WorldWideScience

Sample records for investigate molecular structure

  1. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    cates an easy outlook of the makeup of the molec- ular orbitals in a certain energy range. The energy split between the HOMOs and LUMOs are the crit- ical parameters in special molecular electrical trans- port properties which help in the measure of elec- tron conductivity.42 The HOMO represents the ability to donate an ...

  2. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    The spectroscopic properties of the title compound have beeninvestigated by using IR, UV–Vis and ¹H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two ...

  3. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    MS received 29 December 2015; revised 9 April 2016; accepted 25 May 2016 ... B, open form blue. Scheme 1. Structures and Photochromic reaction of the title compound. 2. Experimental. 2.1 Materials and measurements. The mid-IR spectra were obtained in the ... segment is put between two parallel Au(111) surfaces,.

  4. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    Sci. Vol. 127, No. 12, December 2015, pp. 2137–2149. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0976-x. Molecular structure and DFT investigations on new cobalt(II) chloride complex with superbase guanidine type ligand. SAIED M SOLIMANa,b,∗, MORSY A M ABU-YOUSSEFb,∗. , JΦRG ALBERINGc and.

  5. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    and the new [Co(btmgn)Cl2] complex were charac- terized using different spectroscopic techniques. The. X-ray structure of the [Co(btmgn)Cl2] complex is deter- mined. The electronic and spectroscopic aspects of the ligands as well as the [Co(btmgn)Cl2] were discussed with the aid of DFT quantum chemical calculations.

  6. Molecular structure investigation and tautomerism aspects of (E)-3 ...

    Indian Academy of Sciences (India)

    calculations. The effect of the intermolecular N-H—. O H-bonding interactions on the calculated geometric parameters has been tested. The electronic spectra were assigned with the aid of the TD-DFT calculations. 2. Experimental. 2.1 Synthesis and spectral investigations. A mixture of indolin-2-one 1 (1.5 mmol, 200 mg), ...

  7. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  8. Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7

    Directory of Open Access Journals (Sweden)

    Christopher Peschel

    2017-09-01

    Full Text Available We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.

  9. Molecular dynamics investigation into the structural features and transport properties of C60 in liquid argon.

    Science.gov (United States)

    Fang, Kuan-Chuan; Weng, Cheng-I

    2007-07-05

    Molecular dynamics (MD) simulations were performed to investigate the structural features and transport properties of C60 in liquid argon. The results reveal that an organized structure shell of liquid argon is formed close to the surface of a C60 fullerene molecule, thereby changing the solid/liquid interfacial structure. Furthermore, the simulation indicates that the C60-liquid argon fluid becomes structurally more stable as the C60 molecule volume fraction and the temperature increase. The viscosity of the fluid increases significantly as the C60 molecule loading is increased, particularly at a lower temperature. The thermal conductivity enhancement of the fluid in the present simulations is anomalously an order of magnitude higher than the theoretical predictions from either the Maxwell or the Lu and Liu models, and is found to vary approximately linearly with the C60 molecule volume fraction. The increased thermal conductivity is attributed to the nature of heat conduction in C60 molecule suspensions and an organized structure at the solid/liquid interface.

  10. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  11. Quantum-chemical investigation of molecular structure of bromopyrogallol red and its complexes with rare earths

    International Nuclear Information System (INIS)

    Sivanova, O.V.; Rodnikova, V.N.; Mushtakova, S.P.

    1979-01-01

    The MO LCAO method has been used to study the structure of the molecular and ionized forms of brompyrogallol red (BPGR) and its complex compounds with rare earths. The calculations performed reveal that addition of rare earth ions to BPGR is possible both with respect to the orthooxyquinone group to give a complex with a short wavelength absorption peak and the dioxy group to give a complex compound absorbing in the long wavelength region

  12. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    Science.gov (United States)

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  13. Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation.

    Science.gov (United States)

    Mertz, Blake; Struts, Andrey V; Feller, Scott E; Brown, Michael F

    2012-02-01

    Rhodopsin has served as the primary model for studying G protein-coupled receptors (GPCRs)-the largest group in the human genome, and consequently a primary target for pharmaceutical development. Understanding the functions and activation mechanisms of GPCRs has proven to be extraordinarily difficult, as they are part of a complex signaling cascade and reside within the cell membrane. Although X-ray crystallography has recently solved several GPCR structures that may resemble the activated conformation, the dynamics and mechanism of rhodopsin activation continue to remain elusive. Notably solid-state ((2))H NMR spectroscopy provides key information pertinent to how local dynamics of the retinal ligand change during rhodopsin activation. When combined with molecular mechanics simulations of proteolipid membranes, a new paradigm for the rhodopsin activation process emerges. Experiment and simulation both suggest that retinal isomerization initiates the rhodopsin photocascade to yield not a single activated structure, but rather an ensemble of activated conformational states. This article is part of a Special Issue entitled: Membrane protein structure and function. Copyright © 2011. Published by Elsevier B.V.

  14. Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, Geoffrey [Alfred Univ., NY (United States)

    2017-04-05

    United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

  15. Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations.

    Science.gov (United States)

    Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

    2017-07-07

    Tri-block copolymer styrene-butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG-DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as -OH, C=O, -COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds

  16. Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations

    Science.gov (United States)

    Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

    2017-01-01

    Tri-block copolymer styrene–butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG–DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as –OH, C=O, –COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong

  17. Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Haverkort, Frank; Stradomska, Anna; de Vries, Alex H.; Knoester, Jasper

    2013-01-01

    We perform molecular dynamics (MD) simulations of the self-assembly process of pseudoisocyanine dye molecules with amphiphilic substituents (amphi-PIC). The spontaneous aggregation of cyanine molecules into large molecular J-aggregates with optical functionality has drawn attention for many decades

  18. Investigation of proton pump inhibitors binding with bovine serum albumin and their relationship to molecular structure

    International Nuclear Information System (INIS)

    Zhang Yuping; Shi Shuyun; Peng Mijun

    2012-01-01

    The interactions of three proton pump inhibitors (PPIs), omeprazole, pantoprazole and ilaprazole with bovine serum albumin (BSA) have been investigated by fluorescence, synchronous fluorescence, ultraviolet–visible (UV–vis) and circular dichroism (CD). Various binding parameters have been calculated at various temperatures. The results indicated that omeprazole, pantoprazole and ilaprazole had a strong ability to quench the intrinsic fluorescence of BSA with static quenching mechanism, and the binding affinities were significantly affected by different substituents and polarities as the order ilaprazole>pantoprazole>omeprazole. The site marker competitive experiments indicated that the binding of omeprazole, pantoprazole and ilaprazole to BSA primarily took place in subdomain IIA. The results of thermodynamic parameters ΔG, ΔH and ΔS indicated that electrostatic interaction played a major role for PPIs–BSA association. The distance r between PPIs and BSA was evaluated according to the theory of Förster's energy transfer. The quantitative analysis of synchronous fluorescence and CD spectra showed the change in secondary structure of the BSA upon interaction with PPIs by a reduction of α-helix. All the above results many have relevant insight into the PPIs' availability and distribution. - Highlights: ► The interactions of three PPIs with BSA have been investigated. ► The fluorescence quenching mechanism is static quenching. ► Binding affinities were greatly affected by the substituents and polarities. ► The binding of three PPIs to BSA primarily took place in subdomain IIA.

  19. Investigating Molecular Structures of Bio-Fuel and Bio-Oil Seeds as Predictors To Estimate Protein Bioavailability for Ruminants by Advanced Nondestructive Vibrational Molecular Spectroscopy.

    Science.gov (United States)

    Ban, Yajing; L Prates, Luciana; Yu, Peiqiang

    2017-10-18

    This study was conducted to (1) determine protein and carbohydrate molecular structure profiles and (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural makeup within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO, and cellulosic compounds were obtained for carinata seeds. Carinata and canola seeds showed similar carbohydrate and protein molecular structures by multivariate analyses. Carbohydrate molecular structure profiles were highly correlated to protein rumen degradation and intestinal digestion characteristics. In conclusion, the molecular spectroscopy can detect inherent structural characteristics in carinata and canola seeds in which carbohydrate-relative structural features are related to protein metabolism and utilization. Protein and carbohydrate spectral profiles could be used as predictors of rumen protein bioavailability in cows.

  20. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    International Nuclear Information System (INIS)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

    2010-01-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  1. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Carnevale, V.; Raugei, S.

    2009-01-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  2. Synthesis, molecular structure investigations and antimicrobial activity of 2-thioxothiazolidin-4-one derivatives

    Science.gov (United States)

    Barakat, Assem; Al-Najjar, Hany J.; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Mabkhot, Yahia Nasser; Al-Agamy, Mohamed H. M.; Ghabbour, Hazem A.; Fun, Hoong-Kun

    2015-02-01

    A variety of 2-thioxothiazolidin-4-one derivatives were prepared and their in vitro antimicrobial activities were studied. Most of these compounds showed significant antibacterial activity specifically against Gram-positive bacteria, among which compounds 4a,e,g, 5b,e,g,h and 6f exhibit high levels of antimicrobial activity against Bacillus subtilis ATCC 10400 with Minimum Inhibitory Concentration (MIC) value of 16 μg/mL. All compounds have antifungal activity against Candida albicans. Unfortunately, however, none of the compounds were active against Gram-negative bacteria. The chemical structure of 3 was confirmed by X-ray single crystal diffraction technique. DFT calculations of 3 have been performed on the free C10H7Cl2NO2S2, 3a and the H-bonded complex, C10H7Cl2NO2S2·H2O, 3b to explore the effect of the H-bonding interactions on the geometric and electronic properties of the studied systems. A small increase in bond length was observed in the C12-O6 due to the H-bonding interactions between 3a and water molecule. MEP study has been used to recognize the most reactive sites towards electrophilic and nucleophilic attacks as well as the possible sites for the H-bonding interactions. The TD-DFT calculations have been used to predict theoretically the electronic spectra of the studied compound. The most intense transition band is predicted at 283.9 nm due to the HOMO-2/HOMO-1 to LUMO transitions. NBO analyses were carried out to investigate the stabilization energy of the various intramolecular charge transfer interactions within the studied molecules.

  3. Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations

    Directory of Open Access Journals (Sweden)

    Xiong Xu

    2017-07-01

    Full Text Available Tri-block copolymer styrene–butadiene (SBS is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR and X-ray photoelectron spectroscopy (XPS, and the correlation between oxygen-containing groups and thermal properties (TG–DTG was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as –OH, C=O, –COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult

  4. Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

    Science.gov (United States)

    Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

    2015-07-06

    Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

  5. Complementarity of real-time neutron and synchrotron radiation structural investigations in molecular biology

    International Nuclear Information System (INIS)

    Aksenov, V. L.; Kiselev, M. A.

    2010-01-01

    General problems of the complementarity of different physical methods and specific features of the interaction between neutron and matter and neutron diffraction with respect to the time of flight are discussed. The results of studying the kinetics of structural changes in lipid membranes under hydration and self-assembly of the lipid bilayer in the presence of a detergent are reported. The possibilities of the complementarity of neutron diffraction and X-ray synchrotron radiation and developing a free-electron laser are noted.

  6. Complementarity of real-time neutron and synchrotron radiation structural investigations in molecular biology

    Science.gov (United States)

    Aksenov, V. L.; Kiselev, M. A.

    2010-12-01

    General problems of the complementarity of different physical methods and specific features of the interaction between neutron and matter and neutron diffraction with respect to the time of flight are discussed. The results of studying the kinetics of structural changes in lipid membranes under hydration and self-assembly of the lipid bilayer in the presence of a detergent are reported. The possibilities of the complementarity of neutron diffraction and X-ray synchrotron radiation and developing a free-electron laser are noted.

  7. Raman microprobe investigation of molecular structure and organization in the native state of woody tissue

    Energy Technology Data Exchange (ETDEWEB)

    Atalla, R.H.

    1989-08-01

    Although the primary emphasis of our program has remained with the application of Raman spectroscopy to the study of native tissue, the scope of the work has been expanded to include a number of complementary approaches. These have included Solid State 13C NMR, autoradiography of radiolabeled woody tissue sections, and the generation of biomimetic tertiary aggregates which simulate states of aggregation characteristic of cell walls. Our Raman spectroscopic studies have resulted in progress in the areas of interpretation of the spectral features, and confirmation of the variability of the patterns of orientation of lignin reported earlier. We have assembled and made operational our new microprobe and spectrometer systems acquired under the DOE-URIP program. We have also demonstrated that, operating with gated detection and pulsed laser excitation, we can discriminate against the laser-excited fluorescence characteristic of most woody tissue. Our studies of celluloses, which combine Raman spectroscopy and 13C NMR have shown that all native celluloses are composites of two forms which have the same secondary structure but different tertiary structures.

  8. Synthesis, Molecular Structure and Spectroscopic Investigations of Novel Fluorinated Spiro Heterocycles

    Directory of Open Access Journals (Sweden)

    Mohammad Shahidul Islam

    2015-05-01

    Full Text Available This paper describes an efficient and regioselective method for the synthesis of novel fluorinated spiro-heterocycles in excellent yield by cascade [5+1] double Michael addition reactions. The compounds 7,11-bis(4-fluorophenyl-2,4-dimethyl- 2,4-diazaspiro[5.5] undecane-1,3,5,9-tetraone (3a and 2,4-dimethyl-7,11-bis (4-(trifluoromethylphenyl-2,4-diazaspiro[5.5]undecane-1,3,5,9-tetraone (3b were characterized by single-crystal X-ray diffraction, FT-IR and NMR techniques. The optimized geometrical parameters, infrared vibrational frequencies and NMR chemical shifts of the studied compounds have also been calculated using the density functional theory (DFT method, using Becke-3-Lee-Yang-Parr functional and the 6-311G(d,p basis set. There is good agreement between the experimentally determined structural parameters, vibrational frequencies and NMR chemical shifts of the studied compounds and those predicted theoretically. The calculated natural atomic charges using NBO method showed higher polarity of 3a compared to 3b.The calculated electronic spectra are also discussed based on the TD-DFT calculations.

  9. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    -18 to extend perpendicular to the beta-hairpin plane. This bend was driven by a highly persistent hydrogen-bond between the polar peptide side-chain of TYR7 and the unshielded backbone carbonyl oxygen atom of GLY17. The H-bond formation relieves the unfavorable free energy of insertion of polar groups......All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure......-550]), and to delineate specific peptide-membrane interactions which are responsible for the peptide's membrane binding properties. A novel, previously unknown, "kick" shaped conformation of the peptide was detected, where a bend at the C-terminal beta-strand of the peptide caused the peptide backbone at residues 16...

  10. Ab initio molecular dynamics investigation of the structure and the noncollinear magnetism in liquid oxygen: Occurrence of O4 molecular units

    OpenAIRE

    Oda, Tatsuki; Pasquarello, Alfredo

    2002-01-01

    The ab initio molecular dynamics was performed toinvestigate the noncollinear magnetism of a system with an evolving atomic structure. As such, application to liquid oxygen provides a picture in which the large majority of colliding O2 molecules assume structural and magnetic configurations which closely resemble those in the O4 molecule. Formation of truly long-living molecular O4 units also occurs but involves a considerably smaller fraction of O2 molecules.

  11. A comparative molecular and 3-dimensional structural investigation into cross-continental and novel avian Trypanosoma spp. in Australia.

    Science.gov (United States)

    Cooper, Crystal; Thompson, R C Andrew; Botero, Adriana; Kristancic, Amanda; Peacock, Christopher; Kirilak, Yaowanuj; Clode, Peta L

    2017-05-12

    Molecular and structural information on avian Trypanosoma spp. throughout Australia is limited despite their intrinsic value in understanding trypanosomatid evolution, diversity, and structural biology. In Western Australia tissue samples (n = 429) extracted from 93 birds in 25 bird species were screened using generic PCR primers to investigate the diversity of Trypanosoma spp. To investigate avian trypanosome structural biology the first 3-dimensional ultrastructural models of a Trypanosoma spp. (Trypanosoma sp. AAT) isolated from a bird (currawong, Strepera spp.) were generated using focussed ion beam milling combined with scanning electron microscopy (FIB-SEM). Here, we confirm four intercontinental species of avian trypanosomes in native Australian birds, and identify a new avian Trypanosoma. Trypanosome infection was identified in 18 birds from 13 different bird species (19%). A single new genotype was isolated and found to be closely related to T. culicavium (Trypanosoma sp. CC2016 B002). Other Trypanosoma spp. identified include T. avium, T. culicavium, T. thomasbancrofti, Trypanosoma sp. TL.AQ.22, Trypanosoma sp. AAT, and an uncharacterised Trypanosoma sp. (group C-III sensu Zidková et al. (Infect Genet Evol 12:102-112, 2012)), all previously identified in Australia or other continents. Serially-sectioning Trypanosoma sp. AAT epimastigotes using FIB-SEM revealed the disc-shaped kinetoplast pocket attached perpendicular to the branching mitochondrion. Additionally, the universal minicircle sequence within the kinetoplast DNA and the associated binding protein were determined in Trypanosoma sp. AAT. These results indicate that bird trypanosomes are relatively conserved across continents, while being locally diverse, which supports the hypothesis that bird trypanosomes exist as fewer species than described in the literature. Evidence exists that avian Trypanosoma spp. are infecting mammals and could be transmitted by haemadipsid leeches. Trypanosoma sp

  12. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  13. Investigation on the Molecular Interactions Stabilizing the Structure of α-synuclein Fibril: An In silico Study.

    Science.gov (United States)

    Sanjeev, Airy; Mattaparthi, Venkata S K

    2017-01-01

    Amyloid fibrils represent stable form of many misfolded proteins associated with numerous diseases like Parkinson's Disease (PD), Type II diabetes and Alzheimer's disease (AD). α-synuclein protein is the principal constituent of Lewy bodies that are considered to be pathological hallmark of PD. Recently, a high resolution structure of α-synuclein protein that stacks together forming fibrils in brains of PD patients were identified. What structural features drive pathology of PD can now be possibly answered from the fibril structure of protein. To understand the molecular interactions those are responsible for the stability of the α- synuclein fibril structure. To study the molecular interactions stabilizing the α-synuclein fibril, we have used a high resolution amyloid fibril structure (PDB ID 2N0A). The molecular interactions in fibril structure were studied using PDBSum server. We then looked into the destabilization of α-synuclein fibril by disrupting the salt-bridge holding the strands and probable methods to decompose fibril into structurally distinct units using Top-domain web-server. The effect of salt-bridges on the stability of the fibril structure was studied by mutating one of the residues involved in the formation of salt-bridge using molecular dynamics simulation. Our results indicate a finite salt-bridge (E46-K80) is crucial for stability of protofibril. Besides, we observed hydrogen bonds and non-bonded contacts involved in fibril stabilization. We noticed α-synuclein dimer predominantly exists in conformations distinct from fibril. We characterized the salient molecular interactions in α-synuclein fibril and these findings may be useful to design potential inhibitors for the treatment of PD. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  14. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    of the experimentally determined charge density distribution of a cobalt coordination polymer at 15K is presented in Chapter 4. The study exemplifies the immense advances in experimental charge density analysis made possible by utilization of intense third generation synchrotrons, as even the single crystal structural......This thesis is the result of four years work at the Laboratory of Inorganic Chemistry, Department of Chemistry, Aarhus University. I have decided to divide the thesis into seven chapters, where the two first chapters introduce the theory and compound classes of this dissertation. The next two...... chapters concern transition metal coordination polymers and the last three describe hydroquinone co-crystals and clathrate structures. Even though, the goal of the thesis has been to give account of all the work that I have performed, I have chosen to leave out results of certain projects, and confine...

  15. Neutron diffraction investigation of the crystal and molecular structure of the anisotropic superconductor Hg3AsF6

    International Nuclear Information System (INIS)

    Schultz, A.J.; Williams, J.M.; Miro, N.D.; MacDiarmid, A.G.; Heeger, A.J.

    1978-01-01

    The crystal and molecular structure of Hg 3 AsF 6 has been investigated by single-crystal neutron diffraction. This metallic compound crystallizes in the body-centered tetragonal space group I4 1 /amd with cell dimensions of a = 7.549 (5) A and c = 12.390 (9) A. The crystal structure consists of two orthogonal and nonintersecting linear chains of Hg/sup 0.33+/ cations passing through a lattice of octahedral AsF 6 - anions. The intrachain Hg--Hg distance of 2.64 (2) A is derived from planes of diffuse scattering normal to a* and b*. Since the a and b axis lattice constants are not simple multiples of the Hg--Hg intrachain distance, the mercury chains are incommensurate with the tetragonal lattice; hence we have the apparent formula Hg 2 . 86 AsF 6 . These results are in essential agreement with a previously reported x-ray diffraction study. However, from the neutron diffraction data, we have established that the Hg chains are not strictly one-dimensional. The maximum room-temperature deviation from the chain axis is 0.07 (1) A with neighboring chains distorted away from each other. The closest interchain Hg--Hg contact is 3.24 (2) A. Furthermore, analytical data consistently indicate a stoichiometric empirical formula of Hg 3 AsF 6 . These results together with precise density measurements imply that the incommensurate structure is stabilized by anion vacancies, such that there are four formula weights of Hg 2 . 86 (AsF 6 ) 0 . 953 per unit cell. 4 tables, 2 figures

  16. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    International Nuclear Information System (INIS)

    Kirkpatrick, R. James; Kalinichev, Andrey G.

    2008-01-01

    significantly larger systems. These calculations have allowed us, for the first time, to study the effects of metal cations with different charges and charge density on the NOM aggregation in aqueous solutions. Other computational work has looked at the longer-time-scale dynamical behavior of aqueous species at mineral-water interfaces investigated simultaneously by NMR spectroscopy. Our experimental NMR studies have focused on understanding the structure and dynamics of water and dissolved species at mineral-water interfaces and in two-dimensional nano-confinement within clay interlayers. Combined NMR and MD study of H2O, Na+, and Cl- interactions with the surface of quartz has direct implications regarding interpretation of sum frequency vibrational spectroscopic experiments for this phase and will be an important reference for future studies. We also used NMR to examine the behavior of K+ and H2O in the interlayer and at the surfaces of the clay minerals hectorite and illite-rich illite-smectite. This the first time K+ dynamics has been characterized spectroscopically in geochemical systems. Preliminary experiments were also performed to evaluate the potential of 75As NMR as a probe of arsenic geochemical behavior. The 75As NMR study used advanced signal enhancement methods, introduced a new data acquisition approach to minimize the time investment in ultra-wide-line NMR experiments, and provides the first evidence of a strong relationship between the chemical shift and structural parameters for this experimentally challenging nucleus. We have also initiated a series of inelastic and quasi-elastic neutron scattering measurements of water dynamics in the interlayers of clays and layered double hydroxides. The objective of these experiments is to probe the correlations of water molecular motions in confined spaces over the scale of times and distances most directly comparable to our MD simulations and on a time scale different than that probed by NMR. This work is being done

  17. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.

    1983-01-01

    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  18. Local hydrated structure of an Fe2+/Fe3+ aqueous solution: an investigation using a combination of molecular dynamics and X-ray absorption fine structure methods

    International Nuclear Information System (INIS)

    Ye Qing; Zhou Jing; Zhao Haifeng; Chen Xing; Chu Wangsheng; Zheng Xusheng; Marcelli, Augusto; Wu Ziyu

    2013-01-01

    The hydrated shell of both Fe 2+ and Fe 3+ aqueous solutions are investigated by using the molecular dynamics (MD) and X-ray absorption structure (XAS) methods. The MD simulations show that the first hydrated shells of both Fe 2+ and Fe 3+ are characterized by a regular octahedron with an Fe-O distance of 2.08Å for Fe 2+ and 1.96Å for Fe 3+ , and rule out the occurrence of a Jahn-Teller distortion in the hydrated shell of an Fe 2+ aqueous solution. The corresponding X-ray absorption near edge fine structure (XANES) calculation successfully reproduces all features in the XANES spectra in Fe 2+ and Fe 3+ aqueous solution. A feature that is located at energy 1 eV higher than the white line (WL) in an Fe 3+ aqueous solution may be assigned to the contribution of the charge transfer. (authors)

  19. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  20. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  1. C-Ni-Pd and CNT-Ni-Pd film's molecular and crystalline structure investigations by FTIR spectroscopy and XRD diffraction

    Science.gov (United States)

    Stepińska, Izabela; Czerwosz, ElŻbieta; Diduszko, Ryszard; Kozłowski, Mirosław; Wronka, Halina

    2017-08-01

    In this work molecular and crystalline structure of new type of nanocomposite films were investigated. These films compose of CNT decorated with palladium nanograins. They were prepared on a base of C-Ni films modified in CVD process. C-Ni nanocomposite films were obtained by PVD process and their modification by CVD leads to a growth of CNT film. CNTs-Ni or C-Ni films were treated with additional PVD process with palladium. Nickel and palladium acetate and fulleren C60 are precursors of films in PVD process. FTIR spectroscopy was used to studied the molecular structure of film in every stage of preparation . The crystalline structure of these films was studied by X-ray diffraction. SEM (scanning electron microscopy) was applied to investigate film's surface topography.

  2. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  3. Experimental and theoretical investigation of the molecular, electronic structure and solvatochromism of phenyl salicylate: External electric field effect on the electronic structure

    Science.gov (United States)

    Sıdır, İsa; Sıdır, Yadigar Gülseven

    2017-11-01

    The UV-vis absorption and steady state fluorescence spectra of phenyl salicylate (abbreviated as PS) have been recorded in a series of non-polar, polar protic and polar aprotic solvents at room temperature and the obtained spectral data are used to determine the solvatochromic behavior and the ground and excited state dipole moments. Basis set sensitive molecular structure along with X-ray crystal data are evaluated. The ground state and excited state dipole moments are determined by using Lippert-Mataga, Bakhshiev, Bilot-Kawski and Reichardt solvatochromic shift methods as a function of dielectric constant (ε) and refractive index (n) of the solvents. The larger excited state dipole moment value indicates the more polar PS in the excited state. The rate of μe/μg is found as 2.4239. Solvatochromic behavior of PS is enlightened by using Kamlet-Taft and Catalan models. Kamlet-Taft solvatochromic model indicates that non-specific solute solvent interactions are controlled by solvent dispersion-induction forces and specific interactions are directed by hydrogen-bond donor capacity of solvent. Catalan solvatochromic model designates that solute-solvent interactions are governed by solvent polarizability. Ground and excited state dipole moments are found theoretically by using DFT/B3LYP/6-311++G(d, p) and TDDFT/B3LYP/6-31++G(d, p) methods. External electric field effect on LUMO-HOMO band gap and dipole moment have been investigated by using B3LYP/6-311++G(d, p) method.

  4. A Theoretical Investigation of the Structure and Reactivity of the Molecular Constituents of Oil Sand and Oil Shale

    Energy Technology Data Exchange (ETDEWEB)

    Parish, Carol A. [Univ. of Richmond, VA (United States)

    2016-11-28

    We used a variety of small organic models of asphaltenes to investigate the molecular mechanism for the high temperature decomposition that would take place as part of the oil refinery process. We determined that the decomposition is initiated via four different types of hydrogen migration reactions. According to the energetics of the reactions, the dominant 1,2-H shift mechanism involves two competitive product channels, namely, C2H2 + CH2CS and CS + CH3CCH. The minor channels include the formation of CS + CH2CCH2, H2S + C4H2, HCS + CH2CCH, CS + CH2CHCH, H + C4H3S, and HS + C4H3. We also investigated the alkyl substitution effect by exploring the decomposition pathways of models with alkyl arms. The energetics of such systems were very similar to that for unsubstituted model compounds, which suggests that asphaltene alkylation may not play a significant role in the decomposition of asphaltene compounds. This work was published in the Journal of Physical Chemistry A 2011, 115, 2882-2891. A MECHANISTIC STUDY OF THE 2-THIENYLMETHYL + HO2 RADICAL RECOMBINATION REACTION Radicals are molecules which contain single electrons. They are very reactive. Radical recombination reactions are important in the combustion of fuel oils. Shale oil contains radicals. We used quantum mechanics to explore the reactivity of shale oil model radical compounds. Seventeen product channels corresponding to either addition/elimination or direct hydrogen abstraction were characterized. Direct hydrogen abstraction proceeds via a weakly bonded complex, which leads to 2-methylthiophene, 2-methylene-2,3-dihydrothiophene or 2-methylene-2,5-dihydrothiophene depending upon the 2-thienylmethyl radical reaction site. The addition pathway for the two radical reactants is barrierless with the formation of three adducts, as distinguished by HO

  5. In Situ Spectroscopic Investigation of Molecular Structures of Highly Dispersed Vanadium Oxide on Silica under Various Conditions

    NARCIS (Netherlands)

    Gao, X.; Bare, S.R.; Weckhuysen, B.M.; Wachs, I.E.

    1998-01-01

    The molecularly dispersed V2O5/SiO2 supported oxides were prepared by the incipient wetness impregnation of 2-propanol solutions of V-isopropoxide. The experimental maximum dispersion of surface vanadium oxide species on SiO2 was achieved at ~12 wt % V2O5 ( ~2.6 V atoms/nm^2 ). The surface

  6. electronic and structural investigations

    Indian Academy of Sciences (India)

    2018-03-30

    Mar 30, 2018 ... Indian Academy of Sciences https://doi.org/10.1007/s12034-018-1572-8. Milling effect on the photo-activated properties of TiO2 nanoparticles: electronic and structural investigations. YOUCEF MESSAI1,2, BERTRAND VILENO2,4, DAVID MARTEL3, PHILIPPE TUREK2,4 and. DJAMEL EDDINE MEKKI1,∗.

  7. Theoretical investigation of molecular structure and vibrational spectra of 3,5-Diphenyl-4-(3,4,5-Trimethoxybenzylideneamino)-4H-1,2,4-Triazole Molecular

    International Nuclear Information System (INIS)

    Avci, D.

    2005-01-01

    The molecular geometry and vibrational frequencies of 3,5-diphenyl-4-(3,4,5- trimethoxybenzylideneamino)-4H-1,2,4-triazole in the ground state have been calculated using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of 3,5-diphenyl-4-(3,4,5-trimethoxybenzylideneamino)-4H-1,2,4- triazole with calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems

  8. Structural biology of Molecular machines

    Indian Academy of Sciences (India)

    Administrator

    a structural biology perspective. TANWEER HUSSAIN. Molecular Reproduction, Development and Genetics (MRDG). Indian Institute of Science (IISc). Bangalore. Symposium on “Molecular Machines: a multidiscipline enterprise” 1st July 2017. 28th mid-year meeting of Indian Academy of Sciences at IISc, Bangalore ...

  9. Stereoselective green synthesis and molecular structures of highly functionalized spirooxindole-pyrrolidine hybrids - A combined experimental and theoretical investigation

    Science.gov (United States)

    Kumar, Raju Suresh; Almansour, Abdulrahman I.; Arumugam, Natarajan; Soliman, Saied M.; Kumar, Raju Ranjith; Altaf, Mohammad; Ghabbour, Hazem A.; Krishnamoorthy, Bellie Sundaram

    2018-01-01

    Highly functionalized spirooxindole-pyrrolidine hybrids have been synthesized stereoselectively through a [3 + 2] cycloaddition strategy in an ionic liquid, 1-butyl-3-methylimidazolium bromide ([bmim]Br). The structure of these spiro heterocyclic hybrids was elucidated using one and two dimensional NMR spectroscopy, single crystal X-ray crystallographic studies and Density Functional Theory (DFT) calculations. The calculated geometric parameters are in good agreement with the experimental data obtained from the X-ray structures. The Natural Bond Orbital (NBO) calculations on these molecules confirm the electron rich carbonyl oxygen and electron deficient NH groups. The 1H and 13C NMR chemical shifts calculated using GIAO method are in good agreement with the experimental data. The DFT computed polarizability values also suggest the possible NLO activity of these molecules.

  10. Basic amphipathic model peptides: Structural investigations in solution, studied by circular dichroism, fluorescence, analytical ultracentrifugation and molecular modelling

    Science.gov (United States)

    Mangavel, C.; Sy, D.; Reynaud, J. A.

    1999-05-01

    A twenty amino acid residue long amphipathic peptide made of ten leucine and ten lysine residues and four derivatives, in which a tryptophan, as a fluorescent probe, is substituted for a leucine, are studied. The peptides in water are mainly in an unordered conformation (~90%), and undergo a two state reversible transition upon heating, leading to a partially helical conformation (cold denaturation). Time resolved fluorescence results show that fluorescence decay for the four Trp containing peptides is best described by triple fluorescence decay kinetics. In TFE/water mixture, peptides adopt a single α-helix conformation but the Leu-Trp9 substitution leads to an effective helix destabilizing effect. In salted media, the peptides are fully helical and present a great tendency to self associate by bringing the hydrophobic faces of helices into close contact. This proceeds in non-cooperative multisteps leading to the formation of α helix aggregates with various degrees of complexation. Using modelling, the relative hydrophobic surface areas accessible to water molecules in n-mer structures are calculated and discussed. Nous avons étudié un peptide amphipathique composé de dix lysine et dix leucine, ainsi que quatre dérivés comportant un résidu tryptophane pour les études par fluorescence. Dans l'eau, les peptides ne sont pas structurés (~90%), et se structurent partiellement en hélice α par chauffage (dénaturation froide). Les mesures de déclin de fluorescence font apparaître une cinétique à trois temps de vie. Dans un mélange eau/TFE, les peptides adoptent une conformation en hélice α, mais la substitution Leu-Trp9 possède un effet déstabilisant. En mileu salin, les peptides sont totalement hélicoïdaux et ont tendance à s'agréger de façon à regrouper leur face hydrophobe. Ce processus se fait en plusieurs étapes avec des agrégats de taille variable. L'existence de tels agrégats est discutée sur la base de la modélisation mol

  11. Synthesis, crystal structure analysis, spectral investigations, DFT computations and molecular dynamics and docking study of 4-benzyl-5-oxomorpholine-3-carbamide, a potential bioactive agent

    Science.gov (United States)

    Murthy, P. Krishna; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Suchetan, P. A.

    2017-04-01

    4-benzyl-5-oxomorpholine-3-carbamide has been synthesized; single crystals were grown by slow evaporation solution growth technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman and 1H-NMR. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry of the compound was optimized by using Density Functional Theory (DFT/B3LYP) method with 6-311++G(d,p) basis set in the ground state and geometric parameters are in agreement with the X-ray analysis results of the structure. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wave number was assigned on the basis of potential energy distribution (PED). The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbital's (HOMOs) and lowest unoccupied molecular orbital's (LUMOs). Besides molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behavior and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Potential reactive sites of the title compound have been identified by average local ionization energy and Fukui functions, both mapped to the electron density surface. Bond dissociation energies for all single acyclic bonds have been calculated in order to investigate autoxidation and degradation properties of the title compound. Atoms with pronounced interactions with water molecules have been detected by calculations of radial distribution functions after molecular dynamics simulations. The experimental results are compared with the theoretical calculations using DFT methods for the fortification of the paper. Further the docking studies revealed that the title compound as a docked ligand forms a stable complex with pyrrole inhibitor with a binding affinity value of -7.5 kcal/mol. This

  12. Uncertainties of Molecular Structural Parameters

    International Nuclear Information System (INIS)

    Császár, Attila G.

    2014-01-01

    performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r e BO , and semiexperimental, r e SE ) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

  13. Synthesis, molecular structure, vibrational spectroscopy, optical investigation and DFT study of a novel hybrid material: 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate

    Science.gov (United States)

    Kessentini, A.; Dammak, T.; Belhouchet, M.

    2017-12-01

    In his work we investigate a new halogenotin (IV) organic inorganic material. The structure, determined by single-crystal X-ray diffraction at 293 K of 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate abbreviated 3,3‧(DDS)SnCl6, can be viewed as inorganic layers built from (SnCl6)2- octahedra and H2O molecules, between which, the organic entities [C12H14N2O2S]2+ are inserted. Experimental room-temperature X-ray studies were supported by theoretical methods using density functional theory (DFT). The detailed examination of the vibrational spectra of our material was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. The optical properties in the UV-visible region have been explored by the UV-visible absorption. This material shows a single absorption band centred at 325 nm (318 eV). The energy difference between Occupied, HOMO and Lowest Unoccupied, LUMO orbital which is called energy gap can be used to predict the strength and stability of metal complexes, as well as in determining molecular electrical transport properties. For the calculation of excitation energies in the optical studies we used Time-Dependent Density Functional Theory (TD-DFT). In addition, Mulliken population method and molecular electrostatic potential (MEP) of the title material have been theoretically studied by GAUSSIAN 03 package.

  14. Structural changes of humic acids from sinking organic matter and surface sediments investigated by advanced solid-state NMR: Insights into sources, preservation and molecularly uncharacterized components

    Science.gov (United States)

    Mao, Jingdong; Tremblay, Luc; Gagné, Jean-Pierre

    2011-12-01

    Knowledge of the structural changes that particulate organic matter (POM) undergoes in natural systems is essential for determining its reactivity and fate. In the present study, we used advanced solid-state NMR techniques to investigate the chemical structures of sinking particulate matter collected at different depths as well as humic acids (HAs) extracted from these samples and underlying sediments from the Saguenay Fjord and the St. Lawrence Lower Estuary (Canada). Compared to bulk POM, HAs contain more non-polar alkyls, aromatics, and aromatic C-O, but less carbohydrates (or carbohydrate-like structures). In the two locations studied, the C and N contents of the samples (POM and HAs) decreased with depth and after deposition onto sediments, leaving N-poor but O-enriched HAs and suggesting the involvement of partial oxidation reactions during POM microbial degradation. Advanced NMR techniques revealed that, compared to the water-column HAs, sedimentary HAs contained more protonated aromatics, non-protonated aromatics, aromatic C-O, carbohydrates (excluding anomerics), anomerics, OC q, O-C q-O, OCH, and OCH 3 groups, but less non-polar alkyls, NCH, and mobile CH 2 groups. These results are consistent with the relatively high reactivity of lipids and proteins or peptides. In contrast, carbohydrate-like structures were selectively preserved and appeared to be involved in substitution and copolymerization reactions. Some of these trends support the selective degradation (or selective preservation) theory. The results provide insights into mechanisms that likely contribute to the preservation of POM and the formation of molecules that escape characterization by traditional methods. Despite the depletion of non-polar alkyls with depth in HAs, a significant portion of their general structure survived and can be assigned to a model phospholipid. In addition, little changes in the connectivities of different functional groups were observed. Substituted and copolymerized

  15. Investigation of microstructure and morphology for the Ge on porous silicon/Si substrate hetero-structure obtained by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Gouder, S. [IM2NP Aix-Marseille Universités, UMR CNRS n°7334, Faculté des Sciences St-Jérôme - Case 142, 13397 Marseille Cedex 20 France (France); Electronics Department, University Hadj Lakhdar, Batna 05000 (Algeria); Mahamdi, R. [Electronics Department, University Hadj Lakhdar, Batna 05000 (Algeria); Aouassa, M.; Escoubas, S.; Favre, L.; Ronda, A.; Berbezier, I. [IM2NP Aix-Marseille Universités, UMR CNRS n°7334, Faculté des Sciences St-Jérôme - Case 142, 13397 Marseille Cedex 20 France (France)

    2014-01-01

    Thick porous silicon (PS) buffer layers are used as sacrificial layers to epitaxially grow planar and fully relaxed Ge membranes. The single crystal Ge layers have been deposited by molecular beam epitaxy (MBE) on PS substrate. During deposition, the pore network of PS layers has been filled with Ge. We investigate the structure and morphology of PS as fabricated and after annealing at various temperatures. We show that the PS crystalline lattice is distorted and expanded in the direction perpendicular to the substrate plane due to the presence of chemisorbed –OH. An annealing at high temperature (> 500 °C), greatly changes the PS morphology and structure. This change is marked by an increase of the pore diameter while the lattice parameter becomes tensily strained in the plane (compressed in the direction perpendicular). The morphology and structure of Ge layers are investigated by transmission electron microscopy, high resolution X-ray diffraction and atomic force microscopy as a function of the deposition temperature and deposited thickness. The results show that the surface roughness, level of relaxation and Si-Ge intermixing (Ge content) depend on the growth temperature and deposited thickness. Two sub-layers are distinguished: the layer incorporated inside the PS pores (high level of intermixing) and the layer on top of the PS surface (low level of intermixing). When deposited at temperature > 500 °C, the Ge layers are fully relaxed with a top Si{sub 1−x}Ge{sub x} layer x = 0.74 and a very flat surface. Such layer can serve as fully relaxed ultra-thin SiGe pseudo-substrate with high Ge content. The epitaxy of Ge on sacrificial soft PS pseudo-substrate in the experimental conditions described here provides an easy way to fabricate fully relaxed SiGe pseudo-substrates. Moreover, Ge thin films epitaxially deposited by MBE on PS could be used as relaxed pseudo-substrate in conventional microelectronic technology. - Highlights: • We have developed a rapid

  16. Molecular analysis and antibiotic resistance investigation of ...

    African Journals Online (AJOL)

    Molecular analysis and antibiotic resistance investigation of Staphylococcus aureus isolates associated with staphylococcal food poisoning and nosocomial infections. Y Zhang, S Cheng, G Ding, M Zhu, X Pan, L Zhang ...

