Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Microsolvation of DMSO: Density functional study on the structure and polaraizabilities

The structure and stability for the association of water with dimethyl sulfoxide (DMSO) are investigated using the density functional M06‐2X level theory. Stable complexes are formed by the formation of hydrogen bonding between water and oxygen atom of DMSO molecule, while the electrostatic force between water and DMSO plays a vital role in deciding the structure. The water‐DMSO interactions are stronger than the interwater hydrogen bonds, which can be inferred from the shorter DMSO‐water bond distance compared with the water–water bond distance. The calculated solvent association energy does not saturate, and it remains favorable to attach additional water molecules to the existing water network. The calculated IR spectra shifts supports the formation stronger hydrogen bonding, while the electrostatic potential (ESP) plot supports the existence of weaker electrostatic interaction in the studied clusters. The polarizabilities for the ground state clusters were found to increase monotonically with the cluster size. The presence of additional electrostatic bonding between water and DMSO, devastates the linear hydrogen‐bonding network. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hydration and dewetting near graphite-CH(3) and graphite-COOH plates

The dynamics of water near the nanoscale hydrophobic (graphite-CH(3)) and hydrophilic (graphite-COOH) plates has been studied in detail with molecular dynamics simulations in this paper. It is shown that these designed surfaces (by growing a layer of methyl or carboxyl groups on top of graphite) can have a significant impact on the neighboring water dynamics, with the hydrophilic carboxyl surface having even more profound effects. The water hydrogen bond lifetime is much longer near both types of surfaces than that in the bulk, while on the other hand the water diffusion constant is much smaller than that in the bulk. The difference in the diffusion constant can be as large as a factor of 8 and the difference in the hydrogen bond lifetime can be as large as a factor of 2, depending on the distance from the surface. Furthermore, the water molecules in the first solvation shell of surface atoms show a strong bias in hydroxyl group orientation near the surface, confirming some of the previous findings. Finally, the possible water dewetting transition between two graphite-CH(3) plates and the effect of the strength of the solute-solvent attractions on the water drying transition are investigated. The relationship among the dewetting transition critical distance, van der Waals potential well depth, and water contact angle on the graphite-CH(3) surface is also analyzed on the basis of a simple macroscopic theory, which can be used to predict the dewetting transition critical distance.     

Circular hydrogen bond networks on the surface of beta-ribofuranose in aqueous solution

This paper examines the hydration structure on the surface of beta-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of beta-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of beta-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.     

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.     

Electronic basis of the comparable hydrogen bond properties of small H2CO/(H2O)n and H2NO/(H2O)n systems (n = 1, 2)

The electronic and structural properties of dihydronitroxide/water clusters are investigated and compared to the properties of formaldehyde/water clusters. Exploring the stationary points of their potential energy surfaces (structurally, vibrationally, and energetically) and characterizing their hydrogen bonds (by both atoms in molecules and natural bond orbitals methods) clearly reveal the strong similarity between these two kind of molecular systems. The main difference involves the nature of the hydrogen bond taking place between the X-H bond and the oxygen atom of a water molecule. All the properties of the hydrogen bonds occurring in both kind of clusters can be easily interpreted in terms of competition between intermolecular and intramolecular hyperconjugative interactions.     

The effect of pressure on the hydration structure around hydrophobic solute: a molecular dynamics simulation study

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.     

Energetics of protein backbone hydrogen bonds and their local electrostatic environment

MD simulation study of several peptides including a polyalanine,a helix(pdb:2I9M),and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge(DPPC)to account for the polarization effect in protein dynamics.Results show that the backbone hydrogen-bond strength is generally correlated with its specific local electrostatic environment,measured by the number of water molecules near the hydrogen bond in the first solvation shell.The correlation coefficient is found to be 0.89,0.78,and 0.80,respectively,for polyalanine,2I9M protein,and leucine zipper.In the polyalanine,the energies of the backbone hydrogen bonds are very similar to each other due to their similar local electrostatic environment.The current study helps demonstrate and support the understanding that hydrogen bonds are stronger in a hydrophobic surrounding than in a hydrophilic one.For comparison,the result from simulation using standard force field shows a much weaker correlation between hydrogen bond energy and local electrostatic environment due to the lack of polarization effect in the force field.     

