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Sample records for spectroscopic properties dna

  1. Spectroscopic properties and photoreactivity with DNA of new monofunctional pyridopsoralens

    International Nuclear Information System (INIS)

    Blais, J.; Vigny, P.; Moron, J.; Bisagni, E.

    1984-01-01

    New psoralen derivatives have been synthesized in order to enhance their affinity towards DNA. The spectral properties (absorption, fluorescence emission, fluorescence quantum yield) and the photostability of pyrido[3,4-c]psoralen are first reported. The drastic changes observed in the solubility and in the fluorescence emission when these compounds are added to native DNA give evidence of the formation of non covalent dark complexes. Upon UV irradiation (365 nm) of the complexes, a photobinding occurs. Heat denaturation and renaturation experiments of modified DNA show that only monoadducts are formed. From the analysis of their fluorescence properties the involvement of the 4',5' double bond is assumed. The monofunctional character has also been established for psoralens having a fused pyridine ring in the 4',5' site. However, a fused tetrahydropyrido group in the 4',5' site is inefficient to inactivate this reactive site. (author)

  2. Spectroscopic properties and photoreactivity with DNA of new monofunctional pyridopsoralens

    Energy Technology Data Exchange (ETDEWEB)

    Blais, J.; Vigny, P. (Institut Curie et Universite Paris VI (France). Lab. de Physique et Chimie Biomoleculaire); Moron, J.; Bisagni, E. (Lab. de Synthese Organique, Institut Curie, Orsay (France). Section de Biologie)

    1984-02-01

    New psoralen derivatives have been synthesized in order to enhance their affinity towards DNA. The spectral properties (absorption, fluorescence emission, fluorescence quantum yield) and the photostability of pyrido(3,4-c)psoralen are first reported. The drastic changes observed in the solubility and in the fluorescence emission when these compounds are added to native DNA give evidence of the formation of non covalent dark complexes. Upon UV irradiation (365 nm) of the complexes, a photobinding occurs. Heat denaturation and renaturation experiments of modified DNA show that only monoadducts are formed. From the analysis of their fluorescence properties the involvement of the 4',5' double bond is assumed. The monofunctional character has also been established for psoralens having a fused pyridine ring in the 4',5' site. However, a fused tetrahydropyrido group in the 4',5' site is inefficient to inactivate this reactive site.

  3. Exploring the antioxidant property of bioflavonoid quercetin in preventing DNA glycation: A calorimetric and spectroscopic study

    International Nuclear Information System (INIS)

    Sengupta, Bidisa; Uematsu, Takashi; Jacobsson, Per; Swenson, Jan

    2006-01-01

    Reducing sugars for example glucose, fructose, etc., and their phosphate derivatives non-enzymatically glycate biological macromolecules (e.g., proteins, DNA and lipids) and is related to the production of free radicals. Here we present a novel study, using differential scanning calorimetry (DSC) along with UV/Vis absorption and photon correlation spectroscopy (PCS), on normal and glycated human placenta DNA and have explored the antioxidant property of the naturally occurring polyhydroxy flavone quercetin (3,3',4',5,7-pentahydroxyflavone) in preventing the glycation. The decrease in the absorption intensity of DNA in presence of sugars clearly indicates the existence of sugar molecules between the two bases of a base pair in the duplex DNA molecule. Variations were perceptible in the PCS relaxation profiles of normal and glycated DNA. The melting temperature of placenta DNA was decreased when glycated suggesting a decrease in the structural stability of the double-stranded glycated DNA. Our DSC and PCS data showed, for the first time, that the dramatic changes in the structural properties of glycated DNA can be prevented to a significant extent by adding quercetin. This study provides valuable insights regarding the structure, function, and dynamics of normal and glycated DNA molecules, underlying the manifestation of free radical mediated diseases, and their prevention using therapeutically active naturally occurring flavonoid quercetin

  4. Rhenium complexes of chromophore-appended dipicolylamine ligands: syntheses, spectroscopic properties, DNA binding and X-ray crystal structure

    International Nuclear Information System (INIS)

    Mullice, L.A.; Buurma, N.J.; Pope, S.J.A.; Laye, R.H.; Harding, L.P.

    2008-01-01

    The syntheses of two chromophore-appended dipicolylamine-derived ligands and their reactivity with penta-carbonyl-chloro-rhenium have been studied. The resultant complexes each possess the fac-Re(CO) 3 core. The ligands L 1 1-[bis(pyridine-2-yl-methyl)amino]methyl-pyrene and L 2 2-[bis(pyridine-2-yl-methyl)amino]methyl-quinoxaline were isolated via a one-pot reductive amination in moderate yield. The corresponding rhenium complexes were isolated in good yields and characterised by 1 H NMR, MS, IR and UV-Vis studies. X-Ray crystallographic data were obtained for fac-{Re(CO) 3 (L 1 )}(BF 4 ), C 34 H 26 BF 4 N 4 O 3 Re: monoclinic, P2(1)/c, a 18.327(2) Angstroms, α = 90.00 degrees, b 14.1537(14) Angstroms, β96.263(6) degrees, c = 23.511(3) Angstroms, γ 90.00 Angstroms, 6062.4(11) (Angstroms) 3 , Z=8. The luminescence properties of the ligands and complexes were also investigated, with the emission attributed to the appended chromophore in each case. Isothermal titration calorimetry suggests that fac-{Re(CO) 3 (L 1 )}(BF 4 ) self-aggregates cooperatively in aqueous solution, probably forming micelle-like aggregates with a cmc of 0.18 mM. Investigations into the DNA-binding properties of fac-{Re(CO) 3 (L 1 )}(BF 4 ) were undertaken and revealed that fac-{Re(CO) 3 (L 1 )}(BF 4 ) binding to fish sperm DNA (binding constant 1.5 ± 0.2 * 10 5 M -1 , binding site size 3.2 ± 0.3 base pairs) is accompanied by changes in the UV-Vis spectrum as typically observed for pyrene-based intercalators while the calorimetrically determined binding enthalpy (-14 ± 2 kcal mol -1 ) also agrees favourably with values as typically found for intercalators. (authors)

  5. Optical properties of metals by spectroscopic ellipsometry

    International Nuclear Information System (INIS)

    Arakawa, E.T.; Inagaki, T.; Williams, M.W.

    1979-01-01

    The use of spectroscopic ellipsometry for the accurate determination of the optical properties of liquid and solid metals is discussed and illustrated with previously published data for Li and Na. New data on liquid Sn and Hg from 0.6 to 3.7 eV are presented. Liquid Sn is Drude-like. The optical properties of Hg deviate from the Drude expressions, but simultaneous measurements of reflectance and ellipsometric parameters yield consistent results with no evidence for vectorial surface effects

  6. Specific binding of a dihydropyrimidinone derivative with DNA: Spectroscopic, calorimetric and modeling investigations

    International Nuclear Information System (INIS)

    Wang Gongke; Yan Changling; Wang Dongchao; Li Dan; Lu Yan

    2012-01-01

    One of the dihydropyrimidinone derivative 5-(ethoxycarbonyl)-6-methyl-4-(4-methoxyphenyl) -3,4-dihydropyrimidin-2(1H)-one (EMMD) was synthesized, and its binding properties with calf-thymus DNA (ctDNA) were investigated using spectroscopic, viscometric, isothermal titration calorimetric (ITC) and molecular modeling techniques. Fluorescence spectra suggested that the fluorescence enhancement of the binding interaction of EMMD to ctDNA was a static process with ground state complex formation. The binding constant determined with spectroscopic titration and ITC was found to be in the same order of 10 4 M −1 . According to the results of the viscosity analysis, fluorescence competitive binding experiment, fluorescence quenching studies, absorption spectral and ITC investigations, it can be concluded that EMMD is intercalative binding to ctDNA. Furthermore, the results of molecular modeling confirmed those obtained from spectroscopic, viscosimetric and ITC investigations. Additionally, ITC studies also indicated that the binding interaction is predominantly enthalpy driven. - Highlights: ► Medically important dihydropyrimidinones derivative EMMD is synthesized. ► EMMD is intercalative binding into ctDNA helix. ► Hydrogen bonding may play an essential role in the binding of EMCD with ctDNA. ► This binding interaction is predominantly enthalpy driven.

  7. Spectroscopic Tools for Quantitative Studies of DNA Structure and Dynamics

    DEFF Research Database (Denmark)

    Preus, Søren

    The main objective of this thesis is to develop quantitative fluorescence-based, spectroscopic tools for probing the 3D structure and dynamics of DNA and RNA. The thesis is founded on six peer-reviewed papers covering mainly the development, characterization and use of fluorescent nucleobase...... analogues. In addition, four software packages is presented for the simulation and quantitative analysis of time-resolved and steady-state UV-Vis absorption and fluorescence experiments....

  8. Raman spectroscopic study of plasma-treated salmon DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Joon; Kim, Yong Hee; Choi, Eun Ha [Plasma Bioscience Research Center, Kwangwoon University, Seoul 139-701 (Korea, Republic of); Kwon, Young-Wan [Department of Chemistry, Korea University, Seoul 136-701 (Korea, Republic of)

    2013-01-14

    In this research, we studied the effect of plasma treatment on the optical/structural properties of the deoxyribonucleic acid (DNA) extracted from salmon sperm. DNA-cetyltrimethylammonium (CTMA) films were obtained by complexation of DNA with CTMA. Circular dichroism (CD) and Raman spectra indicated that DNA retained its double helical structure in the solid film. The Raman spectra exhibited several vibration modes corresponding to the nuclear bases and the deoxyribose-phosphate backbones of the DNA, as well as the alkylchains of CTMA. Dielectric-barrier-discharge (DBD) plasma treatment induced structural modification and damage to the DNA, as observed by changes in the ultraviolet-visible absorption, CD, and Raman spectra. The optical emission spectra of the DBD plasma confirmed that DNA modification was induced by plasma ions such as reactive oxygen species and reactive nitrogen species.

  9. Synthesis, Spectroscopic Properties and DFT Calculation of Novel ...

    Indian Academy of Sciences (India)

    L1) identifies its molecular structure and reveals π-π stacking. The synthetic mechanisms for L2, L3 were studied by density functional theory calculations. And a comprehensive study of spectroscopic properties involving experimental data and ...

  10. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA.

    Science.gov (United States)

    Shahal, Tamar; Gilat, Noa; Michaeli, Yael; Redy-Keisar, Orit; Shabat, Doron; Ebenstein, Yuval

    2014-08-19

    5-Hydroxymethylcytosine (5hmC), a modified form of the DNA base cytosine, is an important epigenetic mark linked to regulation of gene expression in development, and tumorigenesis. We have developed a spectroscopic method for a global quantification of 5hmC in genomic DNA. The assay is performed within a multiwell plate, which allows simultaneous recording of up to 350 samples. Our quantification procedure of 5hmC is direct, simple, and rapid. It relies on a two-step protocol that consists of enzymatic glucosylation of 5hmC with an azide-modified glucose, followed by a "click reaction" with an alkyne-fluorescent tag. The fluorescence intensity recorded from the DNA sample is proportional to its 5hmC content and can be quantified by a simple plate reader measurement. This labeling technique is specific and highly sensitive, allowing detection of 5hmC down to 0.002% of the total nucleotides. Our results reveal significant variations in the 5hmC content obtained from different mouse tissues, in agreement with previously reported data.

  11. Spectroscopic profiling and computational study of the binding of tschimgine: A natural monoterpene derivative, with calf thymus DNA

    Science.gov (United States)

    Khajeh, Masoumeh Ashrafi; Dehghan, Gholamreza; Dastmalchi, Siavoush; Shaghaghi, Masoomeh; Iranshahi, Mehrdad

    2018-03-01

    DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (Kb) between TMG and DNA was 2.27 × 104 M- 1, that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking.

  12. In vitro DNA binding studies of lenalidomide using spectroscopic in combination with molecular docking techniques

    Science.gov (United States)

    Xu, Liang; Hu, Yan-Xi; Li, Yan-Cheng; Zhang, Li; Ai, Hai-Xin; Liu, Yu-Feng; Liu, Hong-Sheng

    2018-02-01

    In the present work, the binding interaction between lenalidomide (LEN) and calf thymus DNA (ct-DNA) was systematically studied by using fluorescence, ultraviolet-visible (UV-vis) absorption, circular dichroism (CD) spectroscopies under imitated physiological conditions (pH = 7.4) coupled with molecular docking. It was found that LEN was bound to ct-DNA with high binding affinity (Ka = 2.308 × 105 M-1 at 283 K) through groove binding as evidenced by a slight decrease in the absorption intensity in combination with CD spectra. Thermodynamic parameters (ΔG 0 and ΔS interaction. Furthermore, competitive binding experiments with ethidium bromide and 4‧, 6-dia-midino-2-phenylindoleas probes showed that LEN could preferentially bind in the minor groove of double-stranded DNA. The average lifetime of LEN was calculated to be 7.645 ns. The φ of LEN was measured as 0.09 and non-radiation energy transfer between LEN and DNA had occurred. The results of the molecular docking were consistent with the experimental results. This study explored the potential applicability of the spectroscopic properties of LEN and also investigated its interactions with relevant biological targets. In addition, it will provide some theoretical references for the deep research of simultaneous administration of LEN with other drugs.

  13. Spectroscopic properties of Pr -doped erbium oxalate crystals

    Indian Academy of Sciences (India)

    Spectroscopic properties of praseodymium ions-doped erbium oxalate ... solution with specific gravity 1.04 g/cm3 was mixed homogeneously with 0.5 M oxalic ... of concentrated nitric acid were transferred carefully and gently through the wall ...

  14. Spectroscopic properties of the B meson

    Directory of Open Access Journals (Sweden)

    Devlani Nayneshkumar

    2015-01-01

    Full Text Available Investigation of the B(bq̄; q = u, d meson properties is carried out using variational method within phenomenological quark antiquark potential(coulomb plus power model using the Gaussian wave function. O(1/m correction to the potential energy term and relativistic corrections to the kinetic energy term of the hamiltonian are incorporated. Spin-orbit, spin-spin and tensor interactions are employed to obtain the mass spectra. Various other properties such as the decay constants, e1 and m1 transitions are also obtained

  15. Spectroscopic properties of the Bc system

    International Nuclear Information System (INIS)

    Zenine, N.

    2002-01-01

    We present a calculation of the masses of the low lying levels of the bottom charmed meson system, in the framework of the non relativistic potential model approach. We carry out a comparison with previous calculations.The copious production of b quarks in Zθ decays at the Large Electron-Positron (LEP) collider and in 1.8 TeV proton-antiproton collisions at the Fermilab Tevatron opens for study the rich spectroscopy of mesons and baryons containing b and c quarks. A particularly interesting case is the spectrum of c b states. The spectrum and properties of the above mentioned states have been calculated various times in the past in the framework of the potential model approach [1-6]. The recent experimental observation [7-11] of the B + c . meson has inspired new theoretical interest in the problem. The c b spectrum has been considered again either from the potential approach [12-16] and from the lattice simulation point of view [17-18]. In this work, in the framework of the Non Relativistic (NR) potential model approach, we consider five completely different functional forms of the potential that give reasonable accounts for b b and c c spectra [19-23]. The parameters of these different models [19-23] are fitted to actual quarkonium masses [24]. We calculate the masses of the low-lying levels of the bottom charmed meson system that lie below the threshold for strong decay

  16. Sub-THz spectroscopic characterization of vibrational modes in artificially designed DNA monocrystal

    International Nuclear Information System (INIS)

    Sizov, Igor; Rahman, Masudur; Gelmont, Boris; Norton, Michael L.; Globus, Tatiana

    2013-01-01

    Highlights: • Sub-THz spectroscopy is used to characterize artificially designed DNA monocrystal. • Results are obtained using a novel near field, RT, frequency domain spectrometer. • Narrow resonances of 0.1 cm −1 width in absorption spectra of crystal are observed. • Signature measured between 310 and 490 GHz is reproducible and well resolved. • Absorption pattern is explained in part by simulation results from dsDNA fragment. - Abstract: Sub-terahertz (sub-THz) vibrational spectroscopy is a new spectroscopic branch for characterizing biological macromolecules. In this work, highly resolved sub-THz resonance spectroscopy is used for characterizing engineered molecular structures, an artificially designed DNA monocrystal, built from a short DNA sequence. Using a recently developed frequency domain spectroscopic instrument operating at room temperature with high spectral and spatial resolution, we demonstrated very intense and specific spectral lines from a DNA crystal in general agreement with a computational molecular dynamics (MD) simulation of a short double stranded DNA fragment. The spectroscopic signature measured in the frequency range between 310 and 490 GHz is rich in well resolved and reproducible spectral features thus demonstrating the capability of THz resonance spectroscopy to be used for characterizing custom macromolecules and structures designed and implemented via nanotechnology for a wide variety of application domains. Analysis of MD simulation indicates that intense and narrow vibrational modes with atomic movements perpendicular (transverse) and parallel (longitudinal) to the long DNA axis coexist in dsDNA, with much higher contribution from longitudinal vibrations

  17. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Myungkoo [Iowa State Univ., Ames, IA (United States)

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G2 or G3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N2-dG.

  18. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    International Nuclear Information System (INIS)

    Suh, Myungkoo.

    1995-01-01

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ∼ 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2 -dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2 -dG

  19. Spectroscopic properties of rare earths in optical materials

    CERN Document Server

    Parisi, Jürgen; Osgood, R; Warlimont, Hans; Liu, Guokui; Jacquier, Bernard

    2005-01-01

    Aimed at researchers and graduate students, this book provides up-to-date information for understanding electronic interactions that impact the optical properties of rare earth ions in solids. Its goal is to establish a connection between fundamental principles and the materials properties of rare-earth activated luminescent and laser optical materials. The theoretical survey and introduction to spectroscopic properties include electronic energy level structure, intensities of optical transitions, ion-phonon interactions, line broadening, and energy transfer and up-conversion. An important aspect of the book lies in its deep and detailed discussions on materials properties and the potential of new applications such as optical storage, information processing, nanophotonics, and molecular probes that have been identified in recent experimental studies. This volume will be a valuable reference book on advanced topics of rare earth spectroscopy and materials science.

  20. Spectroscopic properties of vitamin E models in solution

    Science.gov (United States)

    Oliveira, L. B. A.; Colherinhas, G.; Fonseca, T. L.; Castro, M. A.

    2015-05-01

    We investigate the first absorption band and the 13C and 17O magnetic shieldings of vitamin E models in chloroform and in water using the S-MC/QM methodology in combination with the TD-DFT and GIAO approaches. The results show that the solvent effects on these spectroscopic properties are small but a proper description of the solvent shift for 17O magnetic shielding of the hydroxyl group in water requires the use of explicit solute-solvent hydrogen bonds. In addition, the effect of the replacement of hydrogen atoms by methyl groups in the vitamin E models only affects magnetic shieldings.

  1. Modeling the mechanical properties of DNA nanostructures.

    Science.gov (United States)

    Arbona, Jean Michel; Aimé, Jean-Pierre; Elezgaray, Juan

    2012-11-01

    We discuss generalizations of a previously published coarse-grained description [Mergell et al., Phys. Rev. E 68, 021911 (2003)] of double stranded DNA (dsDNA). The model is defined at the base-pair level and includes the electrostatic repulsion between neighbor helices. We show that the model reproduces mechanical and elastic properties of several DNA nanostructures (DNA origamis). We also show that electrostatic interactions are necessary to reproduce atomic force microscopy measurements on planar DNA origamis.

  2. Spectroscopic properties of highly Nd-doped lead phosphate glass

    Energy Technology Data Exchange (ETDEWEB)

    Novais, A.L.F. [Instituto de Física, Universidade Federal de Alagoas, Grupo de Fotônica e Fluidos Complexos, 57072-970 Maceió, AL (Brazil); Dantas, N.O. [Laboratório de Novos Materiais Isolantes e Semicondutores (LNMIS), Instituto de Física, Universidade Federal de Uberlândia, 38400-902 Uberlândia, MG (Brazil); Guedes, I. [Departamento de Física, Universidade Federal do Ceará, Campus do PICI, Caixa Postal 6030, 60455-760 Fortaleza, CE (Brazil); Vermelho, M.V.D., E-mail: vermelho@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, Grupo de Fotônica e Fluidos Complexos, 57072-970 Maceió, AL (Brazil)

    2015-11-05

    The spectroscopic characteristics of highly Nd{sup 3+}-doped lead phosphate glasses (xNd:Pb{sub 3}(PO{sub 4}){sub 2}) have been investigated. The X-ray spectra show that the matrices are glassy up to 25 wt% of Nd{sup 3+} doping. From the Judd–Ofelt analysis we observe that while the Ω{sub (2)} parameter remains constant indicating that the 4f{sup N} and 4f{sup N−1}5 d{sup 1} configurations are not affected by the Nd{sup 3+} doping, the behavior of both Ω{sub (4)} and Ω{sub (6)} changes for 15 wt% of Nd{sup 3+} doping. The reduction of the Ω{sub (6)} parameter is related to the increase of the covalence bonding between the ligands and the Nd{sup 3+} ions. At this particular concentration, the radiative lifetime has a four-fold enhancement. Such behaviors are likely to be related to a modification in the glass structure for high Nd{sup 3+} concentrations. - Graphical abstract: Highly doped lead-phosphate glass matrix, with nominal concentration of up to 25 wt%, maintain the spectroscopic properties without deterioration. The analysis concerning the point of view of Nd{sup 3+} ions showed that high concentrations only affects the rare earth electronic charge density distribution. - Highlights: • Spectroscopic characterization of Nd{sub 2}O{sub 3} highly doped lead phosphate glasses. • Phosphate glass doped with Nd{sup 3+} for applications in photonic devices. • Judd–Ofelt analysis in phosphate glasses doped with Neodymium.

  3. Spectroscopic properties of transition elements and their related magnetic properties

    International Nuclear Information System (INIS)

    Porcher, P.; Malta, O.L.

    1988-01-01

    The optical and magnetic properties of transition elements (nd N and nf N ions) are analysed. The phenomenological parameters introduced in the crystal-ligand field theory, the free ion interactions and crystalline matrix as well as electrostatic repulsion are studied. (M.J.C.) [pt

  4. Exploring the Interactions of the Dietary Plant Flavonoids Fisetin and Naringenin with G-Quadruplex and Duplex DNA, Showing Contrasting Binding Behavior: Spectroscopic and Molecular Modeling Approaches.

    Science.gov (United States)

    Bhattacharjee, Snehasish; Chakraborty, Sandipan; Sengupta, Pradeep K; Bhowmik, Sudipta

    2016-09-01

    Guanine-rich sequences have the propensity to fold into a four-stranded DNA structure known as a G-quadruplex (G4). G4 forming sequences are abundant in the promoter region of several oncogenes and become a key target for anticancer drug binding. Here we have studied the interactions of two structurally similar dietary plant flavonoids fisetin and naringenin with G4 as well as double stranded (duplex) DNA by using different spectroscopic and modeling techniques. Our study demonstrates the differential binding ability of the two flavonoids with G4 and duplex DNA. Fisetin more strongly interacts with parallel G4 structure than duplex DNA, whereas naringenin shows stronger binding affinity to duplex rather than G4 DNA. Molecular docking results also corroborate our spectroscopic results, and it was found that both of the ligands are stacked externally in the G4 DNA structure. C-ring planarity of the flavonoid structure appears to be a crucial factor for preferential G4 DNA recognition of flavonoids. The goal of this study is to explore the critical effects of small differences in the structure of closely similar chemical classes of such small molecules (flavonoids) which lead to the contrasting binding properties with the two different forms of DNA. The resulting insights may be expected to facilitate the designing of the highly selective G4 DNA binders based on flavonoid scaffolds.

  5. Theoretical studies on CH+ ion molecule using configuration interaction method and its spectroscopic properties

    International Nuclear Information System (INIS)

    Machado, F.B.C.

    1985-01-01

    The use of the configuration (CI) method for the calculation of very accurate potential energy curves and dipole moment functions, and then their use in the comprehension of spectroscopic properties of diatomic molecules is presented. The spectroscopic properties of CH + and CD + such as: vibrational levels, spectroscopic constants, averaged dipole moments for all vibrational levels, radiative transition probabilities for emission and absorption, and radiative lifetimes are verificated. (M.J.C.) [pt

  6. Spectroscopic studies on the interaction of mimosine with BSA and DNA

    Science.gov (United States)

    Baltazar, C. J.; Mun, R.; Tajmir-Riahi, H. A.; Bariyanga, J.

    2018-06-01

    Mimosine has shown antitumor activity towards cancer cells. It has also been found to inhibit deoxyribonucleic acid (DNA) but the interaction is not fully understood. Here we report the results of investigation of its interactions with bovine serum albumin (BSA) and DNA in aqueous solution (pH 7.4) using FTIR and UV spectroscopic methods. Mimosine was found to disrupt the conformation of BSA by reducing its α-helix component and promoting a partial unfolding of the protein. In addition, the results indicated that mimosine may bind to DNA by electrostatic attractions via phosphate groups and grooves. The overall binding constant of DNA -mimosine complex was 5 × 10 3 M-1.

  7. Structure and linear spectroscopic properties of near IR polymethine dyes

    International Nuclear Information System (INIS)

    Webster, Scott; Padilha, Lazaro A.; Hu Honghua; Przhonska, Olga V.; Hagan, David J.; Van Stryland, Eric W.; Bondar, Mikhail V.; Davydenko, Iryna G.; Slominsky, Yuriy L.; Kachkovski, Alexei D.

    2008-01-01

    We performed a detailed experimental investigation and quantum-chemical analysis of a new series of near IR polymethine dyes with 5-butyl-7,8-dihydrobenzo[cd]furo[2,3-f]indolium terminal groups. We also synthesized and studied two neutral dyes, squaraine and tetraone, with the same terminal groups and performed a comparison of the spectroscopic properties of this set of 'near IR' dyes (polymethine, squaraine, and tetraone) with an analogous set of 'visible' dyes with simpler benzo[e]indolium terminal groups. From these measurements, we find that the dyes with dihydrobenzo[cd]furo[2,3-f]indolium terminal groups are characterized by a remarkably large shift ∼300 nm (∼200 nm for tetraone) of their absorption bands towards the red region. We discuss the difference in electronic structure for these molecules and show that the 'near IR' dyes are characterized by an additional weak fluorescence band from the higher lying excited states connected with the terminal groups. Absorption spectra for the longest polymethines are solvent-dependent and are characterized by a broadening of the main band in polar solvents, which is explained by ground state symmetry breaking and reduced charge delocalization within the polymethine chromophore. The results of these experiments combined with the agreement of quantum chemical calculations moves us closer to a predictive capability for structure-property relations in cyanine-like molecules

  8. Spectroscopic Evidence for Nonuniform Starspot Properties on II Pegasi

    Science.gov (United States)

    ONeal, Douglas; Saar, Steven H.; Neff, James E.

    1998-01-01

    We present spectroscopic evidence for Multiple Spot temperatures on the RS CVn star II Pegasi (HD 224085). We model the strengths of the 7055 and 8860 A TiO absorption bands in the spectrum of II Peg using weighted sums of inactive comparison spectra: a K star to represent the nonspotted photosphere and an M star to represent the spots. The best fit yields independent measurements of the starspot filling factor (f(sub s) and mean spot temperature (T(sub s)) averaged over the visible hemisphere of the star. During three-fourths of a rotation of II Peg in late 1996, we measure a constant f(sub s) approximately equals 55% +/- 5%. However, (T(sub s) varies from 3350 +/- 60 to 3550 +/- 70 K. We compute (T(sub s) for two simple models: (1) a star with two distinct spot temperatures, and (2) a star with different umbral/penumbral area ratios. The changing (T(sub s) correlates with emission strengths of H(alpha) and the Ca II infrared triplet in the sense that cooler (T(sub s) accompanies weaker emission. We explore possible implications of these results for the physical properties of the spots on II Peg and for stellar surface structure in general.

  9. Geometry-dependent DNA-TiO2 immobilization mechanism: A spectroscopic approach

    Science.gov (United States)

    Silva-Moraes, M. O.; Garcia-Basabe, Y.; de Souza, R. F. B.; Mota, A. J.; Passos, R. R.; Galante, D.; Fonseca Filho, H. D.; Romaguera-Barcelay, Y.; Rocco, M. L. M.; Brito, W. R.

    2018-06-01

    DNA nucleotides are used as a molecular recognition system on electrodes modified to be applied in the detection of various diseases, but immobilization mechanisms, as well as, charge transfers are not satisfactorily described in the literature. An electrochemical and spectroscopic study was carried out to characterize the molecular groups involved in the direct immobilization of DNA structures on the surface of nanostructured TiO2 with the aim of evaluating the influence of the geometrical aspects. X-ray photoelectron spectroscopy at O1s and P2p core levels indicate that immobilization of DNA samples occurs through covalent (Psbnd Osbnd Ti) bonds. X-ray absorption spectra at the Ti2p edge reinforce this conclusion. A new species at 138.5 eV was reported from P2p XPS spectra analysis which plays an important role in DNA-TiO2 immobilization. The Psbnd Osbnd Ti/Osbnd Ti ratio showed that quantitatively the DNA immobilization mechanism is dependent on their geometry, becoming more efficient for plasmid ds-DNA structures than for PCR ds-DNA structures. The analysis of photoabsorption spectra at C1s edge revealed that the molecular groups that participate in the C1s → LUMO electronic transitions have different pathways in the charge transfer processes at the DNA-TiO2 interface. Our results may contribute to additional studies of immobilization mechanisms understanding the influence of the geometry of different DNA molecules on nanostructured semiconductor and possible impact to the charge transfer processes with application in biosensors or aptamers.

  10. Syntheses and spectroscopic properties of mercury(II) and nickel(II ...

    African Journals Online (AJOL)

    Syntheses and spectroscopic properties of mercury(II) and nickel(II) ... The complexes were characterized by IR, diffuse reflectance, 1H NMR spectra and elemental ... coordinating through thiolato sulphur and hydrazinic nitrogen atoms.

  11. Exploration of disulfiram dealings with calf thymus DNA using spectroscopic, electrochemical and molecular docking techniques

    International Nuclear Information System (INIS)

    Subastri, A.; Durga, A.; Harikrishna, K.; Sureshkumar, M.; Jeevaratnam, K.; Girish, K.S.; Thirunavukkarasu, C.

    2016-01-01

    Disulfiram (C 10 H 20 N 2 S 4 ) is an acetaldehyde dehydrogenase inhibitor used in the treatment of chronic alcoholism and it has also been subjected to the clinical trial for cancer in recent times. However, there is no report on the binding effect of this emerging drug with DNA. Hence, the present investigation was taken up to study the binding effect of disulfiram on DNA under physiological conditions. UV–vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism spectroscopy, cyclic voltammetry and molecular docking techniques were employed to determine the interaction mode of disulfiram with DNA. Further, DNA cleavage property of disulfiram was carried out by using agarose gel electrophoresis. The UV–vis absorption, emission and cyclic voltammetry measurements revealed that disulfiram showed the intercalative mode of interaction with DNA. The circular dichroism study exhibited structural changes of partial transition from B-conformation to A-conformation in DNA upon addition of disulfiram. Molecular docking study of disulfiram with DNA depicted intercalative mode of binding by formation of hydrogen and hydrophobic interaction along with docking score of −3.07 kcal/mol. The DNA cleavage study revealed that low concentration of disulfiram (50 µM) protected the DNA from oxidative damage sequentially, while high concentration of disulfiram (100 µM) showed less protective activity. Conversely, it caused DNA damage in the presence of hydroxyl radical oxidative system. Hence, the results obtained from the present investigations provide detailed discernment into DNA interaction effects of disulfiram.

  12. The Spectroscopic and Conductive Properties of Ru(II Complexes with Potential Anticancer Properties

    Directory of Open Access Journals (Sweden)

    Adebayo A. Adeniyi

    2014-01-01

    Full Text Available Different density functional methods (DFT have been used to optimize and study the chemistry of five potential anticancer complexes in terms of their electronic, conductive, and spectroscopic properties. Many of the computed properties in addition to the IR and QTAIM analysis of the NMR are dipole moment vector (μi, linear polarizability tensor (αij, first hyperpolarizability tensors (βijk, polarizability exaltation index (Γ, and chemical hardness (η of the complexes. Stable low energy geometries are obtained using basis set with effective core potential (ECP approximation but, in the computation of atomic or molecular properties, the metal Ru atom is better treated with higher all electron basis set like DGDZVP. The spectroscopic features like the IR of the metal-ligand bonds and the isotropic NMR shielding tensor of the coordinated atoms are significantly influenced by the chemical environment of the participating atoms. The carboxylic and pyrazole units are found to significantly enhance the polarizabilities and hyperpolarizabilities of the complexes while the chloride only improves the polarity of the complexes. Fermi contacts (FC have the highest effect followed by the PSO among all the four Ramsey terms which defined the total spin-spin coupling constant J (HZ of these complexes.

  13. Polarized spectroscopic properties of Nd3+-doped KGd(WO4)2 single crystal

    International Nuclear Information System (INIS)

    Chen Yujin; Lin Yanfu; Gong Xinghong; Tan Qiguang; Zhuang Jian; Luo Zundu; Huang Yidong

    2007-01-01

    The polarized absorption spectra, infrared fluorescence spectra, upconversion visible fluorescence spectra, and fluorescence decay curve of orientated Nd 3+ :KGd(WO 4 ) 2 crystal were measured at room-temperature. Some important spectroscopic parameters were investigated in detail in the framework of the Judd-Ofelt theory and the Fuchtbauer-Ladenburg formula. The effect of the crystal structure on the spectroscopic properties of the Nd 3+ ions was analyzed. The relation among the spectroscopic parameters and the laser performances of the Nd 3+ :KGd(WO 4 ) 2 crystal was discussed

  14. Exploration of disulfiram dealings with calf thymus DNA using spectroscopic, electrochemical and molecular docking techniques

    Energy Technology Data Exchange (ETDEWEB)

    Subastri, A.; Durga, A. [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India); Harikrishna, K.; Sureshkumar, M. [Centre for Bioinformatics, Pondicherry University, Puducherry 605014 (India); Jeevaratnam, K. [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India); Girish, K.S. [Department of Studies & Research in Biochemistry, Tumkur University, Tumkur, Karnataka (India); Thirunavukkarasu, C., E-mail: tchinnasamy@hotmail.com [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India)

    2016-02-15

    Disulfiram (C{sub 10}H{sub 20}N{sub 2}S{sub 4}) is an acetaldehyde dehydrogenase inhibitor used in the treatment of chronic alcoholism and it has also been subjected to the clinical trial for cancer in recent times. However, there is no report on the binding effect of this emerging drug with DNA. Hence, the present investigation was taken up to study the binding effect of disulfiram on DNA under physiological conditions. UV–vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism spectroscopy, cyclic voltammetry and molecular docking techniques were employed to determine the interaction mode of disulfiram with DNA. Further, DNA cleavage property of disulfiram was carried out by using agarose gel electrophoresis. The UV–vis absorption, emission and cyclic voltammetry measurements revealed that disulfiram showed the intercalative mode of interaction with DNA. The circular dichroism study exhibited structural changes of partial transition from B-conformation to A-conformation in DNA upon addition of disulfiram. Molecular docking study of disulfiram with DNA depicted intercalative mode of binding by formation of hydrogen and hydrophobic interaction along with docking score of −3.07 kcal/mol. The DNA cleavage study revealed that low concentration of disulfiram (50 µM) protected the DNA from oxidative damage sequentially, while high concentration of disulfiram (100 µM) showed less protective activity. Conversely, it caused DNA damage in the presence of hydroxyl radical oxidative system. Hence, the results obtained from the present investigations provide detailed discernment into DNA interaction effects of disulfiram.

  15. Synthesis, spectroscopic and redox properties of the mononuclear ...

    Indian Academy of Sciences (India)

    Administrator

    magnetic susceptibility measurements, molar conductivity, cyclic voltammetry, mass ... gens donor atoms show DNA binding and antitumor ... trum can be correlated with the strength of the ... ties, the investigation of redox behaviour has a vital.

  16. Spectroscopic properties for identifying sapphire samples from Ban Bo Kaew, Phrae Province, Thailand

    Science.gov (United States)

    Mogmued, J.; Monarumit, N.; Won-in, K.; Satitkune, S.

    2017-09-01

    Gemstone commercial is a high revenue for Thailand especially ruby and sapphire. Moreover, Phrae is a potential gem field located in the northern part of Thailand. The studies of spectroscopic properties are mainly to identify gemstone using advanced techniques (e.g. UV-Vis-NIR spectrophotometry, FTIR spectrometry and Raman spectroscopy). Typically, UV-Vis-NIR spectrophotometry is a technique to study the cause of color in gemstones. FTIR spectrometry is a technique to study the functional groups in gem-materials. Raman pattern can be applied to identify the mineral inclusions in gemstones. In this study, the natural sapphires from Ban Bo Kaew were divided into two groups based on colors including blue and green. The samples were analyzed by UV-Vis-NIR spectrophotometer, FTIR spectrometer and Raman spectroscope for studying spectroscopic properties. According to UV-Vis-NIR spectra, the blue sapphires show higher Fe3+/Ti4+ and Fe2+/Fe3+ absorption peaks than those of green sapphires. Otherwise, green sapphires display higher Fe3+/Fe3+ absorption peaks than blue sapphires. The FTIR spectra of both blue and green sapphire samples show the absorption peaks of -OH,-CH and CO2. The mineral inclusions such as ferrocolumbite and rutile in sapphires from this area were observed by Raman spectroscope. The spectroscopic properties of sapphire samples from Ban Bo Kaew, Phrae Province, Thailand are applied to be the specific evidence for gemstone identification.

  17. Spectroscopic properties of tetravalent actinide ions in solids

    International Nuclear Information System (INIS)

    Krupa, J.C.

    1987-01-01

    Optical spectroscopy is a powerful tool to study the electronic structure of an optically active transition ion in the condensed phase media and consequently to study the interactions between the central ion and its environment. The main interactions that are essential for an understanding of the energy level distribution of an f N ion in solids is briefly examined and the deduced free-ion and crystal field parameters for Pa 4+ , U 4+ , Np 4+ are compared to those of the isoelectronic configuration lanthanide ions. At last, the actinide series offers an interesting situation since the 5f electrons in the metals are delocalized in the light actinides and then localized, that sould affect the nature of the chemical bonding in the two parts of the series. Is this trend reflected in the An 4+ spectroscopic parameters

  18. Conformational, IR spectroscopic and electronic properties of conium alkaloids and their adducts with C60 fullerene

    Science.gov (United States)

    Zabolotnyi, M. A.; Prylutskyy, Yu I.; Poluyan, N. A.; Evstigneev, M. P.; Dovbeshko, G. I.

    2016-08-01

    Conformational, IR spectroscopic and electronic properties of the components of Conium alkaloids (Conium maculatum) in aqueous environment were determined by model calculations and experiment. With the help of FT-IR spectroscopy the possibility of formation of an adduct between γ-coniceine alkaloid and C60 fullerene was demonstrated, which is important for further application of conium analogues in biomedical purposes.

  19. Elastic properties and spectroscopic studies of Na 2 O–ZnO–B 2 O 3 ...

    Indian Academy of Sciences (India)

    Elastic properties, 11B MAS–NMR and IR spectroscopic studies have been employed to study the structure of Na2O–ZnO–B2O3 glasses. Sound velocities and elastic moduli such as longitudinal, Young's, bulk and shear modulus have been measured at a frequency of 10 MHz as a function of ZnO concentration.

  20. Nonplanar property study of antifungal agent tolnaftate-spectroscopic approach

    Science.gov (United States)

    Arul Dhas, D.; Hubert Joe, I.; Roy, S. D. D.; Balachandran, S.

    2011-09-01

    Vibrational analysis of the thionocarbamate fungicide tolnaftate which is antidermatophytic, antitrichophytic and antimycotic agent, primarily inhibits the ergosterol biosynthesis in the fungus, was carried out using NIR FT-Raman and FTIR spectroscopic techniques. The equilibrium geometry, various bonding features, harmonic vibrational wavenumbers and torsional potential energy surface (PES) scan studies have been computed using density functional theory method. The detailed interpretation of the vibrational spectra has been carried out with the aid of VEDA.4 program. Vibrational spectra, natural bonding orbital (NBO) analysis and optimized molecular structure show the clear evidence for electronic interaction of thionocarbamate group with aromatic ring. Predicted electronic absorption spectrum from TD-DFT calculation has been compared with the UV-vis spectrum. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy were also calculated. Vibrational analysis reveals that the simultaneous IR and Raman activation of the C-C stretching mode in the phenyl and naphthalene ring provide evidence for the charge transfer interaction between the donor and acceptor groups and is responsible for its bioactivity as a fungicide.

  1. Spectroscopic approaches to study DNA damage induced in genome exposed to ionizing radiation and its enzymatic repair

    International Nuclear Information System (INIS)

    Yokoya, Akinari; Fujii, Kentaro; Oka, Toshitaka; Watanabe, Ritsuko

    2012-01-01

    Recent progress on spectroscopic study on physicochemical process of DNA damage induction will be reported. It has been predicted by computer track simulation studies that complex DNA damage, so called clustered DNA damage sites, is produced along the tack particularly of high Linear Energy Transfer (LET) ions. The clustered DNA damage, consisting of two or more isolated lesions such as single strand breaks or nucleobase lesions, is thought to compromise DNA repair enzymes. We have revealed that the nucleobase lesions produced by He 2+ ion impact to simple model DNA (plasmid) are hardly processed by base excision repair enzymes (E. coli DNA glycosylases). Using the third generation synchrotron radiation facility (SPring-8), we have studied unpaired electron species or desorbed ions as intermediates of DNA damage using an EPR apparatus or mass spectrometer installed in the soft X-ray beamline in SPring-8. These aspects are compared with the yields of final products of single- and double-strand breaks and base lesions revealed biochemical techniques. Models of complex DNA damage induction will be proposed considering various modification factors of the damage induction, ionization of valence and inner-shell electrons, OH radicals, hydration layer and the impact of secondary electrons. (author)

  2. Spectroscopic and thermodynamic properties of L-ornithine monohydrochloride

    Energy Technology Data Exchange (ETDEWEB)

    Raja, M. Dinesh [Department of Physics, Bharath University, Chennai – 600073 (India); Kumar, C. Maria Ashok; Arulmozhi, S.; Madhavan, J., E-mail: jmadhavang@yahoo.com [Department of Physics, Loyola College, Chennai – 600034 (India)

    2015-06-24

    L-Ornithine Monohydrochloride (LOMHCL) has been investigated with the help of B3LYP density functional theory with 6-31 G (d, p) basis set. Fourier transform infrared and Fourier transform Raman spectra is to identify the various functional groups. The theoretical frequencies showed very good agreement with experimental values. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H) and temperatures. Second harmonic generation (SHG) efficiency of the grown crystal has been studied.

  3. Optical spectroscopic characterization of human meniscus biomechanical properties

    Science.gov (United States)

    Ala-Myllymäki, Juho; Danso, Elvis K.; Honkanen, Juuso T. J.; Korhonen, Rami K.; Töyräs, Juha; Afara, Isaac O.

    2017-12-01

    This study investigates the capacity of optical spectroscopy in the visible (VIS) and near-infrared (NIR) spectral ranges for estimating the biomechanical properties of human meniscus. Seventy-two samples obtained from the anterior, central, and posterior locations of the medial and lateral menisci of 12 human cadaver joints were used. The samples were subjected to mechanical indentation, then traditional biomechanical parameters (equilibrium and dynamic moduli) were calculated. In addition, strain-dependent fibril network modulus and permeability strain-dependency coefficient were determined via finite-element modeling. Subsequently, absorption spectra were acquired from each location in the VIS (400 to 750 nm) and NIR (750 to 1100 nm) spectral ranges. Partial least squares regression, combined with spectral preprocessing and transformation, was then used to investigate the relationship between the biomechanical properties and spectral response. The NIR spectral region was observed to be optimal for model development (83.0%≤R2≤90.8%). The percentage error of the models are: Eeq (7.1%), Edyn (9.6%), Eɛ (8.4%), and Mk (8.9%). Thus, we conclude that optical spectroscopy in the NIR range is a potential method for rapid and nondestructive evaluation of human meniscus functional integrity and health in real time during arthroscopic surgery.

  4. Spectroscopic and thermal properties of uranium relevant to atomic schemes for laser isotope separation

    International Nuclear Information System (INIS)

    Ahmad, S.A.; Pandey, P.L.

    1980-01-01

    Spectroscopic data on uranium atom and thermal properties of uranium relevant to atomic schemes for laser isotope separation have been presented in this report. All the relevant spectroscopic data reported in literature so far, as well as some other parameters like photo-absorption cross sections, branching ratios, effects of magnetic and electric fields, evaluated using the existing data, have been presented here. Among the thermal properties, parameters like vapour pressure and number densities for U/Liquid U, U/URe 2 and U/UP systems, partition function, percentage population distribution in energy levels, thermal ionisation and velocities of uranium atom have been presented at different temperatures. Different possible collision processes are mentioned and cross-sections of U-U + charge-exchange and U + + e radiative recombination processes have been also evaluated. (author)

  5. Hybrid Biodegradable Hydrogels Obtained from Nanoclay and Carboxymethylcellulose Polysaccharide: Hydrophilic, Kinetic, Spectroscopic and Morphological Properties.

    Science.gov (United States)

    Nascimento, Denis W S; de Moura, Márcia R; Mattoso, Luiz H C; Aouada, Fauze A

    2017-01-01

    In this paper, series of novel nanocomposite hydrogels based on polyacrylamide (PAAm), carboxymethylcellulose (CMC) and nanoclay were synthesized. Hydrophilic, kinetic, spectroscopic and morphological properties were investigated as function of their constituents. Spectroscopic properties confirmed the obtaining of the nanocomposites. It was also observed that the nanocomposites have walls of pores with a more rugged morphology compared with the morphology of the hydrogel without clay, contributing to repel the water molecules. Besides, the results showed that the velocity and quantity of water uptake may be controlled by adjusting of matrix rigidity, i.e., nanoclay content into polymeric matrix. This behavior is required to future application in agriculture fields, specifically as carrier vehicle in controlled release of agrochemicals. Thus, these nanocomposites have technological application.

  6. Influence of Mo impurity on the spectroscopic and scintillation properties of PbWO4 crystals

    International Nuclear Information System (INIS)

    Boehm, M.; Hofstaetter, A.; Luh, M.; Meyer, B.K.; Scharmann, A.; Drobychev, G.Yu.; Grenoble-1 Univ., 74 - Annecy; Peigneux, J.P.

    1997-12-01

    The influence of molybdenum doping on the spectroscopic and scintillation properties of lead tungstate crystals has been investigated. From the results the slow scintillation component as well as the afterglow are found to be due to the Mo impurity. In addition the blue luminescence from excited (WO 4 ) 2- -complex seems to be increasingly suppressed as the doping concentration goes on. Possible mechanisms for the effects have been discussed. (author)

  7. Spectroscopic properties and conformational stability of Concholepas concholepas hemocyanin.

    Science.gov (United States)

    Idakieva, Krassimira; Nikolov, Peter; Chakarska, Irena; Genov, Nicolay; Shnyrov, Valery L

    2008-01-01

    The structure in solution and conformational stability of the hemocyanin from the Chilean gastropod mollusk Concholepas concholepas (CCH) and its structural subunits, CCH-A and CCH-B, were studied using fluorescence spectroscopy and differential scanning calorimetry (DSC). The fluorescence properties of the oxygenated and apo-form (copper-deprived) of the didecamer and its subunits were characterized. Besides tryptophan residues buried in the hydrophobic interior of the protein molecule also exposed fluorophores determine the fluorescence emission of the oxy- and apo-forms of the investigated hemocyanins. The copper-dioxygen system at the binuclear active site quenches the tryptophan emission of the oxy-forms of CCH and its subunits. The removal of this system increases the fluorescence quantum yield and causes structural rearrangement of the microenvironment of the emitting tryptophan residues in the respective apo-forms. Time-resolved fluorescence measurements show that the oxygenated and copper-deprived forms of the CCH and its subunits exist in different conformations. The thermal denaturation of the hemocyanin is an irreversible process, under kinetic control. A successive annealing procedure was applied to obtain the experimental deconvolution of the irreversible thermal transitions. Arrhenius equation parameter for the two-state irreversible model of the thermal denaturation of oxy-CCH at pH 7.2 was estimated. Both factors, oligomerization and the copper-dioxygen system at the active site, are important for stabilizing the structure of the hemocyanin molecule.

  8. Complexation (cucurbit[6]uril-pyrene): Thermodynamic and spectroscopic properties

    Energy Technology Data Exchange (ETDEWEB)

    Sueldo Occello, Valeria N.; Rossi, Rita H. de; Veglia, Alicia V., E-mail: aveglia@fcq.unc.edu.ar

    2015-02-15

    The influence of the macrocyclic compound cucurbit[6]uril (CB6) on the photophysical properties of the fluorophore pyrene (PYR) has been studied. Guest–host interaction was observed by UV–visible spectroscopy and spectrofluorimetry. The fluorescence of PYR was significantly increased in the presence of CB6. The binding equilibrium constants for the complex with 1:1 stoichiometry were determined in HCOOH 55% w/v. The values of the association constants, K{sub A}, and the fluorescence quantum yield ratios between complexed and free substrate, ϕ{sup PYR–CB6}/ϕ{sup PYR}, at different temperatures were (3.1±0.9)×10{sup 2} M{sup −1} and (5.1±0.2), (3.6±0.5)×10{sup 2} M{sup −1} and (5.9±0.1), (4.8±0.7)×10{sup 2} M{sup −1} and (5.5±0.1) at 15.0 °C, 25.0 °C and 40.0 °C, respectively. The enthalpic and entropic contributions to the complexation process were determined, yielding ΔS=(92±3) J mol{sup −1} K{sup −1} and ΔH=(13±1) kJ mol{sup −1}. From these results it can be concluded that the complex formation is mainly driven by the entropic term. The forces involved in the complexation are interpreted from the sign and magnitude of the thermodynamic parameters obtained. The partial inclusion of PYR or the formation of a suspended complex is proposed in base of all the data. The interaction is also demonstrated in the solid state by differential scanning calorimetric (DSC) measurements. - Highlights: • The cucurbit[6]uril (CB6) effects on the absorption and fluorescence of pyrene (PYR) were analyzed. • The association constant (K{sub A}) and the stoichiometry of the complex were determined. • The complex formation was confirmed by differential scanning calorimetry (DSC). • The thermodynamic parameters were determined. • The hydrophobic entropic contribution is the main driving force for the PYR–CB6 complex formation.

  9. Binding of Bisphenol-F, a bisphenol analogue, to calf thymus DNA by multi-spectroscopic and molecular docking studies.

    Science.gov (United States)

    Usman, Afia; Ahmad, Masood

    2017-08-01

    BPF (Bisphenol-F), a member of the bisphenol family, having a wide range of industrial applications is gradually replacing Bisphenol-A. It is a recognized endocrine disrupting chemical (EDC). EDCs have been implicated in increased incidences of breast, prostate and testis cancers besides diabetes, obesity and decreased fertility. Due to the adverse effects of EDCs on human health, attempts have been directed towards their mechanism of toxicity especially at the molecular level. Hence, to understand the mechanism at the DNA level, interaction of BPF with calf thymus DNA was studied employing multi-spectroscopic, voltammetric and molecular docking techniques. Fluorescence spectra, cyclic voltammetry (CV), circular dichroism (CD) and molecular docking studies of BPF with DNA were suggestive of minor groove binding of BPF. UV-visible absorption and fluorescence spectra suggested static quenching due to complex formation between BPF and ctDNA. Hoechst 33258 (HO) and ethidium bromide (EB) displacement studies further confirmed such mode of BPF interaction. Thermodynamic and molecular docking parameters revealed the mechanism of binding of BPF with ctDNA to be favorable and spontaneous due to negative ΔG and occurring through hydrogen bonds and van der waals interactions. BPF induced DNA cleavage under in vitro conditions by plasmid nicking assay suggested it to be genotoxic. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA.

    Science.gov (United States)

    Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

    2018-03-15

    Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 10 3 M -1 , which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) were -63.19kJ mol -1 and -141.92J mol -1 K -1 , indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA

    Science.gov (United States)

    Afrin, Shumaila; Rahman, Yusra; Sarwar, Tarique; Husain, Mohammed Amir; Ali, Abad; Shamsuzzaman; Tabish, Mohammad

    2017-11-01

    Ticlopidine is an anti-platelet drug which belongs to the thienopyridine structural family and exerts its effect by functioning as an ADP receptor inhibitor. Ticlopidine inhibits the expression of TarO gene in S. aureus and may provide protection against MRSA. Groove binding agents are known to disrupt the transcription factor DNA complex and consequently inhibit gene expression. Understanding the mechanism of interaction of ticlopidine with DNA can prove useful in the development of a rational drug designing system. At present, there is no such study on the interaction of anti-platelet drugs with nucleic acids. A series of biophysical experiments were performed to ascertain the binding mode between ticlopidine and calf thymus DNA. UV-visible and fluorescence spectroscopic experiments confirmed the formation of a complex between ticlopidine and calf thymus DNA. Moreover, the values of binding constant were found to be in the range of 103 M- 1, which is indicative of groove binding between ticlopidine and calf thymus DNA. These results were further confirmed by studying the effect of denaturation on double stranded DNA, iodide quenching, viscometric studies, thermal melting profile as well as CD spectral analysis. The thermodynamic profile of the interaction was also determined using isothermal titration calorimetric studies. The reaction was found to be endothermic and the parameters obtained were found to be consistent with those of known groove binders. In silico molecular docking studies further corroborated well with the experimental results.

  12. PHOTOMETRIC AND SPECTROSCOPIC PROPERTIES OF NOVAE IN THE LARGE MAGELLANIC CLOUD

    International Nuclear Information System (INIS)

    Shafter, A. W.

    2013-01-01

    The photometric and spectroscopic properties of the 43 known LMC nova candidates are summarized and reviewed. Of these, photometric data sufficient to establish decline rates are available for 29 novae, while spectroscopic data sufficient to establish the spectroscopic classes are available for 18 systems. Half of the 18 novae belong to the Fe II class, with the remaining nine belonging to either the He/N or the Fe IIb classes. As seen in previous nova studies of M31 and M33, the He/N and Fe IIb novae have on average faster photometric developments than do their Fe II counterparts. Overall, the available photometry confirms earlier studies, and shows conclusively that LMC novae have faster rates of decline than do novae in the Galaxy and M31. It appears that the increased fraction of faster, He/N and Fe IIb novae observed in the LMC compared with M31 is almost certainly the result of differences in the underlying stellar population between the two galaxies. We propose that the younger population seen in the LMC compared with M31's bulge (where most of the novae are found), produces progenitor binaries with higher average white dwarf masses. The higher mean white dwarf mass not only produces a larger fraction of fast, He/N novae compared with M31, but also results in a relatively large recurrent nova population.

  13. Spectroscopic study on the interaction of eugenol with salmon sperm DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun, E-mail: sy_bi@sina.com [College of Chemistry, Changchun Normal University, Changchun 130032 (China); Yan Lili; Wang Yu; Pang Bong; Wang Tianjiao [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2012-09-15

    Fluorescence spectra, absorption spectra, melting temperature, ionic strength effect, and viscosity experiments were described that characterize the interaction of eugenol with salmon sperm DNA in vitro. Eugenol was found to bind but weakly to DNA, with binding constants of 4.23 Multiplication-Sign 10{sup 3}, 3.62 Multiplication-Sign 10{sup 3} and 2.47 Multiplication-Sign 10{sup 3} L mol{sup -1} at 18, 28 and 38 Degree-Sign C respectively. The Stern-Volmer plots at different temperatures suggested that the quenching type of fluorescence of eugenol by DNA was a static quenching. Both the relative viscosity and the melting temperature of DNA were increased by the addition of eugenol. The changes of ionic strength had no affect on the binding. In addition, the binding constant of eugenol with single stranded DNA (ssDNA) was larger than that of eugenol with double stranded DNA (dsDNA). These results revealed that the binding mode of eugenol to DNA was intercalative binding. The thermodynamic parameters {Delta}H, {Delta}G and {Delta}S were also obtained according to the Van't Hoff equations, which suggested that hydrogen bond or van der Waals force might play an important role in a binding of eugenol to DNA. Based on the theory of the Foerster energy transference, the binding distance between DNA and eugenol was determined as 4.40 nm, indicating that the static fluorescence quenching of eugenol by DNA was also a non-radiation energy transfer process. - Highlights: Black-Right-Pointing-Pointer DNA quenched the fluorescence of eugenol. Black-Right-Pointing-Pointer Binding constant, binding site and binding force were determined. Black-Right-Pointing-Pointer Binding mode of eugenol to DNA was intercalative. Black-Right-Pointing-Pointer Energy transfer occurred between eugenol and DNA.

  14. Fiber optic spectroscopic digital imaging sensor and method for flame properties monitoring

    Science.gov (United States)

    Zelepouga, Serguei A [Hoffman Estates, IL; Rue, David M [Chicago, IL; Saveliev, Alexei V [Chicago, IL

    2011-03-15

    A system for real-time monitoring of flame properties in combustors and gasifiers which includes an imaging fiber optic bundle having a light receiving end and a light output end and a spectroscopic imaging system operably connected with the light output end of the imaging fiber optic bundle. Focusing of the light received by the light receiving end of the imaging fiber optic bundle by a wall disposed between the light receiving end of the fiber optic bundle and a light source, which wall forms a pinhole opening aligned with the light receiving end.

  15. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

    Science.gov (United States)

    Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

    2012-05-21

    In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

  16. Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

    Science.gov (United States)

    Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

    2012-10-01

    This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

  17. Theoretical study of H2/+/ spectroscopic properties. II, III. [2p and 3d excited electronic states

    Science.gov (United States)

    Beckel, C. L.; Shafi, M.; Peek, J. M.

    1973-01-01

    Description of the theoretical spectroscopic properties of the 2p pi/sub u/ and 3d sigma/sub g/ excited states of the H2/+/ hydrogen molecular ion. Numerical integration of the Schrodinger equation is used to determine vibration-rotation eigenvalues. Dunham power series expansions are used to determine the equilibrium separation, potential coefficients, and spectroscopic constants. The eigenvalues are used to determine delta-G, Bv, Dv, and Hv.

  18. Spectroscopic studies of the interaction between pirimicarb and calf thymus DNA

    Science.gov (United States)

    Zhang, Guowen; Hu, Xing; Pan, Junhui

    2011-02-01

    The interaction between pirimicarb and calf thymus DNA in physiological buffer (pH 7.4) was investigated with the use of Neutral Red (NR) dye as a spectral probe by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, as well as viscosity measurements and DNA melting techniques. The results revealed that an intercalation binding should be the interaction mode of pirimicarb to DNA. CD spectra indicated that pirimicarb induced conformational changes of DNA. The binding constants of pirimicarb with DNA were obtained by the fluorescence quenching method. The thermodynamic parameters, enthalpy change (Δ Hθ) and entropy change (Δ Sθ) were calculated to be -52.13 ± 2.04 kJ mol -1 and -108.8 ± 6.72 J mol -1 K -1 according to the van't Hoff equation, which suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of pirimicarb to DNA. Further, the alternative least squares (ALS) method was applied to resolve a complex two-way array of the absorption spectra data, which provided simultaneously the concentration information for the three reaction components, pirimicarb, NR and DNA-NR. This ALS analysis indicated that the intercalation of pirimicarb into the DNA by substituting for NR in the DNA-NR complex.

  19. Spectroscopic studies of the interaction between pirimicarb and calf thymus DNA.

    Science.gov (United States)

    Zhang, Guowen; Hu, Xing; Pan, Junhui

    2011-02-01

    The interaction between pirimicarb and calf thymus DNA in physiological buffer (pH 7.4) was investigated with the use of Neutral Red (NR) dye as a spectral probe by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, as well as viscosity measurements and DNA melting techniques. The results revealed that an intercalation binding should be the interaction mode of pirimicarb to DNA. CD spectra indicated that pirimicarb induced conformational changes of DNA. The binding constants of pirimicarb with DNA were obtained by the fluorescence quenching method. The thermodynamic parameters, enthalpy change (ΔHθ) and entropy change (ΔSθ) were calculated to be -52.13±2.04 kJ mol(-1) and -108.8±6.72 J mol(-1) K(-1) according to the van't Hoff equation, which suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of pirimicarb to DNA. Further, the alternative least squares (ALS) method was applied to resolve a complex two-way array of the absorption spectra data, which provided simultaneously the concentration information for the three reaction components, pirimicarb, NR and DNA-NR. This ALS analysis indicated that the intercalation of pirimicarb into the DNA by substituting for NR in the DNA-NR complex. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Unveiling DNA structural properties of promoter regions of ...

    Indian Academy of Sciences (India)

    Aditya Kumar

    Unveiling DNA structural properties of promoter regions of prokaryotic transcriptome and their role in gene expression. Aditya Kumar. Assistant Professor. Molecular Biology & Biotechnology. Tezpur University. Tezpur – 784028, Assam ...

  1. Natural organic UV-absorbent coatings based on cellulose and lignin: designed effects on spectroscopic properties.

    Science.gov (United States)

    Hambardzumyan, Arayik; Foulon, Laurence; Chabbert, Brigitte; Aguié-Béghin, Véronique

    2012-12-10

    Novel nanocomposite coatings composed of cellulose nanocrystals (CNCs) and lignin (either synthetic or fractionated from spruce and corn stalks) were prepared without chemical modification or functionalization (via covalent attachment) of one of the two biopolymers. The spectroscopic properties of these coatings were investigated by UV-visible spectrophotometry and spectroscopic ellipsometry. When using the appropriate weight ratio of CNC/lignin (R), these nanocomposite systems exhibited high-performance optical properties, high transmittance in the visible spectrum, and high blocking in the UV spectrum. Atomic force microscopy analysis demonstrated that these coatings were smooth and homogeneous, with visible dispersed lignin nodules in a cellulosic matrix. It was also demonstrated that the introduction of nanoparticles into the medium increases the weight ratio and the CNC-specific surface area, which allows better dispersion of the lignin molecules throughout the solid film. Consequently, the larger molecular expansion of these aromatic polymers on the surface of the cellulosic nanoparticles dislocates the π-π aromatic aggregates, which increases the extinction coefficient and decreases the transmittance in the UV region. These nanocomposite coatings were optically transparent at visible wavelengths.

  2. DFT calculations on spectroscopic and structural properties of a NLO chromophore

    Science.gov (United States)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2016-03-01

    The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

  3. Structure-Dependent Spectroscopic Properties of Yb3+-Doped Phosphosilicate Glasses Modified by SiO₂.

    Science.gov (United States)

    Wang, Ling; Zeng, Huidan; Yang, Bin; Ye, Feng; Chen, Jianding; Chen, Guorong; Smith, Andew T; Sun, Luyi

    2017-02-28

    Yb 3+ -doped phosphate glasses containing different amounts of SiO₂ were successfully synthesized by the conventional melt-quenching method. The influence mechanism of SiO₂ on the structural and spectroscopic properties was investigated systematically using the micro-Raman technique. It was worth noting that the glass with 26.7 mol % SiO₂ possessed the longest fluorescence lifetime (1.51 ms), the highest gain coefficient (1.10 ms·pm²), the maximum Stark splitting manifold of ²F 7/2 level (781 cm -1 ), and the largest scalar crystal-field N J and Yb 3+ asymmetry degree. Micro-Raman spectra revealed that introducing SiO₂ promoted the formation of P=O linkages, but broke the P=O linkages when the SiO₂ content was greater than 26.7 mol %. Based on the previous 29 Si MAS NMR experimental results, these findings further demonstrated that the formation of [SiO₆] may significantly affect the formation of P=O linkages, and thus influences the spectroscopic properties of the glass. These results indicate that phosphosilicate glasses may have potential applications as a Yb 3+ -doped gain medium for solid-state lasers and optical fiber amplifiers.

  4. Quantum chemical calculations and spectroscopic measurements of spectroscopic and thermodynamic properties of given uranyl complexes in aqueous solutions with possible environmental and industrial applications

    Directory of Open Access Journals (Sweden)

    Višňak Jakub

    2016-01-01

    Full Text Available A brief introduction into computational methodology and preliminary results for spectroscopic (excitation energies, vibrational frequencies in ground and excited electronic states and thermodynamic (stability constants, standard enthalpies and entropies of complexation reactions properties of some 1:1, 1:2 and 1:3 uranyl sulphato- and selenato- complexes in aqueos solutions will be given. The relativistic effects are included via Effective Core Potential (ECP, electron correlation via (TDDFT/B3LYP (dispersion interaction corrected and solvation is described via explicit inclusion of one hydration sphere beyond the coordinated water molecules. We acknowledge limits of this approximate description – more accurate calculations (ranging from semi-phenomenological two-component spin-orbit coupling up to four-component Dirac-Coulomb-Breit hamiltonian and Molecular Dynamics simulations are in preparation. The computational results are compared with the experimental results from Time-resolved Laser-induced Fluorescence Spectroscopy (TRLFS and UV-VIS spectroscopic studies (including our original experimental research on this topic. In case of the TRLFS and UV-VIS speciation studies, the problem of complex solution spectra decomposition into individual components is ill-conditioned and hints from theoretical chemistry could be very important. Qualitative agreement between our quantum chemical calculations of the spectroscopic properties and experimental data was achieved. Possible applications for geochemical modelling (e.g. safety studies of nuclear waste repositories, modelling of a future mining site and analytical chemical studies (including natural samples are discussed.

  5. Spectroscopic study of site selective DNA damage induced by intense soft X-rays

    CERN Document Server

    Fujii, K

    2003-01-01

    To investigate the mechanisms of DNA damage induced by direct photon impact, we observed the near edge X-ray absorption fine structures (NEXAFS) of DNA nucleobases using monochromatic synchrotron soft X-rays around nitrogen and oxygen K-shell excitation regions. Each spectrum obtained has unique structure corresponding to pi* excitation of oxygen or nitrogen 1s electron. These aspects open a way of nucleobase-selective photo-excitation in a DNA molecule using high resolution monochromatized soft X-rays. From the analysis of polarization-dependent intensities of the pi* resonance peak, it is clarified that adenine, guanine an uracil form orientated surface structure. Furthermore from the direct measurement of positive ions desorbed from photon irradiated DNA components, it is revealed that the sugar moiety is a fragile site in a DNA molecule. (author)

  6. Optical properties of gold island films-a spectroscopic ellipsometry study

    Energy Technology Data Exchange (ETDEWEB)

    Loncaric, Martin, E-mail: mloncaric@irb.hr; Sancho-Parramon, Jordi; Zorc, Hrvoje

    2011-02-28

    Metal island films of noble metals are obtained by deposition on glass substrates during the first stage of evaporation process when supported metal nanoparticles are formed. These films show unique optical properties, owing to the localized surface plasmon resonance of free electrons in metal nanoparticles. In the present work we study the optical properties of gold metal island films deposited on glass substrates with different mass thicknesses at different substrate temperatures. The optical characterization is performed by spectroscopic ellipsometry at different angles of incidence and transmittance measurements at normal incidence in the same point of the sample. Fitting of the ellipsometric data allows determining the effective optical constants and thickness of the island film. A multiple oscillator approach was used to successfully represent the dispersion of the effective optical constants of the films.

  7. Modeling the transport properties of epitaxially grown thermoelectric oxide thin films using spectroscopic ellipsometry

    KAUST Repository

    Sarath Kumar, S. R.

    2012-02-01

    The influence of oxygen vacancies on the transport properties of epitaxial thermoelectric (Sr,La)TiO3 thin films is determined using electrical and spectroscopic ellipsometry (SE) measurements. Oxygen vacancy concentration was varied by ex-situ annealing in Ar and Ar/H2. All films exhibited degenerate semiconducting behavior, and electrical conductivity decreased (258–133 S cm−1) with increasing oxygen content. Similar decrease in the Seebeck coefficient is observed and attributed to a decrease in effective mass (7.8–3.2 me ), as determined by SE. Excellent agreement between transport properties deduced from SE and direct electrical measurements suggests that SE is an effective tool for studying oxide thin film thermoelectrics.

  8. Modeling the transport properties of epitaxially grown thermoelectric oxide thin films using spectroscopic ellipsometry

    KAUST Repository

    Sarath Kumar, S. R.; Abutaha, Anas I.; Hedhili, Mohamed N.; Alshareef, Husam N.

    2012-01-01

    The influence of oxygen vacancies on the transport properties of epitaxial thermoelectric (Sr,La)TiO3 thin films is determined using electrical and spectroscopic ellipsometry (SE) measurements. Oxygen vacancy concentration was varied by ex-situ annealing in Ar and Ar/H2. All films exhibited degenerate semiconducting behavior, and electrical conductivity decreased (258–133 S cm−1) with increasing oxygen content. Similar decrease in the Seebeck coefficient is observed and attributed to a decrease in effective mass (7.8–3.2 me ), as determined by SE. Excellent agreement between transport properties deduced from SE and direct electrical measurements suggests that SE is an effective tool for studying oxide thin film thermoelectrics.

  9. Synergistic effects of atmospheric pressure plasma-emitted components on DNA oligomers: a Raman spectroscopic study.

    Science.gov (United States)

    Edengeiser, Eugen; Lackmann, Jan-Wilm; Bründermann, Erik; Schneider, Simon; Benedikt, Jan; Bandow, Julia E; Havenith, Martina

    2015-11-01

    Cold atmospheric-pressure plasmas have become of increasing importance in sterilization processes especially with the growing prevalence of multi-resistant bacteria. Albeit the potential for technological application is obvious, much less is known about the molecular mechanisms underlying bacterial inactivation. X-jet technology separates plasma-generated reactive particles and photons, thus allowing the investigation of their individual and joint effects on DNA. Raman spectroscopy shows that particles and photons cause different modifications in DNA single and double strands. The treatment with the combination of particles and photons does not only result in cumulative, but in synergistic effects. Profilometry confirms that etching is a minor contributor to the observed DNA damage in vitro. Schematics of DNA oligomer treatment with cold atmospheric-pressure plasma. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Influence of Gd2O3 on thermal and spectroscopic properties of aluminosilicate glasses

    Science.gov (United States)

    Kasprzyk, Marta; Środa, Marcin

    2018-06-01

    A series of aluminosilicate glasses 25SiO2·(20-x)Al2O3·40Na2O·15BaO-xGd2O3 with 0 ≤ x ≤ 10 were prepared in order to analyze the influence of gadolinium on thermal and spectroscopic properties of these materials. Increasing of thermal parameters (Tg, Tx, Δcp, ΔT) values with higher Gd2O3 content was determined using DSC method. Crystalline phases, formed during heat treatment, were identified with XRD - NaAlSiO4 and BaSiO3 in glass with 0% mol. Gd2O3 and Gd9.33(SiO4)6O2, NaAlSiO4 and BaAl2Si2O6 in glass with 10% mol. Gd2O3. Spectroscopic analysis - FTIR and Raman - revealed Gd2O3 influence on glass structure in the same way like Al2O3, but some differences appear due to the differ bond strength and ionic radius between Gd and Al. Raman spectra confirmed higher network polymerization (enriched with Q2 units). Optical band gap energy (Eopt) and Urbach energy (ΔE) were calculated from the Tauc plot. Mechanical tests demonstrated lower microhardness with increasing content of Gd2O3 content, as a result of higher concentration of atoms with larger radius.