  17. [Investigation the role of mutations M182T and Q39K in structure of beta-lactamase TEM-72 by molecular dynamics method].

    Science.gov (United States)

    Shcherbinin, D S; Rubtsova, M Yu; Grigorenko, V G; Uporov, I V; Veselovsky, A V; Egorov, A M

    2016-07-01

    Synthesis of b-lactamases is one of the common mechanisms of bacterial resistance to b-lactam antibiotics including penicillins and cephalosporins. The widespread use of antibiotics results in appearance of numerous extended-spectrum b-lactamase variants or resistance to inhibitors. Mutations of 92 residues of TEM type were found. Several mutations are the key mutations that determine the extension of spectrum of substrates. However, roles of the most associated mutations, located far from active site, remain unknown. We have investigated the role of associated mutations in structure of b-lactamase TEM-72, which contain two key mutation (G238S, E240K) and two associated mutations (Q39K, M182T) by means of simulation of molecular dynamics. The key mutation lead to destabilization of the protein globule, characterized by increased mobility of amino acid residues at high temperature of modelling. Mutation M182T lead to stabilization protein, whereas mutation Q39K is destabilizing mutation. It seems that the last mutation serves for optimization of conformational mobility of b-lactamase and may influence on enzyme activity.

  18. Investigations of Nuclear Structure

    Energy Technology Data Exchange (ETDEWEB)

    Sarantites, Demetrios [Washington Univ., St. Louis, MO (United States); Reviol, W. [Washington Univ., St. Louis, MO (United States)

    2015-07-15

    The proposal addresses studies of nuclear structure at low-energies and development of instrumentation for that purpose. The structure studies deal with features of neutron-rich nuclei with unexplored shapes (football- or pear-shaped nuclei). The regions of interest are: neutron rich nuclei like 132-138Sn, or 48-54Ca, and the Zr, Mo, and Ru isotopes. The tools used can be grouped as follows: either Gammasphere or Gretina multi-gamma detector arrays and auxiliary detectors (Microball, Neutron Shell, and the newly completed Phoswich Wall).The neutron-rich nuclei are accessed by radioactive-beam binary reactions or by 252Cf spontaneous fission. The experiments with heavy radioactive beams aim at exciting the beam nuclei by pick-up or transfer a neutron or a proton from a light target like 13C, 9Be, 11B or 14N .For these binary-reaction studies the Phoswich Wall detector system is essential. It is based on four multi-anode photomultiplier tubes on which CsI and thin fast-timing plastic scintillators are attached. Their signals are digitized with a high density microchip system.

  19. Rotational spectra and molecular structure

    CERN Document Server

    Wollrab, James E

    1967-01-01

    Physical Chemistry, A Series of Monographs: Rotational Spectra and Molecular Structure covers the energy levels and rotational transitions. This book is divided into nine chapters that evaluate the rigid asymmetric top molecules and the nuclear spin statistics for asymmetric tops. Some of the topics covered in the book are the asymmetric rotor functions; rotational transition intensities; classes of molecules; nuclear spin statistics for linear molecules and symmetric tops; and classical appearance of centrifugal and coriolis forces. Other chapters deal with the energy levels and effects of ce

  20. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  1. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  2. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene.

    Science.gov (United States)

    Kose, E; Atac, A; Karabacak, M; Nagabalasubramanian, P B; Asiri, A M; Periandy, S

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, (1)H and (13)C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. (13)C and (1)H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Molecular investigations of flaxseed mucilage polysaccharides.

    Science.gov (United States)

    Roulard, Romain; Petit, Emmanuel; Mesnard, François; Rhazi, Larbi

    2016-05-01

    The molecular properties of flaxseed mucilage were determined using a multi-angle laser light scattering (MALLS) detector coupled on-line to size exclusion chromatography (SEC) and asymmetric flow field-flow fractionation (AF4). Water and salt solution were tested as mobile phases. The SEC-MALLS method gave partial information and enabled molecular characterization of disaggregated mucilage molecules. Regardless of the eluent used, the observed Mw ranged from about 1.6 × 10(6) to more than 10 × 10(6) g/mol for mucilage polysaccharides. The AF4-MALLS system enabled a complete analysis of mucilage carbohydrate aggregates in water, in which two populations were satisfactorily separated. The molecular weight distribution (MWD) of molecules ranged from 1.5 × 10(6) to more than 4 × 10(8) g/mol. Experiments showed that the conformational structure of mucilage molecules was strongly influenced by ionic strength. Mucilage carbohydrates exhibited a spherical and compact structure in NaCl solution while they displayed a random-coil conformation in water. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Theoretical molecular structure, vibrational frequencies and NMR investigations of 2-[(1E-2-aza-2-(5-methyl(2-pyridylethenyl]-4-bromobenzen-1-ol

    Directory of Open Access Journals (Sweden)

    Cemal Parlak

    2012-08-01

    Full Text Available The normal mode frequencies and corresponding vibrational assignments, 1H and 13C NMR chemical shifts and structural parameters (bond lengths, bond and dihedral angles of 2-[(1E-2-aza-2-(5-methyl(2-pyridylethenyl]-4-bromobenzen-1-ol (2mpe-4bb Schiff base compound have been theoretically examined by means of Hartree-Fock (HF and Becke-3-Lee-Yang-Parr (B3LYP density functional methods with 6-31G(d and 6-311++G(d,p basis sets. Furthermore, reliable vibrational assignments have made on the basis of potential energy distribution (PED calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO of 2mpe-4bb have been predicted. Theoretical results have been successfully compared with available experimental data in the literature. Regarding the calculations, 2mpe-4bb prefers enol-imine form and DFT method is superior to HF approach except for predicting bond lengths.DOI: http://dx.doi.org/10.4314/bcse.v26i2.11

  5. Evaluating Agronomic Performance and Investigating Molecular Structure of Drought and Heat Tolerant Wild Alfalfa (Medicago sativa L.) Collection from the Southeastern Turkey.

    Science.gov (United States)

    Basbag, Mehmet; Aydin, Ali; Sakiroglu, Muhammet

    2017-02-01

    Drought is a major stress factor for agricultural production including alfalfa production. One way to counterbalance the yield losses is the introgression of drought tolerant germplasm into breeding programs. As an effort to exploit such germplasm, 16 individual plants were selected from the Southeastern Turkey from their natural habitat and clonally propagated in field trials with an ultimate goal to use the germplasm as parents for releasing a synthetic cultivar. Forage yield and forage quality traits were evaluated and molecular genetic diversity among genotypes were determined using inter simple sequence repeat markers. Genotypes showed a variation from growth habit to yield and quality traits indicating sufficient phenotypic variation for diverse breeding efforts (for grazing or harvesting) and long term selection schemes. A large amount of genetic variation was observed even with a limited number of marker and genotypes. However, no pattern of spatial genetic structure was observed for the scale of the study when genetic variation is linked to the geographic origin. We conclude that ex situ natural variation provides a wealth of germplasm that could be incorporated into breeding programs aiming to improve drought tolerance. We also suggest an extensive collection of seeds/plant tissue from unique plants with desirable traits rather than putting more efforts to create a spatial germplasm sampling efforts in narrow regions.

  6. Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: A combined experimental and theoretical study

    Science.gov (United States)

    Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

    2015-01-01

    In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm-1 and 4000-50 cm-1, respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion-1 and anion-2 conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1sbnd C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed.

  7. Preparation and structure investigation of novel Schiff bases using spectroscopic, thermal analyses and molecular orbital calculations and studying their biological activities

    Science.gov (United States)

    Zayed, Ehab M.; Zayed, M. A.; El-Desawy, M.

    2015-01-01

    Two novel Schiff's bases (EB1 and L1) as new macrocyclic compounds were prepared via condensation reactions between bisaldehyde (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde): firstly with hydrazine carbothioamide to give (EB1), secondly with 4,6-diaminopyrimidine-2-thiol to give (L1). EB1 has a general formula C18H20N6O2S2 of mole mass = 416.520, and IUPAC name ((N,N‧Z,N,N‧E)-N,N‧-(((ethane1,2diylbis(oxy))bis(2,1phenylene))bis(methanylylidene))bis(1hydrazinylmethanethioamide). L1 has a general formula C20H16N4O2S of mole mass = 376.10; and IUPAC name 1,2-bis(2-vinylphenoxy)ethane4,6-diaminopyrimidine-2-thiol). The structures of the compounds obtained were characterized based on elemental analysis, FT-IR and 1H NMR spectra, mass, and thermogravimetric analysis (TG, DTG). The activation thermodynamic parameters, such as, ΔE*, ΔH*, ΔS* and ΔG* were calculated from the TG curves using Coats-Redfern method. It is important to investigate their structures to know the active groups and weak bond responsible for their biological activities. The obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculation using PM3 procedure, on the neutral and positively charged forms of these novel Schiff bases. Therefore, comparison between MS and TA helps in selection of the proper pathway representing the decomposition of these compounds to give indication about their structures and consequently their biological activities. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their antimicrobial potential.

  8. Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2006-01-01

    Molecular dynamics simulations of three related helical antimicrobial peptides have been carried out in zwitterionic diphosphocholine (DPC) micelles and anionic sodiumdodecylsulfate (SDS) micelles. These systems can be considered as model mammalian and bacterial membrane interfaces, respectively...

  9. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  10. Structure-Activity Investigation of a G Protein-Biased Agonist Reveals Molecular Determinants for Biased Signaling of the D2 Dopamine Receptor

    Directory of Open Access Journals (Sweden)

    Lani S. Chun

    2018-02-01

    Full Text Available The dopamine D2 receptor (D2R is known to elicit effects through activating two major signaling pathways mediated by either G proteins (Gi/o or β-arrestins. However, the specific role of each pathway in physiological or therapeutic activities is not known with certainty. One approach to the dissection of these pathways is through the use of drugs that can selectively modulate one pathway vs. the other through a mechanism known as functional selectivity or biased signaling. Our laboratory has previously described a G protein signaling-biased agonist, MLS1547, for the D2R using a variety of in vitro functional assays. To further evaluate the biased signaling activity of this compound, we investigated its ability to promote D2R internalization, a process known to be mediated by β-arrestin. Using multiple cellular systems and techniques, we found that MLS1547 promotes little D2R internalization, which is consistent with its inability to recruit β-arrestin. Importantly, we validated these results in primary striatal neurons where the D2R is most highly expressed suggesting that MLS1547 will exhibit biased signaling activity in vivo. In an effort to optimize and further explore structure-activity relationships (SAR for this scaffold, we conducted an iterative chemistry campaign to synthesize and characterize novel analogs of MLS1547. The resulting analysis confirmed previously described SAR requirements for G protein-biased agonist activity and, importantly, elucidated new structural features that are critical for agonist efficacy and signaling bias of the MLS1547 scaffold. One of the most important determinants for G protein-biased signaling is the interaction of a hydrophobic moiety of the compound with a defined pocket formed by residues within transmembrane five and extracellular loop two of the D2R. These results shed new light on the mechanism of biased signaling of the D2R and may lead to improved functionally-selective molecules.

  11. Investigation of pollutant gases with molecular absorption spectroscopy

    International Nuclear Information System (INIS)

    Izairi, N; Ajredini, F.; Shehabi, M.

    2011-01-01

    This paper contains the molecular absorption spectroscopic investigation on environmental pollution by many pollutants. For this purpose a laser absorption spectroscopy at 630 nm wavelength has been applied to excite the molecular spectra in order to identify the presence of main gas pollutants. The following was the experimental procedure. Preliminary the presence of pollutants was identified. The gas champions were taken in live environment, in Tetovo streets where cars moved, and in some points in Tetovo suburbia, during different periods of the day. A special civet, part of the apparatus, has been filled by environmental air, and latter, put into the apparatus. A laser beam pulse passes throughout absorbing gas medium in the civet to excite the gas, and the absorbing spectra were automatically registered. The molecular band spectra registration has been performed by an FT-IR Spectrometer (Spectrum BX FT-IR Perkin Elmer). For this purpose the measurements were focused in spectral region of 2075 cm -1 to 2384 cm -1 for CO 2 and CO bands investigation. The importance of such measurements is to investigate the spectral properties of absorption spectra and molecular structure, and for monitoring the environmental pollution. (Author)

  12. Algorithmic dimensionality reduction for molecular structure analysis.

    Science.gov (United States)

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul

    2008-08-14

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  13. Algorithmic dimensionality reduction for molecular structure analysis

    Science.gov (United States)

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul

    2008-01-01

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation—a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation. PMID:18715062

  14. Algorithmic dimensionality reduction for molecular structure analysis

    Science.gov (United States)

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul

    2008-08-01

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation-a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  15. Investigation of glassy state molecular motions in thermoset polymers

    Science.gov (United States)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  16. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10. A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more.

  17. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    A structure for nucleic acid has already been proposed by Pauling and Corey [1]. They kindly made'their manuscript available to us in advance of publication. Their model consists of three inter-twined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory ...

  18. Molecular structure and centrifugal distortion in methylthioethyne

    NARCIS (Netherlands)

    Engelsen, D. den

    1969-01-01

    The investigation of the microwave spectra of five isotopic species of methylthioethyne, HCCSCH3 enabled a fairly reliable calculation to be made of bond lengths and angles. The centrifugal distortion parameters are related to molecular vibrations.

  19. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  20. Fluorescence Titrations of Bio-relevant Complexes with DNA: Synthesis, Structural Investigation, DNA Binding/Cleavage, Antimicrobial and Molecular Docking Studies.

    Science.gov (United States)

    Arun, Thesingu Rajan; Subramanian, Ramasamy; Packianathan, Seemon; Raman, Natarajan

    2015-07-01

    In the present work, we attempted to develop new metal complexes (Cu(II), Co(II), Ni(II) and Zn(II)) of the imine ligand which was synthesized from 9,10-phenanthrenequinone and para-anisidine. With an intention to make the complexes most stable, very special chelating amino acid has been coordinated to the metal centre. The resultant metal complexes have been characterized by variety of techniques including FT-IR, UV-Vis., (1)H NMR, (13)C NMR, powder XRD, EPR and mass spectral studies. The interaction of the complexes with DNA has been effectively examined and explored by fluorescence titration, UV-Vis absorption, viscometer titration, cyclic voltammetry (CV) and differential pulse voltammetry. Moreover, molecular docking analysis has been performed to understand the nature of binding of the complexes with DNA. These studies prove that CT DNA interaction of the complexes follows intercalation mode. The metal complexes exhibit effective cleavage of pUC19 DNA by an oxidative cleavage mechanism. The antimicrobial screening indicates that these complexes are good antimicrobial agents against various organisms.

  1. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  2. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: a combined experimental and theoretical study.

    Science.gov (United States)

    Arivazhagan, M; Gayathri, R

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ(*) and π(*) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: A combined experimental and theoretical study

    Science.gov (United States)

    Arivazhagan, M.; Gayathri, R.

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ* and π* antibonding orbitals and E(2) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra.

  4. Raman microprobe investigation of molecular structure and organization in the native state of woody tissue. Progress report, April 1, 1987--July 31, 1989

    Energy Technology Data Exchange (ETDEWEB)

    Atalla, R.H.

    1989-08-01

    Although the primary emphasis of our program has remained with the application of Raman spectroscopy to the study of native tissue, the scope of the work has been expanded to include a number of complementary approaches. These have included Solid State 13C NMR, autoradiography of radiolabeled woody tissue sections, and the generation of biomimetic tertiary aggregates which simulate states of aggregation characteristic of cell walls. Our Raman spectroscopic studies have resulted in progress in the areas of interpretation of the spectral features, and confirmation of the variability of the patterns of orientation of lignin reported earlier. We have assembled and made operational our new microprobe and spectrometer systems acquired under the DOE-URIP program. We have also demonstrated that, operating with gated detection and pulsed laser excitation, we can discriminate against the laser-excited fluorescence characteristic of most woody tissue. Our studies of celluloses, which combine Raman spectroscopy and 13C NMR have shown that all native celluloses are composites of two forms which have the same secondary structure but different tertiary structures.

  5. Algorithmic dimensionality reduction for molecular structure analysis

    OpenAIRE

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul

    2008-01-01

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated alg...

  6. Molecular catalysts structure and functional design

    CERN Document Server

    Gade, Lutz H

    2014-01-01

    Highlighting the key aspects and latest advances in the rapidly developing field of molecular catalysis, this book covers new strategies to investigate reaction mechanisms, the enhancement of the catalysts' selectivity and efficiency, as well as the rational design of well-defined molecular catalysts. The interdisciplinary author team with an excellent reputation within the community discusses experimental and theoretical studies, along with examples of improved catalysts, and their application in organic synthesis, biocatalysis, and supported organometallic catalysis. As a result, readers wil

  7. How We Teach Molecular Structure to Freshmen.

    Science.gov (United States)

    Hurst, Michael O.

    2002-01-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  8. Molecular structure, vibrational spectroscopic studies and natural ...

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 74; Issue 5. Molecular structure ... The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out.

  9. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

  10. Investigation of Galactosylated Low Molecular Weight Chitosan ...

    African Journals Online (AJOL)

    the stability towards drug release and for targeting purposes. Chitosan coated liposomes have been formed via ionic interaction between the positively charged chitosan and negatively charged lipid on the surface of the liposomes [9]. The aim of the present investigation was to develop and characterize DOX-bearing, ligand.

  11. Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer

    Science.gov (United States)

    2015-09-01

    compelling evidence linking obesity to aggressive prostate cancer, but the underlying causes of this relationship are unclear. In this study we used whole...1 AWARD NUMBER: W81XWH-14-1-0250 TITLE: Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer PRINCIPAL INVESTIGATOR: Ericka...TITLE AND SUBTITLE Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-14-1-0250

  12. Marine Biotoxins: Laboratory Culture and Molecular Structure

    Science.gov (United States)

    1991-01-21

    4 (B) 108.3 12.1 6.4 - (L) GT - Cambierdiscus toxicus PL - Prorocentrum lima KB - Kahala Beach L - lethal + - toxic symptoms - 15 - Table IV. DaM for...on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Mice, Lab Animals, Maitotoxin, RA I, BD, Marine Toxin , 076 13 Ciquatoxin...most potent naturally occurring toxins known. Their physiological actions are diverse, as are their molecular structures, not all of which have been

  13. On a Molecular Basis, Investigate Association of Molecular Structure with Bioactive Compounds, Anti-Nutritional Factors and Chemical and Nutrient Profiles of Canola Seeds and Co-Products from Canola Processing: Comparison Crusher Plants within Canada and within China as well as between Canada and China.

    Science.gov (United States)

    Gomaa, Walaa M S; Mosaad, Gamal M; Yu, Peiqiang

    2018-04-21

    The objectives of this study were to: (1) Use molecular spectroscopy as a novel technique to quantify protein molecular structures in relation to its chemical profiles and bioenergy values in oil-seeds and co-products from bio-oil processing. (2) Determine and compare: (a) protein molecular structure using Fourier transform infrared (FT/IR-ATR) molecular spectroscopy technique; (b) bioactive compounds, anti-nutritional factors, and chemical composition; and (c) bioenergy values in oil seeds (canola seeds), co-products (meal or pellets) from bio-oil processing plants in Canada in comparison with China. (3) Determine the relationship between protein molecular structural features and nutrient profiles in oil-seeds and co-products from bio-oil processing. Our results showed the possibility to characterize protein molecular structure using FT/IR molecular spectroscopy. Processing induced changes between oil seeds and co-products were found in the chemical, bioenergy profiles and protein molecular structure. However, no strong correlation was found between the chemical and nutrient profiles of oil seeds (canola seeds) and their protein molecular structure. On the other hand, co-products were strongly correlated with protein molecular structure in the chemical profile and bioenergy values. Generally, comparisons of oil seeds (canola seeds) and co-products (meal or pellets) in Canada, in China, and between Canada and China indicated the presence of variations among different crusher plants and bio-oil processing products.

  14. Structure investigations of electrodeposited nickel

    Energy Technology Data Exchange (ETDEWEB)

    Vertes, A.; Czako-Nagy, I.; Lakatos-Varsani, M. (Eoetvoes Lorand Tudomanyegyetem, Budapest (Hungary). Dept. of Physical Chemistry); Kajcsos, Z. (Hungarian Academy of Sciences, Budapest. Central Research Inst. for Physics); Csordas, L. (Eoetvoes Lorand Tudomanyegyetem, Budapest (Hungary). Dept. of Solid State Physics); Brauer, G. (Zentralinstitut fuer Kernforschung, Rossendorf bei Dresden (German Democratic Republic)); Leidheiser, H. Jr. (Lehigh Univ., Bethlehem, PA (USA). Center for Surface and Coatings Research)

    1982-08-01

    Nickel, electrodeposited under different conditions and yielding different values of stress, was investigated by positron annihilation (lifetime and Doppler-broadening), Moessbauer effect and X-ray diffraction measurements. Two-component positron lifetime spectra were obtained. The first component is thought to result from bulk annihilation and trapping at single trapping centres (TC). Estimations of TC-concentrations are obtained by means of the trapping model. The second one possibly denotes annihilation at voids, the number of which is dependent on the stress in the deposit. Results of Doppler-broadening measurements support this interpretation. The Moessbauer results show differences in the magnetic orientation in the three samples examined.

  15. Propagator theory of atomic and molecular structure

    International Nuclear Information System (INIS)

    Oehrn, Y.

    1976-01-01

    It is not at all obvious which methods of use in quantum chemistry can be characterized as being without wavefunctions. There are, however, a number of methods that purpose to calculate atomic and molecular electronic structure and properties without the explicit use of many-electron wavefunctions. Fully realizing the arbitrariness of any classification of such methods as well as the absence of sharp boundaries between any choice of groups, the author separates the three kinds of approaches: (i) Local Density Energy Functional Methods, (ii) Density Matrix Methods, (iii) Propagator or Green's Function Methods. (Auth.)

  16. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    Science.gov (United States)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  17. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  18. Thermal and molecular investigation of laser tissue welding

    Science.gov (United States)

    Small, Ward, IV

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack on both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of the probability of long-term success. Molecular effects induced in the tissue by laser irradiation were investigated by measuring the concentrations of specific collagen covalent crosslinks and measuring the infrared absorption spectra before and after the laser exposure. This investigation yielded results pertaining to both the methods and mechanisms of laser tissue welding. The combination of two-color infrared thermometry to obtain accurate surface temperatures free from emissivity bias and computer modeling illustrated the importance of including evaporation in the simulations, which effectively serves as an inherent cooling mechanism during laser irradiation. Moreover, the hydration state predicted by the model was useful in assessing the role of electrostatic versus covalent bonding in the fusion. These tools also helped elicit differences between dye- enhanced liquid solders and solid-matrix patches in laser-assisted tissue welding, demonstrating the significance of repeatable energy delivery. Surprisingly, covalent bonds

  19. [Molecular structure and fractal analysis of oligosaccharide].

    Science.gov (United States)

    Liu, Wen-long; Wang, Lu-man; He, Dong-qi; Zhang, Tian-lan; Gou, Bao-di; Li, Qing

    2014-10-18

    To propose a calculation method of oligosaccharides' fractal dimension, and to provide a new approach to studying the drug molecular design and activity. By using the principle of energy optimization and computer simulation technology, the steady structures of oligosaccharides were found, and an effective way of oligosaccharides fractal dimension's calculation was further established by applying the theory of box dimension to the chemical compounds. By using the proposed method, 22 oligosaccharides' fractal dimensions were calculated, with the mean 1.518 8 ± 0.107 2; in addition, the fractal dimensions of the two activity multivalent oligosaccharides which were confirmed by experiments, An-2 and Gu-4, were about 1.478 8 and 1.516 0 respectively, while C-type lectin-like receptor Dectin-1's fractal dimension was about 1.541 2. The experimental and computational results were expected to help to find a class of glycoside drugs whose target receptor was Dectin-1. Fractal dimension, differing from other known macro parameters, is a useful tool to characterize the compound molecules' microscopic structure and function, which may play an important role in the molecular design and biological activity study. In the process of oligosaccharides drug screening, the fractal dimension of receptor and designed oligosaccharides or glycoclusters can be calculated respectively. The oligosaccharides with fractal dimension close to that of target receptor should then take priority compared with others, to get the drug molecules with latent activity.

  20. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M.; Prates, Luciana L.; Yu, Peiqiang

    2017-08-01

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions.

  2. [Molecular genetic investigation of sugar beet (Beta vulgaris L.)].

    Science.gov (United States)

    Butorina, A K; Kornienko, A V

    2011-10-01

    Molecular genetic studies of sugar beet (Beta vulgaris L.) are reviewed as a basis for the development of genomics of this species. The methods used to study structural and functional genomics are considered. The results and their application to increase the efficiency of sugar beet breeding are discussed.

  3. Manipulation of molecular structures with magnetic fields

    NARCIS (Netherlands)

    Boamfa, M.I.

    2003-01-01

    The present thesis deals with the use of magnetic fields as a handle to manipulate matter at a molecular level and as a tool to probe molecular properties or inter molecular interactions. The work consists of in situ optical studies of (polymer) liquid crystals and molecular aggregates in high

  4. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...... anthralin, the description of the vibrational structure of the compound is thus complicated by the circumstance that moment directions for transitions polarized perpendicular to the C2 axis (z) are not uniquely determined by symmetry, but can take any direction in the xy plane. The molecular vibrations...... of DHBP were investigated by IR polarization spectroscopy on samples aligned in stretched polyethylene. The observed Linear Dichroic (LD) absorbance curves, corresponding to absorbance measured with the electric vector of the sample beam parallel (U) and perpendicular (V) to the stretching direction, were...

  5. Molecular motion and structure in plastics

    International Nuclear Information System (INIS)

    Doolan, K.R.; Baxter, M.

    2000-01-01

    Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

  6. Relationship between molecular structure and Raman spectra of quinolines

    Science.gov (United States)

    Frosch, Torsten; Popp, Jürgen

    2009-04-01

    DFT calculations were applied to investigate the relationship between the molecular structure and the Raman spectra of quinolines. A variety of different quinolines with increasing complexity was investigated and an aminoquinoline nucleus was found that describes the Raman spectrum of protonated chloroquine. It was discovered that the biological important, rigid C7-chloro group and C4-side chain of chloroquine significantly disturb certain molecular vibrations. The protonation at the N1 position causes dramatic changes of the Raman bands in the wavenumber region between 1500 cm -1 and 1650 cm -1. These bands are putative marker bands of the aminoquinoline drugs for π-π interactions to the hematin targets in malaria infected cells. The calculation of the normal modes and the illustration of the associated atomic displacements are very valuable for a deeper understanding of the associated bands in the Raman spectra.

  7. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2013-07-10

    Jul 10, 2013 ... Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj. 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009- ...

  8. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  9. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009-2010 and ...

  10. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2010-02-01

    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  11. First principles investigation of the structure of a bacteriochlorophyll crystal

    Energy Technology Data Exchange (ETDEWEB)

    Marchi, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)]|[Centre d`Etudes Saclay, Gif-sur-Yvette (France); Hutter, J.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  12. Normal coordinate analysis, molecular structure, vibrational and electronic spectral investigation of 7-(1,3-dioxolan-2-ylmethyl)-1,3-dimethylpurine-2,6-dione by ab initio HF and DFT method

    Science.gov (United States)

    Prabakaran, A.; Muthu, S.

    2014-01-01

    In the present work, the characterization of 7-(1,3-dioxolan-2-ylmethyl)-1,3-dimethylpurine-2,6-dione (7DDMP26D) molecule was carried out by quantum chemical method and vibrational spectral techniques. The FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra of 7DDMP26D were recorded in solid phase. The UV-Vis absorption spectrum of the 7DDMP26D was recorded in the range of 200-400 nm. The molecular geometry, harmonic vibrational frequencies and bonding features of 7DDMP26D in the ground state have been calculated by HF and DFT methods using 6-31G(d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO). The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by time-depended DFT (TD-DFT) approach. The other molecular properties like electrostatic potential (ESP), Fukui function and thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the calculation results were analyzed to simulate infrared, FT-Raman and UV spectra of the title compound which shows better agreement with observed spectra.

  13. DFT charge transfer of hybrid molecular ferrocene/Si structures

    International Nuclear Information System (INIS)

    Calborean, Adrian; Buimaga-Iarinca, Luiza; Graur, Florin

    2015-01-01

    The electrochemical behavior and electronic properties of redox-active ferrocenes grafted onto semiconductor Si(100) substrate were investigated theoretically by first-principles calculations. Organic molecules were attached via the formation of Si-C covalent bonds through two different linkers: vinyl (direct grafting), and N 3 (CH 2 ) 11 (indirect grafting). Redox energies and the electronic properties relating to different spacers in hybrid ferrocene Fc/Si and ferrocenium Fc + /Si structures were theoretically extracted and compared with experimental cyclic voltametry data. Electronic charge transfers are discussed through the alignment positions of the frontier orbitals of the molecule with respect to the Si substrate gap. Periodic boundary conditions were used to investigate the Si(100) as a slab surface and hybrid Fc/Si structures. The resulting projected density of states (PDOS) were compared with molecular results and discussed in the light of experimental data. (paper)

  14. Investigation of uranium molecular species using laser ablation

    Energy Technology Data Exchange (ETDEWEB)

    Curreli, Davide [Univ. of Illinois, Urbana, IL (United States). Dept. of Nuclear, Plasma, and Radiological Engineering

    2017-07-12

    The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

  15. Adsorption properties of the molecule resveratrol on CNT(8,0-10) nanotube: Geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations

    Science.gov (United States)

    Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Hajikolaee, Fatemeh Haji; Balakhanava, Iryna; Alnajjar, Radwan

    2018-05-01

    In the present work the adsorption properties of the molecule Resveratrol (RSV) (trans-3,5,4‧-Trihydroxystilbene) on CNT(8,0-10) nanotube was investigated by Density Functional Theory (DFT) in the gaseous phase for the first time. The non-bonded interaction effects of compounds RSV and CNT(8,0-10) nanotube on the electronic properties, chemical shift tensors and natural charge were determined and discussed. The electronic spectra of the RSV and the complex CNT(8,0-10)/RSV in the gaseous phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for investigation of the maximum wavelength value of the RSV before and after the non-bonded interaction with the CNT(8,0-10) nanotube and molecular orbitals involved in the formation of absorption spectrum of the complex RSV at maximum wavelength.

  16. Preparation and investigation of optical, structural, and ...

    Indian Academy of Sciences (India)

    331–341. Preparation and investigation of optical, structural, and morphological properties of nanostructured. ZnO:Mn thin films. E AMOUPOUR1,∗. , F E GHODSI2, H ANDARVA2 and. A ABDOLAHZADEH ZIABARI3. 1Department of Electronic Engineering, Roudsar & Amlash Branch,. Islamic Azad University, Roudsar, Iran.

  17. Density functional studies of molecular structures of N-methyl ...

    Indian Academy of Sciences (India)

    Administrator

    studies. Sparse experimental data on the gas-phase geometry of DMF reported in the literature compares well with the DFT results on DMF. DFT emerges as a powerful method to calculate molecular structures. Keywords. Density functional theory; alkyl amides; molecular structure of alkyl amides; transition state search; ...

  18. Similarity Measure for Molecular Structure: A Brief Review

    Science.gov (United States)

    Bero, S. A.; Muda, A. K.; Choo, Y. H.; Muda, N. A.; Pratama, S. F.

    2017-09-01

    Similarity or distance measures have been used widely to calculate the similarity or dissimilarity between two samples of dataset. Cheminformatics is known as the domain that dealing with chemical information and both similarity and distance coefficient have been an important role for matching, searching and classification of chemical information. There are various types of similarity/distance coefficient used in molecular structure similarity searching. Generally, the calculation using similarity/distance coefficient is focusing more on 2-dimensional (2D) rather than 3-dimensional (3D) structure. In this paper, the popular similarity/distance coefficients for molecular structure will be reviewed together with the review on 3D molecular structure.

  19. Applications of the Cambridge Structural Database to molecular inorganic chemistry.

    Science.gov (United States)

    Orpen, A Guy

    2002-06-01

    Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

  20. Polymorphism and disorder in caffeine: Dielectric investigation of molecular mobilities

    Science.gov (United States)

    Descamps, M.; Decroix, A. A.

    2014-12-01

    Using dielectric relaxation data we have characterized the molecular mobilities of caffeine both in phase I (stable and metastable) and in phase II. In phase I effects of sublimation and phase transformation kinetics were carefully considered. In plane rotational motions were followed on a wide temperature range. A noticeable antiferroelectric short range order developing at the approach of the glass-like transition is characterized. Condition for occurrence of a critical-like behaviour is discussed. At high temperature the emergence of an additional ultra slow relaxation process is highlighted. Possible molecular mechanisms are proposed for both processes. In phase II the existence of a less intense relaxation process is confirmed. Close similarity with the main process developing in phase I hints at a common origin of the dipolar motions. Careful consideration of recent structure determinations leads to suggest that this process is associated to similar molecular in plane rotations but developing at the surface of crystalline samples. Lower cooperativity at the surface is reflected in the smaller activation entropy of the relaxation.

  1. Theoretical study of electron transport throughout some molecular structures

    Science.gov (United States)

    Abbas, Mohammed A. A.; Hanoon, Falah H.; Al-Badry, Lafy F.

    2017-11-01

    The present work is a theoretical study of the electronic properties of some molecular structures. The system that takes into account in the study is left lead-donor-molecule-acceptor-right lead. The molecule, such as (phenyl, biphenyl, triphenyl, naphthalene, anthracene, and phenanthrene), is threaded by magnetic flux. This work contains two parts. First is computing density of states of the molecular structures as a closed system by density functional theory (DFT). Second is calculating the transmission probability and electric current of such molecular structures as an open system by steady-state theoretical model. Furthermore, the most important effects, taking into consideration are quantum interference, magnetic flux, and interface structure. Our results show that the connection of the molecule to the two leads, the number of rings, the magnetic flux, and the geometrical structure of the molecule play an important role in determining the energy gap of molecular structures.

  2. Experimental investigations of the nuclear structure

    International Nuclear Information System (INIS)

    Gromov, K.Ya.

    1989-01-01

    The problem of experimental investigation into atomic nucleus structure is discussed. Examples of studying the properties of low-lying nucleus states using cyclotron-type accelerators for their production are presented. The consideration is conducted on the base of the Idisol experimental complex created at the Finland. Results of measuring masses of neutron-redundant rubidium nuclei are presented. Schemes of 160 Er and 108 In decay are presented. 12 refs.; 6 figs

  3. Lewis Structures Are Models for Predicting Molecular Structure, Not Electronic Structure

    Science.gov (United States)

    Purser, Gordon H.

    1999-07-01

    This article argues against a close relationship between Lewis dot structures and electron structure obtained from quantum mechanical calculations. Lewis structures are a powerful tool for structure prediction, though they are classical models of bonding and do not predict electronic structure. The "best" Lewis structures are those that, when combined with the VSEPR model, allow the accurate prediction of molecular properties, such as polarity, bond length, bond angle, and bond strength. These structures are achieved by minimizing formal charges within the molecule, even if it requires an expanded octet on atoms beyond the second period. Lewis structures that show an expanded octet do not imply full d-orbital involvement in the bonding. They suggest that the presence of low-lying d-orbitals is important in producing observed molecular structures. Based on this work, the presence of electron density, not a large separation in charge, is responsible for the short bond lengths and large angles in species containing nonmetal atoms from beyond the second period. This result contradicts results obtained from natural population analysis, a method that attempts to derive Lewis structures from molecular orbital calculations.

  4. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    OpenAIRE

    Kyoichi Tezuka; Tatsuhiko Taguchi; Saman Alavi; Amadeu K. Sum; Ryo Ohmura

    2012-01-01

    This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...

  5. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  6. Modified structure of graphene oxide by investigation of structure ...

    Indian Academy of Sciences (India)

    erated in some regions due to hydrogen bonding between functional groups. Trapped water molecules were shown between the GO sheets which strongly affected the distribution of OFGs and their aggregation by hydrogen bonding. Keywords. Graphene oxide; oxygen functional groups; structure investigation; modified ...

  7. Metagenomic Investigation of the Microbial Community Structure and Diversity for Sentinel Coral Reefs and Urbanized Coastal Waters in Southeast Florida, and Molecular Microbial Source Tracking to Characterize Potential LBSP Microbial Contaminant Influences

    Science.gov (United States)

    Sinigalliano, C. D.

    2016-02-01

    Coral reefs and recreational beaches provide critical ecosystem services. However, coastal waters of the Southeast Florida region receive anthropogenic discharges from highly urbanized watersheds via runoff, canals, coastal inlets, and treated wastewater outfalls. There is concern regarding the biological contaminants that enter the coastal zone from land-based sources, especially for viable pathogens and genetic elements that could confer virulence or resistance. Targeted molecular microbial source tracking (MST) by quantitative PCR allows the measurement of specific microbial contaminants such as host-specific fecal indicators. These fecal source markers can help track specific fecal contamination of public health concern in the coastal zone and may also help track exposure of coral reefs to such contamination. A range of pathogens associated with sewage/septic contamination have shown detrimental impact to coral communities, including changes to the biodiversity of coral microbiomes. High-throughput Next-Generation-Sequencing (NGS) and community genomic analysis can provide a comprehensive, culture-independent approach to investigate microbial community diversity in complex environmental samples. The combination of host-specific microbial source tracking by qPCR and metagenomic NGS can provide substantial enhancement to traditional methods of water quality assessment to better protect both environmental biodiversity and human health. Reported here is a multifaceted water quality assessment study of three coastal inlets, two treated wastewater outfalls, and four sentinel coral reef communities in the Southeast Florida coastal zone offshore of Miami-Dade and Broward Counties. This study utilized a combination of bi-monthly sampling for nutrients, fecal indicator bacteria, and human-source molecular source tracking to measure specific contaminants of ecosystem and public health concern. In addition, 16S metagenomic analysis using Illumina Next-Generation Sequencing

  8. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion

  9. Molecular structure of the lecithin ripple phase

    NARCIS (Netherlands)

    de Vries, AH; Yefimov, S; Mark, AE; Marrink, SJ

    2005-01-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in

  10. Molecular investigations of β-thalassemic children in Erbil governorate

    Science.gov (United States)

    Hasan, Ahmad N.; Al-Attar, Mustafa S.

