Structural properties of liquid water

Monte Carlo simulations of molecular configurations of liquid water in theNVT-ensemble atT=298 K using unit cells containing 125 and 1000 molecules were, carried out. Comparison of experimental and calculated radial distribution functions suggests the existence of two types of spatial ordering in water. Structural properties of low-energy molecular clusters and associates of closed cycles of H-bonds were determined. The properties of the network of H-bonds can be described by a set of fundamental constants and one free parameter,viz., the probability of bond formation. The existence of long-range correlations in spatial arrangement of both the molecules and the cycles of bonds was established. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 841–851, May, 1999.     

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 contribution to the water pair interaction potential: Effects on the model liquid structure

Empirical pair potentials of water that take into account the contribution of the OH nonelectrostatic interaction in the hydrogen bond are considered. The effects of this contribution on the radial distribution functions derived by computer simulation are analyzed. Model potentials have been obtained for which the height and position of the first and second peaks of the oxygen-oxygen radial distribution function are comparable with experimental data.Original Russian Text Copyright © 2004 by A. V. Borovkov, M. L. Antipova, V. E. Petrenko, and Yu. M. KesslerTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 678–682, July–August, 2004.Deceased.This revised version was published online in April 2005 with a corrected cover date.     

位于三维超分子网格的螺旋孔道中的螺旋水链（英文）

以偶氮苯-3,5,4′-三羧酸(H3abt)为配体,在水热条件下合成了一个新颖的配合物[Co(H2abt)2(H2O)4]·H2O(1),并通过元素分析、红外光谱、热重分析和X射线单晶衍射对其结构进行了表征.结构分析显示,配合物1具有含螺旋孔道的三维超分子网格结构,两种手性的螺旋水链通过配位作用和氢键固定于螺旋孔道中.     

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 572–581, 2000     

Calculated vibrational spectra of weak hydrogen bonds

Potential energy and dipole moment surfaces for the H-bond SH... S in the dimeric methanethiol have been calculated by the SCF-MO-LCGO method, and the vibrational spectrum — transition frequencies and IR absorption intensities at 20 °K — computed. This spectrum is compared with that of the monomeric species and with experimental results. The resulting dimerization energy is 1.4 kcal/mole.     

The interaction of fluorosilanes with hydrogen fluoride clusters: strongly blue-shifted hydrogen bonds

The equilibrium structures, binding energies, and vibrational spectra of the complexes formed between hydrogen fluoride clusters (HF)_n (1≤n≤4) and the fluorosilanes SiHF₃, SiH₂F₂, and SiH₃F are investigated within the second-order Møller–Plesset perturbation theory method applying extended basis sets. It is shown that Si–FH–F halogen–hydrogen bonds are formed in the most stable open dimers, SiHF₃–HF, SiH₂F₂HF, and SiH₃FHF. No Si–HF–H hydrogen bonds occur in these dimers. Nevertheless, blue shifts of Si–H stretching frequencies are calculated. All three trimers, fluorosilane–(HF)₂, all three tetramers, fluorosilane–(HF)₃, and two of the pentamers, fluorosilane–(HF)₄, form cyclic structures with strong Si–FH–F halogen–hydrogen bonds and weak Si–HF–H contacts, the latter displaying, nevertheless, strongly blue-shifted Si–H stretching frequencies. These blue shifts are comparable in size to those of the corresponding fluoromethane–(HF)_n complexes and are with about +50 cm⁻¹ for the case n=3 among the largest ever calculated and definitely the largest for Si–H bonds. In the title complexes, the formation of the Si–FH–F halogen–hydrogen bonds induces a substantial stretching of this Si–F bond, which in turn leads to a significant contraction of the fluorosilane Si–H bond in the Si–HF–H hydrogen bond. This disposition of the fluorosilane monomers is demonstrated with the aid of suitable potential energy surface scans and appears to be a prerequisite for the formation of strongly blue-shifted hydrogen bonds.     

Intermolecular hydrogen bonds: Comparison of associates in crystals and liquids

The density and sound velocity were measured within wide ranges of temperature for a number of liquids (water, formamide, diols, aliphatic alcohols, cellosolves, ketones), in which various types of H-associate can exist. The temperature dependences of the adiabatic and molar adiabatic compressibility, density, and molar volume are analyzed. The values of the molar adiabatic compressibility permit one to evaluate the dimensionality of H-associates existing in liquids; the values of adiabatic compressibility do not offer this possibility. The terms responsible for the similarity and difference between H-associates in crystals and liquids are discussed.     

Interstitial water and the formation of low barrier hydrogen bonds: A computational model study

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4‐methyl‐1H‐imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the Mim–HAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A Mim–HAc LBHB stabilized with one water molecule observed in diethyl ether (ε = 4.34), with two water molecules in toluene (ε = 2.38), and with three water molecules in vacuo (ε = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (ΔPA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ΔPA values close to zero in charge‐assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

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.     

Using hydrogen bonds to direct the assembly of crowded aromatics

This Minireview details the design, synthesis, and self-assembly of a new class of crowded aromatics that form columnar superstructures. The assembly of these subunits produces helical and polar stacks, whose assembly can be directed with electric fields. In concentrated solutions, these self-assembled helical rods exhibit superhelical arrangements that reflect circularly polarized light at visible wavelengths. Depending on the side chains employed, spin-cast films yield either polar monolayers or isolated strands of molecules that can be visualized with scanning probe microscopy. Also detailed herein are methods to link these mesogens together to produce monodisperse oligomers that fold into defined secondary conformations.     

Structure and cooperativity of the hydrogen bonds in sodium dihydrogen triacetate

Geometry and energetics of low energy conformers of sodium dihydrogen triacetate (SDHTA) and its anion are studied using density functional theory (DFT) at the Becke, Lee‐Yang‐Parr hybrid functional (BLYP) and Becke, three‐parameter, Lee‐Yang‐Parr hybrid functional (B3LYP) levels. For both cases, two structures of comparable energy are found, which have different symmetry with respect to the two hydrogen bonds (HBs). DFT‐based Born–Oppenheimer molecular dynamics simulations are performed for SDHTA, which show that both structures are visited at room temperature conditions. The trajectory analysis further reveals that the two HBs behave anticooperative, that is, on average elongation of one HB is accompanied by a compression of the other one. This is in accord with nuclear magnetic resonance (NMR) experimental studies for a similar counter ion–dihydrogen triacetate complex. © 2012 Wiley Periodicals, Inc.     

A new method for quick predicting the strength of intermolecular hydrogen bonds

A new method is proposed to quick predict the strength of intermolecular hydrogen bonds. The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydrogen-bonded dimers. The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides. Supported by the National Natural Science Foundation of China (Grants Nos. 20573049 and 20633050) and the research fund of the Educational Department of Liaoning Province (2004C019, 20060469)