Hydrogen bonding without borders: an atoms-in-molecules perspective

It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.     

On the mutual diffusion properties of ethanol-water mixtures

The structural organization, the number of hydrogen bonds (H bond), and the self- and mutual diffusion coefficients of ethanol-water mixtures were studied by molecular dynamics simulation. It was found that both the numbers of H bonds per water and per ethanol decrease as the mole fraction of ethanol increases. The composition dependences and the relationships between the self- and the mutual diffusion coefficients were further discussed. The self-diffusion coefficient of water has a large drop as the concentration of ethanol increases from 0 to 0.3 and then it nearly keeps constant, while that of ethanol has a minimum around ethanol mole fraction of 0.5. The mutual diffusion coefficient could be divided into two parts, the kinematic factor and the thermodynamic factor. Both the kinematic and thermodynamic factors for ethanol-water mixtures were calculated. It was found that the change trend of mutual diffusion coefficients with the composition is mainly dependent on the thermodynamic factors.     

Effect of intermolecular hydrogen bonding on the molecular structures of imidazole and 1,2,4-triazole: A study by ab initio molecular orbital calculations

The effect of intermolecular hydrogen bonding in the solid state on the molecular structures of imidazole and 1,2,4-triazole has been studied by SCF ab initio molecular orbital calculations at the HF/6-31G^* level. The crystals of these species contain endless chains of molecules, connected by unusually strong N-H N hydrogen bonds. Our simulation of the crystal field, based on two simple models, unequivocally shows that hydrogen bond formation not only lengthens the N-H bond but also causes a concerted change in the length of two N-C bonds. The change indicates that the contribution of a polar canonical form to the structure of the molecule increases in going from the gaseous phase to the crystal. This provides a rationale for the strong intermolecular hydrogen bond occurring in the solid state. We have also optimized the geometry of the free molecules at the MP2/6-31G^* level, to investigate the effect that correcting for electron correlation has on the equilibrium structure of these systems.     

炼焦煤的官能团结构分析及其黏结性产生机理

以11种炼焦煤为研究对象,分别进行FT-IR和黏结指数G测试。采用Peak Fit软件对FT-IR谱峰进行分峰拟合和定量计算,研究炼焦煤特征官能团含量与其黏结性间的关系。结果表明,煤黏结性大小与其FT-IR吸收峰密切相关,特别是3 000-2 800和3 700-3 000 cm-1两个吸收带;脂肪族结构是煤黏结性形成的主要决定因素,通常脂肪链越短或支链化程度越高,越有利于煤的黏结性形成;含-OH(或-NH)的氢键缔合结构可以与脂肪链协同作用,共同决定煤的黏结性能。不论煤分子有多大,只要是结构单元缩合度较小而作为桥键的脂肪链较多的结构形式,在热解过程中就会生成大量适度分子量、以结构单元为基元的液相物质。氢键是煤中主要的分子间作用形式,当若干形成氢键的官能团聚集缔合时,其相互作用会更强,甚至会形成类似超分子的结构;在形成胶质体阶段,这类氢键缔合的结构也会被打破,并形成以胶质体液相为主的物质。这些液相物质的存在,有利于胶质体的流动、黏连和固化成为半焦,从而最终获得优越的黏结性。     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

鸟嘌呤与氨基酸残基体系的极化力场

发展了应用于鸟嘌呤G和氨基酸残基体系的浮动电荷力场, 该力场明确定义了孤对电子和键的电荷和位置, 通过电荷随着环境的浮动来体现极化效应; 通过氢键拟合函数k_HB描绘了氢键键能. 应用量子化学方法, 对G与氨基酸残基体系从氢键、 几何结构及电荷分布3个方面展开计算及分析, 并以其为基准, 确定参数发展了适用于G与氨基酸残基氢键体系的ABEEMσπ PFF. 采用3种不同力场模拟目标分子的结构和性质. 模拟结果表明, 发展的ABEEMσπ PFF与量子化学方法具有最好的一致性, 可用于模拟生物大分子体系.     