Water-hydrocarbon interfaces: effect of hydrocarbon branching on interfacial structure

Molecular dynamics simulation are performed for the water/hydrocarbon system to study the effect of hydrocarbon branching on interfacial properties. The following two series of hydrocarbons are considered: (1) n-pentane, 2-methyl pentane, and 2,2,4-trimethyl pentane (constant chain length) and (2) n-octane, 2-methyl heptane, and 2,2,4-trimethyl pentane (constant molecular mass). With a simple algorithm for identification of surface sites and mapping nonsurface sites to these surface sites, intrinsic profiles were constructed with respect to the surface layer. Intrinsic density profiles for water and hydrocarbons with respect to the hydrocarbon and water surface, respectively, resemble density profiles of liquids in the presence of a wall. Order parameters were used to study orientation of molecules with respect to the surface normal and the hydrogen bond network was characterized in terms of the number of hydrogen bonds per water molecule and percentage of hydrogen bonded molecules in the first coordination shell. The corresponding intrinsic profiles were obtained. The O-H bond for surface water was found to have two preferential orientations, pointing toward the hydrocarbon phase and parallel to the interface. Hydrocarbon molecules in series 1 orient along the interface with the more branched molecule better aligned. For molecules in series 2, the larger molecular length reduces the alignment of molecules along the interface.     

The role of hydrogen bonding in water-metal interactions

The hydrogen bond interaction between water molecules adsorbed on a Pd <111> surface, a nucleator of two dimensional ordered water arrays at low temperatures, is studied using density functional theory calculations. The role of the exchange and correlation density functional in the characterization of both the hydrogen bond and the water-metal interaction is analyzed in detail. The effect of non local correlations using the van der Waals density functional proposed by Dion et al. [M. Dion, H. Rydberg, E. Schr?der, D. C. Langreth and B. I. Lundqvist, Phys. Rev. Lett., 2004, 92, 246401] is also studied. We conclude that the choice of this potential is critical in determining the cohesive energy of water-metal complexes. We show that the interaction between water molecules and the metal surface is as sensitive to the density functional choice as hydrogen bonds between water molecules are. The reason for this is that the two interactions are very similar in nature. We make a detailed analogy between the water-water bond in the water dimer and the water-Pd bond at the Pd <111> surface. Our results show a strong similarity between these two interactions and based on this we describe the water-Pd bond as a hydrogen bond type interaction. These results demonstrate the need to obtain an accurate and reliable representation of the hydrogen bond interaction in density functional theory.     

A molecular dynamics simulation of the adsorption of water molecules surrounding an Au nanoparticle

This study uses molecular dynamics simulations performed in a parallel computing environment to investigate the adsorption of water molecules surrounding Au nanoparticles of various sizes. An observation of the oxygen and hydrogen atom distributions reveals that the adsorption of the water molecules creates two shell-like formations of water in close vicinity to the Au nanoparticle surface. These shell-like formations are found to be more pronounced around smaller Au nanoparticles. The rearrangement of water molecules in this region reduces the local hydrogen bond strength to below that which is observed in the bulk region. Finally, the simulation results indicate that the absolute value of the interaction energy between the water molecules and the Au nanoparticle is reduced when the water molecules surround a nanoparticle of larger diameter. This observation implies that a stronger adsorption effect exists between smaller Au nanoparticles and water molecules. Hence, the value of the adsorption constant increases for smaller Au nanoparticles.     

X-ray absorption spectroscopy measurements of liquid water

Recent studies, based on X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS), have shown that the hydrogen bond network in liquid water consists mainly of water molecules with only two strong hydrogen bonds. Since this result is controversial, it is important to demonstrate the reliability of the experimental data, which is the purpose of this paper. Here we compare X-ray absorption spectra of liquid water recorded with five very different techniques sensitive to the local environment of the absorbing molecule. Overall, the spectra obtained with photon detection show a very close similarity and even the observable minor differences can be understood. The comparison demonstrates that XAS and XRS can indeed be applied reliably to study the local bonding of the water molecule and thus to reveal the hydrogen bond situation in bulk water.     

