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Sample records for investigate molecular structure

  1. 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,.

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

    Indian Academy of Sciences (India)

    tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

  3. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  4. 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.

  5. 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.

  6. Molecular-orbital and structural descriptors in theoretical investigation of electroreduction of nitrodiazoles

    Directory of Open Access Journals (Sweden)

    BRANKO KOLARIC

    2005-07-01

    Full Text Available It is shown how a simple theoretical approach can be used for the investigation of electro-organic reactions.Mononitroimidazoles and mononitropyrazoles were studied by the semiempirical MNDO-PM3 molecular orbital method. The electrochemical reduction potentials of diazoles have been correlated with the energy of the lowest unoccupied molecular orbital (LUMO. It was found that an admirable correlation could be obtained by the introduction of simple structural descriptors as a correction to the energy of the LUMO. The interaction of a molecule with its surrounding depends on electrostatic potential and on steric hindrance. Most of these steric effects are taken into account using two parameters having a very limited set of integer values. The first (b is the position of a ring substituent regarding ring nitrogens, which accounts for the different orientations of dipole moments and for the different shape of the electrostatic potential. The second (structural parameter (t is the type of the ring, which accounts mostly for different modes of electrode approach, and for different charge polarization patterns in two diazole rings. The extended correlation with ELUMO, b and t, is very good, having a regression coefficient r = 0.991. The intrinsic importance of b and t is exemplified by their high statistical weight.

  7. Molecular- and nm-scale Investigation of the Structure and Compositional Heterogeneity of Naturally Occurring Ferrihydrite

    Science.gov (United States)

    Cismasu, C.; Michel, F. M.; Stebbins, J. F.; Tcaciuc, A. P.; Brown, G. E.

    2008-12-01

    Ferrihydrite is a hydrated Fe(III) nano-oxide that forms in vast quantities in contaminated acid mine drainage environments. As a result of its high surface area, ferrihydrite is an important environmental sorbent, and plays an essential role in the geochemical cycling of pollutant metal(loid)s in these settings. Despite its environmental relevance, this nanomineral remains one of the least understood environmental solids in terms of its structure (bulk and surface), compositional variations, and the factors affecting its reactivity. Under natural aqueous conditions, ferrihydrite often precipitates in the presence of several inorganic compounds such as aluminum, silica, arsenic, etc., or in the presence of organic matter. These impurities can affect the molecular-level structure of naturally occurring ferrihydrite, thus modifying fundamental properties that are directly correlated with solid-phase stability and surface reactivity. Currently there exists a significant gap in our understanding of the structure of synthetic vs. natural ferrihydrites, due to the inherent difficulties associated to the investigation of these poorly crystalline nanophases. In this study, we combined synchrotron- and laboratory-based techniques to characterize naturally occurring ferrihydrite from an acid mine drainage system situated at the New Idria mercury mine in California. We used high-energy X-ray total scattering and pair distribution function analysis to elucidate quantitative structural details of these samples. We have additionally used scanning transmission X-ray microscopy high resolution imaging (30 nm) to evaluate the spatial relationship of major elements Si, Al, and C within ferrihydrite. Al, Si and C K-edge near- edge X-ray absorption fine structure spectroscopy and 27Al nuclear magnetic resonance spectroscopy were used to obtain short-range structural information. By combining these techniques we attain the highest level of resolution permitted by current analytical

  8. Theoretical Investigation on the Molecular Structure, Vibrational and NMR Spectra of N, N, 4-Tri chlorobenzenesulfonamide

    International Nuclear Information System (INIS)

    Cinar, M.

    2008-01-01

    In the present study, the structural properties of N,N,4-Tri chlorobenzenesulfonamide have been studied extensively using Density Functional Theory (DFT) employing B3LYP exchange correlation. The geometry of the molecule was fully optimized, vibrational spectrum was calculated and fundamental vibrations were assigned based on the scaled theoretical wavenumbers. The 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of the compound were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. To investigate the basis set effects, calculations were performed at the 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p) levels. Finally, geometric parameters, vibrational bands and isotropic chemical shifts were compared with available experimental data of compound. The fully optimized geometry of the molecule was found to be consistent with the X-ray crystal structure. The observed and calculated frequencies and chemical shifts were found to be in very good agreement. The computed results appear that the basis set has slight effect on the molecular geometry of N,N,4-Tri chlorobenzenesulfonamide

  9. 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.

  10. Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

    Science.gov (United States)

    Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

    2017-12-01

    Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

  11. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

    Directory of Open Access Journals (Sweden)

    Sathishkumar Natarajan

    2015-12-01

    Full Text Available Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin.

  12. 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.).

  13. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400 (Thailand); Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong [National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Pratontep, Sirapat [College of KMITL Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok (Thailand); Puttipipatkhachorn, Satit, E-mail: uracha@nanotec.or.th [Department of Manufacturing Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400 (Thailand)

    2010-03-26

    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 {gamma}-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 {gamma}-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 ({sup 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 {sup 1}H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of {gamma}-oryzanol inside the lipid nanoparticles, the {sup 1}H-NMR revealed that the chemical shifts of the liquid lipid in {gamma}-oryzanol loaded systems were found at rather higher field than those in {gamma}-oryzanol free systems, suggesting incorporation of {gamma}-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 {gamma}-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models

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

    Science.gov (United States)

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

    2010-03-01

    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 (1H-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 1H-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 1H-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

  16. 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

  17. 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.

  18. Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

    Science.gov (United States)

    Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.

    2013-01-01

    Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646

  19. 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

  20. 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)

  1. 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

  2. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    ···π interactions are accommodated by electrostatic complementarity. The crystal structure of both the α- and the β-polymorph of hydroquinone is presented in Chapter 6 with focus on close intermolecular contacts between the molecules via Hirshfeld surface analysis. The charge density distribution of the empty β....... The last chapter of this dissertation presents the analysis of intermolecular interaction using both the Hirshfeld surface and charge density distribution of the acetonitrile β-hydroquinone clathrate. The local packing and related close contacts are examined by breakdown of the fingerprint plots revealing......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  3. 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

  4. 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)

  5. Structural investigation of water-acetonitrile mixtures: An ab initio, molecular dynamics and X-ray diffraction study

    International Nuclear Information System (INIS)

    Bako, Imre; Megyes, Tuende; Palinkas, Gabor

    2005-01-01

    In this work, we present a study on water-acetonitrile (AN) mixtures by molecular dynamics ab initio and X-ray diffraction techniques. Comparison of the experimental total G(r) functions of the mixtures with the results of molecular dynamics simulation shows an overall good agreement. The properties of hydrogen bonded clusters (water clusters, and water-AN clusters) in these mixtures have been determined. Two different types of AN-water dimers were identified by ab initio quantum chemical calculation. One of these structures proved to be a true H-bonded dimer and the other a dipole bound dimer

  6. 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.

  7. 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.

  8. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    Beyer, Theresa

    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 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 -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

  9. 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

  10. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    Molecular Structure of Nucleic Acids. A Structure for Deoxyribose Nucleic Acid. J. D. Watson and F. H. C. Crick. Medical Research Council Unit for the Study of the Molecular Structure of Biological. Systems, Cavendish Laboratory, Cambridge. April 2. We wish to suggest a structure for the salt of deoxyribose nucleic acid ...

  11. 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.

  12. Structural Molecular Biology 2017 | SSRL

    Science.gov (United States)

    Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

  13. 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

  14. Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation.

    Science.gov (United States)

    Agarwal, Shweta; Tyagi, Gunjan; Chadha, Deepti; Mehrotra, Ranjana

    2017-01-01

    Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (K a ) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×10 2 M -1 , 4.923×10 2 M -1 and 4.223×10 2 M -1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and

  15. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  16. Theoretical investigation of molecular structure and vibrational spectra of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile molecule

    International Nuclear Information System (INIS)

    Avci, D.

    2005-01-01

    The molecular geometry and vibrational frequencies of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile 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 and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of 4,5-bis-(2-isopropyl-5-methylphenoxy) phthalonitrile 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

  17. 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

    -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...... different initial orientations of the peptide converged to the same final equilibrium orientation of the peptide relative to the bilayer. The kick-shaped conformation was observed only in one of the two simulations....... of the peptide in a membrane environment (previously solved only in solution [R.L. Fahrner, T. Dieckmann, S.S.L. Harwig, R.I. Lehrer, D. Eisenberg, J. Feigon, Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes. Chemistry and Biology, 3 (1996) 543...

  18. 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"B"O, and semiexperimental, r_e"S"E) 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

  19. Investigation of Pseudomonas aeruginosa quorum-sensing signaling system for identifying multiple inhibitors using molecular docking and structural analysis methodology.

    Science.gov (United States)

    Soheili, Vahid; Bazzaz, Bibi Sedigheh Fazly; Abdollahpour, Nooshin; Hadizadeh, Farzin

    2015-12-01

    Pseudomonas aeruginosa is an opportunistic human pathogen and a common Gram-negative bacterium in hospital-acquired infections. It causes death in many burn victims, cystic-fibrosis and neutropenic-cancer patients. It is known that P. aeruginosa biofilm maturation and production of cell-associated and extracellular virulence factors such as pyocyanin, elastase and rhamnolipids are under the control of a quorum-sensing (QS) system. Among several proteins involved in the Pseudomonas QS mechanism, LasR and PqsE play an important role in its cascade signaling system. They can cause increases in QS factors, biofilm maturation, and the production of virulence factors. Therefore, inhibition of these proteins can reduce the pathogenicity of P. aeruginosa. According to the structure of corresponding auto-inducers bound to these proteins, in silico calculations were performed with some non-steroidal anti-inflammatory drugs (NSAIDs) to estimate possible interactions and find the co-inhibitors of LasR and PqsE. The results showed that oxicams (Piroxicam and Meloxicam) can interact well with active sites of both proteins with the Ki of 119.43 nM and 4.0 μM for Meloxicam and 201.39 nM and 4.88 μM against LasR and PqsE, respectively. These findings suggested that Piroxicam and Meloxicam can be used as potential inhibitors for control of the P. aeruginosa QS signaling system and biofilm formation, and may be used in the design of multiple inhibitors. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

    Gouder, S.; Mahamdi, R.; Aouassa, M.; Escoubas, S.; Favre, L.; Ronda, A.; Berbezier, I.

    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 1−x Ge 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 and low

  1. Molecular Structure of Membrane Tethers

    NARCIS (Netherlands)

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2012-01-01

    Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains

  2. Spectroscopic and structural investigation of interaction of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt with molecular iodine

    Science.gov (United States)

    Ivolgina, Victoria A.; Chernov'yants, Margarita S.

    2018-06-01

    The interest in the study of heteroaromatic thioamides which are known to exhibit antithyroid activity is stimulated by the variety and an unusual structure their complexes with molecular iodine. The directions of dithiones investigation are diversity enough, however a few works are devoted to the study them as the potential thyreostatics. The ability of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thion potassium salt to form the outer-sphere charge-transfer complex in dilute chloroform solution, coordinating 2 iodine molecules has been studied by UV-vis spectroscopy (lgβ = 7.91). The compound of the 5,5‧-disulfanediylbis(3-phenyl-1,3,4-thiadiazole-2(3H)-thione) - product of irreversible oxidation of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt has been isolated and characterized by X-ray diffraction. Intermolecular interactions between sulfur atoms are observed with very short interatomic distance, shorter than sum of van der Waals radii. The contact between heterocyclic sulfur and heterocyclic nitrogen is also slightly short - 3.169 Å (0.053 Å less than vdW radii sum). This investigation constitutes a starting point for study of novel antithyroid drugs in future.

  3. Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

    Science.gov (United States)

    Ramesh, Gaddam; Reddy, Byru Venkatram

    2018-05-01

    In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of Osbnd H⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6-311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular Osbnd H⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular Osbnd H⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm-1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm-1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO

  4. Investigation of the Influence of PLA Molecular Structure on the Crystalline Forms (α’ and α and Mechanical Properties of Wet Spinning Fibres

    Directory of Open Access Journals (Sweden)

    Michał Puchalski

    2017-01-01

    Full Text Available In this paper, the influence of the molecular structure of polylactide (PLA—characterised by its molar mass and content of d-lactide isomer—on the molecular ordering and α’–α form transition during fibre manufacturing by the wet spinning method is described. Fibres were studied by wide-angle X-ray diffraction (WAXD and differential scanning calorimetry (DSC. Additionally, the physical and mechanical properties of the fibres were determined. This study also examines the preliminary molecular ordering and crystallisation of PLA fibres at various draw ratios. The performed experiments clearly show the dependence of the molecular ordering of PLA on the molar mass and d-lactide content during the wet spinning process. The fibres manufactured from PLA with the lowest content of d-lactide and the lowest molar mass were characterised by a higher tendency for crystallisation and a higher possibility to undergo the disorder-to-order phase transition (α’ to α form. The structural changes in PLA explain the observed changes in the physical and mechanical properties of the obtained fibres.

  5. Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.

    Directory of Open Access Journals (Sweden)

    C George Priya Doss

    Full Text Available Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA.In this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T and rs1803120 (P311S were taken further for structural analysis.Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis.

  6. Containment structure tendon investigation

    International Nuclear Information System (INIS)

    Fulton, J.F.; Murray, K.H.

    1983-01-01

    The paper describes an investigation into the possible causes of lower-than-predicted tendon forces which were measured during past tendon surveillances for a concrete containment. The containment is post tensioned by vertical tendons which are anchored into a rock foundation. The tendons were originally stressed in 1969, and lift-off tests were performed on six occasions subsequent to this date over a period of 11 years. The tendon forces measured in these tests were generally lower than predicted, and by 1979 the prestress level in the containment was only marginally above the design requirement. The tendons were retensioned in 1980, and by this time an investigation into the possible causes was underway. Potential causes investigated include the rock anchors and surrounding rock, elastomeric pad creep, wire stresses, thermal effects, stressing equipment and lift-off procedures, and wire stress relaxation. The investigation activities included stress relaxation testing of wires pulled from actual tendons. The stress relaxation test program included wire specimens at several different temperature and initial stress levels and the effect of a varying temperature history on the stress relaxation property of the wires. For purpose of future force predictions of the retensioned tendons, the test program included tests to determine the effect on stress relaxation due to restressing the wires after they had relaxed for 1000 hours and 10,000 hours. (orig./GL)

  7. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    Science.gov (United States)

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  8. 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,...

  9. 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.

  10. 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:

  11. Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

    Science.gov (United States)

    Costa, Renyer A.; Oliveira, Kelson M. T.; Costa, Emmanoel Vilaça; Pinheiro, Maria L. B.

    2017-10-01

    A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline is presented using the Becke three-parameter Lee-Yang-Parr function (B3LYP) and 6-311G(2d,p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing close values. The calculated HOMO-LUMO gap values showed that the presence of substituents in the benzene ring influences the quantum properties which are directly related to the reactive properties. Theoretical UV spectra agreed well with the measured experimental data, with bands assigned. In addition, Natural Bond Orbitals (NBOs), Mapped molecular electrostatic potential surface (MEPS) and NLO calculations were also performed at the same theory level. The theoretical vibrational analysis revealed several characteristic vibrations that may be used as a diagnostic tool for other strychnobrasiline type alkaloids, simplifying their identification and structural characterization. Molecular docking calculations with DNA Topoisomerase II-DNA complex showed binding free energies values of -8.0 and -9.5 kcal/mol for strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of -10.0 kcal/mol, suggesting that strychnobrasiline derivative alkaloids might exhibit an antineoplastic activity.

  12. Experimental and theoretical investigation on the molecular structure, spectroscopic and electric properties of 2,4-dinitrodiphenylamine, 2-nitro-4-(trifluoromethyl)aniline and 4-bromo-2-nitroaniline

    Science.gov (United States)

    Hernández-Paredes, Javier; Hernández-Negrete, Ofelia; Carrillo-Torres, Roberto C.; Sánchez-Zeferino, Raúl; Duarte-Moller, Alberto; Alvarez-Ramos, Mario E.

    2015-10-01

    2,4-Dinitrodiphenylamine (I), 2-nitro-4-(trifluoromethyl)aniline (II) and 4-bromo-2-nitroaniline (III) have been investigated by DFT and experimental FTIR, Raman and UV-Vis spectroscopies. The gas-phase molecular geometries were consistent with similar compounds already reported in the literature. From the vibrational analysis, the main functional groups were identified and their absorption bands were assigned. Some differences were found between the calculated and the experimental UV-Vis spectra. These differences were analyzed and explained in terms of the TD-DFT/B3LYP limitations, which were mainly attributed to charge-transfer (CT) effects. These findings were in agreement with previous works, which reported that TD-DFT/B3LYP calculations diverge from experimental results when the electronic transitions involve CT. Despite this, TD-DFT/B3LYP calculations provided satisfactory results and a detailed description of the electronic transitions involved in the absorption bands of the UV-Vis spectra. In terms of the NLO properties, it was found that compound (I) is a good candidate for NLO applications and deserves further study due to its good β values. However, the β values for compounds (II) and (III) were negatively affected compared to those found on o-nitroaniline.

  13. 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

    2015-01-25

    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 (C1C16) 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. (1)H and (13)C 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Synthesis, molecular structure, FT-IR and XRD investigations of 2-(4-chlorophenyl)-2-oxoethyl 2-chlorobenzoate: a comparative DFT study.

    Science.gov (United States)

    Chidan Kumar, C S; Fun, Hoong Kun; Tursun, Mahir; Ooi, Chin Wei; Chandraju, Siddegowda; Quah, Ching Kheng; Parlak, Cemal

    2014-04-24

    2-(4-Chlorophenyl)-2-oxoethyl 2-chlorobenzoate has been synthesized, its structural and vibrational properties have been reported using FT-IR and single-crystal X-ray diffraction (XRD) studies. The conformational analysis, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the synthesized compound (C15H10Cl2O3) have been examined by means of Becke-3-Lee-Yang-Parr (B3LYP) density functional theory (DFT) method together with 6-31++G(d,p) basis set. Furthermore, reliable conformational investigation and vibrational assignments have been made by the potential energy surface (PES) and potential energy distribution (PED) analyses, respectively. Calculations are performed with two possible conformations. The title compound crystallizes in orthorhombic space group Pbca with the unit cell dimensions a=12.312(5) Å, b=8.103(3) Å, c=27.565(11) Å, V=2750.0(19) Å(3). B3LYP method provides satisfactory evidence for the prediction of vibrational wavenumbers and structural parameters. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. 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...

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

    African Journals Online (AJOL)

    was coupled with low molecular weight chitosan (LMWC) using carbodiimide chemistry. .... High molecular weight chitosan (minimum 85% ..... membrane permeability of drug and mutual repulsion ... coating thickness and the lower solubility of.

  17. 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.

  18. 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)

  19. 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.

  20. New Pyrazole-Hydrazone Derivatives: X-ray Analysis, Molecular Structure Investigation via Density Functional Theory (DFT) and Their High In-Situ Catecholase Activity.

