Probing the acetylcholinesterase inhibition of sarin: a comparative interaction study of the inhibitor and acetylcholine with a model enzyme cavity

Interaction energies have been estimated between sarin and a model enzyme cavity of acetylcholinesterase (ACHE) using the density functional and M?ller-Plesset second-order perturbation (MP2) levels of theories. The calculated interaction energies have been compared with those of acetylcholine and the same model ACHE cavity. The ACHE...sarin and ACHE...acetylcholine (Ach) structures have been optimized using DFT based two-layer ONIOM hybrid calculations. The nature of interactions has been investigated in detail using an interaction energy partitioning technique. The effects of solvation on the interaction energies have also been taken into account. An inhibition mechanism during the uptake of sarin inside the ACHE cavity has been proposed from the comparison of the energetics of the ACHE...sarin and ACHE...Ach complexes.     

Radiation-induced solid-state polymerization in binary systems. II. Relationship between polymerization rate and physical structure of binary systems

The radiation-induced solid-state polymerization of binary systems consisting of acrylic monomer (acrylamide, acrylic acid) and organic compounds was investigated. In the previous paper on binary systems the authors reported that the rate of polymerization increased in the solid state (eutectic mixture systems). The mechanism of rate increase has been investigated by examination of phase diagrams, viscosities, and surface tension of the binary systems. Viscosity and surface tension are the measure of the molecular interaction of the two-component systems. In addition, the effect of linear crystal growth rate and half maximum width of the x-ray diffraction diagram of the crystallization process were determined. The larger the molecular interaction between the two components, the slower the linear crystal growth rate of monomer. The size of the monomer crystal decreases and the dislocation density of the monomer crystals increases in systems with large molecular interaction. Consequently it can be concluded that the physical structure of a binary solid system is the most important parameter determining the rate increase of solid-state polymerization. Dislocation on the grain boundary is more important than defects inside of the crystal lattice. It was found that the acceleration of polymerization rate is large in binary systems with larger molecular interaction. In some systems such as organic acid—amide systems with strong hydrogen bonds, glassy phases may be formed in which monomer may readily polymerize at very low temperatures.     

Molecular dynamics simulation of polymer dispersed liquid crystal droplets under competing boundary conditions

This paper is devoted to the molecular dynamics simulation of structural organization inside a polydispersed liquid crystal (LC) droplet under competing boundary conditions. The droplet is assumed to be placed at the liquid crystal interface between two different regions of the solid polymer matrix, which accordingly separates the droplet into two hemispheres: the first of these is under radial boundary conditions; the second hemisphere is under bipolar boundary conditions. The droplet is considered as a jagged sphere filled with LC molecules, modelled as classical spins (unit vectors), whose centres of mass are associated with sites of a cubic lattice inside the cavity. The orienting action of the polymer matrix, and hence the resulting boundary conditions, are modelled by the interaction between the internal LC molecules (possessing only orientational degrees of freedom), and those of a delimiting surface layer (a jagged spherical shell), whose orientations are fixed, radial or bipolar, respectively. All interactions are modelled by the short range McMillan pair potential. The molecular orientation inside the LC droplet has been determined for various anchoring strengths of the interaction between internal spins and boundary layers. We have investigated the structure of the spherical defect resulting in the central region of the droplet, as well as of the boojum ‐ like defects existing near the poles of the droplet. It has been found that a change of relative radial and bipolar anchoring strengths can affect both central and boojum ‐ like defects. The effect of an external field on the molecular orientation inside the droplet has also been investigated. It has been found that a sufficiently strong external field increases the radius of the spherical defect placed in the central region of the droplet.     

Molecular dynamics simulation of polymer dispersed liquid crystal droplets under competing boundary conditions

This paper is devoted to the molecular dynamics simulation of structural organization inside a polydispersed liquid crystal (LC) droplet under competing boundary conditions. The droplet is assumed to be placed at the liquid crystal interface between two different regions of the solid polymer matrix, which accordingly separates the droplet into two hemispheres: the first of these is under radial boundary conditions; the second hemisphere is under bipolar boundary conditions. The droplet is considered as a jagged sphere filled with LC molecules, modelled as classical spins (unit vectors), whose centres of mass are associated with sites of a cubic lattice inside the cavity. The orienting action of the polymer matrix, and hence the resulting boundary conditions, are modelled by the interaction between the internal LC molecules (possessing only orientational degrees of freedom), and those of a delimiting surface layer (a jagged spherical shell), whose orientations are fixed, radial or bipolar, respectively. All interactions are modelled by the short range McMillan pair potential. The molecular orientation inside the LC droplet has been determined for various anchoring strengths of the interaction between internal spins and boundary layers. We have investigated the structure of the spherical defect resulting in the central region of the droplet, as well as of the boojum - like defects existing near the poles of the droplet. It has been found that a change of relative radial and bipolar anchoring strengths can affect both central and boojum - like defects. The effect of an external field on the molecular orientation inside the droplet has also been investigated. It has been found that a sufficiently strong external field increases the radius of the spherical defect placed in the central region of the droplet.     