    2017-09-01

    The present work studies the molecular investigation of 40 thalassemic carriers using polymerase chain reaction. Forty thalassemic carriers who were registered and treated at Erbil thalassemic center and twenty apparently healthy children have been included in the present study. Ages of both groups ranged between 1-18 years. Four primers used to detect four different beta thalassemia mutations they were codon 8/9, codon 8, codon 41/42 and IVS-1-5. The two most common mutations detected among thalassemia group were Cd8/9 with 8 cases (20%) and Cd-8 with 6 cases (15%) followed by codon 41/42 with 4 cases (10%) which investigated and detected for the first time in Erbil governorate through the present study and finally IVS-1-5 with 3 cases (7.5%), while no any cases detected among control group.

  11. Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K [Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084 (China); Hajgato, B; Morini, F; Deleuze, M S [Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek (Belgium)], E-mail: ningcg@tsinghua.edu.cn, E-mail: djk-dmp@tsinghua.edu.cn, E-mail: michael.deleuze@uhasselt.be

    2008-09-14

    The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase.

  12. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bianchi, L.

    2000-05-01

    distribution functions, showing that the agreement at the rdf level does not provide a critical evaluation of appropriateness of a chosen potential model to reproduce the observed liquid structure. Both the simulations reproduce equally well the X-X partial comprising of six correlations. The ability of the 3-site model simulations to satisfactorily reproduce this function dominated by contributions from the methyl group, demonstrates that the methyl group does not participate in any bonding in the liquid. However, the main peaks of the simulated Ho-Ho pdf are found to be slightly higher and shifted to larger distances as compared to the ND results. A comparison of the simulated and ND X-Ho inter-molecular functions dominated by H-Ho correlations shows that although the 3-site model reproduces at least qualitatively the experimental features, the six-site model fails badly. The structure of liquid benzene at 298 K is investigated by performing molecular dynamics (MD) simulations in NVE ensemble using three different force field models differing both in their functional form and in the way they were devised. Surprisingly however, they lead to similar results for the pdfs. The structural results from MD simulations are compared with the neutron diffraction (ND) results where the newly C-C, C-H and H-H inter-molecular pdfs are obtained in this study by the H/D substitution on hydrogen atoms of benzene. A good agreement is found between the simulated and experimental total inter-molecular rdfs for C 6 D 6 and C 6 (H/D) 6 experimental, but not for C 6 H 6 . Most of the structural properties of benzene discussed in the past have been based on the models, which showed a reasonable agreement between the simulated and neutron inter-molecular rdf or X-ray C-C pdf The C-C pdf extracted from the present ND studies however differs from the one obtained earlier from the X-ray measurements. Apart from that, the simulated C-C pdf reproduces the corresponding ND function better than that

  13. Structure of bright-rimmed molecular clouds

    International Nuclear Information System (INIS)

    Wootten, A.; Sargent, A.; Knapp, G.; Huggins, P.J.

    1983-01-01

    Five bright-rimmed molecular clouds, NGC 1977, IC 1396, IC 1848 A, B35, and NGC 7822, have been mapped with 30'' resolution in the J = 2--1 lines of 12 co. For the first three, 13 CO maps have also been made. The spatial distributions of temperature, density, and molecular abundance in these clouds have been determined, particularly in the vicinity of the rims. In general, the gas densities increase close to the rims, but temperature enhancements occur over comparatively extended regions. Near the rims the gas kinematics is varied: velocity gradients are observed in several regions, and in IC 1396 line broadening is distinguishable. A detailed study of the excitation of 13 CO demonstrates that near the well-resolved rim in NGC 1977 where C I and carbon recombination lines have been observed, there is a definite decline in the CO abundance. These molecular clouds span a variety of stages of star formation, but in none does the interaction with the adjacent H II region appear to have substantially affected the course of the star-forming history of the cloud

  14. Imaging molecular structure and dynamics using laser driven recollisions

    International Nuclear Information System (INIS)

    Marangos, J.P.; Baker, S.; Torres, R.; Kajumba, N.; Haworth, C.; Robinson, J.; Tisch, J.W.G.; Lein, M.; Chirila, C.; Vozzi, C.

    2006-01-01

    Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO 2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17 tt h - 27 th ) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low I p an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the

  15. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  16. Thermal and molecular investigation of laser tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  17. Molecular Investigation of Pediatric Portuguese Patients with Sensorineural Hearing Loss

    Directory of Open Access Journals (Sweden)

    Célia Nogueira

    2011-01-01

    Full Text Available The understanding of the molecular genetics in sensorineural hearing loss (SNHL has advanced rapidly during the last decade, but the molecular etiology of hearing impairment in the Portuguese population has not been investigated thoroughly. To provide appropriate genetic testing and counseling to families, we analyzed the whole mitochondrial genome in 95 unrelated children with SNHL (53 nonsyndromic and 42 syndromic and searched for variations in two frequent genes, GJB2 and GJB6, in the non-syndromic patients. Mutations in mtDNA were detected in 4.2% of the cases, including a hitherto undescribed change in the mtDNA-tRNATrp gene (namely, m.5558A>G. We also identified mono- or biallelic GJB2 mutations in 20 of 53 non-syndromic cases and also detected two novel mutations (p.P70R and p.R127QfsX84. Our data further reinforce the notion that genetic heterogeneity is paramount in children with SNHL.

  18. Hybrid structures for molecular level sensing

    Science.gov (United States)

    Lemieux, Melburne Charles

    With substantial molecular mobility and segment dynamics relative to metals and ceramics, all polymeric materials, to some extent, are stimuli-responsive by exhibiting pronounced chemical and physical changes in the backbone, side chains, segments, or end groups induced by changes in the local environment. Thus, the push to incorporate polymeric materials as sensing/responsive nanoscale layers into next-generation miniaturized sensor applications is a natural progression. The significance and impact of this research is wide-ranging because it offers design considerations and presents results in perhaps two of the most critical broad areas of nanotechnology: ultrathin multifunctional polymer coatings and miniaturized sensors. In this work, direct evidence is given showing that polymer coatings comprised of deliberately selected molecular segments with very different chemistry can have switchable properties, and that the surface composition can be precisely controlled, and thus properties can be tuned: all in films on the order of 20 nm and less. Furthermore, active sensing layers in the form of plasma-polymerized polymers are successfully incorporated into actual silicon based microsensors resulting in a novel hybrid organic/inorganic materials platform for microfabricated MEMS sensors with record performance far beyond contemporary sensors in terms of detection sensitivity to various environments. The results produced in this research show thermal sensors with more than two orders of magnitude better sensitivity than what is attainable currently. In addition, a humidity response on the order of parts per trillion, which is four orders of magnitude more sensitive than current designs is achieved. Molecular interactions and forces for organic molecules are characterized at the picoscale to optimize polymeric nanoscale layer design that in turn optimize and lead to microscale hybrid sensors with unprecedented sensitivities.

  19. Investigation of multilayer painting by means of molecular spectroscopy

    Directory of Open Access Journals (Sweden)

    Kadikova I.F.

    2017-01-01

    Full Text Available The study of paintings’ layer structure under microscope was implemented in the early XX century; since that time method of cross-section preparation as well as composition of embedded materials changed and capabilities of optical microscopy broadened. Nevertheless, until recently cross-sections were prepared only for analysis of paintings’ layer-specific structure, morphological and technological features, tracks of restoration treatments. Examination of chemical composition required additional sampling as well as division of these samples layer by layer in order to determine pigments and binding media; these procedures didn’t always lead to proper results. Micro-Raman and micro-FTIR spectroscopy allow carrying out investigation of painting cross-sections without any additional preliminary sampling; this is shown on example of investigation of a number of paintings.

  20. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan

    2012-01-01

    Roč. 19, č. 2 (2012), s. 86-87 ISSN 1211-5894. [Struktura 2012. Kolokvium Krystalografické společnosti. 11.06.2012-14.06.2012, Klatovy] R&D Projects: GA ČR GA310/09/1407 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : structure databases * structure-function relations * organic and inorganic materials Subject RIV: EE - Microbiology, Virology

  1. Investigation of Changes in the Microscopic Structure of Anionic Poly(N-isopropylacrylamide-co-Acrylic acid) Microgels in the Presence of Cationic Organic Dyes toward Precisely Controlled Uptake/Release of Low-Molecular-Weight Chemical Compound.

    Science.gov (United States)

    Kureha, Takuma; Shibamoto, Takahisa; Matsui, Shusuke; Sato, Takaaki; Suzuki, Daisuke

    2016-05-10

    Changes in a microscopic structure of an anionic poly(N-isopropylacrylamide-co-acrylic acid) microgel were investigated using small- and wide-angle X-ray scattering (SWAXS). The scattering profiles of the microgels were analyzed in a wide scattering vector (q) range of 0.07 ≤ q/nm(-1) ≤ 20. In particular, the microscopic structure of the microgel in the presence of a cationic dye rhodamine 6G (R6G) was characterized in terms of its correlation length (ξ), which represents the length scale of the spatial correlation of the network density fluctuations, and characteristic distance (d*), which originated from the local packing of isopropyl groups of two neighboring chains. In the presence of cationic R6G, ξ exhibited a divergent-like behavior, which was not seen in the absence of R6G, and d* was decreased with decreasing the volume of the microgel upon increasing temperature. At the same time, the amount of R6G adsorbed per unit mass of the microgel increased upon heating. These results suggested that a coil-to-globule transition of the poly(N-isopropylacrylamide) chains in the present anionic microgel occurred because of efficiently screened, thus, short ranged electrostatic repulsion between the charged groups, and hydrophobic interaction between the isopropyl groups in the presence of cationic R6G. The combination of hydrophobic and electrostatic interaction between the cationic dye and the microgel affected the separation and volume transition behavior of the microgel.

  2. Characterising the Structure of Molecular Clouds

    Science.gov (United States)

    Wong, Graeme Francis

    The Interstellar Medium contains the building blocks of matter in our Galaxy and plays a vital role in the evolution of low mass star formation. The poorly studied molecular clouds of Lupus and Chamaeleon contain ongoing low mass star formation, and are in close proximity to our Solar System. While on the other hand the Carina molecular cloud, poorly observed in radio wavelength, is an active region of star formation and host some of the brightest stars known within our Galaxy. Using tracers like carbon monoxide, atomic neutral carbon, and ammonia, we are able to measure the temperature and density of the gas cloud. This information allows us to understand the initial conditions of the formation of low mass stars. Observations conducted with the 22-m Mopra radio telescope (located at the edge of the Warrumbungle Mountains near Coonabarabran), in the Carbon monoxide (CO) isotopologues 12 CO, 13 CO, C17O, and C18O (1-0) transitions, have mapped the Chamaeleon II cloud, an intermediate mass cloud within the Chamaeleon. Through the sub-arcminute maps, comparisons have been made to previous low resolution (2.5') maps which have been to resolve some of the dense clumps previously identified. Optical depth, column density, and excitation temperature derived from the CO maps, are consistent with previous results. A detailed comparison between identified C18O clumps have shown the different conditions occurring within the clumps, some of which contain or are located near a population of young stellar objects. The Northern region of the Carina Nebular Complex, was observed with NANTEN2, a 4-m radio telescope (located in the Chilean Atacama desert), in the 12CO (4-3) and [C I] 3P1-3P0 emission lines. Previous observations towards this region has either been at poor resolution or had limited coverage. The presented observations, strike a balance between the two; observing in sub-arcmin resolution (0.6') and with an area of 0.9° X 0.5° mapped. Excitation temperature of the 12

  3. Investigating Student Understanding of the Universe: Structure

    Science.gov (United States)

    Hayes, Virginia; Coble, K.; Nickerson, M.; Cochran, G.; Camarillo, C. T.; Bailey, J. M.; McLin, K. M.; Cominsky, L. R.

    2011-05-01

    Chicago State University (CSU) offers an introductory astronomy course that services students from a variety of majors including pre-service teachers. At CSU, we have been investigating methods and tools that will improve student conceptual understanding in astronomy for this diverse group of students. We have analyzed pre-course surveys, pre-course essays, exams, and interviews in an effort to better understand the ideas and difficulties in understanding that students have in regards to the structure of the universe. Analysis of written essays has revealed that our students do have some knowledge of the objects in the universe, but interviews inform us that their understanding of the structure of the universe is superficial. This project is a part of a larger study; also see our posters on student ideas about dark matter, the age and expansion of the universe, and perceptions of astronomical sizes and distances. This work was supported by NASA ROSES E/PO Grant #NNXlOAC89G, as well as by the Illinois Space Grant Consortium and National Science Foundation CCLI Grant #0632563 at Chicago State University and the Fermi E/PO program at Sonoma State University.

  4. Structural studies on Mycobacterium tuberculosis RecA: Molecular ...

    Indian Academy of Sciences (India)

    Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP ...

  5. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  6. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  7. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  8. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  9. Structures of Life: The Role of Molecular Structures in Scientists' Work

    NARCIS (Netherlands)

    Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J

    2008-01-01

    The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

  10. Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

    Science.gov (United States)

    Monk, Joshua D.; Lawson, John W.

    2016-01-01

    Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

  11. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  12. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  13. Building Investigation: Material or Structural Performance

    Directory of Open Access Journals (Sweden)

    Yusof M.Z.

    2014-03-01

    Full Text Available Structures such as roof trusses will not suddenly collapse without ample warning such as significant deflection, tilting etc. if the designer manages to avoid the cause of structural failure at the material level and the structural level. This paper outlines some principles and procedures of PDCA circle and QC tools which can show some clues of structural problems in terms of material or structural performance

  14. Electronic and molecular structure of carbon grains

    Science.gov (United States)

    Almloef, Jan; Luethi, Hans-Peter

    1990-01-01

    Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

  15. Molecular structure-adsorption study on current textile dyes.

    Science.gov (United States)

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  16. The statistics of molecular motor trajectories on different two-dimensional structures

    Science.gov (United States)

    Tabei, S. M. Ali; Jahanmiri-Nezhad, Faezeh; Martin, Michael; Lastine, Colten

    Molecular motors move on a complex cytoskeleton network to transport material within the cell. In this talk, we investigate different scenarios of transport on two-dimensional network structures. We will study different statistical properties of an ensemble of simulated trajectories such as the frequency of directional changes and diffusion statistics. We will investigate how these statistical measures depend on the geometrical properties of the underlying structure.

  17. Molecular Dynamics Investigation of Efficient SO2 Absorption by ...

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    TMG][L]) that absorbs an equimolar amount of SO2 through chemisorption.12 Subsequently, a sig- ...... Visual molecular dynamics J. Mol. Graphics 14 33. 83. Fiorin G, Klein M L and Hénin J 2013 Using collective variables to drive molecular ...

  18. MOSBY: a molecular structure viewer program with portability and extensibility.

    Science.gov (United States)

    Ueno, Yutaka; Asai, Kiyoshi

    2002-03-01

    A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.

  19. Preparation and investigation of optical, structural, and ...

    Indian Academy of Sciences (India)

    determined using point-wise unconstrained minimization approach (PUMA) and fitting the data to the Cauchy formula for thin films [25]. Infrared spectrum of the samples was measured by using Fourier transform infrared (FTIR) spectrophotometer (Bruker model. Vertex 70) for identifying the molecular composition.

  20. Molecular structures guide the engineering of chromatin.

    Science.gov (United States)

    Tekel, Stefan J; Haynes, Karmella A

    2017-07-27

    Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Structural and molecular hair abnormalities in trichothiodystrophy.

    Science.gov (United States)

    Liang, Christine; Morris, Andrea; Schlücker, Sebastian; Imoto, Kyoko; Price, Vera H; Menefee, Emory; Wincovitch, Stephen M; Levin, Ira W; Tamura, Deborah; Strehle, Katrin R; Kraemer, Kenneth H; DiGiovanna, John J

    2006-10-01

    We examined hair from 15 patients with trichothiodystrophy (TTD), a rare inherited disorder with brittle, cystine-deficient hair. They had a wide variety of phenotypes, from brittle hair only to severe intellectual impairment and developmental delay. Polarizing light microscopic examination showed alternating light and dark (tiger tail) bands under polarizing microscopy. Confocal microscopy captured structural features of breaks in intact TTD hairs. The autofluorescent appearance was regular and smooth in normal donors and markedly irregular in sections of TTD hairs possibly reflecting abnormalities in melanin distribution. Scanning electron microscopy revealed numerous surface irregularities. All TTD hair samples had reduced sulfur content. We observed an inverse correlation (R(val)=0.9) between sulfur content and percent of hairs with shaft abnormalities (trichoschisis, trichorrhexis nodosa, or ribbon/twist). There was no association between clinical disease severity and percent of abnormal hairs. Raman spectra of hairs from TTD patients and normal donors revealed a larger contribution of energetically less favored disulfide conformers in TTD hairs. Our data indicate that the brittleness of the TTD hair is dependent upon abnormalities at several levels of organization. These changes make TTD hairs excessively prone to breakage and weathering.

  2. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  3. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    Directory of Open Access Journals (Sweden)

    Mohyeldin Ragab

    2015-01-01

    Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.

  4. Electronic structure of molecular Rydberg states of some small molecules and molecular ion

    International Nuclear Information System (INIS)

    Sun Biao; Li Jiaming

    1993-01-01

    Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

  5. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp......We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  6. Molecular structure and exciton dynamics in organic conjugated polymers

    Science.gov (United States)

    Thomas, Alan K.

    Intermolecular electronic interactions, dipole coupling and orbital overlap, caused by pi-pi stacking in organic conjugated polymers lead to unique structures and properties that can be harnessed for optoelectronic applications. These interactions define structure-function relationships in amorphous and aggregated forms of polymers in the solid state and determine their efficiencies and functionality in electronic devices, from transistors to solar cells. Organic polymer electronic device performance depends critically upon electronic coupling between monomer units -mediated by conformation and packing characteristics - that dictates electronic properties like conductivity and capacitance as well as electronic processes, such as charge carrier generation and transport. This dissertation demonstrates how electronic processes in conjugated polymers are mediated by subtle inter- and intra-chain electronic interactions imparted by the conformational degrees of freedom within their solid state structure and how this effects device performance. To initiate this investigation into structure-function relationships, an examination of nanoparticles representing two limiting aggregation states of the conjugated polymer poly(3-hexylthiophene) (P3HT) was conducted. These aggregates are defined by their predominate form of electronic coupling, inter- or intrachain, called H- and J-aggregates respectively. H- or J-aggregates of P3HT were embedded in an insulating matrix and time-resolved fluorescence intensity modulation spectroscopy was utilized to uncover the existence of efficient singlet-triplet quenching in J aggregates not present in H-aggregates. These studies were extended by examining P3HT H-and J-aggregates under applied electric fields in capacitor type devices using multiple time-resolved and steady-state spectroscopic techniques. These experiments reveal electronic couplings in J aggregates that shift excited state population towards a majority composed of long lived

  7. Molecular epidemiological investigations of plague in Eastern Province of Zambia.

    Science.gov (United States)

    Nyirenda, Stanley S; Hang Ombe, Bernard M; Simulundu, Edgar; Mulenga, Evans; Moonga, Ladslav; Machang U, Robert S; Misinzo, Gerald; Kilonzo, Bukheti S

    2018-01-04

    Plague is a flea-borne zoonotic and invasive disease caused by a gram negative coccobacillus bacterium called Yersinia pestis. Plague has caused three devastating pandemics globally namely: the Justinian, Black Death and Oriental plague. The disease in the Eastern Province of Zambia has been reported in Nyimba and Sinda Districts in the past 15 years. The aim of this study was to investigate the molecular epidemiology of plague in the two affected districts. Polymerase Chain Reaction (PCR), targeting Plasminogen activator gene (pla gene) of Y. pestis, was performed on suspected human bubo aspirates (n = 7), rodents (n = 216), shrews (n = 27) and fleas (n = 1494). Of these, one positive sample from each source or host was subjected to sequencing followed by phylogenetic analysis. The plasminogen activator gene (pla gene) of Y. pestis was detected in 42.8% bubo aspirates, 6.9% rodents, 3.7% shrew and 0.8% fleas. The fleas were from pigs (n = 4), goats (n = 5) and rodents (n = 3). The sequencing and phylogenetic analysis suggested that the pla gene of Y. pestis in Nyimba and Sinda was similar and the isolates demonstrated a high degree of evolutionary relationship with Antiqua strains from the Republic of Congo and Kenya. It can be concluded that pla gene of Y. pestis was present in various hosts in the two districts and the strains circulating in each district were similar and resembles those in the Republic of Congo and Kenya.

  8. Molecular structure of dextran sulphate sodium in aqueous environment

    Science.gov (United States)

    Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

    2018-03-01

    Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

  9. Nanohashtag structures based on carbon nanotubes and molecular linkers

    Science.gov (United States)

    Frye, Connor W.; Rybolt, Thomas R.

    2018-03-01

    Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

  10. Mechanical and Structural Investigation of Porous Bulk Metallic Glasses

    Directory of Open Access Journals (Sweden)

    Baran Sarac

    2015-06-01

    Full Text Available The intrinsic properties of advanced alloy systems can be altered by changing their microstructural features. Here, we present a highly efficient method to produce and characterize structures with systematically-designed pores embedded inside. The fabrication stage involves a combination of photolithography and deep reactive ion etching of a Si template replicated using the concept of thermoplastic forming. Pt- and Zr-based bulk metallic glasses (BMGs were evaluated through uniaxial tensile test, followed by scanning electron microscope (SEM fractographic and shear band analysis. Compositional investigation of the fracture surface performed via energy dispersive X-ray spectroscopy (EDX, as well as Auger spectroscopy (AES shows a moderate amount of interdiffusion (5 at.% maximum of the constituent elements between the deformed and undeformed regions. Furthermore, length-scale effects on the mechanical behavior of porous BMGs were explored through molecular dynamics (MD simulations, where shear band formation is observed for a material width of 18 nm.

  11. Structural investigation of a new antimicrobial thiazolidine compound

    Energy Technology Data Exchange (ETDEWEB)

    Cozar, I. B.; Pîrnău, A. [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath Street, RO-400293 Cluj-Napoca (Romania); Vedeanu, N.; Nastasă, C. [Iuliu Hatieganu University of Medicine and Pharmacy, Faculty of Pharmacy, RO-400023 Cluj-Napoca (Romania)

    2013-11-13

    Thiazoles and their derivatives have attracted the interest over the last decades because of their varied biological activities: antibacterial, antiviral, antifungal, inflammation or in the treatment of allergies. A new synthesized compound 3-[2-(4-Methyl-2-phenyl-thiazol-5-yl)-2-oxo-ethyl]-thazolidine-2,4-dione was investigated by FT-IR, FT-Raman, {sup 1}H, {sup 13}C NMR spectroscopies and also by DFT calculations at B3LYP/6-31G(d) level of theory. The very good correlation found between the experimental and theoretical data shows that the optimized molecular structure is very close to reality. Also the NMR spectra show a monomeric behaviour of this compound in solutions.

  12. Theoretical investigation on structural evolution, energetic stability ...

    Indian Academy of Sciences (India)

    Abstract. We systematically studied the geometrical structures, relative stabilities, electronic properties and chemical hardness of AunCd (n=1–12) clusters based on the framework of the density functional theory using relativistic all-electron methods. Low-lying energy structures include two-dimensional and three- ...

  13. Investigation of the relationship between structural empowerment ...

    African Journals Online (AJOL)

    satisfaction, and organizational commitment. These re- sults strengthen those of previous studies reporting work place structures/processes/contributions leading to su- perior care environments12. Modifying the work place structure and improving nurs- es access to opportunities (organizational support, in- formation and ...

  14. Relation between molecular electronic structure and nuclear spin-induced circular dichroism

    DEFF Research Database (Denmark)

    Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

    2017-01-01

    with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state......The recently theoretically described nuclear spin-induced circular dichroism (NSCD) is a promising method for the optical detection of nuclear magnetization. NSCD involves both optical excitations of the molecule and hyperfine interactions and, thus, it offers a means to realize a spectroscopy...... with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...

  15. Fluid structure and molecular interaction of acetophenone derivatives

    Indian Academy of Sciences (India)

    pp. 1129-1137. Fluid structure and molecular interaction of acetophenone derivatives. K K GUPTA and P J sINGH. Department of Physics, Government MSJ (PG) College, Bharatpur 321 001, India. E-mail: kkguptakkg@indiatimes.com. MS received 4 June 2003; revised 2 January 2004; accepted 2 January 2004. Abstract.

  16. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    Molecular cloning, sequence analysis and structure prediction of the related to b 0,+ amino acid transporter (rBAT) in Cyprinus carpio L. ... The amplified product was 2370 bp, including a 42 bp 5'-untranslated region, a 288 bp 3'-untranslated region, and a 2040 bp open reading frame (ORF), which encoded 679 amino acids ...

  17. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    neutron diffraction data [12]. 3. Method of analysis. 3.1 General background. In the following paragraph we present the extraction of total neutron molecular structure .... carbon and oxygen contributions and important information about the hydrogen positions ... the hydroxyl group OD1 is at a staggered position, as expected.

  18. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.

    1977-12-01

    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  19. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Administrator

    4,5 proposed a density matrix divide-and-conquer (DC) method for electronic structure calculation of large molecules. The method is based on partitioning the density matrix and is applicable to both HF and DFT level of theories. Subsequently, Gadre et al. 6 formulated the. Molecular Tailoring Approach (MTA) for evaluating.

  20. Learning Molecular Structures in a Tangible Augmented Reality Environment

    Science.gov (United States)

    Asai, Kikuo; Takase, Norio

    2011-01-01

    This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

  1. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  2. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its molecular conformation is presented. 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky and an improved method of data analysis is given. The intermolecular structural ...

  3. Density functional studies of molecular structures of N-methyl ...

    Indian Academy of Sciences (India)

    Density functional theory was applied to the calculation of molecular structures of N-methyl formamide (NMF), N,N-dimethyl formamide (DMF), and N,Ndimethyl acetamide (DMA). DFT calculations on NMF, DMF, and DMA were performed using a combination of the local functional of Vosko, Wilk, and Nusair (VWN) with the ...

  4. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

  5. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  6. Exploring antioxidant reactivity and molecular structure of phenols ...

    Indian Academy of Sciences (India)

    MERCEDES BECERRA-HERRERA

    2017-07-11

    Jul 11, 2017 ... Abstract. Phenolic compounds can be considered as the most important bioactive compounds in Mediterranean diet. However, many of the complex connections between phenols antioxidant reactivity and their molecular structure remain unsolved. To shine light on these issues, the antioxidant reactivity of ...

  7. Exploring antioxidant reactivity and molecular structure of phenols ...

    Indian Academy of Sciences (India)

    Phenolic compounds can be considered as themost important bioactive compounds in Mediterranean diet. However, many of the complex connections between phenols antioxidant reactivity and their molecular structure remain unsolved. To shine light on these issues, the antioxidant reactivity of 15 relevant phenolic ...

  8. Cambridge Structural Database as a tool for studies of general structural features of organic molecular crystals

    International Nuclear Information System (INIS)

    Kuleshova, Lyudmila N; Antipin, Mikhail Yu

    1999-01-01

    The review surveys and generalises data on the use of the Cambridge Structural Database (CSD) for studying and revealing general structural features of organic molecular crystals. It is demonstrated that software and facilities of the CSD allow one to test the applicability of a number of known concepts of organic crystal chemistry (the principle of close packing, the frequency of occurrence of space groups, the preferred formation of centrosymmetrical molecular crystals, etc.) on the basis of abundant statistical data. Examples of the use of the Cambridge Structural Database in engineering of molecular crystals and in the systematic search for compounds with specified properties are given. The bibliography includes 122 references.

  9. The interaction between 4-aminoantipyrine and bovine serum albumin: Multiple spectroscopic and molecular docking investigations

    International Nuclear Information System (INIS)

    Teng Yue; Liu Rutao; Li Chao; Xia Qing; Zhang Pengjun

    2011-01-01

    4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.

  10. Investigation of molecular size of transcription factor TFIIE in solution.

    Science.gov (United States)

    Itoh, Yoshiyuki; Unzai, Satoru; Sato, Mamoru; Nagadoi, Aritaka; Okuda, Masahiko; Nishimura, Yoshifumi; Akashi, Satoko

    2005-11-15

    Human general transcription factor IIE (TFIIE), a component of a transcription preinitiation complex associated with RNA polymerase II, was characterized by size-exclusion chromatography, mass spectrometry, analytical ultracentrifugation, and small-angle X-ray scattering (SAXS). Recombinant human TFIIE was purified to homogeneity and shown to contain equimolar amounts of TFIIEalpha (50 kDa) and TFIIEbeta (35 kDa) by SDS-PAGE. In the analysis of size-exclusion chromatography of the purified sample, as already reported, TFIIE was shown to be a 170-kDa alpha(2)beta(2) heterotetramer. However, by using electrospray ionization mass spectrometry the purified sample gave the molecular mass of 84,152 +/- 5, indicating that TFIIE is an alphabeta heterodimer but not a heterotetramer. Analytical ultracentrifugation experiment of TFIIE provided that only a single component with the molecular mass of ca. 80,000 existed in solution, also suggesting an alphabeta heterodimer. In addition, its extraordinarily rod-like molecular shape was confirmed by SAXS. It is likely that the rod-like molecular shape of TFIIE has misled larger molecular size in size-exclusion chromatography, which was calibrated by globular proteins. It is demonstrated that TFIIE exists as a heterodimer under our present conditions in solution, although two molecules of heterodimer might be required for the formation of the preinitiation complex with RNA polymerase II for starting the transcription process. (c) 2005 Wiley-Liss, Inc.

  11. Inverse Finite Method Investigation for Adaptive Structures

    Data.gov (United States)

    National Aeronautics and Space Administration — This research project is evaluating an innovative technique that uses fiber optic strain sensors to measure structural deformations and full field strains. An...

  12. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    DEFF Research Database (Denmark)

    Celebioglu, Hilal Yilmaz

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers...... submaxillary mucin (BSM), a major salivary protein, were studied using high and low field Nuclear Magnetic Resonance (NMR), Dynamic Light Scattering (DLS), and Circular Dichroism (CD) spectroscopy. The zeta potentials of the proteins were also measured to provide information on the role of electrostatic forces...

  13. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  14. Investigations of the Structure of Titanate Nanoscrolls

    International Nuclear Information System (INIS)

    Sheppard, D.A.; Buckley, C.E.

    2005-01-01

    Full text: Nanosized materials have attracted much research lately due to their unique properties and their potential application in nanoelectronic and optoelectronic devices. Nanostructured materials have also sparked interest as possible hydrogen storage candidates. Research at Curtin University has shown titanate nanoscrolls to absorb modest amounts of hydrogen at low temperatures. Whether or not this capacity can be improved will be dependent on a thorough understanding of the structure and the way it interacts with hydrogen. Titanate nanoscrolls are made via a soft chemical process that involves ageing TiO 2 powder in a concentrated NaOH solution. The resultant nanoscrolls, once filtered and washed, are typically 8-10 nm in diameter and hundreds of nanometers long. The walls consist of 3-5 layers and the diameter of the hollow centre is typically 5 nm. A number of different structures have been assigned to nanoscrolls produced via the soft chemical process. These include anatase, H 2 Ti 3 O 7 , lepidocrocite-type structure and H 2 Ti 4 O 9 .H 2 O. Many of these structures are similar, consisting of titanate type layers, and qualitatively reproduce the X-ray diffraction data. However, preliminary data suggests that these structures are inconsistent with neutron diffraction data. Here we attempt a more quantitative analysis of the structure than those published previously using neutron and X-ray diffraction. (authors)

  15. Microstructural Investigation and MolecularWeight Determination of 1, 2-Polybutadiene by Nuclear Magnetic Resonance Spectroscopy

    Directory of Open Access Journals (Sweden)

    Farshid Ziaee

    2013-01-01

    Full Text Available In this research, the microstructural of low molecular weight 1,2-polybutadiene (1,2-PBD was conducted by 1H and 13C nuclear magnetic resonance spectroscopy (NMR to determine the isomeric contents of 1,4-cis, 1,4-trans and 1,2-vinyl in 1,2-PBD polymer structures. Number average molecular weight for low molecular weight 1,2-PBD was measured by NMR techniques and the results were compared with gel permeation chromatography. Due to the presence of methyl end group and its comparison with repeating units in 1,2-PBD microstructure, the number average molecular weight was calculated by NMR techniques. For calculation of surface areas, carbon and protons of methyl groups were characterized using distortion enhancement by polarization transfer (DEPT methods. For proton assignment of methyl end groups in 1H NMR spectral analysis the heteronuclear multiple quantum coherence (HMQC method was employed. Finally, stereoregularity and tacticity of 1,2-PBD were investigated through pentad and heptad sequences splitting of olefinic methylene and methine carbons pendant groups with various NMR acquisition temperatures from 20 to 50oC. 13C NMR spectra showed that with increasing of NMR acquisition temperature, the number of split peaks of two olefinic carbons increased.

  16. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  17. Experimental investigation of bubble plume structure instability

    Energy Technology Data Exchange (ETDEWEB)

    Marco Simiano; Robert Zboray; Francois de Cachard [Thermal-Hydraulics Laboratory, Paul Scherrer Institut, 5232 Villigen PSI (Switzerland); Djamel Lakehal; George Yadigaroglu [Institute of Energy Technology, Swiss Federal Institute of Technology, ETH-Zentrum/CLT, 8092 Zurich (Switzerland)

    2005-07-01

    Full text of publication follows: The hydrodynamic properties of a 3D bubble plume in a large water pool are investigated experimentally. Bubble plumes are present in various industrial processes, including chemical plants, stirred reactors, and nuclear power plants, e.g. in BWR suppression pools. In these applications, the main issue is to predict the currents induced by the bubbles in the liquid phase, and to determine the consequent mixing. Bubble plumes, especially large and unconfined ones, present strong 3D effects and a superposition of different characteristic length scales. Thus, they represent relevant test cases for assessment and verification of 3D models in thermal-hydraulic codes. Bubble plumes are often unsteady, with fluctuations in size and shape of the bubble swarm, and global movements of the plume. In this case, local time-averaged data are not sufficient to characterize the flow. Additional information regarding changes in plume shape and position is required. The effect of scale on the 3D flow structure and stability being complex, there was a need to conduct studies in a fairly large facility, closer to industrial applications. Air bubble plumes, up to 30 cm in base diameter and 2 m in height were extensively studied in a 2 m diameter water pool. Homogeneously sized bubbles were obtained using a particular injector. The main hydrodynamic parameters. i.e., gas and liquid velocities, void fraction, bubble shape and size, plume shape and position, were determined experimentally. Photographic and image processing techniques were used to characterize the bubble shape, and double-tip optical probes to measure bubble size and void fraction. Electromagnetic probes measured the recirculation velocity in the pool. Simultaneous two-phase flow particle image velocimetry (STPFPIV) in a vertical plane containing the vessel axis provided instantaneous velocity fields for both phases and therefore the relative velocity field. Video recording using two CCD

  18. Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages.

    Science.gov (United States)

    Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang

    2017-10-18

    The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

  19. Molecular Cloud Structures and Massive Star Formation in N159

    Science.gov (United States)

    Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

    2018-02-01

    The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

  20. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    Science.gov (United States)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov–Popov–Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  1. Structural investigation of a new composite process

    Science.gov (United States)

    Mayer, Philippe; Becker, Eric; Bigot, Régis; Kaïci, Bruno

    2017-10-01

    This work presents a study done on a new patented forming process, created to produce massive composite parts used for structural applications in automotive and aeronautics industries. The study presented in this paper deals with an experimental setup, used to characterize thick composite cylinders. The author presents the characterization of these cylinders and a new analysis method, in order to understand the consolidation steps of the composite in this forming process. The structural health of the part is illustrated by the analysis of the intra-bundle and inter-bundle porosities, by micrographs characterizations.

  2. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    It is fully characterized by CHN analysis, FTIR, XRD, UV-Vis-NIR DRS, 31P MAS NMR, TGA and SEM. The FTIR spectrum of the compound shows the fingerprint vibrational bands of both Keggin molecular anions and imidazolium cations. The aromatic C-H stretch region (2700-3250 cm-1) of imidazolium cation is split due ...

  3. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    Wintec

    A solid hybrid molecular material containing 1-butyl 3-methyl imidazolium cations and. Keggin anions of phosphotungstic acid has been synthesized. It is fully characterized by CHN analysis,. FTIR, XRD, UV-Vis-NIR DRS,. 31. P MAS NMR, TGA and SEM. The FTIR spectrum of the compound shows the fingerprint vibrational ...

  4. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

    Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  5. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  6. Structure-Activity Relationships on the Molecular Descriptors Family Project at the End

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2007-12-01

    Full Text Available Molecular Descriptors Family (MDF on the Structure-Activity Relationships (SAR, a promising approach in investigation and quantification of the link between 2D and 3D structural information and the activity, and its potential in the analysis of the biological active compounds is summarized. The approach, attempts to correlate molecular descriptors family generated and calculated on a set of biological active compounds with their observed activity. The estimation as well as prediction abilities of the approach are presented. The obtained MDF SAR models can be used to predict the biological activity of unknown substrates in a series of compounds.

  7. Design of Carborane Molecular Architectures via Electronic Structure Computations

    International Nuclear Information System (INIS)

    Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

    2009-01-01

    Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

  8. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  9. Structure investigations of some beryllium materials

    International Nuclear Information System (INIS)

    Faeldt, I.; Lagerberg, G.

    1960-05-01

    Metallographic structure, microhardness and texture have been studied on various types of beryllium metal including hot pressed powder, a rolled strip and an extruded tube It was found that beryllium exhibits its highest hardness in directions perpendicular to the basal plane. Good ideas of the prevailing textures were obtained with an ordinary X-ray diffractometer

  10. Investigation of the relationship between structural empowerment ...

    African Journals Online (AJOL)

    Specifically in health care settings, nurse leaders play an essential role in creating supportive work environments to avert these negative trends and increase nurse job satisfaction. Objective: The purpose of this study was to examine the relationship between structural empowerment and organizational commitment of ...

  11. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton. Key words: Gossypium hirsutum, pigment gland, zinc binding ...

  12. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  13. Mechanistic investigation of Fe(III) oxide reduction by low molecular weight organic sulfur species

    Science.gov (United States)

    Eitel, Eryn M.; Taillefert, Martial

    2017-10-01

    Low molecular weight organic sulfur species, often referred to as thiols, are known to be ubiquitous in aquatic environments and represent important chemical reductants of Fe(III) oxides. Thiols are excellent electron shuttles used during dissimilatory iron reduction, and in this capacity could indirectly affect the redox state of sediments, release adsorbed contaminants via reductive dissolution, and influence the carbon cycle through alteration of bacterial respiration processes. Interestingly, the reduction of Fe(III) oxides by thiols has not been previously investigated in environmentally relevant conditions, likely due to analytical limitations associated with the detection of thiols and their oxidized products. In this study, a novel electrochemical method was developed to simultaneously determine thiol/disulfide pair concentrations in situ during the reduction of ferrihydrite in batch reactors. First order rate laws with respect to initial thiol concentration were confirmed for Fe(III) oxyhydroxide reduction by four common thiols: cysteine, homocysteine, cysteamine, and glutathione. Zero order was determined for both Fe(III) oxyhydroxide and proton concentration at circumneutral pH. A kinetic model detailing the molecular mechanism of the reaction was optimized with proposed intermediate surface structures. Although metal oxide overall reduction rate constants were inversely proportional to the complexity of the thiol structure, the extent of metal reduction increased with structure complexity, indicating that surface complexes play a significant role in the ability of these thiols to reduce iron. Taken together, these results demonstrate the importance of considering the molecular reaction mechanism at the iron oxide surface when investigating the potential for thiols to act as electron shuttles during dissimilatory iron reduction in natural environments.