The effect of methyl group on the cooperativity between three types of hydrogen bond: O?H···O,C?H···O,and O?H···π

The effect of the methyl group on the cooperativity between three types of hydrogen bond (O H···O, C H···O, and O H···π) in cyclic complex involving an acetylene and two waters has been studied on the basis of high-level ab initio calculations. The total interaction energy of three hydrogen bonds increases as the number of methyl group in the complex increases. The binding distances of O H···π and O H···O hydrogen bonds shorten, while that of C H···O hydrogen bond elongates with increasing methyl group. This indicates that addition of methyl group leads to enhancement of O H···π and O H···O hydrogen bonds, and weakening of C H···O hydrogen bond, as also shown in frequency shift, chemical shifts, charge populations, and stabilization energies of orbital interactions. Although the presence of methyl group has a complicated effect on different type of hydrogen bond, the cooperativity of three hydrogen bonds increases in general with the addition of methyl group. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅲ): Equation of state and fluctuations

The equation of the state of the hydrogen bonding fluid system of AaDd type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover, the number density fluctuations of both molecules and hydrogen bonds as well as their spatial correlation property are investigated. Furthermore, an equation describing relation between the number density correlation function of "molecules-hydrogen bonds" and that of molecules and hydrogen bonds is derived. As application,taking the van der Waals hydrogen bonding fluid as an example, we considered the effect of hydrogen bonds on its relevant statistical properties.     

The progression of strong and weak hydrogen bonds in a series of ethylenediammonium dithiocyanate derivatives--a new bonding protocol for macromolecules?

The experimental charge densities for a series of sym-N-methyl-substituted ethylenediammonium dithiocyanate salts have been investigated based on low-temperature and high-resolution X-ray diffraction data. This series of organic dications provides both strong and weak hydrogen bonding networks that vary depending on the N-H : SCN(-) (donor/acceptor) ratios. The number of N-HN hydrogen bonds connected to each cation increases (linear to bifurcated) as the number of N-H donor groups increases. The bifurcated thiocyanate anions also form a less energetic N-HS hydrogen bond. The presence of more than one hydrogen bond acceptor on each thiocyanate anion results in a competition between the sulfur and nitrogen atoms in forming both strong and weak hydrogen bonds. The formation of a significant number of weak hydrogen bonds is shown to play a crucial role in stabilizing these organic ionic crystals. The progression of these organic dications (smaller to larger N-H : SCN(-) ratios) results in the weaker hydrogen bonds playing a smaller role in stabilizing the crystalline structures. In addition, the electron density along the saddle point has been shown to vary significantly from weak hydrogen bonds to van der Waals interactions. This has led to a better understanding of the progression of hydrogen bonding in the crystalline states of sym-N-methyl substituted ethylenediammonium dithiocyanate salts and provides insight into the relationship between strong and weak hydrogen bonds in organic ionic crystals.     

Hydrogen bond dynamics and microscopic structure of confined water inside carbon nanotubes

We have investigated the density and temperature dependences of microscopic structure and hydrogen bond dynamics of water inside carbon nanotubes (CNTs) using molecular dynamics simulation. The CNTs are treated as rigid, and smoothly truncated extended simple point charge water model is adopted. The results show that as the overall density increases, the atomic density profiles of water inside CNTs become sharper, the peaks shift closer to the wall, and a new peak of hydrogen atomic density appears between the first (outermost) and second layer. The intermittent hydrogen bond correlation function C(HB)(t) of water inside CNTs decays slower than that of bulk water, and the rate of decay decreases as the tube diameter decreases. C(HB)(t) clearly decays more slowly for the first layer of water than for other regions inside CNTs. The C(HB)(t) of the interlayer hydrogen bonds decays faster than those of the other regions and even faster than that of the bulk water. On the other hand, the hydrogen bond lifetimes of the first layer are shorter than those of the inner layer(s). Interlayer hydrogen bond lifetimes are clearly shorter than those of the constituent layers. As a whole, the hydrogen bond lifetimes of water inside CNTs are shorter than those of bulk water, while the relaxation of C(HB)(t) is slower for the confined water than for bulk water. In other words, hydrogen bonds of water inside CNTs break more easily than those of bulk water, but the water molecules remain in each other's vicinity and can easily reform the bonds.     