    Science.gov (United States)

    Karrouchi, Khalid; Yousfi, El Bekkaye; Sebbar, Nada Kheira; Ramli, Youssef; Taoufik, Jamal; Ouzidan, Younes; Ansar, M'hammed; Mabkhot, Yahia N; Ghabbour, Hazem A; Radi, Smaail

    2017-10-25

    The development of low-cost catalytic systems that mimic the activity of tyrosinase enzymes (Catechol oxidase) is of great promise for future biochemistry technologic demands. Herein, we report the synthesis of new biomolecules systems based on hydrazone derivatives containing a pyrazole moiety ( L1 - L6 ) with superior catecholase activity. Crystal structures of L1 and L2 biomolecules were determined by X-ray single crystal diffraction (XRD). Optimized geometrical parameters were calculated by density functional theory (DFT) at B3LYP/6-31G (d, p) level and were found to be in good agreement with single crystal XRD data. Copper (II) complexes of the compounds ( L1 - L6 ), generated in-situ, were investigated for their catalytic activities towards the oxidation reaction of catechol to ortho -quinone with the atmospheric dioxygen, in an attempt to model the activity of the copper containing enzyme tyrosinase. The studies showed that the activities depend on four parameters: the nature of the ligand, the nature of counter anion, the nature of solvent and the concentration of ligand. The Cu(II)-ligands, given here, present the highest catalytic activity (72.920 μmol·L -1 ·min -1 ) among the catalysts recently reported in the existing literature.

  1. Biocompatible Materials Based on Self-Assembling Peptides on Ti25Nb10Zr Alloy: Molecular Structure and Organization Investigated by Synchrotron Radiation Induced Techniques

    Directory of Open Access Journals (Sweden)

    Valeria Secchi

    2018-03-01

    Full Text Available In this work, we applied advanced Synchrotron Radiation (SR induced techniques to the study of the chemisorption of the Self Assembling Peptide EAbuK16, i.e., H-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-NH2 that is able to spontaneously aggregate in anti-parallel β-sheet conformation, onto annealed Ti25Nb10Zr alloy surfaces. This synthetic amphiphilic oligopeptide is a good candidate to mimic extracellular matrix for bone prosthesis, since its β-sheets stack onto each other in a multilayer oriented nanostructure with internal pores of 5–200 nm size. To prepare the biomimetic material, Ti25Nb10Zr discs were treated with aqueous solutions of EAbuK16 at different pH values. Here we present the results achieved by performing SR-induced X-ray Photoelectron Spectroscopy (SR-XPS, angle-dependent Near Edge X-ray Absorption Fine Structure (NEXAFS spectroscopy, FESEM and AFM imaging on Ti25Nb10Zr discs after incubation with self-assembling peptide solution at five different pH values, selected deliberately to investigate the best conditions for peptide immobilization.

  2. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... 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...

  3. The Molecular Structure of Penicillin

    Science.gov (United States)

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  4. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  5. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  6. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  7. One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT), X-ray Analysis, and Their Biological Activities.

    Science.gov (United States)

    Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z E

    2016-06-28

    Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity.

  8. 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.

  9. 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

  10. Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

    Science.gov (United States)

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John... encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

  11. Learning surface molecular structures via machine vision

    Science.gov (United States)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  12. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

  13. Molecular Structure of Human-Liver Glycogen.

    Directory of Open Access Journals (Sweden)

    Bin Deng

    Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

  14. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  15. 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

  16. Characteristics studies of molecular structures in drugs

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-05-01

    Full Text Available In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined. Furthermore, the Wiener related indices of distance-regular structure are also considered.

  17. Molecular structure, Hirshfeld surface analysis, theoretical investigations and nonlinear optical properties of a novel crystalline chalcone derivative: (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl)prop-2-en-1-one

    Science.gov (United States)

    Pramodh, B.; Lokanath, N. K.; Naveen, S.; Naresh, P.; Ganguly, S.; Panda, J.

    2018-06-01

    In the present work, the crystal structure of a novel chalcone derivative, (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl) prop-2-en-1-one has been confirmed by X-ray diffraction studies. Hirshfeld surface analysis was carried out to explore the intermolecular interactions. From the Hirshfeld surface analysis it was observed that H⋯H (26.7%) and C⋯H (26.3%) are the major contributors to the intermolecular interactions which stabilizes the crystal structure. The coordinates were optimized using the density functional theory (DFT) calculations using B3LYP hybrid functions with 6-31G(d) basis set. The structural parameters obtained from XRD studies compliment with those calculated using DFT calculations. The HOMO and LUMO energy gap was found to be 4.1778 eV. The molecular electrostatic potential (MEP) was plotted to identify the possible reactions sites of the molecule. Further, non-linear optical (NLO) properties were investigated by calculating hyperpolarizabilities which indicate that the title compound would be a potential candidate for the NLO applications.

  18. Marine Biotoxins: Laboratory Culture and Molecular Structure

    Science.gov (United States)

    1991-01-21

    ciguateric carnivorous fishes in concentrations ranging from I to 10 ppb. Its molecular structure has been elucidated. It has been isolated from toxic...American Chemical Society, Washington, DC, 1984, pp 217-329. 6. Med. J. Australia 1986, 145 (11/12), 558; 584-5M). 7. "Toxic Plants and Animals A Guide...isolated and grown in the laboratory. Lethality of crude acetone and methanol extracts were assa~ed by ip injection into mice. In vitro cytotoxicity and

  19. Synthesis, molecular structure, FT-IR, Raman, XRD and theoretical investigations of (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one.

    Science.gov (United States)

    Chidan Kumar, Chandraju Sadolalu; Fun, Hoong Kun; Parlak, Cemal; Rhyman, Lydia; Ramasami, Ponnadurai; Tursun, Mahir; Chandraju, Siddegowda; Quah, Ching Kheng

    2014-11-11

    A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory method, employing, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P2₁/c with the unit cell parameters a=5.7827(8)Å, b=14.590(2)Å, c=16.138(2)Å and β=89.987 (°). The CC bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. 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.

  1. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  2. Structural investigations of yeast mannans

    International Nuclear Information System (INIS)

    Rademacher, K.H.

    1983-01-01

    Cell wall mannans were isolated from 8 different Candida species and separated in oligosaccharides by partial acetolysis. After gel chromatography specific acetolysis patterns were obtained. The 13 C NMR spectra of mannans and oligosaccharides were recorded. Signals at delta = 93.1 - 105.4 were assigned to certain chemical structures. Both the spectral patterns and the acetolysis patterns of the yeast mannans can be used for the discrimination of related yeasts. (author)

  3. C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach

    International Nuclear Information System (INIS)

    Boccia, A.; Lanzilotto, V.; Marrani, A. G.; Zanoni, R.; Stranges, S.; Alagia, M.; Fronzoni, G.; Decleva, P.

    2012-01-01

    We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the σ/π hyperconjugation in EtFC and the π-conjugation in VFC and EFC.

  4. Molecular structure of the lecithin ripple phase

    Science.gov (United States)

    de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

    2005-04-01

    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 one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation | structural model

  5. Structure investigations of electrodeposited nickel

    International Nuclear Information System (INIS)

    Vertes, A.; Czako-Nagy, I.; Lakatos-Varsanyi, M.; Brauer, G.; Leidheiser, H. Jr

    1981-01-01

    Electrodeposited nickel samples were 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), their concentrations are obtained from the trapping model. The second one possibly denotes annihilation at voids, the number of which is dependent on the stress in the deposit. The Moessbauer results show differences in the magnetic orientation in the three samples examined. (author)

  6. Ab initio study of structural and mechanical property of solid molecular hydrogens

    Science.gov (United States)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  7. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae.

    Science.gov (United States)

    Li, Yiming; Syvitski, Ray T; Chu, Grace C; Ikeda-Saito, Masao; Mar, Gerd N La

    2003-02-28

    The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

  8. 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...

  9. Molecular orientation and electronic structure at organic heterojunction interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

    2015-10-01

    Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

  10. 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

  11. 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.

  12. Projected quasiparticle theory for molecular electronic structure

    Science.gov (United States)

    Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

    2011-09-01

    We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

  13. An investigation onto the molecular structure of 5-chloro-3-(2-(4-ethylpiperazine-1-il)-2-oxoethyl)benzo[d]thiazole-2(3H)-on drug molecule before and after atmospheric pressure plasma treatment

    Science.gov (United States)

    Tanışlı, Murat; Taşal, Erol; Şahin, Neslihan; Dikmen, Gökhan

    2018-05-01

    The spectra of molecular structure for the 5-chloro-3-(2-(4-ethylpiperazine-1-il)-2-oxoethyl)benzo[d]thiazole-2(3H)-on drug molecule (abbreviated as 5KEB) before and after the atmospheric pressure plasma treatments (APPTs) of neon (Ne) and argon (Ar) were investigated. The Fourier transform infrared (FT-IR), ultraviolet visible (UV-Vis) spectra and NMR measurements of the 5KEB drug molecule dissolved in toluene and ethanol solvents were recorded and examined for liquid phases. Then FT-IR, UV-Vis spectra and NMR measurements were analysed. It is seen that some bonds of 5KEB molecule were decomposed. There were also unobserved vibrational modes. After the Ne plasma at the atmospheric pressure applied to 5KEB drug molecule dissolved in toluene, the bonds as 9Ssbnd 8C; 9Ssbnd 8C = 10 O, 8Csbnd 7N, 7Nsbnd 8C = 10O were vanished, and then the new bonds of the 7N = 8C, 7N = 8C = 10 O, 9Ssbnd 5Csbnd 4Csbnd 7N = 8C = 10O were observed. New photoproducts may be defined as the stretching peaks, stretching vibrational modes for 5KEB drug molecule in liquid phase prepared with ethanol and toluene solvents after APPT. Also, after Ar plasma at atmospheric pressure applied here, the 9Ssbnd 8C bond of the 5KEB drug molecule dissolved in toluene was broken. The isomerization process in UV-Vis was defined by π-π* and n-π* electronic transitions. According to NMR results, protons of pyridine ring, protons of CH2 group bonded to carbonyl group and protons of CH3 group more affected than other protons from Ar and Ne APPTs and these protons were eliminated by Ar and Ne APPTs.

  14. 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

  15. 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.

  16. Molecular structure and vibrational spectroscopy of isoproturon

    Science.gov (United States)

    Vrielynck, L.; Dupuy, N.; Kister, J.; Nowogrocki, G.

    2006-05-01

    The crystal structure of isoproturon [ N-(4-isopropylphenyl)- N', N'-dimethylurea] has been determined: the compound crystallizes in the space group Pbca with unit cell parameters a=10.186(2) Å, b=11.030(2) Å, c=20.981(4) Å. The structure was solved and refined down to R1=0.0508 and ωR2=0.12470 for 3056 reflections. The crystalline molecular network of this pesticide is stabilized, as for many molecules of the same family, by π-π interactions but especially by a medium-strong N-H⋯C dbnd6 O intermolecular hydrogen bond (2.14 Å). The X-ray parameters were then compared with the results of DFT quantum chemical calculation computed with the GAUSSIAN 94 package. A tentative assignment of the ATR-FT-IR and Raman spectra was proposed supported by vibrational mode calculation and spectroscopic data on benzenic and urea derivatives available in the literature. The presence of a tight band around 3300 cm -1, which can be assigned to the NH bond stretching mode as well as the low frequency position of the amide I band at 1640 cm -1, sensitive to solvent polarity, confirms the existence of a quite strong intermolecular hydrogen bond between neighboring molecules in the crystal of isoproturon.

  17. 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 ...

  18. Structural investigation of biogenic ferrihydrite nanoparticles dispersion

    International Nuclear Information System (INIS)

    Balasoiu, M.; Ishchenko, L.A.; Stolyar, S.V.; Iskhakov, R.S.; Rajkher, Yu.L.; Kuklin, A.I.; Solov'ev, D.V.; Arzumanyan, G.M.; Kurkin, T.S.; Aranghel, D.

    2010-01-01

    Structural properties of biogenic ferrihydrite nanoparticles produced by bacteria Klebsiella oxytoca are investigated. Investigations of morphology and size of particles dispersed in water by means of high-resolution transmission electron microscopy and small angle X-ray scattering measurements were performed. By model calculations followed by fitting procedure the structural parameters of a cylinder of radius R = (4.87 ± 0.02) nm and height L = (2.12 ± 0.04) nm are obtained

  19. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  20. 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.

  1. Quantum chemical investigations on the molecular structure, FTIR, UV-Vis and HOMO-LUMO analysis of 15-16-epoxy-7b, 9a dihydroxylabdane 13(16), 14-dien-6-one

    Science.gov (United States)

    Uppal, Anshul; Pathania, Kamni; Khajuria, Yugal

    2018-05-01

    The structural, spectroscopic (Fourier Transform Infrared (FT-IR), Ultra-Violet Visible (UV-VIS)) and thermodynamic properties of 15, 16-epoxy-7b, 9a dihydroxylabdane-13(16), 14-dien-6-one were studied by using both experimental techniques and theoretical methods. The FTIR spectrum of the title compound was recorded in the spectral range 4000-400 cm-1. The UV-VIS spectrum was measured in the spectral range 190-800 nm. The quantum chemistry calculations have been performed to compute optimized geometry, molecular parameters, vibrational frequencies along with intensities using Hartree Fock (HF) theory and Density Functional Theory (DFT) with 6-31G basis set. The calculated HOMO-LUMO energies show that the charge transfer occurs within the molecule. The temperature dependence of the thermodynamic properties like heat capacity, entropy and enthalpy of the optimized structure were obtained. Finally, a comparison between the experimental data and the calculated results presented a good agreement.

  2. Molecular Diagnostics of the Internal Structure of Starspots and Sunspots

    Science.gov (United States)

    Afram, N.; Berdyugina, S. V.; Fluri, D. M.; Solanki, S. K.; Lagg, A.; Petit, P.; Arnaud, J.

    2006-12-01

    We have analyzed the usefulness of molecules as a diagnostic tool for studying solar and stellar magnetism with the molecular Zeeman and Paschen-Back effects. In the first part we concentrate on molecules that are observed in sunspots such as MgH and TiO. We present calculated molecular line profiles obtained by assuming magnetic fields of 2-3 kG and compare these synthetic Stokes profiles with spectro-polarimetric observations in sunspots. The good agreement between the theory and observations allows us to turn our attention in the second part to starspots to gain insight into their internal structure. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and compare synthetic Stokes profiles with our recent observations.

  3. 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 impurity. Transforming the equation to the noninertial frame of reference coupled with the center of mass we investigate the soliton behavior in the close vicinity of the impurity. With the help of the lens transformation we show that the soliton width is governed by an Ermakov-Pinney equation. We also...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  4. Structure and Interface Properties of Nanophase Ceramics: Multimillion Particle Molecular-Dynamics Simulations on Parallel Computer

    National Research Council Canada - National Science Library

    Kalia, Rajiv

    1997-01-01

    Large-scale molecular-dynamics (MD) simulations were performed to investigate: (1) sintering process, structural correlations, and mechanical behavior including dynamic fracture in microporous and nanophase Si3N4...

  5. Structural and spectroscopic investigation of glycinium oxalurate

    Science.gov (United States)

    Kavitha, T.; Pasupathi, G.; Marchewka, M. K.; Anbalagan, G.; Kanagathara, N.

    2017-09-01

    Glycinium oxalurate (GO) single crystals has been synthesized and grown by the slow solvent evaporation method at room temperature. Single crystal X-ray diffraction study confirms that GO crystal crystallizes in the monoclinic system with centrosymmetric space group P121/c1. The grown crystals are built up from single protonated glycinium residues and single dissociated oxalurate anions. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the glycine and oxaluric acid residues forms a three-dimensional network. Hydrogen bonded network present in the crystal gives notable vibrational effect. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on HF and density functional theory B3LYP methods with 6-311++G(d,p) basis set. Frontier molecular orbital energies and other related electronic properties are calculated. The natural bonding orbital (NBO) charges have been calculated and interpreted. The molecular electrostatic potential map has been constructed and discussed in detail.

  6. 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.

  7. 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.

  8. A molecular investigation of adsorption onto mineral pigments

    Science.gov (United States)

    Ninness, Brian J.

    Pigment suspensions are important in several processes such as ceramics, paints, inks, and coatings. In the wet state, pigments are combined with a variety of chemical species such as polymers, surfactants, and polyelectrolytes which produce a complex colloidal system. The adsorption, desorption, and redistribution of these species at the pigment-aqueous solution interface can have an impact on the behavior in both the wet state or its final dried state. The goal of this work is to establish a molecular picture of the adsorption properties of these pigmented systems. A novel in situ infrared technique has been developed which allows the detection of adsorbed surface species on pigment particles in an aqueous environment. The technique involves the use of a polymeric binder to anchor the colloidal pigment particles to the surface of an internal reflection element (IRE). The binder only weakly perturbs about 25% of the reactive surface sites (hydroxyl groups) on silica. The reaction of succinic anhydride with an aminosilanized silica surface has been quantified using this technique. The adsorption dynamics of the cationic surfactant cetyltrimethylammonium bromide (C16TAB) at the TiO2-aqueous solution interface has been investigated using Fourier transform infrared-attenuated total reflection spectroscopy (FTIR-ATR) and electrokinetic analysis. At low bulk concentrations, C16TAB is shown to adsorb as isolated islands with a "defective" bilayer structure. Anionic probe molecules are shown to effectively "tune" the adsorbed surfactant microstructure. The results indicate that the structure of the adsorbed surfactant layer, and not the amount of adsorbed surfactant, dictates the subsequent adsorption behavior of the system. Atomic Layer Deposition is used to deposit a TiO2 layer onto the surfaces of silica and kaolin pigments. The process involves the cyclic reaction sequence of the vapors of TiCl4 and H2O. Three complete deposition cycles are needed before the surfaces

  9. Theoretical investigations of molecular wires: Electronic spectra and electron transport

    Science.gov (United States)

    Palma, Julio Leopoldo

    The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

  10. Molecular structure and motion in zero field magnetic resonance

    International Nuclear Information System (INIS)

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

  11. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    OpenAIRE

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferre...

  12. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1984-02-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

  13. Structural investigations of some metallic glasses

    International Nuclear Information System (INIS)

    Sietsma, J.

    1987-03-01

    Metallic glasses were prepared by the melt spinning technique from iron and nickel alloys (Fe-Ni-P; Fe-B; Ni-Nb; Ni-B). Structure investigations were made by means of neutron diffraction experiments. Distribution functions and range orders were determined. (Auth.)