  11. Spectroscopic analysis of radiation-generated changes in tensile properties of a polyetherimide film

    International Nuclear Information System (INIS)

    Long, E.R. Jr.; Long, S.A.T.

    1985-05-01

    The effects of electron radiation on Ultem, a polyetherimide were studied for doses from 2 x 10 to the 9th power to 6 x 10 to the 9th power rad. Specimens were studied for tensile property testing and for electron paramagnetic resonance and infrared spectroscopic measurements of molecular structure. A Faraday cup design and a method for remote temperature measurement were developed. The spectroscopic data show that radiation caused dehydrogenation of methyl groups, rupture of main-chain ether linkage, and opening of imide rings, all to form radicals and indicate that the so-formed atomic hydrogen attached to phenyl radicals, but not to phenoxyl radicals, which would have formed hydroxyls. The observed decays of the radiation-generated phenoxyl, gem-dimethyl, and carbonyl radicals were interpreted as a combining of the radicals to form crosslinking. This crosslinking is the probable cause of the major reduction in the elongation of the tensile specimens after irradiation. Subsequent classical solubility tests indicate that the irradiation caused massive crosslinking

  12. Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

    Science.gov (United States)

    Zhu, Pan; Zhang, Guowen; Ma, Yadi; Zhang, Yepeng; Miao, Hong; Wu, Yongning

    2013-08-01

    The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 104 L mol-1. Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13 ± 1.89 kJ mol-1 and -22.79 ± 1.21 J mol-1 K-1, respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

  13. Spectroscopic and molecular modeling study on the interaction of ctDNA with 3′-deoxy-3′-azido doxorubicin

    International Nuclear Information System (INIS)

    Geng, Shaoguang; Cui, Yanrui; Liu, Qingfeng; Cui, Fengling; Zhang, Guisheng; Chi, Yanwei; Peng, Hao

    2013-01-01

    The method of synthesizing 3′-deoxy-3′-azido doxorubicin (ADOX) directly from doxorubicin has been developed. This study presents the interaction between ADOX and calf thymus deoxyribonucleic acid (ctDNA) by using spectroscopic methods and molecular modeling techniques. Iodide quenching, fluorescence polarization, viscosity and molecular modeling studies of ADOX–ctDNA interactions indicated that ADOX was an intercalator of ctDNA and preferentially bound to C–G rich regions of ctDNA. Simultaneously, spectroscopic results indicated that the quenching mechanism of ADOX–ctDNA was a static quenching. According to thermodynamic parameters, electrostatic force played roles in the interaction of ADOX with ctDNA. -- Highlights: ●An approach to 3′-deoxy-3′-azido doxorubicin (ADOX) from doxorubicin was developed. ●The quenching mechanism of ADOX with ctDNA was a static quenching type. ●The binding mode between ADOX and ctDNA was intercalative binding. ●The results of molecular docking corroborated results of spectra investigations

  14. Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Moral, Monica; Garcia, Gregorio [Departamento de Quimica Fisica y Analitica, Facultad de Ciencias Experimentales, Universidad de Jaen, Campus las Lagunillas, E23071 Jaen (Spain); Penas, Antonio [Departamento de Quimica Inorganica y Organica, Facultad de Ciencias Experimentales, Universidad de Jaen, Campus las Lagunillas, E23071 Jaen (Spain); Garzon, Andres; Granadino-Roldan, Jose M. [Departamento de Quimica Fisica y Analitica, Facultad de Ciencias Experimentales, Universidad de Jaen, Campus las Lagunillas, E23071 Jaen (Spain); Melguizo, Manuel [Departamento de Quimica Inorganica y Organica, Facultad de Ciencias Experimentales, Universidad de Jaen, Campus las Lagunillas, E23071 Jaen (Spain); Fernandez-Gomez, Manuel, E-mail: mfg@ujaen.es [Departamento de Quimica Fisica y Analitica, Facultad de Ciencias Experimentales, Universidad de Jaen, Campus las Lagunillas, E23071 Jaen (Spain)

    2012-10-26

    Highlights: Black-Right-Pointing-Pointer We study properties of Ph{sub 2}Tz and (PhTz){sub n}Ph as candidates for organic electronics. Black-Right-Pointing-Pointer The synthesis of Ph{sub 2}Tz was performed through a modified Pinner-type reaction. Black-Right-Pointing-Pointer IR/Raman spectra allowed to conclude that Ph{sub 2}Tz is nearly planar in liquid phase. Black-Right-Pointing-Pointer Electronic structure was studied by UV-Vis/TD-DFT methods in different solvents. Black-Right-Pointing-Pointer Bandgap, E{sub LUMO}, electron mobility predict some n-type character for limit polymer. -- Abstract: This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph{sub 2}Tz) and some oligomeric derivatives. Ph{sub 2}Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

  15. Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

    International Nuclear Information System (INIS)

    Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

    2012-01-01

    Highlights: ► We study properties of Ph 2 Tz and (PhTz) n Ph as candidates for organic electronics. ► The synthesis of Ph 2 Tz was performed through a modified Pinner-type reaction. ► IR/Raman spectra allowed to conclude that Ph 2 Tz is nearly planar in liquid phase. ► Electronic structure was studied by UV–Vis/TD-DFT methods in different solvents. ► Bandgap, E LUMO , electron mobility predict some n-type character for limit polymer. -- Abstract: This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph 2 Tz) and some oligomeric derivatives. Ph 2 Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV–Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

  16. Physicotechnical, spectroscopic and thermogravimetric properties of powdered cellulose and microcrystalline cellulose derived from groundnut shells

    Directory of Open Access Journals (Sweden)

    Chukwuemeka P. Azubuike

    2012-09-01

    Full Text Available α-Cellulose and microcrystalline cellulose powders, derived from agricultural waste products, that have for the pharmaceutical industry, desirable physical (flow properties were investigated. α–Cellulose (GCN was extracted from groundnut shell (an agricultural waste product using a non-dissolving method based on inorganic reagents. Modification of this α -cellulose was carried out by partially hydrolysing it with 2N hydrochloric acid under reflux to obtain microcrystalline cellulose (MCGN. The physical, spectroscopic and thermal properties of the derived α-cellulose and microcrystalline cellulose powders were compared with Avicel® PH 101, a commercial brand of microcrystalline cellulose (MCCA, using standard methods. X-ray diffraction and infrared spectroscopy analysis showed that the α-cellulose had lower crystallinity. This suggested that treatment with 2N hydrochloric acid led to an increase in the crystallinity index. Thermogravimetric analysis showed quite similar thermal behavior for all cellulose samples, although the α-cellulose had a somewhat lower stability. A comparison of the physical properties between the microcrystalline celluloses and the α-cellulose suggests that microcrystalline cellulose (MCGN and MCCA might have better flow properties. In almost all cases, MCGN and MCCA had similar characteristics. Since groundnut shells are agricultural waste products, its utilization as a source of microcrystalline cellulose might be a good low-cost alternative to the more expensive commercial brand.

  17. An Ultraviolet Resonance Raman Spectroscopic Study of Cisplatin and Transplatin Interactions with Genomic DNA.

    Science.gov (United States)

    Geng, Jiafeng; Aioub, Mena; El-Sayed, Mostafa A; Barry, Bridgette A

    2017-09-28

    Ultraviolet resonance Raman (UVRR) spectroscopy is a label-free method to define biomacromolecular interactions with anticancer compounds. Using UVRR, we describe the binding interactions of two Pt(II) compounds, cisplatin (cis-diamminedichloroplatinum(II)) and its isomer, transplatin, with nucleotides and genomic DNA. Cisplatin binds to DNA and other cellular components and triggers apoptosis, whereas transplatin is clinically ineffective. Here, a 244 nm UVRR study shows that purine UVRR bands are altered in frequency and intensity when mononucleotides are treated with cisplatin. This result is consistent with previous suggestions that purine N7 provides the cisplatin-binding site. The addition of cisplatin to DNA also causes changes in the UVRR spectrum, consistent with binding of platinum to purine N7 and disruption of hydrogen-bonding interactions between base pairs. Equally important is that transplatin treatment of DNA generates similar UVRR spectral changes, when compared to cisplatin-treated samples. Kinetic analysis, performed by monitoring decreases of the 1492 cm -1 band, reveals biphasic kinetics and is consistent with a two-step binding mechanism for both platinum compounds. For cisplatin-DNA, the rate constants (6.8 × 10 -5 and 6.5 × 10 -6 s -1 ) are assigned to the formation of monofunctional adducts and to bifunctional, intrastrand cross-linking, respectively. In transplatin-DNA, there is a 3.4-fold decrease in the rate constant of the slow phase, compared with the cisplatin samples. This change is attributed to generation of interstrand, rather than intrastrand, adducts. This longer reaction time may result in increased competition in the cellular environment and account, at least in part, for the lower pharmacological efficacy of transplatin.

  18. Optical properties of LiGaS2: an ab initio study and spectroscopic ellipsometry measurement

    International Nuclear Information System (INIS)

    Atuchin, V V; Lin, Z S; Isaenko, L I; Lobanov, S I; Kesler, V G; Kruchinin, V N

    2009-01-01

    Electronic and optical properties of lithium thiogallate crystal, LiGaS 2 , have been investigated by both experimental and theoretical methods. The plane-wave pseudopotential method based on DFT theory has been used for band structure calculations. The electronic parameters of Ga 3d orbitals have been corrected by the DFT+U methods to be consistent with those measured with x-ray photoemission spectroscopy. Evolution of optical constants of LiGaS 2 over a wide spectral range was determined by developed first-principles theory and dispersion curves were compared with optical parameters defined by spectroscopic ellipsometry in the photon energy range 1.2-5.0 eV. Good agreement has been achieved between theoretical and experimental results.

  19. Does the Intramolecular Hydrogen Bond Affect the Spectroscopic Properties of Bicyclic Diazole Heterocycles?

    Directory of Open Access Journals (Sweden)

    Paweł Misiak

    2018-01-01

    Full Text Available The formation of an intramolecular hydrogen bond in pyrrolo[1,2-a]pyrazin-1(2H-one bicyclic diazoles was analyzed, and the influence of N-substitution on HB formation is discussed in this study. B3LYP/aug-cc-pVDZ calculations were performed for the diazole, and the quantum theory of atoms in molecules (QTAIM approach as well as the natural bond orbital (NBO method was applied to analyze the strength of this interaction. It was found that the intramolecular hydrogen bond that closes an extra ring between the C=O proton acceptor group and the CH proton donor, that is, C=O⋯H–C, influences the spectroscopic properties of pyrrolopyrazine bicyclic diazoles, particularly the carbonyl frequencies. The influence of N-substitution on the aromaticity of heterocyclic rings is also discussed in this report.

  20. Preparation and spectroscopic properties of Yb-doped and Yb-Al-codoped high silica glasses

    International Nuclear Information System (INIS)

    Qiao Yanbo; Wen Lei; Wu Botao; Ren Jinjun; Chen Danping; Qiu Jianrong

    2008-01-01

    Yb-doped and Yb-Al-codoped high silica glasses have been prepared by sintering nanoporous glasses. The absorption, fluorescent spectra and fluorescent lifetimes have been measured and the emission cross-section and minimum pump intensities were calculated. Codoping aluminum ions enhanced the fluorescence intensity of Yb-doped high silica glass obviously. The emission cross-sections of Yb-doped and Yb-Al-codoped high silica glasses were 0.65 and 0.82 pm 2 , respectively. The results show that Yb-Al-codoped high silica glass has better spectroscopic properties for a laser material. The study of high silica glass doped with ytterbium is helpful for its application in Yb laser systems, especially for high-power and high-repetition lasers

  1. Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

    Science.gov (United States)

    Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta’ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

    2016-01-01

    The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology. PMID:27435636

  2. Transitional circuitry for studying the properties of DNA

    Science.gov (United States)

    Trubochkina, N.

    2018-01-01

    The article is devoted to a new view of the structure of DNA as an intellectual scheme possessing the properties of logic and memory. The theory of transient circuitry, developed by the author for optimal computer circuits, revealed an amazing structural similarity between mathematical models of transition silicon elements and logic and memory circuits of solid state transient circuitry and atomic models of parts of DNA.

  3. Spectroscopic study of a DNA brush synthesized in situ by surface initiated enzymatic polymerization.

    Science.gov (United States)

    Khan, M Nuruzzaman; Tjong, Vinalia; Chilkoti, Ashutosh; Zharnikov, Michael

    2013-08-29

    We used a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the chemical integrity, purity, and possible internal alignment of single-strand (ss) adenine deoxynucleotide (poly(A)) DNA brushes. The brushes were synthesized by surface-initiated enzymatic polymerization (SIEP) on a 25-mer of adenine self-assembled monolayer (SAM) on gold (A25-SH), wherein the terminal 3'-OH of the A25-SH serve as the initiation sites for SIEP of poly(A). XPS and NEXAFS spectra of poly(A) brushes were found to be almost identical to those of A25-SH initiator, with no unambiguous traces of contamination. Apart from the well-defined chemical integrity and contamination-free character, the brushes were found to have a high degree of orientational order, with an upright orientation of individual strands, despite their large thickness up to ~55 nm, that corresponds to a chain length of at least several hundred nucleotides for individual ssDNA molecules. The orientational order exhibited by these poly(A) DNA brushes, mediated presumably by base stacking, was found to be independent of the brush thickness as long as the packing density was high enough. The well-defined character and orientational ordering of the ssDNA brushes make them a potentially promising system for different applications.

  4. DNA interaction studies of new nano metal based anticancer agent: validation by spectroscopic methods

    International Nuclear Information System (INIS)

    Tabassum, Sartaj; Chandra Sharma, Girish; Arjmand, Farukh; Azam, Ameer

    2010-01-01

    A new nano dimensional heterobimetallic Cu-Sn containing complex as a potential drug candidate was designed, synthesized and characterized by analytical and spectral methods. The electronic absorption and electron paramagnetic resonance parameters of the complex revealed that the Cu(II) ion exhibits a square pyramidal geometry with the two pyrazole nitrogen atoms, the amine nitrogen atom and the carboxylate oxygen of the phenyl glycine chloride ligand located at the equatorial sites and the coordinated chloride ion occupying an apical position. 119 Sn NMR spectral data showed a hexa-coordinated environment around the Sn(IV) metal ion. TEM, AFM and XRD measurements illustrate that the complex could induce the condensation of CT-DNA to a particulate nanostructure. The interaction of the Cu-Sn complex with CT-DNA was investigated by UV-vis absorption and emission spectroscopy, as well as cyclic voltammetric measurements. The results indicated that the complex interacts with DNA through an electrostatic mode of binding with an intrinsic binding constant K b = 8.42 x 10 4 M -1 . The Cu-Sn complex exhibits effective cleavage of pBR322 plasmid DNA by an oxidative cleavage mechanism, monitored at different concentrations both in the absence and in the presence of reducing agents.

  5. DNA interaction studies of new nano metal based anticancer agent: validation by spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Tabassum, Sartaj; Chandra Sharma, Girish; Arjmand, Farukh [Department of Chemistry, Aligarh Muslim University, Aligarh-202002 (India); Azam, Ameer [Center of Excellence in Materials Science (Nanomaterials), Department of Applied Physics, Aligarh Muslim University, Aligarh 202002, UP (India)

    2010-05-14

    A new nano dimensional heterobimetallic Cu-Sn containing complex as a potential drug candidate was designed, synthesized and characterized by analytical and spectral methods. The electronic absorption and electron paramagnetic resonance parameters of the complex revealed that the Cu(II) ion exhibits a square pyramidal geometry with the two pyrazole nitrogen atoms, the amine nitrogen atom and the carboxylate oxygen of the phenyl glycine chloride ligand located at the equatorial sites and the coordinated chloride ion occupying an apical position. {sup 119}Sn NMR spectral data showed a hexa-coordinated environment around the Sn(IV) metal ion. TEM, AFM and XRD measurements illustrate that the complex could induce the condensation of CT-DNA to a particulate nanostructure. The interaction of the Cu-Sn complex with CT-DNA was investigated by UV-vis absorption and emission spectroscopy, as well as cyclic voltammetric measurements. The results indicated that the complex interacts with DNA through an electrostatic mode of binding with an intrinsic binding constant K{sub b} = 8.42 x 10{sup 4} M{sup -1}. The Cu-Sn complex exhibits effective cleavage of pBR322 plasmid DNA by an oxidative cleavage mechanism, monitored at different concentrations both in the absence and in the presence of reducing agents.

  6. DNA origami compliant nanostructures with tunable mechanical properties.

    Science.gov (United States)

    Zhou, Lifeng; Marras, Alexander E; Su, Hai-Jun; Castro, Carlos E

    2014-01-28

    DNA origami enables fabrication of precise nanostructures by programming the self-assembly of DNA. While this approach has been used to make a variety of complex 2D and 3D objects, the mechanical functionality of these structures is limited due to their rigid nature. We explore the fabrication of deformable, or compliant, objects to establish a framework for mechanically functional nanostructures. This compliant design approach is used in macroscopic engineering to make devices including sensors, actuators, and robots. We build compliant nanostructures by utilizing the entropic elasticity of single-stranded DNA (ssDNA) to locally bend bundles of double-stranded DNA into bent geometries whose curvature and mechanical properties can be tuned by controlling the length of ssDNA strands. We demonstrate an ability to achieve a wide range of geometries by adjusting a few strands in the nanostructure design. We further developed a mechanical model to predict both geometry and mechanical properties of our compliant nanostructures that agrees well with experiments. Our results provide a basis for the design of mechanically functional DNA origami devices and materials.

  7. Sequence dependent DNA conformations: Raman spectroscopic studies and a model of action of restriction enzymes

    International Nuclear Information System (INIS)

    Nishimura, Y.

    1985-01-01

    Raman spectra have been examined to clarify the polymorphic forms of DNA, A, B, and Z forms. From an analysis the authors found that the guanine ring breathing vibration is sensitive to its local conformation. Examination of nine crystals of guanosine residues in which the local conformations are well established revealed that a guanosine residue with a C3'endo-anti gives a strong line at 666+-2 cm/sup -1/, O4'endo-anti at 682 cm/sup -1/, C1'exo-anti at 673 cm/sup -1/, C2'endo-anti at 677 cm/sup -1/ and syn-forms around 625 cm/sup -1/. Using this characteristic line, they were able to obtain the local conformations of guanosine moieties in poly(dG-dC). Such a sequence derived variation is suggested to be recognized by sequence specific proteins such as restriction enzymes. The authors found a correlation between sequence dependent DNA conformation and a mode of action of restriction enzymes. The cutting mode of restriction enzymes is classified into three groups. The classification of whether the products have blunt ends, two-base-long cohesive ends, or four-base-long cohesive ends depends primarily on the substrate, not on the enzyme. It is suggested that sequence dependent DNA conformation causes such a classification by the use of the Calladine-Dickerson analysis. In the recognition of restriction enzymes, the methyl group in a certain sequence is considered to play an important role by changing the local conformation of DNA

  8. Static and Dynamic Properties of DNA Confined in Nanochannels

    Science.gov (United States)

    Gupta, Damini

    Next-generation sequencing (NGS) techniques have considerably reduced the cost of high-throughput DNA sequencing. However, it is challenging to detect large-scale genomic variations by NGS due to short read lengths. Genome mapping can easily detect large-scale structural variations because it operates on extremely large intact molecules of DNA with adequate resolution. One of the promising methods of genome mapping is based on confining large DNA molecules inside a nanochannel whose cross-sectional dimensions are approximately 50 nm. Even though this genome mapping technology has been commercialized, the current understanding of the polymer physics of DNA in nanochannel confinement is based on theories and lacks much needed experimental support. The results of this dissertation are aimed at providing a detailed experimental understanding of equilibrium properties of nanochannel-confined DNA molecules. The results are divided into three parts. In first part, we evaluate the role of channel shape on thermodynamic properties of channel confined DNA molecules using a combination of fluorescence microscopy and simulations. Specifically, we show that high aspect ratio of rectangular channels significantly alters the chain statistics as compared to an equivalent square channel with same cross-sectional area. In the second part, we present experimental evidence that weak excluded volume effects arise in DNA nanochannel confinement, which form the physical basis for the extended de Gennes regime. We also show how confinement spectroscopy and simulations can be combined to reduce molecular weight dispersity effects arising from shearing, photo-cleavage, and nonuniform staining of DNA. Finally, the third part of the thesis concerns the dynamic properties of nanochannel confined DNA. We directly measure the center-of-mass diffusivity of single DNA molecules in confinement and show that that it is necessary to modify the classical results of de Gennes to account for local chain

  9. Synthesis, spectroscopic characterization and structural investigations of a new charge transfer complex of 2,6-diaminopyridine with 3,5-dinitrobenzoic acid: DNA binding and antimicrobial studies

    Science.gov (United States)

    Khan, Ishaat M.; Ahmad, Afaq; Kumar, Sarvendra

    2013-03-01

    A new charge transfer (CT) complex [(DAPH)+(DNB)-] consisting of 2,6-diaminopyridine (DAP) as donor and 3,5-dinitrobenzoic acid (DNB-H) as acceptor, was synthesized and characterized by FTIR, 1H and 13C NMR, ESI mass spectroscopic and X-ray crystallographic techniques. The hydrogen bonding (N+-H⋯O-) plays an important role to consolidate the cation and anion together. CT complex shows a considerable interaction with Calf thymus DNA. The CT complex was also tested for its antibacterial activity against two Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis and two Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa strains by using Tetracycline as standard, and antifungal property against Aspergillus niger, Candida albicans, and Penicillium sp. by using Nystatin as standard. The results were compared with standard drugs and significant conclusions were obtained. A polymeric net work through H-bonding interactions between neighboring moieties was observed. This has been attributed to the formation of 1:1 type CT complex.

  10. Synthesis and spectroscopic properties of transfermium isotopes with Z = 105, 106 and 107

    International Nuclear Information System (INIS)

    Streicher, B.

    2006-01-01

    The quest for production of new elements has been on for several decades. On the way up the ladder of nuclear chart the systematic research of nuclear properties of elements in transfermium region has been severely overlooked. This drawback is being rectified in past few years by systematic synthesis of especially even-even and odd-A isotopes of these elements. This work proceeds forward also with major contribution of velocity filter SHIP, placed at GSI, Darmstadt. This experimental device represents a unique possibility due to high (up to 1 pμA) beam currents provided by UNILAC accelerator and advancing detection systems to study by means of decay spectroscopy the nuclear structure of isotopes for the elements, possibly up to proton number Z = 110. As the low lying single-particle levels are especially determined by the unpaired nucleon, the odd mass nuclei provide a valuable source of information about the nuclear structure. Such results can be directly compared with the predictions of the calculations based on macroscopic-microscopic model of nuclear matter, thus proving an unambiguous test of the correctness of present models and their power to predict nuclear properties towards yet unknown regions. This work concentrates on the spectroscopic analysis of few of such nuclei. Namely it deals with isotopes 261 Sg and 257 Rf with one unpaired neutron, as well as isotopes 257 Db and 253 Lr with one unpaired proton configuration. Moreover, the analysis of odd-odd nuclei of the the decay sequence 262 Bg → 258 Db → 254 Lr → produced in various experiments at SHIP is discussed in detail. Exhaustive spectroscopic analysis of these data is provided, revealing new information on α, β, EC and SF decay modes of these very heavy isotopes, and deepening the knowledge of the low lying single-particle level structure. Outcomes resulting from the comparison with the systematics of experimentally derived nuclear properties as well as with the predictions of the

  11. Synthesis and spectroscopic properties of transfermium isotopes with Z = 105, 106 and 107

    Energy Technology Data Exchange (ETDEWEB)

    Streicher, B [Comenius University, Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biopgysics, 84218 Bratislava (Slovakia)

    2006-07-01

    The quest for production of new elements has been on for several decades. On the way up the ladder of nuclear chart the systematic research of nuclear properties of elements in transfermium region has been severely overlooked. This drawback is being rectified in past few years by systematic synthesis of especially even-even and odd-A isotopes of these elements. This work proceeds forward also with major contribution of velocity filter SHIP, placed at GSI, Darmstadt. This experimental device represents a unique possibility due to high (up to 1 p{mu}A) beam currents provided by UNILAC accelerator and advancing detection systems to study by means of decay spectroscopy the nuclear structure of isotopes for the elements, possibly up to proton number Z = 110. As the low lying single-particle levels are especially determined by the unpaired nucleon, the odd mass nuclei provide a valuable source of information about the nuclear structure. Such results can be directly compared with the predictions of the calculations based on macroscopic-microscopic model of nuclear matter, thus proving an unambiguous test of the correctness of present models and their power to predict nuclear properties towards yet unknown regions. This work concentrates on the spectroscopic analysis of few of such nuclei. Namely it deals with isotopes {sup 261}Sg and {sup 257}Rf with one unpaired neutron, as well as isotopes {sup 257}Db and {sup 253}Lr with one unpaired proton configuration. Moreover, the analysis of odd-odd nuclei of the the decay sequence {sup 262}Bg {yields} {sup 258}Db {yields} {sup 254}Lr {yields} produced in various experiments at SHIP is discussed in detail. Exhaustive spectroscopic analysis of these data is provided, revealing new information on {alpha}, {beta}, EC and SF decay modes of these very heavy isotopes, and deepening the knowledge of the low lying single-particle level structure. Outcomes resulting from the comparison with the systematics of experimentally derived

  12. DNA Nucleotides Detection via capacitance properties of Graphene

    Science.gov (United States)

    Khadempar, Nahid; Berahman, Masoud; Yazdanpanah, Arash

    2016-05-01

    In the present paper a new method is suggested to detect the DNA nucleotides on a first-principles calculation of the electronic features of DNA bases which chemisorbed to a graphene sheet placed between two gold electrodes in a contact-channel-contact system. The capacitance properties of graphene in the channel are surveyed using non-equilibrium Green's function coupled with the Density Functional Theory. Thus, the capacitance properties of graphene are theoretically investigated in a biological environment, and, using a novel method, the effect of the chemisorbed DNA nucleotides on electrical charges on the surface of graphene is deciphered. Several parameters in this method are also extracted including Electrostatic energy, Induced density, induced electrostatic potential, Electron difference potential and Electron difference density. The qualitative and quantitative differences among these parameters can be used to identify DNA nucleotides. Some of the advantages of this approach include its ease and high accuracy. What distinguishes the current research is that it is the first experiment to investigate the capacitance properties of gaphene changes in the biological environment and the effect of chemisorbed DNA nucleotides on the surface of graphene on the charge.

  13. Synthesis, characterization, spectroscopic properties and DFT study of a new pyridazinone family

    Science.gov (United States)

    Arrue, Lily; Rey, Marina; Rubilar-Hernandez, Carlos; Correa, Sebastian; Molins, Elies; Norambuena, Lorena; Zarate, Ximena; Schott, Eduardo

    2017-11-01

    Nitrogen compounds are widely investigated due to their pharmacological properties such as antihypertensive, antinociceptive, antibacterial, antifungal, analgesic, anticancer and inhibition activities and lately even as pesticide. In this context, we present the synthesis of new compounds: (E)-6-(3,4-dimethoxyphenyl)-3-(3-(3,4-dimethoxyphenyl)acryloyl)-1-(4-R-phenyl)- 5,6-dihydropyridazin-4(1H)-one (with R = sbnd H(1), -Cl(2), -Br(3), sbnd I(4) and sbnd COOH(5)) that was carried out by reaction of (1E, 6E)-1,7-bis(3,4-dimethoxyphenyl)hepta-1,6-diene-3,5-dione with a substituted phenylamine with general formula p-R-C6H4sbnd NH2 (R = sbnd H (1), sbnd Cl (2), -Br(3), sbnd I(4) and sbnd COOH(5)). This is the first synthesis report of a pyridazinone using as precursors a curcuminoid derivative and a diazonium salt formed in situ. All compounds were characterized by EA, FT-IR, UV-Vis, Emission,1H- and13C-NMR spectroscopy and the crystalline and molecular structure of 4 was solved by X-rays diffraction method. DFT and TD-DFT quantum chemical calculations were also employed to characterize the compounds and provide a rational explanation to the spectroscopic properties. To assess the biological activity of the systems, we focused on pesticide tests on compound 2, which showed an inhibitory effect in plant growth of Agrostis tenuis Higland.

  14. Spectroscopic study on variations in illite surface properties after acid-base titration.

    Science.gov (United States)

    Liu, Wen-xin; Coveney, R M; Tang, Hong-xiao

    2003-07-01

    FT-IR, Raman microscopy, XRD, 29Si and 27Al MAS NMR, were used to investigate changes in surface properties of a natural illite sample after acid-base potentiometric titration. The characteristic XRD lines indicated the presence of surface Al-Si complexes, preferable to Al(OH)3 precipitates. In the microscopic Raman spectra, the vibration peaks of Si-O and Al-O bonds diminished as a result of treatment with acid, then increased after hydroxide back titration. The varied ratio of signal intensity between (IV)Al and (VI)Al species in 27Al MAS NMR spectra, together with the stable BET surface area after acidimetric titration, suggested that edge faces and basal planes in the layer structure of illite participated in dissolution of structural components. The combined spectroscopic evidence demonstrated that the reactions between illite surfaces and acid-leaching silicic acid and aluminum ions should be considered in the model description of surface acid-base properties of the aqueous illite.

  15. Spectroscopic Properties of Erbium Ions Doped in Bismuth Boro-Silicate Glasses

    Science.gov (United States)

    Bhardwaj, Sunil; Shukla, Rajni; Sanghi, Sujata; Agarwal, Ashish; Pal, Inder

    Glasses with composition 20B2O3.(79.5-x)Bi2O3.xSiO2 (10 ≤ x ≤ 40) containing 0.5mol% of Er3+ ions were prepared by melt-quench technique. Optical absorption and fluorescence spectra were recorded at room temperature for all glass samples. Based on the Judd-Offelt theory, spectroscopic properties of Er3+ ions are discussed by changing the host glass compositions. The intensity parameters Ω2, Ω4, and Ω6 are determined by applying least square analysis method. The variation of Ω2 and Ω6 with Bi2O3 content has been attributed to changes in the asymmetry of the ligand field at the rare earth ion site and to the changes in the rare earth oxygen (RE-O) covalency. The variation of Ω4 with Bi2O3 content has been attributed to rigidity of the samples. Using these intensity parameters various radiative properties like spontaneous emission probability, branching ratio, radiative life time and stimulated emission cross-section of various emission lines have been evaluated. An intense green luminescence bands with maximum around 516 nm and 536 nm are assigned to the 2H11/2→ 4I15/2 and 4S3/2→ 4I15/2 transitions respectively has been obtained.

  16. Supergiant fast X-ray transients with Swift: Spectroscopic and temporal properties

    Science.gov (United States)

    Romano, P.; Mangano, V.; Ducci, L.; Esposito, P.; Farinelli, R.; Ceccobello, C.; Vercellone, S.; Burrows, D. N.; Kennea, J. A.; Krimm, H. A.; Gehrels, N.

    2012-12-01

    Supergiant fast X-ray transients (SFXTs) are a class of high-mass X-ray binaries with possible counterparts in the high energy gamma rays. The Swift SFXT Project1 has conducted a systematic investigation of the properties of SFTXs on timescales ranging from minutes to years and in several intensity states (from bright flares, to intermediate intensity states, and down to almost quiescence). We also performed broad-band spectroscopy of outbursts, and intensity-selected spectroscopy outside of outbursts. We demonstrated that while the brightest phase of the outburst only lasts a few hours, further activity is observed at lower fluxes for a remarkably longer time, up to weeks. Furthermore, we assessed the fraction of the time these sources spend in each phase, and their duty cycle of inactivity. We present the most recent results from our investigation. The spectroscopic and, most importantly, timing properties of SFXTs we have uncovered with Swift will serve as a guide in search for the high energy emission from these enigmatic objects.

  17. Designing Optical Properties in DNA-Programmed Nanoparticle Superlattices

    Science.gov (United States)

    Ross, Michael Brendan

    A grand challenge of modern science has been the ability to predict and design the properties of new materials. This approach to the a priori design of materials presents a number of challenges including: predictable properties of the material building blocks, a programmable means for arranging such building blocks into well understood architectures, and robust models that can predict the properties of these new materials. In this dissertation, we present a series of studies that describe how optical properties in DNA-programmed nanoparticle superlattices can be predicted prior to their synthesis. The first chapter provides a history and introduction to the study of metal nanoparticle arrays. Chapter 2 surveys and compares several geometric models and electrodynamics simulations with the measured optical properties of DNA-nanoparticle superlattices. Chapter 3 describes silver nanoparticle superlattices (rather than gold) and identifies their promise as plasmonic metamaterials. In chapter 4, the concept of plasmonic metallurgy is introduced, whereby it is demonstrated that concepts from materials science and metallurgy can be applied to the optical properties of mixed metallic plasmonic materials, unveiling rich and tunable optical properties such as color and asymmetric reflectivity. Chapter 5 presents a comprehensive theoretical exploration of anisotropy (non-spherical) in nanoparticle superlattice architectures. The role of anisotropy is discussed both on the nanoscale, where several desirable metamaterial properties can be tuned from the ultraviolet to near-infrared, and on the mesoscale, where the size and shape of a superlattice is demonstrated to have a pronounced effect on the observed far-field optical properties. Chapter 6 builds upon those theoretical data presented in chapter 5, including the experimental realization of size and shape dependent properties in DNA-programmed superlattices. Specifically, nanoparticle spacing is explored as a parameter that

  18. Structural properties of replication origins in yeast DNA sequences

    International Nuclear Information System (INIS)

    Cao Xiaoqin; Zeng Jia; Yan Hong

    2008-01-01

    Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

  19. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  20. Protective role of quercetin against copper(II)-induced oxidative stress: A spectroscopic, theoretical and DNA damage study.

    Science.gov (United States)

    Jomova, Klaudia; Lawson, Michael; Drostinova, Lenka; Lauro, Peter; Poprac, Patrik; Brezova, Vlasta; Michalik, Martin; Lukes, Vladimir; Valko, Marian

    2017-12-01

    The radical scavenging and metal chelating properties of flavonoids indicate that they may play a protective role in diseases with perturbed metal homeostasis such as Alzheimer's disease. In this work we investigated the effect of the coordination of quercetin to copper(II) in view of the formation of ROS in Cu-catalyzed Fenton reaction. ABTS and DPPH assays confirmed that the copper(II)-quercetin complex exhibits a stronger radical scavenging activity than does quercetin alone. EPR spin trapping experiments have shown that chelation of quercetin to copper significantly suppressed the formation of hydroxyl radicals in the Cu(II)-Fenton reaction. DNA damage experiments revealed a protective effect for quercetin, but only at higher stoichiometric ratios of quercetin relative to copper. DNA protective effect of quercetin against ROS attack was described by two mechanisms. The first mechanism lies in suppressed formation of ROS due to the decreased catalytic action of copper in the Fenton reaction, as a consequence of its chelation and direct scavenging of ROS by free quercetin. Since the Cu-quercetin complex intercalates into DNA, the second mechanism was attributed to a suppressed intercalating ability of the Cu-quercetin complex due to the mildly intercalating free quercetin into DNA, thus creating a protective wall against stronger intercalators. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Synthesis, spectroscopic characterization, biological screenings, DNA binding study and POM analyses of transition metal carboxylates

    Science.gov (United States)

    Uddin, Noor; Sirajuddin, Muhammad; Uddin, Nizam; Tariq, Muhammad; Ullah, Hameed; Ali, Saqib; Tirmizi, Syed Ahmed; Khan, Abdur Rehman

    2015-04-01

    This article contains the synthesis of a novel carboxylic acid derivative, its transition metal complexes and evaluation of biological applications. Six carboxylate complexes of transition metals, Zn(II) and Hg(II), have been successfully synthesized and characterized by FT-IR and NMR (1H, 13C). The ligand, HL, (4-[(2,6-Diethylphenyl)amino]-4-oxobutanoic acid) was also characterized by single crystal X-ray analysis. The complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date show the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than that of the free ligand. The ligand and its complexes were screened for antifungal and antileishmanial activities. The results showed that the ligand and its complexes are active with few exceptions. UV-visible spectroscopy and viscometry results reveal that the ligand and its complexes interact with the DNA via intercalative mode of interaction. A new and efficient strategy to identify the pharmacophores and anti-pharmacophores sites in carboxylate derivatives for the antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out.

  2. Fluoxetine and Norfluoxetine Revisited: New Insights into the Electrochemical and Spectroscopic Properties

    Science.gov (United States)

    Garrido, E. Manuela; Garrido, Jorge; Calheiros, Rita; Marques, M. Paula M.; Borges, Fernanda

    2009-08-01

    The extent to which humans and wildlife are exposed to the vast array of anthropogenic chemicals and their degradation products, along with related naturally occurring compounds, is nowadays an important issue. The study of the physical-chemical properties of the compounds and/or degradation products is an important subject because some of them are intrinsically related to its resistance to degradation and/or bioaccumulation. Accordingly, the study of the electrochemical behavior of the selective serotonin reuptake inhibitor fluoxetine and its main metabolite norfluoxetine was investigated. The identification of the oxidation processes was done via two fluoxetine analogues, 1-(benzyloxy)-4-(trifluoromethyl)benzene and N-methyl-3-phenylpropan-1-amine hydrochloride. The oxidative processes occurring in fluoxetine are pH-dependent and were ascribed to the chemical moieties present in the molecule: the secondary amine group and the substituted aromatic nucleus. To perform an unequivocal ascription, the structural preferences of the drug and metabolite were also determined, by Raman spectroscopy coupled to quantum mechanical calculations (at the DFT level). The analytical data obtained in this work will allow the development of a rapid and unequivocal spectroscopic procedure suitable for fluoxetine identification, as well as to distinguish between the drug and its main metabolite.

  3. Imaging properties of small-pixel spectroscopic x-ray detectors based on cadmium telluride sensors

    International Nuclear Information System (INIS)

    Koenig, Thomas; Schulze, Julia; Zuber, Marcus; Rink, Kristian; Oelfke, Uwe; Butzer, Jochen; Hamann, Elias; Cecilia, Angelica; Zwerger, Andreas; Fauler, Alex; Fiederle, Michael

    2012-01-01

    Spectroscopic x-ray imaging by means of photon counting detectors has received growing interest during the past years. Critical to the image quality of such devices is their pixel pitch and the sensor material employed. This paper describes the imaging properties of Medipix2 MXR multi-chip assemblies bump bonded to 1 mm thick CdTe sensors. Two systems were investigated with pixel pitches of 110 and 165 μm, which are in the order of the mean free path lengths of the characteristic x-rays produced in their sensors. Peak widths were found to be almost constant across the energy range of 10 to 60 keV, with values of 2.3 and 2.2 keV (FWHM) for the two pixel pitches. The average number of pixels responding to a single incoming photon are about 1.85 and 1.45 at 60 keV, amounting to detective quantum efficiencies of 0.77 and 0.84 at a spatial frequency of zero. Energy selective CT acquisitions are presented, and the two pixel pitches' abilities to discriminate between iodine and gadolinium contrast agents are examined. It is shown that the choice of the pixel pitch translates into a minimum contrast agent concentration for which material discrimination is still possible. We finally investigate saturation effects at high x-ray fluxes and conclude with the finding that higher maximum count rates come at the cost of a reduced energy resolution. (paper)

  4. Spectroscopic properties of Er3+-doped fluorotellurite glasses containing various modifiers

    Science.gov (United States)

    Burtan-Gwizdała, Bożena; Reben, Manuela; Cisowski, Jan; Grelowska, Iwona; Yousef, El Sayed; Algarni, Hamed; Lisiecki, Radosław; Nosidlak, Natalia

    2017-11-01

    We have investigated the optical and spectroscopic properties of new Er3+-doped fluorotellurite glasses with the basic molar composition 75%TeO2-10%P2O5-10%ZnO-5%PbF2, modified by replacing 5%TeO2 by four various metal oxides, namely MgO, PbO, SrO and CdO. The ellipsometric data have provided a Sellmeier-type dispersion relation of the refractive index of the investigated glasses. The optical absorption edge has been described within the Urbach approach, while the absorption and fluorescence spectra have been analyzed in terms of the standard Judd-Ofelt theory along with the photoluminescence decay of the 4I13/2 and 4S3/2 levels of the Er3+ ion. The absorption and emission spectra of the 4I15/2 ↔ 4I13/2 infrared transition have been analyzed within the McCumber theory to yield the peak emission cross-section and figure of merit (FOM) for the amplifier gain. It appears that the glass containing MgO as a modifier is characterized by the largest FOM suggesting that the fluorotellurite matrix with this oxide can be a good novel host for Er3+ ion doping. Finally, we propose a new simple method to calculate the mean transition energy of the McCumber approach as the arithmetic average of the barycenter wavenumbers of absorption and emission spectra.

  5. Spectroscopic properties of Er{sup 3+}-doped antimony oxide glass

    Energy Technology Data Exchange (ETDEWEB)

    Ouannes, K.; Soltani, M.T. [Laboratoire de Physique Photonique et Nanomatériaux Multifonctionnels, Université de Biskra, BP 145 RP, 07000 Biskra (Algeria); Poulain, M. [UMR 6226 – Verres et Céramiques – Campus de Beaulieu, Université' de Rennes 1, 35042 Rennes (France); Boulon, G.; Alombert-Goget, G.; Guyot, Y.; Pillonnet, A. [Institut Lumière Matière, UMR 5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne (France); Lebbou, K., E-mail: kheireddine.lebbou@univ-lyon1.fr [Institut Lumière Matière, UMR 5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne (France)

    2014-08-01

    Highlight: • As a function of Er concentration, glasses corresponding to the 60Sb{sub 2}O{sub 3}–20WO{sub 3}–(19 − x) Na{sub 2}O–1Bi{sub 2}O{sub 3}, xEr{sub 2}O{sub 3} formula were prepared. The quantum efficiency shows that this glass could be promised for laser devices. - Abstract: Spectroscopic properties of Er{sup 3+} ions have been studied in the 60Sb{sub 2}O{sub 3}–20WO{sub 3}–19Na{sub 2}O–1Bi{sub 2}O{sub 3} (SWNB) glasses doped with 0.25 and 0.50 mol% Er{sub 2}O{sub 3} respectively. The Judd–Ofelt parameters measured from the absorption spectra have been used to calculate the radiative life-time (τ{sub r}) and the stimulated emission cross section. The low phonon energy, a reduced quenching effect and a high quantum efficiency of 90% for the 1.53 μm expected laser emission into pumping at 980 nm are in favor of promising material laser application.

  6. Microscopic and spectroscopic properties of Langmuir–Blodgett films composed of flavins and their aggregation structures

    International Nuclear Information System (INIS)

    Lim, Jong Kuk; Jo, Jihee; Jang, Dasol; Jang, Hyeong Ju

    2015-01-01

    Isoalloxazine derivatives (flavins) are commonly found in natural systems that are involved in an electron transfer process, such as photosynthetic or metabolic systems, and are also frequently used as electron donors in organic-based electronic devices. As an example, molecular photodiodes composed of 7,8-dimethyl-10-dodecyl isoalloxazine (DDI) have been fabricated by the Langmuir–Blodgett (LB) technique, and such devices showed characteristic properties of photodiodes. The efficiency of molecular photodiodes is dependent on the assembled structure of the LB films, which is related to the morphology of the LB films. For that reason, Lim has investigated the morphology of LB films, and found that rod-shaped domains are formed when a DDI monolayer is transferred to a solid substrate above a specific surface pressure (Thin Solid Films, 531 (2013) 499). In that paper, rod-shaped domains were revealed to be collapsed triple layers, i.e., double layers collapsed on the monolayer; however, the detailed aggregation structure of the constituent molecules (DDI) has not been studied. Herein, we investigate the microscopic and spectroscopic properties of LB films composed of DDI. We apply the extended dipole model to explain spectral changes in the absorption spectra and propose an aggregation structure for DDI in the LB films. - Highlights: • Aggregation structure of DDI in LB films was experimentally investigated. • Theoretical estimation is in good agreement with experimental result. • Molecular aggregation structure for DDI in LB films was proposed. • Molecular configuration in LB films is changed from side-by-side to face-to-face.

  7. Spectroscopic properties of Ho{sup 3+}-doped K-Sr-Al phosphate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Linganna, K.; Rathaiah, M.; Venkatramu, V. [Yogi Vemana University, Department of Physics, Kadapa (India); Jayasankar, C.K. [Sri Venkateswara University, Department of Physics, Tirupati (India)

    2014-05-15

    Trivalent holmium-doped K-Sr-Al phosphate glasses (P{sub 2}O{sub 5}-K{sub 2}O-SrO-Al{sub 2}O{sub 3}-Ho{sub 2}O{sub 3}) were prepared, and their spectroscopic properties have been evaluated using absorption, emission, and excitation measurements. The Judd-Ofelt theory has been used to derive spectral intensities of various absorption bands from measured absorption spectrum of 1.0 mol% Ho{sub 2}O{sub 3}-doped K-Sr-Al phosphate glass. The Judd-Ofelt intensity parameters (Ω{sub λ}, x 10{sup -20} cm{sup 2}) have been determined of the order of Ω{sub 2} = 11.39, Ω{sub 4} = 3.59, and Ω{sub 6} = 2.92, which in turn used to derive radiative properties such as radiative transition probability, radiative lifetime, branching ratios, etc. for excited states of Ho{sup 3+} ions. The radiative lifetimes for the {sup 5}F{sub 4}, {sup 5}S{sub 2}, and {sup 5}F{sub 5} levels of Ho{sup 3+} ions are found to be 169, 296, and 317 μs, respectively. The stimulated emission cross-section for 2.05-μm emission was calculated by the McCumber theory and found to be 9.3 x 10{sup -21} cm{sup 2}. The wavelength-dependent gain coefficient with population inversion rate has been evaluated. The results obtained in the titled glasses are discussed systematically and compared with other Ho{sup 3+}-doped systems to assess the possibility for visible and infrared device applications. (orig.)

  8. Optical and spectroscopic properties of neodymium doped cadmium-sodium borate glasses

    Science.gov (United States)

    Mohan, Shaweta; Thind, Kulwant Singh

    2017-10-01

    Neodymium doped cadmium sodium borate glasses having composition xCdO-(40-x) Na2CO3-59.5H3BO3-0.5Nd2O3; x = 10, 20 and 30 mol% were prepared by conventional melt-quenching technique. X-ray diffraction studies confirmed the amorphous nature of the prepared glasses. Conventional methods were used to determine the physical properties such as density, molar volume, refractive index, and rare earth ion concentration. The Judd-Ofelt theory was applied on the optical absorption spectra of the glasses to evaluate the three phenomenological intensity parameters Ω2, Ω4 and Ω6. The calculated intensity parameters were further used to predict the radiative transition probability (A), radiative lifetime (τR) and branching ratio (βR) for the various fluorescent levels of Nd3+ ion in the prepared glass series. The effect of the compositional changes on the spectroscopic characteristics of Nd3+ ions have been studied and reported. The value of Ω2 is found to decrease with the decrease in the sodium content and the corresponding increase in the cadmium content. This can be ascribed to the changes in the asymmetry of the ligand field at the rare earth ion site and the change in rare earth oxygen (RE-O) covalency. Florescence spectra has been used to determine the peak wavelength (λp), effective line widths (Δλeff) and stimulated emission cross-section (σp) for the 4F3/2 → 4I9/2,4I11/2,4I13/2 transitions of the Nd3+ ion. The reasonably higher values of branching ratios and stimulated emission cross-section for the prepared glasses points towards the efficacy of these glasses as laser host materials. However, the glass with more sodium content is found to show better lasing properties.

  9. Deformation properties of even-even Os, Pt, Hg nuclei and spectroscopic properties of odd Re, Os, Ir, Pt, Au, Hg nuclei from self-consistent calculations

    CERN Document Server

    Desthuilliers-Porquet, M G; Quentin, P; Sauvage-Letessier, J

    1981-01-01

    Static properties of even-even Os, Pt, Hg nuclei have been obtained from HF+BCS calculations. Single-particle wave functions which come from these self-consistent calculations have been used to calculate some spectroscopic properties of odd Re, Os, Ir, Pt, Au, and Hg nuclei, within the rotor-quasiparticle coupling model. The authors' calculations are able to give a good description of most of available experimental data. (12 refs).

  10. Synthesis, spectroscopic characterization and acoustic, volumetric, transport and thermal properties of hydroxyl ammonium based ionic liquids

    International Nuclear Information System (INIS)

    Losetty, Venkatramana; Chennuri, Bharath Kumar; Gardas, Ramesh L.

    2016-01-01

    Graphical abstract: Density, ρ (■) in kg · m"−"3, speed of sound, u (●) in m · s"−"1, dynamic viscosity, η (▴) in mPa · s, electrical conductivity, σ (♦) in S · cm"−"1of [BHEA][TFA] as the function of temperature and at 0.1 MPa pressure. - Highlights: • N-butyl-(N-hydroxyethyl) ammonium based protic ionic liquids (PILs) were synthesized. • Density, speed of sound, electrical conductivity and viscosity were measured for studied PILs. • Transport property data were fitted to Vogel–Tammann–Fulcher (VTF) equation. • FT-IR spectrum was helpful to explain the hydrogen bonding between ions. • Measured and derived properties were analyzed in terms of chemical structure of PILs. - Abstract: In the present work, solvent-free synthesis of two hydroxyethyl ammonium-based ionic liquids (ILs) at room temperature was carried out namely, N-butyl-(N-hydroxyethyl) ammonium trifluoroacetate ([BHEA][TFA]) and N-butyl-(N-hydroxyethyl) ammonium nitrate ([BHEA][NO_3]). The synthesized ionic liquids were characterized by various spectroscopic techniques such as "1H-NMR, "1"3C-NMR and FTIR. Furthermore, density (ρ), speed of sound (u), electrical conductivity (σ) and viscosity (η) have been measured within the temperature range from T = (303.15 to 343.15) K and at 0.1 MPa pressure. The measured density and viscosity values were fitted to the linear and Vogel–Tammann–Fulcher (VTF) equation, respectively. The temperature dependence conductivity of the measured ILs was fitted to a similar equation type of viscosity (VTF). Furthermore, the refractive index was measured at T = 303.15 K, in turn molar refraction (R_m) and free volume (f_V) were calculated using the Lorentz–Lorenz equation. The thermodynamic properties such as thermal expansion coefficient (α), isentropic compressibility (β_S) and intermolecular free length (L_f) were calculated by using the experimental values of density and speed of sound. The thermal decomposition temperature (T

  11. Optical and spectroscopic properties of Eu-doped tellurite glasses and glass ceramics

    International Nuclear Information System (INIS)

    Stambouli, W.; Elhouichet, H.; Gelloz, B.; Férid, M.

    2013-01-01

    in the nanocrystals precipitated in the glass ceramics. -- Highlights: ► Structural, thermal and optical properties of Eu 3+ doped tellurite glass, vitoceramic and ceramic were investigated. ► Judd–Ofelt model is used to determine the spectroscopic parameters of Eu 3+ doped tellurite glass and ceramic. ► Large improvements of the emission cross-section, gain bandwidth and quantum efficiency of Eu were found after thermal annealing of the glass

  12. Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

    Science.gov (United States)

    Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

    2018-03-01

    The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

  13. Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

    2018-03-01

    Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

  14. Pharmaceutical properties of two ethenzamide-gentisic acid cocrystal polymorphs: Drug release profiles, spectroscopic studies and theoretical calculations.

    Science.gov (United States)

    Sokal, Agnieszka; Pindelska, Edyta; Szeleszczuk, Lukasz; Kolodziejski, Waclaw

    2017-04-30

    The aim of this study was to evaluate the stability and solubility of the polymorphic forms of the ethenzamide (ET) - gentisic acid (GA) cocrystals during standard technological processes leading to tablet formation, such as compression and excipient addition. In this work two polymorphic forms of pharmaceutical cocrystals (ETGA) were characterized by 13 C and 15 N solid-state nuclear magnetic resonance and Fourier transformed infrared spectroscopy. Spectroscopic studies were supported by gauge including projector augmented wave (GIPAW) calculations of chemical shielding constants.Polymorphs of cocrystals were easily identified and characterized on the basis of solid-state spectroscopic studies. ETGA cocrystals behaviour during direct compressionand tabletting with excipient addition were tested. In order to choose the best tablet composition with suitable properties for the pharmaceutical industry dissolution profile studies of tablets containing polymorphic forms of cocrystals with selected excipients were carried out. Copyright © 2017. Published by Elsevier B.V.

  15. Spectroscopic and visible luminescence properties of rare earth ions in lead fluoroborate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Anjaiah, G. [Department of Physics, Osmania University, Hyderabad 500007 (India); Nayab Rasool, SK. [Department of Physics, Sri Venkateswara University, Tirupati 517502 (India); Kistaiah, P., E-mail: pkistaiah@yahoo.com [Department of Physics, Osmania University, Hyderabad 500007 (India)

    2015-03-15

    The lanthanide doped lead lithium calcium zinc fluoroborate glasses (LLCZFB:Ln) of composition 20PbF{sub 2}+10Li{sub 2}O+5Cao+5ZnO+59B{sub 2}O{sub 3}+1Ln{sub 2}O{sub 3} (where Ln=Sm, Eu and Dy in mol%) were prepared by conventional melt quench technique. The amorphous nature of these glasses was confirmed by X-ray diffraction studies. The glass transition temperatures (T{sub g}) were studied by DSC analysis. The glass structure and spectroscopic properties were investigated using optical absorption, vibrational and fluorescence spectra. The FT-IR spectra and Raman spectra reveal the presence of BO{sub 3}, BO{sub 4} and non-bridging oxygen's. The Judd–Ofelt intensity parameters Ω{sub λ} (λ=2, 4, 6) were determined from the spectral intensities of absorption bands. These parameters were used to calculate the radiative parameters such as radiative transition probability (A{sub R}), radiative life time (τ{sub R}) and branching ratio (β{sub r}) for various excited luminescent states of rare earth ions. The visible emission spectra for different rare earth ions were recorded by exciting the samples at different wavelengths and the decay rates for the different rare earth ions were measured. Using the emission spectra, full width half maxima (FWFM), stimulated emission cross section (σ{sup E}{sub p}) were evaluated. The nature of decay profiles of {sup 4}F{sub 9/2}, {sup 4}G{sub 5/2} and {sup 5}D{sub 0} states of Dy, Sm and Eu ions respectively are analyzed. Comparison of luminescence features of these glasses and also with those reported for different glass hosts indicates that the LLCZFB:Dy glass has strong luminescence in the visible region. - Highlights: • LLCZFB:Ln glasses are prepared with Ln: Sm, Eu and Dy. • Glasses are characterized by XRD, FTIR, Raman, absorption and emission spectra. • J–O theory is used to calculate different radiative properties. • Green, yellow and red emissions are observed. • Glasses are useful for the development

  16. Structural, thermal and spectroscopic properties of highly Er3+-doped novel oxyfluoride glasses for photonic application

    Energy Technology Data Exchange (ETDEWEB)

    Kesavulu, C.R. [Department of Physics, Changwon National University, Changwon 641-773 (Korea, Republic of); Sreedhar, V.B.; Jayasankar, C.K. [Department of Physics, Sri Venkateswara University, Tirupati 517502 (India); Jang, Kiwan [Department of Physics, Changwon National University, Changwon 641-773 (Korea, Republic of); Shin, Dong-Soo [Department of Chemistry, Changwon National University, Changwon 641-773 (Korea, Republic of); Yi, Soung Soo, E-mail: ssyi@silla.ac.kr [Department of Electronic Materials Engineering, Silla University, Busan 617-736 (Korea, Republic of)

    2014-03-01

    Graphical abstract: - Highlights: • Er{sup 3+}-doped novel oxyfluoride glasses have been prepared by melt quenching technique. • Structural, thermal and spectroscopic properties have been carried out. • SALSFEr glasses exhibit intense green and weak red emissions at 365 nm excitation. • Major laser transition for Er{sup 3+} ion in SALSFEr glasses is {sup 4}I{sub 13/2} → {sup 4}I{sub 15/2} (1.53 μm). • These results suggest the possibility of using SALSFEr glasses as photonic devices. - Abstract: The Er{sup 3+}-doped novel oxyfluoride glasses of composition (43 − x)SiO{sub 2}–10Al{sub 2}O{sub 3}–24LiF–23SrF{sub 2}–xEr{sub 2}O{sub 3}, where x = 1.0, 2.0, 4.0 and 6.0 mol%, have been prepared by conventional melt quenching technique and are characterized through X-ray diffraction (XRD), differential thermal analysis (DTA), Raman, Fourier transform infrared (FT-IR) analysis, optical absorption spectra, visible (vis) and near-infrared (NIR) emission spectra measurements. Judd–Ofelt (JO) intensity parameters (Ω{sub λ}, λ = 2, 4 and 6) have been derived from the absorption spectrum of 1.0 mol% Er{sub 2}O{sub 3} doped glass and are in turn used to calculate radiative properties for the important luminescent levels of Er{sup 3+} ions. The studied glasses show intense green and weak red visible emissions under 365 nm excitation. The decrease in visible emission intensities with concentration of Er{sup 3+} ions has been explained due to energy transfer processes between Er{sup 3+} ions. Upon excitation at 980 nm laser diode, an intense 1.53 μm NIR emission has been observed with the maximum full width at half maximum (FWHM) for Er{sup 3+}-doped oxyfluoride glasses. The higher Er{sup 3+} ion doping capability and relatively high gain and broad emission at 1.5 μm are the most notable features of these glasses to realize efficient short-length optical amplifiers.

  17. Multi-spectroscopic method study the interaction of anti-inflammatory drug ketoprofen and calf thymus DNA and its analytical application

    Science.gov (United States)

    Guo, Hongqin; Cai, Changqun; Gong, Hang; Chen, Xiaoming

    2011-06-01

    Interactions of the anti-inflammatory drug ketoprofen with calf thymus DNA (ctDNA) in aqueous solution have been studied by multi-spectroscopic method including resonance light scattering (RLS) technique, ultraviolet spectra (UV), 1H NMR, etc. The characteristics of RLS spectra, the effective factors and optimum conditions of the reaction have been unequivocally investigated. Mechanism investigations have shown that ketoprofen can bind to ctDNA by groove binding and form large particles, which resulted in the enhancement of RLS intensity. In Critic acid-Na 2HPO 4 buffer (pH = 6.5), ketoprofen has a maximum peak 451.5 nm and the RLS intensity is remarkably enhanced by trace amount of ctDNA due to the interaction between ketoprofen and ctDNA. The enhancement of RLS signal is directly proportional to the concentration of ctDNA in the range of 1.20 × 10 -6-1.0 × 10 -5 mol/L, and its detection limit (3 σ) is 1.33 × 10 -9 mol/L. The method is simple, rapid, practical and relatively free from interference generated by coexisting substance, and was applied to the determination of trace amounts of nucleic acid in synthetic samples with satisfactory results.

  18. Spectroscopic and electric dipole properties of Sr+Ar and SrAr systems including high excited states

    Science.gov (United States)

    Hamdi, Rafika; Abdessalem, Kawther; Dardouri, Riadh; Al-Ghamdi, Attieh A.; Oujia, Brahim; Gadéa, Florent Xavier

    2018-01-01

    The spectroscopic properties of the fundamental and several excited states of Sr+Ar and SrAr, Van der Waals systems are investigated by employing an ab initio method in a pseudo-potential approach. The potential energy curves and the spectroscopic parameters are displayed for the 1-10 2Σ+, 1-6 2Π and 1-3 2Δ electronic states of the Sr+Ar molecule and for the 1-6 1Σ+, 1-4 3Σ+, 1-3 1,3Π and 1-3 1,3Δ states of the neutral molecule SrAr. In addition, from these curves, the vibrational levels and their energy spacing are deduced for Σ+, Π and Δ symmetries. The spectra of the permanent and transition dipole moments are studied for the 1,3Σ+ states of SrAr, which are considered to be two-electron systems and 2Σ+ states of the single electron Sr+Ar ion. The spectroscopic parameters obtained for each molecular system are compared with previous theoretical and experimental works. A significant correlation revealed the accuracy of our results.

  19. Statistical properties and fractals of nucleotide clusters in DNA sequences

    International Nuclear Information System (INIS)

    Sun Tingting; Zhang Linxi; Chen Jin; Jiang Zhouting

    2004-01-01

    Statistical properties of nucleotide clusters in DNA sequences and their fractals are investigated in this paper. The average size of nucleotide clusters in non-coding sequence is larger than that in coding sequence. We investigate the cluster-size distribution P(S) for human chromosomes 21 and 22, and the results are different from previous works. The cluster-size distribution P(S 1 +S 2 ) with the total size of sequential Pu-cluster and Py-cluster S 1 +S 2 is studied. We observe that P(S 1 +S 2 ) follows an exponential decay both in coding and non-coding sequences. However, we get different results for human chromosomes 21 and 22. The probability distribution P(S 1 ,S 2 ) of nucleotide clusters with the size of sequential Pu-cluster and Py-cluster S 1 and S 2 respectively, is also examined. In the meantime, some of the linear correlations are obtained in the double logarithmic plots of the fluctuation F(l) versus nucleotide cluster distance l along the DNA chain. The power spectrums of nucleotide clusters are also discussed, and it is concluded that the curves are flat and hardly changed and the 1/3 frequency is neither observed in coding sequence nor in non-coding sequence. These investigations can provide some insights into the nucleotide clusters of DNA sequences

  20. Creating Spin-One Fermions in the Presence of Artificial Spin-Orbit Fields: Emergent Spinor Physics and Spectroscopic Properties

    Science.gov (United States)

    Kurkcuoglu, Doga Murat; de Melo, C. A. R. Sá

    2018-05-01

    We propose the creation and investigation of a system of spin-one fermions in the presence of artificial spin-orbit coupling, via the interaction of three hyperfine states of fermionic atoms to Raman laser fields. We explore the emergence of spinor physics in the Hamiltonian described by the interaction between light and atoms, and analyze spectroscopic properties such as dispersion relation, Fermi surfaces, spectral functions, spin-dependent momentum distributions and density of states. Connections to spin-one bosons and SU(3) systems is made, as well relations to the Lifshitz transition and Pomeranchuk instability are presented.

  1. Effect of gamma radiation on the spectroscopic properties of Bromocresol green-polyvinyl chloride film

    International Nuclear Information System (INIS)

    Bera, Anuradha; Ram, Surendra; Singh, Shailendra K.; Vaijapurkar, S.G.

    2009-01-01

    Bromocresol Green (BCG) - Polyvinyl chloride (PVC) film was prepared by dispersing the dye in the polymer matrix in a suitable solvent medium in the presence of an organic base and then solvent casting the formulation in the form of transparent colored film. Preliminary studies through UV-Vis Spectroscopic measurements show that the prepared PVC - dye films was sensitive to gamma radiation almost linearly in the dose range upto 8 kGy range. This spectroscopic change becomes visually distinguishable from 4 kGy onwards until 8 kGy where it finally changes color from green to yellow, beyond which no significant optical change was observed. The gamma response of the film could be tailored by varying the concentration of the pH sensitive dye and the organic base. (author)

  2. Spectroscopic properties and quenching processes of Yb3+ in Fluoride single crystals for laser applications

    International Nuclear Information System (INIS)

    Bensalah, A.; Ito, M.; Guyot, Y.; Goutaudier, C.; Jouini, A.; Brenier, A.; Sato, H.; Fukuda, T.; Boulon, G.

    2007-01-01

    Spectroscopic characterization is carried out to identify Stark's levels of Yb 3+ transitions in several fluoride crystals grown either by the Czochralski technique or by the laser-heated pedestal growth method. Yb 3+ concentration dependence of the decay time is analyzed in order to understand involved concentration quenching mechanisms. Laser tests under saphire:Ti pumping are presented for all our materials as well as under diode pumping for Yb:CaF 2

  3. Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis

    Science.gov (United States)

    Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh

    2016-09-01

    The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298 K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb = (7.6 ± 0.21) × 105) between complex and protein have been obtained at 298 K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2 ± 0.11) × 106 M- 1. Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.

  4. Spectroscopic mapping of the physical properties of supernova remnant N 49

    Science.gov (United States)

    Pauletti, D.; Copetti, M. V. F.

    2016-10-01

    Context. Physical conditions inside a supernova remnant can vary significantly between different positions. However, typical observational data of supernova remnants are integrated data or contemplate specific portions of the remnant. Aims: We study the spatial variation in the physical properties of the N 49 supernova remnant based on a spectroscopic mapping of the whole nebula. Methods: Long-slit spectra were obtained with the slit (~4' × 1.03″) aligned along the east-west direction from 29 different positions spaced by 2″ in declination. A total of 3248 1D spectra were extracted from sections of 2″ of the 2D spectra. More than 60 emission lines in the range 3550 Å to 8920 Å were measured in these spectra. Maps of the fluxes and of intensity ratios of these emission lines were built with a spatial resolution of 2″ × 2″. Results: An electron density map has been obtained using the [S II] λ6716 /λ6731 line ratio. Values vary from ~500 cm-3 at the northeast region to more than 3500 cm-3 at the southeast border. We calculated the electron temperature using line ratio sensors for the ions S+, O++, O+, and N+. Values are about 3.6 × 104 K for the O++ sensor and about 1.1 × 104 K for other sensors. The Hα/Hβ ratio map presents a ring structure with higher values that may result from collisional excitation of hydrogen. We detected an area with high values of [N II] λ6583/Hα extending from the remnant center to its northeastern border, which may be indicating an overabundance of nitrogen in the area due to contamination by the progenitor star. We found a radial dependence in many line intensity ratio maps. We observed an increase toward the remnant borders of the intensity ratio of any two lines in which the numerator comes before in the sequence [O III] λ5007, [O III] λ4363, [Ar III] λ7136, [Ne III] λ3869, [O II] λ7325, [O II] λ3727, He II λ4686, Hβ λ4861, [N II] λ6583, He I λ6678, [S II] λ6731, [S II] λ6716, [O I] λ6300, [Ca II]

  5. Structure-Dependent Spectroscopic Properties of Yb3+-Doped Phosphosilicate Glasses Modified by SiO2

    Directory of Open Access Journals (Sweden)

    Ling Wang

    2017-02-01

    Full Text Available Yb3+-doped phosphate glasses containing different amounts of SiO2 were successfully synthesized by the conventional melt-quenching method. The influence mechanism of SiO2 on the structural and spectroscopic properties was investigated systematically using the micro-Raman technique. It was worth noting that the glass with 26.7 mol % SiO2 possessed the longest fluorescence lifetime (1.51 ms, the highest gain coefficient (1.10 ms·pm2, the maximum Stark splitting manifold of 2F7/2 level (781 cm−1, and the largest scalar crystal-field NJ and Yb3+ asymmetry degree. Micro-Raman spectra revealed that introducing SiO2 promoted the formation of P=O linkages, but broke the P=O linkages when the SiO2 content was greater than 26.7 mol %. Based on the previous 29Si MAS NMR experimental results, these findings further demonstrated that the formation of [SiO6] may significantly affect the formation of P=O linkages, and thus influences the spectroscopic properties of the glass. These results indicate that phosphosilicate glasses may have potential applications as a Yb3+-doped gain medium for solid-state lasers and optical fiber amplifiers.

  6. Structure-Dependent Spectroscopic Properties of Yb3+-Doped Phosphosilicate Glasses Modified by SiO2

    Science.gov (United States)

    Wang, Ling; Zeng, Huidan; Yang, Bin; Ye, Feng; Chen, Jianding; Chen, Guorong; Smith, Andew T.; Sun, Luyi

    2017-01-01

    Yb3+-doped phosphate glasses containing different amounts of SiO2 were successfully synthesized by the conventional melt-quenching method. The influence mechanism of SiO2 on the structural and spectroscopic properties was investigated systematically using the micro-Raman technique. It was worth noting that the glass with 26.7 mol % SiO2 possessed the longest fluorescence lifetime (1.51 ms), the highest gain coefficient (1.10 ms·pm2), the maximum Stark splitting manifold of 2F7/2 level (781 cm−1), and the largest scalar crystal-field NJ and Yb3+ asymmetry degree. Micro-Raman spectra revealed that introducing SiO2 promoted the formation of P=O linkages, but broke the P=O linkages when the SiO2 content was greater than 26.7 mol %. Based on the previous 29Si MAS NMR experimental results, these findings further demonstrated that the formation of [SiO6] may significantly affect the formation of P=O linkages, and thus influences the spectroscopic properties of the glass. These results indicate that phosphosilicate glasses may have potential applications as a Yb3+-doped gain medium for solid-state lasers and optical fiber amplifiers. PMID:28772601

  7. Analysis of the Interaction of Dp44mT with Human Serum Albumin and Calf Thymus DNA Using Molecular Docking and Spectroscopic Techniques

    Directory of Open Access Journals (Sweden)

    Zhongjie Xu

    2016-06-01

    Full Text Available Di-2-pyridylketone-4,4,-dimethyl-3-thiosemicarbazone (Dp44mT exhibits significant antitumor activity. However, the mechanism of its pharmacological interaction with human serum albumin (HSA and DNA remains poorly understood. Here, we aimed to elucidate the interactions of Dp44mT with HSA and DNA using MTT assays, spectroscopic methods, and molecular docking analysis. Our results indicated that addition of HSA at a ratio of 1:1 did not alter the cytotoxicity of Dp44mT, but did affect the cytotoxicity of the Dp44mT-Cu complex. Data from fluorescence quenching and UV-VIS absorbance measurements demonstrated that Dp44mT could bind to HSA with a moderate affinity (Ka = approximately 104 M−1. CD spectra revealed that Dp44mT could slightly disrupt the secondary structure of HSA. Dp44mT could also interact with Ct-DNA, but had a moderate binding constant (KEB = approximately 104 M−1. Docking studies indicated that the IB site of HSA, but not the IIA and IIIA sites, could be favorable for Dp44mT and that binding of Dp44mT to HSA involved hydrogen bonds and hydrophobic force, consistent with thermodynamic results from spectral investigations. Thus, the moderate binding affinity of Dp44mT with HSA and DNA partially contributed to its antitumor activity and may be preferable in drug design approaches.