  14. On the use of test gases of various radii to investigate molecular sieving in leak channels.

    Science.gov (United States)

    Lim, William W; Bucknall, Martin P; Adler, Lewis; McKenzie, David R; Suaning, Gregg J

    2015-08-01

    Evidence of the effect of molecule size (molecular sieving) was discovered in leak channels similar to those found in hermetically sealed implantable bionics. A range of test gases of different molecular sizes was used to investigate the relative leak rates of several different samples. A contemporary model of molecular sieving is shown to be in partial agreement with our data.

  15. Solution structure of human insulin-like growth factor 1: A nuclear magnetic resonance and restrained molecular dynamics study

    International Nuclear Information System (INIS)

    Cooke, R.M.; Harvey, T.S.; Campbell, I.D.

    1991-01-01

    The solution structure of human insulin-like growth factor 1 has been investigated with a combination of nuclear magnetic resonance and restrained molecular dynamics methods. The results show that the solution structure is similar to that of insulin, but minor differences exist. The regions homologous to insulin are well-defined, while the remainder of the molecular exhibits greater disorder. The resultant structures have been used to visualize the sites for interaction with a number of physiologically important protein

  16. Molecular property investigations of an ortho-hydroxy Schiff base type compound with the first-principle molecular dynamics approach.

    Science.gov (United States)

    Jezierska-Mazzarello, Aneta; Vuilleumier, Rodolphe; Panek, Jarosław J; Ciccotti, Giovanni

    2010-01-14

    The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(N-methyl-alpha-iminoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O...H...N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1) assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm(-1) is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O...H...N bridge in a vacuum. The 1D Schrodinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal.

  17. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra.

    Science.gov (United States)

    Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M; Cinar, Mehmet

    2013-11-01

    The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Modified structure of graphene oxide by investigation of structure ...

    Indian Academy of Sciences (India)

    The structure of graphite oxide and graphene oxide (GO) has been studied previously using various analyses and computer simulations. Although some oxygen functional groups (OFGs) are accepted as the main functionalities in GO, the structure of GO has remained elusive. In this regard, GO was produced using the ...

  19. Investigation of Vibration Reduction through Structural Optimization.

    Science.gov (United States)

    1980-07-01

    energy calculations (Equation 13) were beyond the scope of this study. However, by using the Direct Mctrix Abstraction Program ( DMAP ) capability in NASTRAN ...Fuselage vertical bending 26.96 29.47 6th Skid mode 29.04 - 25 The AH-lG elastic-line NASTRAN model (including the DMAP ALTER procedure developed for...energy method for reducing vibration response, primarily via structural stiffness changes, using NASTRAN beam-element repre- sentation of the WI-G with

  20. The resource investigation and community structure characteristics ...

    African Journals Online (AJOL)

    Chinese fir is one of the most important commercial timber species in south China. Mycorrhizal fungi has been applied in many trees and showed important effect on enhancing the productive forces and the soil activities, but there is little report about the mycorrhizal fungi on Chinese fir. So this paper investigated the ...

  1. Structural investigation on gamma-irradiated polyacrylamide ...

    Indian Academy of Sciences (India)

    Small-angle neutron scattering (SANS) and ultraviolet (UV)–visible spectroscopictechniques are used to investigate the microstructural changes in polyacrylamide (PAAm) hydrogels on gamma irradiation. SANS measurements have revealed the presence of inhomogeneities in nanometre scale and reduction of their size ...

  2. Structural investigation on gamma-irradiated polyacrylamide ...

    Indian Academy of Sciences (India)

    Abstract. Small-angle neutron scattering (SANS) and ultraviolet (UV)–visible spectroscopic techniques are used to investigate the microstructural changes in polyacrylamide (PAAm) hydro- gels on gamma irradiation. SANS measurements have revealed the presence of inhomogeneities in nanometre scale and reduction of ...

  3. Theoretical investigation on crystal structure, detonation ...

    Indian Academy of Sciences (India)

    Density functional theory calculations were performed to study the new polynitro cage compound with the similar framework of HNIW. IR spectrum, heat of formation and thermodynamic properties were predicted. The bond dissociation energies and bond orders for the weakest bonds were analysed to investigate the ...

  4. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    Science.gov (United States)

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Structural and Molecular Modeling Features of P2X Receptors

    Directory of Open Access Journals (Sweden)

    Luiz Anastacio Alves

    2014-03-01

    Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

  6. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  7. Interaction Between New Anti-cancer Drug Syndros and CNT(6,6-6) Nanotube for Medical Applications: Geometry Optimization, Molecular Structure, Spectroscopic (NMR, UV/Vis, Excited state), FMO, MEP and HOMO-LUMO Investigation

    Science.gov (United States)

    Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Kumar, Rakesh

    2018-03-01

    In the present work, Density Functional Theory (DFT) was first time employed to investigate the interaction between new drug (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol (Syndros) and the CNT(6,6-6) Nanotube in the gaseous phase. The interaction effects of compounds Syndros and CNT (6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was also determined and discussed. The electronic spectra of the Syndros and the complex CNT(6,6-6)/Syndros in the gas phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for the formation of adsorption effect on maximum wavelength of the Syndros. Nucleus-Independent Chemical Shifts (NICS) calculations have also been carried out for the compound Syndors and the complex CNT(6,6-6)/Syndros and the aromaticity of the compound Syndors before and after interaction with the CNT(6,6-6) Nanotube was investigated.

  8. Synthesis, structures and theoretical investigation of

    Science.gov (United States)

    Weigend; Wirth; Ahlrichs; Fenske

    2000-02-04

    The silylated derivative of thiophosphoric acid (S)P(SSiMe3)3 is used as a convenient starting compound for the synthesis of multinuclear Cu and Au cluster complexes. (S)P(SSiMe3)3 reacts with CuCI/PPh3 and [AuCClPPh3] to give the following compounds: [Cu4(P2S6)(PPh3)4] (1), [Cu6(P2S6)Cl2-(PPh3)6] (2) and [Au4(P2S6)(PPh3)4](3). According to X-ray structure determination, these compounds contain P2S6(4-) ions, in which S atoms act as ligands for Cu+ and Au+ ions. Although 1 and 3 have the same stoichiometry, bonding of the metal ions to the P2S6 skeleton displays small but remarkable differences. Au is twofold coordinated, whereas Cu shows a threefold coordination. Ab initio calculations have been carried out to rationalise these structural differences. The theoretical treatment of the corresponding Ag compound indicates the latter to be less stable.

  9. Electronic Structure Investigation of Doping C60 with Metal Oxide

    Science.gov (United States)

    Wang, Chenggong; Gao, Yongli

    2014-03-01

    Fullerene (C60) has been used extensively as an acceptor material in organic photovoltaic (OPV) cells. Other applications including n-channel organic thin film transistors (OTFT) and C60 based organic superconductors have been reported more than a decade ago. We have investigated p-doping of C60 with molybdenum oxide (MoOx) with ultra-violet photoemission spectroscopy (UPS), inverse photoemission spectroscopy (IPES) and atomic force microscopy (AFM). Both surface doping and bulk doping by MoOx are studied. It was found that the thermally evaporated MoOx inter-layer substantially increased the surface workfunction. This increased surface workfunction strongly attract electrons towards the MoOx layer at the C60/MoOx interface, resulting in strong inversion of C60. Energy levels of C60 relax gradually as the thickness of C60 increases. An exceptionally long (greater than 400 Angstrom) band bending is observed during this relaxation in C60. Such a long band bending has not been observed for other organic/MoOx interface. For the bulk doping, MoOx doping ratios from 1% to over 100% were investigated. The saturation occurs at approximately 20 %, when the highest occupied molecular level (HOMO) of C60 starts to be pinned at the Fermi level. These studies demonstrate effective ways to manipulate the electronic structures of the fullerene. This work is supported by the National Science Foundation Grant No. DMR-1303742.

  10. Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

    International Nuclear Information System (INIS)

    Wang, J.; Gutierre, M.S.

    2010-01-01

    This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

  11. Investigation of IFMIF target assembly structure design

    International Nuclear Information System (INIS)

    Ida, Mizuho; Nakamura, Hiroo; Sugimoto, Masayoshi; Yamamura, Toshio

    2006-10-01

    In the International Fusion Materials Irradiation Facility (IFMIF), the back-wall of target assembly is the part suffered the highest neutron-flux. The back-wall and the assembly are designed to have lips for cutting/welding at the back-wall replacement. To reduce thermal stress and deformation of the back-wall under neutron irradiation, contact pressure between the back-wall and the assembly is one of dominant factors. Therefore, an investigation was performed for feasible clamping pressure of a mechanical clamp set in limited space around the back-wall. It was clarified that the clamp can give a pressure difference up to 0.4 MPa between the contact pressure and atmosphere pressure in the test cell room. Also a research was performed for the dissimilar metal welding in the back-wall. Use of 309 steel was found adequate as the intermediate filler metal through the research of previous welding. Maintaining a temperature of the target assembly so as to avoid a freezing of liquid lithium is needed at the lithium charge into the loop before the beam injection. The assembly is covered with thermal insulation. Therefore, a research and an investigation were performed for compact and light thermal-insulation effective even under helium (i.e. high heat-conduction) condition of the test cell room. The result was as follows; in the case that a thermal conductivity 0.008 W/m·K of one of found insulation materials is available in the temperature range up to 300degC of the IFMIF target assembly, needed thickness and weight of the insulation were respectively only 8.2 mm and 32 kg. Also a research was performed for high-heat-density heaters to maintain temperature of the back-wall which can not be cover with insulation due to limited space. A heater made of silicon-nitride was found to be adequate. Total heat of 8.4 kW on the back-wall was found to be achievable through an investigations of heater arrange. Also an investigation was performed for remote-handling device to

  12. Investigation of Nuclear Partonic Structure. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, Henry J. [Univ. of California, Berkeley, CA (United States); Engelage, J. M.

    2016-08-30

    Our research program had two primary goals during the period of this grant, to search for new and rare particles produced in high-energy nuclear collisions and to understand the internal structure of nuclear matter. We have developed electronics to pursue these goals at the Relativistic Heavy Ion Collider (RHIC) in the Solenoidal Tracker at RHIC (STAR) experiment and the AnDY experiment. Our results include discovery of the anti-hyper-triton, anti- 3Λ-barH, which opened a new branch on the chart of the nuclides, and the anti-alpha, anti- 4He, the heaviest form of anti-matter yet seen, as well as uncovering hints of gluon saturation in cold nuclear matter and observation of jets in polarized proton-proton collisions that will be used to probe orbital motion inside protons.

  13. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

    Science.gov (United States)

    Couvineau, Alain; Laburthe, Marc

    2012-05-01

    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  14. Exponential Repulsion Improves Structural Predictability of Molecular Docking

    Czech Academy of Sciences Publication Activity Database

    Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

    2016-01-01

    Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

  15. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  16. Theoretical study on the molecular and crystal structures of nitrogen ...

    Indian Academy of Sciences (India)

    The molecular and crystal structure of the adduct NF3·BF3 was studied computationally using density functional theory. It shows that the adduct exists in the form of a complex but is not ionic. The heats of formation in the gas and the condensed phase of the adduct are −1266.09 and −1276.37 kJ·mol−1, respectively, which ...

  17. Lithium diffusion in silicon and induced structure disorder: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Huanyu Wang

    2013-11-01

    Full Text Available Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively. Moreover, lithium diffuses easier in the Li-Si alloy structure of higher lithium concentration with deeper injection depth. The silicon's structure will be damaged gradually during the charge and discharge process. However, it will also recover to initial state to a great extent after relaxation. Therefore, the damage of lithium diffusion to silicon anode in the structure of low lithium concentration is reversible to a great degree. In addition, the silicon structure of crystal orientation perform better properties in both lithium's diffusivity and structural stability.

  18. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  19. Structural modeling and molecular dynamics simulation of the actin filament.

    Science.gov (United States)

    Splettstoesser, Thomas; Holmes, Kenneth C; Noé, Frank; Smith, Jeremy C

    2011-07-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized. Copyright © 2011 Wiley-Liss, Inc.

  20. Infectious Bronchitis Virus Variants: Molecular Analysis and Pathogenicity Investigation

    Directory of Open Access Journals (Sweden)

    Shu-Yi Lin

    2017-09-01

    Full Text Available Infectious bronchitis virus (IBV variants constantly emerge and pose economic threats to poultry farms worldwide. Numerous studies on the molecular and pathogenic characterization of IBV variants have been performed between 2007 and 2017, which we have reviewed herein. We noted that viral genetic mutations and recombination events commonly gave rise to distinct IBV genotypes, serotypes and pathotypes. In addition to characterizing the S1 genes, full viral genomic sequencing, comprehensive antigenicity, and pathogenicity studies on emerging variants have advanced our understanding of IBV infections, which is valuable for developing countermeasures against IBV field outbreaks. This review of IBV variants provides practical value for understanding their phylogenetic relationships and epidemiology from both regional and worldwide viewpoints.

  1. Investigating Viruses during the Transformation of Molecular Biology.

    Science.gov (United States)

    Moss, Bernard

    2017-03-10

    This Reflections article describes my early work on viral enzymes and the discovery of mRNA capping, how my training in medicine and biochemistry merged as I evolved into a virologist, the development of viruses as vaccine vectors, and how scientific and technological developments during the 1970s and beyond set the stage for the interrogation of nearly every step in the reproductive cycle of vaccinia virus (VACV), a large DNA virus with about 200 genes. The reader may view this article as a work in progress, because I remain actively engaged in research at the National Institutes of Health (NIH) notwithstanding 50 memorable years there. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Investigating the Lithospheric Structure of Southern Madagascar

    Science.gov (United States)

    Tilmann, Frederik; Yuan, Xiaohui; Rümpker, Georg; Gerard, Rambolamana; Elisa, Rindraharisaona; Priestley, Keith

    2014-05-01

    there is some so-far poorly characterised seismicity. We present preliminary results on the lithospheric crust and mantle structure based on surface wave dispersion and waveform modelling, focussing on the contrast between the metamorphic areas in the east and the presumably stretched regions in the west. Interstation Green's functions have been obtained from all pairs of vertical broadband records, with coherent Rayleigh waves being identifiable for periods of 3-40 s. In addition, two-station phase dispersion measurements have allowed us to determine phase dispersion between 25 and 60 s. The ambient noise and earthquake data both indicate a slow-down of surface propagation in the western part of the array for periods 45 s.

  3. Investigating the influence of effective parameters on molecular characteristics of bovine serum albumin nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rohiwal, S.S.; Satvekar, R.K.; Tiwari, A.P.; Raut, A.V.; Kumbhar, S.G.; Pawar, S.H., E-mail: pawar_s_h@yahoo.com

    2015-04-15

    Graphical abstract: The physiochemical properties of nanoparticles provide the basic aspects about the conformational transitions which could have a strong bearing on the bioavailability for bioactive molecules such as peptides and hormones. - Highlights: • Synthesis and surface and structural properties of Bovine Serum Albumin nanoparticles (BSANPs). • Study of conformational transitions of BSANPs by spectroscopic techniques. • Studies on the effect of pH and protein concentration on formulation of BSANPs. - Abstract: The protein nanoparticles formulation is a challenging task as they are prone to undergo conformational transitions while processing which may affect bioavailability for bioactive compounds. Herein, a modified desolvation method is employed to prepare Bovine Serum Albumin nanoparticles, with controllable particle size ranging from 100 to 300 nm and low polydispersity index. The factors influencing the size and structure of BSA NPs viz. protein concentration, pH and the conditions for purification are well investigated. The structure of BSA NPs is altered due to processing, and may affect the effective binding ability with drugs and bioactive compounds. With that aims, investigations of molecular characteristics of BSA NPs are carried out in detail by using spectroscopic techniques. UV–visible absorption and Fourier Transform Infrared demonstrate the alteration in protein structure of BSA NPs whereas the FT-Raman spectroscopy investigates changes in the secondary and tertiary structures of the protein. The conformational changes of BSA NPs are observed by change in fluorescence intensity and emission maximum wavelength of tryptophan residue by fluorescence spectroscopy. The field emission scanning electron and atomic force microscopy micrographs confirm the size and semi-spherical morphology of the BSA NPs. The effect of concentration and pH on particle size distribution is studied by particle size analyzer.

  4. 16O + 16O molecular structures of superdeformed states in S isotopes

    Science.gov (United States)

    Taniguchi, Y.

    2017-06-01

    Structures of excited states in S isotopes are investigated by using the antisymmetrized molecular dynamics and generator coordinate method (GCM). The GCM basis wave functions are calculated via energy variation with a constraint on the quadrupole deformation parameter β. By applying the GCM after parity and angular momentum projections, the coexistence of positive- and negative-parity superdeformed (SD) bands are predicted in 33-36S except for negative-parity states in 36S. The SD bands have structures of 16O + 16O + valence neutron(s) in molecular orbitals around the two 16O cores in a cluster picture. The configurations of the valence neutron(s) in the SD states are δ and/or π molecular orbitals.

  5. Benzyl alcohol–ammonia (1: 1) cluster structure investigated by ...

    Indian Academy of Sciences (India)

    Laser-induced fluorescence excitation and IR-UV double resonance spectroscopy have been used to determine the hydrogen-bonded structure of benzyl alcohol-ammonia (1:1) cluster in a jet-cooled molecular beam. In addition, ab initio quantum chemical calculations have been performed at HF/6-31G and HF/6-31G(d, ...

  6. A clinical and molecular investigation of two South African families ...

    African Journals Online (AJOL)

    consistently present and structural brain abnormalities can occur.[6]. Importantly, boys with SGBS ... 2 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg,. South Africa, and National .... Proband B's mother was a healthy woman of normal intellect.

  7. Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

    Science.gov (United States)

    Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

    2018-05-01

    For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

  8. Ultrafast electron diffraction: oriented molecular structures in space and time.

    Science.gov (United States)

    Baskin, J Spencer; Zewail, Ahmed H

    2005-11-11

    The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.

  9. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  10. Multi-Probe Investigation of Proteomic Structure of Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B; Wheeler, K E

    2008-01-24

    Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also

  11. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    Science.gov (United States)

    Heffernan, Natalie; Brunton, Nigel P.; FitzGerald, Richard J.; Smyth, Thomas J.

    2015-01-01

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. PMID:25603345

  12. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    Directory of Open Access Journals (Sweden)

    Natalie Heffernan

    2015-01-01

    Full Text Available Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis. Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs. These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  13. Molecular Structural Characteristics of Polysaccharide Fractions from Canarium album (Lour.) Raeusch and Their Antioxidant Activities.

    Science.gov (United States)

    Zeng, Hongliang; Miao, Song; Zheng, Baodong; Lin, Shan; Jian, Yeye; Chen, Shen; Zhang, Yi

    2015-11-01

    The objective of this study was to investigate the multiple relations between the preliminary molecular structural characteristics and antioxidant activities of polysaccharides from Canarium album (Lour.) Raeusch (CPS). Three polysaccharide fractions, CPS1, CPS2, and CPS3, were isolated from CPS by column chromatography. CPS1 and CPS3 were mainly composed of neutral polysaccharides linked by α- and β-glycosidic linkages while CPS2 was pectin polysaccharides mainly linked by β-glycosidic linkages. According to the SEC-MALLS-RI system, the molecular weight of CPS1 was greater compared to CPS2 and CPS3, and the molecular weight and radius of CPS did not display positive correlation. The chain conformation analysis indicated CPS1 and CPS2 were typical highly branched polysaccharides while CPS3 existed as a globular shape in aqueous. Furthermore, the antioxidant activity of CPS2 was better than that of CPS3, while that of CPS1 was the weakest. The antioxidant activities of polysaccharide fractions were affected by their monosaccharide composition, glycosidic linkage, molecular weight, and chain conformation. This functional property was a result of a combination of multiple molecular structural factors. CPS2 was the major antioxidant component of CPS and it could be exploited as a valued antioxidant product. The molecular structural characteristics, antioxidant activities, and structure-function relationships of polysaccharide fractions from Canarium album were first investigated in this study. The results provided background and practical knowledge for the deep-processed products of C. album with high added value. CPS2 was the major antioxidant component of CPS, which could be exploited as a valued antioxidant ingredient in food and pharmaceutical industries. © 2015 Institute of Food Technologists®

  14. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree-Fock (HF) method; density functional theory (DFT); Møller-Plesset second order (MP2) method; molecular electron density (MED); molecular electrostatic potential.

  15. Molecular Investigation of the Stem Snap Point in Textile Hemp

    Directory of Open Access Journals (Sweden)

    Marc Behr

    2017-12-01

    Full Text Available Fibre crops are important natural resources, as they sustainably provide bast fibres, an economically-valuable raw material used in the textile and biocomposite sectors. Among fibre crops, textile hemp (Cannabis sativa L. is appreciated for its long and strong gelatinous bast fibres. The stem of fibre crops is a useful system for cell wall-oriented studies, because it shows a strong tissue polarity with a lignified inner core and a cellulosic hypolignified cortex, as well as a basipetal lignification gradient. Along the stem axis of fibre crops, a specific region, denoted snap point, marks the transition from elongation (above it to fibre thickening (below it. After empirically determining the snap point by tilting the plant, we divided the stem segment containing it into three non-overlapping consecutive regions measuring 1 cm each, and carried out targeted RT-qPCR on cell wall-related genes separately, in outer and inner tissues. Different gene clusters can be observed, two of which are the major gene groups, i.e., one group with members expressed at higher levels in the inner tissues, and one group whose genes are more expressed in the cortex. The present results provide a molecular validation that the snap point is characterised by a gradient of events associated with the shift from fibre elongation to thickening.

  16. Molecular structural changes of plasticized PVC after UV light exposure.

    Science.gov (United States)

    Hankett, Jeanne M; Collin, William R; Chen, Zhan

    2013-12-19

    Plasticized poly(vinyl chloride) (PVC) materials for industrial, medical, and household use are often intentionally exposed to UV light, though its impact on the molecular integrity and toxicity of the surface and bulk of PVC materials is still not well understood. This paper investigates the surface and bulk molecular changes of plasticized PVC films with 25, 10, or 0 wt % bis-2-ethylhexyl phthalate (DEHP) plasticizer after exposure to short wave (254 nm) or long wave (365 nm) UV light. Surface analytical techniques including sum frequency generation vibrational spectroscopy (SFG) revealed short wave UV exposure induced major molecular changes on the plasticized PVC surfaces, resulting in increased surface hydrophilicity and decreased CH3 content with increasing exposure time. Additionally, it was deduced from multiple techniques that the surface and the bulk of the plastic exposed to short wave UV contained phthalic monoesters and phthalic acid formed from multistep radical reactions. In contrast, when exposed to long wave UV, molecular content and ordering on the surfaces of the plastic remained relatively unchanged and the introduction of DEHP in plastic helped protect PVC chains from degradation. Results from this study demonstrate short wave UV exposure will result in plastic surfaces containing phthalates and phthalate-related products accessible to contact by living organisms.

  17. Molecular structure investigation and tautomerism aspects of (E)-3 ...

    Indian Academy of Sciences (India)

    Saudi M N S, El Semary M M A and El Sawaf G 2002. Pharmazie 57 519. 17. Amal Raj A, Raghunathan R, Sridevikumari M R and. Raman N 2003 Bioorg. Med. Chem. 11 407. 18. Heydri R and Tahamipour B 2011 Chin. Chem. Lett. 22. 1281. 19. Nanubolu J B, Sridhar B and Ravikumar K 2014. CrystEngComm 16 10602.

  18. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez

    2013-01-01

    Full Text Available We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM, using the nonequilibrium version of the IEF-PCM model.

  19. Molecular self-assembly for biological investigations and nanoscale lithography

    Science.gov (United States)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  20. Chemistry and structure of giant molecular clouds in energetic environments

    Science.gov (United States)

    Anderson, Crystal Nicole

    2016-09-01

    Throughout the years many studies on Galactic star formation have been conducted. This resulted in the idea that giant molecular clouds (GMCs) are hierarchical in nature with substructures spanning a large range of sizes. The physical processes that determine how molecular clouds fragment, form clumps/cores and then stars depends strongly on both recent radiative and mechanical feed- back from massive stars and, on longer term, from enhanced cooling due to the buildup of metals. Radiative and mechanical energy input from stellar populations can alter subsequent star formation over a large part of a galaxy and hence is relevant to the evolution of galaxies. Much of our knowledge of star formation on galaxy wide scales is based on scaling laws and other parametric descriptions. But to understand the overall evolution of star formation in galaxies we need to watch the feedback processes at work on giant molecular cloud (GMC) scales. By doing this we can begin to answer how strong feedback environments change the properties of the substructure in GMCs. Tests of Galactic star formation theory to other galaxies has been a challenging process due to the lack of resolution with current instruments. Thus, only the nearest galaxies allow us to resolve GMCs and their substructures. The Large Magellanic Cloud (LMC), is one of the closest low metallicity dwarf galaxies (D˜ 50 kpc) and is close enough that current instruments can resolve the sub- structure of its GMCs to gas tracers (e.g. HCO+, HCN, HNC, CS, C2H, N2H+) detected in the LMC at 1.5-40 pc scales and in NGC 5253 at 40 pc scales. I then compare the molecular gas detections to the Central Molecular Zone in our Galaxy. Dense molecular gas was detected in all of the sources. For the regions in the LMC, molecular lines of CS, N2H+, C 2H, HNC, HCO+ and HCN were all detected in N159W and N113 while only HCN, HCO+, HNC, and C2H were detected in 30Dor-10. Toward NGC 5253 only HCO+, HCN, C2H and CS were detected. I observe

  1. Close-packed (polytypic) structures in molecular-dynamics simulations

    International Nuclear Information System (INIS)

    Moody, M.; Ray, J.R.; Rahman, A.

    1987-01-01

    Molecular-dynamics (MD) computer-simulation studies are used to study close-packed structures found in solid-phase atomic systems interacting via a Morse potential (parametrized to model Ni). A graphical display of particle positions [a (112-bar0) projection] within the parallelepiped forming the MD cell is illustrated. Such a graphic projection allows accurate, complete, and readily visual recognition of the stacking order of close-packed planes and is a much more effective way of identifying polytypes than a study of the pair-distribution function for the structure. These illustrations demonstrate the polytypic nature of previously and newly recognized MD close-packed structures. When assuming compatibility with periodic boundary conditions, as is conventional in MD, only certain polytypes are allowed for an MD simulation system. A discussion of compatibility between close-packed structures and the periodic boundary conditions is presented. The pair coordination numbers, geometrical structure-factor intensities, and potential-energy lattice sums are then calculated for some of these compatible structures. This paper concludes that, through careful consideration, a considerable variety of close-packed physical systems may be appropriately modeled with use of MD computer simulation. Conversely, proper interpretation of the data obtained during such studies may require awareness of the findings presented here

  2. Molecular structure of a tolyl derivative of γ-pyrone

    Science.gov (United States)

    Tranfić Bakić, Marina; Cetina, Mario; Mazalović, Sanja

    2018-01-01

    A study of the molecular structure of a new derivative of γ-pyrone, which is assumed to be of biological and pharmacological importance, has been carried out. The detailed insight into the structure of the γ-pyrone derivative was obtained by 1H NMR, 13C NMR, IR and Raman spectroscopy. Furthermore, its crystal structure was determined by single crystal X-ray diffraction method and its behavior in solutions was examined by UV/Vis and fluorescence spectroscopy. Assignment of the vibrational spectra of the studied compound is presented and correlated to some structural parameters. DFT calculations, namely geometry optimization, frequency calculations, and NBO population analysis, were performed at B3LYP/6-311G++(d,p) level of theory and the obtained data was compared to the experimental results to further elucidate the structural details. In addition, energies of the electronic transitions were estimated using DFT calculations at the same level of theory, and the calculated results showed good agreement with experimental data. It was shown that longer Csbnd C and shorter Cdbnd C bonds alternate in the pyrone ring and that the structure of the studied γ-pyrone derivative comprises two intramolecular Csbnd H⋯O bonds. All the results pointed to relatively weak π-electron delocalization inside the pyrone moiety and significantly stronger π-electron delocalization through tolyl substituents.

  3. Contributions to Advances in Blend Pellet Products (BPP) Research on Molecular Structure and Molecular Nutrition Interaction by Advanced Synchrotron and Globar Molecular (Micro)Spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, VÍctor H; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  4. Molecular and Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017)

    Science.gov (United States)

    2017-10-01

    term goal is to identify molecular mechanisms regulating tau that can be used as diagnostics and to develop therapeutics for CTE. The immediate goal...AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017) PRINCIPAL...INTRODUCTION: Repetitive mild traumatic brain injury leads to neurological symptoms and chronic traumatic encephalopathy (CTE). The molecular changes

  5. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  6. 3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis

    Directory of Open Access Journals (Sweden)

    Jiraporn Ungwitayatorn

    2008-02-01

    Full Text Available A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR studies using molecular field analysis (MFA. The substitutional requirements for favorable antioxidant activity were investigated and a predictive model that could be used for the design of novel antioxidants was derived. Regression analysis was carried out using genetic partial least squares (G/PLS method. A highly predictive and statistically significant model was generated. The predictive ability of the developed model was assessed using a test set of 5 compounds (r2pred = 0.924. The analyzed MFA model demonstrated a good fit, having r2 value of 0.868 and crossvalidated coefficient r2cv value of 0.771.

  7. The diverse and expanding role of mass spectrometry in structural and molecular biology.

    Science.gov (United States)

    Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

    2016-12-15

    The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  8. Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil.

    Science.gov (United States)

    Mayer, Fabiana Quoos; Dos Reis, Emily Marques; Bezerra, André Vinícius Andrade; Cerva, Cristine; Rosa, Júlio; Cibulski, Samuel Paulo; Lima, Francisco Esmaile Sales; Pacheco, Susi Missel; Rodrigues, Rogério Oliveira

    2017-06-01

    The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. A molecular dynamic investigation for shock induced phase transition of water

    Science.gov (United States)

    Mitra, Nilanjan; Neogi, Anupam

    2015-06-01

    Atomistic equilibrium molecular dynamics (EMD) was carried out to investigate shock induced phase transition of bulk liquid water. Multi-scale shock technique (MSST) was utilized to investigate low (US = 2 . 5km /s) to strong (US = 6 . 5km /s) intensity shock response on an extended flexible three point model up to 100 ns. The thermodynamic pathway of phase transition from liquid water to ice VII was investigated using temporal variation of thermodynamic state variables, power spectrum analyses of O-H bond vibration along with temporal evolution of pair correlation function between O-O, O-H and H-H atoms. Static structure factor along with pair-distribution function extended up to 20 Å was calculated and compared against the ideal ice VII to get information regarding long range ordering. Bragg reflection at different crystal planes were evaluated to investigate percentage of crystallinity of the shocked sample. Specific questions answered in this work involves: What is the exact time frame after the passage of shock at certain intensity in which nucleation of solid phase can be observed? Is it a complete or partial phase transition? Are external nucleators essential for this transformation? What is the percentage of crystallinity of the nucleated phase?

  10. Effect of water vapour on the molecular structures of supported vanadium oxide catalysts at elevated temperatures

    NARCIS (Netherlands)

    Jehng, Jih-Mirn; Deo, G.; Weckhuysen, B.M.; Wachs, I.E.

    1996-01-01

    The effect of water vapor on the molecular structures of V2O3-supported catalysts (SiO2, Al2o3, TiO2, and CeO2) was investigated by in situ Raman spectroscopy as a function of temperature (from 500°C to 120°C). Under dry conditions only isolated surface VO4 species are present on the dehydrated SiO2

  11. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  12. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    Science.gov (United States)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  13. Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

    International Nuclear Information System (INIS)

    Firment, L.E.

    1977-01-01

    The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

  14. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    Iwahashi, Makio

    2005-01-01

    Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

  15. Equilibrium theory of molecular fluids: Structure and freezing transitions

    Science.gov (United States)

    Ram, Jokhan

    2014-05-01

    In this article we review equilibrium theory of molecular fluids which includes structure and freezing transitions. The application of the theory to evaluate the pair correlation functions using Integral Equation methods and Computer Simulations have been discussed. Freezing of classical complex fluids based on the density functional approach is also discussed and compare a variety of its versions. Transitions discussed are sensitive to the value of direct correlation functions of the effective liquid which is required as an input information in the theory. Accurate evaluation of pair correlation functions is emphasized. Calculation of these correlation functions which pose problems in the case of ordered phases is discussed. The pair correlation functions of the ordered phase, which are supposed to be made up of two contributions, one that preserves the symmetry of the isotropic phase and a second that breaks it, are discussed. A new free-energy functional developed for an inhomogeneous system that contains both symmetry conserved and symmetry broken parts of the direct pair correlation function is discussed. The most useful three dimensional reference interaction site model (3D-RISM) and its extension done recently by many workers is discussed. Application of this theory to a large variety of complex systems in combination with the density functional theory method implemented in the Amsterdam density functional software package is discussed. Coupling of the 3D-RISM salvation theory with molecular dynamics in the Amber molecular dynamics package is also given. The importance of the density functional theory for the study of the structure and phase behaviour of hard polyhedral is also discussed. The dynamical density functional and its generalized form applied for many important class of problems such as binary mixture, anisotropic particles dynamics of freezing and wetting, colloidal samples, particle self diffusion in complex environment, colloidal sedimentation

  16. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  17. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy : A molecular dynamics simulation study

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    2003-01-01

    The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been

  18. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

  19. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jianjun [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL; Monticelli, Luca [Institut National de la Santé et de la Recherche Médicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada; Katsaras, John [ORNL

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  20. The effect of molecular mass on the polymorphism and crystalline structure of isotactic polypropylene

    Directory of Open Access Journals (Sweden)

    2010-02-01

    Full Text Available This study is devoted to the investigation of the effect of molecular mass on the α-, β- and γ-crystallization tendency of isotactic polypropylene (iPP. The crystalline structure was studied by wide angle X-ray scattering (WAXS and by polarised light microscopy (PLM. The melting and crystallization characteristics were determined by differential scanning calorimetry (DSC. The results indicate clearly that iPP with low molecular mass crystallizes essentially in α-modification. However, it crystallizes in β-form in the presence of a highly efficient and selective β-nucleating agent. The α- and β-modifications form in wide molecular mass range. The decreasing molecular mass results in increased structural instability in both α- and β-modifications and consequently enhanced inclination to recrystallization during heating. The formation of γ-modification could not be observed, although some literature sources report that γ-form develops in iPP with low molecular mass.

  1. Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    Science.gov (United States)

    Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

    2008-12-11

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  2. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    Science.gov (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  3. Pure and Modified Co-Poly(amide-12-b-ethylene oxide) Membranes for Gas Separation Studied by Molecular Investigations.

    Science.gov (United States)

    De Lorenzo, Luana; Tocci, Elena; Gugliuzza, Annarosa; Drioli, Enrico

    2012-06-28

    This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET) as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST) and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships.

  4. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  5. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    Science.gov (United States)

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  7. Molecular flexibility and structural instabilities in crystalline L-methionine

    NARCIS (Netherlands)

    Fischer, Jennifer; Lima, Jose A.; Freire, Paulo T. C.; Melo, Francisco E. A.; Havenith, Remco W. A.; Mendes Filho, Josue; Broer, Ria; Eckert, Juergen; Bordallo, Heloisa N.

    2013-01-01

    We have investigated the dynamics in polycrystalline samples of L-methionine related to the structural transition at about 307 K by incoherent inelastic and quasielastic neutron scattering, X-ray powder diffraction as well as ab-initio calculations. L-Methionine is a sulfur amino acid which can be

  8. Atomic and electronic structures of carbon nanotube covalent connecting with graphene by oxygen molecular

    Science.gov (United States)

    Wei, Jianwei; Wei, Qiang; Ma, Zengwei; Zeng, Hui

    2016-02-01

    Based on density functional theories, we have investigated the nanostructure in which boron and nitrogen co-doped carbon nanotube (CNT)/graphene (GR) were connected by an oxygen molecular. The geometry structure and electronic properties of the system were calculated carefully. The band structures indicate that the impurity state of oxygen transfer the semiconducting co-doped carbon nanotube/graphene into a semimetallic composite material. The results show that the connection can be achieved with energy release under a wider range of distance between the nanotube and graphene. It indicates that the connection between the nanotube and the graphene might be a self-assemble process.

  9. Investigations on structural, optical and magnetic properties of ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 40; Issue 1. Investigations on structural, optical and magnetic properties of solution-combustion-synthesized nanocrystalline iron molybdate. KRITHIKADEVI RAMACHANDRAN SIVA CHIDAMBARAM BALRAJ BASKARAN ARULMOZHI MUTHUKUMARASAMY JOHN ...

  10. Structures of water molecular nanotube induced by axial tensile strains

    Energy Technology Data Exchange (ETDEWEB)

    Li, H. [Key Laboratory of Liquid Structures and Heredity of Materials, Ministry of Education, School of Materials Science and Engineering, Shandong University (China)], E-mail: lihuilmy@hotmail.com; Zhang, X.Q. [Physics Department, Ocean University of China, Qingdao (China); Liew, K.M. [Department of Building and Constructions, City University of Hong Kong, Kowloon (Hong Kong); Liu, X.F. [Key Laboratory of Liquid Structures and Heredity of Materials, Ministry of Education, School of Materials Science and Engineering, Shandong University (China)

    2008-10-06

    Five well-ordered nano-ice structures embedded in carbon nanotubes are obtained in this study. These five nano-ice phases all exhibit single walled tubular morphologies, including the pentagon, hexagon ice nanotubes whose structures are quite different from bulk ice. Our simulation results indicate that water molecules tend to rearrange into surface ring structures to reduce the number of free OH groups. The structural behavior of these ice nanotubes inside CNTs subject to axial stress is also investigated. The ice nanotubes tend to be drawn to ice nanorings or ice nanospring during the mechanical stretching. The distribution function exhibits typical order-to-disorder transition of the water network confined in carbon nanotube during the stretching. By analysis, we suggest that it is unlikely that additional water molecules will enter the tubes because of the increased volume available if the tubes are stretched at contact with a water reservoir.

  11. Spectral investigations of structural peculiarities in some compound ethers

    Science.gov (United States)

    Pogorelov, Valerii E.; Astashkin, Yuri; Bukalo, Vyacheslav; Kutulya, Lidiya A.; Semenova, Galina N.

    2000-02-01

    The results of spectral investigation of two liquid crystalline isomers at different temperature pre-history are reported. The temperature depended transformations of vibrational Raman spectra and their connections with the change of structure of these substances were investigated. Spectral region was 1100-1760 cm-1, temperature interval was from 203 K to 398 K. Both general and special regularities under thermo-structural transformations were noted.

  12. Isotope chemistry and molecular structure. Carbon and oxygen isotope chemistry

    International Nuclear Information System (INIS)

    Bigeleisen, J.; Hom, R.C.; Ishida, T.