  14. MOLECULAR STRUCTURE AND VIBRATIONAL FREQUENCIES OF

    Directory of Open Access Journals (Sweden)

    Fatih UCUN

    2009-02-01

    Full Text Available Abstract: The molecular structure, vibrational frequencies and the corresponding assignments of N-aminophthalimide (NAPH in the ground state have been calculated using the Hartree-Fock (HF and density functional methods (B3LYP with 6-31G (d, p basis set. The calculations were utilized in the CS symmetry of NAPH. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that B3LYP is superior to the scaled HF method. Theoretical infrared intensities and Raman activities were also reported. Key words: N-aminophthalimide; vibrations; IR spectra; Raman spectra; HF; DFT N-AMİNOFİTALOMİD'İN MOLEKÜLER YAPISI VE TİTREŞİM FREKANSLARI Özet: Temel haldeki N-aminofitalamidin (NAPH moleküler yapısı, titreşim frekansları ve uygun mod tanımlamaları, 6-31 G (d, p temel setli Hartree-Fock (HF ve yoğunluk fonksiyonu metodları (B3LYP kullanılarak hesaplandı. Hesaplamalar, NAPH'ın CS simetrisine uyarlandı. Elde edilen titreşim frekansları ve optimize geometrik parametreleri (bağ uzunlukları ve bağ açıları, deneysel değerlerle iyi bir uyum içinde olduğu görüldü. Deneysel ve teorik sonuçların karşılaştırılması, B3LYP'nin HF metodundan daha üstün olduğunu gösterdi. Ayrıca teorik infrared şiddetleri ve Raman aktiviteleri verildi. Anahtar Kelimeler: N-aminofitalamidin; titreşimler; IR spektrumu; Raman Spektrumu; HF; DFT

  15. Thermal behaviour of molecular sieves (SAPO-11/AIPO-11 type) investigated by synchrotron radiation X-ray diffraction (SRXD)

    International Nuclear Information System (INIS)

    Neissendorfer, F.; Jahn, E.; Gusenko, S.N.; Sheromov, M.A.

    1991-01-01

    The structure of molecular sieves is important for a successful application as a catalyzer. The final structure of the synthetic product depends on the technological steps. This process was investigated by in-situ Synchrotron radiation X-ray diffraction. Structural changes in the molecular sieves exist not only during the heating process but also during the following cooling process. (author) 3 figs., 2 refs

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

    OpenAIRE

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

    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 ...

  17. 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 by a

  18. 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

  19. 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

  20. Molecular simulations of hydrated proton exchange membranes. The structure

    Energy Technology Data Exchange (ETDEWEB)

    Marcharnd, Gabriel [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie; Bordeaux Univ., Talence (France). Dept. of Chemistry; Bopp, Philippe A. [Bordeaux Univ., Talence (France). Dept. of Chemistry; Spohr, Eckhard [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie

    2013-01-15

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion {sup registered} (Dupont) and Hyflon {sup registered} (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. (orig.)

  1. 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

  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. 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.

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

    International Nuclear Information System (INIS)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K; Hajgato, B; Morini, F; Deleuze, M S

    2008-01-01

    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

  5. The hierarchical structure of molecular clouds

    International Nuclear Information System (INIS)

    Chieze, J.P.

    1987-01-01

    The mass-radius-velocity dispersion relations observed among the members of cool molecular complexes is interpreted in terms of fragmentation at the gravitational instability threshold in a roughly constant pressure environment. The mass range of the self-similar fragmentation hierarchy is governed by the thermal instability thresholds. Using a realistic equation of state, the gravitational stability of thermally stable clumps is analysed as a function of both the local gas pressure and extinction of the mean interstellar radiation field

  6. The Role of Molecular Structure and Conformation in Polymer Electronics

    NARCIS (Netherlands)

    von Hauff, Elizabeth

    2011-01-01

    ABSTRACT Conjugated polymers have unique material properties that make them promising for a wide range of applications. The potential lies in the virtually infinite possibilities for creating new materials for specific applications by simply chemically tuning the molecular structure. Conjugated

  7. 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.

  8. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1983-01-01

    Galactic CO line emission at 115 GHz has been surveyed in the region 12 0 less than or equal to l less than or equal to 60 0 and -1 0 less than or equal to b less than or equal to 1 0 in order to study the distribution of molecular clouds in the inner galaxy; an inner strip 0 0 .5 wide has been sampled every beamwidth (0 0 .125), the rest every two beamwidths. Comparison of the survey with similar HI data reveals a detailed correlation with the most intense 21-cm features, implying that the CO and HI trace the same galactic features and have the same large-scale kinematics. To each of the classical 21-cm (HI) spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is developed in which all of the CO emission from the inner galaxy arises from spiral arms. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide. A variety of methods are employed to estimate distances and masses for the largest clouds detected by the inner-galaxy survey and a catalogue is compiled. The catalogued clouds, the largest of which have masses of several 10 6 M/sub sunmass/ and linear dimensions in excess of 100 pc, are found to be excellent spiral-arm tracers. One of the nearest of the clouds, that associated with the supernova remnant W44, is fully mapped in both CO and 13 CO and is discussed in detail

  9. Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

    Science.gov (United States)

    Khan, Nazir Ahmad; Booker, Helen; Yu, Peiqiang

    2014-07-16

    The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value.

  10. 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.

  11. 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.

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

    Indian Academy of Sciences (India)

    2015-01-11

    Jan 11, 2015 ... The molecular geometry of RecA and the location of the nucleotide binding site ...... the residue in all the glycerol complexes clusters together along with the two ..... an X-ray and molecular dynamics investigation on banana.

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

    OpenAIRE

    Celebioglu, Hilal Yilmaz; Chronakis, Ioannis S.; Lee, Seunghwan; Guðjónsdóttir, María

    2017-01-01

    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 epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their f...

  14. Chemical structure investigation on SFEF fractions of Dagang vacuum residue

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Z.; Yan, G.; Zhao, S.; Guo, S. [China Univ. of Petroleum, Beijing (China). State Key Laboratory of Heavy Oil Processing; Zhang, Z. [Beijing Aeronautical Technology Research Center, Beijing (China)

    2006-07-01

    One of the most important problems in petroleum chemistry is the molecular structure and composition of heavy oil fractions and its importance in applications pertaining to the recovery, refining, and upgrading of petroleum. This paper presented an investigation into the chemical structure on supercritical fluid extraction and fraction (SFEF) factions of Dagang vacuum residue. Dagang vacuum residue was cut into sixteen fractions and a tailing with SFEF instrument. Then, using a chromatography, all SFEF fractions were further separated into four group compositions, notably saturated hydrocarbons, aromatic hydrocarbons, resins and asphaltenes (SARA). Last, the chemical structure was explored through a thorough analysis of the products from the ruthenium ions-catalyzed oxidation (RICO) reaction of those aromatics, resins and asphaltenes. The paper discussed the experiment in terms of samples and chemicals; supercritical fluid extraction and fraction; SARA separation; and RICO. The results and discussions focused on alkyl side chains attached to aromatic carbon; polymethylene bridges connecting two aromatic units; benzenecarboxylic acids an aromatic units; and others. The study has brought to light useful characterization on covalent molecular structure of two typical SFEF fractions, notably the tenth and fifteen fraction. 17 refs., 6 tabs., 16 figs., 1 appendix.

  15. Instructional Approach to Molecular Electronic Structure Theory

    Science.gov (United States)

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  16. SAXS and TEM Investigation of Bentonite Structure

    International Nuclear Information System (INIS)

    Matusewicz, Michal; Liljestroem, Ville; Muurinen, Arto; Serimaa, Ritva

    2013-01-01

    A preliminary investigation of bentonite structure using Small-Angle X-ray Scattering (SAXS) and Transmission Electron Microscopy (TEM) is presented. Three types of clay were used: unchanged MX-80 bentonite and purified clays with sodium or calcium ions. Quantitative information in nano-scale - basal spacing, mean crystallite size - was obtained from SAXS, which was complemented by TEM to give qualitative information from micron to nanometre scale. SAXS seems to be a more reliable source of quantitative data than TEM. SAXS gives the averaged information about basal spacing. TEM in this study gives more qualitative information, but in a greater resolution range. The presented work is a starting point to combine more methods to obtain a better idea of bentonite structure. (authors)

  17. 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

  18. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Ould-Kaddour, F.; Barrat, J.L.

    1991-05-01

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  19. Stability investigations of relaxing molecular gas flows. Results and perspectives

    Science.gov (United States)

    Grigor'ev, Yurii N.; Ershov, Igor V.

    2017-10-01

    This article presents results of systematic investigations of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The effect can be a new way for control stability and laminar turbulent transition in aerodynamic flows. The consideration of suppression of inviscid acoustic waves in 2D shear flows is presented. Nonlinear evolution of large-scale vortices and Kelvin — Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both classical linear and nonlinear energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of this article is to show the new dissipative effect, which can be used for flow control and laminarization.

  20. Electronic structure and molecular dynamics of Na2Li

    Science.gov (United States)

    Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

    Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

  1. Molecular and structural aspects of oocyte maturation

    NARCIS (Netherlands)

    Hölzenspies, J.J.

    2009-01-01

    In the mammalian ovary, oocytes are contained within follicles, specialized structures that facilitate oocyte growth and development. During the reproductive cycle, several follicles are recruited into growth, and through a process of selection, one (human, cow) or several (mouse, pig) of these

  2. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research ... Purpose: To determine the exact structure and antimicrobial activity of 2-(3-(4 phenylpiperazin-1-yl) ... Besides HOMO– LUMO energy gap was performed at B3LYP/6-31G (d,p) level of theory.

  3. Molecular dynamics investigation on adsorption layer of alcohols at the air/brine interface.

    Science.gov (United States)

    Nguyen, Cuong V; Phan, Chi M; Ang, Ha M; Nakahara, Hiromichi; Shibata, Osamu; Moroi, Yoshikiyo

    2015-01-01

    Alcohols are a significant group of surfactants which have been employed extensively in industry to improve the interfacial effects. Recently, the change in surface potential (ΔV) of two isomeric hexanols, methyl isobutyl carbinol (MIBC) and 1-hexanol, was investigated by using an ionizing (241)Am electrode. It clearly showed the opposite effects between MIBC and 1-hexanol in the interfacial zone: one enhanced the presence of cations, whereas the other enhanced the presence of anions. This study employs molecular dynamics simulation to provide new insights into the interactions between alcohol molecules and ions as well as water at the molecular level. The results qualitatively agreed with the experimental data and verified the significance of MIBC branching structure on the molecular arrangement within the interfacial zone. The results also highlighted the role of the second water layer on the interfacial properties.

  4. Density functional study of molecular interactions in secondary structures of proteins.

    Science.gov (United States)

    Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

    2016-01-01

    Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

  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. 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.

  7. MOLECULAR STRUCTURE AND STABILITY E. Vessally* Payame ...

    African Journals Online (AJOL)

    Preferred Customer

    planar conformers are also found for NO, CO, SiO, GeO, O, C, Si, Ge. Isodesmic reactions to determine the stabilities of XO and X are considered. Nuclear independent chemical shifts, NICS, are calculated for the investigation of the homo-aromatic character of XO and X. The optimised geometries show the bonding in the.

  8. 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

  9. 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.

  10. 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.)

  11. 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.

  12. Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

    Science.gov (United States)

    Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

    2018-05-01

    Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

  13. 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.

  14. Crystal and molecular structure of 2-thiouridine

    Energy Technology Data Exchange (ETDEWEB)

    Hawkinson, S W

    1977-01-01

    The ''minor'' nucleoside 2-thiouridine, C/sub 9/H/sub 12/O/sub 5/N/sub 2/S, crystallizes in a monoclinic cell, space group P2/sub 1/ with a = 5.049 (2), b = 7.526 (2), c = 14.050 (3) A, ..beta.. = 90.17 (2)/sup 0/, and d = 1.619 g cm/sup -3/ (for Z = 2) at 22 +- 2/sup 0/C. The structure was derived from 1334 unique intensities measured with an Oak Ridge computer-controlled diffractometer to a limit of sin theta/lambda = 0.65 A/sup -1/ with Nb-filtered Mo K..cap alpha.. radiation. Atomic parameters were obtained by a combination of Patterson and Fourier techniques and refined by full-matrix least squares to a final R(F) value of 0.023 for all data. The bond lengths and angles in the molecule agree well with those of other thiopyrimidines (C(2) - S = 1.677 A). The conformation of the sugar ring relative to the base is anti with a torsion angle chi(O(1')--C(1') ..-->.. N(1)--C(6)) of 17/sup 0/. The sugar exists in the 3'-endo conformation. The O(5')--C(5') bond is gauche to C(4) - O(1') and trans to C(4')--C(3') (torsion angles of 74 and -169/sup 0/ respectively). The molecules are linked together in the crystal by hydrogen bonds in an intricate network which is identical to that inferred by Kojic-Prodic, Liminga, Sljukic and Ruzic-Toros (Acta Cryst. (1974), B30, 1550-1555) for the crystal structure of 5,6-dihydro-2-thiouridine. 2 figures; 6 tables.

  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. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  17. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

  18. Chemical protection and sensitization to ionizing radiation:molecular investigations

    International Nuclear Information System (INIS)

    Badiello, R.

    1980-01-01

    Chemical radioprotection and radiosensitization are induced by the presence of certain chemical compounds, which reduce or enhance the effect of ionizing radiation on living organisms. Such substances are either naturally present or may be artificially introduced in the living cells. Chemical radioprotectors are interesting for possible application in the health protection of both professionally exposed workers and patients treated by radiation for diagnostic and thereapeutic purposes. Interest in chemical radiosensitization has increased recently because of its potential application in the radiotherapy of tumours. Both radioprotection and radiosensitization occur by means of complicated mechanisms, which at first correspond to very fast reactions. The mechanism of the interaction between such substances and radiation-induced biological radicals has been investigated by means of pulse radiolysis and rapid mixing techniques. Examples of the application of these techniques are given to illustrate how information has been obtained on the molecular basis of radiation chemical modi-fication at the cellular level. In particular some interactions between model systems of biological interest (DNA, DNA components, enzymes, amino acids, etc.) and sulphur-containing radioprotectors (glutathione, cysteine, etc.) and/or electroaffinic radiosensitizers, are described. (H.K.)

  19. 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.

  20. 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

  1. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  2. 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.

  3. 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

  4. Investigation of nuclear structures using transition probabilities

    International Nuclear Information System (INIS)

    Dewald, A.; Moeller, O.; Peusquens, R.

    2002-01-01

    Magnetic rotation which appears as regular M1 bands in the spectra, is a well established phenomenon in several Pb isotopes. In the A = 130 region where similar M1 bands are known, e.g. in 124 Xe and 128 Ba, it is still not clear whether it does exists. Crucial experimental observables are the B (M1) values which -are expected to decrease with in creasing spin. At Strasbourg a recoil distance measurement (RDM) with the EUROBALL spectrometer at Strasbourg and the Koeln plunger using the reaction 110 Pd( 18 O, 4n) 124 Xe at a beam energy of 86 MeV yielded preliminary lifetimes of ground band states and states of the M1 band. The deduced B(M1) values show the expected behaviour for magnetic rotation. It is also shown that the experimental B(M1) values can be described as well on the basis of a rotational band. The measured B(E2) values are used to investigate the nuclear deformation of 124 Xe as well as the interaction of the ground state band with two s-bands. Spherical deformed shape coexistence is investigated by means of electromagnetic transition probabilities in the case of 188 Pb. Lifetimes were measured in 188 Pb using a novel combination of the Koeln plunger device with the GSFMA set-up at ATLAS. The reaction 40 Ca ( 152 Sm, 4n) 188 Pb at a beam energy of 725 MeV in inverse kinematics is used. It is found that the lowest 2 + state is predominantly of prolate structure

  5. 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.

  6. 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.

  7. 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 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...... 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 calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

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

    Indian Academy of Sciences (India)

    Wintec

    Near IR spectral region (1000–2500 nm) shows the elimination of water in the compound which ... 1-Butyl 3-methyl imidazolium bromide; molecular material; phosphotungstic acid; near IR. ..... attributable to the first overtone of hydroxyl groups,.

  9. 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…

  10. 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...

  11. 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.

  12. 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...

  13. 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

  14. 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...

  15. 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.

  16. 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.

  17. 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.

  18. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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 ...

  6. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

  7. Structure and texture investigations by neutron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Vratislav, S [Ceske Vysoke Uceni Technicke, Prague (Czechoslovakia). Fakulta Jaderna a Fysikalne Inzenyrska

    1982-01-01

    Analysis of the KSN-2 neutron diffractometer parameters helped improve the KSN-2 resolution to 7.5x10/sup -3/. Structure analysis of compounds with elementary cell volume down to 5 nm/sup 3/ can now be performed. Resolution analysis of the neutron powder diffractometer and its conclusions are described, results of the structure determination of zeolites and the magnetic structure determination of perovskites are given. The three-dimensional distribution function and its use in calculating the elastic modulus of aluminium sheets are mentioned.

  8. 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 ...

  9. 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...

  10. 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)

  11. Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

    Science.gov (United States)

    Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

    2018-04-01

    The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

  12. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  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. 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

  15. Fluid-structure interaction investigations for pipelines

    International Nuclear Information System (INIS)

    Altstadt, E.; Carl, H.; Weiss, R.

    2003-12-01

    In existing Nuclear Power Plants water hammers can occur in case of an inflow of sub-cooled water into pipes or other parts of the equipment, which are filled with steam or steam-water mixture. They also may appear as the consequence of fast valve closing or opening actions or of breaks in pipelines, with single phase or two-phase flow. In the latter case, shock waves in two-phase flow must be expected. In all cases, strong dynamic stresses are induced in the wall of the equipment. Further, the change of the momentum of the liquid motion and the deformation of the component due to the dynamic stresses generate high loads on the support structures of the component, in which the water hammer respectively the shock wave occurs. The influence of the fluid-structure interaction on the magnitude of the loads on pipe walls and support structures is not yet completely understood. In case of a dynamic load caused by a pressure wave, the stresses in pipe walls, especially in bends, are different from the static case. The propagating pressure wave may cause additional non-symmetric deformations which increase the equivalent stresses in comparison to the symmetric load created by a static inner pressure. On the other hand, fluid-structure interaction causes the structure to deform, which leads to a decrease of the resulting stresses. The lack of experimental data obtained at well defined geometric boundary conditions is a significant obstacle for the validation of codes which consider fluid-structure interaction. Furthermore, up to now the feedback from structural deformations to the fluid mechanics has not been fully implemented in existing calculation software codes. Therefore, at FZR a cold water hammer test facility (CWHTF) was designed and built up. (orig.)

  16. 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

  17. 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 (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral 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.

  18. 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.

  19. 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.

  20. 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.

  1. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

    1991-01-01

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  2. Experimental investigation of molecular beam injection in HL-1 tokamak

    International Nuclear Information System (INIS)

    Yao Lianghua; Diao Guangyao; Wang Zhanhe; Deng Huichen; Luo Junlin; Duan Xuru; Cui Zhengying

    1993-07-01

    A new method of gas puffing is presented. The molecular beam, formed by high pressure deuterium gas through Larval nozzle and skimmer slit, is injected into the HL-1 vacuum vessel. The deuterium molecular current from the nozzle passing through the skimmer is about 3 x 10 20 /s. At the line average electron density of 5.2 x 10 19 m -3 , the beam velocity is about 100 m/s. As the plasma density and temperature increasing, the influxes of deuterium particles attenuate quickly. When the molecular beam injection (MBI) just returned to normal gas puffing, the D α emission rapidly decreases, meanwhile, the particles move toward plasma center, the electron density is continuously peaking. The line average electron density rising lasts 45 ms. The thermal energy of plasma and confinement time for particles and energy are also increasing. the MBI is a direct and efficient gas fuelling mode, and the injected particles can reach to inside about 8 cm of plasma and q ≅ 2 confinement region. Its efficiency of injection is about 50%. After the MBI, the particle recycling coefficient R on the wall is 0.6 which is 10% lower than that of normal gas puffing

  3. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  4. 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.

