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Sample records for capturing molecular structural

  1. Protein-Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure.

    Science.gov (United States)

    Andersen, Amity; Reardon, Patrick N; Chacon, Stephany S; Qafoku, Nikolla P; Washton, Nancy M; Kleber, Markus

    2016-06-21

    Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na(+)-montmorillonite (001), Ca(2+)-montmorillonite (001), goethite (100), and Na(+)-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na(+)-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation. PMID:27243116

  2. Molecular Profiling of Activated Neurons by Phosphorylated Ribosome Capture

    OpenAIRE

    Knight, Zachary A.; Tan, Keith; Birsoy, Kivanc; Schmidt, Sarah; Garrison, Jennifer L.; Wysocki, Robert W.; Emiliano, Ana; Ekstrand, Mats I.; Friedman, Jeffrey M.

    2012-01-01

    The mammalian brain is composed of thousands of interacting neural cell types. Systematic approaches to establish the molecular identity of functional populations of neurons would advance our understanding of neural mechanisms controlling behavior. Here, we show that ribosomal protein S6, a structural component of the ribosome, becomes phosphorylated in neurons activated by a wide range of stimuli. We show that these phosphorylated ribosomes can be captured from mouse brain homogenates, there...

  3. Molecular profiling of activated neurons by phosphorylated ribosome capture.

    Science.gov (United States)

    Knight, Zachary A; Tan, Keith; Birsoy, Kivanc; Schmidt, Sarah; Garrison, Jennifer L; Wysocki, Robert W; Emiliano, Ana; Ekstrand, Mats I; Friedman, Jeffrey M

    2012-11-21

    The mammalian brain is composed of thousands of interacting neural cell types. Systematic approaches to establish the molecular identity of functional populations of neurons would advance our understanding of neural mechanisms controlling behavior. Here, we show that ribosomal protein S6, a structural component of the ribosome, becomes phosphorylated in neurons activated by a wide range of stimuli. We show that these phosphorylated ribosomes can be captured from mouse brain homogenates, thereby enriching directly for the mRNAs expressed in discrete subpopulations of activated cells. We use this approach to identify neurons in the hypothalamus regulated by changes in salt balance or food availability. We show that galanin neurons are activated by fasting and that prodynorphin neurons restrain food intake during scheduled feeding. These studies identify elements of the neural circuit that controls food intake and illustrate how the activity-dependent capture of cell-type-specific transcripts can elucidate the functional organization of a complex tissue. PMID:23178128

  4. Molecular dynamics Gibbs free energy calculations for CO2 capture and storage in structure I clathrate hydrates in the presence of SO2, CH4, N2, and H2S impurities

    International Nuclear Information System (INIS)

    Graphical abstract: Highlights: → Gibbs free energies of CO2 substitution in the structure I hydrate with other guests are computed. → Molecular dynamics based thermodynamic integration method is used. → The pressure and temperature of the CO2 substitution correspond with experimental hydrate synthesis conditions. → SO2 and H2S are more stable in the structure I hydrate. → The contributions to the electrostatic and van der Waals forces to the Gibbs free energies are evaluated separately. - Abstract: The capture of CO2 from flue gas in coal, natural gas, and other fossil fuel burning power stations and storage of CO2 in depleted gas reservoirs in the form of the solid clathrate hydrate have been suggested as methods of carbon capture and storage. These methods have the benefit of only needing water as the CO2 capturing material. The flue gas contains impurities including SO2, CH4, N2, and H2S which can interfere with the CO2 hydrate formation process. Some of these gases may also be found as residuals in depleted natural gas reservoirs. In this work, we use the molecular dynamics thermodynamic integration method to calculate the Gibbs free energy of the substitution reactions at conditions relevant to carbon capture (T = 200 K and 0.1 MPa and at 273 K and 1.0 MPa conditions), clathrate[CO2,p,T]+Y(fluid,p,T)→clathrate[Y,p,T]+CO2(fluid,p,T) where Y is the impurity species in the flue. Knowledge of the Gibbs free energy for this reaction will allow us to determine whether the impurities need to be eliminated from the flue or can participate in the hydrate formation process as neutral species without affecting the stability of the desired CO2 clathrate hydrate. For the thermodynamic integration, we use the nonlinear mixing scheme. In addition to calculating the ΔG for the above reaction, the contributions of different terms in the intermolecular potential of the guest molecules to the ΔG will be determined.

  5. 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

  6. Theory and Application of Dissociative Electron Capture in Molecular Identification

    CERN Document Server

    Havey, C D; Jones, T; Voorhees, K J; Laramee, J A; Cody, R B; Clougherty, D P; Eberhart, Mark; Voorhees, Kent J.; Laramee, James A.; Cody, Robert B.; Clougherty, Dennis P.

    2006-01-01

    The coupling of an electron monochromator (EM) to a mass spectrometer (MS) has created a new analytical technique, EM-MS, for the investigation of electrophilic compounds. This method provides a powerful tool for molecular identification of compounds contained in complex matrices, such as environmental samples. EM-MS expands the application and selectivity of traditional MS through the inclusion of a new dimension in the space of molecular characteristics--the electron resonance energy spectrum. However, before this tool can realize its full potential, it will be necessary to create a library of resonance energy scans from standards of the molecules for which EM-MS offers a practical means of detection. Here, an approach supplementing direct measurement with chemical inference and quantum scattering theory is presented to demonstrate the feasibility of directly calculating resonance energy spectra. This approach makes use of the symmetry of the transition-matrix element of the captured electron to discriminat...

  7. Proton capture reactions and nuclear structure

    International Nuclear Information System (INIS)

    Experimental studies are described of the structure of 40Ca and 42Sc with measurements at proton-capture of (p, gamma) reactions. Where possible, an attempt has been made to interpret the results of the measurements in termsof existing models. The 40Ca and 42Sc nuclides were excited by bombarding 39K and 41Ca targets, respectively with low energy protons (Ep = 0.3-3.0 MeV), that were produced by the Utrecht 3MV van de Graaff accelerator. From the measured energy and intensity of the gamma-rays created in the subsequent decay of the cuclei, information was obtained on the existence and properties of their excited states. In addition properties of two T = 3/2 levels at high excitation energy of the 9Be nucleus were investigated. These levels were excited by the resonant absorption of gamma-rays from the 11B(p, gamma)12C reaction. The results of the measurements are interpreted by a comparison to the analoque β-decay of 9Li and to shell model calculations. The total decay energy of the superallowed O+ → O+ transition between the ground states of 42Sc and 42Ca was determined by measurements in Utrecht of the proton separation energy Sp of 42Sc and in Oak Ridge of Sn of 42Sc and 42Ca. The results were used for verification of the conserved vector current hypothesis, which implies that the ft values of all superallowed O+ → O+ β-decays are the same. An attempt was made to describe properties of odd-parity states of A = 37-41 nuclei with a variant of the Warburton, Becker, Millener and Brown (WBMB) interaction.Finally a new method for the assignment of nuclear spins by a simple statistical analysis of spectroscopic information is proposed. (author). 169 refs.; 22 figs.; 24 schemes; 29 tabs

  8. Capturing Polyradical Protein Cations after an Electron Capture Event: Evidence for their Stable Distonic Structures in the Gas Phase

    Science.gov (United States)

    Baba, Takashi; Campbell, J. Larry

    2015-08-01

    We report on the formation and "capture" of polyradical protein cations after an electron capture event. Performed in a unique electron-capture dissociation (ECD) instrument, these experiments can generate reduced forms of multiply protonated proteins by sequential charge reduction using electrons with ~1 eV. The true structures of these possible polyradicals is considered: Do the introduced unpaired electrons recombine quickly to form a new two-electron bond, or do these unpaired electrons exist as radical sites with appropriate chemical reactivity? Using an established chemical probe—radical quenching with molecular oxygen—we demonstrate that these charge-reduced protein cations are indeed polyradicals that form adducts with up to three molecules of oxygen (i.e., tri-radical protein cations) that are stable for at least 100 ms.

  9. Longitudinal capture in the radio-frequency-quadrupole structure

    International Nuclear Information System (INIS)

    The radio-frequency-quadrupole (RFQ) linac structure not only can attain easily transverse focusing in the low-beta region, but also can obtain very high capture efficiency because of its low beta-lambda and low-particle rigidity. An optimization study of the zero space-charge longitudinal capture in an RFQ linac that yields configurations with large capture efficiency is described

  10. Molecular Spectrum Capture by Tuning the Chemical Potential of Graphene

    Directory of Open Access Journals (Sweden)

    Yue Cheng

    2016-05-01

    Full Text Available Due to its adjustable electronic properties and effective excitation of surface plasmons in the infrared and terahertz frequency range, research on graphene has attracted a great deal of attention. Here, we demonstrate that plasmon modes in graphene-coated dielectric nanowire (GNW waveguides can be excited by a monolayer graphene ribbon. What is more the transverse resonant frequency spectrum of the GNW can be flexibly tuned by adjusting the chemical potential of graphene, and amplitude of the resonance peak varies linearly with the imaginary part of the analyte permittivity. As a consequence, the GNW works as a probe for capturing the molecular spectrum. Broadband sensing of toluene, ethanol and sulfurous anhydride thin layers is demonstrated by calculating the changes in spectral intensity of the propagating mode and the results show that the intensity spectra correspond exactly to the infrared spectra of these molecules. This may open an effective avenue to design sensors for detecting nanometric-size molecules in the terahertz and infrared regimes.

  11. Molecular Spectrum Capture by Tuning the Chemical Potential of Graphene

    Science.gov (United States)

    Cheng, Yue; Yang, Jingjing; Lu, Qiannan; Tang, Hao; Huang, Ming

    2016-01-01

    Due to its adjustable electronic properties and effective excitation of surface plasmons in the infrared and terahertz frequency range, research on graphene has attracted a great deal of attention. Here, we demonstrate that plasmon modes in graphene-coated dielectric nanowire (GNW) waveguides can be excited by a monolayer graphene ribbon. What is more the transverse resonant frequency spectrum of the GNW can be flexibly tuned by adjusting the chemical potential of graphene, and amplitude of the resonance peak varies linearly with the imaginary part of the analyte permittivity. As a consequence, the GNW works as a probe for capturing the molecular spectrum. Broadband sensing of toluene, ethanol and sulfurous anhydride thin layers is demonstrated by calculating the changes in spectral intensity of the propagating mode and the results show that the intensity spectra correspond exactly to the infrared spectra of these molecules. This may open an effective avenue to design sensors for detecting nanometric-size molecules in the terahertz and infrared regimes. PMID:27240372

  12. CO{sub 2} Capture from Flue Gas Using Solid Molecular Basket Sorbents

    Energy Technology Data Exchange (ETDEWEB)

    Fillerup, Eric; Zhang, Zhonghua; Peduzzi, Emanuela; Wang, Dongxiang; Guo, Jiahua; Ma, Xiaoliang; Wang, Xiaoxing; Song, Chunshan

    2012-08-31

    The objective of this project is to develop a new generation of solid, regenerable polymeric molecular basket sorbent (MBS) for more cost-efficient capture and separation of CO{sub 2} from flue gas of coal-fired power plants. The primary goal is to develop a cost-effective MBS sorbent with better thermal stability. To improve the cost-effectiveness of MBS, we have explored commercially available and inexpensive support to replace the more expensive mesoporous molecular sieves like MCM-41 and SBA- 15. In addition, we have developed some advanced sorbent materials with 3D pore structure such as hexagonal mesoporous silica (HMS) to improve the CO{sub 2} working capacity of MBS, which can also reduce the cost for the whole CO{sub 2} capture process. During the project duration, the concern regarding the desorption rate of MBS sorbents has been raised, because lower desorption rate increases the desorption time for complete regeneration of the sorbent which in turn leads to a lower working capacity if the regeneration time is limited. Thus, the improvement in the thermal stability of MBS became a vital task for later part of this project. The improvement in the thermal stability was performed via increasing the polymer density either using higher molecular weight PEI or PEI cross-linking with an organic compound. Moreover, we have used the computational approach to estimate the interaction of CO{sub 2} with different MBSs for the fundamental understanding of CO{sub 2} sorption, which may benefit the development, design and modification of the sorbents and the process.

  13. Atomic and molecular structure

    International Nuclear Information System (INIS)

    This book is a textbook for an introductory course of atomic physics for students of chemistry. After an introduction to the mathematical and physical foundations the quantum mechanical theory of atoms is described starting from simple examples of quantum mechanics. Then the atomic structure and the chemical bending are extensively discussed. This book is also suited for physicists who are especially interested in the atomic structure and the theory of chemical reactions. (HSI)

  14. Supra-molecular networks for CO2 capture

    Science.gov (United States)

    Sadowski, Jerzy; Kestell, John

    Utilizing capabilities of low-energy electron microscopy (LEEM) for non-destructive interrogation of the real-time molecular self-assembly, we have investigated supramolecular systems based on carboxylic acid-metal complexes, such as trimesic and mellitic acid, doped with transition metals. Such 2D networks can act as host systems for transition-metal phthalocyanines (MPc; M = Fe, Ti, Sc). The electrostatic interactions of CO2 molecules with transition metal ions can be tuned by controlling the type of TM ion and the size of the pore in the host network. We further applied infrared reflection-absorption spectroscopy (IRRAS) to determine of the molecular orientation of the functional groups and the whole molecule in the 2D monolayers of carboxylic acid. The kinetics and mechanism of the CO2 adsorption/desorption on the 2D molecular network, with and without the TM ion doping, have been also investigated. This research used resources of the Center for Functional Nanomaterials, which is the U.S. DOE Office of Science User Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.

  15. Molecular gate membrane for CO{sub 2} capture

    Energy Technology Data Exchange (ETDEWEB)

    Singo Kazama; Shuhong Duan; Chie Ohno; Takayuki Kouketsu; Yumi Shimada; Firoz A. Chowdhury; Ichiro Fujiwara; Kenji Haraya; Kazukiyo Nagai; Benny Freeman; Koichi Yamada [Research Institute of Innovative Technology for the Earth (RITE), Kyoto (Japan)

    2005-07-01

    Composite hollow fiber membrane of highly CO{sub 2} selective molecular gate was formed by the in situ modification technique. An active layer of poly(amidoamine) (PAMAM) dendrimer, which has been shown the property of high CO{sub 2}-selective molecular gate, was prepared on the surface of a hollow fiber substrate by using modification technique of surface coating. For the substrate, a polysulfone (PSF) hollow fiber membrane fabricated in RITE was used. The PSF hollow fiber itself has no selectivity of CO{sub 2} on N{sub 2}, on the other hand, the CO{sub 2}/N{sub 2} selectivity of composite membrane treated by PAMAM attained to 67. Membrane systems of CO{sub 2} and H{sub 2} separation from a hypothetical IGCC process gas were investigated. Potential CO{sub 2}/H{sub 2} selectivity of 100 in the molecular gate membrane would offer the reasonable separation of CO{sub 2} from H{sub 2}. 1 ref., 4 figs., 2 tabs.

  16. Molecular electronic-structure theory

    CERN Document Server

    Helgaker, Trygve; Olsen, Jeppe

    2014-01-01

    Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluati

  17. Intermediate structure in the 238U neutron capture cross section

    International Nuclear Information System (INIS)

    Recent measurements of the 238U neutron capture cross section show large fluctuations in the unresolved resonance region. To test whether or not the observed long-range fluctuation of the neutron capture represent departures from the compound nuclear model, the Wald-Wolfowitz runs and correlation tests were applied to the 238U neutron capture data obtained at ORELA. The Wald-Wolfowitz runs test deals with the statistic, R, which is the number of unbroken sequences of data points above or below a given reference line. This statistic is to be compared with the expected value of runs E(R) +- sigma(R) arising from randomly distributed data. In the correlation test we have computed the first serial correlation coefficient of the data as well as its expected value and variance for a set of random data. In both tests one computes the probability, P, for the given statistical entity to depart from its expected value by more than epsilon standard deviations. Both tests confirm the presence of intermediate structure between 5 and 100 keV. The range of the structure far exceeds the width of the experimental resolution and level widths. 3 tables, 2 figures

  18. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

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

  19. Ordered structures of molecular bottlebrushes

    NARCIS (Netherlands)

    ten Brinke, G.; Ikkala, O.

    1997-01-01

    In this review 'molecular bottlebrushes' are flexible polymers densely loaded with equally flexible side chains. Interest in these structures arises from the possibility of lyotropic behaviour in dilute solution in a good solvent, as well as the possibility, of highly, ordered microphase-separated s

  20. Ordered Structures of Molecular Bottlebrushes

    NARCIS (Netherlands)

    Brinke, Gerrit ten; Ikkala, Olli

    1997-01-01

    In this review 'molecular bottlebrushes' are flexible polymers densely loaded with equally flexible side chains. Interest in these structures arises from the possibility of lyotropic behaviour in dilute solution in a good solvent, as well as the possibility of highly ordered microphase-separated sta

  1. Laser capture microdissection enables cellular and molecular studies of tooth root development

    OpenAIRE

    Sun, Jian-Xun; Horst, Orapin V; Bumgarner, Roger; Lakely, Bryce; Somerman, Martha J; Zhang, Hai

    2012-01-01

    Epithelial–mesenchymal interactions (EMIs) are critical for tooth development. Molecular mechanisms mediating these interactions in root formation is not well understood. Laser capture microdissection (LCM) and subsequent microarray analyses enable large scale in situ molecular and cellular studies of root formation but to date have been hindered by technical challenges of gaining intact histological sections of non-decalcified mineralized teeth or jaws with well-preserved RNA. Here,we descri...

  2. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    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 structures

  3. 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

  4. Molecular Simulation on Microstructure of Ionic Liquids in Capture of CO2

    Institute of Scientific and Technical Information of China (English)

    YUE Zhen-uo; LIU Xiao-min; ZHAO Yu-ling; ZHANG Xiao-chun; LU Xing-mei; ZHANG Suo-jiang

    2011-01-01

    Molecular dynamic simulation is used to study the microstructure of four kinds of ionic liquids (ILs),[Emim]PF6,[Emim][Tf2N],[PC6,6,6,14]PF6 and [PC6,6,6,14][Tf2N] in the capture process of CO2.Radial distribution function (RDF) and spatial distribution function (SDF) are used to analyze the microscopic properties of these systems.The calculated results show that the space distribution of CO2 around ILs determines the capability of ionic liquids for capturing CO2.Based on the analysis of SDF,CO2 and PF6- are overlapped partially around [Emim]+ in [Emim]PF6-CO2 mixture.When the anion is [Tf2N]-,cations are mainly distributed on one side of [Tf2N]- near N atom,and CO2 is concentrated on two sides near the fluoroalkylgroup (-CF3),and there is little overlapped district between cation and CO2.In [PC6,6,6,14]PF6-CO2 mixture,layered structure is found and CO2 is much nearer to PF6- than [PC6,6,6,14]+.Based on the analysis of RDF,in the phosphonium-based ILs,the highest distribution densities of anions and CO2 around cations are about 6 and 3 times as their average ones respectively,while in the imidazolium-based ILs,they are about 3 and 2 respectively,this means that the distributions of CO2 and anions around the imidazolium-based ILs are more evenly distributed than those around the phosphonium-bascd ILs.

  5. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  6. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  7. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH.

    Science.gov (United States)

    Cheng, Chin Jung; Daggett, Valerie

    2014-01-01

    Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process. PMID:24970211

  8. Molecular Dynamics Simulations Capture the Misfolding of the Bovine Prion Protein at Acidic pH

    Directory of Open Access Journals (Sweden)

    Chin Jung Cheng

    2014-02-01

    Full Text Available Bovine spongiform encephalopathy (BSE, or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP, which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process.

  9. Rotational spectra and molecular structure

    CERN Document Server

    Wollrab, James E

    1967-01-01

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

  10. 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,...

  11. Ontological Status of Molecular Structure

    Directory of Open Access Journals (Sweden)

    Giuseppe Del Re

    1998-11-01

    Full Text Available Molecular structure (MS has been treated as a convention or an epiphenomenon by physicists and quantum chemists interpreting the mathematical formalism of quantum mechanics as the essential reality criterion in the submicroscopic world (R2 world. This paper argues that, (a even in the R2 world there is a class of entities which are real per se, even though they cannot be separated from their material support, and MS may belong to that class; (b MS actualizes a particular molecule from the many potentialities of a given set of nuclei and electrons, all present in the same Schroedinger equation; (c MS is a fact established in the XIXth century, albeit as a result of circumstantial evidence (because of its belonging to the R2 world; (d the fact that MS is known, as all objects of the atomic world, in terms of analogies with macroscopic models, is not valid grounds for questioning its reality; (e MS is a set of topological as well as geometrical relations. All along the discussion, observability according to Bohr, Heisenberg, Feynman is taken as the essential criterion of reality in the R2 world. On its basis, quantum mechanics is by no means in conflict with the reality of molecular structure and shape. On the other hand, the question of the minimum lifetime required for a MS proper to exist should be left open, pending a detailed analysis of measurement techniques.

  12. Electron spectroscopy and molecular structure

    International Nuclear Information System (INIS)

    Electron spectroscopy can now be applied to solids, liquids and gases. Some fields of research require ultrahigh vacuum conditions, in particular those directly concerned with surface phenomena on the monolayer level. Liquids have just recently been subject to studies and several improvements and extensions of this technique can be done. Much advance has lately been achieved in the case of gases, where the pressure range presently is 10-5-1 torr. Signal-to-background ratios for core lines can be approximately 1000:1 and the resolution has been increased to the extent that vibrational fine structures of 1s levels in some small molecules have been observed. These improvements are based on the monochromatization of the exciting AlKα radiation. Under such conditions the background is furthermore so much reduced that shake-up structures are more generally accessible for closer studies. ESCA shifts are also much easier to resolve and to measure with higher precision, around 0.02 eV. The photoionization dynamics including atomic and molecular relaxations has been investigated, both experimentally and theoretically. In the valence electron region improvements in energy resolution and in the application of the intensity model based on the MO-LCAO approximation greatly facilitate the assignments of the valence orbitals. Accumulation of empirical evidences gathered from series of similar chemical species and also better methods of calculation, both ab initio and semiempirical, have gradually resulted in a much better understanding of the molecular orbital description. The experience of the latest ESCA instrument with monochromatization has motivated an attempt to design an optimized apparatus according to the general principles of this prototype. A considerable gain in intensity can be made at an improved resolution set by the inherent diffraction pattern of the focussing spherical quartz crystals. (author)

  13. A Versatile Simple Capture Assay for Assessing the Structural Integrity of MHC Multimer Reagents.

    Directory of Open Access Journals (Sweden)

    Brendan K Reed

    Full Text Available Antigen-specific T cell responses can be visualized using MHC:peptide multimers. In cases where robust T cell controls are not readily available to assess the integrity of multimer reagents prior to analyzing limited sample, the ability to assess the structural integrity of MHC multimers before their use in critical experiments would be useful. We present a method to probe the structural integrity of MHC multimers using antibodies specific for conformational determinants. Beads coated with anti-mouse Ig are incubated with conformation-specific mouse monoclonal antibody and then with fluorescently tagged MHC multimer. The ability of the bead to capture the labeled multimer can be measured semi-quantitatively by flow cytometry. In this manner, the correct folding of MHC multimers can be visualized and batches of multimer can be compared for quality control. Because there are multiple conformational epitopes formed by various molecular interactions among heavy chain, peptide, and β2M, this capture assay can assess the fidelity of each aspect of multimer structure, depending on the availability of antibodies. The described approach could be particularly useful for studies using irreplaceable samples, including patient samples collected in clinical trials.

  14. Search for electromagnetic transitions between molecular states : results from the radiative capture channel

    International Nuclear Information System (INIS)

    This paper discusses the characterization of the cluster nature of resonances in 12C+12C and 12C+16O by measuring their γ decay. Results from resonant radiative capture measurements in these systems are presented. Spin attributions as well as specificities of the decay pattern are described. For the 12C+12C system, identification of γ transitions within the molecular band are discussed as well as a new method to measure the eventual persistence of the resonant behaviour down to astrophysical energies

  15. Molecular basis for mid-region amyloid-β capture by leading Alzheimer's disease immunotherapies

    OpenAIRE

    Crespi, Gabriela A. N.; Hermans, Stefan J.; Parker, Michael W.; Luke A. Miles

    2015-01-01

    Solanezumab (Eli Lilly) and crenezumab (Genentech) are the leading clinical antibodies targeting Amyloid-β (Aβ) to be tested in multiple Phase III clinical trials for the prevention of Alzheimer's disease in at-risk individuals. Aβ capture by these clinical antibodies is explained here with the first reported mid-region Aβ-anti-Aβ complex crystal structure. Solanezumab accommodates a large Aβ epitope (960 Å2 buried interface over residues 16 to 26) that forms extensive contacts and hydrogen b...

  16. Fluid-structure interaction in blood flow capturing non-zero longitudinal structure displacement

    OpenAIRE

    Bukac, Martina; Canic, Suncica; Glowinski, Roland; Tambaca, Josip; Quaini, Annalisa

    2012-01-01

    We present a new model and a novel loosely coupled partitioned numerical scheme modeling fluid-structure interaction (FSI) in blood flow allowing non-zero longitudinal displacement. Arterial walls are modeled by a {linearly viscoelastic, cylindrical Koiter shell model capturing both radial and longitudinal displacement}. Fluid flow is modeled by the Navier-Stokes equations for an incompressible, viscous fluid. The two are fully coupled via kinematic and dynamic coupling conditions. Our numeri...

  17. Probing the Electron Capture Dissociation Mass Spectrometry of Phosphopeptides with Traveling Wave Ion Mobility Spectrometry and Molecular Dynamics Simulations

    Science.gov (United States)

    Kim, Doyong; Pai, Pei-Jing; Creese, Andrew J.; Jones, Andrew W.; Russell, David H.; Cooper, Helen J.

    2015-06-01

    Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, we seek to rationalize the observed ECD behavior through a combination of ECD of model peptides, traveling wave ion mobility mass spectrometry and molecular dynamics simulations. The results suggest that for doubly protonated ions of phosphopeptide APLpSFRGSLPKSYVK a salt-bridge structure is favored, whereas for the doubly-protonated ions of APLSFRGSLPKpSYVK ionic hydrogen bonds predominate.

  18. Electron capture by slow highly-charged neon and argon ions from molecular and atomic hydrogen

    International Nuclear Information System (INIS)

    Electron capture cross sections for low velocity (106-107 cm/s) highly charged Ne/sup q+/ (2 less than or equal to q less than or equal to 7) and Ar/sup q+/ (2 less than or equal to q less than or equal to 10) projectiles incident on molecular and atomic hydrogen targets have been measured. A recoil ion source that uses the collisions of fast heavy (1 MeV/amu) ions with target gas atoms was utilized to produce slow highly charged ions. Atomic hydrogen was produced by dissociating hydrogen molecules in a thermal oven. Measurements and analysis of the data for the atomic hydrogen oven target are discussed in detail. The measured absolute cross sections were compared with the published data and the predictions of theoretical models

  19. Structures for capturing CO.sub.2, methods of making the structures, and methods of capturing CO.sub.2

    Science.gov (United States)

    Jones, Christopher W; Hicks, Jason C; Fauth, Daniel J; McMahan, Gray

    2012-10-30

    Briefly described, embodiments of this disclosure, among others, include carbon dioxide (CO.sub.2) sorption structures, methods of making CO.sub.2 sorption structures, and methods of using CO.sub.2 sorption structures.

  20. Structure parameters in molecular tunneling ionization theory

    Science.gov (United States)

    Wang, Jun-Ping; Li, Wei; Zhao, Song-Feng

    2014-04-01

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  1. Structure parameters in molecular tunneling ionization theory

    International Nuclear Information System (INIS)

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  2. Molecular basis for mid-region amyloid-β capture by leading Alzheimer's disease immunotherapies.

    Science.gov (United States)

    Crespi, Gabriela A N; Hermans, Stefan J; Parker, Michael W; Miles, Luke A

    2015-01-01

    Solanezumab (Eli Lilly) and crenezumab (Genentech) are the leading clinical antibodies targeting Amyloid-β (Aβ) to be tested in multiple Phase III clinical trials for the prevention of Alzheimer's disease in at-risk individuals. Aβ capture by these clinical antibodies is explained here with the first reported mid-region Aβ-anti-Aβ complex crystal structure. Solanezumab accommodates a large Aβ epitope (960 Å(2) buried interface over residues 16 to 26) that forms extensive contacts and hydrogen bonds to the antibody, largely via main-chain Aβ atoms and a deeply buried Phe19-Phe20 dipeptide core. The conformation of Aβ captured is an intermediate between observed sheet and helical forms with intramolecular hydrogen bonds stabilising residues 20-26 in a helical conformation. Remarkably, Aβ-binding residues are almost perfectly conserved in crenezumab. The structure explains the observed shared cross reactivity of solanezumab and crenezumab with proteins abundant in plasma that exhibit this Phe-Phe dipeptide. PMID:25880481

  3. Molecular modeling of nucleic acid structure

    OpenAIRE

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

    2001-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

  4. Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores.

    Science.gov (United States)

    Belkin, Maxim; Aksimentiev, Aleksei

    2016-05-25

    The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA-ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surface-slip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid

  5. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins

    OpenAIRE

    Law, Sean M.; Ahlstrom, Logan S.; Panahi, Afra; Brooks, Charles L.

    2014-01-01

    Molecular recognition by intrinsically disordered proteins (IDPs) plays a central role in many critical cellular processes. Toward achieving detailed mechanistic understanding of IDP–target interactions, here we employ the “Hamiltonian mapping” methodology, which is rooted in the weighted histogram analysis method (WHAM), for the fast and efficient calibration of structure-based models in studies of IDPs. By performing reference simulations on a given Hamiltonian, we illustrate for two model ...

  6. 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.

  7. Molecular structure by Coulomb explosion imaging of stored molecular ions

    International Nuclear Information System (INIS)

    An experimental scheme, which combines Coulomb explosion imaging (CEI) with storage of fast molecular ions, has been introduced recently at the TSR heavy ion storage ring facility in Heidelberg. CEI is an experimental technique that provides direct observation of the nuclear conformations within small molecules. The combination of CEI with the storage ring technique enables the control of the internal excitation of the measured molecules, which is an essential condition to the interpretation of CEI results in terms of ''structure'' assigned to specific molecular states. This structure is measured as a function of storage time, thus enabling one to study processes of slow intramolecular dynamics such as isomerization, metastable states, etc. Moreover in this scheme, CEI can be used as a diagnostic tool for the intramolecular excitation, while other molecular interactions (e.g. with electrons or photons) are investigated. In this report, the CEI principle and the new experimental setup are described with an emphasis on the new prospects for studies in molecular physics. CEI measurements of stored CH2+ and NH2+ molecular ions are presented. The study of the angular distribution in these molecules as a function of their vibrational relaxation to the ground state, reveals unexpected behavior near the linear conformation which is inconsistent with the current adiabatic theories

  8. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    International Nuclear Information System (INIS)

    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 13CO 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.

  9. Quantum mechanics of molecular structures

    CERN Document Server

    Yamanouchi, Kaoru

    2012-01-01

    At a level accessible to advanced undergraduates, this textbook explains the fundamental role of quantum mechanics in determining the structure, dynamics, and other properties of molecules. Readers will come to understand the quantum-mechanical basis for harmonic oscillators, angular momenta and scattering processes. Exercises are provided to help readers deepen their grasp of the essential phenomena.

  10. Structured Molecular Gas Reveals Galactic Spiral Arms

    CERN Document Server

    Sawada, Tsuyoshi; Koda, Jin

    2012-01-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function (BDF) and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO 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 formati...

  11. 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...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  12. Reaction dynamics following electron capture of chlorofluorocarbon adsorbed on water cluster : a direct density functional theory molecular dynamics study

    OpenAIRE

    Tachikawa, Hiroto; ABE, Shigeaki

    2007-01-01

    The electron capture dynamics of halocarbon and its water complex have been investigated by means of the full dimensional direct density functional theory molecular dynamics method in order to shed light on the mechanism of electron capture of a halocarbon adsorbed on the ice surface. The CF2Cl2 molecule and a cyclic water trimer (H2O)3 were used as halocarbon and water cluster, respectively. The dynamics calculation of CF2Cl2 showed that both C–Cl bonds are largely elongated after the electr...

  13. 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 ma

  14. Study on Molecular Structure of TATFIW

    Institute of Scientific and Technical Information of China (English)

    LI Li-jie; LI Yan-yue; LU Lin; CHEN Shu-sen; CHEN Hua-xiong; JIN Shao-hua; ZHAO Xin-qi

    2008-01-01

    The molecular structure of triacetyltriformylhexaazaisowurtzitane (TATFIW) is optimized by using Gaussian98 software package at the level of B3LYP/6-31G. Theoretically analyzed the TATFIW molecular structure, namely bond length, bond angle, dihedral angle and the charge distribution, it was found that hydrogen bond exists in TATFIW, and acetyl is easily taken off than formyl in the nitrolysis with nitric-sulfuric mixed acid. These results mentioned above agree with experiments. The comparison of calculated vibration frequency and intensity with the experiment values are also given.