  8. Growth and spectroscopic properties of Tm3+:NaBi(MoO4)2 single crystal

    Science.gov (United States)

    Gusakova, N. V.; Mudryi, A. V.; Demesh, M. P.; Yasukevich, A. S.; Pavlyuk, A. A.; Kornienko, A. A.; Dunina, E. B.; Khodasevich, I. A.; Orlovich, V. A.; Kuleshov, N. V.

    2018-06-01

    In this work we report the spectroscopic properties of Tm3+:NaBi(MoO4)2 crystals with the dopant concentrations of 0.7 at.% and 3 at.%. The energy levels of the Tm3+ in the NaBi(MoO4)2 host were determined from polarized optical absorption and photoluminescence spectra measured at 77.4 K. Radiative properties of the crystals were calculated in context of Judd-Ofelt theory. Raman spectra of the crystal were studied. The concentration dependences of emission decay times of 3H4 and 3F4 levels were analyzed. The potential of the crystal for building tunable and ultrafast pulse lasers is shown on the base of cross sections and gain coefficient in the range of 1.9 μm.

  9. Effect of Molecular Weight on the Thermal and Spectroscopic Properties of Poly(vinyl alcohol) Films

    International Nuclear Information System (INIS)

    Khafagy, R.M.; Abd El-Kader, K.M.; Badr, Y.A.

    2009-01-01

    Thin films of Poly(vinyl alcohol) (PVA) with molecular weights 5000, 17000,72000 and 125000 g/mol were prepared by casting technique.Samples were thermally and spectroscopically investigated using TGA, DSC, FTIR and FT-Raman spectroscopy, in order to show how the thermal stability and structure of PVA might be correlated with its molecular weight. Thermal analysis showed that samples degrade in two steps mechanism. The mechanism observed for degradation in an inert atmosphere was in accordance with the accepted mechanism of elimination followed by pyrolisation. PVA 5000MW and PVA 17000Mw showed almost similar thermal behavior due to their expected similar structure. PVA 72000Mw showed lower thermal stability since it is characterized with the presence of the unstable C-O-C ether linkages, which lead to the fast melting of this sample. PVA 125000Mw showed the highest thermal stability because crosslinking of the main chains takes place due to introducing additional PVA units, which substitute each over oxygen atom. ΔH values obtained from DSC showed good accordance with TGA and Drtg analysis. Moreover, FTIR and FT-Raman results agreed well with thermal analysis, and confirmed our supposed structural changes which might take place as the molecular weight of the sample changes: since the water uptake, presence of ether linkages, and double bonds formulation due to crosslinking, were confirmed with FTIR and FT-Raman spectral analysis. The crystallinity percentage of the samples was calculated from Raman spectra and results confirmed our spectroscopic explanations. The thermal and spectroscopic behavior of the samples was explained as a result of the competitive action of at least three factors due to increasing the molecular weight: (i) diminution of the existing physical network due to changes in hydrogen bonding; (ii) formation of a chemical network; and (iii) introduction of flexible moieties due to the specific chemical structure after crosslinking

  10. Investigation of the optical properties of MoS{sub 2} thin films using spectroscopic ellipsometry

    Energy Technology Data Exchange (ETDEWEB)

    Yim, Chanyoung; O' Brien, Maria; Winters, Sinéad [School of Chemistry, Trinity College Dublin, Dublin 2 (Ireland); Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2 (Ireland); McEvoy, Niall [Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2 (Ireland); Mirza, Inam; Lunney, James G. [Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2 (Ireland); School of Physics, Trinity College Dublin, Dublin 2 (Ireland); Duesberg, Georg S., E-mail: duesberg@tcd.ie [School of Chemistry, Trinity College Dublin, Dublin 2 (Ireland); Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2 (Ireland); Advanced Materials and BioEngineering Research (AMBER) Centre, Trinity College Dublin, Dublin 2 (Ireland)

    2014-03-10

    Spectroscopic ellipsometry (SE) characterization of layered transition metal dichalcogenide (TMD) thin films grown by vapor phase sulfurization is reported. By developing an optical dispersion model, the extinction coefficient and refractive index, as well as the thickness of molybdenum disulfide (MoS{sub 2}) films, were extracted. In addition, the optical band gap was obtained from SE and showed a clear dependence on the MoS{sub 2} film thickness, with thinner films having a larger band gap energy. These results are consistent with theory and observations made on MoS{sub 2} flakes prepared by exfoliation, showing the viability of vapor phase derived TMDs for optical applications.

  11. Investigation of the optical properties of MoS2 thin films using spectroscopic ellipsometry

    International Nuclear Information System (INIS)

    Yim, Chanyoung; O'Brien, Maria; Winters, Sinéad; McEvoy, Niall; Mirza, Inam; Lunney, James G.; Duesberg, Georg S.

    2014-01-01

    Spectroscopic ellipsometry (SE) characterization of layered transition metal dichalcogenide (TMD) thin films grown by vapor phase sulfurization is reported. By developing an optical dispersion model, the extinction coefficient and refractive index, as well as the thickness of molybdenum disulfide (MoS 2 ) films, were extracted. In addition, the optical band gap was obtained from SE and showed a clear dependence on the MoS 2 film thickness, with thinner films having a larger band gap energy. These results are consistent with theory and observations made on MoS 2 flakes prepared by exfoliation, showing the viability of vapor phase derived TMDs for optical applications

  12. Optical properties of monolayer transition metal dichalcogenides probed by spectroscopic ellipsometry

    KAUST Repository

    Liu, Hsiang-Lin

    2014-11-17

    Spectroscopic ellipsometry was used to characterize the complex refractive index of chemical-vapor-deposited monolayer transition metal dichalcogenides (TMDs). The extraordinary large value of the refractive index in the visible frequency range is obtained. The absorption response shows a strong correlation between the magnitude of the exciton binding energy and band gap energy. Together with the observed giant spin-orbit splitting, these findings advance the fundamental understanding of their novel electronic structures and the development of monolayer TMDs-based optoelectronic and spintronic devices.

  13. Optical properties of monolayer transition metal dichalcogenides probed by spectroscopic ellipsometry

    KAUST Repository

    Liu, Hsiang-Lin; Shen, Chih-Chiang; Su, Sheng-Han; Hsu, Chang-Lung; Li, Ming-Yang; Li, Lain-Jong

    2014-01-01

    Spectroscopic ellipsometry was used to characterize the complex refractive index of chemical-vapor-deposited monolayer transition metal dichalcogenides (TMDs). The extraordinary large value of the refractive index in the visible frequency range is obtained. The absorption response shows a strong correlation between the magnitude of the exciton binding energy and band gap energy. Together with the observed giant spin-orbit splitting, these findings advance the fundamental understanding of their novel electronic structures and the development of monolayer TMDs-based optoelectronic and spintronic devices.

  14. Perturbed Angular Correlation (PAC)/NMR spectroscopic properties and dynamics of compounds containing metal ions

    DEFF Research Database (Denmark)

    Arcisauskaité, Vaida

    have been used to elucidate Hg coordination in proteins. Computational chemistry calculations have a potential to contribute to the interpretation of this spectroscopic data, as calculated diagonalised electric field gradient (EFG) tensor components (jVzzj jVyyj jVxxj) and NMR shielding constants...... steps towards understanding how Zn(II) reaches its target position in biological systems in vivo and in vitro experiments in aqueous solution, is the detailed investigation of water exchange reactions for Zn(II)(aq). A very advanced (albeit not complete) picture of structure and dynamics of solvated Zn...

  15. Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

    International Nuclear Information System (INIS)

    Slone, Scott Michael; Li, Chen-Yu; Aksimentiev, Aleksei; Yoo, Jejoong

    2016-01-01

    The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design. (paper)

  16. Spectroscopic properties of a two-dimensional time-dependent Cepheid model. I. Description and validation of the model

    Science.gov (United States)

    Vasilyev, V.; Ludwig, H.-G.; Freytag, B.; Lemasle, B.; Marconi, M.

    2017-10-01

    Context. Standard spectroscopic analyses of Cepheid variables are based on hydrostatic one-dimensional model atmospheres, with convection treated using various formulations of mixing-length theory. Aims: This paper aims to carry out an investigation of the validity of the quasi-static approximation in the context of pulsating stars. We check the adequacy of a two-dimensional time-dependent model of a Cepheid-like variable with focus on its spectroscopic properties. Methods: With the radiation-hydrodynamics code CO5BOLD, we construct a two-dimensional time-dependent envelope model of a Cepheid with Teff = 5600 K, log g = 2.0, solar metallicity, and a 2.8-day pulsation period. Subsequently, we perform extensive spectral syntheses of a set of artificial iron lines in local thermodynamic equilibrium. The set of lines allows us to systematically study effects of line strength, ionization stage, and excitation potential. Results: We evaluate the microturbulent velocity, line asymmetry, projection factor, and Doppler shifts. The microturbulent velocity, averaged over all lines, depends on the pulsational phase and varies between 1.5 and 2.7 km s-1. The derived projection factor lies between 1.23 and 1.27, which agrees with observational results. The mean Doppler shift is non-zero and negative, -1 km s-1, after averaging over several full periods and lines. This residual line-of-sight velocity (related to the "K-term") is primarily caused by horizontal inhomogeneities, and consequently we interpret it as the familiar convective blueshift ubiquitously present in non-pulsating late-type stars. Limited statistics prevent firm conclusions on the line asymmetries. Conclusions: Our two-dimensional model provides a reasonably accurate representation of the spectroscopic properties of a short-period Cepheid-like variable star. Some properties are primarily controlled by convective inhomogeneities rather than by the Cepheid-defining pulsations. Extended multi-dimensional modelling

  17. Influence of silver nanoparticles on the spectroscopic properties of Sm3+ doped boro-phosphate glasses

    Science.gov (United States)

    Suthanthirakumar, P.; Marimuthu, K.

    2016-05-01

    The Sm3+ doped novel boro-phosphate glasses containing silver nanoparticles (NPs) (SmBPxA) have been prepared following the melt quenching technique and their structural and spectroscopic behavior were studied through HR-TEM, optical absorption and photoluminescence spectral measurements. The TEM analysis validates the existence of Ag NPs with an average diameter of ~8 nm. The Surface plasmon resonance (SPR) band of silver NPs was found at around 600 nm from the absorption spectrum of the Sm3+ ions free glass sample. The optical band gap energy (Eopt) corresponding to the direct and indirect allowed transitions and the Urbach energy (ΔE) values were determined from the absorption spectral measurements. The luminescence intensity is found to get enhance when the Ag NPs were embedded along with the Sm3+ ions in the prepared glasses due to the local electric field effect around the rare earth (RE) ion site produced by the SPR of Ag NPs.

  18. The Spectral Properties and Photostability of DNA, RNA and Oligonucleotides

    International Nuclear Information System (INIS)

    Kudrya, V.Yu.; Yashchuk, V.M.

    2012-01-01

    The present work discusses the results of comparative investigations of the optical absorption, luminescence, and photostability of the biomacromolecules (DNA, RNA), as well as synthetic poly- and oligonucleotides. The separate nucleotides in DNA and RNA are examined as almost independent absorbing centers. It is confirmed that the main triplet excitons traps responsible for the DNA phosphorescence emission are AT-complexes in DNA. In contrast to DNA, the main triplet excitons traps in RNA are adenosine bases. These bases are the most photostable against UV-irradiation as compared with all other nucleotides in both DNA and RNA. The fact of the photostability of adenosine bases and the AT-complex provides the existence of the DNA/RNA self-protection mechanisms against a damage caused by UV-irradiation. It is found the deoxyribonucleotides are more photostable than the corresponding ribonucleotides. So, the results presented here show that DNA is more photostable than RNA.

  19. Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

    Science.gov (United States)

    Park, Jin-Young; Woon, David E.

    2004-01-01

    Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

  20. The effect of ionic environment and mercury(II) binding on the alternative structures of DNA. An infrared spectroscopic study

    Science.gov (United States)

    Keller, P. B.; Hartman, K. A.

    Infrared spectroscopy was used to measure the effects of NaCl, NaNO 3 and HgCl 2 on the structure and structural transitions of DNA in hydrated films. The following conclusions are supported by the data. (1) The transition from the B- to the A-structural form in films of salt-free, calf-thymus DNA occurs between 86 and 75% r.h. Previous failures to obtain this transition in salt-free films and the finding that ca 4% (w/w) NaCl is needed to observe the B to A transition in films of DNA appear to be anomalies produced by the very slow kinetics for this transition. (2) The addition of NaCl to DNA increases the quantity of water absorbed at a given r.h. value and shifts the B to A transition to lower r.h. values. (3) Highly hydrated DNA (100% r.h.) with or without added NaCl exists in the B-helical structure for all samples examined. (4) DNA films containing one NaNO 3 per 6.7 nucleotide residues remained in the B-helical form to very low values of hydration. (5) The interaction of HgCl 2 with DNA to form the type I complex prevents the transition of DNA from the B- to the A-helical form but a conformational variation within the B family of structures was observed to occur between 94 and 75% r.h. (6) The primary sites of binding of Hg 2+ in the type-1 complex with the DNA are the AT base pairs. Hg 2+ binds to the N3 atom of thymine. Binding of Hg 2+ to AT pairs perturbs the CG pairs but has only a minor effect on the sugar—phosphate conformation.

  1. Effect of F- ions on physical and spectroscopic properties of Yb3+-doped TeO2-based glasses

    International Nuclear Information System (INIS)

    Wang Guonian; Dai Shixun; Zhang Junjie; Xu Shiqing; Hu Lili; Jiang Zhonghong

    2005-01-01

    The effects of F - ions on physical and spectroscopic properties of the Yb 3+ in tellurite glass system are investigated. The results show that the glass system takes on good thermal stability with the content of ZnF 2 lower than 15 mol%, both the emission cross-section and the fluorescence lifetime of Yb 3+ ions increase evidently which indicate that such oxyfluoride tellurite glass system is a promising laser host matrix for high power generation. FT-IR spectra were used to analyze the effect of F- ions on the structure of tellurite glasses and OH - groups in this glass system. Analysis demonstrates that addition of fluoride decreases the symmetry of the structure of tellurite glasses which increases the emission cross-section and removes the OH - groups, and which improves the measured fluorescence lifetime of Yb 3+ ions

  2. Optical properties of LiGaS{sub 2}: an ab initio study and spectroscopic ellipsometry measurement

    Energy Technology Data Exchange (ETDEWEB)

    Atuchin, V V [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Lin, Z S [Beijing Center for Crystal R and D, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, PO Box 2711, Beijing 100190 (China); Isaenko, L I; Lobanov, S I [Laboratory of Crystal Growth, Institute of Geology and Mineralogy, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Kesler, V G [Laboratory of Physical Bases of Integrated Microelectronics, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Kruchinin, V N, E-mail: zslin@mail.ipc.ac.c [Laboratory for Ellipsometry of Semiconductor Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation)

    2009-11-11

    Electronic and optical properties of lithium thiogallate crystal, LiGaS{sub 2}, have been investigated by both experimental and theoretical methods. The plane-wave pseudopotential method based on DFT theory has been used for band structure calculations. The electronic parameters of Ga 3d orbitals have been corrected by the DFT+U methods to be consistent with those measured with x-ray photoemission spectroscopy. Evolution of optical constants of LiGaS{sub 2} over a wide spectral range was determined by developed first-principles theory and dispersion curves were compared with optical parameters defined by spectroscopic ellipsometry in the photon energy range 1.2-5.0 eV. Good agreement has been achieved between theoretical and experimental results.

  3. Spectroscopic properties and thermal stability of Er3+-doped tungsten-tellurite glass for waveguide amplifier application

    International Nuclear Information System (INIS)

    Zhao Shilong; Wang Xiuli; Fang Dawei; Xu Shiqing; Hu Lili

    2006-01-01

    Tungsten-tellurite glass with molar composition of 60TeO 2 -30WO 3 -10Na 2 O has been investigated for developing planar broadband waveguide amplifier application. Spectroscopic properties and thermal stability of Er 3+ -doped tungsten-tellurite glass have been discussed. The results show that the introduction of WO 3 increases significantly the glass transition temperature and the maximum phonon energy. Er 3+ -doped tungsten-tellurite glass exhibits high glass transition temperature (377 deg. C), large emission cross-section (0.91 x 10 -20 cm 2 ) at 1532 nm and broad full width at half maximum (FWHM), which make it preferable for broadband Er 3+ -doped waveguide amplifier application

  4. Comparative investigation on the spectroscopic properties of Pr3+-doped boro-phosphate, boro-germo-silicate and tellurite glasses

    Science.gov (United States)

    Zhang, Liaolin; Dong, Guoping; Peng, Mingying; Qiu, Jianrong

    We report on the spectroscopic properties of Pr3+-doped boro-phosphate, boro-germo-silicate and tellurite glasses. The stimulated absorption and emission cross sections were estimated. Only one emission at 596 nm and 605 nm is observed in Pr3+-doped boro-phosphate and boro-germo-silicate glasses, respectively, while three emissions at 605 nm, 612 nm and 645 nm are observed in Pr3+-doped tellurite glass when excited at 467 nm. The fluorescence lifetime at 600 nm in Pr3+-doped boro-phosphate, boro-germo-silicate and tellurite glasses is 137 μs, 73 μs and 51 μs, respectively. The emissions from Pr3+-doped boro-phosphate, boro-germo-silicate and tellurite glasses show different decay behaviors and can be well explained by multiphonon relaxation theory.

  5. Spectroscopic and neutron detection properties of rare earth and titanium doped LiAlO 2 single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dickens, Peter T.; Marcial, José; McCloy, John; McDonald, Benjamin S.; Lynn, Kelvin G.

    2017-10-01

    In this study, LiAlO2 crystals doped with rare-earth elements and Ti were produced by the CZ method and spectroscopic and neutron detection properties were investigated. Photoluminescence revealed no clear luminescent activation of LiAlO2 by the rare-earth dopants though some interesting luminescence was observed from secondary phases within the crystal. Gamma-ray pulse height spectra collected using a 137Cs source exhibited only a Compton edge for the crystals. Neutron modeling using Monte Carlo N-Particle Transport Code revealed most neutrons used in the detection setup are thermalized, and while using natural lithium in the crystal growth, which contains 7.6 % 6Li, a 10 mm Ø by 10 mm sample of LiAlO2 has a 70.7 % intrinsic thermal neutron capture efficiency. Furthermore, the pulse height spectra collected using a 241Am-Be neutron source demonstrated a distinct neutron peak.

  6. Spectroscopic identification and anti-biofilm properties of polar metabolites from the medicinal plant Helichrysum italicum against Pseudomonas aeruginosa.

    Science.gov (United States)

    D'Abrosca, Brigida; Buommino, Elisabetta; D'Angelo, Grazia; Coretti, Lorena; Scognamiglio, Monica; Severino, Valeria; Pacifico, Severina; Donnarumma, Giovanna; Fiorentino, Antonio

    2013-11-15

    Two new acylated styrylpyrones, one 5-methoxy-1(3H)-isobenzofuranone glucoside and a hydroxymethyl-orcinol derivative, along with sixteen known aromatic metabolites, including lignans, quinic acid derivatives low-molecular weight phenol glucosides, have been isolated from the methanol extract of Helichrysum italicum, a medicinal plant typical of the Mediterranean vegetation. The structures of these compounds have been elucidated on the basis of extensive 2D-NMR spectroscopic analyses, including COSY, TOCSY, HSQC, CIGAR-HMBC, H2BC and HSQC-TOCSY, along with Q-TOF HRMS(2) analysis. Selected compounds were evaluated for their anti-biofilm properties against Pseudomonas aeruginosa. Copyright © 2013. Published by Elsevier Ltd.

  7. Evidences of long lived cages in functionalized polymers: Effects on chromophore dynamic and spectroscopic properties

    Science.gov (United States)

    Prampolini, Giacomo; Monti, Susanna; De Mitri, Nicola; Barone, Vincenzo

    2014-05-01

    the two signals, the spectrum in toluene being significantly broader than its polymer analog. This difference can be quantified with a decrease in full width at half maximum (FWFM) of about 19%. The computed emission spectra are instead displayed in Figure 5 bottom panel. A systematic blue shift of ∼20 nm in the peaks positions, that results in maxima located at 340 (toluene) and 344 nm (polymer), can be ascribed to the chosen DFT functional, as discussed in detail in Ref. [13], where the choice of the functional was discussed specifically for the NfO-TEMPO chromophore. More important, the broadening of the experimental line shapes and their general trends are very well reproduced by the dynamical computational approach: the FWHM is indeed reduced by almost the same amount (17%) and the different slopes in band decays are also reproduced with rather good accuracy.In summary, the computational strategy defined in this Letter has been able to reproduce the effects of a complex anisotropic medium, namely an amorphous polymer matrix, on the fluorescence emission of a dye grafted onto its chains, disclosing the key features of the caging process responsible for the reduced rotational motion of the naphthoyloxy moiety. The narrowing of the electronic spectral signals was a consequence of this entrapment. The comparison of these findings with the outcomes in toluene solution reveals a highly dynamic behavior of the short-lived solvent cage and suggests that rationally engineering polymer structures used to obtain selective immobilization strategies could be a powerful technique for improving some spectroscopic properties of the dyes and specific features of composites materials. Furthermore, the proposed procedure is general enough to be applied also for more polar and interacting environments, in order to unravel both energetic and entropic effects, that can effectively tune the performances of novel dye-based devices.

  8. Spectroscopic properties of nitrogen doped hydrogenated amorphous carbon films grown by radio frequency plasma-enhanced chemical vapor deposition

    International Nuclear Information System (INIS)

    Hayashi, Y.; Yu, G.; Rahman, M. M.; Krishna, K. M.; Soga, T.; Jimbo, T.; Umeno, M.

    2001-01-01

    Nitrogen doped hydrogenated amorphous carbon thin films have been deposited by rf plasma-enhanced chemical vapor deposition using CH 4 as the source of carbon and with different nitrogen flow rates (N 2 /CH 4 gas ratios between 0 and 3), at 300 K. The dependence modifications of the optical and the structural properties on nitrogen incorporation were investigated using different spectroscopic techniques, such as, Raman spectroscopy, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy, ultraviolet-visible (UV-VIS) spectroscopy, electron spin resonance (ESR), photoluminescence (PL) and spectroscopic ellipsometry (SE). Raman spectroscopy and IR absorption reveal an increase in sp 2 -bonded carbon or a change in sp 2 domain size with increasing nitrogen flow rate. It is found that the configuration of nitrogen atoms incorporated into an amorphous carbon network gradually changes from nitrogen atoms surrounded by three (σ bonded) to two (π bonded) neighboring carbons with increasing nitrogen flow rate. Tauc optical gap is reduced from 2.6 to 2.0 eV, and the ESR spin density and the peak-to-peak linewidth increase sharply with increasing nitrogen flow rate. Excellent agreement has been found between the measured SE data and modeled spectra, in which an empirical dielectric function of amorphous materials and a linear void distribution along the thickness have been assumed. The influence of nitrogen on the electronic density of states is explained based on the optical properties measured by UV-VIS and PL including nitrogen lone pair band. [copyright] 2001 American Institute of Physics

  9. Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

    Science.gov (United States)

    Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Boon Tong, Goh; Abdul Rahman, Saadah

    2016-01-01

    Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field.

  10. Spectroscopic (UV/VIS, Raman and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    Full Text Available Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100, is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT. As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field.

  11. Properties of the chromatin assembled on DNA injected into Xenopus oocytes and eggs

    International Nuclear Information System (INIS)

    Gargiulo, G.; Wasserman, W.; Worcel, A.

    1983-01-01

    The onset of DNA synthesis occurs between 10 and 30 minutes after activation of the egg and thus the transition from nuclease-sensitive to nuclease-resistant supercoils may take place on the newly replicated DNA. To test this possibility, the nonradioactive circular 5-kb DNA carrying the Drosophila histone gene repeat and [α -32 P]dCTP were coinjected into fertilized eggs. Such protocol labels both the injected, replicated heterologous DNA and the replicated endogenous, maternal Xenopus DNA. The labeled, presumably replicated, supercoiled DNA is resistant to micrococcal nuclease as expected. The endogenous, high-molecular-weight Xenopus DNA is degraded to 180-bp nucleosomal DNA. Thus, the nuclease resistance is not a general property of chromatin during the cleavage stage of the Xenopus embryo but is a peculiar feature of the injected DNA. 42 references, 5 figures

  12. Spectroscopic study

    International Nuclear Information System (INIS)

    Flores, M.; Rodriguez, R.; Arroyo, R.

    1999-01-01

    This work is focused about the spectroscopic properties of a polymer material which consists of Polyacrylic acid (Paa) doped at different concentrations of Europium ions (Eu 3+ ). They show that to stay chemically joined with the polymer by a study of Nuclear Magnetic Resonance (NMR) of 1 H, 13 C and Fourier Transform Infrared Spectroscopy (Ft-IR) they present changes in the intensity of signals, just as too when this material is irradiated at λ = 394 nm. In according with the results obtained experimentally in this type of materials it can say that is possible to unify chemically the polymer with this type of cations, as well as, varying the concentration of them, since that these are distributed homogeneously inside the matrix maintaining its optical properties. These materials can be obtained more quickly and easy in solid or liquid phase and they have the best conditions for to make a quantitative analysis. (Author)

  13. Low-dimensional compounds containing cyanido groups. XXVIII. Crystal structure, spectroscopic and magnetic properties of two copper(II) tetracyanidoplatinate complexes with 1,2-diaminopropane

    Czech Academy of Sciences Publication Activity Database

    Vavra, M.; Potočňák, I.; Dušek, Michal; Čižmár, E.; Ozerov, M.; Zvyagin, S.A.

    2015-01-01

    Roč. 225, May (2015), s. 202-208 ISSN 0022-4596 Institutional support: RVO:68378271 Keywords : spectroscopic studies * magnetic properties * crystal structure * [Pt(CN) ]2- anion * 1,2-diaminopropane Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.265, year: 2015

  14. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA using boric acid-functionalized nano-microsphere fluorescent probes.

    Science.gov (United States)

    Chen, Hua-Yan; Wei, Jing-Ru; Pan, Jiong-Xiu; Zhang, Wei; Dang, Fu-Quan; Zhang, Zhi-Qi; Zhang, Jing

    2017-05-15

    5-hydroxymethylcytosine (5hmC) is the sixth base of DNA. It is involved in active DNA demethylation and can be a marker of diseases such as cancer. In this study, we developed a simple and sensitive 2-(4-boronophenyl)quinoline-4-carboxylic acid modified poly (glycidyl methacrylate (PBAQA-PGMA) fluorescent probe to detect the 5hmC content of genomic DNA based on T4 β-glucosyltransferase-catalyzed glucosylation of 5hmC. The fluorescence-enhanced intensity recorded from the DNA sample was proportional to its 5-hydroxymethylcytosine content and could be quantified by fluorescence spectrophotometry. The developed probe showed good detection sensitivity and selectivity and a good linear relationship between the fluorescence intensity and the concentration of 5 hmC within a 0-100nM range. Compared with other fluorescence detection methods, this method not only could determine trace amounts of 5 hmC from genomic DNA but also could eliminate the interference of fluorescent dyes and the need for purification. It also could avoid multiple labeling. Because the PBAQA-PGMA probe could enrich the content of glycosyl-5-hydroxymethyl-2-deoxycytidine from a complex ground substance, it will broaden the linear detection range and improve sensitivity. The limit of detection was calculated to be 0.167nM after enrichment. Furthermore, the method was successfully used to detect 5-hydroxymethylcytosine from mouse tissues. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Prompt and Afterglow Emission Properties of Gamma-Ray Bursts with Spectroscopically Identified Supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Yuki; Ramirez-Ruiz, E.; Granot, J.; Kouveliotou, C.; Woosley, S.E.; Patel, S.K.; Rol, E.; Zand, J.J.M.in' t; a; Wijers, R.A.M.J.; Strom, R.; /USRA, Huntsville

    2006-07-12

    We present a detailed spectral analysis of the prompt and afterglow emission of four nearby long-soft gamma-ray bursts (GRBs 980425, 030329, 031203, and 060218) that were spectroscopically found to be associated with type Ic supernovae, and compare them to the general GRB population. For each event, we investigate the spectral and luminosity evolution, and estimate the total energy budget based upon broadband observations. The observational inventory for these events has become rich enough to allow estimates of their energy content in relativistic and sub-relativistic form. The result is a global portrait of the effects of the physical processes responsible for producing long-soft GRBs. In particular, we find that the values of the energy released in mildly relativistic outflows appears to have a significantly smaller scatter than those found in highly relativistic ejecta. This is consistent with a picture in which the energy released inside the progenitor star is roughly standard, while the fraction of that energy that ends up in highly relativistic ejecta outside the star can vary dramatically between different events.

  16. Exploring the Evolution of Star Formation and Dwarf Galaxy Properties with JWST /MIRI Serendipitous Spectroscopic Surveys

    Energy Technology Data Exchange (ETDEWEB)

    Bonato, Matteo; Sajina, Anna; McKinney, Jed; Marchesini, Danilo; Roebuck, Eric; Shipley, Heath [Department of Physics and Astronomy, Tufts University, 574 Boston Avenue, Medford, MA (United States); Zotti, Gianfranco De [INAF, Osservatorio Astronomico di Padova, Vicolo Osservatorio 5, I-35122 Padova (Italy); Baronchelli, Ivano; Yan, Lin [California Institute of Technology, Pasadena, CA (United States); Negrello, Mattia [School of Physics and Astronomy, Cardiff University, Queens Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); Kurinsky, Noah [Department of Physics, Stanford University, Stanford, CA (United States); Pope, Alexandra [Department of Astronomy, University of Massachusetts Amherst, Amherst, MA (United States); Noriega-Crespo, Alberto [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD (United States); Kirkpatrick, Allison [Department of Astronomy, Yale University, New Haven, CT (United States)

    2017-02-20

    The James Webb Space Telescope ’s Medium Resolution Spectrometer (MRS), will offer nearly two orders of magnitude improvement in sensitivity and >3× improvement in spectral resolution over our previous space-based mid-IR spectrometer, the Spitzer IRS. In this paper, we make predictions for spectroscopic pointed observations and serendipitous detections with the MRS. Specifically, pointed observations of Herschel sources require only a few minutes on source integration for detections of several star-forming and active galactic nucleus lines, out to z = 3 and beyond. But the same data will also include tens of serendipitous 0 ≲ z ≲ 4 galaxies per field with infrared luminosities ranging ∼10{sup 6}–10{sup 13} L {sub ☉}. In particular, for the first time and for free we will be able to explore the L {sub IR} < 10{sup 9} L {sub ☉} regime out to z ∼ 3. We estimate that with ∼ 100 such fields, statistics of these detections will be sufficient to constrain the evolution of the low- L end of the infrared luminosity function, and hence the star formation rate function. The above conclusions hold for a wide range in the potential low- L end of the IR luminosity function, and account for the PAH deficit in low- L , low-metallicity galaxies.

  17. Spectroscopic and radiative properties study of Nd3+ doped cadmium-phosphate glasses

    International Nuclear Information System (INIS)

    Mahmoud, K.H.

    2010-01-01

    A spectroscopic investigation is performed on Nd 3+ doped cadmium-phosphate glasses. The Judd-Ofelt analysis is applied to the glass system in order to evaluate their potential as both glass laser and amplifier materials. The phenomenological Judd-Ofelt parameters Ω (2) , Ω (4) , and Ω (6) are determined, their values are 4.80x10 -20 , 6.18x10 -20 , and 7.14x10 -20 cm -2 , respectively. The quality factor for glass system is 0.86. Predicted radiative decay rates and branching ratios of transitions from Nd 3+4 F 3/2 state to the 4 I J manifolds are determined and analyzed. The calculated lifetime of the 4 F 3/2 metastable state of Nd 3+ is 31 μs. The results showed that 4 F 3/2 to 4 I 11/2 transition, with fluorescence at 1056 nm, has the most potential for laser application. Photoluminescence up-conversion under excitation at 488 nm laser light exhibits three emission bands of Nd 3+ ions at 541 (green), 601 (orange), and 677 nm (red). These emission bands are assigned to 4 G 7/2 → 4 I 9/2 , 4 G 7/2 → 4 I 11/2 , and 4 G 7/2 → 4 I 13/2 transitions, respectively. Analysis of luminescence spectra enhances the use of glass system in optical displays, lasers, and optical memory devices.

  18. Elastic properties and spectroscopic studies of Na2O–ZnO–B2O3 ...

    Indian Academy of Sciences (India)

    Unknown

    Therefore, the choice of the most appropriate material for particular application requires a knowledge of its mechanical properties. Hence, elastic properties are ... son's ratio and θD the Debye temperature. Vl and Vt are longitudinal and shear sound velocities, respectively. The mean sound velocity, Vm, is defined by the ...

  19. Spectroscopic investigation of the redox properties of CoAPO molecular sieves

    NARCIS (Netherlands)

    Peeters, M.P.J.; Hooff, van J.H.C.; Sheldon, R.A.; Zholobenko, V.L.; Kustov, L.M.; Kazansky, V.B.; Balmoos, von R.; Higgins, J.B.; Treacy, M.M.J

    1993-01-01

    Acid sites in CoAPO-5 and CoAPO-11 and redox properties of these Co-substituted aluminophosphates have been investigated using UV- and IR-spectroscopy. The data obtained show that CoAPO exhibits quite unusual acidic and redox properties. The absence of the bridged OH-group seems to be a common

  20. DNA complexes with Ni nanoparticles: structural and functional properties

    Energy Technology Data Exchange (ETDEWEB)

    Tatarinova, Olga N.; Smirnov, Igor P. [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation); Safenkova, Irina V. [A.N. Bach Institute of Biochemistry (Russian Federation); Varizhuk, Anna M.; Pozmogova, Galina E., E-mail: pozmge@gmail.com [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation)

    2012-10-15

    Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid-nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

  1. DNA complexes with Ni nanoparticles: structural and functional properties

    International Nuclear Information System (INIS)

    Tatarinova, Olga N.; Smirnov, Igor P.; Safenkova, Irina V.; Varizhuk, Anna M.; Pozmogova, Galina E.

    2012-01-01

    Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid–nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

  2. DNA Structures on Silicon and Diamond

    NARCIS (Netherlands)

    Pop, Simona D.; Hinrichs, Karsten; Wenmackers, Sylvia; Cobet, Christoph; Esser, Norbert; Zahn, Dietrich R.T.; Hinrichs, Karsten; Eichhorn, Klaus-Jochen

    2014-01-01

    In the design of DNA-based hybrid devices, it is essential to have knowledge of the structural, electronic and optical properties of these biomolecular films. Spectroscopic ellipsometry is a powerful technique to probe and asses these properties. In this chapter, we review its application to

  3. Surface-enhanced Raman spectroscopic study of DNA and 6-mercapto-1-hexanol interactions using large area mapping

    DEFF Research Database (Denmark)

    Frøhling, Kasper Bayer; Alstrøm, Tommy Sonne; Bache, Michael

    2016-01-01

    intensities and peak positions it is possible to directly inspect the interplay between DNA and 6-mercapto-1-hexanol on gold covered nanopillars. It is demonstrated that optimised functionalization parameters can be extracted from the Raman spectra directly. Using the peak-fitting approach it is possible...

  4. Determination of membrane disruption and genomic DNA binding of cinnamaldehyde to Escherichia coli by use of microbiological and spectroscopic techniques.

    Science.gov (United States)

    He, Tian-Fu; Zhang, Zhi-Hong; Zeng, Xin-An; Wang, Lang-Hong; Brennan, Charles S

    2018-01-01

    This work was aimed to investigate the antibacterial action of cinnamaldehyde (CIN) against Escherichia coli ATCC 8735 (E. coli) based on membrane fatty acid composition analysis, alterations of permeability and cell morphology as well as interaction with genomic DNA. Analysis of membrane fatty acids using gas chromatography-mass spectrometry (GC-MS) revealed that the proportion of unsaturated fatty acids (UFA) and saturated fatty acids (SFA) were the major fatty acids in plasmic membrane, and their levels were significantly changed after exposure of E. coli to CIN at low concentrations. For example, the proportion of UFA decreased from 39.97% to 20.98%, while the relative content of SFA increased from 50.14% to 67.80% as E. coli was grown in increasing concentrations of CIN (from 0 to 0.88mM). Scanning electron microscopy (SEM) showed that the morphology of E. coli cells to be wrinkled, distorted and even lysed after exposure to CIN, which therefore decreased the cell viability. The binding of CIN to genomic DNA was probed using fluorescence, UV-Visible absorption spectra, circular dichroism, molecular modeling and atomic force microscopy (AFM). Results indicated that CIN likely bound to the minor groove of genomic DNA, and changed the secondary structure and morphology of this biomacromolecule. Therefore, CIN can be deem as a kind of natural antimicrobial agents, which influence both cell membrane and genomic DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Overview of ultraviolet and infrared spectroscopic properties of Yb3+ doped borate and oxy-borates compounds

    International Nuclear Information System (INIS)

    Sablayrolles, J.

    2006-12-01

    The trivalent ytterbium ion can give rise to two emissions with different spectroscopic properties: the first one, with a short lifetime, in the ultraviolet (charge transfer emission) is used in detectors such as scintillators, and the other one, with a long lifetime, in the infrared (4f-4f emission) for laser applications. The strong link between material structure and properties is illustrated through ytterbium luminescence study, in the ultraviolet and infrared, inserted in the borate Li 6 Y(BO 3 ) 3 and two oxy-borates: LiY 6 O 5 (BO 3 ) 3 and Y 17,33 B 8 O 38 . For the first time an ytterbium charge transfer emission in oxy-borates has been observed. The calculation of the single configurational coordinate diagram, as well as the thermal quenching, has been conducted under a fundamental approach on the ytterbium - oxygen bond. The study of the ytterbium infrared spectroscopy in these compounds has been realised and an energy level attribution is proposed in the particular case of the borate Li 6 Y(BO 3 ) 3 : Yb 3+ . An original approach is introduced with the study of the charge transfer states for the three compounds by looking at the infrared emission. The first laser performances in three operating modes (continuous wave, Q-switch and mode locking) of a Li 6 Y(BO 3 ) 3 : Yb 3+ crystal are reported. (author)

  6. Parametrization of optical properties of indium-tin-oxide thin films by spectroscopic ellipsometry: Substrate interfacial reactivity

    Science.gov (United States)

    Losurdo, M.; Giangregorio, M.; Capezzuto, P.; Bruno, G.; de Rosa, R.; Roca, F.; Summonte, C.; Plá, J.; Rizzoli, R.

    2002-01-01

    Indium-tin-oxide (ITO) films deposited by sputtering and e-gun evaporation on both transparent (Corning glass) and opaque (c-Si, c-Si/SiO2) substrates and in c-Si/a-Si:H/ITO heterostructures have been analyzed by spectroscopic ellipsometry (SE) in the range 1.5-5.0 eV. Taking the SE advantage of being applicable to absorbent substrate, ellipsometry is used to determine the spectra of the refractive index and extinction coefficient of the ITO films. The effect of the substrate surface on the ITO optical properties is focused and discussed. To this aim, a parametrized equation combining the Drude model, which considers the free-carrier response at the infrared end, and a double Lorentzian oscillator, which takes into account the interband transition contribution at the UV end, is used to model the ITO optical properties in the useful UV-visible range, whatever the substrate and deposition technique. Ellipsometric analysis is corroborated by sheet resistance measurements.

  7. Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies

    Science.gov (United States)

    Ikhlas, Shoeb; Ahmad, Masood

    2018-02-01

    Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).

  8. Magnetic Properties of the DNA-Quaternary Ammonium Surfactant Complexes Studied by EMR Spectroscopy and SQUID Measurement

    National Research Council Canada - National Science Library

    Kwon, Young-Wan; Do, Eui D; Choi, Dong H; Jin, Jung-Il; Lee, Chang H; Koh, Eui K; Grote, James Gerard

    2008-01-01

    .... In particular, interest in nanoscience and nanotechnology is accelerating the exploration of DNA for various properties such as electrical conductivity electron or hole transport and optical properties...

  9. Production of a handbook: Nd-doped glass spectroscopic and physical properties

    International Nuclear Information System (INIS)

    Saroyan, R.A.

    1979-01-01

    The production of Lawrence Livermore Laboratory publication M-095, a handbook containing a collection of properties of Nd 3+ -doped glasses, is described. The pros and cons of the method are presented. The bulk of the report is contained in detailed appendices which cover major aspects of production

  10. Spectroscopic properties of chromium(III) in zirconium barium fluoride glass (ZBLA)

    International Nuclear Information System (INIS)

    Balda, R.; Fernandez, J.; Illarramendi, M.A.; Elejalde, M.J.

    1988-01-01

    The optical properties of trivalent chromium ions in ZBLA glass have been studied for different concentrations of Cr 3 + . Optical absorption, luminescence and lifetimes have been investigated in a wide range of temperatures. The relative quantum efficiencies of these systems have been determined from the integrated luminescence decay curves as a function of the excitation wavelength

  11. The Synthesis and Luminescence-spectroscopic Properties of Fluorescent Condensation Polymers

    Science.gov (United States)

    Barashkov, Nikolai N.

    1985-07-01

    The results of studies on the synthesis of polycondensation phosphorus-containing aliphatic and aromatic polymers as well as the products of polymer-analogue transformations with phosphorus-groups in the side chain are examined. The light absorption and luminescent properties of the polymers obtained and of model compounds having an analogous structure are discussed. The bibliography includes 108 references.

  12. Effects of alkali ions on thermal stability and spectroscopic properties of Er{sup 3+}-doped gallogermanate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Shi, D.M.; Zhao, Y.G.; Wang, X.F.; Liao, G.H. [Department of Materials Science and Engineering, Luoyang Institute of Science and Technology, Luoyang 471023 (China); Zhao, C. [Department of Physics, South China University of Technology, Guangzhou 510641 (China); MOE Key Lab of Specially Functional Materials and Institute of Optical Communication Materials, South China University of Technology, Guangzhou 510641 (China); Peng, M.Y. [MOE Key Lab of Specially Functional Materials and Institute of Optical Communication Materials, South China University of Technology, Guangzhou 510641 (China); Zhang, Q.Y., E-mail: qyzhang@scut.edu.c [MOE Key Lab of Specially Functional Materials and Institute of Optical Communication Materials, South China University of Technology, Guangzhou 510641 (China)

    2011-02-01

    Since information transportation capacity of optical communication network increases rapidly, new optical materials are always demanded with gain bandwidth desirably much broader than traditional erbium-doped silica fiber amplifier (EDFA). We show here in this paper the erbium-doped gallogermanate glasses with a full-width at half-maximum (FWHM) more than 50 nm. Incorporation of alkali ions such as Li{sup +}, Na{sup +}, K{sup +} into the system can on the one hand improve the thermal stability of the glasses, and on the other hand enhance the emission at 1.5 {mu}m due to the {sup 4}I{sub 13/2{yields}}{sup 4}I{sub 15/2} transition of Er{sup 3+} and suppress the upconversion process at the same time. This particularly works best for the case of K{sup +} inclusion. This work might give a general idea on controlling the Er{sup 3+} luminescence by simply adjusting the glass component and find a potential laser glass applicable to developing new broadband fiber amplifier. -- Research highlights: {yields} We report on spectroscopic properties of Er{sup 3+}-doped Ga{sub 2}O{sub 3}-GeO{sub 2}-R{sub 2}O (GGR, R=Li, Na and K) glasses for 1.53 {mu}m fiber amplifier. Effects of alkali metal ions on the thermal stability and spectroscopic properties of Er{sup 3+}-doped GGR glasses have been investigated. {yields} Incorporation of alkali ions such as Li{sup +}, Na{sup +}, K{sup +} into the system can on the one hand improve the thermal stability of the glasses, and on the other hand enhance the emission at 1.5 {mu}m due to the {sup 4}I{sub 13/2{yields}}{sup 4}I{sub 15/2} transition of Er{sup 3+} and suppress the upconversion process at the same time. This particularly works best for the case of K{sup +} inclusion. This work might give a general idea on controlling the Er{sup 3+} luminescence by simply adjusting the glass component and find a potential laser glass applicable to developing new broadband fiber amplifier.

  13. Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    The present report demonstrates that the conformational properties of DNA in solution are sensitive to the type of monovalent ion. Results are based on the ability of a polarizable force field using the classical Drude oscillator to reproduce experimental solution X-ray scattering data more accurately than two nonpolarizable DNA models, AMBER Parmbsc0 and CHARMM36. The polarizable model is then used to calculate scattering profiles of DNA in the presence of four different monovalent salts, Li...

  14. A treatise on benzimidazole based Schiff base metal(II) complexes accentuating their biological efficacy: Spectroscopic evaluation of DNA interactions, DNA cleavage and antimicrobial screening

    Energy Technology Data Exchange (ETDEWEB)

    Kumaravel, Ganesan; Raman, Natarajan, E-mail: ramchem1964@gmail.com

    2017-01-01

    Two novel imidazole derived Schiff bases, (Z)-1-(1H-benzo[d]imidazol-2-yl)-N-benzylidenemethanamine (L{sup 1}) and 1-(1H-benzo[d]imidazol-2-yl)-N-(4-nitrobenzylidene) methanamine, and a series of their transition metal complexes of the types [M(L{sup 1}){sub 2}]Cl{sub 2} and [M(L{sup 2}){sub 2}]Cl{sub 2} where, M = Cu(II), Ni(II), Co(II) and Zn(II) have been designed and synthesized. These compounds were characterized by various spectral and physicochemical data. UV–Vis, magnetic susceptibility and molar conductivity data indicate that all the complexes adopt square planar geometry. The EPR spectral data of the Cu(II) complexes have provided supportive evidence to the conclusion derived on the basis of electronic absorption and magnetic moment values. Moreover, the interaction of complexes with DNA via intercalation has been explored by absorption, fluorescence spectroscopy, cyclic voltammetry, viscosity and circular dichroism. Agarose gel electrophoresis technique reveals that the complexes are good metallonucleases. All the compounds have relatively high antibacterial and antifungal potencies. Among the metal complexes, Cu(II) complexes exhibit higher efficacy against all the pathogens. - Highlights: • Synthesis of new and efficient benzimidazole based DNA targeting complexes • Synthesis of efficient metallointercalators • Excellent DNA exploiting ability of Cu(II) complexes • Efficient antimicrobial agents against various pathogens.

  15. Influence of bismuth on structural, elastic and spectroscopic properties of Nd{sup 3+} doped Zinc–Boro-Bismuthate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Gaurav; Sontakke, Atul D.; Karmakar, P.; Biswas, K.; Balaji, S.; Saha, R.; Sen, R.; Annapurna, K., E-mail: annapurnak@cgcri.res.in

    2014-05-01

    The present investigation reports, influence of bismuth addition on structural, elastic and spectral properties of [(99.5−x) {4ZnO−3B_2O_3}−0.5Nd{sub 2}O{sub 3}−x Bi{sub 2}O{sub 3} where x=0, 5, 10, 20, 30, 40, 50 and 60] glasses. The measured FTIR reflectance spectra facilitated a thorough insight of methodical modifications that are arising in the glass structure from borate (build by BO{sub 3} and BO{sub 4} units) to bismuthate (BiO{sub 3} and BiO{sub 6} units) network due to the increase of bismuth content ensuing with a steady decrease in host phonon energy (ν{sub ph}). The elastic properties estimated from measured longitudinal and shear ultrasonic velocities (U{sub L} and U{sub s}) demonstrated the reduction in network rigidity of glasses on Bi{sub 2}O{sub 3} inclusion. The three phenomenological Judd–Ofelt intensity parameters (Ω{sub 2,4,6}) were obtained from recorded absorption spectra of Nd{sup 3+} ions in these glasses and have been used to predict radiative properties as a function of variation in bismuth content. The reduced host phonon energy and high optical basicity effect due to Bi{sub 2}O{sub 3} incorporation remarkably improved the Nd{sup 3+} luminescence properties such as emission intensity, quantum yield and emission cross-section. The quantum yield showed a strong increase from mere 16% in Zinc–Borate glass to almost 73% in 60 mol% Bi{sub 2}O{sub 3} containing glass. Similarly, the emission cross-section for Nd{sup 3+4}F{sub 3/2}→{sup 4}I{sub 11/2} laser transition raised from 2.43×10{sup −20} cm{sup 2} to 3.95×10{sup −20} cm{sup 2} in studied concentration suggesting a strong improvement in Nd{sup 3+} laser spectroscopic properties in Zinc–Boro-Bismuthate glass. These materials may be promising for compact solid state infrared lasers. - Highlights: • Continuous structural changes associated with reduction in host phonon energy by Bi{sub 2}O{sub 3} inclusion. • Ultrasonic velocity study revealed reduced Debye

  16. Supergiant Fast X-ray Transients with Swift: spectroscopic and temporal properties

    OpenAIRE

    Romano, P.; Mangano, V.; Ducci, L.; Esposito, P.; Farinelli, R.; Ceccobello, C.; Vercellone, S.; Burrows, D. N.; Kennea, J. A.; Krimm, H. A.; Gehrels, N.

    2012-01-01

    Supergiant fast X-ray transients (SFXTs) are a class of high-mass X-ray binaries with possible counterparts in the high energy gamma rays. The Swift SFXT Project has conducted a systematic investigation of the properties of SFTXs on timescales ranging from minutes to years and in several intensity states (from bright flares, to intermediate intensity states, and down to almost quiescence). We also performed broad-band spectroscopy of outbursts, and intensity-selected spectroscopy outside of o...

  17. Chemical and structural properties of Pd nanoparticle-decorated graphene-Electron spectroscopic methods and QUASES

    Czech Academy of Sciences Publication Activity Database

    Lesiak, B.; Jiříček, Petr; Bieloshapka, Igor

    2017-01-01

    Roč. 404, May (2017), s. 300-309 ISSN 0169-4332 R&D Projects: GA MŠk LM2015088 Institutional support: RVO:68378271 Keywords : graphite (Gr) * graphene oxide (GO) * reduced graphene oxide (RGO) * Pd nanoparticles * XPS * QUASES * REELS * chemical and structural properties Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 3.387, year: 2016

  18. Tuning porosity and radial mechanical properties of DNA origami nanotubes via crossover design

    Science.gov (United States)

    Ma, Zhipeng; Kawai, Kentaro; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

    2017-06-01

    DNA origami nanotubes are utilized as structural platforms for the fabrication of various micro/nanosystems for drug delivery, optical or biological sensing, and even nanoscale robots. Their radial structural and mechanical properties, which play a crucial role in the effective use of micro/nanosystems, have not been fully studied. In particular, the effects of crossovers, which are basic structures for rationally assembling double-stranded DNA (dsDNA) helices into a nanotube configuration, have not yet been characterized experimentally. To investigate the effects of crossovers on the porosity and the radial mechanical properties of DNA origami nanotubes, we fabricated a DNA origami nanotube with varied crossover designs along the nanotube axis. The radial geometry of the DNA origami nanotube is experimentally characterized by both atomic force microscopy (AFM) and electron cryomicroscopy (cryo-EM). Moreover, the radial mechanical properties of the DNA origami nanotube including the radial modulus are directly measured by force-distance-based AFM. These measurements reveal that the porosity and the radial modulus of DNA origami nanotubes can be tuned by adjusting the crossover design, which enables the optimal design and construction of DNA origami nanostructures for various applications.

  19. DNA binding properties of the small cascade subunit Csa5.

    Directory of Open Access Journals (Sweden)

    Michael Daume

    Full Text Available CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon Thermoproteus tenax was shown to target and degrade DNA in vitro, dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. T. tenax Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.

  20. Spectroscopic and luminescent properties of Co2+ doped tin oxide thin films by spray pyrolysis

    Directory of Open Access Journals (Sweden)

    K. Durga Venkata Prasad

    2016-07-01

    Full Text Available The wide variety of electronic and chemical properties of metal oxides makes them exciting materials for basic research and for technological applications alike. Oxides span a wide range of electrical properties from wide band-gap insulators to metallic and superconducting. Tin oxide belongs to a class of materials called Transparent Conducting Oxides (TCO which constitutes an important component for optoelectronic applications. Co2+ doped tin oxide thin films were prepared by chemical spray pyrolysis synthesis and characterized by powder X-ray diffraction, SEM, TEM, FT-IR, optical, EPR and PL techniques to collect the information about the crystal structure, coordination/local site symmetry of doped Co2+ ions in the host lattice and the luminescent properties of the prepared sample. Powder XRD data revealed that the crystal structure belongs to tetragonal rutile phase and its lattice cell parameters are evaluated. The average crystallite size was estimated to be 26 nm. The morphology of prepared sample was analyzed by using SEM and TEM studies. Functional groups of the prepared sample were observed in the FT-IR spectrum. Optical absorption and EPR studies have shown that on doping, Co2+ ions enter in the host lattice as octahedral site symmetry. PL studies of Co2+ doped SnO2 thin films exhibit blue and yellow emission bands. CIE chromaticity coordinates were also calculated from emission spectrum of Co2+ doped SnO2 thin films.

  1. Ionization-potential depression and other dense plasma statistical property studies - Application to spectroscopic diagnostics.

    Science.gov (United States)

    Calisti, Annette; Ferri, Sandrine; Mossé, Caroline; Talin, Bernard

    2017-02-01

    The radiative properties of an emitter surrounded by a plasma, are modified through various mechanisms. For instance the line shapes emitted by bound-bound transitions are broadened and carry useful information for plasma diagnostics. Depending on plasma conditions the electrons occupying the upper quantum levels of radiators no longer exist as they belong to the plasma free electron population. All the charges present in the radiator environment contribute to the lowering of the energy required to free an electron in the fundamental state. This mechanism is known as ionization potential depression (IPD). The knowledge of IPD is useful as it affects both the radiative properties of the various ionic states and their populations. Its evaluation deals with highly complex n-body coupled systems, involving particles with different dynamics and attractive ion-electron forces. A classical molecular dynamics (MD) code, the BinGo-TCP code, has been recently developed to simulate neutral multi-component (various charge state ions and electrons) plasma accounting for all the charge correlations. In the present work, results on IPD and other dense plasma statistical properties obtained using the BinGo-TCP code are presented. The study focuses on aluminum plasmas for different densities and several temperatures in order to explore different plasma coupling conditions.

  2. A spectroscopic study of the chromatic properties of GafChromic™EBT3 films

    Energy Technology Data Exchange (ETDEWEB)

    Callens, M., E-mail: maarten.callens@kuleuven-kulak.be; Van Den Abeele, K. [Wave Propagation and Signal Processing, KU Leuven–KULAK, Kortrijk 8500 (Belgium); Crijns, W.; Depuydt, T.; Haustermans, K. [Department of Radiation Oncology, University Hospitals Leuven, Leuven 3000 (Belgium); Simons, V. [imec, Kapeldreef 75, Leuven 3001 (Belgium); De Wolf, I. [imec, Kapeldreef 75, Leuven 3001, Belgium and Department of Materials Engineering, KU Leuven, Leuven 3001 (Belgium); Maes, F. [Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven 3001 (Belgium); D’hooge, J. [Department of Cardiovascular Sciences, KU Leuven, Leuven 3000 (Belgium); D’Agostino, E. [DoseVue NV, Hasselt 3500 (Belgium); Wevers, M.; Pfeiffer, H. [Department of Materials Engineering, KU Leuven, Leuven 3001 (Belgium)

    2016-03-15

    Purpose: This work provides an interpretation of the chromatic properties of GafChromic™EBT3 films based on the chemical nature of the polydiacetylene (PDA) molecules formed upon interaction with ionizing radiation. The EBT3 films become optically less transparent with increasing radiation dose as a result of the radiation-induced polymerization of diacetylene monomers. In contrast to empirical quantification of the chromatic properties, less attention has been given to the underlying molecular mechanism that induces the strong decrease in transparency. Methods: Unlaminated GafChromic™EBT3 films were irradiated with a 6 MV photon beam to dose levels up to 20 Gy. The optical absorption properties of the films were investigated using visible (vis) spectroscopy. The presence of PDA molecules in the active layer of the EBT3 films was investigated using Raman spectroscopy, which probes the vibrational modes of the molecules in the layer. The vibrational modes assigned to PDA’s were used in a theoretical vis-absorption model to fit our experimental vis-absorption spectra. From the fit parameters, one can assess the relative contribution of different PDA conformations and the length distribution of PDA’s in the film. Results: Vis-spectroscopy shows that the optical density increases with dose in the full region of the visible spectrum. The Raman spectrum is dominated by two vibrational modes, most notably by the ν(C≡C) and the ν(C=C) stretching modes of the PDA backbone. By fitting the vis-absorption model to experimental spectra, it is found that the active layer contains two distinct PDA conformations with different absorption properties and reaction kinetics. Furthermore, the mean PDA conjugation length is found to be 2–3 orders of magnitude smaller than the crystals PDA’s are embedded in. Conclusions: Vis- and Raman spectroscopy provided more insight into the molecular nature of the radiochromic properties of EBT3 films through the identification of

  3. Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

    Science.gov (United States)

    Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

    2018-03-01

    Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

  4. Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

    Science.gov (United States)

    Sørensen, L. K.; Fleig, T.; Olsen, J.

    2009-08-01

    Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

  5. Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

    International Nuclear Information System (INIS)

    Soerensen, L K; Fleig, T; Olsen, J

    2009-01-01

    Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

  6. Theoretical modeling of the spectroscopic absorption properties of luciferin and oxyluciferin: A critical comparison with recent experimental studies

    Energy Technology Data Exchange (ETDEWEB)

    Anselmi, Massimiliano, E-mail: m.anselmi@caspur.it [Department of Chemistry, University of Rome ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy); Marocchi, Simone [Department of Chemistry, University of Rome ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy); Aschi, Massimiliano [Department of Chemistry, Chemical Engineering and Materials, University of L' Aquila, Via Vetoio (Coppito 1), 67100 Coppito, L' Aquila (Italy); Amadei, Andrea [Department of Chemistry, University of Rome ' Tor Vergata' , Via della Ricerca Scientifica 1, 00133 Rome (Italy)

    2012-01-02

    Highlights: Black-Right-Pointing-Pointer The calculated absorption spectra were compared with experimental data. Black-Right-Pointing-Pointer Shapes and absorption maxima were reproduced for luciferin and oxyluciferin spectra. Black-Right-Pointing-Pointer The effect of the solvent largely changes the electronic transition probabilities. Black-Right-Pointing-Pointer Higher excitations provide an important contribution to the main absorption peak. - Abstract: Firefly luciferin and its oxidated form, oxyluciferin, are two heterocyclic compounds involved in the enzymatic reaction, catalyzed by redox proteins called luciferases, which provides the bioluminescence in a wide group of arthropods. Whereas the electronic absorption spectra of D-luciferin in water at different pHs are known since 1960s, only recently reliable experimental electronic spectra of oxyluciferin have become available. In addition oxyluciferin is involved in a triple chemical equilibria (deprotonation of the two hydroxyl groups and keto-enol tautomerism of the 4-hydroxythiazole ring), that obligates to select during an experiment a predominant species, tuning pH or solvent polarity besides introducing chemical modifications. In this study we report the absorption spectra of luciferin and oxyluciferin in each principal chemical form, calculated by means of perturbed matrix method (PMM), which allowed us to successfully introduce the effect of the solvent on the spectroscopic absorption properties, and compare the result with available experimental data.

  7. Effect of radiative trapping on measurement of the spectroscopic properties of Yb sup 3 sup + :phosphate glasses

    CERN Document Server

    Dai Shi Xun; Wen Lei; Hu Li Li; Jiang Zhong Hon

    2003-01-01

    The effect of radiative trapping on measurement of the spectroscopic properties of Yb sup 3 sup + -doped phosphate glasses was investigated as a function of Yb sup 3 sup + concentration at different thicknesses. It was found that radiative trapping exists generally in Yb sup 3 sup + :phosphate glasses, even at low concentration. As a result, the measured lifetime of Yb sup 3 sup + in phosphate glasses is usually larger than the calculated one. The maximum discrepancies between them at high concentration are found to be <42%. The calculated lifetime should be used as a reference in determining the true value of the measured lifetime because of it being lengthened largely by radiative trapping. On the other hand, the shape of fluorescence spectrum exhibits remarkable changes due to the radiative trapping. What is more, the intensity increase of DELTA lambda sub e sub f sub f at high concentration is greater than that of low doping. The DELTA lambda sub e sub f sub f increases 36% from 53 to 72 nm with thickn...

  8. Spectroscopic properties of Er3+ and Yb3+ co-doped glass ceramics containing SrF2 nanocrystals

    International Nuclear Information System (INIS)

    Qiao Xvsheng; Fan Xianping; Wang Minquan; Zhang Xianghua

    2009-01-01

    The spectroscopic properties of Er 3+ /Yb 3+ co-doped 50SiO 2 -10Al 2 O 3 -20ZnF 2 -20SrF 2 glass and glass ceramic containing SrF 2 nanocrystals were investigated. The formation of SrF 2 nanocrystals in the glass ceramic was confirmed by XRD. The oscillator strengths for several transitions of the Er 3+ ions in the glass ceramic have been obtained and the Judd-Ofelt parameters were then determined. The XRD result and Judd-Ofelt parameters suggested that Er 3+ and Yb 3+ ions had efficiently enriched in the SrF 2 nanocrystals in the glass ceramic. The lifetime of excited states has been used to reveal the surroundings of luminescent Er 3+ and Yb 3+ and energy transfer (ET) mechanism between Er 3+ and Yb 3+ . Much stronger upconversion luminescence and longer lifetime of the Er 3+ /Yb 3+ co-doped glass ceramic were observed in comparison with the Er 3+ /Yb 3+ co-doped glass, which could be ascribed to more efficient ET from Yb 3+ to Er 3+ due to the enrichment of Yb 3+ and Er 3+ and the shortening of the distance between lanthanide ions in the precipitated SrF 2 nanocrystals.

  9. Lipid chain saturation and the cholesterol in the phospholipid membrane affect the spectroscopic properties of lipophilic dye nile red

    Science.gov (United States)

    Halder, Animesh; Saha, Baishakhi; Maity, Pabitra; Kumar, Gopinatha Suresh; Sinha, Deepak Kumar; Karmakar, Sanat

    2018-02-01

    We have studied the effect of composition and the phase state of phospholipid membranes on the emission spectrum, anisotropy and lifetime of a lipophilic fluorescence probe nile red. Fluorescence spectrum of nile red in membranes containing cholesterol has also been investigated in order to get insights into the influence of cholesterol on the phospholipid membranes. Maximum emission wavelength (λem) of nile red in the fluid phase of saturated and unsaturated phospholipids was found to differ by 10 nm. The λem was also found to be independent of chain length and charge of the membrane. However, the λem is strongly dependent on the temperature in the gel phase. The λem and rotational diffusion rate decrease, whereas the anisotropy and lifetime increase markedly with increasing cholesterol concentration for saturated phosoholipids, such as, dimyristoyl phosphatidylcholine (DMPC) in the liquid ordered phase. However, these spectroscopic properties do not alter significantly in case of unsaturated phospholipids, such as, dioleoyl phosphatidylcholine (DOPC) in liquid disordered phase. Interestingly, red edge excitation shift (REES) in the presence of lipid-cholesterol membranes is the direct consequences of change in rotational diffusion due to motional restriction of lipids in the presence of cholesterol. This study provides correlations between the membrane compositions and fluorescence spectral features which can be utilized in a wide range of biophysical fields as well the cell biology.

  10. Synthesis, spectroscopic and catalytic properties of some new boron hybrid molecule derivatives by BF2 and BPh2 chelation

    Science.gov (United States)

    Kilic, Ahmet; Alcay, Ferhat; Aydemir, Murat; Durgun, Mustafa; Keles, Armagan; Baysal, Akın

    2015-05-01

    A new series of Schiff base ligands (L1-L3) and their corresponding fluorine/phenyl boron hybrid complexes [LnBF2] and [LnBPh2] (n = 1, 2 or 3) have been synthesized and well characterized by both analytical and spectroscopic methods. The Schiff base ligands and their corresponding fluorine/phenyl boron hybrid complexes have been characterized by NMR (1H, 13C and 19F), FT-IR, UV-Vis, LC-MS, and fluorescence spectroscopy as well as melting point and elemental analysis. The fluorescence efficiencies of phenyl chelate complexes are greatly red-shifted compared to those of the fluorine chelate analogs based on the same ligands, presumably due to the large steric hindrance and hard π → π∗ transition of the diphenyl boron chelation, which can effectively prevent molecular aggregation. The boron hybrid complexes were applied to the transfer hydrogenation of acetophenone derivatives to 1-phenylethanol derivatives in the presence of 2-propanol as the hydrogen source. The catalytic studies showed that boron hybrid complexes are good catalytic precursors for transfer hydrogenation of aromatic ketones in 0.1 M iso-PrOH solution. Also, we have found that both steric and electronic factors have a significant impact on the catalytic properties of this class of molecules.

  11. Effect of Gd substitution on structure and spectroscopic properties of (Lu,Gd)2O3:Eu ceramic scintillator

    Science.gov (United States)

    Cao, Maoqing; Hu, Zewang; Ivanov, Maxim; Dai, Jiawei; Li, Chaoyu; Kou, Huamin; Shi, Yun; Chen, Haohong; Xu, Jiayue; Pan, Yubai; Li, Jiang

    2018-02-01

    In this paper, (Lu1-xGdx)2O3:Eu (x = 0, 0.1, 0.3, 0.5, 0.7, 0.9) ceramics were consolidated by the solid-state reaction method combined with vacuum sintering without sintering aids. We investigated the effect of the varying contents of Gd2O3 on the structure and spectroscopic properties of (Lu1-xGdx)2O3:Eu ceramics. X-ray diffraction (XRD) patterns indicate that proper amount of Gd2O3 can incorporate well with Lu2O3 and form Lu2O3-Gd2O3 solid solution. However, excessive Gd3+-doping in Lu2O3 will lead to the cubic phase transforming into monoclinic even hexagonal phase. The Gd3+ substitution no more than 50% of Lu2O3 enhances the radioluminescence, and reduces the fluorescence lifetime. Transmittance, photoluminescence, and radiation damage of the (Lu1-xGdx)2O3:Eu scintillation ceramics were also studied.

  12. Synthesis, molecular structure, spectroscopic properties and stability of (Z)-N-methyl-C-2,4,6-trimethylphenylnitrone

    Science.gov (United States)

    Lasri, Jamal; Ismail, Ali I.; Haukka, Matti; Soliman, Saied M.

    2015-02-01

    New N-methyl-C-2,4,6-trimethylphenylnitrone 1 has been synthesized starting from N-methylhydroxylamine and mesitaldehyde. The product was fully characterized using different spectroscopic techniques; FTIR, NMR, UV-Vis, high resolution mass spectrometry and X-ray diffraction. The relative stability and percent of population of its two possible isomers (E and Z) were calculated using the B3LYP/6-311++G(d,p) method in gas phase and in solution. In agreement with the X-ray results, it was found that Z-isomer is the most stable one in both gas phase and solution. The molecular geometry, vibrational frequencies, gauge-including atomic orbital (GIAO), and chemical shift values were also calculated using the same level of theory. The TD-DFT results of the studied nitrone predicted a π-π∗ transition band at 285.1 nm (fosc = 0.3543) in the gas phase. The rest of the spectral bands undergo either hyperchromic or hypsochromic shifts in the presence of solvent. Polarizability and HOMO-LUMO gap values were used to predict the nonlinear optical properties (NLO) of the studied compound. NBO analysis has been used to determine the most accurate Lewis structure of the studied molecule.

  13. Thermal, structural and spectroscopic properties of Pr3+-doped lead zinc borate glasses modified by alkali metal ions

    Directory of Open Access Journals (Sweden)

    M.V. Sasi kumar

    2017-07-01

    Full Text Available This paper offers a study on Pr3+-doped alkali and mixed-alkali borate glasses prepared by the melt quenching technique and characterized by thermal, structural and spectroscopic studies. The amorphous nature of the glassy systems was identified based on X-ray diffraction. The thermal behaviour of glasses was studied using differential thermal analysis (DTA. The functional groups contained in the glasses were identified by Fourier transform infrared spectroscopy (FTIR. Spectral intensities were evaluated from the absorption spectra and used for calculating J–O intensity parameters, Ωλ (λ = 2, 4 and 6. Further, these parameters were used for calculating different radiative properties. The best radiative state was identified as the laser transition state among the various states. Emission analysis was performed for this state by calculating the branching ratios and stimulated emission cross sections (σp for all the prepared glasses. These studies suggest that borate glasses are useful for visible fluorescence.

  14. Redox properties of iron-bearing clays and MX-80 bentonite – Electrochemical and spectroscopic characterization

    Energy Technology Data Exchange (ETDEWEB)

    Hofstetter, Th. B.; Sosedova, Y.; Gorski, C.; Voegelin, A.; Sander, M.

    2014-03-15

    The characterization of the redox properties of Fe-bearing minerals in the presence and absence of dissolved Fe{sup 2+} is of major relevance for the assessment of redox reactions in natural and engineered environments such as radioactive waste repositories. In this study, we developed an electrochemical approach based on the use of soluble organic electron transfer mediators, which enabled us to quantify the redox properties of Fe-bearing clay minerals, MX- 80 bentonite and combinations of clay minerals, Fe oxides and dissolved Fe{sup 2+}. Using mediated electrochemical oxidation and reduction, we quantified the electron accepting and donating capacities of ferrous smectite SWa-1, Wyoming montmorillonite SWy-2 and MX-80 bentonite at pH 7.5. All structural Fe in clay minerals was redox-active in contrast to that present in other, not further defined phases of MX-80. The materials investigated were redoxactive over a very wide range of Eh-values, that is the Fe{sup 2+}/Fe{sub total} ratio of the minerals changed from 0 to 100 % between +600 and -600 mV (vs. SHE). Redox properties were highly path-dependent due to structural changes of the minerals as revealed from the study of native and redox-cycled clay minerals after repeated reduction and re-oxidation cycles. Irreversible alteration of the mineral structure, however, was less obvious for materials with lower total Fe content such as MX-80 bentonite and SWy-2. Systems containing native montmorillonites (SWy-2 or MX-80), goethite and dissolved Fe{sup 2+} were also able to buffer the reduction potential E{sub H} between 0 and -300 mV. Regardless of their Fe oxidation state, Fe-bearing minerals are redox-active over a wide potential range and therefore very relevant as redox buffers determining the fate of redox-active radionuclides and metals in waste repositories. (authors)

  15. Redox properties of iron-bearing clays and MX-80 bentonite – Electrochemical and spectroscopic characterization

    International Nuclear Information System (INIS)

    Hofstetter, Th. B.; Sosedova, Y.; Gorski, C.; Voegelin, A.; Sander, M.