Molecular Dynamics Simulation of Glucomannan Solution

1 INTRODUCTION Konjac Glucomanan (KGM), found in konjac plant with molecular weight ranging from 2×105 to 2×106[1], is neutral polyoses with excellent water solubility. The structural studies of KGM have been well presented, but its accurate structure has not been clearly clarified so far, so the investigation is still in progress. According to the previous studies[2～4], the conjectural structure of KGM is as follows: KGM is natural polyoses formed by D-glucose and D-mannose link…     

The influence of hydrogen bonds on the globular structure of HP-copolymers

We present the results of computer modeling of coil-globule transition of HP-copolymer which can form hydrogen bonds between some specific monomer units (hydrogen bond units). Langevin dynamics approach is used for the simulation of coil-globule transition. We study the influence of the number and distribution of hydrogen bond units along primary sequence on the formation of globular conformations.     

Hydrogen Bonding of Carboxylic Acids in Aqueous Solutions—UV Spectroscopy, Viscosity, and Molecular Simulation of Acetic Acid

The UV spectra of aqueous acetic acid solutions up to 2M were investigated. At these wavelengths, the carboxylic acids exhibit an absorption peak, attributed to the C=O group, which shifts when hydrogen bonds are formed.. The measured spectra were best fitted to several bands, either of Gaussian or Lorentzian shape, which can be explained as several types of structural units formed by hydrogen bonds established between acetic acid and water molecules and between acetic acid molecules themselves. Molecular dynamics simulation of these mixtures was also performed, confirming the occurrence of several types of hydrogen bonds and showing the presence of dimers at higher concentrations. The viscosity and density of these solutions were also measured at different concentrations and temperatures. These results give a more complete picture of the hydrogen bond network of the system.     

Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅲ): Equation of state and fluctuations

The equation of the state of the hydrogen bonding fluid system of A_aD_d type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover, the number density fluctuations of both molecules and hydrogen bonds as well as their spatial correlation property are investigated. Furthermore, an equation describing relation between the number density correlation function of “molecules-hydrogen bonds” and that of molecules and hydrogen bonds is derived. As application, taking the van der Waals hydrogen bonding fluid as an example, we considered the effect of hydrogen bonds on its relevant statistical properties. Supported by the National Natural Science Foundation of China (Grant Nos. 20303006 and 20574016), the Natural Science Foundation of Hebei Province (Grant Nos. B2006000959 and B2004000093) and the Natural Science Foundation of Education Committee of Hebei Province (Grant No. 2003101)     

Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

The effect of hydrogen bonds around the active site of Anabaena [2Fe-2S] ferredoxin (Fd) on a vertical ionization potential of the reduced state (IP(red)) is examined based on the density functional theory (DFT) calculations. The results indicate that a single hydrogen bond increases the relative stability of the reduced state, and shifts IP(red) to a reductive side by 0.31–0.33 eV, regardless of the attached sulfur atoms. In addition, the IP(red) value can be changed by the number of hydrogen bonds around the active site. The results also suggest that the redox potential of [2Fe-2S] Fd is controlled by the number of hydrogen bonds because IP(red) is considered to be a major factor in the redox potential. Furthermore, there is a possibility that the redox potentials of artificial iron-sulfur clusters can be finely controlled by the number of the hydrogen bonds attached to the sulfur atoms of the cluster.     

Anomalous Density and Permittivity Effects on the Structure of Water

The relationship between the structural peculiarities of the hydrogen bond net and the anomalous behavior of density and dielectric permittivity of water is investigated. The degree of ordering in the network of hydrogen bonds is described in terms of the structural functions, among which the most important ones are tetrahedricity and the mean number of hydrogen bonds per molecule. The temperature dependence of the number of hydrogen bonds per molecule is discussed in terms of the analysis of the experimental temperature dependences of density and permittivity of water on the saturation line. The estimated density of hexagonal ice at the melting point is reproduced in terms of the concepts suggested for analysis; the estimate is rather close to the experimental value. Possible applications of the new approach are discussed.     

Computer simulation of the hydrogen bond lifetime and the mechanism of the structural rearrangement of water

The concept of a hydrogen bond lifetime is analyzed in a computer experiment. It is shown that different definitions of the lifetime of a hydrogen bond characterize definite stages in the microdynamics of a liquid. The lifetimes of hydrogen bonds are calculated for water using the TIP4P and TIP4B-HB model potentials. A number of features in the mechanism of the structural rearrangement of the nearest surrounding is determined by comparing them.     