  15. Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

    Energy Technology Data Exchange (ETDEWEB)

    Laves, Kevin S.; Loeb, Susan C.

    2006-01-01

    ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examined at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.

  16. Capturing the transient species at the electrode-electrolyte interface by in situ dynamic molecular imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jiachao; Zhou, Yufan; Hua, Xin; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-09-01

    The electrochemical interface between the solid electrode and liquid electrolyte has long been studied because of its importance in electrical energy storage, material synthesis, catalysis, and energy conversions.1 However, such interfaces are complex and extremely difficult to observe directly and are poorly under-stood due to lack of true in situ tools.2 Although electrochemical techniques have been widely used to investigate such interfaces, they are based on macroscopic models or current changes that could not provide direct ionic and molecular information of the interfacial structure. Many in situ and ex situ spectroscopy and microscopy techniques have been used to study the solid–liquid (s–l) interface.3,4 In situ TEM in sealed liquid cells has notably become a popular choice to provide structural information of s–l at the atomic level.5,6 However, real-time spatial mapping of the ionic and molecular intermediate species at the dynamic inter-face still remains a key challenge.

  17. Anatomy of molecular structures in $^{20}$Ne

    CERN Document Server

    Zhou, E F; Li, Z P; Meng, J; Ring, P

    2015-01-01

    We present a beyond mean-field study of clusters and molecular structures in low-spin states of $^{20}$Ne with a multireference relativistic energy density functional, where the dynamical correlation effects of symmetry restoration and quadrupole-octupole shapes fluctuation are taken into account with projections on parity, particle number and angular momentum in the framework of the generator coordinate method. Both the energy spectrum and the electric multipole transition strengths for low-lying parity-doublet bands are better reproduced after taking into account the dynamical octupole vibration effect. Consistent with the finding in previous antisymmetrized molecular dynamics studies, a rotation-induced dissolution of the $\\alpha+^{16}$O molecular structure in $^{20}$Ne is predicted and this peculiar phenomenon is partially attributed to the special deformation-dependent moment of inertia.

  18. Molecular Association and Structure of Hydrogen Peroxide.

    Science.gov (United States)

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  19. Irreversible Change of the Pore Structure of ZIF-8 in Carbon Dioxide Capture with Water Coexistence

    DEFF Research Database (Denmark)

    Liu, Huang; Guo, Ping; Regueira Muñiz, Teresa;

    2016-01-01

    showed an irreversible change of its framework, which occurs during the CO2 capture process. It was found that there is an irreversible chemical reaction among ZIF-8, water, and CO2, which creates both zinc carbonate (or zinc carbonate hydroxides) and single 2-methylimidazole crystals, and therefore the......The performance of zeolitic imidazolate framework 8 (ZIF-8) for CO2 capture under three different conditions (wetted ZIF-8, ZIF-8/water slurry, and ZIF-8/water-glycol slurry) was systemically investigated. This investigation included the study of the pore structure stability of ZIF-8 by using X...... pore structure of ZIF-8 collapses. It is suggested therefore that care must be taken when using ZIF-8 or products containing ZIF-8 for gas capture, gas separation, or other applications where both water and acid gases coexist....

  20. Solvents for CO2 capture. Structure-activity relationships combined with vapour-liquid-equilibrium measurements

    NARCIS (Netherlands)

    Mergler, Y.L.; Rumley-Van Gurp, R.; Brasser, P.; Koning, M.C. de; Goetheer, E.L.V.

    2011-01-01

    In this study a systematic approach was chosen to test and characterize amine systems for CO2 capture. Vapour-liquid-equilibrium measurements were performed on a homologue series of amines, with ethylene amine as base structure. Various functional groups were used that ranged in chemical and physica

  1. Mercury capture by selected Bulgarian fly ashes: Influence of coal rank and fly ash carbon pore structure on capture efficiency

    Science.gov (United States)

    Kostova, I.J.; Hower, J.C.; Mastalerz, Maria; Vassilev, S.V.

    2011-01-01

    Mercury capture by fly ash C was investigated at five lignite- and subbituminous-coal-burning Bulgarian power plants (Republika, Bobov Dol, Maritza East 2, Maritza East 3, and Sliven). Although the C content of the ashes is low, never exceeding 1.6%, the Hg capture on a unit C basis demonstrates that the low-rank-coal-derived fly ash carbons are more efficient in capturing Hg than fly ash carbons from bituminous-fired power plants. While some low-C and low-Hg fly ashes do not reveal any trends of Hg versus C, the 2nd and, in particular, the 3rd electrostatic precipitator (ESP) rows at the Republika power plant do have sufficient fly ash C range and experience flue gas sufficiently cool to capture measurable amounts of Hg. The Republika 3rd ESP row exhibits an increase in Hg with increasing C, as observed in other power plants, for example, in Kentucky power plants burning Appalachian-sourced bituminous coals. Mercury/C decreases with an increase in fly ash C, suggesting that some of the C is isolated from the flue gas stream and does not contribute to Hg capture. Mercury capture increases with an increase in Brunauer-Emmett-Teller (BET) surface area and micropore surface area. The differences in Hg capture between the Bulgarian plants burning low-rank coal and high volatile bituminous-fed Kentucky power plants suggests that the variations in C forms resulting from the combustion of the different ranks also influence the efficiency of Hg capture. ?? 2010 Elsevier Ltd.

  2. Turbulent Velocity Structure in Molecular Clouds

    CERN Document Server

    Ossenkopf, V; Ossenkopf, Volker; Low, Mordecai-Mark Mac

    2002-01-01

    We compare velocity structure observed in the Polaris Flare molecular cloud at scales ranging from 0.015 pc to 20 pc to the velocity structure of a suite of simulations of supersonic hydrodynamic and MHD turbulence computed with the ZEUS MHD code. We examine different methods of characterising the structure, including a scanning-beam size-linewidth relation, structure functions, velocity and velocity difference probability distribution functions (PDFs), and the Delta-variance wavelet transform, and use them to compare models and observations. The Delta-variance is most sensitive in detecting characteristic scales and varying scaling laws, but is limited in the observational application by its lack of intensity weighting. We compare the true velocity PDF in our models to simulated observations of velocity centroids and average line profiles in optically thin lines, and find that the line profiles reflect the true PDF better. The observed velocity structure is consistent with supersonic turbulence showing a com...

  3. Dynamics of fragment capture for cluster structures of weakly bound 7Li

    International Nuclear Information System (INIS)

    Role of cluster structures of 7Li on reaction dynamics have been studied by performing exclusive measurements of prompt-γ rays from residues with scattered particles at energy, E/Vb = 1.6, with 198Pt target. Yields of the residues resulting after capture of t and 4,5,6He, corresponding to different excitation energies of the composite system were estimated. The results were compared with three body classical-dynamical model for breakup fusion, constrained by the measured fusion, α and t capture cross-sections. The cross-section of residues from capture of α and t agreed well with the prediction of the model showing dominance of the two step process - breakup fusion, while those from tightly bound 6He showed massive transfer to be the dominant mechanism. (authors)

  4. Dynamics of fragment capture for cluster structures of weakly bound 7Li

    Directory of Open Access Journals (Sweden)

    Shrivastava A.

    2013-12-01

    Full Text Available Role of cluster structures of 7Li on reaction dynamics have been studied by performing exclusive measurements of prompt-γ rays from residues with scattered particles at energy, E/Vb = 1.6, with 198Pt target. Yields of the residues resulting after capture of t and 4,5,6He, corresponding to different excitation energies of the composite system were estimated. The results were compared with three body classical-dynamical model for breakup fusion, constrained by the measured fusion, α and t capture cross-sections. The cross-section of residues from capture of α and t agreed well with the prediction of the model showing dominance of the two step process - breakup fusion, while those from tightly bound 6He showed massive transfer to be the dominant mechanism.

  5. Molecular structure and interfacial behaviour of polymers.

    OpenAIRE

    Lent, van, J.

    1989-01-01

    The aim of this study was to investigate the influence of the molecular structure on the interfacial behaviour of polymers. Theoretical models were developed for three different systems. All these models are based on the self-consistent field theory of Scheutjens and Fleer for the adsorption of homopolymers.This self-consistent field theory is a lattice model. All possible polymer conformations on the lattice are taken into account. The potential of a conformation is sum of the local potentia...

  6. The Structure of Cold Molecular Cloud Cores

    OpenAIRE

    Ward-Thompson, D.; D. J. Nutter; Kirk, J M; Andre, P.

    2003-01-01

    A brief summary is presented of our current knowledge of the structure of cold molecular cloud cores that do not contain protostars, sometimes known as starless cores. The most centrally condensed starless cores are known as pre-stellar cores. These cores probably represent observationally the initial conditions for protostellar collapse that must be input into all models of star formation. The current debate over the nature of core density profiles is summarised. A cautionary note is sounded...

  7. The molecular structure of future fuels

    OpenAIRE

    Hellier, P. R.

    2013-01-01

    Future fuels will be developed from a variety of biomass and fossil sources, and must seek to address the adverse environmental impacts of current fossil fuel usage. To this end, understanding how the molecular structure of a fuel impacts on the processes of combustion and emissions production is critical in selecting suitable feed-stocks and conversion methods. This work presents experimental studies carried out on a compression ignition engine equipped with a novel low volume fuel system. T...

  8. 2004 Reversible Associations in Structure & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  9. Magnetic Capture of a Molecular Biomarker from Synovial Fluid in a Rat Model of Knee Osteoarthritis.

    Science.gov (United States)

    Yarmola, Elena G; Shah, Yash; Arnold, David P; Dobson, Jon; Allen, Kyle D

    2016-04-01

    Biomarker development for osteoarthritis (OA) often begins in rodent models, but can be limited by an inability to aspirate synovial fluid from a rodent stifle (similar to the human knee). To address this limitation, we have developed a magnetic nanoparticle-based technology to collect biomarkers from a rodent stifle, termed magnetic capture. Using a common OA biomarker--the c-terminus telopeptide of type II collagen (CTXII)--magnetic capture was optimized in vitro using bovine synovial fluid and then tested in a rat model of knee OA. Anti-CTXII antibodies were conjugated to the surface of superparamagnetic iron oxide-containing polymeric particles. Using these anti-CTXII particles, magnetic capture was able to estimate the level of CTXII in 25 μL aliquots of bovine synovial fluid; and under controlled conditions, this estimate was unaffected by synovial fluid viscosity. Following in vitro testing, anti-CTXII particles were tested in a rat monoiodoacetate model of knee OA. CTXII could be magnetically captured from a rodent stifle without the need to aspirate fluid and showed tenfold changes in CTXII levels from OA-affected joints relative to contralateral control joints. Combined, these data demonstrate the ability and sensitivity of magnetic capture for post-mortem analysis of OA biomarkers in the rat. PMID:26136062

  10. Molecular sieve supported ionic liquids as efficient adsorbent for CO2 capture

    Directory of Open Access Journals (Sweden)

    Yang Na

    2015-01-01

    Full Text Available [NH3e-mim][BF4], [OHe-mim][BF4] and [HOEAm] were selected and supported onto molecular sieves NaY, USY, SAPO-34 and MCM-41, to prepare supported ionic liquids. It was found that [NH3e-mim][BF4]/NaY has excellent CO2 adsorption performance, with adsorption capacity of 0.108 mmolCO2/g. This paper investigates the optimal adsorption conditions and recyclability of [NH3e-mim][BF4]/NaY. The results show that [NH3e-mim][BF4]/NaY has good CO2 adsorption under the condition of 20°C and 20% ILs loading amount. By vacuum heating, CO2 adsorption capacity reaches 0.451mmolCO2/g at fifth runs and reduces to 0.29mmolCO2/g at tenth runs. The structure and characterization of the [NH3e-mim][BF4]/NaY was examined by FT-IR, XRD, SEM and TG-DSC. TG-DSC also shows that it has good thermostability below 50°C.

  11. Low-cost structured-light based 3D capture system design

    Science.gov (United States)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  12. Interatomic Coulombic electron capture in atomic, molecular, and quantum dot systems

    Directory of Open Access Journals (Sweden)

    Bande Annika

    2015-01-01

    Full Text Available The interatomic Coulombic electron capture (ICEC process has recently been predicted theoretically for clusters of atoms and molecules. For an atom A capturing an electron e(ε it competes with the well known photorecombination, because in an environment of neutral or anionic neighboring atoms B, A can transfer its excess energy in the ultrafast ICEC process to B which is then ionized. The cross section for e(ε + A + B → A− + B+ + e(ε′ has been obtained in an asymptotic approximation based on scattering theory for several clusters [1,2]. It was found that ICEC starts dominating the PR for distances among participating species of nanometers and lower. Therefore, we believe that the ICEC process might be of importance in the atmosphere, in biological systems, plasmas, or in nanostructured materials. As an example for the latter, ICEC has been investigated by means of electron dynamics in a model potential for semiconductor double quantum dots (QDs [3]. In the simplest case one QD captures an electron while the outgoing electron is emitted from the other. The reaction probability for this process was found to be relatively large.

  13. 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...

  14. Molecular Modeling of the Chain Structures of Polybenzoxazines

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

  15. Molecular structure of actinides in biochemistry

    International Nuclear Information System (INIS)

    In case of internal contamination, drugs used for decorporation are scarce and do not act very specifically. For instance the sole de-corporating drug recommended for plutonium decontamination is a water-soluble ligand named DTPA (Diethylene-Triamino-Pentaacetate). The transport of DTPA to its organ-target and its bio-availability on the spot are not satisfactorily understood. The conventional method to develop new ligands is based on molecular approaches but it is not sufficient. A new method that combines methods from structural biochemistry with methods of bio-inorganic chemistry and with methods from physico-chemistry (particularly X-ray absorption spectroscopy) is so far the best way to understand molecular speciation and to detail the local arrangement of atoms around a cation for instance, which are valuable information to understand the behaviour of a ligand. EXAFS (Extended X-ray Absorption Fine structure Spectroscopy) measurements suggest that during the formation of a complex involving an actinide (An) and a ligand, the inter-atomic distance An-O decreases when the atomic number of the cation increases while it is the reverse in the case of An-N

  16. Laser slowing of CaF molecules to near the capture velocity of a molecular MOT

    CERN Document Server

    Hemmerling, Boerge; Ravi, Aakash; Anderegg, Loic; Drayna, Garrett K; Hutzler, Nicholas R; Collopy, Alejandra L; Ye, Jun; Ketterle, Wolfgang; Doyle, John M

    2016-01-01

    Laser slowing of CaF molecules down to the capture velocity of a magneto-optical trap (MOT) for molecules is achieved. Starting from a two-stage buffer gas beam source, we apply frequency-broadened "white-light" slowing and observe approximately 6x10^4 CaF molecules with velocities near 10\\,m/s. CaF is a candidate for collisional studies in the mK regime. This work represents a significant step towards magneto-optical trapping of CaF.

  17. Nuclear structure of 170Tm from neutron-capture and (d,p)-reaction measurements

    International Nuclear Information System (INIS)

    We have made experimental measurements in 170Tm of the following: secondary γ rays, conversion electrons, and γ-γ coincidences from thermal neutron capture in 169Tm, primary γ rays from average resonance capture with 2-keV and 24-keV neutron beams, and proton spectra from the (d,p) reaction on 169Tm. From these data and those of previous investigations, we have identified more than 130 excited levels in 170Tm below 1550 keV. Of these, 62 (with connecting transitions) are placed in 18 rotational bands with assigned Nilsson configurations. These results are in good agreement with a semiempirical modeling of 170Tm level structure. Values for seven Gallagher-Moszkowski splittings and four Newby shifts have been obtained. These matrix elements show remarkably good agreement with calculation. Among the observed Kπ=1- and 2- rotational bands, configuration mixing appears to play a significant role. copyright 1996 The American Physical Society

  18. Role of the cluster structure of 7Li in the dynamics of fragment capture

    International Nuclear Information System (INIS)

    Exclusive measurements of prompt γ-rays from the heavy-residues with various light charged particles in the 7Li + 198Pt system, at an energy near the Coulomb barrier (E/Vb∼1.6) are reported. Recent dynamic classical trajectory calculations, constrained by the measured fusion, α- and t-capture cross-sections have been used to explain the excitation energy dependence of the residue cross-sections. These calculations distinctly illustrate a two-step process, breakup followed by fusion, in case of the capture of t and α clusters; whereas for 6He+p and 5He+d configurations, massive transfer is inferred to be the dominant mechanism. The present work clearly demonstrates the role played by the cluster structures of 7Li in understanding the reaction dynamics at energies around the Coulomb barrier.

  19. Molecularly imprinted polymers: compromise between flexibility and rigidity for improving capture of template analogues.

    Science.gov (United States)

    Pardo, Antonelle; Mespouille, Laetitia; Dubois, Philippe; Blankert, Bertrand; Duez, Pierre

    2014-03-17

    New synthetic strategies for molecularly imprinted polymers (MIPs) were developed to mimic the flexibility and mobility exhibited by receptor/enzyme binding pockets. The MIPs were prepared by bulk polymerization with quercetin as template molecule, acrylamide as functional monomer, ethylene glycol dimethacrylate as cross-linker, and THF as porogen. The innovative grafting of specific oligoethylene glycol units onto the imprinted cavities allowed MIPs to be obtained that exhibit extended selectivity towards template analogues. This synthetic strategy gives promising perspectives for the design of molecular recognition of molecules based on a congruent pharmacophore, which should be of interest for drug development. PMID:24615923

  20. Plant sex chromosomes: molecular structure and function.

    Science.gov (United States)

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  1. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    Science.gov (United States)

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; Li, F.; Pai, C.-H.; Wan, Y.; Wu, Y. P.; Gu, Y. Q.; Mori, W. B.; Joshi, C.; Lu, W.

    2016-07-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.

  2. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    Science.gov (United States)

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; Li, F.; Pai, C.-H.; Wan, Y.; Wu, Y. P.; Gu, Y. Q.; Mori, W. B.; Joshi, C.; Lu, W.

    2016-01-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method. PMID:27403561

  3. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe.

    Science.gov (United States)

    Zhang, C J; Hua, J F; Xu, X L; Li, F; Pai, C-H; Wan, Y; Wu, Y P; Gu, Y Q; Mori, W B; Joshi, C; Lu, W

    2016-01-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method. PMID:27403561

  4. Molecular Component Structures Mediated Formation of Self-assemblies

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the result ed self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-as semblies was discussed in terms of intermolecular interactions.

  5. 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.

  6. Molecular sieve supported ionic liquids as efficient adsorbent for CO2 capture

    OpenAIRE

    Yang Na; Wang Rui

    2015-01-01

    [NH3e-mim][BF4], [OHe-mim][BF4] and [HOEAm] were selected and supported onto molecular sieves NaY, USY, SAPO-34 and MCM-41, to prepare supported ionic liquids. It was found that [NH3e-mim][BF4]/NaY has excellent CO2 adsorption performance, with adsorption capacity of 0.108 mmolCO2/g. This paper investigates the optimal adsorption conditions and recyclability of [NH3e-mim][BF4]/NaY. The results show that [NH3e-mim][BF4]/NaY has good CO2 adsorption under the ...

  7. A Structure-Based Mechanism for Vesicle Capture by the Multisubunit Tethering Complex Dsl1

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Y.; Yip, C; Tripathi, A; Huie, D; Jeffrey, P; Walz, T; Hughson, F

    2009-01-01

    Vesicle trafficking requires membrane fusion, mediated by SNARE proteins, and upstream events that probably include tethering, an initial long-range attachment between a vesicle and its target organelle. Among the factors proposed to mediate tethering are a set of multisubunit tethering complexes (MTCs). The Dsl1 complex, with only three subunits, is the simplest known MTC and is essential for the retrograde traffic of COPI-coated vesicles from the Golgi to the ER. To elucidate structural principles underlying MTC function, we have determined the structure of the Dsl1 complex, revealing a tower containing at its base the binding sites for two ER SNAREs and at its tip a flexible lasso for capturing vesicles. The Dsl1 complex binds to individual SNAREs via their N-terminal regulatory domains and also to assembled SNARE complexes; moreover, it is capable of accelerating SNARE complex assembly. Our results suggest that even the simplest MTC may be capable of orchestrating vesicle capture, uncoating, and fusion.

  8. Filamentary structure in the Orion molecular cloud

    International Nuclear Information System (INIS)

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation

  9. The Determination of Molecular Structure from Rotational Spectra

    Science.gov (United States)

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  10. A structured approach for selecting carbon capture process models : A case study on monoethanolamine

    NARCIS (Netherlands)

    van der Spek, Mijndert; Ramirez, Andrea

    2014-01-01

    Carbon capture and storage is considered a promising option to mitigate CO2 emissions. This has resulted in many R&D efforts focusing at developing viable carbon capture technologies. During carbon capture technology development, process modeling plays an important role. Selecting an appropriate pro

  11. Molecular structure and motion in zero field magnetic resonance

    International Nuclear Information System (INIS)

    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

  12. Molecular-orbital treatment of electron capture in an external magnetic field: collisions of B4+ ions with H atoms

    International Nuclear Information System (INIS)

    A semiclassical close-coupling equation is formulated for the electron-capture process in ion-atom collisions under the influence of an external magnetic field. The direction of the magnetic field is chosen to be parallel to an initial velocity vector of a projectile. As we deal with the case for the magnetic field strength less than the critical field strength (2.35 x 105 T), the second- and higher-order terms for the magnetic field are neglected. Eigenfunctions in zero magnetic field are employed as a basis set for expansion. The equation obtained is the same in structure as that at zero magnetic field except that the relative velocity υ is replaced by the scaled velocity υB. Effects due to the magnetic field are: (i) dynamic couplings, similar to rotational couplings and (ii) the Zeeman splitting of energies. The phase factor due to the gauge transformation is similar in form to the electron-translation factor. We apply this close-coupling equation to a study of electron-capture processes in a singlet (B4+ + H) system at 0 ≤ B ≤ 2.35 x 104 T, for which the zero-field results have been reported earlier. (author)

  13. Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

    International Nuclear Information System (INIS)

    Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD

  14. Investigation of CO2 capture mechanisms of liquid-like nanoparticle organic hybrid materials via structural characterization

    KAUST Repository

    Park, Youngjune

    2011-01-01

    Nanoparticle organic hybrid materials (NOHMs) have been recently developed that comprise an oligomeric or polymeric canopy tethered to surface-modified nanoparticles via ionic or covalent bonds. It has already been shown that the tunable nature of the grafted polymeric canopy allows for enhanced CO 2 capture capacity and selectivity via the enthalpic intermolecular interactions between CO2 and the task-specific functional groups, such as amines. Interestingly, for the same amount of CO2 loading NOHMs have also exhibited significantly different swelling behavior compared to that of the corresponding polymers, indicating a potential structural effect during CO2 capture. If the frustrated canopy species favor spontaneous ordering due to steric and/or entropic effects, the inorganic cores of NOHMs could be organized into unusual structural arrangements. Likewise, the introduction of small gaseous molecules such as CO2 could reduce the free energy of the frustrated canopy. This entropic effect, the result of unique structural nature, could allow NOHMs to capture CO2 more effectively. In order to isolate the entropic effect, NOHMs were synthesized without the task-specific functional groups. The relationship between their structural conformation and the underlying mechanisms for the CO2 absorption behavior were investigated by employing NMR and ATR FT-IR spectroscopies. The results provide fundamental information needed for evaluating and developing novel liquid-like CO2 capture materials and give useful insights for designing and synthesizing NOHMs for more effective CO2 capture. © the Owner Societies 2011.

  15. Topological Indices Study of Molecular Structure in Anticancer Drugs

    OpenAIRE

    Wei Gao; Weifan Wang; Mohammad Reza Farahani

    2016-01-01

    Numerous studies indicate that there is strong inherent relationship between the chemical characteristics of chemical compounds and drugs (e.g., boiling point and melting point) and their molecular structures. Topological indices defined on these chemical molecular structures can help researchers better understand the physical features, chemical reactivity, and biological activity. Thus, the study of the topological indices on chemical structure of chemical materials and drugs can make up for...

  16. Capturing ultrafast photoinduced local structural distortions of BiFeO3.

    Science.gov (United States)

    Wen, Haidan; Sassi, Michel; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell G; Rosso, Kevin M; Zhang, Xiaoyi

    2015-01-01

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials. PMID:26463128

  17. Capturing ultrafast photoinduced local structural distortion of BiFeO3

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Haidan [Argonne National Lab. (ANL), Argonne, IL (United States); Sassi, Michel [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Luo, Zhenlin [Univ. of Science and Technology of China, Hefei (China); Adamo, Carolina [Cornell Univ., Ithaca, NY (United States); Schlom, Darrell G. [Cornell Univ., Ithaca, NY (United States); Cornell Univ., Ithaca, NY (United States). Kavli Inst. for Nanoscale Science; Rosso, Kevin M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zhang, Xiaoyi [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-10-14

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials.

  18. Capturing structure and function in an embryonic heart with Biophotonic tools

    Directory of Open Access Journals (Sweden)

    Ganga eKarunamuni

    2014-09-01

    Full Text Available Disturbed cardiac function (flow, excitation, contraction, calcium transients at an early stage of development has been shown to correlate with and may lead to cellular/molecular, functional and structural cardiac anomalies at later stages culminating in the congenital heart defects (CHDs that present at birth. It is not surprising that cardiac function, which drives embryonic and extraembryonic circulation, is also connected to neural and placental development. While our knowledge of molecular and cellular steps in cardiac development is growing rapidly, our understanding of the role of cardiovascular function in the embryo is still rudimentary. One reason for the scanty information in this area is that the tools to study early cardiac function are limited. Recently developed and adapted Biophotonic tools may overcome the challenges of studying the tiny fragile beating heart. In this chapter, the strengths and limitations of Biophotonic tools will be described with emphasis on Optical Coherence Tomography (OCT. OCT can be used for detailed structural and functional studies of the tubular and looping avian embryo heart under physiological conditions. The same hearts can be subsequently rapidly and quantitatively phenotyped at a later stage using OCT. When combined with other tools such as Optimal Mapping (OM and Optical Pacing (OP, OCT has the potential to reveal in spatial and temporal detail the biophysical changes that can potentially impact mechanotransduction pathways. This information may provide better explanations for the etiology of the CHDs when interwoven with our understanding of the multiple molecular pathways that have been described to be involved. Examples of application of these tools to study the etiology of CHDs are presented. Directions for future directions and advances in the use of Biophotonic tools are discussed.

  19. Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data

    Science.gov (United States)

    Coggins, L.G., Jr.; Pine, William E., III; Walters, C.J.; Martell, S.J.D.

    2006-01-01

    We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. ?? Copyright by the American Fisheries Society 2006.

  20. Molecular structural order and anomalies in liquid silica

    OpenAIRE

    Shell, M. S.; Debenedetti, P. G.; Panagiotopoulos, A. Z.

    2002-01-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends ...

  1. Tritium capture by clay mineral structure during its propagation in aeration zone

    International Nuclear Information System (INIS)

    The underlay compositions in aeration zone have been contaminated near radioactive waste repositories as a result of radiation accident in which tritium leakage from repositories had been occurred. The tritium distribution in aeration zone and its moving into the first aquifer are investigated. Measurements of tritium activity in aeration zone have reviled, that tritium is captured by OH - groups of clay minerals. The measuring and modeling process of tritium capture by OH - groups of clay minerals let to estimate an amount of tritium, captured by OH - groups and typical times of capture and retention. It was shown that the tritium capture by OH - groups of clay minerals during its propagation into environment in some times improve the protective properties of the barrier consisting of clay minerals

  2. Molecular and Crystal Structures of Three Berberine Derivatives

    OpenAIRE

    Jiří Dostál; Zdirad Žák; Marek NeÄÂas; Milan PotáÄÂek; Stanislav Man

    2001-01-01

    Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  3. Molecular and Crystal Structures of Three Berberine Derivatives

    Directory of Open Access Journals (Sweden)

    Jiří Dostál

    2001-04-01

    Full Text Available Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  4. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    Science.gov (United States)

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  5. Carbon capture and sequestration (CCS) technological innovation system in China: Structure, function evaluation and policy implication

    International Nuclear Information System (INIS)

    Carbon capture and sequestration (CCS) can be an important technology option for China in addressing global climate change and developing clean energy technologies. Promoted by international climate conventions and supported by government research and development programs, an increasing number of CCS pilot and demonstration projects have been launched in China. In this study, we analyze the structure of China’s CCS effort from a technological innovation system (TIS) perspective. Within this system, key socio-political components, including institutions, actor-networks, and technology development, are examined to evaluate the state of the innovation system. The study assessed the perceived capacity of seven functional areas of the CCS innovation system through a survey of key CCS actors and stakeholders. The findings suggest that China’s CCS innovation system has a strong functional capacity for knowledge and technology development. It is significantly weaker in the innovative functions of knowledge diffusion, market formation, facilitating entrepreneurs and new entrants into the CCS market. Based on the evaluation of China’s technological innovation system to develop CCS, the article articulates specific public policies to formulate a more robust innovation system to traverse the “valley of death” from research and development to commercial deployment and accelerate energy innovation in China. - Highlights: ► We analyze and evaluate China’s CCS innovation system from TIS perspective. ► Strong and systematic CCS innovation system structure has come into being in China. ► The system has acquired high knowledge development and accumulation. ► Weak innovation functions are identified: market creation, guidance, etc. ► Public policies are needed to improve the innovation system performance.

  6. Capturing Thoughts, Capturing Minds?

    DEFF Research Database (Denmark)

    Nielsen, Janni

    2004-01-01

    Think Aloud is cost effective, promises access to the user's mind and is the applied usability technique. But 'keep talking' is difficult, besides, the multimodal interface is visual not verbal. Eye-tracking seems to get around the verbalisation problem. It captures the visual focus of attention....... However, it is expensive, obtrusive and produces huge amount of data. Besides, eye-tracking do not give access to user's mind. Capturing interface/cursor tracking may be cost effective. It is easy to install, data collection is automatic and unobtrusive and replaying the captured recording to the user and...

  7. Structural basis for arabinoxylo‐oligosaccharide capture by the probiotic Bifidobacterium animalis subsp. lactis Bl‐04

    DEFF Research Database (Denmark)

    Hansen, Morten Ejby; Fredslund, Folmer; Vujicic‐Zagar, Andreja;

    2013-01-01

    Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo‐oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria...... in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactis Bl‐04. The binding protein BlAXBP, which is associated with an ATP‐binding cassette (ABC) transporter that mediates the uptake of AXOS, displays an exceptionally...... broad specificity for arabinosyl‐decorated and undecorated xylo‐oligosaccharides, with preference for tri‐ and tetra‐saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in...

  8. Experimental determination of neutron capture cross sections of fast reactor structure materials integrated in intermediate energy spectra. Vol. 2: description of experimental structure

    International Nuclear Information System (INIS)

    A selection of technical documents is given concerning the experimental determination of the neutron capture cross-sections of fast reactor structural materials (Fe, Cr, Ni...) integrated over the intermediate energy spectra. The experimental structure project and modifications of the reactor RB2 for this experiment, together with criticality and safety calculations, are presented

  9. Cost structure of a postcombustion CO{sub 2} capture system using CaO

    Energy Technology Data Exchange (ETDEWEB)

    J. Carlos Abanades; G. Grasa; M. Alonso; N. Rodriguez; E.J. Anthony; L.M. Romeo [Instituto Nacional del Carbon, (CSIC), Oviedo (Spain)

    2007-08-01

    This paper presents the basic economics of an emerging concept for CO{sub 2} capture from flue gases in power plants. The complete system includes three key cost components: a full combustion power plant, a second power plant working as an oxy-fired fluidized bed calciner, and a fluidized bed carbonator interconnected with the calciner and capturing CO{sub 2} from the combustion power plant. The simplicity in the economic analysis is possible because the key cost data for the two major first components are well established in the open literature. It is shown that there is clear scope for a breakthrough in capture cost to around 15 $/t of CO{sub 2} avoided with this system. This is mainly because the capture system is generating additional power (from the additional coal fed to the calciner) and because the avoided CO{sub 2} comes from the capture of the CO{sub 2} generated by the coal fed to the calciner and the CO{sub 2} captured (as CaCO{sub 3}) from the flue gases of the existing power plant, that is also released in the calciner. 8 refs., 2 figs., 1 tab.

  10. Distribution of naphthoquinones, plumbagin, droserone, and 5-O-methyl droserone in chitin-induced and uninduced Nepenthes khasiana: molecular events in prey capture.