    1976-01-01

    The relationships between force constants and the isotope chemistry of carbon and oxygen are calculated for H 2 O, CO 2 , CH 2 O, CH 4 , C 2 H 4 , C 2 H 6 , and C 6 H 6 . Significant differences are found from the general features of protium--deuterium isotope chemistry. These are shown to be associated with a structural effect. Hydrogen is always an end atom except for hydrogen bonded moleules. Carbon is generally tetrahedrally bonded and its isotope chemistry shows significant contributions from the interaction between stretching and bending modes. These interactions lead to deviations in additivity of the total isotope effect from the contributions of the individual force constants. Stretching forces dominate the isotope chemistry of carbon and oxygen as they do in hydrogen. They account for 70%--90% of the reduced partition function ratios. Correlations are made between the stretching force contributions and molecular structure. It is shown that while significant differences exist between the specific contributions calculated from different force fields for methane, ethane, and benzene, the absolute value of ln(s/s') f is rather insensitive to the detailed structures of the F matrices studied

  13. Transmission electron microscopy and the molecular structure of icosahedral viruses.

    Science.gov (United States)

    San Martín, Carmen

    2015-09-01

    The field of structural virology developed in parallel with methodological advances in X-ray crystallography and cryo-electron microscopy. At the end of the 1970s, crystallography yielded the first high resolution structure of an icosahedral virus, the T=3 tomato bushy stunt virus at 2.9Å. It took longer to reach near-atomic resolution in three-dimensional virus maps derived from electron microscopy data, but this was finally achieved, with the solution of complex icosahedral capsids such as the T=25 human adenovirus at ∼3.5Å. Both techniques now work hand-in-hand to determine those aspects of virus assembly and biology that remain unclear. This review examines the trajectory followed by EM imaging techniques in showing the molecular structure of icosahedral viruses, from the first two-dimensional negative staining images of capsids to the latest sophisticated techniques that provide high resolution three-dimensional data, or snapshots of the conformational changes necessary to complete the infectious cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Controlling molecular deposition and layer structure with supramolecular surface assemblies

    Science.gov (United States)

    Theobald, James A.; Oxtoby, Neil S.; Phillips, Michael A.; Champness, Neil R.; Beton, Peter H.

    2003-08-01

    Selective non-covalent interactions have been widely exploited in solution-based chemistry to direct the assembly of molecules into nanometre-sized functional structures such as capsules, switches and prototype machines. More recently, the concepts of supramolecular organization have also been applied to two-dimensional assemblies on surfaces stabilized by hydrogen bonding, dipolar coupling or metal co-ordination. Structures realized to date include isolated rows, clusters and extended networks, as well as more complex multi-component arrangements. Another approach to controlling surface structures uses adsorbed molecular monolayers to create preferential binding sites that accommodate individual target molecules. Here we combine these approaches, by using hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules. We find that the open network acts as a two-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules, with the network itself also serving as a template for the formation of a fullerene layer.

  15. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.

    2006-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  17. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  18. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1975-01-01

    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

  19. Durability of marine concrete structures - field investigations and modelling

    NARCIS (Netherlands)

    Polder, R.B.; Rooij, M.R. de

    2005-01-01

    This article presents a series of investigations on six concrete structures along the North Sea coast in The Netherlands. They had ages between 18 and 41 years and most of them were made using Blast Furnace Slag cement. Visual inspections showed corrosion damage in only one structure, related to

  20. Durability of marine concrete structures - field investigations and modelling

    NARCIS (Netherlands)

    Polder, R.B.; Rooij, M.R. de

    2006-01-01

    This article presents a series of investigations on six concrete structures along the North Sea coast in The Netherlands. They had ages between 18 and 41 years and most of them were made using Blast Furnace Slag cement. Visual inspections showed corrosion damage in only one structure, related to

  1. Investigations on structural disorder-induced modifications in the ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 39; Issue 4. Investigations on structural disorder-induced ... Structural studies using X-ray diffraction (XRD) measurements confirmed the single phasic nature of all the samples without any detectable impurities. The A-site size disorder ( σ 2 A) increased from 3.81 × 10 ...

  2. Molecular characterization of myoglobin from Sciurus vulgaris meridionalis: Primary structure, kinetics and spectroscopic studies.

    Science.gov (United States)

    Di Giuseppe, Antonella M A; Russo, Luigi; Russo, Rosita; Ragucci, Sara; Caso, J Valentina; Isernia, Carla; Chambery, Angela; Di Maro, Antimo

    2017-05-01

    Myoglobins (Mbs) are heme-proteins involved in dioxygen storage necessary for metabolic respiration. Mbs are intensely investigated as archetype to investigate structure/function relationship in globular proteins. In this work, the myoglobin from Sciurus vulgaris meridionalis has been for the first time isolated and purified with a high yield and homogeneity. The primary structure characterization has been performed by applying a strategy based on high resolution tandem mass spectrometry. Proximal (position 93, α-helix F8) and distal (position 64, α-helix E7) histidinyl residues as well as most of the amino acid residues (i.e., Leu29, Lys45, Thr67, Val68) involved in the autoxidation mechanism are conserved in the squirrel Mb. The structural and dynamical properties of the squirrel Mb have been also deeply investigated by CD, NMR. Furthermore, molecular dynamics studies of Mbs from different species have been performed. In addition, the functional properties of squirrel Mb have been characterized by determining its autoxidation kinetic and thermal stability in comparison with crested porcupine and reindeer Mbs. Interestingly, a higher autoxidation rate was revealed for squirrel Mb with respect to reindeer and crested porcupine Mbs. Even considering the very similar structural fold, molecular dynamics data show a higher conformational mobility of squirrel Mb with respect to reindeer and crested porcupine. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Influence of the molecular structure on hydrolyzability of epoxy resins

    International Nuclear Information System (INIS)

    Pays, M.F.

    1996-01-01

    EDF has decided to use glass reinforced composites for certain pipework in Pressurized Water Reactors (service water, emergency-supplied service water, fine pipe works, etc...) as a replacement for traditional materials. In practice, steel is prone to rapid corrosion in these circuits; introducing composites could prove economically viable if their long term behaviour can be demonstrated. However, composite materials can undergo deterioration in service through hydrolysis of the resin or the fibre-matrix interface. Different resins can be chosen depending on the programmed use. A first study has covered the hydrolyzability of polyester and vinyl ester resins. The present document undertakes the resistance to hydrolysis of epoxy resins, concentrating on those reputed to withstand high temperatures. This research uses model monomer, linking the molecular structure of the materials to their resistance to hydrolysis. (author)

  4. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  5. Hamiltonian flow over saddles for exploring molecular phase space structures

    Science.gov (United States)

    Farantos, Stavros C.

    2018-03-01

    Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

  6. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  7. Shear response of grain boundaries with metastable structures by molecular dynamics simulations

    Science.gov (United States)

    Zhang, Liang; Lu, Cheng; Shibuta, Yasushi

    2018-04-01

    Grain boundaries (GBs) can play a role as the favored locations to annihilate point defects, such as interstitial atoms and vacancies. It is thus highly probable that different boundary structures can be simultaneously present in equilibrium with each other in the same GB, and thus the GB achieves a metastable state. However, the structural transition and deformation mechanism of such GBs are currently not well understood. In this work, molecular dynamics simulations were carried out to study the multiple structures of a Σ5(310)/[001] GB in bicrystal Al and to investigate the effect of structural multiplicity on the mechanical and kinetic properties of such a GB. Different GB structures were obtained by changing the starting atomic configuration of the bicrystal model, and the GB structures had significantly different atomic density. For the Σ5(310) GB with metastable structures, GB sliding was the dominant mechanism at a low temperature (T = 10 K) under shear stress. The sliding mechanism resulted from the uncoordinated transformation of the inhomogeneous structural units. The nucleation of voids was observed during GB sliding at the low temperature, and the voids subsequently evolved to a nanocrack at the boundary plane. Increasing the temperature can induce the structural transition of local GB structures and can change their overall kinetic properties. GB migration with occasional GB sliding dominated the deformation mechanism at elevated temperatures (T = 300 and 600 K), and the migration process of the metastable GB structures is closely related to the thermally assisted diffusion mechanism.

  8. Raman spectroscopy based investigation of molecular changes associated with an early stage of dengue virus infection

    Science.gov (United States)

    Bilal, Maria; Bilal, Muhammad; Saleem, Muhammad; Khurram, Muhammad; Khan, Saranjam; Ullah, Rahat; Ali, Hina; Ahmed, Mushtaq; Shahzada, Shaista; Ullah Khan, Ehsan

    2017-04-01

    Raman spectroscopy based investigations of the molecular changes associated with an early stage of dengue virus infection (DENV) using a partial least squares (PLS) regression model is presented. This study is based on non-structural protein 1 (NS1) which appears after three days of DENV infection. In total, 39 blood sera samples were collected and divided into two groups. The control group contained samples which were the negative for NS1 and antibodies and the positive group contained those samples in which NS1 is positive and antibodies were negative. Out of 39 samples, 29 Raman spectra were used for the model development while the remaining 10 were kept hidden for blind testing of the model. PLS regression yielded a vector of regression coefficients as a function of Raman shift, which were analyzed. Cytokines in the region 775-875 cm-1, lectins at 1003, 1238, 1340, 1449 and 1672 cm-1, DNA in the region 1040-1140 cm-1 and alpha and beta structures of proteins in the region 933-967 cm-1 have been identified in the regression vector for their role in an early stage of DENV infection. Validity of the model was established by its R-square value of 0.891. Sensitivity, specificity and accuracy were 100% each and the area under the receiver operator characteristic curve was found to be 1.

  9. Changes in molecular structure and properties of irradiated polymers of different compositions - ESR and NMR study

    International Nuclear Information System (INIS)

    Carswell-Pomerantz, T.; Babanalbandi, A.; Dong, L.; Hill, D.J.T.; Perera, M.C.S.; Pomery, P.J.; Saadat, G.; Whittaker, A.K.

    1999-01-01

    Investigations of molecular structural changes in polymers during exposure to high energy radiation is the long term interest of the Polymer Materials and Radiation Group at the University of Queensland. Recently, the group had looked at a range of polymers including natural and synthetic rubbers, methacrylates and polyesters. The objective of the work has been to investigate the relationships between polymer structure and sensitivity towards high energy radiation, including gamma radiation. This report will focus on the Electron Spin Resonance (ESR) and Nuclear Magnetic Resonance (NMR) studies of the effects of gamma irradiation on these polymers. Other methods such as Gas Chromatography (GC), Gel Permeation Chromatography (GPC), Fourier Transformed Infra Red (FTIR), Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA) and Dynamic Mechanical Analysis (DMA) have also been used as these methods combine with ESR and NMR, to provide a more complete picture of the mechanism of the structural changes. (author)

  10. Di- and sesquiterpenoids from Cystoseira genus: structure, intra-molecular transformations and biological activity.

    Science.gov (United States)

    Gouveia, Vera; Seca, Ana M L; Barreto, M Carmo; Pinto, Diana C G A

    2013-06-01

    Natural products have been the single most productive source of leads for the development of drugs, because of the great variety of their chemical structures. Previous chemical investigation of members of the genus Cystoseira resulted in the discovery of various bioactive secondary metabolites. The secondary metabolites isolated and characterized are very interesting, both from the biological activity and structural complexity points of view, which make this genus an attractive target for further investigations. The present review covers the research progress on natural products isolated from this genus since January 1995 until now, concerning the isolation and structural elucidation of the secondary metabolites from Cystoseira species. In this contribution significant biological properties are briefly discussed. Simultaneously, we gradually construct an intra-molecular pathway that logically interrelates the isolated compounds.

  11. Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

  12. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  13. 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.

  14. Molecular structure of tetramethylgermane from gas electron diffraction

    Science.gov (United States)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  15. Bonding and structure in dense multi-component molecular mixtures.

    Science.gov (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  16. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun, E-mail: chjsong@zzu.edu.cn; Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn

    2014-10-15

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking.

  17. Structural investigation of aroylhydrazones in dimethylsulphoxide/water mixtures

    Science.gov (United States)

    Galić, Nives; Dijanošić, Adriana; Kontrec, Darko; Miljanić, Snežana

    Molecular structures of aroylhydrazones derived from salicylaldehyde, o-vanilin and nicotinic acid hydrazide in DMSO and DMSO/H2O mixtures have been studied by NMR, UV-Vis, ATR and Raman spectroscopy. The addition of water to the system did not induce the tautomeric conversion of the existing form constituted of the ketoamino hydrazide part and the enolimino aldehyde part, but it was involved in the formation of hydrated molecules. Vibrational spectra (ATR and Raman) clearly indicated hydrogen bonding of the studied hydrazones through the carbonyl, amino and hydroxyl groups with water molecules. Increasing the water content conversion from E to Z isomer was not observed.

  18. Retinal structure, function, and molecular pathologic features in gyrate atrophy.

    Science.gov (United States)

    Sergouniotis, Panagiotis I; Davidson, Alice E; Lenassi, Eva; Devery, Sophie R; Moore, Anthony T; Webster, Andrew R

    2012-03-01

    To describe phenotypic variability and to report novel mutational data in patients with gyrate atrophy. Retrospective case series. Seven unrelated patients (10 to 52 years of age) with clinical and biochemical evidence of gyrate atrophy. Detailed ophthalmologic examination, fundus photography, fundus autofluorescence (FAF) imaging, spectral-domain optical coherence tomography, and microperimetry testing were performed. The coding region and intron-exon boundaries of ornithine aminotransferase (OAT) were analyzed. OAT mRNA was isolated from peripheral blood leucocytes of 1 patient and analyzed. OAT mutation status and resultant clinical, structural, and functional characteristics. Funduscopy revealed circular areas of chorioretinal atrophy, and FAF imaging showed sharply demarcated areas of increased or preserved signal in all 7 patients. Spectral-domain optical coherence tomography revealed multiple intraretinal cystic spaces and hyperreflective deposit in the ganglion cell layer of all study subjects. Round tubular, rosette-like structures located in the outer nuclear layer of the retinae of the 4 older patients were observed (termed outer retinal tubulation). Thickening was evident in the foveolae of younger patients, despite the posterior pole appearing relatively preserved. Macular function, assessed by microperimetry, was preserved over areas of normal or increased autofluorescence. However, sensitivity was reduced even in structurally intact parts of the retina. The molecular pathologic features were determined in all study subjects: 9 mutations, 4 novel, were detected in the OAT gene. OAT mRNA was isolated from blood leukocytes, and monoallelic expression of a mutated allele was demonstrated in 1 patient. Fundus autofluorescence imaging can reveal the extent of neurosensory dysfunction in gyrate atrophy patients. Macular edema is a uniform finding; the fovea is relatively thick in early stages of disease and retinal tubulation is present in advanced disease

  19. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino

    2002-01-01

    by titration calorimetry. A simple dimer dissociation model was used to derive the information about the heat and the constant of dissociation from asphaltenes of Mexico and Alaska obtained from the calorimetric data. The association enthalpies calculated were found to be in excellent agreement with those...... bond mechanism depends on the heteroatoms involved, the extension of the aromatic regions, and the steric interference present in the asphaltene molecules. The simulation results have been compared with experimental values of enthalpy of association of two different petroleum asphaltenes obtained...... measured, although the simulation only employed the interaction between averaged molecular structures....

  20. An NMR Investigation of Phase Structure and Chain Dynamics in the Polyethylene/Montmorillonite Nanocomposites

    Directory of Open Access Journals (Sweden)

    Wei Li

    2013-01-01

    Full Text Available Novel exfoliated and interacted polyethylene (PE/montmorillonite (MMT nanocomposites prepared by in situ polymerization were characterized by solid-state nuclear magnetic resonance (NMR. The phase structure and molecular mobility were investigated by proton and carbon NMR under static and magic-angle spinning (MAS conditions. The results showed that incorporation of MMT layer enhanced the polyethylene crystallinity behavior. The chain mobility of crystalline phase, interphase and amorphous phase was hindered in the nanocomposites. The phase structure and chain dynamics were also investigated upon changing the temperature. The orthorhombic and monoclinic phases were detected according to the 13CP/MAS NMR. Quantitative characterization of the phase structure was also conducted by 13C DP/MAS upon changing the temperature. Finally, the difference in the phase structure and chain dynamics in each phase of PE/nanocomposites was compared based on the NMR results when fiber filler was introduced.

  1. The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

    Directory of Open Access Journals (Sweden)

    Benjamin Allen

    2015-02-01

    Full Text Available Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

  2. Performance based investigations of structural systems under fire

    DEFF Research Database (Denmark)

    Gentili, Filippo; Crosti, Chiara; Giuliani, Luisa

    2010-01-01

    Prescriptive measures and procedures developed over the past here are mostly aimed at preventing structural failures of single elements for the time required for the evacuation. The response to fire and fire effects of the structural system as a whole remains often unknown and the survival of the...... structures are presented and discussed, with particular attention to methodological aspects. The effects of different assumptions in the modeling and in the definition of the collapse are highlighted, as critical aspects of a performance-based investigation....... these kinds of events, the mitigation of possible collapse induced by fire should be achieved. In this respect, a performance-based investigation of the structure aimed at highlight fire effects and fire-induced collapse mechanisms becomes of interest. In the paper collapse mechanisms of some simple...

  3. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    International Nuclear Information System (INIS)

    Eisenberg, David S.

    2008-01-01

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  4. Synthesis, characterization, crystal structure and quantum chemical investigations of three novel coumarin-benzenesulfonohydrazide derivatives

    Science.gov (United States)

    Chethan Prathap, K. N.; Lokanath, N. K.

    2018-04-01

    Coumarin derivatives are an important class of heterocyclic compounds due to their physical and biological properties. Coumarin derivatives have been identified with many significant electro-optical properties and biological activities. Three novel coumarin derivatives containing benzene sulfonohydrazide group were synthesized by condensation reaction. The synthesized compounds were characterized by various spectroscopic techniques (Mass, 1H/13C NMR and FTIR). Thermal and optical properties were investigated by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and UV-Vis spectroscopic studies. Finally their structures were confirmed by single crystal X-ray diffraction (XRD) studies. The three compounds exhibit diverse intermolecular interactions, as observed by the crystal packing and Hirshfeld surface analysis. Further, their structures were optimized by density functional theory (DFT) calculations using B3LYP hybrid functionals with 6-311G+(d,p) level basis set. The Mulliken charge, molecular electrostatic potential (MEP), frontier molecular orbitals (HOMO-LUMO) were investigated. The experimentally determined parameters were compared with those calculated theoretically and they complement each other with a very good correlation. The transitions among the molecular orbitals were investigated using time-dependent density functional theory (TD-DFT) and the electronic absorption spectra obtained showed very good agreement with the experimentally measured UV-Vis spectra. Furthermore, non-linear optical (NLO) properties were investigated by calculating polarizabilities and hyperpolarizabilities. All three compounds exhibit significantly high hyperpolarizabilities compared to the reference material urea, which makes them potential candidates for NLO applications.

  5. X-ray diffraction, neutron diffraction and analysis of molecular structures

    International Nuclear Information System (INIS)

    Fontecilla-Camps, J.C.

    1997-01-01

    The only method that is capable to show the atomic structure of most of macromolecules is the X ray diffraction; neutron diffraction is mostly used for the localization of hydrogen atoms, too light to be detected by X ray diffraction. With the growing number of known structures, the molecular crystallographic study may combine the molecular replacement technique and the co-crystallization method, or use the new Laue method, and leads to the functional and topological analysis of biological molecular structures

  6. Molecular structure and modeling studies of azobenzene derivatives containing maleimide groups.

    Science.gov (United States)

    Cojocaru, Corneliu; Airinei, Anton; Fifere, Nicusor

    2013-01-01

    The molecular orbital calculations have been carried out to investigate the structure and stability of (E) / (Z) isomers of some azobenzene derivatives containing maleimide groups. A special attention has been devoted to the compound (E)-1, (E)-1-(4-(phenyldiazenyl)phenyl)-1H-pyrrole-2,5-dione, for which the available crystallographic experimental data have been used to validate the modeling structures computed at the theoretical levels AM1, PM3, RHF/6-31+G(d,p) and B3LYP/6-31+G(d,p). To this end, the discrepancy between experimental and calculated structural parameters has been ascertained in terms of root-mean-square deviation (RMSD). The quantum calculations at the level RHF/6-31+G(d,p) yield the most accurate results on (E)-1 structure giving a deviation error from crystallographic data of about 5.00% for bond lengths and 0.97% for interatomic angles. The theoretical electronic absorption spectra of azobenzene derivatives of concern have been computed by means of configuration-interaction method (CI) at the level of semi-empirical Hamiltonians (AM1 and PM3). Likewise, the molecular energy spectra, electrostatic potential and some quantitative structure activity relationship (QSAR) properties of studied molecules have been computed and discussed in the paper.

  7. Light-operated machines based on threaded molecular structures.

    Science.gov (United States)

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  8. Synthesis and computer-aided structural investigation of potentially photochromic spirooxazines

    International Nuclear Information System (INIS)

    Chi, L.

    2000-03-01

    Quantum mechanical methods, PPP-MO and ZINDO, were used to predict the electronic spectra of the ring-opened forms and ring-closed forms respectively of a series of spirooxazines. Molecular mechanics was used to optimise the molecular geometry and to calculate the molecular final energy (steric energy) using the MM2 force field method. An all-valence-electron quantum mechanical method was employed to calculate the heats of formation using AM1 parameters, and the data were used to provide a measure of the stability of the molecules. This computer-aided structural investigation has provided an enhanced understanding of the spirooxazine system and methods with the potential to predict photochromic behaviour have emerged. The synthesis of a series of heterocyclic analogues of the well-known spironaphthoxazines based on quinolines, coumarin and pyrazolones were attempted. The properties of the compounds obtained were correlated with the results of the calculations. (author)

  9. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  10. On-line system for investigation of atomic structure

    International Nuclear Information System (INIS)

    Amus'ya, M.Ya.; Chernysheva, L.V.

    1983-01-01

    A description of the on-line ATOM system is presented that enables to investigate the structure of atomic electron shells and their interactions with different scattering particles-electrons, positronse photons, mesons - with the use of computerized numerical solutions. The problem is stated along with mathematical description of atomic properties including theoretical and numerical models for each investigated physical process. The ATOM system structure is considered. The Hartree-Fock method is used to determine the wave functions of the ground and excited atomic states. The programs are written in the ALGOL langauge. Different atomic characteristics were possible to be calculated for the first time with an accuracy exceeding an experimental one

  11. On the molecular structure, vibrational spectra, HOMO-LUMO, molecular electrostatic potential, UV-Vis, first order hyperpolarizability, and thermodynamic investigations of 3-(4-chlorophenyl)-1-(1yridine-3-yl) prop-2-en-1-one by quantum chemistry calculations

    Science.gov (United States)

    Rahmani, Rachida; Boukabcha, Nourdine; Chouaih, Abdelkader; Hamzaoui, Fodil; Goumri-Said, Souraya

    2018-03-01

    A recent experimental study has allowed synthesis of a new organic nonlinear optical material 3-(4-chlorophenyl)-1-(pyridin-3-yl)prop-2-en-1-one(CPP) with a high second harmonic generation efficiency. We apply density functional theory (DFT, GGA and B3LYP) and Hartree-Fock (HF) methods to calculate the vibrational wavenumbers. They are assigned with by using the potential energy distribution method. The calculated first hyperpolarizability of the title compound is comparable with the reported values of similar derivatives and 25 times that of the standard NLO material urea. The HOMO-LUMO calculations lead to consider GGA-PBE as the best functional to determine the electronic band gap of CPP molecule. We complete this study with assignment of the vibrational modes and perform a comparison with the experimental results. The analysis of MEP map shows that the most reactive site of the CPP molecule is the site containing the oxygen atom. Furthermore, because of the enhancement of molecular vibration within the CPP molecule, the thermodynamic parameters are increasing with the increase of temperature. The FTIR, Raman and NMR spectra are calculated using DFT approach and corroborate the experimental available data.

  12. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  13. Structural and vibrational dynamics of molecular solids under variable temperature and pressure

    Science.gov (United States)

    Schatschneider, Bohdan Hindulak

    An ultra-high resolution FTIR study (0.01cm-1) coupled with molecular simulations of para-terphenyl (PTP) under variable temperatures and pressures has been conducted in an effort to better understand the molecular dynamics (MD) of organic molecular crystals. PTP's use as an electrooptic material and as a host matrix for single molecular spectroscopy has created significant interest into the systems dynamics under variable conditions. Our high resolution study reveals many structure and dynamics changes in the PTP matrix as a result of changes in temperature and pressure. Further spectroscopic analysis using MD verifies these structural and dynamics alterations. Accurately modeled pressure and temperature phase transitions between the low-temperature low-pressure triclinic phase and the high-pressure high-temperature monoclinic phase of PTP was accomplished by a one-parameter optimization of the torsion potential component of the polymer consistent force field (PCFF) along with incorporation of COMPASS' (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies) non-bond parameters. Initial MD simulations implementing the universal force field COMPASS could not adequately model the experimental crystal structure at 113K, nor could it reproduce the known transition temperature at ambient pressure or yield a well-defined transition pressure at low temperature. Therefore, we needed to create a new potential which was shown to reproduce the solid-solid phase transitions. The previously never simulated pressure induced solid-solid phase transition of PTP at low temperature (20K) and varying pressures (0-1GPa) was modeled. The symmetry based crystal/molecular rearrangement shows a compression and distortion of the unit cell and corresponding angles along with a flattening of the once twisted PTP molecules at high pressures (>0.5GPa). A fourth crystal phase (Phase IV) has been successfully identified through analysis of the individual molecule

  14. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2013-07-01

    Full Text Available Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  15. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    Science.gov (United States)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  16. Investigation of the Josephin Domain protein-protein interaction by molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Marco A Deriu

    Full Text Available Spinocerebellar ataxia (SCA 3, the most common form of SCA, is a neurodegenerative rare disease characterized by polyglutamine tract expansion and self-assembly of Ataxin3 (At3 misfolded proteins into highly organized fibrillar aggregates. The At3 N-terminal Josephin Domain (JD has been suggested as being responsible for mediating the initial phase of the At3 double-step fibrillogenesis. Several issues concerning the residues involved in the JD's aggregation and, more generally, the JD clumping mechanism have not been clarified yet. In this paper we present an investigation focusing on the JD protein-protein interaction by means of molecular modeling. Our results suggest possible aminoacids involved in JD contact together with local and non-local effects following JD dimerization. Surprisingly, JD conformational changes following the binding may involve ubiquitin binding sites and hairpin region even though they do not pertain to the JD interaction surfaces. Moreover, the JD binding event has been found to alter the hairpin open-like conformation toward a closed-like arrangement over the simulated timescale. Finally, our results suggest that the JD aggregation might be a multi-step process, with an initial fast JD-JD binding mainly driven by Arg101, followed by slower structural global rearrangements involving the exposure to the solvent of Leu84-Trp87, which might play a role in a second step of JD aggregation.

  17. Structure of solvent-free grafted nanoparticles: Molecular dynamics and density-functional theory

    KAUST Repository

    Chremos, Alexandros

    2011-01-01

    The structure of solvent-free oligomer-grafted nanoparticles has been investigated using molecular dynamics simulations and density-functional theory. At low temperatures and moderate to high oligomer lengths, the qualitative features of the core particle pair probability, structure factor, and the oligomer brush configuration obtained from the simulations can be explained by a density-functional theory that incorporates the configurational entropy of the space-filling oligomers. In particular, the structure factor at small wave numbers attains a value much smaller than the corresponding hard-sphere suspension, the first peak of the pair distribution function is enhanced due to entropic attractions among the particles, and the oligomer brush expands with decreasing particle volume fraction to fill the interstitial space. At higher temperatures, the simulations reveal effects that differ from the theory and are likely caused by steric repulsions of the expanded corona chains. © 2011 American Institute of Physics.

  18. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow

    DEFF Research Database (Denmark)

    Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear...... of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex...... rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates...

  19. Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics.

    Science.gov (United States)

    Jezierska, Aneta; Panek, Jarosław J

    2009-06-01

    The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure. 2008 Wiley Periodicals, Inc.

  20. A quantum chemical investigation of the electronic structure of thionine.

    Science.gov (United States)

    Rodriguez-Serrano, Angela; Daza, Martha C; Doerr, Markus; Marian, Christel M

    2012-02-01

    We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of π→π* (S(1), S(2), T(1), T(2)) and n→π* (S(3), T(3)) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S(1) and T(1) states (~0.02 eV). The relaxation effects on the energies of S(2) and T(2) are moderate (0.14-0.20 eV). The very small emission energy results in a very low fluorescence rate. While we were not able to locate the energetic minimum of the S(3) state, we found a non-planar minimum for the T(3) state with an energy which is very close to the energy of the S(1) minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→π* states S(3) and T(3) are strongly blueshifted (0.33 and 0.46 eV), while the π→π* states are only slightly affected (<0.06 eV). This journal is © The Royal Society of Chemistry and Owner Societies 2012

  1. X-ray diffraction and molecular-dynamics studies: Structural analysis of phases in diglyceride monolayers

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Larsen, Niels Bent; Bjørnholm, T.

    1998-01-01

    We report a detailed structural analysis of the phases of 1,2-sn-dipalmitoylglycerol Langmuir monolayers at room temperature. Pressure-induced transitions have been investigated by combination of molecular-dynamics simulations and grazing-incidence x-ray diffraction (XRD). The diglyceride film......; At the lowest pressure the tilt angle reaches approximate to 14 degrees in a direction close to a nearest neighbor direction. Both arrangements of the alkyl chains are confirmed by XRD. For higher order and fractional order Bragg peaks, simulations predict higher intensities than observed with XRD. This may...

  2. Theoretical studies on the molecular structure, conformational preferences, topological and vibrational analysis of allicin

    Science.gov (United States)

    Durlak, Piotr; Berski, Sławomir; Latajka, Zdzisław

    2016-01-01

    The molecular structure, conformational preferences, topological and vibrational analysis of allicin has been investigated at two different approaches. Calculations have been carried out on static (DFT and MP2) levels with an assortment of Dunning's basis sets and dynamic CPMD simulations. In this both case within the isolated molecule approximation. The results point out that at least twenty different conformers coexist on the PES as confirmed by the flexible character of this molecule. The topological analysis of ELF showed very similar nature of the Ssbnd S and Ssbnd O bonds. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed.

  3. MICRO-STRUCTURAL INVESTIGATION OF SOME ARTIFACTS DISCOVERED AT POROLISSUM

    Directory of Open Access Journals (Sweden)

    MUNTEANU Mihai

    2014-09-01

    Full Text Available the paper presents the investigation of two fragments of roman bronze artefacts, discovered during archaeological works performed at Porolissum, an important military and economical point on the northern limes of Dacia Province. One of the analyzed fragments (Mi1 was taken from a consistent fragment of a Roman bronze statue, while the second (Mi2 was among a lot of small metal pieces, discovered in the same investigated area. Using highly sophisticated micro-structural analysing techniques – X-Ray diffraction, the paper investigates the possibility that the Mi2 fragment may have belonged to the same statue from which the sample Mi1 was taken

  4. The Latent Structure of Psychopathy in Youth: A Taxometric Investigation

    Science.gov (United States)

    Vasey, Michael W.; Kotov, Roman; Frick, Paul J.; Loney, Bryan R.

    2005-01-01

    Using taxometric procedures, the latent structure of psychopathy was investigated in two studies of children and adolescents. Prior studies have identified a taxon (i.e., a natural category) associated with antisocial behavior in adults as well as children and adolescents. However, features of this taxon suggest that it is not psychopathy but…

  5. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination...

  6. Structural appraisal of the Gadag schist belt from gravity investigations

    Indian Academy of Sciences (India)

    Semi-detailed gravity investigations were carried out over an area of approximately 2750 sq km with maximum N-S and E-W extents of 55 and 50km respectively in the Gadag region in the Dharwar craton with a view to obtain a clearer perception of the structural configuration of the region. From qualitative analysis of the ...

  7. Spectral investigation of a complex space charge structure in plasma

    International Nuclear Information System (INIS)

    Gurlui, S.; Dimitriu, D. G.; Ionita, C.; Schrittwieser, R. W.

    2009-01-01

    Complex space charge structures bordered by electrical double layers were spectrally investigated in argon plasma in the domain 400-1000 nm, identifying the lines corresponding to the transitions from different excited states of argon. The electron excitation temperature in the argon atoms was estimated from the spectral lines intensity ratio. (authors)

  8. Investigation on pore structure and small-scale agglomeration ...

    Indian Academy of Sciences (India)

    Investigation on pore structure and small-scale agglomeration behaviour in liquid phase sintered. SiC using small angle neutron scattering. D SEN1,∗, J BAHADUR1, S MAZUMDER1, T MAHATA2, M SYAMBABU2 and. P K SINHA2. 1Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.

  9. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

    Science.gov (United States)

    Walsh, Tiffany R

    2017-07-18

    An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

  10. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured using...

  11. Effects of molecular structural variants on serum Krebs von den Lungen-6 levels in sarcoidosis

    Directory of Open Access Journals (Sweden)

    Shigemura Masahiko

    2012-07-01

    Full Text Available Abstract Background Serum Krebs von den Lungen-6 (KL-6, which is classified as human mucin-1 (MUC1, is used as a marker of sarcoidosis and other interstitial lung diseases. However, there remain some limitations due to a lack of information on the factors contributing to increased levels of serum KL-6. This study was designed to investigate the factors contributing to increased levels of serum KL-6 by molecular analysis. Methods Western blot analysis using anti-KL-6 antibody was performed simultaneously on the bronchoalveolar lavage fluid (BALF and serum obtained from 128 subjects with sarcoidosis. Results KL-6/MUC1 in BALF showed three bands and five band patterns. These band patterns were associated with the MUC1 genotype and the KL-6 levels. KL-6/MUC1 band patterns in serum were dependent on molecular size class in BALF. Significantly increased levels of serum KL-6, serum/BALF KL-6 ratio and serum soluble interleukin 2 receptor were observed in the subjects with influx of high molecular size KL-6/MUC1 from the alveoli to blood circulation. The multivariate linear regression analysis involving potentially relevant variables such as age, gender, smoking status, lung parenchymal involvement based on radiographical stage and molecular size of KL-6/MUC1 in serum showed that the molecular size of KL-6/MUC1 in serum was significant independent determinant of serum KL-6 levels. Conclusions The molecular structural variants of KL-6/MUC1 and its leakage behavior affect serum levels of KL-6 in sarcoidosis. This information may assist in the interpretation of serum KL-6 levels in sarcoidosis.

  12. MOLECULAR STRUCTURE OF AMYOTROPHIC LATERAL SCLEROSIS IN RUSSIAN POPULATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Abramycheva

    2016-01-01

    Full Text Available Materials and methods. 285 Russian patients with amyotrophic lateral sclerosis (ALS including 260 patients with a sporadic form and 25 with a familial form were examined for mutations in SOD1, C9orf72, TARDBP,  ANG and other genes and the presence of associations among polymorphic sites in ATXN2 (polyCAG and VEGF (-2578С/А genes.Molecular genetic analysis was performed using direct sequencing, fragment analysis and real-time polymerase chain reaction. On the last stage, rare ALS candidate genes were evaluated using a next generation sequencing (NGS panel.Results. Total rate of the identified mutations in the examined ALS cohort was 9.5 %. The most frequently observed defects were mutations in the SOD1 (24.0 % in familial ALS and 4.6 % in sporadic ALS and C9orf72 (pathological hexanucleotide repeat expansion was identified in 1.8 % cases of ALS, all sporadic genes. The TARDBP gene didn’t contain any mutations, though in the ALS group deletion c.715-126delG located in intron 5 of the TARDBP gene was significantly over-represented – 38.0 % vs. 26.6 % (χ2 = 13.17; р = 0.002. Mutations in the ANG gene were identified in 1.05 % of ALS patients (all cases were sporadic. In 1 (0.35 % sporadic case a G1082A mutation in the DCTN1 gene was identified. The examined group significantly more frequently carried a risk allele of the ATXN2 gene with an “intermediate” (28–33  number of CAG repeats – 5.0 % vs. 1.7 % in the control group (χ2 = 3.89; р = 0.0486. In Russian ALS patients, an association between the disease and the presence of a risk А-allele and homozygote genotype А/А of -2578С/А polymorphism in the VEGF gene was identified (χ2 = 7.14; р = 0.008 and χ2 = 13.46; р = 0.001 for the rates in the ALS population and in the control population, respectively, which is confirmed by the odds ratio.Conclusion. In the current article, molecular structure of ALS in the Russian population was examined, rates of individual genetic forms

  13. Structural investigation of e-beam cured epoxy resins through solid state NMR

    International Nuclear Information System (INIS)

    Alessi, Sabina; Spinella, Alberto; Caponetti, Eugenio; Dispenza, Clelia; Spadaro, Giuseppe

    2012-01-01

    In this paper the network structure of e-beam cured DGEBF based epoxy resins is investigated. Two epoxy systems, having different reactivity and cured in different process conditions, were analyzed through solid state NMR spectroscopy. The analysis shows that the more reactive system has higher cross-linking density and higher uniformity of network distribution. Similar information were obtained, in a previous work, on the same systems through dynamic mechanical thermal analysis. It is worth noting that unlike DMTA tests, which interfere with the molecular structure of the analyzed material, due to the heating during the analysis itself, more reliable information, without any artefact, are obtained by solid state NMR, carried out at constant room temperature. - Highlights: ► The structure of two e-beam cured epoxy systems is investigated through solid state NMR. ► The aim is to have direct information about the structure without inducing modifications. ► The different molecular structures are able to emphasize the response of solid state NMR. ► T 1 H, T 1ρ H and T CH measurements indicate different cross-linking degrees. ► The NMR results are in agreement with DMTA analysis performed in a previous paper.

  14. Correlation between the molecular structure and the inhibiting effect of some benzimidazole derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Niamien, P.M., E-mail: niamienfr@yahoo.fr [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Essy, F.K.; Trokourey, A.; Yapi, A.; Aka, H.K. [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Diabate, D. [Laboratoire de chimie physique, Universite de Cocody-Abidjan, 22 BP 582 Abidjan (Cote d' Ivoire); Institut UTINAM-UMR CNRS 6213 Equipe capteurs et membranes 25013 Besancon cedex, 22 BP 582 Abidjan 22 (Cote d' Ivoire)

    2012-09-14

    Quantum chemical parameters of 2-thiobenzylbenzimidazole (TBBI), 2-thiomethylbenzimidazole (TMBI), and 2-mercaptobenzimidazole (MBI) were calculated. The correlation between molecular structure of these compounds and their inhibition efficiency IE (%) against copper corrosion in 1 M HNO{sub 3} was found by considering Density Functional Theory DFT/B3LYP/6-31G (d, p) level. The properties most relevant to their potential action as corrosion inhibitors have been calculated: highest occupied molecular orbital energy (E{sub HOMO}), lowest unoccupied molecular orbital energy (E{sub LUMO}), energy gap ({Delta}E), dipole moment ({mu}) and parameters that provide informations about the chemical reactivity: electronegativity ({chi}), global hardness ({eta}), global softness ({sigma}) and electrophilicity index ({omega}). All calculations have been performed using the Gaussian 03W suite of programs. It was found that theoretical data support experimental results. -- Highlights: Black-Right-Pointing-Pointer Benzimidazole derivatives (TBBI, TMBI, MBI) as corrosion inhibitors of copper in 1 M HNO{sub 3}. Black-Right-Pointing-Pointer The inhibition process evaluated by weight loss indicates that the investigated compounds are good inhibitors of copper. Black-Right-Pointing-Pointer The inhibition efficiency is found to be in the following order: TBBI > TMBI > MBI. Black-Right-Pointing-Pointer The studied molecules adsorbed on the metal surface according to the Langmuir adsorption isotherm. Black-Right-Pointing-Pointer Most of the calculated molecular parameters by DFT/B3LYP/6-31G (d, p) show excellent correlation with the inhibition efficiency.