    2014-03-01

    The characterization of the redox properties of Fe-bearing minerals in the presence and absence of dissolved Fe"2"+ is of major relevance for the assessment of redox reactions in natural and engineered environments such as radioactive waste repositories. In this study, we developed an electrochemical approach based on the use of soluble organic electron transfer mediators, which enabled us to quantify the redox properties of Fe-bearing clay minerals, MX- 80 bentonite and combinations of clay minerals, Fe oxides and dissolved Fe"2"+. Using mediated electrochemical oxidation and reduction, we quantified the electron accepting and donating capacities of ferrous smectite SWa-1, Wyoming montmorillonite SWy-2 and MX-80 bentonite at pH 7.5. All structural Fe in clay minerals was redox-active in contrast to that present in other, not further defined phases of MX-80. The materials investigated were redoxactive over a very wide range of Eh-values, that is the Fe"2"+/Fe_t_o_t_a_l ratio of the minerals changed from 0 to 100 % between +600 and -600 mV (vs. SHE). Redox properties were highly path-dependent due to structural changes of the minerals as revealed from the study of native and redox-cycled clay minerals after repeated reduction and re-oxidation cycles. Irreversible alteration of the mineral structure, however, was less obvious for materials with lower total Fe content such as MX-80 bentonite and SWy-2. Systems containing native montmorillonites (SWy-2 or MX-80), goethite and dissolved Fe"2"+ were also able to buffer the reduction potential E_H between 0 and -300 mV. Regardless of their Fe oxidation state, Fe-bearing minerals are redox-active over a wide potential range and therefore very relevant as redox buffers determining the fate of redox-active radionuclides and metals in waste repositories. (authors)

  16. Spectroscopic properties of the S1 state of linear carotenoids after excess energy excitation

    Science.gov (United States)

    Kuznetsova, Valentyna; Southall, June; Cogdell, Richard J.; Fuciman, Marcel; Polívka, Tomáš

    2017-09-01

    Properties of the S1 state of neurosporene, spheroidene and lycopene were studied after excess energy excitation in the S2 state. Excitation of carotenoids into higher vibronic levels of the S2 state generates excess vibrational energy in the S1 state. The vibrationally hot S1 state relaxes faster when carotenoid is excited into the S2 state with excess energy, but the S1 lifetime remains constant regardless of which vibronic level of the S2 state is excited. The S∗ signal depends on excitation energy only for spheroidene, which is likely due to asymmetry of the molecule, facilitating conformations responsible for the S∗ signal.

  17. Influence of dopant concentration on spectroscopic properties of Sr2CeO4:Yb nanocrystals

    Science.gov (United States)

    Stefanski, M.; Kędziorski, A.; Hreniak, D.; Strek, W.

    2017-12-01

    Optical properties of Sr2CeO4:Yb nanocrystals synthesized via Pechini's method are reported. The samples were characterized by X-ray diffraction data measurements. The unit cell parameters were determined using Rietveld refinement. It was found that they decreased with increasing amount of Yb ions. The absorption, excitation, emission spectra and luminescence decay profiles of the Sr2CeO4:Yb nanocrystals were investigated. It was observed that optical properties were strongly dependent on Yb concentration. It was found that Yb3+-O2- charge transfer transitions have great influence on the absorption spectra. It can be seen in the emission spectra that in addition to standard bands/lines corresponding to Ce-O metal-to-ligand charge transfer of Sr2CeO4 and f-f transitions of Yb3+, there is emission band centered at 744 nm. Its intensity depends on the concentration of the dopant. Recorded decay times become shorter with increasing dopant concentration due to the Yb3+ concentration quenching. Excitation spectra indicate the energy transfer from Ce-O charge transfer states to Yb3+2F5/2 state. The issue of appearance of down-conversion process in Sr2CeO4:Yb nanocrystals is considered.

  18. Dielectric properties of DNA oligonucleotides on the surface of silicon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Bagraev, N. T., E-mail: bagraev@mail.ioffe.ru [St. Petersburg Polytechnic University (Russian Federation); Chernev, A. L. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation); Klyachkin, L. E. [St. Petersburg Polytechnic University (Russian Federation); Malyarenko, A. M. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation); Emel’yanov, A. K.; Dubina, M. V. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation)

    2016-10-15

    Planar silicon nanostructures that are formed as a very narrow silicon quantum well confined by δ barriers heavily doped with boron are used to study the dielectric properties of DNA oligonucleotides deposited onto the surface of the nanostructures. The capacitance characteristics of the silicon nanostructures with oligonucleotides deposited onto their surface are determined by recording the local tunneling current–voltage characteristics by means of scanning tunneling microscopy. The results show the possibility of identifying the local dielectric properties of DNA oligonucleotide segments consisting of repeating G–C pairs. These properties apparently give grounds to correlate the segments with polymer molecules exhibiting the properties of multiferroics.

  19. Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy.

    Science.gov (United States)

    Meroni, Alice; Lazzaro, Federico; Muzi-Falconi, Marco; Podestà, Alessandro

    2018-01-01

    We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

  20. Effect of Ga2O3 on the spectroscopic properties of erbium-doped boro-bismuth glasses.

    Science.gov (United States)

    Ling, Zhou; Ya-Xun, Zhou; Shi-Xun, Dai; Tie-Feng, Xu; Qiu-Hua, Nie; Xiang, Shen

    2007-11-01

    The spectroscopic properties and thermal stability of Er3+-doped Bi2O3-B2O3-Ga2O3 glasses are investigated experimentally. The effect of Ga2O3 content on absorption spectra, the Judd-Ofelt parameters Omega t (t=2, 4, 6), fluorescence spectra and the lifetimes of Er3+:4I 13/2 level are also investigated, and the stimulated emission cross-section is calculated from McCumber theory. With the increasing of Ga2O3 content in the glass composition, the Omega t (t=2, 4, 6) parameters, fluorescence full width at half maximum (FWHM) and the 4I 13/2 lifetimes of Er3+ first increase, reach its maximum at Ga2O3=8 mol.%, and then decrease. The results show that Er3+-doped 50Bi2O3-42B2O3-8Ga2O3 glass has the broadest FWHM (81nm) and large stimulated emission cross-section (1.03 x1 0(-20)cm2) in these glass samples. Compared with other glass hosts, the gain bandwidth properties of Er+3-doped Bi2O3-B2O3-Ga2O3 glass is better than tellurite, silicate, phosphate and germante glasses. In addition, the lifetime of 4I 13/2 level of Er(3+) in bismuth-based glass, compared with those in other glasses, is relative low due to the high-phonon energy of the B-O bond, the large refractive index of the host and the existence of OH* in the glass. At the same time, the glass thermal stability is improved in which the substitution of Ga2O3 for B2O3 strengthens the network structure. The suitability of bismuth-based glass as a host for a Er3+-doped broadband amplifier and its advantages over other glass hosts are also discussed.

  1. Nonlinear optical and G-Quadruplex DNA stabilization properties of novel mixed ligand copper(II) complexes and coordination polymers: Synthesis, structural characterization and computational studies

    Science.gov (United States)

    Rajasekhar, Bathula; Bodavarapu, Navya; Sridevi, M.; Thamizhselvi, G.; RizhaNazar, K.; Padmanaban, R.; Swu, Toka

    2018-03-01

    The present study reports the synthesis and evaluation of nonlinear optical property and G-Quadruplex DNA Stabilization of five novel copper(II) mixed ligand complexes. They were synthesized from copper(II) salt, 2,5- and 2,3- pyridinedicarboxylic acid, diethylenetriamine and amide based ligand (AL). The crystal structure of these complexes were determined through X-ray diffraction and supported by ESI-MAS, NMR, UV-Vis and FT-IR spectroscopic methods. Their nonlinear optical property was studied using Gaussian09 computer program. For structural optimization and nonlinear optical property, density functional theory (DFT) based B3LYP method was used with LANL2DZ basis set for metal ion and 6-31G∗ for C,H,N,O and Cl atoms. The present work reveals that pre-polarized Complex-2 showed higher β value (29.59 × 10-30e.s.u) as compared to that of neutral complex-1 (β = 0.276 × 10-30e.s.u.) which may be due to greater advantage of polarizability. Complex-2 is expected to be a potential material for optoelectronic and photonic technologies. Docking studies using AutodockVina revealed that complex-2 has higher binding energy for both G-Quadruplex DNA (-8.7 kcal/mol) and duplex DNA (-10.1 kcal/mol). It was also observed that structure plays an important role in binding efficiency.

  2. Transition metal impurities in fluorides: Role of electronic structure of fluorine on spectroscopic properties

    DEFF Research Database (Denmark)

    Trueba, A.; Garcia-Fernandez, P.; García Lastra, Juan Maria

    2011-01-01

    This work examines the relation between optical properties of a MF6q− complex (M=transition–metal cation) and the chemical bonding paying especial attention to the role played by the electronic structure of fluorine. A main goal of the present study is to understand why if the effective Racah...... parameters, B and C, as well as the cubic splitting parameter, 10Dq, all depend on the covalency nevertheless the latter one is much more sensitive to a hydrostatic pressure than the former ones. The analysis carried out in this work, together with the results of ab initio calculations on CrF63− embedded...... detail. At the same time the reasons avoiding its measurement from optical spectra are pointed out as well. The present results stress that the microscopic origin of an optical parameter like 10Dq can certainly be very subtle....

  3. DC electrical, thermal, and spectroscopic properties of various condensation polyimides containing surface cobalt oxide

    Science.gov (United States)

    Rancourt, J. D.; Boggess, R. K.; Horning, L. S.; Taylor, L. T.

    1987-01-01

    Doping polyimides with cobalt ion causes the room temperature direct current electrical resistivity to decrease relative to the polymer alone, the reduction being most pronounced for the air-side of the cobalt modified polyimides. At a constant electrical field, resistivity for the volume, air-side and glass-side modes decreases yet further with an increase in temperature as expected for semiconductors and insulators. X-ray photoelectron spectroscopy indicates the air-side of the cobalt modified polyimides is predominantly Co3O4. The bulk resistivity of the air-side and activation energy of conduction for this surface are comparable to high purity sintered Co3O4. Charging characteristics at room temperature indicate a substantial polymer matrix contribution to both the glass-side and volume mode measurements but a negligible contribution to the air-side electrical properties. Volume electrical resistivity for similar additive levels is reduced by increasing the molecular flexibility of the host polymer.

  4. THE WHIQII SURVEY: METALLICITIES AND SPECTROSCOPIC PROPERTIES OF LUMINOUS COMPACT BLUE GALAXIES

    International Nuclear Information System (INIS)

    Tollerud, Erik J.; Barton, Elizabeth J.; Cooke, Jeff; Van Zee, Liese

    2010-01-01

    As part of the WIYN High Image Quality Indiana-Irvine (WHIQII) survey, we present 123 spectra of faint emission-line galaxies, selected to focus on intermediate redshift (0.4 ∼ 23 -O 32 plane that differs from luminous local galaxies and is more consistent with dwarf irregulars at the present epoch, suggesting that cosmic 'downsizing' is observable in even the most fundamental parameters that describe star formation. These properties for our sample are also generally consistent with lying between local galaxies and those at high redshift, as expected by this scenario. Surprisingly, our sample exhibits no detectable correlation between compactness and metallicity, strongly suggesting that at these epochs of rapid star formation, the morphology of compact star-forming galaxies is largely transient.

  5. Spectroscopic, thermal, and electrical properties of MgO/ polyvinyl pyrrolidone/ polyvinyl alcohol nanocomposites

    Science.gov (United States)

    Mohammed, Gh.; El Sayed, Adel M.; Morsi, W. M.

    2018-04-01

    In this study, we aimed to control the optical and electrical properties of polyvinyl alcohol (PVA) in order to broaden its industrial and technological applications, which we achieved by blending PVA with polyvinyl pyrrolidone (PVP) and adding sol-gel prepared MgO nanopowder. The blended film and nanocomposite films were prepared using the solution casting technique. X-ray diffraction analyses showed that the crystallite size was ∼18.4 nm for MgO and the highest degree of crystallinity (XC) in the films was about 24.34% at 1.0 wt% MgO. High resolution transmission electron microscopy determined the nanoribbon morphology of MgO. Scanning electron microscopy (SEM) indicated the uniform distribution of the MgO nanoribbons on the surfaces of the PVA/PVP films. SEM and Fourier transform infrared spectroscopy also confirmed the interaction between the blend and MgO fillers. The effects of the additives on the glass transition (Tg) and melting (Tm) temperatures were evaluated by differential thermal analysis and differential scanning calorimetry. The appearance of one melting point confirmed the miscibility of the two polymers. According to ultraviolet-visible-near infrared spectroscopy measurements, the optical properties and optical constants of PVA could be adjusted by the addition of PVP and MgO, where the optical band gap (Eg) determined for PVA increased with the PVP content, whereas it decreased to 4.8 eV as the MgO content increased. The DC conductivity (σdc) of the films increased whereas the activation energy (Ea) decreased after the addition of MgO, possibly because the nanoribbon shape fixed the preferred conducting pathways. In addition, MgO could break the H-bond in sbnd OH groups of the blends to allow the free movement of the molecular chains.

  6. Evaluation of the physicochemical properties of liposomes as potential carriers of anticancer drugs: spectroscopic study

    International Nuclear Information System (INIS)

    Pentak, Danuta

    2016-01-01

    Vesicle size and composition are a critical parameter for determining the circulation half-life of liposomes. Size influences the degree of drug encapsulation in liposomes. The geometry, size, and properties of liposomes in an aqueous environment have to be described to enable potential applications of liposome systems as drug carriers. The characteristics of multiple thermotropic phase transitions are also an important consideration in liposomes used for analytical and bioanalytical purposes. The aim of this study was to evaluate the physicochemical properties of liposomes which accommodate hydrophilic and amphiphilic drugs used in cancer therapy. The studied liposomes were prepared with the involvement of the modified reverse-phase evaporation method (mREV). The prepared liposomes had a diameter of 70–150 nm. The analyzed compounds were 1-β-d-arabinofuranosylcytosine, cyclophosphamide, and ifosfamide. In literature, there is no information about simultaneous incorporation of cytarabine, ifosfamide, and cyclophosphamide, in spite of the fact that these drugs have been used for more than 30 years. A combination of the examined drugs is used in CODOX-M/IVAC therapy. CODOX-M/IVAC (cyclophosphamide, doxorubicin, high-dose methotrexate/ifosfamide, etoposide, and high-dose cytarabine) is one of the currently preferred intensive-dose chemotherapy regimens for Burkitt lymphoma (BL). The present research demonstrates the pioneering studies of incorporation of ifosfamide into liposome vesicles, location of and competition between the analyzed drugs and liposome vesicles. The applied methods were nuclear magnetic resonance (NMR), atomic force microscopy (AFM), differential scanning calorimetry (DSC).Graphical Abstract.

  7. [Study on spectroscopic characterization and property of PES/ micro-nano cellulose composite membrane material].

    Science.gov (United States)

    Tang, Huan-Wei; Zhang, Li-Ping; Li, Shuai; Zhao, Guang-Jie; Qin, Zhu; Sun, Su-Qin

    2010-03-01

    In the present paper, the functional groups of PES/micro-nano cellulose composite membrane materials were characterized by Fourier transform infrared spectroscopy (FTIR). Also, changes in crystallinity in composite membrane materials were analyzed using X-ray diffraction (XRD). The effects of micro-nano cellulose content on hydrophilic property of composite membrane material were studied by measuring hydrophilic angle. The images of support layer structure of pure PES membrane material and composite membrane material were showed with scanning electron microscope (SEM). These results indicated that in the infrared spectrogram, the composite membrane material had characteristic peaks of both PES and micro-nano cellulose without appearance of other new characteristics peaks. It revealed that there were no new functional groups in the composite membrane material, and the level of molecular compatibility was achieved, which was based on the existence of inter-molecular hydrogen bond association between PES and micro-nano cellulose. Due to the existence of micro-nano cellulose, the crystallinity of composite membrane material was increased from 37.7% to 47.9%. The more the increase in micro-nano cellulose mass fraction, the better the van de Waal force and hydrogen bond force between composite membrane material and water were enhanced. The hydrophilic angle of composite membrane material was decreased from 55.8 degrees to 45.8 degrees and the surface energy was raised from 113.7 to 123.5 mN x m(-2). Consequently, the hydrophilic property of composite membrane material was improved. The number of pores in the support layer of composite membrane material was lager than that of pure PES membrane. Apparently, pores were more uniformly distributed.

  8. Evaluation of the physicochemical properties of liposomes as potential carriers of anticancer drugs: spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Pentak, Danuta, E-mail: danuta.pentak@us.edu.pl [University of Silesia, Department of Materials Chemistry and Chemical Technology, Institute of Chemistry (Poland)

    2016-05-15

    Vesicle size and composition are a critical parameter for determining the circulation half-life of liposomes. Size influences the degree of drug encapsulation in liposomes. The geometry, size, and properties of liposomes in an aqueous environment have to be described to enable potential applications of liposome systems as drug carriers. The characteristics of multiple thermotropic phase transitions are also an important consideration in liposomes used for analytical and bioanalytical purposes. The aim of this study was to evaluate the physicochemical properties of liposomes which accommodate hydrophilic and amphiphilic drugs used in cancer therapy. The studied liposomes were prepared with the involvement of the modified reverse-phase evaporation method (mREV). The prepared liposomes had a diameter of 70–150 nm. The analyzed compounds were 1-β-d-arabinofuranosylcytosine, cyclophosphamide, and ifosfamide. In literature, there is no information about simultaneous incorporation of cytarabine, ifosfamide, and cyclophosphamide, in spite of the fact that these drugs have been used for more than 30 years. A combination of the examined drugs is used in CODOX-M/IVAC therapy. CODOX-M/IVAC (cyclophosphamide, doxorubicin, high-dose methotrexate/ifosfamide, etoposide, and high-dose cytarabine) is one of the currently preferred intensive-dose chemotherapy regimens for Burkitt lymphoma (BL). The present research demonstrates the pioneering studies of incorporation of ifosfamide into liposome vesicles, location of and competition between the analyzed drugs and liposome vesicles. The applied methods were nuclear magnetic resonance (NMR), atomic force microscopy (AFM), differential scanning calorimetry (DSC).Graphical Abstract.

  9. Spectroscopic and thermal properties of Sm3+ doped iron lead bismuthate glasses

    Science.gov (United States)

    Narwal, P.; Yadav, A.; Dahiya, M. S.; Vishal, Rohit, Agarwal, A.; Khasa, S.

    2018-05-01

    The results of the structural, physical, thermal and electrical properties of the glass compositions xFe2O3•(100-x)(3Bi2O3•PbO)• Sm2O3(1 mol%) where x=0, 1, 5, 10, 12, 15 mol% prepared via melt quench technique were studied. The synthesized compositions were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and differential thermal analysis (DTA). The IR study reveals that present system is build up with lead in tetrahedral coordination and bismuth in trigonal as well as octahedral coordination. Density and molar volume have been calculated using Archimedes principle, and the variation in their values has been correlated with structural changes in the glass matrix based on the IR study. The variation in the characteristic temperatures (glass transition temperature Tg, crystallization temperature Tp and melting temperature Tm) with different heating rate and change in the composition of iron oxide were analyzed and reported in the present study.

  10. Spectroscopic properties of tetravalent uranium in the incommensurate phase of thorium tetrabromide

    International Nuclear Information System (INIS)

    Delamoye, P.

    1985-04-01

    This thesis includes: the complete visible and infrared absorption (emission) spectra of U 4+ as doping ion in pure ThBr 4 , as well as the magnetic circular dichroism (MCD) measurements have been examined. At liquid - He temperature the absorption spectra consist of broad absorption bands with two edge singularities. The apparently continuous character of fluorescence lines in selective excitation experiments, and the MCD profiles suggest the existence of a continuous distribution of U 4+ sites in the host crystal. Raman scattering results indicate the existence of a displacive phase transition at Tsub(c) = 95 K. X-ray and neutron powder diffraction data show additional lines. Single-crystal neutron diffraction measurements indicate that below Tsub(c) ThBr 4 has a displacively modulated structure. Inelastic neutron scattering leads us to understand the dynamics of the phase transition. In conclusion this study led us to give a complete interpretation of the optical properties of an ion embedded in an incommensurate structure [fr

  11. Electronic and spectroscopic properties of early 3d metal atoms on a graphite surface

    Science.gov (United States)

    Rakotomahevitra, A.; Garreau, G.; Demangeat, C.; Parlebas, J. C.

    1995-07-01

    High-sensitivity magneto-optic Kerr effect experiments failed to detect manifestations of magnetism in epitaxial films of V on Ag(100) substrates. More recently V 3s XPS of freshly evaporated V clusters on graphite exhibited the appearance of a satellite structure which has then been interpreted by the effect of surface magnetic moments on V. It is the absence of unambiguous results on the electronic properties of early 3d supported metals that prompts us to examine the problem. Our purpose is twofold. In a first part, after a total energy calculation within a tight-binding method which yields the equilibrium position of a given adatom, we use the Hartree-Fock approximation to find out a possible magnetic solution of V (or Cr) upon graphite for a reasonable value of the exchange integral Jdd. In a second part the informations given by the density of states of the graphite surface as well as the additional states of the adsorbed atom are taken into account through a generalised impurity Anderson Hamiltonian which incorporates the various Coulomb and exchange interactions necessary to analyse the 3s XPS results.

  12. Chemical behavior and spectroscopic properties of rare earth borates in glazes

    Energy Technology Data Exchange (ETDEWEB)

    Lezhnina, Marina M., E-mail: marina@fh-muenster.de [Muenster University of Applied Sciences, Department of Chemical Engineering, Stegerwaldstr. 39, 48565 Steinfurt (Germany); Kätker, Heike [Muenster University of Applied Sciences, Department of Chemical Engineering, Stegerwaldstr. 39, 48565 Steinfurt (Germany); Kaiser, Martin [Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin (Germany); Stegemann, Linda [University of Muenster, Physical Institute, Heisenbergstr. 11, 48149 Muenster (Germany); Voss, Eckhard [Wendel GmbH, Am Güterbahnhof 30, 35683 Dillenburg (Germany); Resch-Genger, Ute [Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin (Germany); Strassert, Cristian [University of Muenster, Physical Institute, Heisenbergstr. 11, 48149 Muenster (Germany); Kynast, Ulrich [Muenster University of Applied Sciences, Department of Chemical Engineering, Stegerwaldstr. 39, 48565 Steinfurt (Germany)

    2016-02-15

    Efficient Near UV excited materials (350<λ<400 nm) responding with green line emission are sparse in comparison to higher energy UV excited emitters (λ<350 nm), while corresponding red line emitters are more abundant, albeit typically also restricted to excitation wavelengths below 400 nm. This situation is disadvantageous for several important actual and potential applications. Among these, excitation with high power UV-LEDs and laser diodes are of particular interest. Here we present results on green emitting YBO{sub 3}:Ce, Tb, which can be excited with 370–380 nm radiation at quantum efficiencies of up to 60% and decay times in excess of 2 ms. Moreover, as powderous phosphors typically require stable matrices to be hosted in, we investigated low melting, lead- and fluoride-free glasses for their capability to accommodate the phosphor and yet retain its optical properties. In these, we even observed an increase of the quantum efficiencies of up to 70% at decay times approaching 3 ms. Finally, we characterized the thermal quenching behavior, which showed a clear advantage of the phosphors in glassy matrices. - Highlights: • YBO3:Ce, Tb revisited as a reference material for Near UV excitation. • Absolute quantum yields determined independently at different institutions. • Efficient luminescence from glazing YBO{sub 3}:Ce,Tb with glass forming compositions. • Glaze composites retain or surpass pure phosphor’s optical performance.

  13. Spectroscopic properties of triangular silver nanoplates immobilized on polyelectrolyte multilayer-modified glass substrates

    Science.gov (United States)

    Rabor, Janice B.; Kawamura, Koki; Muko, Daiki; Kurawaki, Junichi; Niidome, Yasuro

    2017-07-01

    Fabrication of surface-immobilized silver nanostructures with reproducible plasmonic properties by dip-coating technique is difficult due to shape alteration. To address this challenge, we used a polyelectrolyte multilayer to promote immobilization of as-received triangular silver nanoplates (TSNP) on a glass substrate through electrostatic interaction. The substrate-immobilized TSNP were characterized by absorption spectrophotometry and scanning electron microscopy. The bandwidth and peak position of localized surface plasmon resonance (LSPR) bands can be tuned by simply varying the concentration of the colloidal solution and immersion time. TSNP immobilized from a higher concentration of colloidal solution with longer immersion time produced broadened LSPR bands in the near-IR region, while a lower concentration with shorter immersion time produced narrower bands in the visible region. The shape of the nanoplates was retained even at long immersion time. Analysis of peak positions and bandwidths also revealed the point at which the main species of the immobilization had been changed from isolates to aggregates.

  14. A DFT Study of the Geometrical, Spectroscopical and Reactivity Properties of Diindolylmethane-Phenylboronic Acid Hybrids

    Directory of Open Access Journals (Sweden)

    Amira Jalil Fragoso-Medina

    2017-10-01

    Full Text Available The structure of the ortho-, meta- and para- hybrid diindolylmethane-phenylboronic acids and their interactions were optimized with by a quantum chemical method, using density functional theory at the (DFT level. Thus, infrared bands were assigned based on the scaled theoretical wavenumbers by correlating the respective experimental data of the molecules. In addition, the corresponding 1H-/13C-/11B-NMR experimental and theoretical chemical shifts were correlated. The target molecules showed a poor treatment of the OH shifts in the GIAO method due to the absence of explicit solvent effects in these calculations; therefore, they were explicitly considered with acetone molecules. Moreover, the electron density at the hydrogen bond critical point increased, generating stabilization energy, from weak to moderate or weak to strong, serving as an indicator of the strength of the hydrogen bond between the different intermolecular interactions. Finally, some properties related to the reactive behavior of the target molecules associated with their cytotoxic effects and metabolic pathways were also calculated.

  15. Multiscale properties of DNA primary structure: cross-scale correlations

    International Nuclear Information System (INIS)

    Altajskij, M.V.; Ivanov, V.V.; Polozov, R.V.

    2000-01-01

    Cross-scale correlations of wavelet coefficients of the DNA coding sequences are calculated and compared to that of the generated random sequence of the same length. The coding sequences are shown to have strong correlation between large and small scale structures, while random sequences have not

  16. Virulence properties and random amplification of polymorphic DNA ...

    African Journals Online (AJOL)

    Genotypic and phenotypic characterization as well as studies on the virulence factors of Candida albicans isolates obtained from oral cavity of patients was carried out using random amplified polymorphic DNA (RAPD) fingerprinting and epithelial cells adherence assay, respectively. RAPD patterns revealed the presence of ...

  17. Optical properties of DNA-hosted silver clusters

    NARCIS (Netherlands)

    Markešević, Nemanja

    2015-01-01

    DNA-hosted silver clusters (Ag:DNAs) have attracted a lot of attention due to their small size (~20 atoms), wide range of applications in chemistry and biology, and sequence-dependent optical tunability. Most of the previous studies are focused on the ensemble of emitters in solution. However,

  18. Moessbauer spectroscopic studies of the magnetic and structural properties of novel nanophase magnetic materials

    International Nuclear Information System (INIS)

    Milford, G.H.

    2000-08-01

    57 Fe Moessbauer Spectroscopy and complementary techniques have been used to characterise the physical and magnetic properties of a variety of novel nanophase iron containing magnetic particles, over a range of temperatures, and applied magnetic fields. Two series of commercially produced advanced metal particle pigments and tapes intended for use as magnetic recording media have been characterised using Transmission and Conversion Electron Moessbauer Spectroscopy at 4.2K, 77K and 293K. Moessbauer Spectra at 4.2K and 293K have identified two different forms of iron within the samples, an iron alloy core and an Fe 3+ oxide passivation layer. The first series of metal particle pigments studied is split into two separate groups, the core of the first group consists of a disordered Fe/Co alloy. Whereas the second group of metal particle pigments studied within the series have shown different characteristics than the previous samples, as the core is no longer a simple Fe/Co alloy. In addition to this the particle size is significantly reduced in the final sample within the series. This may be due to the presence of an Fe 2+ component, which appears to reduce the amount of Fe 3+ component necessary to passivate the particles by approximately half. The second series of samples have been used in part to investigate the out of plane angle of the metal particle pigments and its relationship with the squareness of the metal particle tapes. It is vital to minimise the out of plane angle of the metal particle tapes to obtain the optimum magnetic properties of the metal particle pigment. It has been shown that a decreasing out of plane angle leads to an increase in the squareness of the tapes. As a consequence of this the switching field distribution can be narrowed on metal particle tapes by reducing the out of plane angle. A further investigation has been carried out on the metal particle pigments coated onto tapes using Conversion Electron Moessbauer Spectroscopy, in order to

  19. Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of Co(II)- picolinate complex

    Energy Technology Data Exchange (ETDEWEB)

    Tamer, Ömer, E-mail: omertamer@sakarya.edu.tr; Avcı, Davut; Atalay, Yusuf

    2015-11-15

    A cobalt(II) complex of picolinate was synthesized, and its structure was fully characterized by the applying of X-ray diffraction method as well as FT-IR, FT-Raman and UV–vis spectroscopies. In order to both support the experimental results and convert study to more advanced level, density functional theory calculations were performed by using B3LYP level. Single crystal X-ray structural analysis shows that cobalt(II) ion was located to the center of distorted octahedral geometry. The C=O, C=C and C=N stretching vibrations were found as highly active and strong peaks, inducing the molecular charge transfer within Co(II) complex. The small energy gap between frontier molecular orbital energies was another indicator of molecular charge transfer interactions within Co(II) complex. The nonlinear optical properties of Co(II) complex were investigated at DFT/B3LYP level, and the hypepolarizability parameter was found to be decreased due to the presence of inversion symmetry. The natural bond orbital (NBO) analysis was performed to investigate molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength for Co(II) complex. Finally, molecular electrostatic potential (MEP) and spin density distributions for Co(II) complex were evaluated. - Highlights: • Co(II) complex of picolinate was prepared. • Its FT-IR, FT-Raman and UV–vis spectra were measured. • DFT calculations were performed to support experimental results. • Small HOMO-LUMO energy gap is an indicator of molecular charge transfer. • Spin density localized on Co(II) as well as O and N atoms.

  20. Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro.

    Science.gov (United States)

    Santos, L; Santos, E B H; Dias, J M; Cunha, A; Almeida, A

    2014-08-01

    The influence of photochemical transformations of chromophoric dissolved organic matter (CDOM) on microbial communities was evaluated in the estuarine system Ria de Aveiro. Two sites, representative of the marine and brackish water zones of the estuary, were surveyed regularly in order to determine seasonal and vertical profiles of variation of CDOM properties. Optical parameters of CDOM indicative of aromaticity and molecular weight were used to establish CDOM sources, and microbial abundance and activity was characterized. Additionally, microcosm experiments were performed in order to simulate photochemical reactions of CDOM and to evaluate microbial responses to light-induced changes in CDOM composition. The CDOM of the two estuarine zones showed different spectral characteristics, with significantly higher values of the specific ultra-violet absorbance at 254 nm (SUVA254) (5.5 times) and of the absorption coefficient at 350 nm (a350) (12 times) and lower SR (S275-295/S350-400) ratio at brackish water compared with the marine zone, reflecting the different amounts and prevailing sources of organic matter, as well as distinct riverine and oceanic influences. At the marine zone, the abundance of bacteria and the activity of Leu-AMPase correlated with a350 and a254, suggesting a microbial contribution to the HMW CDOM pool. The irradiation of DOM resulted in a decrease of the values of a254 and a350 and an increase of the slope S275-295 and of the ratios E2 : E3 (a250/a365) and SR, which in turn increase its bioavailability. However, the extent of photoinduced transformations and microbial responses was dependent on the initial optical characteristics of CDOM. In Ria de Aveiro both photochemical and microbial processes yielded optical changes in CDOM and the overall results of these combined processes determine the fate of CDOM in the estuarine system and have an influence on local productivity and in adjacent coastal areas.

  1. Spectroscopic techniques for measuring ion diode space-charge distributions and ion source properties

    Energy Technology Data Exchange (ETDEWEB)

    Filuk, A B; Bailey, J E; Adams, R G [Sandia Labs., Albuquerque, NM (United States); and others

    1997-12-31

    The authors are using time- and space-resolved visible spectroscopy to measure applied-B ion diode dynamics on the 20 TW Particle Beam Fusion Accelerator II. Doppler broadening of fast Li atoms, as viewed parallel to the anode, is used in a charge-exchange model to obtain the Li{sup +} ion divergence within 100 {mu}m of the anode surface. The characteristic Stark/Zeeman shifts in spectra of alkali neutrals or singly-ionized alkaline-earths are used to measure the strong electric (10{sup 9} V/m) an magnetic ({approx} 6 T) fields in the diode gap. Large Stark shifts within 0.5 mm of the anode indicate the LiF emits with a finite field threshold rather than with Child-Langmuir-type emission, and the small slope in the electric field indicates an unexpected build-up of electrons near the anode. In the diode gap, the authors aim to unfold fields to quantify the time-dependent ion and electron space-charge distributions that determine the ion beam properties. Observed electric field non-uniformities give local beam deflections that can be comparable to the total beam microdivergence. The authors are implementing active laser absorption and laser-induced fluorescence spectroscopy on low-density Na atoms injected into the diode gap prior to the power pulse. The small Doppler broadening in the Na spectra should allow simultaneous electric and magnetic field mapping with improved spatial resolution. (author). 4 figs., 13 refs.

  2. Spectroscopic properties of Pr{sup 3+} ions embedded in lithium borate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Ramteke, D.D. [Department of Applied Physics, Visvesvaraya National Institute of Technology, Nagpur 440010 (India); Department of Physics, University of the Free State, P.O. Box 339, Bloemfontein 9300 (South Africa); Swart, H.C., E-mail: swarthc@ufs.ac.za [Department of Physics, University of the Free State, P.O. Box 339, Bloemfontein 9300 (South Africa); Gedam, R.S., E-mail: rupesh_gedam@rediffmail.com [Department of Applied Physics, Visvesvaraya National Institute of Technology, Nagpur 440010 (India)

    2016-01-01

    A series of lithium borate glasses with different Pr{sup 3+} contents were prepared by the melt quench technique to explore the new material for solid state light applications. We found that the addition of Pr{sup 3+} ions in the glass matrix has a profound effect on the properties of the glasses. The presence of Pr{sup 3+} ions in the glass matrix created various absorption bands compared to the base glass. These bands were due to the ground state ({sup 3}H{sub 4}) of the Pr{sup 3+} to the various excited states. Optical energy band gap was calculated by Tauc's method which showed a decreasing trend with an increase in the Pr{sup 3+} content. This might be due to structural changes when the glass structure became rigid due to the Pr{sup 3+} ions and this was confirmed by the density results. Rigidity of the glass structure was further confirmed by the Fourier transformed infrared results. The excitation spectra showed bands at {sup 3}H{sub 4}→{sup 3}P{sub 2}, {sup 3}P{sub 1} and {sup 3}P{sub 0} nm. The {sup 3}H{sub 4}→{sup 3}P{sub 2} band was used to study the unresolved {sup 1}D{sub 2}→{sup 3}H{sub 4} and {sup 3}P{sub 0}→{sup 3}H{sub 6} transitions of the Pr{sup 3+} ions.

  3. Spectroscopic and Mechanical Properties of a New Generation of Bulk Fill Composites.

    Science.gov (United States)

    Monterubbianesi, Riccardo; Orsini, Giovanna; Tosi, Giorgio; Conti, Carla; Librando, Vito; Procaccini, Maurizio; Putignano, Angelo

    2016-01-01

    Objectives: The aims of this study were to in vitro evaluate the degree of conversion and the microhardness properties of five bulk fill resin composites; in addition, the performance of two curing lamps, used for composites polymerization, was also analyzed. Materials and Methods: The following five resin-based bulk fill composites were tested: SureFil SDR®, Fill Up!™, Filtek™, SonicFill™, and SonicFill2™. Samples of 4 mm in thickness were prepared using Teflon molds filled in one increment and light-polymerized using two LED power units. Ten samples for each composite were cured using Elipar S10 and 10 using Demi Ultra. Additional samples of SonicFill2, (3 and 5 mm-thick) were also tested. The degree of conversion (DC) was determined by Raman spectroscopy, while the Vickers microhardness (VMH) was evaluated using a microhardness tester. The experimental evaluation was carried out on top and bottom sides, immediately after curing (t0), and, on bottom, after 24 h (t24). Two-ways analysis of variance was applied to evaluate DC and VMH-values. In all analyses, the level of significance was set at p composites recorded satisfactory DCs on top and bottom sides. At t0, the top of SDR and SonicFill2 showed the highest DCs-values (85.56 ± 9.52 and 85.47 ± 1.90, respectively), when cured using Elipar S10; using Demi Ultra, SonicFill2 showed the highest DCs-values (90.53 ± 2.18). At t0, the highest DCs-values of bottom sides were recorded by SDR (84.64 ± 11.68), when cured using Elipar S10, and Filtek (81.52 ± 4.14), using Demi Ultra. On top sides, Demi Ultra lamp showed significant higher DCs compared to the Elipar S10 ( p composites showed higher VMH than the flowable or dual curing composites.

  4. Spectroscopic properties of reaction center pigments in photosystem II core complexes: revision of the multimer model.

    Science.gov (United States)

    Raszewski, Grzegorz; Diner, Bruce A; Schlodder, Eberhard; Renger, Thomas

    2008-07-01

    Absorbance difference spectra associated with the light-induced formation of functional states in photosystem II core complexes from Thermosynechococcus elongatus and Synechocystis sp. PCC 6803 (e.g., P(+)Pheo(-),P(+)Q(A)(-),(3)P) are described quantitatively in the framework of exciton theory. In addition, effects are analyzed of site-directed mutations of D1-His(198), the axial ligand of the special-pair chlorophyll P(D1), and D1-Thr(179), an amino-acid residue nearest to the accessory chlorophyll Chl(D1), on the spectral properties of the reaction center pigments. Using pigment transition energies (site energies) determined previously from independent experiments on D1-D2-cytb559 complexes, good agreement between calculated and experimental spectra is obtained. The only difference in site energies of the reaction center pigments in D1-D2-cytb559 and photosystem II core complexes concerns Chl(D1). Compared to isolated reaction centers, the site energy of Chl(D1) is red-shifted by 4 nm and less inhomogeneously distributed in core complexes. The site energies cause primary electron transfer at cryogenic temperatures to be initiated by an excited state that is strongly localized on Chl(D1) rather than from a delocalized state as assumed in the previously described multimer model. This result is consistent with earlier experimental data on special-pair mutants and with our previous calculations on D1-D2-cytb559 complexes. The calculations show that at 5 K the lowest excited state of the reaction center is lower by approximately 10 nm than the low-energy exciton state of the two special-pair chlorophylls P(D1) and P(D2) which form an excitonic dimer. The experimental temperature dependence of the wild-type difference spectra can only be understood in this model if temperature-dependent site energies are assumed for Chl(D1) and P(D1), reducing the above energy gap from 10 to 6 nm upon increasing the temperature from 5 to 300 K. At physiological temperature, there are

  5. Temperature influence on spectroscopic properties and 2.7-μm lasing of Er:YAP crystal

    Science.gov (United States)

    Švejkar, Richard; Šulc, Jan; Němec, Michal; Jelínková, Helena; Nejezchleb, Karel; Čech, Miroslav

    2018-02-01

    The spectroscopic and laser properties of Er:YAP crystal, that is appropriate for generation at 2.7 μm, in temperature range 78 - 400 K are presented. The sample of Er:YAP (1 at. % of Er3+) had face-polished plan-parallel faces without anti-reflection coatings (thickness 4.47 mm). During experiments the Er:YAP was attached to temperature controlled copper holder and it was placed in vacuum chamber. The transmission and emission spectra together with the fluorescence decay time were measured depending on temperature. The Er:YAP crystal was longitudinally pumped by radiation from laser diode that works in pulse regime (repetition rate 66.6 Hz, pulse duration 1.5 ms, pump wavelength 972.5 nm) or in CW regime. Laser resonator was hemispherical, 145 mm in length with flat pumping mirror (HR @ 2.7 μm) and spherical output coupler (r = 150 mm, R = 95 % @ 2.5 - 2.8 μm). The fluorescence decay time of manifold 4I11/2 (upper laser level) became shorter and intensity of up-conversion radiation was increasing with decreasing temperature. In pulsed regime, the highest slope efficiency with respect to absorbed mean power was 1.27 % at 78 K. The maximum output of mean power was 3.5 mW at 78 K, i.e. 8.7 times higher than measured this value at 300 K. The maximal output power 27 mW with slope efficiency up to 3.5 % was achieved in CW. The radiation generated by Er:YAP laser (2.73 μm) is close to absorption peak of water (3 μm) thus this wavelength can be use in medicine and spectroscopy.

  6. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties.

    Science.gov (United States)

    Pan, Gaofeng; Jiang, Limin; Tang, Jijun; Guo, Fei

    2018-02-08

    DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods-especially machine learning methods-have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k -gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria-area under the receiver operating characteristic curve (AUC), Matthew's correlation coefficient (MCC), accuracy (ACC), sensitivity (SN), and specificity-are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  7. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties

    Directory of Open Access Journals (Sweden)

    Gaofeng Pan

    2018-02-01

    Full Text Available DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods—especially machine learning methods—have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k-gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria—area under the receiver operating characteristic curve (AUC, Matthew’s correlation coefficient (MCC, accuracy (ACC, sensitivity (SN, and specificity—are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  8. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  9. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    International Nuclear Information System (INIS)

    Snodin, Benedict E. K.; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-01-01

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na + ] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

  10. Influence of different water-ethanol solvent systems on the spectroscopic and physico-chemical properties of the macrocyclic compounds pheophytin and chlorophyll a

    International Nuclear Information System (INIS)

    Moreira, Leonardo M.; Rodrigues, Maira R.; Oliveira, Hueder P. M. de; Lima, Adriana; Soares, Rafael R. S.; Batistela, Vagner R.; Gerola, Adriana P.; Hioka, Noboru; Severino, Divinomar; Baptista, Mauricio S.; Machado, Antonio Eduardo da Hora

    2010-01-01

    This work focus on the influence of solvent on the photophysical properties of chlorophyll a and pheophytin. Both compounds are related to the photosynthesis process and are considered prototypes of photosensitizers in Photodynamic Therapy. Fluorescence measurements were developed using water/ethanol mixtures at different compositions, since both solvents could be employed in biological applications. The spectroscopic properties of these compounds undergo profound changes depending on water content in the ethanol due to auto-aggregation processes. The major hydrophobicity and the lower dielectric constant of ethanol when compared with water precluded significantly the auto-aggregation process of these compounds. (author)

  11. Substituent and solvent effects on spectroscopic properties of 2-amino-1,3-dicyano-5,6,7,8-tetrahydronaphthalene derivatives

    International Nuclear Information System (INIS)

    Józefowicz, M.; Bajorek, A.; Pietrzak, M.; Heldt, J.R.; Heldt, J.

    2014-01-01

    In this article, we report the photophysical properties of six, newly synthesized donor-substituted 2-amino-1,3-dicyano-5,6,7,8-tetrahydronaphthalene fluorophores. The steady-state and time-resolved spectroscopic experiments have been used to investigate the substituent and solvent effects on the locally excited (LE) and intramolecular charge transfer (ICT) emission. We demonstrate that the spectroscopic characteristics (fluorescence quantum yields, fluorescence decay times, radiative rate constants, and ground and excited state dipole moments) of the studied D–A dyes, as well as the reorganization energies characterizing the solute–solvent interactions and intramolecular torsion motions greatly depend on different substituents and microenvironment. On the basis of the experimental results and our previous quantum-chemical calculations, it was shown that two emitting charge transfer states: non-relaxed (ICT) NR and relaxed (ICT) R exist in six biphenyl derivatives dissolved in polar solvents (e.g., THF), whereas in non-polar medium (MCH) the existence of two emissive states have been attributed to non-relaxed and relaxed, locally excited state ((LE) NR , (LE) R ). - Highlights: • Spectroscopic properties greatly depend on different substituents and microenvironment. • Investigated dyes form a typically spectrally inhomogeneous system. • Two emitting charge transfer states (ICT) NR and (ICT) R exist in polar solvents. • In non-polar medium locally excited fluorescence is possible from (LE) NR and (LE) R states

  12. Isolation, characterization, spectroscopic properties and quantum chemical computations of an important phytoalexin resveratrol as antioxidant component from Vitis labrusca L. and their chemical compositions

    Science.gov (United States)

    Güder, Aytaç; Korkmaz, Halil; Gökce, Halil; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

    2014-12-01

    In this study, isolation and characterization of trans-resveratrol (RES) as an antioxidant compound were carried out from VLE, VLG and VLS. Furthermore, antioxidant activities were evaluated by using six different methods. Finally, total phenolic, flavonoid, ascorbic acid, anthocyanin, lycopene, β-carotene and vitamin E contents were carried out. In addition, the FT-IR, 13C and 1H NMR chemical shifts and UV-vis. spectra of trans-resveratrol were experimentally recorded. Quantum chemical computations such as the molecular geometry, vibrational frequencies, UV-vis. spectroscopic parameters, HOMOs-LUMOs energies, molecular electrostatic potential (MEP), natural bond orbitals (NBO) and nonlinear optics (NLO) properties of title molecule have been calculated by using DFT/B3PW91 method with 6-311++G(d,p) basis set in ground state for the first time. The obtained results show that the calculated spectroscopic data are in a good agreement with experimental data.

  13. Breaking Symmetry in Time-Dependent Electronic Structure Theory to Describe Spectroscopic Properties of Non-Collinear and Chiral Molecules

    Science.gov (United States)

    Goings, Joshua James

    Time-dependent electronic structure theory has the power to predict and probe the ways electron dynamics leads to useful phenomena and spectroscopic data. Here we report several advances and extensions of broken-symmetry time-dependent electronic structure theory in order to capture the flexibility required to describe non-equilibrium spin dynamics, as well as electron dynamics for chiroptical properties and vibrational effects. In the first half, we begin by discussing the generalization of self-consistent field methods to the so-called two-component structure in order to capture non-collinear spin states. This means that individual electrons are allowed to take a superposition of spin-1/2 projection states, instead of being constrained to either spin-up or spin-down. The system is no longer a spin eigenfunction, and is known a a spin-symmetry broken wave function. This flexibility to break spin symmetry may lead to variational instabilities in the approximate wave function, and we discuss how these may be overcome. With a stable non-collinear wave function in hand, we then discuss how to obtain electronic excited states from the non-collinear reference, along with associated challenges in their physical interpretation. Finally, we extend the two-component methods to relativistic Hamiltonians, which is the proper setting for describing spin-orbit driven phenomena. We describe the first implementation of the explicit time propagation of relativistic two-component methods and how this may be used to capture spin-forbidden states in electronic absorption spectra. In the second half, we describe the extension of explicitly time-propagated wave functions to the simulation of chiroptical properties, namely circular dichroism (CD) spectra of chiral molecules. Natural circular dichroism, that is, CD in the absence of magnetic fields, originates in the broken parity symmetry of chiral molecules. This proves to be an efficient method for computing circular dichroism spectra

  14. DNA Hydrogel with Tunable pH-Responsive Properties Produced by Rolling Circle Amplification.

    Science.gov (United States)

    Xu, Wanlin; Huang, Yishun; Zhao, Haoran; Li, Pan; Liu, Guoyuan; Li, Jing; Zhu, Chengshen; Tian, Leilei

    2017-12-22

    Recently, smart DNA hydrogels, which are generally formed by the self-assembly of oligonucleotides or through the cross-linking of oligonucleotide-polymer hybrids, have attracted tremendous attention. However, the difficulties of fabricating DNA hydrogels limit their practical applications. We report herein a novel method for producing pH-responsive hydrogels by rolling circle amplification (RCA). In this method, pH-sensitive cross-linking sites were introduced into the polymeric DNA chains during DNA synthesis. As the DNA sequence can be precisely defined by its template, the properties of such hydrogels can be finely tuned in a very facile way through template design. We have investigated the process of hydrogel formation and pH-responsiveness to provide rationales for functional hydrogel design based on the RCA reaction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Irradiation effects on electrical properties of DNA solution/Al Schottky diodes

    Science.gov (United States)

    Al-Ta'ii, Hassan Maktuff Jaber; Periasamy, Vengadesh; Iwamoto, Mitsumasa

    2018-04-01

    Deoxyribonucleic acid (DNA) has emerged as one of the most exciting organic material and as such extensively studied as a smart electronic material since the last few decades. DNA molecules have been reported to be utilized in the fabrication of small-scaled sensors and devices. In this current work, the effect of alpha radiation on the electrical properties of an Al/DNA/Al device using DNA solution was studied. It was observed that the carrier transport was governed by electrical interface properties at the Al-DNA interface. Current ( I)-voltage ( V) curves were analyzed by employing the interface limited Schottky current equations, i.e., conventional and Cheung and Cheung's models. Schottky parameters such as ideality factor, barrier height and series resistance were also determined. The extracted barrier height of the Schottky contact before and after radiation was calculated as 0.7845, 0.7877, 0.7948 and 0.7874 eV for the non-radiated, 12, 24 and 36 mGy, respectively. Series resistance of the structure was found to decline with the increase in the irradiation, which was due to the increase in the free radical root effects in charge carriers in the DNA solution. Results pertaining to the electronic profiles obtained in this work may provide a better understanding for the development of precise and rapid radiation sensors using DNA solution.

  16. DNA in the material world: electrical properties and nano-applications.

    Science.gov (United States)

    Triberis, Georgios P; Dimakogianni, Margarita

    2009-01-01

    Contradictory experimental findings and theoretical interpretations have spurred intense debate over the electrical properties of the DNA double helix. In the present review article the various factors responsible for these divergences are discussed. The enlightenment of this issue could improve long range chemistry of oxidative DNA damage and repair processes, monitoring protein-DNA interactions and possible applications in nano-electronic circuit technology. The update experimental situation concerning measurements of the electrical conductivity is given. The character of the carriers responsible for the electrical conductivity measured in DNA is investigated. A theoretical model for the temperature dependence of the electrical conductivity of DNA is presented, based on microscopic models and percolation theoretical arguments. The theoretical results, excluding or including correlation effects, are applied to recent experimental findings for DNA, considering it as a one dimensional molecular wire. The results indicate that correlation effects are probably responsible for large hopping distances in DNA samples. Other theoretical conductivity models proposed for the interpretation of the responsible transport mechanism are also reviewed. Some of the most known and pioneering works on DNA's nano-applications, future developments and perspectives along with current technological limitations and patents are presented and discussed.

  17. Action of an ionizing radiation and hydrodynamic effect on matrix properties of DNA during extracellular synthesis of RNA, and thiophosphate protection of matrix properties of T2-DNA against. gamma. -radiation. [gamma radiation

    Energy Technology Data Exchange (ETDEWEB)

    Shekhtman, Ya L; Domashenko, A D; Kamzolova, S G; Medvedkov, A A [AN SSSR, Pushchino-na-Oke. Inst. Biologicheskoj Fiziki

    1976-05-01

    Action of an ionizing radiation and the hydrodynamic effect of the matrix activity of thymus DNA and T2 phase DNA have been studied in vitro in the RNA: polymerase system of E.coli B. Also studied have been the thiophosphate protection of matrix properties of T2-DNA against ..gamma..-radiation.

  18. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Spectroscopic and dielectric properties of titanium doped MgO-Al{sub 2}O{sub 3}-B{sub 2}O{sub 3} glass system

    Energy Technology Data Exchange (ETDEWEB)

    Raju, G Naga; Ramesh, N Ch; Naresh, P; Krishna, T L; Srinivasulu, K; Sudhkar, K S V; Rao, P Venkateswara, E-mail: gnag_9@rediffmail.com [Department of Physics, Acharya Nagarjuna University-Nuzvid Campus, Nuzvid - 521 201 (India)

    2009-07-15

    In this paper we have reported the influence of titanium ions on different spectroscopic and dielectric properties of MgO-Al{sub 2}O{sub 3}-B{sub 2}O{sub 3} glasses. The analysis of result of all these studies has indicated that as the concentration of TiO{sub 2} increased in the glass matrix, there is a gradual transformation of titanium ions from octahedral position to tetrahedral positions and cause to increase the rigidity of glass network.

  20. Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.

    Science.gov (United States)

    Schimelman, Jacob B; Dryden, Daniel M; Poudel, Lokendra; Krawiec, Katherine E; Ma, Yingfang; Podgornik, Rudolf; Parsegian, V Adrian; Denoyer, Linda K; Ching, Wai-Yim; Steinmetz, Nicole F; French, Roger H

    2015-02-14

    The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

  1. High-pressure effect in spectroscopic and structural properties of Sm{sup 3+} doped GeO{sub 2}-PbO glass

    Energy Technology Data Exchange (ETDEWEB)

    Rovani, Pablo Roberto; Herrera, Alvaro; Azevedo, Gustavo de Medeiros; Balzaretti, Naira Maria, E-mail: rovani.pr@gmail.com [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre (Brazil)

    2016-07-01

    Full text: The effect of densification under high pressure (7.7 GPa) on spectroscopic and structural properties of Ge{sub 2}O-PbO glass doped with Sm{sup 3+} ion were investigated. Raman spectroscopy and Extended X-ray Absorption Fine Structure (EXAFS) were used to investigate the effect of high pressure on the structural properties. The spectroscopic properties were investigated through the absorption and luminescence spectra recorded at room temperature The splitting in the VIS-NIR fluorescence bands increased after densification. Judd-Ofelt (J-O) theory was applied to evaluate phenomenological JO intensity parameters Ω (λ = 2, 4 and 6). The effect of high pressure on the transition probabilities (A{sub R}), radiative lifetimes (t{sub R}), branching ratio (b{sub R}) and stimulated emission cross-section s(l{sub p}) was also investigated. The results obtained from EXAFS indicated changes around the vicinity of Sm{sup 3+} ion which would explain the quenching in emission intensities in the visible range. A novel band related to the transition {sup 4}G{sub 5/2} to {sup 6}F{sub 11/2} was observed in the Sm{sup 3+} doped GeO{sub 2}-PbO. The obtained results may be useful for compact light sources, optical devices in the visible region and optoelectronic devices. (author)

  2. Spliced DNA Sequences in the Paramecium Germline: Their Properties and Evolutionary Potential

    Science.gov (United States)

    Catania, Francesco; McGrath, Casey L.; Doak, Thomas G.; Lynch, Michael

    2013-01-01

    Despite playing a crucial role in germline-soma differentiation, the evolutionary significance of developmentally regulated genome rearrangements (DRGRs) has received scant attention. An example of DRGR is DNA splicing, a process that removes segments of DNA interrupting genic and/or intergenic sequences. Perhaps, best known for shaping immune-system genes in vertebrates, DNA splicing plays a central role in the life of ciliated protozoa, where thousands of germline DNA segments are eliminated after sexual reproduction to regenerate a functional somatic genome. Here, we identify and chronicle the properties of 5,286 sequences that putatively undergo DNA splicing (i.e., internal eliminated sequences [IESs]) across the genomes of three closely related species of the ciliate Paramecium (P. tetraurelia, P. biaurelia, and P. sexaurelia). The study reveals that these putative IESs share several physical characteristics. Although our results are consistent with excision events being largely conserved between species, episodes of differential IES retention/excision occur, may have a recent origin, and frequently involve coding regions. Our findings indicate interconversion between somatic—often coding—DNA sequences and noncoding IESs, and provide insights into the role of DNA splicing in creating potentially functional genetic innovation. PMID:23737328

  3. DNA binding properties of dioxin receptors in wild-type and mutant mouse hepatoma cells

    International Nuclear Information System (INIS)

    Cuthill, S.; Poellinger, L.

    1988-01-01

    The current model of action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) entails stimulation of target gene transcription via the formation of dioxin-receptor complexes and subsequent accumulation of the complexes within the cell nucleus. Here, the authors have analyzed the DNA binding properties of the dioxin receptor in wild-type mouse hepatoma (Hepa 1c1c7) cells and a class of nonresponsive mutant cells which fail to accumulate dioxin-receptor complexes within the nucleus in vivo. In vitro, both the wild-type and mutant [ 3 H]dioxin-receptor complexes exhibited low affinity for DNA-cellulose (5-8% and around 4% retention, respectively) in the absence of prior biochemical manipulations. However, following chromatography on heparin-Sepharose, the wild-type but not the mutant dioxin receptor was transformed to a species with an increased affinity for DNA (40-50% retention on DNA-cellulose). The gross molecular structure of the mutant, non DNA binding dioxin receptor did not appear to be altered as compared to that of the wild-type receptor. These results imply that the primary deficiency in the mutant dioxin receptor form may reside at the DNA binding level and that, in analogy to steroid hormone receptors, DNA binding of the receptor may be an essential step in the regulation of target gene transcription by dioxin

  4. Biochemical properties of mammalian TREX1 and its association with DNA replication and inherited inflammatory disease.

    Science.gov (United States)

    Lindahl, Tomas; Barnes, Deborah E; Yang, Yun-Gui; Robins, Peter

    2009-06-01

    The major DNA-specific 3'-5' exonuclease of mammalian cells is TREX1 (3' repair exonuclease 1; previously called DNase III). The human enzyme is encoded by a single exon and, like many 3' exonucleases, exists as a homodimer. TREX1 degrades ssDNA (single-stranded DNA) more efficiently than dsDNA (double-stranded DNA), and its catalytic properties are similar to those of Escherichia coli exonuclease X. However, TREX1 is only found in mammals and has an extended C-terminal domain containing a leucine-rich sequence required for its association with the endoplasmic reticulum. In normal S-phase and also in response to genotoxic stress, TREX1 at least partly redistributes to the cell nucleus. In a collaborative project, we have demonstrated TREX1 enzyme deficiency in Aicardi-Goutières syndrome. Subsequently, we have shown that AGS1 cells exhibit chronic ATM (ataxia telangiectasia mutated)-dependent checkpoint activation, and these TREX1-deficient cells accumulate ssDNA fragments of a distinct size generated during DNA replication. Other groups have shown that the syndromes of familial chilblain lupus as well as systemic lupus erythematosus, and the distinct neurovascular disorder retinal vasculopathy with cerebral leukodystrophy, can be caused by dominant mutations at different sites within the TREX1 gene.

  5. Photophysicochemical, calf thymus DNA binding and in vitro photocytotoxicity properties of tetra-morpholinoethoxy-substituted phthalocyanines and their water-soluble quaternized derivatives.

    Science.gov (United States)

    Koçan, Halit; Kaya, Kerem; Özçeşmeci, İbrahim; Sesalan, B Şebnem; Göksel, Meltem; Durmuş, Mahmut; Burat, Ayfer Kalkan

    2017-12-01

    In this study, morpholinoethoxy-substituted metal-free (3), zinc(II) (4) and indium(III) (5) phthalocyanines were synthesized. These phthalocyanines were converted to their water-soluble quaternized derivatives (3Q-5Q) using excess methyl iodide as a quaternization agent. All these phthalocyanines (Pcs) were characterized by elemental analysis and different spectroscopic methods such as FT-IR, 1 H NMR, UV-Vis and mass spectrometry. The photophysical and photochemical properties such as fluorescence and generation of singlet oxygen were investigated for determination of these phthalocyanines as photosensitizers in photodynamic therapy (PDT) applications. The binding properties of quaternized phthalocyanines (3Q-5Q) to calf thymus DNA (CT-DNA) were investigated by UV-Vis and fluorescence spectrophotometric methods. The quenching effect of all quaternized phthalocyanines on the fluorescence intensity of SYBR Green-DNA complex was determined. The mixtures of 3Q, 4Q or 5Q and DNA solutions were used to determine the change in T m of double helix DNA with thermal denaturation profile. In addition, thermodynamic parameters considering their aggregation in buffer solution, which shows the spontaneity of the reactions between DNA and quaternized Pcs were investigated. On the other hand, in vitro phototoxicity and cytotoxicity behavior of the quaternized water-soluble phthalocyanine photosensitizers (3Q-5Q) were tested against the cervical cancer cell line named HeLa for evaluation of their suitability for treatment of cancer by PDT method. Peripherally tetra-substituted neutral and quaternized metal-free and metallophthalocyanines (MPcs) (Zn, In) bearing morpholinoethoxy groups were prepared. The binding of quaternized compounds (3Q-5Q) to CT-DNA were examined using UV-Vis, fluorescence spectra, thermal denaturation profiles and K SV values. Besides, thermodynamic studies indicated that binding of 3Q-5Q to DNA was spontaneous. On the other hand, in vitro phototoxicity and

  6. Structural Changes Induced in Grapevine (Vitis vinifera L. DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study

    Directory of Open Access Journals (Sweden)

    Nicoleta E. Dina

    2016-05-01

    Full Text Available In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L. varieties, respectively, are analyzed in the wavenumber range 300–1800 cm−1. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs infrared (IR laser pulse irradiation (λ = 1100 nm are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm−1 of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA, eight different grapevine varieties were discriminated.

  7. New transition metal complexes of 2,4-dihydroxybenzaldehyde benzoylhydrazone Schiff base (H2dhbh): Synthesis, spectroscopic characterization, DNA binding/cleavage and antioxidant activity

    Science.gov (United States)

    Aboafia, Seyada A.; Elsayed, Shadia A.; El-Sayed, Ahmed K. A.; El-Hendawy, Ahmed M.

    2018-04-01

    New complexes [VO2(Hdhbh)] (1), [VO(phen)(dhbh)].1.5H2O (2), [Zn(Hdhbh)2] (3), [MoO2(dhbh)(D)] (D = H2O (4) or MeOH (5)), [Ru(PPh3)(dhbh)Cl(H2O)] (6), and [Pd(Hdhbh)Cl]·H2O (7) (H2dhbh = Schiff base derived from 2,4-dihydroxybenzaldehyde and benzoylhydrazone) have been isolated and characterized by IR, 1H NMR, Mass, UV-Visible and ESR spectroscopy. They were also investigated by cyclic voltammetry, thermal and magnetic measurements and the structure of complex cis-[MoO2(dhbh)(H2O)] (4) was solved by X-ray crystallography. Analytical data showed that H2dhbh behaves as monobasic/or dibasic tridentate ligand via phenolate O, azomethine N and amide O/or deprotonated amide O atoms. Antioxidant activity of the complexes has been evaluated against DPPH (2,2-diphenyl-1-picrylhydrazyl) radical and it has been found that oxovandium (IV) complex (2) displays the highest radical scavenging potency comparable to ascorbic acid as a standard antioxidant. The DNA binding properties of the ligand and its complexes have been investigated by electronic spectroscopy together with DNA cleavage by gel electrophoresis whose results showed also that vanadium (IV) complex (2) has a significant oxidative cleavage among other complexes.

  8. Potential energy curves and spectroscopic properties of X2Σ+ and A2Π states of 13C14N

    International Nuclear Information System (INIS)

    Liao Jian-Wen; Yang Chuan-Lu

    2014-01-01

    The potential energy curves (PECs) of X 2 Σ + and A 2 Π states of the CN molecule have been calculated with the multi-reference configuration interaction method and the aug-cc-pwCV5Z basis set. Based on the PECs, all of the vibrational and rotational levels of the 13 C 14 N molecule are obtained by solving the Schrödinger equation of the molecular nuclear motion. The spectroscopic parameters are determined by fitting the Dunham coefficients with the levels. Both the levels and the spectroscopic parameters are in good qualitative agreement with the experimental data available. The analytical potential energy functions are also deduced from the calculated PECs. The present results can provide a helpful reference for future spectroscopy experiments or dynamical calculations of the molecule. (atomic and molecular physics)

  9. Spectroscopic properties and quenching processes of Yb{sup 3+} in Fluoride single crystals for laser applications

    Energy Technology Data Exchange (ETDEWEB)

    Bensalah, A. [Physical Chemistry of Luminescent Materials, Claude Bernard/Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France) and Institute for Multidisciplinary Research of Advanced Materials, Tohoku University, Sendai 980-8577 (Japan)]. E-mail: amina-bensalah@enscp.fr; Ito, M. [Physical Chemistry of Luminescent Materials, Claude Bernard/Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France); Guyot, Y. [Physical Chemistry of Luminescent Materials, Claude Bernard/Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France); Goutaudier, C. [Physical Chemistry of Luminescent Materials, Claude Bernard/Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France); Jouini, A. [Physical Chemistry of Luminescent Materials, Claude Bernard /Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France); Institute for Multidisciplinary Research of Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Brenier, A. [Physical Chemistry of Luminescent Materials, Claude Bernard/Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France); Sato, H. [Institute for Multidisciplinary Research of Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Fukuda, T. [Institute for Multidisciplinary Research of Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Boulon, G. [Physical Chemistry of Luminescent Materials, Claude Bernard /Lyon1 University, UMR 5620, CNRS Bat. A. Kastler, 10 rue Ampere, 69622 Villeurbanne (France)

    2007-01-15

    Spectroscopic characterization is carried out to identify Stark's levels of Yb{sup 3+} transitions in several fluoride crystals grown either by the Czochralski technique or by the laser-heated pedestal growth method. Yb{sup 3+} concentration dependence of the decay time is analyzed in order to understand involved concentration quenching mechanisms. Laser tests under saphire:Ti pumping are presented for all our materials as well as under diode pumping for Yb:CaF{sub 2}.

  10. Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

    Science.gov (United States)

    Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

    2015-05-01

    The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN (1Σ) and hydrideisocyanidezinc HZnNC (1Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]+ composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn+ (2Σ) and HCNZn+ (2Σ).

  11. Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

    International Nuclear Information System (INIS)

    Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

    2015-01-01

    The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader’s quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN ( 1 Σ) and hydrideisocyanidezinc HZnNC ( 1 Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn] + composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn + ( 2 Σ) and HCNZn + ( 2 Σ)

  12. Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen, E-mail: cbb@qf.uva.es [Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-05-14

    The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader’s quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN ({sup 1}Σ) and hydrideisocyanidezinc HZnNC ({sup 1}Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]{sup +} composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn{sup +} ({sup 2}Σ) and HCNZn{sup +} ({sup 2}Σ)

  13. Properties of Thermus ruber Strains Isolated from Icelandic Hot Springs and DNA:DNA Homology of Thermus ruber and Thermus aquaticus

    Science.gov (United States)

    Sharp, Richard J.; Williams, Ralph A. D.

    1988-01-01

    Seventeen pink-pigmented strains of the genus Thermus were isolated from samples collected from thermal areas of Iceland. The strains were examined by using phenotypic characterization and DNA:DNA homology and were compared with recognized strains. Visually, the strains could be divided into three groups based on their pigmentation; however, spectroscopic studies of the pigments indicated little difference among them. Most strains required a vitamin supplement for growth and used fructose, maltose, mannose, or sucrose as the sole carbon source. In the presence of nitrate, two strains were able to grow under anaerobic conditions. The optimum growth temperature was 60°C; growth did not occur at 30 or 70°C. PMID:16347714

  14. Cytotoxic Activities and DNA Binding Properties of 1-Methyl-7H-indeno[1,2-b]Quinolinium-7-(4-dimethylamino) Benzylidene Triflate

    OpenAIRE

    Li, Wen; Ji, Yuan Yuan; Wang, Jian Wen; Zhu, Yong Ming

    2012-01-01

    The interaction of calf thymus DNA (ct-DNA) with a novel synthesized pyrazolo[1,5-a]indole compound 1-methyl-7H-indeno[1,2-b]quinolinium-7-(4-dimethylamino) benzylidene triflate (MIDBT) was extensively studied by various spectroscopic techniques, viscosity measurements, and gel electrophoresis. The UV-visible observation implied that the compound interacted with ct-DNA by two binding modes, intercalating into the DNA base pairs and attaching to the helix exterior of DNA. The results of the fl...

  15. Probing of O2 vacancy defects and correlated magnetic, electrical and photoresponse properties in indium-tin oxide nanostructures by spectroscopic techniques

    Science.gov (United States)

    Ghosh, Shyamsundar; Dev, Bhupendra Nath

    2018-05-01

    Indium-tin oxide (ITO) 1D nanostructures with tunable morphologies i.e. nanorods, nanocombs and nanowires are grown on c-axis (0 0 0 1) sapphire (Al2O3) substrate in oxygen deficient atmosphere through pulsed laser deposition (PLD) technique and the effect of oxygen vacancies on optical, electrical, magnetic and photoresponse properties is investigated using spectroscopic methods. ITO nanostructures are found to be enriched with significant oxygen vacancy defects as evident from X-ray photoelectron and Raman spectroscopic analysis. Photoluminescence spectra exhibited intense mid-band blue emission at wavelength of region of 400-450 nm due to the electronic transition from conduction band maxima (CBM) to the singly ionized oxygen-vacancy (VO+) defect level within the band-gap. Interestingly, ITO nanostructures exhibited significant room-temperature ferromagnetism (RTFM) and the magnetic moment found proportional to concentration of VO+ defects which indicates VO+ defects are mainly responsible for the observed RTFM in nanostructures. ITO nanowires being enriched with more VO+ defects exhibited strongest RTFM as compared to other morphologies. Current voltage (I-V) characteristics of ITO nanostructures showed an enhancement of current under UV light as compared to dark which indicates such 1D nanostructure can be used as photovoltaic material. Hence, the study shows that there is ample opportunity to tailor the properties of ITOs through proper defect engineering's and such photosensitive ferromagnetic semiconductors might be promising for spintronic and photovoltaic applications.

