N2,O2水溶液光谱的分子动力学模拟

用分子动力学模拟方法研究了N2和O2水溶液的光谱性质．给出了能描述分子内部运动的溶质－溶剂相互作用势．对溶质和溶剂原子的速度自相关函数（VACF）作了计算．讨论了所得VACF的性质并计算了其谱密度．溶质分子振动谱出现的红移，与液态N2，O2的Raman实验结果相吻合．模拟得出的转动谱表明了溶剂分子对溶质转动运动的阻滞，模拟结果也表明VACF计算对溶液和液体光谱的研究十分有效．     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

The structure of the mixed OH + H2O overlayer on Pt[111

The structure of the mixed p(3 x 3)-(3OH + 3H2O) phase on Pt[111] has been investigated by low-energy electron diffraction-IV structure analysis. The OH + H2O overlayer consists of hexagonal rings of coplanar oxygen atoms interlinked by hydrogen bonds. Lateral shifts of the O atoms away from atop sites result in different O-O separations and hexagons with only large separations (2.81 and 3.02 angstroms) linked by hexagons with alternating separations of 2.49 and 2.813.02 angstroms. This unusual pattern is consistent with a hydrogen-bonded network in which water is adsorbed in cyclic rings separated by OH in a p(3 x 3) structure. The top-most two layers of the Pt atoms relax inwards with respect to the clean surface and both show vertical buckling of up to 0.06 angstroms. In addition, significant shifts away from the lateral bulk positions have been found for the second layer of Pt atoms.     

Coordination of water to organolead(IV) nitrates: The examples of [PbPh2(NO3)2(H2O)2] and [PbMe3(NO3)(H2O)]

The compound [PbPh₂(NO₃)₂(H₂O)₂] was synthesized and characterized by spectroscopic methods (IR; ¹H, ¹³C and ²⁰⁷Pb NMR) and mass spectrometry. An X-ray diffraction study showed that the crystal is a supramolecular tridimensional network of hydrogen-bonded PbPh₂(NO₃)₂(H₂O)₂ units in which the Pb atom is octacoordinated and adopts a distorted hexagonal bipyramidal geometry, with four O (bidentate nitrate) and two O (water) atoms in equatorial positions and two C-phenyl atoms in axial positions. The crystal of [PbMe₃(NO₃)(H₂O)], obtained as a byproduct in the synthesis of PbMe₂(NO₃)₂, contains chains of hydrogen-bonded PbMe₃(NO₃)(H₂O) units in which the Pb atom is pentacoordinated with a slightly distorted trigonal bipyramidal environment. In this arrangement the three C-methyl atoms are equatorial and the O atoms from the monodentate nitrate and the water molecule are axial.     

苯并三氮唑及其羧酸酯衍生物对铜缓蚀机理的分子动力学模拟研究

用分子动力学(MD)方法, 模拟计算了5种铜缓蚀剂[苯并三氮唑(BTA)、苯并三氮唑-5-羧酸甲酯(MBTC)、苯并三氮唑-5-羧酸丁酯(BBTC)、苯并三氮唑-5-羧酸己酯(HBTC)、苯并三氮唑-5-羧酸辛酯(OBTC)]与Cu₂O晶体的相互作用. 结果发现, 中性条件下缓蚀剂分子与Cu₂O晶体的结合能均大于酸性条件下的数值, 但两种条件下结合能的大小排序均为OBTC＞HBTC＞BBTC＞MBTC＞BTA. 对体系各种相互作用以及对关联函数g(r)的分析表明, 体系结合能主要由库仑作用提供, Cu₂O晶体中的Cu原子与缓蚀剂分子中的N原子之间形成了配位键. 在与Cu₂O(001)晶面结合过程中, BTA及其衍生物分子发生了扭曲变形, 但形变能远小于体系的非键相互作用能.     

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.     