  15. Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Galo E. Balatti

    2017-10-01

    Full Text Available In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a peptides in water in the presence of a pre-equilibrated lipid bilayer; (b peptides inside the hydrophobic core of the membrane; and (c random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.

  16. Supramolecular macrocycles based on porphyrins- correlation of molecular structure and biological photoactivity

    International Nuclear Information System (INIS)

    Ion, R. M.; Oprea, F.; Bacinschi, Z.; Scarlat, F.; Scarlat, Fl.; Niculescu, V.I.R.

    2002-01-01

    Porphyrins and phthalocyanines are organic dyes which can be used as highly fluorescent species in laser technology, in photography, as radiation power indicators, as photosensitizers in photodynamic therapy of cancerous disease. Porphyrins constitute a class of the molecules which contain four pyrrole rings linked by the methane carbon bridges whereas the phthalocyanine molecules are composed of four indole units - pyrrole rings linked by nitrogen atoms conjugated with benzene rings. A large group of porphyrins and phthalocyanines can be chemically modified by introducing metal in the center of the pyrrole rings or by attaching the peripheral groups to the outer rings of the methane bridges or isoindole units, respectively. In this study five groups of tetraphenylporphyrins (TPP) and phthalocyanines (Pc) were investigated: - metal (Me)-free dyes without any substitutes, - non-substituted porphyrins and phthalocyanines but complexed with metal (Me) - Zn, Mg, Mn, Co, Cu, Pt, Pd, Pb and others, - metal-complexed dyes substituted with aromatic rings, - metal-complexed dyes substituted with fluorines, - metal-complexed dyes substituted with long organic chains (alkyl or alkyloxy). The difference in the TPP and Pc molecular structure, the kind of metal incorporated into the main molecular core or the variation in the peripheral groups attached to the molecular skeleton are expected to affect the effectiveness of dyes in photocurrent generation. Since there is a competition between the charge separation process and other deactivation processes in the molecule, in our study photochemical investigations (photodynamic action) are usually accompanied with the spectroscopic examinations (absorption, fluorescence- which give information on the (non-) radiative processes) of dyes. In the paper we have presented the review of our study on the correlation between the molecular structure of dyes and their photoactive properties. (authors)

  17. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    Science.gov (United States)

    Xiao, Xueliang; Hu, Jinlian

    2016-05-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

  18. A raman microprobe investigation of the molecular architecture of loblolly pine tracheids

    Science.gov (United States)

    James S. Bond; Rajai H. Atalla

    1999-01-01

    Our understanding of the molecular architecture of intact, native plant cell walls is very limited. Traditional methods of investigation disturb the tissue to varying degrees and conclusions based on these methods may be intimately related to the technique used. A promising new technique to study native-state organization is polarized Raman spectroscopy. In this...

  19. Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

    NARCIS (Netherlands)

    Esposito, Alessandro

    2006-01-01

    This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These

  20. Molecular biological methods (DGGE) as a tool to investigate nitrification inhibition in wastewater treatment.

    Science.gov (United States)

    Kreuzinger, N; Farnleitner, A; Wandl, G; Hornek, R; Mach, R

    2003-01-01

    Incomplete nitrification at an activated sludge plant for biological pre-treatment of rendering plant effluents led to a detailed investigation on the origin and solution of this problem. Preliminary studies revealed that an inhibition of ammonia oxidising microorganisms (AOM) by process waters of the rendering plant was responsible for the situation. We were able to show a correlation between the existence of specific AOM and nitrification capacity expressed as oxygen uptake rate for maximal nitrification (OURNmax). Only Nitrosospira sp. was found in the activated sludge of the rendering plant and another industrial wastewater treatment plant with problems in nitrification, while reference plants without nitrification problems showed Nitrosomonas spp. as the predominant ammonia oxidising bacteria. By accompanying engineering investigations and experiments (cross-feeding experiments, operation of a two-stage laboratory plant) with molecular biological methods (DGGE--Denaturing Gradient Gel Electrophoresis) we were able to elaborate an applicable solution for the rendering plant. Laboratory experiments with a two-stage process layout finally provided complete nitrification overcoming the inhibiting nature of process waters from the rendering plant. DGGE analysis of the second stage activated sludge from the laboratory plant showed a shift in population structure from Nitrosospira sp. towards Nitrosomonas spp. simultaneous to the increase of nitrification capacity. Nitrification capacities comparable to full-scale municipal wastewater treatment plants could be maintained for more than two months. As the design of wastewater treatment plants for nitrification is linked to the growth characteristics of Nitrosomonas spp., established criteria can be applied for the redesign of the full-scale plant.

  1. Investigation on the crystal growth, molecular structure and nonlinear optical susceptibilities of 2-[2-(4-Ethoxy-phenyl)-vinyl]-1-ethyl-stilbazolium iodide (EESI) by Z-scan technique using He-Ne laser for third-order nonlinear optical applications

    Science.gov (United States)

    Senthil, K.; Kalainathan, S.; Kondo, Y.; Hamada, F.; Yamada, M.

    2017-05-01

    Organic 2-[2-(4-Ethoxy-phenyl)-vinyl]-1-ethyl-stilbazolium iodide (EESI), a derivative of the stilbazolium family single crystal was synthesized by condensation method. Nearly perfect as-gown single crystals of EESI structure was confirmed by single-crystal X-ray diffraction studies. The crystal has a triclinic system with the space group P-1, the molecule consists of one pyridinium cation, one iodide anion, and 0·5H2O molecules. The nature of charge transfer, molecular properties, electrostatic potential map, and HOMO-LUMO energy gap of EESI have been theoretically investigated by Sparton'10 V1.0.1 program. The optical transparency of EESI was studied by Uv-Visible spectral analysis. The growth features were observed during the etching studies using a Carl Zeiss optical microscope (50X magnification). The mechanical behavior of the crystal was estimated by Vickers microhardness test, which shows reverse indentation size effect (RISE) with good mechanical stability. Both the dielectric constant and dielectric loss increases with the increasing temperature and attain almost constant at higher frequencies, which justify the crystal quality and essential parameter for electro-optic device applications. The complex impedance analysis explains the electrical property of EESI. TGA and DTA measurements determined the thermal stability of the grown crystal. Laser-induced damage threshold energy measurements exhibit that the excellent resistance with good threshold energy up to 2.08 GW/cm2 that was found to be more than that of some known organic and inorganic NLO crystals. Photoconductivity of EESI crystal confirms that the positive photoconductivity nature. Also, the third-order nonlinear optical (NLO) properties of EESI were investigated by using the single beam Z-scan technique under the Visible light (632.8 nm) region. The results show that EESI has effective third-order nonlinear optical property with the nonlinear refractive index n2 =1.787×10-11m2/W, third

  2. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations.

    Science.gov (United States)

    Shawon, Jakaria; Khan, Akib Mahmud; Rahman, Adhip; Hoque, Mohammad Mazharol; Khan, Mohammad Abdul Kader; Sarwar, Mohammed G; Halim, Mohammad A

    2016-10-01

    Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

  3. Molecular, structural, and phylogenetic analyses of Taxus chinensis JAZs.

    Science.gov (United States)

    Zhang, Meng; Chen, Ying; Nie, Lin; Jin, Xiaofei; Fu, Chunhua; Yu, Longjiang

    2017-07-15

    Taxus spp. are ancient gymnosperms that produce a unique secondary metabolite, namely, taxol, an anticancer drug. JAZ proteins are key regulators of the JA signaling pathway, which control taxol biosynthesis. However, the JAZ proteins of Taxus spp. are poorly studied. In this work, nine JAZ genes from Taxus chinensis were identified using our previous transcriptome data and named as TcJAZ1-TcJAZ9. Of these nine TcJAZ proteins, eight contain Jas and TIFY domains, and the Jas domain of TcJAZ6 is incomplete. Most TcJAZs and PsJAZs are not related to AtJAZs and OsJAZs. Phylogenetic analysis divided all JAZ proteins from Arabidopsis thaliana, Oryza sativa, Picea sitchensis, and T. chinensis into eight subgroups; gymnosperms JAZs were classified into subgroups V-VIII, and angiosperm JAZs were categorized into subgroups I-V. Three motifs of subgroups VI-VIII were identified in gymnosperm JAZs, indicating that gymnosperm JAZ proteins exhibit a different evolutionary process from those of angiosperms. The expression patterns of nine TcJAZs showed that TcJAZ2/3/8 was a key regulator, indicating their important roles in T. chinensis. Results revealed that gymnosperm JAZs differ from angiosperm JAZs in terms of molecular structure. Three novel conserved motifs were found in TcJAZs and PsJAZs. This study provides a basis for research on JA regulatory system in Taxus spp. and for elucidating the significance of JA signaling pathway to land plants. Copyright © 2017. Published by Elsevier B.V.

  4. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex

    KAUST Repository

    Anneser, Markus R.

    2016-02-26

    The dioxygen reactivity of a cyclic iron(II) tetra–NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(III) whereas in the latter case an oxide bridged Fe(III) dimer is formed. In acetone, an Fe(III)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(III)–O–Fe(III) dimer is formed from the Fe(III) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(II) complex in both solvents is a reversible process. For the regeneration of the initial Fe(II) complex both organic and inorganic reducing agents can be used.

  5. Pure and Modified Co-Poly(amide-12-b-ethylene oxide Membranes for Gas Separation Studied by Molecular Investigations

    Directory of Open Access Journals (Sweden)

    Luana De Lorenzo

    2012-06-01

    Full Text Available This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships.

  6. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    Science.gov (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  7. Murine transgenic embryonic stem cell lines for the investigation of sinoatrial node-related molecular pathways

    Directory of Open Access Journals (Sweden)

    Stefanie Schmitteckert

    2017-12-01

    Full Text Available The elucidation of molecular mechanisms that restrict the potential of pluripotent stem cells and promote cardiac lineage differentiation is of crucial relevance, since embryonic stem cells (ESCs hold great potential for cell based heart therapies. The homeodomain transcription factor Shox2 is essential for the development and proper function of the native cardiac pacemaker, the sinoatrial node. This prompted us to develop a cardiac differentiation model using ESC lines isolated from blastocysts of Shox2-deficient mice. The established cell model provides a fundamental basis for the investigation of molecular pathways under physiological and pathophysiological conditions for evaluating novel therapeutic approaches.

  8. Quasi- and inelastic neutron scattering to investigate the molecular dynamics of discotic molecules in the bulk

    Directory of Open Access Journals (Sweden)

    Krause Christina

    2015-01-01

    Full Text Available In- and quasielastic neutron scattering is employed to investigate both the vibrational density of states and the molecular dynamics of two homologous discotic liquid crystals (DLC with different length of the alkyl side chain based on a triphenylene derivate. For both compounds characteristic low frequency excess contributions to the vibrational density of states are found. Therefore it is concluded that these liquid crystals show a glass-like behaviour. Elastic scans further show that in these materials a rich molecular dynamics takes place.

  9. SUDDEN UNEXPLAINED JUVENILE DEATH AND THE ROLE OF MEDICOLEGAL INVESTIGATION: UPDATE ON MOLECULAR AUTOPSY

    Directory of Open Access Journals (Sweden)

    Antonina Argo

    2012-04-01

    Full Text Available In the past few years, contributions of molecular biology assays to the investigation of sudden juvenile death have permitted to clarify some of the pathogenetic aspects of sudden arrhythmic death, opening the way to preventive action on victims’ relatives. We reviewed literature on the genetics of sudden juvenile death, and on molecular biology assays performed on autoptic samples. Biological investigation permits the detection of genetic mutations underlying the susceptibility to sudden cardiac death of individuals with rare inherited forms of arrhythmia (Long QT Syndrome, Brugada Syndrome, Lev’s disease etc. through the analysis of critical sequences codifying for ion channel subunits (HERG, KvLQT1, MinK, Mirp1, SCN5A, KCNQ1, KCNH2, KCNE1, KCNE2. The main objective of post-mortem investigation in sudden juvenile death is the detection of treatable monogenic inherited disorders, in order to prevent further deaths among the relatives of the deceased patient.

  10. The Investigation of Structure Heterogeneous Joint Welds in Pipelines

    Directory of Open Access Journals (Sweden)

    Lyubimova Lyudmila

    2016-01-01

    Full Text Available Welding joints of dissimilar steels don’t withstand design life. One of the important causes of premature destructions can be the acceleration of steel structural degradation due to cyclic mechanical and thermal gradients. Two zones of tube from steel 12H18N9T, exhibiting the structural instability at early stages of the decomposition of a supersaturated solid austenite solution, were subjected to investigation. Methods of x-ray spectral and structure analysis, micro hardnessmetry were applied for the research. Made the following conclusions, inside and outside tube wall surfaces of hazardous zones in welding joint have different technological and resource characteristics. The microhardness very sensitive to changes of metal structure and can be regarded as integral characteristic of strength and ductility. The welding processes are responsible for the further fibering of tube wall structure, they impact to the characteristics of hot-resistance and long-term strength due to development of ring cracks in the welding joint of pipeline. The monitoring of microhardness and structural phase conversions can be used for control by changes of mechanical properties in result of post welding and reductive heat treatment of welding joints.

  11. INVESTIGATION OF STRUCTURAL AND MECHANICAL PROPERTIES OF FOUNDRY WASTES

    Directory of Open Access Journals (Sweden)

    D. N. Shabanov

    2006-01-01

    Full Text Available The purpose of the paper is to investigate utilization of foundry wastes for production of building materials. The paper shows how to solve the problem concerning recycling of wastes and economy of natural resources. Waste moulding sand and granulated cupola slag are considered in the paper. The paper has studied structural and mechanical properties of the investigated powders. Optimal ratios of the used material fi*actions ensuring obtaining of silicate brick that meets the requirements of the current standards have been determined in the paper. 

  12. Application of ellipsometric and interference methods in MOS structures investigations

    Energy Technology Data Exchange (ETDEWEB)

    Rzodkiewicz, W; Borowicz, L; Piskorski, K [Institute of Electron Technology, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)

    2007-04-15

    Changes in some electrical and photoelectric parameters in the plane of aluminum gate, particularly in the effective contact potential difference (ECPD or {phi}{sub MS} factor) have been observed in MOS System Studies Department of Institute of Electron Technology for the first time. It has been found that the MS distribution over the gate area has a characteristic domelike shape, with the highest values ate the center of the gate, lower at the gate edges and still lower at gate corners. In order to find out why these values were changed in such way, we have investigated optical properties of the dielectric in the neighborhood of metal gate. Hence, in this work, interferometry and spectroscopic ellipsometry as well as scattered Raman radiation analysis have been used in the investigation of metal-oxide-semiconductor (MOS) structures. The above mentioned methods turned out to be very useful for the possible explanation of changes in photoelectric characteristics of MOS structures with aluminum gate.

  13. Application of ellipsometric and interference methods in MOS structures investigations

    Science.gov (United States)

    Rzodkiewicz, W.; Borowicz, L.; Piskorski, K.

    2007-04-01

    Changes in some electrical and photoelectric parameters in the plane of aluminum gate, particularly in the effective contact potential difference (ECPD or phiMS factor) have been observed in MOS System Studies Department of Institute of Electron Technology for the first time. It has been found that the MS distribution over the gate area has a characteristic domelike shape, with the highest values ate the center of the gate, lower at the gate edges and still lower at gate corners. In order to find out why these values were changed in such way, we have investigated optical properties of the dielectric in the neighborhood of metal gate. Hence, in this work, interferometry and spectroscopic ellipsometry as well as scattered Raman radiation analysis have been used in the investigation of metal-oxide-semiconductor (MOS) structures. The above mentioned methods turned out to be very useful for the possible explanation of changes in photoelectric characteristics of MOS structures with aluminum gate.

  14. Investigation of the interaction of naringin palmitate with bovine serum albumin: spectroscopic analysis and molecular docking.

    Directory of Open Access Journals (Sweden)

    Xia Zhang

    Full Text Available BACKGROUND: Bovine serum albumin (BSA contains high affinity binding sites for several endogenous and exogenous compounds and has been used to replace human serum albumin (HSA, as these two compounds share a similar structure. Naringin palmitate is a modified product of naringin that is produced by an acylation reaction with palmitic acid, which is considered to be an effective substance for enhancing naringin lipophilicity. In this study, the interaction of naringin palmitate with BSA was characterised by spectroscopic and molecular docking techniques. METHODOLOGY/PRINCIPAL FINDINGS: The goal of this study was to investigate the interactions between naringin palmitate and BSA under physiological conditions, and differences in naringin and naringin palmitate affinities for BSA were further compared and analysed. The formation of naringin palmitate-BSA was revealed by fluorescence quenching, and the Stern-Volmer quenching constant (KSV was found to decrease with increasing temperature, suggesting that a static quenching mechanism was involved. The changes in enthalpy (ΔH and entropy (ΔS for the interaction were detected at -4.11 ± 0.18 kJ·mol(-1 and -76.59 ± 0.32 J·mol(-1·K(-1, respectively, which indicated that the naringin palmitate-BSA interaction occurred mainly through van der Waals forces and hydrogen bond formation. The negative free energy change (ΔG values of naringin palmitate at different temperatures suggested a spontaneous interaction. Circular dichroism studies revealed that the α-helical content of BSA decreased after interacting with naringin palmitate. Displacement studies suggested that naringin palmitate was partially bound to site I (subdomain IIA of the BSA, which was also substantiated by the molecular docking studies. CONCLUSIONS/SIGNIFICANCE: In conclusion, naringin palmitate was transported by BSA and was easily removed afterwards. As a consequence, an extension of naringin applications for use in food, cosmetic

  15. Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA.

    Directory of Open Access Journals (Sweden)

    David M Engelthaler

    2011-10-01

    Full Text Available Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification.

  16. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  17. INVESTIGATION OF THERMAL BEHAVIOR OF MULTILAYERED FIRE RESISTANT STRUCTURE

    Directory of Open Access Journals (Sweden)

    R. GUOBYS

    2016-09-01

    Full Text Available This paper presents experimental and numerical investigations of thermal behavior under real fire conditions of new generation multilayered fire resistant structure (fire door, dimensions H × W × D: 2090 × 980 × 52 mm combining high strength and fire safety. This fire door consists of two steel sheets (thickness 1.5 and 0.7 mm with stone wool ( = 33 kg/m3, k = 0.037 W/mK, E = 5000 N/m2,  = 0.2 insulating layer in between. One surface of the structure was heated in fire furnace for specified period of time of 60 min. Temperature and deformation of opposite surface were measured from outside at selected measuring points during fire resistance test. Results are presented as temperature-time and thermal deformation-time graphs. Experimental results were compared with numerical temperature field simulation results obtained from SolidWorks®Simulation software. Numerical results were found to be in good agreement with experimental data. The percent differences between door temperatures from simulation and fire resistance test don’t exceed 8%. This shows that thermal behaviour of such multilayered structures can be investigated numerically, thus avoiding costly and time-consuming fire resistance tests. It is established that investigated structure should be installed in a way that places thicker steel sheet closer to the potential heat source than thinner one. It is also obtained that stone wool layer of higher density should be used to improve fire resistance of the structure.

  18. Investigating the dynamic properties of an MOS-transistor structure

    OpenAIRE

    Likhobabin, N. P.; Politanskii, L. F.; Vatamanyuk, P. P.

    1990-01-01

    The literature provides practically no information on the operation of MOS-transistor switches in the low-temperature range. The purpose of the present work was to study the dynamic parameters in the temperature range from 77 to 400 K. The investigations were carried out on horizontal high-voltage MOS structures having a drift region and a polysilicon gate, which had been fabricated on KDB80 plates.

  19. An empirical investigation of governance structures in the hotel industry

    OpenAIRE

    Dahlstrom, Robert; Haugland, Sven Arne; Nygaard, Arne; Rokkan, Aksel Ivar

    2002-01-01

    The study investigates alternative governance forms in the hotel industry. We analyze the choice among independently owned firms, voluntary chains, franchising, and vertically integrated chains. Based on agency theory, we argue that the need for control over service quality, financial risk, and the market environment affect the choice of governance form. Prior agency research emphasizes alternative governance structures employed by principals given local market conditions, agent incentives, a...

  20. Variable temperature investigation of the atomic structure of gold nanoparticles

    International Nuclear Information System (INIS)

    Young, N P; Kirkland, A I; Huis, M A van; Zandbergen, H W; Xu, H

    2010-01-01

    The characterisation of nanoparticle structures is the first step towards understanding and optimising their utility in important technological applications such as catalysis. Using newly developed in-situ transmission electron microscopy (TEM) specimen holders, the temperature dependent atomic structure of gold nanoparticles in the size range 5-12 nm has been investigated. In this size interval, the decahedral morphology has been identified as the most favourable structure at or above room temperature, while particle surface roughening becomes evident above 600 0 C. An icosahedral transition has also been identified at low temperature in particles under 9 nm in diameter. These experimental results are consistent with recently published temperature dependent equilibrium phase maps for gold nanoparticles.

  1. Optical investigation of functional structures in isolated perfused pig heart

    Science.gov (United States)

    Rauh, Robert; Boehnert, Markus; Mahlke, Christine; Kessler, Manfred D.

    2000-11-01

    Light scattering in tissue of mammals and humans is affected by subcellular structures. Since these structures correlate well with the status of cells and tissue, light scattering seems to be ideal for monitoring of functional tissue state. By use of EMPHO SSK Oxyscan we investigated functional parameters in a novel kind of isolated perfused pig heart model. In this perfusion model we use organs obtained by the local slaughterhouse that are reanimated at our institute by application of a heart-lung machine. By creating 3D-images of tissue scattering we found an interesting relation between anatomical structures of myocardium and the 3D-images. Additionally, we detected coherence between backscattered light intensity and functional tissue status. Furthermore, we got a sight into the redox state of cytochrome aa3, b and c by creating difference spectra. We believe that this new kind of tissue imaging method will give us the opportunity to get new insights into myocardial function.

  2. Molecular evolution, intracellular organization, and the quinary structure of proteins.

    OpenAIRE

    McConkey, E H

    1982-01-01

    High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

  3. Investigation of optical properties of Ag: PMMA nanocomposite structures

    Science.gov (United States)

    Ponelyte, S.; Palevicius, A.; Guobiene, A.; Puiso, J.; Prosycevas, I.

    2010-05-01

    In the recent years fundamental research involving the nanodimensional materials has received enormous momentum for observing and understanding new types of plasmonic materials and their physical phenomena occurring in the nanoscale. Mechanical and optical properties of these polymer based nanocomposite structures depend not only on type, dimensions and concentration of filler material, but also on a kind of polymer matrix used. By proper selection of polymer matrix and nanofillers, it is possible to engineer nanocomposite materials with certain favorable properties. One of the most striking features of nanocomposite materials is that they can expose unique optical properties that are not intrinsic to natural materials. In these researches, nanocomposite structures were formed using polymer (PMMA) as a matrix, and silver nanoparticles as fillers. By hot embossing procedure a diffraction grating was imprinted on formed layers. The effect of UV exposure time on nanocomposite structures morphology, optical (diffraction effectiveness, absorbance) and mechanical properties was investigated. Results were confirmed by UV-VIS spectrometer, Laser Diffractometer, PMT- 3 and AFM. Investigations proposed new nanocomposite structures as plasmonic materials with improved optical and mechanical properties, which may be applied for a number of technological applications: micro-electro-mechanical devices, optical devices, various plasmonic sensors, or even in DNA nanotechnology.

  4. Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study

    Science.gov (United States)

    Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

    2017-11-01

    We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (Cd) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of Cd with positive and negative surface potentials.

  5. Investigation of coherent molecular resonances in quantum dot–metallic nanoparticle systems using their spontaneous emission

    International Nuclear Information System (INIS)

    Sadeghi, S.M.; Patty, K.D.

    2014-01-01

    In the presence of metallic nanoparticles the nature of the optical excitations (pumping) of semiconductor quantum dots can be determined by their molecular states and resonances formed via coherent coupling of excitons and plasmons. We show that the spontaneous emission of such quantum dots can provide key information regarding formation and characteristics of such molecular properties. This includes an ultra-fast switching process associated with optical transition between the molecular states of the quantum dot-metallic nanoparticle system or its plasmonic meta-resonance when the intensity of the laser field responsible for the exciton–plasmon coupling reaches a critical value. We also show that by varying the intensity of this laser, the spontaneous emission exhibits characteristic features indicating tunability of the molecular resonances and excitation-power dependence of plasmonic fields of the metallic nanoparticles. - Highlights: • Investigation of collective molecular properties of quantum dot-metallic nanoparticle systems. • Impact of such collective properties on the optical excitation of quantum dots. • Effects of exciton–plasmon coupling in the spontaneous emission of the quantum dots. • Signatures of plasmonic meta-resonances in the fluorescence of quantum dots

  6. The effect of hot multistage drawing on molecular structure and optical properties of polyethylene terephthalate fibers

    Directory of Open Access Journals (Sweden)

    Aminoddin Haji

    2012-08-01

    Full Text Available In this work, mechanical and structural parameters related to the optical properties of polyethylene terephthalate (PET fibers drawn at hot multistage have been investigated. The changes in optical parameters upon changing draw ratio are used to obtain the mechanical orientation factors and , various orientation functions f2(θ, f4(θ and f6(θ, and amorphous and crystalline orientation functions (f a and f c. Also, the numbers of random links between the network junction points (N1, the average optical orientation (Fav, and the distribution function of segment ω(cos θ were calculated. In addition, an empirical formula was suggested to correlate changes in the birefringence with the draw ratio and its constants were determined. The study demonstrated change on the molecular orientation functions and structural parameters upon hot multistage drawing. Significant variations in the characteristic properties of the drawn PET fibers were due to reorientation of the molecules caused by applied heat and external tension.

  7. Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

    Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

  8. Molecular dynamics simulation of chemical sputtering of hydrogen atom on layer structured graphite

    International Nuclear Information System (INIS)

    Ito, A.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.

    2008-10-01

    Chemical sputtering of hydrogen atom on graphite was simulated using molecular dynamics. Especially, the layer structure of the graphite was maintained by interlayer intermolecular interaction. Three kinds of graphite surfaces, flat (0 0 0 1) surface, armchair (1 1 2-bar 0) surface and zigzag (1 0 1-bar 0) surface, are dealt with as targets of hydrogen atom bombardment. In the case of the flat surface, graphene layers were peeled off one by one and yielded molecules had chain structures. On the other hand, C 2 H 2 and H 2 are dominant yielded molecules on the armchair and zigzag surfaces, respectively. In addition, the interaction of a single hydrogen isotope on a single graphene is investigated. Adsorption, reflection and penetration rates are obtained as functions of incident energy and explain hydrogen retention on layered graphite. (author)

  9. Molecular structure and conformations of caramboxin, a natural neurotoxin from the star fruit: A computational study

    Science.gov (United States)

    Pichierri, Fabio

    2015-01-01

    Using density functional theory calculations we investigate the molecular structure and conformations of caramboxin, a neurotoxin recently isolated from the star fruit Averroha carambola. Among the seven conformers that exist within an energy window of ∼16.0 kcal/mol, two of them are the most favored ones with an energy difference of less than 2.0 kcal/mol. The computed chemical shifts of these two low-energy conformers are in good agreement with the experimental values determined in deuterated dimethylsulfoxide thus confirming the 2D chemical structure assigned to the neurotoxin. A topological analysis of the theoretical electronic charge density of four caramboxin conformers reveals the existence of intramolecular CH⋯O/N interactions which, in addition to the classical OH⋯O/N H-bonding interactions, contribute to decrease the conformational freedom of the neurotoxin.

  10. Supramolecular Structure and Mechanical Characteristics of Ultrahigh-Molecular-Weight Polyethylene-Inorganic Nanoparticle Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Okhlopkova, T. A.; Borisova, R. V.; Nikiforov, L. A.; Spiridonov, A. M.; Okhlopkova, A. A.; Cho, Jin-Ho [North-Eastern Federal University, Yakutsk (Russian Federation); Jeong, Dae-Yong [Inha University, Incheon (Korea, Republic of)

    2016-04-15

    We investigated the mechanical properties and structure of polymeric nanocomposites (PNCs) with anultrahigh-molecular-weight polyethylene (UHMWPE) matrix and aluminum and silicon oxide and nitride nanoparticle (NP) fillers. Mixing with a paddle mixer or by joint mechanical activation in a planetary mill was used for the PNC preparation. Joint mechanical activation afforded PNCs with better mechanical properties than paddle mixing. Scanning electron microscopy suggested that the poorer mechanical properties can be attributed to the disordered regions and imperfect spherulites in the PNC supramolecular structure arising from paddle mixing. The better mechanical properties observed with joint mechanical activation may derive from the uniform NP distribution in the polymer matrix and absence of disordered regions.

  11. Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure.

    Science.gov (United States)

    Hiramatsu, Michiaki; Ichikawa, Yuki; Tomoshige, Shusuke; Makishima, Makoto; Muranaka, Atsuya; Uchiyama, Masanobu; Yamaguchi, Takao; Hashimoto, Yuichi; Ishikawa, Minoru

    2016-08-05

    Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  13. Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

    Science.gov (United States)

    Stojanov, M; Magalhaes, B; Terletsky, V; Basset, P; Prod'hom, G; Greub, G; Senn, L; Blanc, D S

    2016-02-01

    Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases.

  14. Phase sensitive molecular dynamics of self-assembly glycolipid thin films: A dielectric spectroscopy investigation

    Science.gov (United States)

    Velayutham, T. S.; Ng, B. K.; Gan, W. C.; Majid, W. H. Abd.; Hashim, R.; Zahid, N. I.; Chaiprapa, Jitrin

    2014-08-01

    Glycolipid, found commonly in membranes, is also a liquid crystal material which can self-assemble without the presence of a solvent. Here, the dielectric and conductivity properties of three synthetic glycolipid thin films in different thermotropic liquid crystal phases were investigated over a frequency and temperature range of (10-2-106 Hz) and (303-463 K), respectively. The observed relaxation processes distinguish between the different phases (smectic A, columnar/hexagonal, and bicontinuous cubic Q) and the glycolipid molecular structures. Large dielectric responses were observed in the columnar and bicontinuous cubic phases of the longer branched alkyl chain glycolipids. Glycolipids with the shortest branched alkyl chain experience the most restricted self-assembly dynamic process over the broad temperature range studied compared to the longer ones. A high frequency dielectric absorption (Process I) was observed in all samples. This is related to the dynamics of the hydrogen bond network from the sugar group. An additional low-frequency mechanism (Process II) with a large dielectric strength was observed due to the internal dynamics of the self-assembly organization. Phase sensitive domain heterogeneity in the bicontinuous cubic phase was related to the diffusion of charge carriers. The microscopic features of charge hopping were modelled using the random walk scheme, and two charge carrier hopping lengths were estimated for two glycolipid systems. For Process I, the hopping length is comparable to the hydrogen bond and is related to the dynamics of the hydrogen bond network. Additionally, that for Process II is comparable to the bilayer spacing, hence confirming that this low-frequency mechanism is associated with the internal dynamics within the phase.

  15. Investigation of the disc-and-washer structure

    International Nuclear Information System (INIS)

    Mavrogenes, G.; Gallagher, W.J.

    1981-01-01

    About 1971 a proposed accelerating structure was described by the radiotechnical Institute, Moscow, which was intended for proton acceleration in a planned meson factory linac. The structure has several quite useful features and has been subsequently investigated by AECL (Chalk River, Canada), LASL (UC Los Alamos, NM) and Argonne National Laboratory. A sketch of the structure is shown which reveals the origin of the name disc-and-washer structure (DAW). The origin and development of the concept upon which the structure is founded is provided from considerations of a chain of individual TM-01 cavities designed to produce kinetic energy gain to a bunched beam transiting their common axis. It is assumed the cavities are individually excited without inter-coupling; so that for maximum energy gain there is a specific phasing requirement based on the transit time from the previous cavity. Such a system would be very complex to operate and would only be considered in the special case of a few cavities as, for example, the LASL PHERMEX

  16. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  17. Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

    Science.gov (United States)

    Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

    2018-03-06

    Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

  18. Molecular identification of blow flies recovered from human cadavers during crime scene investigations in Malaysia.

    Science.gov (United States)

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Isa, Mohd Noor Mat; Azirun, Mohd Sofian

    2012-12-01

    Forensic entomology applies knowledge about insects associated with decedent in crime scene investigation. It is possible to calculate a minimum postmortem interval (PMI) by determining the age and species of the oldest blow fly larvae feeding on decedent. This study was conducted in Malaysia to identify maggot specimens collected during crime scene investigations. The usefulness of the molecular and morphological approach in species identifications was evaluated in 10 morphologically identified blow fly larvae sampled from 10 different crime scenes in Malaysia. The molecular identification method involved the sequencing of a total length of 2.2 kilo base pairs encompassing the 'barcode' fragments of the mitochondrial cytochrome oxidase I (COI), cytochrome oxidase II (COII) and t-RNA leucine genes. Phylogenetic analyses confirmed the presence of Chrysomya megacephala, Chrysomya rufifacies and Chrysomya nigripes. In addition, one unidentified blow fly species was found based on phylogenetic tree analysis.

  19. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  20. Spatial and mass distributions of molecular clouds and spiral structure

    International Nuclear Information System (INIS)

    Kwan, J.; Valdes, F.; National Optical Astronomy Observatories, Tucson, AZ)

    1987-01-01

    The growth of molecular clouds resulting from cloud-cloud collisions and coalescence in the Galactic ring between 4 and 8 kpc are modeled, taking into account the presence of a spiral potential and the mutual cloud-cloud gravitational attraction. The mean lifetime of molecular clouds is determined to be about 200 million years. The clouds are present in both spiral arm and interarm regions, but a spiral pattern in their spatial distribution is clearly discernible, with the more massive clouds showing a stronger correlation with the spiral arms. As viewed from within the Galactic disk, however, it is very difficult to ascertain that the molecular cloud distribution in longitude-velocity space has a spiral pattern. 19 references

  1. Investigation on the thermographic detection of corrosion in RC structures

    Science.gov (United States)

    Tantele, Elia A.; Votsis, Renos A.; Kyriakides, Nicholas; Georgiou, Panagiota G.; Ioannou, Fotia G.

    2017-09-01

    Corrosion of the steel reinforcement is the main problem of reinforced concrete (RC) structures. Over the past decades, several methods have been developed aiming to detect the corrosion process early in order to minimise the structural damage and consequently the repairing costs. Emphasis was given in developing methods and techniques of non-destructive nature providing fast on-the-spot detection and covering large areas rather that concentrating on single locations. This study, investigates a non-destructive corrosion detection technique for reinforced concrete, which is based on infrared thermography and the difference in thermal characteristics of corroded and non-corroded steel rebars. The technique is based on the principle that corrosion products have poor heat conductivity, and they inhibit the diffusion of heat that is generated in the reinforcing bar due to heating. For the investigation RC specimens, have been constructed in the laboratory using embedded steel bars of different corrosion states. Afterward, one surface of the specimens was heated using an electric device while thermal images were captured at predefined time instants on the opposite surface with an IR camera. The test results showed a clear difference between the thermal characteristics of the corroded and the non-corroded samples, which demonstrates the potential of using thermography in corrosion detection in RC structures.

  2. Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

    Science.gov (United States)

    Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

    2017-08-01

    The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

  3. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    2017-01-01

    Full Text Available The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR, are the main endocrine therapies for prostate cancer (PCa. But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  4. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists.

    Science.gov (United States)

    Wang, Yuwei; Han, Rui; Zhang, Huimin; Liu, Hongli; Li, Jiazhong; Liu, Huanxiang; Gramatica, Paola

    2017-01-01

    The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7 α -substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD) simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  5. Nanoscale insight into the exfoliation mechanism of graphene with organic dyes: effect of charge, dipole and molecular structure.

    Science.gov (United States)

    Schlierf, Andrea; Yang, Huafeng; Gebremedhn, Elias; Treossi, Emanuele; Ortolani, Luca; Chen, Liping; Minoia, Andrea; Morandi, Vittorio; Samorì, Paolo; Casiraghi, Cinzia; Beljonne, David; Palermo, Vincenzo

    2013-05-21

    We study the mechanism of surface adsorption of organic dyes on graphene, and successive exfoliation in water of these dye-functionalized graphene sheets. A systematic, comparative study is performed on pyrenes functionalized with an increasing number of sulfonic groups. By combining experimental and modeling investigations, we find an unambiguous correlation between the graphene-dye interaction energy, the molecular structure and the amount of graphene flakes solubilized. The results obtained indicate that the molecular dipole is not important per se, but because it facilitates adsorption on graphene by a "sliding" mechanism of the molecule into the solvent layer, facilitating the lateral displacement of the water molecules collocated between the aromatic cores of the dye and graphene. While a large dipole and molecular asymmetry promote the adsorption of the molecule on graphene, the stability and pH response of the suspensions obtained depend on colloidal stabilization, with no significant influence of molecular charging and dipole.

  6. An investigation of the structure of disordered materials by using neutron diffraction

    International Nuclear Information System (INIS)

    Petri, I.

    1999-01-01

    The structure of several semiconducting, metallic and ionic disordered materials was investigated using neutron diffraction and the results were compared with those obtained from recent ab initio molecular dynamics methods. The method of isotopic substitution was applied to measure the full set of partial structure factors, S αβ (Q), for the liquid semiconductor GeSe and the covalent network glass GeSe 2 . Their short range ordering and for GeSe 2 also the intermediate range ordering were identified and a substantial number of 'defects' such as homopolar bonds were detected in both systems. Further, the structure of liquid GeSe 2 with increasing temperature was studied at the total structure factor level. Also, changes in the topology of Ge x Se 1-x glasses in the range 0 ≤ x ≤ 0.4 were observed and investigated by measuring the total structure factors. As far as possible our results were compared with those from molecular dynamics studies. The Ge-Se system was found to serve as a sensitive test-system for these studies, giving an insight into the strengths and limitations of them. For instance, problems are found in the region of the homopolar bonds for g GeGe (r) and for the first sharp diffraction peak in the Bhatia-Thornton concentration-concentration structure factor that could not be reproduced. The structure of liquid lithium was measured and particular attention was paid to the inelasticity and resolution function corrections. The ion-ion and ion-valence electron partial structure factors were obtained and found to be in good agreement with ab initio molecular dynamics studies. The method of first order difference functions in neutron diffraction in combination with H/D substitution was applied to 2 molal solutions of Cu(ClO 4 ) 2 in perchloric acid to measure the Cu-H and, to a first order approximation, the Cu-O partial structure factor. A (4 + 1) distortion of the hydration shell around the Cu 2+ ion was measured. (author)

  7. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein Digestibility and Solubility

    Directory of Open Access Journals (Sweden)

    Mingmei Bai

    2016-08-01

    Full Text Available The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003; moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004. On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001 and solubility (p = 0.002. These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

  8. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...