    Science.gov (United States)

    Raj, Gopan; Kurup, Rajani; Hussain, Abdul Azeez; Baby, Sabulal

    2011-11-01

    Prey capture and digestion in Nepenthes spp. through their leaf-evolved biological traps involve a sequence of exciting events. Sugar-rich nectar, aroma chemicals, narcotic alkaloid secretions, slippery wax crystals, and other biochemicals take part in attracting, capturing, and digesting preys in Nepenthes pitchers. Here we report the distribution of three potent naphthoquinones in Nepenthes khasiana and their roles in prey capture. Plumbagin was first detected in N. khasiana, and its content (root: 1.33 ± 0.02%, dry wt.) was the highest found in any natural source. Chitin induction enhanced plumbagin levels in N. khasiana (root: 2.17 ± 0.02%, dry wt.). Potted N. khasiana plants with limited growth of roots and aerial parts, showed higher levels of plumbagin accumulation (root: 1.92 ± 0.02%; root, chitin induction: 3.30 ± 0.21%, dry wt.) compared with field plants. Plumbagin, a known toxin, insect ecdysis inhibitor, and antimicrobial, was also found embedded in the waxy layers at the top prey capture region of N. khasiana pitchers. Chitin induction, mimicking prey capture, produced droserone and 5-O-methyl droserone in N. khasiana pitcher fluid. Both these naphthoquinone derivatives provide antimicrobial protection to the pitcher fluid from visiting preys. A two-way barrier was found between plumbagin and its two derivatives. Plumbagin was never detected in the pitcher fluid whereas both its derivatives were only found in the pitcher fluid on chitin induction or prey capture. The three naphthoquinones, plumbagin, droserone, and 5-O-methyl droserone, act as molecular triggers in prey capture and digestion in the carnivorous plant, N. khasiana. PMID:21862483

  11. Corrections to measurements of pion capture ratios

    International Nuclear Information System (INIS)

    The authors conclude that the electromagnetic corrections to the C/O pion capture ratios deduced from the summed intensities of pionic Balmer series are small, and much less than their experimental errors. The magnitude of the correction due to nuclear absorption depends on the initial angular momentum distribution which in turn depends on molecular structure. The dependence of the capture ratios on molecular structure has raised serious questions about the effect on dose calculations for pion radiotherapy and on the definition of tissue equivalence for pions. (U.K.)

  12. Adsorbed films containing tetrazole on steel surface. 1. Molecular structure

    International Nuclear Information System (INIS)

    By the method of IR- and X-ray electron spectroscopy the molecular structure of the compound formed on steel during exposure to aqueous corrosion - active solution containing tetrazole (tet) is investigated. Most possibility tet act as bridging bidentate ligand form surface complex [Fe(tet)2(H2O)]m which is network polymeric structure. 29 refs.; 4 figs

  13. Modelling molecular flexibility for crystal structure prediction

    OpenAIRE

    Uzoh, O. G.

    2015-01-01

    In the crystal packing of molecules wherein a single bond links aromatic groups, a change in the torsion angle can optimise close packing of the molecule. The improved intermolecular interactions, Uinter, outweigh the conformational energy penalty, ΔEintra, to give a more stable lattice energy, Elatt = Uinter + ΔEintra. This thesis uses this lattice energy model hierarchically in a new Crystal Structure Prediction (CSP) algorithm, CrystalPredictor version 1.6, which varies the low-barrier tor...

  14. Crystal and molecular structure of paclitaxel (taxol).

    OpenAIRE

    Mastropaolo, D; Camerman, A; Luo, Y.; Brayer, G. D.; Camerman, N

    1995-01-01

    Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus severa...

  15. 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.

  16. Modelling of Spectroscopic and Structural Properties using Molecular Dynamics

    OpenAIRE

    Francesco Muniz Miranda

    2013-01-01

    The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins ...

  17. 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.

  18. Neutron capture and total cross-section measurements on fast reactor structural materials

    International Nuclear Information System (INIS)

    The neutron capture and total cross-sections of a series of nuclides in the mass range 46 to 62 have been measured at Harwell by the time-of-flight method. The capture cross-sections were measured for incident neutron energies from a few eV to 800 keV using the neutron booster target of the 45 MeV electron linac. High resolution total cross-section measurements were made with the transmission facility on the 160 MeV proton synchrocyclotron. The results of preliminary analyses of the data are presented on the capture cross-sections of Fe, 47Ti, and 49Ti and the total cross-sections of 56Fe, 58Ni and 60Ni. (author)

  19. Linking numerical simulations of molecular cloud structure with observations.

    Science.gov (United States)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  20. Hydrogen isotope capture and permeability in structural materials under conditions simulating plasma disruption

    International Nuclear Information System (INIS)

    Method of thermodesorption analysis was applied to investigate deuterium capture and desorption out of austenitic (Kh18N10T) and ferritic-martensitic (Kh13) steels and high-nickel alloy type Kh20N45 irradiated by high-temperature pulsed plasma jets. The influence of preliminary plasma processing of nickel on its hydrogen permeability in the process of irradiation by monoenergetic hydrogen ions was also under study. Ferritic-martensitic steels was also under study. Ferritic-martensitic steels were found to capture deuterium twice as much compared to austenitic steels. Preliminary plasma processing resulted in suppression of hydrogen permeability of nickel. 12 refs., 5 figs.,

  1. Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description

    CERN Document Server

    Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco

    2015-01-01

    A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...

  2. Experimental study of the collision mechanisms involved in one-electron capture by slow N5+ ions in atomic and molecular hydrogen

    International Nuclear Information System (INIS)

    Translational energy spectroscopy (TES) in the range 214-857 eV amu-1 has been used to study the collision mechanisms involved in one-electron capture by slow helium-like N5+ in both atomic and molecular hydrogen. In the case of N5+-H2 collisions, our measurements show that non-dissociative electron capture leading to the N4+ (n=3) states is the main product channel at the higher impact energies with smaller contributions to the N4+ (n=4) states. While this has also been observed in previous studies based on photon emission spectroscopy (PES), there are substantial differences in both magnitude and energy dependence between the TES and PES results. Theoretical predictions for n=3 formation are also in poor accord with experiment. Unlike previous PES measurements, the present TES study has been able to identify the presence of dissociative one-electron capture channels and two-electron autoionizing capture channels, both leading to N4+ (n=2) formation. Two-electron autoionizing electron capture is found to be the main collision mechanism leading to N4+ ions at the lowest energies considered. Our measurements of one-electron capture in N5+ + H(1s) are in excellent accord with previous higher measurements based on PES and now provide a useful extension to energies below 1 keV amu-1. In this case, only the N4+ (n=4) and N4+ (n=3) product channels are observed, with contributions from the latter becoming insignificant at our lowest energies

  3. On the structure of molecular clouds

    CERN Document Server

    Ballesteros-Paredes,; D'Alessio,; P.,; Hartmann,; W., L

    2012-01-01

    We show that the inter-cloud Larson scaling relation between mean volume density and size $\\rho\\propto R^{-1}$, which in turn implies that mass $M\\propto R^2$, or that the column density $N$ is constant, is an artifact of the observational methods used. Specifically, setting the column density threshold near or above the peak of the column density probability distribution function Npdf ($N\\sim 10^{21}$ cm\\alamenos 2) produces the Larson scaling as long as the Npdf decreases rapidly at higher column densities. We argue that the physical reasons behind local clouds to have this behavior are that (1) this peak column density is near the value required to shield CO from photodissociation in the solar neighborhood, and (2) gas at higher column densities is rare because it is susceptible to gravitational collapse into much smaller structures in specific small regions of the cloud. Similarly, we also use previous results to show that if instead a threshold is set for the volume density, the density will appear to be...

  4. Crystal and molecular structure of aflatrem

    Directory of Open Access Journals (Sweden)

    Bruno N. Lenta

    2015-11-01

    Full Text Available The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the molecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabicyclo[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabicyclo[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the molecule exhibits a tilt of 2.02 (1° between its two rings. In the crystal, O—H...O hydrogen bonds connect molecules into chains along [010]. Weak N—H...π interactions connect these chains, forming sheets parallel to (10-1.

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

    Science.gov (United States)

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

    2013-03-01

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

  6. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    Science.gov (United States)

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

    2013-03-21

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

  7. Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

    Directory of Open Access Journals (Sweden)

    Yann Bouret

    Full Text Available We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

  8. Optimization techniques in molecular structure and function elucidation

    OpenAIRE

    Sahinidis, Nikolaos V.

    2009-01-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly ...

  9. Molecular Structure of DNA by Scanning Tunneling Microscopy

    Science.gov (United States)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  10. THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION

    NARCIS (Netherlands)

    TORDA, AE; VANGUNSTEREN, WF

    1991-01-01

    We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where

  11. A SAPO-11 Silicoaluminophosphate Molecular Sieve with Stable Crystal Structure

    Institute of Scientific and Technical Information of China (English)

    Yue Ming LIU; Feng Mei ZHANG; Hai Hong WU; Hai Jiao ZHANG; Jian Guo YANG; Xing Tian SHU; Ming Yuan HE

    2004-01-01

    A SAPO-11 silicoaluminophosphate molecular sieve with stable crystal structure was synthesized for the first time. After removing template by calcination, its crystal space group still retains Icm2 which the as-synthesized has. The catalyst deriving from the present SAPO-11materials shows higher isomerization selectivity and higher paraffin hydroisomerization yield than those reported elsewhere.

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

    DEFF Research Database (Denmark)

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

    1995-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

  14. Tailoring the Pore Environment of Metal-Organic and Molecular Materials Decorated with Inorganic Anions: Platforms for Highly Selective Carbon Capture

    Science.gov (United States)

    Nugent, Patrick S.

    Due to their high surface areas and structural tunability, porous metal-organic materials, MOMs, have attracted wide research interest in areas such as carbon capture, as the judicious choice of molecular building block (MBB) and linker facilitates the design of MOMs with myriad topologies and allows for a systematic variation of the pore environment. Families of MOMs with modular components, i.e. MOM platforms, are eminently suitable for targeting the selective adsorption of guest molecules such as CO2 because their pore size and pore functionality can each be tailored independently. MOMs with saturated metal centers (SMCs) that promote strong yet reversible CO2 binding in conjunction with favorable adsorption kinetics are an attractive alternative to MOMs containing unsaturated metal centers (UMCs) or amines. Whereas MOMs with SMCs and exclusively organic linkers typically have poor CO2 selectivity, it has been shown that a versatile, long known platform with SMCs, pillared square grids with inorganic anion pillars and pcu topology, exhibits high and selective CO 2 uptake, a moderate CO2 binding affinity, and good stability under practical conditions. As detailed herein, the tuning of pore size and pore functionality in this platform has modulated the CO2 adsorption properties and revealed variants with unprecedented selectivity towards CO 2 under industrially relevant conditions, even in the presence of moisture. With the aim of tuning pore chemistry while preserving pore size, we initially explored the effect of pillar substitution upon the carbon capture properties of a pillared square grid, [Cu(bipy)2(SiF6)] (SIFSIX-1-Cu). Room temperature CO2, CH4, and N 2 adsorption isotherms revealed that substitution of the SiF6 2- ("SIFSIX") inorganic pillar with TiF6 2- ("TIFSIX") or SnF62- ("SNIFSIX") modulated CO2 uptake, CO2 affinity (heat of adsorption, Qst), and selectivity vs. CH4 and N2. TIFSIX-1-Cu and SNIFSIX-1-Cu were calculated to exhibit the highest CO2/N 2

  15. Molecular solids of actinide hexacyanoferrate: Structure and bonding

    International Nuclear Information System (INIS)

    The hexacyanometallate family is well known in transition metal chemistry because the remarkable electronic delocalization along the metal-cyano-metal bond can be tuned in order to design systems that undergo a reversible and controlled change of their physical properties. We have been working for few years on the description of the molecular and electronic structure of materials formed with [Fe(CN)6]n- building blocks and actinide ions (An = Th, U, Np, Pu, Am) and have compared these new materials to those obtained with lanthanide cations at oxidation state +III. In order to evaluate the influence of the actinide coordination polyhedron on the three-dimensional molecular structure, both atomic number and formal oxidation state have been varied : oxidation states +III, +IV. EXAFS at both iron K edge and actinide LIII edge is the dedicated structural probe to obtain structural information on these systems. Data at both edges have been combined to obtain a three-dimensional model. In addition, qualitative electronic information has been gathered with two spectroscopic tools : UV-Near IR spectrophotometry and low energy XANES data that can probe each atom of the structural unit : Fe, C, N and An. Coupling these spectroscopic tools to theoretical calculations will lead in the future to a better description of bonding in these molecular solids. Of primary interest is the actinide cation ability to form ionic - covalent bonding as 5f orbitals are being filled by modification of oxidation state and/or atomic number.

  16. Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

    Science.gov (United States)

    Camproux, A C; Tufféry, P

    2005-08-01

    Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. We have recently set up a Hidden Markov Model to optimally compress protein three-dimensional conformations into a one-dimensional series of letters of a structural alphabet. Such a model learns simultaneously the shape of representative structural letters describing the local conformation and the logic of their connections, i.e. the transition matrix between the letters. Here, we move one step further and report some evidence that such a model of protein local architecture also captures some accurate amino acid features. All the letters have specific and distinct amino acid distributions. Moreover, we show that words of amino acids can have significant propensities for some letters. Perspectives point towards the prediction of the series of letters describing the structure of a protein from its amino acid sequence. PMID:16040198

  17. Probing the Electron Capture Dissociation Mass Spectrometry of Phosphopeptides with Traveling Wave Ion Mobility Spectrometry and Molecular Dynamics Simulations

    OpenAIRE

    Kim, Doyong; Pai, Pei-Jing; Creese, Andrew J.; Jones, Andrew W.; Russell, David H.; Cooper, Helen J.

    2015-01-01

    Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, w...

  18. Molecular simulation of multi-component adsorption processes related to carbon capture in a high surface area, disordered activated carbon

    OpenAIRE

    Di Biase, Emanuela; Sarkisov, Lev

    2015-01-01

    We employ a previously developed model of a high surface area activated carbon, based on a random packing of small fragments of a carbon sheet, functionalized with hydroxyl surface groups, to explore adsorption of water and multicomponent mixtures under conditions representing typical carbon capture processes. Adsorption of water is initialized and proceeds through the growth of clusters around the surface groups, in a process predominantly governed by hydrogen bond interactions. In contrast,...

  19. Design of Carborane Molecular Architectures via Electronic Structure Computations

    Directory of Open Access Journals (Sweden)

    Josep M. Oliva

    2009-01-01

    Full Text Available Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of polycarborane 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 photoenergy processes.

  20. Capturing molecular structural dynamics by 100 ps time-resolved X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. The X-ray positional active feedback to crystals in a monochromator combined with a figure-of-merit scan of the laser beam position has been utilized as an essential tool to stabilize the spatial overlap of the X-ray and laser beams at the sample position. As a typical example, a time-resolved XAFS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented

  1. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    Science.gov (United States)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  2. 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

  3. A detailed study of cholinium chloride and levulinic acid deep eutectic solvent system for CO2 capture via experimental and molecular simulation approaches.

    Science.gov (United States)

    Ullah, Ruh; Atilhan, Mert; Anaya, Baraa; Khraisheh, Majeda; García, Gregorio; ElKhattat, Ahmed; Tariq, Mohammad; Aparicio, Santiago

    2015-08-28

    Choline chloride + levulinic acid deep eutectic solvent is studied as a suitable material for CO2 capturing purposes. The most relevant physicochemical properties of this solvent are reported together with the CO2 solubility as a function of temperature. The corrosivity of this solvent is studied showing better performance than amine-based solvents. A theoretical study using both density functional theory and molecular dynamics approaches is carried out to analyze the properties of this fluid from the nanoscopic viewpoint, and their relationship with the macroscopic behavior of the system and its ability for CO2 capturing. The behavior of the liquid-gas interface is also studied and its role on the CO2 absorption mechanism is analyzed. The reported combined experimental and theoretical approach leads to a complete picture of the behavior of this new sorbent with regard to CO2, which together with its low cost, and the suitable environmental and toxicological properties of this solvent, lead to a promising candidate for CO2 capturing technological applications. PMID:26214080

  4. Effect of the porous structure in carbon materials for CO2 capture at atmospheric and high-pressure

    OpenAIRE

    Casco, Mirian Elizabeth; Martínez Escandell, Manuel; Silvestre Albero, Joaquín; Rodríguez Reinoso, Francisco

    2014-01-01

    Activated carbons prepared from petroleum pitch and using KOH as activating agent exhibit an excellent behavior in CO2 capture both at atmospheric (∼168 mg CO2/g at 298 K) and high pressure (∼1500 mg CO2/g at 298 K and 4.5 MPa). However, an exhaustive evaluation of the adsorption process shows that the optimum carbon structure, in terms of adsorption capacity, depends on the final application. Whereas narrow micropores (pores below 0.6 nm) govern the sorption behavior at 0.1 MPa, large microp...

  5. Molecular Medicine: Synthesis and In Vivo Detection of Agents for use in Boron Neutron Capture Therapy. Final Report

    International Nuclear Information System (INIS)

    The primary objective of the project was the development of in vivo methods for the detection and evaluation of tumors in humans. The project was focused on utilizing positron emission tomography (PET) to monitor the distribution and pharmacokinetics of a current boron neutron capture therapy (BNCT) agent, p-boronophenylalanine (BPA) by labeling it with a fluorine-18, a positron emitting isotope. The PET data was then used to develop enhanced treatment planning protocols. The study also involved the synthesis of new tumor selective BNCT agents that could be labeled with radioactive nuclides for the in vivo detection of boron

  6. Molecular Medicine: Synthesis and In Vivo Detection of Agents for use in Boron Neutron Capture Therapy. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabalka, G. W.

    2005-06-28

    The primary objective of the project was the development of in vivo methods for the detection and evaluation of tumors in humans. The project was focused on utilizing positron emission tomography (PET) to monitor the distribution and pharamacokinetics of a current boron neutron capture therapy (BNCT) agent, p-boronophenylalanine (BPA) by labeling it with a fluorine-18, a positron emitting isotope. The PET data was then used to develop enhanced treatment planning protocols. The study also involved the synthesis of new tumor selective BNCTagents that could be labeled with radioactive nuclides for the in vivo detection of boron.

  7. Imaging molecular structure and dynamics using laser driven recollisions

    International Nuclear Information System (INIS)

    Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17tth - 27th) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low Ip an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the

  8. Electron capture decay of {sup 116}In and nuclear structure of double {beta} decays

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, M.; Garcia, A.; Ortiz, C.E.; Kaloskamis, N.I. [University of Notre Dame, Notre Dame, Indiana 46556 (United States); Hindi, M.M. [Physics Department, Tennessee Technological University, Cookeville, Tennessee 38505 (United States); Norman, E.B. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Davids, C.N. [Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Civitarese, O. [Department of Physics, University of La Plata, C. C. 67, 1900-La Plata (Argentina); Suhonen, J. [Department of Physics, University of Jyvaeskylae, P.O. Box 35, SF-40351, Jyvaeskylae (Finland)

    1998-08-01

    Quasiparticle-random-phase-approximation (QRPA) calculations of double {beta} decays have not been able to reproduce data in the A=100 system. We propose the A=116 system{emdash}because of its smaller deformation{emdash}as a simpler system to test QRPA calculations. We present results of two experiments we performed, which determine the electron-capture-decay branch of {sup 116}In to be (2.27{plus_minus}0.63){times}10{sup {minus}2}{percent}, from which we deduce logft=4.39{sub {minus}0.15}{sup +0.10}. We present QRPA calculations and compare their predictions to experimental data. Finally we use these calculations to predict the 2{nu} double-{beta}-decay rate of {sup 116}Cd to the ground and excited states of {sup 116}Sn. {copyright} {ital 1998} {ital The American Physical Society}

  9. Electron capture decay of 116In and nuclear structure of double β decays

    International Nuclear Information System (INIS)

    Quasiparticle-random-phase-approximation (QRPA) calculations of double β decays have not been able to reproduce data in the A=100 system. We propose the A=116 system emdash because of its smaller deformation emdash as a simpler system to test QRPA calculations. We present results of two experiments we performed, which determine the electron-capture-decay branch of 116In to be (2.27±0.63)x10-2%, from which we deduce logft=4.39-0.15+0.10. We present QRPA calculations and compare their predictions to experimental data. Finally we use these calculations to predict the 2ν double-β-decay rate of 116Cd to the ground and excited states of 116Sn. copyright 1998 The American Physical Society

  10. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  11. A new parametrizable model of molecular electronic structure

    OpenAIRE

    Laikov, Dimitri N.

    2011-01-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good...

  12. Preparation and structure characterization of nanospherical MCM- 41 molecular sieves

    OpenAIRE

    Chen, Ting; WEI Yiting; Guo, Yajun; CHU Lianfeng; Guo, Yaping

    2013-01-01

    Nanospherical MCM-41 molecular sieves have been synthesized by using hexadecyl trimethyl ammonium bromide (CTAB) as templates and tetraethyl orthosilicate (TEOS) as silicon sources. XRD,SEM,FT-IR,TEM,and N2 adsorption-desorption isotherms were used to investigate the effects of the reaction temperature and aging time on the morphology and structure of the samples. The results show that the nanospherical MCM-41 particles can be obtained at reaction temperatures between 20 to 80℃. With the reac...

  13. Structural basis for arabinoxylo-oligosaccharide capture by the probiotic Bifidobacterium animalis subsp lactis Bl-04

    OpenAIRE

    Ejby, Morten; Fredslund, Folmer; Vujicic-Zagar, Andreja; Svensson, Birte; Slotboom, Dirk Jan; Abou Hachem, Maher

    2013-01-01

    Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo-oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactisBl-04. The binding protein BlAXBP, which is associated with an...

  14. Dynamical structure of fluid mercury: Molecular-dynamics simulations

    OpenAIRE

    Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki

    2007-01-01

    We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...

  15. Optimization techniques in molecular structure and function elucidation.

    Science.gov (United States)

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  16. Microspectroscopy as applied to the study of wood molecular structure

    DEFF Research Database (Denmark)

    Fackler, Karin; Thygesen, Lisbeth Garbrecht

    2013-01-01

    -induced dimensional changes, decay resistance or mechanical properties. It is, however, important to choose the right technique for the purpose at hand and to apply it in a suitable way if any new insights are to be gained. This review presents and compares three different microspectroscopic techniques: infrared......Microspectroscopy gives access to spatially resolved information on the molecular structure and chemical composition of a material. For a highly heterogeneous and anisotropic material like wood, such information is essential when assessing structure/property relationships such as moisture...

  17. Tailoring the Pore Environment of Metal-Organic and Molecular Materials Decorated with Inorganic Anions: Platforms for Highly Selective Carbon Capture

    Science.gov (United States)

    Nugent, Patrick S.

    Due to their high surface areas and structural tunability, porous metal-organic materials, MOMs, have attracted wide research interest in areas such as carbon capture, as the judicious choice of molecular building block (MBB) and linker facilitates the design of MOMs with myriad topologies and allows for a systematic variation of the pore environment. Families of MOMs with modular components, i.e. MOM platforms, are eminently suitable for targeting the selective adsorption of guest molecules such as CO2 because their pore size and pore functionality can each be tailored independently. MOMs with saturated metal centers (SMCs) that promote strong yet reversible CO2 binding in conjunction with favorable adsorption kinetics are an attractive alternative to MOMs containing unsaturated metal centers (UMCs) or amines. Whereas MOMs with SMCs and exclusively organic linkers typically have poor CO2 selectivity, it has been shown that a versatile, long known platform with SMCs, pillared square grids with inorganic anion pillars and pcu topology, exhibits high and selective CO 2 uptake, a moderate CO2 binding affinity, and good stability under practical conditions. As detailed herein, the tuning of pore size and pore functionality in this platform has modulated the CO2 adsorption properties and revealed variants with unprecedented selectivity towards CO 2 under industrially relevant conditions, even in the presence of moisture. With the aim of tuning pore chemistry while preserving pore size, we initially explored the effect of pillar substitution upon the carbon capture properties of a pillared square grid, [Cu(bipy)2(SiF6)] (SIFSIX-1-Cu). Room temperature CO2, CH4, and N 2 adsorption isotherms revealed that substitution of the SiF6 2- ("SIFSIX") inorganic pillar with TiF6 2- ("TIFSIX") or SnF62- ("SNIFSIX") modulated CO2 uptake, CO2 affinity (heat of adsorption, Qst), and selectivity vs. CH4 and N2. TIFSIX-1-Cu and SNIFSIX-1-Cu were calculated to exhibit the highest CO2/N 2

  18. The Pivotal Role of Alumina Pore Structure in HF Capture and Fluoride Return in Aluminum Reduction

    Science.gov (United States)

    McIntosh, Grant J.; Agbenyegah, Gordon E. K.; Hyland, Margaret M.; Metson, James B.

    2016-07-01

    Fluoride emissions during primary aluminum production are mitigated by dry scrubbing on alumina which, as the metal feedstock, also returns fluoride to the pots. This ensures stable pot operation and maintains process efficiency but requires careful optimization of alumina for both fluoride capture and solubility. The Brunauer-Emmett-Teller (BET) surface area of 70-80 m2 g-1 is currently accepted. However, this does not account for pore accessibility. We demonstrate using industry-sourced data that pores <3.5 nm are not correlated with fluoride return. Reconstructing alumina pore size distributions (PSDs) following hydrogen fluoride (HF) adsorption shows surface area is not lost by pore diameter shrinkage, but by blocking the internal porosity. However, this alone cannot explain this 3.5 nm threshold. We show this is a consequence of surface diffusion-based inhibition with surface chemistry probably playing an integral role. We advocate new surface area estimates for alumina which account for pore accessibility by explicitly ignoring <3.5 nm pores.

  19. Preparation and structure characterization of nanospherical MCM- 41 molecular sieves

    Directory of Open Access Journals (Sweden)

    CHEN Ting

    2013-04-01

    Full Text Available Nanospherical MCM-41 molecular sieves have been synthesized by using hexadecyl trimethyl ammonium bromide (CTAB as templates and tetraethyl orthosilicate (TEOS as silicon sources. XRD,SEM,FT-IR,TEM,and N2 adsorption-desorption isotherms were used to investigate the effects of the reaction temperature and aging time on the morphology and structure of the samples. The results show that the nanospherical MCM-41 particles can be obtained at reaction temperatures between 20 to 80℃. With the reaction temperature increasing,the diameter of the nanospheres increases. When the reaction temperature reaches 110℃,MCM-41 molecular sieves exhibit irregular particle morphology. With the aging time of 0-15 h,the dispersion of nanospherical MCM-41 molecular sieves is very good. However,as the aging time increases,the particle size is also increased,while agglomeration is also more serious. Besides,the optimal synthesis conditions of the nanospherical MCM-41 molecular sieves were obtained by analyzing their formation mechanism.

  20. Structural and morphological characterization of active intermontane basins: a case of the Gubbio captured basin (Umbria Pre-Apennines, Italy)

    Science.gov (United States)

    Cavitolo, Paolo; Menichetti, Marco; Nesci, Olivia; Savelli, Daniele; Troiani, Francesco

    2014-05-01

    Intermontane basins characterize many orogenic chains, where they are originated either by crustal stretching or gravitational collapse of the axial zones of the chain. Extensional and/or transtensional mechanisms generate structures with geometries controlled by fault-bounded depressed areas, which in some cases are seismogenetic. The western sector of the Northern Apennines in Central Italy is characterized by several intermontane basins filled by continental Plio-Pleistocene sediments. At present, a few of these basins are depressed endorheic areas, whereas most of them have been captured by river upstream erosion. The morphotectonic characterization at both regional and local scale of these structures is crucial considering the associated geological hazards due to clustered seismicity and seismic-related slope-instability along the basin-margins. This work presents a multi-disciplinary approach based on new and existing data to define the structural geometries, landforms and processes related to the genesis and the morphoevolution of the intermountain valleys/captured-basins in Central Italy. Quantitative geomorphological analyses from Digital Terrain Models (DTMs) are compared with geological and structural data and with geophysical investigations of active and sismogenetic faults bordering the Gubbio valley in the Umbria Pre-Apennines in central Italy. This 4 km-wide valley extends for ca. 20 km in NW-SE direction and is bounded along the NE margin by a SW-dipping listric normal fault with an offset of 1500 m. The area locates along one of the main seismogenic portion of the Apennine chain and recorded historical (i.e., April 29, 1984: Ms 5.3) and many instrumental earthquakes. In this study, new data on the slope-instability along the basin-margins and the influence of active tectonics and gravitational phenomena on the streams incision and aggradation are also provided.

  1. A 3D visualization system for molecular structures

    Science.gov (United States)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  2. Molecular Structure and Target Recognition of Neuronal Calcium Sensor Proteins

    Directory of Open Access Journals (Sweden)

    James Ames

    2012-02-01

    Full Text Available Neuronal calcium sensor (NCS proteins, a sub-branch of the calmodulin superfamily, are expressed in the brain and retina where they transduce calcium signals and are genetically linked to degenerative diseases. The amino acid sequences of NCS proteins are highly conserved but their physiological functions are quite distinct. Retinal recoverin and guanylate cyclase activating proteins (GCAPs both serve as calcium sensors in retinal rod cells, neuronal frequenin (NCS1 modulates synaptic activity and neuronal secretion, K+ channel interacting proteins (KChIPs regulate ion channels to control neuronal excitability, and DREAM (KChIP3 is a transcriptional repressor that regulates neuronal gene expression. Here we review the molecular structures of myristoylated forms of NCS1, recoverin, and GCAP1 that all look very different, suggesting that the sequestered myristoyl group helps to refold these highly homologous proteins into very different structures. The molecular structure of NCS target complexes have been solved for recoverin bound to rhodopsin kinase, NCS-1 bound to phosphatidylinositol 4-kinase, and KChIP1 bound to A-type K+ channels. We propose that N-terminal myristoylation is critical for shaping each NCS family member into a different structure, which upon Ca2+-induced extrusion of the myristoyl group exposes a unique set of previously masked residues that interact with a particular physiological target.

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

    International Nuclear Information System (INIS)

    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

  4. Capturing hammerhead ribozyme structures in action by modulating general base catalysis.

    Directory of Open Access Journals (Sweden)

    Young-In Chi

    2008-09-01

    Full Text Available We have obtained precatalytic (enzyme-substrate complex and postcatalytic (enzyme-product complex crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.

  5. Assessing the structure and temporal dynamics of seabird communities: the challenge of capturing marine ecosystem complexity

    OpenAIRE

    Moreno, Rocio; Stowasser, Gabriele; McGill, Rona A.R.; Bearhop, Stuart; Phillips, Richard A.

    2016-01-01

    Summary 1.Understanding interspecific interactions, and the influences of anthropogenic disturbance and environmental change on communities, are key challenges in ecology. Despite the pressing need to understand these fundamental drivers of community structure and dynamics, only 17% of ecological studies conducted over the past three decades have been at the community level. 2.Here, we assess the trophic structure of the procellariiform community breeding at South Georgia, to identify ...

  6. Radiation track structure simulation in a molecular medium

    International Nuclear Information System (INIS)

    A problem in the simulation of track structures is identified; because the underlying medium is assumed to be a continuum in the simulation, events (and therefore chemical species) can be generated unphysically close together. The problem is particularly severe for low-energy electrons, which are responsible for inducing most of the observed chemistry. Two modified simulation methods are proposed to investigate this effect. The first method modifies the density of the medium using the radial distribution function, to ensure that events can not be generated closer to one another than nearest neighbour molecules. The second method simulates the track in a molecular medium, using configurations generated by molecular dynamics. When gas phase cross-sections are used these two methods have large effects on the mean electron range and the mean inter-event distance, but surprisingly, they act in opposite directions. When condensed phase cross-sections are used the effects are much smaller. (author)

  7. Molecular structure and pathophysiological roles of the Mitochondrial Calcium Uniporter.

    Science.gov (United States)

    Mammucari, Cristina; Raffaello, Anna; Vecellio Reane, Denis; Rizzuto, Rosario

    2016-10-01

    Mitochondrial Ca(2+) uptake regulates a wide array of cell functions, from stimulation of aerobic metabolism and ATP production in physiological settings, to induction of cell death in pathological conditions. The molecular identity of the Mitochondrial Calcium Uniporter (MCU), the highly selective channel responsible for Ca(2+) entry through the IMM, has been described less than five years ago. Since then, research has been conducted to clarify the modulation of its activity, which relies on the dynamic interaction with regulatory proteins, and its contribution to the pathophysiology of organs and tissues. Particular attention has been placed on characterizing the role of MCU in cardiac and skeletal muscles. In this review we summarize the molecular structure and regulation of the MCU complex in addition to its pathophysiological role, with particular attention to striated muscle tissues. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26968367

  8. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    Science.gov (United States)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  9. STRUCTURAL ANALYSIS AND MOLECULAR DYNAMICS STUDY OF PHB SYNTHASE

    Directory of Open Access Journals (Sweden)

    T. Femlin Blessia

    2012-02-01

    Full Text Available Polyhydroxybutyrate (PHB is a polyhydroxyalkanoate (PHA, a polymer belonging to polyesters class and is composed of hydroxy fatty acids. PHB is produced by microorganisms apparently in response to conditions of physiological stress. PHB synthases are the key enzymes of PHB biosynthesis. The PHB synthases obtained from Chromobacterium violaceum, belongs to the class I PHA synthases. Due to the limited structural information of PHB synthase, its functional properties including catalysis are unknown. Therefore, this study seeks to investigate the structural and functional properties of PHB synthase (phaC by predicting its three dimensional structure using bioinformatics methods. Present 15 ns molecular dynamics study provides an overall insight about some of the parameters such as energy, RMSD (Root Mean Square Deviation, SASA (Solvent Accessible Surface Area, hydrogen bonds, etc., Protein-protein docking reveals the binding mode of the protein in the active dimer state.

