单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature

We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.     

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.     

Hydrogen bond and residence dynamics of ion-water and water-water pairs in supercritical aqueous ionic solutions: dependence on ion size and density

We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.     

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.     

Short strong hydrogen bonds: can they explain enzymic catalysis?

It has been proposed that some remarkable enzymic catalytic effects can be explained by the existence of unusually strong hydrogen bonds within the enzyme's active site. Although such hydrogen bonds may be short, and may have unusual properties, there is no evidence that unusually strong hydrogen bonds exist in solution or in enzyme active sites. Thus there is no basis for invoking strong hydrogen bonds to explain enzymic rate enhancements.     

Intramolecular hydrogen bonds with large proton polarizability in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines

Heteroconjugated NO⁺H … N NO … H⁺N and homoconjugated NO⁺H … ON NO … H⁺ON intramolecular hydrogen bonds formed in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines were studied by IR and NMR spectroscopy. All these hydrogen bonds show large proton polarizability. In the case of the heteroconjugated hydrogen bonds the proton transfer equilibrium shifts from compounds 1 to 3 to the left hand side since the interaction of the hydrogen bond with the solvent environment decreases in this series of compounds. With compound 1 the hydrogen bonds are slightly weaker and longer, hence the wavenumber dependence of the intensity of the continuum caused by these hydrogen bonds is slightly changed with compound 1 compared with compound 2. In the case of compound 3 the intensity of the continuum decreases because of increasing screening of the hydrogen bonds. In the series of homoconjugated hydrogen bonds, from compound 4 to 6 the intense continuum vanishes, and only the band of the 0–1 proton transition at 950 cm⁻¹ remains. The vanishing of the continuum is caused by increasing screening of the hydrogen bonds against their solvent environments by bulky groups, and thus, this change demonstrates again that the interaction of the hydrogen bond with large proton polarizabilities is a necessary prerequisite for IR continua to appear.     

LCAO-MO-SCF-Calculations on the stability and Sterochernistry of hydrogen bonds

CNDO and INDO calculations were performed on numerous structures with hydrogen bonds of different strength. An almost linear relationship is found between the strength of weak hydrogen bonds and the amount of charge transfered.π-electrons and lone pairs are nearly equivalent in hydrogen bonding. The stereochemistry of hydrogen bonds is determined largely by additional interactions betweenσ-bonds of the two molecules. Since proton affinities are calculated too large by the CNDO method, an error is introduced in the potential curves for proton transfer in weak hydrogen bonds. In systems with strong hydrogen bonds both structures with the proton on the right and left have almost the same energy and hence the potential curves for proton transfer are free of the errors mentioned above.     

Insertion reactions of dimethylsilylene: relative reactivity towards oxygenz.sbnd;hydrogen,siliconhydrogen,and siliconz.sbnd;alkoxy bonds

Photochemically-generated dimethylsilylene is found in competition experiments to insert preferentially into oxygenhydrogen bonds of alcohols compared to either siliconhydrogen bonds of silanes or siliconoxygen bonds of alkoxysilanes. This selectivity for OH bonds compared to SiH bonds is quite high in tetrahydrofuran and in dilute hydrocarbon solutions. However, it decreases in more concentrated hydrocarbon solutions. These effects are discussed in terms of aggregation of alcohols, hydrogen bonding, and solvent-mediated dimethylsilylene reactivity.     

Monitoring selected hydrogen bonds in crystal hydrates of amino acid salts: combining variable-temperature single-crystal X-ray diffraction and polarized Raman spectroscopy