  9. Ring structures on natural molybdenum disulfide investigated by scanning tunneling and scanning force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Heckl, W.M.; Ohnesorge, F.; Binnig, G. (IBM Research Division, Muenchen (West Germany)); Specht, M. (Univ. Muenchen (West Germany)); Hashmi, M. (MPIf. Plasmaphysics, Garching (West Germany))

    In this paper the authors present a study of ring-like structures of two different sizes on a nanometer scale found on natural molybdenum disulfide (MoS{sub 2}). Investigation by scanning tunneling and scanning force microscopy as well as secondary-ion mass spectroscopy indicate that these rings might originate from included molecules. Synthetic compared to natural MoS{sub 2} shows characteristic differences. The origin of these striking structures could be the morphology of organic or even remnants of biological material included at the geological time when the mineral was formed and could therefore be regarded as a result of a molecular fossilization process. The alternative explanation that the ring structure is a nonmorphological and purely electronic effect caused by a point defect like a dopant is also discussed.

  10. First-principles investigation on structural and electronic properties of antimonene nanoribbons and nanotubes

    Science.gov (United States)

    Nagarajan, V.; Chandiramouli, R.

    2018-03-01

    The electronic properties of antimonene nanotubes and nanoribbons hydrogenated along the zigzag and armchair borders are investigated with the help of density functional theory (DFT) method. The structural stability of antimonene nanostructures is confirmed with the formation energy. The electronic properties of hydrogenated zigzag and armchair antimonene nanostructures are studied in terms of highest occupied molecular orbital (HOMO) & lowest unoccupied molecular orbital (LUMO) gap and density of states (DOS) spectrum. Moreover, due to the influence of buckled orientation, hydrogen passivation and width of antimonene nanostructures, the HOMO-LUMO gap widens in the range of 0.15-0.41 eV. The findings of the present study confirm that the electronic properties of antimonene nanostructures can be tailored with the influence of width, orientation of the edges, passivation with hydrogen and morphology of antimonene nanostructures (nanoribbons, nanotubes), which can be used as chemical sensor and for spintronic devices.

  11. A structured framework for improving outbreak investigation audits

    Directory of Open Access Journals (Sweden)

    Durrheim David N

    2009-12-01

    Full Text Available Abstract Background Outbreak investigation is a core function of public health agencies. Suboptimal outbreak investigation endangers both public health and agency reputations. While audits of clinical medical and nursing practice are conducted as part of continuous quality improvement, public health agencies rarely make systematic use of structured audits to ensure best practice for outbreak responses, and there is limited guidance or policy to guide outbreak audit. Methods A framework for prioritising which outbreak investigations to audit, an approach for conducting a successful audit, and a template for audit trigger questions was developed and trialled in four foodborne outbreaks and a respiratory disease outbreak in Australia. Results The following issues were identified across several structured audits: the need for clear definitions of roles and responsibilities both within and between agencies, improved communication between agencies and with external stakeholders involved in outbreaks, and the need for development of performance standards in outbreak investigations - particularly in relation to timeliness of response. Participants considered the audit process and methodology to be clear, useful, and non-threatening. Most audits can be conducted within two to three hours, however, some participants felt this limited the scope of the audit. Conclusion The framework was acceptable to participants, provided an opportunity for clarifying perceptions and enhancing partnership approaches, and provided useful recommendations for approaching future outbreaks. Future challenges include incorporating feedback from broader stakeholder groups, for example those of affected cases, institutions and businesses; assessing the quality of a specific audit; developing training for both participants and facilitators; and building a central capacity to support jurisdictions embarking on an audit. The incorporation of measurable performance criteria or

  12. Investigation of thermal conduction in symmetric and asymmetric nanoporous structures

    Science.gov (United States)

    Yu, Ziqi; Ferrer-Argemi, Laia; Lee, Jaeho

    2017-12-01

    Nanoporous structures with a critical dimension comparable to or smaller than the phonon mean free path have demonstrated significant thermal conductivity reductions that are attractive for thermoelectric applications, but the presence of various geometric parameters complicates the understanding of governing mechanisms. Here, we use a ray tracing technique to investigate phonon boundary scattering phenomena in Si nanoporous structures of varying pore shapes, pore alignments, and pore size distributions, and identify mechanisms that are primarily responsible for thermal conductivity reductions. Our simulation results show that the neck size, or the smallest distance between nearest pores, is the key parameter in understanding nanoporous structures of varying pore shapes and the same porosities. When the neck size and the porosity are both identical, asymmetric pore shapes provide a lower thermal conductivity compared with symmetric pore shapes, due to localized heat fluxes. Asymmetric nanoporous structures show possibilities of realizing thermal rectification even with fully diffuse surface boundaries, in which optimal arrangements of triangular pores show a rectification ratio up to 13 when the injection angles are optimally controlled. For symmetric nanoporous structures, hexagonal-lattice pores achieve larger thermal conductivity reductions than square-lattice pores due to the limited line of sight for phonons. We also show that nanoporous structures of alternating pore size distributions from large to small pores yield a lower thermal conductivity compared with those of uniform pore size distributions in the given porosity. These findings advance the understanding of phonon boundary scattering phenomena in complex geometries and enable optimal designs of artificial nanostructures for thermoelectric energy harvesting and solid-state cooling systems.

  13. Structural changes on a molecular basis of canola meal by conditioning temperature and time during pelleting process in relation to physiochemical (energy and protein) properties relevant to ruminants.

    Science.gov (United States)

    Huang, Xuewei; Zhang, Huihua; Yu, Peiqiang

    2017-01-01

    The objectives of this study were: (1) To investigate the effects of conditioning temperature (70, 80, 90°C), time (30, 60 sec), and interaction (temperature × time) during the pelleting process on internal protein molecular structure changes of the co-products; (2) To identify differences in protein molecular structures among pellets that were processed under different conditions, and between unprocessed mash and pellets; 3) To quantify protein molecular structure changes in relation to predicted energy and protein utilization in dairy cows. The final goal of this program was to show how processing conditions changed internal feed structure on a molecular basis and how molecular structure changes induced by feed processing affected feed milk value in dairy cows. The hypothesis in this study was that processing-induced protein inherent structure changes affected energy and protein availability in dairy cattle and the sensitivity and response of protein internal structure to the different pelleting process conditions could be detected by advanced molecular spectroscopy. The protein molecular structures, amides I and II, amide I to II ratios, α-helix structure, β-sheet structure, and α to β structure ratios, were determined using the advanced vibrational molecular spectroscopy (ATR-FT/IR). The energy values were determined using NRC2001 summary approach in terms of total digestible nutrients, metabolizable and net energy for lactation. The protein and carbohydrate subfactions that are related to rumen degradation characteristics and rumen undegraded protein supply were determined using updated CNCPS system. The experiment design was a RCBD and the treatment design was a 3x2 factorial design. The results showed that pelleting induced changes in protein molecular structure. The sensitivity and response of protein inherent structure to the pelleting depended on the conditioning temperature and time. The protein molecular structure changes were correlated (P < 0

  14. Molecular Packing Structure of Mesogenic Octa-Hexyl Substituted Phthalocyanine Thin Film by X-ray Diffraction Analysis.

    Science.gov (United States)

    Ohmori, Masashi; Higashi, Takuya; Fujii, Akihiko; Ozaki, Masanori

    2016-04-01

    The molecular packing structure in a thin film of the liquid crystalline phthalocyanine, 1,4,8,11,15,18,22,25-octahexylphthalocyanine (C6PcH2), which is a promising small-molecular material for solution-processable organic thin-film solar cells, has been investigated by X-ray diffraction (XRD) measurement. The crystal structure of C6PcH2 in the spin-coated film was determined to be a centered rectangular structure (a = 36.4 Å, b = 20.3 Å). The tilt angle of the phthalocyanine core normal vector was 34-39° from the column axis, and the shortest intermolecular distance was 3.9-4.0 A. The crystal structure determined by XRD analysis was ascertained to be consistent with that calculated by Fourier analvsis.

  15. Nuclear structure of the transactinides – investigated by decay spectroscopy

    Directory of Open Access Journals (Sweden)

    Heßberger Fritz Peter

    2016-01-01

    Full Text Available Superheavy elements owe their stability due to a subtle balance between the disruptive Coulomb force and the attractive nuclear forces. Thus they represent an ideal laboratory to study basic interactions. The essential tools are detailed investigations of radioactive decay properties and nuclear structure of superheavy nuclei. The results of those studies will deliver valuable input to improve theoretical models. To fulfill this demand conclusive data of high quality are necessary, which is presently not so easy to meet due to small production cross sections and technical limitations (beam intensities, detection probabilities. Possibilities and problems concerning extraction of decay properties and nuclear structure information on the basis of a low number of observed decay events will be discussed for three illustrative examples, 257Rf, 257Lr, and 288Fl.

  16. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its ... is still open in view of differences in diffraction, simulation and other results [1,2,6–. 9]. The neutron diffraction is ... molecular conformation hitherto obtained from X-ray diffraction data [10] has lim- itation since hydrogen ...

  17. Theoretical investigations on the structure and potential binding sites of antineoplaston A10 and experimental findings.

    Science.gov (United States)

    Michalska, D

    1990-01-01

    The essential biological importance of antineoplastons has motivated the present theoretical and experimental studies on the structure and potential binding sites of Antineoplaston A10, 3-phenylacetylamino-2,6-piperidinedione. Semi-empirical molecular orbital calculations SCF-LCAO-MO were performed using the MNDO method. The calculated molecular geometry of A10 is in very good agreement with the recently obtained X-ray structure of synthetic A10. Experimental investigations of the Raman spectra of A10 and its N,N-dideuterated derivative confirm the theoretical predictions concerning the structure and hydrogen bonding of A10. Analysis of calculated charge distribution reveals that the negative charges are localized on the ring nitrogen and on the exocyclic oxygen atoms of A10 and are similar to the corresponding charges computed for some pyrimidine bases. This indicates that Antineoplaston A10 may have similar binding sites. It is concluded that the mechanism of action of Antineoplaston A10 may in part be related to its structural and chemical resemblance with deoxythymidine and uridine. A10 may act as a nucleoside antagonist and interact very closely with adenosine units in nucleic acids and enzymes, which may interfere with protein synthesis in neoplastic cells.

  18. Structural investigation of carbon/carbon composites by neutron scattering

    International Nuclear Information System (INIS)

    Prem, Manfred; Krexner, Gerhard; Peterlik, Herwig

    2006-01-01

    Carbon/carbon (C/C) composite material was investigated by means of small-angle as well as wide-angle elastic neutron scattering. The C/C-composites were built up from bi-directionally woven fabrics from PAN-based carbon fibers. Pre-impregnation with phenolic resin was followed by pressure curing and carbonization at 1000 deg. C and a final heat treatment at either 1800 or 2400 deg. C. Measurements of the samples were performed in orientations arranging the carbon fibers, respectively, parallel and perpendicular to the incoming beam. Structural features of the fibers as well as the inherently existing pores are presented and the influence of the heat treatment is discussed. The results are compared to earlier X-ray investigations of carbon fibers and C/C-composites

  19. Investigation of knowledge structure of nuclear data evaluation code

    International Nuclear Information System (INIS)

    Uenaka, Junji; Kambayashi, Shaw

    1988-08-01

    In this report, investigation results of knowledge structure in a nuclear data evaluation code are described. This investigation is related to the natural language processing and the knowledge base in the research theme of Human Acts Simulation Program (HASP) begun at the Computing Center of JAERI in 1987. By using a machine translation system, an attempt has been made to extract a deep knowledge from Japanese sentences which are equivalent to a FORTRAN program CASTHY for nuclear data evaluation. With the knowledge extraction method used by the authors, the verification of knowledge is more difficult than that of the prototyping method in an ordinary AI technique. In the early stage of building up a knowledge base system, it seems effective to extract and examine knowledge fragments of limited objects. (author)

  20. Real time spectroscopic ellipsometry investigation of homoepitaxial GaN grown by plasma assisted molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tong-Ho; Choi, Soojeong; Wu, Pae; Brown, April [Department of Electrical and Computer Engineering, Duke University, 128 Hudson Hall, Durham, NC (United States); Losurdo, Maria; Giangregorio, Maria M.; Bruno, Giovanni [Institute of Inorganic Methodologies and of Plasmas, IMIP-CNR and INSTM UdR Bari, via Orabona, 4, 70126 Bari (Italy); Moto, Akihiro [Innovation Core SEI, Inc., 3235 Kifer Road, Santa Clara, CA 95051 (United States)

    2006-06-15

    The growth of GaN by plasma assisted molecular beam epitaxy on GaN template substrates (GaN on sapphire) is investigated with in-situ multi-channel spectroscopic ellipsometry. Growth is performed under various Ga/N flux ratios at growth temperatures in the range 710-780 C. The thermal roughening of the GaN template caused by decomposition of the surface is investigated through the temporal variation of the GaN pseudodielectric function over the temperature range of 650 C to 850 C. The structural, morphological, and optical properties are also discussed. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. Structure-activity relationships and molecular docking of thirteen synthesized flavonoids as horseradish peroxidase inhibitors.

    Science.gov (United States)

    Mahfoudi, Reguia; Djeridane, Amar; Benarous, Khedidja; Gaydou, Emile M; Yousfi, Mohamed

    2017-10-01

    For the first time, the structure-activity relationships of thirteen synthesized flavonoids have been investigated by evaluating their ability to modulate horseradish peroxidase (HRP) catalytic activity. Indeed, a modified spectrophotometrically method was carried out and optimized using 4-methylcatechol (4-MC) as peroxidase co-substrate. The results show that these flavonoids exhibit a great capacity to inhibit peroxidase with Ki values ranged from 0.14±0.01 to 65±0.04mM. Molecular docking has been achieved using Auto Dock Vina program to discuss the nature of interactions and the mechanism of inhibition. According to the docking results, all the flavonoids have shown great binding affinity to peroxidase. These molecular modeling studies suggested that pyran-4-one cycle acts as an inhibition key for peroxidase. Therefore, potent peroxidase inhibitors are flavonoids with these structural requirements: the presence of the hydroxyl (OH) group in 7, 5 and 4' positions and the absence of the methoxy (O-CH 3 ) group. Apigenin contributed better in HRP inhibitory activity. The present study has shown that the studied flavonoids could be promising HRP inhibitors, which can help in developing new molecules to control thyroid diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Dynamic molecular structure retrieval from low-energy laser-induced electron diffraction spectra

    Science.gov (United States)

    Vu, Dinh-Duy T.; Phan, Ngoc-Loan T.; Hoang, Van-Hung; Le, Van-Hoang

    2017-12-01

    A recently developed quantitative rescattering theory showed that a laser-free elastic cross section can be separated from laser-induced electron diffraction (LIED) spectra. Based upon this idea, Blaga et al investigated the possibility of reconstructing molecular structure from LIED spectra (2012 Nature 483 7388). In the above study, an independent atoms model (IAM) was used to interpret high-energy electron–molecule collisions induced by a mid-infrared laser. Our research aims to extend the application range of this structural retrieval method to low-energy spectra induced by more common near-infrared laser sources. The IAM is insufficient in this case, so we switch to a more comprehensive model—the multiple scattering (MS) theory. From the original version concerning only neutral targets, we upgrade the model so that it is compatible with electron–ion collisions at low energy. With available LIED experiment data of CO2 and O2, the upgraded MS is shown to be greatly effective as a tool for molecular imaging from spectra induced by a near-infrared laser. The captured image is at about 2 fs after the ionization, shorter than the period 4–6 fs by using the mid-infrared laser in Blaga’s experiment.

  3. Structural investigations of sodium caseinate micelles in complex environments

    Energy Technology Data Exchange (ETDEWEB)

    Huck Iriart, C.; Herrera, M.L.; Candal, R. [Universidad de Buenos Aires, Buenos Aires (Argentina); Oliveira, C.L.P. [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil); Torriani, I. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil)

    2012-07-01

    Full text: The most frequent destabilization mechanisms in Sodium Caseinate (NaCas) emulsions are creaming and flocculation. Coarse or fine emulsions with low protein con- tent destabilize mainly by creaming. If migration mechanism is suppressed, flocculation may become the main mechanism of destabilization. Small Angle X-Ray Scattering (SAXS) technique was applied to investigate sodium caseinate micelles structure in different environments. As many natural products, Sodium Caseinate samples have large polydisperse size distribution. The experimental data was analyzed using advanced modeling approaches. The Form Factor for the Caseinate micelle subunits was described by an ellipsoidal core shell model and the structure factor was split into two contributions, one corresponding to the particle-particle interactions and another one for the long range correlation of the subunits in the supramolecular structure. For the first term the hard sphere structure factor using the Percus-Yevick approximation for closure relation was used and for the second term a fractal model was applied. Three concentrations of sodium Caseinate (2, 5 and 7.5 %wt.) were measured in pure water, sugar solutions (20 %wt.) and in three different lipid phase emulsions containing 10 %wt. sunflower seed, olive and fish oils. Data analysis provided an average casein subunit radius of 4 nm, an average distance between the subunits of around 20nm and a fractal dimension value of around 3 for all samples. As indicated by the values of the correlation lengths for the set of studied samples, the casein aggregation is strongly affected by simple sugar additions and it is enhanced by emulsion droplets hydrophobic interaction. As will be presented, these nanoscale structural results provided by scattering experiments is consistent with macroscopic results obtained from several techniques, providing a new understanding of NaCas emulsions. (author)

  4. The Atom in a Molecule: Implications for Molecular Structure and Properties

    Science.gov (United States)

    2016-05-23

    Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  5. Molecular dynamics modeling self-organization of pyramid-like structures after crystallization of nanodrops in the field of solid surface

    International Nuclear Information System (INIS)

    Samsonov, V.M.; Murav'ev, S.D.; Pushkar', M.Yu.

    2005-01-01

    The process of nanodrop crystallization in the field of solid surface was investigated on the basis of the isothermal molecular dynamics. The initial stage of the process corresponds to the spreading under a constant cooling rate. The crystallization resulted in the formation of layered pyramid-like structures. A comparative analysis of forms and conditions was made, which yielded the pyramid-like structure formation in molecular dynamics simulation and in the experiments with Ge/Si systems [ru

  6. Structural and Electronic Investigations of Complex Intermetallic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Hyunjin [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  7. Studies on vibrational structure of diatomic molecular states

    International Nuclear Information System (INIS)

    Sun Weiguo; Hou Shilin; Ren Weiyi; Feng Hao

    2002-01-01

    Alternative expressions for vibrational and rotational spectrum constants and energies of diatomic molecular electronic states are suggested based on the perturbation theory. An algebraic method (AM) is proposed to generate converged full vibrational spectrum from limited energy data, and a potential variational method (PVM) is suggested to produce the vibrational force constants f n 's and rotational spectrum constants using the perturbation formulae and the AM vibrational constants. Applying this method to several diatomic electronic states, the calculation results show that: 1) the AM E υ max converges to correct molecular dissociation energy; 2) the AM not only reproduce the input energies, but also generate the E υ 's of high vibrational excited states which may be difficult to be obtained experimentally or theoretically; 3) the PVM vibrational force constants f n 's may be used to measure the relative chemical bond strength of different diatomic electronic states for a molecule quantitatively

  8. Design Investigation on Applicable Mesh Structures for Medical Stent Applications

    Science.gov (United States)

    Asano, Shoji; He, Jianmei

    2017-11-01

    In recent years, utilization of medical stents is one of effective treatments for stenosis and occlusion occurring in a living body’s lumen indispensable for maintenance of human life such as superficial femoral artery (SFA) occlusion. However, there are concerns about the occurrence of fatigue fractures caused by stress concentrations, neointimal hyperplasia and the like due to the shape structure and the manufacturing method in the conventional stents, and a stent having high strength and high flexibility is required. Therefore, in this research, applicable mesh structures for medical stents based on the design concepts of high strength, high flexibility are interested to solve various problem of conventional stent. According to the shape and dimensions of SFA occlusion therapy stent and indwelling delivery catheter, shape design of the meshed stent are performed using 3-dimensional CAD software Solid Works first. Then analytical examination on storage characteristics and compression characteristics of such mesh structure applied stent models were carried out through finite element analysis software ANSYS Workbench. Meshed stent models with higher strength and higher flexibility with integral molding are investigated analytically. It was found that the storage characteristics and compression characteristics of meshed stent modles are highly dependent on the basic mesh shapes with same surface void ratio. Trade-off relationship between flexibility and storage characteristics is found exited, it is required to provide appropriate curvatures during basic mesh shape design.

  9. Structure and dynamics of alkali borate glasses: a molecular dynamics study

    NARCIS (Netherlands)

    Verhoef, A.H; den Hartog, H. W.

    Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at

  10. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  11. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    Energy Technology Data Exchange (ETDEWEB)

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  12. Utility of checklist to describe experimental methods for investigating molecular biomarkers.

    Science.gov (United States)

    Chiarella, Pieranna; Carbonari, Damiano; Iavicoli, Sergio

    2015-01-01

    In research articles, detailed description of experimental methods and reagents is fundamental for correct reproducibility of the published data. This becomes even more important when such data contribute to identify molecular targets and toxicity biomarkers whose role is crucial in the physiology and pathology of human health. Methods & Objectives: To achieve good reproducibility of data we took advantage of others' experiences and analyzed molecular biology and immunodetection techniques in 32 journal articles investigating the human NRF2 and Keap1 genes involved in the cell response to oxidative stress. In conclusion of the analysis, we assessed deficiency of information in the published methods, making it difficult to select appropriate protocols. Underlining the importance of assay reproducibility, this paper proposes the utility of a minimum information checklist of methods for biomarker detection.

  13. Molecular-Orbital Structure in Neutron-Rich Be and C Isotopes

    International Nuclear Information System (INIS)

    Itagaki, N.; Okabe, S.; Ikeda, K.; Tanihata, I.

    2000-01-01

    The structure of 10 Be and 12 Be are investigated using a microscopic α+α+n+n+··· model based on the molecular orbit (MO) model. The model space employed is extended from the traditional MO models, and the low-lying states are characterized by three basic orbits (3/2 - , 1/2 - and 1/2 + ) for the valence neutrons. The orbits perpendicular to the α-α axis with one node (3/2 - and 1/2 - ) are called π-orbit and one along the α-α axis (1/2 + ) is called σ-orbit, which has two nodes. In 10 Be, all of the observed positive-parity bands and the negative-parity bands are described within the model. The second 0 + state, which has dominantly the (1/2 + ) 2 configuration for the two valence neutrons, is shown to have a particularly enlarged α-α structure. The kinetic energy of the two valence neutrons occupying along the α-α axis is reduced remarkably due to the strong α clustering and simultaneously, the spin-orbit interaction plays unexpectedly important role to make the energy of this state much lower. The rotational band structure with enhanced α-α is compared with the experimental data. 12 Be is also investigated using α+α+4n model. The energy surface is shown to exhibit the similar characteristics, that the remarkable α clustering and the contribution of the spin-orbit interaction make the binding of the ground state with the (3/2 - ) 2 (1/2 - ) 2 configuration for valence neutrons properly stronger in comparison with the (3/2 - ) 2 (1/2 - ) 2 configuration. These effects play crucial roles in accounting for breaking of the N = 8 (closed p-shell) magic number. The molecular-like structure of the C isotopes is also investigated and the orbits are introduced around three α-clusters. The neutrons in π-orbit increase the binding and stabilize the linear-chain configuration of three α against the breathing-like break-up. On the other hand, the σ-orbits prevent the bending motion of the three-α chain. The combination of these configuration for the

  14. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  15. Laser-induced blurring of molecular structure information in high harmonic spectroscopy

    DEFF Research Database (Denmark)

    Risoud, Francois; Leveque, Camille; Labeye, Marie

    2017-01-01

    High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either...

  16. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

    Science.gov (United States)

    Cramer, Patrick

    2017-08-18

    Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Molecular dynamics simulations of the local structures and transport coefficients of molten alkali chlorides.

    Science.gov (United States)

    Wang, Jia; Sun, Ze; Lu, Guimin; Yu, Jianguo

    2014-08-28

    Systematic results from molecular dynamics simulations of molten alkali chlorides (ACl) serials are presented in detail in this paper. The effects of temperature and cationic size on the structures and transport properties of molten salts have been investigated and analyzed. The local structures of molten ACl have been studied via the analysis of radial distribution functions and angular distribution functions. The coordination number of ACl decreases when ACl melts from solid and increases as cationic radius increases. Molten LiCl takes a distorted tetrahedral complex as the microconfiguration, while other melts have the tendency to keep the original local structure of the corresponding crystal. Temperature has no significant effect on the local structures of molten ACls. The results also show that the Tosi-Fumi potential predicts positive temperature dependences for self-diffusion coefficients and ionic conductivity, and negative temperature dependences for both viscosity and thermal conductivity of molten ACls. Ionic diffusivity decreases as cationic radius increases from LiCl to CsCl. The simulation results are in agreement with the experimental data available in the literature.

  18. Molecular dynamics study on the structure I clathrate-hydrate of methane + ethane mixture

    International Nuclear Information System (INIS)

    Erfan-Niya, Hamid; Modarress, Hamid; Zaminpayma, Esmaeil

    2011-01-01

    Molecular dynamics (MD) simulations are used to study the structure I stability of methane + ethane clathrate-hydrates at temperatures 273, 275 and 277 K. NVT- and NPT-ensembles are utilized in MD simulation, and each consists of 3 x 3 x 3 replica unit cells containing 46 water molecules which are considered as the host molecules and up to eight methane + ethane molecules considered as the guest molecules. In MD simulations for host-host interactions, the potential model used was a type of simple point charge (SPC) model, and for guest-guest and host-guest interactions the potential used was Lennard-Jones model. In the process of MD simulation, achieving equilibrium of the studied system was recognized by stability in calculated pressure for NVT-ensemble and volume for NPT-ensemble. To understand the characteristic configurations of the structure I hydrate, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules as well as other properties including kinetic energy, potential energy and total energy were calculated. The results show that guest molecules interaction with host molecules cannot decompose the hydrate structure, and these results are consistent with most previous experimental and theoretical investigations that methane + ethane mixtures form structure I hydrates over the entire mixture composition range.

  19. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  20. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein In vitro Digestibility and Solubility.

    Science.gov (United States)

    Bai, Mingmei; Qin, Guixin; Sun, Zewei; Long, Guohui

    2016-08-01

    The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003); moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004). On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (pproteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

  1. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Galasso, V., E-mail: galasso@univ.trieste.it [Dipartimento di Scienze Chimiche, Universita di Trieste, I-34127 Trieste (Italy)

    2010-08-23

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, {sup 13}C NMR chemical shifts, and absorption spectrum account for the unique structural backbone, chemical behaviour, and spectroscopic properties of usnic acid, the cortical pigment and potent reactive of lichens. - Abstract: The molecular structure of usnic acid was investigated by the density functional theory (DFT). Two keto-enol tautomers are nearly isoenergetic and more stable than other tautomers. Noteworthy is the energy difference among the three intramolecular O-H...O hydrogen bonds. The DFT/PCM calculated dissociation constants account for the acidic sequence of the three OH-groups. The electronic structure was also studied by calculating IR/Raman, NMR, and absorption features. A reliable assignment of the 'fingerprint' carbonyl stretching modes was supported by calculations on related molecules. The calculated NMR chemical shifts fit expectation in terms of a fast interconversion between the two most preferred tautomers. A variety of {pi} {yields} {pi}* and n {yields} {pi}* excitations, localized on a single ring or involving a charge-transfer between the two lateral rings of the molecule, gives rise to the broad UV-absorption bands. This property accounts for the efficient protection against damaging solar radiation provided by usnic acid for lichens.

  2. Parallel molecular dynamics simulations of pressure-induced structural transformations in cadmium selenide nanocrystals

    Science.gov (United States)

    Lee, Nicholas Jabari Ouma

    Parallel molecular dynamics (MD) simulations are performed to investigate pressure-induced solid-to-solid structural phase transformations in cadmium selenide (CdSe) nanorods. The effects of the size and shape of nanorods on different aspects of structural phase transformations are studied. Simulations are based on interatomic potentials validated extensively by experiments. Simulations range from 105 to 106 atoms. These simulations are enabled by highly scalable algorithms executed on massively parallel Beowulf computing architectures. Pressure-induced structural transformations are studied using a hydrostatic pressure medium simulated by atoms interacting via Lennard-Jones potential. Four single-crystal CdSe nanorods, each 44A in diameter but varying in length, in the range between 44A and 600A, are studied independently in two sets of simulations. The first simulation is the downstroke simulation, where each rod is embedded in the pressure medium and subjected to increasing pressure during which it undergoes a forward transformation from a 4-fold coordinated wurtzite (WZ) crystal structure to a 6-fold coordinated rocksalt (RS) crystal structure. In the second so-called upstroke simulation, the pressure on the rods is decreased and a reverse transformation from 6-fold RS to a 4-fold coordinated phase is observed. The transformation pressure in the forward transformation depends on the nanorod size, with longer rods transforming at lower pressures close to the bulk transformation pressure. Spatially-resolved structural analyses, including pair-distributions, atomic-coordinations and bond-angle distributions, indicate nucleation begins at the surface of nanorods and spreads inward. The transformation results in a single RS domain, in agreement with experiments. The microscopic mechanism for transformation is observed to be the same as for bulk CdSe. A nanorod size dependency is also found in reverse structural transformations, with longer nanorods transforming more

  3. Synthesis, crystal structure analysis, spectral (NMR, FT-IR, FT-Raman and UV-Vis) investigations, molecular docking studies, antimicrobial studies and quantum chemical calculations of a novel 4-chloro-8-methoxyquinoline-2(1H)-one: An effective antimicrobial agent and an inhibition of DNA gyrase and lanosterol-14α-demethylase enzymes

    Science.gov (United States)

    Murugavel, S.; Sundramoorthy, S.; Lakshmanan, D.; Subashini, R.; Pavan Kumar, P.

    2017-03-01

    The novel title compound 4-chloro-8-methoxyquinoline-2(1H)-one (4CMOQ) has been synthesized by slow evaporation solution growth technique at room temperature. The synthesized 4CMOQ molecule was characterized experimentally by FT-IR, FT-Raman, UV-Vis, NMR and single crystal diffraction (XRD) and theoretically by quantum chemical calculations. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311++G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. The nuclear magnetic resonance spectra (1H and 13C NMR) are obtained by using the gauge-invariant atomic orbital (GIAO) method. The change in electron density (ED) in the antibonding orbital's and stabilization energies E(2) of the molecule have been evaluated by natural bond orbital (NBO) analysis to give clear evidence of stabilization. Moreover, electronic characteristics such as HOMO and LUMO energies, Mulliken atomic charges and molecular electrostatic potential surface are investigated. Absorption spectrum analysis, nonlinear optical properties, chemical reactivity descriptors and thermodynamic features are also outlined theoretically. Molecular docking studies were executed to understand the inhibitory activity of 4CMOQ against DNA gyrase and Lanosterol 14 α-demethylase. The antimicrobial activity of 4CMOQ was determined against bacterial strains such as Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and fungal strains such as Aspergillus niger, Monascus purpureus and Penicillium citrinum. The obtained results show that the compound exhibited good to moderate antimicrobial activity.

  4. Structural studies on Mycobacterium tuberculosis RecA: Molecular ...

    Indian Academy of Sciences (India)

    2015-01-11

    Jan 11, 2015 ... with the protein, characterized in the structures reported here, could be useful for design of inhibitors against. M. tuberculosis RecA. .... rotating anode generator, both using a MAR345 image plate. The crystal to detector ...... structures of Mycobacterium tuberculosis peptidyl-tRNA hydro- lase. J. Mol. Biol.

  5. Application of molecular spectroscopy to the determination of organic structures

    International Nuclear Information System (INIS)

    Leicknam, J.P.

    1976-01-01

    Some brief accounts are presented followed by a discussion about various physico-chemical techniques: Raman spectrometry, infrared spectrometry, resonance Raman spectrometry, conformational analysis and polarized Rayleigh diffusion. Applications of the Nuclear Magnetic Resonance to nucleotide structure in aqueous solution are described as well as some applications of neutron scattering to the study of organic structures [fr

  6. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  7. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  8. Effect of molecular structure of aniline-formaldehyde copolymers on corrosion inhibition of mild steel in hydrochloric acid solution.

    Science.gov (United States)

    Zhang, Yan; Nie, Mengyan; Wang, Xiutong; Zhu, Yukun; Shi, Fuhua; Yu, Jianqiang; Hou, Baorong

    2015-05-30

    Aniline-formaldehyde copolymers with different molecular structures have been prepared and investigated for the purpose of corrosion control of mild steel in hydrochloric acid. The copolymers were synthesized by a condensation polymerization process with different ratios of aniline to formaldehyde in acidic precursor solutions. The corrosion inhibition efficiency of as-synthesized copolymers for Q235 mild steel was investigated in 1.0 mol L(-1) hydrochloric acid solution by weight loss measurement, potentiodynamic polarization, and electrochemical impedance spectroscopy, respectively. All the results demonstrate that as-prepared aniline-formaldehyde copolymers are efficient mixed-type corrosion inhibitors for mild steels in hydrochloric acid. The corrosion inhibition mechanism is discussed in terms of the role of molecular structure on adsorption of the copolymers onto the steel surface in acid solution. Copyright © 2015. Published by Elsevier B.V.

  9. Investigation on the vibrational and structural properties of a self-structured bridged silsesquioxane.

    Science.gov (United States)

    Creff, Gaëlle; Arrachart, Guilhem; Hermet, Patrick; Wadepohl, Hubert; Almairac, Robert; Maurin, David; Sauvajol, Jean-Louis; Carcel, Carole; Moreau, Joël J E; Dieudonné, Philippe; Man, Michel Wong Chi; Bantignies, Jean-Louis

    2012-04-28

    The crystalline structure of ureidopyrimidinone-based silane (UPY) has been determined. The local and long range order structuring of the bridged silsesquioxane (MUPY) resulting from the sol-gel hydrolysis-condensation of the former precursor has been investigated by MFTIR (Mid Fourier Transform InfraRed) combined with DFT (Density Functional Theory) and XRD (X-ray diffraction) studies. These studies showed that a long range structuring exists within the organic fragments with the transcription of the DDAA (Donor-Donor-Acceptor-Acceptor) H-bonding array from UPY to MUPY whereas a disordered siloxane network was revealed in the hybrid material. This journal is © the Owner Societies 2012

  10. Numerical and experimental investigation on structure-borne sound transmission in multilayered concrete structures

    Science.gov (United States)

    Asakura, T.; Toyoda, M.; Miyajima, T.

    2018-01-01

    Environmental vibrations in cities are transmitted to buildings and propagate through the buildings via complex paths composed of the structural elements in the building, such as concrete slabs, beams, and columns. In this study, the transmission characteristics of such structure-borne sound in building structures composed of concrete were experimentally and numerically investigated. The vibration and radiated sound characteristics of a five-storey concrete structure obtained experimentally through an excitation test using the hammering method and numerically through wave-based numerical calculations are presented and compared. In this study, the finite-difference time-domain (FDTD) method, which treats the target structure as a composition of two-dimensional plate and one-dimensional beam elements to enable a low-cost calculation, is applied as a wave-based scheme. The propagation characteristics of the vibration and sound within the same floor and across different floors were investigated by considering various combinations of receiver and source points, and the structure-borne sound transmission characteristics of a concrete structure with frame elements are discussed.

  11. Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

    KAUST Repository

    Ganot, P.

    2014-09-21

    Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives to reconstruct the phylogeny of the molecular components of SJs. Although Claudins and SJ cytoplasmic adaptor components appeared successively throughout metazoan evolution, the structural components of SJs arose at the time of Placozoa/Cnidaria/Bilateria radiation. We also show that in the scleractinian coral Stylophora pistillata, the structural SJ component Neurexin IV colocalizes with the cortical actin network at the apical border of the cells, at the place of SJs. We propose a model for SJ components in Cnidaria. Moreover, our study reveals an unanticipated diversity of SJ structural component variants in cnidarians. This diversity correlates with gene-specific expression in calcifying and noncalcifying tissues, suggesting specific paracellular pathways across the cell layers of these diploblastic animals.

  12. Investigation of the graphene-electrolyte interface in Li-air batteries: A molecular dynamics study

    Science.gov (United States)

    Pavlov, S. V.; Kislenko, S. A.

    2018-01-01

    In this work the behavior of the main reactants (Li+, O2) of the oxygen reduction reaction (ORR) in acetonitrile solvent near the multi-layer graphene edge has been studied. It was observed by molecular dynamics simulations that the concentration distributions of the Li+ and O2 represent a “chessboard” structure. It was ascertained that the concentrations of the lithium ions and oxygen molecules reach their maximum values near the graphene edges pushed out from the surface, which may act as nucleation centers for the formation of crystalline products of the ORR. The maps of the free energy were estimated for the Li+ and O2. Energy optimal trajectories for the adsorption of oxygen molecules and lithium ions were found. Moreover, the distributions of the electric potential were obtained near the following carbon surfaces: single- and multi-layer graphene edge, graphene plane, which shows the qualitative differences in the double-layer structure.

  13. A parity function for studying the molecular electronic structure

    DEFF Research Database (Denmark)

    Schmider, Hartmut

    1996-01-01

    Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...... are qualitatively even more affected by the presence of chemical bonds than a complementary projection, the reciprocal form factor. In this paper we discuss, on the grounds of a variety of examples, how this rather simple function may aid the understanding of the chemical bond on a one-particle level. (C) 1996...

  14. Molecular conformation and structural correlations of liquid D-1 ...

    Indian Academy of Sciences (India)

    Inelasticity parameters: a = 3.22374 × 10−3 Е2, b = 0.404782 × 10−5 Е4. Constant for Debye–Waller terms: λ0 = 0.0384, χ2 = 0.134823 × 10−5. Election. Molecular diffraction [12] parameters. Present. X-ray [5]. (gas phase). MD [6]. rCC (Е). 1.477 ± 0.003. 1.520. 1.540. 1.530. rCO (Е). 1.443 ± 0.012. 1.420. 1.410. 1.430. rCD ...

  15. Molecular-Field Calculation of the Magnetic Structure in Erbium

    DEFF Research Database (Denmark)

    Jensen, J.

    1976-01-01

    A molecular-field calculation of the magnetic configurations in Er is found to reproduce the neutron diffraction results of the three different magnetic phases and to give a reasonable fit to the magnetization data at 4.2K. The two-ion coupling is considered to be described by the inter......-planar coupling parameters deduced from the dispersion of the spin waves in the low temperature conical phases. The four (effective) crystal-field parameters are determined by the fit to the experimental data. Projecting the magnetic moments present in the intermediate phase of Er (18-52.4K) to a common origin...

  16. Molecular structure and transport dynamics in Nafion and sulfonated poly(ether ether ketone ketone) membranes

    Energy Technology Data Exchange (ETDEWEB)

    Chen, P.Y.; Chiu, C.P.; Hong, C.W. [Department of Power Mechanical Engineering, National Tsing Hua University, 101, Sec. 2, Kwang Fu Road, Hsinchu 30013 (China)

    2009-12-01

    An atomistic simulation technique is performed to investigate the molecular structure and transport dynamics inside a hydrated Nafion membrane and a hydrated sulfonated poly(ether ether ketone ketone) (SPEEKK) membrane. The simulation system consists of the representative fragments of the polymer electrolytes, hydronium ions and solvent molecules, such as water plus methanol molecules. Simulation results show that the hydrated SPEEKK has less phase separation among hydrophobic and hydrophilic regions in comparison with the Nafion. Those water channels formed in the SPEEKK are much narrower compared to those in the Nafion. These characteristics lead to a lower mobility of hydronium ions and water molecules and hence relatively lower diffusion coefficient of methanol in the SPEEKK. It results in the reduction of the methanol permeation problem in direct methanol fuel cells. (author)

  17. Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

    Science.gov (United States)

    Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

    2018-04-01

    Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P < .01); (2) The ATR-Ft/VMS molecular technique was able to detect the processing induced CHO molecular structure changes; (3) Induced CHO molecular structure spectral features are significantly correlated (P < .05) to CHO subfractions, CHO biodegradation and biodigestion and could be applied to potentially predict CHO biodegradation (R2 = 0.87, RSD = 0.74, P < .01) and intestinal digestible undegraded CHO (R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

  18. Investigation of Wireless Sensor Networks for Structural Health Monitoring

    Directory of Open Access Journals (Sweden)

    Ping Wang

    2012-01-01

    Full Text Available Wireless sensor networks (WSNs are one of the most able technologies in the structural health monitoring (SHM field. Through intelligent, self-organising means, the contents of this paper will test a variety of different objects and different working principles of sensor nodes connected into a network and integrated with data processing functions. In this paper the key issues of WSN applied in SHM are discussed, including the integration of different types of sensors with different operational modalities, sampling frequencies, issues of transmission bandwidth, real-time ability, and wireless transmitter frequency. Furthermore, the topology, data fusion, integration, energy saving, and self-powering nature of different systems will be investigated. In the FP7 project “Health Monitoring of Offshore Wind Farms,” the above issues are explored.

