纯水溶液中的氢键交换反应路径

利用分子动力学模拟方法对纯水溶液的氢键转化动力学性质进行了深入的微观探讨,溶液中非氢键构型为寿命较短(0.1～0.2 ps)的过渡态构型,我们发现氢键交换通过两种过渡构型完成,氢键角度扭曲激发后与氢键第一壳层水分子沿路径1交换,氢键径向拉伸激发后与氢键第二壳层水分子沿路径2交换,过渡态路径的选择具有温度依赖性.氢键转化需在旧氢键受体氢键过量和新氢键受体氢键不足,同时满足交换反应空间结构要求下才能完成.氢键交换反应对水分子平动和转动行为起着决定作用.     

氢键准则在DMSO水溶液中应用的评价

利用分子动力学模拟方法, 分别采用几何准则和能量准则分析了不同浓度下的二甲基亚砜(DMSO)水溶液的氢键统计和动力学等特性. 结果显示, 两种氢键准则可以很好地反映出溶液的氢键性质随浓度的变化趋势. 通过分析比较发现, 由于几何准则不能有效地排除具有弱对势能的分子对, 因此其统计的氢键数量要大于能量准则的结果.此外, 能量准则对于分子间相对取向的区分存在不足, 进而引起氢键寿命的计算结果偏大.因此,为使氢键分析更加准确, 本文建议使用几何-能量混合型氢键准则.     

铵根离子在水溶液中的跳跃转动机理

铵根离子的动力学行为与生命体内的生物和化学过程密切相关.依据流体力学理论,由于铵根离子与水分子之间存在多个强氢键,其转动应较慢,但实验结果并非如此,其转动的微观机理尚不清晰.本文分子动力学模拟研究表明,水溶液中铵根离子主要以快速、大角度的跳跃方式进行转动,像水分子一样遵从扩展分子跳跃转动模型.通过微观转动模式的分解和两种转动弛豫时间的比较发现,相对其氢键骨架的扩散转动,跳跃转动对其转动速率贡献更大,并随浓度增大不断强化.与水分子氢键交换方式相比,铵根离子更倾向于在非氢键相连的水分子间发生交换.     

乙二醇的分子间氢键结构动力学的飞秒非线性红外光谱

利用稳态线性红外光谱和飞秒泵浦-探测红外光谱技术, 研究了在乙腈(MeCN)、丙酮(AC)、四氢呋喃(THF)和二甲基亚砜(DMSO)溶剂中乙二醇(EG)的结构和羟基(―OH)伸缩振动动力学. 结果表明, 乙二醇的―OH伸缩振动的频率位置、峰宽以及振动弛豫动力学都表现出强烈的溶剂依赖性. 乙二醇溶液中至少存在两种形式的分子间氢键, 一种是溶质-溶剂团簇的分子间氢键, 另一种是溶质-溶质团簇的分子间氢键. 量子化学计算预测的―OH伸缩振动频率的溶剂依赖性与我们的红外光谱实验观测结果一致. 进一步, 我们发现在乙腈中参与形成溶质-溶剂团簇氢键的乙二醇―OH伸缩振动具有最慢的弛豫动力学, 丙酮和四氢呋喃次之, 而最快的弛豫动力学过程发生在二甲基亚砜中. 在每一溶剂条件下, 乙二醇/乙二醇溶质团簇中―OH伸缩振动弛豫都更快一些. 本文结果有助于认识在溶质-溶质、溶质-溶剂分子团簇共存的体系中不同分子间氢键的结构动力学特性.     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

十二烷基硫酸钠对聚乙烯醇亚浓水溶液流变行为的影响

表面活性剂会影响聚乙烯醇(PVA)分子间及分子内氢键形成,进而改变其水溶液的流变响应.本文在确定十二烷基硫酸钠(SDS)在PVA亚浓水溶液中的临界聚集浓度(CAC)和临界胶束浓度(CMCP)基础上,考察了SDS对PVA亚浓溶液(10 wt%)流变行为的影响.研究发现,不同浓度SDScsur对PVA水溶液稳态流变行为的影响差异较大:(1)当csur CMCP,随着csur增加,胶束起物理交联点作用,ηa增大,复合溶液的动态储能模量亦显著增大.加入SDS后,PVA体系内结合水的数目降低,但当csur> CMC后,结合水的数目几乎不变,黏流活化能也表现出相近的变化规律.与稀溶液相比,SDS对PVA亚浓溶液的降黏幅度较大.     

甲酰胺水溶液的分子动力学模拟

为了解重要的生化模型甲酰胺在水溶液中的微观结构, 采用全原子力场在全浓度范围内对甲酰胺溶液进行了分子动力学模拟, 得到了溶液的径向分布函数, 分析计算了溶质和溶剂分子间的相互作用, 对甲酰胺和水分子的氢键缔合情况进行了分析. 研究发现羰基侧的H原子与水分子能形成C—H…O弱相互作用. 在作者早期的研究中发现, 此相互作用对于阻碍甲酰胺的异构化具有重要意义, 特别是当甲酰胺在溶液中含量增大时, 此相互作用更加不能忽视. 全浓度溶液的模拟表明, 甲酰胺在稀浓度区可以促进水局部结构的增强, 随FM浓度增加, 由水的自身缔合转变为水与FM的交叉缔合, 在FM高浓度区, 两者的交叉缔合将逐渐被甲酰胺自身的线状缔合代替.     

