Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

Equivalent potential of water for electronic structure of asparagine

The equivalent potential of water for the electronic structure of asparagine(Asn) is constructed by using the first‐principles, all‐electron, ab initio calculation. The process is composed of three steps. The first step is to determine the geometric structure of Asn+nH₂O system with a minimum energy. The second step is to calculate the electronic structure of Asn with the potential of water molecules by using the self‐consistent cluster‐embedding (SCCE) method, based on the result obtained in the first step. The last step is to calculate the electronic structure of Asn with the potential of dipole after replacing water molecules with dipoles. The results show that the major effect of water molecules on Asn' electronic structure be raising the occupied electronic states by 0.034 Ry on average and narrowing energy gap by 0.91%. The effect of water on the electronic structure of Asn can be well simulated by using dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

软胶体粒子形成束晶的动力学模拟

利用广义指数模型描述软胶体粒子, 结合分子动力学模拟研究软胶体粒子形成束晶的动力学过程. 通过等温压缩和等密度降温2个不同的过程, 研究了束晶形成过程中结构变化特征和动力学路径对结构的影响规律. 研究发现, 与蒙特卡洛模拟结果相比, 分子动力学模拟得到的结构随着密度的变化有明显的迟滞现象, 这是由于考虑了真实的动力学因素引起的差异. 此外, 在相同温度和压力下通过不同的动力学路径得到的相结构不完全相同, 这是由于动力学形成过程会对相结构产生很大的影响.     

Secondary structure of globules of copolymers consisting of amphiphilic and hydrophilic units: Effect of potential range

The relation of the coil-globule transition in macromolecules consisting of amphiphilic and hydrophilic monomer units to the radius of action of the interaction potential is investigated by the method of computer-assisted experiments. The internal structure of globules formed by such macromolecules is significantly dependent on the radius of action of the potential. In the case of the long-range potential, the globule is characterized by the blob structure, while in the case of the short-range potential, a quasi-helical structure forms. In this structure, the skeleton of a macromolecule forms a helical turn, and the direction of twisting may vary from one turn to another. The coil-globule transition in such macromolecules proceeds through formation of the necklace conformation from quasi-helical micelle beads. For sufficiently long macromolecules, the dimensions of such globules are linearly dependent on the degree of polymerization.     

Computational Analysis of a Double Nozzle Structure Plasma Cutting Torch

Double arcing phenomenon is a limit to increasing the capacity of the plasma cutting torch. In an attempt to enhance the ability of being invulnerable to the double arcing, a double nozzle structure is introduced in this paper. The reason why the double nozzle structure is less vulnerable to the double arcing phenomenon than single nozzle structure is explored. Double nozzle structure allows the longer nozzle which may cause stronger shock wave. In order to evaluate the influence of shock wave on the cutting ability, the influence of nozzle length on the double nozzle structure plasma arc is investigated. The modeling results show that the longer nozzle produces the stronger shock wave outside the nozzle outlet, but the energy flux and momentum flux become concentrated after the shock wave and increases with the increasing of nozzle length. So the double nozzle structure improves the cutting ability of the plasma torch and meanwhile be less vulnerable to the double arcing phenomenon.     

Observation of a chevron hybrid structure in the smectic A phase of a liquid crystal device

Small angle X-ray diffraction experiments show the emergence of a chevron structure on cooling from the nematic phase into the smectic A phase of the commercial mixture S3 (Merck Ltd, UK), in a display device. The chevron angle increases from 0 at the nematicsmectic transition temperature, T NS, to a maximum value of 8.5 , which is reached when the sample is 15 C below T NS. Between 5 C and 15 C below the transition temperature a quasi bookshelf structure emerges, in addition to the prevailing chevron structure; such a structure has not been hitherto reported. There is no further resolvable change in the device structure on cooling lower than T NS -15 C. The chevron structure is due to the combination of layer thinning and fixed surface layers, as confirmed by a comparison of layer spacing calculated from the Bragg angle equation and from the layer thinning equation ( d = d nematic cos delta, where delta is the chevron angle).     

Low-energy electron induced restructuring of water monolayers on NaCl(100)

The influence of electron irradiation on the controversially discussed monolayer structure of H(2)O on NaCl(100) is investigated with helium atom diffraction before and after a low-damage low-energy electron diffraction (LEED) experiment. The ordered (1x1) structure observed initially with He atoms is found to be transformed to a stable c(4x2) structure after a 90 eV electron dosage of only 10(15) electrons cm(-2) or about 2 incident electrons per adsorbate molecule. Based on previously reported structure models for the two phases, the transition is attributed to a reorientation, and a possible compression of the water film induced by the electrons.     