氢键桥联双核铜配合物磁耦合的密度泛函研究

在密度泛函理论的基础上,应用对称性破损方法研究了氢键桥联双核铜模型配合物的磁耦合行为以及磁耦合常数随O-O距离的变化趋势.计算结果表明,反铁磁耦合作用来源于Cu原子的d_x²-y²和氧原子的p_x或p_y磁轨道的部分重叠,而H原子不参与磁耦合作用.磁耦合常数J与O-O距离r之间存在指数关系,而不是线性关系.     

水、甲醇和乙醇液体微结构性质的Car-Parrinello 分子动力学模拟

采用Car-Parrinello 分子动力学(CPMD)方法分别研究了水、甲醇和乙醇的液体微结构性质.研究结果显示:在水、甲醇和乙醇三个体系中O…O径向分布函数曲线的第一个峰位置分别为0.278、0.276 和0.275nm; O…H径向分布函数曲线的第一个峰位置分别为0.178、0.176和0.177 nm.表明基团(氢原子、甲基、乙基)的差异对O…O第一个峰的位置影响很小.但基团的差异对径向分布函数峰高的影响却很显著,由水到乙醇第一个峰的高度逐渐变高.空间分布函数表明氧原子和氢原子在溶剂分子周围有取向地分布,这与径向分布函数所表现出尖锐的第一个峰相一致.氢键分布分析显示,水、甲醇和乙醇的平均氢键数分别为3.62、1.99 和1.87,表明水形成了网状氢键结构,而甲醇、乙醇形成链状氢键结构.     

Hydro­gen bonds in the framework of bis{2-[bis(2-amino­ethyl)­amino]­ethanol}nickel(II) diperchlorate

The title molecule, [Ni(C₆H₁₇N₃O)₂](ClO₄)₂, possesses a crystallographic centre of symmetry at the Ni^II position. The coordination geometry around the Ni^II atom is distorted octahedral, consisting of six N atoms from two tripodal poly­amine ligands, while the ethanol O atoms of the ligands remain uncoordinated. The crystal packing shows two-dimensional layers and an infinite three-dimensional framework which is stabilized by a hydrogen-bonded network.     

Computational models for proton transfer in biological systems

A computational scheme based on a “mixed basis set” approach is applied to the study of the structure and the energetics in proton transfer systems. Five hydrogen-bonded systems of the type (CH₃H_nA ‥ H ‥ BH_mCH₃)⁺, where A and B can be N, O, or S, have been investigated with various minimal and extended basis sets. Calculations with the extended basis set yield double-well potential energy curves, which the minimal basis set is unable to reproduce. Calculations with the mixed basis set, constructed from an extended basis set on the atoms engaged in the hydrogen transfer part and a minimal basis set on the rest of the molecule, give predictions of geometries, potential energy curves, and relative energies similar to the results from the extended basis set. Inclusion of polarization functions in the mixed basis set becomes essential in systems that contain third row atoms. This scheme should become useful in studies of large molecules in which different parts can be represented at different levels of computational complexity.     

Mechanism of glucose oxidation by quinoprotein soluble glucose dehydrogenase: insights from molecular dynamics studies

We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme.PQQ.glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme.PQQ.glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H[bond]OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 A) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1[bond]H of glucose to the >C5[double bond]O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5[double bond]O. The rearrangement of [bond](H)C5(O-)[bond]C4([double bond]O)[bond] of II to [bond]C5(OH)[double bond]C4(OH)[bond] of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4[double bond]O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4[double bond]O4 oxygen and that of the O5 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.     