  5. STRUCTURAL STUDY AND INVESTIGATION OF NMR TENSORS ...

    African Journals Online (AJOL)

    theory. The structural and vibrational properties of dopamine-4-N7GUA and ... There is evidence, however, that DA is involved in the ... spectra to the results of ab initio gauge-invariant atomic orbital (GIAO) [14-17] and continuous- ..... Nicholls, G. Proteins, transmitter & synapses, Blackwell Scientific Publication: Scotland;.

  6. Structure investigations of some beryllium materials

    Energy Technology Data Exchange (ETDEWEB)

    Faeldt, I; Lagerberg, G

    1960-05-15

    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.

  7. Investigation of defect structures in solids

    Energy Technology Data Exchange (ETDEWEB)

    Dienel, G; Hubrig, W H; Schenk, M; Syhre, H [Zentralinstitut fuer Kernforschung, Rossendorf bei Dresden (German Democratic Republic)

    1976-01-01

    Some central points of interest of research in the field of defect structures in solids dealt with at the Central Institute of Nuclear Research at Rossendorf in the last years are presented. Studies on f.c.c. and b.c.c. metals, radiation-induced phase transitions in perovskites and ion-implanted silicon are described in some detail.

  8. 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

  9. Theoretical investigation on the molecular structure, Infrared, Raman and NMR spectra of para-halogen benzenesulfonamides, 4-X-C 6H 4SO 2NH 2 (X = Cl, Br or F)

    Science.gov (United States)

    Karabacak, Mehmet; Çınar, Mehmet; Çoruh, Ali; Kurt, Mustafa

    2009-02-01

    In the present study, the structural properties of para-halogen benzenesulfonamides, 4-XC 6H 4SO 2NH 2 (4-chlorobenzenesulfonamide (I), 4-bromobenzenesulfonamide (II) and 4-fluorobenzenesulfonamide (III)) have been studied extensively utilizing ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP exchange correlation. The vibrational frequencies were calculated and scaled values were compared with experimental values. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The effects of the halogen substituent on the characteristic benzenesulfonamides bands in the spectra are discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecules were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. Finally, geometric parameters, vibrational bands and chemical shifts were compared with available experimental data of the molecules. The fully optimized geometries of the molecules were found to be consistent with the X-ray crystal structures. The observed and calculated frequencies and chemical shifts were found to be in very good agreement.

  10. 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

  11. 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

  12. 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.

  13. Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations.

    Science.gov (United States)

    Song, Wei; Guo, Jun-Tao

    2015-01-01

    Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) simulations. Protein flexibility has been considered as a key factor in molecular recognition, which is intrinsically a dynamic process involving fine structural fitting between binding components. In this study, we performed comparative MD simulations on wild-type and F10V mutant P22 Arc repressor in both free and complex conformations. The F10V mutant has lower DNA-binding specificity though both the bound and unbound main-chain structures between the wild-type and F10V mutant Arc are highly similar. We found that the DNA-binding motif of wild-type Arc is structurally more flexible than the F10V mutant in the unbound state, especially for the six DNA base-contacting residues in each dimer. We demonstrated that the flexible side chains of wild-type Arc lead to a higher DNA-binding specificity through forming more hydrogen bonds with DNA bases upon binding. Our simulations also showed a possible conformational selection mechanism for Arc-DNA binding. These results indicate the important roles of protein flexibility and dynamic properties in protein-DNA-binding specificity.

  14. 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.

  15. Isotope chemistry and molecular structure. The WINIMAX weighting factor

    International Nuclear Information System (INIS)

    Lee, M.W.; Bigeleisen, J.

    1979-01-01

    The modulating coefficients for the finite polynomial expansion of the logarithm of the reduced partition function, lnb (u), of a harmonic oscillator have been obtained for the range of 0 6 . It is shown that this weighting function is near optimum to insure minimum amplitudes of oscillation in the expansion of lnb (u) as a function of the order of the expansion and to include most of the important molecular structure information contained in the moments of the eigenvalues. Beyond Σu/sub i/ 6 , there is little new structural information

  16. Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer

    Science.gov (United States)

    2015-09-01

    cholesterol ↑ triglycerides Aim • Examine tissue-level alterations associated with obesity using whole transcriptome expression profiles of tumor and...the tumor tissue of obese patients included chromatin modification and remodeling genes involved in the regulation of chromatin structure and function...methylation, alterations in chromatin structure also represent an important component of transcription deregulation during tumor progression

  17. 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...... epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their functional properties related to the food oral processing is presented at the first chapter of the thesis (Paper...... V). Most of the studies suggest an electrostatic attraction between positively charged food proteins with negatively charged moieties of mucins (mainly on glycosylated region of mucins). The structural changes occurring during the interaction between BLG, the major whey protein, and bovine...

  18. 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 ...

  19. 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 ...

  20. 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.

  1. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Science.gov (United States)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

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

    Indian Academy of Sciences (India)

    Administrator

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree– ..... energy decomposition analysis also performed and which clearly ... through molecular dynamics simulation furnished by. Takeguchi,. 46.

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

    African Journals Online (AJOL)

    is variable, with some individuals having normal development and others exhibiting ... consistently present and structural brain abnormalities can occur.[6] .... have right-sided hydronephrosis secondary to pelvoureteric ... the left kidney.

  4. Investigation of matrix-isolated species: spectroscopy and molecular modelling

    International Nuclear Information System (INIS)

    Nemukhin, A V; Grigorenko, B L; Bochenkova, A V; Khriachtchev, L Yu; Raesaenen, M

    2007-01-01

    The results of experimental and theoretical approaches to the study of some stable and unstable chemical species in low-temperature noble gas matrices are considered. The characteristic features of matrix effects manifested in the spectra of the SH radicals in krypton matrices are discussed. The structure and the spectra of HArF in argon matrices and the structure and dynamics of the intermolecular complexes HXeOH with water are analysed.

  5. 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

  6. 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.

  7. Tunneling and resonant conductance in one-dimensional molecular structures

    International Nuclear Information System (INIS)

    Kozhushner, M.A.; Posvyanskii, V.S.; Oleynik, I.I.

    2005-01-01

    We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

  8. 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.

  9. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mathiazhagan, S., E-mail: smathi.research@gmail.com; Anup, S., E-mail: anupiist@gmail.com

    2016-08-19

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  10. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    International Nuclear Information System (INIS)

    Mathiazhagan, S.; Anup, S.

    2016-01-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  11. 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.

  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. Tackling The Dragon: Investigating Lensed Galaxy Structure

    Science.gov (United States)

    Fortenberry, Alexander; Livermore, Rachael

    2018-01-01

    Galaxies have been seen to have a rapid decrease in star formation beginning at a redshift of around 1-2 up to the present day. To understand the processes underpinning this change, we need to observe the inner structure of galaxies and understand where and how the stellar mass builds up. However, at high redshifts our observable resolution is limited, which hinders the accuracy of the data. The lack of resolution at high redshift can be counteracted with the use of gravitational lensing. The magnification provided by the gravitational lens between us and the galaxies in question enables us to see extreme detail within the galaxies. To begin fine-tuning this process, we used Hubble data of Abell 370, a galaxy cluster, which lenses a galaxy know as “The Dragon” at z=0.725. With the increased detail proved by the gravitational lens we provide a detailed analysis of the galaxy’s spatially resolved star formation rate, stellar age, and masses.

  14. 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.

  15. Towards structural models of molecular recognition in olfactory receptors.

    Science.gov (United States)

    Afshar, M; Hubbard, R E; Demaille, J

    1998-02-01

    The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

  16. 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.

  17. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    Science.gov (United States)

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry. PMID:22455919

  18. Quantum Chemical Calculations and Experimental Investigations of Molecular Actinide Oxides

    NARCIS (Netherlands)

    Kovács, Attila; Konings, Rudy J. M.; Gibson, John K.; Infante, Ivan; Gagliardi, Laura

    2015-01-01

    The available experimental and theoretical information on gaseous actinide oxides covering both the neutral and the ionic species are reviewed. The ground-state electronic structures of the oxides of An = Th-Cm have been obtained by the well-tested SOCASPT2 method, and therefore they are very likely

  19. Structure of a molecular liquid GeI4

    International Nuclear Information System (INIS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-01-01

    A molecular liquid GeI 4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge–I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I–I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å −1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed. (paper)

  20. The general atomic and molecular electronic structure system HONDO: Version 7.0

    International Nuclear Information System (INIS)

    Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

    1989-01-01

    We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

  1. 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...... 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...

  2. 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.

  3. Investigation of nuclear structures using transition probabilities

    CERN Document Server

    Dewald, A; Peusquens, R

    2002-01-01

    Magnetic rotation which appears as regular M1 bands in the spectra, is a well established phenomenon in several Pb isotopes. In the A = 130 region where similar M1 bands are known, e.g. in sup 1 sup 2 sup 4 Xe and sup 1 sup 2 sup 8 Ba, it is still not clear whether it does exists. Crucial experimental observables are the B (M1) values which -are expected to decrease with in creasing spin. At Strasbourg a recoil distance measurement (RDM) with the EUROBALL spectrometer at Strasbourg and the Koeln plunger using the reaction sup 1 sup 1 sup 0 Pd( sup 1 sup 8 O, 4n) sup 1 sup 2 sup 4 Xe at a beam energy of 86 MeV yielded preliminary lifetimes of ground band states and states of the M1 band. The deduced B(M1) values show the expected behaviour for magnetic rotation. It is also shown that the experimental B(M1) values can be described as well on the basis of a rotational band. The measured B(E2) values are used to investigate the nuclear deformation of sup 1 sup 2 sup 4 Xe as well as the interaction of the ground s...

  4. Alternative Radioligands for Investigating the Molecular Pharmacology of Melatonin Receptors.

    Science.gov (United States)

    Legros, Céline; Brasseur, Chantal; Delagrange, Philippe; Ducrot, Pierre; Nosjean, Olivier; Boutin, Jean A

    2016-03-01

    Melatonin exerts a variety of physiologic activities that are mainly relayed through the melatonin receptors MT1 and MT2 Low expressions of these receptors in tissues have led to widespread experimental use of the agonist 2-[(125)I]-iodomelatonin as a substitute for melatonin. We describe three iodinated ligands: 2-(2-[(2-iodo-4,5-dimethoxyphenyl)methyl]-4,5-dimethoxy phenyl) (DIV880) and (2-iodo-N-2-[5-methoxy-2-(naphthalen-1-yl)-1H-pyrrolo[3,2-b]pyridine-3-yl])acetamide (S70254), which are specific ligands at MT2 receptors, and N-[2-(5-methoxy-1H-indol-3-yl)ethyl]iodoacetamide (SD6), an analog of 2-[(125)I]-iodomelatonin with slightly different characteristics. Here, we further characterized these new ligands with regards to their molecular pharmacology. We performed binding experiments, saturation assays, association/dissociation rate measurements, and autoradiography using sheep and rat tissues and recombinant cell lines. Our results showed that [(125)I]-S70254 is receptor, and can be used with both cells and tissue. This radioligand can be used in autoradiography. Similarly, DIV880, a partial agonist [43% of melatonin on guanosine 5'-3-O-(thio)triphosphate binding assay], selective for MT2, can be used as a tool to selectively describe the pharmacology of this receptor in tissue samples. The molecular pharmacology of both human melatonin receptors MT1 and MT2, using a series of 24 ligands at these receptors and the new radioligands, did not lead to noticeable variations in the profiles. For the first time, we described radiolabeled tools that are specific for one of the melatonin receptors (MT2). These tools are amenable to binding experiments and to autoradiography using sheep or rat tissues. These specific tools will permit better understanding of the role and implication in physiopathologic processes of the melatonin receptors. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  5. 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.

  6. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  7. 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; Zhang, Huihua; 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.

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

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    J. Chem. Sci. Vol. 129, No. 7, July 2017, pp. 859–872. c Indian Academy of Sciences. ... Ionic liquids are appropriate candidates for the absorption of acid gases such as SO2. Six anion- ... nificant number of task-specific ILs were designed and used to ...... investigation of a pilot-scale jet bubbling reactor for wet flue gas ...

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

    Indian Academy of Sciences (India)

    corrections to energy and Gibbs free energy were calcu- lated at the ... importance. We noted that the energy barrier between .... would be predicted that the carbonyl oxygen atom and ... spin allowed singlet-singlet excitations were calculated.

  10. Free radicals. High-resolution spectroscopy and molecular structure

    International Nuclear Information System (INIS)

    Hirota, E.

    1983-01-01

    High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

  11. 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)

  12. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    Science.gov (United States)

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites.

  13. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N; Komvopoulos, K

    2014-01-01

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures

  14. Spectroscopic and TDDFT investigation on highly selective fluorogenic chemosensor and construction of molecular logic gates

    Energy Technology Data Exchange (ETDEWEB)

    Basheer, Sabeel M [Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015 (India); Kumar, Saravana Loganathan Ashok [Department of Chemistry, GRT Institute of Engineering Technology, Tiruttani (India); Kumar, Moorthy Saravana [Research and PG Department of Chemistry, Saraswathi Narayanan College, Madurai 625022 (India); Sreekanth, Anandaram, E-mail: sreekanth@nitt.edu [Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015 (India)

    2017-03-01

    1,5-Bis(2-fluorene)thiocarbohydrazone (FBTC) was designed and synthesized for selective sensing of fluoride and copper ions. The binding constants of FBTC towards fluoride and copper ions have been calculated using the Benesi-Hildebrand equation, and FBTC has more binding affinity towards copper ion than fluoride ion. The {sup 1}H NMR and {sup 13}C NMR titration studies strongly support the deprotonation was taken from the N–H protons followed by the formation of hydrogen bond via N–H{sup …}F. To understand the fluoride ion sensing mechanism, theoretical investigation had been carried out using the density functional theory and time-dependent density functional theory. The theoretical data well reproduced the experimental results. The deprotonation process has a moderate transition barrier (481.55 kcal/mol). The calculated ΔE and ΔG values (− 253.92 and − 192.41 kcal/mol respectively) suggest the feasibility of sensing process. The potential energy curves give the optimized structures of FBTC-F complex in the ground state and excited state, which states the proton transition occurs at the excited state. The excited state proton transition mechanism was further confirmed with natural bond orbital analysis. The reversibility of the sensor was monitored by the alternate addition of F{sup −} and Cu{sup 2+} ions, which was explained with “Read-Erase-Write-Read” behaviour. The multi-ion detection of sensor used to construct the molecular logic gate, such as AND, OR, NOR and INHIBITION logic gates. - Highlight: • Synthesis and characterised the thiosemicarbohydrazone derivative • Experimental evolution of selective fluoride and copper sensing via both colorimetric and spectroscopic studies • The proposed sensing mechanism of fluoride and copper ion were further confirmed with DFT and TD-DFT investigation • Receptor was turned as molecular switches and molecular logic gates.

  15. Multi-Probe Investigation of Proteomic Structure of Pathogens

    International Nuclear Information System (INIS)

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

    2008-01-01

    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

  16. 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.

  17. 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.

  18. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-07

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

    OpenAIRE

    Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

    2002-01-01

    The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

  20. Chemical structure and properties of low-molecular furin inhibitors

    Directory of Open Access Journals (Sweden)

    T. V. Osadchuk

    2016-12-01

    Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

  1. 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.

  2. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    Science.gov (United States)

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  3. 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

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Skin hydration: interplay between molecular dynamics, structure and water uptake in the stratum corneum.

    Science.gov (United States)

    Mojumdar, Enamul Haque; Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

    2017-11-16

    Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca. 85% relative humidity (RH). The abrupt changes in SC molecular properties coincide with changes in SC macroscopic swelling properties as well as mechanical properties in the SC. The flexible terminals at the solid keratin filaments can be compared to flexible polymer brushes in colloidal systems, creating long-range repulsion and extensive swelling in water. We further show that the addition of urea to the SC at reduced RH leads to similar molecular and macroscopic responses as the increase in RH for SC without urea. The findings provide new molecular insights to deepen the understanding of how intermediate filament organization responds to changes in the surrounding environment.

  11. 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

  12. 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 molecular 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

  13. Functional Annotation of Ion Channel Structures by Molecular Simulation.

    Science.gov (United States)

    Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

    2016-12-06

    Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Zeynab Mohammad Hosseini Naveh

    Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

  15. SGC method for predicting the standard enthalpy of formation of pure compounds from their molecular structures

    International Nuclear Information System (INIS)

    Albahri, Tareq A.; Aljasmi, Abdulla F.

    2013-01-01

    Highlights: • ΔH° f is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH° f with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH° f with a correlation coefficient of 0.90. • Better definition of the atom-type molecular groups is presented. • The method is better than others in terms of combined simplicity, accuracy and generality. - Abstract: A theoretical method for predicting the standard enthalpy of formation of pure compounds from various chemical families is presented. Back propagation artificial neural networks were used to investigate several structural group contribution (SGC) methods available in literature. The networks were used to probe the structural groups that have significant contribution to the overall enthalpy of formation property of pure compounds and arrive at the set of groups that can best represent the enthalpy of formation for about 584 substances. The 51 atom-type structural groups listed provide better definitions of group contributions than others in the literature. The proposed method can predict the standard enthalpy of formation of pure compounds with an AAD of 11.38 kJ/mol and a correlation coefficient of 0.9934 from only their molecular structure. The results are further compared with those of the traditional SGC method based on MNLR as well as other methods in the literature

  16. Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

    Science.gov (United States)

    He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

    2015-09-01

    Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Model of molecular structure of the insoluble organic matter isolated from Murchison meteorite

    Science.gov (United States)

    Derenne, Sylvie; Robert, François

    2010-09-01

    The molecular structure of the insoluble organic matter (IOM) from Murchison meteorite has been investigated by our group for several years using a large set of analytical methods including various spectroscopies (Fourier transform infrared spectroscopy, nuclear magnetic resonance, electron paramagnetic resonance, X-ray absorption near-edge spectroscopy), high resolution electron microscopy, and thermal (pyrolyses in the presence or not of tetramethylammonium hydroxide) and chemical (RuO4 oxidation) degradations. Taken together, these techniques provided a wealth of qualitative and quantitative information, from which we derived 11 elemental and molecular parameters on the same IOM residue. In addition to the basic elemental composition, these parameters describe the distribution of the different types of carbon, nitrogen, and sulfur atoms as well as the size of the polyaromatic units. For this molecular structure, we therefore propose a model which fits with these 11 molecular quantitative parameters. Several cosmochemical implications are derived from this structure. Based on the fact that aromatic moieties are highly substituted and aliphatic chains highly branched, it can be anticipated that the synthesis of this IOM occurred through successive additions of single carbon units in the gas-phase ending by a spontaneous cyclization for chain length ≥7 C. As a whole, these observations favor an organosynthesis in the solar T-Tauri disk.