Atomic structure and bonding interaction in a layered molybdenum disulfide compound with trimethylphenylammonium cations

The atomic structure of the layered nanocrystalline molybdenum disulfide compound with trimethylphenylammonium cations has been determined for the first time using X-ray powder diffraction analysis adapted for turbostratically disordered systems and quantum chemical density functional theory calculations. It has been demonstrated that, in this compound, a conducting modification of MoS₂ monolayers is stabilized, which is metastable under common conditions. Bonding interaction inside the molybdenum disulfide layers as well as between these layers and organic cations, revealed in the framework of Bader’s atoms in molecules theory, has been considered.     

磷脂酶A2及其复合物的分子动力学研究

本文运用分子动力学方法对磷脂酶A2的自由态以及有机小分子形成的复合物进行了研究．通过模型构建分子动力学模拟得到了磷脂酶A2与配体结合的模型，与磷脂酶A2的自由态相比，其口袋更为宽松，组成口袋的残基的结构趋于稳定，但催化残基的柔性变大．研究结果为药物分子设计提供了有用的信息．     

Radicals formed in cytosine–hydrochloride(thiocytosine) single crystals: Insights from a DFT study

Specific properties of chlorine interaction with thiocytosine in comparison to chlorine interaction with cytosine in the system formed by the incorporation of small amount of thiocytosine in a cytosine–hydrochloride crystal lattice have been investigated by DFT calculations of the g-tensor of sulfur centered radical. Taking account of the crystal environment of the radical site it has been shown that the main reason for difficulties in interpretation of spectroscopic as well as theoretical results in this model system is the considerable spin density spread on both chlorine and sulfur atoms. From comparison of the results for the proposed model structure with accessible spectroscopic data, the specific direction in which charge transfer in the investigated system may take place has been pointed out.     

The Transannular Interaction in [2.2]Paracyclophane: Repulsive or Attractive?

The molecular structure and charge density distribution in the crystal of [2.2]paracyclophane derived from the high‐resolution single crystal X‐ray diffraction data at 100 K is reported together with ab initio calculations of this molecule. Analysis of the atomic, anisotropic displacement parameters in a “rigid‐body” model approximation has revealed that the molecule is ordered in the crystal. Topological analysis of the electron density and potential‐energy density‐distribution functions has demonstrated that there is no “through‐space” interaction between the rings in the molecule. The role of the ethylene bridges and distortion of the aromatic desks on the inter‐ring interaction are discussed.     

Modeling Steroid 5alpha-reductase and Characterizing Its Potential Active Sites

Steroid 5alpha-reductase of human is an enzyme in the biosynthetic pathway from testosterone (T) to dihydrotestosterone (DHT). Up to now, no crystal structure of this enzyme has been reported. However, knowledge of the tertiary structure and possible active sites is essential for understanding the catalysis mechanism and for the design of inhibitors. A model with putative active sites has been created and evaluated by using homology modeling and molecular docking techniques based on the bioinformatics knowledge. The homology model is optimized in Swiss PDB Viewer with MM method and substrate structures before docking are also optimized on HF/6-31G. The active site for the docking of NADP, T, DHT and Finasteride is located near the N-terminus of enzyme. Four active amino acids in the active site are identified as Ala26, Arg53, Arg176 and Lys177. Reaction procedure, binding pattern of active sites, the types of weak interaction and so on are also discussed.     

Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals

Experimental and theoretical studies of electron densities and the corresponding derived entities such as electrostatic potentials have been the primary means of understanding the chemical nature and electronic properties of crystalline substances. Conventional crystal calculation methods such as the embedded cluster models are capable of performing calculations on small and medium-sized molecules, while periodic ab initio methods can treat crystals with up to 200 atoms per unit cell. A linear scaling method, viz. the molecular tailoring approach, has recently been developed for obtaining ab initio quality one-electron properties. In the present study, the molecular tailoring approach is employed to generate electron density, electrostatic potential and interaction density maps with the ibuprofen crystal as a test case. The interaction density and electrostatic potential maps produced in the present work succinctly bring out the actual crystalline environment around a given reference molecule by including the interactions with atoms in its neighborhood. The results obtained from the molecular tailoring approach may thus be expected to enhance our understanding of the environment in the crystalline material with reasonably small computational effort.Contribution to the Jacopo Tomasi Honorary Issue     

Determining the strengths of hydrogen bonds in solid-state ammonia and urea: insight from periodic DFT calculations

Plane-wave density functional theory has been applied to determine the strengths of hydrogen bonds in the phase I crystal structures of ammonia and urea. For ammonia, each component of the trifurcated hydrogen bond has been found to be almost as strong as a standard N-H.N interaction, and for urea the strengths of the two different N-H.O interactions have been determined by a quantum mechanical technique for the first time.     