Predicting behaviour of hydrogen bonds with varying temperature, in particular-correlating donor-acceptor distances in the O-H···O hydrogen bonds with the frequencies of O-H stretching vibrations is important for understanding dynamics of biomolecules and phase transitions in crystals. A commonly used correlation suggested earlier in the literature is based on statistical analysis of different compounds [A. Novak, Structure and Bonding, 1974, 18, 177; K. Nakamoto, M. Margoshes, R. E. Rundle, J. Am. Chem. Soc., 1955, 77, 6480]. The present study is a rare example when correlations between geometry and energy parameters have been found for selected individual hydrogen bonds in the same crystalline compound at multiple temperatures. The properties of several types of O-H···O hydrogen bonds in bis(DL-serinium) oxalate dihydrate and DL-alaninium semi-oxalate monohydrate have been studied by a combination of variable-temperature single-crystal X-ray diffraction and polarized Raman spectroscopy. The changes in the hydrogen bonds geometry could be compared with the changes of the corresponding spectral modes. The correlation suggested by Novak is roughly followed, better for medium and weak, than for short hydrogen bonds. Fine details of spectral changes differ for individual bonds. The way how H-bonds are affected by cooling depends on their environment in the crystal structure. Short O-H···O hydrogen bonds in bis(DL-serinium) oxalate dihydrate expand or remain almost unchanged on cooling, whereas in DL-alaninium semi-oxalate monohydrate all strong H-bonds are compressed under these conditions. The distortion of individual hydrogen bonds on temperature variations is correlated with the anisotropy of lattice strain.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Intramolecular easily polarizable charged and non-charged hydrogen bonds: IR continua and hydrogen bond length

Substances with intramolecular, easily polarizable hydrogen bonds of different length are compared. Long hydrogen bonds cause IR continua which show band-like structures in the region 2800–1800 cm^?1, extending with weaker intensity toward smaller wave-numbers over the whole region studied. Medium length bonds cause continua beginning at 3200 cm^?1 and extending over the whole region studied. Very short, easily polarizable hydrogen bonds, such as the bond in the HAuCl₄ salt of NN'-tetramethyl-o-xylildiamine di-N-oxide, cause continua with very great intensity in the region 1500–850 cm^?1. Comparison of the experimental with calculated continua shows very good agreement with regard to wavenumber regions in which easily polarizable hydrogen bonds of different length cause IR continua.By comparing all these intramolecular, easily polarizable hydrogen bonds causing IR continua it is shown that the charge of the hydrogen bonds is not the decisive property for the occurrence of the continua but rather the shape of the proton potentials. Continua may occur only with hydrogen bonds with double minima or broad flat proton potential.     

Quantitative information about the hydrogen bond strength in dilute aqueous solutions of methanol from the temperature dependence of the Raman spectra of the decoupled OD stretch

We have obtained quantitative information about the hydrogen bond strength in pure water and in dilute aqueous solutions of methanol by analyzing the temperature dependence of Raman spectra of the decoupled OD stretch from 21 to 160 degrees C with the hydrogen bond energy dispersion method. A minimum at 2440 cm(-1) assigned to strong icelike hydrogen bonds and a maximum at 2650 cm(-1) due to maximally (but not completely) broken hydrogen bonds result in all cases. The energy of the minimum decreases upon addition of methanol due to formation of stronger water-methanol hydrogen bonds, whereas the energy of the maximum increases because water hydrogen atoms in the vicinity of the methyl group might participate in "more broken" hydrogen bonds than in bulk water.     

Role of hydrogen bonds in protein-DNA recognition: effect of nonplanar amino groups

Amino groups are one of the various types of hydrogen bond donors, abundantly found in protein main chains, protein side chains, and DNA bases. The polar hydrogen atoms of these groups exhibit short ranged, specific, and directional hydrogen bonds, which play a decisive role in the specificity and stability of protein-DNA complexes. To date, planar amino groups are only considered for the analysis of protein-DNA interfacial hydrogen bonds. This assumption regarding hydrogen atom positions possibly failed to establish the expected role of hydrogen bonds in protein-DNA recognition. We have performed ab initio quantum chemical studies on amino acid side chains and DNA bases containing amino groups as well as on specific hydrogen bonded residue pairs selected from high-resolution protein-DNA complex crystal structures. Our results suggest that occurrences of pyramidal amino groups are more probable in comparison with the usually adopted planar geometry. This increases the quality of the existing hydrogen bonds in almost all cases. Further, detailed analysis of protein-DNA interfacial hydrogen bonds in 107 crystal structures using the in-house program "pyrHBfind" indicates that consideration of energetically more preferred nonplanar amino groups improves the geometry of hydrogen bonds and also gives rise to new contacts amounting to nearly 14.5% of the existing interactions. Large improvements have been observed specifically for the amino groups of guanine, which faces the DNA minor groove and thus helps to resolve the problem of insufficient directional contacts observed in many minor groove binding complexes. Apart from guanine, improvement observed for asparagine, glutamine, adenine, or cytosine also indicates that the consideration of nonplanar amino groups leads to a more realistic scenario of hydrogen bonds occurring between protein and DNA residues.     