Binding energies of hydrogen-bonded complexes from extrapolation with localized basis sets

By incorporating effective basis sets containing diffuse functions only in the interaction region of hydrogen-bonded complexes into the simple extrapolation scheme suitable for such basis sets, an accurate estimation of the MP2 basis set limit hydrogen-bonding energies of formic acid tetramer, formamide tetramer, alanine-water, phenol-water, and guanine-cytosine base pair is made with all estimates falling within 0.1-0.3 kcalmol of the reference basis set limits. The basis sets for extrapolation are composed of the cc-pVDZ and cc-pVDZ plus highest polarization functions from the cc-pVTZ set, or cc-pVDZ and cc-pVTZ set, all of which are augmented by the diffuse functions of the atoms in the interaction region of hydrogen bond. In contrast to the extrapolated estimates by this method, density functional theory binding energies with B3LYP, B971, and TPSS methods yield the differences from the reference values as large as 3.9 kcalmol with much higher computational cost in most cases, signifying the efficacy of the employed extrapolation scheme for study of large hydrogen-bonded complexes.     

Weakly coordinating anions HA2-generated from oxoanions A- and their conjugate acids. Coordination equilibria,ionic conductivities,and the structures of [Cu2(H(CH3SO3)2)4]n and [Cu(CO)(H(CF3CO2)2)]2

The coordination or ion pairing of the hydrogen-bonded anions H(CF3CO2)2- and H(CH3SO3)2- to NEt4+, Li+, Cu+, and/or Cu2+ was investigated. The structure of [Cu2(H(CH3SO3)2)4]n consists of centrosymmetric dimeric moieties that contain two homoconjugated (CH3SO2O-H...OSO2CH3)- anions per Cu2+ ion, forming typical Jahn-Teller tetragonally elongated CuO6 coordination spheres. The oxygen atoms involved in the nearly linear O-H...O hydrogen bonds (O...O approximately 2.62 A) are not coordinated to the Cu2+ ions. The structure of Cu2(CO)2(H(CF3-CO2)2)2 consists of pseudo-C2-symmetric dimers that contain one homoconjugated (CF3COO-H...OCOCF3)- anion per Cu+ ion, forming highly distorted tetrahedral Cu(CO)O3 coordination spheres. Three of the four oxygen atoms in each hydrogen-bonded H(CF3CO2)2- anion are coordinated to the Cu+ ions, including one of the oxygen atoms in each O-H...O hydrogen bond (O...O approximately 2.62 A). Infrared spectra (v(CO) values) of Cu(CO)(CF3CO2) or Cu(CO)(CH3SO3) dissolved in acetonitrile or benzene, with and without added CF3COOH or CH3SO3H, respectively, demonstrate that HA2- anions involving carboxylates or sulfonates are more weakly coordinating than the parent anions RCO2- and RSO3-. Direct current conductivities of THF solutions of Li(CF3CO2) containing varying concentrations of added CF3COOH further demonstrate that Li+ and NEt4+ ion pair much more weakly with H(CF3CO2)2- than with CF3CO2-.     

Local order in aqueous NaCl solutions and pure water: X-ray scattering and molecular dynamics simulations study

The microstructures of pure water and aqueous NaCl solutions over a wide range of salt concentrations (0-4 m) under ambient conditions are characterized by X-ray scattering and molecular dynamics (MD) simulations. MD simulations are performed with the rigid SPC water model as a solvent, while the ions are treated as charged Lennard-Jones particles. Simulated data show that the first peaks in the O...O and O...H pair correlation functions clearly decrease in height with increasing salt concentration. Simultaneously, the location of the second O...O peak, the signature of the so-called tetrahedral structure of water, gradually disappears. Consequently, the degree of hydrogen bonding in liquid water decreases when compared to pure fluid. MD results also show that the hydration number around the cation decreases as the salt concentration increases, which is most likely because some water molecules in the first hydration shell are occasionally substituted by chlorine. In addition, the fraction of contact ion pairs increases and that of solvent-separated ion pairs decreases. Experimental data are analyzed to deduce the structure factors and the pair correlation functions of each system. X-ray results clearly show a perturbation of the association structure of the solvent and highlight the appearance of new interactions between ions and water. A model of intermolecular arrangement via MD results is then proposed to describe the local order in each system, as deduced from X-ray scattering data.     

Proton relay in a one-dimensional hydrogen-bonded chain composed of water molecules and a squaric acid derivative.