Molecular and crystal structure of 1-(2-hydroxyethyl)-1,2-dihydro-3,4,6-trimethyl-2-oxopyrimidinium iodide: the N-alkylation product of xymedone

The structure of xymedone iodo methylate is determined by X-ray crystallography. The molecular and crystal structure of the compound is analyzed in comparison with xymedone whose X-ray crystallographic data have been obtained previously. The molecular and electronic structures of both compounds and noncovalent interactions in the ionic pair of xymedone iodo methylate are analyzed using the data of the quantum topological calculations. It is shown that the presence of the iodine anion results in an increase in the delocalization of the π electron density inside the heterocyclic moiety, the charge redistribution inside the molecule, and consequently, in significant distinctions in crystal packings.     

Ethane adsorption in slit-shaped micropores: influence of molecule orientation on adsorption capacity

Adsorption of ethane in a slit shaped micropore system has been studied by Monte Carlo molecular simulation by considering this hydrocarbon as a two interacting sites molecule. Ethane adsorption in pore sizes from 0.41 to 1.66 nm was simulated at 303 K. Microscopic characteristics of the adsorbed phase have been studied for pores of different size, comparing two density profiles: the molecule centre of mass profile and the molecular interaction site profile. Averaged angle distribution of molecule positions with respect to the slit plane across the pore width has been also obtained by simulation. These results were related to ethane molecule packing efficiency, which is also related to the adsorption capacity in terms of the adsorbed phase density. Packing efficiency presents an oscillation shape as the result of the adsorbate disorder inside the pore. Pressure influence on the adsorption has been studied by following pore filling by simulation. When pore condensation takes place and for pressures above condensation, fluid-fluid interactions are determinant in molecule disorder observed between the two adsorbed layers.     

Probing the non-analytic properties of exciton band structures by reflection spectroscopy

A method of probing the exciton band structure about the centre of the Brillouin zone is developed. Oblique angle reflectance spectra at angles of incidence up to 80° for a (001) face of an anthracene crystal have been obtained for both an air-crystal and a silica-crystal interface. A method for transforming the reflectance data to optical constants is developed and used. From this method the direction of propagation of radiation k? at any frequency inside the crystal for any incident angle can be determined. For a model of an isotropic crystal consisting of anisotropic molecules, dipole-dipole theory for an arbitrary k? is developed, exciton band structures from this theory are calculated and theoretical spectra based on these calculated band structures are presented. The theoretical spectra are in very good agreement with the experimental data. Information about the exciton density of states is deduced from the results.     

Studies of surface processes of electrocatalytic reduction of CO_2 on Pt(210), Pt(310) and Pt(510)

Surface processes of CO2 reduction on Pt(210), Pt(310), and Pt(510) electrodes were studied by cyclic voltammetry. Different surface structures of these platinum single crystal electrodes were obtained by various treatment conditions. The experimental results illustrated that the electrocatalytic activity of Pt single crystal electrodes towards CO2 reduction is decreased in an order of Pt(210)>Pt(310)>Pt(510), i.e., with the decrease of (110) step density on well-defined surfaces. When the surfaces were reconstructed due to oxygen adsorption, the catalytic activity of all the three electrodes has been enhanced to a cer- tain extent. Although the activity order remains unchanged, the electrocatalytic activity has been en- hanced more significantly as the density of (110) step sites is more intensive on the Pt single crystal surface. It has revealed that the more open the surface structure is, the more active the Pt single crystal electrode will be, and the easier for the electrode to be transformed into a surface structure that exhib- its higher activity under external inductions. However, the relatively ordered surfaces of Pt single crystal electrode are comparatively stable under the same external inductions. The present study has gained knowledge on the interaction between CO2 and Pt single crystal electrode surfaces at a micro- scopic level, and thrown new insight into understanding the surface processes of electrocatalytic re- duction of CO2.     

LiNiO2及掺杂化合物的结构与稳定性的第一性原理研究

应用第一原理局域密度泛函对LiNiO2及其掺杂化合物的晶体结构、能带结构和态密度进行了研究.结果表明:锂镍氧系正极材料是电子的良导体,在充放电过程中具有良好的稳定性,适合做锂离子电池的正极材料;在LiNiO2晶体中主要是O和Ni之间成键,镍离子和氧离子的相互作用比较强,Li在嵌入层状结构材料后部分失去电子,以离子状态存在.     

豆荚型纳米材料C60@SWNTs的制备和表征

通过气相扩散的方法将C60填入单壁碳纳米管（SWNTs）,制备了豆荚型纳米材料C60@SWNTs,并利用高分辨电子显微镜（HRTEM）和拉曼光谱（Raman spectra）对其进行了表征.结果均证明C60以较高的比例填充入单壁碳纳米管中.HRTEM结果表明,填入单壁碳纳米管的C60之间的距离与面心立方C60晶体中C60之间的距离有细微的差别,说明C60分子与SWNTs间存在弱的范德华相互作用.此外,还观察到在电子束的照射下,C60在SWNT中两两聚合的现象.