  10. Ordered molecular layer structure of lubricating oil adsorbed films

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Low-angle X-ray diffraction has been applied to analyze the structure of stearic acid LB films and self-grown surface adsorbed films of aluminium product metalworking lubricants. The results show that LB films exhibit a good layer-like ordered structure in the normal direction of film-carrying surface, while in the tangential direction, they do not show a cyclically ordered molecular arrangement; as for the self-grown surface adsorbed films of aluminium sheet and strip metalworking lubricants, their molecules are orderly arranged to certain degree in both the tangential and the normal directions of film-carrying surface, and they have a short-range ordered structure. Moreover, the better the orientation of normal molecules is, the higher the oil film strength is, and the smaller the friction factor is.

  11. 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

  12. Capturing in Vivo Plant Metabolism by Real-Time Analysis of Low to High Molecular Weight Volatiles.

    Science.gov (United States)

    Barrios-Collado, César; García-Gómez, Diego; Zenobi, Renato; Vidal-de-Miguel, Guillermo; Ibáñez, Alfredo J; Martinez-Lozano Sinues, Pablo

    2016-02-16

    We have deployed an efficient secondary electrospray ionization source coupled to an Orbitrap mass analyzer (SESI-MS) to investigate the emissions of a Begonia semperflorens. We document how hundreds of species can be tracked with an unparalleled time resolution of 2 min during day-night cycles. To further illustrate the capabilities of this system for volatile organic compounds (VOCs) analysis, we subjected the plant to mechanical damage and monitored its response. As a result, ∼1200 VOCs were monitored displaying different kinetics. To validate the soundness of our in vivo measurements, we fully characterized some key compounds via tandem mass spectrometry (MS/MS) and confirmed their expected behavior based on prior gas chromatography/mass spectrometry (GC/MS) studies. For example, β-caryophyllene, which is directly related to photosynthesis, was found to show a periodic day-night pattern with highest concentrations during the day. We conclude that the capability of SESI-MS to capture highly dynamic VOC emissions and wide analyte coverage makes it an attractive tool to complement GC/MS in plant studies. PMID:26814403

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

    International Nuclear Information System (INIS)

    Neutron diffraction (ND) measurements on liquid methanol (CD3OD, CD3O(H/D), CD3OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), Gdist(r) and inter-molecular, Ginter(r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, GXHo(r) (X=C, O, and H - a methyl hydrogen) and GXX(r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, GXHo(r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct GXX(r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular GXX(r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), gHoHo(r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular GXHo(r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial distribution functions

  14. Assessing the structure and temporal dynamics of seabird communities: the challenge of capturing marine ecosystem complexity.

    Science.gov (United States)

    Moreno, Rocío; Stowasser, Gabriele; McGill, Rona A R; Bearhop, Stuart; Phillips, Richard A

    2016-01-01

    Understanding interspecific interactions, and the influences of anthropogenic disturbance and environmental change on communities, are key challenges in ecology. Despite the pressing need to understand these fundamental drivers of community structure and dynamics, only 17% of ecological studies conducted over the past three decades have been at the community level. Here, we assess the trophic structure of the procellariiform community breeding at South Georgia, to identify the factors that determine foraging niches and possible temporal changes. We collected conventional diet data from 13 sympatric species between 1974 and 2002, and quantified intra- and inter-guild, and annual variation in diet between and within foraging habits. In addition, we tested the reliability of stable isotope analysis (SIA) of seabird feathers collected over a 13-year period, in relation to those of their potential prey, as a tool to assess community structure when diets are diverse and there is high spatial heterogeneity in environmental baselines. Our results using conventional diet data identified a four-guild community structure, distinguishing species that mainly feed on crustaceans; large fish and squid; a mixture of crustaceans, small fish and squid; or carrion. In total, Antarctic krill Euphausia superba represented 32%, and 14 other species a further 46% of the combined diet of all 13 predators, underlining the reliance of this community on relatively few types of prey. Annual variation in trophic segregation depended on relative prey availability; however, our data did not provide evidence of changes in guild structure associated with a suggested decline in Antarctic krill abundance over the past 40 years. Reflecting the differences in δ(15) N of potential prey (crustaceans vs. squid vs. fish and carrion), analysis of δ(15) N in chick feathers identified a three-guild community structure that was constant over a 13-year period, but lacked the trophic cluster representing

  15. Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.

    Science.gov (United States)

    Wu, Hong; Xu, Dingguo; Yang, Mingli; Zhang, Xingdong

    2016-05-10

    The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules. PMID:27096760

  16. [Cardiac potassium channels: molecular structure, physiology, pathophysiology and therapeutic implications].

    Science.gov (United States)

    Mironov, N Iu; Golitsyn, S P

    2013-01-01

    Potassium channels and currents play essential roles in cardiac repolarization. Potassium channel blockade by class III antiarrhythmic drugs prolongs cardiac repolarization and results in termination and prevention of cardiac arrhythmias. Excessive inhomogeneous repolarization prolongation may lead to electrical instability and proarrhythmia (Torsade de Pointes tachycardia). This review focuses on molecular structure, physiology, pathophysiology and therapeutic potential of potassium channels of cardiac conduction system and myocardium providing information on recent findings in pathogenesis of cardiac arrhythmias, including inherited genetic abnormalities, and future perspectives. PMID:24654438

  17. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    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)

  18. Three decades of structure- and property-based molecular design

    DEFF Research Database (Denmark)

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been...... of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries...

  19. Diffuse large B-cell lymphoma patient-derived xenograft models capture the molecular and biological heterogeneity of the disease.

    Science.gov (United States)

    Chapuy, Bjoern; Cheng, Hongwei; Watahiki, Akira; Ducar, Matthew D; Tan, Yuxiang; Chen, Linfeng; Roemer, Margaretha G M; Ouyang, Jing; Christie, Amanda L; Zhang, Liye; Gusenleitner, Daniel; Abo, Ryan P; Farinha, Pedro; von Bonin, Frederike; Thorner, Aaron R; Sun, Heather H; Gascoyne, Randy D; Pinkus, Geraldine S; van Hummelen, Paul; Wulf, Gerald G; Aster, Jon C; Weinstock, David M; Monti, Stefano; Rodig, Scott J; Wang, Yuzhuo; Shipp, Margaret A

    2016-05-01

    Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease defined by transcriptional classifications, specific signaling and survival pathways, and multiple low-frequency genetic alterations. Preclinical model systems that capture the genetic and functional heterogeneity of DLBCL are urgently needed. Here, we generated and characterized a panel of large B-cell lymphoma (LBCL) patient-derived xenograft (PDX) models, including 8 that reflect the immunophenotypic, transcriptional, genetic, and functional heterogeneity of primary DLBCL and 1 that is a plasmablastic lymphoma. All LBCL PDX models were subjected to whole-transcriptome sequencing to classify cell of origin and consensus clustering classification (CCC) subtypes. Mutations and chromosomal rearrangements were evaluated by whole-exome sequencing with an extended bait set. Six of the 8 DLBCL models were activated B-cell (ABC)-type tumors that exhibited ABC-associated mutations such as MYD88, CD79B, CARD11, and PIM1. The remaining 2 DLBCL models were germinal B-cell type, with characteristic alterations of GNA13, CREBBP, and EZH2, and chromosomal translocations involving IgH and either BCL2 or MYC Only 25% of the DLBCL PDX models harbored inactivating TP53 mutations, whereas 75% exhibited copy number alterations of TP53 or its upstream modifier, CDKN2A, consistent with the reported incidence and type of p53 pathway alterations in primary DLBCL. By CCC criteria, 6 of 8 DLBCL PDX models were B-cell receptor (BCR)-type tumors that exhibited selective surface immunoglobulin expression and sensitivity to entospletinib, a recently developed spleen tyrosine kinase inhibitor. In summary, we have established and characterized faithful PDX models of DLBCL and demonstrated their usefulness in functional analyses of proximal BCR pathway inhibition. PMID:26773040

  20. Capturing the Energy Absorbing Mechanisms of Composite Structures under Crash Loading

    Science.gov (United States)

    Wade, Bonnie

    As fiber reinforced composite material systems become increasingly utilized in primary aircraft and automotive structures, the need to understand their contribution to the crashworthiness of the structure is of great interest to meet safety certification requirements. The energy absorbing behavior of a composite structure, however, is not easily predicted due to the great complexity of the failure mechanisms that occur within the material. Challenges arise both in the experimental characterization and in the numerical modeling of the material/structure combination. At present, there is no standardized test method to characterize the energy absorbing capability of composite materials to aide crashworthy structural design. In addition, although many commercial finite element analysis codes exist and offer a means to simulate composite failure initiation and propagation, these models are still under development and refinement. As more metallic structures are replaced by composite structures, the need for both experimental guidelines to characterize the energy absorbing capability of a composite structure, as well as guidelines for using numerical tools to simulate composite materials in crash conditions has become a critical matter. This body of research addresses both the experimental characterization of the energy absorption mechanisms occurring in composite materials during crushing, as well as the numerical simulation of composite materials undergoing crushing. In the experimental investigation, the specific energy absorption (SEA) of a composite material system is measured using a variety of test element geometries, such as corrugated plates and tubes. Results from several crush experiments reveal that SEA is not a constant material property for laminated composites, and varies significantly with the geometry of the test specimen used. The variation of SEA measured for a single material system requires that crush test data must be generated for a range of

  1. Molecular structural order and anomalies in liquid silica.

    Science.gov (United States)

    Shell, M Scott; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

    2002-07-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water. PMID:12241346

  2. Neighborhood structure influences the convergence in light capture efficiency and carbon gain: an architectural approach for cloud forest shrubs.

    Science.gov (United States)

    Guzmán Q, J Antonio; Cordero S, Roberto A

    2016-06-01

    Although plant competition is recognized as a fundamental factor that limits survival and species coexistence, its relative importance on light capture efficiency and carbon gain is not well understood. Here, we propose a new framework to explain the effects of neighborhood structures and light availability on plant attributes and their effect on plant performance in two understory shade-tolerant species (Palicourea padifolia (Roem. & Schult.) C.M. Taylor & Lorence and Psychotria elata (Swartz)) within two successional stages of a cloud forest in Costa Rica. Features of plant neighborhood physical structure and light availability, estimated by hemispherical photographs, were used to characterize the plant competition. Plant architecture, leaf attributes and gas exchange parameters extracted from the light-response curve were used as functional plant attributes, while an index of light capture efficiency (silhouette to total area ratio, averaged over all viewing angles, STAR) and carbon gain were used as indicators of plant performance. This framework is based in a partial least square Path model, which suggests that changes in plant performance in both species were affected in two ways: (i) increasing size and decreasing distance of neighbors cause changes in plant architecture (higher crown density and greater leaf dispersion), which contribute to lower STAR and subsequently lower carbon gain; and (ii) reductions in light availability caused by the neighbors also decrease plant carbon gain. The effect of neighbors on STAR and carbon gain were similar for the two forests sites, which were at different stages of succession, suggesting that the architectural changes of the two understory species reflect functional convergence in response to plant competition. Because STAR and carbon gain are variables that depend on multiple plant attributes and environmental characteristics, we suggest that changes in these features can be used as a whole-plant response approach to

  3. Observation of edge filamentary structure motion during supersonic molecular-beam injection using a fast camera in Heliotron J

    International Nuclear Information System (INIS)

    A perpendicular-view fast video camera has been installed in Heliotron J to observe the behavior of filamentary structures of edge plasma turbulence across the last closed flux surface (LCFS). Supersonic molecular-beam injection (SMBI) can greatly increase the edge Hα emission; hence, we used the high imaging rate and shutter speed of the camera to capture the behavior of the fast propagating filamentary structures. A high-pass fast Fourier transform filter on the time dimension was adopted to extract the fluctuation component from the raw data for each pixel. The motion of the filamentary structures was clearly visible when we applied an amplitude threshold to identify the intense structures. In addition, a time-resolved 2D cross-correlation technique was adopted to estimate the poloidal phase velocity of turbulence. The motion direction was found to be reversed dramatically just after an SMBI pulse. (author)

  4. Molecular structure and reversible photodegradation in anthraquinone dyes

    CERN Document Server

    Dhakal, Prabodh

    2016-01-01

    Reversible photodegradation is a process that has been observed in several dye molecules, but the underlying mechanisms are not still well understood. In this contribution, we characterize a series of anthraquinone dyes to determine how self-healing depends on molecular structure. Past studies have used probing techniques that rely on linear absorption, two-photon fluorescence, and amplified spontaneous emission. Each of these probes provide an indirect measure of the populations of the damaged and undamaged species, requiring calibrations or assumptions to be made that might affect the accuracy of the results. The present studies use fluorescence as a probe, which is shown to directly measure the undamaged population. It is found that certain anthraquinone classes share common structural features that are associated with self healing. Furthermore, the time and temperature dependence of photodegradation and self-healing is found to be consistent with the domain model of self healing.

  5. Study on multimers and their structures in molecular association mixture

    Institute of Scientific and Technical Information of China (English)

    YAMAGUCHI; Yoshinori; OZAKI; Yukihiro

    2007-01-01

    Self-association system of(R)-1,3-butanediol in dilute carbon tetrachloride(CCl4)solution is studied as a model of molecular association mixture.Analysis methods including FSMWEFA(fixed-size moving window evolving factor analysis)combined with PCA(principal component analysis),SIMPLISMA (simple-to-use interactive self-modeling mixture analysis),and ITTFA(iterative target transformation factor analysis)are adopted to resolve infrared spectra of(R)-1,3-butanediol solution.Association number and equilibrium constant are computed.(R)-1,3-butanediol in dilute inert solution is determined as a monomer-trimer equilibrium system.Theoretical investigation of trimer structures is carried out with DFT(density functional theory),and structural factors are analyzed.

  6. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    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), 13C-NMR spin-lattice relaxation time (T1), 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 KMnO4 solution is incorrect. (2) By using the LB film of 3H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14C-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. T1 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)

  7. Methods for empirical formula, molecular structure determination and colloid characterisation

    International Nuclear Information System (INIS)

    Determination of empirical formula and of molecular structures in issues pertinent to the fuel cycle, waste management and remediation, as well as in risk assessment associated with radionuclide release and its migration to the near and far field of a repository present a particular challenge. Speciation techniques in these areas are needed for extraction chemistry of actinides, aquatic reactions of actinide ions (e.g. tetravalent actinide hydrolysis, formation of ternary complexes and redox chemistry), reactions at the water/mineral interface, formation of secondary phases and the formation of and interaction with colloids. The range of concentrations of interest is extreme, from relatively pure substances such as the fuels themselves, to tracer levels in far-field release scenarios. Actinide speciation in extractant solutions used for separation techniques for partitioning technologies involves investigation of solutions with often acidic pH, whereas speciation in cement pore waters, for example, can involve very basic solutions. Finally, the amount of sample available may be limited, e.g. pore water samples can be as small as μL quantities. There exist a variety of techniques for determining empirical formula and molecular structure of radionuclide species. The actual contents and components of the sample at hand in addition to the degree of complexity required dictates the method that is chosen. The speciation of radionuclides is often governed by their association with or formation to colloids. The characterisation of such colloids is imperative and their quantification and characterisation is, therefore, included as a separate treatise. (author)

  8. Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.

    Science.gov (United States)

    Caputo, Alessandro T; Alonzi, Dominic S; Marti, Lucia; Reca, Ida-Barbara; Kiappes, J L; Struwe, Weston B; Cross, Alice; Basu, Souradeep; Lowe, Edward D; Darlot, Benoit; Santino, Angelo; Roversi, Pietro; Zitzmann, Nicole

    2016-08-01

    The biosynthesis of enveloped viruses depends heavily on the host cell endoplasmic reticulum (ER) glycoprotein quality control (QC) machinery. This dependency exceeds the dependency of host glycoproteins, offering a window for the targeting of ERQC for the development of broad-spectrum antivirals. We determined small-angle X-ray scattering (SAXS) and crystal structures of the main ERQC enzyme, ER α-glucosidase II (α-GluII; from mouse), alone and in complex with key ligands of its catalytic cycle and antiviral iminosugars, including two that are in clinical trials for the treatment of dengue fever. The SAXS data capture the enzyme's quaternary structure and suggest a conformational rearrangement is needed for the simultaneous binding of a monoglucosylated glycan to both subunits. The X-ray structures with key catalytic cycle intermediates highlight that an insertion between the +1 and +2 subsites contributes to the enzyme's activity and substrate specificity, and reveal that the presence of d-mannose at the +1 subsite renders the acid catalyst less efficient during the cleavage of the monoglucosylated substrate. The complexes with iminosugar antivirals suggest that inhibitors targeting a conserved ring of aromatic residues between the α-GluII +1 and +2 subsites would have increased potency and selectivity, thus providing a template for further rational drug design. PMID:27462106

  9. Molecular interrogation of the feeding behaviour of field captured individual insects for interpretation of multiple host plant use.

    Directory of Open Access Journals (Sweden)

    James P Hereward

    Full Text Available The way in which herbivorous insect individuals use multiple host species is difficult to quantify under field conditions, but critical to understanding the evolutionary processes underpinning insect-host plant relationships. In this study we developed a novel approach to understanding the host plant interactions of the green mirid, Creontiades dilutus, a highly motile heteropteran bug that has been associated with many plant species. We combine quantified sampling of the insect across its various host plant species within particular sites and a molecular comparison between the insects' gut contents and available host plants. This approach allows inferences to be made as to the plants fed upon by individual insects in the field. Quantified sampling shows that this "generalist" species is consistently more abundant on two species in the genus Cullen (Fabaceae, its primary host species, than on any other of its numerous listed hosts. The chloroplast intergenic sequences reveal that C. dilutus frequently feeds on plants additional to the one from which it was collected, even when individuals were sampled from the primary host species. These data may be reconciled by viewing multiple host use in this species as an adaptation to survive spatiotemporally ephemeral habitats. The methodological framework developed here provides a basis from which new insights into the feeding behaviour and host plant relationships of herbivorous insects can be derived, which will benefit not only ecological interpretation but also our understanding of the evolution of these relationships.

  10. 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'…

  11. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    Science.gov (United States)

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale.

  12. Capturing the Magnetic and Structural Phase Transition of Ferh using Extreme Ultraviolet Light

    Science.gov (United States)

    Zusin, Dmitriy; Grychtol, Patrik; Gentry, Christian; Murnane, Margaret; Kapteyn, Henry; Canton, Sophie; Knut, Ronny; Shaw, Justin; Nembach, Hans; Silva, Thomas; Ceballos, Alejandro; Bordel, Catherine; Fischer, Peter; Hellman, Frances

    2015-03-01

    The temperature dependent transition from the anti-ferromagnetic to the ferromagnetic phase in FeRh is accompanied by a modification of its crystal lattice. The interplay between the magnetic and the structural transition is a matter of strong debate. It is important to better understand the mechanism(s) of the transition since it can be induced by femtosecond laser pulses and, unlike slower (nanosecond) magnetic phase transitions, does not seem to be limited by heat transfer. In this work, we use extreme ultraviolet light generated by a tabletop high harmonics source to perform element-selective investigations of the temperature-dependent magneto-optical response of a thin film FeRh sample. We study the optically induced phase transition using two ultrafast pump-probe spectroscopy approaches: by monitoring the time-resolved transversal magneto-optical Kerr effect (T-MOKE) and the transient change in reflectivity. PF acknowledges support from BES MSD DOE # DE-AC02-05-CH11231 and LFRIR program (# 2012K1A4A3053565) through NRF Korea funded by MEST, and JILA from DOE # DE-FG02-09ER4665.

  13. 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.

  14. 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.

  15. Molecular graphics-structural and molecular graphics descriptors in a QSAR study of 17-a-acetoxyprogesterones

    OpenAIRE

    Kiralj Rudolf; Ferreira Márcia M. C.

    2003-01-01

    Quantitative Structure-Activity Relationship study on 21 oral progestogens, 19 of which are 17-alpha-acetoxyprogesterones, was performed by using Partial Least Squares. Fairly good regression models were achieved, the best being Q²=0.707, R²=0.811 with two Principal Components and four descriptors. Most of the molecular descriptors were generated from molecular graphics of DFT 6-31G** optimized geometries (molecular graphics descriptors) or were additionally combined with experimental structu...

  16. Selective capture and rapid identification of Panax notoginseng metabolites in rat faeces by the integration of magnetic molecularly imprinted polymers and high-performance liquid chromatography coupled with orbitrap mass spectrometry.

    Science.gov (United States)

    Cai, Qizhi; Yang, Zaiyue; Chen, Ning; Zhou, Xuemin; Hong, Junli

    2016-07-15

    In the present work, an advanced pretreatment method magnetic molecular imprinted polymers-dispersive solid phase extraction (MMIPs-DSPE) combined with the high sensitivity LTQ-Orbitrap mass spectrometry was applied to the complicated metabolites analysis of Traditional Chinese Medicines (TCMs) in complex matrices. The ginsenoside Rb1 magnetic molecular imprinted polymers (Rb1-MMIPs) were successfully synthesized for specific recognition and selective enrichment of Panax notoginseng saponin metabolites in rat faeces. The polymers were prepared by using Fe3O4@SiO2 as the supporting material, APTES as the functional monomer and TEOS as the cross-linker. The Rb1-MMIPs showed quick separation (10.8 emu/g), large adsorption capacity (636μmol/g), high selectivity and fast binding kinetics (25min). Dispersion solid-phase extraction using Rb1-MMIPs (Rb1-MMIPs-DSPE) integrated with LTQ-Orbitrap MS was applied to fish out and identify saponin metabolites from rat faeces, and totally 58 related compounds were detected within 20min, including 26 PPD-group and 32 PPT-group notoginsenoside metabolites. Parallel tests showed that Rb1-MMIPs-DSPE obtained the lowest matrix effects of 0.98-14.84% and captured the largest number of structural analogues compared with traditional pretreatment methods organic solvent extraction (OSE) and solid phase extraction (SPE). PMID:27295967

  17. Capturing state-dependent dynamic events of GABAA-receptors: a microscopic look into the structural and functional insights.

    Science.gov (United States)

    Payghan, Pavan V; Bera, Indrani; Bhattacharyya, Dhananjay; Ghoshal, Nanda

    2016-08-01

    The γ-amino butyric acid type A receptors (GABAA-Rs) are the key players in the mammalian brain that meditate fast inhibitory neurotransmission events. The structural integrity of these ligand-gated ion channel controls chloride ion permeability, which in turn monitors important pharmacological functions. Despite ample studies on GABAA-Rs, there was a need for a study on full-length receptor structures, devoted to track structure-function correlations based on their dynamic behavior consideration. We have employed molecular dynamics simulations accompanied by other biophysical methods to shed light on sequential and unaddressed questions like How GABAA-R structure facilitates the entry of GABA molecules at its two orthosteric binding sites? After entry, what structural features and changes monitor site-wise GABA binding differences? In the same context, what are the roles and responsibilities of loops such as C and F? On physiologically relevant time scales, how open to close state transition occurs? How salt bridges such as E155-R207 and E153-R207 maintain state-dependent C-loop structures? In an attempt, our simulation study unravels the complete course of GABA binding-unbinding pathway. This provides us with the relevant understanding of state-dependent dynamic events of GABAA-Rs. PMID:26372345

  18. A new parametrizable model of molecular electronic structure

    Science.gov (United States)

    Laikov, Dimitri N.

    2011-10-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure - making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost.

  19. Microsecond molecular dynamics simulations of the open state structure of a bacterial voltage-gated sodium channel reveal mechanisms of ion selectivity and conduction

    OpenAIRE

    Ulmschneider, Martin B.; Bagneris, Claire; McCusker, Emily C.; Ulmschneider, J.P.; Wallace, Bonnie A.

    2013-01-01

    Microsecond atomic detail equilibrium molecular dynamics simulations based on the open-state crystal structure (McCusker et al, 2012, Nature Comm) of a bacterial voltage-gated sodium channel (NavMs) have been employed to characterize the mechanisms underlying ion selectivity and conductance of the channel embedded in a lipid bilayer membrane. This approach captured the full plethora of conduction events, revealing a complex mixture of single and multi-ion phenomena, with decoupled rapid bi-di...

  20. How does the molecular network structure influence PDMS elastomer wettability?

    Science.gov (United States)

    Melillo, Matthew; Genzer, Jan

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from medical devices to absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into PDMS networks is of critical importance for the design and use of another application - microfluidic devices. We have systematically studied the effects of polymer molecular weight, loading of tetra-functional crosslinker, end-group chemical functionality, and the extent of dilution of the curing mixture on the mechanical and surface properties of end-linked PDMS networks. The gel and sol fractions, storage and loss moduli, liquid swelling ratios, and water contact angles have all been shown to vary greatly based on the aforementioned variables. Similar trends were observed for the commercial PDMS material, Sylgard-184. Our results have confirmed theories predicting the relationships between modulus and swelling. Furthermore, we have provided new evidence for the strong influence that substrate modulus and molecular network structure have on the wettability of PDMS elastomers. These findings will aid in the design and implementation of efficient microfluidics and other PDMS-based materials that involve the transport of liquids.

  1. 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.

  2. A new parametrizable model of molecular electronic structure

    CERN Document Server

    Laikov, Dimitri N

    2011-01-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the paramtrization procedure -- making a direct link...

  3. Molecular structure and thermodynamic properties of scandium halides

    International Nuclear Information System (INIS)

    Experimental data on molecular constants of mono-, di- and trihalides of scandium, as well as di-scandium hexahalides of the composition ScXn and Sc2X6 (X = F - I; n = 1 - 3), have been analyzed. Specific features of the compounds molecule structure are considered. The values of molecular constants have been evaluated by the methods of statistical thermodynamics and thermodynamic properties of all scandium halides mentioned in the temperature range of 100 - 6000 K and 298.15 - 1000 K respectively for scandium monohalides and for di-, tri-, hexahalides have been calculated. The values of thermodynamic functions Cp Deg, Φ Deg (T), H Deg (T) - H Deg (0) at 298.15 K published for the first time equal respectively for ScF: 32.734; 192.186; 222.232; 8.958; for ScCl: 45.782; 203.351; 237.356; 10.138; for ScBr: 49.449; 215.090; 252.783; 11.238; for ScI: 42.605; 227.517; 265.635; 12.259

  4. 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 ...

  5. Towards a molecular description of intermediate filament structure and assembly

    International Nuclear Information System (INIS)

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central α-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling

  6. Electronic Structure and Molecular Dynamics Calculations for KBH4

    Science.gov (United States)

    Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas

    2012-02-01

    In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-12-31

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-01

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

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

    International Nuclear Information System (INIS)

    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)

  10. 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.

  11. Inter-molecular β-sheet structure facilitates lung-targeting siRNA delivery

    Science.gov (United States)

    Zhou, Jihan; Li, Dong; Wen, Hao; Zheng, Shuquan; Su, Cuicui; Yi, Fan; Wang, Jue; Liang, Zicai; Tang, Tao; Zhou, Demin; Zhang, Li-He; Liang, Dehai; Du, Quan

    2016-03-01

    Size-dependent passive targeting based on the characteristics of tissues is a basic mechanism of drug delivery. While the nanometer-sized particles are efficiently captured by the liver and spleen, the micron-sized particles are most likely entrapped within the lung owing to its unique capillary structure and physiological features. To exploit this property in lung-targeting siRNA delivery, we designed and studied a multi-domain peptide named K-β, which was able to form inter-molecular β-sheet structures. Results showed that K-β peptides and siRNAs formed stable complex particles of 60 nm when mixed together. A critical property of such particles was that, after being intravenously injected into mice, they further associated into loose and micron-sized aggregates, and thus effectively entrapped within the capillaries of the lung, leading to a passive accumulation and gene-silencing. The large size aggregates can dissociate or break down by the shear stress generated by blood flow, alleviating the pulmonary embolism. Besides the lung, siRNA enrichment and targeted gene silencing were also observed in the liver. This drug delivery strategy, together with the low toxicity, biodegradability, and programmability of peptide carriers, show great potentials in vivo applications.

  12. Genetic structure of Triatoma venosa (Hemiptera: Reduviidae: molecular and morphometric evidence

    Directory of Open Access Journals (Sweden)

    Erika Vargas

    2006-02-01

    Full Text Available Triatoma venosa presents a restricted geographical distribution in America and is considered as a secondary vector of Chagas disease in Colombia and Ecuador. A total of 120 adult insects were collected in domestic and peridomestic habitats in an endemic area of the department of Boyacá, Colombia, in order to determine their genetic structure through morphometric and molecular techniques. The head and wings of each specimen were used for the analyses of size, shape, and sexual dimorphism. A significant sexual dimorphism was found, although no differences in size among the studied groups were detected. Differences were found in the analyzed structures except for male heads. DNA was extracted from the legs in order to carry out the internal transcriber space-2 (ITS-2 amplification and the randon amplified polymorphic DNA (RAPD analyses. Length polymorphisms were not detected in the ITS-2. Fst and Nm values were estimated (0.047 and 3.4, respectively. The high genetic flow found among the insects captured in the domicile and peridomiciliary environment does not permit a genetic differentiation, thus establishing the peridomicile as an important place for epidemiological surveillance.

  13. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    Science.gov (United States)

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  14. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    Science.gov (United States)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

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

    Science.gov (United States)

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

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers. PMID:26520533

  16. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

    Science.gov (United States)

    Pabit, Suzette A.; Katz, Andrea M.; Tolokh, Igor S.; Drozdetski, Aleksander; Baker, Nathan; Onufriev, Alexey V.; Pollack, Lois

    2016-05-01

    Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

  17. Mineral-Biochar Composites: Molecular Structure and Porosity.

    Science.gov (United States)

    Rawal, Aditya; Joseph, Stephen D; Hook, James M; Chia, Chee H; Munroe, Paul R; Donne, Scott; Lin, Yun; Phelan, David; Mitchell, David R G; Pace, Ben; Horvat, Joseph; Webber, J Beau W

    2016-07-19

    Dramatic changes in molecular structure, degradation pathway, and porosity of biochar are observed at pyrolysis temperatures ranging from 250 to 550 °C when bamboo biomass is pretreated by iron-sulfate-clay slurries (iron-clay biochar), as compared to untreated bamboo biochar. Electron microscopy analysis of the biochar reveals the infusion of mineral species into the pores of the biochar and the formation of mineral nanostructures. Quantitative (13)C nuclear magnetic resonance (NMR) spectroscopy shows that the presence of the iron clay prevents degradation of the cellulosic fraction at pyrolysis temperatures of 250 °C, whereas at higher temperatures (350-550 °C), the clay promotes biomass degradation, resulting in an increase in both the concentrations of condensed aromatic, acidic, and phenolic carbon species. The porosity of the biochar, as measured by NMR cryoporosimetry, is altered by the iron-clay pretreatment. In the presence of the clay, at lower pyrolysis temperatures, the biochar develops a higher pore volume, while at higher temperature, the presence of clay causes a reduction in the biochar pore volume. The most dramatic reduction in pore volume is observed in the kaolinite-infiltrated biochar at 550 °C, which is attributed to the blocking of the mesopores (2-50 nm pore) by the nonporous metakaolinite formed from kaolinite. PMID:27284608

  18. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    International Nuclear Information System (INIS)

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH2 groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  19. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    Energy Technology Data Exchange (ETDEWEB)

    Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

    2009-05-15

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

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

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2013-07-01

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

  1. Automatic molecular structure perception for the universal force field.

    Science.gov (United States)

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616

  2. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    Science.gov (United States)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

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

  3. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  4. Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

    OpenAIRE

    Gutierrez, R.; Caetano, R.; Woiczikowski, P. B.; Kubar, T.; Elstner, M; Cuniberti, G.

    2009-01-01

    Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either fr...

  5. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    International Nuclear Information System (INIS)

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method

  6. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    Science.gov (United States)

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  7. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    Science.gov (United States)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  8. Neurobiological mechanisms of treatment resistant depression: Functional, structural and molecular imaging studies

    NARCIS (Netherlands)

    B.P. de Kwaasteniet

    2015-01-01

    This thesis investigated the neurobiological mechanisms of TRD using functional, structural and molecular imaging studies. First the neurobiological mechanisms of MDD were investigated and revealed decreased functional connectivity between the ventral and dorsal network. Thereafter, structural conne

  9. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.

    Science.gov (United States)

    Springer, Mark S; Signore, Anthony V; Paijmans, Johanna L A; Vélez-Juarbe, Jorge; Domning, Daryl P; Bauer, Cameron E; He, Kai; Crerar, Lorelei; Campos, Paula F; Murphy, William J; Meredith, Robert W; Gatesy, John; Willerslev, Eske; MacPhee, Ross D E; Hofreiter, Michael; Campbell, Kevin L

    2015-10-01

    The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in

  10. Structural effect of the in situ generated titania on its ability to oxidize and capture the gas-phase elemental mercury.