  18. 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.

  19. 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.

  20. Molecular structures from density functional calculations with simulated annealing

    International Nuclear Information System (INIS)

    Jones, R.O.

    1991-01-01

    The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, the difficulties have meant that they have focused on systems with relatively few local minima, or have used experiments or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results. (orig.)

  1. 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.

  2. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  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. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Science.gov (United States)

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  5. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  6. 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.

  7. Roles of water in protein structure and function studied by molecular liquid theory.

    Science.gov (United States)

    Imai, Takashi

    2009-01-01

    The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

  8. 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

  9. 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 ...

  10. Molecular Origin of the Vibrational Structure of Ice Ih.

    Science.gov (United States)

    Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

    2017-06-15

    An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

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

    KAUST Repository

    Das, Mita; Perry, John D.; Koros, William J.

    2010-01-01

    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.

  12. 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.

  13. 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.

  14. 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.

  15. On the nodal structure of atomic and molecular Wigner functions

    International Nuclear Information System (INIS)

    Dahl, J.P.; Schmider, H.

    1996-01-01

    In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

  16. 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)

  17. 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.

  18. 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'.

  19. Structural investigation of nitrogen-linked saccharinate-tetrazole

    Science.gov (United States)

    Gómez-Zavaglia, A.; Ismael, A.; Cabral, L. I. L.; Kaczor, A.; Paixão, J. A.; Fausto, R.; Cristiano, M. L. S.

    2011-09-01

    The molecular structure of nitrogen-linked saccharinate-tetrazole, N-(1,1-dioxo-1,2-benzisothiazol-3-yl)-amine-1 H-tetrazole (BAT), was investigated in the crystalline state using X-ray crystallography and infrared and Raman spectroscopies, and isolated in argon matrix by infrared spectroscopy. Interpretation of the experimental results was supported by quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory. In the neat crystalline solid (space group C2/ c, a = 21.7493(3) Å, b = 8.85940(10) Å, c = 10.76900(10) Å, β = 103.3300(10) deg; Z = 8), BAT units exist in the (1 H)-tetrazole aminosaccharin tautomeric form, with the NH spacer establishing a hydrogen bond to the nitrogen in position-4 of the tetrazole group of a neighbour molecule, and the NH group of the tetrazole fragment forming a bifurcated H-bond to the saccharyl nitrogen of the same molecule and to one of the oxygen atoms of a second neighbour molecule. On the other hand, according to both the matrix isolation infrared studies and the theoretical calculations, the isolated BAT molecule exists preferentially as the (1 H)-tetrazole iminosaccharin tautomer, where the main stabilizing interaction is the intramolecular H-bond established between the NH group of the saccharyl ring and the tetrazole nitrogen atom in position 4. A detailed conformational analysis of the studied molecule and full assignment of the vibrational spectra for both the matrix-isolated compound and crystalline sample were undertaken.

  20. 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.

  1. 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

  2. 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)

  3. 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.

  4. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Huiding Xie

    2015-11-01

    Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  5. 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.

  6. Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups

    Science.gov (United States)

    Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.

    2018-01-01

    Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

  7. Structural and molecular basis of starch viscosity in hexaploid wheat.

    Science.gov (United States)

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  8. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  9. 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.

  10. 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.

  11. Molecular clouds in the North American and Pelican Nebulae: structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaobo; Xu, Ye; Yang, Ji, E-mail: shbzhang@pmo.ac.cn [Purple Mountain Observatory, and Key Laboratory for Radio Astronomy, Chinese Academy of Sciences, Nanjing 210008 (China)

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  12. International seminar on structural investigations on pulsed neutron sources. Proceedings

    International Nuclear Information System (INIS)

    Aksenov, V.L.; Balagurov, A.M.; Taran, Yu.V.

    1993-01-01

    The proceedings of the International seminar on structural investigations using pulsed neutron sources are presented. The seminar is dedicated to the memory of Dr. Yu.M. Ostanevich, a world acknowledged physicist. The problems of structural analysis using pulsed neutron source at the IBR-2 reactor are discussed

  13. Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Lang, Lin [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Tian, Zean; Xiao, Shifang [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Deng, Huiqiu, E-mail: hqdeng@hnu.edu.cn [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Ao, Bingyun [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Chen, Piheng, E-mail: chenpiheng@caep.cn [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Hu, Wangyu [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

    2017-02-15

    Highlights: • The structural evolution of Cu{sub 64.5}Zr{sub 35.5} MG under irradiation was studied. • The structure clusters were analyzed using the LSCA method. • Most of these radiation damages have been self-recovered quickly. - Abstract: Molecular dynamics simulations have been performed to investigate the structural evolution of Cu{sub 64.5}Zr{sub 35.5} metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

  14. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  15. 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.

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

    International Nuclear Information System (INIS)

    Wang, Ruiyong; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun; Chang, Junbiao

    2014-01-01

    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. Investigation of the structure of filter cakes from bore flushing

    Energy Technology Data Exchange (ETDEWEB)

    Hartmann, A; Oezerler, M; Marx, C; Hartmann, A; Oezerler, M; Marx, C; Poege, S; Young, F

    1985-01-01

    After a description of the tasks and functions of the filter cake in bores, the requirements for filter cakes are explained. The aim of the investigation is finding a correlation between the filter cake structures and the prehistory of flushing. The technique of preparing the samples and previous results from investigations with electron microscopes are introduced and discussed.

  18. Investigation into the use of molecular hydrogen on the growth of gallium nitride via metal-organic molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Billingsley, Daniel; Pritchett, David; Henderson, Walter; Carver, Alexander G.; Burnham, Shawn D.; Doolittle, W.A. [Georgia Institute of Technology, School of Electrical and Computer Engineering, 777 Atlantic Dr., Atlanta, GA 30332 (United States)

    2008-07-01

    Molecular hydrogen (H{sub 2}) has been investigated as a means to improve ammonia nitridation efficiency and attempts to reduce carbon contamination in ammonia-based metal-organic molecular beam epitaxy (MOMBE). A 30% improvement in crystalline quality, inferred from XRD, as well as an increase in subsequent GaN bulk growth rate was observed when bare sapphire was subject to H{sub 2} annealing before nitridation. However, the use of H{sub 2} during GaN homoepitaxy on GaN templates resulted in increased carbon contamination and decreased growth rate of GaN. The results demonstrate promise and proper uses of H{sub 2} during GaN growth under certain conditions. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  19. Effect of the molecular structure of phenolic novolac precursor resins on the properties of phenolic fibers

    International Nuclear Information System (INIS)

    Ying, Yong-Gang; Pan, Yan-Ping; Ren, Rui; Dang, Jiang-Min; Liu, Chun-Ling

    2013-01-01

    A series of phenolic resins with different weight-average molecular weights (M w ) and ortho/para (O/P) ratios were prepared. The effect of the phenolic precursor resin structure on the structure and properties of the resulting phenolic fibers was investigated. The structures of the resins and fibers were characterized by nuclear magnetic resonance spectroscopy, gel permeation chromatography, melt rheometry, dynamic mechanical analysis, and thermogravimetric analysis. The results show that the O/P ratio, unsubstituted ortho and para carbon ratio (O u /P u ), and M w of the phenolic resins play an important role in determining the properties of the phenolic fibers. The tensile strength of the phenolic fibers increases with increasing novolac precursor O u /P u ratios, corresponding to low O/P ratios, at comparable resin M w values. Also, the tensile strength of the phenolic fibers increases with increasing novolac M w values at comparable O/P ratios. Phenolic fibers with high tensile strength and good flame resistance characteristics were generated from a phenolic precursor resin, possessing a high weight-average molecular weight and a low O/P value. - Highlights: • Phenolic resins with different weight-average molecular weights and ortho/para ratios have been prepared. • The tensile strength of the phenolic fibers increases with reducing novolac O/P ratio. • The tensile strength of the phenolic fibers increases with increasing novolac M w

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

    Science.gov (United States)

    Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A

    2015-02-01

    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.

  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. Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

    Directory of Open Access Journals (Sweden)

    Giuseppe Mele

    2011-12-01

    Full Text Available Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral data were reported and analyzed in context of the individual molecular features introduced by the meso substituents into the porphyrin moiety base. Raw experimental spectral data, including 1H- and 13C-NMR, UV-Vis, FTIR, XRD, and other relevant physicochemical details have been provided for a specially chosen reference zinc porphyrin functionalized by tert-butylphenyl groups.

  3. Electronic structure and molecular orbital study of hole-transport material triphenylamine derivatives

    International Nuclear Information System (INIS)

    Wang, B.-C.; Liao, H.-R.; Chang, J.-C.; Chen Likey; Yeh, J.-T.

    2007-01-01

    Recently, triphenylamine (TPA), 4,4'-bis(phenyl-m-tolylamino)biphenyl (TPD), 4,4'-bis(1-naphthylphenylamino)biphenyl (NPB) and their derivatives are widely used in the organic light-emitting diode (OLED) devices as a hole-transporting material (HTM) layer. We have optimized twenty different structures of HTM materials by using density functional theory (DFT), B3LYP/6-31G method. All these different structures contain mono-amine and diamine TPA derivatives. The energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) along with molecular orbitals for these HTMs are also determined. We have found that the central amine nitrogen atom and the phenyl ring, which is next to the central amine nitrogen atom, show significant contribution to the HOMO and LUMO, respectively. The sum of the calculated bond angles (α+β+γ) of the central amine nitrogen atom has been applied to describe the bonding and the energy difference for HOMO and LUMO in these TPA derivatives. Electronic structure calculations have been performed for these TPA derivatives. Again, the LCAO-MO patterns of HOMO and LUMO levels of these derivatives are used to investigate their electron density. A series of electron-transporting steps are predicted for these compounds employing these calculated results

  4. 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

  5. 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.

  6. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2014-09-30

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

  7. Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules

    International Nuclear Information System (INIS)

    Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

    2009-01-01

    We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

  8. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

    Science.gov (United States)

    DiMaio, Frank

    2017-01-01

    Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

  9. A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

    Science.gov (United States)

    Foley, Henry C.

    1990-01-01

    The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.

  10. Molecular structures of fructans from Agave tequilana Weber var. azul.

    Science.gov (United States)

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  11. Molecular structures of some 8-isoanalogues of steroid estrogens

    International Nuclear Information System (INIS)

    Starova, G.L.; Eliseev, I.I.; Abusalimov, Sh.N.; Tsogoeva, S.B.; Shavva, A.G.

    2001-01-01

    The molecular structures of three steroids, namely, 17β-acetoxy-3-methoxy-8-isoestra-1,3,5(10)-triene (I), 17β-acetoxy-3-methoxy-7α-methyl-8-isoestra-1,3,5(10)-triene (II), and 17β-acetoxy-3-methoxy-1-methyl-8-isoestra-1,3,5(10)-triene (III), are determined by X-ray diffraction analysis. It is shown that the substituents in the A and B rings of the compounds of the 8-iso series have a slight effect on the conformation of the steroid skeleton as a whole, which manifests itself only in insignificant distortions of the B and D rings. The methyl group in the 1-position (compound III) affects the geometric parameters of the steroid nucleus less than the same substituent in the 7-position (compound II). A sharp decrease in the uterotropic activity of compounds II and III (compared to compound I) revealed in biological studies can be attributed to unfavorable steric interactions of the substituents in the A and B rings with the estradiol receptor

  12. A study of the molecular structure in CR-39

    International Nuclear Information System (INIS)

    Stejny, J.; Portwood, T.

    1986-01-01

    A technique is presented for examining the molecular structure of CR-39 by analysis of the etch products from hydrolysis of the polymer network. The CR-39 network consists of polyallyl chains jointed by diethyleneglycol dicarbonate links. The etching cuts the carbonate links and liberates the polyallyl chains which makes them amenable to common analytical methods. Gel Permeation Chromatography was used to characterize the chain lengths and their distribution. It was found that the average length is rather short and that it decreases with increasing concentration of the initiator. This technique has been also used to identify the radiation sensitive link in the CR-39 network. It was found that the length of polyallyl chain is not changed in 60 Co γ-irradiated plastic while the etch rate significantly increases. This shows that the polyallyl chains are relatively inert and not responsible for the radiation sensitivity of CR-39 and that it is the diethyleneglycol dicarbonate links which are damaged by radiation. (author)

  13. 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

  14. 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.

  15. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi [Department of Chemistry, Aalto University, FI-00076 Aalto (Finland)

    2014-01-15

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration.

  16. 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)

  17. Numerical investigation of elastic mechanical properties of graphene structures

    International Nuclear Information System (INIS)

    Georgantzinos, S.K.; Giannopoulos, G.I.; Anifantis, N.K.

    2010-01-01

    The computation of the elastic mechanical properties of graphene sheets, nanoribbons and graphite flakes using spring based finite element models is the aim of this paper. Interatomic bonded interactions as well as van der Waals forces between carbon atoms are simulated via the use of appropriate spring elements expressing corresponding potential energies provided by molecular theory. Each layer is idealized as a spring-like structure with carbon atoms represented by nodes while interatomic forces are simulated by translational and torsional springs with linear behavior. The non-bonded van der Waals interactions among atoms which are responsible for keeping the graphene layers together are simulated with the Lennard-Jones potential using appropriate spring elements. Numerical results concerning the Young's modulus, shear modulus and Poisson's ratio for graphene structures are derived in terms of their chilarity, width, length and number of layers. The numerical results from finite element simulations show good agreement with existing numerical values in the open literature.

  18. 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.

  19. 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

  20. Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics simulations

    NARCIS (Netherlands)

    Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.; Spek, A.L.; Hilbers, P.A.J.; Meijer, E.W.

    2007-01-01

    The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The

  1. Molecular structure and vibrational spectra of Bis(melaminium) terephthalate dihydrate: A DFT computational study

    Science.gov (United States)

    Tanak, Hasan; Marchewka, Mariusz K.; Drozd, Marek

    2013-03-01

    The experimental and theoretical vibrational spectra of Bis(melaminium) terephthalate dihydrate were studied. The Fourier transform infrared (FT-IR) spectra of the Bis(melaminium) terephthalate dihydrate and its deuterated analogue were recorded in the solid phase. The molecular geometry and vibrational frequencies of Bis(melaminium) terephthalate dihydrate in the ground state have been calculated by using the density functional method (B3LYP) with 6-31++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The molecule contains the weak hydrogen bonds of Nsbnd H⋯O, Nsbnd H⋯N and Osbnd H⋯O types, and those bonds are calculated with DFT method. In addition, molecular electrostatic potential, frontier molecular orbitals and natural bond orbital analysis of the title compound were investigated by theoretical calculations. The lack of the second harmonic generation (SHG) confirms the presence of macroscopic center of inversion.

  2. X-ray detectors for structure investigations constructed at JINR

    Energy Technology Data Exchange (ETDEWEB)

    Chernenko, S P [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Cheremukhina, G A [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Fateev, O V [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Smykov, L P [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Vasiliev, S E [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Zanevsky, Yu V [LHE Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Kheiker, D M [Institute of Crystallography, Leninsky prosp. 59, 117333 Moscow (Russian Federation); Popov, A N [Institute of Crystallography, Leninsky prosp. 59, 117333 Moscow (Russian Federation)

    1994-09-01

    The performance characteristics of a few high resolution position-sensitive detectors constructed at JINR are presented. The detectors supplied with original software operate with an IBM PC/AT. One of these devices has been succesfully applied for protein molecule structure investigations and the other for studies of the structure-forming process during combustion. The preliminary parameters of the high count rate MWPC with parallel electronics and the testing results of the microstrip detector are given. ((orig.))

  3. 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

  4. Investigations of Structural Requirements for BRD4 Inhibitors through Ligand- and Structure-Based 3D QSAR Approaches

    Directory of Open Access Journals (Sweden)

    Adeena Tahir

    2018-06-01

    Full Text Available The bromodomain containing protein 4 (BRD4 recognizes acetylated histone proteins and plays numerous roles in the progression of a wide range of cancers, due to which it is under intense investigation as a novel anti-cancer drug target. In the present study, we performed three-dimensional quantitative structure activity relationship (3D-QSAR molecular modeling on a series of 60 inhibitors of BRD4 protein using ligand- and structure-based alignment and different partial charges assignment methods by employing comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA approaches. The developed models were validated using various statistical methods, including non-cross validated correlation coefficient (r2, leave-one-out (LOO cross validated correlation coefficient (q2, bootstrapping, and Fisher’s randomization test. The highly reliable and predictive CoMFA (q2 = 0.569, r2 = 0.979 and CoMSIA (q2 = 0.500, r2 = 0.982 models were obtained from a structure-based 3D-QSAR approach using Merck molecular force field (MMFF94. The best models demonstrate that electrostatic and steric fields play an important role in the biological activities of these compounds. Hence, based on the contour maps information, new compounds were designed, and their binding modes were elucidated in BRD4 protein’s active site. Further, the activities and physicochemical properties of the designed molecules were also predicted using the best 3D-QSAR models. We believe that predicted models will help us to understand the structural requirements of BRD4 protein inhibitors that belong to quinolinone and quinazolinone classes for the designing of better active compounds.

  5. 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.

  6. Effects of Electrode Distances on Geometric Structure and Electronic Transport Properties of Molecular 4,4'-Bipyridine Junction

    International Nuclear Information System (INIS)

    Li Zongliang; Zou Bin; Wang Chuankui; Luo Yi

    2006-01-01

    Influences of electrode distances on geometric structure of molecule and on electronic transport properties of molecular junctions have been investigated by means of a generalized quantum chemical approach based on the elastic scattering Green's function method. Numerical results show that, for organic molecule 4,4'-bipyridine, the geometric structure of the molecule especially the dihedral angle between the two pyridine rings is sensitive to the distances between the two electrodes. The currents of the molecular junction are taken nonlinearly increase with the increase of the bias. Shortening the distance of the metallic electrodes will result in stronger coupling and larger conductance

  7. A Theoretical Investigation on Rectifying Performance of a Single Motor Molecular Device

    International Nuclear Information System (INIS)

    Lei Hui; Tan Xun-Qiong

    2015-01-01

    We report ab initio calculations of the transport behavior of a phenyl substituted molecular motor. The calculated results show that the transport behavior of the device is sensitive to the rotation degree of the rotor part. When the rotor part is parallel with the stator part, a better rectifying performance can be found in the current-voltage curve. However, when the rotor part revolves to vertical with the stator part, the currents in the positive bias region decrease slightly. More importantly, the rectifying performance disappears. Thus this offers us a new method to modulate the rectifying behavior in molecular devices. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  8. Investigation of RNA structure in satellite panicum mosaic virus

    International Nuclear Information System (INIS)

    Makino, D.L.; Day, J.; Larson, S.B.; McPherson, A.

