Definition Of Hydrogen Bond Research Articles

Nuclear Quantum Effects in Proton or Hydrogen Transfer.

Proton or hydrogen transfers, basic chemical reactions, proceed either by thermally activated barrier crossing or via tunneling. Studies of molecules undergoing single or double proton or hydrogen transfer in the ground or excited electronic state reveal that tunneling can dominate under conditions usually considered to favor the thermal process. Moreover, the tunneling probability strongly varies for excitation of certain vibrational modes, which changes the effective barrier and/or proton transfer distance. When the reaction is fast compared to vibrational relaxation, the mode selectivity can still be maintained for molecules in solutions at 293 K. These observations point to dangers of relating the calculated minimum energy paths and the associated barriers to the experimentally obtained activation energies. The multidimensional character of the reaction coordinate is obvious; it can dramatically change for slowly and rapidly relaxing environments. We postulate that the hydrogen bond definition should be extended by specifically including the role of molecular vibrations.

Hydrogen bond types which do not fit accepted definitions.

There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).

Molecular aggregation in liquid water: Laplace spectra and spectral clustering of H-bonded network

Molecular dynamics simulations of pure ambient liquid water were performed. Hydrogen bond network properties were determined by calculation of eigenvectors and eigenvalues of the Laplace matrix. We investigated how these quantities depend on the system size, the coordination number and periodic boundary conditions taking into account different hydrogen bond definitions. It was found that the first peak of the Laplace spectra contains six eigenvalues. These results suggest that six communities are always formed in our simulated systems independently of the number of molecules in the cubic box. By the help of the spectral clustering method, which is an acceptable indicator of the global properties of H-bonded network, two different H-bonded environments were identified. The tetrahedrality of the water molecules is significantly larger at the surface than inside the clusters. This difference can be related to the coexistence of HDL and LDL domains in liquid water. Furthermore, our work also emphasizes that the periodic boundary conditions always cause clustering in the system.

One Hundred Years After the Latimer and Rodebush Paper, Hydrogen Bonding Remains an Elephant!

Latimer and Rodebush (J Am Chem Soc 42: 1419–1433, 1920) discussed the ways a Lewis dot structure could be drawn for liquid water and proposed that the H held between two octets constitutes a bond in 1920. When it was realized that the other molecule of life, DNA, owes its double helix structure to specific hydrogen bonds between A–T (two) and C–G (three) base pairs, the interest in hydrogen bonding grew dramatically. While hydrogen bonding could be readily seen in water and DNA, it was not so easy to understand leading to continuous debates about what it means. This article gives a personal perspective of the evolution of hydrogen bonding since the Latimer and Rodebush paper to the recent IUPAC definition of hydrogen bond, published in 2011 and now. Is there a third C–H···O hydrogen bond in the A–T base pair?

Definition of Free O-H Groups of Water at the Air-Water Interface.

Free O-H groups of water are often found at the water-hydrophobic medium interface, e.g. for water contact with hydrophobic protein residues, or at the water-air interface. In surface-specific vibrational spectroscopic studies using sum-frequency generation (SFG) spectroscopy, free O-H groups are experimentally well characterized in the O-H stretch region by a sharp 3700 cm-1 peak. Although these free O-H groups are often defined as the O-H groups which are not hydrogen-bonded to other water molecules, a direct correlation between such non-hydrogen-bonded O-H groups and the 3700 cm-1 SFG response has been lacking. Our data show that commonly used hydrogen bond definitions do not adequately capture the free O-H groups contributing to the 3700 cm-1 peak. We thus formulate a new definition for capturing the subensemble of the surface free O-H groups using the intermolecular distance and the angle formed by the water dimer, through the comparison of the ∼3700 cm-1 SFG response and the responses from the selected free O-H groups at the HOD-air interface. Using these optimized free O-H group definitions, we infer the fraction of interfacial water molecules with free O-H groups of 28%, a vibrational lifetime of the free O-H groups of 1.3 ps, and the angle formed by the free O-H groups and the surface normal of 67° at the water-air interface. We expect that this improved free O-H group definition can be helpful in exploring the structure and dynamics of the interfacial water.

Cluster formation and percolation in ethanol-water mixtures

Results of systematic molecular dynamics studies of ethanol-water mixtures, over the entire concentration range, were reported previously that agree with experimental X-ray diffraction data. These simulated systems are analyzed in this work to examine cluster formation and percolation, using four different hydrogen bond definitions. Percolation analyses revealed that each mixture (even the one containing 80mol% ethanol) is above the 3D percolation threshold, with fractal dimensions, df, between 2.6 and 2.9, depending on concentration. Monotype water cluster formation was also studied in the mixtures: 3D water percolation can be found in systems with less than 40mol% ethanol, with fractal dimensions between 2.53 and 2.84. These observations can be put in parallel with experimental data on some thermodynamic quantities, such as the excess partial molar enthalpy and entropy.

The Relation Between Lipase Thermostability and Dynamics of Hydrogen Bond and Hydrogen Bond Network Based on Long Time Molecular Dynamics Simulation.