  16. Exploration of spectroscopic properties of solvated tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III)red hybrid organic complex for solution processed OLEDs and displays

    Energy Technology Data Exchange (ETDEWEB)

    Chitnis, Dipti [Department of Physics, RTM Nagpur University, Nagpur 440033 (India); Thejokalyani, N., E-mail: thejokalyani@rediffmail.com [Department of Applied Physics, Laxminarayan Institute of Technology, Nagpur 440033 (India); Dhoble, S.J. [Department of Physics, RTM Nagpur University, Nagpur 440033 (India)

    2017-05-15

    In order to explore the spectroscopic properties of a novel europium activated hybrid organic tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III), Eu(TTA){sub 3}bipy phosphor in various solvents at different pH and molar concentrations, UV–vis optical absorption and photoluminescence spectra were carried out. With a variation in the solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid, formic acid) media, staggering differences in optical absorptions and optical densities were noticed with hypsochromic shift in the absorption peaks. The optical density was found to be maximum for the complex with pH= 7.0 and the intensity as well as optical density gradually decreased when pH is lowered to 6.0 or raised to 8.0 (at an interval of 0.5), proving that the complex is pH sensitive. It's optical energy gap and stokes shift values in various organic solvents were also calculated on the basis of Lippert-Mataga plot. The exploration of spectroscopic properties of solvated Eu(TTA){sub 3}bipy complex demonstrates its prospective for solution processed OLEDs and display devices. - Graphical abstract: Pictorial depiction of photoluminescence in solvated Eu(TTA){sub 3}bipy complex under UV light.

  17. Accurate predictions of spectroscopic and molecular properties of 27 Λ-S and 73 Ω states of AsS radical

    Science.gov (United States)

    Shi, Deheng; Song, Ziyue; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue

    2016-01-01

    The PECs are calculated for the 27 Λ-S states and their corresponding 73 Ω states of AsS radical. Of these Λ-S states, only the 22Δ and 54Π states are replulsive. The 12Σ+, 22Σ+, 42Π, 34Δ, 34Σ+, and 44Π states possess double wells. The 32Σ+ state possesses three wells. The A2Π, 32Π, 12Φ, 24Π, 34Π, 24Δ, 34Δ, 16Σ+, and 16Π states are inverted with the SO coupling effect included. The 14Σ+, 24Σ+, 24Σ-, 24Δ, 14Φ, 16Σ+, and 16Π states, the second wells of 12Σ+, 34Σ+, 42Π, 44Π, and 34Δ states, and the third well of 32Σ+ state are very weakly-bound states. The PECs are extrapolated to the CBS limit. The effect of SO coupling on the PECs is discussed. The spectroscopic parameters are evaluated, and compared with available measurements and other theoretical ones. The vibrational properties of several weakly-bound states are determined. The spectroscopic properties reported here can be expected to be reliably predicted ones.

  18. Exploration of spectroscopic properties of solvated tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III)red hybrid organic complex for solution processed OLEDs and displays

    International Nuclear Information System (INIS)

    Chitnis, Dipti; Thejokalyani, N.; Dhoble, S.J.

    2017-01-01

    In order to explore the spectroscopic properties of a novel europium activated hybrid organic tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III), Eu(TTA) 3 bipy phosphor in various solvents at different pH and molar concentrations, UV–vis optical absorption and photoluminescence spectra were carried out. With a variation in the solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid, formic acid) media, staggering differences in optical absorptions and optical densities were noticed with hypsochromic shift in the absorption peaks. The optical density was found to be maximum for the complex with pH= 7.0 and the intensity as well as optical density gradually decreased when pH is lowered to 6.0 or raised to 8.0 (at an interval of 0.5), proving that the complex is pH sensitive. It's optical energy gap and stokes shift values in various organic solvents were also calculated on the basis of Lippert-Mataga plot. The exploration of spectroscopic properties of solvated Eu(TTA) 3 bipy complex demonstrates its prospective for solution processed OLEDs and display devices. - Graphical abstract: Pictorial depiction of photoluminescence in solvated Eu(TTA) 3 bipy complex under UV light.

  19. Similarity of satellite DNA properties in the order Rodentia

    Energy Technology Data Exchange (ETDEWEB)

    Mazrimas, J A; Hatch, F T

    1977-09-01

    We have characterized satellite DNAs from 9 species of kangaroo rat (Dipodomys) and have shown that the HS-..cap alpha.. and HS-..beta.. satellites, where present, are nearly identical in all species as to melting transition midpoint (Tm), and density in neutral CsCl, alkaline CsCl, and Cs/sub 2/SO/sub 4/-Ag/sup +/ gradients. However, the MS satellites exist in two internally similar classes. The satellite DNAs from three other rodents were characterized (densities listed are in neutral CsCl). The pocket gopher, Thomomys bottae, contains Th-..cap alpha.. (1.713 g/ml) and Th-..beta.. (1.703 g/ml). The guinea pig (Cavia porcellus) contains Ca-..cap alpha.., Ca-..beta.., and Ca-..gamma.. at densities of 1.706 g/ml, 1.704 g/ml, and 1.704 g/ml, respectively. The antelope ground squirrel (Ammospermophilus harrisi) contains Am-..cap alpha.., 1.708 g/ml, Am-..beta.., 1.717 g/ml, and Am-..gamma.., 1.707 g/ml. The physical and chemical properties of the alpha-satellites from the above four rodents representing four different families in two suborders of Rodentia were compared. They show nearly identical Tm, nucleoside composition of single strands, and single strand densities in alkaline CsCl. Similar comparisons on the second or third satellite DNAs from these rodents also indicate a close relationship to each other. Thus the high degree of similarity of satellite sequences found in such a diverse group of rodents suggests a cellular function that is subject to natural selection, and implies that these sequences have been conserved over a considerable span of evolutionary time since the divergence of these rodents about 50 million years ago.

  20. Similarity of satellite DNA properties in the order Rodentia

    Energy Technology Data Exchange (ETDEWEB)

    Mazrimas, J A; Hatch, F T

    1977-09-01

    Satellite DNAs from 9 species of kangaroo rat (Dipodomys) have been characterized and have shown that the HS-..cap alpha.. and HS-..beta.. satellites, where present, are nearly identical in all species as to melting transition midpoint (Tm), and density in neutral CsCl, alkaline CsCl, and Cs/sub 2/SO/sub 4/-Ag/sup +/ gradients. However, the MS satellites exist in two internally similar classes. The satellite DNAs from three other rodents were characterized (densities listed are in neutral CsCl). The pocket gopher, Thomomys bottae, contains Th-..cap alpha.. (1.713 g/ml) and Th..beta.. (1.703 g/ml). The guinea pig (Cavia porcellus) contains Ca-..cap alpha.., Ca-..beta.. and Ca-..gamma.. at densities of 1.706 g/ml, 1.704 g/ml and 1.704 g/ml, respectively. The antelope ground squirrel (Ammospermophilus harrisi) contains Am-..cap alpha.., 1.708 g/ml, Am-..beta.., 1.717 g/ml, and Am-..gamma.., 1.707 g/ml. The physical and chemical properties of the alpha-satellites from the above four rodents representing four different families in two suborders of Rodentia were compared. They show nearly identical Tm, nucleoside composition of single strands, and single strand densities in alkaline CsCl. Similar comparisons on the second or third satellite DNAs from these rodents also indicate a close relationship to each other. Thus the high degree of similarity of satellite sequences found in such a diverse group of rodents suggests a cellular function that is subject to natural selection, and implies that these sequences have been conserved over a considerable span of evolutionary time since the divergence of these rodents about 50 million years ago.

  1. repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

    Science.gov (United States)

    Liu, Bin; Liu, Fule; Fang, Longyun; Wang, Xiaolong; Chou, Kuo-Chen

    2015-04-15

    In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facilitate the studies of DNAs and nucleotides, we developed a Python package called representations of DNAs (repDNA) for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides. There are three feature groups composed of 15 features. The first group calculates three nucleic acid composition features describing the local sequence information by means of kmers; the second group calculates six autocorrelation features describing the level of correlation between two oligonucleotides along a DNA sequence in terms of their specific physicochemical properties; the third group calculates six pseudo nucleotide composition features, which can be used to represent a DNA sequence with a discrete model or vector yet still keep considerable sequence-order information via the physicochemical properties of its constituent oligonucleotides. In addition, these features can be easily calculated based on both the built-in and user-defined properties via using repDNA. The repDNA Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/repDNA/. bliu@insun.hit.edu.cn or kcchou@gordonlifescience.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Some new methyl-8-methoxypsoralens: synthesis, photobinding to DNA, photobiological properties and molecular modelling.

    Science.gov (United States)

    Gia, O; Anselmo, A; Pozzan, A; Antonello, C; Magno, S M; Uriarte, E

    1997-01-01

    The tricyclic structure of known natural photochemotherapeutic drugs such as 8-methoxypsoralen and 5-methoxypsoralen is often taken as a model in the search of new photosensitizer agents with less phototoxic and mutagenic effects. This paper describes the synthesis, characterization, photobinding to DNA, photobiological properties and computational chemistry of some 8-methoxypsoralen derivatives bearing two or three methyl groups at the key positions of the two photoactive double bonds. Results showed that photoreactivity and photobiological behaviour depend on the pattern of methyl substitutions. Antiproliferative activity in cell lines shows good correlation with DNA interaction data.

  3. Base-pairing preferences, physicochemical properties and mutational behaviour of the DNA lesion 8-nitroguanine †

    OpenAIRE

    Bhamra, Inder; Compagnone-Post, Patricia; O’Neil, Ian A.; Iwanejko, Lesley A.; Bates, Andrew D.; Cosstick, Richard

    2012-01-01

    8-Nitro-2′-deoxyguanosine (8-nitrodG) is a relatively unstable, mutagenic lesion of DNA that is increasingly believed to be associated with tissue inflammation. Due to the lability of the glycosidic bond, 8-nitrodG cannot be incorporated into oligodeoxynucleotides (ODNs) by chemical DNA synthesis and thus very little is known about its physicochemical properties and base-pairing preferences. Here we describe the synthesis of 8-nitro-2′-O-methylguanosine, a ribonucleoside analogue of this lesi...

  4. Effect of protonation on the electronic properties of DNA base pairs: applications for molecular electronics.

    Science.gov (United States)

    Mallajosyula, Sairam S; Pati, Swapan K

    2007-10-11

    Protonation of DNA basepairs is a reversible phenomenon that can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen-bonding pattern of the DNA basepairs undergoes a change. We study the effect of protonation on the electronic properties of the DNA basepairs to probe for possible molecular electronics applications. We find that, under mild acidic pH conditions, the A:T basepair shows excellent rectification behavior that is, however, absent in the G:C basepair. The mechanism of rectification has been discussed using a simple chemical potential model. We also consider the noncanonical A:A basepair and find that it can be used as efficient pH dependent molecular switch. The switching action in the A:A basepair is explained in the light of pi-pi interactions, which lead to efficient delocalization over the entire basepair.

  5. Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties.

    Science.gov (United States)

    Linko, Veikko; Leppiniemi, Jenni; Paasonen, Seppo-Tapio; Hytönen, Vesa P; Toppari, J Jussi

    2011-07-08

    We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

  6. Computational Approach for Studying Optical Properties of DNA Systems in Solution

    DEFF Research Database (Denmark)

    Nørby, Morten Steen; Svendsen, Casper Steinmann; Olsen, Jógvan Magnus Haugaard

    2016-01-01

    In this paper we present a study of the methodological aspects regarding calculations of optical properties for DNA systems in solution. Our computational approach will be built upon a fully polarizable QM/MM/Continuum model within a damped linear response theory framework. In this approach...... the environment is given a highly advanced description in terms of the electrostatic potential through the polarizable embedding model. Furthermore, bulk solvent effects are included in an efficient manner through a conductor-like screening model. With the aim of reducing the computational cost we develop a set...... of averaged partial charges and distributed isotropic dipole-dipole polarizabilities for DNA suitable for describing the classical region in ground-state and excited-state calculations. Calculations of the UV-spectrum of the 2-aminopurine optical probe embedded in a DNA double helical structure are presented...

  7. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  8. Sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA

    Science.gov (United States)

    Woehrstein, Johannes B.; Strauss, Maximilian T.; Ong, Luvena L.; Wei, Bryan; Zhang, David Y.; Jungmann, Ralf; Yin, Peng

    2017-01-01

    Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure–based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub–100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target. PMID:28691083

  9. DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

    Science.gov (United States)

    Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

    The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

  10. Radiosensitizing and cytotoxic properties of DNA targeted phenanthridine-linked nitroheterocycles of varying electron affinities

    International Nuclear Information System (INIS)

    Cowan, D.S.M.; Rauth, A.M.; Toronto Univ., ON; Matejovic, J.F.; McClelland, R.A.; Wardman, P.

    1994-01-01

    2-Nitroimidazoles targeted to DNA via intercalation have previously been shown to be as much as 10-100 times more efficient on a molar basis than the untargeted nitroimidazole, misonidazole, in vitro as hypoxic cell selective radiosensitizers and cytotoxins based on extracellular concentrations. In this work the effect of varying the nitroaromatic group has been examined through the preparation of a DNA-targeted 4-nitroimidazole (4-MeNLP-3), a 5-nitroimidazole (5-NLP-3) and a 5-nitrofuran (FEP-2) linked to phenanthridinium ions. With the previously synthesized 2-nitroimidazoles, this provides a series of DNA targeted compounds of varying electron affinity as well as structure at the nitroaromatic position. The present series of compounds was tested for partition coefficient, DNA binding ability, reduction potentials and in vitro radiosensitizing and cytotoxic abilities. The results obtained indicate that targeting such compounds to DNA diminishes the dependency of radiosensitizing and cytotoxic properties on reduction potential and may allow significant uncoupling of toxicity from radiosensitizing ability. (author)

  11. A novel method to obtain chitosan/DNA nanospheres and a study of their release properties

    International Nuclear Information System (INIS)

    Masotti, Andrea; Bordi, Federico; Ortaggi, Giancarlo; Marino, Federica; Palocci, Cleofe

    2008-01-01

    Polysaccharides and other cationic polymers have recently been used in pharmaceutical research and industry for their properties to control the release of antibiotics, DNA, proteins, peptide drugs or vaccines, and they have also been extensively studied as non-viral DNA carriers for gene delivery and therapy. Among them, chitosan is the most used since it can promote long-term release of incorporated drugs. This work is focused on the preparation of chitosan and chitosan/DNA nanospheres by using a novel and simple osmosis-based method, recently patented. The morphology of chitosan/DNA particles is spherical (as observed by scanning electron microscopy, SEM) and the nanospheres' average diameter is 38 ± 4 nm (obtained by dynamic light scattering, DLS). With this method, DNA is incorporated with high yield (up to 30%) and the release process is gradual and prolonged in time. The novelty of the reported method resides in the general applicability to various synthetic or natural biopolymers. Solvent, temperature and membrane cut-off are the physicochemical parameters that one is able to use to control the overall osmotic process, leading to several nanostructured systems with different size and shape that may be used in several biotechnological applications

  12. A novel method to obtain chitosan/DNA nanospheres and a study of their release properties

    Science.gov (United States)

    Masotti, Andrea; Bordi, Federico; Ortaggi, Giancarlo; Marino, Federica; Palocci, Cleofe

    2008-02-01

    Polysaccharides and other cationic polymers have recently been used in pharmaceutical research and industry for their properties to control the release of antibiotics, DNA, proteins, peptide drugs or vaccines, and they have also been extensively studied as non-viral DNA carriers for gene delivery and therapy. Among them, chitosan is the most used since it can promote long-term release of incorporated drugs. This work is focused on the preparation of chitosan and chitosan/DNA nanospheres by using a novel and simple osmosis-based method, recently patented. The morphology of chitosan/DNA particles is spherical (as observed by scanning electron microscopy, SEM) and the nanospheres' average diameter is 38 ± 4 nm (obtained by dynamic light scattering, DLS). With this method, DNA is incorporated with high yield (up to 30%) and the release process is gradual and prolonged in time. The novelty of the reported method resides in the general applicability to various synthetic or natural biopolymers. Solvent, temperature and membrane cut-off are the physicochemical parameters that one is able to use to control the overall osmotic process, leading to several nanostructured systems with different size and shape that may be used in several biotechnological applications.

  13. Influence of different amino substituents in position 1 and 4 on spectroscopic and acid base properties of 9,10-anthraquinone moiety.

    Science.gov (United States)

    Wcisło, Anna; Niedziałkowski, Paweł; Wnuk, Elżbieta; Zarzeczańska, Dorota; Ossowski, Tadeusz

    2013-05-01

    A series of novel 1-amino and 1,4-diamino-9,10-anthraquinones, substituted with different alkyl groups, were synthesized as the result of alkylation with amino substituents. All the obtained aminoanthraquinone derivatives were characterized by NMR, IR spectroscopy and mass spectrometry. The spectroscopic properties of these compounds were determined by using UV-Vis spectroscopy in acetonitrile, and in the mixture of acetonitrile and methanol at different pH ranges. The effects of various substituents present in the newly developed anthraquinone derivatives and their ability to form hydrogen bonds between the carbonyl oxygen atom of anthraquinone moiety and nitrogen atom of N-H group in 1-aminoanthraquinone (1-AAQ) and 1,4-diaminoanthraquinone (1,4-DAAQ) were studied. Additionally, the effects of hydrogen bond formation between O-H group in hydroxyethylamino substituent and the carbonyl oxygen atom of anthraquinone were investigated. The spectroscopic behavior of the studied derivatives strongly depended on the solvent-solute interactions and the nature of solvent. The values of pKa for the new anthraquinones were determined by the combined potentiometric and spectrophotometric titration methods. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Optical properties of Au–TiO{sub 2} and Au–SiO{sub 2} granular metal thin films studied by Spectroscopic Ellipsometry

    Energy Technology Data Exchange (ETDEWEB)

    Bakkali, H., E-mail: hicham.bakkali@mail.uca.es [Departamento de Física de la Materia Condensada and Instituto de Microscopía Electrónica y Materiales (IMEYMAT), Universidad de Cadiz, 11510 Puerto Real, Cádiz (Spain); Centro de Ciencias Aplicadas y Desarrollo Tecnológico (CCADET), Universidad Nacional Autónoma de México (UNAM), México, D.F. 04510 (Mexico); Blanco, E.; Dominguez, M. [Departamento de Física de la Materia Condensada and Instituto de Microscopía Electrónica y Materiales (IMEYMAT), Universidad de Cadiz, 11510 Puerto Real, Cádiz (Spain); Mora, M.B. de la [CONACyT Research Fellow-CCADET, Universidad Nacional Autónoma de México (UNAM), México, D.F. 04510 (Mexico); Sánchez-Aké, C.; Villagrán-Muniz, M. [Centro de Ciencias Aplicadas y Desarrollo Tecnológico (CCADET), Universidad Nacional Autónoma de México (UNAM), México, D.F. 04510 (Mexico)

    2017-05-31

    Highlights: • Gold NPs embedded in TiO{sub 2} or SiO{sub 2} are fabricated by single RF magnetron sputtering. • Films thickness and optical constants are determined by Spectroscopic Ellipsometry. - Abstract: We report on the optical properties in the dielectric regime of gold nanostructured granular thin films fabricated through sputter deposition with a composite target at room temperature and over a wide photon energy range (0.62–4.13 eV) by means of Spectroscopic Ellipsometry. The thickness and the films effective optical constants are successfully determined using an approach based on multiple Gaussian oscillators. In the quasi-static regime, i.e., 2R ≪ λ, and in the dipole approximation, examining the real and imaginary parts, ε{sub 1}, ε{sub 2}, of the dielectric function, it is shown that the dc optical conductivity is almost negligible (σ = ωε{sub 0}ε{sub 2} ≪ 10{sup −5} Ω cm{sup −1}) and only the capacitive contribution holds for the electron-phonon relaxation in localized surface plasmon of the gold particles. Furthermore, we find that the resonant frequencies ω{sub p} becomes red-shifted when the particles are electromagnetically coupled to each other or when the surrounding medium dielectric constant, ε{sub m}, increases, thus exhibiting a wide spectral tuning range of 1.95–2.24 eV.

  15. A plasma modified cellulose-chitosan porous membrane allows efficient DNA binding and provides antibacterial properties: A step towards developing a new DNA collecting card.

    Science.gov (United States)

    Chumwangwapee, Sasiwimon; Chingsungnoen, Artit; Siri, Sineenat

    2016-11-01

    In forensic DNA analyses, biological specimens are collected and stored for subsequent recovery and analysis of DNA. A cost-effective and efficient DNA recovery approach is therefore a need. This study aims to produce a plasma modified cellulose-chitosan membrane (pCE-CS) that efficiently binds and retains DNA as a potential DNA collecting card. The pCE-CS membrane was produced by a phase separation of ionic liquid dissolving CE and CS in water with subsequent surface-modification by a two-step exposure of argon plasma and nitrogen gas. Through plasma modification, the pCE-CS membrane demonstrated better DNA retention after a washing process and higher rate of DNA recovery as compared with the original CE-CS membrane and the commercial FTA card. In addition, the pCE-CS membrane exhibited anti-bacterial properties against both Escherichia coli and Staphylococcus aureus. The results of this work suggest a potential function of the pCE-CS membrane as a DNA collecting card with a high recovery rate of captured DNA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

    Directory of Open Access Journals (Sweden)

    Soler-López Montserrat

    2011-10-01

    Full Text Available Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site and TTS (Transcription Termination Site (at least in yeast is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.

  17. Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats

    Czech Academy of Sciences Publication Activity Database

    Zemánek, Michal; Kypr, Jaroslav; Vorlíčková, Michaela

    2005-01-01

    Roč. 36, - (2005), s. 23-32 ISSN 0141-8130. [Študentská vedecká konferencia. Bratislava, 9.03.2003-10.03.2003] R&D Projects: GA MZd(CZ) NM7634; GA AV ČR(CZ) IAA4004201 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA conformational properties * length polymorphism * microsatellite sequences Subject RIV: BO - Biophysics Impact factor: 1.684, year: 2005

  18. Spectroscopic properties of a two-dimensional time-dependent Cepheid model. II. Determination of stellar parameters and abundances

    Science.gov (United States)

    Vasilyev, V.; Ludwig, H.-G.; Freytag, B.; Lemasle, B.; Marconi, M.

    2018-03-01

    Context. Standard spectroscopic analyses of variable stars are based on hydrostatic 1D model atmospheres. This quasi-static approach has not been theoretically validated. Aim. We aim at investigating the validity of the quasi-static approximation for Cepheid variables. We focus on the spectroscopic determination of the effective temperature Teff, surface gravity log g, microturbulent velocity ξt, and a generic metal abundance log A, here taken as iron. Methods: We calculated a grid of 1D hydrostatic plane-parallel models covering the ranges in effective temperature and gravity that are encountered during the evolution of a 2D time-dependent envelope model of a Cepheid computed with the radiation-hydrodynamics code CO5BOLD. We performed 1D spectral syntheses for artificial iron lines in local thermodynamic equilibrium by varying the microturbulent velocity and abundance. We fit the resulting equivalent widths to corresponding values obtained from our dynamical model for 150 instances in time, covering six pulsational cycles. In addition, we considered 99 instances during the initial non-pulsating stage of the temporal evolution of the 2D model. In the most general case, we treated Teff, log g, ξt, and log A as free parameters, and in two more limited cases, we fixed Teff and log g by independent constraints. We argue analytically that our approach of fitting equivalent widths is closely related to current standard procedures focusing on line-by-line abundances. Results: For the four-parametric case, the stellar parameters are typically underestimated and exhibit a bias in the iron abundance of ≈-0.2 dex. To avoid biases of this type, it is favorable to restrict the spectroscopic analysis to photometric phases ϕph ≈ 0.3…0.65 using additional information to fix the effective temperature and surface gravity. Conclusions: Hydrostatic 1D model atmospheres can provide unbiased estimates of stellar parameters and abundances of Cepheid variables for particular

  19. SPECTRAL CLASSIFICATION AND PROPERTIES OF THE O Vz STARS IN THE GALACTIC O-STAR SPECTROSCOPIC SURVEY (GOSSS)

    Energy Technology Data Exchange (ETDEWEB)

    Arias, Julia I.; Barbá, Rodolfo H.; Sabín-Sanjulián, Carolina [Departamento de Física y Astronomía, Universidad de La Serena, Av. Cisternas 1200 Norte, La Serena (Chile); Walborn, Nolan R. [Space Telescope Science Institute, 3700 San Martin Drive, MD 21218, Baltimore (United States); Díaz, Sergio Simón [Instituto de Astrofísica de Canarias, E-38200, Departamento de Astrofísica, Universidad de La Laguna, E-38205, La Laguna, Tenerife (Spain); Apellániz, Jesús Maíz [Centro de Astrobiología, CSIC-INTA, campus ESAC, Camino Bajo del Castillo s/n, E-28 692 Madrid (Spain); Gamen, Roberto C. [Instituto de Astrofísica de La Plata (CONICET, UNLP), Facultad de Ciencias Astronómicas y Geofísicas, Universidad Nacional de La Plata, Paseo del Bosque s/n, 1900 La Plata (Argentina); Morrell, Nidia I. [Las Campanas Observatory, Carnegie Observatories, Casilla 601, La Serena (Chile); Sota, Alfredo [Instituto de Astrofísica de Andalucía-CSIC, Glorieta de la Astronomía s/n, E-18 008 Granada (Spain); Marco, Amparo; Negueruela, Ignacio, E-mail: jarias@userena.cl [Departamento de Física, Ingeniería de Sistemas y Teoría de la Señal, Escuela Politécnica Superior, Universidad de Alicante, Carretera San Vicente del Raspeig s/n, E03690, San Vicente del Raspeig (Spain); and others

    2016-08-01

    On the basis of the Galactic O Star Spectroscopic Survey (GOSSS), we present a detailed systematic investigation of the O Vz stars. The currently used spectral classification criteria are rediscussed, and the Vz phenomenon is recalibrated through the addition of a quantitative criterion based on the equivalent widths of the He i λ 4471, He ii λ 4542, and He ii λ 4686 spectral lines. The GOSSS O Vz and O V populations resulting from the newly adopted spectral classification criteria are comparatively analyzed. The locations of the O Vz stars are probed, showing a concentration of the most extreme cases toward the youngest star-forming regions. The occurrence of the Vz spectral peculiarity in a solar-metallicity environment, as predicted by the fastwind code, is also investigated, confirming the importance of taking into account several processes for the correct interpretation of the phenomenon.

  20. SPECTRAL CLASSIFICATION AND PROPERTIES OF THE O Vz STARS IN THE GALACTIC O-STAR SPECTROSCOPIC SURVEY (GOSSS)

    International Nuclear Information System (INIS)

    Arias, Julia I.; Barbá, Rodolfo H.; Sabín-Sanjulián, Carolina; Walborn, Nolan R.; Díaz, Sergio Simón; Apellániz, Jesús Maíz; Gamen, Roberto C.; Morrell, Nidia I.; Sota, Alfredo; Marco, Amparo; Negueruela, Ignacio

    2016-01-01

    On the basis of the Galactic O Star Spectroscopic Survey (GOSSS), we present a detailed systematic investigation of the O Vz stars. The currently used spectral classification criteria are rediscussed, and the Vz phenomenon is recalibrated through the addition of a quantitative criterion based on the equivalent widths of the He i λ 4471, He ii λ 4542, and He ii λ 4686 spectral lines. The GOSSS O Vz and O V populations resulting from the newly adopted spectral classification criteria are comparatively analyzed. The locations of the O Vz stars are probed, showing a concentration of the most extreme cases toward the youngest star-forming regions. The occurrence of the Vz spectral peculiarity in a solar-metallicity environment, as predicted by the fastwind code, is also investigated, confirming the importance of taking into account several processes for the correct interpretation of the phenomenon.

  1. Comparative investigation on the spectroscopic properties of Pr³⁺-doped boro-phosphate, boro-germo-silicate and tellurite glasses.

    Science.gov (United States)

    Zhang, Liaolin; Dong, Guoping; Peng, Mingying; Qiu, Jianrong

    2012-07-01

    We report on the spectroscopic properties of Pr(3+)-doped boro-phosphate, boro-germo-silicate and tellurite glasses. The stimulated absorption and emission cross sections were estimated. Only one emission at 596 nm and 605 nm is observed in Pr(3+)-doped boro-phosphate and boro-germo-silicate glasses, respectively, while three emissions at 605 nm, 612 nm and 645 nm are observed in Pr(3+)-doped tellurite glass when excited at 467 nm. The fluorescence lifetime at 600 nm in Pr(3+)-doped boro-phosphate, boro-germo-silicate and tellurite glasses is 137 μs, 73 μs and 51 μs, respectively. The emissions from Pr(3+)-doped boro-phosphate, boro-germo-silicate and tellurite glasses show different decay behaviors and can be well explained by multiphonon relaxation theory. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV-visible, Raman, DFT and TD-DFT calculations

    International Nuclear Information System (INIS)

    Cornard, Jean-Paul; Rasmiwetti; Merlin, Jean-Claude

    2005-01-01

    We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol

  3. Spectroscopic studies on the interactions of 5-ethyl-6-phenyl-3,8-bis((3-aminoalkyl)propanamido)phenanthridin-5-ium derivatives with G-quadruplex DNA

    Science.gov (United States)

    Yalçın, Ergin; Duyar, Halil; Ihmels, Heiko; Seferoğlu, Zeynel

    2018-05-01

    An improved microwave-induced synthesis of five ethidium derivatives (Ethidium derivatives, 2a-d) is presented. As the derivatives 2a-d have been proposed previously to be telomerase inhibitors, the binding interactions of these ethidium derivatives with G-quadruplex DNA were evaluated by means of photometric and fluorimetric titration, thermal DNA denaturation, CD and 1H NMR spectroscopy. In particular, the compound bearing 3,8-bis(pyrrolidin-1-yl)propanamido substituent 2a exhibits high selectivity for G-quadruplex DNA relative to duplex DNA.

  4. Accurate predictions of spectroscopic and molecular properties of 27 Λ-S and 73 Ω states of AsS radical.

    Science.gov (United States)

    Shi, Deheng; Song, Ziyue; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue

    2016-01-15

    The PECs are calculated for the 27 Λ-S states and their corresponding 73 Ω states of AsS radical. Of these Λ-S states, only the 2(2)Δ and 5(4)Π states are replulsive. The 1(2)Σ(+), 2(2)Σ(+), 4(2)Π, 3(4)Δ, 3(4)Σ(+), and 4(4)Π states possess double wells. The 3(2)Σ(+) state possesses three wells. The A(2)Π, 3(2)Π, 1(2)Φ, 2(4)Π, 3(4)Π, 2(4)Δ, 3(4)Δ, 1(6)Σ(+), and 1(6)Π states are inverted with the SO coupling effect included. The 1(4)Σ(+), 2(4)Σ(+), 2(4)Σ(-), 2(4)Δ, 1(4)Φ, 1(6)Σ(+), and 1(6)Π states, the second wells of 1(2)Σ(+), 3(4)Σ(+), 4(2)Π, 4(4)Π, and 3(4)Δ states, and the third well of 3(2)Σ(+) state are very weakly-bound states. The PECs are extrapolated to the CBS limit. The effect of SO coupling on the PECs is discussed. The spectroscopic parameters are evaluated, and compared with available measurements and other theoretical ones. The vibrational properties of several weakly-bound states are determined. The spectroscopic properties reported here can be expected to be reliably predicted ones. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. The prion protein has DNA strand transfer properties similar to retroviral nucleocapsid protein.

    Science.gov (United States)

    Gabus, C; Auxilien, S; Péchoux, C; Dormont, D; Swietnicki, W; Morillas, M; Surewicz, W; Nandi, P; Darlix, J L

    2001-04-06

    The transmissible spongiform encephalopathies are fatal neurodegenerative diseases that are associated with the accumulation of a protease-resistant form of the cellular prion protein (PrP). Although PrP is highly conserved and widely expressed in vertebrates, its function remains a matter of speculation. Indeed PrP null mice develop normally and are healthy. Recent results show that PrP binds to nucleic acids in vitro and is found associated with retroviral particles. Furthermore, in mice the scrapie infectious process appears to be accelerated by MuLV replication. These observations prompted us to further investigate the interaction between PrP and nucleic acids, and compare it with that of the retroviral nucleocapsid protein (NC). As the major nucleic acid-binding protein of the retroviral particle, NC protein is tightly associated with the genomic RNA in the virion nucleocapsid, where it chaperones proviral DNA synthesis by reverse transcriptase. Our results show that the human prion protein (huPrP) functionally resembles NCp7 of HIV-1. Both proteins form large nucleoprotein complexes upon binding to DNA. They accelerate the hybridization of complementary DNA strands and chaperone viral DNA synthesis during the minus and plus DNA strand transfers necessary to generate the long terminal repeats. The DNA-binding and strand transfer properties of huPrP appear to map to the N-terminal fragment comprising residues 23 to 144, whereas the C-terminal domain is inactive. These findings suggest that PrP could be involved in nucleic acid metabolism in vivo. Copyright 2001 Academic Press.

  6. Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs.

    Science.gov (United States)

    Ma, Zhipeng; Huang, Yunfei; Park, Seongsu; Kawai, Kentaro; Kim, Do-Nyun; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Yamada, Hirofumi; Tabata, Osamu

    2018-01-01

    DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency-modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic-shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns. The bending rigidity of crossovers is determined to be only one-third of that of the DNA helix, based on interhelical electrostatic forces reported elsewhere, and the measured pitches of the 3-turn crossover design rhombic-shaped nanostructures undergoing negligible bending. To evaluate the robustness of their structural integrity, they are intentionally and simultaneously stressed using force-controlled atomic force microscopy. DNA crossovers are verified to have a stabilizing effect on the structural robustness, while the nicks have an opposite effect. The structural and mechanical properties of DNA origami and the effects of crossovers and nicks revealed in this paper can provide information essential for the design of versatile DNA origami structures that exhibit specified and desirable properties. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Spectroscopic data

    CERN Document Server

    Melzer, J

    1976-01-01

    During the preparation of this compilation, many people contributed; the compilers wish to thank all of them. In particular they appreciate the efforts of V. Gilbertson, the manuscript typist, and those of K. C. Bregand, J. A. Kiley, and W. H. McPherson, who gave editorial assistance. They would like to thank Dr. J. R. Schwartz for his cooperation and encouragement. In addition, they extend their grati­ tude to Dr. L. Wilson of the Air Force Weapons Laboratory, who gave the initial impetus to this project. v Contents I. I ntroduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 . . . . . . . . . . . . . . . . 11. Organization ofthe Spectroscopic Table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Methods of Production and Experimental Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Band Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2...

  8. Ab initio study of spectroscopic properties of bimetallic molecules MeB (where Me=Li, Na, K, Br, Cs, Fr) using CCSD(T) and MRCI methods

    International Nuclear Information System (INIS)

    Cukovicova, M.; Cernusak, I.

    2010-01-01

    For our study we have chosen a series of diatomic molecules MeB (where Me = Li, Na, K, Rb, Cs, Fr). These molecules present experimentally unknown species, hence we were motivated to predict theoretically potential energy curves, equilibrium bond lengths, harmonic frequencies, constants of anharmonicity, dipole moments and dissociation energies for the ground and low-lying excited states using high level ab initio techniques. Based on previous state averaged MRCI calculations in ANO-S basis set of NaB and KB molecules, we have focused on four lowest-lying electronic states, ground state 3Π and excited states 1Σ+, 1Π and 3Σ+. All four states dissociate to the atoms in ground states 2P1/2(B) and 2S1/2(Me). 3Π, 1Σ+, 1Π and 3Σ+ electronic states we investigated employing CCSD(T) method using relativistic ANO-RCC basis set. Our calculations include scalar relativistic effects via the second order one-component (spin-free) Douglas-Kroll-Hess Hamiltonian. Relativistic effects become remarkable in the case of heavy atoms, hence properties of CsB and FrB molecules may differ from trend of properties in row from LiB to FrB. Spectroscopic properties of particular state were obtained from the analysis of the potential energy curves using VIBROT and DUNHAM programs.

  9. Chemical and physical properties of the normal and aging lens: spectroscopic (UV, fluorescence, phosphorescence, and NMR) analyses

    International Nuclear Information System (INIS)

    Lerman, S.

    1987-01-01

    In vitro [UV absorption, fluorescence, phosphorescence, and nuclear magnetic resonance (NMR)] spectroscopic studies on the normal human lens demonstrate age-related changes which can be correlated with biochemical and photobiologic mechanisms occurring during our lifetime. Chronic cumulative UV exposure results in an age-related increase of photochemically induced chromophores and in color of the lens nucleus. This enables the lens to filter the incident UV radiation, thereby protecting the underlying aging retina from UV photodamage. We have measured the age-related increase in lens fluorescence in vivo on more than 300 normal subjects (1st to 9th decade) by UV slitlamp densitography. These data show a good correlation with the in vitro lens fluorescence studies reported previously and demonstrate that molecular photodamage can be monitored in the lens. In vitro NMR (human and animal lenses) and in vivo experiments currently in progress are rapidly elucidating the physicochemical basis for transparency and the development of light scattering areas. Surface scanning NMR can monitor organophosphate metabolism in the ocular lens in vivo as well as in vitro. These studies demonstrate the feasibility of using biophysical methods (optical spectroscopy and NMR analyses) to delineate age-related parameters in the lens, in vivo as well as in vitro. 46 references

  10. Structural, thermal, dielectric spectroscopic and AC impedance properties of SiC nanoparticles doped PVK/PVC blend

    Science.gov (United States)

    Alghunaim, Naziha Suliman

    2018-06-01

    Nanocomposite films based on poly (N-vinylcarbazole)/polyvinylchloride (PVK/PVC) blend doped with different concentrations of Silicon Carbide (SiC) nanoparticles have been prepared. The X-ray diffraction, Ultra violet-visible spectroscopy, thermogravimetric analysis and electrical spectroscopic has been used to characterize these nanocomposites. The X-ray analysis confirms the semi-crystalline nature of the films. The intensity of the main X-ray peak is decreased due to the interaction between the PVK/PVC and SiC. The main SiC peaks are absent due to complete dissolution of SiC in polymeric matrices. The UV-Vis spectra indicated that the band gap optical energy is affected by adding SiC nanoparticles because the charges transfer complexes between PVK/PVC with amount of SiC. The thermal stability is improved and the estimated values of ε‧ and ε″ are increased with increasing for SiC content due to the free charge carriers which in turn increase the ionic conductivity of the doped samples. The plots of tan δ with frequency are studied. A single peak from the plot between tan δ and Log (f) is appeared and shifted towards the higher frequency confirmed the presence of relaxing dipoles moment.

  11. Influence of silver nanoparticles on the spectroscopic properties of Sm{sup 3+} doped boro-phosphate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Suthanthirakumar, P.; Marimuthu, K., E-mail: emari-ram2000@yahoo.com [Department of Physics, Gandhigram Rural University, Gandhigram - 624 302 (India)

    2016-05-23

    The Sm{sup 3+} doped novel boro-phosphate glasses containing silver nanoparticles (NPs) (SmBPxA) have been prepared following the melt quenching technique and their structural and spectroscopic behavior were studied through HR-TEM, optical absorption and photoluminescence spectral measurements. The TEM analysis validates the existence of Ag NPs with an average diameter of ~8 nm. The Surface plasmon resonance (SPR) band of silver NPs was found at around 600 nm from the absorption spectrum of the Sm{sup 3+} ions free glass sample. The optical band gap energy (E{sub opt}) corresponding to the direct and indirect allowed transitions and the Urbach energy (ΔE) values were determined from the absorption spectral measurements. The luminescence intensity is found to get enhance when the Ag NPs were embedded along with the Sm{sup 3+} ions in the prepared glasses due to the local electric field effect around the rare earth (RE) ion site produced by the SPR of Ag NPs.

  12. Optical properties and surface characterization of pulsed laser-deposited Cu2ZnSnS4 by spectroscopic ellipsometry

    International Nuclear Information System (INIS)

    Crovetto, Andrea; Cazzaniga, Andrea; Ettlinger, Rebecca B.; Schou, Jørgen; Hansen, Ole

    2015-01-01

    Cu 2 ZnSnS 4 films prepared by pulsed laser deposition at different temperatures are characterized by spectroscopic ellipsometry. The focus is on confirming results from direct measurement techniques, by finding appropriate models of the surface overlayer for data fitting, and extracting the dielectric function of the films. It is found that the surface overlayer changes with film thickness and deposition temperature. Adopting different ellipsometry measurements and modeling strategies for each film, dielectric functions are extracted and compared. As the deposition temperature is increased, the dielectric functions exhibit additional critical points related to optical transitions in the material other than absorption across the fundamental band gap. In the case of a thin film < 200 nm thick, surface features observed by scanning electron microscopy and atomic force microscopy are accurately reproduced by ellipsometry data fitting. - Highlights: • Inhomogeneous Cu 2 ZnSnS 4 films are prepared by pulsed laser deposition. • The film surface includes secondary phases and topographic structures. • We model a film surface layer that fits ellipsometry data. • Ellipsometry data fits confirm results from direct measurement techniques. • We obtain the dielectric function of inhomogeneous Cu 2 ZnSnS 4 films

  13. Synthesis, characterization and spectroscopic properties of a new Nd{sup 3+}-doped Co-picromerite-type Tutton salt

    Energy Technology Data Exchange (ETDEWEB)

    Souamti, A., E-mail: souamtiahmed88@gmail.com [Laboratoire d' Application de la Chimie aux Ressources et Substances Naturelles et à l' Environnement, Département de Chimie, Université de Carthage, Faculté des Sciences de Bizerte, Zarzouna, Bizerte 7021 (Tunisia); Martín, I.R. [Departamento de Física, Universidad de La Laguna, 38206 La Laguna (Spain); Zayani, L. [Laboratoire d' Application de la Chimie aux Ressources et Substances Naturelles et à l' Environnement, Département de Chimie, Université de Carthage, Faculté des Sciences de Bizerte, Zarzouna, Bizerte 7021 (Tunisia); Hernández-Rodríguez, M.A.; Soler-Carracedo, K.; Lozano-Gorrín, A.D. [Departamento de Física, Universidad de La Laguna, 38206 La Laguna (Spain); Lalla, E. [Extreme Light Infrastructure – Nuclear Physics (ELI-NP), Horia Hulubei, National Institute of Physics and Nuclear Engineering (IFIN HH), 30, Reactorului Street, P.O. Box MG-6, 077125 Magurele, jud. Ilfov (Romania); Chehimi, D. Ben Hassen [Laboratoire d' Application de la Chimie aux Ressources et Substances Naturelles et à l' Environnement, Département de Chimie, Université de Carthage, Faculté des Sciences de Bizerte, Zarzouna, Bizerte 7021 (Tunisia)

    2016-09-15

    Single crystals of Nd{sup 3+}-doped Co-picromerite has been synthesized by the slow evaporation method. After two weeks on hold, the crystals obtained were characterized by different techniques, indeed X-ray powder diffraction (XRPD) shows that these compounds crystallize in the monoclinic system with space group P21/a. Complete dehydration of the double salt was obtained before reaching 200 °C with a phase transition of KS around 570 °C. The IR spectroscopic study confirms the vibrational modes of the sulfate groups and water molecules. Exciting at 473 nm, the emission peaks associated with the 4F{sub 5/2}→4I{sub 9/2}, 4F{sub 3/2}→4I{sub 9/2} and 4F{sub 3/2}→4I{sub 11/2} transitions were observed. The luminescence decay curve was analyzed in the frame of the Inokuti-Hirayama model in order to obtain the intrinsic lifetime and the energy transfer parameter among Nd{sup 3+}ions.

  14. THE REST-FRAME OPTICAL SPECTROSCOPIC PROPERTIES OF LY α -EMITTERS AT z  ∼ 2.5: THE PHYSICAL ORIGINS OF STRONG LY α EMISSION

    Energy Technology Data Exchange (ETDEWEB)

    Trainor, Ryan F. [Department of Astronomy, University of California, Berkeley, 501 Campbell Hall, Berkeley, CA 94720 (United States); Strom, Allison L.; Steidel, Charles C. [Cahill Center for Astrophysics, MC 249-17, 1200 E California Boulevard, Pasadena, CA 91125 (United States); Rudie, Gwen C., E-mail: trainor@berkeley.edu [Carnegie Observatories, 813 Santa Barbara Street, Pasadena, CA 91101 (United States)

    2016-12-01

    We present the rest-frame optical spectroscopic properties of 60 faint ( R {sub AB} ∼ 27; L ∼ 0.1 L {sub *}) Ly α -selected galaxies (LAEs) at z  ≈ 2.56. These LAEs also have rest-UV spectra of their Ly α emission line morphologies, which trace the effects of interstellar and circumgalactic gas on the escape of Ly α photons. We find that the LAEs have diverse rest-optical spectra, but their average spectroscopic properties are broadly consistent with the extreme low-metallicity end of the populations of continuum-selected galaxies selected at z  ≈ 2–3. In particular, the LAEs have extremely high [O iii] λ 5008/H β ratios (log([O iii]/H β ) ∼ 0.8) and low [N ii] λ 6585/H α ratios (log([N ii]/H α ) < 1.15). Coupled with a detection of the [O iii] λ 4364 auroral line, these measurements indicate that the star-forming regions in faint LAEs are characterized by high electron temperatures (T{sub e} ≈ 1.8 × 10{sup 4} K), low oxygen abundances (12 + log(O/H) ≈ 8.04, Z{sub neb} ≈ 0.22 Z {sub ⊙}), and high excitations with respect to their more luminous continuum-selected analogs. Several of our faintest LAEs have line ratios consistent with even lower metallicities, including six with 12 + log(O/H) ≈ 6.9–7.4 (Z {sub neb} ≈ 0.02–0.05 Z{sub ⊙}). We interpret these observations in light of new models of stellar evolution (including binary interactions) that have been shown to produce long-lived populations of hot, massive stars at low metallicities. We find that strong, hard ionizing continua are required to reproduce our observed line ratios, suggesting that faint galaxies are efficient producers of ionizing photons and important analogs of reionization-era galaxies. Furthermore, we investigate the physical trends accompanying Ly α emission across the largest current sample of combined Ly α and rest-optical galaxy spectroscopy, including both the 60 KBSS-Ly α LAEs and 368 more luminous galaxies at similar redshifts. We

  15. Charge transport properties of DNA aperiodic molecule: The role of interbase hopping in Watson-Crick base pair

    Science.gov (United States)

    Sinurat, E. N.; Yudiarsah, E.

    2017-07-01

    The charge transport properties of DNA aperiodic molecule has been studied by considering various interbase hopping parameter on Watson-Crick base pair. 32 base pairs long double-stranded DNA aperiodic model with sequence GCTAGTACGTGACGTAGCTAGGATATGCCTGA on one chain and its complement on the other chain is used. Transfer matrix method has been used to calculate transmission probabilities, for determining I-V characteristic using Landauer Büttiker formula. DNA molecule is modeled using tight binding hamiltonian combined with the theory of Slater-Koster. The result show, the increment of Watson-Crick hopping value leads to the transmission probabilities and current of DNA aperiodic molecule increases.

  16. Sedimentation properties of DNA-membrane complexes and yield of DNA breaks at irradiation of mammalian cells

    International Nuclear Information System (INIS)

    Erzgraber, G.; Kozubek, S.; Lapidus, I.L.

    1985-01-01

    The dependence of the relative sedimentation velocity of DNA-membrane complexes on the dose of irradiation and time of incubation of Chinese Hamster cells is analysed. It is concluded that the initial part of the curve provides the information on the occurrence of single strand breaks in DNA; the position of the local maximum allows us to calculate the yield of DNA double strand breaks. The reparation decay constant can be estimated as well

  17. Spectroscopic investigation on interaction and sonodynamic damage of Riboflavin to DNA under ultrasonic irradiation by using Methylene Blue as fluorescent probe

    Science.gov (United States)

    Wang, Qi; Wu, Qiong; Wang, Jun; Chen, Dandan; Fan, Ping; Wang, Baoxin

    2014-01-01

    In this paper, the Riboflavin (RF) as a sonosensitizer and Methylene Blue (MB) as a fluorescent probe were used to study the interaction and sonodynamic damage to Deoxyribonucleic Acid (DNA) by fluorescence and UV-vis spectroscopy. The results showed that the RF could efficiently bind to DNA in aqueous solution and exchange with the MB through competing reaction. And then, under ultrasonic irradiation, the RF could obviously damage the DNA. In addition, the influencing factors such as ultrasonic irradiation time and RF concentration on the sonodynamic damage to DNA were also considered. The experimental results showed that the sonodynamic damage degree increase with the increase of ultrasonic irradiation time and RF concentration. Perhaps, this paper may offer some important subjects for broadening the application of RF in sonodynamic therapy (SDT) technologies for tumor treatment.

  18. Electronic properties of Al/DNA/p-Si MIS diode: Application as temperature sensor

    International Nuclear Information System (INIS)

    Guellue, O.; Tueruet, A.

    2011-01-01

    Research highlights: → This work proposes that DNA molecules should be considered, among other candidates, as a potential organic thin film for metal-interface layer-semiconductor devices. → We successfully fabricated Al/DNA/p-Si device with interlayer by a simple cast method. → The temperature is found to significantly effect the electrical properties of the Al/DNA/p-Si device. → The facts: (i) that the technology of the fabrication of a Al/DNA/p-Si Schottky diode much simpler and economical than that for the Si p-n junction and (ii) the sensibility of the Al/DNA/p-Si Schottky diode as temperature sensor is 42% higher than that of a Si p-n junction, indicate that the Al/DNA/p-Si Schottky diode is a good alternative as temperature sensor. - Abstract: The current-voltage (I-V) measurements were performed in the temperature range (200-300 K) on Al/DNA/p-Si Schottky barrier type diodes. The Schottky diode shows non-ideal I-V behaviour with ideality factors n equal to 1.34 ± 0.02 and 1.70 ± 0.02 at 300 K and 200 K, respectively, and is thought to have a metal-interface layer-semiconductor (MIS) configuration. The zero-bias barrier height Φ b determined from the I-V measurements was 0.75 ± 0.01 eV at 300 K and decreases to 0.61 ± 0.01 eV at 200 K. The forward voltage-temperature (V F -T) characteristics were obtained from the I-V measurements in the temperature range 200-300 K at different activation currents (I F ) in the range 20 nA-6 μA. The V F -T characteristics were linear for three activation currents in the diode. From the V F -T characteristics at 20 nA, 100 nA and 6 μA, the values of the temperature coefficients of the forward bias voltage (dV F /dT) for the diode were determined as -2.30 mV K -1 , -2.60 mV K -1 and -3.26 mV K -1 with a standard error of 0.05 mV K -1 , respectively.

  19. Electronic properties of Al/DNA/p-Si MIS diode: Application as temperature sensor

    Energy Technology Data Exchange (ETDEWEB)

    Guellue, O., E-mail: omergullu@gmail.com [Batman University, Science and Art Faculty, Department of Physics, 72060 Batman (Turkey); Osmaniye Korkut Ata University, Science and Art Faculty, Department of Physics, 80000 Osmaniye (Turkey); Tueruet, A. [Atatuerk University, Science Faculty, Department of Physics, 25240 Erzurum (Turkey)

    2011-01-21

    Research highlights: > This work proposes that DNA molecules should be considered, among other candidates, as a potential organic thin film for metal-interface layer-semiconductor devices. > We successfully fabricated Al/DNA/p-Si device with interlayer by a simple cast method. > The temperature is found to significantly effect the electrical properties of the Al/DNA/p-Si device. > The facts: (i) that the technology of the fabrication of a Al/DNA/p-Si Schottky diode much simpler and economical than that for the Si p-n junction and (ii) the sensibility of the Al/DNA/p-Si Schottky diode as temperature sensor is 42% higher than that of a Si p-n junction, indicate that the Al/DNA/p-Si Schottky diode is a good alternative as temperature sensor. - Abstract: The current-voltage (I-V) measurements were performed in the temperature range (200-300 K) on Al/DNA/p-Si Schottky barrier type diodes. The Schottky diode shows non-ideal I-V behaviour with ideality factors n equal to 1.34 {+-} 0.02 and 1.70 {+-} 0.02 at 300 K and 200 K, respectively, and is thought to have a metal-interface layer-semiconductor (MIS) configuration. The zero-bias barrier height {Phi}{sub b} determined from the I-V measurements was 0.75 {+-} 0.01 eV at 300 K and decreases to 0.61 {+-} 0.01 eV at 200 K. The forward voltage-temperature (V{sub F}-T) characteristics were obtained from the I-V measurements in the temperature range 200-300 K at different activation currents (I{sub F}) in the range 20 nA-6 {mu}A. The V{sub F}-T characteristics were linear for three activation currents in the diode. From the V{sub F}-T characteristics at 20 nA, 100 nA and 6 {mu}A, the values of the temperature coefficients of the forward bias voltage (dV{sub F}/dT) for the diode were determined as -2.30 mV K{sup -1}, -2.60 mV K{sup -1} and -3.26 mV K{sup -1} with a standard error of 0.05 mV K{sup -1}, respectively.

  20. CHARACTERIZATION OF A SAMPLE OF INTERMEDIATE-TYPE AGNs. I. SPECTROSCOPIC PROPERTIES AND SERENDIPITOUS DISCOVERY OF NEW DUAL AGNs

    Energy Technology Data Exchange (ETDEWEB)

    Benitez, Erika; Cruz-Gonzalez, Irene; Martinez, Benoni; Jimenez-Bailon, Elena [Instituto de Astronomia, Universidad Nacional Autonoma de Mexico, Apdo. Postal 70-264, Mexico D.F. 04510 (Mexico); Mendez-Abreu, Jairo; Lopez-Martin, Luis [Instituto de Astrofisica de Canarias, E-38200 La Laguna, Tenerife (Spain); Fuentes-Carrera, Isaura [Escuela Superior de Fisica y Matematicas, Instituto Politecnico Nacional (ESFM-IPN), U.P. Adolfo Lopez Mateos, Mexico D.F. 07730 (Mexico); Leon-Tavares, Jonathan [Aalto University Metsaehovi Radio Observatory, Metsaehovintie 114, FI-02540, Kylmaelae (Finland); Chavushyan, Vahram H., E-mail: erika@astro.unam.mx [Instituto Nacional de Astrofisica, Optica y Electronica, Apdo. Postal 51-216, 72000 Puebla (Mexico)

    2013-01-20

    A sample of 10 nearby intermediate-type active galactic nuclei (AGNs) drawn from the Sloan Digital Sky Survey is presented. The aim of this work is to provide estimations of the black hole (BH) mass for the sample galaxies from the dynamics of the broad-line region. For this purpose, a detailed spectroscopic analysis of the objects was done. Using Baldwin-Phillips-Terlevich diagnostic diagrams, we have carefully classified the objects as true intermediate-type AGNs and found that 80%{sup +7.2%} {sub -17.3%} are composite AGNs. The BH mass estimated for the sample is within 6.54 {+-} 0.16 < log M {sub BH} < 7.81 {+-} 0.14. Profile analysis shows that five objects (J120655.63+501737.1, J121607.08+504930.0, J141238.14+391836.5, J143031.18+524225.8, and J162952.88+242638.3) have narrow double-peaked emission lines in both the red (H{alpha}, [N II] {lambda}{lambda}6548,6583 and [S II] {lambda}{lambda}6716, 6731) and the blue (H{beta} and [O III] {lambda}{lambda}4959, 5007) regions of the spectra, with velocity differences ({Delta}V) between the double peaks within 114 km s{sup -1} < {Delta}V < 256 km s{sup -1}. Two of them, J121607.08+504930.0 and J141238.14+391836.5, are candidates for dual AGNs since their double-peaked emission lines are dominated by AGN activity. In searches of dual AGNs, type 1, type II, and intermediate-type AGNs should be carefully separated, due to the high serendipitous number of narrow double-peaked sources (50% {+-} 14.4%) found in our sample.

  1. Multireference configuration interaction study on spectroscopic properties of low-lying electronic states of As2 molecule

    International Nuclear Information System (INIS)

    Wang Jie-Min; Liu Qiang

    2013-01-01

    The potential energy curves (PECs) of four electronic states (X 1 Σ g + , e 3 Δ u , a 3 Σ u − , and d 3 Π g ) of an As 2 molecule are investigated employing the complete active space self-consistent field (CASSCF) method followed by the valence internally contracted multireference configuration interaction (MRCI) approach in conjunction with the correlation-consistent aug-cc-pV5Z basis set. The effect on PECs by the relativistic correction is taken into account. The way to consider the relativistic correction is to employ the second-order Douglas-Kroll Hamiltonian approximation. The correction is made at the level of a cc-pV5Z basis set. The PECs of the electronic states involved are extrapolated to the complete basis set limit. With the PECs, the spectroscopic parameters (T e , R e , ω e , ω e x e , ω e y e , α e , β e , γ e , and B e ) of these electronic states are determined and compared in detail with those reported in the literature. Excellent agreement is found between the present results and the experimental data. The first 40 vibrational states are studied for each electronic state when the rotational quantum number J equals zero. In addition, the vibrational levels, inertial rotation and centrifugal distortion constants of d 3 Π g electronic state are reported which are in excellent agreement with the available measurements. Comparison with the experimental data shows that the present results are both reliable and accurate. (atomic and molecular physics)

  2. Charge transport properties of a twisted DNA molecule: A renormalization approach

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, M.L. de; Ourique, G.S.; Fulco, U.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Moura, F.A.B.F. de; Lyra, M.L. [Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió-AL (Brazil)

    2016-10-20

    In this work we study the charge transport properties of a nanodevice consisting of a finite segment of the DNA molecule sandwiched between two metallic electrodes. Our model takes into account a nearest-neighbor tight-binding Hamiltonian considering the nucleobases twist motion, whose solutions make use of a two-steps renormalization process to simplify the algebra, which can be otherwise quite involved. The resulting variations of the charge transport efficiency are analyzed by numerically computing the main features of the electron transmittance spectra as well as their I × V characteristic curves.

  3. Tunable optical properties of plasmonic Au/Al2O3 nanocomposite thin films analyzed by spectroscopic ellipsometry accounting surface characteristics.

    Science.gov (United States)

    Jaiswal, Jyoti; Mourya, Satyendra; Malik, Gaurav; Chandra, Ramesh

    2018-05-01

    In the present work, we have fabricated plasmonic gold/alumina nanocomposite (Au/Al 2 O 3 NC) thin films on a glass substrate at room temperature by RF magnetron co-sputtering. The influence of the film thickness (∼10-40  nm) on the optical and other physical properties of the samples was investigated and correlated with the structural and compositional properties. The X-ray diffractometer measurement revealed the formation of Au nanoparticles with average crystallite size (5-9.2 nm) embedded in an amorphous Al 2 O 3 matrix. The energy-dispersive X ray and X-ray photoelectron spectroscopy results confirmed the formation of Au/Al 2 O 3 NC quantitatively and qualitatively and it was observed that atomic% of Au increased by increasing thickness. The optical constants of the plasmonic Au/Al 2 O 3 NC thin films were examined by variable angle spectroscopic ellipsometry in the wide spectral range of 246-1688 nm, accounting the surface characteristics in the optical stack model, and the obtained results are expected to be unique. Additionally, a thickness-dependent blueshift (631-590 nm) of surface plasmon resonance peak was observed in the absorption spectra. These findings of the plasmonic Au/Al 2 O 3 NC films may allow the design and fabrication of small, compact, and efficient devices for optoelectronic and photonic applications.

  4. Global minimum-energy structure and spectroscopic properties of I2(*-) x n H2O clusters: a Monte Carlo simulated annealing study.

    Science.gov (United States)

    Pathak, Arup Kumar; Mukherjee, Tulsi; Maity, Dilip Kumar

    2010-01-18

    The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I(2)(*-) x n H(2)O (n=1-10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin-orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I-I stretching band but enhances the intensity of the O-H stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of O-H bonds in a cyclic water network are observed for I(2)(*-) x n H(2)O clusters with n > or = 3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I(2)(*-) in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl(2)(*-) and Br(2)(*-).

  5. A theoretical study on the geometry and spectroscopic properties of ground-state and local minima isomers of (CuS)n=2-6 clusters

    Science.gov (United States)

    Luque-Ceballos, Jonathan C.; Posada-Borbón, Alvaro; Herrera-Urbina, Ronaldo; Aceves, R.; Juárez-Sánchez, J. Octavio; Posada-Amarillas, Alvaro

    2018-03-01

    Spectroscopic properties of gas-phase copper sulfide clusters (CuS)n (n = 2-6) are calculated using Density Functional Theory (DFT) and time-dependent (TD) DFT approaches. The energy landscape of the potential energy surface is explored through a basin-hopping DFT methodology. Ground-state and low-lying isomer structures are obtained. The global search was performed at the B3PW91/SDD level of theory. Normal modes are calculated to validate the existence of optimal cluster structures. Energetic properties are obtained for the ground-state and isomer clusters and their relative energies are evaluated for probing isomerization. This is a few tenths of an eV, except for (CuS)2 cluster, which presents energy differences of ∼1 eV. Notable differences in the infrared spectra exist between the ground-state and first isomer structures, even for the (CuS)5 cluster, which has in both configurations a core copper pyramid. TDDFT provides the simulated absorption spectrum, presenting a theoretical description of optical absorption bands in terms of electronic excitations in the UV and visible regions. Results exhibit a significant dependence of the calculated UV/vis spectra on clusters size and shape regarding the ground state structures. Optical absorption is strong in the UV region, and weak or forbidden in the visible region of the spectrum.

  6. Physicochemical, antioxidant, DNA cleaving properties and antimicrobial activity of fisetin-copper chelates.

    Science.gov (United States)

    Łodyga-Chruscińska, Elżbieta; Pilo, Maria; Zucca, Antonio; Garribba, Eugenio; Klewicka, Elżbieta; Rowińska-Żyrek, Magdalena; Symonowicz, Marzena; Chrusciński, Longin; Cheshchevik, Vitalij T

    2018-03-01

    Fisetin (3,3',4',7-tetrahydroxyflavone) metal chelates are of interest as this plant polyphenol has revealed broad prospects for its use as natural medicine in the treatment of various diseases. Metal interactions may change or enhance fisetin biological properties so understanding fisetin metal chelation is important for its application not only in medicine but also as a food additive in nutritional supplements. This work was aimed to determine and characterize copper complexes formed in different pH range at applying various metal/ligand ratios. Fisetin and Cu(II)-fisetin complexes were characterized by potentiometric titrations, UV-Vis (Ultraviolet-visible spectroscopy), EPR, ESI-MS, FTIR and cyclic voltammetry. Their effects on DNA were investigated by using circular dichroism, spectrofluorimetry and gel electrophoresis methods. The copper complex with the ratio of Cu(II)/fisetin 1/2 exhibited significant DNA cleavage activity, followed by complete degradation of DNA. The influence of copper(II) ions on antioxidant activity of fisetin in vitro has been studied using DPPH, ABTS and mitochondrial assays. The results have pointed out that fisetin or copper complexes can behave both as antioxidants or pro-oxidants. Antimicrobial activity of the compounds has been investigated towards several bacteria and fungi. The copper complex of Cu(II)/fisetin 1/2 ratio showed higher antagonistic activity against bacteria comparing to the ligand and it revealed a promising antifungal activity. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. NMR characterization of the DNA binding properties of a novel Hoechst 33258 analogue peptide building block

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Behrens, Carsten; Jacobsen, Jens Peter

    2002-01-01

    A novel aryl-bis-benzimidazole amino acid analogue of the DNA-binding compound Hoechst 33258 has recently been designed for incorporation in peptide combinatorial libraries by replacing the N-methylpiperazine group with a carboxyl group and the hydroxy group with an amino-methyl group. The DNA......-binding properties of the aryl-bis-benzimidazole monomer with the C-terminus derivatized with 3-(dimethylamino)-propylamine has been investigated in this paper by (1)H NMR studies of two different complexes with two different DNA sequences: A(5) d(5'-GCCA(5)CG-3'):d(5'-CGT(5)GGC-3') and A(3)T(3) d(5'-CGA(3)T(3)CG-3...... preference with the bis-benzimidazole moiety displaced toward the 3'-end from the center of the duplex. Two families of models of the complexes with A(5) and A(3)T(3) were derived with restrained molecular dynamics based on a large set of 70 and 61, respectively, intermolecular ligand NOEs. Both models give...

  8. Base-pairing preferences, physicochemical properties and mutational behaviour of the DNA lesion 8-nitroguanine.

    Science.gov (United States)

    Bhamra, Inder; Compagnone-Post, Patricia; O'Neil, Ian A; Iwanejko, Lesley A; Bates, Andrew D; Cosstick, Richard

    2012-11-01

    8-Nitro-2'-deoxyguanosine (8-nitrodG) is a relatively unstable, mutagenic lesion of DNA that is increasingly believed to be associated with tissue inflammation. Due to the lability of the glycosidic bond, 8-nitrodG cannot be incorporated into oligodeoxynucleotides (ODNs) by chemical DNA synthesis and thus very little is known about its physicochemical properties and base-pairing preferences. Here we describe the synthesis of 8-nitro-2'-O-methylguanosine, a ribonucleoside analogue of this lesion, which is sufficiently stable to be incorporated into ODNs. Physicochemical studies demonstrated that 8-nitro-2'-O-methylguanosine adopts a syn conformation about the glycosidic bond; thermal melting studies and molecular modelling suggest a relatively stable syn-8-nitroG·anti-G base pair. Interestingly, when this lesion analogue was placed in a primer-template system, extension of the primer by either avian myeloblastosis virus reverse transcriptase (AMV-RT) or human DNA polymerase β (pol β), was significantly impaired, but where incorporation opposite 8-nitroguanine did occur, pol β showed a 2:1 preference to insert dA over dC, while AMV-RT incorporated predominantly dC. The fact that no 8-nitroG·G base pairing is seen in the primer extension products suggests that the polymerases may discriminate against this pairing system on the basis of its poor geometric match to a Watson-Crick pair.

  9. Base-pairing preferences, physicochemical properties and mutational behaviour of the DNA lesion 8-nitroguanine†

    Science.gov (United States)

    Bhamra, Inder; Compagnone-Post, Patricia; O’Neil, Ian A.; Iwanejko, Lesley A.; Bates, Andrew D.; Cosstick, Richard

    2012-01-01

    8-Nitro-2′-deoxyguanosine (8-nitrodG) is a relatively unstable, mutagenic lesion of DNA that is increasingly believed to be associated with tissue inflammation. Due to the lability of the glycosidic bond, 8-nitrodG cannot be incorporated into oligodeoxynucleotides (ODNs) by chemical DNA synthesis and thus very little is known about its physicochemical properties and base-pairing preferences. Here we describe the synthesis of 8-nitro-2′-O-methylguanosine, a ribonucleoside analogue of this lesion, which is sufficiently stable to be incorporated into ODNs. Physicochemical studies demonstrated that 8-nitro-2′-O-methylguanosine adopts a syn conformation about the glycosidic bond; thermal melting studies and molecular modelling suggest a relatively stable syn-8-nitroG·anti-G base pair. Interestingly, when this lesion analogue was placed in a primer-template system, extension of the primer by either avian myeloblastosis virus reverse transcriptase (AMV-RT) or human DNA polymerase β (pol β), was significantly impaired, but where incorporation opposite 8-nitroguanine did occur, pol β showed a 2:1 preference to insert dA over dC, while AMV-RT incorporated predominantly dC. The fact that no 8-nitroG·G base pairing is seen in the primer extension products suggests that the polymerases may discriminate against this pairing system on the basis of its poor geometric match to a Watson–Crick pair. PMID:22965127

  10. Synthesis and characterization of new unsymmetrical Schiff base Zn (II) and Co (II) complexes and study of their interactions with bovin serum albumin and DNA by spectroscopic techniques

    Science.gov (United States)

    Sedighipoor, Maryam; Kianfar, Ali Hossein; Sabzalian, Mohammad R.; Abyar, Fatemeh

    2018-06-01

    Two novel tetra-coordinated Cobalt(II) and Zinc (II) chelate series with the general formula of [Co (L)·2H2O] (1) and [Zn (L)] (2) [L = N-2-hydroxyacetophenon-N‧-2-hydroxynaphthaldehyde-1,2 phenylenediimine)] with biologically active Schiff base ligands were synthesized and recognized by elemental analysis and multi-nuclear spectroscopy (IR and 1H and 13C NMR); then, their biological activities including DNA and protein interactions were studied. The interaction of the synthesized compounds with bovine serum albumin (BSA) was investigated via fluorescence spectroscopy, showing the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary BSA structure in the presence of the complexes. The interaction of these compounds with CT-DNA was considered by UV-Vis technique, emission titration, viscosity measurements, helix melting methods, and circular dichroism (CD) spectroscopy, confirming that the complexes were bound to CT-DNA by the intercalation binding mode. Furthermore, the complexes had the capability to displace the DNA-bound MB, as shown by the competitive studies of these complexes with methylene blue (MB), thereby suggesting the intercalation mode for the competition. Finally, the theoretical studies carried out by the docking method were performed to calculate the binding constants and recognize the binding site of the BSA and DNA by the complexes. In addition, in vitro and in silico studies showed that the compounds were degradable by bacterial and fungal biodegradation activities.