    Science.gov (United States)

    Lee, Tai Gyu; Hyun, Jung Eun

    2006-01-01

    Structural effect of the in situ generated TiO(2) sorbent particle was examined for its ability to capture elemental mercury under UV irradiation in a simulated combustion flue gas. Titania particles were prepared by thermal gas-phase oxidation of Titanium (IV) isopropoxide (TTIP) using a high temperature electric furnace reactor. The structural characteristics of the in situ generated TiO(2) at various synthesis temperatures were investigated; size distribution and the geometric mean diameter were measured using a scanning mobility particle sizer, while fractal dimension and radius of gyration were evaluated from the transmission electron microscopy images. Results from the Hg(0) capture experiment show that with increasing titania synthesis temperature, the overall aggregate size increases and the morphology becomes more open-structured to gas-phase Hg(0) and UV light, resulting in the improved mercury removal capability. PMID:15949836

  11. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  12. Effect of molecular structure and slump loss resistance of polycarboxylate superplasticizers on self-compacting concrete

    Institute of Scientific and Technical Information of China (English)

    LAN Zi-dong

    2016-01-01

    A new kind of polycarboxylate superplasticizer with high slump loss resistance was obtained by designing scheduled molecular structure. The number average molecular mass of the polymer was characterized by thegel permeation chromatography measurements. And chemical structure of the polymer was observed by the Fouriertransform infrared spectroscopy(FT-IR). The results showthat the good workablemaintaining ofself-compacting concretecould be achieved through direct adjustmentof number average molecular mass and different unsaturated monomer in synthetic process. The FT-IR analysis illustrated that the high slump loss resistance of polycarboxylate superplasticizers with ester and carboxyl group and expectations of molecular structure were designed.

  13. Molecular Structural and Properties of 3-chloro-4 (dichloromethyl)-5-hydroxy-2 [5H] -furanone (MX)

    Institute of Scientific and Technical Information of China (English)

    李欣; 龙运前; 齐晶瑶; 王郁萍

    2004-01-01

    3 - chloro - 4 (dichloromethyl) - 5 - hydroxy - 2 [5H] - furanone (MX) formed during chlorination of water containing natural organic substances, is a very potent bacterial mutgen. Molecular mechanics calculations to evaluate the conformation of structure, and to determine structure relationship properties are put forward. The investigations allow the correlation of molecular structures of MX with its properties, such as mass,partial charges, steric energy, frontier molecular orbital. The VRML molecular models have been investigated using Virtual Reality software. The spectral simulation of MX is illustrated. The principal aim is to develop an efficient method which control of MX.

  14. Structural Characteristics of Low Molecular Weight Laminarin Prepared by Ionizing Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong-il [Chonnam National University, Gwangju (Korea, Republic of)

    2013-12-15

    Recently, it has been reported that low molecular weight laminarin had the enhanced biological activities. In this study, molecular structure of low molecular weight laminarin prepared by ionizing irradiation was studied. Low molecular weight laminarin samples of 13.5, 8.5, 7, and 6 kDa were obtained from 15 kDa laminarin by irradiation. From gel permeation chromatography data, low molecular weight laminarin was shown to have low polydispersity. To define the changes of functional groups in laminarin with different molecular weights, Fourier-transform infrared analysis was carried out. There was found no significant changes of functional groups in low molecular weight laminarin, except the increase of carbonyl group. The granular fissures from scanning electron microscopy showed the breakage of glycosidic bond in low molecular weight laminarin. These results could be utilized for the investigation of the enhanced biological activities of low molecular weight polysaccharides including laminarin.

  15. Structural Characteristics of Low Molecular Weight Laminarin Prepared by Ionizing Irradiation

    International Nuclear Information System (INIS)

    Recently, it has been reported that low molecular weight laminarin had the enhanced biological activities. In this study, molecular structure of low molecular weight laminarin prepared by ionizing irradiation was studied. Low molecular weight laminarin samples of 13.5, 8.5, 7, and 6 kDa were obtained from 15 kDa laminarin by irradiation. From gel permeation chromatography data, low molecular weight laminarin was shown to have low polydispersity. To define the changes of functional groups in laminarin with different molecular weights, Fourier-transform infrared analysis was carried out. There was found no significant changes of functional groups in low molecular weight laminarin, except the increase of carbonyl group. The granular fissures from scanning electron microscopy showed the breakage of glycosidic bond in low molecular weight laminarin. These results could be utilized for the investigation of the enhanced biological activities of low molecular weight polysaccharides including laminarin

  16. Laser capture.

    Science.gov (United States)

    Potter, S Steven; Brunskill, Eric W

    2012-01-01

    This chapter describes detailed methods used for laser capture microdissection (LCM) of discrete subpopulations of cells. Topics covered include preparing tissue blocks, cryostat sectioning, processing slides, performing the LCM, and purification of RNA from LCM samples. Notes describe the fine points of each operation, which can often mean the difference between success and failure. PMID:22639264

  17. Extremely small hole capture cross sections in HfO2/HfxSiyOz/p-Si structures

    Science.gov (United States)

    Yousif, M. Y. A.; Johansson, M.; Engström, O.

    2007-05-01

    Defects in Al /HfO2/HfxSiyOz/p-Si capacitors have been characterized using thermally stimulated current at temperatures between 30 and 300K. The hole activation energy and capture cross section were extracted from the results. The authors observed shallow traps that move with changing the discharging voltage, giving rise to activation energies in the range 0.03-0.14eV. Postmetallization anneal passivated these traps and a deeper trap appears with a significantly lower shift with the discharging voltage. Very small apparent capture cross sections (capture cross section times tunneling probability) have been extracted (10-26-10-18cm2). Simulations agree very well with experimental data.

  18. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    Science.gov (United States)

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  19. Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

    OpenAIRE

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

    2001-01-01

    An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat the energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.

  20. Molecular weight dependence of domain structure in silica-siloxane molecular composites

    International Nuclear Information System (INIS)

    This paper reports that a detailed investigation of the molecular weight dependence of silica growth in in situ filled polydimethylsiloxane/tetraethylorthosilicate (PDMS/TEOS) materials was conducted using small angle neutron scattering (SANS). Composite materials were produced by using TEOS to simultaneously produce the glassy filler phase and to crosslink linear, hydroxyl terminated PDMS of variable molecular weight, M. Correlated domains of glassy filler were produced. The morphology of the in situ filled material showed a definite dependence on the molecular weight of the precursor polymer. The scale, R, of the glassy domains follows de Gennes' description of phase separation in a crosslinked system (R α M1/2)

  1. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: a non-equilibrium molecular dynamics study

    CERN Document Server

    Lemarchand, Claire A; Todd, Billy D; Daivis, Peter J; Hansen, Jesper S

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear is investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity and normal stress differences of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid. The corresponding molecular structure is studied at the same shear rates and temperatures. The Cooee bitumen is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. The nanoaggregates are shown to break up at very high shear rates, leading only to a minor effect on the viscosity of the mixture. At low shear rates, bitumen can be seen as a colloidal suspension of nanoaggregates in a solvent. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified...

  2. Designing π-stacked molecular structures to control heat transport through molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Kiršanskas, Gediminas [Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Mathematical Physics and Nanometer Structure Consortium (nmC-LU), Lund University, Box 118, 221 00 Lund (Sweden); Li, Qian; Solomon, Gemma C. [Nano-Science Center and Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Flensberg, Karsten [Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Leijnse, Martin [Solid State Physics and Nanometer Structure Consortium (nmC-LU), Lund University, 221 00 Lund (Sweden)

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  3. Insights from the Molecular Dynamics Simulation of Cellobiohydrolase Cel6A Molecular Structural Model from Aspergillus fumigatus NITDGPKA3.

    Science.gov (United States)

    Dodda, Subba Reddy; Sarkar, Nibedita; Aikat, Kaustav; Krishnaraj, Navanietha R; Bhattacharjee, Sanchari; Bagchi, Angshuman; Mukhopadhyay, Sudit S

    2016-01-01

    Global demand for bioethanol is increasing tremendously as it could help to replace the conventional fossil fuel and at the same time supporting the bioremediation of huge volume of cellulosic wastes generated from different sources. Ideal genetic engineering approaches are essential to improve the efficacy of the bioethanol production processes for real time applications. A locally isolated fungal strain Aspergillus fumigatus NITDGPKA3 was used in our laboratory for the hydrolysis of lignocellulose with good cellulolytic activity when compared with other contemporary fungal strains. An attempt is made to sequence the cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, model its structure to predict its catalytic activity towards improving the protein by genetic engineering approaches. Herein, the structure of the sequenced Cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, modelled by homology modelling and its validation is reported. Further the catalytic activity of the modelled CBH enzyme was assessed by molecular docking analysis. Phylogenetic analysis showed that CBH from A. fumigatus NITDGPKA3 belongs to the Glycohydro 6 (Cel6A) super family. Molecular modeling and molecular dynamics simulation suggest the structural and functional mechanism of the enzyme. The structures of both the cellulose binding (CBD) and catalytic domain (CD) have been compared with most widely studied CBH of Trichoderma reesei. The molecular docking with cellulose suggests that Gln 248, Pro 287, Val236, Asn284, and Ala288 are the main amino acids involved in the hydrolysis of the β, 1-4, glycosidic bonds of cellulose. PMID:27109185

  4. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  5. 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.

  6. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to...

  7. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  8. Molecular and structural preservation of dehydrated bio-tissue for THz spectroscopy

    Science.gov (United States)

    Png, Gretel M.; Choi, Jin Wook; Guest, Ian; Ng, Brian W.-H.; Mickan, Samuel P.; Abbott, Derek; Zhang, Xi-Cheng

    2007-12-01

    Terahertz transmission through freshly excised biological tissue is limited by the tissue's high water content. Tissue fixation methods that remove water, such as fixation in Formalin, destroy the structural information of proteins hence are not suitable for THz applications. Dehydration is one possible method for revealing the tissue's underlying molecular structure and components. In this study, we measured the THz responses over time of dehydrating fresh, necrotic and lyophilized rat tissue. Our results show that as expected, THz absorption increases dramatically with drying and tissue freshness can be maintained through lyophilization. Dehydrated biological tissue with retained molecular structure can be useful for future laser-based THz wave molecular analysis.

  9. Synaptic tagging and capture in a biophysical model

    OpenAIRE

    Benjamin Auffarth

    2014-01-01

    There is wide consensus that synaptic plasticity (prominently long-term potentiation; LTP) is the underlying mechanism for learning and memory storage (cf Nabavi 2014). Open issues include the molecular pathways and networks and structural processes leading to functional and structural changes at the synaptic and dendritic levels in terms of channels and spines. Synaptic tagging and capture (STC; Frey and Morris 1997; Redondo and Morris 2011) is a predominant model for investigating LTP. Acco...

  10. 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...

  11. A Molecular Dynamics Approach to Grain Boundary Structure and Migration

    DEFF Research Database (Denmark)

    Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans

    1974-01-01

    It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...

  12. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  13. Molecular conformation and structural correlations of liquid D-1-propanol through neutron diffraction

    Indian Academy of Sciences (India)

    A Sahoo; S Sarkar; P S R Krishna; V Bhagat; R N Joarder

    2008-07-01

    An analysis of neutron diffraction data of liquid deuterated 1-propanol at room temperature to extract its molecular conformation is presented. Being a big molecule with twelve atomic sites, the analysis is tricky and needs careful consideration. The resulting molecular parameters are compared with electron diffraction (gas phase), X-ray diffraction (liquid phase) and MD simulation results. Information about the hydrogen-bonded intermolecular structure in liquid is extracted and nature of the probable molecular association suggested.

  14. Molecular Characterisation of Structural Chromosomal Abnormalities Associated with Congenital Disorders

    OpenAIRE

    Mansouri, Mahmoud R.

    2006-01-01

    Chromosomal abnormalities are defined as changes in the chromosome structure and fall in one of two categories. The first category is numerical alterations while the second category consists of structural abnormalities. Structural chromosomal abnormalities do not always interrupt genes in order to cause disease. They can also affect gene expression by separating a gene and its promoter element from distant regulatory elements. We have used characterisation of structural chromosomal abnormalit...

  15. Reply to comments on `Structure effects in the $^{15}$N($n,\\gamma$)$^{16}$N radiative capture reaction from the Coulomb dissociation of $^{16}$N'

    CERN Document Server

    Shubhchintak,; Chatterjee, R

    2016-01-01

    We reply to the comments (arXiv:1605.07499 [nucl-th]) on "Structure effects in the $^{15}$N($n,\\gamma$)$^{16}$N radiative capture reaction from the Coulomb dissociation of $^{16}$N". We have investigated the issue of "energy dependence of branching ratios" and believe that this energy dependence is due to the proper inclusion of the non-resonant continuum in the post-form reaction theory. Interestingly, this energy dependence is sensitive to the relative orbital angular momentum content of the state. We reiterate that we have attempted to resolve the discrepancy in the spectroscopic factors of low-lying $^{16}$N levels and that it is essential to know the low energy $^{15}$N($n,\\gamma$)$^{16}$N capture cross section, especially below 0.25 MeV.

  16. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    Science.gov (United States)

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-Lin; Du, Guan-Hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2) ) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw ) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives. PMID:26648584

  17. 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.

  18. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Science.gov (United States)

    de la Llave, Ezequiel; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-01

    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.

  19. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    International Nuclear Information System (INIS)

    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

  20. Neutron Capture and Neutron Halos

    OpenAIRE

    A.Mengoni; Otsuka, T; Nakamura, T.(International Center for Elementary Particle Physics and Department of Physics, The University of Tokyo, Tokyo, Japan); Ishihara, M.

    1996-01-01

    The connection between the neutron halo observed in light neutron rich nuclei and the neutron radiative capture process is outlined. We show how nuclear structure information such as spectroscopic factors and external components of the radial wave function of loosely bound states can be derived from the neutron capture cross section. The link between the direct radiative capture and the Coulomb dissociation process is elucidated.

  1. Structure of Ionic Liquids and their Mixtures with Molecular Solvents

    Czech Academy of Sciences Publication Activity Database

    Rotrekl, Jan

    Prague : Institute of Chemical Process Fundamentals of the ASCR, v. v. i, 2014 - (Bendová, M.; Wagner, Z.), s. 10-11 ISBN 978-80-86186-61-0. [Bažant Postgraduate Conference 2014. Prague (CZ), 19.06.2014] R&D Projects: GA MŠk LD14090 Institutional support: RVO:67985858 Keywords : molecular solvent * ionic liquids * thermodynamic characterization Subject RIV: CF - Physical ; Theoretical Chemistry

  2. 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.

  3. The large-scale structure of molecular clouds

    International Nuclear Information System (INIS)

    This thesis deals with the large-scale properties of molecular clouds. Most extensive studies of these clouds are made in 12CO line at 2.6 mm and this line being optically thick, the analysis is strongly dependent on the much less abundant 13CO. In addition there exists some discord about the abundance of CO with respect to H2. The results of observations of large clouds in the local arm are presented: the clouds near Mon OB 1 and Mon OB 2, the Ophiuchus complex near Sco OB2 and the extended complexes of molecular clouds in Taurus. Observations of local clouds between l = 1000 and l = 1400 near the galactic plane are also discussed, as is the distribution of molecular clouds and other spiral arm tracers in the Perseus arm. The author concludes with a comparison of different models of cloud formation. In his opinion the model of Blitz and Shu agrees best with the observations in this part of the galaxy. However he considers it improbable that every individual cloud was formed in that way. It is more likely that a number of clouds with a range of sizes is formed at the same time and that they gradually move apart, which may be the situation in the Perseus arm around l = 1100. (Auth.)

  4. Molecular dynamics simulations on structural conformations of rhodopsin and prion proteins

    International Nuclear Information System (INIS)

    Molecular dynamics simulations were performed to investigate the structural conformation of the rhodopsin and prion proteins. We have estimated the effect of specific disease-related amino acid mutations on the dynamics and conformational changes

  5. SERS and RAIR for Molecular Structure of Phenylazonaphthalene terminated Self-Assembled Monolayer

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The SAMs of 10-[4-(4-phenylazo)naphth-l-oxyl]-l-decanethiol (Compound 1) on gold were prepared. Their molecular structures were determined by surface enhanced Raman spectroscopy (SERS) and reflection absorption infrared spectroscopy (RAIR).

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

    International Nuclear Information System (INIS)

    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)

  7. Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures.

    Science.gov (United States)

    Cole, Jason C; Groom, Colin R; Korb, Oliver; McCabe, Patrick; Shields, Gregory P

    2016-04-25

    This paper describes a novel way to use the structural information contained in the Cambridge Structural Database (CSD) to drive geometry optimization of organic molecules. We describe how CSD structural information is transformed into objective functions for gradient-based optimization to provide good quality geometries for a large variety of organic molecules. Performance is assessed by minimizing different sets of organic molecules reporting RMSD movements for bond lengths, valence angles, torsion angles, and heavy atom positions. PMID:26977906

  8. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    Energy Technology Data Exchange (ETDEWEB)

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  9. Influence of the molecular structure of biofuels on combustion in a compression ignition engine

    OpenAIRE

    Schönborn, A

    2009-01-01

    This thesis presents an experimental study on the influence of the molecular structure of potential biofuels on combustion in a compression ignition engine. The molecular structure of a fuel is amongst the most fundamental parameter controlling its physical and chemical characteristics, and is thus critical to the combustion process within an engine. The approach employed in this work was to study the combustion of several individual molecules in a series of experiments whilst var...

  10. Cyclo (Tyrosyl-Prolyl) Produced by Streptomyces sp.: Bioactivity and Molecular Structure Elucidation

    OpenAIRE

    ROFIQ SUNARYANTO; BAMBANG MARWOTO; LIESBETINI HARTOTO; ZAINAL ALIM MAS'UD; TUN TEDJA IRAWADI

    2011-01-01

    Determination of bioactivity by minimum inhibitory concentration (MIC) methods and molecular structure identification of antibiotic produced by Streptomyces sp. have been carried out. The antibiotic was produced by liquid culture using Streptomyces sp. isolate. Purification of antibiotic was carried out by silica gel column chromatography and preparative HPLC. Molecular structure identification was carried out using ESI-MS, 1H NMR, 13C NMR, and 13C DEPT NMR. Pure antibiotic showed inhibition ...

  11. Molecular weight and antioxidant effects on the structure of irradiated linear low density polyethylene

    International Nuclear Information System (INIS)

    Linear copolymers of ethylene and butene-1 with uniform chemical microstructure and very narrow molecular weight distribution are used to study the effects of ionizing radiation. The well characterized copolymers are irradiated at room temperature with γ-rays from a 60Co source. To follow the evolution of the molecular structure with the radiation doses, changes in molecular weight averages Mn and Mw are measured by membrane osmometry, light scattering and GPC. The influence of the original linear polymer molecular weight is examined in the range of 50,000-100,000. The effects of antioxidant are explored irradiating samples with and without additive. (author)

  12. 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. PMID:17054018

  13. Structural basis for molecular recognition at serotonin receptors.

    Science.gov (United States)

    Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D; Gao, Xiang; Zhou, X Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L; Cherezov, Vadim; Stevens, Raymond C; Xu, H Eric

    2013-05-01

    Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs. PMID:23519210

  14. Evolution of molecular structure in alkoxide-derived lithium niobate

    International Nuclear Information System (INIS)

    This paper reports on structural rearrangements during the sol-gel processing of lithium niobate investigated by FTIR and Raman spectroscopic methods. The reaction of lithium ethoxide with niobium ethoxide resulted in the formation of a bimetallic alkoxide, LiNb(OEt)6, which could be crystallized from solution. Single crystals were comprised of helical polymeric units consisting of niobium octahedra linked by lithium in cetrahedral (distorted) coordination. Successive crystallizations from solution allowed for the enhanced purification of the alkoxide precursor. Hydrolysis of the bimetallic alkoxide resulted in the formation of an amorphous network structure, which contained niobium-oxygen octahedral units modified by lithium. Heat-treatment facilitated structural rearrangements for the niobium environment, which allowed for the formation of the lithium niobate crystal structure. Further heat-treatment above 700 degrees C resulted in structural changes associated with lithium oxide volatility

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

    International Nuclear Information System (INIS)

    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

  16. 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...

  17. The structural biology of molecular recognition by vancomycin.

    Science.gov (United States)

    Loll, P J; Axelsen, P H

    2000-01-01

    Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used world-wide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition. PMID:10940250

  18. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    Science.gov (United States)

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-01

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches. PMID:26876376

  19. Crystal and molecular structure of Np(4) sulfate

    International Nuclear Information System (INIS)

    Monocrystals are prepared and crystal structure of Np(SO4)2·4H2O is detected: a=14.597(4), b=11.036(2), c=5.663(2) A, space group - Pnma. The structure is layered, electroneutral layers of [Np(SO4)2(H2O)4]n are perpendicular to [100] direction, hydrogen bonds combine layers into three-dimensional packing. Coordination Np(4) polyhedron is quadratic prism and is formed by oxygen atoms of bidentate-bridge sulfate ions and four water molecules. Np-O bond lengths and bond angles are determined. Peculiarities of structure of double neptunium sulfates with K, Na, Cs in dependence on ligand number and effect of outer spheric cations and water molecules on structure of coordination spheres of Np atoms are considered

  20. Structural Basis for Molecular Recognition at Serotonin Receptors

    OpenAIRE

    Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Gao, Xiang; Zhou, Edward X.; Melcher, Karsten; Zhang, Chenghai

    2013-01-01

    Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist anti-migraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserv...

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Marcia, Marco, E-mail: marco.marcia@yale.edu; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas [Yale University, New Haven, CT 06511 (United States); Rajashankar, Kanagalaghatta [Argonne National Laboratory, Argonne, IL 60439 (United States); Pyle, Anna Marie, E-mail: marco.marcia@yale.edu [Yale University, New Haven, CT 06511 (United States); Yale University, New Haven, CT 06511 (United States); Howard Hughes Medical Institute, Chevy Chase, MD 20815 (United States)

    2013-11-01

    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.

  3. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    OpenAIRE

    Sha, Wei

    2008-01-01

    In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the ...

  4. How to capture patients’ concerns and related changes: Comparing the MYCaW questionnaire, semi-structured interview and a priority list of outcome areas

    DEFF Research Database (Denmark)

    Ostenfeld-Rosenthal, Ann; Johannessen, Helle

    2014-01-01

    Objectives To compare the capacity of the MYCaW questionnaire, a priority list of concerns covered by validated questionnaires, and semi-structured interviews to identify patients’ personalized concerns and related changes. Design In a pragmatic trial on the effectiveness of energy healing as...... convergences and divergences of the outcome measures are identified, and strengths and weaknesses of the three methods in regard to capturing personalized concerns and changes are discussed. Results Three patterns were identified: (1) in the intervention groups concerns stated in MYCaW were adjusted after...

  5. 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...

  6. The Molecular Structure of the Liquid Ordered Phase

    Science.gov (United States)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  7. 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.

  8. Effect of Molecular Structure on the Performance of Polyacrylic Acid Superplasticizer

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rongguo; GUO Huiling; LEI Jiaheng; ZHANG Anfu; GU Huajun

    2007-01-01

    The effects of structure parameters, such as molecular structure, segment kinds, molecular weight, and organic functional groups, on the performance of polyacrylic acid superplasticizer were discussed. According to the differences of chain sections, functional groups, etc, polyacrylic acid superplasticizer could be divided into A, B, C three parts. Among them, A chain section included sulfonic acid groups, B chain section carboxyl groups, C chain section polyester. Polyacrylic acid superplasticizers with different matching of A, B, C chain sections, different length of C chain section and different molecular weights were synthesized by acrylic acid, polyethylene glycol, sodium methyl allylsulfonate; the relation between the molecular structure and performance was also studied. The expetimental results indicate that the water-reduction ratio increases obviously with the increment of the proportion of sodium methyl allylsulfonate chain section in the molecular; the slump retention increases greatly with the increment of the proportion of acrylic acid chain section; the dispersion of cement particles increases with the increment of the chain length of polyethylene glycol; when the molecular weight is in the range of 5000, the dispersion and slump retentibity increase with the increment of the average molecular weight of polymers.

  9. Molecular structure and nonequilibrium polarizations: recent experiments on polar gases

    International Nuclear Information System (INIS)

    Senftleben-Beenakker experiments are reported on the thermal conductivity and visosity of polyatomic gases. Polar molecules of linear and symmetric top structure have been investigated in a magnetic field. NH3-noble gas mixtures and CH3CN mixtures have been studied. The results indicate the concentration dependence of the various non-equilibrium polarizations for these specific systems. (C.F.)

  10. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    Science.gov (United States)

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  11. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    Science.gov (United States)

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers. PMID:26752623

  12. Molecular conformation and liquid structure of 2-propanol through neutron diffraction

    Indian Academy of Sciences (India)

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

    2010-05-01

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its molecular conformation is presented. 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky and an improved method of data analysis is given. The intermolecular structural correlations, i.e., hydrogen-bonded liquid structure, can be modelled accurately to extract the nature of the average hydrogen-bonded molecular association in liquid state at room temperature. Like other alcohols these are mostly hexamer ring chain (HRC) clusters. The cluster analysis of recent X-ray data available in the literature also support the same liquid structure.

  13. Using molecular structure for reliable predicting enthalpy of melting of nitroaromatic energetic compounds

    International Nuclear Information System (INIS)

    In this work, a reliable simple method has been introduced for predicting enthalpy of melting of nitroaromatic energetic compounds through their molecular structures. This method can be used for a wide range of nitroaromatics including halogenated nitroaromatic compounds. The contribution of hydrogen bonding and polar groups as well as structural parameters can be used to improve the predicted values on the basis of the number of carbon, nitrogen and oxygen atoms. The predicted results show that this method gives reliable prediction of standard enthalpy of melting with respect to the best available methods for different nitroaromatic compounds including high explosives with complex molecular structures.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Eisenberg, David S.

    2008-07-15

    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

  16. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  17. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  18. Do Giant Molecular Clouds Care About the Galactic Structure?

    CERN Document Server

    Fujimoto, Yusuke; Wakayama, Mariko; Habe, Asao

    2014-01-01

    We investigate the impact of galactic environment on the properties of simulated giant molecular clouds formed in a M83-type barred spiral galaxy. Our simulation uses a rotating stellar potential to create the grand design features and resolves down to 1.5 pc. From the comparison of clouds found in the bar, spiral and disc regions, we find that the typical GMC is environment independent, with a mass of 5e+5 Msun and radius 11 pc. However, the fraction of clouds in the property distribution tails varies between regions, with larger, more massive clouds with a higher velocity dispersion being found in greatest proportions in the bar, spiral and then disc. The bar clouds also show a bimodality that is not reflected in the spiral and disc clouds except in the surface density, where all three regions show two distinct peaks. We identify these features as being due to the relative proportion of three cloud types, classified via the mass-radius scaling relation, which we label A, B and C. Type A clouds have the typi...

  19. Crystal and molecular structure of perindopril erbumine salt

    Science.gov (United States)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  20. Molecular Structure of Humin and Melanoidin via Solid State NMR

    OpenAIRE

    Herzfeld, Judith; Rand, Danielle; Matsuki, Yoh; Daviso, Eugenio; Mak-Jurkauskas, Melody; Mamajanov, Irena

    2011-01-01

    Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective 13C substitution, 1H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simpl...

  1. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    Science.gov (United States)

    Czupinski, O.; Bator, G.; Ciunik, Z.; Jakubas, R.; Medycki, W.; Swiergiel, J.

    2002-09-01

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO4 has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 21, with Z = 8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the 1 H nuclear magnetic resonance second moment (M2) and spin-lattice relaxation time T1. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH)+ cations and ClO4- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO4 is observed over the whole temperature range studied.

  2. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    International Nuclear Information System (INIS)

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO4 has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 21, with Z=8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the 1H nuclear magnetic resonance second moment (M2) and spin-lattice relaxation time T1. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH)+ cations and ClO4- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO4 is observed over the whole temperature range studied. (author)

  3. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    Energy Technology Data Exchange (ETDEWEB)

    Czupinski, O.; Bator, G.; Ciunik, Z.; Jakubas, R. [Faculty of Chemistry, University of Wroclaw, Wroclaw (Poland); Medycki, W.; Swiergiel, J. [Institute of Molecular Physics, PAS, Poznan (Poland)

    2002-09-16

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO{sub 4} has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 2{sub 1}, with Z=8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the {sup 1}H nuclear magnetic resonance second moment (M{sub 2}) and spin-lattice relaxation time T{sub 1}. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH){sup +} cations and ClO{sub 4}- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO{sub 4} is observed over the whole temperature range studied. (author)

  4. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    Science.gov (United States)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  5. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

    International Nuclear Information System (INIS)

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnaha-Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drive strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles

  6. A Quantitative Structure Property Relationship for Prediction of Flash Point of Alkanes Using Molecular Connectivity Indices

    Institute of Scientific and Technical Information of China (English)

    Morteza Atabati; Reza Emamalizadeh

    2013-01-01

    Many structure-property/activity studies use graph theoretical indices,which are based on the topological properties of a molecule viewed as a graph.Since topological indices can be derived directly from the molecular structure without any experimental effort,they provide a simple and straightforward method for property prediction.In this work the flash point of alkanes was modeled by a set of molecular connectivity indices (x),modified molecular connectivity indices (mx(1)h) and valance molecular connectivity indices (mxv),with mxv calculated using the hydrogen perturbation.A stepwise Multiple Linear Regression (MLR) method was used to select the best indices.The predicted flash points are in good agreement with the experimental data,with the average absolute deviation 4.3 K.

  7. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    International Nuclear Information System (INIS)

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed

  8. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    Directory of Open Access Journals (Sweden)

    Dallakian Pavel

    2011-02-01

    Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

  9. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    Directory of Open Access Journals (Sweden)

    Peiqiang Yu

    2007-01-01

    Full Text Available The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1 using the newly advanced synchrotron technology (S-FTIR as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2 revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3 prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4 obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  10. Nuclear structure of 241Pu from neutron-capture, (d,p)-, and (d,t)-reaction measurements

    International Nuclear Information System (INIS)

    We report experimental measurements in 241Pu of the following: primary and secondary γ rays and conversion electrons from thermal neutron capture in 240Pu;γ rays from 245Cm α decay; proton and triton spectra, respectively, from (d,p) and (d,t) reactions on 240Pu and 242Pu targets. From these data and those of other investigations, we have identified 53 excited levels in 241Pu below 1400 keV. Of these, 44 are placed in 10 rotational bands (with connecting transitions) that have been assigned Nilsson configurations. For the bands below 1 MeV in 241Pu that are largely of single-particle character, there is good correspondence with similar bands in 239U and with the theoretical model of Gareev et al. For those bands in 241Pu where there is mixing between single-particle and vibrational modes, we find some significant deviations from theoretical predictions. For example, the (5) /(2) [622]circle-times 0- state at 519 keV appears to mix less with other states than predicted, while a trio of Kπ= (1) /(2) - bands show unexpected mixing patterns. copyright 1998 The American Physical Society

  11. Molecular modeling of the ion channel-like nanotube structure of amyloid β-peptide

    Institute of Scientific and Technical Information of China (English)

    JIAO Yong; YANG Pin

    2007-01-01

    The ion channel-like nanotube structure of the oligomers of amyloid β-peptide (Aβ) was first investigated by molecular modeling. The results reveal that the hydrogen bond net is one of the key factors to stabilize the structure. The hydrophobicity distribution mode of the side chains is in favor of the structure inserting into the bilayers and forming a hydrophilic pore. The lumen space is under the control of the negative potential, weaker but spreading continuously, to which the cation selectivity attributes; meanwhile, the alternate distribution of the stronger positive and negative potentials makes the electrostatic distribution of the structure framework balance, which is also one of the key factors stabilizing the structure. The results lay the theoretical foundation for illuminating the structure stability and the ion permeability, and give a clue to elucidating the molecular mechanism of Alzheimer's disease (AD) and designing novel drugs to prevent or reverse AD at the root.

  12. Structure of beryllium isotopes in fermionic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Torabi, Bahram Ramin

    2009-02-16

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  13. Structure of beryllium isotopes in fermionic molecular dynamics

    International Nuclear Information System (INIS)

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  14. Study of the molecular structure of uranium hexafluoride

    International Nuclear Information System (INIS)

    The vibrational spectrum of uranium hexafluoride has been studied in both the gaseous and solid states. The study of gaseous UF6 confirms the regular octahedral structure of the fluorine atoms around the central U atom and makes it possible to evaluate some of the vibrational frequencies. From these, some new force constants have been determined. A tetragonal distortion is observed on solid UF6; this distortion has only observed up till now by means of X-ray diffraction and nuclear magnetic resonance techniques. (author)

  15. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

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

    OpenAIRE

    Huanyu Wang; Xiao Ji; Chi Chen; Kui Xu; Ling Miao

    2013-01-01

    Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively...

  17. Crystal and molecular structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline

    Indian Academy of Sciences (India)

    K V Arjuna Gowda; M K Kokila; Puttaraja; M V Kulkarni; N C Shivaprakash

    2000-09-01

    The crystal structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline (II) has been determined by X-ray structure analysis. This belongs to a class of benzylidene anilines. The structure was solved by direct method. The molecular packing of the non-planar molecules are held by Van der Waals and F$\\cdots\\cdot$H7, O$\\cdots\\cdot$Cl, F$\\cdots\\cdot$F and N$\\cdots\\cdot$H interactions.