三元水溶液体系中氢键作用与分子结构的拉曼光谱研究

采用拉曼光谱研究了水-乙腈-二甲基亚砜三元水溶液体系中氢键作用对分子结构的影响.结果表明,在三元水溶液中乙腈C≡N键的电子云向碳原子发生偏移,二甲基亚砜中S=O双键的电子云向硫原子发生偏移;在三元体系中乙腈和二甲基亚砜与水形成氢键时存在明显的竞争关系,出现乙腈分子和二甲基亚砜分子共用1个水分子形成复合物的情况,并且随着水含量的增加,共用水分子的情况逐渐消失.     

离子对水溶液微观结构和动力学的影响

离子对水溶液结构和动力学性质的影响具有特异性,本文对此进行了一系列的分子模拟研究,发现一价单原子离子的溶解结构与阴离子-阳离子、离子-水和水-水之间的竞争作用有关,离子间成对趋势符合Collins规则,以水分子为桥的离子对结构是离子在水中溶解的重要方式,并具有不对称性.在Na SCN和KSCN极稀水溶液中,盐对水分子活动性影响体现为阴、阳离子效应的叠加,符合Hofmeister离子序和Jones-Dole黏度B系数的定量趋势,随着浓度增大,离子协同性和离子团簇的影响逐渐增强,浓溶液中普遍具有拖慢效应.水溶液中水分子转动与氢键交换相关,存在大角度跳跃转动和氢键对协同扩散转动两种方式,阴离子效应主要体现在对跳跃转动的影响,由阴离子与水分子间氢键强度决定,阳离子主要通过间接方式同时影响两种方式,影响程度与电荷密度有关.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

New model pair potential for water. Effect of inclusion of specific O⋯H interactions on the topology and dynamics of the hydrogen-bond network

Classical molecular dynamics was used to calculate the topologic and dynamic characteristics of H-bond networks in water, using various model potentials. The explicit inclusion of intermolecular interactions of oxygen and hydrogen atoms leads to a model involving additional stabilization of tetrahedrally coordinated molecules and, as a consequence, increased number of such molecules in the system. The H-bond lifetimes point to a strongly correlated molecular motion in the immediate environment.     

Stabilizing role of lithium in structures of complex oxide compounds as an instrument for crystal chemical design

Various hydrogen bond lifetime distribution functions, used to describe the breaking and formation dynamics of these bonds in a computer experiment, are examined and relationships between them are found. The procedures for calculating these functions by the molecular dynamics method are described and the results for water models of 3456 molecules at 310 K are reported. The peak of short-lived spurious H-bonds, which results from short-time violations of hydrogen bonding criteria induced by dynamic intermolecular vibrations of molecules, prevails in the types of distributions most often referred to in the literature. A special distribution that appears to have not been used before is proposed. Along with short-lived bonds, it manifests long-lived ones whose lifetime is determined by the genuine, or random, hydrogen bond breaking rather than by dynamic. A technique to exclude dynamic effects and reveal the genuine H-bond breaking is proposed. This allows the evaluation of the average lifetime of “true” H-bonds that turns out to exceed 3 ps.     

Outline of a transition-state hydrogen-bond theory

Though the H-bond is well characterized as a D–H:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O–HO energies range from 0.1 to 31 kcal mol⁻¹). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK_a equalization principle, showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid–base properties (PA or pK_a) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference ΔpK_a=pK_AH(D–H)−pK_BH(A–H⁺) or, alternatively, ΔPA=PA(D⁻)−PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D–HA to DH–A via the DHA transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N–HO to NH–O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.     

Fluorescence properties of fluorescein, tetramethylrhodamine and Texas Red linked to a DNA aptamer

We report the picosecond time-scale fluorescence dynamics of a dye-labeled DNA oligonucleotide or "aptamer" designed to bind specifically to Immunoglobulin E. Comparison of the photophysics of Texas Red (TR), fluorescein and 5'-carboxytetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for measurements of oligonucleotide structure and dynamics. The fluorescence decay of the TR-aptamer is a simple single exponential with a weak temperature dependence. The fluorescence decay of the fluorescein-aptamer (fl-aptamer) is pH dependent and displays a complex temperature dependence with significant changes on melting of the aptamer tertiary structure. Despite its similarities to TR, TAMRA is strongly quenched when conjugated to the aptamer and displays complex fluorescence kinetics best described by a distributed rate model. Using the maximum entropy method, we have discovered two highly temperature-dependent fluorescence lifetimes for the TAMRA-aptamer. One of these lifetimes is similar to that of free TAMRA and displays the same temperature dependence. The other lifetime is quenched and displays a temperature dependence characteristic of a charge transfer reaction. These data set TR apart as an attractive alternative to TAMRA and fluorescein for studies such as fluorescence polarization and fluorescence resonance energy transfer, where environmental sensitivity of the probe is not desired.     

Structure and dynamics of water confined in dimethyl sulfoxide.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior.     

The topological and dynamic characteristics of H-bond networks in water according to computer simulation results

The classic molecular dynamics methods were employed to calculate the topological and dynamic characteristics of H-bond networks in water with the use of various model potentials. The explicit inclusion of specific intermolecular interactions between oxygen and hydrogen atoms additionally stabilized tetrahedrally coordinated molecules and, as a consequence, increased their number in the system. The lifetimes of H-bonds were found to characterize high correlation of movements of nearest environment molecules.     

Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach

Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Proper and improper hydrogen bonds in liquid water

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.