The influence of different structure representations on the clustering of an RNA nucleotides data set

The last couple of years an overwhelming amount of data has emerged in the field of biomolecular structure determination. To explore information hidden in these structure databases, clustering techniques can be used. The outcome of the clustering experiments largely depends, among others, on the way the data is represented; therefore, the choice how to represent the molecular structure information is extremely important. This article describes what the influence of the different representations on the clustering is and how it can be analyzed by means of a dendrogram comparison method. All experiments are performed using a data set consisting of RNA trinucleotides. Besides the most basic structure representation, the Cartesian coordinates representation, several other structure representations are used.     

Effect of change of water structure on the phase transition of liposomes of dipalmitoyl phosphatidylcholine

The role of water structure around model membrane systems (e.g., liposomes) on phase transition of the lipid dipalmitoyl phosphatidylcholine was investigated. Water structure was altered by changing pH and by addition of solutes which are known breakers and makers of water structure. The structure makers broadened the zone of transition and changed the overall phase transition profile, while the main effect of structure breakers was to cause a shift in the transition temperature. The observed variation of Chapman transition temperature and broadening of zone of transition with varying pH is discussed in terms of altered water structure around the membrane–aqueous interface. Binding studies with the dye 1-anilino-8-napthalene sulfonate showed that structure makers or breakers did not bind to the liposome surface directly. Thus the structure makers and breakers act on the membranes perhaps by altering the water structure differentially. Possible associated mechanisms of action are discussed.     

Features of the real structure of pseudoboehmites: Violations of the structure and layer packing caused by crystallization water

Rietveld structure refinement and simulation of the diffraction patterns of partially disordered materials are used to study the real structure of nanoscale pseudoboehmite samples obtained by different technologies. The effect of various violations in the structure of these nanomaterials on diffraction patterns is analyzed. The introduction of corrections for the Lorentz and polarization factors in the determination of the cell parameter b by the position of the 020 diffraction peak in the pattern is shown to be important. A model for the atomic structure of pseudoboehmite is proposed. The model involves additional water molecules as compared to the structure of boehmite. The water molecules in the interlayer space of the layered boehmite structure are found to violate its regularity, which results in a decrease in the size of crystallites.     

Statistical Modeling of Water Structure in a Near-Electrode Layer

The structure of water near the electrode surface is studied by a molecular dynamics method, the electrode is assumed to be a structureless conducting surface, a cell of 216 water molecules is used. It is shown that the structure of water in a near-electrode area formed under the electric field influence differs greatly from that in the bulk. The effect of anisotropy of water structure normally to the surface is found. The effect consists of a lower diffusion mobility of molecules in this direction, quantitatively depends on the surface charge density, and decays with increasing distance from the surface. The main role in forming the water structure in the near-electrode layer is played by electrostatic interaction.     

The effect of backbone constraints: the case of water oxidation by the oxygen-evolving complex in PSII

The procedure for fixing atoms of amino acid residues in cluster model calculations on enzymes is reviewed. Examples from recent calculations on photosystem II (PSII) and Mo,Cu-dependent CO dehydrogenase are given. In this context, the cluster model work on finding a mechanism for O-O bond formation and a structure of the oxygen-evolving complex in PSII is also reviewed. In that work, fixing certain atoms played an important role. The main part of the present study concerns the mechanism in PSII using models based on the new high-resolution (1.9 ?) X-ray structure, which is compared to that using the old, theoretically suggested, structure. It is concluded that the mechanism remains the same, with a similar barrier height. Finally, a connection between the OEC structure and Mn,Ca-containing minerals is also briefly discussed.     

Revising Space Groups from Simulated SHELXfcf Structure Factors. More Examples of Incorrect Space Groups, an Example of a Chemically-Incorrect Structure and the Special Case of Pgl to PRevisions

1 INTRODUCTION Although the incorrect assignment of the space groups of crystal structures has been addressed in a number of reports, instances of crystal structures refined in incorrect symmetry turn up even in the recent literature[1～4]. A simple method of space group revision makes use of the published atomic coordinates and temperature factors to simulate the diffraction intensities; the structure is then 搒olved?in the correct space group from the simulated hkl-F2 data[5] and an O…     

Deriving the 3D structure of organic molecules from their infrared spectra

The representation of the 3D structure of a molecule by a radial distribution function (RDF) code is described. The use of the RDF code for the simulation of an infrared spectrum by a counterpropagation (CPG) neural network is shown. Furthermore, a CPG network can also be operated in reverse mode: on input of an infrared spectrum an RDF code is obtained for which a 3D structure can be searched in a database. An empirical modelling process is used to refine this 3D structure to obtain a three-dimensional model of the molecular structure that corresponds to the infrared spectrum.     