    2006-01-01

    Three new crystal forms of satellite panicum mosaic virus (SPMV) were grown and their structures solved from X-ray diffraction data using molecular replacement techniques. The crystals were grown under conditions of pH and ionic strength that were appreciably different then those used for the original structure determination. In rhombohedral crystals grown at pH 8.5 and low ionic strength PEG 3350 solutions, Fourier syntheses revealed segments, ten amino acid residues long, of amino-terminal polypeptides not previously seen, as well as masses of electron density within concavities on the interior of the capsid, which appeared in the neighborhoods of icosahedral five- and threefold axes. The densities were compatible with secondary structural domains of RNA, and they included a segment of double helical RNA of about four to five base pairs oriented, at least approximately, along the fivefold axes. The distribution of RNA observed for SPMV appears to be distinctly different than the encapsidated nucleic acid conformation previously suggested for another satellite virus, satellite tobacco mosaic virus. This study further shows that analysis of viruses in crystals grown under different chemical conditions may reveal additional information regarding the structure of encapsidated RNA

  9. Influence of the molecular structure on hydrolysability of unsaturated polyesters

    International Nuclear Information System (INIS)

    Pays, M.F.; Denis, V.

    1993-09-01

    EDF has decided to replace conventional materials by glass reinforced plastics for certain PWR water distribution systems (raw water system, essential service water system, firefighting water distribution system, etc...). Since steel corrodes rapidly in these pipings, introducing composite materials will be economically beneficial if the long-term resistance of these materials can be guaranteed. However, due to hydrolysis of the resin or of the fiber-matrix interface, composite materials deteriorations may occur during service life. This paper reports on the hydrolysis resistance of polyester and vinylester resins. - Model monomers were studied to relate the molecular structure to the hydrolysis resistance. Two ester categories were determined, the diacids and the diols. For the diacids, we obtained the following classification in increasing order of resistance: < maleates < ethoxysuccinates < succinates < fumerates < terephtalates < orthophtalates < isophtalates and for the diols: trioxyethylene glycol << butane diol ∼ ethylene glycol < neopentyl glycol < bisphenol A. The positions obtained for neopentyl glycol and isophtalic acid on this scale justify their inclusion in the formulation of hydrolysis-resistant resins. Since aliphatic unsaturated esters are highly sensitive to hydrolysis, the cross linking procedures for these materials, notably the post-cure stages, must be the subject of particular care. - The hydrolytic degradation of cross linked materials was studied. It was shown that hydrolysis could be monitored by a simple gravimetric method. Used in association with accelerated aging tests, it predicts the time lapse to initiation of the phenomenon. The better hydrolysis resistance of vinylester resins as compared with unsaturated polyesters has been demonstrated. However, forecasting over a 30-year life span is difficult to guarantee in that this involves indicating in the resin specifications the in-service stress which it will be required to

  10. Investigation of naproxen drug using mass spectrometry, thermal analyses and semi-empirical molecular orbital calculation

    Directory of Open Access Journals (Sweden)

    M.A. Zayed

    2017-03-01

    Full Text Available Naproxen (C14H14O3 is a non-steroidal anti-inflammatory drug (NSAID. It is important to investigate its structure to know the active groups and weak bonds responsible for medical activity. In the present study, naproxen was investigated by mass spectrometry (MS, thermal analysis (TA measurements (TG/DTG and DTA and confirmed by semi empirical molecular orbital (MO calculation, using PM3 procedure. These calculations included, bond length, bond order, bond strain, partial charge distribution, ionization energy and heat of formation (ΔHf. The mass spectra and thermal analysis fragmentation pathways were proposed and compared to select the most suitable scheme representing the correct fragmentation pathway of the drug in both techniques. The PM3 procedure reveals that the primary cleavage site of the charged molecule is the rupture of the COOH group (lowest bond order and high strain which followed by CH3 loss of the methoxy group. Thermal analysis of the neutral drug reveals a high response to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 80–400 °C. These mass losses appear as two endothermic and one exothermic peaks which required energy values of 255.42, 10.67 and 371.49 J g−1 respectively. The initial thermal ruptures are similar to that obtained by mass spectral fragmentation (COOH rupture. It was followed by the loss of the methyl group and finally by ethylene loss. Therefore, comparison between MS and TA helps in selection of the proper pathway representing its fragmentation. This comparison is successfully confirmed by MO-calculation.

  11. 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.

  12. Geometric and electronic structures of molecular ions from high energy collisions

    International Nuclear Information System (INIS)

    Groeneveld, K.O.

    1983-01-01

    This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

  13. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  14. Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Cordeiro, Joao M.M., E-mail: cordeiro@dfq.feis.unesp.br [ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom); Soper, Alan K. [ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom)

    2011-03-18

    Graphical abstract: Structure of liquid NMF and DMSO mixtures investigated using a combination of neutron diffraction techniques augmented with isotopic substitution and empirical potential structure refinement simulations. Research highlights: {yields} NMF-DMSO mixture is a well-structured liquid. {yields} The liquid structure is driven by strong hydrogen bonds. {yields} There is a preference for NMF-DMSO hydrogen bonding compared to the NMF-NMF. {yields} There are very stable NMF-DMSO dimers dispersed through the liquid. {yields} The peptide structure is very well solvated in DMSO. - Abstract: The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF-DMSO hydrogen bonding, compared to the NMF-NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF-DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60{sup o}. The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

  15. Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

    International Nuclear Information System (INIS)

    Cordeiro, Joao M.M.; Soper, Alan K.

    2011-01-01

    Graphical abstract: Structure of liquid NMF and DMSO mixtures investigated using a combination of neutron diffraction techniques augmented with isotopic substitution and empirical potential structure refinement simulations. Research highlights: → NMF-DMSO mixture is a well-structured liquid. → The liquid structure is driven by strong hydrogen bonds. → There is a preference for NMF-DMSO hydrogen bonding compared to the NMF-NMF. → There are very stable NMF-DMSO dimers dispersed through the liquid. → The peptide structure is very well solvated in DMSO. - Abstract: The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF-DMSO hydrogen bonding, compared to the NMF-NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF-DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60 o . The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

  16. 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…

  17. 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.

  18. The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

    Science.gov (United States)

    Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

    2011-01-01

    Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

  19. 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

  20. An Investigation of the Intellectual Structure of Opinion Mining Research

    Science.gov (United States)

    Zhu, Yongjun; Kim, Meen Chul; Chen, Chaomei

    2017-01-01

    Introduction: Opinion mining has been receiving increasing attention from a broad range of scientific communities since early 2000s. The present study aims to systematically investigate the intellectual structure of opinion mining research. Method: Using topic search, citation expansion, and patent search, we collected 5,596 bibliographic records…

  1. 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…

  2. 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)

  3. 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.

  4. 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.

  5. Crystal and molecular structure of dysprosium (3) n-aminobenzoate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    The X ray diffraction investigation of the Dy(NH 2 C 6 H 4 COO) 3 x3H 2 O complex is carried out. Triclinic crystals have lattice parameters α=11.095(15), b=9.099(17), c=12.780 (15)A, α=108.051(12), β=89.072(10); γ=104.954(12) 0 , space group P anti 1, Z=2. The structure consists of dimer molecules. The third water molecule in the formula is an outer spherical one. The average lengths of Dy-O and Dy-OH 2 are 2.39 and 2.40 A respectively, the average value of Dy-O in bridge carboxylates (2.26A) is remarkably shorter. Hydrogen bonds between amine ligand ends, carboxylic groups oxygen and water molecules bind complex molecules into the three-dimensional frame [ru

  6. 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.

  7. Neutron scattering investigations of the lipid bilayer structure pressure dependence

    Directory of Open Access Journals (Sweden)

    D. V. Soloviov

    2012-03-01

    Full Text Available Lipid bilayer structure investigation results obtained with small angle neutron scattering method at the Joint Institute for Nuclear Research IBR-2M nuclear reactor (Dubna, Russia are presented. Experiment has been per-formed with small angle neutron scattering spectrometer YuMO, upgraded with the apparatus for performing P-V-T measurements on the substance under investigation. D2O-1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC liquid system, presenting the model of natural live membrane, has been taken as the sample for investiga-tions. The lipid bilayer spatial period was measured in experiment along with isothermal compressibility simulta-neously at different pressures. It has been shown, that the bilayer structural transition from ripple (wavelike gel-phase phase to liquid-crystal phase is accompanied with anomalous rise of isothermal compressibility, indicat-ing occurrence of the phase transition.

  8. Neutron scattering investigations of the lipid bilayer structure pressure dependence

    International Nuclear Information System (INIS)

    Solovjov, D.V.; Gordelyij, V.Yi.; Gorshkova, Yu.Je.; Yivan'kov, O.Yi.; Koval'ov, Yu.S.; Kuklyin, A.Yi.; Solovjov, D.V.; Bulavyin, L.A.; Yivan'kov, O.Yi.; Nyikolajenko, T.Yu.; Kuklyin, A.Yi.; Gordelyij, V.Yi.; Gordelyij, V.Yi.

    2012-01-01

    Lipid bilayer structure investigation results obtained with small angle neutron scattering method at the Joint Institute for Nuclear Research IBR-2M nuclear reactor (Dubna, Russia) are presented. Experiment has been performed with small angle neutron scattering spectrometer YuMO, upgraded with the apparatus for performing PV-T measurements on the substance under investigation. D 2 O-1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liquid system, presenting the model of natural live membrane, has been taken as the sample for investigations. The lipid bilayer spatial period was measured in experiment along with isothermal compressibility simultaneously at different pressures. It has been shown, that the bilayer structural transition from ripple (wavelike gel-phase) phase to liquid-crystal phase is accompanied with anomalous rise of isothermal compressibility, indicating occurrence of the phase transition.

  9. Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Hajilar, Shahin, E-mail: shajilar@iastate.edu [Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA 50011-1066 (United States); Shafei, Behrouz, E-mail: shafei@iastate.edu [Department of Civil, Construction and Environmental Engineering, Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011-1066 (United States)

    2016-12-15

    The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanical properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates. - Graphical abstract: Fracture mechanism of portlandite under uniaxial strain in the z-direction. - Highlights: • The structural, thermal, and mechanical properties of portlandite are investigated. • The coefficients of thermal expansion are determined. • The stress-strain relationships are studied in three orthogonal directions. • The effects of temperature and strain rate on mechanical properties are examined. • The plastic energy required for fracture in the crystalline structure is reported.

  10. 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 ...

  11. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    Science.gov (United States)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  12. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    International Nuclear Information System (INIS)

    Asafi, M S; Tekpinar, M; Yildirim, A

    2016-01-01

    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. (paper)

  13. 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.

  14. 16O+16O molecular nature of the superdeformed band of 32S and the evolution of the molecular structure

    International Nuclear Information System (INIS)

    Kimura, Masaaki; Horiuchi, Hisashi

    2004-01-01

    The relation between the superdeformed band of 32 S and 16 O+ 16 O molecular bands is studied by the deformed-basis antisymmetrized molecular dynamics with the Gogny D1S force. It is found that the obtained superdeformed band members of S have a considerable amount of the 16 O+ 16 O component. Above the superdeformed band, we have obtained two excited rotational bands which have more prominent character of the 16 O+ 16 O molecular band. These three rotational bands are regarded as a series of 16 O+ 16 O molecular bands which were predicted by using the unique 16 O- 16 O optical potential. As the excitation energy and principal quantum number of the relative motion increase, the 16 O+ 16 O cluster structure becomes more prominent but at the same time, the band members are fragmented into several states

  15. Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

    Science.gov (United States)

    Cordeiro, João M. M.; Soper, Alan K.

    2011-03-01

    The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF-DMSO hydrogen bonding, compared to the NMF-NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF-DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60°. The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

  16. Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study.

    Science.gov (United States)

    Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K

    2017-11-21

    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 (C d ) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of C d with positive and negative surface potentials.

  17. Structural phase transition and failure of nanographite sheets under high pressure: a molecular dynamics study

    International Nuclear Information System (INIS)

    Zhang Bin; Liang Yongcheng; Sun Huiyu

    2007-01-01

    Nanographite sheets under high compressive stresses at ambient temperature have been investigated through molecular dynamics simulations using the Tersoff-Brenner potential. Nanographite undergoes a soft to hard phase transition at a certain compressive stress, about 15 GPa. With increasing compressions, the bonding structures of nanographite are changed, interlayer sp 3 -bonds are formed, and nanographite transforms into a superhard carbon phase (SCP). Further compressions lead to the instabilities of the SCP. Although the detailed lattice structure of the SCP remains elusive, its compressive strength can approach 150 GPa, comparable to that of diamond. The maximum failure stresses of nanographite sheets are sensitive to the inter-and intra-layer interstices. Our results may explain paradoxical experimental results in the available literature

  18. 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.

  19. 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)

  20. 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.

  1. Supramolecular Structure and Mechanical Characteristics of Ultrahigh-Molecular-Weight Polyethylene-Inorganic Nanoparticle Nanocomposites

    International Nuclear Information System (INIS)

    Okhlopkova, T. A.; Borisova, R. V.; Nikiforov, L. A.; Spiridonov, A. M.; Okhlopkova, A. A.; Cho, Jin-Ho; Jeong, Dae-Yong

    2016-01-01

    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.

  2. Investigation of supersonic jets shock-wave structure

    Science.gov (United States)

    Zapryagaev, V. I.; Gubanov, D. A.; Kavun, I. N.; Kiselev, N. P.; Kundasev, S. G.; Pivovarov, A. A.

    2017-10-01

    The paper presents an experimental studies overview of the free supersonic jet flow structure Ma = 1.0, Npr = 5, exhausting from a convergent profiled nozzle into a ambient space. Also was observed the jets in the presence of artificial streamwise vortices created by chevrons and microjets located on the nozzle exit. The technique of experimental investigation, schlieren-photographs and schemes of supersonic jets, and Pitot pressure distributions, are presented. A significant effect of vortex generators on the shock-wave structure of the flow is shown.

  3. Milestone in the NTB phase investigation and beyond: direct insight into molecular self-assembly.

    Science.gov (United States)

    Ivšić, Trpimir; Vinković, Marijana; Baumeister, Ute; Mikleušević, Ana; Lesac, Andreja

    2014-12-14

    Although liquid-crystalline materials are most widely exploited for flat-panel displays, their ability to self-organize into periodically ordered nanostructures gives rise to a broad variety of additional applications. The recently discovered low-temperature nematic phase (N(TB)) with unusual characteristics generated considerable attention within the scientific community: despite the fact that the molecules from which the phase is composed are not chiral, the helicoidal structure of the phase is strongly implicated. Here we report on combined experimental, computational and spectroscopic studies of the structural aspects influencing formation of the N(TB) phase as well as on the molecular organization within the phase. In an extensive DFT study, the structure-property prerequisite was traced to a "bent-propeller" shape of the molecule. We also demonstrate the first utilization of liquid state NMR for direct analysis of intermolecular interactions within thermotropic liquid-crystalline phases, providing new insight into molecular packing that can lead towards design of novel chiral functional materials. The synergy of experimental, computational and NMR studies suggests a syn-parallel helical molecular organization within the N(TB) phase.

  4. 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.

  5. Molecular structure and correlations in liquid D-2-propanol through neutron diffraction

    International Nuclear Information System (INIS)

    Sahoo, A.; Sarkar, S.; Joarder, R.N.; Krishna, P.S.R.

    2003-01-01

    Like t-butanol, 2-propanol molecules are quite big with substantial amount of asymmetry in the structure and so the analysis of the neutron diffraction data is tricky. A modified method of analysis, similar to one for liquid t-butanol, enables extraction of the detailed molecular conformation and intermolecular correlations through neutron diffraction. The pre-peak in the structure function, a signature of chain molecular association together with partially identified inter-molecular correlations yield some information about the nature of possible H-bonded molecular clusters in the liquid state. (author)

  6. 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.

  7. Mutation analysis and molecular modeling for the investigation of ligand-binding modes of GPR84.

    Science.gov (United States)

    Nikaido, Yoshiaki; Koyama, Yuuta; Yoshikawa, Yasushi; Furuya, Toshio; Takeda, Shigeki

    2015-05-01

    GPR84 is a G protein-coupled receptor for medium-chain fatty acids. Capric acid and 3,3'-diindolylmethane are specific agonists for GPR84. We built a homology model of a GPR84-capric acid complex to investigate the ligand-binding mode using the crystal structure of human active-state β2-adrenergic receptor. We performed site-directed mutagenesis to subject ligand-binding sites to our model using GPR84-Giα fusion proteins and a [(35)S]GTPγS-binding assay. We compared the activity of the wild type and mutated forms of GPR84 by [(35)S]GTPγS binding to capric acid and diindolylmethane. The mutations L100D `Ballesteros-Weinstein numbering: 3.32), F101Y (3.33) and N104Q (3.36) in the transmembrane helix III and N357D (7.39) in the transmembrane helix VII resulted in reduced capric acid activity but maintained the diindolylmethane responses. Y186F (5.46) and Y186H (5.46) mutations had no characteristic effect on capric acid but with diindolylmethane they significantly affected the G protein activation efficiency. The L100D (3.32) mutant responded to decylamine, a fatty amine, instead of a natural agonist, the fatty acid capric acid, suggesting that we have identified a mutated G protein-coupled receptor-artificial ligand pairing. Our molecular model provides an explanation for these results and interactions between GPR84 and capric acid. Further, from the results of a double stimulation assay, we concluded that diindolylmethane was a positive allosteric modulator for GPR84. © The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

    Science.gov (United States)

    2017-05-05

    Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

  13. 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

  14. An arc detector for neutron crystal structure investigations

    Energy Technology Data Exchange (ETDEWEB)

    Habib, N [Reactor and Neutron Physics Dept., Nuclear Research Center. AEA, Cairo (Egypt)

    1997-12-31

    An arc detector for neutron structure investigations of powder crystals using time-of-flight technique is described. In order to enable the measurement of integral intensity from about 1/4 of the Debye-Scherrer ring and for simplicity reasons, the scattering angle 20-90 degree was chosen and a special arc collimator was built. The arc collimator-detector had a divergency of about 20 minutes of arc, and the distance between detector-sample was 64 cm. Four {sup 3} He detectors were fixed on the arc of the collimator. Both efficiency and space sensitivity of the detector were determined using a point neutron source. Results of measurements show that parameters of the arc detector are acceptable for high resolution crystal structure investigations. 6 figs.

  15. 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.

  16. 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.

  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. Investigations on the local structure and the spin-Hamiltonian ...

    Indian Academy of Sciences (India)

    2016-07-13

    Jul 13, 2016 ... (2016) 87: 22 c Indian Academy of Sciences. DOI 10.1007/s12043-016-1234-6. Investigations on the local structure and the spin-Hamiltonian parameters for the tetragonal Cu. 2+ centre in ZnGeF6·6H2O crystal. LI CHAO-YING. ∗. , HUANG YING and ZHENG XUE MEI. School of Physics and Electronic ...