  18. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    Science.gov (United States)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  19. Correlations between molecular structure and charge distribution in organometallic complexes of lanthanoids and actinoids

    International Nuclear Information System (INIS)

    The correlation between molecular structure and charge distribution was investigated in organometallic compounds of the lanthanoid (4f-) and actinoid (5f-) elements. These compounds are suitable models for two reasons: a) they are soluble in nonpolar solvents and b) in both series, there is a possibility for continuous variation of the ionic size of the central ion. Detailed investigation of several compound-classes with different molecular symmetry, has given important information concerning the influence of the molecular structure on the macroscopic charge distribution in the molecule. The anisotropy of the charge distribution in the molecule increases with decreasing of the molecular symmetry. Contrary to predictions previously discussed in the literature, it has been shown, that the molecular symmetry primarily does not depend on sterical interactions, but on the Coulomb-interaction between the central ion and the ligand. Using different models which take into account the molecular geometry and the charge distribution, it was possible to calculate the partial electrical moments between ligand and central ion for several coordinating atoms of the used ligands. The contribution of the f-electrons to the total charge distribution around the central ion can be quantitatively calculated from the molecular polarizability and the total charge distribution of the investigated molecule. (orig./RB)

  20. Molecular Clouds in the North American and Pelican Nebulae: Structures

    CERN Document Server

    Zhang, Shaobo; Yang, Ji

    2013-01-01

    We present observations of 4.25 square degree area toward the North American and Pelican Nebulae in the $J = 1-0$ transitions of $^{12}$CO, $^{13}$CO, and C$^{18}$O. Three molecules show different emission area with their own distinct structures. These different density tracers reveal several dense clouds with surface density over 500 $M_\\odot$ pc$^{-2}$ and a mean H$_2$ column density of 5.8, 3.4, and 11.9$\\times10^{21}$ cm$^{-2}$ for $^{12}$CO, $^{13}$CO, and C$^{18}$O, respectively. We obtain a total mass of $5.4\\times10^4 M_\\odot$ ($^{12}$CO), $2.0\\times10^4 M_\\odot$ ($^{13}$CO), and $6.1\\times10^3 M_\\odot$ (C$^{18}$O) in the complex. The distribution of excitation temperature shows two phase of gas: cold gas ($\\sim$10 K) spreads across the whole cloud; warm gas ($>$20 K) outlines the edge of 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 including t...

  1. Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

    Energy Technology Data Exchange (ETDEWEB)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

    2007-07-01

    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)

  2. EFFECTS OF MATRIX MOLECULAR WEIGHT ON STRUCTURE AND REINFORCEMENT OF HIGH DENSITY POLYETHYLENE/MICA COMPOSITES

    Institute of Scientific and Technical Information of China (English)

    Li Chen; Yu-fang Xiang; Ke Wang; Qin Zhang; Rong-ni Du; Qiang Fu

    2011-01-01

    Three types of high-density polyethylene (HDPE) with different molecular weights (high, medium and Iow) were adopted to evaluate the influence of matrix molecular weight on the structure-property relation of injection-molded HDPE/mica composites through a combination of SEM, 2d-WAXS, DSC, DMA and tensile testing. Various structural factors including orientation, filler dispersion, interfacial interaction between HDPE and mica, etc., which can impact the macroscopic mechanics, were compared in detail among the three HDPE/mica composites. The transcrystallization of HDPE on the mica surface was observed and it exhibited strong matrix molecular weight dependence. Obvious transcrystalline structure was found in the composite with Iow molecular weight HDPE, whereas it was hard to be detected in the composites with increased HDPE molecular weight. The best reinforcement effect in the composite with low molecular weight HDPE can be understood as mainly due to substantially improved interracial adhesion between matrix and mica filler, which arises from the transerystallization mechanism.

  3. Two-dimensional topological insulator molecular networks: dependence on structure, symmetry, and composition

    Science.gov (United States)

    Tan, Liang Z.; Louie, Steven G.

    2014-03-01

    2D molecular networks can be fabricated from a wide variety of molecular building blocks, arranged in many different configurations. Interactions between neighboring molecular building blocks result in the formation of new 2D materials. Examples of 2D organic topological insulators, that contain molecular building blocks and heavy elements arranged in a hexagonal lattice, have been recently proposed by Feng Liu and coworkers (Nano Lett., 13, 2842 (2013)). In this work, we present a systematic study of the design space of 2D molecular network topological insulators, elucidating the role of structure, symmetry, and composition of the networks. We show that the magnitude and presence of spin-orbit gaps in the electronic band structure is strongly dependent on the symmetry properties and arrangement of the individual components of the molecular lattice. We present general rules to maximize the magnitude of spin-orbit gaps and perform ab-initio calculations on promising structures derived from these guidelines. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NSF through XSEDE resources at NICS.

  4. Capturing Structural Complexity of Innovation Diffusion through System Dynamics: A Discussion on Model Development, Calibration and Simulation Results

    OpenAIRE

    Sanjay Bhushan

    2013-01-01

    This paper shows the utility of systems approach by extending the traditional innovation models and incorporating and integrating into them selective critical structural variables to map their interaction and explain the inherent dynamism. Conventionally, the approaches in explaining the innovation diffusion process assume that the process takes place in a stable and homogeneous system in which the innovation diffuses or spreads without being affected by the system’s structural variables ev...

  5. Muon capture probability of carbon and oxygen for CO, CO2, and COS under low-pressure gas conditions

    International Nuclear Information System (INIS)

    When a negatively charged muon is stopped in a substance, it is captured by an atom of the substance, and the muonic atom is formed. The muon capture process is significantly affected by the chemical environment of the atom and factors such as molecular structure (chemical effect). In this study, we performed muon irradiation for low-pressure CO, CO2, and COS molecules and measured the muonic X-rays emitted immediately after muon capture by an atom. In this paper, we quantitatively discuss the muon capture probability of each type of atom using the LMM model. (author)

  6. Role of crystal structure on CO2 capture by limestone derived CaO subjected to carbonation/recarbonation/calcination cycles at Ca-looping conditions

    International Nuclear Information System (INIS)

    Highlights: • CO2 capture of limestone subjected to carbonation/recarbonation/calcination cycles is affected by diffusion. • A reduction of crystallinity by ball milling favors diffusion and promotes recarbonation. • Thermal annealing enhances crystallinity and hinders recarbonation. • Milling promotes friability whereas annealing enhances the resistance of particles to fragmentation. • The solid crystal structure determines the efficiency of the novel Ca-looping concept. - Abstract: Large scale pilot plants are currently demonstrating the feasibility of the Calcium-looping (CaL) technology built on the multicyclic calcination/carbonation of natural limestone for post-combustion and pre-combustion CO2 capture. Yet, limestone derived CaO exhibits a drop of conversion when subjected to multiple carbonation/calcination cycles, which lessens the efficiency of the technology. In this paper we analyze a novel CaL concept recently proposed to mitigate this drawback based on the introduction of an intermediate stage wherein carbonation is intensified at high temperature and high CO2 partial pressure. It is shown that carbonation in this stage is mainly driven by solid-state diffusion, which is determined by the solid’s crystal structure. Accordingly, a reduction of crystallinity by ball milling, which favors diffusion, serves to promote recarbonation. Conversely, thermal annealing, which enhances crystallinity, hinders recarbonation. An initial fast phase has been identified in the recarbonation stage along which the rate of carbonation is also a function of the crystal structure indicating a relevant role of surface diffusion. This is consistent with a recently proposed mechanism for nucleation of CaCO3 on the CaO surface in islands with a critical size determined by surface diffusion. A further issue analyzed has been the effects of pretreatment and cycling on the mechanical strength of the material, whose fragility hampers the CaL process efficiency

  7. Crystal and molecular structure of cadmium diformiatodiaquo-bis-(nicotinamide)

    International Nuclear Information System (INIS)

    The structural investigation of the cadmium formiate complex with nicotinamide Cd(HCOO)2(AHA)2(H2O)2, AHA=NC5H4-CONH2, is performed. The parameters of the triclinic lattice are α=7.451 (1), b=7.549(2), c=8.787(3)A, α=109.88(2), β=100.16(2), γ=96.92(2), space group. P anti 1, Z=1. Each of the ligands occupies a coordination place, forming transoctahedral surroundings around Cd. The AHA ligand is coordinated by pyridine nitrogen Cd-N 2.336(5), distances Cd-O(HCOO) 2.285(7), Cd-O(H2O) 2.342(7)

  8. Molecular Variability in Barley Structural Mutants Produced by Gamma Irradiation

    International Nuclear Information System (INIS)

    Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used to survey gamma ray induced genetic variation in a set of 13 originally produced structural barley (H. vulgare L.) mutants from cv. Freya; including 8 single translocation lines, 3 double translocation lines and 2 multiple reconstructed karyotypes. Both marker systems contributed to the evaluation of the radiation induced DNA alterations and revealed in general 0.49% polymorphisms in the studied genotypes. AFLPs were observed with 3 out of 10 PstI/MseI primer combinations. Transmissible microsatellite instability at loci with perfect (AT)n repeats located in the introns of the rubisco activase and waxy was documented in three mutant lines. The results emphasize that in addition to point mutations, small indels (2bp) form the major group of the gamma induced DNA alterations. (author)

  9. Changes in physical properties and molecular structure of butyl rubber during γ-irradiation

    International Nuclear Information System (INIS)

    Butyl rubber samples have been aged by γ-irradiation at 250C in air. The change in molecular structure due to chain scission and formation of oxygenated groups also change the number-average molecular weight, tensile strength and density of butyl rubber. The rubber predominantly undergoes chain scission upon γ-irradiation up to a dose of 50 Mrad, but there is also substantial chain crosslinking above 50 Mrad. The yield G(x) has been found, which provides an insight into the mechanism of the radiolytic degradation. Hydroperoxide is the major product and unsaturation is incorporated in the polymer back bone. The change in molecular structure due to recombination and chain scission are followed by the formation of a more ordered structure and hence an increase in density. (author)

  10. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  11. Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance.

    Science.gov (United States)

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  12. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    Directory of Open Access Journals (Sweden)

    Fei Shi

    2011-01-01

    Full Text Available Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions.

  13. Modification of LDPE molecular structure by gamma irradiation for bioapplications

    International Nuclear Information System (INIS)

    The surface properties of low-density polyethylene (LDPE) can be modified by the grafting of 2-hydroxyethyl methacrylate (HEMA). This was done aiming at the production of new materials suitable for bioapplications. Samples with different monomer concentrations were prepared from LDPE particles by gamma irradiation, following different irradiation protocols, including irradiation in presence and absence of air. The samples were characterized by thermal analysis techniques (DSC and TGA) and by Fourier transform infrared spectroscopy (FTIR). The results obtained show a decrease in the crystallinity of the supporting matrix for copolymers with high yields of grafting. However, the new materials prepared maintain good structural order resulting from the protective effect of polyHEMA grafted onto LDPE backbone. These effects can improve the diffusion of other species deeper inside the matrix and increase the material hydrophilicity. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield. These were used in the production of new LDPE films with enhanced hydrophilic properties

  14. Study of the molecular structure and dynamics of bakelite with neutron cross section measurements

    International Nuclear Information System (INIS)

    The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 8000 C. (F.E.). 65 refs, 31 figs, 5 tabs

  15. Linking microbial community structure to biogeochemical function in coastal marine sediments: Stable isotope probing combined with magnetic bead capture

    NARCIS (Netherlands)

    T. Miyatake

    2011-01-01

    Microbial community structure and its biogeochemical functions in marine sediments can be successfully linked by using the improved Mag-SIP method in combination with other approaches. In this thesis, we were able to provide detailed information on the microorganisms responsible for the utilization

  16. A molecular dynamics calculation of the fluctuation structure in the diatomic fluids around the critical points

    International Nuclear Information System (INIS)

    The principle of corresponding state on the fluctuation structure, which is the spatial distribution of various clusters of molecules caused by density fluctuations, in supercritical states around the critical points has been investigated. In this paper, we performed Molecular Dynamics (MD) simulation to extract the fluctuation structure around the critical points of 2-Center-Lennard-Jones (2CLJ) fluids, whose characteristics change by their molecular elongations. First, we indentified some critical points of 2CLJ fluids with comparatively shorter elongations applying Lotfi's function, which correctly describes the liquid-vapor coexistence line of Lennard-Jones (LJ) fluid, and successfully defined each critical point. Next, two methods were applied in the estimation of the fluctuation structure: one is the evaluation of the dispersion of the number of molecules at a certain domain, and the other is the calculation of static structure factor. As a result, in 2CLJ fluids which have shorter molecular elongations comparatively, the principle of corresponding state is satisfied because of the small differences in the fluctuation structures extracted in the present two methods. On the other hand, some results imply that the fluctuation may decrease in 2CLJ fluids which have the longer molecular elongations although more accurate evaluation of the critical points in those fluids is necessary for the further investigation. (author)

  17. Molecular and electronic structure of actinide hexa-cyanoferrates

    International Nuclear Information System (INIS)

    The goal of this work is to improve our knowledge on the actinide-ligand bond properties. To this end, the hexacyanoferrate entities have been used as pre-organized ligand. We have synthesized, using mild chemistry, the following series of complexes: AnIV[FeII(CN)6].xH2O (An = Th, U, Np, Pu); AmIII[FeIII(CN)6].xH2O; Pu III[CoIII(CN)6].xH2O and K(H?)AnIII[FeII(CN)6].xH2O (An = Pu, Am). The metal oxidation states have been obtained thanks to the νCN, stretching vibration and to the actinide LIII absorption edge studies. As Prussian Blue, the AnIV[FeII(CN)6].xH2O (An = Np, Pu) are class II of Robin and Day compounds. X-ray Diffraction has shown besides that these complexes crystallize in the P63/m space group, as the isomorphic LaKFe(CN)6.4H2O complex used as structural model. The EXAFS oscillations at the iron K edge and at the An LIII edge allowed to determine the An-N, An-O, Fe-C and Fe-N distances. The display of the multiple scattering paths for both edges explains the actinide contribution absence at the iron edge, whereas the iron signature is present at the actinide edge. We have shown that the actinide coordination sphere in actinides hexa-cyanoferrates is comparable to the one of lanthanides. However, the actinides typical behavior towards the lanthanides is brought to the fore by the AnIV versus LnIII ions presence in this family of complexes. Contrarily to the 4f electrons, the 5f electrons influence the electronic properties of the compounds of this family. However, the gap between the An-N and Ln-N distances towards the corresponding metals ionic radii do not show any covalence bond evolution between the actinide and lanthanide series. (author)

  18. 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.

  19. Probing the 12C-12C and 12C-16O molecular states by radiative capture reactions: present status and future

    International Nuclear Information System (INIS)

    Complete γ-decay in the 12C(12C,γ)24Mg and 12C(16O,γ)28Si reactions has been measured at energies close to the Coulomb Barrier using the DRAGON spectrometer and its associated BGO γ-array at the TRIUMF facility. The experimental data show an important feeding of doorway states around 10-11 MeV in both reactions. Comparisons with simulations allow to extract the full capture cross section and the main spin involved in the process. Different models are confronted to the results: completely statistical, semi-statistical with an unique entrance spin and cluster. The resolution of the BGO enables to eliminate a fully statistical scenario but is not enough to disentangle the two remaining scenarios. It is shown that the future PARIS array composed of the recently developed LaBr3 scintillators will have capabilities to distinguish between these two scenarios. (authors)

  20. Crystal Structures of Precise Functional Copolymers: Atomistic Molecular Dynamics Simulations and Comparisons with Experiments

    Science.gov (United States)

    Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.

    Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.

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

    Directory of Open Access Journals (Sweden)

    Huanyu Wang

    2013-11-01

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

  2. Linking microbial community structure to biogeochemical function in coastal marine sediments: Stable isotope probing combined with magnetic bead capture

    OpenAIRE

    Stal, L.J.; Boschker, H.T.S.; Miyatake, T.

    2011-01-01

    Microbial community structure and its biogeochemical functions in marine sediments can be successfully linked by using the improved Mag-SIP method in combination with other approaches. In this thesis, we were able to provide detailed information on the microorganisms responsible for the utilization of major substrates in marine sediments. It was shown that a number of important groups in the microbial community played a broader role than expected. Some surprising results are that oxygenic pho...

  3. 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 < 0.001) contents of oil (44.54 vs 41.42% dry matter (DM)) and CP (24.94 vs 20.91% DM) compared to those of the brown-seeded varieties. The CP in yellow seeds contained lower (P < 0.01) contents of true protein subfraction (81.31 vs 92.71% CP) and more (P < 0.001) extensively degraded (70.8 vs 64.9% CP) in rumen resulting in lower (P < 0.001) content of 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. PMID:24931851

  4. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    Science.gov (United States)

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  5. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry.

    Science.gov (United States)

    May, Jody Christopher; Gant-Branum, Randi Lee; McLean, John Allen

    2016-06-01

    Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine. PMID:27132126

  6. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    Energy Technology Data Exchange (ETDEWEB)

    Tiwari, Sanat Kumar, E-mail: sanat-tiwari86@yahoo.co.in; Das, Amita; Sen, Abhijit; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar - 382428 (India)

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  7. Molecular Structures and Mechanical Properties of Microbe Rapid Coagulation Natural Rubber

    Institute of Scientific and Technical Information of China (English)

    LIANG Yue; HUANG Mao-Fang; ZENG Zong-Qiang

    2011-01-01

    In this work,molecular structures,dynamic mechanical properties and glass transition temperatures of microbe coagulated natural rubber(NR) samples were analyzed by using pyrolysis gas chromatography-mass spectrometry(py-GC/MS),rubber process analyzer(RPA) and dynamic mechanical thermal analysis(DMA).And the cross-linked network structures and mechanical properties of the corresponding NR vulcanizates were further determined by using nuclear magnetic resonance(NMR) crosslink density spectrometer(XLDS-15) and universal testing machines.The results show that NR raw rubber produced by rapidly coagulated with microorganism exhibits a simple molecular structure composition and good dynamic mechanical properties,and the corresponding NR vulcanizates possess the aggregation structure of high cross-linked density,a high glass transition temperature of-61.5 ℃ and high mechanical properties(tensile strength reaches 25.2 MPa),as compared with that coagulated with acetic acid.

  8. NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

    CERN Document Server

    1984-01-01

    That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

  9. Atomic and molecular physics, physicochemical properties of biologically important structure, and high-voltage research

    International Nuclear Information System (INIS)

    Research in atomic and molecular physics is reported. Studies included: experimental evidence for the existence of a Ramsauer-Townsend minimum in liquid methane and liquid argon; discovery of a Ramsauer-Townsend minimum in gaseous ethane and propane; motion of thermal electrons in n-alkane vapors; electron mobilities in high pressure gases; electron capture and drift in liquid media; electron attachment to molecules in dense gases; attachment of slow electrons to hexafluorobenzene; fragmentation of atmospheric halocarbons under electron impact; negative ion resonances and threshold electron excitation spectra of organic molecules; theoretical studies of negative-ion resonance states of organic molecules; kinetics of electron capture by sulfur hexafluoride in solution; interactions of slow electrons with benzene and benzene derivatives; Stokes and anti-Stokes fluorescence of 1 : 12-benzoperylene in solution; photoionization of molecules in liquid media; construction of high-voltage breakdown apparatus for gaseous insulation studies; measurements of the breakdown strengths of gaseous insulators and their relation to basic electron-collision processes; accuracy of the breakdown voltage measurements; and assembling basic data on electronegative gases of significance to breakdown

  10. Molecular dynamics modelling of mechanical properties of polymers for adaptive aerospace structures

    Science.gov (United States)

    Papanikolaou, Michail; Drikakis, Dimitris; Asproulis, Nikolaos

    2015-02-01

    The features of adaptive structures depend on the properties of the supporting materials. For example, morphing wing structures require wing skin materials, such as rubbers that can withstand the forces imposed by the internal mechanism while maintaining the required aerodynamic properties of the aircraft. In this study, Molecular Dynamics and Minimization simulations are being used to establish well-equilibrated models of Ethylene-Propylene-Diene Monomer (EPDM) elastomer systems and investigate their mechanical properties.

  11. Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

    Institute of Scientific and Technical Information of China (English)

    YAN; Han; ZHU; HaoMiao; SHEN; Jian

    2007-01-01

    Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The results showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".

  12. One-Dimensional Palladium Wires: Influence of Molecular Changes on Supramolecular Structure

    OpenAIRE

    Campbell, Michael Glenn; Zheng, Shao-Liang; Ritter, Tobias

    2013-01-01

    Nanostructured materials based on one-dimensional (1D) metal wires are of potential utility; however, to date, there is a lack of synthetic methods that allow for variation of structure and therefore properties. Here we report the use of molecular control elements to alter the solid-state structures of 1D palladium wires, including Pd–Pd bond distances and the porosity of the supramolecular framework.

  13. Molecular Dynamics Study on Mechanical Properties in the Structure of Self-Assembled Quantum Dot

    OpenAIRE

    Tatsuya Yamaguchi; Ken-ichi Saitoh

    2012-01-01

    Stress and strain in the structure of self-assembled quantum dots constructed in the Ge/Si(001) system is calculated by using molecular dynamics simulation. Pyramidal hut cluster composed of Ge crystal with {105} facets surfaces observed in the early growth stage are computationally modeled. We calculate atomic stress and strain in relaxed pyramidal structure. Atomic stress for triplet of atoms is approximately defined as an average value of pairwise (virial) quantity inside triplet, which is...

  14. Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers

    DEFF Research Database (Denmark)

    Nilsson, Louis; Sljivancanin, Zeljko; Balog, Richard; Xu, Wei; Linderoth, Trolle René; Lægsgaard, Erik; Stensgaard, Ivan; Hammer, Bjørk; Besenbacher, Flemming; Hornekær, Liv

    2012-01-01

    Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen. The...... method can in principle be applied to obtain nanopatterned hydrogen structures on free standing graphene and graphene laid down on insulating substrates, hereby opening up for the possibility of substrate independent bandgap engineering of graphene....

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

    OpenAIRE

    Giuseppe Mele; Małgorzata A. Broda; Krzysztof Ejsmont; Gabriela Dyrda; Rudolf Słota

    2011-01-01

    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 repr...

  16. Presentation of thermodynamic functions of isotopic forms using terms of molecular structure

    International Nuclear Information System (INIS)

    Precise mathematical representation of vibration contributions to thermodynamic functions and to their isotopic differences as a matrix of contributions of natural vibration coordinates associated with structural elements of a molecule is developed. The obtained representation permit to unambiguously interpret the given values in terms of molecular structure without using the notion of vibration frquency. It is shown to have essential advantages at interpretation of isotopic effects

  17. Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic

    OpenAIRE

    Kirchhausen, Tom; Owen, David; Harrison, Stephen C.

    2014-01-01

    Clathrin is a molecular scaffold for vesicular uptake of cargo at the plasma membrane, where its assembly into cage-like lattices underlies the clathrin-coated pits of classical endocytosis. This review describes the structures of clathrin, major cargo adaptors, and other proteins that participate in forming a clathrin-coated pit, loading its contents, pinching off the membrane as a lattice-enclosed vesicle, and recycling the components. It integrates as much of the structural information as ...

  18. Molecular dynamics of folding of secondary structures in Go-type models of proteins

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek

    1999-01-01

    We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamic...

  19. EMBEDDED MOLECULAR CLUSTER APPROACH TO THE ELECTRONIC STRUCTURE OF AMORPHOUS AND LIQUID METALS

    OpenAIRE

    Delley, B.; Ellis, D.; Freeman, A

    1980-01-01

    In this approach to the electronic structure of amorphous and liquid metals, we represent the system by molecular clusters which are embedded in an external potential chosen as a suitable representation of the rest of the system. We have determined the electronic structure of a number of Cu, Zr and Cu-Zr clusters using the self-consistent discrete variational-LCAO approach within local density functional theory. Effects due to deviations from perfect crystalline symmetry are analyzed. Total d...

  20. 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

    2016-09-01

    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. PMID:27235585

  1. Statistical tests for the detection of intermediate structure: Application to the structure of the 238U neutron capture cross section between 5 keV and 0.1 MeV

    International Nuclear Information System (INIS)

    Recent measurements of the 238U neutron capture cross section show a considerable amount of fluctuation between 5 and 100 keV. Statistical tests performed on the measured cross section suggest that the fluctuations are not compatible with the statistical model of nuclear reactions and imply the existence of intermediate structure, which is interpreted in terms of doorway states. The validity of the statistical tests used here is confirmed by numerical experiments with simulated cross sections generated by the Monte Carlo method, in accordance with the statistical method. The behavior of the capture cross section is compared to those of the subthreshold fission cross section and of the inelastic scattering cross section. The threshold anomaly at the opening of the inelastic channel at 45 keV is seen in the form of a rounded step

  2. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    Science.gov (United States)

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  3. Structural organization of surfactant aggregates in vacuo: a molecular dynamics and well-tempered metadynamics study.

    Science.gov (United States)

    Longhi, Giovanna; Fornili, Sandro L; Turco Liveri, Vincenzo

    2015-07-01

    Experimental investigations using mass spectrometry have established that surfactant molecules are able to form aggregates in the gas phase. However, there is no general consensus on the organization of these aggregates and how it depends on the aggregation number and surfactant molecular structure. In the present paper we investigate the structural organization of some surfactants in vacuo by molecular dynamics and well-tempered metadynamics simulations to widely explore the space of their possible conformations in vacuo. To study how the specific molecular features of such compounds affect their organization, we have considered as paradigmatic surfactants, the anionic single-chain sodium dodecyl sulfate (SDS), the anionic double-chain sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and the zwitterionic single-chain dodecyl phosphatidyl choline (DPC) within a wide aggregation number range (from 5 to 100). We observe that for low aggregation numbers the aggregates show in vacuo the typical structure of reverse micelles, while for large aggregation numbers a variety of globular aggregates occur that are characterized by the coexistence of interlaced domains formed by the polar or ionic heads and by the alkyl chains of the surfactants. Well-tempered metadynamics simulations allows us to confirm that the structural organizations obtained after 50 ns of molecular dynamics simulations are practically the equilibrium ones. Similarities and differences of surfactant aggregates in vacuo and in apolar media are also discussed. PMID:26050747

  4. Relationship between chemical structure and the occupational asthma hazard of low molecular weight organic compounds

    OpenAIRE

    Jarvis, J; Seed, M; Elton, R; Sawyer, L.; Agius, R.

    2005-01-01

    Aims: To investigate quantitatively, relationships between chemical structure and reported occupational asthma hazard for low molecular weight (LMW) organic compounds; to develop and validate a model linking asthma hazard with chemical substructure; and to generate mechanistic hypotheses that might explain the relationships.

  5. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38. ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.300, year: 2014

  6. 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...

  7. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures...

  8. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  9. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...

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

    CERN Document Server

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

    2002-01-01

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

  11. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    Science.gov (United States)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  12. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    International Nuclear Information System (INIS)

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample

  13. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    Science.gov (United States)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  14. Loading Actinides in Multilayered Structures for Nuclear Waste Treatment: The First Case Study of Uranium Capture with Vanadium Carbide MXene.

    Science.gov (United States)

    Wang, Lin; Yuan, Liyong; Chen, Ke; Zhang, Yujuan; Deng, Qihuang; Du, Shiyu; Huang, Qing; Zheng, Lirong; Zhang, Jing; Chai, Zhifang; Barsoum, Michel W; Wang, Xiangke; Shi, Weiqun

    2016-06-29

    Efficient nuclear waste treatment and environmental management are important hurdles that need to be overcome if nuclear energy is to become more widely used. Herein, we demonstrate the first case of using two-dimensional (2D) multilayered V2CTx nanosheets prepared by HF etching of V2AlC to remove actinides from aqueous solutions. The V2CTx material is found to be a highly efficient uranium (U(VI)) sorbent, evidenced by a high uptake capacity of 174 mg g(-1), fast sorption kinetics, and desirable selectivity. Fitting of the sorption isotherm indicated that the sorption followed a heterogeneous adsorption model, most probably due to the presence of heterogeneous adsorption sites. Density functional theory calculations, in combination with X-ray absorption fine structure characterizations, suggest that the uranyl ions prefer to coordinate with hydroxyl groups bonded to the V-sites of the nanosheets via forming bidentate inner-sphere complexes. PMID:27267649

  15. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    Science.gov (United States)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    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 are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  16. Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier

    Science.gov (United States)

    Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

    2003-03-01

    Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  17. IR spectrum simulation of molecular structure model of Shendong coal vitrinite by using quantum chemistry method.

    Science.gov (United States)

    Jia, Jian-Bo; Wang, Ying; Li, Feng-Hai; Yi, Gui-Yun; Zeng, Fan-Gui; Guo, Hong-Yu

    2014-01-01

    The structure of coal needs to be understood from a molecular point of view for clean, effective and high value-added utilization of coal. In the literature, molecular structure model of Shendong coal vitrinite (SV) was established by the authors on the basis of experimental results of ultimate analysis and 13C NMR, and the calculated 13C NMR spectrum of SV model was consistent with the experimental spectrum. In order to further verify the accuracy of SV structure model established by the authors, the infrared spectrum of SV structure model was calculated using quantum chemistry semi-empirical VAMP in this thesis. The results showed that the peak shape of calculated IR spectrum of SV structure model was similar to the experiment's, but the wave number of calculated IR spectrum was obviously higher than that of experimental spectrum. According to the calculated results for model compounds by using the same method, calculated vibrational frequency was higher than that of experiment for the same functional groups. Hence, the calculated IR spectrum should be corrected. After correction the calculated IR spectrum of SV structure model matched well with the experimental spectrum. In other words, the SV structure model can truly reflect the structure characteristics of SV. PMID:24783531

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

    International Nuclear Information System (INIS)

    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

  19. Structure and stability of copper clusters: A tight-binding molecular dynamics study

    International Nuclear Information System (INIS)

    In this paper we propose a tight-binding molecular dynamics with parameters fitted to first-principles calculations on the smaller clusters and with an environment correction, to be a powerful technique for studying large transition-metal/noble-metal clusters. In particular, the structure and stability of Cun clusters for n=3-55 are studied by using this technique. The results for small Cun clusters (n=3-9) show good agreement with ab initio calculations and available experimental results. In the size range 10≤n≤55 most of the clusters adopt icosahedral structure which can be derived from the 13-atom icosahedron, the polyicosahedral 19-, 23-, and 26-atom clusters, and the 55-atom icosahedron, by adding or removing atoms. However, a local geometrical change from icosahedral to decahedral structure is observed for n=40-44 and return to the icosahedral growth pattern is found at n=45 which continues. Electronic 'magic numbers' ( n=2, 8, 20, 34, 40) in this regime are correctly reproduced. Due to electron pairing in highest occupied molecular orbitals (HOMOs), even-odd alternation is found. A sudden loss of even-odd alternation in second difference of cluster binding energy, HOMO-LUMO (LUMO, lowest unoccupied molecular orbital) gap energy and ionization potential is observed in the region n∼40 due to structural change there. Interplay between electronic and geometrical structure is found

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

    Energy Technology Data Exchange (ETDEWEB)

    Albahri, Tareq A., E-mail: toalbahri@gmail.com; Aljasmi, Abdulla F.

    2013-09-20

    Highlights: • ΔH°{sub f} is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH°{sub f} with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH°{sub 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.

  1. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

    CERN Document Server

    Singh, Raghvendra Pratap; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...

  2. Structure-activity relationship study between baicalein and wogonin by spectrometry, molecular docking and microcalorimetry.

    Science.gov (United States)

    Tu, Bao; Li, Rong-Rong; Liu, Zhi-Juan; Chen, Zhi-Feng; Ouyang, Yu; Hu, Yan-Jun

    2016-10-01

    Flavones (e.g. baicalein and wogonin) extensively used worldwide in food preparation and traditional medicine. In this study, a systematically comparative study of their structure-activity relationships (SAR) on their interaction with BSA, antioxidant activity and antibacterial activity has been carried out by spectrometry, molecular docking and microcalorimetry. Our results show that the skeleton structure of flavones, the number of hydroxyl groups, the type of functional group, conjugated system and the steric hindrance may be responsible for their different biological activity. These findings not only would lay a scientific foundation for discovering and designing flavones-based food and drug, may also help us to understanding the structure-activity relationship between flavones at the molecular level. PMID:27132840

  3. Molecular Dynamics Study of Carbon Nanotubes/Polyamide Reverse Osmosis Membranes: Polymerization, Structure, and Hydration.