19F-19F spin-spin coupling constant surfaces for (HF)2 clusters: the orientation and distance dependence of the sign and magnitude of J(F-F)

Ab initio calculations using the equation-of-motion coupled cluster method have been carried out to investigate 19F-19F spin-spin coupling constants for a pair of HF molecules. The overall features of the J(F-F) coupling surface with respect to the F-F distance and the orientation of the pair of HF molecules reflect those of the Fermi-contact (FC) surface, although the FC term may not be a good quantitative estimate of J(F-F). The hydrogen-bonded HF dimer exhibits unusual behavior compared to other hydrogen-bonded complexes, since both the FC term and 2hJ(F-F) exhibit variations in sign and magnitude as the F-F distance changes and the linearity of the hydrogen bond is destroyed. The FC term for F-F coupling is relative small and negative for the equilibrium dimer. At the dimer F-F distance, the maximum negative value for the FC term is found for the linear arrangement F-H...H-F, while the maximum positive value is found for the linear H-F...F-H arrangement, despite the fact that neither of these structures is bound. Changes in the sign and magnitude of the FC term are analyzed using the nuclear magnetic resonance triplet wave function model, which relates the orientation of magnetic nuclei to the phases of the wave functions for excited triplet states that couple to the ground state. The FC term for a particular orientation is a result of competing positive and negative contributions from different triplet states, the sign of each contribution being determined by the alignment of the nuclear magnetic moments in that state. Factors are identified which must play a role in determining which types of wave functions dominate.     

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

Molecular interpretation of water structuring and destructuring effects: hydration of alkanediols

Molecular electrostatic potential (MESP) guidelines are employed for understanding the reactivity and hydration patterns in alkanediol molecules. The deeper oxygen lone pair MESP minima indicate stronger basicity of 1,n-diols and 2,4-pentanediol (2,4-PeD) as compared to that of vicinal diols. The existence and strength of the intramolecular hydrogen bond in diols are gauged in terms of the electron density at the bond saddle points. A model named electrostatic potential for intermolecular complexation (EPIC) is used for generating the structures of hydrated complexes, which are subsequently subjected to ab initio calculations at M?ller-Plesset second-order perturbation level of theory. Further, the nature of water...water as well as diol...water interactions is appraised employing many-body energy decomposition analysis. It is seen that water...water interactions are more favorable in vicinal diol...6H(2)O than those in 1,n-diol...6H(2)O (n=3, 4, 5,...) complexes. Exactly opposite trends are shown by diol...water interaction energies. Thus vicinal diols, being more effective at strengthening water...water network, are expected to act as water structuring agents, whereas the non-vicinal diols are expected to be water destructuring agents.     

多肽中氢键强度的理论研究

用B3LYP/6-31G^*法优化了多肽分子的几何构型,计算了各个构型的电荷分布和氢键酸度,进而对多肽分子中的氢键强度进行了研究.结果表明,多肽分子中氢键的强度同时取决于形成氢键的H…O原子间距R和N-H…O之间的键角β;多肽分子倾向于形成R值小、β值大的大环氢键.3₁₀螺旋结构的多肽分子中的氢键具有协同效应,分子越大,分子中氢键越多,氢键的协同效应越强.     

Hydrogen bonded structure and dynamics of liquid-vapor interface of water-ammonia mixture: an ab initio molecular dynamics study

We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.     

On the hydrogen bond networks in the water-methanol mixtures: topology, percolation and small-world

Statistical mechanics based topological analysis and island (or cluster) statistics were used to study the hydrogen bond (H-bond) networks in the water-methanol mixtures with the following methanol mole fractions (x(m)): 0.00, 0.10, 0.20, 0.25, 0.28, 0.30, 0.32, 0.36, 0.38, 0.42, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00. NPT-Monte Carlo simulations were performed at room conditions using the TIP5P model potential for water and united-atoms (OPLS) for methanol to generate the H-bond networks. We have found evidence for non-ideal behavior of mixtures with x(m) ≈ 0.3. Several structural and topological properties present strong dependence with the mixture composition. Island statistics indicate a change from the percolated to non-percolate regime at x(m) ≈ 0.5. Statistical analysis of the islands' nature (homo-clusters: same type of molecules × hetero-clusters: two types of molecules) yields a preferential formation of homo-clusters that quantifies the local composition and preferential solvation ("microimmiscibility"). The topology of the hydrogen bond networks was characterized by local (clustering coefficients, average degrees), semi-global (path lengths) and global (spectral densities) properties. Small-world patterns (highly clustered and small path lengths) appear for x(m) in the range 0.40-0.70, and the momenta in the spectral densities correlate quite well with previous analysis based on rings, chains and branched chains topologies. It also seems that small quantities of methanol in water cause disruption of the continuous fully connected H-bond networks formed by water molecules.