  19. The Monotonicity Puzzle: An Experimental Investigation of Incentive Structures

    Directory of Open Access Journals (Sweden)

    Jeannette Brosig

    2010-05-01

    Full Text Available Non-monotone incentive structures, which - according to theory - are able to induce optimal behavior, are often regarded as empirically less relevant for labor relationships. We compare the performance of a theoretically optimal non-monotone contract with a monotone one under controlled laboratory conditions. Implementing some features relevant to real-world employment relationships, our paper demonstrates that, in fact, the frequency of income-maximizing decisions made by agents is higher under the monotone contract. Although this observed behavior does not change the superiority of the non-monotone contract for principals, they do not choose this contract type in a significant way. This is what we call the monotonicity puzzle. Detailed investigations of decisions provide a clue for solving the puzzle and a possible explanation for the popularity of monotone contracts.

  20. UPS and DFT investigation of the electronic structure of gas-phase trimesic acid

    Energy Technology Data Exchange (ETDEWEB)

    Reisberg, L., E-mail: rebban@ut.ee [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Pärna, R. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund (Sweden); Kikas, A.; Kuusik, I.; Kisand, V. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Hirsimäki, M.; Valden, M. [Surface Science Laboratory, Optoelectronics Research Centre, Tampere University of Technology, FIN-33101 Tampere (Finland); Nõmmiste, E. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia)

    2016-11-15

    Highlights: • In the current study outer valence band electronic structure of benzene-1,3,5-tricarboxylic acid was interpreted. • Experimental and calculated trimesic acid (TMA) spectrum were compared to ones of benzene and benzoic acid. • It is shown that similarities between MO energies and shapes for benzene and TMA exists. • Addition of carboxyl groups to the benzene ring clearly correlates with increasing binding energy of HOMO. - Abstract: Benzene-1,3,5-tricarboxylic acid (trimesic acid, TMA) molecules in gas-phase have been investigated by using valence band photoemission. The photoelectron spectrum in the binding energy region from 9 to 22 eV is interpreted by using density functional theory calculations. The electronic structure of TMA is compared with benzene and benzoic acid in order to demonstrate changes in molecular orbital energies induced by addition of carboxyl groups to benzene ring.

  1. Synthesis and molecular structure of manganese complexes with ...

    Indian Academy of Sciences (India)

    Administrator

    Manganese-dioxygen complexes are assumed to play significant roles in physiologically important enzymatic reactions including superoxide dismutation, decomposition of hydrogen peroxide and dioxygen evolution from water catalysed by manganese containing proteins 1. Accordingly, the characterization of structurally ...

  2. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    Science.gov (United States)

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-07

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches.

  3. Juvenile neuronal ceroid-lipofuscinosis: clinical and molecular investigation in a large family in Brazil

    Directory of Open Access Journals (Sweden)

    Eugênia Ribeiro Valadares

    2011-02-01

    Full Text Available OBJECTIVE: Juvenile Neuronal Ceroid-Lipofuscinosis (JNCL, CLN 3, Batten Disease (OMIM #204200 belongs to the most common group of neurodegenerative disorders of childhood. We report the clinical data and molecular analysis of a large Brazilian family. METHOD: Family composed of two consanguineous couples and thirty-two children. Clinical data of ten JNCL patients and molecular analyses on 13 participants were obtained. RESULTS: The large 1.02 kb deletion was detected. The most severe phenotype, with autistic behavior, tics and parkinsonism was seen in a 12-year-old female and a milder phenotype in a 14-year-old male. Nyctalopia was the first symptom in one deceased child. The visual loss of six patients has been first observed in the school and not at home. CONCLUSION: The report highlights the phenotypical intrafamily variation in 10 affected children of this family. The molecular investigation of this large family in our metabolic center turned possible the diagnosis, right approach and genetic counseling.

  4. Taking action: A cross-modal investigation of discourse structure

    Directory of Open Access Journals (Sweden)

    Elsi eKaiser

    2012-06-01

    Full Text Available Segmenting stimuli into events and understanding the relations between those events is crucial for understanding the world. For example, on the linguistic level, successful language use requires the ability to recognize semantic coherence relations between events (e.g. causality, similarity. However, relatively little is known about the mental representation of discourse structure. We report two experiments that used a cross-modal priming paradigm to investigate how humans represent the relations between events. Participants repeated a motor action modeled by the experimenter (e.g. rolled a ball towards mini bowling pins to knock them over, and then completed an unrelated sentence-continuation task (e.g. provided a continuation for Peter scratched John. …. In two experiments, we tested whether and how the coherence relations represented by the motor actions (e.g., causal events vs. non-causal events influence participants’ performance in the linguistic task. Our analyses focused on the coherence relations between the prompt sentences and participants’ continuations, as well as the referential shifts in the continuations. As a whole, the results suggest that the mental representations activated by motor actions overlap with the mental representations used during linguistic discourse-level processing, but nevertheless contain fine-grained information about sub-types of causality (reaction vs. consequence. In addition, the findings point to parallels between shifting one’s attention from one event to another and shifting one’s attention from one referent to another, and indicate that the event structure of causal sequences is conceptualized more like single events than like two distinct events. As a whole, the results point towards common representations activated by motor sequences and discourse-semantic relations, and further our understanding of the mental representation of discourse structure, an area that is still not yet well-understood.

  5. Structure investigation of organic molecules on Au(111) surfaces; Strukturuntersuchung organischer Molekuele auf Au(111)-Oberflaechen

    Energy Technology Data Exchange (ETDEWEB)

    Kazempoor, Michel

    2009-02-02

    The present work covers two topics namely the coadsorption of formic acid and water on Au(111) and the structure of biphenylalkanthiole SAMs on Au(111) surfaces. The coadsorption of formic acid and water on Au(111) surfaces has been investigated by means of vibrational and photoelectron spectroscopy (HREELS, XPS). Formic acid adsorbs at 90 K molecularly with vibrational modes characteristic for flat lying zig-zag chains in the mono- and multilayer regime, like in solid formic acid. The structure of the flat lying formic acid chains was determined by low energy electron diffraction (LEED) as a (2r3 x r19) unit cell. Annealing results in a complete desorption at 190 K. Sequential adsorption of formic acid and water at 90 K shows no significant chemical interaction. Upon annealing the coadsorbed layer to 140 K a hydrogenbonded cyclic complex of formic acid with one water molecule could be identified using isotopically labelled adsorbates. Upon further annealing this complex decomposes leaving molecularly adsorbed formic acid on the surface at 160 K, accompanied by a proton exchange between formic acid and water. The influence of the alkane spacer chain length on the structure of biphenylalkanethiols on Au(111) surfaces was investigated as well. A systematic study was done on BPn-SAMs deposited from the gas phase. For every chain length a structure was found by LEED. Furthermore the influence of temperature on the structure was investigated in the range from room temperature up to about 400 K. To obviate influences from different preparation methods BP3 and BP4 was deposited from gas phase and from solution. No LEED spots were observed on BP4 SAMs deposited from solution. For BP3 an influence of the preparation could be excluded. For all BPn-SAMs a good agreement between LEED and STM data's was found. Nevertheless different unit cells were determined by LEED and STM consistent structures could be suggested considering the unit cell size given by LEED and the

  6. Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.

    Science.gov (United States)

    Serrano, Jorge; Moros, Javier; Laserna, J Javier

    2015-03-03

    Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule.

  7. Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein.

    Science.gov (United States)

    Hasiów-Jaroszewska, Beata; Czerwoniec, Anna; Pospieszny, Henryk; Elena, Santiago F

    2011-06-24

    Pepino mosaic virus (PepMV) is considered one of the most dangerous pathogens infecting tomatoes worldwide. The virus is highly diverse and four distinct genotypes, as well as inter-strain recombinants, have already been described. The isolates display a wide range on symptoms on infected plant species, ranging from mild mosaic to severe necrosis. However, little is known about the mechanisms and pattern of PepMV molecular evolution and about the role of individual proteins in host-pathogen interactions. The nucleotide sequences of the triple gene block 3 (TGB3) from PepMV isolates varying in symptomatology and geographic origin have been analyzed. The modes and patterns of molecular evolution of the TGBp3 protein were investigated by evaluating the selective constraints to which particular amino acid residues have been subjected during the course of diversification. The tridimensional structure of TGBp3 protein has been modeled de novo using the Rosetta algorithm. The correlation between symptoms development and location of specific amino acids residues was analyzed. The results have shown that TGBp3 has been evolving mainly under the action of purifying selection operating on several amino acid sites, thus highlighting its functional role during PepMV infection. Interestingly, amino acid 67, which has been previously shown to be a necrosis determinant, was found to be under positive selection. Identification of diverse selection events in TGB3p3 will help unraveling its biological functions and is essential to an understanding of the evolutionary constraints exerted on the Potexvirus genome. The estimated tridimensional structure of TGBp3 will serve as a platform for further sequence, structural and function analysis and will stimulate new experimental advances.

  8. An investigation on non-invasive fungal sinusitis; Molecular identification of etiologic agents

    Directory of Open Access Journals (Sweden)

    Abdolrasoul Mohammadi

    2017-01-01

    Full Text Available Background: Fungal sinusitis is increasing worldwide in the past two decades. It is divided into two types including invasive and noninvasive. Noninvasive types contain allergic fungal sinusitis (AFS and fungus ball. AFS is a hypersensitivity reaction to fungal allergens in the mucosa of the sinonasal tract in atopic individuals. The fungus ball is a different type of noninvasive fungal rhinosinusitis which is delineated as an accumulation of debris and fungal elements inside a paranasal sinus. Fungal sinusitis caused by various fungi such as Aspergillus species, Penicillium, Mucor, Rhizopus, and phaeohyphomycetes. The aim of the present study is to identify fungal species isolated from noninvasive fungal sinusitis by molecular methods. Materials and Methods: During 2015–2016, a total of 100 suspected patients were examined for fungal sinusitis. Functional endoscopic sinus surgery was performed using the Messerklinger technique. Clinical samples were identified by phenotypic and molecular methods. Polymerase chain reaction (PCR sequencing of ITS1-5.8S-ITS2 region and PCR-restriction fragment length polymorphism with Msp I restriction enzyme was performed for molecular identification of molds and yeasts, respectively. Results: Twenty-seven out of 100 suspected cases (27% had fungal sinusitis. Nasal congestion (59% and headache (19% were the most common clinical signs among patients. Fifteen patients (55.5% were male and 12 patients (44.5% were female. Aspergillus flavus was the most prevalent fungal species (26%, followed by Penicillium chrysogenum (18.5% and Candida glabrata species complex (15%. Conclusion: Since clinical manifestations, computed tomography scan, endoscopy, and histopathological findings are very nonspecific in AFS and fungus ball; therefore, molecular investigations are compulsory for precise identification of etiologic agents and appropriate management of these fungal infections.

  9. Advanced understanding on electronic structure of molecular semiconductors and their interfaces

    Science.gov (United States)

    Akaike, Kouki

    2018-03-01

    Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

  10. Role of redox centre in charge transport investigated by novel self-assembled conjugated polymer molecular junctions.

    Science.gov (United States)

    Wang, Zongrui; Dong, Huanli; Li, Tao; Hviid, Rune; Zou, Ye; Wei, Zhongming; Fu, Xiaolong; Wang, Erjing; Zhen, Yonggang; Nørgaard, Kasper; Laursen, Bo W; Hu, Wenping

    2015-06-18

    Molecular electronics describes a field that seeks to implement electronic components made of molecular building blocks. To date, few studies have used conjugated polymers in molecular junctions despite the fact that they potentially transport charge more efficiently than the extensively investigated small-molecular systems. Here we report a novel type of molecular tunnelling junction exploring the use of conjugated polymers, which are self-assembled into ultrathin films in a distinguishable 'planar' manner from the traditional vertically oriented small-molecule monolayers. Electrical measurements on the junctions reveal molecular-specific characteristics of the polymeric molecules in comparison with less conjugated small molecules. More significantly, we decorate redox-active functionality into polymeric backbones, demonstrating a key role of redox centre in the modulation of charge transport behaviour via energy level engineering and external stimuli, and implying the potential of employing tailor-made polymeric components as alternatives to small molecules for future molecular-scale electronics.

  11. Synthesis, structure, spectroscopic investigations, and computational studies of optically pure β-ketoamide

    Energy Technology Data Exchange (ETDEWEB)

    Mtat, D.; Touati, R. [Université de Monastir, Laboratoire de Synthèse Organique Asymétrique et Catalyse Homogène (UR11ES56), Faculté des Sciences (Tunisia); Guerfel, T., E-mail: taha-guerfel@yahoo.fr [Université de Kairouan, Laboratoire d’Electrochimie, Matériaux et Environnement (Tunisia); Walha, K. [Université de Sfax, M.E.S.Lab. Faculté des Sciences de Sfax (Tunisia); Ben Hassine, B. [Université de Monastir, Laboratoire de Synthèse Organique Asymétrique et Catalyse Homogène (UR11ES56), Faculté des Sciences (Tunisia)

    2016-12-15

    Chemical preparation, X-ray single crystal diffraction, IR and NMR spectroscopic investigations of a novel nonlinear optical organic compound (C{sub 17}H{sub 22}NO{sub 2}Cl) are described. The compound crystallizes in the orthorhombic system with the non-centrosymmetric sp. gr. P2{sub 1}2{sub 1}2{sub 1}. In the crystal structure, molecules are interconnected by N–H…O hydrogen bonds forming infinite chains along a axis. The Hirshfeld surface and associated fingerprint plots of the compound are presented to explore the nature of intermolecular interactions and their relative contributions in building the solid-state architecture. The molecular HOMO–LUMO compositions and their respective energy gaps are also drawn to explain the activity of the compound. The first hyperpolarizability β{sub tot} of the title compound is determined using DFT calculations. The optical properties are also investigated by UV–Vis absorption spectrum.

  12. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...... efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from...... an MD trajectory, as another route for final phase acceleration. Our suggestions may be implemented within most MD quench implementations with a few, straightforward lines of code, thus maintaining the appealing simplicity of the MD quench algorithms. In this paper, we also bridge the conceptual gap...

  13. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1969-01-01

    This volume is a consequence of a series of seminars presented by the authors at the Infrared Spectroscopy Institute, Canisius College, Buffalo, New York, over the last nine years. Many participants on an intermediate level lacked a sufficient background in mathematics and quantum mechan­ ics, and it became evident that a non mathematical or nearly nonmathe­ matical approach would be necessary. The lectures were designed to fill this need and proved very successful. As a result of the interest that was developed in this approach, it was decided to write this book. The text is intended for scientists and students with only limited theore­ tical background in spectroscopy, but who are sincerely interested in the interpretation of molecular spectra. The book develops the detailed selection rules for fundamentals, combinations, and overtones for molecules in several point groups. Detailed procedures used in carrying out the normal coordinate treatment for several molecules are also presented. Numerous examples...

  14. The Structural, Functional and Molecular Organization of the Brainstem

    Directory of Open Access Journals (Sweden)

    Rudolf eNieuwenhuys

    2011-06-01

    Full Text Available According to Wilhelm His (1891, 1893 the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature and the ventral basal plate (motor in nature. Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this ‘four-functional-zones’ concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1 the magnocellular vestibular nucleus situated in the viscerosensory zone; (2 the basal plate containing a number of evidently non-motor centres (superior and inferior olives. Nevertheless the ‘functional zonal model’ has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioural profiles, as ‘local hypertrophies’ of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units.

  15. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes

    Science.gov (United States)

    Eskhan, Asma Omar

    Atomic force microscopy has been used to quantify the adherence and mechanical properties of an array of L. monocytogenes strains and their surface biopolymers. First, eight L. monocytogenes strains that represented the two major lineages of the species were compared for their adherence and mechanics at cellular and molecular levels. Our results indicated that strains of lineage' II were characterized by higher adhesion and Young's moduli, longer and more rigid surface biopolymers and lower specific and nonspecific forces when compared to lineage' I strains. Additionally, adherence and mechanical properties of eight L. monocytogenes epidemic and environmental strains were probed. Our results pointed to that environmental and epidemic strains representative of a given lineage were similar in their adherence and mechanical properties when investigated at a cellular level. However, when the molecular properties of the strains were considered, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. Second, the role of environmental pH conditions of growth on the adhesion and mechanics of a pathogenic L. monocytogenes EGDe was investigated. Our results pointed to a transition in the adhesion energies for cells cultured at pH 7. In addition, when the types of molecular forces that govern the adhesion were quantified using Poisson statistical approach and using a new proposed method, specific hydrogen-bond energies dominated the bacterial adhesion process. Such a finding is instrumental to researchers designing methods to control bacterial adhesion. Similarly, bacterial cells underwent a transition in their mechanical properties. We have shown that cells cultured at pH 7 were the most rigid compared to those cultured in lower or higher pH conditions of growth. Due to transitions observed in adherence and mechanics when cells were cultured at pH 7, we hypothesized that

  16. Spectroscopic and computational investigation of the structure and pharmacological activity of 1-benzylimidazole

    Directory of Open Access Journals (Sweden)

    A. Madanagopal

    2017-11-01

    Full Text Available The chemical and pharmacological activity of the compound 1-benzylimidazole was analysed using vibrational, NMR and UV-Visible spectroscopic tools. The necessary data were obtained by recording FT-IR, FT-Raman, NMR and UV-Visible spectra. 1H and 13C NMR spectral chemical shifts were observed and investigated to understand the basis of the antiparasitic, antifungal and antimicrobial activities. The elaborate electronic excitational absorptions in which bathochromic shifts in the UV-Visible spectrum are linked to strong cardiotonic activity are noteworthy. The pharmacodynamic activity was related to the molecular polarization as analysed according to different analytical parameters. The molecular reactivity was studied according to the dislocation of charge levels in frontier molecular orbitals. NBO analysis was carried out to delineate the asymmetric charge interaction transitions among orbitals, which were correlated with the pharmacological behaviour of the compound. The enantiomer errors in the electronic structure have been analysed by simulating ECD and VCD spectra. Keywords: 1-Benzylimidazole, Pharmacological, FT-IR, FT-Raman, NMR, Cardiotonic activity, Enantiomer, ECD and VCD spectra

  17. Electronic structure of monolayer 1T′-MoTe2 grown by molecular beam epitaxy

    Directory of Open Access Journals (Sweden)

    Shujie Tang

    2018-02-01

    Full Text Available Monolayer transition metal dichalcogenides (TMDCs in the 1T′ structural phase have drawn a great deal of attention due to the prediction of quantum spin Hall insulator states. The band inversion and the concomitant changes in the band topology induced by the structural distortion from 1T to 1T′ phases are well established. However, the bandgap opening due to the strong spin-orbit coupling (SOC is only verified for 1T′-WTe2 recently and still debated for other TMDCs. Here we report a successful growth of high-quality monolayer 1T′-MoTe2 on a bilayer graphene substrate through molecular beam epitaxy. Using in situ angle-resolved photoemission spectroscopy (ARPES, we have investigated the low-energy electronic structure and Fermi surface topology. The SOC-induced breaking of the band degeneracy points between the valence and conduction bands is clearly observed by ARPES. However, the strength of SOC is found to be insufficient to open a bandgap, which makes monolayer 1T′-MoTe2 on bilayer graphene a semimetal.

  18. Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

    Energy Technology Data Exchange (ETDEWEB)

    Fröhlich, Markus G., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D., E-mail: SewellT@missouri.edu; Thompson, Donald L., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States)

    2014-01-14

    The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

  19. Anomalous Ambipolar Transport of Organic Semiconducting Crystals via Control of Molecular Packing Structures.

    Science.gov (United States)

    Park, Beomjin; Kim, Kyunghun; Park, Jaesung; Lim, Heeseon; Lanh, Phung Thi; Jang, A-Rang; Hyun, Chohee; Myung, Chang Woo; Park, Seungkyoo; Kim, Jeong Won; Kim, Kwang S; Shin, Hyeon Suk; Lee, Geunsik; Kim, Se Hyun; Park, Chan Eon; Kim, Jin Kon

    2017-08-23

    Organic crystals deposited on 2-dimensional (2D) van der Waals substrates have been widely investigated due to their unprecedented crystal structures and electrical properties. van der Waals interaction between organic molecules and the substrate induces epitaxial growth of high quality organic crystals and their anomalous crystal morphologies. Here, we report on unique ambipolar charge transport of a "lying-down" pentacene crystal grown on a 2D hexagonal boron nitride van der Waals substrate. From in-depth analysis on crystal growth behavior and ultraviolet photoemission spectroscopy measurement, it is revealed that the pentacene crystal at the initial growth stage have a lattice-strained packing structure and unique energy band structure with a deep highest occupied molecular orbital level compared to conventional "standing-up" crystals. The lattice-strained pentacene few layers enable ambipolar charge transport in field-effect transistors with balanced hole and electron field-effect mobilities. Complementary logic circuits composed of the two identical transistors show clear inverting functionality with a high gain up to 15. The interesting crystal morphology of organic crystals on van der Waals substrates is expected to attract broad attentions on organic/2D interfaces for their electronic applications.

  20. Electronic structure of monolayer 1T'-MoTe2 grown by molecular beam epitaxy

    Science.gov (United States)

    Tang, Shujie; Zhang, Chaofan; Jia, Chunjing; Ryu, Hyejin; Hwang, Choongyu; Hashimoto, Makoto; Lu, Donghui; Liu, Zhi; Devereaux, Thomas P.; Shen, Zhi-Xun; Mo, Sung-Kwan

    2018-02-01

    Monolayer transition metal dichalcogenides (TMDCs) in the 1T' structural phase have drawn a great deal of attention due to the prediction of quantum spin Hall insulator states. The band inversion and the concomitant changes in the band topology induced by the structural distortion from 1T to 1T' phases are well established. However, the bandgap opening due to the strong spin-orbit coupling (SOC) is only verified for 1T'-WTe2 recently and still debated for other TMDCs. Here we report a successful growth of high-quality monolayer 1T'-MoTe2 on a bilayer graphene substrate through molecular beam epitaxy. Using in situ angle-resolved photoemission spectroscopy (ARPES), we have investigated the low-energy electronic structure and Fermi surface topology. The SOC-induced breaking of the band degeneracy points between the valence and conduction bands is clearly observed by ARPES. However, the strength of SOC is found to be insufficient to open a bandgap, which makes monolayer 1T'-MoTe2 on bilayer graphene a semimetal.

  1. Molecular Weight and Structural Properties of Biodegradable PLA Synthesized with Different Catalysts by Direct Melt Polycondensation

    Directory of Open Access Journals (Sweden)

    Hyung Woo Lee

    2015-09-01

    Full Text Available Production of biodegradable polylactic acid (PLA from biomassbased lactic acid is widely studied for substituting petro-based plastics or polymers. This study investigated PLA production from commercial lactic acid in a batch reactor by applying a direct melt polycondensation method with two kinds of catalyst, γ-aluminium(III oxide (γ-Al2O3 or zinc oxide (ZnO, in reduced pressure. The molecular weight of the synthesized PLA was determined by capillary viscometry and its structural properties were analyzed by functional group analysis using FT-IR. The yields of polymer production with respect to the theoretical conversion were 47% for γ-Al2O3 and 35% for ZnO. However, the PLA from ZnO had a higher molecular weight (150,600 g/mol than that from γ-Al2O3 (81,400 g/mol. The IR spectra of the synthesized PLA from both catalysts using polycondensation show the same behavior of absorption peaks at wave numbers from 4,500 cm-1 to 500 cm-1, whereas the PLA produced by two other polymerization methods – polycondensation and ring opening polymerization –showed a significant difference in % transmittance intensity pattern as well as peak area absorption at a wave number of 3,500 cm-1 as –OH vibration peak and at 1,750 cm-1 as –C=O carbonyl vibrational peak.

  2. Condensed Tannins from Ficus virens as Tyrosinase Inhibitors: Structure, Inhibitory Activity and Molecular Mechanism

    Science.gov (United States)

    Chai, Wei-Ming; Feng, Hui-Ling; Zhuang, Jiang-Xing; Chen, Qing-Xi

    2014-01-01

    Condensed tannins from Ficus virens leaves, fruit, and stem bark were isolated and their structures characterized by 13C nuclear magnetic resonance spectrometry, high performance liquid chromatography electrospray ionization mass spectrometry, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The results showed that the leaves, fruit, and stem bark condensed tannins were complex mixtures of homo- and heteropolymers of B-type procyanidins and prodelphinidins with degrees of polymerization up to hexamer, dodecamer, and pentadecamer, respectively. Antityrosinase activities of the condensed tannins were studied. The results indicated that the condensed tannins were potent tyrosinase inhibitors. The concentrations for the leaves, fruit, and stem bark condensed tannins leading to 50% enzyme activity were determined to be 131.67, 99.89, and 106.22 μg/ml on monophenolase activity, and 128.42, 43.07, and 74.27 μg/ml on diphenolase activity. The inhibition mechanism, type, and constants of the condensed tannins on the diphenolase activity were further investigated. The results indicated that the condensed tannins were reversible and mixed type inhibitors. Fluorescence quenching, copper interacting, and molecular docking techniques were utilized to unravel the molecular mechanisms of the inhibition. The results showed that the hydroxyl group on the B ring of the condensed tannins could chelate the dicopper irons of the enzyme. Moreover, the condensed tannins could reduce the enzyme product o-quinones into colourless compounds. These results would contribute to the development and design of antityrosinase agents. PMID:24637701

  3. Condensed tannins from Ficus virens as tyrosinase inhibitors: structure, inhibitory activity and molecular mechanism.

    Science.gov (United States)

    Chen, Xiao-Xin; Shi, Yan; Chai, Wei-Ming; Feng, Hui-Ling; Zhuang, Jiang-Xing; Chen, Qing-Xi

    2014-01-01

    Condensed tannins from Ficus virens leaves, fruit, and stem bark were isolated and their structures characterized by 13C nuclear magnetic resonance spectrometry, high performance liquid chromatography electrospray ionization mass spectrometry, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The results showed that the leaves, fruit, and stem bark condensed tannins were complex mixtures of homo- and heteropolymers of B-type procyanidins and prodelphinidins with degrees of polymerization up to hexamer, dodecamer, and pentadecamer, respectively. Antityrosinase activities of the condensed tannins were studied. The results indicated that the condensed tannins were potent tyrosinase inhibitors. The concentrations for the leaves, fruit, and stem bark condensed tannins leading to 50% enzyme activity were determined to be 131.67, 99.89, and 106.22 μg/ml on monophenolase activity, and 128.42, 43.07, and 74.27 μg/ml on diphenolase activity. The inhibition mechanism, type, and constants of the condensed tannins on the diphenolase activity were further investigated. The results indicated that the condensed tannins were reversible and mixed type inhibitors. Fluorescence quenching, copper interacting, and molecular docking techniques were utilized to unravel the molecular mechanisms of the inhibition. The results showed that the hydroxyl group on the B ring of the condensed tannins could chelate the dicopper irons of the enzyme. Moreover, the condensed tannins could reduce the enzyme product o-quinones into colourless compounds. These results would contribute to the development and design of antityrosinase agents.

  4. Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia).

    Science.gov (United States)

    Kawagoshi, Taiki; Nishida, Chizuko; Ota, Hidetoshi; Kumazawa, Yoshinori; Endo, Hideki; Matsuda, Yoichi

    2008-01-01

    Crocodilians have several unique karyotypic features, such as small diploid chromosome numbers (30-42) and the absence of dot-shaped microchromosomes. Of the extant crocodilian species, the Siamese crocodile (Crocodylus siamensis) has no more than 2n = 30, comprising mostly bi-armed chromosomes with large centromeric heterochromatin blocks. To investigate the molecular structures of C-heterochromatin and genomic compartmentalization in the karyotype, characterized by the disappearance of tiny microchromosomes and reduced chromosome number, we performed molecular cloning of centromeric repetitive sequences and chromosome mapping of the 18S-28S rDNA and telomeric (TTAGGG)( n ) sequences. The centromeric heterochromatin was composed mainly of two repetitive sequence families whose characteristics were quite different. Two types of GC-rich CSI-HindIII family sequences, the 305 bp CSI-HindIII-S (G+C content, 61.3%) and 424 bp CSI-HindIII-M (63.1%), were localized to the intensely PI-stained centric regions of all chromosomes, except for chromosome 2 with PI-negative heterochromatin. The 94 bp CSI-DraI (G+C content, 48.9%) was tandem-arrayed satellite DNA and localized to chromosome 2 and four pairs of small-sized chromosomes. The chromosomal size-dependent genomic compartmentalization that is supposedly unique to the Archosauromorpha was probably lost in the crocodilian lineage with the disappearance of microchromosomes followed by the homogenization of centromeric repetitive sequences between chromosomes, except for chromosome 2.

  5. Study on the variations of molecular structures of some biomolecules induced by free electron laser using FTIR spectroscopy

    Science.gov (United States)

    Yang, Limin; Xu, Yizhuang; Su, Yunlan; Wu, Jinguang; Zhao, Kui; Wang, Mingkai; Xu, Jinqiang; Dai, Zhiping; Chen, Jia'er

    2007-05-01

    In this study, free electron laser (FEL) with selective wavelength was used to induce structure changes of biomolecules, which were characterized by FTIR spectroscopy. For understanding of the interactions between FEL and biomolecules as well as biological tissues, the biomolecules investigated are ATP, ADP, AMP, t-RNA, D-ribose and the complex of SmCl 3- D-ribose. Their FTIR spectra before and after irradiation of FEL show molecular structure variations of the samples after irradiation of FEL, especially the rearrangement of their hydrogen bond networks. Along with the various irradiation wavelengths, irradiation time and molecular structures, the changes after irradiation are different for these molecules. In the FTIR spectra after irradiation, the phenomenon that the bands split into several peaks indicates the existence of several structures, conformations and configurations, which may be prompted by multiple photons process induced by FEL. After irradiation, the changes in their IR spectra indicate the occurrence of stable or metastable states of the molecules after irradiation, which illustrated that IR spectroscopy is a sensitive probe of molecular structure and provides us a method to detect the information related to the mechanism of the irradiation process.

  6. Magnetic structure of molecular magnet Fe[Fe(CN) 6

    Indian Academy of Sciences (India)

    We have studied the magnetic structure of Fe[Fe(CN)6]·4H2O, prepared by precipitation method, using neutron diffraction technique. Temperature dependent DC magnetization study down to 4.2 K shows that the compound undergoes from a high temperature disordered (paramagnetic) to an ordered magnetic phase ...

  7. Efficient synthesis and molecular structure of 2-hydroxyisophthaldehyde

    NARCIS (Netherlands)

    Zondervan, C; van den Beuken, E.K; Kooijman, H.; Spek, A.L.; Feringa, B.L.

    1997-01-01

    A new highly effective procedure has been developed for the preparation of 2-hydroxyisophthaldehyde from 2,6-dimethylphenol. The X-ray crystal structure shows infinite chains of molecules joined by hydrogen bonds. (C) 1997 Published by Elsevier Science Ltd.

  8. Molecular dynamic study of the U-Mo alloy structure

    International Nuclear Information System (INIS)

    Kolotova, L.N.; Smirnova, D.E.; Starikov, S.V.

    2015-01-01

    The method of atomistic simulations was used to study the structure of the quasi-equilibrium tetragonal phase U-Mo, formed during crystallization of the melt. Radial distribution function and bond-angle distribution function were calculated for the analysis of uranium and molybdenum structures in the alloy. The lattice constants of the uranium-molybdenum alloy were obtained for different concentrations of molybdenum. Results of calculations are in good agreement with experimental data and confirm the anisotropy of the lattice at low molybdenum concentrations. Temperature of the transition from anisotropic tetragonal phase to a body-centered cubic phase was calculated for different concentrations of molybdenum. It was found that the anisotropy is a consequence of the local arrangement of uranium atoms in the U-Mo alloy structure. It is shown that the anisotropy disappears with increase of molybdenum concentration not due to changes in the uranium atoms arrangement. It disappears because the number of molybdenum atoms – “stabilization centers of isotropy” increases. Also dependence of the enthalpy of mixing for uranium-molybdenum alloy on molybdenum concentration was calculated. It is shown that anomalous enthalpy of mixing - molybdenum concentration dependence, known from the experiments, can be obtained only when the atomic structure of the alloy is taking into account. [ru

  9. Refining of crystal structures of macromolecules with molecular dynamics

    International Nuclear Information System (INIS)

    Mascarenhas, Y.P.

    1988-01-01

    In this work, the refining of crystal structures of macromolecules is discussed. The annealing method is employed and it can be previewed that, this method, will be largely used in the future for protein crystallography. (A.C.A.S.) [pt

  10. The crystal and molecular structure of 2,3-diazanaphthalene

    NARCIS (Netherlands)

    Huiszoon, C.; van de Waal, B.W.; van Egmond, A.B.; Harkema, Sybolt

    1972-01-01

    The structure of 2,3-diazanaphthalene (phthalazine) has been determined by X-ray methods. Cell constants and intensity data were obtained with a single-crystal diffractometer. The space group is Pbca. Cell constants are 13.695, 10.557 and 9.285 A. There are eight nearly planar molecules in the unit

  11. The crystal and molecular structure of 2,7-diazanaphthalene

    NARCIS (Netherlands)

    Huiszoon, C.; van Hummel, G.J.; van den Ham, D.M.W.

    1977-01-01

    X-ray diffraction data were collected at 20°C on a computer-controlled Philips diffractometer (PW 1100). The structure was solved by direct methods and refined by the full-matrix least-squares method to an R of 0.065 (weighted R 0.046). The molecule in the crystal is of lower symmetry than C2,.. The

  12. Molecular structure and intramolecular hydrogen bonding in 2 ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 4 ... To understand the substitution effects on the nature of IHB and the electronic structure of the chelated ring system, the vibrational frequencies, 1H chemical shift, topological parameters, natural bond orders and natural charges over atoms involved in the ...

  13. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    AJL

    2012-04-19

    Apr 19, 2012 ... The 3-D protein model in this study was predicted by the comparative protein modeling program SWISS-MODEL automated protein modeling server, based upon deep- sea bacterium Geobacillus sp. strain HTA-462. (2ze0A.pdb) Protein Data Bank structure file (Figure 8). DISCUSSION. The rBAT proteins ...

  14. Molecular structures of viruses from Raman optical activity

    DEFF Research Database (Denmark)

    Blanch, Ewan W.; Hecht, Lutz; Syme, Christopher D.

    2002-01-01

    A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity to chira...

  15. CNDO/SCF MOLECULAR ORBITAL STRUCTURAL STUDIES AND ...

    African Journals Online (AJOL)

    a

    at 77 oK has been studied using UV and visible spectroscopy [4]. Lahir has studied charge transfer complex formation between, oxytetracycline and tetracycline, with purines, pyrimidines and amino acids [5]. A CNDO study of the tautomeric structure of uracil and its effect on the electrochemical corrosion behavior of mild ...

  16. Structural Investigation of Biological and Semiconductor Nanostructures with Nonlinear Multicontrast Microscopy

    Science.gov (United States)

    Cisek, Richard

    Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities

  17. Investigation of the molecular relationship between breast cancer and obesity by candidate gene prioritization methods

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi

    2015-10-01

    Full Text Available Background: Cancer and obesity are two major public health concerns. More than 12 million cases of cancer are reported annually. Many reports confirmed obesity as a risk factor for cancer. The molecular relationship between obesity and breast cancer has not been clear yet. The purpose of this study was to investigate priorities of effective genes in the molecular relationship between obesity and breast cancer. Methods: In this study, computer simulation method was used for prioritizing the genes that involved in the molecular links between obesity and breast cancer in laboratory of systems biology and bioinformatics (LBB, Tehran University, Tehran, Iran, from March to July 2014. In this study, ENDEAVOUR software was used for prioritizing the genes and integrating multiple data sources was used for data analysis. Training genes were selected from effective genes in obesity and/or breast cancer. Two groups of candidate genes were selected. The first group was included the existential genes in 5 common region chromosomes (between obesity and breast cancer and the second group was included the results of genes microarray data analysis of research Creighton, et al (In 2012 on patients with breast cancer. The microarray data were analyzed with GER2 software (R online software on GEO website. Finally, both training and candidate genes were entered in ENDEAVOUR software package. Results: The candidate genes were prioritized to four style and five genes in ten of the first priorities were repeated twice. In other word, the outcome of prioritizing of 72 genes (Product of microarray data analysis and genes of 5 common chromosome regions (Between obesity and breast cancer showed, 5 genes (TNFRSF10B, F2, IGFALS, NTRK3 and HSP90B1 were the priorities in the molecular connection between obesity and breast cancer. Conclusion: There are some common genes between breast cancer and obesity. So, molecular relationship is confirmed. In this study the possible effect

  18. Bicelles: A natural 'molecular goniometer' for structural, dynamical and topological studies of molecules in membranes.

    Science.gov (United States)

    Diller, Anna; Loudet, Cécile; Aussenac, Fabien; Raffard, Gérard; Fournier, Sylvie; Laguerre, Michel; Grélard, Axelle; Opella, Stanley J; Marassi, Francesca M; Dufourc, Erick J

    2009-06-01

    Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called 'bicelles' that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14-18 carbons) and short chain phospholipids (6-8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural 'molecular goniometer' for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes.

  19. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations.

    Science.gov (United States)

    Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha

    2018-02-01

    Filamentous temperature-sensitive protein Z (FtsZ) is a protein encoded by the FtsZ gene that assembles into a Z-ring at the future site of the septum of bacterial cell division. Structurally, FtsZ is a homolog of eukaryotic tubulin but has low sequence similarity; this makes it possible to obtain FtsZ inhibitors without affecting the eukaryotic cell division. Computational studies were performed on a series of substituted 3-arylalkoxybenzamide derivatives reported as inhibitors of FtsZ activity in Staphylococcus aureus. Quantitative structure-activity relationship models (QSAR) models generated showed good statistical reliability, which is evident from r 2 ncv and r 2 loo values. The predictive ability of these models was determined and an acceptable predictive correlation (r 2 Pred ) values were obtained. Finally, we performed molecular dynamics simulations in order to examine the stability of protein-ligand interactions. This facilitated us to compare free binding energies of cocrystal ligand and newly designed molecule B1. The good concordance between the docking results and comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) contour maps afforded obliging clues for the rational modification of molecules to design more potent FtsZ inhibitors.

  20. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone. Copyright © 2012 Elsevier Ltd. All rights reserved.