    Science.gov (United States)

    Araki, Takumi; Cruz-Silva, Rodolfo; Tejima, Syogo; Takeuchi, Kenji; Hayashi, Takuya; Inukai, Shigeki; Noguchi, Toru; Tanioka, Akihiko; Kawaguchi, Takeyuki; Terrones, Mauricio; Endo, Morinobu

    2015-11-11

    Carbon nanotubes/polyamide (PA) nanocomposite thin films have become very attractive as reverse osmosis (RO) membranes. In this work, we used molecular dynamics to simulate the influence of single walled carbon nanotubes (SWCNTs) in the polyamide molecular structure as a model case of a carbon nanotubes/polyamide nanocomposite RO membrane. It was found that the addition of SWCNTs decreases the pore size of the composite membrane and increases the Na and Cl ion rejection. Analysis of the radial distribution function of water confined in the pores of the membranes shows that SWCNT+PA nanocomposite membranes also exhibit smaller clusters of water molecules within the membrane, thus suggesting a dense membrane structure (SWCNT+PA composite membranes were 3.9% denser than bare PA). The results provide new insights into the fabrication of novel membranes reinforced with tubular structures for enhanced desalination performance. PMID:26505521

  4. Molecular dynamics simulations of silicate and borate glasses and melts : structure, diffusion dynamics and vibrational properties

    OpenAIRE

    Scherer, Christoph

    2015-01-01

    Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...

  5. Molecular size distribution and structure investigations of humic substances in groundwater

    International Nuclear Information System (INIS)

    A non-ionic macroporous polymeric sorbent DAX-8 was applied to the isolation of humic and fulvic acids from groundwater. This procedure was able to isolate approximately 40% of the DOC as humic solutes. For the investigation of the structure and molecular size distribution of the isolated humic solutes, the hyphenated SEC-ESIMS system with a quadrupole mass spectrometer and a UV detector were utilized. For the higher-molecular-weight humic acids, the ESI-MS loses sensitivity compared with the parallel UV detection, because of the difficulty in getting the ionized humic compounds to fly efficiently through the mass spectrometer. (orig.)

  6. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity.

    Science.gov (United States)

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-07-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  7. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    CERN Document Server

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  8. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    Directory of Open Access Journals (Sweden)

    Yajiang Hao

    2015-07-01

    Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  9. Distant electron tunneling controlled by external fields in molecular nano structures

    International Nuclear Information System (INIS)

    The influence of stochastic, periodic, and magnetic fields on a long-range electron tunneling in donor - bridge - acceptor and electrode - molecular wire - electrode structures is studied theoretically. The description of a bridge-mediated electron tunneling between donor and acceptor groups is shown to be possible via the introduction of effective transfer rates. The principal distinction in the dependence of low-temperature elastic and inelastic tunnel currents mediated by a molecular wire with bridging paramagnetic ions on an applied magnetic field is considered. The appearance of the field-induced inversion and suppression effects is widely discussed

  10. The structure and molecular orientation of polytetrafluoroethylene coatings deposited from active gas phase

    International Nuclear Information System (INIS)

    The molecular structure of polytetrafluoroethylene (PTFE) coatings deposited on aluminium substrates was investigated by the method of attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR). It has been shown experimentally that PTFE coatings deposited by the electron-beam dispersion method have molecular orientation and are ordered nonmonotonously during the process of coating growth. Maximum order and orientation of molecules along the normal to the substrate are observed in an interfacial layer located within up to 100 nm to the substrate. The observed morphological and orientation features of the formed layers were explained using the proposed adsorption-diffusion mechanism of polymer coating formation.

  11. Structural and Dynamic Properties of Amorphous Silicon:Tight-Binding Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    HUANG Shi-Ping; WANG Wen-Chuan

    2004-01-01

    @@ The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Ql are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.

  12. Molecules and Models The molecular structures of main group element compounds

    CERN Document Server

    Haaland, Arne

    2008-01-01

    This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

  13. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  14. Demonstration of molecular beam epitaxy and a semiconducting band structure for I-Mn-V compounds

    International Nuclear Information System (INIS)

    Our ab initio theory calculations predict a semiconducting band structure of I-Mn-V compounds. We demonstrate on LiMnAs that high-quality materials with group-I alkali metals in the crystal structure can be grown by molecular beam epitaxy. Optical measurements on the LiMnAs epilayers are consistent with the theoretical electronic structure. Our calculations also reproduce earlier reports of high antiferromagnetic ordering temperature and predict large, spin-orbit-coupling-induced magnetic anisotropy effects. We propose a strategy for employing antiferromagnetic semiconductors in high-temperature semiconductor spintronics.

  15. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob; Jacobsen, Karsten Wedel; Braun, K.F.; Rieder, K.H.; Laegsgaard, E.; Besenbacher, Flemming

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the...... simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  16. THE ROTATING MOLECULAR STRUCTURES AND THE IONIZED OUTFLOW ASSOCIATED WITH IRAS 16547-4247

    International Nuclear Information System (INIS)

    We present Very Large Array 1.3 cm radio continuum and water maser observations as well as Submillimeter Array SO2 (226.300 GHz) and 1.3 mm dust continuum observations toward the massive star formation region IRAS 16547-4247. We find evidence of multiple sources in the central part of the region. There is evidence of a rotating structure associated with the most massive of these sources, traced at small scales (∼50 AU) by the water masers. At large scales (∼1000 AU), we find a velocity gradient in the SO2 molecular emission with a barely resolved structure that can be modeled as a rotating ring or two separate objects. The velocity gradients of the masers and of the molecular emission have the same sense and may trace the same structure at different size scales. The position angles of the structures associated with the velocity gradients are roughly perpendicular to the outflow axis observed in radio continuum and several molecular tracers. We estimate the mass of the most massive central source to be around 30 solar masses from the velocity gradient in the water maser emission. The main source of error in this estimate is the radius of the rotating structure. We also find water masers that are associated with the large-scale molecular outflow of the system, as well as water masers that are associated with other sources in the region. Our results suggest that the formation of this source, one of the most luminous protostars or protostellar clusters known, is taking place with the presence of ionized jets and disk-like structures.

  17. Fine- and hyperfine-structure effects in molecular photoionization: II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

    CERN Document Server

    Germann, Matthias

    2016-01-01

    Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine- structure effects in one-photon ionization of molecules presented in the preceding companion article. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ioni...

  18. Molecular early main group metal hydrides: synthetic challenge, structures and applications.

    Science.gov (United States)

    Harder, Sjoerd

    2012-11-25

    Within the general area of early main group metal chemistry, the controlled synthesis of well-defined metal hydride complexes is a rapidly developing research field. As group 1 and 2 metal complexes are generally highly dynamic and lattice energies for their [MH](∞) and [MH(2)](∞) salts are high, the synthesis of well-defined soluble hydride complexes is an obvious challenge. Access to molecular early main group metal hydrides, however, is rewarding: these hydrocarbon-soluble metal hydrides are highly reactive, have found use in early main group metal catalysis and are potentially also valuable molecular model systems for polar metal hydrides as a hydrogen storage material. The article focusses specifically on alkali and alkaline-earth metal hydride complexes and discusses the synthetic challenge, molecular structures, reactivity and applications. PMID:23012695

  19. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    Science.gov (United States)

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

    2014-01-01

    Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder. PMID:24816101

  20. Unoccupied electronic structure and molecular orientation of rubrene; from evaporated films to single crystals

    Science.gov (United States)

    Ueba, T.; Park, J.; Terawaki, R.; Watanabe, Y.; Yamada, T.; Munakata, T.

    2016-07-01

    Two-photon photoemission (2PPE) spectroscopy and ultraviolet photoemission spectroscopy (UPS) have been performed for rubrene single crystals and evaporated thin films on highly oriented pyrolytic graphite (HOPG). The changes in the 2PPE intensity from the single crystals by the polarization of the light and by the angle of the light incident plane against the crystalline axes indicate that the molecular arrangement on the surface is similar to that in the bulk crystal. On the other hand, in the case of evaporated films, the polarization dependence of 2PPE indicates that the tetracene backbone becomes standing upright as the thickness increases. In spite of the alignment of molecules, the broadened 2PPE spectral features for thick films suggest that the films are amorphous and molecules are in largely different environments. The film structures are confirmed by scanning tunneling microscopy (STM). The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) derived levels of the single crystal are shifted by + 0.18 and - 0.20 eV, respectively, from those of the 0.8 ML film. The shifts are attributed to the packing density of molecules. It is shown that the unoccupied electronic structure is more sensitively affected by the film structure than the occupied electronic structure.

  1. Method for predicting the standard net heat of combustion for pure hydrocarbons from their molecular structure

    International Nuclear Information System (INIS)

    Highlights: • QSPR method predicts ΔHc∘ of pure hydrocarbons from their molecular structures alone. • The method is better than others in terms of simplicity and accuracy. • ΔHc∘ is calculated using a simple correlation. • The calculated values of 32 atom-type groups predict ΔHc∘ with 0.71% error and 0.998 R2. • The method is notable for being the first to predict ΔHc∘ of hydrocarbon isomers. - Abstract: A group contribution method is used to predict the standard net heat of combustion of pure hydrocarbons from their molecular structures. A multivariable nonlinear regression based on the least square method was used to arrive at a set of 32 atom-type structural groups that can best represent the standard net heat of combustion for about 452 pure hydrocarbon substances. The proposed method is very simple, requires no experimental data, and can predict the standard net heat of combustion from the knowledge of the molecular structure alone with an average absolute error of 0.71% and a correlation coefficient of 0.9982. The method can predict the standard net heat of combustion of hydrocarbon isomers as well

  2. Molecular dynamics studies on the structural stability of wild-type dog prion protein.

    Science.gov (United States)

    Zhang, Jiapu; Liu, David D W

    2011-06-01

    Prion diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) and chronic wasting disease in cattle are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601-2614 (2008)). Thus, it is very worth studying the molecular structures of dog prion protein to obtain insights into the immunity of dogs to prion diseases. This paper studies the molecular structural dynamics of wild-type dog prion protein. The comparison analyses with rabbit prion protein show that the dog prion protein has stable molecular structures whether under neutral or low pH environments. We also find that the salt bridges such as D177-R163 contribute to the structural stability of wild-type rabbit prion protein under neutral pH environment. PMID:21469747

  3. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    International Nuclear Information System (INIS)

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder

  4. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

    2014-05-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  5. Complex Structure in Class 0 Protostellar Envelopes II: Kinematic Structure from Single-Dish and Interferometric Molecular Line Mapping

    CERN Document Server

    Tobin, John J; Chiang, Hsin-Fang; Looney, Leslie W; Bergin, Edwin A; Chandler, Claire J; Masque, Josep M; Maret, Sebastien; Heitsch, Fabian

    2011-01-01

    We present a study of dense molecular gas kinematics in seventeen nearby protostellar systems using single-dish and interferometric molecular line observations. The non-axisymmetric envelopes around a sample of Class 0/I protostars were mapped in the N2H+ (J=1-0) tracer with the IRAM 30m, CARMA and PdBI as well as NH3 (1,1) with the VLA. The molecular line emission is used to construct line-center velocity and linewidth maps for all sources to examine the kinematic structure in the envelopes on spatial scales from 0.1 pc to ~1000 AU. The direction of the large-scale velocity gradients from single-dish mapping is within 45 degrees of normal to the outflow axis in more than half the sample. Furthermore, the velocity gradients are often quite substantial, the average being ~2.3 km\\s\\pc. The interferometric data often reveal small-scale velocity structure, departing from the more gradual large-scale velocity gradients. In some cases, this likely indicates accelerating infall and/or rotational spin-up in the inner...

  6. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    Science.gov (United States)

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule. PMID:25233034

  7. Investigation of Terminal Group Effect on Electron Transport Through Open Molecular Structures

    International Nuclear Information System (INIS)

    The effect of terminal groups on the electron transport through metal-molecule-metal system has been investigated using nonequilibrium Green's function (NEGF) formalism combined with extended Huckel theory (EHT). Au-molecule-Au junctions are constructed with borazine and BCN unit structure as core molecule and sulphur (S), oxygen (O), selenium (Se) and cyano-group (CN) as terminal groups. The electron transport characteristics of the borazine and BCN molecular systems are analyzed through the transmission spectra and the current-voltage curve. The results demonstrate that the terminal groups modifying the transport behaviors of these systems in a controlled way. Our result shows that, selenium is the best linker to couple borazine to Au electrode and oxygen is the best one to couple BCN to Au electrode. Furthermore, the results of borazine systems are compared with that of BCN molecular systems and are discussed. Simulation results show that the conductance through BCN molecular systems is four times larger than the borazine molecular systems. Negative differential resistance behavior is observed with borazine-CN system and the saturation feature appears in BCN systems. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  8. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    Science.gov (United States)

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

  9. Molecular structure in correlation with electrochemical properties of mixed-ligand cobalt(III complexes

    Directory of Open Access Journals (Sweden)

    K. BABIĆ-SAMARDZIJA

    2008-07-01

    Full Text Available Four mixed-ligand cobalt(III complexes (1–4 of the general formula [Co(Rdtccyclam](ClO42 and [Co(Raccyclam](ClO42 (cyclam = 1,4,8,11-tetraazacyclotetradecane; Rdtc = thiomorpholine-(Timdtc or 2-methylpiperidine-(2-Mepipdtc dithiocarbamates; Rac = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionato (Hfac or 2,2,6,6-tetramethyl-3,5-heptanedionato (Tmhd, respectively were electro­chemically examined on a glassy carbon and an iron electrode in perchloric acid solution. The obtained results showed the influence of these complexes on hydrogen evolution, the oxygen reduction reaction and iron dissolution. The exhibited effects of the complexes on these reactions depend on structure related to the bidentate dithiocarbamato or b-diketonato ligand. The electrochemical properties of the complexes were correlated with molecular structure and parameters derived from spectral analysis and molecular modeling.

  10. Molecular dynamical and structural studies for the bakelite by neutron cross section measurements

    International Nuclear Information System (INIS)

    Neutron reaction cross sections were determined by transmission and scattering measurements, to study the dynamics and molecular structure of calcined bakelites. Total cross sections were determined, with a deviation smaller than 5%, from the literature values, by neutron transmission method and a specially devised approximation. These cross sections were then correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. Double differential scattering cross sections, scattering law values and frequency distributions were determined with 15% error using the neutron inelastic scattering method. The frequency distributions as well as the overall results from all experimental techniques used in this work allowed to suggest a structural model like polycyclic hydrocarbons, for calcined bakelite at 8000 C. (author)

  11. Molecular Dynamics Simulation of the Structure and Properties of Lithium Phosphate Glasses

    Energy Technology Data Exchange (ETDEWEB)

    Liang, J-J; Cygan, R.T.; Alam, T.M.

    1999-07-09

    A new forcefield model was developed for the computer simulation of phosphate materials that have many important applications in the electronics and biomedical industries. The model provides a fundamental basis for the evaluation of phosphate glass structure and thermodynamics. Molecular dynamics simulations of a series of lithium phosphate glass compositions were performed using the forcefield model. A high concentration of three-membered rings (P{sub 3}O{sub 3}) occurs in the glass of intermediate composition (0.2 Li{sub 2}O {center_dot} 0.8P{sub 2}O{sub 5}) that corresponds to the minimum in the glass transition temperature curve for the compositional series. Molecular orbital calculations of various phosphate ring clusters indicate an increasing stabilization of the phosphate ring structure going from two- to four-membered rings.

  12. A nitrogen-vacancy spin based molecular structure microscope using multiplexed projection reconstruction

    CERN Document Server

    Lazariev, Andrii

    2015-01-01

    Methods and techniques to measure and image beyond the state-of-the-art have always been influential in propelling basic science and technology. Because current technologies are venturing into nanoscopic and molecular-scale fabrication, atomic-scale measurement techniques are inevitable. One such emerging sensing method uses the spins associated with nitrogen-vacancy (NV) defects in diamond. The uniqueness of this NV sensor is its atomic size and ability to perform precision sensing under ambient conditions conveniently using light and microwaves (MW). These advantages have unique applications in nanoscale sensing and imaging of magnetic fields from nuclear spins in single biomolecules. During the last few years, several encouraging results have emerged towards the realization of an NV spin-based molecular structure microscope. Here, we present a projection-reconstruction method that retrieves the three-dimensional structure of a single molecule from the nuclear spin noise signatures. We validate this method ...

  13. Equilibrium and dynamics of ionic solutions and molten salts: from the primitive model to molecular structures

    International Nuclear Information System (INIS)

    In this HDR (Accreditation to supervise researches) thesis, the author first recalls his research thesis work which addressed the study of structural properties of simple electrolyte solutions by neutron scattering and interpretation by using integral equations of statistic mechanics. He also evokes other related research works he supervised, and more recent research works he performed on a GDR Practis issue (the solubility of ionic compounds) in collaboration with German and Italian researchers. Thus, the author describes how his scientific activity has known a double evolution: on the experimental point of view (determination of scattering coefficients on long durations), and on the modelling point of view (transition from a model based on a continuous solvent to a model based on molecular structures, which meant a transition from integral equations of Brownian dynamics to a molecular dynamics)

  14. Molecular Weight and Proposed Structure of the Angelica sinensis Polysaccharide-iron Complex

    Institute of Scientific and Technical Information of China (English)

    WANG,Kai-Ping; CHEN,Zhi-Xiang; ZHANG,Yu; WANG,Pei-Pei; WANG,Ji-Hong; DAI,Li-Quan

    2008-01-01

    The molecular weight and the proposed structure of the Angelica sinensis polysaccharide-iron complex (APIC) were studied.Fourier transform infrared spectroscopy,X-ray powder diffraction,differential scanning calorimetry,transmission electron microscopy,electron paramagnetic resonance,thermogravimetric analysis,atomic force microscopy,and gel filtration chromatography were used to characterize APIC,which is a macromolecule complex composed of Angelica sinensis polysaccharide (ASP) and iron.The structure of APIC was proposed to be a polynuclear ferrihydrite core chelated firmly by an encircling framework of ASP chains,forming a core molecule,which is surrounded by a removable outer protective sheath of colloidal ASP.And the molecular formula of APIC was proposed to be { [(Fe2O3·2.2H2O)1043(ASP)32](ASP)12 },with MW=270000 Da.

  15. Effect of molecular structure on the thermal properties and water sorption of thin gelatin films

    International Nuclear Information System (INIS)

    The thin gelatin films, prepared by casting of gelatin solutions at different drying temperatures, had different molecular morphologies as monitored, using wide angle X-ray diffraction and differential scanning calorimetry techniques. It was revealed that gelatin films dried at lower temperatures showed markedly higher crystalline or helical structure with slightly higher Tg and lower ΔCp than those for the hot dried film with more coiled structure. These films exhibited different interactions with water, which were assessed, using dynamic vapour sorption experiments. The sorption capacity of these films increased with increasing the degree of molecular order. There was no difference between the diffusion coefficients obtained upon sorption and desorption steps for each gelatin samples. The diffusion coefficient did not show any significant dependence on water content

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

    OpenAIRE

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit

    2014-01-01

    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 superla...

  17. Molecular Simulation Study on the Influence of Dimethylsulfoxide on the Structure of Phospholipid Bilayers

    OpenAIRE

    Sum, Amadeu K.; de Pablo, Juan J.

    2003-01-01

    Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayer/water systems were performed in the presence of dimethylsulfoxide (DMSO) at 2, 5, 10, and 100 mol % DMSO (lipid-free basis). The equilibrium structure and several dynamic properties were determined for these systems. Results show that DMSO penetrates much deeper into the bilayer than water does. It is also found that DMSO molecules do not interact with the polar groups of the lipid headgroup, but exhibit a p...

  18. The relationship between crystal structure and NMR relaxation in molecular solids with tert-butyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Rheingold, Arnold L.; DiPasquale, Antonio G. [Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (United States); Beckmann, Peter A. [Department of Physics, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, PA 19010-2899 (United States)], E-mail: pbeckman@brynmawr.edu

    2008-04-03

    We correlate an X-ray determination of the molecular and crystal structures of 2-tert-butylanthracene and 2-tert-butylanthraquinone reported here with the previously reported dynamical nuclear magnetic resonance determination of the motions of the tert-butyl groups and their resident methyl groups in the solid state [P.A. Beckmann, K.S. Burbank, M.M.W. Lau, J.N. Ree, T.L. Weber, Chem. Phys. 290 (2003) 241].

  19. The relationship between crystal structure and NMR relaxation in molecular solids with tert-butyl groups

    International Nuclear Information System (INIS)

    We correlate an X-ray determination of the molecular and crystal structures of 2-tert-butylanthracene and 2-tert-butylanthraquinone reported here with the previously reported dynamical nuclear magnetic resonance determination of the motions of the tert-butyl groups and their resident methyl groups in the solid state [P.A. Beckmann, K.S. Burbank, M.M.W. Lau, J.N. Ree, T.L. Weber, Chem. Phys. 290 (2003) 241

  20. Are the program packages for molecular structure calculations really black boxes?

    OpenAIRE

    ANA MRAKOVIC; MILICA DRVENDZIJA; ALEKSANDRA SAMOLOV; MILENA PETKOVIC; MILJENKO PERIC

    2007-01-01

    In this communication it is shown that the widely held opinion that compact program packages for quantum–mechanical calculations of molecular structure can safely be used as black boxes is completely wrong. In order to illustrate this, the results of computations of equilibrium bond lengths, vibrational frequencies and dissociation energies for all homonuclear diatomic molecules involving the atoms from the first two rows of the Periodic Table, performed using the Gaussian program package are...

  1. Synthesis, Structural Studies and Molecular Modelling of a Novel Imidazoline Derivative with Antifungal Activity.

    Science.gov (United States)

    Wróbel, Tomasz M; Kosikowska, Urszula; Kaczor, Agnieszka A; Andrzejczuk, Sylwia; Karczmarzyk, Zbigniew; Wysocki, Waldemar; Urbańczyk-Lipkowska, Zofia; Morawiak, Maja; Matosiuk, Dariusz

    2015-01-01

    Six novel imidazoline derivatives were synthesized and tested in antifungal assays. One of the compounds, N-cyclohexyl-2-imino-3-(4-nitrophenyl)imidazolidine-1-carboxamide showed moderate activity against several clinical strains of Candida albicans. Its structure was solved by X-ray crystallography and its mode of action was deduced using molecular modelling. It was found to be similar to that of fluconazole. The potential for further optimization including SAR of the compound is briefly discussed. PMID:26287137

  2. Synthesis, Structural Studies and Molecular Modelling of a Novel Imidazoline Derivative with Antifungal Activity

    Directory of Open Access Journals (Sweden)

    Tomasz M. Wróbel

    2015-08-01

    Full Text Available Six novel imidazoline derivatives were synthesized and tested in antifungal assays. One of the compounds, N-cyclohexyl-2-imino-3-(4-nitrophenylimidazolidine-1-carboxamide showed moderate activity against several clinical strains of Candida albicans. Its structure was solved by X-ray crystallography and its mode of action was deduced using molecular modelling. It was found to be similar to that of fluconazole. The potential for further optimization including SAR of the compound is briefly discussed.

  3. Structural insights into the molecular ruler mechanism of the endoplasmic reticulum aminopeptidase ERAP1

    OpenAIRE

    Amit Gandhi; Damodharan Lakshminarasimhan; Yixin Sun; Hwai-Chen Guo

    2011-01-01

    Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an essential component of the immune system, because it trims peptide precursors and generates the N--restricted epitopes. To examine ERAP1's unique properties of length- and sequence-dependent processing of antigen precursors, we report a 2.3 Å resolution complex structure of the ERAP1 regulatory domain. Our study reveals a binding conformation of ERAP1 to the carboxyl terminus of a peptide, and thus provides direct evidence for the molecular...

  4. 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 un...... indicate that in the simulated monolayer the finite size with periodic boundary conditions imposes a higher degree of order....

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

    NARCIS (Netherlands)

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

    2001-01-01

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

  6. Molecular and crystal structure of liquid crystalline p-octyloxyphenyl p′-pentyloxybenzoate

    International Nuclear Information System (INIS)

    The crystal and molecular structure of p-octyloxyphenyl p′-pentyloxybenzoate C5H11-O-C6H4-C(O)-O-C6H4-O-C8H17, which forms a nematic mesophase upon melting, was determined by X-ray diffraction. There is one system of weak directional intermolecular C-H…π interactions responsible for the formation of the nematic phase in these crystals.

  7. Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

    OpenAIRE

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very litt...

  8. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    International Nuclear Information System (INIS)

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H2 in Si, and the obtained dispersion law is analyzed

  9. Electrotunable friction with ionic liquid lubricants: how important is the molecular structure of the ions?

    OpenAIRE

    Fajardo, O. Y.; Bresme, Fernando; Kornyshev, Alexei A.; Urbakh, Michael

    2015-01-01

    Using non-equilibrium molecular dynamics simulations and a coarse grained model of ionic liquids, we have investigated the impact that the shape and the intramolecular charge distribution of the ions have on the electrotuneable friction with ionic-liquid nanoscale films. We show that the electric-field induces significant structural changes in the film, leading to dramatic modifications of the friction force. Comparison of the present work with previous studies using different models of ionic...

  10. X-ray interferometric method of determination of super molecular structure parameters of polymers

    International Nuclear Information System (INIS)

    A new method for determining the density of polymeric substances is proposed. It is based on the determination of the path-Iength differences in moire patterns. The method is characterized by simplicity and accuracy of results. The densities of polychloroprene and polystrol are determined with high accuracy. The knowledge of the dependence of polymer density on the stretching degree allows one to reveal the dynamics of changes of the super molecular structure at the deformation of polymer

  11. Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

    OpenAIRE

    Gallas, J M; Littrell, K. C.; Seifert, S; Zajac, G W; Thiyagarajan, P.

    1999-01-01

    Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the pre...

  12. Molecular dynamics explorations of active site structure in designed and evolved enzymes

    OpenAIRE

    Osuna Oliveras, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L.; Houk, Kendall N.

    2015-01-01

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explora...

  13. The Electronic Structure of Organic Molecular Materials : Theoretical and Spectroscopic Investigations

    OpenAIRE

    Brumboiu, Iulia Emilia

    2014-01-01

    In the present thesis the electronic properties of two organic molecules were studied by means of density functional theory (DFT) in connection to their possible applications in organic photovoltaics and molecular spintronics respectively. The first analysed system is the C60 derivative PCBM extensively used in polymer solar cells for the charge separation process. Since fullerenes have been shown to undergo modifications as a result of light exposure, investigating their electronic structure...

  14. Presenting your structures: the CCP4mg molecular-graphics software

    OpenAIRE

    McNicholas, S.; Potterton, E.; Wilson, K. S.; Noble, M. E. M.

    2011-01-01

    CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects an...

  15. PASBio: predicate-argument structures for event extraction in molecular biology

    OpenAIRE

    Shah Parantu K; Wattarujeekrit Tuangthong; Collier Nigel

    2004-01-01

    Abstract Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sen...

  16. Structural changes in ultra-high molecular weight polyethylene after irradiation with accelerated electrons

    Czech Academy of Sciences Publication Activity Database

    Synková, Hana; Šlouf, Miroslav; Baldrian, Josef; Sikora, Antonín; Kovářová, Jana; Stephan, M.

    Paris: International Union of Pure and Applied Chemistry, 2004, 5.3.5. [IUPAC International Symposium on Macromolecules, World Polymer Congress MACRO /40./. Paris (FR), 04.07.2004-09.07.2004] R&D Projects: GA ČR GA106/04/1118 Institutional research plan: CEZ:AV0Z4050913 Keywords : ultrahigh molecular weight polyethylene * irradiation * supramolecular structure Subject RIV: CD - Macromolecular Chemistry http://www.e-polymers.org/paris/data/L2387.pdf

  17. Mesoscopic superposition and sub-Planck-scale structure in molecular wave packets

    OpenAIRE

    Ghosh, Suranjana; Chiruvelli, Aravind; Banerji, J.; P. K. Panigrahi

    2005-01-01

    We demonstrate the possibility of realizing sub-Planck-scale structures in the mesoscopic superposition of molecular wave packets involving vibrational levels. The time evolution of the wave packet, taken here as the SU(2) coherent state of the Morse potential describing hydrogen iodide molecules, produces macroscopicquantum- superposition-like states, responsible for the above phenomenon. We investigate the phase-space dynamics of the coherent state through the Wigner function approach and i...

  18. Boron neutron capture therapy of EGFR or EGFRvIII positive gliomas using either boronated monoclonal antibodies or epidermal growth factor as molecular targeting agents

    Energy Technology Data Exchange (ETDEWEB)

    Yang, W. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States); Barth, R.F. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States)], E-mail: rolf.barth@osumc.edu; Wu, G. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States); Tjarks, W. [College of Pharmacy, Ohio State University, Columbus, OH 43210 (United States); Binns, P.; Riley, K. [Nuclear Reactor Laboratory and Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, MA 02215 (United States)

    2009-07-15

    In the present report we have summarized studies carried out over the past five years on molecular targeting of the epidermal growth factor receptor (EGFR) and its mutant isoform, EFGRvIII, for BNCT of genetically engineered F98 rat gliomas, expressing either wildtype (F98{sub EGFR}) or mutant receptors (F98{sub npEGFRvIII}). EGF or the monoclonal antibodies (mAbs), cetuximab (IMC-C225) and L8A4, which recognize wildtype EGFR and EGFRvIII, respectively, were heavily boronated using polyamidoamine (PAMAM) dendrimers (BD) linked to the targeting vehicles by means of heterobifunctional reagents. Boronated EGF or mAbs, alone or in combination with i.v. boronophenylalanine (BPA), were administered intracerebrally (i.c.) by either intratumoral (i.t.) injection or convection enhanced delivery (CED) to rats bearing F98 gliomas following which BNCT was initiated. The best survival data were obtained in rats bearing F98{sub npEGFRvIII} gliomas that had received CED of BD-L8A4 either alone or in combination with i.v. boronophenylalanine (BPA). Studies carried out in rats bearing composite tumors (F98{sub EGFR}/F98{sub npEGFRvIII}) demonstrated that it was essential to target both tumor cell populations in order to obtain an optimal therapeutic effect. Based on these observations, we have concluded that EGFR targeting vehicles are useful, but not stand-alone boron delivery agents due to the heterogeneity of receptor expression in brain tumors. They could, however, be quite useful in combination with the two drugs that currently are being used clinically, BPA and sodium borocaptate (BSH) for BNCT of either brain tumors or head and neck cancers.

  19. 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.

  20. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    International Nuclear Information System (INIS)

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7Tc) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

  1. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    Energy Technology Data Exchange (ETDEWEB)

    Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

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

    International Nuclear Information System (INIS)

    A series of phenolic resins with different weight-average molecular weights (Mw) 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 (Ou/Pu), and Mw 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 Ou/Pu ratios, corresponding to low O/P ratios, at comparable resin Mw values. Also, the tensile strength of the phenolic fibers increases with increasing novolac Mw 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 Mw

  3. 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.

  4. Resolving detailed molecular structures in complex organic mixtures and modeling their secondary organic aerosol formation

    Science.gov (United States)

    Goodman-Rendall, Kevin A. S.; Zhuang, Yang R.; Amirav, Aviv; Chan, Arthur W. H.

    2016-03-01

    Characterization of unresolved complex mixtures (UCMs) remains an ongoing challenge towards developing detailed and accurate inputs for modeling secondary organic aerosol (SOA) formation. Traditional techniques based on gas chromatography/electron impact-mass spectrometry induce excessive fragmentation, making it difficult to speciate and quantify isomers precisely. The goal of this study is to identify individual organic isomers by gas chromatography/mass spectrometry with supersonic molecular beam (SMB-GC/MS, also known as GC/MS with Cold EI) and to incorporate speciated isomers into an SOA model that accounts for the specific structures elucidated. Two samples containing atmospherically relevant UCMs are analyzed. The relative isomer distributions exhibit remarkably consistent trends across a wide range of carbon numbers. Constitutional isomers of different alkanes are speciated and individually quantified as linear, branched - for the first time by position of branching - multiply branched, or unsaturated - by degree of ring substitution and number of rings. Relative amounts of exact molecular structures are used as input parameters in an SOA box model to study the effects of molecular structures on SOA yields and volatility evolution. Highly substituted cyclic, mono-substituted cyclic, and linear species have the highest SOA yields while branched alkanes formed the least SOA. The rate of functionalization of a representative UCM is found to be in agreement with current volatility basis set (VBS) parameterizations based on detailed knowledge of composition and known oxidation mechanisms, confirming the validity of VBS parameters currently used in air quality models.

  5. Effects of molecular structure on microscopic heat transport in chain polymer liquids.

    Science.gov (United States)

    Matsubara, Hiroki; Kikugawa, Gota; Bessho, Takeshi; Yamashita, Seiji; Ohara, Taku

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7Tc) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs. PMID:25933776

  6. CH5M3D: an HTML5 program for creating 3D molecular structures

    OpenAIRE

    Earley, Clarke W

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also pr...

  7. Strain and structure in nano Ag films deposited on Au: Molecular dynamics simulation

    International Nuclear Information System (INIS)

    Molecular dynamics simulations are applied to analyze the stress and structure of nano Ag thin films deposited on the Au substrate. The interactions in the system are described by the embedded atom method. The kinematical theory of scattering is employed to identify the structure obtained from simulations data. Results shows that the silver layers are adjusted to the crystalline lattice of the gold buffer layers, and during the deposition process only compressive stress is observed. In all the cases the distribution of stress does not depend on temperature.