The crystal structure of a hydrated crystal of bis(squaryl)biphenyl (BSQB*4H2O), in which two squaric acid moieties are connected with a 4,4'-biphenyl unit, was characterized by the presence of a one-dimensional hydrogen-bonded chain composed of BSQB and water molecules. X-ray crystallographic analysis showed that BSQB exists in a dianion form and that, on average, two of the four water molecules are protonated. The enhanced temperature dependence of the thermal parameters of the oxygen atoms of the water molecules suggested dynamic disorder of the water molecules. The solid-state magic angle spinning deuterium NMR spectrum of BSQB*4D2O revealed that deuterons are exchanged between heavy water molecules and oxonium ions with an exchange rate of ca. 700 Hz around 250 K and that deuterons start to migrate in a hydrogen-bonded cluster of water molecules. Ac dielectric measurements were also used to examine the dynamic process in the hydrated crystal. The dielectric permittivity of the crystal dramatically increased above 250 K with a distinct frequency dependence (epsilon' = 4.7 x 10(4) at 340 K and 1 kHz). The frequency dependence of tan delta at 290 K exhibited a maximum at 3.0 kHz, and this maximum shifted to lower frequencies when the temperature of the crystal decreased. These experimental results suggested that in the one-dimensional hydrogen-bonded chain of BSQB*4H2O a proton relay between oxonium ions and water molecules occurred within a cluster of four water molecules and that the relay was transmitted to the adjacent cluster mediated by the modulation of the negative charge distribution of the BSQB dianion. These phenomena were interpreted as the solitonic migration of the charged domain boundaries along the one-dimensional hydrogen-bonded chain.     

纳米Al2O3颗粒对纯Fe液诱导凝固过程的分子动力学模拟

采用分子动力学(MD)方法模拟了不同半径大小的纳米Al2O3颗粒夹杂在三个温度下(1750、1730和1710K)对纯Fe液的诱导凝固过程,并分析了作为诱导核心的纳米Al2O3颗粒的结构演变及其对Fe原子体系的凝固过程的影响.发现在诱导过程中,纳米Al2O3颗粒的内部保持较好的晶型结构,仅表面原子有结构变形;诱导凝固的Fe原子主要为面心立方(fcc)和密排六方(hcp)原子;纳米Al2O3颗粒的尺寸越大,发生诱导凝固的温度越高;诱导凝固得到的Fe晶体的晶格取向受纳米Al2O3颗粒在Fe液中的漂移程度影响.     

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.     

醇及脱氧核糖与水分子间三体作用强度的快速准确计算

快速准确预测醇及脱氧核糖分子与水形成的氢键复合物的三体作用强度, 对准确模拟水环境下蛋白质和DNA的结构和功能至关重要. 基于对多体极化作用的理解, 在可极化偶极-偶极作用模型(PBFF)基础上, 将体系中的极性化学键视为化学键偶极, 通过模拟键偶极的极化计算了醇及脱氧核糖与水分子形成的氢键复合物的三体作用能. 通过拟合甲醇与水氢键复合物的三体作用能随分子间距离变化的能量曲线确定了所需的参数. 将模型和所确定的参数应用于计算更多的甲醇、 乙醇及脱氧核糖与水氢键复合物的三体作用能, 检验了模型的准确性和参数的可转移性. 计算结果表明, 可极化偶极-偶极作用模型及所确定的参数能够较好地预测具有不同结构的氢键复合物的三体作用强度, 其精度可与MP2方法的计算精度相当.     

Repeated Elements of the Structure of Liquid Monoethanolamine

For the first time, in F-structures of liquid monoethanolamine that were constructed by molecular dynamics simulations at various temperatures, repetition of structural triangles formed by hydrogen-bonded coordinating atoms (O and N) was revealed. A correlation was found between the revealed features of the molecular dynamics structures and the characteristics of monoethanolamine clusters determined by quantum mechanical calculations. It was shown that there are two main types of triangular motifs that ensure strong binding in the system owing to peculiarities of the electron distribution.