Semiempirical study of compounds with O-H?O intramolecular hydrogen bond

Application of MNDO, AM1, PM3, MNDO/H, and MNDO/M methods to a set of compounds with intramolecular hydrogen bonds suggested that none of these methods accurately modeled the characteristics of the hydrogen bonds. Since the MNDO/H and MNDO/M methods work well for intermolecular hydrogen bonds, we followed their example and modified MNDO for intramolecular hydrogen bonds by altering the empirical core–core repulsion energy function for all pairs of atoms involved in intramolecular O-H? O bonds. The resulting modified method models the behavior of these bonds quite well, especially as regards their geometry and the barrier to proton transfer. © 1992 by John Wiley & Sons, Inc.     

The effect of hydrogen bonding on structural parameters I: An ab initio study of the keto and enol tautomers of formamide and their hydrogen bonded dimers

In order to study the variation of CO and CN bond lengths as functions of the hydrogen bond length, a series of ab initio calculations have been performed on the keto and enol tautomers of formamide. The formation of hydrogen bonds leads to an increase in the conjugation of the NCO fragment. This increase is expressed as a lengthening of the double bonds and a corresponding shortening of the single bonds. These changes are found to vary with the length of the hydrogen bonds and analytical expressions for these variations of the bond lengths have been derived. The potential functions for dimerization, i.e. formation of, respectively, two N-H ·· O and two O-H ·· N hydrogen bonds have also been found. The results obtained indicate significant differences between the two types of hydrogen bonds.     

由分子间氢键导致的丝素构象转变的FT-IR研究

用FT－IR研究发现，在丙烯腈与丙烯酸甲酯的共聚物（PANMA）与聚L-丙氨酸（PLAL）的共混体系中，丝素（SF）与PANMA的共混体系及SF与聚丙烯酸钠（NA）的共混体系中，含有羰基或其它极性基团的高分子与SF形成强弱不等的氢键．由于氢键的形成,使SF分子不得不调整自身的构象，从而引起其构象转变．讨论了可能的分子间氢键的结构．     

Molecular interaction of (ethanol)2-water heterotrimers

The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.     

The influence of water molecule coordination to a metal ion on water hydrogen bonds

The geometry of hydrogen bonds in the crystal structures from the Cambridge Structural Database and calculated data show that water coordination to a metal ion has a remarkable influence on hydrogen bonds. The calculated energies of hydrogen bonds of coordinated water are much stronger, even if the aqua complex is neutral.     

Hydrogen bond strength modulates the mechanical strength of ferric-thiolate bonds in rubredoxin

It has long been recognized that hydrogen bonds formed by protein backbone amides with cysteinyl S(γ) atoms play important roles in modulating the functional and structural properties of the iron-sulfur centers in proteins. Here we use single molecule atomic force microscopy, cyclic voltammetry, and protein engineering techniques to investigate directly how the strength of N-H···S(γ) hydrogen bonds in the secondary coordination sphere affects the mechanical stability of Fe(III)-thiolate bonds of rubredoxin. Our results show that the mechanical stability of Fe(III)-thiolate bonds in rubredoxin correlates with the strength of N-H···S(γ) hydrogen bonds as reflected by the midpoint reduction potential, providing direct evidence that N-H···S(γ) hydrogen bonds play important roles in modulating the mechanical and kinetic properties of the Fe(III)-thiolate bonds of iron-sulfur proteins and corroborating the important roles of the protein environment in tuning the properties of metal-thiolate bonds.