  11. Quasiparticle properties of DNA bases from GW calculations in a Wannier basis

    Science.gov (United States)

    Qian, Xiaofeng; Marzari, Nicola; Umari, Paolo

    2009-03-01

    The quasiparticle GW-Wannier (GWW) approach [1] has been recently developed to overcome the size limitations of conventional planewave GW calculations. By taking advantage of the localization properties of the maximally-localized Wannier functions and choosing a small set of polarization basis we reduce the number of Bloch wavefunctions products required for the evaluation of dynamical polarizabilities, and in turn greatly reduce memory requirements and computational efficiency. We apply GWW to study quasiparticle properties of different DNA bases and base-pairs, and solvation effects on the energy gap, demonstrating in the process the key advantages of this approach. [1] P. Umari,G. Stenuit, and S. Baroni, cond-mat/0811.1453

  12. Effects of thermal annealing on the optical, spectroscopic, and structural properties of tris (8-hydroxyquinolinate) gallium films grown on quartz substrates

    Energy Technology Data Exchange (ETDEWEB)

    Muhammad, Fahmi Fariq, E-mail: fahmi982@gmail.com [Low Dimensional Materials Research Center, Department of Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Department of Physics, Faculty of Science and Engineering, University of Koya, Koya, Kurdistan Region (Iraq); Sulaiman, Khaulah [Low Dimensional Materials Research Center, Department of Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia)

    2011-10-03

    Highlights: {yields} Achieving a broad absorption band for Gaq3 covering the whole UV and some parts of visible spectra. {yields} Increasing photoluminescence emission to five times stronger than that of pristine film. {yields} Conformational changes towards the formation of crystalline {alpha}-Gaq3 polymorph. {yields} Determination of glass transition temperature for Gaq3 (T{sub g} 182 deg. C) and Alq3 (T{sub g} = 173 deg. C). {yields} Improving and understanding the physical properties of Gaq3 film by means of thermal treatment. - Abstract: In this study we report the optical, spectroscopic, and structural properties of vacuum deposited tris (8-hydroxyquinolinate) gallium film upon thermal annealing in the temperature range from 85 deg. C to 255 deg. C under a flowing nitrogen gas for 10 min. The optical UV-vis-NIR and luminescence spectroscopy measurements were performed to estimate the absorption bands, optical energy gap (E{sub g}), and photoluminescence (PL) of the films. Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) techniques were used to probe the spectroscopic and structural nature of the films. We show that, by annealing the films from 85 deg. C to 235 deg. C, it is possible to achieve an enhanced absorption and increased photoluminescence to five times stronger than that of the pristine film. The PL quenching at 255 deg. C was attributed to the presence of plainer chains allow easy going for excitons to a long distance due to the crystalline region formation of {alpha}-Gaq3 polymorph. The reduction in E{sub g} and infrared absorption bands upon annealing were referred to the enhancement in {pi}-{pi} interchain interaction and conformational changes by re-arrangement of the Gaq3 quinolinate ligands, respectively. Stokes shift for the films were observed and calculated. From the differential scanning calorimetry, DSC measurements, higher glass transition temperature was observed for Gaq3 (T{sub g} = 182 deg. C) compared to

  13. Thermodynamic and spectroscopic investigations of TMPyP4 association with guanine- and cytosine-rich DNA and RNA repeats of C9orf72.

    Science.gov (United States)

    Alniss, Hasan; Zamiri, Bita; Khalaj, Melisa; Pearson, Christopher E; Macgregor, Robert B

    2018-01-22

    An expansion of the hexanucleotide repeat (GGGGCC)n·(GGCCCC)n in the C9orf72 promoter has been shown to be the cause of Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The C9orf72 repeat can form four-stranded structures; the cationic porphyrin (TMPyP4) binds and distorts these structures. Isothermal titration calorimetry (ITC), and circular dichroism (CD) were used to study the binding of TMPyP4 to the C-rich and G-rich DNA and RNA oligos containing the hexanucleotide repeat at pH 7.5 and 0.1 M K + . The CD spectra of G-rich DNA and RNA TMPyP4 complexes showed features of antiparallel and parallel G-quadruplexes, respectively. The shoulder at 260 nm in the CD spectrum becomes more intense upon formation of complexes between TMPyP4 and the C-rich DNA. The peak at 290 nm becomes more intense in the c-rich RNA molecules, suggesting induction of an i-motif structure. The ITC data showed that TMPyP4 binds at two independent sites for all DNA and RNA molecules. For DNA, the data are consistent with TMPyP4 stacking on the terminal tetrads and intercalation. For RNA, the thermodynamics of the two binding modes are consistent with groove binding and intercalation. In both cases, intercalation is the weaker binding mode. These findings are considered with respect to the structural differences of the folded DNA and RNA molecules and the energetics of the processes that drive site-specific recognition by TMPyP4; these data will be helpful in efforts to optimize the specificity and affinity of the binding of porphyrin-like molecules. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Photoreactivity of biologically active compounds. XVII. Influence of solvent interactions on spectroscopic properties and photostability of primaquine.

    Science.gov (United States)

    Kristensen, S

    2005-06-01

    The influence of solvent interactions on absorption properties, fluorescence properties (emission spectra and quantum yields) and relative photochemical degradation rates of primaquine has been investigated, in order to evaluate photochemical reaction mechanisms and chemical properties of the compound. The first absorption band (n - pi*) of primaquine is only slightly dependent on properties of the solvent, which can be ascribed to a strong, intramolecular hydrogen bond between the quinoline N and amine group in the ground state (S0). Amphiprotic solvents with predominant acidic properties (water and methanol) will to some extent stabilize the molecule and initiate hypsochromic shifts of the absorption band by protic interactions, while the other solvents (amphiprotic, basic and neutral) influence the absorption spectrum by general solvent effects only. The excited singlet (S1*) state of primaquine interacts more efficiently with the surrounding solvents than the S0 state, as evaluated by the Stokes shifts. The pKa value of the quinoline N is likely to increase in the S1* state, which is important for the observed protic interactions with amphiprotic solvents of predominant acidity. Specific solvent effects are highly important for the efficiency of the fluorescence (fluorescence quantum yields; phi f). The fluorescence is quenched by amphiprotic solvents, likely due to a rupture of the intramolecular bond and protonation of the quinolone N, and enhanced by polar, non-protic (basic) solvents, probably by stabilization of the delta intramolecular hydrogen bond. The observed photochemical degradation rates of primaquine in amphiprotic media are positively correlated with phi f, indicating that the photochemical degradation of primaquine is dependent on intramolecular hydrogen bonding and non protonated lone-pair electrons at the quinoline N. The intramolecular ring-formation with a subsequent increased lipophilic character and (lack of) interactions with the

  15. The Redshift Evolution of Rest-UV Spectroscopic Properties in Lyman-break Galaxies at z ∼ 2–4

    Science.gov (United States)

    Du, Xinnan; Shapley, Alice E.; Reddy, Naveen A.; Jones, Tucker; Stark, Daniel P.; Steidel, Charles C.; Strom, Allison L.; Rudie, Gwen C.; Erb, Dawn K.; Ellis, Richard S.; Pettini, Max

    2018-06-01

    We present the first comprehensive evolutionary analysis of the rest-frame UV spectroscopic properties of star-forming galaxies at z ∼ 2–4. We match samples at different redshifts in UV luminosity and stellar mass, and perform systematic measurements of spectral features and stellar population modeling. By creating composite spectra grouped according to Lyα equivalent width (EW) and various galaxy properties, we study the evolutionary trends among Lyα, low- and high-ionization interstellar (LIS and HIS) absorption features, and integrated galaxy properties. We also examine the redshift evolution of Lyα and LIS absorption kinematics, and fine-structure emission EWs. The connections among the strengths of Lyα, LIS lines, and dust extinction are redshift independent, as is the decoupling of the Lyα and HIS line strengths, and the bulk outflow kinematics as traced by the LIS lines. Stronger Lyα emission is observed at higher redshift at fixed UV luminosity, stellar mass, SFR, and age. Much of this variation in the average Lyα strength with redshift, and the variation in Lyα strength at fixed redshift, can be explained in terms of variations in the neutral gas covering fraction and/or dust content in the ISM and CGM. However, based on the connection between Lyα and C III] emission strengths, we additionally find evidence for variations in the intrinsic production rate of Lyα photons at the highest Lyα EWs. The challenge now is to understand the observed evolution of the neutral gas covering fraction and dust extinction within a coherent model for galaxy formation, and make robust predictions for the escape of ionizing radiation at z > 6.

  16. The effect of micro-environment on luminescence of aequorin: the role of amino acids and explicit water molecules on spectroscopic properties of coelenteramide.

    Science.gov (United States)

    Li, Zuo-Sheng; Zou, Lu-Yi; Min, Chun-Gang; Ren, Ai-Min

    2013-10-05

    Despite the fact that the luminescence reaction mechanism of aequorin has been intensively investigated, details in luminescence such as the effect of important amino acids residues and explicit water molecules on spectroscopic properties of coelenteramide remain unclear. In this work, the effect of amino acids residues His16, Tyr82, Trp86, Phe113, Trp129, Tyr132, explicit water molecules Wat505 and Wat405 on the spectral properties of CLM(-) has been studied by CAM-B3LYP, TD M06L and TD CAM-B3LYP methods in hydrophobic environment and aqueous solution. In hydrophobic environment, the amino acids or water molecules have no significant effect on the absorption. Tyr82 and Trp86 move close to CLM(-) changes the hydrogen bond network, and thus, the spectral properties is significantly affected by the hydrogen bonds between His16H(+)+Tyr82+Trp86 and CLM(-). Tyr82, Trp86 hydrogen bonding to CLM(-) upshifts the excited energy and helps emission spectra shift to blue region. Therefore, it is concluded that His16H(+)+Tyr82+Trp86 modify the emission spectra. The molecular electrostatic potential indicated that the greater electron density is located at the oxygen atom of 6-p-hydroxyphenyl group of CLM(-), and it facilitates the formation of hydrogen bond with His16H(+)+Tyr82+Trp86. It is a critical condition for the modification of emission spectra. It is expected to help to understand the interactions between emitter and amino acids in the micro environment. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Spectroscopic and Electrochemical Properties of Lithium-Rich LiFePO4 Cathode Synthesized by Solid-State Reaction

    Science.gov (United States)

    Rosaiah, P.; Hussain, O. M.; Zhu, Jinghui; Qiu, Yejun

    2017-08-01

    Lithium iron phosphate (Li x FePO4) is synthesized by a solid-state reaction method. The structural, electrical and electrochemical properties are studied in detail. It is found that the increment of lithium concentration (up to x = 1.05) does not affect the structure of LiFePO4 but improves its electrical conductivity as well as electrochemical performance. Surface morphological studies exhibited the formation of rod-like nanoparticles with small size. Electric and dielectric properties are also investigated over a frequency range of 1 Hz-1 MHz at different temperatures. The conductivity increased with increasing temperature, which follows the Arrhenius relation with the activation energy of about 0.31 eV. And the electrochemical tests found that the Li1.05FePO4 cathode possessed improved discharge capacity with better cycling performance.

  18. Utilizing ultrathin DNA/poly-lysine multilayer films to create liquid/liquid interfaces: spectroscopic characterization, interfacial reactions and nanoparticle adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hye Jin; Wark, Alastair W; Corn, Robert M [Department of Chemistry, University of California-Irvine, Irvine, CA 92697 (United States)

    2007-09-19

    Alternating electrostatic multilayer adsorption of poly-L-lysine (pLys) and DNA is used to create well-defined biopolymer multilayers for use as an ultrathin aqueous phase in liquid-liquid interfacial measurements. The molecular structure and thickness of the polyelectrolyte multilayers are determined using a combination of polarization modulation FT-IR reflection-absorption spectroscopy (PM-FTIRRAS) and FT-surface plasmon resonance (FT-SPR) thickness measurements. Electroactive species such as ferri/ferrocyanide ions can be incorporated into the DNA/pLys polyelectrolyte multilayers. The ion transport activity of these electroactive films when in contact with 1,2-dichoroethane is verified by electrochemical measurements. Micron-sized patterns of these multilayers are created by either photopatterning, vapour-deposited spot patterning or microfluidic stencil processing, and are used in conjunction with fluorescence and surface plasmon resonance imaging (SPRI) to monitor (i) the intercalation of dye molecules into DNA/pLys ultrathin films, (ii) the electrostatic adsorption of gold nanoparticles onto DNA/pLys multilayers and (iii) the spatially controlled incorporation and reaction of enzymes into patterned biopolymer multilayers.

  19. Ab initio calculation of the electronic structure and spectroscopic properties of spinel γ-Sn3N4

    International Nuclear Information System (INIS)

    Ching, W. Y.; Rulis, Paul

    2006-01-01

    The electronic structure and physical properties of γ-Sn 3 N 4 in the spinel structure are investigated by first-principles calculations. The calculated band structure, electronic bonding, and optical properties are compared with two well-studied spinel nitrides γ-Si 3 N 4 and γ-Ge 3 N 4 . γ-Sn 3 N 4 is a semiconductor with a direct band gap of 1.40 eV and an attractive small electron effective mass of 0.17. Its optical properties are different from that of γ-Si 3 N 4 and γ-Ge 3 N 4 because of the difference in the conduction band minimum. The Sn K, Sn L 3 , Sn M 5 , and N K edges of the x-ray-absorption near-edge structure spectra in γ-Sn 3 N 4 are calculated using a supercell approach and are found to be rich in structures. These spectra are discussed in the context of the electronic structure of the unoccupied conduction band in the presence of the electron core-hole interaction. These calculated spectra can be used for the characterization of this novel compound

  20. Correlation of surface contour, optoelectronic and spectroscopic properties of Cu(In,Ga)Se{sub 2} by SNOM and AFM

    Energy Technology Data Exchange (ETDEWEB)

    Neumann, Oliver; Heise, Stephan J.; Brueggemann, Rudolf; Meessen, Max; Bauer, Gottfried H. [Institute of Physics, Carl von Ossietzky University Oldenburg (Germany); Witte, Wolfram; Hariskos, Dimitrios [Zentrum fuer Sonnenenergie- und Wasserstoff-Forschung Baden-Wuerttemberg (ZSW), Stuttgart (Germany)

    2012-07-01

    Chalcopyrite absorbers exhibit local fluctuations of structural, optical and optoelectronic properties. We study the correlation of the surface contour and the local properties such as the integrated photoluminescence (PL) yield and the splitting of the quasi-Fermi levels in a Cu(In,Ga)Se{sub 2}-based thin-film system at room temperature by AFM and spatially resolved PL measurements at the identical position with a scanning near-field optical microscope (SNOM). The Cu(In,Ga)Se{sub 2} layer is deposited on glass, etched with bromine-methanol to smooth the surface for a more homogeneous incoupling of laser light, and passivated with cadmium sulfide. Our measurements reveal a high structural correlation between surface contour, integrated PL yield and quasi-Fermi level splitting. Additionally, we observe trenches in the surface contour which correspond to a dip or to a peak in the splitting of the quasi-Fermi levels and integrated PL yield. Furthermore some trenches show spectral variation of the PL compared to their direct environment. We discuss these observations with respect to the optoelectronic property and the composition of the absorber.

  1. Novel vanillin derivatives: Synthesis, anti-oxidant, DNA and cellular protection properties.

    Science.gov (United States)

    Scipioni, Matteo; Kay, Graeme; Megson, Ian; Kong Thoo Lin, Paul

    2018-01-01

    Antioxidants have been the subject of intense research interest mainly due to their beneficial properties associated with human health and wellbeing. Phenolic molecules, such as naturally occurring Resveratrol and Vanillin, are well known for their anti-oxidant properties, providing a starting point for the development of new antioxidants. Here we report, for the first time, the synthesis of a number of new vanillin through the reductive amination reaction between vanillin and a selection of amines. All the compounds synthesised, exhibited strong antioxidant properties in DPPH, FRAP and ORAC assays, with compounds 1b and 2c being the most active. The latter also demonstrated the ability to protect plasmid DNA from oxidative damage in the presence of the radical initiator AAPH. At cellular level, neuroblastoma SH-SY5Y cells were protected from oxidative damage (H 2 O 2 , 400 μM) with both 1b and 2c. The presence of a tertiary amino group, along with the number of vanillin moieties in the molecule contribute for the antioxidant activity. Furthermore, the delocalization of the electron pair of the nitrogen and the presence of an electron donating substituent to enhance the antioxidant properties of this new class of compounds. In our opinion, vanillin derivatives 1b and 2c described in this work can provide a viable platform for the development of antioxidant based therapeutics. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  2. Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

    Science.gov (United States)

    Denning, Elizabeth J; Mackerell, Alexander D

    2011-04-20

    Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geometric and conformational properties. Based on these results, it is suggested that the As-DNA will have similar conformational properties to phosphorus-based DNA, including the maintenance of base stacking.

  3. Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking

    Science.gov (United States)

    Karami, Kazem; Rafiee, Mina; Lighvan, Zohreh Mehri; Zakariazadeh, Mostafa; Faal, Ali Yeganeh; Esmaeili, Seyed-Alireza; Momtazi-Borojeni, Amir Abbas

    2018-02-01

    [Pd{(C,N)sbnd C6H4CH (CH3)NH}(CUR)] (3) and [Pd2{(C,N)sbnd C6H4CH(CH3)NH2}2(μ-N3CS2)] (4) [cur = 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dion] novel organometallic complexes with biologically active ligands have been prepared and characterized via elemental analysis, multinuclear spectroscopic techniques (1H, and 13C NMR and IR) and their biological activities, including antitumoral activity and DNA-protein interactions have been investigated. Fluorescence spectroscopy used to study the interaction of the complexes with BSA have shown the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary structure of BSA in the presence of the complexes. In the meantime, spectroscopy and competitive titration have been applied to investigate the interaction of complexes with Warfarin and Ibuprofen site markers for sites I and II, respectively, with BSA. The results have suggested that the locations of complexes 3 and 4 are sites II and I, respectively. UV-Vis spectroscopy, emission titration and helix melting methods have been used to study the interaction of these complexes with CT-DNA, indicating that complexes are bound to CT-DNA by intercalation binding mode. In addition, good cytotoxic activity against MCF-7 (human breast cancer) and JURKAT (human leukemia) cell line has been shown by both complexes whereas low cytotoxicity was exerted on normal peripheral blood mononuclear cells.

  4. Growth and spectroscopic properties of Yb{sup 3+}-doped Li{sub 6}Y(BO{sub 3}){sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Brenier, A. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France)]. E-mail: brenier@pcml.univ-lyon1.fr; Yoshikawa, A. [Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Lebbou, K. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Jouini, A. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Aloui-Lebbou, O. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Boulon, G. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Fukuda, T. [Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan)

    2007-10-15

    The spectroscopic properties of high-quality Czochralski grown 20% Yb{sup 3+}-doped Li{sub 6}Y(BO{sub 3}){sub 3} single crystal as new promising laser material are presented. The crystal was seeded-grown in the <0 1 0> direction and its crystallinity was measured using X-ray rocking curve analysis. Low temperature transmission spectrum exhibits broad bands in a short range of wavelengths and two sharp lines at 972.5 and 978 nm, interpreted as two zero-lines of two nonequivalent Yb{sup 3+} centers inside the lattice. The fluorescence lifetimes associated to these two intense lines are different: 0.867 and 1.33 ms. An attempt of determination of the Stark sublevels energies of the {sup 4}F{sub 5/2} and {sup 4}F{sub 7/2} manifolds of the two Yb{sup 3+} nonequivalent ions is given. The polarized absorption and emission spectra were also recorded at room temperature and we conclude that the most favorable emission line for laser application could be around 1042 nm in n {sub g} polarization.

  5. Physicochemical and spectroscopic properties of natural organic matter (NOM) from various sources and implications for ameliorative effects on metal toxicity to aquatic biota

    Energy Technology Data Exchange (ETDEWEB)

    Al-Reasi, Hassan A.; Wood, Chris M. [Department of Biology, McMaster University, Hamilton, ON, L8S 4K1 (Canada); Smith, D. Scott, E-mail: ssmith@wlu.camailto [Department of Chemistry, Wilfrid Laurier University, Waterloo, ON, N2L 3C5 (Canada)

    2011-06-15

    Natural organic matter (NOM), expressed as dissolved organic carbon (DOC in mg C L{sup -1}), is an ubiquitous complexing agent in natural waters, and is now recognized as an important factor mitigating waterborne metal toxicity. However, the magnitude of the protective effect, judged by toxicity measures (e.g. LC50), varies substantially among different NOM sources even for similar DOC concentrations, implying a potential role of NOM physicochemical properties or quality of NOM. This review summarizes some key quality parameters for NOM samples, obtained by reverse osmosis, and by using correlation analyses, investigates their contribution to ameliorating metal toxicity towards aquatic biota. At comparable and environmentally realistic DOC levels, molecular spectroscopic characteristics (specific absorbance coefficient, SAC, and fluorescence index, FI) as well as concentrations of fluorescent fractions obtained from mathematical mixture resolution techniques (PARAFAC), explain considerable variability in the protective effects. NOM quality clearly influences the toxicity of copper (Cu) and lead (Pb). NOM quality may also influence the toxicity of silver (Ag), cadmium (Cd) and inorganic mercury (Hg), but as yet insufficient data are available to unequivocally support the latter correlations between toxicity reduction and NOM quality predictors. Cu binding capacities, protein-to-carbohydrate ratio, and lipophilicity, show insignificant correlation to the amelioration offered by NOMs, but these conclusions are based on data for Norwegian NOMs with very narrow ranges for the latter two parameters. Certainly, various NOMs alleviate metal toxicity differentially and therefore their quality measures should be considered in addition to their quantity.

  6. Redox properties of structural Fe in clay minerals. 2. Electrochemical and spectroscopic characterization of electron transfer irreversibility in ferruginous smectite, SWa-1.

    Science.gov (United States)

    Gorski, Christopher A; Klüpfel, Laura; Voegelin, Andreas; Sander, Michael; Hofstetter, Thomas B

    2012-09-04

    Structural Fe in clay minerals is an important, albeit poorly characterized, redox-active phase found in many natural and engineered environments. This work develops an experimental approach to directly assess the redox properties of a natural Fe-bearing smectite (ferruginous smectite, SWa-1, 12.6 wt % Fe) with mediated electrochemical reduction (MER) and oxidation (MEO). By utilizing a suite of one-electron-transfer mediating compounds to facilitate electron transfer between structural Fe in SWa-1 and a working electrode, we show that the Fe2+/Fe3+ couple in SWa-1 is redox-active over a large range of potentials (from E(H) = -0.63 V to +0.61 V vs SHE). Electrochemical and spectroscopic analyses of SWa-1 samples that were subject to reduction and re-oxidation cycling revealed both reversible and irreversible structural Fe rearrangements that altered the observed apparent standard reduction potential (E(H)(ø)) of structural Fe. E(H)(ø)-values vary by as much as 0.56 V between SWa-1 samples with different redox histories. The wide range of E(H)-values over which SWa-1 is redox-active and redox history-dependent E(H)(ø)-values underscore the importance of Fe-bearing clay minerals as redox-active phases in a wide range of redox regimes.

  7. A Comparison of Modifications Induced by Li3+ and Ag14+ Ion Beam in Spectroscopic Properties of Bismuth Alumino-Borosilicate Glass Thin Films

    Directory of Open Access Journals (Sweden)

    Ravneet Kaur

    2013-01-01

    Full Text Available Ion irradiation effects on the glass network and structural units have been studied by irradiating borosilicate glass thin film samples with 50 MeV Li3+ and 180 MeV Ag14+ swift heavy ions (SHI at different fluence rates ranging from 1012 ions/cm2 to 1014 ions/cm2. Glass of the composition (65-x Bi2O3-10Al2O3-(65-y B2O3-25SiO2 (x = 45, 40; y = 20, 25 has been prepared by melt quench technique. To study the effects of ionizing radiation, the glass thin films have been prepared from these glasses and characterized using XRD, FTIR, and UV-Vis spectroscopic techniques. IR spectra are used to study the structural arrangements in the glass before and after irradiation. The values of optical band gap, Urbach energy, and refractive index have been calculated from the UV-Vis measurements. The variation in optical parameters with increasing Bi2O3 content has been analyzed and discussed in terms of changes occurring in the glass network. A comparative study of the influence of Li3+ ion beam on structural and optical properties of the either glass system with Ag14+ ion is done. The results have been explained in the light of the interaction that SHI undergo on entering the material.

  8. Spectroscopic properties of the 1.4 microm emission of Tm3+ ions in TeO2-WO3-PbO glasses.

    Science.gov (United States)

    Balda, R; Lacha, L M; Fernández, J; Arriandiaga, M A; Fernández-Navarro, J M; Muñoz-Martin, D

    2008-08-04

    In this work, we report the spectroscopic properties of the infrared 3H4-->3F4 emission of Tm3+ ions in two different compositions of glasses based on TeO2, WO3, and PbO for three Tm2O3 concentrations (0.1,0.5, and 1 wt%). Judd-Ofelt intensity parameters have been determined and used to calculate the radiative transition probabilities and radiative lifetimes. The infrared emission at around 1490 nm corresponding to the 3H4-->F4 transition has two noticeable features if compared to fluoride glasses used for S-band amplifiers. On one hand, it is broader by nearly 30 nm, and on the other, the stimulated emission cross section is twice the value for fluoride glasses. Both the relative intensity ratio of the 1490 nm emission to 1820 nm and the measured lifetime of the 3H4 level decrease as concentration increases, due to the existence of energy transfer via cross-relaxation among Tm3+ ions. The analysis of the decays from the 3H4 level with increasing concentration indicates the presence of a dipole-dipole quenching process assisted by energy migration.

  9. The influence of TeO2 on thermal stability and 1.53 μm spectroscopic properties in Er(3+) doped oxyfluorite glasses.

    Science.gov (United States)

    Wang, Fengchao; Cai, Muzhi; Chen, Rong; Jing, Xufeng; Li, Bingpeng; Tian, Ying; Zhang, Junjie; Xu, Shiqing

    2015-11-05

    In this work, the thermal and spectroscopic properties of Er(3+)-doped oxyfluorite glass based on AMCSBYT (AlF3-MgF2-CaF2-SrF2-BaF2-YF3-TeO2) system for different TeO2 concentrations from 6 to 21 mol% is reported. After adding a suitable content of TeO2, the thermal ability of glass improves significantly whose ΔT and S can reach to 118 °C and 4.47, respectively. The stimulated emission cross-section reaches to 7.80×10(-21) cm(2) and the fluorescence lifetime is 12.18 ms. At the same time, the bandwidth characteristics reach to 46.41×10(-21) cm(2) nm and the gain performance is 63.73×10(-21) cm(2) ms. These results show that the optical performances of this oxyfluorite glass are very well. Hence, AMCSBYT glass with superior performances might be a useful material for applications in optical amplifier around 1.53 μm. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Spectroscopic properties and energy transfer analysis of Tm3+-doped BaF2-Ga2O3-GeO2-La2O3 glass.

    Science.gov (United States)

    Yu, Shenglei; Yang, Zhongmin; Xu, Shanhui

    2010-05-01

    This paper reports on the spectroscopic properties and energy transfer analysis of Tm(3+)-doped BaF(2)-Ga(2)O(3)-GeO(2)-La(2)O(3) glasses with different Tm(2)O(3) doping concentrations (0.2, 0.5, 2.0, 2.5, 3.0, 3.5, 3.5, 4.0 wt%). Mid-IR fluorescence intensities in the range of 1,300 nm-2,200 nm have been measured when excited under an 808 nm LD for all the samples with the same pump power. Energy level structure and Judd-Ofelt parameters have been calculated based on the absorption spectra of Tm(3+), cross-relaxation rates and multi-phonon relaxation rates have been estimated with different Tm(2)O(3) doping concentrations. The maximum fluorescence intensity at around 1.8 mum has been obtained in Tm(2)O(3)-3 wt% sample and the maximum value of calculated stimulated emission cross-section of Tm(3+) in this sample is about 0.48 x 10(-20) cm(2) at 1,793 nm, and there is not any crystallization peak in the DSC curve of this sample, which indicate the potential utility of Tm(3+)-doped BaF(2)-Ga(2)O(3)-GeO(2)- La(2)O(3) glass for 2.0-microm optical fiber laser.

  11. The influence of the Cys46/Cys55 disulfide bond on the redox and spectroscopic properties of human neuroglobin.

    Science.gov (United States)

    Bellei, Marzia; Bortolotti, Carlo Augusto; Di Rocco, Giulia; Borsari, Marco; Lancellotti, Lidia; Ranieri, Antonio; Sola, Marco; Battistuzzi, Gianantonio

    2018-01-01

    Neuroglobin is a monomeric globin containing a six-coordinate heme b, expressed in the nervous system, which exerts an important neuroprotective role. In the human protein (hNgb), Cys46 and Cys55 form an intramolecular disulfide bond under oxidizing conditions, whose cleavage induces a helix-to-strand rearrangement of the CD loop that strengthens the bond between the heme iron and the distal histidine. Hence, it is conceivable that the intramolecular disulfide bridge modulates the functionality of human neuroglobin by controlling exogenous ligand binding. In this work, we investigated the influence of the Cys46/Cys55 disulfide bond on the redox properties and on the pH-dependent conformational equilibria of hNgb, using UV-vis spectroelectrochemistry, cyclic voltammetry, electronic absorption spectroscopy and magnetic circular dichroism (MCD). We found that the SS bridge significantly affects the heme Fe(III) to Fe(II) reduction enthalpy (ΔH°' rc ) and entropy (ΔS°' rc ), mostly as a consequence of changes in the reduction-induced solvent reorganization effects, without affecting the axial ligand-binding interactions and the polarity and electrostatics of the heme environment. Between pH3 and 12, the electronic properties of the heme of ferric hNgb are sensitive to five acid-base equilibria, which are scarcely affected by the Cys46/Cys55 disulfide bridge. The equilibria occurring at extreme pH values induce heme release, while those occurring between pH5 and 10 alter the electronic properties of the heme without modifying its axial coordination and low spin state. They involve the sidechains of non-coordinating aminoacids close to the heme and at least one heme propionate. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Spectroscopic Properties of Star-Forming Host Galaxies and Type Ia Supernova Hubble Residuals in a Nearly Unbiased Sample

    Energy Technology Data Exchange (ETDEWEB)

    D' Andrea, Chris B. [Univ. of Pennsylvania, Philadelphia, PA (United States); et al.

    2011-12-20

    We examine the correlation between supernova host galaxy properties and their residuals on the Hubble diagram. We use supernovae discovered during the Sloan Digital Sky Survey II - Supernova Survey, and focus on objects at a redshift of z < 0.15, where the selection effects of the survey are known to yield a complete Type Ia supernova sample. To minimize the bias in our analysis with respect to measured host-galaxy properties, spectra were obtained for nearly all hosts, spanning a range in magnitude of -23 < M_r < -17. In contrast to previous works that use photometric estimates of host mass as a proxy for global metallicity, we analyze host-galaxy spectra to obtain gas-phase metallicities and star-formation rates from host galaxies with active star formation. From a final sample of ~ 40 emission-line galaxies, we find that light-curve corrected Type Ia supernovae are ~ 0.1 magnitudes brighter in high-metallicity hosts than in low-metallicity hosts. We also find a significant (> 3{\\sigma}) correlation between the Hubble residuals of Type Ia supernovae and the specific star-formation rate of the host galaxy. We comment on the importance of supernova/host-galaxy correlations as a source of systematic bias in future deep supernova surveys.

  13. Spectroscopic and structural properties of polycrystalline Y{sub 2}Si{sub 2}O{sub 7} doped with Er{sup 3+}

    Energy Technology Data Exchange (ETDEWEB)

    Marciniak, L., E-mail: L.Marciniak@int.pan.wroc.pl [Institute for Low Temperature and Structure Research, Polish Academy of Sciences, Wroclaw (Poland); Hreniak, D.; Strek, W. [Institute for Low Temperature and Structure Research, Polish Academy of Sciences, Wroclaw (Poland); Piccinelli, F., E-mail: fabio.piccinelli@univr.it [Laboratorio di Chimica dello Stato Solido, DB, Università di Verona and INSTM, UdR Verona, Strada Le Grazie 15, 37134 Verona (Italy); Speghini, A.; Bettinelli, M. [Laboratorio di Chimica dello Stato Solido, DB, Università di Verona and INSTM, UdR Verona, Strada Le Grazie 15, 37134 Verona (Italy); Miritello, M., E-mail: maria.miritello@ct.infn.it [CNR-IMM MATIS and Dipartimento di Fisica e Astronomia, Università di Catania, Via S. Sofia 64, 95123 Catania (Italy); Lo Savio, R.; Cardile, P.; Priolo, F. [CNR-IMM MATIS and Dipartimento di Fisica e Astronomia, Università di Catania, Via S. Sofia 64, 95123 Catania (Italy)

    2016-02-15

    Powders of yttrium disilicate (Y{sub 2}Si{sub 2}O{sub 7}) doped with Er{sup 3+} have been prepared by the sol–gel method. The structure of the obtained powders has been determined. Room temperature emission spectra have been recorded and excited state decay profiles have been analyzed. Differences between the spectroscopic properties of Er{sup 3+} in monoclinic α-Y{sub 2}Si{sub 2}O{sub 7} (space group P-1) and β-Y{sub 2}Si{sub 2}O{sub 7} (space group C2/m) polymorphs have been investigated and shown. The significant broadening of the emission spectra recorded for the α phase compared to the one for the β phase was discussed in terms of higher number of Y{sup 3+} sites (4) present in the α phase with respect to only one Y{sup 3+} site in the case of β phase. The higher value of the luminescence decay time of β phase (11.2 ms) compared to the α phase (8.5 ms) is associated with the higher site symmetry of β-Y{sub 2}Si{sub 2}O{sub 7}. Moreover it was found that Er{sup 3+} concentration affects the shape of the {sup 4}I{sub 13/2}→{sup 4}I{sub 15/2} emission band. It results in changes of the relative emission intensities of peaks localized at 1527 nm and 1532 nm; this indicates changes of the Y{sup 3+} sites occupation on increasing the Er{sup 3+} concentration. The luminescence lifetime was observed to decrease with the increase of Er{sup 3+} concentration. The spectroscopic results have been compared with the ones relative to thin films of Y{sub 2}Si{sub 2}O{sub 7}:Er{sup 3+} with a similar composition. The lower value of the luminescence decay time observed for thin films compared to the powder of α phase was explained with the changes of the particles packing resulting in the change of the effective refractive index.

  14. SPECTROSCOPIC STUDY OF EFFECTS OF TETRAALKYLAMMONIUM CATIONS ON F--SENSING PROPERTIES OF CALIX[4]PYRROLE BORADIAZAINDACENE DYE

    Directory of Open Access Journals (Sweden)

    Yongjun Lv

    Full Text Available A novel meso-tetracyclohexylcalix[4]pyrrole-based boradiazaindacene dye 3 was synthesized and characterized. F--binding properties of the dye in the presence of tetrabutylammonium (TBA+, tetraethylammonium (TEA+, and tetramethylammonium (TMA+ counter ions were investigated by UV-Vis, fluorescence, and NMR spectroscopies. Dye 3 displayed various degrees of absorption red shift, fluorescence quenching, and downfield shifts of NH signals for the three fluoride salts. The association constants of these salts mainly depend on cation size effects and ion-pairing effects and were in the order KTMA+ > KTEA+ > KTBA+. Thus, we speculate that both F- and tetraalkylammonium cations are concomitantly located above and below a bowl-shaped calix[4]pyrrole cup in an ion-paired complex, respectively.

  15. Investigation of PA-CVD of TiN: relations between process parameters, spectroscopic measurements and layer properties

    International Nuclear Information System (INIS)

    Rie, K.T.; Gebauer, A.; Woehle, J.

    1993-01-01

    The plasma-assisted chemical vapour deposition of TiN layers on steel substrates was investigated for various process parameters in this work. Optical emission spectroscopy (OES) was used to identify the species in the electrical discharge during the deposition process. The layer properties of the deposited TiN layers were determined by various methods (scanning electron microscopy, energy- and wavelength-dispersive X-ray analysis). The deposited layers have a constant amount of titanium, while the contents of nitrogen and chlorine show a contrary behaviour for different deposition parameters. The hardness of the layers is related among other things to the chlorine content. The OES investigations show that the Ti + and N 2 + emission is related to the layer growth rate. The formation of TiN in a gas phase reaction degrades the quality of the layers, such as their hardness. (orig.)

  16. Properties of an endonuclease activity in Micrococcus luteus acting on γ-irradiated DNA and on apurinic DNA

    International Nuclear Information System (INIS)

    Schaefer, G.; Haas, P.; Coquerelle, Th.; Hagen, U.

    1980-01-01

    A protein fraction from Micrococcus luteus with endonuclease activity against γ-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against γ-irradiated DNA was stimulated five-fold with 5 mM Mg ++ , whereas that against apurinic sites was less dependent on the Mg ++ concentration. 100 mM KCl inhibited the γ-ray endonuclease, but not the apurinic endonuclease activity. In γ-irradiated DNA the protein recognized 1.65 endonuclease sensitive sites per radiation-induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The was evaluated resulting in a Ksub(m)-value of 73 nM. (author)

  17. Properties of an endonuclease activity in Micrococcus luteus acting on. gamma. -irradiated DNA and on apurinic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, G; Haas, P; Coquerelle, Th; Hagen, U [Kernforschungszentrum Karlsruhe G.m.b.H. (Germany, F.R.). Inst. fuer Genetik und fuer Toxikologie von Spaltstoffen

    1980-01-01

    A protein fraction from Micrococcus luteus with endonuclease activity against ..gamma..-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against ..gamma..-irradiated DNA was stimulated five-fold with 5 mM Mg/sup + +/, whereas that against apurinic sites was less dependent on the Mg/sup + +/ concentration. 100 mM KCl inhibited the ..gamma..-ray endonuclease, but not the apurinic endonuclease activity. In ..gamma..-irradiated DNA the protein recognized 1.65 endonuclease sensitive sites per radiation-induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The was evaluated resulting in a Ksub(m)-value of 73 nM.

  18. In-depth investigation on physicochemical and thermal properties of magnesium (II gluconate using spectroscopic and thermoanalytical techniques

    Directory of Open Access Journals (Sweden)

    Mahendra Kumar Trivedi

    2017-10-01

    Full Text Available Magnesium gluconate is a classical organometallic pharmaceutical compound used for the prevention and treatment of hypomagnesemia as a source of magnesium ion. The present research described the in-depth study on solid state properties viz. physicochemical and thermal properties of magnesium gluconate using sophisticated analytical techniques like PXRD, PSA, FT-IR, UV–Vis spectroscopy, TGA/DTG, and DSC. Magnesium gluconate was found to be crystalline in nature along with the crystallite size ranging from 14.10 to 47.35 nm. The particle size distribution was at d(0.1=6.552 µm, d(0.5=38.299 µm, d(0.9=173.712 µm and D(4,3=67.122 µm along with the specific surface area of 0.372 m2/g. The wavelength for the maximum absorbance was at 198.0 nm. Magnesium gluconate exhibited 88.51% weight loss with three stages of thermal degradation process up to 895.18 °C from room temperature. The TGA/DTG thermograms of the analyte indicated that magnesium gluconate was thermally stable up to around 165 °C. Consequently, the melting temperature of magnesium gluconate was found to be 169.90 °C along with the enthalpy of fusion of 308.7 J/g. Thus, the authors conclude that the achieved results from this study are very useful in pharmaceutical and nutraceutical industries for the identification, characterization and qualitative analysis of magnesium gluconate for preformulation studies and also for developing magnesium gluconate based novel formulation.

  19. Influence of cobalt ions on spectroscopic and dielectric properties of Sb2O3 doped lithium fluoroborophosphate glasses

    Science.gov (United States)

    Kumar, G. Ravi; Srikumar, T.; Rao, M. C.; Venkat Reddy, P.; Srinivasa Rao, Ch

    2018-03-01

    Glasses with compositions (20–x) LiF–10 Sb2O3–10 B2O3–60 P2O5: x CoO (0 disorder in the glass network with increasing concentration of CoO up to 0.15 mol%. The reversal trend has been observed beyond 0.15 mol% suggesting an increasing polymerization of glass network. The optical properties of LiF–Sb2O3–B2O3–P2O5: CoO glasses were analyzed by optical absorption and photoluminescence studies. The observations from OA and PL spectral studies suggested that the gradual increase of octahedral Co2+ ions with the increase in the concentration of CoO up to 0.15 mol%. At higher concentration i.e. above 0.15 mol% of CoO, there was a reduction in the concentration of octahedral Co2+ ions. The electrical properties of the glass samples were studied by both DC and AC conductivity studies. The dielectric dispersion analysis was also performed on the prepared glass samples. The results of these studies indicated that there is a mixed conduction (both ionic and polaronic) and the polaron hoping seems to prevail over ionic conduction in the glasses containing CoO less than 0.15 mol%. The increasing space charge polarization is responsible for enhanced values of dielectric constant, dielectric loss and AC conductivity for all frequency and temperature ranges with the increase in concentration of CoO up to 0.15 mol%.

  20. Spectroscopic properties of Eu{sup 3+}:KLa(WO{sub 4}){sub 2} novel red phosphors

    Energy Technology Data Exchange (ETDEWEB)

    Rasu, K. Kavi; Balaji, D.; Babu, S. Moorthy, E-mail: babusm@yahoo.com

    2016-02-15

    Eu{sup 3+}:KLa(WO{sub 4}){sub 2} (Eu:KLW) phosphors were prepared through Pechini type sol–gel method. Low temperature synthesis was achieved through polyesterification between citric acid and ethylene glycol during the growth procedure. The properties of phosphors were analysed using X-ray diffractogram (XRD), scanning electron microscopy (SEM), Raman and luminescence spectroscopy. An effective energy transfer from the tungstate matrix to the activator Eu{sup 3+} was observed. Intense red emission in Eu:KLW phosphors was observed while excited with f–f transitions of Eu{sup 3+}. The Judd–Ofelt (J–O) intensity parameters Ω{sub 2} and Ω{sub 4} were obtained from the emission intensities of {sup 5}D{sub 0}→{sup 7}F{sub 2},{sub 4,} respectively by taking the magnetic dipole {sup 5}D{sub 0}→{sup 7}F{sub 1} emission band intensity as reference. The CIE colour co-ordinates of the Eu:KLW red phosphors was calculated (x=0.650, y=0.348), which are close to NTSC standard values. - Highlights: • Eu:KLW phosphors were synthesized by pechini type sol–gel method. • Structural, morphological, vibrational and luminescence properties were well investigation. • Eu{sup 3+}:KLa(WO{sub 4}){sub 2} phosphors has strong red emission at about 615 nm ({sup 5}D{sub 0}→{sup 7}F{sub 2}) under the excitation of near UV and blue LEDs regions. • Decay measurement and Judd–Ofelt parameter were calculated and dicussed. • These phosphors can serve as a potential candidate for red source for White LEDs application.

  1. A far ultraviolet spectroscopic study of the reflectance, luminescence and electronic properties of SrMgF4 single crystals

    International Nuclear Information System (INIS)

    Ogorodnikov, I.N.; Pustovarov, V.A.; Omelkov, S.I.; Isaenko, L.I.; Yelisseyev, A.P.; Goloshumova, A.A.; Lobanov, S.I.

    2014-01-01

    The electronic properties of single crystals of SrMgF 4 have been determined using low-temperature (10–293 K) time-resolved vacuum ultraviolet synchrotron radiation spectroscopy, far ultraviolet (3.7–36 eV) reflectance spectra and calculations for the spectra of optical functions. The bandgap of investigated compound was found at E g =12.55eV, the energy threshold for creation of the unrelaxed excitons at E n=1 =11.37eV, and the low-energy fundamental absorption edge at 10.3 eV. Two groups of photoluminescence (PL) bands have been identified: the exciton-type emissions at 2.6–3.3 and 3.3–4.2 eV and defect-related emissions at 1.8–2.6 and 4.2–5.5 eV. It was shown that PL excitation (PLE) for the exciton-type emission bands occurs mainly at the low-energy tail of the fundamental absorption of the crystal with a maximum at 10.7 eV. At excitation energies above E g the energy transfer from the host lattice to the PL emission centers is inefficient. The paper discusses the origin of the excitonic-type PLE spectra taking into account the results of modeling the PLE spectra shape in the framework of a simple diffusion theory and surface energy losses. -- Highlights: • Far-ultraviolet reflection spectra of SrMgF 4 were studied. • Photoluminescence (PL) emission and PL excitation spectra were studied. • Optical function spectra were calculated on the basis of experimental data. • Electronic structure properties of undoped SrMgF 4 crystals were determined

  2. #%In-depth investigation on physicochemical and thermal properties of magnesium (II) gluconate using spectroscopic and thermoanalytical techniques

    Institute of Scientific and Technical Information of China (English)

    #

    2017-01-01

    Magnesium gluconate is a classical organometallic pharmaceutical compound used for the prevention and treatment of hypomagnesemia as a source of magnesium ion. The present research described the in-depth study on solid state properties viz. physicochemical and thermal properties of magnesium gluconate using sophisticated analytical techniques like Powder X-ray diffraction (PXRD), particle size analysis ( PSA), Fourier transform infrared (FT-IR) spectrometry, ultraviolet–visible (UV–Vis) spectroscopy, thermogravimetric analysis (TGA)/differential thermogravimetric analysis (DTG), and differential scanning calorimetry (DSC). Magnesium gluconate was found to be crystalline in nature along with the crystallite size ranging from 14.10 to 47.35 nm. The particle size distribution was at d(0.1)=6.552 μm, d(0.5)=38.299 μm, d(0.9)=173.712 μm and D(4,3)=67.122 μm along with the specific surface area of 0.372 m2/g. The wavelength for the maximum absorbance was at 198.0 nm. Magnesium gluconate exhibited 88.51% weight loss with three stages of thermal degradation process up to 895.18 ℃ from room temperature. The TGA/DTG thermograms of the analyte indicated that magnesium gluconate was thermally stable up to around 165 ℃. Consequently, the melting temperature of magnesium gluconate was found to be 169.90 ℃ along with the enthalpy of fusion of 308.7 J/g. Thus, the authors conclude that the achieved results from this study are very useful in pharmaceutical and nutraceutical industries for the identification, characterization and qualitative analysis of magnesium gluconate for preformulation studies and also for developing magnesium gluconate based novel formulation.

  3. DNA-mediated gene transfer into human diploid fibroblasts derived from normal and ataxia-telangiectasia donors: parameters for DNA transfer and properties of DNA transformants

    International Nuclear Information System (INIS)

    Debenham, P.G.; Webb, M.B.T.; Masson, W.K.; Cox, R.

    1984-01-01

    An investigation was made of the feasibility of DNA-mediated gene transfer into human diploid fibroblasts derived from patients with the radiation sensitive syndrome ataxia-telangiectasia (A-T) and from a normal donor. Although they are markedly different in their growth characteristics, both normal and A-T strains give similar frequencies for DNA transfer in a model system using the recombinant plasmid pSV2-gpt. pSV2-gpt DNA transformants arise with a frequency between 10 -5 and 10 -4 per viable cell. Analysis of such transformants, although possible, is severely handicapped by the limited clonal life span of diploid human cells. Despite these problems it may be concluded that diploid human fibroblasts are competent recipients for DNA-mediated gene transfer and the putative repair deficiency of A-T does not markedly effect the efficiency of this process. (author)

  4. Antioxidant and cyto/DNA protective properties of apple pomace enriched bakery products.

    Science.gov (United States)

    Sudha, M L; Dharmesh, Shylaja M; Pynam, Hasitha; Bhimangouder, Shivaleela V; Eipson, Sushma W; Somasundaram, Rajarathnam; Nanjarajurs, Shashirekha M

    2016-04-01

    Apple pomace (AP), the residue that remains after the extraction of juice from apple accounts for ~25 % of total apple weight. Current study is aimed at identification of phytochemicals and utilization of Dehydrated apple pomace (DAP) in the preparation of bakery products with potential health benefits. DAP was prepared by drying the pomace obtained by crushing peeled apple fruits. DAP was incorporated into bakery products such as bun, muffin and cookies for value addition. Bioactivity such as free radical scavenging, cyto/DNA protectivity was evaluated in these products. DAP contained 17 g/100 g starch, 49.86 g/100 g fructose and 37 g/100 g dietary fibre. The phenolics and flavonoids content was 1.5 mg/g and 3.92 mg/g, respectively. Increase in DAP resulted in decreased volume and enhanced firmness of buns and muffins. DAP at 15 % in buns, 30 % in muffins and 20 % in cookies were found to be acceptable. DAP blended products exhibited better free radical scavenging as well as cyto/DNA protective properties suggesting the retention of bioactivity after baking. Addition of DAP potentially enhanced the bioactivity of the products evaluated.

  5. 1-Amino-4-hydroxy-9,10-anthraquinone - An analogue of anthracycline anticancer drugs, interacts with DNA and induces apoptosis in human MDA-MB-231 breast adinocarcinoma cells: Evaluation of structure-activity relationship using computational, spectroscopic and biochemical studies.

    Science.gov (United States)

    Mondal, Palash; Roy, Sanjay; Loganathan, Gayathri; Mandal, Bitapi; Dharumadurai, Dhanasekaran; Akbarsha, Mohammad A; Sengupta, Partha Sarathi; Chattopadhyay, Shouvik; Guin, Partha Sarathi

    2015-12-01

    The X-ray diffraction and spectroscopic properties of 1-amino-4-hydroxy-9,10-anthraquinone (1-AHAQ), a simple analogue of anthracycline chemotherapeutic drugs were studied by adopting experimental and computational methods. The optimized geometrical parameters obtained from computational methods were compared with the results of X-ray diffraction analysis and the two were found to be in reasonably good agreement. X-ray diffraction study, Density Functional Theory (DFT) and natural bond orbital (NBO) analysis indicated two types of hydrogen bonds in the molecule. The IR spectra of 1-AHAQ were studied by Vibrational Energy Distribution Analysis (VEDA) using potential energy distribution (PED) analysis. The electronic spectra were studied by TDDFT computation and compared with the experimental results. Experimental and theoretical results corroborated each other to a fair extent. To understand the biological efficacy of 1-AHAQ, it was allowed to interact with calf thymus DNA and human breast adino-carcinoma cell MDA-MB-231. It was found that the molecule induces apoptosis in this adinocarcinoma cell, with little, if any, cytotoxic effect in HBL-100 normal breast epithelial cell.

  6. Vanillin and isovanillin: Comparative vibrational spectroscopic studies, conformational stability and NLO properties by density functional theory calculations

    Science.gov (United States)

    Balachandran, V.; Parimala, K.

    This study is a comparative analysis of FT-IR and FT-Raman spectra of vanillin (3-methoxy-4-hydroxybenzaldehyde) and isovanillin (3-hydroxy-4-methoxybenzaldehyde). The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for both molecules using the B3LYP density functional theory (DFT) with the standard 6-311++G∗∗ basis set. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. The calculated harmonic vibrational frequencies are compared with experimental FT-IR and FT-Raman spectra. The geometrical parameters and total energies of vanillin and isovanillin were obtained for all the eight conformers (a-h) from DFT/B3LYP method with 6-311++G∗∗ basis set. The computational results identified the most stable conformer of vanillin and isovanillin as in the "a" form. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecules have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.

  7. STAR FORMATION PROPERTIES IN BARRED GALAXIES (SFB). I. ULTRAVIOLET TO INFRARED IMAGING AND SPECTROSCOPIC STUDIES OF NGC 7479

    International Nuclear Information System (INIS)

    Zhou Zhimin; Meng Xianmin; Wu Hong; Cao Chen

    2011-01-01

    Large-scale bars and minor mergers are important drivers for the secular evolution of galaxies. Based on ground-based optical images and spectra as well as ultraviolet data from the Galaxy Evolution Explorer and infrared data from the Spitzer Space Telescope, we present a multi-wavelength study of star formation properties in the barred galaxy NGC 7479, which also has obvious features of a minor merger. Using various tracers of star formation, we find that under the effects of both a stellar bar and a minor merger, star formation activity mainly takes place along the galactic bar and arms, while the star formation rate changes from the bar to the disk. With the help of spectral synthesis, we find that strong star formation took place in the bar region about 100 Myr ago, and the stellar bar might have been ∼10 Gyr old. By comparing our results with the secular evolutionary scenario from Jogee et al., we suggest that NGC 7479 is possibly in a transitional stage of secular evolution at present, and it may eventually become an earlier type galaxy or a luminous infrared galaxy. We also note that the probable minor merger event happened recently in NGC 7479, and we find two candidates for minor merger remnants.

  8. Thermal, spectroscopic and laser properties of Nd3+ in gadolinium scandium gallium garnet crystal produced by optical floating zone method

    Science.gov (United States)

    Tian, Li; Wang, Shuxian; Wu, Kui; Wang, Baolin; Yu, Haohai; Zhang, Huaijin; Cai, Huaqiang; Huang, Hui

    2013-12-01

    A neodymium-doped gadolinium scandium gallium garnet (Nd:GSGG) single crystal with dimensions of Φ 5 × 20 mm2 has been grown by means of optical floating zone (OFZ). X-ray powder diffraction (XRPD) result shows that the as-grown Nd:GSGG crystal possesses a cubic structure with space group Ia3d and a cell parameter of a = 1.2561 nm. Effective elemental segregation coefficients of the Nd:GSGG as-grown crystal were calculated by using X-ray fluorescence (XRF). The thermal properties of the Nd:GSGG crystal were systematically studied by measuring the specific heat, thermal expansion and thermal diffusion coefficient, and the thermal conductivity of this crystal was calculated. The absorption and luminescence spectra of Nd:GSGG were measured at room temperature (RT). By using the Judd-Ofelt (J-O) theory, the theoretical radiative lifetime was calculated and compared with the experimental result. Continuous wave (CW) laser performance was achieved with the Nd:GSGG at the wavelength of 1062 nm when it was pumped by a laser diode (LD). A maximum output power of 0.792 W at 1062 nm was obtained with a slope efficiency of 11.89% under a pump power of 7.36 W, and an optical-optical conversion efficiency of 11.72%.

  9. Infrared Spectroscopic Studies of the Properties of Dust in the Ejecta of Galactic Oxygen-Rich Asymptotic Giant Branch Stars

    Science.gov (United States)

    Sargent, Benjamin A.; Srinivasan, Sundar; Kastner, Joel; Meixner, Margaret; Riley, Allyssa

    2018-06-01

    We are conducting a series of infrared studies of large samples of mass-losing asymptotic giant branch (AGB) stars to explore the relationship between the composition of evolved star ejecta and host galaxy metallicity. Our previous studies focused on mass loss from evolved stars in the relatively low-metallicity Large and Small Magellanic Clouds. In our present study, we analyze dust in the mass-losing envelopes of AGB stars in the Galaxy, with special focus on the ejecta of oxygen-rich (O-rich) AGB stars. We have constructed detailed dust opacity models of AGB stars in the Galaxy for which we have infrared spectra from, e.g., the Spitzer Space Telescope Infrared Spectrograph (IRS). This detailed modeling of dust features in IRS spectra informs our choice of dust properties to use in radiative transfer modeling of the broadband SEDs of Bulge AGB stars. We investigate the effects of dust grain composition, size, shape, etc. on the AGB stars' infrared spectra, studying both the silicate dust and the opacity source(s) commonly attributed to alumina (Al2O3). BAS acknowledges funding from NASA ADAP grant 80NSSC17K0057.

  10. Phosphorus(V)-corrole: synthesis, spectroscopic properties, theoretical calculations, and potential utility for in vivo applications in living cells.

    Science.gov (United States)

    Liang, Xu; Mack, John; Zheng, Li-Min; Shen, Zhen; Kobayashi, Nagao

    2014-03-17

    The synthesis and properties of phosphorus(V) 5,10,15-tris(4-methoxycarbonylphenyl)corrole (1) have been investigated, and its potential utility for bioimaging applications in living cells has been explored. As would normally be anticipated for corrole complexes, the intensity of the Q(0,0) bands of 1 is greater than those of comparable phosphorus(V) tetraphenylporphyrins, but the ΦF values (0.25 for 1) are found to be comparable. A detailed analysis of the electronic structure of the complex was carried out by comparing electronic absorption and MCD spectral data to the results of TD-DFT calculations. The meso-aryl substituents, which enhance the lipophilicity of 1 and hence result in its localization in intracellular membranes during HeLa cell experiments, are predicted to result in a narrowing of the HOMO-LUMO gap and hence a red shift of the Q(0,0) bands toward the optical window in biological tissues.

  11. Fabrication and spectroscopic properties of Co:MgAl2O4 transparent ceramics by the HIP post-treatment

    Science.gov (United States)

    Luo, Wei; Ma, Peng; Xie, Tengfei; Dai, Jiawei; Pan, Yubai; Kou, Huamin; Li, Jiang

    2017-07-01

    Cobalt-doped magnesium aluminate spinel (Co:MgAl2O4) is one of the most important saturable absorbers for the passive Q-switching of solid-state lasers operating at eye-safe wavelength of 1.5 μm. In this work, highly transparent Co:MgAl2O4 ceramics were fabricated by vacuum sintering combined with hot isostatic pressing (HIP) post-treatment, using the mixture of the commercial spinel and the lab-made Co:MgAl2O4 powder as the raw materials. The densification mechanism of Co:MgAl2O4 transparent ceramics was discussed. The microstructure and optical properties of the samples were investigated. The ground state absorption cross section (σGSA) was calculated from the fitted curve of the absorption coefficient spectrum. The results show that Co:MgAl2O4 ceramics fabricated by vacuum sintering at 1500 °C for 5 h and then HIP post-treatment at 1650 °C for 3 h perform good transparency, whose in-line transmittance exceeds 80% at 2500 nm. Moreover, the ground state absorption cross section of 0.02 at.% Co:MgAl2O4 ceramics is calculated to be 3.35 × 10-19 cm2 at the wavelength of 1540 nm, which is promising for the application to the passive Q-switching of solid-state laser operating in the near infrared region (NIR).

  12. Synthesis, Crystal Growth, Spectroscopic and Electrical Properties of 5-tert-Butyl-1,2,3-trinitrobenzene

    Directory of Open Access Journals (Sweden)

    S. Sahaya Jude Dhas

    2013-01-01

    Full Text Available 5-tert-Butyl-1,2,3-trinitrobenzene (TBTB was synthesized and characterized by NMR so as to confirm the structure. Single crystals were obtained from methanol by solvent evaporation technique at room temperature. Optically transparent single crystals with dimension up to 17×4×3 mm3 have been grown by submerged seed solution method within a period of 30 days. The modes of vibration of different molecular groups present in the title compound were identified by FTIR and FT-Raman spectral analyses, and it was found with the tabulation that both of the spectral vibrations are very close to each other confirming the existence of specific functional groups in the crystal. Optical behaviour of the crystal was analyzed by UV-Vis absorption studies, and the value of the optical band gap energy (Eg of the crystal has been determined using the optical absorption spectrum. The dielectric behaviour and AC conductivity of the grown crystals were also analyzed, and it is shown that both properties vary with respect to frequency and do not vary in accordance with temperature.

  13. X-ray photoelectron spectroscopic depth profilometry of nitrogen implanted in materials for modification of their surface properties

    International Nuclear Information System (INIS)

    Sarkissian, A.H.; Paynter, R.; Stansfield, B.L.

    1996-01-01

    The modification of the surface properties of materials has a wide range of industrial applications. For example, the authors change the electrical characteristics of semiconductors, improve surface hardness, decrease friction, increase resistance to corrosion, improve adhesion, etc. Nitriding is one of the most common processes used in industry for surface treatment. Nitrogen ion implantation is one technique often used to achieve this goal. Ion implantation offers the power to control the deposition profile, and can be achieved by either conventional ion beam implantation or plasma assisted ion implantation. They have used the technique of plasma assisted ion implantation to implant nitrogen in several materials, including titanium, silicon and stainless steel. The plasma source is a surface ECR source developed at INRS-Energie et Materiaux. The depth profile of the implanted ions has been measured by X-ray photoelectron spectroscopy. They have also conducted simulations using the TRIM-95 code to predict the depth profile of the implanted ions. Comparisons of the measured results with those from simulations are used to deduce information regarding the plasma composition and the collisional effects in the plasma. A fast responding, current and voltage measuring circuit with fiber optic links is being developed, which allows more accurate quantitative measurements. Further experiments to study the characteristics of the plasma, and their effects on the characteristics of the implanted surfaces are in progress, and the results are presented at this meeting

  14. Spectroscopic analysis of 8-hydroxyquinoline-5-sulphonic acid and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Sheena Mary, Y.; Panicker, C. Yohannan; Resmi, K. S.; Suma, S.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.

    2017-12-01

    A detailed interpretation of the FT-IR and FT-Raman spectra has been performed on the basis of the observed and calculated infrared and Raman spectra as well as calculated potential energy distribution values. Comparison of Raman and SERS spectra suggests a tilted orientation of the rings on the metal surface. The dipole moment, polarizability and first and second order hyperpolarizability values of the molecule were calculated. Global reactivity parameters were predicted. The relative reactivities towards electrophilic and nucleophilic attack are predicted using molecular electrostatic potential map. Average local ionization energy (ALIE) and Fukui functions have been inspected in order to investigate local reactivity properties of title molecule. The importance of autoxidation and hydrolysis mechanisms for the title molecule has been assessed by DFT calculations of bond dissociation energies (BDE) and by calculations of radial distribution functions (RDFs) after molecular dynamics (MD) simulations. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.

  15. Density, viscosity, surface tension, and spectroscopic properties for binary system of 1,2-ethanediamine + diethylene glycol

    International Nuclear Information System (INIS)

    Li, Lihua; Zhang, Jianbin; Li, Qiang; Guo, Bo; Zhao, Tianxiang; Sha, Feng

    2014-01-01

    Graphical abstract: Excess property of the binary system 1,2-ethanediamine (EDA) + diethylene glycol (DEG). - Highlights: • Densities and viscosities of EDA + DEG at 298.15–318.150 K were listed. • Thermodynamics data of EDA + DEG at 298.15–318.15 K were calculated. • Surface tension of EDA + DEG at 298.15 K was measured. • Intermolecular interaction of EDA with DEG was discussed. - Abstract: This paper reports density and viscosity data at T = 298.15, 303.15, 308.15, 313.15, and 318.15 K and surface tension data at 298.15 K for the binary system 1,2-ethanediamine (EDA) + diethylene glycol (DEG) as a function of composition under atmospheric pressure. From the experimental density and viscosity data, the excess molar volume and viscosity deviation were calculated, and the results were fitted to a Redlich–Kister equation to obtain the coefficients and to estimate the standard deviations between the experimental and calculated quantities. Based on the kinematic viscosity data, enthalpy of activation for viscous flow, entropy of activation for the viscous flow, and Gibbs energies of activation of viscous flow were calculated. In addition, based on Fourier transform infrared spectra, UV–vis spectra, and electrical conductivity for the system EDA + DEG with various concentrations, intermolecular interaction of EDA with DEG was discussed

  16. Theoretical study of electronic structures and spectroscopic properties of Ga 3Sn, GaSn 3, and their ions

    Science.gov (United States)

    Zhu, Xiaolei

    2007-01-01

    Ground and excited states of mixed gallium stannide tetramers (Ga 3Sn, Ga 3Sn +, Ga 3Sn -, GaSn 3, GaSn 3+, and GaSn 3-) are investigated employing the complete active space self-consistent-field (CASSCF), density function theory (DFT), and the coupled-cluster single and double substitution (including triple excitations) (CCSD(T)) methods. The ground states of Ga 3Sn, Ga 3Sn +, and Ga 3Sn - are found to be the 2A 1, 3B 1, and 1A 1 states in C2v symmetry with a planar quadrilateral geometry, respectively. The ground states of GaSn 3 and GaSn 3- is predicted to be the 2A 1 and 1A 1 states in C2v point group with a planar quadrilateral structure, respectively, while the ground state of GaSn 3+ is the 1A 1 state with ideal triangular pyramid C3v geometry. Equilibrium geometries, vibrational frequencies, binding energies, electron affinities, ionization energies, and other properties of Ga 3Sn and GaSn 3 are computed and discussed. The anion photoelectron spectra of Ga 3Sn - and GaSn 3- are also predicted. It is interesting to find that the amount of charge transfer between Ga and Sn 2 atoms in the 1A 1 state of GaSn 3+ greatly increases upon electron ionization from the 2A 1 state of GaSn 3, which may be caused by large geometry change. On the other hand, the results of the low-lying states of Ga 3Sn and GaSn 3 are compared with those of Ga 3Si and GaSi 3.

  17. Spectroscopic properties of 1.8 μm emission in Tm3+ doped bismuth silicate glass

    International Nuclear Information System (INIS)

    Zhao, Guoying; Tian, Ying; Wang, Xin; Fan, Huiyan; Hu, Lili

    2013-01-01

    The emission properties around 1.8 μm in Tm 3+ doped bismuth silicate glass have been investigated. Based on the obtained Raman spectroscopy and differential scanning calorimetry curves, it is found the introduced Bi 2 O 3 can efficiently reduce the phonon energy of silicate glass to 926 cm −1 . The energy gap between glass transition temperature and onset temperature of crystallization is 169 °C. The OH − content maintains lower in glass by bubbling dry O 2 during the melting process. The cut-off wavelength in mid-infrared range is as long as 5 μm. Bismuth silicate glass has high radiative transition probability of 238.80 s −1 corresponding to the Tm 3+ : 3 F 4 → 3 H 6 transition compared with conventional silicate glasses. The strongest emission at 1.8 μm with a large full width at half-maximum of 238 nm is achieved from this bismuth silicate glass doped with 0.9 mol% Tm 2 O 3 . Its fluorescence lifetime at 1.8 μm is 640 μs. - Highlights: ► The 1.8 μm fluorescence of Tm 3+ -doped bismuth silicate glass is investigated. ► The prepared glass has lower phonon energy than other typical silicate glasses. ► A broadband 1.8 μm emission with the FWHM of 238 nm is observed. ► The fluorescence lifetime of Tm 3+ : 3 F 4 level reaches 640 μs.

  18. Role of Cu in engineering the optical properties of SnO2 nanostructures: Structural, morphological and spectroscopic studies

    Science.gov (United States)

    Kumar, Virender; Singh, Kulwinder; Jain, Megha; Manju; Kumar, Akshay; Sharma, Jeewan; Vij, Ankush; Thakur, Anup

    2018-06-01

    We have carried out a systematic study to investigate the effect of Cu doping on the optical properties of SnO2 nanostructures synthesized by chemical route. Synthesized nanostructures were characterized using X-ray diffraction (XRD), Field emission scanning electron microscopy (FE-SEM), High resolution transmission electron microscopy (HR-TEM), Energy dispersive X-ray spectroscopy, Raman spectroscopy, Fourier transform infrared (FTIR) spectroscopy, UV-visible and Photoluminescence (PL) spectroscopy. The Rietveld refinement analysis of XRD patterns of Cu-doped SnO2 samples confirmed the formation of single phase tetragonal rutile structure, however some localized distortion was observed for 5 mol% Cu-doped SnO2. Crystallite size was found to decrease with increase in dopant concentration. FE-SEM images indicated change in morphology of samples with doping. HR-TEM images revealed that synthesized nanostructures were nearly spherical and average crystallite size was in the range 12-21 nm. Structural defects, crystallinity and size effects on doping were investigated by Raman spectroscopy and results were complemented by FTIR spectroscopy. Optical band gap of samples was estimated from reflectance spectra. We have shown that band gap of SnO2 can be engineered from 3.62 to 3.82 eV by Cu doping. PL emission intensity increased as the doping concentration increased, which can be attributed to the development of defect states in the forbidden transition region of band gap of SnO2 with doping. We have also proposed a band model owing to defect states in SnO2 to explain the observed PL in Cu doped SnO2 nanostructures.

  19. An insight into the metal coordination and spectroscopic properties of artistic Fe and Fe/Cu logwood inks

    Science.gov (United States)

    Bronzato, Maddalena; Zoleo, Alfonso; Biondi, Barbara; Centeno, Silvia A.

    2016-01-01

    Fe- and Fe/Cu-based logwood inks were synthesized following recipes in nineteenth and early twentieth century manuals and were characterized by EPR, ESI-MS, FTIR, and Raman spectroscopies. This multi-technique approach allowed us to shed light on the structures of the complexes responsible for the inks' colors and to obtain vibrational signatures that can be used to identify the different inks in works of art and in historic documents. Information on the nature and chemical properties of the complexes formed between a dye and a mordant is important as these determine, at least in part, their lightfastness. EPR permitted to determine the coordination environment of the metallic ions. The results of the ESI-MS analysis demonstrated, for the first time, the breakdown of the hematein molecule during the ink preparation, and that the colorants are formed by the complexation of the metallic ions by hematein breakdown products, mainly catechol and/or bicyclic compounds. The FTIR spectra obtained were found to be dominated by bands due to the binding medium and sulfates used as reagents. The Raman analysis showed that the characteristic features for the different inks studied depend on the historic recipe used, attesting to the challenges that their identification and characterization in works of art present. In the Raman spectra of the inks applied on paper, broadening of bands in the 750-400 cm- 1 range are observed when compared to the spectra of the inks' powders, possibly due to the interaction of the compounds with the cellulose in the substrate.

  20. Tunable CsPbBr3/Cs4PbBr6 phase transformation and their optical spectroscopic properties.

    Science.gov (United States)

    Chen, Xiao; Chen, Daqin; Li, Junni; Fang, Gaoliang; Sheng, Hongchao; Zhong, Jiasong

    2018-04-24

    As a novel type of promising materials, metal halide perovskites are a rising star in the field of optoelectronics. On this basis, a new frontier of zero-dimensional perovskite-related Cs4PbBr6 with bright green emission and high stability has attracted an enormous amount of attention, even though its photoluminescence still requires to clarification. Herein, the controllable phase transformation between three-dimensional CsPbBr3 and zero-dimensional Cs4PbBr6 is easily achieved in a facile ligand-assisted supersaturated recrystallization synthesis procedure via tuning the amount of surfactants, and their unique optical properties are investigated and compared in detail. Both Cs4PbBr6 and CsPbBr3 produce remarkably intense green luminescence with quantum yields up to 45% and 80%, respectively; however, significantly different emitting behaviors are observed. The fluorescence lifetime of Cs4PbBr6 is much longer than that of CsPbBr3, and photo-blinking is easily detected in the Cs4PbBr6 product, proving that the zero-dimensional Cs4PbBr6 is indeed a highly luminescent perovskite-related material. Additionally, for the first time, tunable emissions over the visible-light spectral region are demonstrated to be achievable via halogen composition modulations in the Cs4PbX6 (X = Cl, Br, I) samples. Our study brings a simple method for the phase control of CsPbBr3/Cs4PbBr6 and demonstrates the intrinsic luminescence nature of the zero-dimensional perovskite-related Cs4PbX6 products.