  19. Electronic structure of Mo and W investigated with positron annihilation

    Energy Technology Data Exchange (ETDEWEB)

    Dutschke, Markus [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Sekania, Michael [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Andronikashvili Institute of Physics, Tbilisi (Georgia); Benea, Diana [Faculty of Physics, Babes-Bolyai University, Cluj-Napoca (Romania); Department of Chemistry, Ludwig Maximilian University of Munich (Germany); Ceeh, Hubert; Weber, Joseph A.; Hugenschmidt, Christoph [FRM II, Technische Universitaet Muenchen, Garching (Germany); Chioncel, Liviu [Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg (Germany); Augsburg Center for Innovative Technologies, University of Augsburg (Germany)

    2016-07-01

    We perform electronic structure calculations to analyze the momentum distribution of the transition metals molybdenum and tungsten. We study the influence of positron-electron and the electron-electron interactions on the shape of the two-dimensional angular correlation of positron annihilation radiation (2D-ACAR) spectra. Our analysis is performed within the framework of the combined Density Functional (DFT) and Dynamical Mean-Field Theory (DMFT). Computed spectra are compared with recent experimental investigations.

  20. An Algorithm for Investigating the Structure of Material Surfaces

    Directory of Open Access Journals (Sweden)

    M. Toman

    2003-01-01

    Full Text Available The aim of this paper is to summarize the algorithm and the experience that have been achieved in the investigation of grain structure of surfaces of certain materials, particularly from samples of gold. The main parts of the algorithm to be discussed are:1. acquisition of input data,2. localization of grain region,3. representation of grain size,4. representation of outputs (postprocessing.

  1. 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...

  2. 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.

  3. FTIR of binary lead borate glass: Structural investigation

    Science.gov (United States)

    Othman, H. A.; Elkholy, H. S.; Hager, I. Z.

    2016-02-01

    The glass samples were prepared according to the following formula: (100-x) B2O3 - x PbO, where x = 20-80 mol% by melt quenching method. The density of the prepared samples was measured and molar volume was calculated. IR spectra were measured for the prepared samples to investigate the glass structure. The IR spectra were deconvoluted using curves of Gaussian shape at approximately the same frequencies. The deconvoluted data were used to study the effect of PbO content on all the structural borate groups. Some structural parameters such as density, packing density, bond length and bond force constant were theoretically calculated and were compared to the obtained experimental results. Deviation between the experimental and theoretically calculated parameters reflects the dual role of PbO content on the network of borate glass.

  4. Variable temperature investigation of the atomic structure of gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Young, N P; Kirkland, A I [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Huis, M A van; Zandbergen, H W [Kavli Insitute of Nanoscience, Delft University of Technolgy, Lorentzweg 1, NL-2628CJ, Delft (Netherlands); Xu, H, E-mail: neil.young@materials.ox.ac.u [Department of Geology and Geophysics, and Materials Science Program, University of Wisconsin-Madison, Madison, Wisconsin (United States)

    2010-07-01

    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{sup 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.

  5. 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.

  6. 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.

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

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017) PRINCIPAL...this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data ...sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden

  9. A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants.

    Science.gov (United States)

    He, Muyang; Li, Weikang; Zheng, Qingchuan; Zhang, Hongxing

    2018-01-11

    Alectinib, a highly selective next-genetation anaplastic lymphoma kinase (ALK) inhibitor, has demonstrated promising antitumor activity in patients with ALK-positive non-small cell lung carcinomas (NSCLC). However, the therapeutic benefits of alectinib is inescapably hampered by the development of acquired resistant mutations in ALK. Despite the availability of ample experimental mutagenesis data, the molecular origin and the structural motifs under alectinib binding affinity deficiencies are still ambiguous. Here, molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) calculation approaches were employed to elucidate the mechanisms of alectinib resistance induced by the mutations I1171N, V1180L, and L1198F. The MD results reveal that the studied mutations could trigger the dislocation of alectinib as well as conformational changes at the inhibitor binding site, thus induce the interactional changes between alectinib and mutants. The most influenced regions are the ligand binding entrance and the hinge region, which are considered to be the dominant binding motifs accounting for the binding affinity loss in mutants. The "key and lock mechanism" between the ethyl group at position 9 of alectinib and a recognition cavity in the hinge region of ALK is presented to illustrate the major molecular origin of drug resistance. Our results provide mechanistic insight into the effect of ALK mutations resistant to alectinib, which could contribute to further rational design of inhibitors to combat the acquired resistance. © 2018 Wiley Periodicals, Inc.

  10. Analytical and molecular dynamical investigations of the influence of molecular vibrations upon the (e,2e) electron momentum distributions of furan

    International Nuclear Information System (INIS)

    Morini, F; Deleuze, M S; Watanabe, N; Takahashi, M

    2015-01-01

    The role of molecular vibrations has been theoretically investigated in the electronic ground state on the (e, 2e) valence orbital momentum profiles of furan by means of two complementary approaches. The first one relies upon the principles of Born-Oppenheimer Molecular Dynamics (BOMD), whereas the second one, referred as Harmonic Analytical Quantum Mechanical (HAQM) approach, includes on quantum-mechanical (paper)

  11. 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...

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

    Indian Academy of Sciences (India)

    By analyzing the simulation trajectory of molecular packing within ... The total charges of NF3 and BF3 are nearly zero. (0.075e and ... ity due to the charge density distribution. After hav- .... sity distributions are not discrete like a spectral density.

  13. Molecular structure descriptors in the computer-aided design of biologically active compounds

    International Nuclear Information System (INIS)

    Raevsky, Oleg A

    1999-01-01

    The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

  14. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  15. 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

  16. 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.

  17. 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.

  18. 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)

  19. Electron transport in dipyridazine and dipyridimine molecular junctions: a first-principles investigation

    Science.gov (United States)

    Parashar, Sweta

    2018-05-01

    We present density functional theory-nonequilibrium Green’s function method for electron transport of dipyridazine and dipyridimine molecular junctions with gold, copper and nickel electrodes. Our investigation reveals that the junctions formed with gold and copper electrodes bridging dipyridazine molecule through thiol anchoring group enhance current as compared to the junctions in which the molecule and electrode were coupled directly. Further, nickel electrode displays weak decrease of current with increase of voltage at about 1.2 V. The result is fully rationalized by means of the distribution of molecular orbitals as well as shift in molecular energy levels and HOMO-LUMO gap with applied bias voltage. Our findings are compared with theoretical and experimental results available for other molecular junctions. Present results predict potential avenues for changing the transport behavior by not only changing the electrodes, but also the position of nitrogen atom and type of anchoring-atom that connect molecule and electrodes, thus extending applications of dipyridazine and dipyridimine molecule in future integrated circuits.

  20. Classification of proteins: available structural space for molecular modeling.

    Science.gov (United States)

    Andreeva, Antonina

    2012-01-01

    The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

  1. Ciona intestinalis notochord as a new model to investigate the cellular and molecular mechanisms of tubulogenesis.

    Science.gov (United States)

    Denker, Elsa; Jiang, Di

    2012-05-01

    Biological tubes are a prevalent structural design across living organisms. They provide essential functions during the development and adult life of an organism. Increasing progress has been made recently in delineating the cellular and molecular mechanisms underlying tubulogenesis. This review aims to introduce ascidian notochord morphogenesis as an interesting model system to study the cell biology of tube formation, to a wider cell and developmental biology community. We present fundamental morphological and cellular events involved in notochord morphogenesis, compare and contrast them with other more established tubulogenesis model systems, and point out some unique features, including bipolarity of the notochord cells, and using cell shape changes and cell rearrangement to connect lumens. We highlight some initial findings in the molecular mechanisms of notochord morphogenesis. Based on these findings, we present intriguing problems and put forth hypotheses that can be addressed in future studies. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Structural investigation of chemically synthesized ferrite magnetic nanomaterials

    Science.gov (United States)

    Uyanga, E.; Sangaa, D.; Hirazawa, H.; Tsogbadrakh, N.; Jargalan, N.; Bobrikov, I. A.; Balagurov, A. M.

    2018-05-01

    In recent times, interest in ferrite magnetic nanomaterials has considerably grown, mainly due to their highly promising medical and biological applications. Spinel ferrite powder samples, with high heat generation abilities in AC magnetic fields, were studied for their application to the hyperthermia treatment of cancer tumors. These properties of ferrites strongly depend on their chemical composition, ion distribution between crystallographic positions, magnetic structure and method of preparation. In this study, crystal and magnetic structures of several magnetic spinels were investigated by neutron diffraction. The explanation of the mechanism triggering the heat generation ability in the magnetic materials, and the electronic and magnetic states of ferrite-spinel type structures, were theoretically defined by a first-principles method. Ferrites with the composition of CuxMg1-xFe2O4 have been investigated as a heat generating magnetic nanomaterial. Atomic fraction of copper in ferrite was varied between 0 and 100% (that is, x between 0 and 1.0 with 0.2 steps), with the copper dope limit corresponding to appear a tetragonal phase.

  3. 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.

  4. Effect of electron beam radiation on the structure and mechanical properties of ultra high molecular weight polyethylene fibers

    International Nuclear Information System (INIS)

    Li Shujun; Sun Weijun; Liu Xiuju; Gao Yongzhong; Li Huisheng

    1998-01-01

    Ultra high molecular weight polyethylene fibers have been crosslinked by electron beam. The structure and mechanical properties of them have been investigated in different irradiation atmospheres. The obtained results show that the gel content and crosslinking density increase with the increase of dose, the swelling ratio and average molecular weight of crosslinked net decrease with the increase of dose, the tensile strength and failure elongation decrease with the increase of dose, the tensile modulus increases with the increase of dose. When the samples are irradiated in air, vacuum and acetylene atmospheres, the effect of irradiation in acetylene atmosphere is best

  5. 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.)

  6. Effect of steam explosion pre-treatment on molecular structure of ...

    African Journals Online (AJOL)

    Purpose: To examine the effect of steam-explosion (SE) strength on the molecular ... pressure-holding time on the molecular structure of the sweet potato starch were ... overheated liquid and then their pores are filled ... expands and exerts pressure on the cell walls, ... oscillation using distilled water as the dispersing agent.

  7. 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....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

  8. 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.

  9. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    International Nuclear Information System (INIS)

    Swygenhoven, H. van; Caro, A.

    1997-01-01

    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

  10. 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.

  11. Chemical/molecular structure of the dentin-enamel junction is dependent on the intratooth location.

    Science.gov (United States)

    Xu, Changqi; Yao, Xiaomei; Walker, Mary P; Wang, Yong

    2009-03-01

    The dentin-enamel junction (DEJ) plays an important role in preventing crack propagation from enamel into dentin. This function stems from its complex structure and materials properties that are different from either dentin or enamel. The molecular structural differences in both mineral and organic matrix across the DEJ zone were investigated by two-dimensional confocal Raman microspectroscopic mapping/imaging technique. The intensity ratios of 1450 (CH, matrix)/960 (P-O, mineral) decreased gradually to nearly zero across the DEJ. The width of this transition zone was dependent on the intratooth location, with 12.9 +/- 3.2 microm width at occlusal positions and 6.2 +/- 1.3 microm at cervical positions. The difference in width was significant (P < 0.001). Concurrently, spectral differences in both organic and inorganic matrices across the DEJ were also noted. For example, the ratios of 1243 (amide III)/1450 (CH) within the DEJ were lower than the values in dentin; however, the ratios of 1665 (amide I)/1450 (CH) within the DEJ were higher than those values in dentin. In addition, the ratios of 1070 (carbonate)/960 (phosphate) within the dentin were lower than the values in the DEJ. Raman images indicated that the distribution of the above ratios across the DEJ zone were also different at occlusal and cervical positions. The results suggest that the intratooth-location-dependent structure of the DEJ may be related to its function. Micro-Raman spectroscopic/imaging analysis of the DEJ provides a powerful means of identifying the functional width and molecular structural differences across the DEJ.

  12. Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

    Science.gov (United States)

    Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

    2011-03-01

    The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

  13. Influence of substrate quality on structural properties of AlGaN/GaN superlattices grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Schubert, F. [NaMLab gGmbH, Nöthnitzer Straße 64, 01187 Dresden (Germany); Merkel, U.; Schmult, S. [TU Dresden, Institute of Semiconductors and Microsystems, Nöthnitzer Straße 64, 01187 Dresden (Germany); Mikolajick, T. [NaMLab gGmbH, Nöthnitzer Straße 64, 01187 Dresden (Germany); TU Dresden, Institute of Semiconductors and Microsystems, Nöthnitzer Straße 64, 01187 Dresden (Germany)

    2014-02-28

    Short-period AlGaN/GaN superlattices were established as versatile test structures to investigate the structural properties of molecular beam epitaxy (MBE)-grown GaN and AlGaN layers and their dependence on the GaN substrate quality. X-ray diffractometry data of the investigated superlattices allow access to relevant structural parameters such as aluminum mole fraction and layer thicknesses. The occurrence of theoretically predicted intense high-order satellite peaks and pronounced interface fringes in the diffraction pattern reflects abrupt interfaces and perfect 2-dimensional growth resulting in smooth surfaces. The data unambiguously demonstrate that the structural quality of the MBE grown layers is limited by the structural properties of the GaN substrate.

  14. Structural Investigations of Complex Oxides using Synchrotron Radiation

    International Nuclear Information System (INIS)

    Hans-Conrad zur Loye

    2007-01-01

    The work is a collaborative effort between Prof. Hanno zur Loye at the University of South Carolina and Dr. Tom Vogt at Brookhaven National Laboratory. The collaborative research focuses on the synthesis and the structural characterization of perovskites and perovskite related oxides and will target new oxide systems where we have demonstrated expertise in synthesis, yet lack the experimental capabilities to answer important structural issues. Synthetically, we will focus on two subgroups of perovskite structures, the double and triple perovskites, and the 2H-perovskite related oxides belonging to the A 3n+3m A(prime) 3M+n B 3m+n O 9m+6n family. In the first part of the proposal, our goal of synthesizing and structurally characterizing new ruthenium, iridium, rhodium and ruthenium containing double and triple perovskites, with the emphasis on exercising control over the oxidation state(s) of the metals, is described. These oxides will be of interest for their electronic and magnetic properties that will be investigated as well

  15. Population age structure and asset returns: an empirical investigation.

    Science.gov (United States)

    Poterba, J M

    1998-10-01

    "This paper investigates the association between population age structure, particularly the share of the population in the 'prime saving years' 45-60, and the returns on stocks and bonds. The paper is motivated by the claim that the aging of the 'Baby Boom' cohort in the United States is a key factor in explaining the recent rise in asset values. It also addresses the associated claim that asset prices will decline when this large cohort reaches retirement age and begins to reduce its asset holdings. This paper begins by considering household age-asset accumulation profiles. Data from the Survey of Consumer Finances suggest that while cross-sectional age-wealth profiles peak for households in their early 60s, cohort data on the asset ownership of the same households show a much less pronounced peak.... The paper then considers the historical relationship between demographic structure and real returns on Treasury bills, long-term government bonds, and corporate stock. The results do not suggest any robust relationship between demographic structure and asset returns.... The paper concludes by discussing factors such as international capital flows and forward-looking behavior on the part of market participants that could weaken the relationship between age structure and asset returns in a single nation." excerpt

  16. Molecular structures and functional relationships in clostridial neurotoxins.

    Science.gov (United States)

    Swaminathan, Subramanyam

    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. Journal compilation © 2011 FEBS. No claim to original US government works.

  17. Nuclear magnetic resonance structure investigations on crosslinked polyesters

    International Nuclear Information System (INIS)

    Grobelny, J.

    1999-01-01

    Styrene-crosslinked mixed polyesters derived from maleic anhydride, 2,2-di(4-hydroxypropoxyphenyl)propane, oligo(propylene oxide) and 1,2-propylene glycol were investigated by high-resolution solid-state 13 C NMR spectroscopy. The structural modifications accompanying crosslinking were characterized in terms of spin-lattice relaxation times as a function of unsaturated polyester composition. Copolymerization and crosslinking effects were individually evaluated and the latter effect was related to variations in crosslinking density associated with the chemical structure of the unsaturated prepolymer. As the crosslinking effect is suppressed, the mechanical properties undergo expected changes, e.g., impact strength is increased and modulus of elasticity in tension is decreased. (author)

  18. The investigation on the structure, fabrication and applications of graphene

    Science.gov (United States)

    Du, Donghe

    By investigating the structure of graphene oxide (GO), the long-wavelength photoluminescence of GO is evidenced to be originated from the excimer formation between GO basal plane and oxidative debris (ODs) attached on the GO sheets. The thermally unstable ODs would induce micro-explosion of GO upon heating. A novel method is developed to supress the explosion and achieve simultaneous thermal reduction and nitrogen doping of graphene oxide in air. The high quality N-doped graphene demonstrate excellent electrocatalytic property in oxygen reduction reaction. Furthermore, an electronic textile material is fabricated by coating chemically reduced GO on a piece of non-woven fabric (GNWF). GNWF can be applied as wearable sensors to detect physiological signals of human body. This research work deepens the understanding on the structure and property of graphene based materials and provides a cost-effective fabrication method for large scale production of graphene, and hence facilitates the commercialization of graphene.

  19. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

    Science.gov (United States)

    Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

    2006-06-01

    The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.

  20. 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.

  1. 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...... that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band...

  2. Conformation of phylogenetic relationship of Penaeidae shrimp based on morphometric and molecular investigations.

    Science.gov (United States)

    Rajakumaran, P; Vaseeharan, B; Jayakumar, R; Chidambara, R

    2014-01-01

    Understanding of accurate phylogenetic relationship among Penaeidae shrimp is important for academic and fisheries industry. The Morphometric and Randomly amplified polymorphic DNA (RAPD) analysis was used to make the phylogenetic relationsip among 13 Penaeidae shrimp. For morphometric analysis forty variables and total lengths of shrimp were measured for each species, and removed the effect of size variation. The size normalized values obtained was subjected to UPGMA (Unweighted Pair-Group Method with Arithmetic Mean) cluster analysis. For RAPD analysis, the four primers showed reliable differentiation between species, and used correlation coefficient between the DNA banding patterns of 13 Penaeidae species to construct UPGMA dendrogram. Phylogenetic relationship from morphometric and molecular analysis for Penaeidae species found to be congruent. We concluded that as the results from morphometry investigations concur with molecular one, phylogenetic relationship obtained for the studied Penaeidae are considered to be reliable.

  3. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    International Nuclear Information System (INIS)

    Galasso, V.

    2010-01-01

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, 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 π → π* and n → π* 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.

  4. 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.

  5. 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.

  6. 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 (pdigestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

  7. 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.

  8. Adsorption and double layer charging in molecular sieve carbons in relation to molecular dimensions and pore structures

    International Nuclear Information System (INIS)

    Koresh, J.