Compared with the wild type of lipase (WTL), mutant lipase 6B has twelve mutations (A15S, F17S, A20E, N89Y, G111D, L114P, A132D, M134E, M137P, I157M, S163P, N166Y). The melting temperature of 6B (78.2°C) is much higher than that of WTL (56°C). Hydrogen bond (HB) play an important role in stabilizing the protein. It is important to analyze how mutations affect hydrogen bond and hydrogen bond network and explain how hydrogen bond and hydrogen bond network affect lipase thermostability by the change of the intensity of HB and HB networks with temperature changing. Study the dynamics of HB and HB networks to find that how HBs and HB networks change over time and over temperature in WTL and 6B. Long time MD simulations of WTL and 6B are carried out to analyze how mutations affect hydrogen bond and hydrogen bond network. All proteins were simulated at 300K, 325K, 350K, 375K, 400K for 300ns respectively. The definition of HB is that the distance between acceptor and donor is smaller than a cutoff 3.0 Å and the angle between Donor-H and H-Acceptor is larger than 120o. If two or more HBs connect together, they formed HB network. In the network, residues that formed HB represent nodes, the HB interactions between residues represent edges. The persistence value of HB is computed by . The persistence values of HBs formed by mutations A15S, A20E, G111D, M137P, N166Y are significantly different from that of WTL. HB Glu20-Ser24, Asp111-Asp144, Leu160-Tyr166 and Lys170-Tyr166 are important to stabilize 6B. In addition, the HB networks dynamics show that there are three HB networks are more stable in mutants than that in WTL. The first HB network makes β3, β5, loop and 310-helix closely connect with each other at mutants. The second HB network increases the rigidity of the loop, αC, β3 and β5. The third HB network enhances the interaction between loops, αB and αC. The higher HB persistence value generally means that the HB is more stable. These mutations directly improve the stability of these HBs referring to their persistence values, which show that mutations strengthen the ability of HBs to withstand high temperature and then stabilize the secondary structure. It is thus clear that the mutations change the stability of HBs and the HB networks, which are responsible for increasing protein thermostability.

Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure.

DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system.

Aqueous Solutions of Ionic Liquids: Microscopic Assembly.

Aqueous solutions of ionic liquids are of special interest, due to the distinctive properties of ionic liquids, in particular, their amphiphilic character. A better understanding of the structure-property relationships of such systems is hence desirable. One of the crucial molecular-level interactions that influences the macroscopic behavior is hydrogen bonding. In this work, we conduct molecular dynamics simulations to investigate the effects of ionic liquids on the hydrogen-bond network of water in dilute aqueous solutions of ionic liquids with various combinations of cations and anions. Calculations are performed for imidazolium-based cations with alkyl chains of different lengths and for a variety of anions, namely, [Br](-), [NO3](-), [SCN](-) [BF4](-), [PF6](-), and [Tf2N](-). The structure of water and the water-ionic liquid interactions involved in the formation of a heterogeneous network are analyzed by using radial distribution functions and hydrogen-bond statistics. To this end, we employ the geometric criterion of the hydrogen-bond definition and it is shown that the structure of water is sensitive to the amount of ionic liquid and to the anion type. In particular, [SCN](-) and [Tf2N](-) were found to be the most hydrophilic and hydrophobic anions, respectively. Conversely, the cation chain length did not influence the results.

Instantaneous, parameter-free methods to define a solute's hydration shell.

A range of methods are presented to calculate a solute's hydration shell from computer simulations of dilute solutions of monatomic ions and noble gas atoms. The methods are designed to be parameter-free and instantaneous so as to make them more general, accurate, and consequently applicable to disordered systems. One method is a modified nearest-neighbor method, another considers solute-water Lennard-Jones overlap followed by hydrogen-bond rearrangement, while three methods compare various combinations of water-solute and water-water forces. The methods are tested on a series of monatomic ions and solutes and compared with the values from cutoffs in the radial distribution function, the nearest-neighbor distribution functions, and the strongest-acceptor hydrogen bond definition for anions. The Lennard-Jones overlap method and one of the force-comparison methods are found to give a hydration shell for cations which is in reasonable agreement with that using a cutoff in the radial distribution function. Further modifications would be required, though, to make them capture the neighboring water molecules of noble-gas solutes if these weakly interacting molecules are considered to constitute the hydration shell.

Фізична природа водневого зв’язку

The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\,\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\,\,The conventional model of H-bonds as sharply directed and saturated bridges between water molecules is incompatible with the behavior of the specific volume, evaporation heat, and self-diffusion and kinematic shear viscosity coefficients of water. On the other hand, it is shown that the variation of the dipole moment of a water molecule and the frequency shift of valence vibrations of a hydroxyl group can be totally explained in the framework of the electrostatic model of H-bond.\,\,At the same time, the temperature dependences of the heat capacity of water in the liquid and vapor states clearly testify to the existence of weak H-bonds.\,\,The analysis of a water dimer shows that the contribution of weak H-bonds to its ground state energy is approximately 4--5 times lower in comparison with the energy of electrostatic interaction between water molecules.\,\,A conclusion is made that H-bonds have the same nature in all other cases where they occur.