  1. Microstructural, spectroscopic, and antibacterial properties of silver-based hybrid nanostructures biosynthesized using extracts of coriander leaves and seeds

    Directory of Open Access Journals (Sweden)

    Luna C

    2016-09-01

    Full Text Available Carlos Luna,1 Enrique Díaz Barriga-Castro,2 Alberto Gómez-Treviño,3 Nuria O Núñez,4 Raquel Mendoza-Reséndez1 1Research Center of Mathematics and Physics, Faculty of Mathematics and Physics, Autonomous University of Nuevo León, Nuevo León, Mexico; 2Central Laboratory of Analytical Instrumentation, Research Center for Applied Chemistry, Coahuila, Mexico; 3Laboratory of Molecular Biology, Faculty of Chemistry, Autonomous University of Nuevo León, Nuevo León, Mexico; 4Colloidal Materials Research Group, Institute of Materials Science of Seville, Spanish National Research Council, University of Seville, Seville, Spain Abstract: Coriander leaves and seeds have been highly appreciated since ancient times, not only due to their pleasant flavors but also due to their inhibitory activity on food degradation and their beneficial properties for health, both ascribed to their strong antioxidant activity. Recently, it has been shown that coriander leaf extracts can mediate the synthesis of metallic nanoparticles through oxidation/reduction reactions. In the present study, extracts of coriander leaves and seeds have been used as reaction media for the wet chemical synthesis of ultrafine silver nanoparticles and nanoparticle clusters, with urchin- and tree-like shapes, coated by biomolecules (mainly, proteins and polyphenols. In this greener route of nanostructure preparation, the active biocompounds of coriander simultaneously play the roles of reducing and stabilizing agents. The morphological and microstructural studies of the resulting biosynthesized silver nanostructures revealed that the nanostructures prepared with a small concentration of the precursor Ag salt (AgNO3 =5 mM exhibit an ultrafine size and a narrow size distribution, whereas particles synthesized with high concentrations of the precursor Ag salt (AgNO3 =0.5 M are polydisperse and formation of supramolecular structures occurs. Fourier transform infrared and Raman spectroscopy

  2. Topological and metric properties of linear and circular DNA chains in nano-slits and nano-channels

    Science.gov (United States)

    Orlandini, Enzo; Micheletti, Cristian

    2014-03-01

    Motivated by recent advancements in single DNA molecule experiments, based on nanofluidic devices, we investigate numerically the metric and topological properties of a modelof open and circular DNA chains confined inside nano-slits and nano-channles. The results reveal an interesting characterization of the metric crossover behaviour in terms of the abundance, type and length of occuring knots. In particular we find that the knotting probability is nonmonotonic for increasing confinement and can be largely enhanced or suppressed, compared to the bulk case, by simply varying the slit or channel trasversal dimension. The observed knot population consists of knots that are far simpler than for DNA chains in spherical (i.e. cavities or capsids) confinement. These results suggest that nanoslits and nanochannels can be properly designed to produce open DNA chains hosting simple knots or to sieve DNA rings according to their knotted state. Finally we discuss the implications that the presence of knots may have on the dynamical properties of confined DNA chains such as chain elongation, injection/ejection processes and entanglement relaxation. We acknowledge financial support from the Italian ministry of education, grant PRIN 2010HXAW77.

  3. Spectroscopic investigation of the chemical and electronic properties of chalcogenide materials for thin-film optoelectronic devices

    Science.gov (United States)

    Horsley, Kimberly Anne

    optoelectronic properties of these films. Through publication and/or discussion with collaborators, each project presented in this dissertation contributed to the understanding of the chemical and electronic properties of the material surface, near-surface bulk, and/or interfaces formed. The information gained on these unique chalcogenide materials will assist in designing more efficient and successful optoelectronic devices for the next generation of solar cells and LEDs.

  4. Substrate specificity, metal binding properties, and spectroscopic characterization of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae.

    Science.gov (United States)

    Bienvenue, David L; Gilner, Danuta M; Davis, Ryan S; Bennett, Brian; Holz, Richard C

    2003-09-16

    The catalytic and structural properties of divalent metal ion cofactor binding sites in the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. Co(II)-substituted DapE enzyme was 25% more active than the Zn(II)-loaded form of the enzyme. Interestingly, Mn(II) can activate DapE, but only to approximately 20% of the Zn(II)-loaded enzyme. The order of the observed k(cat) values are Co(II) > Zn(II) > Cd(II) > Mn(II) >Ni(II) approximately equal Cu(II) approximately equal Mg(II). DapE was shown to only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and was inactive toward D,L-, L,D-, and D,D-SDAP. DapE was also inactive toward several acetylated amino acids as well as D,L-succinyl aminopimelate, which differs from the natural substrate, L,L-SDAP, by the absence of the amine group on the amino acid side chain. These data imply that the carboxylate of the succinyl moiety and the amine form important interactions with the active site of DapE. The affinity of DapE for one versus two Zn(II) ions differs by nearly 2.2 x 10(3) times (K(d1) = 0.14 microM vs K(d2) = 300 microM). In addition, an Arrhenius plot was constructed from k(cat) values measured between 16 and 35 degrees C and was linear over this temperature range. The activation energy for [ZnZn(DapE)] was found to be 31 kJ/mol with the remaining thermodynamic parameters calculated at 25 degrees C being DeltaG(++) = 64 kJ/mol, DeltaH(++) = 28.5 kJ/mol, and DeltaS(++) = -119 J mol(-1) K(-1). Electronic absorption and EPR spectra of [Co_(DapE)] and [CoCo(DapE)] indicate that the first Co(II) binding site is five-coordinate, while the second site is octahedral. In addition, any spin-spin interaction between the two Co(II) ions in [CoCo(DapE)] is very weak. The kinetic and spectroscopic data presented herein suggest that the DapE from H. influenzae has similar divalent metal binding properties to the aminopeptidase from Aeromonas proteolytica (AAP), and

  5. Understanding the mechanical properties of DNA origami tiles and controlling the kinetics of their folding and unfolding reconfiguration.

    Science.gov (United States)

    Chen, Haorong; Weng, Te-Wei; Riccitelli, Molly M; Cui, Yi; Irudayaraj, Joseph; Choi, Jong Hyun

    2014-05-14

    DNA origami represents a class of highly programmable macromolecules that can go through conformational changes in response to external signals. Here we show that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement. The reconfiguration kinetics was experimentally studied as a function of incubation temperature, initial origami concentration, missing staples, and origami geometry. A kinetic model was developed by introducing the j factor to describe the reaction rates in the cyclization process. We found that the cyclization efficiency (j factor) increases sharply with temperature and depends strongly on the structural flexibility and geometry. A simple mechanical model was used to correlate the observed cyclization efficiency with origami structure details. The mechanical analysis suggests two sources of the energy barrier for DNA origami folding: overcoming global twisting and bending the structure into a circular conformation. It also provides the first semiquantitative estimation of the rigidity of DNA interhelix crossovers, an essential element in structural DNA nanotechnology. This work demonstrates efficient DNA origami reconfiguration, advances our understanding of the dynamics and mechanical properties of self-assembled DNA structures, and should be valuable to the field of DNA nanotechnology.

  6. A new ion-exchange adsorbent with paramagnetic properties for the separation of genomic DNA.

    Science.gov (United States)

    Feng, Guodong; Jiang, Luan; Wen, Puhong; Cui, Yali; Li, Hong; Hu, Daodao

    2011-11-21

    A new ion-exchange adsorbent (IEA) derived from Fe(3)O(4)/SiO(2)-GPTMS-DEAE with paramagnetic properties was prepared. Fe(3)O(4) nanoparticles were firstly prepared in water-in-oil microemulsion. The magnetic Fe(3)O(4) particles were modified in situ by hydrolysis and condensation reactions with tetraethoxysilane (TEOS) to form the core-shell Fe(3)O(4)/SiO(2). The modified particles were further treated by 3-glycidoxypropyltrimethoxysilane (GPTMS) to form Fe(3)O(4)/SiO(2)-GPTMS nanoparticles. Fe(3)O(4)/SiO(2)-GPTMS-DEAE nanoparticles (IEA) were finally obtained through the condensation reaction between the Cl of diethylaminoethyl chloride-HCl (DEAE) and the epoxy groups of GPTMS in the Fe(3)O(4)/SiO(2)-GPTMS. The obtained IEA has features of paramagnetic and ion exchange properties because of the Fe(3)O(4) nanoparticles and protonated organic amine in the sample. The intermediates and final product obtained in the synthesis process were characterized. The separation result of genomic DNA from blood indicated that Fe(3)O(4)/SiO(2)-GPTMS-DEAE nanoparticles have outstanding advantages in operation, selectivity, and capacity.

  7. Genome-wide DNA polymorphisms in Kavuni, a traditional rice cultivar with nutritional and therapeutic properties.

    Science.gov (United States)

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; Parani, Madasamy

    2016-05-01

    Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.

  8. Alpha-momorcharin: a ribosome-inactivating protein from Momordica charantia, possessing DNA cleavage properties.

    Science.gov (United States)

    Wang, Shuzhen; Zheng, Yinzhen; Yan, Junjie; Zhu, Zhixuan; Wu, Zhihua; Ding, Yi

    2013-11-01

    Ribosome-inactivating proteins (RIPs) function to inhibit protein synthesis through the removal of specific adenine residues from eukaryotic ribosomal RNA and rending the 60S subunit unable to bind elongation factor 2. They have received much attention in biological and biomedical research due to their unique activities toward tumor cells, as well as the important roles in plant defense. Alpha-momorcharin (α-MC), a member of the type I family of RIPs, is rich in the seeds of Momordica charantia L. Previous studies demonstrated that α-MC is an effective antifungal and antibacterial protein. In this study, a detailed analysis of the DNase-like activity of α-MC was conducted. Results showed that the DNase-like activity toward plasmid DNA was time-dependent, temperature-related, and pH-stable. Moreover, a requirement for divalent metal ions in the catalytic domain of α-MC was confirmed. Additionally, Tyr(93) was found to be a critical residue for the DNase-like activity, while Tyr(134), Glu(183), Arg(186), and Trp(215) were activity-related residues. This study on the chemico-physical properties and mechanism of action of α-MC will improve its utilization in scientific research, as well as its potential industrial uses. These results may also assist in the characterization and elucidation of the DNase-like enzymatic properties of other RIPs.

  9. The use of gum Arabic as "Green" stabilizer of poly(aniline) nanocomposites: a comprehensive study of spectroscopic, morphological and electrochemical properties.

    Science.gov (United States)

    Quintanilha, Ronaldo C; Orth, Elisa S; Grein-Iankovski, Aline; Riegel-Vidotti, Izabel C; Vidotti, Marcio

    2014-11-15

    Herein we show the synthesis and characterization of water dispersible composites formed by poly(aniline) and the natural polymer gum Arabic (GA), used as stabilizer. The materials were synthesized via a rapid and straightforward method and were fully characterized by different techniques such as UV-Vis, Raman, FTIR, TEM, SEM and cyclic voltammetry. TEM and SEM images revealed that the proportion of stabilizer highly influences the growth mechanism of the nanostructures. It was found spherical particles, elongated structures and large agglomerates at the lower, intermediate and at the higher GA amount, respectively. Accordingly to fluorescence spectra, different hydrophobic structures are formed depending on the GA amount in aqueous solutions, possibly acting as hosting sites for the PANI growth. In order to further study the PANI polymerization in the presence of GA, kinetics experiments were performed and showed that nucleation is the limiting step for the composite growth and a model is proposed. Spectroscopic experiments showed that the presence of GA affects the PANI conformation, avoiding the formation of phenazine structures which highly impairs the electroactivity of PANI. The material integrity is achieved by strong hydrogen bond interactions between PANI and GA as evidenced by the study of specific NH bands in FTIR and Raman analyses. The intensity of the hydrogen bonds decreased upon higher amounts of GA, probably due to steric impediment around the NH sites. Cyclic voltammograms showed a good electroactivity behavior of the modified electrodes presenting distinguishable diffusional processes through the adsorbed composites. By this way, we have thoroughly investigated the formation and properties of new conducting polymer composite materials. Taken into account the low toxicity of GA and the excellent dispersity in water, the materials can successfully be applied in bioelectrochemical applications or as green corrosion inhibitors. Copyright © 2014

  10. Antioxidant and DNA damage protective properties of anthocyanin-rich extracts from Hibiscus and Ocimum: a comparative study.

    Science.gov (United States)

    Sarkar, Biswatrish; Kumar, Dhananjay; Sasmal, Dinakar; Mukhopadhyay, Kunal

    2014-01-01

    Anthocyanin extracts (AEs) from Ocimum tenuiflorum (leaf), Hibiscus rosa-sinensis (petal) and Hibiscus sabdariffa (calyx) were investigated and compared for in vitro antioxidant activity and DNA damage protective property. Total phenolic content (TPC) and total anthocyanin content (TAC) of the AEs were determined and the major anthocyanins were characterised. In vitro antioxidant activities were assessed by ferric-reducing antioxidant power (FRAP) assay, 2,2-diphenyl-1-picryl hydrazyl (DPPH) radical-scavenging activity, 2-deoxy-D-ribose degradation assay and lipid peroxidation assay. The protective property of the AEs was also examined against oxidative DNA damage by H2O2 and UV using pUC19 plasmid. All the AEs particularly those from O. tenuiflorum demonstrated efficient antioxidant activity and protected DNA from damage. Strong correlation between antioxidant capacity and TPC and TAC was observed. Significant correlation between antioxidant capacity and TPC and TAC ascertained that phenolics and anthocyanins were the major contributors of antioxidant activity.

  11. New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sangmin, E-mail: taeinlee2011@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Chung, Jeong Min [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Yun, Hyung Joong; Won, Jonghan [Advanced Nano Surface Research Group, Korea Basic Science Institute, 169-148 Gwahak-ro, Daejeon, 305-333 (Korea, Republic of); Jung, Hyun Suk, E-mail: hsjung@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of)

    2016-01-22

    Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.

  12. New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

    International Nuclear Information System (INIS)

    Lee, Sangmin; Chung, Jeong Min; Yun, Hyung Joong; Won, Jonghan; Jung, Hyun Suk

    2016-01-01

    Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.

  13. A cDNA encoding a pRB-binding protein with properties of the transcription factor E2F

    DEFF Research Database (Denmark)

    Helin, K; Lees, J A; Vidal, M

    1992-01-01

    The retinoblastoma protein (pRB) plays an important role in the control of cell proliferation, apparently by binding to and regulating cellular transcription factors such as E2F. Here we describe the characterization of a cDNA clone that encodes a protein with properties of E2F. This clone, RBP3...

  14. On some surprising statistical properties of a DNA fingerprinting technique called AFLP

    NARCIS (Netherlands)

    Gort, G.

    2010-01-01

    AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary

  15. DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway

    NARCIS (Netherlands)

    van den Broek, B.; Noom, M.C.; Wuite, G.J.L.

    2005-01-01

    Type II restriction endonucleases protect bacteria against phage infections by cleaving recognition sites on foreign double-stranded DNA (dsDNA) with extraordinary specificity. This capability arises primarily from large conformational changes in enzyme and/or DNA upon target sequence recognition.

  16. Electrochemical, spectroscopic, and photophysical properties of structurally diverse polyazine-bridged Ru(II),Pt(II) and Os(II),Ru(II),Pt(II) supramolecular motifs.

    Science.gov (United States)

    Knoll, Jessica D; Arachchige, Shamindri M; Wang, Guangbin; Rangan, Krishnan; Miao, Ran; Higgins, Samantha L H; Okyere, Benjamin; Zhao, Meihua; Croasdale, Paul; Magruder, Katherine; Sinclair, Brian; Wall, Candace; Brewer, Karen J

    2011-09-19

    Five new tetrametallic supramolecules of the motif [{(TL)(2)M(dpp)}(2)Ru(BL)PtCl(2)](6+) and three new trimetallic light absorbers [{(TL)(2)M(dpp)}(2)Ru(BL)](6+) (TL = bpy = 2,2'-bipyridine or phen = 1,10-phenanthroline; M = Ru(II) or Os(II); BL = dpp = 2,3-bis(2-pyridyl)pyrazine, dpq = 2,3-bis(2-pyridyl)quinoxaline, or bpm = 2,2'-bipyrimidine) were synthesized and their redox, spectroscopic, and photophysical properties investigated. The tetrametallic complexes couple a Pt(II)-based reactive metal center to Ru and/or Os light absorbers through two different polyazine BL to provide structural diversity and interesting resultant properties. The redox potential of the M(II/III) couple is modulated by M variation, with the terminal Ru(II/III) occurring at 1.58-1.61 V and terminal Os(II/III) couples at 1.07-1.18 V versus Ag/AgCl. [{(TL)(2)M(dpp)}(2)Ru(BL)](PF(6))(6) display terminal M(dπ)-based highest occupied molecular orbitals (HOMOs) with the dpp(π*)-based lowest unoccupied molecular orbital (LUMO) energy relatively unaffected by the nature of BL. The coupling of Pt to the BL results in orbital inversion with localization of the LUMO on the remote BL in the tetrametallic complexes, providing a lowest energy charge separated (CS) state with an oxidized terminal Ru or Os and spatially separated reduced BL. The complexes [{(TL)(2)M(dpp)}(2)Ru(BL)](6+) and [{(TL)(2)M(dpp)}(2)Ru(BL)PtCl(2)](6+) efficiently absorb light throughout the UV and visible regions with intense metal-to-ligand charge transfer (MLCT) transitions in the visible at about 540 nm (M = Ru) and 560 nm (M = Os) (ε ≈ 33,000-42,000 M(-1) cm(-1)) and direct excitation to the spin-forbidden (3)MLCT excited state in the Os complexes about 720 nm. All the trimetallic and tetrametallic Ru-based supramolecular systems emit from the terminal Ru(dπ)→dpp(π*) (3)MLCT state, λ(max)(em) ≈ 750 nm. The tetrametallic systems display complex excited state dynamics with quenching of the (3)MLCT emission at

  17. The redox properties of the natural iron-bearing clay mineral ferruginous smectite SWA-1: a combined electrochemical and spectroscopic study

    International Nuclear Information System (INIS)

    Gorski, Christopher A.; Voegelin, Andreas; Sander, Michael; Hofstetter, Thomas B.

    2012-01-01

    . Our results indicate that the reduction and oxidation of SWa-1 is complex and partly irreversible, implying that classically used thermodynamic relationships (i.e., the Nernst equation and Gibbs free energy) cannot be used to describe SWa-1 redox reactions. SWa-1 is redox active over a much wider potential range (approx. 1.0 V) than would be expected for a single electron transferring species (i.e., Fe 2+ /Fe 3+ ) in Nernstian system, which is attributed to redox interdependence between octahedral Fe sites. SWa-1 reduction and oxidation is also shown to be inherently thermodynamically irreversible based on oxidation and reduction paths following different Fe 2+ /Fe 3+ versus applied potential (E H ) curves depending on the initial redox state of the SWa-1. By modeling the Fe 2+ /Fe 3+ versus applied potential curves, we were able to fit apparent standard reduction potential values for native and dithionite-reduced SWa-1 that can be used in future studies. Current work is underway to determine the effect of pH on the redox properties of Fe-bearing clay minerals. Spectroscopic observations indicate that the reduction and subsequent re-oxidation of all the clay minerals studied was chemically irreversible, as indicated by the native and re-oxidized samples exhibiting differences in Moessbauer and XAS spectra. Further characterization of the Moessbauer spectra suggest that certain spectral features are indicative of the reduction potential (Eh) at which structural Fe 3+ reduction occurs. Our results point out that the complex redox behavior of Fe-bearing clay minerals must be taken into account to understand and predict the fate of radionuclides in matrices containing Fe-bearing clay minerals. The spectroscopic and electrochemical characterization of Fe-bearing clay minerals in this study also provides a means to account for these factors in future studies. Finally, we show that mediated electrochemistry offers new avenues to assess the redox properties of other redox

  18. SYNTHESES, SPECTROSCOPIC AND MAGNETIC PROPERTIES ...

    African Journals Online (AJOL)

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    suspension of II reacts with Mn(II), Ni(II), Cd(II), Fe(III) and UO2(VI) ions and ... There has been considerable interest in the synthesis and use of ... chelating abilities in recent years due to their practical convenience, operational flexibility and.

  19. Photorepair of UV damage to DNA: purification and properties of DNA photolyase (the DNA-photoreactivating enzyme). Progress report, August 1, 1975--July 31, 1976

    International Nuclear Information System (INIS)

    Werbin, H.

    1976-01-01

    Progress is reported on the following research projects: separation of photolyase subunits by sucrose gradient sedimentation; determination of whether fluorescent material is the chromophore for photolyase; studies on tryptophane and lysine residues to determine whether these are involved in the binding and photolytic steps; nmr spectrum of activator of photolyase; damage to pea chromatin by solar near uv and repair of damage; tryptophan residues in yeast DNA photolyase; photolyase in pea seedlings; and nuclear magnetic resonance spectra of purified activator

  20. Mossbauer spectroscopic studies in ferroboron

    Science.gov (United States)

    Yadav, Ravi Kumar; Govindaraj, R.; Amarendra, G.

    2017-05-01

    Mossbauer spectroscopic studies have been carried out in a detailed manner on ferroboron in order to understand the local structure and magnetic properties of the system. Evolution of the local structure and magnetic properties of the amorphous and crystalline phases and their thermal stability have been addressed in a detailed manner in this study. Role of bonding between Fe 4s and/or 4p electrons with valence electrons of boron (2s,2p) in influencing the stability and magnetic properties of Fe-B system is elucidated.

  1. Composition and immuno-stimulatory properties of extracellular DNA from mouse gut flora.

    Science.gov (United States)

    Qi, Ce; Li, Ya; Yu, Ren-Qiang; Zhou, Sheng-Li; Wang, Xing-Guo; Le, Guo-Wei; Jin, Qing-Zhe; Xiao, Hang; Sun, Jin

    2017-11-28

    To demonstrate that specific bacteria might release bacterial extracellular DNA (eDNA) to exert immunomodulatory functions in the mouse small intestine. Extracellular DNA was extracted using phosphate buffered saline with 0.5 mmol/L dithiothreitol combined with two phenol extractions. TOTO-1 iodide, a cell-impermeant and high-affinity nucleic acid stain, was used to confirm the existence of eDNA in the mucus layers of the small intestine and colon in healthy Male C57BL/6 mice. Composition difference of eDNA and intracellular DNA (iDNA) of the small intestinal mucus was studied by Illumina sequencing and terminal restriction fragment length polymorphism (T-RFLP). Stimulation of cytokine production by eDNA was studied in RAW264.7 cells in vitro . TOTO-1 iodide staining confirmed existence of eDNA in loose mucus layer of the mouse colon and thin surface mucus layer of the small intestine. Illumina sequencing analysis and T-RFLP revealed that the composition of the eDNA in the small intestinal mucus was significantly different from that of the iDNA of the small intestinal mucus bacteria. Illumina Miseq sequencing showed that the eDNA sequences came mainly from Gram-negative bacteria of Bacteroidales S24-7. By contrast, predominant bacteria of the small intestinal flora comprised Gram-positive bacteria. Both eDNA and iDNA were added to native or lipopolysaccharide-stimulated Raw267.4 macrophages, respectively. The eDNA induced significantly lower tumor necrosis factor-α/interleukin-10 (IL-10) and IL-6/IL-10 ratios than iDNA, suggesting the predominance for maintaining immune homeostasis of the gut. Our results indicated that degraded bacterial genomic DNA was mainly released by Gram-negative bacteria, especially Bacteroidales-S24-7 and Stenotrophomonas genus in gut mucus of mice. They decreased pro-inflammatory activity compared to total gut flora genomic DNA.

  2. Phonon and free-charge carrier properties in group-III nitride heterostructures investigated by spectroscopic ellipsometry and optical Hall effect

    Science.gov (United States)

    Schoeche, Stefan

    The material class of group-III nitrides gained tremendous technological importance for optoelectronic and high-power/high-frequency amplification devices. Tunability of the direct band gap from 0.65 eV (InN) to 6.2 eV (AlN) by alloying, high breakthrough voltages and intrinsic mobilities, as well as the formation of highly mobile 2d electron gases (2DEG) at heterointerfaces make these compounds ideal for many applications. GaN and Ga-rich alloys are well studied and current research is mainly device-oriented. For example, choice and quality of the gate dielectric significantly influence device performance in high-electron mobility transistors (HEMT) which utilize highly mobile 2DEGs at heterointerfaces. Experimental access to the 2DEG channel properties without influence from parasitic currents or contact properties are desirable. In- and Al-rich ternary alloys are less explored than Ga-rich compounds. For InN and In-rich alloys, while many material parameters such as stiffness constants or effective mass values are largely unknown, reliable p-type doping is a major challenge, also because p-type conducting channels are buried within highly conductive n-type material formed at the surface and interfaces preventing electrical characterization. For AlN and high-Al content alloys, doping mechanisms are not understood and reliable fabrication of material with high free-charge carrier (FCC) concentrations was achieved just recently. Difficulties to form ohmic contacts impair electrical measurements and optical characterization is impeded by lack of high-energy excitation sources. In this work, spectroscopic ellipsometry over the wide spectral range from the THz to VUV in combination with optical Hall effect (generalized ellipsometry with applied magnetic field) from THz to MIR are applied in order to investigate the phonon modes and FCC properties in group-III nitride heterostructures. Adequate model descriptions and analysis strategies are introduced which allow

  3. Enzymatic properties of the bacteriophage phi X174 A protein on superhelical phi X174 DNA: a model for the termination of the rolling circle DNA replication

    NARCIS (Netherlands)

    van der Ende, A.; Langeveld, S. A.; Teertstra, R.; van Arkel, G. A.; Weisbeek, P. J.

    1981-01-01

    Incubation of phi X174 replication form I DNA with the A* protein of phi X174 in the presence of MN2+ results in the formation of three different types of DNA molecules: open circular form DNA (RFII), linear form DNA (RFIII) and the relaxed covalently closed form DNA (RFIV). The RFII and RFIII DNAs

  4. XRCC1 and PCNA are loading platforms with distinct kinetic properties and different capacities to respond to multiple DNA lesions

    Directory of Open Access Journals (Sweden)

    Leonhardt Heinrich

    2007-09-01

    Full Text Available Abstract Background Genome integrity is constantly challenged and requires the coordinated recruitment of multiple enzyme activities to ensure efficient repair of DNA lesions. We investigated the dynamics of XRCC1 and PCNA that act as molecular loading platforms and play a central role in this coordination. Results Local DNA damage was introduced by laser microirradation and the recruitment of fluorescent XRCC1 and PCNA fusion proteins was monitored by live cell microscopy. We found an immediate and fast recruitment of XRCC1 preceding the slow and continuous recruitment of PCNA. Fluorescence bleaching experiments (FRAP and FLIP revealed a stable association of PCNA with DNA repair sites, contrasting the high turnover of XRCC1. When cells were repeatedly challenged with multiple DNA lesions we observed a gradual depletion of the nuclear pool of PCNA, while XRCC1 dynamically redistributed even to lesions inflicted last. Conclusion These results show that PCNA and XRCC1 have distinct kinetic properties with functional consequences for their capacity to respond to successive DNA damage events.

  5. XRCC1 and PCNA are loading platforms with distinct kinetic properties and different capacities to respond to multiple DNA lesions

    Science.gov (United States)

    Mortusewicz, Oliver; Leonhardt, Heinrich

    2007-01-01

    Background Genome integrity is constantly challenged and requires the coordinated recruitment of multiple enzyme activities to ensure efficient repair of DNA lesions. We investigated the dynamics of XRCC1 and PCNA that act as molecular loading platforms and play a central role in this coordination. Results Local DNA damage was introduced by laser microirradation and the recruitment of fluorescent XRCC1 and PCNA fusion proteins was monitored by live cell microscopy. We found an immediate and fast recruitment of XRCC1 preceding the slow and continuous recruitment of PCNA. Fluorescence bleaching experiments (FRAP and FLIP) revealed a stable association of PCNA with DNA repair sites, contrasting the high turnover of XRCC1. When cells were repeatedly challenged with multiple DNA lesions we observed a gradual depletion of the nuclear pool of PCNA, while XRCC1 dynamically redistributed even to lesions inflicted last. Conclusion These results show that PCNA and XRCC1 have distinct kinetic properties with functional consequences for their capacity to respond to successive DNA damage events. PMID:17880707

  6. Studies of torsional properties of DNA and nucleosomes using angular optical trapping

    Science.gov (United States)

    Sheinin, Maxim Y.

    DNA in vivo is subjected to torsional stress due to the action of molecular motors and other DNA-binding proteins. Several decades of research have uncovered the fascinating diversity of DNA transformations under torsion and the important role they play in the regulation of vital cellular processes such as transcription and replication. Recent studies have also suggested that torsion can influence the structure and stability of nucleosomes---basic building blocks of the eukaryotic genome. However, our understanding of the impact of torsion is far from being complete due to significant experimental challenges. In this work we have used a powerful single-molecule experimental technique, angular optical trapping, to address several long-standing issues in the field of DNA and nucleosome mechanics. First, we utilized the high resolution and direct torque measuring capability of the angular optical trapping to precisely measure DNA twist-stretch coupling. Second, we characterized DNA melting under tension and torsion. We found that torsionally underwound DNA forms a left-handed structure, significantly more flexible compared to the regular B-DNA. Finally, we performed the first comprehensive investigation of the single nucleosome behavior under torque and force. Importantly, we discovered that positive torque causes significant dimer loss, which can have implications for transcription through chromatin.

  7. Simple Laboratory methods to measure cell proliferation using DNA synthesis property

    Directory of Open Access Journals (Sweden)

    Madhavan H N

    2007-01-01

    Full Text Available This is a mini-review on the techniques to measure proliferation of cells by estimation of DNA synthesis. This is not an exhaustive review of literature, but a bird’s eye view of a few selected articles which may provide the technical details to the readers.The nucleus of a cell occupies about 10-30% of the cells space, depends on the type of genetic material (DNA -DeoxyriboNucleic Acid. DNA is a long, double-stranded, helical molecule which carries the genetic information. Duplication of the DNA takes place by the phenomena of replication. One copy of double-stranded DNA molecule forms two double-stranded DNA molecules. DNA replication is the fundamental process used in all living organisms as it is the basis for biological inheritance. This process is known also as Mitosis in somatic cells. In Mitosis, the duplication process results in two genetically identical "daughter" cells from a single "parent" cell. The resulting double-stranded DNA molecules are identical; proof reading and error-checking mechanisms exist to ensure near perfect pair. Mitosis is divided into six phases: prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis.

  8. Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

    DEFF Research Database (Denmark)

    Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

    2006-01-01

    BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

  9. Miscoding and mutagenic properties of 8-oxoguanine and abasic sites: Ubiquitous lesions in damaged DNA

    International Nuclear Information System (INIS)

    Grollman, A.P.; Takeshita, Masaru

    1995-01-01

    More than twenty oxidatively-damaged bases, including 8-oxoguanine, have been found to occur in genomic DNA. Some of these lesions block DNA replication and are potentially lethal; others generate mutations which can initiate carcinogenesis and promote cellular aging. In this report, the authors focus attention on the mutagenicity and repair of 8-oxoguanine. Kasai and Nishimura's discovery that hydroxyl radicals react with guanine residues in DNA to form 8-oxoguanine and the development of sensitive methods for the detection and quantitation of this modified base led to the observation that approximately 1 in 10 5 guanine residues in mammalian DNA are oxidized at the C-8 position. DNA containing 8-oxoguanine and synthetic analogs of the abasic site have been used to investigate the miscoding and mutagenic potential of these ubiquitous lesions. Studies in the laboratory were facilitated by the development of solid state synthetic methods by which these lesions could be introduced at defined positions in DNA. In this paper, the authors review studies in which 8-oxoguanine and abasic sites have been used in model systems to explore various early events in the replication of selectively damaged DNA

  10. Enzymatic and spectroscopic properties of a thermostable [NiFe]‑hydrogenase performing H2-driven NAD+-reduction in the presence of O2.

    Science.gov (United States)

    Preissler, Janina; Wahlefeld, Stefan; Lorent, Christian; Teutloff, Christian; Horch, Marius; Lauterbach, Lars; Cramer, Stephen P; Zebger, Ingo; Lenz, Oliver

    2018-01-01

    Biocatalysts that mediate the H 2 -dependent reduction of NAD + to NADH are attractive from both a fundamental and applied perspective. Here we present the first biochemical and spectroscopic characterization of an NAD + -reducing [NiFe]‑hydrogenase that sustains catalytic activity at high temperatures and in the presence of O 2 , which usually acts as an inhibitor. We isolated and sequenced the four structural genes, hoxFUYH, encoding the soluble NAD + -reducing [NiFe]‑hydrogenase (SH) from the thermophilic betaproteobacterium, Hydrogenophilus thermoluteolus TH-1 T (Ht). The HtSH was recombinantly overproduced in a hydrogenase-free mutant of the well-studied, H 2 -oxidizing betaproteobacterium Ralstonia eutropha H16 (Re). The enzyme was purified and characterized with various biochemical and spectroscopic techniques. Highest H 2 -mediated NAD + reduction activity was observed at 80°C and pH6.5, and catalytic activity was found to be sustained at low O 2 concentrations. Infrared spectroscopic analyses revealed a spectral pattern for as-isolated HtSH that is remarkably different from those of the closely related ReSH and other [NiFe]‑hydrogenases. This indicates an unusual configuration of the oxidized catalytic center in HtSH. Complementary electron paramagnetic resonance spectroscopic analyses revealed spectral signatures similar to related NAD + -reducing [NiFe]‑hydrogenases. This study lays the groundwork for structural and functional analyses of the HtSH as well as application of this enzyme for H 2 -driven cofactor recycling under oxic conditions at elevated temperatures. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Cytotoxic and DNA-damaging properties of glyphosate and Roundup in human-derived buccal epithelial cells.

    Science.gov (United States)

    Koller, Verena J; Fürhacker, Maria; Nersesyan, Armen; Mišík, Miroslav; Eisenbauer, Maria; Knasmueller, Siegfried

    2012-05-01

    Glyphosate (G) is the largest selling herbicide worldwide; the most common formulations (Roundup, R) contain polyoxyethyleneamine as main surfactant. Recent findings indicate that G exposure may cause DNA damage and cancer in humans. Aim of this investigation was to study the cytotoxic and genotoxic properties of G and R (UltraMax) in a buccal epithelial cell line (TR146), as workers are exposed via inhalation to the herbicide. R induced acute cytotoxic effects at concentrations > 40 mg/l after 20 min, which were due to membrane damage and impairment of mitochondrial functions. With G, increased release of extracellular lactate dehydrogenase indicative for membrane damage was observed at doses > 80 mg/l. Both G and R induced DNA migration in single-cell gel electrophoresis assays at doses > 20 mg/l. Furthermore, an increase of nuclear aberrations that reflect DNA damage was observed. The frequencies of micronuclei and nuclear buds were elevated after 20-min exposure to 10-20 mg/l, while nucleoplasmatic bridges were only enhanced by R at the highest dose (20 mg/l). R was under all conditions more active than its active principle (G). Comparisons with results of earlier studies with lymphocytes and cells from internal organs indicate that epithelial cells are more susceptible to the cytotoxic and DNA-damaging properties of the herbicide and its formulation. Since we found genotoxic effects after short exposure to concentrations that correspond to a 450-fold dilution of spraying used in agriculture, our findings indicate that inhalation may cause DNA damage in exposed individuals.

  12. Hair Dye–DNA Interaction: Plausible Cause of Mutation

    Directory of Open Access Journals (Sweden)

    Swati Maiti

    2015-09-01

    Full Text Available Hair dye is one of the most popular cosmetic products which are used more widely and frequently to improve an individual’s appearance. Although the genotoxic effects of dye ingredients are widely reported, hair dye in its usable form is not reported extensively. In this contribution, we report the possible mode of interaction of hair dye with DNA which leads to genotoxicity. The effect of dye DNA interaction was studied on the most popular and globally used hair dye with Calf Thymus DNA and plasmid DNA. This interaction of dye DNA was studied by spectroscopic analyses and gel electrophoresis. The result had shown positive interaction of dye with DNA. Gel electrophoresis study confirms the binding of dye with DNA which results in linearization and fragmentation of the plasmid DNA. Dye–DNA interaction causes fragmentation and oxidation of DNA in absence of any catalyst, implies high toxicity of commercial hair dyes. Thus, it can be deduced from the present studies that hair dye in its usable form may lead to its penetration through skin affecting genomic DNA possesses genotoxic property and can be treated as one of the most common mutagen.

  13. Single-strand breaks induced in Bacillus subtilis DNA by ultraviolet light: action spectrum and properties

    International Nuclear Information System (INIS)

    Peak, M.J.; Peak, J.G.

    1982-01-01

    The induction of single-strand breaks (alkali-labile bonds plus frank breaks) in the DNA of Bacillus subtilis irradiated in vivo by monochromatic UV light at wavelengths from 254 to 434nm was measured. The spectrum consists of a major far-UV (below 320nm) component and a minor near-UV shoulder. A mutant deficient in DNA polymerase I accumulates breaks caused by near-UV (above 320nm) wavelengths faster than the wild-type strain proficient in polymerase I. Measurable breaks in extracted DNA are induced at a higher frequency than those induced in vivo. Anoxia, glycerol, and diazobicyclo (2.2.2.) octane inhibit break formation in extracted DNA. Alkali-labile bonds induced by 365-nm UV radiation are largely (78%) covalent bond chain breaks, the remainder consists of true alkali-labile bonds, probably apurinic and apyrimidinic sites. (author)

  14. Spectroscopic classification of transients

    DEFF Research Database (Denmark)

    Stritzinger, M. D.; Fraser, M.; Hummelmose, N. N.

    2017-01-01

    We report the spectroscopic classification of several transients based on observations taken with the Nordic Optical Telescope (NOT) equipped with ALFOSC, over the nights 23-25 August 2017.......We report the spectroscopic classification of several transients based on observations taken with the Nordic Optical Telescope (NOT) equipped with ALFOSC, over the nights 23-25 August 2017....

  15. Lethal and mutagenic properties of MMS-generated DNA lesions in Escherichia coli cells deficient in BER and AlkB-directed DNA repair.

    Science.gov (United States)

    Sikora, Anna; Mielecki, Damian; Chojnacka, Aleksandra; Nieminuszczy, Jadwiga; Wrzesinski, Michal; Grzesiuk, Elzbieta

    2010-03-01

    Methylmethane sulphonate (MMS), an S(N)2-type alkylating agent, generates DNA methylated bases exhibiting cytotoxic and mutagenic properties. Such damaged bases can be removed by a system of base excision repair (BER) and by oxidative DNA demethylation catalysed by AlkB protein. Here, we have shown that the lack of the BER system and functional AlkB dioxygenase results in (i) increased sensitivity to MMS, (ii) elevated level of spontaneous and MMS-induced mutations (measured by argE3 --> Arg(+) reversion) and (iii) induction of the SOS response shown by visualization of filamentous growth of bacteria. In the xth nth nfo strain additionally mutated in alkB gene, all these effects were extreme and led to 'error catastrophe', resulting from the presence of unrepaired apurinic/apyrimidinic (AP) sites and 1-methyladenine (1meA)/3-methylcytosine (3meC) lesions caused by deficiency in, respectively, BER and AlkB dioxygenase. The decreased level of MMS-induced Arg(+) revertants in the strains deficient in polymerase V (PolV) (bearing the deletion of the umuDC operon), and the increased frequency of these revertants in bacteria overproducing PolV (harbouring the pRW134 plasmid) indicate the involvement of PolV in the error-prone repair of 1meA/3meC and AP sites. Comparison of the sensitivity to MMS and the induction of Arg(+) revertants in the double nfo alkB and xth alkB, and the quadruple xth nth nfo alkB mutants showed that the more AP sites there are in DNA, the stronger the effect of the lack of AlkB protein. Since the sum of MMS-induced Arg(+) revertants in xth, nfo and nth xth nfo and alkB mutants is smaller than the frequency of these revertants in the BER(-) alkB(-) strain, we consider two possibilities: (i) the presence of AP sites in DNA results in relaxation of its structure that facilitates methylation and (ii) additional AP sites are formed in the BER(-) alkB(-) mutants.

  16. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

    Energy Technology Data Exchange (ETDEWEB)

    Orimoto, Yuuichi, E-mail: orimoto.yuuichi.888@m.kyushu-u.ac.jp [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Aoki, Yuriko [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012 (Japan)

    2016-07-14

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

  17. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

    International Nuclear Information System (INIS)

    Orimoto, Yuuichi; Aoki, Yuriko

    2016-01-01

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

  18. DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68.

    Directory of Open Access Journals (Sweden)

    Jorge Mansilla-Soto

    2009-07-01

    Full Text Available Rep68 is a multifunctional protein of the adeno-associated virus (AAV, a parvovirus that is mostly known for its promise as a gene therapy vector. In addition to its role as initiator in viral DNA replication, Rep68 is essential for site-specific integration of the AAV genome into human chromosome 19. Rep68 is a member of the superfamily 3 (SF3 helicases, along with the well-studied initiator proteins simian virus 40 large T antigen (SV40-LTag and bovine papillomavirus (BPV E1. Structurally, SF3 helicases share two domains, a DNA origin interaction domain (OID and an AAA(+ motor domain. The AAA(+ motor domain is also a structural feature of cellular initiators and it functions as a platform for initiator oligomerization. Here, we studied Rep68 oligomerization in vitro in the presence of different DNA substrates using a variety of biophysical techniques and cryo-EM. We found that a dsDNA region of the AAV origin promotes the formation of a complex containing five Rep68 subunits. Interestingly, non-specific ssDNA promotes the formation of a double-ring Rep68, a known structure formed by the LTag and E1 initiator proteins. The Rep68 ring symmetry is 8-fold, thus differing from the hexameric rings formed by the other SF3 helicases. However, similiar to LTag and E1, Rep68 rings are oriented head-to-head, suggesting that DNA unwinding by the complex proceeds bidirectionally. This novel Rep68 quaternary structure requires both the DNA binding and AAA(+ domains, indicating cooperativity between these regions during oligomerization in vitro. Our study clearly demonstrates that Rep68 can oligomerize through two distinct oligomerization pathways, which depend on both the DNA structure and cooperativity of Rep68 domains. These findings provide insight into the dynamics and oligomeric adaptability of Rep68 and serve as a step towards understanding the role of this multifunctional protein during AAV DNA replication and site-specific integration.

  19. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Amy L Bauer

    2010-11-01

    Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

  20. Electronic properties of an organic molecule within MCM-41 host: a spectroscopic and theoretical study toward elucidating the variation in band gaps of the guest species

    CERN Document Server

    Zhang, L Z; Tang Guo Qing; Liao Dai Zhen

    2003-01-01

    An organic molecule salicylidene-1,2-ethanediamine 1, has been encapsulated in the nanocavities of MCM-41 and this nanocomposite material has been investigated by X-ray diffraction, absorption and emission spectroscopy. Results from the spectroscopic measurements show that the bathochromic shift of the 0-0 transitions is correlated with the reduction of the HOMO-LUMO band gap accompanying by the energy changes of the frontier orbitals. Theoretical studies indicate that the energy levels of HOMO and LUMO increase when 1 is confined, and the HOMO is more sensitive than the LUMO.

  1. Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

    DEFF Research Database (Denmark)

    Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe

    2013-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...... in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2...

  2. DNA-interactive properties of crotamine, a cell-penetrating polypeptide and a potential drug carrier.

    Directory of Open Access Journals (Sweden)

    Pei-Chun Chen

    Full Text Available Crotamine, a 42-residue polypeptide derived from the venom of the South American rattlesnake Crotalus durissus terrificus, has been shown to be a cell-penetrating protein that targets chromosomes, carries plasmid DNA into cells, and shows specificity for actively proliferating cells. Given this potential role as a nucleic acid-delivery vector, we have studied in detail the binding of crotamine to single- and double-stranded DNAs of different lengths and base compositions over a range of ionic conditions. Agarose gel electrophoresis and ultraviolet spectrophotometry analysis indicate that complexes of crotamine with long-chain DNAs readily aggregate and precipitate at low ionic strength. This aggregation, which may be important for cellular uptake of DNA, becomes less likely with shorter chain length. 25-mer oligonucleotides do not show any evidence of such aggregation, permitting the determination of affinities and size via fluorescence quenching experiments. The polypeptide binds non-cooperatively to DNA, covering about 5 nucleotide residues when it binds to single (ss or (ds double stranded molecules. The affinities of the protein for ss- vs. ds-DNA are comparable, and inversely proportional to salt levels. Analysis of the dependence of affinity on [NaCl] indicates that there are a maximum of ∼3 ionic interactions between the protein and DNA, with some of the binding affinity attributable to non-ionic interactions. Inspection of the three-dimensional structure of the protein suggests that residues 31 to 35, Arg-Trp-Arg-Trp-Lys, could serve as a potential DNA-binding site. A hexapeptide containing this sequence displayed a lower DNA binding affinity and salt dependence as compared to the full-length protein, likely indicative of a more suitable 3D structure and the presence of accessory binding sites in the native crotamine. Taken together, the data presented here describing crotamine-DNA interactions may lend support to the design of more

  3. Influence of degree of methyl methacrylate polymerization on spectroscopic properties of ethyl 5-(4-aminophenyl)- and 5-(4-dimethylaminophenyl)-3-amino-2,4-dicyanobenzoate

    International Nuclear Information System (INIS)

    Józefowicz, M.; Bajorek, A.; Pietrzak, M.; Jędrzejewska, B.; Heldt, J.R.; Heldt, J.

    2013-01-01

    The influence of degree of methyl methacrylate (MM) polymerization on the both emission modes (LE—locally excited and ICT—intramolecular charge transfer) of the fluorescence spectrum of ethyl 5-(4-aminophenyl)-3-amino-2,4-dicyanobenzoate (EAADCy) and ethyl 5-(4-dimethylaminophenyl)-3-amino-2,4-dicyanobenzoate (EDMAADCy) has been studied using steady-state and time-resolved spectroscopic technique. The purpose of these studies was to find a relationship between the changes in the spectroscopic characteristics (fluorescence intensity, wavelength of maximum intensity, fluorescence full-width at half maximum, emission anisotropy, fluorescence decay time) of the tested compounds and degree of monomer conversion into polymer. On the basis of the experimental results, it was shown that the ICT fluorescence full-width at half maximum for EDMAADCy shows a linear dependence on the time of MM polymerization. Our findings predestine the molecule EDMAADCy to be used as fluorescence probe for monitoring the polymerization process of MM. - Highlights: ► The fluorescence excitation and emission spectra in MM possess a complex nature. ► Fluorescence decay kinetics for different degrees of polymerization of MM were investigated. ► The ICT fluorescence FWHM for EDMAADCy shows a linear dependence on the time of polymerization. ► EDMAADCy can be used as fluorescence probe for monitoring the polymerization process of MM

  4. Usefulness of charge-transfer complexation for the assessment of sympathomimetic drugs: Spectroscopic properties of drug ephedrine hydrochloride complexed with some π-acceptors

    Science.gov (United States)

    Refat, Moamen S.; Ibrahim, Omar B.; Saad, Hosam A.; Adam, Abdel Majid A.

    2014-05-01

    Recently, ephedrine (Eph) assessment in food products, pharmaceutical formulations, human fluids of athletes and detection of drug toxicity and abuse, has gained a growing interest. To provide basic data that can be used to assessment of Eph quantitatively based on charge-transfer (CT) complexation, the CT complexes of Eph with 7‧,8,8‧-tetracyanoquinodimethane (TCNQ), dichlorodicyanobenzoquinone (DDQ), 1,3-dinitrobenzene (DNB) or tetrabromothiophene (TBT) were synthesized and spectroscopically investigated. The newly synthesized complexes have been characterized via elemental analysis, IR, Raman, 1H NMR, and UV-visible spectroscopy. The formation constant (KCT), molar extinction coefficient (εCT) and other spectroscopic data have been determined using the Benesi-Hildebrand method and its modifications. The sharp, well-defined Bragg reflections at specific 2θ angles have been identified from the powder X-ray diffraction patterns. Thermal decomposition behavior of these complexes was also studied, and their kinetic thermodynamic parameters were calculated with Coats-Redfern and Horowitz-Metzger equations.

  5. Effects of Calcium Ions on the Thermostability and Spectroscopic Properties of the LH1-RC Complex from a New Thermophilic Purple Bacterium Allochromatium tepidum.

    Science.gov (United States)

    Kimura, Yukihiro; Lyu, Shuwen; Okoshi, Akira; Okazaki, Koudai; Nakamura, Natsuki; Ohashi, Akira; Ohno, Takashi; Kobayashi, Manami; Imanishi, Michie; Takaichi, Shinichi; Madigan, Michael T; Wang-Otomo, Zheng-Yu

    2017-05-18

    The light harvesting-reaction center (LH1-RC) complex from a new thermophilic purple sulfur bacterium Allochromatium (Alc.) tepidum was isolated and characterized by spectroscopic and thermodynamic analyses. The purified Alc. tepidum LH1-RC complex showed a high thermostability comparable to that of another thermophilic purple sulfur bacterium Thermochromatium tepidum, and spectroscopic characteristics similar to those of a mesophilic bacterium Alc. vinosum. Approximately 4-5 Ca 2+ per LH1-RC were detected by inductively coupled plasma atomic emission spectroscopy and isothermal titration calorimetry. Upon removal of Ca 2+ , the denaturing temperature of the Alc. tepidum LH1-RC complex dropped accompanied by a blue-shift of the LH1 Q y absorption band. The effect of Ca 2+ was also observed in the resonance Raman shift of the C3-acetyl νC═O band of bacteriochlorophyll-a, indicating changes in the hydrogen-bonding interactions between the pigment and LH1 polypeptides. Thermodynamic parameters for the Ca 2+ -binding to the Alc. tepidum LH1-RC complex indicated that this reaction is predominantly driven by the largely favorable electrostatic interactions that counteract the unfavorable negative entropy change. Our data support a hypothesis that Alc. tepidum may be a transitional organism between mesophilic and thermophilic purple bacteria and that Ca 2+ is one of the major keys to the thermostability of LH1-RC complexes in purple bacteria.

  6. Effect of hydrophobic interactions on properties and stability of DNA-polyelectrolyte complexes

    Czech Academy of Sciences Publication Activity Database

    Filippov, Sergey K.; Koňák, Čestmír; Kopečková, P.; Starovoytova, Larisa; Špírková, Milena; Štěpánek, Petr

    2010-01-01

    Roč. 26, č. 7 (2010), s. 4999-5006 ISSN 0743-7463 R&D Projects: GA ČR GA202/09/2078 EU Projects: European Commission(XE) 512087 - GIANT Institutional research plan: CEZ:AV0Z40500505 Keywords : DNA * polyplex * cholesterol Subject RIV: BO - Biophysics Impact factor: 4.269, year: 2010

  7. Energetic and binding properties of DNA upon interaction with dodecyl trimethylammonium bromide.

    Science.gov (United States)

    Bathaie, S Z; Moosavi-Movahedi, A A; Saboury, A A

    1999-02-15

    The interaction of dodecyl trimethylammonium bromide (DTAB), a cationic surfactant, with calf thymus DNA has been studied by various methods, including potentiometric technique using DTAB-selective plastic membrane electrode at 27 and 37 degreesC, isothermal titration microcalorimetry and UV spectrophotometry at 27 degreesC using 0.05 M Tris buffer and 0.01 M NaCl at pH 7.4. The free energy is calculated from binding isotherms on the basis of Wyman binding potential theory and the enthalpy of binding according to van't Hoff relation. The enthalpy of unfolding has been determined by subtraction of the enthalpy of binding from the microcalorimetric enthalpy. The results show that, after the interaction of first DTAB molecule to DNA (base molarity) through the electrostatic interaction, the second DTAB molecule also binds to DNA through electrostatic interaction. At this stage, the predom-inant DNA conformational change occurs. Afterwards up to 20 DTAB molecules, below the critical micelle concentration of DTAB, bind through hydrophobic interactions.

  8. Purification and DNA-binding properties of RNA polymerase from Bacillus subtilis.

    Science.gov (United States)

    Giacomoni, P U

    1980-05-01

    Four RNA-polymerizing activities having different subunit composition can be purified from uninfected and from SPO1-infected Bacillus subtilis. Lysozyme and sodium deoxycholate are used for lysing the cells. Polymin P is used for precipitating nucleic acids and DEAE-cellulose chromatography allows separation of enzymatic activity from the residual Polymin P. After these common steps, one can purify core + sigma + delta by chromatography on single-stranded DNA-agarose followed by gel filtration while pure core + sigma can be obtained by chromatography on double-stranded DNA cellulose. Core + delta is obtained by high-salt sucrose/glycerol gradient centrifugation. The host enzyme modified by the product of gene 28 of phage SPO1 can be purified from SPO1 infected cells by chromatography on DNA cellulose (or CNA agarose) followed by chromatography on phosphocellulose. The pH and salt dependance of the initial rate of RNA synthesis of core + sigma has been investigated using SPO1 and SPP1 DNA as templates. The optimum pH for the initial rate of transcription is 8.2 at 30 degrees C in 50 mM N,N-bis(2-hydroxyethyl)glycine buffer, and the optimum Na+ concentration is between 0.1 and 0.15 M. The kinetics of formation and of dissociation of non-filterable complexes between SPP1 DNA and core + sigma have been analyzed at different cationic concentrations. The value of the rate constant of dissociation in 0.1 M NaCl at 30 degrees C is kd = 2.16 x 10(-4) S-1. The value of the rate constant of association, under the same conditions, is ka = 5.5 x 10(8) M-1 S-1; this value is compatible with a diffusion-controlled reaction for promoter selection.

  9. Spectroscopic and radiation-resistant properties of Er,Pr:GYSGG laser crystal operated at 2.79 μm

    International Nuclear Information System (INIS)

    Zhao Xu-Yao; Sun Dun-Lu; Luo Jian-Qiao; Zhang Hui-Li; Fang Zhong-Qing; Quan Cong; Li Xiu-Li; Cheng Mao-Jie; Zhang Qing-Li; Yin Shao-Tang

    2017-01-01

    We demonstrate the spectroscopic and laser performance before and after 100 Mrad gamma-ray irradiation on an Er,Pr:GYSGG crystal grown by the Czochralski method. The additional absorption of Er,Pr:GYSGG crystal is close to zero in the 968 nm pumping and 2.7–3 μm laser wavelength regions. The lifetimes of the upper and lower levels show faint decreases after gamma-ray irradiation. The maximum output powers of 542 and 526 mW with the slope efficiencies of 17.7% and 17.0% are obtained, respectively, on the GYSGG/Er,Pr:GYSGG composite crystal before and after the gamma-ray irradiation. These results suggest that Er,Pr:GYSGG crystal as a laser gain medium possesses a distinguished anti-radiation ability for application in space and radiant environments. (paper)

  10. A Novel Property of DNA – As a Bioflotation Reagent in Mineral Processing

    Science.gov (United States)

    Vasanthakumar, Balasubramanian; Ravishankar, Honnavar; Subramanian, Sankaran

    2012-01-01

    Environmental concerns regarding the use of certain chemicals in the froth flotation of minerals have led investigators to explore biological entities as potential substitutes for the reagents in vogue. Despite the fact that several microorganisms have been used for the separation of a variety of mineral systems, a detailed characterization of the biochemical molecules involved therein has not been reported so far. In this investigation, the selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using the cellular components of Bacillus species. The key constituent primarily responsible for the flotation of sphalerite has been identified as DNA, which functions as a bio-collector. Furthermore, using reconstitution studies, the obligatory need for the presence of non-DNA components as bio-depressants for galena has been demonstrated. A probable model involving these entities in the selective flotation of sphalerite from the mineral mixture has been discussed. PMID:22768298

  11. A novel property of DNA - as a bioflotation reagent in mineral processing.

    Science.gov (United States)

    Vasanthakumar, Balasubramanian; Ravishankar, Honnavar; Subramanian, Sankaran

    2012-01-01

    Environmental concerns regarding the use of certain chemicals in the froth flotation of minerals have led investigators to explore biological entities as potential substitutes for the reagents in vogue. Despite the fact that several microorganisms have been used for the separation of a variety of mineral systems, a detailed characterization of the biochemical molecules involved therein has not been reported so far. In this investigation, the selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using the cellular components of Bacillus species. The key constituent primarily responsible for the flotation of sphalerite has been identified as DNA, which functions as a bio-collector. Furthermore, using reconstitution studies, the obligatory need for the presence of non-DNA components as bio-depressants for galena has been demonstrated. A probable model involving these entities in the selective flotation of sphalerite from the mineral mixture has been discussed.

  12. A novel property of DNA - as a bioflotation reagent in mineral processing.

    Directory of Open Access Journals (Sweden)

    Balasubramanian Vasanthakumar

    Full Text Available Environmental concerns regarding the use of certain chemicals in the froth flotation of minerals have led investigators to explore biological entities as potential substitutes for the reagents in vogue. Despite the fact that several microorganisms have been used for the separation of a variety of mineral systems, a detailed characterization of the biochemical molecules involved therein has not been reported so far. In this investigation, the selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using the cellular components of Bacillus species. The key constituent primarily responsible for the flotation of sphalerite has been identified as DNA, which functions as a bio-collector. Furthermore, using reconstitution studies, the obligatory need for the presence of non-DNA components as bio-depressants for galena has been demonstrated. A probable model involving these entities in the selective flotation of sphalerite from the mineral mixture has been discussed.

  13. Assessment of the photoprotection properties of sunscreens by chromatographic measurement of DNA damage in skin explants.

    Science.gov (United States)

    Mouret, Stéphane; Bogdanowicz, Patrick; Haure, Marie-José; Castex-Rizzi, Nathalie; Cadet, Jean; Favier, Alain; Douki, Thierry

    2011-01-01

    Evaluation of the photoprotection provided by sunscreens is performed either through the induction of erythema and expressed as the sun protection factor (SPF), or by the UVA-mediated persistent pigment darkening (PPD). None of these two endpoints has a link with skin cancer, the most deleterious consequence of excess exposure to solar UV radiation. We thus set up a complementary approach to evaluate the protection provided by sunscreens to the genome of human skin. This is based on the quantification of the thymine cyclobutane dimer (TT-CPD), the main DNA lesion induced by both UVB and UVA radiations. Irradiations were performed ex vivo on human skin explants and the level of TT-CPD in DNA was determined by HPLC associated with tandem mass spectrometry. The technique was first optimized and validated with three standard sunscreens. The study was then extended to the evaluation of a commercial high SPF sunscreen exhibiting efficient UVA photoprotection. The DNA protecting factor was found to reflect the ratio between UVB and UVA photoprotection, although the absolute values of the genomic protection were, as a general trend, lower than either SPF or PPD. These data show the usefulness of the proposed approach for the evaluation of the genoprotection afforded by sunscreens. © 2010 The Authors. Photochemistry and Photobiology © 2010 The American Society of Photobiology.

  14. Hamster endogenous retrovirus (HaER) - distinct properties of structural proteins and DNA polymerase

    International Nuclear Information System (INIS)

    Goldschmied-Reouven, A.; Yaniv, A.

    1983-01-01

    The structural proteins as well as some features of the RNA-dependent DNA polymerase of the hamster endogenous retrovirus (HaER) were examined. The polypeptide pattern of this virus is substantially different from that of other known retroviruses in containing major polypeptides with molecular weights of 68000, 59000, 27000, 24000 daltons. Double antibody competitive radioimmunoassays showed that the HaER particles do not share any detectable antigenic relatedness with the murine viruses' p30, but manifest a considerable relatedness with the feline leukemia virus p27 and a slight cross-reactivity with the rat virus major protein. The RNA-dependent DNA polymerase of HaER virus has a molecular size of approximately 73000 daltons and in contrast to other mammalian retroviruses shows no significant preference for Mn 2+ over Mg 2+ . Apart from the lack of antigenic relatedness between the HaER virus proteins and the p30 protein of murine viruses, there is also no antigenic relatedness between HaER and murine viruses insofar as their DNA polymerase is concerned. (Author)

  15. Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer.

    Science.gov (United States)

    Almeida, Michell O; Barros, Daiane A S; Araujo, Sheila C; Faria, Sergio H D M; Maltarollo, Vinicius G; Honorio, Kathia M

    2017-09-05

    Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O 15 (donor NBO) and BD* (π) N 1 -H 10 (acceptor NBO), being that the value of this interaction is 7.72kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer

    Science.gov (United States)

    Almeida, Michell O.; Barros, Daiane A. S.; Araujo, Sheila C.; Faria, Sergio H. D. M.; Maltarollo, Vinicius G.; Honorio, Kathia M.

    2017-09-01

    Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89 nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89 eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O15 (donor NBO) and BD* (π) N1-H10 (acceptor NBO), being that the value of this interaction is 7.72 kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment.

  17. Spectroscopic investigation of Indium Bromide for lighting purposes

    NARCIS (Netherlands)

    Mulders, H.C.J.; Kroesen, G.M.W.; Haverlag, M.; Haverlag, M.; Kroesen, G.M.W.; Tagushi, T.

    2010-01-01

    Laser Induced Fluorescence was used to study the radiative properties of InBr for lighting purposes. Results include the temperature dependence of the fluorescence decay time, spectroscopic constants and rotational temperature determination from a LIF spectrum.

  18. Electronic properties and assambly of DNA-based molecules on gold surfaces

    DEFF Research Database (Denmark)

    Salvatore, Princia

    , highly base specific voltammetric peak in the presence of spermidine ions. A capacitive origin was attributed to this peak, and a novel route to detection of hybridization and base pair mismatches proposed on the basis of the high sensitivity to base pair mismatches showed by such ON-based monolayers...... as widely employed as Au(111) surfaces). In particular, SERS offered a valuable and rapid way ofcharacterising interactions between the DNA-based molecules and the NP surface, with no need for complex sample preparation....

  19. New ELISA technique for analysis of p53 protein/DNA binding properties

    Czech Academy of Sciences Publication Activity Database

    Jagelská, Eva; Brázda, Václav; Pospíšilová, Š.; Vojtěšek, B.; Paleček, Emil

    2002-01-01

    Roč. 267, č. 2 (2002), s. 227-235 ISSN 0022-1759 R&D Projects: GA ČR GA301/00/D001; GA AV ČR IAB5004203; GA ČR GA301/00/P094; GA ČR GA301/02/0831; GA MZd NC6404; GA MZd NC5343; GA AV ČR IAA4004110 Institutional research plan: CEZ:AV0Z5004920 Keywords : ELISA * p53 * DNA-binding Subject RIV: BO - Biophysics Impact factor: 2.598, year: 2002

  20. Conjugation of Benzylvanillin and Benzimidazole Structure Improves DNA Binding with Enhanced Antileukemic Properties

    Science.gov (United States)

    Al-Mudarris, Ban A.; Chen, Shih-Hsun; Liang, Po-Huang; Osman, Hasnah; Jamal Din, Shah Kamal Khan; Abdul Majid, Amin M. S.

    2013-01-01

    Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy)-3-methoxybenzaldehyde) compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl)-2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2XP, and (R) and (S)-1-(2-benzyloxy-3-methoxyphenyl)-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1), the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1) has weak anticancer activity even after it was combined with the benzimidazole (2MP), but after addition of another benzylvanillin structure (2XP), stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS) significantly improved the

  1. Crystalline phase, profile characteristics and spectroscopic properties of Er3+/Tm3+-diffusion-codoped LiNbO3 crystal

    International Nuclear Information System (INIS)

    Sun, Wen-Bao; Zhang, Zi-Bo; Sun, Hong-Xue; Wong, Wing-Han; Yu, Dao-Yin; Pun, Edwin Yue-Bun

    2017-01-01

    Er 3+ /Tm 3+ -codoped LiNbO 3 crystal was prepared by co-diffusion of stacked Er and Tm metal films coated onto surface of off-congruent, Li-deficient LiNbO 3 substrate produced by Li-poor vapor transport equilibration technique. The crystalline phase on the diffused surface was analyzed by X-ray single-crystal diffraction. The Er 3+ and Tm 3+ profile characteristics were studied by secondary ion mass spectrometry. The emission spectra were measured under the 980 or 795 nm wavelength excitation, and the emission and absorption cross section spectra were calculated based upon McCumber theory. The lifetimes of some emissions were measured. The results show that the Er 3+ and Tm 3+ ions presence is in the form of LiNbO 3 phase. Both ions obey to Gaussian profile with a diffusion depth 21.5 μm. In the codoping case, both ions keep their respective spectroscopic features of only doping case and do not affect each other. The codoping enables to combine the wavelength emissions of both ions and the resultant emission band in the telecommunication window around 1.5 μm is as wide as 150 nm, providing the possibility of S+C+L broadband amplification by employing commercial 980 and 795 nm laser diodes as the pump sources. The Er 3+ /Tm 3+ -codoped LN is a promising host material for integrated optics. - Graphical abstract: Er 3+ /Tm 3+ -codoped LiNbO 3 crystal was prepared by co-diffusion of stacked Er and Tm metal films. The crystalline phase, diffusion profile and cross section spectra of Er 3+ and Tm 3+ ions in the diffusion layer have been investigated. The results show that the presence of Er 3+ and Tm 3+ ions is in the LiNbO 3 phase. Both ions follow Gaussian profile with a diffusion depth 21.5 μm. Both ions keep their respective spectroscopic features of only doping case. Excited state absorption is the dominant process for 795-nm-upconvered fluorescence of Tm 3+ . The codoping enables to combine the wavelength emissions of both ions and provide the possibility of S

  2. Crystalline phase, profile characteristics and spectroscopic properties of Er{sup 3+}/Tm{sup 3+}-diffusion-codoped LiNbO{sub 3} crystal

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Wen-Bao [Department of Opto-electronics and Information Engineering, School of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072 (China); Key Laboratory of Optoelectronic Information Technology, Ministry of Education (Tianjin University), Tianjin 300072 (China); Zhang, Zi-Bo [Department of Engineering, Pierre and Marie Curie University (University of Paris VI), 4 place Jussieu, 75005 Paris (France); Sun, Hong-Xue [Department of Opto-electronics and Information Engineering, School of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072 (China); Key Laboratory of Optoelectronic Information Technology, Ministry of Education (Tianjin University), Tianjin 300072 (China); Wong, Wing-Han, E-mail: eewhwong@cityu.edu.hk [Department of Opto-electronics and Information Engineering, School of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072 (China); Key Laboratory of Optoelectronic Information Technology, Ministry of Education (Tianjin University), Tianjin 300072 (China); Department of Electronic Engineering and State Key Laboratory of Millimeter Waves, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong (China); Yu, Dao-Yin [Department of Opto-electronics and Information Engineering, School of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072 (China); Key Laboratory of Optoelectronic Information Technology, Ministry of Education (Tianjin University), Tianjin 300072 (China); Pun, Edwin Yue-Bun [Department of Electronic Engineering and State Key Laboratory of Millimeter Waves, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong (China); and others

    2017-04-15

    Er{sup 3+}/Tm{sup 3+}-codoped LiNbO{sub 3} crystal was prepared by co-diffusion of stacked Er and Tm metal films coated onto surface of off-congruent, Li-deficient LiNbO{sub 3} substrate produced by Li-poor vapor transport equilibration technique. The crystalline phase on the diffused surface was analyzed by X-ray single-crystal diffraction. The Er{sup 3+} and Tm{sup 3+} profile characteristics were studied by secondary ion mass spectrometry. The emission spectra were measured under the 980 or 795 nm wavelength excitation, and the emission and absorption cross section spectra were calculated based upon McCumber theory. The lifetimes of some emissions were measured. The results show that the Er{sup 3+} and Tm{sup 3+} ions presence is in the form of LiNbO{sub 3} phase. Both ions obey to Gaussian profile with a diffusion depth 21.5 μm. In the codoping case, both ions keep their respective spectroscopic features of only doping case and do not affect each other. The codoping enables to combine the wavelength emissions of both ions and the resultant emission band in the telecommunication window around 1.5 μm is as wide as 150 nm, providing the possibility of S+C+L broadband amplification by employing commercial 980 and 795 nm laser diodes as the pump sources. The Er{sup 3+}/Tm{sup 3+}-codoped LN is a promising host material for integrated optics. - Graphical abstract: Er{sup 3+}/Tm{sup 3+}-codoped LiNbO{sub 3} crystal was prepared by co-diffusion of stacked Er and Tm metal films. The crystalline phase, diffusion profile and cross section spectra of Er{sup 3+} and Tm{sup 3+} ions in the diffusion layer have been investigated. The results show that the presence of Er{sup 3+} and Tm{sup 3+} ions is in the LiNbO{sub 3} phase. Both ions follow Gaussian profile with a diffusion depth 21.5 μm. Both ions keep their respective spectroscopic features of only doping case. Excited state absorption is the dominant process for 795-nm-upconvered fluorescence of Tm{sup 3+}. The

  3. Ultrasensitive Electrochemical Detection of Clostridium perfringens DNA Based Morphology-Dependent DNA Adsorption Properties of CeO2 Nanorods in Dairy Products

    Directory of Open Access Journals (Sweden)

    Xingcan Qian

    2018-06-01

    Full Text Available Foodborne pathogens such as Clostridium perfringens can cause diverse illnesses and seriously threaten to human health, yet far less attention has been given to detecting these pathogenic bacteria. Herein, two morphologies of nanoceria were synthesized via adjusting the concentration of NaOH, and CeO2 nanorod has been utilized as sensing material to achieve sensitive and selective detection of C. perfringens DNA sequence due to its strong adsorption ability towards DNA compared to nanoparticle. The DNA probe was tightly immobilized on CeO2/chitosan modified electrode surface via metal coordination, and the DNA surface density was 2.51 × 10−10 mol/cm2. Under optimal experimental conditions, the electrochemical impedance biosensor displays favorable selectivity toward target DNA in comparison with base-mismatched and non-complementary DNA. The dynamic linear range of the proposed biosensor for detecting oligonucleotide sequence of Clostridium perfringens was from 1.0 × 10−14 to 1.0 × 10−7 mol/L. The detection limit was 7.06 × 10−15 mol/L. In comparison, differential pulse voltammetry (DPV method quantified the target DNA with a detection limit of 1.95 × 10−15 mol/L. Moreover, the DNA biosensor could detect C. perfringens extracted DNA in dairy products and provided a potential application in food quality control.

  4. Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles.

    Science.gov (United States)

    Al-Ta'ii, Hassan Maktuff Jaber; Periasamy, Vengadesh; Amin, Yusoff Mohd

    2015-05-21

    Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0-20 min) of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung's and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung's methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles.

  5. Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles

    Directory of Open Access Journals (Sweden)

    Hassan Maktuff Jaber Al-Ta'ii

    2015-05-01

    Full Text Available Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0–20 min of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung’s and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung’s methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles.

  6. Spectroscopic properties of Er3+/Yb3+ Co-doped zinc boro-tellurite glasses for 1.5 xB5m broadband optical amplifiers

    Science.gov (United States)

    Suthanthirakumar, P.; Karthikeyan, P.; Vijayakumar, R.; Marimuthu, K.