Temperature scanning FTIR analysis of hydrogen bonding states of various saccharides in amorphous matrixes below and above their glass transition temperatures

Temperature scanning Fourier transform infrared, TS-FTIR, spectroscopy of various amorphous sugar matrixes was conducted to investigate the relationship between the glass transition temperature, T(g), of an amorphous sugar matrix and the nature of the hydrogen bonds in the matrix. An amorphous sugar matrix was prepared by air-drying an aqueous solution of sugar, and the degree of formation of hydrogen bonds in the matrix was evaluated at different temperatures using the peak positions of the IR band corresponding to the O-H stretching vibration at around 3400 cm(-1). The T(g) value increased with increasing peak position of the O-H stretching vibration at T(g) and were correlated reasonably well with the magnitude of the peak shift by the temperature increase (from 25 degrees C) to the T(g) value. This demonstrates that the amorphous sugar matrix, in which the segments are fixed by fewer hydrogen bonds, has a higher thermal resistance. The glycosidic linkage largely contributes to the restriction of the segments, pyranose ring, rather than a hydrogen bond. As the degree of polymerization of pyranose rings increases, the degree of hydrogen bond formation needed to hold the matrix in a fixed position decreases. However, the magnitude of the restriction of pyranose rings by a glycosidic linkage changes depending on the type: the restrictions imposed by alpha-1,1 and -1,6 glycosidic linkages are the tightest and most flexible of all of the types of glycosidic linkages, respectively.     

Contribution of multicentered short hydrogen bond arrays to potency of active site-directed serine protease inhibitors

We describe and compare the pH dependencies of the potencies and of the bound structures of two inhibitor isosteres that form multicentered short hydrogen bond arrays at the active sites of trypsin, thrombin, and urokinase type plasminogen activator (urokinase or uPA) over certain ranges of pH. Depending on the pH, short hydrogen bond arrays at the active site are mediated by two waters, one in the oxyanion hole (H(2)O(oxy)) and one on the other (S2) side of the inhibitor (H(2)O(S2)), by one water (H(2)O(oxy)), or by no water. The dramatic variation in the length of the active site hydrogen bonds as a function of pH, of inhibitor, and of enzyme, along with the involvement or absence of ordered water, produces a large structural manifold of active site hydrogen bond motifs. Diverse examples of multicentered and two-centered short hydrogen bond arrays, both at and away from the active site, recently discovered in several protein crystal systems, suggest that short hydrogen bonds in proteins may be more common than has been recognized. The short hydrogen bond arrays resemble one another with respect to ionic nature, highly polar environment, multitude of associated ordinary hydrogen bonds, and disparate pK(a) values of participating groups. Comparison of structures and K(i) values of trypsin complexes at pH values where the multicentered short hydrogen bond arrays mediating inhibitor binding are present or absent indicate that these arrays have a minor effect on inhibitor potency. These features suggest little covalent nature within the short hydrogen bonds, despite their extraordinary shortness (as short as 2.0 A).     

高岭石-水体系中水分子结构的分子动力学模拟

以Hendricks模型为初始结构, 利用CLAYFF力场对高岭石-水体系进行无晶体学限制的分子动力学模拟. 结果表明, 层间水有三种类型: I型类似于Costanzo提出的“洞水”分子, 其HH矢量(水分子中从一个氢原子位置指向另一个氢原子位置的方向矢量)平行于(001)平面, 而C2轴稍微倾斜于(001)面法线; II型类似于“连接水”, 一个氢氧键指向临近的层间四面体氧形成氢键, 另一个氢氧键与(001)面近似平行; III型水分子在层间近似保持为竖直状, 一个氢与层间四面体氧形成氢键, 而另一个氢与对面层的羟基氧形成氢键. 高岭石羟基氢沿(001)晶面法线的浓度曲线显示一部分羟基指向变为近似平行于(001)面, 羟基氧因此能够暴露出来与层间水分子氢形成氢键. 此外, 模拟中还观察到部分II型水分子氧偏离于层间的平均位置而更靠近四面体层, 这和Costanzo的实验结果一致, 可能是X射线谱图中(002)弱衍射峰出现的原因.