Order and correlation contributions to the entropy of hydrophobic solvation.

The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom's test-particle insertion method, and other methods and models are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.

Towards a unified description of the hydrogen bond network of liquid water: a dynamics based approach.

The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.

ChemInform Abstract: Naming Interactions from the Electrophilic Site

AbstractReview: 76 refs.

Naming Interactions from the Electrophilic Site

It is proposed that noncovalent interactions, wherein it is possible to identify an element or moiety working as the electrophile, are named by referring to the Group of the Periodic Table the electrophilic atom belongs to. The resulting terminology generalizes a criterion which was used in the recent IUPAC definition of halogen bond and inspired the definition of hydrogen bond. A systematic, unambiguous, and periodic naming is obtained and applies to the majority of the attractive interactions formed by the elements of Groups 1, 2, 13–17 and, possibly, to some interactions formed by the elements of other Groups.

CH-π hydrogen bonds in biological macromolecules.

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

The quest for self-consistency in hydrogen bond definitions

In the last decades several hydrogen-bond definitions were proposed by classical computer simulations. Aiming at validating their self-consistency on a wide range of conditions, here we present a comparative study of six among the most common hydrogen-bond definitions for temperatures ranging from 220 K to 400 K and six classical water models. Our results show that, in the interval of temperatures investigated, a generally weak agreement among definitions is present. Moreover, cutoff choice for geometrically based definitions depends on both temperature and water model. As such, analysis of the same water model at different temperatures as well as different water models at the same temperature would require the development of specific cutoff values. Interestingly, large discrepancies were found between two hydrogen-bond definitions which were recently introduced to improve on more conventional methods. Our results reinforce the idea that a more universal way to characterize hydrogen bonds in classical molecular systems is needed.

Water's non-tetrahedral side

The case for liquid water having non-tetrahedral as well as tetrahedral coordination is put forward. Given the dependence of structure on the hydrogen bond definition, a recent conceptual breakthrough has been the topological hydrogen bond definition which overcomes the shortcomings of traditional cut-off-based hydrogen bond definitions. It identifies the hydrogen bonds in water's first coordination shell using assumed transition states as boundaries instead of fixed cut-offs. Here, the topological definition is applied to liquid water to characterise the distances, angles and energies of the hydrogen bonds for the different types of coordinations found. These coordinations include bent, trigonal, tetrahedral, trigonal bipyramidal, and octahedral structures, as well as bifurcated hydrogens, bifurcated oxygens and cyclic dimers, and larger polygons. All species are shown to have properties consistent with their classification, justifying their assignments, and supporting the structure of water as a continuous, single phase mixture. However, a detailed analysis to assess the existence of the assumed transition states reveals the remarkable finding that hydrogen bond switching via a bifurcated hydrogen under certain circumstances is a barrierless process. The likelihood of a switch depends on both the acceptor numbers and on the proximity of a donor to its acceptor. Specifically, a donor in an acceptor's outermost subshell switches uphill to an acceptor of the same or higher coordination to the starting acceptor, downhill to an acceptor of lower coordination by two or more, or sits bifurcated between two acceptors if the new acceptor has a coordination lower by only one. Which it is depends intimately on the donor molecule's oscillations and on other hydrogen bond switches that control the nearby acceptors' coordinations. Finally, a search is conducted for long-range structure in water in terms of asymmetry in the distribution of the donor-acceptor bias but none is found.

Conjugation in hydrogen-bonded systems

Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both σ- and π-binding between molecules. The σ-kind density distribution determines the mutual orientation of molecules. A π-system may be delocalized conjugated, which provides additional stabilization of molecular clusters. In those clusters where the sequence of hydrogen bonds is not planar, a peculiar kind of π-conjugation exists. HF2 − and H5O2 + ions are characterized by quasi-triple bonds between the electronegative atoms. The most long-lived species stabilized by π-binding are structural rings and closed or open hoops composed of fused rings. It is conjugated π system that determines the cooperativity phenomenon. New definition of hydrogen bond is proposed.

Estudo das ligações de hidrogênio para dímeros formados pelas moléculas de H2O, NH3, HF, HCl e HBr através de cálculos baseados em primeiros princípios

HYDROGEN BOND STUDY BY AB INITIO CALCULATIONS FOR DIMERS FORMED FROM H2O, NH3, HF, HCl AND HBr MONOMERS. Hydrogen bond energies of fifteen dimers were calculated using the large basis set 6-311++G(3df,3pd), at HartreeFock (HF) level including Moller-Plesset (MP2) calculations. The procedure for obtaining such energies were based on the dimer’s energy rise provoked by increasing in intermolecular distance of the system component units. Deviations from a strictly linear hydrogen bond were investigated and rotational barriers were also computed allowing the calculation of the second order attractive interactions. In order to provide a more objective definition of hydrogen bond, a lower energy limit was proposed in place of the merely empirical parameters employed in the classical definition.