  8. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    OpenAIRE

    Dallakian Pavel; Haider Norbert

    2011-01-01

    Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality i...

  9. First-principles study of the electronic and molecular structure of protein nanotubes

    Science.gov (United States)

    Okamoto, Hajime; Takeda, Kyozaburo; Shiraishi, Kenji

    2001-09-01

    The electronic and molecular structures of protein nanotubes (PNT's) have been investigated theoretically by first-principles electronic structure calculations. The results have been discussed in comparison to those of the polypeptide open chains (POC's) and polypeptide closed rings (PCR's) in order to give a systematic understanding. Focusing on the intra-ring and inter-ring hydrogen bonds (HB's), we also investigate the PCR stacking mechanism. The present calculation reveals that PNT's are semiconductors and that an extra proton in the tube interior has the potential to be an electron acceptor.

  10. Mesoscopic superposition and sub-Planck scale structure in molecular wave packets

    CERN Document Server

    Ghosh, S; Banerji, J; Panigrahi, P K; Ghosh, Suranjana; Chiruvelli, Aravind

    2005-01-01

    We demonstrate the possibility of realizing sub-Planck scale structures in the mesoscopic superposition of molecular wave packets involving vibrational levels. The time evolution of the wave packet, taken here as the SU(2) coherent state of the Morse potential describing hydrogen iodide molecule, produces cat-like states, responsible for the above phenomenon. We investigate the phase space dynamics of the coherent state through the Wigner function approach and identify the interference phenomena behind the sub-Planck scale structures. The optimal parameter ranges are specified for observing these features.

  11. Small-scale structure in the Rosette molecular cloud revealed by Herschel

    OpenAIRE

    Di Francesco, J.; Sadavoy, S.; Motte, F; Schneider, N.; Hennemann, M.; Csengeri, T.; Bontemps, S.; Z. Balog; Zavagno, A.; André, Ph.; Saraceno, P.; Griffin, M; Men'shchikov, A.; Abergel, A; Baluteau, J. -P.

    2010-01-01

    We present a preliminary analysis of the small-scale structure found in new 70-520 μm continuum maps of the Rosette molecular cloud (RMC), obtained with the SPIRE and PACS instruments of the Herschel Space Observatory. We find 473 clumps within the RMC using a new structure identification algorithm, with sizes up to ~1.0 pc in diameter. A comparison with recent Spitzer maps reveals that 371 clumps are "starless" (without an associated young stellar object), while 102 are "protostellar". Using...

  12. Quantum chemistry the development of ab initio methods in molecular electronic structure theory

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

    This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

  13. Caracterização molecular do vírus da raiva isolado de Desmodus rotundus capturados no Estado do Rio de Janeiro Molecular characterization of rabies virus isolated from Desmodus rotundus captured in Rio de Janeiro State

    Directory of Open Access Journals (Sweden)

    L.F.P. Vieira

    2010-04-01

    Full Text Available Caracterizou-se filogeneticamente o vírus da raiva, isolado de morcegos hematógafos (Demodus rotundus. Cento e noventa e nove D. rotundus foram capturados em cinco abrigos, no Norte e Noroeste do Estado do Rio de Janeiro e sul do Espírito Santo. Sete deles foram positivos para a raiva. Amostras desses vírus foram sequenciadas e comparadas com sequências provenientes de diversos estados brasileiros. As sequências de vírus da raiva isoladas, na região norte do Estado do Rio de Janeiro, mostraram características que as distinguem de amostras de vírus isoladas em outras regiões do país, no entanto foram idênticas às isoladas de bovinos no noroeste do Rio de Janeiro.Rabies samples isolated from vampire bats captured in the Rio de Janeiro State were phylogenetically analyzed. One hundred and ninety nine vampire bats were captured from five shelters from North and Northwest of Rio de Janeiro and South of Espírito Santo States. Seven of them were positive for rabies. Theses samples were sequenced and compared with rabies virus sequences from several Brazilian states. The sequences of rabies virus, isolated in the present work, from North of Rio de Janeiro State, showed characteristics that differ of the sequences isolated from bats from other Brazilian regions. However, they were identical to samples isolated from cattle in Northwest of Rio de Janeiro state.

  14. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Directory of Open Access Journals (Sweden)

    Alessandro Marchiori

    Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  15. In-silico bonding schemes to encode chemical bonds involving sharing of electrons in molecular structures.

    Science.gov (United States)

    Punnaivanam, Sankar; Sathiadhas, Jerome Pastal Raj; Panneerselvam, Vinoth

    2016-05-01

    Encoding of covalent and coordinate covalent bonds in molecular structures using ground state valence electronic configuration is achieved. The bonding due to electron sharing in the molecular structures is described with five fundamental bonding categories viz. uPair-uPair, lPair-uPair, uPair-lPair, vPair-lPair, and lPair-lPair. The involvement of lone pair electrons and the vacant electron orbitals in chemical bonding are explained with bonding schemes namely "target vacant promotion", "source vacant promotion", "target pairing promotion", "source pairing promotion", "source cation promotion", "source pairing double bond", "target vacant occupation", and "double pairing promotion" schemes. The bonding schemes are verified with a chemical structure editor. The bonding in the structures like ylides, PCl5, SF6, IF7, N-Oxides, BF4(-), AlCl4(-) etc. are explained and encoded unambiguously. The encoding of bonding in the structures of various organic compounds, transition metals compounds, coordination complexes and metal carbonyls is accomplished. PMID:27041446

  16. Molecular dynamics approach to water structure of HII mesophase of monoolein

    Science.gov (United States)

    Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

    2012-02-01

    The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

  17. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies. PMID:26758200

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

    Energy Technology Data Exchange (ETDEWEB)

    Cooke, R.M.; Harvey, T.S.; Campbell, I.D. (Univ. of Oxford (England))

    1991-06-04

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

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

    International Nuclear Information System (INIS)

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

  20. A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil

    Science.gov (United States)

    Kattan, D.; Alcolea Palafox, M.; Rathor, S. K.; Rastogi, V. K.

    2016-02-01

    The four unit cells found in the crystals of the biomolecule 5-Nitrouracil were simulated as tetramer forms by density functional calculations. Four tetramer forms were fully optimized. Specific scale factors and scaling equations deduced from uracil molecule were employed in the predicted wavenumbers of 5-nitrouracil. The experimental FT-Raman and FT-IR spectra were recorded in the solid state. Comprehensive interpretation of the experimental FT-IR and FT-Raman spectra of the compound under study in the solid state is based on potential energy distribution. A good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. A complete vibrational assignment in the isolated state was also carried out aided by the theoretical harmonic frequency analysis and the results compared with those reported in Ar matrix. The scaled wavenumbers were used in the reassignment of several experimental bands. A comparison between the molecular structure and charge distribution of 5-Nitrouracil with related 5-uracil derivatives was presented. The effect of the nitro substitution in the 5th position of the pyrimidine ring was evaluated.

  1. A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures

    Science.gov (United States)

    Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.

    2014-03-01

    Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.

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

    Directory of Open Access Journals (Sweden)

    Shigemura Masahiko

    2012-07-01

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

  3. Density functional theory study of the structural, electronic, lattice dynamical, and thermodynamic properties of Li4SiO4 and its capability for CO2 capture

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua; Parlinski, K.

    2011-01-01

    The structural, electronic, lattice dynamical, optical, thermodynamic, and CO{sub 2} capture properties of monoclinic and triclinic phases of Li{sub 4}SiO{sub 4} are investigated by combining density functional theory with phonon lattice dynamics calculations. We found that these two phases have some similarities in their bulk and thermodynamic properties. The calculated bulk modulus and the cohesive energies of these two phases are close to each other. Although both of them are insulators, the monoclinic phase of Li{sub 4}SiO{sub 4} has a direct band gap of 5.24 eV while the triclinic Li{sub 4}SiO{sub 4} phase has an indirect band gap of 4.98 eV. In both phases of Li{sub 4}SiO{sub 4}, the s orbital of O mainly contributes to the lower-energy second valence band (VB{sub 2}) and the p orbitals contribute to the fist valence band (VB{sub 1}) and the conduction bands (CBs). The s orbital of Si mainly contributes to the lower portions of the VB1 and VB{sub 2}, and Si p orbitals mainly contribute to the higher portions of the VB{sub 1} and VB{sub 2}. The s and p orbitals of Li contribute to both VBs and to CBs, and Li p orbitals have a higher contribution than the Li s orbital. There is possibly a phonon soft mode existing in triclinic {gamma}-Li{sub 4}SiO{sub 4}; in the monoclinic Li{sub 4}SiO{sub 4}, there are three phonon soft modes, which correspond to the one type of Li disordered over a few sites. Their LO-TO splitting indicates that both phases of Li{sub 4}SiO{sub 4} are polar anisotropic materials. The calculated infrared absorption spectra for LO and TO modes are different for these two phases of Li{sub 4}SiO{sub 4}. The calculated relationships of the chemical potential versus temperature and CO{sub 2} pressure for reaction of Li{sub 4}SiO{sub 4} with CO{sub 2} shows that Li{sub 4}SiO{sub 4} could be a good candidate for a high-temperature CO{sub 2} sorbent while used for postcombustion capture technology.

  4. 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)

    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 (C3 to C8), 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

  5. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    Science.gov (United States)

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism. PMID:26208627

  6. Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene

    Directory of Open Access Journals (Sweden)

    Kubicki JD

    2000-09-01

    Full Text Available Molecular simulations (energy minimizations and molecular dynamics of an n-hexane soot model developed by Smith and co-workers (M. S. Akhter, A. R. Chughtai and D. M. Smith, Appl. Spectrosc., 1985, 39, 143; ref. 1 were performed. The MM+ (N. L. Allinger, J. Am. Chem. Soc., 1977, 395, 157; ref. 2 and COMPASS (H. Sun, J. Phys. Chem., 1998, 102, 7338; ref. 3 force fields were tested for their ability to produce realistic soot nanoparticle structure. The interaction of pyrene with the model soot was simulated. Quantum mechanical calculations on smaller soot fragments were carried out. Starting from an initial 2D structure, energy minimizations are not able to produce the observed layering within soot with either force field. Results of molecular dynamics simulations indicate that the COMPASS force field does a reasonably accurate job of reproducing observations of soot structure. Increasing the system size from a 683 to a 2732 atom soot model does not have a significant effect on predicted structures. Neither does the addition of water molecules surrounding the soot model. Pyrene fits within the soot structure without disrupting the interlayer spacing. Polycyclic aromatic hydrocarbons (PAH, such as pyrene, may strongly partition into soot and have slow desorption kinetics because the PAH-soot bonding is similar to soot–soot interactions. Diffusion of PAH into soot micropores may allow the PAH to be irreversibly adsorbed and sequestered so that they partition slowly back into an aqueous phase causing dis-equilibrium between soil organic matter and porewater.

  7. Molecular and Electronic Structure of Cyclic Trinuclear Gold(I) Carbeniate Complexes: Insights for Structure/Luminescence/Conductivity Relationships

    Energy Technology Data Exchange (ETDEWEB)

    McDougaldJr, Roy N [University of North Texas; Chilukuri, Bhaskar [University of North Texas; Jia, Huiping [University of Texas at Dallas; Perez, Michael R [University of Texas at Dallas; Rabaa, Hassan [Ibn Tofail Univ, ESCTM, Morocco; Wang, Xiaoping [ORNL; Nesterov, Vladimir [University of North Texas; Cundari, Thomas R. [University of North Texas; Gnade, Bruce E [University of Texas at Dallas; Omary, Mohammad A [University of North Texas

    2014-01-01

    An experimental and computational study of correlations between solid-state structure and optical/electronic properties of cyclotrimeric gold(I) carbeniates, [Au-3(RN=COR')(3)] (R, R' = H, Me, Bu-n, or (c)Pe), is reported. Synthesis and structural and photophysical characterization of novel complexes [Au-3(MeN=(COBu)-Bu-n)(3)], [Au-3((BuN)-Bu-n=COMe)(3)], [Au-3((BuN)-Bu-n=(COBu)-Bu-n)(3)], and [Au-3((c)PeN=COMe)(3)] are presented. Changes in R and R' lead to distinctive variations in solid-state stacking, luminescence spectra, and conductive properties. Solid-state emission and excitation spectra for each complex display a remarkable dependence on the solid-state packing of the cyclotrimers. The electronic structure of [Au-3(RN=COR')(3)] was investigated via molecular and solid-state simulations. Calculations on [Au-3(HN=COH)(3)] models indicate that the infinitely extended chain of eclipsed structures with equidistant Au-Au intertrimer aurophilic bonding can have lower band gaps, smaller Stokes shifts, and reduced reorganization energies (lambda). The action of one cyclotrimer as a molecular nanowire is demonstrated via fabrication of an organic field effect transistor and shown to produce a p-type field effect. Hole transport for the same cyclotrimer-doped within a poly(9-vinylcarbazole) host-produced a colossal increase in current density from similar to 1 to similar to 1000 mA/cm(2). Computations and experiments thus delineate the complex relationships between solid-state morphologies, electronic structures, and optoelectronic properties of gold(I) carbeniates.

  8. Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

    Directory of Open Access Journals (Sweden)

    Leandro Martínez

    Full Text Available The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD and Root Mean Square Fluctuations (RMSF of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

  9. Molecular view modeling of atmospheric organic particulate matter: Incorporating molecular structure and co-condensation of water

    Science.gov (United States)

    Pankow, James F.; Marks, Marguerite C.; Barsanti, Kelley C.; Mahmud, Abdullah; Asher, William E.; Li, Jingyi; Ying, Qi; Jathar, Shantanu H.; Kleeman, Michael J.

    2015-12-01

    Most urban and regional models used to predict levels of organic particulate matter (OPM) are based on fundamental equations for gas/particle partitioning, but make the highly simplifying, anonymized-view (AV) assumptions that OPM levels are not affected by either: a) the molecular characteristics of the condensing organic compounds (other than simple volatility); or b) co-condensation of water as driven by non-zero relative humidity (RH) values. The simplifying assumptions have allowed parameterized chamber results for formation of secondary organic aerosol (SOA) (e.g., "two-product" (2p) coefficients) to be incorporated in chemical transport models. However, a return towards a less simplistic (and more computationally demanding) molecular view (MV) is needed that acknowledges that atmospheric OPM is a mixture of organic compounds with differing polarities, water, and in some cases dissolved salts. The higher computational cost of MV modeling results from a need for iterative calculations of the composition-dependent gas/particle partition coefficient values. MV modeling of OPM that considered water uptake (but not dissolved salts) was carried out for the southeast United States for the period August 29 through September 7, 2006. Three model variants were used at three universities: CMAQ-RH-2p (at PSU), UCD/CIT-RH-2p (at UCD), and CMAQ-RH-MCM (at TAMU). With the first two, MV structural characteristics (carbon number and numbers of functional groups) were assigned to each of the 2p products used in CMAQv.4.7.1 such that resulting predicted Kp,i values matched those in CMAQv.4.7.1. When water uptake was allowed, most runs assumed that uptake occurred only into the SOA portion, and imposed immiscibility of SOA with primary organic aerosol (POA). (POA is often viewed as rather non-polar, while SOA is commonly viewed as moderately-to-rather polar. Some runs with UCD/CIT-RH-2p were used to investigate the effects of POA/SOA miscibility.) CMAQ-RH-MCM used MCM to

  10. Influence of stretchening load and radiation on molecular structure of isotactic polypropylene

    International Nuclear Information System (INIS)

    Change of molecular structure of oriented isotactic polypropylene film in dependence on stretching load, and neutron radiation is investigated. The investigations were carried out by IR spectroscopy and dielectric relaxation methods using of the absorption bands sensitive to conformation states of macromolecular chains, molecular ordering and to intermolecular interaction. It was mainly used the band at 973 cm-1 . This IR band assignment to mixes mainly of deformation modes of the CH3 and CH2 groupings and stretching modes of CH2-CH3 groups. Under influence of stretching load takes place shifting to lower frequencies and asymmetrical sharp change of the IR band. The observation spectroscopic effects some authors tried to explain before by decreasing of the valent bonds and valent angle force constant values of the overstressed section of passage molecular chains and later also by the grouply forming the 'dilatons' - the regions of anharmonic dilatation in the polymer. But the forming such matter 'dilatons' needs very high of the fluctuation energy values and therefore such process have very lower probability. Our investigation shows that the above pointed spectral effects changes under stretching load takes place because of configuration distortion of helical structure of macromolecules, conformation transformation of some molecular sections and weakening of intermolecular interaction. Molecular regroupings were occurred more for polymer sample with smaller crystallinity and spectral changes were accordingly more appreciable for such sample. The further spectral changes with increase of stretchening load afterwards conformation regroupings in amorphous regions took place mainly for of stretching and weakening of intermolecular bonds in polymer crystallites. It explains the large convertibility of mentioned spectral changes caused by loading and unloading of highly oriented polymer sample. The tension of macromolecular sections and displacement of molecular

  11. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  12. Weak links between fast mobility and local structure in molecular and atomic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  13. Weak links between fast mobility and local structure in molecular and atomic liquids

    International Nuclear Information System (INIS)

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-14

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

  15. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    International Nuclear Information System (INIS)

    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented

  16. Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures

    Science.gov (United States)

    Rosas-Trigueros, Jorge Luis; Correa-Basurto, José; Guadalupe Benítez-Cardoza, Claudia; Zamorano-Carrillo, Absalom

    2011-01-01

    Bax is a member of the Bcl-2 protein family that participates in mitochondrion-mediated apoptosis. In the early stages of the apoptotic pathway, this protein migrates from the cytosol to the outer mitochondrial membrane, where it is inserted and usually oligomerizes, making cytochrome c-compatible pores. Although several cellular and structural studies have been reported, a description of the stability of Bax at the molecular level remains elusive. This article reports molecular dynamics simulations of monomeric Bax at 300, 400, and 500 K, focusing on the most relevant structural changes and relating them to biological experimental results. Bax gradually loses its α-helices when it is submitted to high temperatures, yet it maintains its globular conformation. The resistance of Bax to adopt an extended conformation could be due to several interactions that were found to be responsible for maintaining the structural stability of this protein. Among these interactions, we found salt bridges, hydrophobic interactions, and hydrogen bonds. Remarkably, salt bridges were the most relevant to prevent the elongation of the structure. In addition, the analysis of our results suggests which conformational movements are implicated in the activation/oligomerization of Bax. This atomistic description might have important implications for understanding the functionality and stability of Bax in vitro as well as within the cellular environment. PMID:21936009

  17. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena [Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

    2013-11-01

    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.

  18. 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.

  19. Effects of Irradiation on the Structure-activity Relationship of Konjac Glucomannan Molecular Chain Membrane

    Institute of Scientific and Technical Information of China (English)

    WU Chun-Hua; PENG Shu-Hui; WEN Cheng-Rong; WANG Li-Xia; XIONG Bo; LIU Ya-Nan; FAN Lin-Lin; YAO Min-Na; PANG Jie

    2012-01-01

    To know the effects of irradiation on the konjac glucomannan (KGM) molecular chain membrane, KGM membrane solution was treated with the irradiation dose of 0-20 kGy in this study, and the structure and properties of KGM membrane were analyzed with Infrared spectrum, Raman spectrum, X-ray, SEM scanning and so on. The results revealed that the effects of different irradiation doses on the KGM molecular chain structure were different. Higher irradiation dose (20 kGy) resulted in partial damage against KGM membrane crystal structure, and there was no obvious change for the amorphous structure; with membrane property test, the tensile strength of KGM membrane gradually increased with the increase of irradiation dose and its elongation at break reduced, but these changes were not significant, WVP value reduced; with SEM, the membrane surface treated with irradiation was smoother even than the membrane without treatment. In addition, when increasing the irradiation dose, membrane surface became more even, and arrangement was more orderly and compact. KGM membrane nrooerties, and it is an ideal Irradiation modification could effectively improve the modification method.

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

    Science.gov (United States)

    Xiao, Xueliang; Hu, Jinlian

    2016-01-01

    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. PMID:27230823

  1. Structural studies on Mycobacterium tuberculosis RecA: Molecular plasticity and interspecies variability

    Indian Academy of Sciences (India)

    Anu V Chandran; J Rajan Prabu; Astha Nautiyal; K Neelakanteshwar Patil; K Muniyappa; M Vijayan

    2015-03-01

    Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the `switch’ residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.

  2. Fabrication variables affecting the structure and properties of supported carbon molecular sieve membranes for hydrogen separation

    KAUST Repository

    Briceño, Kelly

    2012-10-01

    A high molecular weight polyimide (Matrimid) was used as a precursor for fabricating supported carbon molecular sieve membranes without crack formation at 550-700°C pyrolysis temperature. A one-step polymer (polyimide) coating method as precursor of carbon layer was used without needing a prior modification of a TiO 2 macroporous support. The following fabrication variables were optimized and studied to determine their effect on the carbon structure: polymeric solution concentration, solvent extraction, heating rate and pyrolysis temperature. Two techniques (Thermogravimetric analysis and Raman spectroscopy) were used to determine these effects on final carbon structure. Likewise, the effect of the support was also reported as an additional and important variable in the design of supported carbon membranes. Atomic force microscopy and differential scanning calorimetry quantified the degree of influence. Pure gas permeation tests were performed using CH 4, CO, CO 2 and H 2. The presence of a molecular sieving mechanism was confirmed after defects were plugged with PDMS solution at 12wt%. Gas selectivities higher than Knudsen theoretical values were reached with membranes obtained over 650°C, showing as best values 4.46, 4.70 and 10.62 for H 2/N 2, H 2/CO and H 2/CH 4 ratio, respectively. Permeance values were over 9.82×10 -9mol/(m 2Pas)during pure hydrogen permeation tests. © 2012 Elsevier B.V.

  3. Stability of Y/MCM-48 composite molecular sieve with mesoporous and microporous structures

    Directory of Open Access Journals (Sweden)

    Qian Zhao

    2014-12-01

    Full Text Available Y/MCM-48 composite molecular sieve was hydrothermally synthesized at different crystallization temperatures and crystallization times using ethyl orthosilicate as Si source and cetyltrimethyl ammonium bromide as template with the aid of fluoride ions and was characterized by X-ray diffraction, N2 physical adsorption technique, scanning electron microscopy and transmission electron microscopy. The thermal, hydrothermal, acidic, and basic stabilities of the Y/MCM-48 composite were investigated. The results show that Y/MCM-48 composite molecular sieve with meso- and microporous structures was synthesized successfully at 120 °C for 36 h. The Y/MCM-48 composite has the surface area of 864 m2/g and the average pore size is ca. 2.48 nm. The bi-porous structure in composite molecular sieve still maintains its stability even after thermal treatment at 800 °C for 4 h or hydrothermal treatment at 100 °C for 48 h. After treatment in 1 mol/L hydrochloric acid solution or 1 mol/L sodium hydroxide solution for 48 h, the Y/MCM-48 composite exhibits good acidic stability. The acidic stability is superior to the basic stability at the same treatment time.

  4. The Structure of a Low-Metallicity Giant Molecular Cloud Complex

    CERN Document Server

    Leroy, A K; Bot, C; Engelbracht, C W; Gordon, K; Israel, F P; Rubio, M; Sandstrom, K; Stanimirović, S

    2009-01-01

    To understand the impact of low metallicities on giant molecular cloud (GMC) structure, we compare far infrared dust emission, CO emission, and dynamics in the star-forming complex N83 in the Wing of the Small Magellanic Cloud. Dust emission (measured by Spitzer as part of the S3MC and SAGE-SMC surveys) probes the total gas column independent of molecular line emission and traces shielding from photodissociating radiation. We calibrate a method to estimate the dust column using only the high-resolution Spitzer data and verify that dust traces the ISM in the HI-dominated region around N83. This allows us to resolve the relative structures of H2, dust, and CO within a giant molecular cloud complex, one of the first times such a measurement has been made in a low-metallicity galaxy. Our results support the hypothesis that CO is photodissociated while H2 self-shields in the outer parts of low-metallicity GMCs, so that dust/self shielding is the primary factor determining the distribution of CO emission. Four piec...

  5. 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.

  6. Molecular replacement studies on crystal structure of allophycocyanin from red algae Porphyra yezoensis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Using the crystal structure of allophycocyanin from cyanobacterium Spirulina platensis (APC-SP) as a search model,the crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) has been studied by molecular replacement methods.The APC-PY crystals (Form 3) belong to the space group of R32,cell dimensions a=b= 10.53 nm,c=18.94 nm,α= β= 90°,γ=120°;there is one αβ monomer in each crystallographic asymmetric unit in the cell.The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1% for reflection data from 1.0 to 0.4 nm.Using the results by molecular replacement,the initial model of APC-PY was built,and the coincidence of the chromophore in APC-PY initial model with its 2Fo-Fc OMIT map further confirms the results by molecular replacement.

  7. Molecular replacement studies on crystal structure of allophycocyanin from red algae Porphyra yezoensis

    Institute of Scientific and Technical Information of China (English)

    刘锦玉; 江涛; 张季平; 常文瑞; 梁栋材

    2000-01-01

    Using the crystal structure of allophycocyanin from cyanobacterium Spirulina platensis (APC-SP) as a search model, the crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) has been studied by molecular replacement methods. The APC-PY crystals (Form 3) belong to the space group of R32, cell dimensions a = b = 10.53 nm, c = 18.94 nm, α =β = 90°, γ= 120°; there is one αβ monomer in each crystallographic asymmetric unit in the cell. The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1 % for reflection data from 1.0 to 0.4 nm. Using the results by molecular replacement, the initial model of APC-PY was built, and the coincidence of the chromophore in APC-PY initial model with its 2Fo-FC OMIT map further confirms the results by molecular replacement.

  8. Applications of the Information Theory to Problems of Molecular Electronic Structure and Chemical Reactivity

    Directory of Open Access Journals (Sweden)

    Roman F. Nalewajski

    2002-04-01

    Full Text Available Abstract: Recent studies on applications of the information theoretic concepts to molecular systems are reviewed. This survey covers the information theory basis of the Hirshfeld partitioning of molecular electron densities, its generalization to many electron probabilities, the local information distance analysis of molecular charge distributions, the charge transfer descriptors of the donor-acceptor reactive systems, the elements of a “thermodynamic” description of molecular charge displacements, both “vertical” (between molecular fragments for the fixed overall density and “horizontal” (involving different molecular densities, with the entropic representation description provided by the information theory. The average uncertainty measures of bond multiplicities in molecular “communication” systems are also briefly summarized. After an overview of alternative indicators of the information distance (entropy deficiency, missing information between probability distributions the properties of the “stockholder” densities, which minimize the entropy deficiency relative to the promolecule reference, are summarized. In particular, the surprisal analysis of molecular densities is advocated as an attractive information-theoretic tool in the electronic structure theory, supplementary to the familiar density difference diagrams. The subsystem information density equalization rules satisfied by the Hirshfeld molecular fragments are emphasized: the local values of alternative information distance densities of subsystems are equal to the corresponding global value, characterizing the molecule as a whole. These local measures of the information content are semi-quantitatively related to the molecular density difference function. In the density functional theory the effective external potentials of molecular fragments are defined, for which

  9. Radiative electron capture

    International Nuclear Information System (INIS)

    Some data are presented for radiative electron capture by fast moving ions. The radiative electron capture spectrum is shown for O8+ in Ag, along with the energy dependence of the capture cross-section. A discrepancy between earlier data, theoretical prediction, and the present data is pointed out. (3 figs) (U.S.)

  10. Translocation Properties of Primitive Molecular Machines and Their Relevance to the Structure of the Genetic Code

    CERN Document Server

    Aldana, M; Larralde, H; Martínez-Mekler, G; Aldana, Maximino; Cocho, Germinal; Larralde, Hernan; Martinez-Mekler, Gustavo

    2002-01-01

    We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles(rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi one dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present day genetic sequences, we show that the ab...

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

    Science.gov (United States)

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

    2016-05-01

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

  12. Structural and electronic characterization of self-assembled molecular nanoarchitectures by X-ray photoelectron spectroscopy.

    Science.gov (United States)

    Gulino, Antonino

    2013-02-01

    Molecular monolayers and similar nanoarchitectures are indicative of the promising future of nanotechnology. Therefore, many scientists recently devoted their efforts to the synthesis, characterization, and properties of mono- and multilayer-based systems. In this context, X-ray photoelectron spectroscopy is an important technique for the in-depth chemical and structural characterization of nanoscopic systems. In fact, it is a surface technique suitable for probing thicknesses of the same order of the photoelectron inelastic mean free paths (a few tens of ångströms) and allows one to immediately obtain qualitative and quantitative data, film thickness, surface coverage, molecule footprint, oxidation states, and presence of functional groups. Nevertheless, other techniques are important in obtaining a complete spectroscopic characterization of the investigated systems. Therefore, in the present review we report on X-ray photoelectron spectroscopy of self-assembled molecular mono- and multilayer materials including some examples on which other characterization techniques produced important results. PMID:23014858

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

    DEFF Research Database (Denmark)

    Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter; Todd, Billy; Hansen, Jesper Schmidt

    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 are...... viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex...

  14. Molecular Adsorption Changes the Quantum Structure of Oxide-Supported Gold Nanoparticles: Chemisorption versus Physisorption.

    Science.gov (United States)

    Stiehler, Christian; Calaza, Florencia; Schneider, Wolf-Dieter; Nilius, Niklas; Freund, Hans-Joachim

    2015-07-17

    STM conductance spectroscopy and mapping has been used to analyze the impact of molecular adsorption on the quantized electronic structure of individual metal nanoparticles. For this purpose, isophorone and CO2, as prototype molecules for physisorptive and chemisorptive binding, were dosed onto monolayer Au islands grown on MgO thin films. The molecules attach exclusively to the metal-oxide boundary, while the interior of the islands remains pristine. The Au quantum well states are perturbed due to the adsorption process and increase their mutual energy spacing in the CO2 case but move together in isophorone-covered islands. The shifts disclose the nature of the molecule-Au interaction, which relies on electron exchange for the CO2 ligands but on dispersive forces for the organic species. Our experiments reveal how molecular adsorption affects individual quantum systems, a topic of utmost relevance for heterogeneous catalysis. PMID:26230817

  15. Effects of Contact Atomic Structure on Electronic Transport in Molecular Junction

    International Nuclear Information System (INIS)

    Based on nonequilibrium Green's function and first-principles calculations, we investigate the change in molecular conductance caused by different adsorption sites with the presence of additional Au atom around the metal-molecule contact in the system that benzene sandwiched between two Au(111) leads. The motivation is the variable situations that may arise in break junction experiments. Numerical results show that the enhancement of conductance induced by the presence of additional Au is dependent on the adsorption sites of anchoring atom. When molecule is located on top site with the presence of additional Au atoms, it can increase molecular conductance remarkably and present negative differential resistance under applied bias which cannot be found in bridge and hollow sites. Furthermore, the effects of different distance between additional Au and sulfur atoms in these three adsorption sites are also discussed. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  16. Materials for organic photovoltaics: insights from detailed structural models and molecular simulations

    Directory of Open Access Journals (Sweden)

    Po Riccardo

    2012-10-01

    Full Text Available This paper contains a brief discussion of the role of detailed structural and computational studies, within the general field of organic photovoltaics. We review some of our recent work on poly(3-butylthiophene (P3BT and on [6,6]phenyl-C61-butyric acid methyl ester (PCBM. The first is a prototypical hole-transporting material, whose crystal forms I.’ and II were solved by us through the combined use of powder Xray diffraction, electron diffraction and molecular modelling. PCBM is a widely used fullerene derivative with electron-transporting properties. It has a rich polymorphism, which to date remains largely unexplored. Our molecular dynamics simulations have revealed interesting features of its solid-state organization, including that in the amorphous phase.

  17. Pathophysiology of heart failure in broiler chickens: structural, biochemical, and molecular characteristics.

    Science.gov (United States)

    Olkowski, A A

    2007-05-01

    Modern strains of fast-growing meat type poultry are highly susceptible to heart failure. Heart-related mortalities are observed predominantly in fast-growing broiler chickens, with ascites and sudden death syndrome being the most common heart-related conditions in modern broiler flocks. This paper examines the role of structural, molecular, and biochemical factors pertinent to the pathophysiology of heart failure in fast-growing broilers. Evidence explaining the pathogenesis of acute and chronic heart failure, in the context of the underlying molecular and biochemical changes in the cardiomyocytes, contractile apparatus, and extracellular matrix in the ventricular myocardium are critically evaluated and discussed with reference to the clinical signs associated with deterioration of heart pump function. The secondary pathophysiological effects on the cardiovascular system, resulting from hemodynamic changes associated with the failing heart pump, are also reviewed and critically discussed. PMID:17435038

  18. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  19. Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity

    Energy Technology Data Exchange (ETDEWEB)

    Gupta,Y.; Nair, D.; Wharton, R.; Aggarwal, A.

    2008-01-01

    Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycBreverse and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a 'spacer.' The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.

  20. Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

    Science.gov (United States)

    Gupta, Yogesh K; Nair, Deepak T; Wharton, Robin P; Aggarwal, Aneel K

    2008-04-01

    Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycB(reverse) and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a "spacer." The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo. PMID:18328718