    1982-09-01

    The pore structure of a fibrous carbon molecular sieve was studied by adsorption of molecular probes. Mild activation steps enabled the graduated opening of critical pore dimensions in the range 3.1-5.0 A, which keeps adsorption selectivity between molecules differing by 0.2 A in cross section diameter, to be considerably greater than 100/1. High adsorption stereospecificity over a wide pore dimension range enabled the studied adsorbates to be ordered in a sequence of increasing critical molecular dimension. Estimation of molecular dimensions by various experimental methods was discussed and their relevance to nonspherical molecules was evaluated. Polar molecules assume different dimensions depending on whether the carbon surface was polar (oxidized) or not. Hydrogen acquires, surprisingly, large width in accordance with its high liquid molar volume. Adsorbent-adsorbate interactions play a crucial role in determining molecular dimensions. Adsorption of ions from aqueous solutions into the developed ultramicropores of fibrous carbon electrodes was also studied. The dependence of the double layer capacitance and the charging rate on the pore critical dimension and on surface oxidation was studied using linear potential sweep voltametry. (Author)

  9. 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)

  10. 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

  11. 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 R2 = 0.87, RSD = 0.74, P 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.

  12. 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)

  13. Structural investigations of sodium caseinate micelles in complex environments

    International Nuclear Information System (INIS)

    Huck Iriart, C.; Herrera, M.L.; Candal, R.; Oliveira, C.L.P.; Torriani, I.

    2012-01-01

    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)

  14. 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

  15. 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

  16. 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...

  17. 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...

  18. 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.

  19. 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...... undergoes two phase transitions occurring at 38.3 and 39.8 Angstrom(2)/molecule. Simulation indicates that the first transition involves a reorientation of the headgroups while simulation and XRD show that in the second transition the order parameter is the tilt angle of the alkyl chains. A methodology......; 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...

  20. Spatial distribution of intra-molecular water and polymeric components in polyelectrolyte dendrimers revealed by small angle scattering investigations

    Science.gov (United States)

    Wu, Bin; Li, Xin; Do, Changwoo; Kim, Tae-Hwan; Shew, Chwen-Yang; Liu, Yun; Yang, Jun; Hong, Kunlun; Porcar, Lionel; Chen, Chun-Yu; Liu, Emily L.; Smith, Gregory S.; Herwig, Kenneth W.; Chen, Wei-Ren

    2011-10-01

    An experimental scheme using contrast variation small angle neutron scattering technique is developed to investigate the structural characteristics of amine-terminated poly(amidoamine) dendrimers solutions. Using this methodology, we present the dependence of both the intra-dendrimer water and the polymer distribution on molecular protonation, which can be precisely adjusted by tuning the pH of the solution. Assuming spherical symmetry of the spatial arrangement of the constituent components of dendrimer, and that the atomic ratio of hydrogen-to-deuterium for the solvent residing within the cavities of dendrimer is identical to that for the solvent outside the dendrimer, the intra-dendrimer water distribution along the radial direction is determined. Our result clearly reveals an outward relocation of the peripheral groups, as well as enhanced intra-dendrimer hydration, upon increasing the molecular protonation and, therefore, allows the determination of segmental backfolding in a quantitative manner. The connection between these charge-induced structural changes and our recently observed progressively active segmental dynamics is also discussed.

  1. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  2. 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

  3. 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.

  4. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

    Science.gov (United States)

    2018-01-01

    With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

  5. 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.

  6. Entomologic and molecular investigation into Plasmodium vivax transmission in Singapore, 2009.

    Science.gov (United States)

    Ng, Lee-Ching; Lee, Kim-Sung; Tan, Cheong-Huat; Ooi, Peng-Lim; Lam-Phua, Sai-Gek; Lin, Raymond; Pang, Sook-Cheng; Lai, Yee-Ling; Solhan, Suhana; Chan, Pei-Pei; Wong, Kit-Yin; Ho, Swee-Tuan; Vythilingam, Indra

    2010-10-29

    Singapore has been certified malaria free since November 1982 by the World Health Organization and despite occasional local transmission, the country has maintained the standing. In 2009, three clusters of malaria cases were reported in Singapore. Epidemiological, entomological and molecular studies were carried out to investigate the three clusters, namely Mandai-Sungei Kadut, Jurong Island and Sembawang. A total of 29 malaria patients, with no recent travel history, were reported in the three clusters. Molecular analysis based on the msp3α and msp1 genes showed two independent local transmissions: one in Mandai-Sungei Kadut and another in Sembawang. Almost all cases within each cluster were epidemiologically linked. In Jurong Island cluster, epidemiological link remains uncertain, as almost all cases had a unique genetic profile. Only two cases shared a common profile and were found to be linked to the Mandai-Sungei Kadut cluster. Entomological investigation found Anopheles sinensis to be the predominant Anopheline in the two areas where local transmission of P. vivax was confirmed. Anopheles sinensis was found to be attracted to human bait and bites as early as 19:45 hrs. However, all Anopheles mosquitoes caught were negative for sporozoites and oocysts by dissection. Investigation of P. vivax cases from the three cluster areas confirmed the occurrence of local transmission in two areas. Although An. sinensis was the predominant Anopheline found in areas with confirmed transmission, the vector/s responsible for the outbreaks still remains cryptic.

  7. Entomologic and molecular investigation into Plasmodium vivax transmission in Singapore, 2009

    Directory of Open Access Journals (Sweden)

    Solhan Suhana

    2010-10-01

    Full Text Available Abstract Background Singapore has been certified malaria free since November 1982 by the World Health Organization and despite occasional local transmission, the country has maintained the standing. In 2009, three clusters of malaria cases were reported in Singapore. Methods Epidemiological, entomological and molecular studies were carried out to investigate the three clusters, namely Mandai-Sungei Kadut, Jurong Island and Sembawang. Results A total of 29 malaria patients, with no recent travel history, were reported in the three clusters. Molecular analysis based on the msp3α and msp1 genes showed two independent local transmissions: one in Mandai-Sungei Kadut and another in Sembawang. Almost all cases within each cluster were epidemiologically linked. In Jurong Island cluster, epidemiological link remains uncertain, as almost all cases had a unique genetic profile. Only two cases shared a common profile and were found to be linked to the Mandai-Sungei Kadut cluster. Entomological investigation found Anopheles sinensis to be the predominant Anopheline in the two areas where local transmission of P. vivax was confirmed. Anopheles sinensis was found to be attracted to human bait and bites as early as 19:45 hrs. However, all Anopheles mosquitoes caught were negative for sporozoites and oocysts by dissection. Conclusion Investigation of P. vivax cases from the three cluster areas confirmed the occurrence of local transmission in two areas. Although An. sinensis was the predominant Anopheline found in areas with confirmed transmission, the vector/s responsible for the outbreaks still remains cryptic.

  8. Magnetic effects on the solvent properties investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

    2014-03-15

    This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

  9. 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.

  10. Investigations of the Formation of Molecular Hydrogen on Dust Grain Analogues

    Science.gov (United States)

    Vidali, Gianfranco; Roser, Joseph E.; Manico, Giulio; Pirronello, Valerio

    2002-01-01

    In the last four years we have been working to investigate the formation of molecular hydrogen on surfaces of materials of astrophysical interest, such as silicates, carbonaceous particles and ices, and in conditions approximating the ones present in a variety of astrophysical environments. Our experimental studies - the first of their kind and complemented with computer simulations and theoretical analyses - have given not only hydrogen recombination rates under different ISM conditions, but they have also offered new insights into this fundamental astrophysical problem. Here we summarize our experimental methods and most significant results.

  11. 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.

  12. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    International Nuclear Information System (INIS)

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  13. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  14. Molecular structure, functionality and applications of oxidized starches: A review.

    Science.gov (United States)

    Vanier, Nathan Levien; El Halal, Shanise Lisie Mello; Dias, Alvaro Renato Guerra; da Rosa Zavareze, Elessandra

    2017-04-15

    During oxidation, the hydroxyl groups of starch molecules are first oxidized to carbonyl groups, then to carboxyl groups. The contents of the carbonyl and carboxyl groups in a starch molecule therefore indicate the extent of starch oxidation. The mechanisms of starch oxidation with different oxidizing agents, including sodium hypochlorite, hydrogen peroxide, ozone and sodium periodate, are described in this review. The effects of these oxidizing agents on the molecular, physicochemical, thermal, pasting and morphological properties of starch are described as well. In addition, the main industrial applications of oxidized starches are presented. The present review is important for understanding the effects of oxidation on starch properties, and this information may facilitate the development of novel oxidized starches for both food and non-food applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. 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...

  16. 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.

  17. Characterization of the Structural, Mechanical, and Electronic Properties of Fullerene Mixtures: A Molecular Simulations Description

    KAUST Repository

    Tummala, Naga Rajesh; Aziz, Saadullah; Coropceanu, Veaceslav; Bredas, Jean-Luc

    2017-01-01

    We investigate mixtures of fullerenes and fullerene derivatives, the most commonly used electron accepting materials in organic solar cells, by using a combination of molecular dynamics and density functional theory methods. Our goal is to describe

  18. 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.

  19. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    Science.gov (United States)

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

  20. Investigating the structure and fragmentation of a highly filamentary IRDC

    Science.gov (United States)

    Henshaw, J. D.; Caselli, P.; Fontani, F.; Jiménez-Serra, I.; Tan, J. C.; Longmore, S. N.; Pineda, J. E.; Parker, R. J.; Barnes, A. T.

    2016-11-01

    We present 3.7 arcsec (˜0.05 pc) resolution 3.2 mm dust continuum observations from the Institut de Radioastronomie Millimétrique Plateau de Bure Interferometer, with the aim of studying the structure and fragmentation of the filamentary infrared dark cloud (IRDC) G035.39-00.33. The continuum emission is segmented into a series of 13 quasi-regularly spaced (λobs ˜ 0.18 pc) cores, following the major axis of the IRDC. We compare the spatial distribution of the cores with that predicted by theoretical work describing the fragmentation of hydrodynamic fluid cylinders, finding a significant (a factor of ≳ 8) discrepancy between the two. Our observations are consistent with the picture emerging from kinematic studies of molecular clouds suggesting that the cores are harboured within a complex network of independent sub-filaments. This result emphasizes the importance of considering the underlying physical structure, and potentially, dynamically important magnetic fields, in any fragmentation analysis. The identified cores exhibit a range in (peak) beam-averaged column density (3.6 × 1023 cm-2 < NH, c < 8.0 × 1023 cm-2), mass (8.1 M⊙ < Mc < 26.1 M⊙), and number density (6.1 × 105 cm-3 < nH, c, eq < 14.7 × 105 cm-3). Two of these cores, dark in the mid-infrared, centrally concentrated, monolithic (with no traceable substructure at our PdBI resolution), and with estimated masses of the order ˜20-25 M⊙, are good candidates for the progenitors of intermediate-to-high-mass stars. Virial parameters span a range 0.2 < αvir < 1.3. Without additional support, possibly from dynamically important magnetic fields with strengths of the order of 230 μG < B < 670 μG, the cores are susceptible to gravitational collapse. These results may imply a multilayered fragmentation process, which incorporates the formation of sub-filaments, embedded cores, and the possibility of further fragmentation.

  1. Multiparticle 3D imaging technique to study the structure of molecular ions

    International Nuclear Information System (INIS)

    Koenig, W.; Faibis, A.; Kanter, E.P.; Vager, Z.; Zabransky, B.J.

    1984-01-01

    When energetic molecular ions (E/sub ion/ = 0.1 to 0.5 MeV/amu) pass through thin solid targets a Coulomb explosion ensues due to the rapid (approx. 10 -17 s) stripping of the valence electrons. This process has been successfully used to derive stereochemical information on diatomic and on selected triatomic ions. In order to investigate more complex molecular ions as well as to obtain more accurate and detailed structure information, a large area, multiparticle, position- and time-sensitive detector has been developed to detect all atomic fragments in coincidence. The requirement of multiparticle detection independent of the relative particle positions leads to a rather complex data-readout and -reduction system containing approx. 650 analog-to-digital conversions per event. The system relies heavily on techniques developed for high energy physics experiments during recent years. The single event resolution of the apparatus with respect to bond-lengths and -angles has been studied by Monte Carlo simulations and is typically a few percent

  2. 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.

  3. Molecular structure, vibrational spectra and DFT computational studies of melaminium N-acetylglycinate dihydrate

    Science.gov (United States)

    Tanak, H.; Pawlus, K.; Marchewka, M. K.

    2016-10-01

    Melaminium N-acetylglycinate dihydrate, an organic material has been synthesized and characterized by X-ray diffraction, FT-IR, and FT-Raman spectroscopies for the protiated and deuteriated crystals. The title complex crystallizes in the triclinic system, and the space group is P-1 with a = 5.642(1) Å, b = 7.773(2) Å, c = 15.775(3) Å, α = 77.28(1)°, β = 84.00(1)°, γ = 73.43(1)° and Z = 2. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional method (B3LYP) with the 6-311++G(d,p) basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. The intermolecular hydrogen bonding interactions of the title compound have been investigated using the natural bonding orbital analysis. It reveals that the O-H···O, N-H···N and N-H···O intermolecular interactions significantly influence crystal packing of this molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, thermodynamic properties, frontier orbitals and chemical reactivity descriptors were also performed at 6-311++G(d,p) level of theory.

  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. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    International Nuclear Information System (INIS)

    Tanak, Hasan; Koysal, Yavuz; Isik, Samil; Yaman, Hanifi; Ahsen, Vefa

    2011-01-01

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained

  6. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    Energy Technology Data Exchange (ETDEWEB)

    Tanak, Hasan [Amasya University, Amasys (Turkmenistan); Koysal, Yavuz; Isik, Samil [Ondokuz Mayis University, Samsun (Turkmenistan); Yaman, Hanifi; Ahsen, Vefa [Gebze Institute of Technology Department of Chemistry, Gebze-Kocaeli (Turkmenistan)

    2011-02-15

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained.

  7. 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.

  8. 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

  9. 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 ...

  10. Energy-related atomic and molecular structure and scattering studies: Final report

    International Nuclear Information System (INIS)

    1987-01-01

    The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

  11. SEM investigation of incandescent lamp mantle structure on durability

    International Nuclear Information System (INIS)

    Gerneke, D.; Lang, C.

    2002-01-01

    Full text: The incandescent mantle as used on pressure and non-pressure liquid fuel lamps has been in use for over 100 years. What remains unexplained is the way in which the resistance to mechanical shock and the decline in tensile strength with usage is experienced. It has been suggested that to improve durability it is necessary to continuously burn a new mantle for the first two to three hours. The known factors in mantle durability and mechanical strength are chemical composition and fabric weave. This study was undertaken to investigate the effects of burning time and temperature on thorium oxide mantles. The operating temperature of mantles on a range of kerosene pressure lamps was measured and found to be between 800 and 1100 deg C. Heat treatments of thorium based Coleman mantles were carried out in a laboratory furnace within these ranges of temperatures for periods ranging from 2 minutes to 2 hours. The mantles were then viewed in a LEO S440 analytical SEM. Results at 800 deg C show a distinct change in surface morphology with increasing exposure time. At the shorter times (2-5 minutes) the surface was relatively smooth. With increased time periods (15 - 120 minutes) the surface was observed to have a large lumpy structure. At 1100 deg C the difference in surface morphology was not apparent between the shortest and longest times. The surface appears much smoother and no lumpy structure was observed. This suggests that when a mantle is operated at the higher temperature of 1100 deg C the structure of the Thorium oxide is quickly transformed into the known stronger amorphous form. This is taken as the observed smooth structure seen in the SEM images of the 1100 deg C samples. Thus the mantle is expected to be more resistant to mechanical shock and have increased durability. Practical field test results confirm these observations. The mantle on a lamp that is operating efficiently, burns brightly, will far outlast a mantle on an inefficient lamp which bums

  12. 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.

  13. 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.

  14. Investigating performance of microchannel evaporators with different manifold structures

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Junye; Qu, Xiaohua; Qi, Zhaogang; Chen, Jiangping [Institute of Refrigeration and Cryogenics, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai 200240 (China)

    2011-01-15

    In this paper, the performances of microchannel evaporators with different manifold structures are experimentally investigated. Eight evaporator samples with 7 different designs of the I/O manifold and 5 different designs of the return manifold are made for this study. The performances of the evaporator samples are tested on a psychometric calorimeter test bench with the refrigerant 134A at a real automotive AC condition. The results on the variations of the cooling capacity and air temperature distribution of the evaporator due to the deflector designs in the I/O manifold and flow hole arrangements in the return manifold are presented and analyzed. By studying the KPI's for the performance of an evaporator, the design trade-off for an evaporator designer is summarized and discussed. (author)

  15. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    International Nuclear Information System (INIS)

    Bowsher, James; Giles, William; Yin, Fang-Fang; Yan, Susu; Roper, Justin

    2014-01-01

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  16. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    Energy Technology Data Exchange (ETDEWEB)

    Bowsher, James, E-mail: james.bowsher@duke.edu; Giles, William; Yin, Fang-Fang [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Yan, Susu [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Roper, Justin [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2014-01-15

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  17. 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

  18. 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.

  19. Investigation of hadronic structure by solving QCD on a lattice

    International Nuclear Information System (INIS)

    Grandy, J.M.

    1992-01-01

    Various aspects of hadronic structure are investigated by means of lattice calculations. The measurements focus on equal-time quark wavefunctions, correlations of density operators, and vacuum correlators of hadronic currents, with additional measurements of Wilson loops and hadron masses as a consistency check. The wavefunctions are shown to be consistent with a confinement model prediction. The effect of hyperfine splitting on the wavefunctions is shown to agree closely with the quark model prediction. The computed quark density correlations for the pion, rho, and proton at long range are compared with the expected asymptotic behavior. The density correlation also provides a basis for comparing the spatial extent of quark pairs surrounding the hadron with the extent of the valence quark wavefunction. Vacuum correlation functions of hadronic currents are compared with phenomenological fits to experimental data and sum rule calculations. Hadronic observable calculations are performed by evaluating path integrals in imaginary time using a Monte Carlo technique. Lattices with 16 points in the time direction and spatial volume of 12 3 and 16 3 points are used. The physical lattice spacing is 0.2 fm, and the physical volume of the lattice is large enough that the effect of spatial boundary conditions on the long range structure of the particles can be corrected in a linear fashion

  20. A Non-Structural Investigation of VIX Risk Neutral Density

    DEFF Research Database (Denmark)

    Barletta, Andrea; Santucci de Magistris, Paolo; Violante, Francesco

    We propose a non-structural pricing method to derive the risk-neutral density (RND) implied by options on the CBOE Volatility Index (VIX). The methodology is based on orthogonal polynomial expansions around a kernel density and yields the RND of the underlying asset without the need for a paramet......We propose a non-structural pricing method to derive the risk-neutral density (RND) implied by options on the CBOE Volatility Index (VIX). The methodology is based on orthogonal polynomial expansions around a kernel density and yields the RND of the underlying asset without the need...... for a parametric specification. The classic family of Laguerre expansions is extended to include the GIG and the generalized Weibull kernels, thus relaxing the conditions required on the tail decay rate of the RND to ensure convergence. We show that the proposed methodology yields an accurate approximation...... of the RND in a large variety of cases, also when the no-arbitrage and efficient option prices are contaminated by measurement errors. Our empirical investigation, based on a panel of traded VIX options, reveals some stylized facts on the RND of VIX. We find that a common stochastic factor drives the dynamic...