    2015-06-01

    A new series of Er3+/Yb3+ co-doped Zinc boro-tellurite glasses with the chemical composition (40-x-y)B2O3+ 25TeO2+20ZnO+15BaO+xYb2O3+yEr2O3 (where x = 0.1, 0.5, 1 and 3; y =1 in wt %) were prepared by melt quenching technique and their spectroscopic behavior were studied through UV-Vis-NIR absorption and NIR luminescence measurements. The bonding parameters (β ¯ and δ) and Judd-Ofelt (JO) intensity parameters Ωλ (λ=2, 4 and 6) have been calculated from the band positions of the absorption spectra. A broad near-infrared emission band at 1540 nm with a full width at half maximum around 80 nm was observed from the NIR luminescence spectra by monitoring an excitation at 980 nm. The absorption cross-section and emission cross-section for the4I13/2→4I15/2 transition of the Er3+ ions were also determined using McCumber theory and the results were discussed and reported.

  7. The Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST) Quasar Survey: Quasar Properties from Data Release Two and Three

    Science.gov (United States)

    Dong, X. Y.; Wu, Xue-Bing; Ai, Y. L.; Yang, J. Y.; Yang, Q.; Wang, F.; Zhang, Y. X.; Luo, A. L.; Xu, H.; Yuan, H. L.; Zhang, J. N.; Wang, M. X.; Wang, L. L.; Li, Y. B.; Zuo, F.; Hou, W.; Guo, Y. X.; Kong, X.; Chen, X. Y.; Wu, Y.; Yang, H. F.; Yang, M.

    2018-05-01

    This is the second installment for the Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST) Quasar Survey, which includes quasars observed from 2013 September to 2015 June. There are 9024 confirmed quasars in DR2 and 10911 in DR3. After cross-match with the Sloan Digital Sky Survey (SDSS) quasar catalogs and NED, 12126 quasars are discovered independently. Among them, 2225 quasars were released by SDSS DR12 QSO catalog in 2014 after we finalized the survey candidates. 1801 sources were identified by SDSS DR14 as QSOs. The remaining 8100 quasars are considered as newly founded, and among them, 6887 quasars can be given reliable emission line measurements and the estimated black hole masses. Quasars found in LAMOST are mostly located at low-to-moderate redshifts, with a mean value of 1.5. The highest redshift observed in DR2 and DR3 is 5. We applied emission line measurements to Hα, Hβ, Mg II, and C IV. We deduced the monochromatic continuum luminosities using photometry data, and estimated the virial black hole masses for the newly discovered quasars. Results are compiled into a quasar catalog, which will be available online.

  8. Spectroscopic surveys of LAMOST

    International Nuclear Information System (INIS)

    Zhao Yongheng

    2015-01-01

    The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST), a new type of reflecting Schmidt telescope, has been designed and produced in China. It marks a breakthrough for large scale spectroscopic survey observation in that both large aperture and wide field of view have been achieved. LAMOST has the highest spectrum acquisition rate, and from October 2011 to June 2014 it has obtained 4.13 million spectra of celestial objects, of which 3.78 million are spectra of stars, with the stellar parameters of 2.20 million stars included. (author)

  9. Stk1-mediated phosphorylation stimulates the DNA-binding properties of the Staphylococcus aureus SpoVG transcriptional factor.

    Science.gov (United States)

    Bischoff, Markus; Brelle, Solène; Minatelli, Sabrina; Molle, Virginie

    2016-05-13

    The stage V sporulation protein G (SpoVG) homolog of Staphylococcus aureus is a modulator of virulence factor synthesis and antibiotic resistance in this clinically important gram-positive pathogen. Here we demonstrate that SpoVG can be phosphorylated by the staphylococcal Ser/Thr protein kinase Stk1 and that phosphorylation positively affects its DNA-binding properties. Mass spectrometric analyses and site directed mutagenesis identified Thr4, Thr13, Thr24 and Ser41 as phospho-acceptors. Stk1-mediated phosphorylation markedly enhanced the DNA binding activity of SpoVG towards the promoter regions of target genes such as capA, lip, and nuc1. Similarly, trans-complementation of the S. aureus ΔyabJ-spoVG mutant SM148 with a SpoVG derivative that mimics constitutive phosphorylation, SpoVG_Asp, exhibited capA, lip, and nuc1 transcript levels that were comparable to the levels seen with the wild-type, whereas trans-complementation with a phosphoablative variant of SpoVG (SpoVG_Ala) produced transcript levels similar to the ones seen in SM148. Our data suggest that the expression/activity of this transcription factor is tightly controlled in S. aureus by transcriptional, post-transcriptional and post-translational mechanisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. U4+ spectroscopic properties in Dsub(2d) with ThCl4, UCl4 and ThSiO4

    International Nuclear Information System (INIS)

    Khan Malek, C.

    1985-01-01

    This thesis is concerned with the study of the electronic structure of the tetravalent actinide ions in solid state. The technique used was high resolution optical spectroscopy. We deal with the U 4+ ion (sf 2 ) in the monocrystals ThCl 4 , UCl 4 , and ThSiO 4 where the U 4+ ion is substituded for the Th 4+ ion by doping. Visible and infrared optical spectra were recorded between 300 and 4.2K. With these three compounds, it is possible to compare the influence of different environments of Dsub(2d) symmetry: real symmetry for U 4+ in UCl 4 and ThSiO 4 ; approximate symmetry in ThCl 4 , whose structure is incommensurate and modulated at low temperature. The fitting of the data was carried out by diagonalizing the hamiltonian which describes the interactions of the U 4+ ion in a crystal field with its environment. This fitting procedure led to a coherent set of spectroscopic parameters. The fluorescence of U 4+ was observed in ThCl 4 and ThSiO 4 and the effect of the incommensurate structure of ThCl 4 on the optical spectra was studied. The symmetry of the U 4+ sites was identified by site selective excitation experiments and a relationship between the incommensurate structure and the lifetime of U 4+ energy levels was found. In conclusion, the U 4+ energy levels in a relatively low crystal field were determined for compounds that have a similar coordination polyhedron about the actinide ion. The values for these energy levels were then compared to those of lanthanide and 3d elements [fr

  11. Kinematic, Photometric, and Spectroscopic Properties of Faint White Dwarf Stars Discovered in the HALO7D Survey of the Milky Way Galaxy

    Science.gov (United States)

    Harris, Madison; Cunningham, Emily; Guhathakurta, Puragra; Cheshire, Ishani; Gupta, Nandita

    2018-01-01

    White dwarf (WD) stars represent the final phase in the life of solar-mass stars. The extreme low luminosity of WDs means that most detailed measurements of such stars are limited to samples in the immediate neighborhood of the Sun in the thin disk of the Milky Way galaxy. We present spectra, line-of-sight (LOS) velocities, and proper motions (PMs) of a sample of faint (m_V ~ 19.0–24.5) white dwarfs (WDs) from the HALO7D survey. HALO7D is a Keck II/DEIMOS spectroscopic survey of unprecedented depth (8–24 hour integrations) in the CANDELS fields of main sequence turnoff stars in the Milky Way's outer halo. Faint WD stars are rare but useful by-products of this survey. We identify the sample of WDs based on their characteristic broad spectral Balmer absorption features, and present a Bayesian method for measuring their LOS velocities. Using their broadband colors, LOS velocities and PMs measured with the Hubble Space Telescope, we identify candidate halo members among the WDs based on the predicted velocity distributions from the Besançon numerical model of stellar populations in the Milky Way galaxy. The WDs found in the HALO7D survey will yield new insights on the old stellar population associated with the Milky Way's thick disk and halo. Funding for this research was provided by the National Science Foundation and NASA/STScI. NG and IC's participation in this research was under the auspices of the Science Internship Program at the University of California Santa Cruz.

  12. Properties of internalization factors contributing to the uptake of extracellular DNA into tumor-initiating stem cells of mouse Krebs-2 cell line.

    Science.gov (United States)

    Dolgova, Evgeniya V; Potter, Ekaterina A; Proskurina, Anastasiya S; Minkevich, Alexandra M; Chernych, Elena R; Ostanin, Alexandr A; Efremov, Yaroslav R; Bayborodin, Sergey I; Nikolin, Valeriy P; Popova, Nelly A; Kolchanov, Nikolay A; Bogachev, Sergey S

    2016-05-25

    Previously, we demonstrated that poorly differentiated cells of various origins, including tumor-initiating stem cells present in the ascites form of mouse cancer cell line Krebs-2, are capable of naturally internalizing both linear double-stranded DNA and circular plasmid DNA. The method of co-incubating Krebs-2 cells with extracellular plasmid DNA (pUC19) or TAMRA-5'-dUTP-labeled polymerase chain reaction (PCR) product was used. It was found that internalized plasmid DNA isolated from Krebs-2 can be transformed into competent Escherichia coli cells. Thus, the internalization processes taking place in the Krebs-2 cell subpopulation have been analyzed and compared, as assayed by E. coli colony formation assay (plasmid DNA) and cytofluorescence (TAMRA-DNA). We showed that extracellular DNA both in the form of plasmid DNA and a PCR product is internalized by the same subpopulation of Krebs-2 cells. We found that the saturation threshold for Krebs-2 ascites cells is 0.5 μg DNA/10(6) cells. Supercoiled plasmid DNA, human high-molecular weight DNA, and 500 bp PCR fragments are internalized into the Krebs-2 tumor-initiating stem cells via distinct, non-competing internalization pathways. Under our experimental conditions, each cell may harbor 340-2600 copies of intact plasmid material, or up to 3.097 ± 0.044×10(6) plasmid copies (intact or not), as detected by quantitative PCR. The internalization dynamics of extracellular DNA, copy number of the plasmids taken up by the cells, and competition between different types of double-stranded DNA upon internalization into tumor-initiating stem cells of mouse ascites Krebs-2 have been comprehensively analyzed. Investigation of the extracellular DNA internalization into tumor-initiating stem cells is an important part of understanding their properties and possible destruction mechanisms. For example, a TAMRA-labeled DNA probe may serve as an instrument to develop a target for the therapy of cancer, aiming at elimination of

  13. Interaction of gold nanoparticles with Pfu DNA polymerase and effect on polymerase chain reaction.

    Science.gov (United States)

    Sun, L-P; Wang, S; Zhang, Z-W; Ma, Y-Y; Lai, Y-Q; Weng, J; Zhang, Q-Q

    2011-03-01

    The interaction of gold nanoparticles with Pfu DNA polymerase has been investigated by a number of biological, optical and electronic spectroscopic techniques. Polymerase chain reaction was performed to show gold nanoparticles' biological effect. Ultraviolet-visible and circular dichroism spectra analysis were applied to character the structure of Pfu DNA polymerase after conjugation with gold nanoparticles. X-ray photoelectron spectroscopy was used to investigate the bond properties of the polymerase-gold nanoparticles complex. The authors demonstrate that gold nanoparticles do not affect the amplification efficiency of polymerase chain reaction using Pfu DNA polymerase, and Pfu DNA polymerase displays no significant changes of the secondary structure upon interaction with gold nanoparticles. The adsorption of Pfu DNA polymerase to gold nanoparticles is mainly through Au-NH(2) bond and electrostatic interaction. These findings may have important implications regarding the safety issue as gold nanoparticles are widely used in biomedical applications.

  14. Covalently bound DNA on naked iron oxide nanoparticles: Intelligent colloidal nano-vector for cell transfection.

    Science.gov (United States)

    Magro, Massimiliano; Martinello, Tiziana; Bonaiuto, Emanuela; Gomiero, Chiara; Baratella, Davide; Zoppellaro, Giorgio; Cozza, Giorgio; Patruno, Marco; Zboril, Radek; Vianello, Fabio

    2017-11-01

    Conversely to common coated iron oxide nanoparticles, novel naked surface active maghemite nanoparticles (SAMNs) can covalently bind DNA. Plasmid (pDNA) harboring the coding gene for GFP was directly chemisorbed onto SAMNs, leading to a novel DNA nanovector (SAMN@pDNA). The spontaneous internalization of SAMN@pDNA into cells was compared with an extensively studied fluorescent SAMN derivative (SAMN@RITC). Moreover, the transfection efficiency of SAMN@pDNA was evaluated and explained by computational model. SAMN@pDNA was prepared and characterized by spectroscopic and computational methods, and molecular dynamic simulation. The size and hydrodynamic properties of SAMN@pDNA and SAMN@RITC were studied by electron transmission microscopy, light scattering and zeta-potential. The two nanomaterials were tested by confocal scanning microscopy on equine peripheral blood-derived mesenchymal stem cells (ePB-MSCs) and GFP expression by SAMN@pDNA was determined. Nanomaterials characterized by similar hydrodynamic properties were successfully internalized and stored into mesenchymal stem cells. Transfection by SAMN@pDNA occurred and GFP expression was higher than lipofectamine procedure, even in the absence of an external magnetic field. A computational model clarified that transfection efficiency can be ascribed to DNA availability inside cells. Direct covalent binding of DNA on naked magnetic nanoparticles led to an extremely robust gene delivery tool. Hydrodynamic and chemical-physical properties of SAMN@pDNA were responsible of the successful uptake by cells and of the efficiency of GFP gene transfection. SAMNs are characterized by colloidal stability, excellent cell uptake, persistence in the host cells, low toxicity and are proposed as novel intelligent DNA nanovectors for efficient cell transfection. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. TRLIFS study of Eu(III) spectroscopic properties to obtain structural and thermodynamic informations on lanthanide-malonamide complexes in the Eu(III)/NaNO3/tetraethylmalonamide system

    International Nuclear Information System (INIS)

    Couston, L.; Charbonnel, M.C.; Flandin, J.L.; Rancier, F.; Moulin, C.

    2004-01-01

    Improvement of the nuclear fuel reprocessing involves separating the minor actinides (Am(III) and Cm(III)) from the fission products. In the French strategy, the first step consists in the separation of the trivalent actinides and lanthanides from high-level liquid waste, for which malonamides RR'NCO(CHR '' )CONRR' are promising ligands. These molecules have been optimized for reprocessing but still require basic chemical studies to describe the complexation mechanisms at a molecular scale. This paper discusses a thermodynamic and structural study of a Ln(III)-malonamide complex formed with the hydrosoluble tetraethylmalonamide ligand (TEMA = (C 2 H 5 ) 2 NCOCH 2 CON(C 2 H 5 ) 2 ) dissolved in a nitrate medium. Despite the simplified chemical system obtained with TEMA, its weak chemical affinity and its physical properties pushed the analytical techniques to their limits. The sensitivity of time-resolved laser-induced fluorescence spectroscopy (TRLIFS) combined with the major luminescent spectroscopic properties of Eu(III) (hypersensitive band and fluorescence lifetime) were successfully used to determine the equilibrium constant and hydration number in the Eu(III), TEMA, and NO 3 - system. Fluorescence lifetimes, connected with the first coordination sphere of the solvated metal, clearly show the inner-sphere location of nitrate in the Eu(NO 3 ) 2+ complex, the outer-sphere location of TEMA in the Eu(TEMA) 3+ complex, and the outer-sphere location of both ligands in the Eu(NO 3 )(TEMA) 2+ complex. (orig.)

  16. Hydrothermal synthesis, structural elucidation, spectroscopic studies, thermal behavior and luminescence properties of a new 3-d compound: FeAlF2(C10H8N2)(HPO4)2(H2O)

    Science.gov (United States)

    Bouzidia, Nabaa; Salah, Najet; Hamdi, Besma; Ben Salah, Abdelhamid

    2017-04-01

    The study of metal phosphate has been a proactive field of research thanks to its applied and scientific importance, especially in terms of the development of optical devices such as solid state lasers as well as optical fibers. The present paper seeks to investigate the synthesis, crystal structure, elemental analysis and properties of FeAlF2(C10H8N2)(HPO4)2(H2O) compound investigated by spectroscopic studies (FT-IR and FT-Raman), thermal behavior and luminescence. The Hirshfeld surface analysis and 2-D fingerprint plot have been performed to explore the behavior of these weak interactions and crystal cohesion. This investigation shows that the molecules are connected by hydrogen bonds of the type Osbnd H⋯O and Osbnd H⋯F. In addition, the 2,2'‒bipyridine ligand plays a significant role in the construction of 3-D supramolecular framework via π‒π stacking. FT‒IR and FT‒Raman spectra were used so as to ease the responsibilities of the vibration modes of the title compound. The thermal analysis (TGA) study shows a mass loss evolution as a temperature function. Finally, the optical properties were evaluated by photoluminescence spectroscopy.

  17. Shell model and spectroscopic factors

    International Nuclear Information System (INIS)

    Poves, P.

    2007-01-01

    In these lectures, I introduce the notion of spectroscopic factor in the shell model context. A brief review is given of the present status of the large scale applications of the Interacting Shell Model. The spectroscopic factors and the spectroscopic strength are discussed for nuclei in the vicinity of magic closures and for deformed nuclei. (author)

  18. (CAG)(n)-hairpin DNA binds to Msh2-Msh3 and changes properties of mismatch recognition.

    Science.gov (United States)

    Owen, Barbara A L; Yang, Zungyoon; Lai, Maoyi; Gajec, Maciej; Gajek, Maciez; Badger, John D; Hayes, Jeffrey J; Edelmann, Winfried; Kucherlapati, Raju; Wilson, Teresa M; McMurray, Cynthia T

    2005-08-01

    Cells have evolved sophisticated DNA repair systems to correct damaged DNA. However, the human DNA mismatch repair protein Msh2-Msh3 is involved in the process of trinucleotide (CNG) DNA expansion rather than repair. Using purified protein and synthetic DNA substrates, we show that Msh2-Msh3 binds to CAG-hairpin DNA, a prime candidate for an expansion intermediate. CAG-hairpin binding inhibits the ATPase activity of Msh2-Msh3 and alters both nucleotide (ADP and ATP) affinity and binding interfaces between protein and DNA. These changes in Msh2-Msh3 function depend on the presence of A.A mispaired bases in the stem of the hairpin and on the hairpin DNA structure per se. These studies identify critical functional defects in the Msh2-Msh3-CAG hairpin complex that could misdirect the DNA repair process.

  19. Electronic structure, Fermi surface topology and spectroscopic optical properties of LaBaCo{sub 2}O{sub 5.5} compound

    Energy Technology Data Exchange (ETDEWEB)

    Reshak, A.H. [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, Pilsen 306 14 (Czech Republic); Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia); Al-Douri, Y. [Institute of Nano Electronic Engineering, University Malaysia Perlis, 01000 Kangar, Perlis (Malaysia); Khenata, R. [Laboratoire de Physique Quantique et de Modélisation Mathématique (LPQ3M), Département de Technologie, Université de Mascara, Mascara 29000 (Algeria); Khan, Wilayat; Khan, Saleem Ayaz [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, Pilsen 306 14 (Czech Republic); Azam, Sikander, E-mail: sikander.physicst@gmail.com [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, Pilsen 306 14 (Czech Republic)

    2014-08-01

    We have investigated the electronic band structure, Fermi surface topology, chemical bonding and optical properties of LaBaCo{sub 2}O{sub 5.5} compound. The first-principle calculations based on density functional theory (DFT) by means of the full-potential linearized augmented plane-wave method were employed. The atomic positions of LaBaCo{sub 2}O{sub 5.5} compound were optimized by minimizing the forces acting on atoms. We employed the local density approximation (LDA), generalized gradient approximation (GGA) and Engel–Vosko GGA (EVGGA) to treat the exchange correlation potential by solving Kohn–Sham equations. Electronic structure and bonding properties are studied throughout the calculation of densities of states, Fermi surfaces and charge densities. Furthermore, the optical properties are investigated via the calculation of the dielectric tensor component in order to characterize the linear optical properties. Optical spectra are analyzed by means of the electronic structure, which provides theoretical understanding of the conduction mechanism of the investigated compound. - Highlights: • DFT-FPLAPW method used for calculating the properties of LaBaCo{sub 2}O{sub 5.5} compound. • This study shows that nature of the compound is metallic. • Crystallographic plane which shows covalent character of O–Co bond. • The optical properties were also calculated and analyzed. • The Fermi surface of LaBaCo{sub 2}O{sub 5.5} is composed of five bands crossing along Γ–Z direction.

  20. Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

    Directory of Open Access Journals (Sweden)

    Yogini P. Bhavsar

    2011-01-01

    Full Text Available Topological variants of single-strand DNA (ssDNA structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC and 1,3-diaza-2-oxophenoxazine (tC∘, can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.

  1. Synthesis, characterization, DNA-binding, and DNA-photocleavage properties of [Co(bpy)2(7-NO2-dppz)]3+, [Co(dmb)2(7-NO2-dppz)]3+, and [Co(phen)2(7-NO2-dppz)]3+ complexes: (7-nitro-dppz = 7-nitro dipyrido[3,2-a:2'-3'-c]phenazine; bpy = 2,2'-bipyridine; dmb = 4,4'-dimethyl-2,2'-bipyridine; phen = 1,10-phenanthroline) and their toxicity on different microorganisms.

    Science.gov (United States)

    Reddy, Kotha Laxma; Reddy, Y Harish Kumar; Kumar, K Ashwini; Vidhisha, S; Satyanarayana, S

    2009-03-01

    The polypyridyl ligand 7-Nitro dipyrido[3,2-a:2'-3'-c]phenazine (7-Nitro-dppz) and its complexes [Co(bpy)(2)(7-NO(2)-dppz)](3+)(1) (bpy = 2,2'-bipyridine), [Co(dmb)(2)(7-NO(2)-dppz)](3+)(2), (dmb = 4,4'-dimethyl-2,2'-bipyridine), and [Co(phen)(2)(7-NO(2)-dppz)](3+)(3) (phen = 1,10-phenanthroline) were synthesized and characterized by UV/VIS, IR, elemental analysis, (1)H and (13)C-NMR, and mass spectra. The binding properties of the three complexes to CT-DNA were investigated by different spectroscopic methods and viscosity measurements and DNA cleavage assay. The experimental results suggest that these complexes bind to CT-DNA through an intercalative mode. Also, the three complexes promote the photocleavage of plasmid pBR-322 DNA under irradiation. Toxicological effects of the selected complexes were estimated with different microorganisms.

  2. Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

    Science.gov (United States)

    2011-01-01

    Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der

  3. Theoretical investigations on the structural, spectroscopic, electronic and thermodynamic properties of (3-Oxo-3H-benzo[f]chromen-1yl methyl N,N-dimethylcarbamodithioate-1ex

    Directory of Open Access Journals (Sweden)

    Kara Mehmet

    2017-10-01

    Full Text Available Hartree-Fock and Density Functional Theory (B3LYP, B3PW91 calculations for the ground state of (3-Oxo-3Hbenzo[ f]chromen-1-yl methyl N,N-dimethylcarbamodithioate have been presented and the calculated structural parameters and energetic properties have been compared with the available X-ray diffraction data. The vibrational frequencies have been calculated using optimized geometry of the molecule. The conformational properties of the molecule have been determined by computing molecular energy properties, in which torsional angle varied from -180° to +180° in steps of 10°. Moreover, natural bond orbital analysis and atomic charge analysis have been performed. Besides, HOMO and LUMO energies have been calculated and their pictures have been presented. Finally, molecular electrostatic potential and thermodynamic properties have been calculated. It is seen that the obtained theoretical results agree well with the available experimental values. In all the calculations, except for optimization and vibrational calculations, B3LYP level of theory with 6-311++G(d,p basis set has been used.

  4. Low-dimensional compounds containing cyano groups. XVII. Crystal structure, spectroscopic, thermal and magnetic properties of [Cu(bmen)2][Pt(CN)4] (bmen=N,N'-dimethylethylenediamine)

    International Nuclear Information System (INIS)

    Potocnak, Ivan; Vavra, Martin; Cizmar, Erik; Kajnakova, Marcela; Radvakova, Alena; Steinborn, Dirk; Zvyagin, Sergei A.; Wosnitza, Jochen; Feher, Alexander

    2009-01-01

    The synthesis, structural analysis, spectroscopic studies, susceptibility and specific-heat measurements of {[Cu(bmen) 2 ][Pt(CN) 4 ]} n (bmen=N,N'-dimethylethylenediamine) are presented. X-ray crystal-structure analysis revealed that the [Pt(CN) 4 ] 2- building blocks are combined with [Cu(bmen) 2 ] 2+ units to form a chain-like structure along the a axis. The Cu(II) atoms are hexacoordinated by four nitrogen atoms in the equatorial plane belonging to two molecules of bidentate bmen ligands with average Cu-N distance of 2.043(18) A. The axial positions are occupied by two nitrogen atoms from bridging [Pt(CN) 4 ] 2- anions at a longer axial Cu-N distance of 2.490(4) A. The compound is characterized by the presence of a weak antiferromagnetic exchange coupling J/k B =0.6 K. Despite the one-dimensional (1D) character of the structure, the analysis of the magnetic properties and specific heat at very low temperatures shows that [Cu(bmen) 2 ][Pt(CN) 4 ] behaves as a two-dimensional (2D) square-lattice Heisenberg magnet with weak interlayer coupling. - Graphical abstract: The synthesis, structural analysis, spectroscopic studies, susceptibility and specific-heat measurements of {[Cu(bmen) 2 ][Pt(CN) 4 ]} n (bmen=N,N'-dimethylethylenediamine) are presented. X-ray crystal-structure analysis revealed that the [Pt(CN) 4 ] 2- building blocks are combined with [Cu(bmen) 2 ] 2+ units to form a chain-like structure. The compound is characterized by the presence of a weak antiferromagnetic exchange coupling J/k B =-0.6 K. Despite the one-dimensional character of the structure, the analysis of the magnetic properties and specific heat at very low temperatures shows that [Cu(bmen) 2 ][Pt(CN) 4 ] behaves as a two-dimensional square-lattice Heisenberg magnet with weak interlayer coupling

  5. Latest Results on Top Quark Properties: \\\\ Deciphering the DNA of the heaviest quark

    CERN Document Server

    Gallinaro, Michele

    2017-01-01

    The top quark, the heaviest known elementary particle discovered at the Fermilab Tevatron more than twenty years ago, has taken a central role in the study of fundamental interactions. Due to its large mass, the top quark provides a unique environment for tests of the standard model. With a cumulative luminosity of more than 100~fb$^{-1}$ collected at $\\sqrt{s}=7,8,13$~TeV by each of the ATLAS and CMS experiments at the Large Hadron Collider in the first ten years of operation, top quark physics is probing uncharted territories in precision and rare measurements with sensitivity to New Physics processes. This document summarizes the latest experimental measurements and studies of top quark properties.

  6. The Spectroscopic Properties of Lyα-Emitters at z ˜2.7: Escaping Gas and Photons from Faint Galaxies

    Science.gov (United States)

    Trainor, Ryan F.; Steidel, Charles C.; Strom, Allison L.; Rudie, Gwen C.

    2015-08-01

    We present a spectroscopic survey of 318 faint ({R}˜ 27, L˜ 0.1{L}*), Lyα-emission-selected galaxies (LAEs) in regions centered on the positions of hyperluminous QSOs (HLQSOs) at 2.5\\lt z\\lt 3. A sample of 32 LAEs with rest-frame optical emission line spectra from Keck/Multi-Object Spectrometer For InfraRed Exploration (MOSFIRE) are used to interpret the LAE spectra in the context of their systemic redshifts. The fields are part of the Keck Baryonic Structure Survey, which includes substantial ancillary multi-wavelength imaging from both the ground and space. From a quantitative analysis of the diverse Lyα spectral morphologies, including line widths, asymmetries, and multi-peaked profiles, we find that peak widths and separations are typically smaller than among samples of more luminous continuum-selected galaxies (Lyman-break galaxies and their analogs; LBGs) at similar redshifts. We find tentative evidence for an association between Lyα spectral morphology and external illumination by the nearby HLQSO. Using the MOSFIRE subsample, we find that the peak of the resolved (R ≈ 1300) Lyα line is shifted by +200 km s-1 with respect to systemic across a diverse set of galaxies including both LAEs and LBGs. We also find a small number of objects with significantly blueshifted Lyα emission, a potential indicator of accreting gas. The Lyα-to-Hα line ratios measured for the MOSFIRE subset suggest that the LAEs in this sample have Lyα escape fractions {f}{esc,{Ly}α } ≈ 30%, significantly higher than typical LBG samples. Using redshifts calibrated by our MOSFIRE sample, we construct composite LAE spectra, finding the first evidence for metal-enriched outflows in such intrinsically faint high-redshift galaxies. These outflows have smaller continuum covering fractions ({f}{{c}}≈ 0.3) and velocities ({v}{ave} ≈ 100-200 km s-1, {v}{max} ≈ 500 km s-1) than those associated with typical LBGs, suggesting that the gas covering fraction is a likely driver of

  7. State-of-the-art ab initio potential energy curve for the xenon atom pair and related spectroscopic and thermophysical properties

    Science.gov (United States)

    Hellmann, Robert; Jäger, Benjamin; Bich, Eckard

    2017-07-01

    A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.

  8. Electrochemical and spectroscopic properties of 1:2 Ni complexes of 1,3-substitued (CH3, OCH3) phenyl-5-phenylformazans

    International Nuclear Information System (INIS)

    Tezcan, Habibe; Uzluk, Elif; Aksu, Mehmet Levent

    2008-01-01

    In this study, new 1:2 nickel complexes of 1-[o-, m-, p-(methyl, metoxyphenyl)]-3-(p-metoxyphenyl)-5-phenylformazans were synthesized. Their structures were elucidated and spectral behaviors were investigated with the use of elemental analysis, GC-mass, 1 H NMR, 13 C NMR, IR, and UV-vis spectra. The redox characteristics of these compounds have been investigated in nonaqueous dimethylsulfoxide at platinum and ultramicro platinum (10 μm) electrodes. Through controlled potential electrolysis, the oxidation products of each class of compounds can be separated and identified. The oxidation mechanism is suggested and it is proved. It was observed the oxidation mechanism take place in a single step two-electron or one-electron transfer to a disproportionation or dimerization reactions following the radical formation step. Eventually the relation between their absorption properties and electrochemical properties was examined

  9. State-of-the-art ab initio potential energy curve for the xenon atom pair and related spectroscopic and thermophysical properties.

    Science.gov (United States)

    Hellmann, Robert; Jäger, Benjamin; Bich, Eckard

    2017-07-21

    A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.

  10. CaF{sub 2}(Eu{sup 2+}):LiF - Structural and spectroscopic properties of a new system for neutron detection

    Energy Technology Data Exchange (ETDEWEB)

    Trojan-Piegza, Joanna, E-mail: jtp@eto.wchuwr.p [Department of Manufacturing Engineering, Boston University, 15 St. Mary' s Street, Boston, MA 02215 (United States); Faculty of Chemistry, Wroclaw University, 14 F. Joliot-Curie Street, Wroclaw 50-383 (Poland); Glodo, Jarek [RMD Inc., Watertown, MA (United States); Sarin, Vinod Kumar [Department of Manufacturing Engineering, Boston University, 15 St. Mary' s Street, Boston, MA 02215 (United States)

    2010-02-15

    A series of composites of CaF{sub 2}(Eu{sup 2+}) and LiF with different Ca/Li ratios were fabricated via liquid phase consolidation. Luminescent properties of these samples were investigated. Radioluminescence shows the typical Eu{sup 2+} blue emission in all the compositions. The energy spectra measured under gamma and neutron irradiation indicates that the most promising composition for neutron detection is the eutectic.

  11. Structural, electronic, topological and vibrational properties of a series of N-benzylamides derived from Maca (Lepidium meyenii) combining spectroscopic studies with ONION calculations

    Science.gov (United States)

    Chain, Fernando E.; Ladetto, María Florencia; Grau, Alfredo; Catalán, César A. N.; Brandán, Silvia Antonia

    2016-02-01

    In the present work, the structural, topological and vibrational properties of four members of the N-benzylamides series derived from Maca (Lepidium meyenii) whose names are, N-benzylpentadecanamide, N-benzylhexadecanamide, N-benzylheptadecanamide and N-benzyloctadecanamide, were studied combining the FTIR, FT-Raman and 1H and 13C-NMR spectroscopies with density functional theory (DFT) and ONION calculations. Furthermore, the N-benzylacetamide, N-benzylpropilamide and N-benzyl hexanamide derivatives were also studied in order to compare their properties with those computed for the four macamides. These seven N-benzylamides series have a common structure, C8H8NO-R, being R the side chain [-(CH2)n-CH3] with a variable n number of CH2 groups. Here, the atomic charges, molecular electrostatic potentials, stabilization energies, topological properties of those macamides were analyzed as a function of the number of C atoms of the side chain while the frontier orbitals were used to compute the gap energies and some descriptors in order to predict their reactivities and behaviors in function of the longitude of the side chain. Here, the force fields, the complete vibrational assignments and the corresponding force constants were only reported for N-benzylacetamide, N-benzyl hexanamide and N-benzylpentadecanamide due to the high number of vibration normal modes that present the remains macamides.

  12. Evaluation of the structural, electronic, topological and vibrational properties of N-(3,4-dimethoxybenzyl)-hexadecanamide isolated from Maca (Lepidium meyenii) using different spectroscopic techniques

    Science.gov (United States)

    Chain, Fernando; Iramain, Maximiliano Alberto; Grau, Alfredo; Catalán, César A. N.; Brandán, Silvia Antonia

    2017-01-01

    N-(3,4-dimethoxybenzyl)-hexadecanamide (DMH) was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet- Visible (UV-Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance (1H and 13C NMR) spectroscopies. The structural, electronic, topological and vibrational properties were evaluated in gas phase and in n-hexane employing ONIOM and self-consistent force field (SCRF) calculations. The atomic charges, molecular electrostatic potentials, stabilization energies and topological properties of DMH were analyzed and compared with those calculated for N-(3,4-dimethoxybenzyl)-acetamide (DMA) in order to evaluate the effect of the side chain on the properties of DMH. The reactivity and behavior of this alkamide were predicted by using the gap energies and some descriptors. Force fields and the corresponding force constants were reported for DMA only in gas phase and n-hexane due to the high number of vibration normal modes showed by DMH, while the complete vibrational assignments are presented for DMA and both forms of DMH. The comparisons between the experimental FTIR, FT-Raman, UV-Visible and 1H and 13C NMR spectra with the corresponding theoretical ones showed a reasonable concordance.

  13. On tungstates of divalent cations (I). Structural investigation and spectroscopic properties of Sr{sub 2}[WO{sub 5}] and Ba{sub 2}[WO{sub 5}

    Energy Technology Data Exchange (ETDEWEB)

    Jantz, Stephan G.; Dialer, Marwin; Hoeppe, Henning A. [Lehrstuhl fuer Festkoerperchemie, Universitaet Augsburg (Germany); Pielnhofer, Florian [Abteilung Nanochemie, Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)

    2017-12-13

    The crystal structures of Sr{sub 2}[WO{sub 5}] [Pna2{sub 1}, a = 7.2457(3) Aa, b = 10.8867(5) Aa, c = 5.5391(3) Aa, Z = 4, R{sub int} = 0.0671, R{sub 1} = 0.0495, wR{sub 2} = 0.0462] and Ba{sub 2}[WO{sub 5}] [Pnma, a = 7.3828(2) Aa, b = 5.71420(10) Aa, c = 11.4701(3) Aa, Z = 4, R{sub int} = 0.0294, R{sub 1} = 0.0146, wR{sub 2} = 0.0284] are revised, based on single-crystal XRD data. Furthermore spectroscopic data (infrared, Raman, and UV/Vis) assisted by DFT calculations are discussed and first results on the luminescence properties of Sr{sub 2}[WO{sub 5}]:Eu{sup 3+} are presented. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Modulating the electronic properties of asymmetric push–pull and symmetric Zn(II)-diarylporphyrinates with para substituted phenylethynyl moieties in 5,15 meso positions: A combined electrochemical and spectroscopic investigation

    International Nuclear Information System (INIS)

    Mussini, Patrizia Romana; Orbelli Biroli, Alessio; Tessore, Francesca; Pizzotti, Maddalena; Biaggi, Cinzia; Di Carlo, Gabriele; Lobello, Maria Grazia; De Angelis, Filippo

    2012-01-01

    Graphical abstract: - Abstract: Push–pull Zn(II)-porphyrinates have recently shown attracting performances as light harvesting systems in dye-sensitized solar cells (DSSCs). To fully exploit their intrinsically high efficiency it is important to finely tune their HOMO and LUMO levels, which can be achieved by proper choice of the push and pull substituents. Of course such target-oriented molecular design requires the availability of reliable relationships between molecular structure and electronic properties; therefore we have carried out a combined electrochemical, spectroscopic and computational investigation on a wide, systematic range of Zn(II)-porphyrinates 5,15 meso substituted with phenylethynyl linkers, including a first symmetric series carrying on the opposite terminals the same substituent (-N(CH 3 ) 2 , -OCH 3 , -COOCH 3 , -COOH, -NO 2 ); and a second push–pull one, with the terminal positions carrying one donor and one acceptor group belonging to the series above. Moreover, two suitably modified porphyrins allowed evaluation of the effects of (i) the presence or absence of the phenyl group in the linker between the porphyrin core and the acceptor group, and (ii) the effect of perfluorination on the same phenyl group. A rationalization scheme is proposed encompassing the whole porphyrin set, affording inter alia interesting clues on the different localization of the redox centres and effective conjugation between the porphyrin core and the side chains as a function of the molecular design.

  15. Spectroscopic studies of copper enzymes

    International Nuclear Information System (INIS)

    Dooley, D.M.; Moog, R.; Zumft, W.; Koenig, S.H.; Scott, R.A.; Cote, C.E.; McGuirl, M.

    1986-01-01

    Several spectroscopic methods, including absorption, circular dichroism (CD), magnetic CD (MCD), X-ray absorption, resonance Raman, EPR, NMR, and quasi-elastic light-scattering spectroscopy, have been used to probe the structures of copper-containing amine oxidases, nitrite reductase, and nitrous oxide reductase. The basic goals are to determine the copper site structure, electronic properties, and to generate structure-reactivity correlations. Collectively, the results on the amine oxidases permit a detailed model for the Cu(II) sites in these enzymes to be constructed that, in turn, rationalizes the ligand-binding chemistry. Resonance Raman spectra of the phenylhydrazine and 2,4-dinitrophenyl-hydrazine derivatives of bovine plasma amine oxidase and models for its organic cofactor, e.g. pyridoxal, methoxatin, are most consistent with methoxatin being the intrinsic cofactor. The structure of the Cu(I) forms of the amine oxidases have been investigated by X-ray absorption spectroscopy (XAS); the copper coordination geometry is significantly different in the oxidized and reduced forms. Some anomalous properties of the amine oxidases in solution are explicable in terms of their reversible aggregation, which the authors have characterized via light scattering. Nitrite and nitrous oxide reductases display several novel spectral properties. The data suggest that new types of copper sites are present

  16. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2015-01-01

    In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

  17. Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA

    International Nuclear Information System (INIS)

    Fuentes-Cabrera, Miguel A.; Sumpter, Bobby G.; Sponer, Judit; Sponer, Jiri; Petit, Leon; Wells, Jack C.

    2007-01-01

    M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong

  18. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  19. Exploring Relations Between BCG & Cluster Properties in the SPectroscopic IDentification of eROSITA Sources Survey from 0.05 < z < 0.3

    Science.gov (United States)

    Furnell, Kate E.; Collins, Chris A.; Kelvin, Lee S.; Clerc, Nicolas; Baldry, Ivan K.; Finoguenov, Alexis; Erfanianfar, Ghazaleh; Comparat, Johan; Schneider, Donald P.

    2018-04-01

    We present a sample of 329 low to intermediate redshift (0.05 data from ROSAT, maximum likelihood outputs from an optical cluster-finder algorithm and visual inspection. Using SDSS imaging data, we fit Sérsic profiles to our BCGs in three bands (g, r, i) with SIGMA, a GALFIT-based software wrapper. We examine the reliability of our fits by running our pipeline on ˜104 psf-convolved model profiles injected into 8 random cluster fields; we then use the results of this analysis to create a robust subsample of 198 BCGs. We outline three cluster properties of interest: overall cluster X-ray luminosity (LX), cluster richness as estimated by REDMAPPER (λ) and cluster halo mass (M200), which is estimated via velocity dispersion. In general, there are significant correlations with BCG stellar mass between all three environmental properties, but no significant trends arise with either Sérsic index or effective radius. There is no major environmental dependence on the strength of the relation between effective radius and BCG stellar mass. Stellar mass therefore arises as the most important factor governing BCG morphology. Our results indicate that our sample consists of a large number of relaxed, mature clusters containing broadly homogeneous BCGs up to z ˜ 0.3, suggesting that there is little evidence for much ongoing structural evolution for BCGs in these systems.

  20. Effects of countercations on the structures and redox and spectroscopic properties of diruthenium catecholate complexes with ligand-unsupported Ru-Ru bonds.

    Science.gov (United States)

    Chang, Ho-Chol; Mochizuki, Katsunori; Kitagawa, Susumu

    2005-05-30

    The molecular structures and physicochemical properties of diruthenium complexes with ligand-unsupported Ru-Ru bonds, generally formulated as [A2{Ru2(DTBCat)4}] (DTB = 3,5- or 3,6-di-tert-butyl; Cat(2-) = catecholate), were studied in detail by changing the countercations. First, the binding structures of the cations in a family of [{A(DME)n}2{Ru2(3,5-DTBCat)4}] (n = 2 for A+ = Li+ and Na+ and n = 1 for A+ = K+ and Rb+) were systematically examined to reveal the effects of the cations on the molecular structures and electrochemical properties. Second, the complex (n-Bu4N)2[Ru2(3,6-DTBCat)4] with a cation-free structure was synthesized using tetra-n-butylammonium cations. The complex clearly demonstrates first that the ligand-unsupported Ru-Ru bonds are essentially stabilized by the dianionic nature of the catecholate derivatives without any other bridging or supporting species. In contrast, the redox potentials and absorption spectra of the complexes can sensitively respond to the countercations depending upon the polarity of the solvents.

  1. Synthesis, X-ray crystallography characterization, vibrational spectroscopic, molecular electrostatic potential maps, thermodynamic properties studies of N,N'-di(p-thiazole)formamidine.

    Science.gov (United States)

    Rofouei, M K; Fereyduni, E; Sohrabi, N; Shamsipur, M; Attar Gharamaleki, J; Sundaraganesan, N

    2011-01-01

    In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of N,N'-di(p-thiazole)formamidine (DpTF). DpTF has been synthesized and characterized by elemental analysis, FT-IR, FT-Raman, 1H NMR, 13C NMR spectroscopy and X-ray single crystal diffraction. The FT-IR and FT-Raman spectra of DpTF were recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods using 6-31G(d) basis set. The FT-IR and FT-Raman spectra of DpTF was calculated at the HF/B3LYP/6-31G(d) level and were interpreted in terms of potential energy distribution (PED) analysis. The scaled theoretical wavenumber showed very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of DpTF was reported. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m°, Sm°, Hm° and temperatures. Furthermore, molecular electrostatic potential maps (MESP) and total dipole moment properties of the compound have been calculated. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. The Study of Anti-/Pro-Oxidant, Lipophilic, Microbial and Spectroscopic Properties of New Alkali Metal Salts of 5-O-Caffeoylquinic Acid

    Directory of Open Access Journals (Sweden)

    Monika Kalinowska

    2018-02-01

    Full Text Available Lithium, sodium, potassium, rubidium and caesium salts of 5-O-caffeoylquinic acid (chlorogenic acid, 5-CQA were synthesized and described by FT-IR (infrared spectroscopy, FT-Raman (Raman spectroscopy, UV (UV absorption spectroscopy, 1H (400.15 MHz, 13C (100.63 MHz NMR (nuclear magnetic resonance spectroscopy. The quantum–chemical calculations at the B3LYP/6-311++G** level were done in order to obtain the optimal structures, IR spectra, NBO (natural bond orbital atomic charges, HOMO (highest occupied molecular orbital and LUMO (lowest unoccupied molecular orbital orbitals and chemical reactivity parameters for 5-CQA and Li, Na and K 5-CQAs (chlorogenates. The DPPH (α, α-diphenyl-β-picrylhydrazyl and FRAP (ferric reducing antioxidant power assays were used for the preliminary estimation of the antioxidant properties of alkali metal chlorogenates and chlorogenic acid. In the DPPH assay the EC50 parameter were equal to 7.39 μM for 5-CQA and was in the range of 4.50–5.89 μM for salts. The FRAP values for two different concentrations (5 and 2.5 μM of the studied compounds were respectively 114.22 and 72.53 μM Fe2+ for 5-CQA, whereas for salts they were 106.92–141.13 and 78.93–132.00 μM Fe2+. The 5-CQA and its alkali metal salts possess higher antioxidant properties than commonly applied antioxidants (BHA, BHT, l-ascorbic acid. The pro-oxidant action of these compounds on trolox oxidation was studied in the range of their concentration 0.05–0.35 μM. The lipophilicity (logkw of chlorogenates and chlorogenic acid was determined by RP-HPLC (reverse phase—high performance liquid chromatography using five different columns (C8, PHE (phenyl, CN (cyano, C18, IAM (immobilized artificial membrane. The compounds were screened for their in vitro antibacterial activity against E. coli, Bacillus sp., Staphylococcus sp., Streptococcus pyogenes and antifungal activity against Candida sp. The 5-CQA possessed lower antibacterial (minimal inhibitory

  3. A subspace approach to high-resolution spectroscopic imaging.

    Science.gov (United States)

    Lam, Fan; Liang, Zhi-Pei

    2014-04-01

    To accelerate spectroscopic imaging using sparse sampling of (k,t)-space and subspace (or low-rank) modeling to enable high-resolution metabolic imaging with good signal-to-noise ratio. The proposed method, called SPectroscopic Imaging by exploiting spatiospectral CorrElation, exploits a unique property known as partial separability of spectroscopic signals. This property indicates that high-dimensional spectroscopic signals reside in a very low-dimensional subspace and enables special data acquisition and image reconstruction strategies to be used to obtain high-resolution spatiospectral distributions with good signal-to-noise ratio. More specifically, a hybrid chemical shift imaging/echo-planar spectroscopic imaging pulse sequence is proposed for sparse sampling of (k,t)-space, and a low-rank model-based algorithm is proposed for subspace estimation and image reconstruction from sparse data with the capability to incorporate prior information and field inhomogeneity correction. The performance of the proposed method has been evaluated using both computer simulations and phantom studies, which produced very encouraging results. For two-dimensional spectroscopic imaging experiments on a metabolite phantom, a factor of 10 acceleration was achieved with a minimal loss in signal-to-noise ratio compared to the long chemical shift imaging experiments and with a significant gain in signal-to-noise ratio compared to the accelerated echo-planar spectroscopic imaging experiments. The proposed method, SPectroscopic Imaging by exploiting spatiospectral CorrElation, is able to significantly accelerate spectroscopic imaging experiments, making high-resolution metabolic imaging possible. Copyright © 2014 Wiley Periodicals, Inc.

  4. Comparative study of crystallographic, spectroscopic, and laser properties of Tm3+ in NaT(WO4)2 (T=La, Gd, Y, and Lu) disordered single crystals

    Science.gov (United States)

    Cano-Torres, J. M.; Rico, M.; Han, X.; Serrano, M. D.; Cascales, C.; Zaldo, C.; Petrov, V.; Griebner, U.; Mateos, X.; Koopmann, P.; Kränkel, C.

    2011-11-01

    Tetragonal double tungstate single crystals with formula NaT(WO4)2 have been grown by the Czochralski (T = Gd, La, Y) or by the top-seeded solution growth (T = Lu) methods with Tm concentration between 8 × 1018 and 7.85 × 1020 cm-3. The spectroscopic properties of Tm3+ in these crystals are related with the peculiarities of their I4¯ crystalline structure. Sixty-five percent of La ions in NaLa(WO4)2 are in the 2d site, while in the other crystal hosts, the lanthanide occupies preferentially the 2b site (59% in T = Gd, 74% in T = Y, and 58% in T = Lu). As a consequence, the linewidths of spectral bands associated with the electronic transitions are significantly narrower in NaLa(WO4)2 than in the rest of the isostructural crystals considered. Polarized spectroscopic measurements at 5 K and at higher temperatures, along with energy level simulation of the 4f12 configuration using a single-electron Hamiltonian, including free-ion and crystal field interactions, allowed us to determine the irreducible representation and energy of Stark levels up to the 3P0 multiplet and thus to obtain realistic partition functions (Z) used for emission cross-section calculations. In particular, for the 3F4(u) → 3H6(l) laser transition at λ ≈ 2 μm, this provides: Zl/Zu = 1.436 (T = Gd), 1.464 (T = La), 1.448 (T = Y), and 1.471 (T = Lu). Radiative lifetimes calculated by the Judd-Ofelt and Füchtbauer-Ladenburg methods are in agreement and decrease in the following order T = Gd, La, Y, and Lu, however, nonradiative losses are stronger for T = Gd and La crystals; therefore, experimental lifetimes of 1D2, 1G4, 3H4, and 3F4 Tm3+ multiplets do not change too much with crystal host. For 4.68 at.% Tm:NaY(WO4)2 crystal continuous-wave laser operation is obtained with ≈42% of slope efficiency and a record (for this crystal class) tuning capability of λ = 1847-2069 nm. The broad bandwidths, ΔλFWHM > 20 nm, of the free-running laser emission are promising for ultrafast (fs) mode

  5. Thickness, morphology, and optoelectronic characteristics of pristine and surfactant-modified DNA thin films

    International Nuclear Information System (INIS)

    Arasu, Velu; Reddy Dugasani, Sreekantha; Son, Junyoung; Gnapareddy, Bramaramba; Ha Park, Sung; Jeon, Sohee; Jeong, Jun-Ho

    2017-01-01

    Although the preparation of DNA thin films with well-defined thicknesses controlled by simple physical parameters is crucial for constructing efficient, stable, and reliable DNA-based optoelectronic devices and sensors, it has not been comprehensively studied yet. Here, we construct DNA and surfactant-modified DNA thin films by drop-casting and spin-coating techniques. The DNA thin films formed with different control parameters, such as drop-volume and spin-speed at given DNA concentrations, exhibit characteristic thickness, surface roughness, surface potential, and absorbance, which are measured by a field emission scanning electron microscope, a surface profilometer, an ellipsometer, an atomic force microscope, a Kelvin probe force microscope, and an UV–visible spectroscope. From the observations, we realized that thickness significantly affects the physical properties of DNA thin films. This comprehensive study of thickness-dependent characteristics of DNA and surfactant-modified DNA thin films provides insight into the choice of fabrication techniques in order for the DNA thin films to have desired physical characteristics in further applications, such as optoelectronic devices and sensors. (paper)

  6. Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA

    Czech Academy of Sciences Publication Activity Database

    Fuentes-Cabrera, M.; Sumpter, B.G.; Šponer, Judit E.; Šponer, Jiří; Petit, L.; Wells, J.C.

    2007-01-01

    Roč. 111, č. 4 (2007), s. 870-879 ISSN 1520-6106 R&D Projects: GA AV ČR(CZ) 1QS500040581; GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : metalated DNA * ab initio * electronic properties of DNA Subject RIV: BO - Biophysics Impact factor: 4.086, year: 2007

  7. A combined experimental and computational study of 3-bromo-5-(2,5-difluorophenyl) pyridine and 3,5-bis(naphthalen-1-yl)pyridine: Insight into the synthesis, spectroscopic, single crystal XRD, electronic, nonlinear optical and biological properties

    Science.gov (United States)

    Ghiasuddin; Akram, Muhammad; Adeel, Muhammad; Khalid, Muhammad; Tahir, Muhammad Nawaz; Khan, Muhammad Usman; Asghar, Muhammad Adnan; Ullah, Malik Aman; Iqbal, Muhammad

    2018-05-01

    Carbon-carbon coupling play a vital role in the synthetic field of organic chemistry. Two novel pyridine derivatives: 3-bromo-5-(2,5-difluorophenyl)pyridine (1) and 3,5-bis(naphthalen-1-yl)pyridine (2) were synthesized via carbon-carbon coupling, characterized by XRD, spectroscopic techniques and also investigated by using density functional theory (DFT). XRD data and optimized DFT studies are found to be in good correspondence with each other. The UV-Vis analysis of compounds under study i.e. (1) and (2) was obtained by using "TD-DFT/B3LYP/6-311 + G(d,p)" level of theory to explain the vertical transitions. Calculated FT-IR and UV-Vis results are found to be in good agreement with experimental FT-IR and UV-Vis findings. Natural bond orbital (NBO) study was performed using B3LYP/6-311 + G(d,p) level to find the most stable molecular structure of the compounds. Frontier molecular orbital (FMO) analysis were performed at B3LYP/6-311 + G(d,p) level of theory, which indicates that the molecules might be bioactive. Moreover, the bioactivity of compounds (1) and (2) have been confirmed by the experimental activity in terms of zones of inhibition against bacteria and fungus. Chemical reactivity of compounds (1) and (2) was indicated by mapping molecular electrostatic potential (MEP) over the entire stabilized geometries of the compounds under study. The nonlinear optical properties were computed with B3LYP/6-311 + G(d,p) level of theory which are found greater than the value of urea due to conjugation effect. Two state model has been further employed to explain the nonlinear optical properties of compounds under investigation.

  8. Accurate dipole moment curve and non-adiabatic effects on the high resolution spectroscopic properties of the LiH molecule

    Science.gov (United States)

    Diniz, Leonardo G.; Kirnosov, Nikita; Alijah, Alexander; Mohallem, José R.; Adamowicz, Ludwik

    2016-04-01

    A very accurate dipole moment curve (DMC) for the ground X1Σ+ electronic state of the 7LiH molecule is reported. It is calculated with the use of all-particle explicitly correlated Gaussian functions with shifted centers. The DMC - the most accurate to our knowledge - and the corresponding highly accurate potential energy curve are used to calculate the transition energies, the transition dipole moments, and the Einstein coefficients for the rovibrational transitions with ΔJ = - 1 and Δv ⩽ 5 . The importance of the non-adiabatic effects in determining these properties is evaluated using the model of a vibrational R-dependent effective reduced mass in the rovibrational calculations introduced earlier (Diniz et al., 2015). The results of the present calculations are used to assess the quality of the two complete linelists of 7LiH available in the literature.

  9. Electronic structure of Ge-2 and Ge-2 and thermodynamic properties of Ge-2 from all electron ab initio investigations and Knudsen effusion mass spectroscopic measurements

    DEFF Research Database (Denmark)

    Shim, Irene; Baba, M. Sai; Gingerich, K.A.

    2002-01-01

    The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term and for t......The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term...... excited states are presented. Thermal functions based on the theoretically determined molecular parameters were used to derive the thermodynamic properties of the Ge-2 molecule from new mass spectrometric equilibrium data. The literature value for the dissociation energy of Ge-2 has been re...

  10. Influence of phosphorous precursors on spectroscopic properties of Er3+-activated SiO2-HfO2-P2O5 planar waveguides

    International Nuclear Information System (INIS)

    Vasilchenko, I; Carpentiero, A; Chiappini, A; Chiasera, A; Ferrari, M; Vaccari, A; Lukowiak, A; Righini, G C; Vereshagin, V

    2014-01-01

    (70-x)SiO 2 -30HfO 2 -xP 2 O 5 (x= 5, 10 mol %) glass planar waveguides activated by 0.5 mol% Er 3 + ions were prepared by sol-gel route. Several phosphorous precursors have been investigated for the synthesis of a dielectric stable sol useful for the realization of planar waveguides. The waveguides were investigated by different diagnostic techniques. The optical properties such as refractive index, thickness, number of propagating modes and attenuation coefficient were measured at 632.8 and 543.5 nm by prism coupling technique. Transmission measurements were carried out in order to assess the transparency of the deposited films. Photoluminescence measurements and lifetime decay curves of the Er 3 + transition (4 I 13/2 → 4 I 15/2 ) were performed in order to investigate the role of P 2 O 5

  11. Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations

    Science.gov (United States)

    Sinha, Leena; Karabacak, Mehmet; Narayan, V.; Cinar, Mehmet; Prasad, Onkar

    2013-05-01

    Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.

  12. Synthesis, structural and spectroscopic properties of acentric triple molybdate Cs{sub 2}NaBi(MoO{sub 4}){sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Savina, A.A. [Laboratory of Oxide Systems, Baikal Institute of Nature Management, SB RAS, Ulan-Ude 670047 (Russian Federation); Department of Chemistry, Buryat State University, Ulan-Ude 670000 (Russian Federation); Atuchin, V.V., E-mail: atuchin@isp.nsc.ru [Laboratory of Optical Materials and Structures, Rzhanov Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Functional Electronics Laboratory, Tomsk State University, Tomsk 634050 (Russian Federation); Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, Novosibirsk 630090 (Russian Federation); Solodovnikov, S.F. [Laboratory of Crystal Chemistry, Nikolaev Institute of Inorganic Chemistry, SB RAS, Novosibirsk 630090 (Russian Federation); Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090 (Russian Federation); Solodovnikova, Z.A. [Laboratory of Crystal Chemistry, Nikolaev Institute of Inorganic Chemistry, SB RAS, Novosibirsk 630090 (Russian Federation); Krylov, A.S. [Laboratory of Molecular Spectroscopy, Kirensky Institute of Physics, SB RAS, Krasnoyarsk 660036 (Russian Federation); Maximovskiy, E.A. [Laboratory of Epitaxial Layers, Nikolaev Institute of Inorganic Chemistry, SB RAS, Novosibirsk 630090 (Russian Federation); Laboratory of Research Methods of Composition and Structure of Functional Materials, Novosibirsk State University, Novosibirsk 630090 (Russian Federation); Molokeev, M.S. [Laboratory of Crystal Structure, Kirensky Institute of Physics, SB RAS, Krasnoyarsk 660036 (Russian Federation); Oreshonkov, A.S [Laboratory of Molecular Spectroscopy, Kirensky Institute of Physics, SB RAS, Krasnoyarsk 660036 (Russian Federation); Department of Photonics and Laser Technology, Siberian Federal University, Krasnoyarsk 660079 (Russian Federation); Pugachev, A.M. [Laboratory of Condenced Matter Spectroscopy, Institute of Automation and Electrometry, SB RAS, Novosibirsk 90, 630090 (Russian Federation); and others

    2015-05-15

    New ternary molybdate Cs{sub 2}NaBi(MoO{sub 4}){sub 3} is synthesized in the system Na{sub 2}MoO{sub 4}–Cs{sub 2}MoO{sub 4}–Bi{sub 2}(MoO{sub 4}){sub 3}. The structure of Cs{sub 2}NaBi(MoO{sub 4}){sub 3} of a new type is determined in noncentrosymmetric space group R3c, a=10.6435(2), c=40.9524(7) Å, V=4017.71(13) Å{sup 3}, Z=12 in anisotropic approximation for all atoms taking into account racemic twinning. The structure is completely ordered, Mo atoms are tetrahedrally coordinated, Bi(1) and Bi(2) atoms are in octahedra, and Na(1) and Na(2) atoms have a distorted trigonal prismatic coordination. The Cs(1) and Cs(2) atoms are in the framework cavities with coordination numbers 12 and 10, respectively. No phase transitions were found in Cs{sub 2}NaBi(MoO{sub 4}){sub 3} up to the melting point at 826 K. The compound shows an SHG signal, I{sub 2w}/I{sub 2w}(SiO{sub 2})=5 estimated by the powder method. The vibrational properties are evaluated by Raman spectroscopy, and 26 narrow lines are measured. - Graphical abstract: - Highlights: • The crystal structure of Cs{sub 2}NaBi(MoO{sub 4}){sub 3} is defined. • The molybdate Cs{sub 2}NaBi(MoO{sub 4}){sub 3} is stable up to melting point at 826 K. • Vibrational properties of Cs{sub 2}NaBi(MoO{sub 4}){sub 3} are evaluated by Raman spectroscopy.

  13. Some properties and cDNA cloning of proteinaceous toxins from two species of lionfish (Pterois antennata and Pterois volitans).

    Science.gov (United States)

    Kiriake, Aya; Shiomi, Kazuo

    2011-11-01

    Lionfish, members of the genera Pterois, Parapterois and Dendrochirus, are well known to be venomous, having venomous glandular tissues in dorsal, pelvic and anal spines. The lionfish toxins have been shown to cross-react with the stonefish toxins by neutralization tests using the commercial stonefish antivenom, although their chemical properties including structures have been little characterized. In this study, an antiserum against neoverrucotoxin, the stonefish Synanceia verrucosa toxin, was first raised in a guinea pig and used in immunoblotting and inhibition immunoblotting to confirm that two species of Pterois lionfish (P. antennata and P. volitans) contain a 75kDa protein (corresponding to the toxin subunit) cross-reacting with neoverrucotoxin. Then, the amino acid sequences of the P. antennata and P. volitans toxins were successfully determined by cDNA cloning using primers designed from the highly conserved sequences of the stonefish toxins. Notably, either α-subunits (699 amino acid residues) or β-subunits (698 amino acid residues) of the P. antennata and P. volitans toxins share as high as 99% sequence identity with each other. Furthermore, both α- and β-subunits of the lionfish toxins exhibit high sequence identity (70-80% identity) with each other and also with the β-subunits of the stonefish toxins. As reported for the stonefish toxins, the lionfish toxins also contain a B30.2/SPRY domain (comprising nearly 200 amino acid residues) in the C-terminal region of each subunit. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Synthesis, Characterization and DNA Binding Activity of a Potential DNA Intercalator

    International Nuclear Information System (INIS)

    Siti Norain Harun; Yaakob Razak; Haslina Ahmad

    2016-01-01

    A novel complex, (Ru(dppz) 2 (p-MOPIP)) 2+ (dppz = dipyrido-(3,2-a:20,30-c]phenazine, p-MOPIP = 2-(4-methoxyphenyl) imidazo(4,5-f)(1,10]phenanthroline) has been synthesized and characterized by elemental analysis, 1 H Nuclear Magnetic Resonance spectroscopy, mass spectrometry, Fourier Transform Infrared analysis, Ultra Violet visible and fluorescence spectroscopy. Herein, the complex was designed by adding p-MOPIP as an intercalating ligand and dppz as the ancillary ligand. The DNA binding properties of the complex with Calf Thymus DNA (CT-DNA) were investigated using spectroscopic methods. The UV-visible absorption band observed at 460 nm corresponded to the metal-to-ligand charge transfer (MLCT) while bands at 358 and 281 nm corresponded to intra-ligand (IL) π-π * transitions of the ligand scaffold in p-MOPIP and dppz. The intrinsic binding constant, K b for this complex was 1.67x10 6 M -1 and this suggested that this complex, (Ru(dppz) 2 (p-MOPIP)) 2+ bound to DNA via the intercalative mode. Interestingly, the interaction of this complex with CT-DNA also had a molecular light switch effect. (author)

  15. Synthesis and characterization of nitrile functionalized silver(I)-N-heterocyclic carbene complexes: DNA binding, cleavage studies, antibacterial properties and mosquitocidal activity against the dengue vector, Aedes albopictus.

    Science.gov (United States)

    Asekunowo, Patrick O; Haque, Rosenani A; Razali, Mohd R; Avicor, Silas W; Wajidi, Mustafa F F

    2018-04-25

    A series of four benzimidazolium based nitrile-functionalized mononuclear-Ag(I)-N-heterocyclic carbene and binuclear-Ag(I)-N-heterocyclic carbene (Ag(I)-NHC) hexafluorophosphate complexes (5b-8b) were synthesized by reacting the corresponding hexafluorophosphate salts (1b-4b) with Ag 2 O in acetonitrile, respectively. These compounds were characterized by 1 H NMR, 13 C NMR, IR, UV-visible spectroscopic techniques, elemental analyses and molar conductivity. Additionally, 8b was structurally characterized by single crystal X-ray diffraction technique. Preliminary in vitro antibacterial evaluation was conducted for all the compounds against two standard bacteria; gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacterial strains. Most of the Ag(I)-NHC complexes (5b-8b) showed moderate to good antibacterial activity with MIC values in the range of 12.5-100 μg/mL. Especially, compound 8b exhibited promising anti-Staphylococcus aureus activity with a low MIC value (12.5 μg/mL). However, all the hexafluorophosphate salts (1b-4b) were inactive against the bacteria strains. The preliminary interactive investigation revealed that the most active compound, 8b, could effectively intercalate into DNA to form 8b-DNA complex which shows a better binding ability for DNA (K b  = 3.627 × 10 6 ) than the complexes 5b-7b (2.177 × 10 6 , 8.672 × 10 5 and 6.665 × 10 5 , respectively). Nuclease activity of the complexes on plasmid DNA and Aedes albopictus genomic DNA was time-dependent, although minimal. The complexes were larvicidal to the mosquito, with 5b, 6b and 8b being highly active. Developmental progression from the larval to the adult stage was affected by the complexes, progressively being toxic to the insect's development with increasing concentration. These indicate the potential use of these complexes as control agents against bacteria and the dengue mosquito Ae. albopictus. Copyright © 2018 Elsevier Masson SAS. All

  16. Spectroscopic properties and laser performance at 1,066 nm of a new laser crystal Nd:GdTaO4

    Science.gov (United States)

    Peng, Fang; Yang, Huajun; Zhang, Qingli; Luo, Jianqiao; Liu, Wenpeng; Sun, Dunlu; Dou, Renqin; Sun, Guihua

    2015-03-01

    A new laser medium Nd3+:GdTaO4 single crystal with high optical quality was grown successfully by the Czochralski method, and its high-efficiency laser operation at 1,066 nm was demonstrated for the first time. The absorption cross section of the crystal at 808 nm is 5.098 × 10-20 cm2, and the full width at half maximum of this absorption band is about 6 nm. Spectral properties are investigated by Judd-Ofelt theory. The stimulated emission cross section at 1,066 nm is 3.9 × 10-19 cm2, and the fluorescence lifetime of 4F3/2 level is 178.4 μs. A diode end-pumped Nd:GdTaO4 laser at 1,066 nm with the maximum output power of 2.5 W is achieved in the continuous-wave mode. The optical-to-optical conversion efficiency and slope efficiency are 34.6 and 36 %, respectively. In addition, the fluorescence branching ratio of 4F3/2 → 4I9/2 transition reaches 44.4 %, indicating that Nd:GdTaO4 may be an efficient laser medium at 920 nm. All the results demonstrate that Nd:GdTaO4 crystal is a good candidate for laser diode-pumped laser material.

  17. Spectroscopic, electrochemical and photovoltaic properties of Pt(ii) and Pd(ii) complexes of a chelating 1,10-phenanthroline appended perylene diimide.

    Science.gov (United States)

    Işık Büyükekşi, Sebile; Şengül, Abdurrahman; Erdönmez, Seda; Altındal, Ahmet; Orman, Efe Baturhan; Özkaya, Ali Rıza

    2018-02-20

    In this study, a bis-chelating bridging perylene diimide ditopic ligand, namely N,N'-di(1,10-phenanthroline)-1,6,7,12-tetrakis-(4-methoxyphenoxy)perylene tetracarboxylic acid diimide (1), was synthesized and characterized. Further reactions of 1 with d 8 metal ions such as Pt(ii) and Pd(ii) having preferential square-planar geometry afforded the novel triads [(Cl 2 )M(ii)-(1)-M(ii)(Cl 2 )] where M(ii) = Pt(ii) (2), and Pd(ii) (3), respectively. The isolated triads and the key precursor were fully characterized by FT-IR, 1D-NMR ( 1 H NMR and 13 C DEPT NMR), 2D-NMR ( 1 H- 1 H COSY, 1 H- 13 C HSQC, 1 H- 13 C HMBC), MALDI-TOF mass and UV/Vis spectroscopy. The electrochemical properties of 1, 2 and 3 were investigated by cyclic voltammetry as well as in situ spectroelectrochemistry and also in situ electrocolorimetric measurements. These compounds were shown to exhibit net colour changes suitable for electrochromic applications. The compounds exhibited remarkably narrow HOMO-LUMO gaps, leading to their ease of reduction at low negative potentials. More importantly, dye-sensitized solar cells (DSSCs) were also fabricated using 1-3 to clarify the potential use of these complexes as a sensitizer. Analysis of the experimental data indicated that 2 has good potential as a sensitizer material for DSSCs.

  18. Structures and Spectroscopic Properties of F-(H2O) n with n = 1-10 Clusters from a Global Search Based On Density Functional Theory.

    Science.gov (United States)

    Shi, Ruili; Wang, Pengju; Tang, Lingli; Huang, Xiaoming; Chen, Yonggang; Su, Yan; Zhao, Jijun

    2018-04-05

    Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F - (H 2 O) n with n = 1-10. The F - (H 2 O) n clusters prefer structures in which the F - anion remains at the surface of the structure and coordinates with four water molecules, as the F - (H 2 O) n clusters have strong F - -H 2 O interactions as well as strong hydrogen bonds between H 2 O molecules. The strong interaction between the F - anion and adjacent H 2 O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule. The simulated infrared (IR) spectra of the F - (H 2 O) 1-5 clusters obtained via second-order vibrational perturbation theory (VPT2) and including anharmonic effects reproduce the experimental results quite well. The strong interaction between the F - anion and water molecules results in a large redshift (600-2300 cm -1 ) of the adjacent O-H stretching mode. Natural bond orbital (NBO) analysis of the lowest-energy structures of the F - (H 2 O) 1-10 clusters illustrates that charge transfer from the lone pair electron orbital of F - to the antibonding orbital of the adjacent O-H is mainly responsible for the strong interaction between the F - anion and water molecules, which leads to distinctly different geometric and vibrational properties compared with neutral water clusters.

  19. Synthesis, aggregation and spectroscopic studies of novel water soluble metal free, zinc, copper and magnesium phthalocyanines and investigation of their anti-bacterial properties

    Science.gov (United States)

    Bayrak, Rıza; Akçay, Hakkı Türker; Beriş, Fatih Şaban; Şahin, Ertan; Bayrak, Hacer; Demirbaş, Ümit

    2014-12-01

    In this study, novel phthalonitrile derivative (3) was synthesized by the reaction between 4-nitrophthalonitrile (2) and a triazole derivative (1) containing pyridine moiety. Crystal structure of compound (3) was characterized by X-ray diffraction. New metal free and metallo-phthalocyanine complexes (Zn, Cu, and Mg) were synthesized using the phthalonitrile derivative (3). Cationic derivatives o