Revising Space Groups from Simulated SHELX·fcf Structure Factors. More Examples of Incorrect Space Groups, an Example of a Chemically-Incorrect Structure and the Special Case of P1 to P(-1) Revisions

The structure factors of any crystal structure can be simulated from its atomic coordinates (and temperature factors) in a SHELXL-97 run on a dummy hkl in which only the scale factor is refined. The squares of the structure factors are retrieved from thefcf, and such simulated data are used in the revision of the space groups of several incorrectly-refined crystal structures. Two cases, a P1 to Pl- revision and a chemically-incorrect structure that is refined in a correct space group, are discussed.     

Structure of the surface layer of mercury and adhesion of Langmuir monolayers on it

A model crystalline approximant of the surface layer (SL) structure of liquid mercury is formed using the algorithm, previously applied to form a crystalline approximant of the SL structure of water, the experimental data on the SL structure of mercury, and the stereochemical data for Hg atoms in the α-Hg crystalline phase and bulk liquid mercury. The correspondence of the metrics of the crystalline approximant proposed for the SL structure of mercury and Langmuir monolayers composed of organic molecules with hydrocarbon tails and different hydrophilic groups on liquid mercury to the position of molecules along mercury SL is shown.     

Moving of a nonhomogeneous, porous floc normal to a rigid plate

The boundary effect on the moving of a porous, nonhomogeneous, spherical floc normal to a rigid plate is analyzed theoretically for the case of low to medium Reynolds number. In particular, the drag force acting on the floc under various conditions is evaluated. A two-layer structure is adopted to simulate the nonhomogeneous nature of a floc. We show that if a floc is away from the plate, the streamlines surrounding the floc are distorted, but the degree of distortion becomes less significant if the floc is near the plate. The modified drag coefficient of a porous floc is orders of magnitude smaller than that of the corresponding rigid particle. For a fixed volume-averaged permeability, the effect of the presence of the plate on the behavior of a nonhomogeneous floc is more significant than that of a homogeneous floc, and this effect depends largely on the structure of a floc. The nonhomogeneous structure of a floc leads to a positive deviation from a Stokes-law-like correlation in the modified drag coefficient, and the smaller the volume-averaged permeability of a floc the greater the deviation. The presence of the plate has the effect of reducing this deviation. The nonhomogeneous structure of a floc on its modified drag coefficient is pronounced when it is close to a boundary.     

Effects of tertiary amine accelerators on curing of epoxide resins

The effects of seven tertiary amine accelerators on curing of bisphenol-type epoxide resins using azelaic acid as a curing agent have been investigated. The structure of the cured resins is characterized and reaction and structure schemes are proposed. The reaction mechanism and the resulting structure of the resin depend on the basicity of the accelerator. With increasing accelerator basicity crosslinking in the cured resin increases. Characterization results indicate that the network structure consists of ether bonds or a mixture of ether and ester bonds; the linear structure consists of only ester bonds. The structure and, therefore, the properties of the cured epoxide resin may thus be regulated by selection of the amine basicity.     

Modelling of nano-alloying and structural evolution of bimetallic core-shell nanoparticles obtained via the microemulsion route

A Monte Carlo model has been developed to describe the formation of bimetallic nanoparticles via the microemulsion route. The motivation stems from the need to understand the kinetics of nanoparticle formation in microemulsion droplets in order to determine the best experimental conditions to synthesize a nanoparticle with a given structure. We focus our study on the influence of the homogeneous and heterogeneous critical nucleus sizes of both metals on nanoparticle structure, as well as the role played by the surfactant film flexibility. The study reveals that the final structure is sensitive to changes in the critical nucleus numbers, because these parameters determine the rate of nucleation. An increase in the difference between nucleation rates of both metals gives rise to a better segregation of metals in the final nanoparticle. Likewise, as long as the formation of heterogeneous seeds is faster, the degree of alloying is greater. Finally, a fast material intermicellar exchange leads to a better mixture of metals, so the influence of the critical nucleus sizes on nanoparticle structure becomes less pronounced as the flexibility of surfactant film is increased.