Hydrogen Bond Model Research Articles

High-temperature superconductivity using a model of hydrogen bonds

Recently, there has been much interest in high-temperature superconductors and more recently in hydrogen-based superconductors. This work offers a simple model that explains the behavior of the superconducting gap based on naive BCS (Bardeen-Cooper-Schrieffer) theory and reproduces most effects seen in experiments, including the isotope effect and [Formula: see text] enhancement as a function of pressure. We show that this is due to a combination of the factors appearing in the gap equation: the matrix element between the proton states and the level splitting of the proton.

DFT/TDDFT theoretical investigation on the excited-state intermolecular hydrogen bonding interactions, photoinduced charge transfer, and vibrational spectroscopic properties of deprotonated deoxyadenosine monophosphate [dAMP-H]− anion in aqueous solution: Upon photoexcitation of hydrogen-bonded model complexes [dAMP-H]−–nH2O (n = 0, 1, 2, 3, 4)

In this work, the excited-state intermolecular hydrogen bonding interactions, photoinduced charge transfer, and vibrational spectroscopic properties of deprotonated deoxyadenosine monophosphate [dAMP-H]− anion in aqueous solution were investigated by the DFT/TDDFT method. The intermolecular hydrogen-bonded model complexes [dAMP-H]−–nH2O (n=0, 1, 2, 3, 4) in both the ground state and electronic excited state were first discussed. Analysis of frontier molecular orbitals reveals an intramolecular charge transfer (ICT) state for [dAMP-H]−–nH2O (n=0, 1, 2) complexes in which charge transfer occurs from the phosphate group to the base. However, it becomes a locally excited (LE) state for [dAMP-H]−–nH2O (n=3, 4) complexes, which only locates on the adenine moiety. The excited energies of the first excited state of [dAMP-H]−–nH2O (n=0, 1, 2, 3) increase gradually during the introduction of water molecules, but decreases with the fourth water molecule at adenine site. The fourth water molecule has little influence on the structure but significant to the photoexcitation. Upon electronic excitation, stretching vibration frequencies of NH and OH of hydrogen bonds: N5H10⋯O9, O9H19⋯O10 and O10H21⋯O3 are red-shifted. The excited-state bond lengths of these hydrogen bonds are also shortened. Therefore, the total intermolecular hydrogen bonding interaction at the base moiety is significantly strengthened in the electronic excited state.

Fluid transition layer between rigid solute and liquid solvent: is there depletion or enrichment?

The fluid layer between solute and liquid solvent is studied by combining the density functional theory with the probabilistic hydrogen bond model. This combination allows one to obtain the equilibrium distribution of fluid molecules, taking into account the hydrogen bond contribution to the external potential whereto they are subjected near the solute. One can find the effective width of the fluid solvent-solute transition layer and fluid average density in that layer, and determine their dependence on temperature, solvent-solute affinity, vicinal hydrogen bond (hb) energy alteration ratio, and solute radius. Numerical calculations are performed for the solvation of a plate and spherical solutes of four different radii in two model solvents (associated liquid and non-associated one) in the temperature range from 293 K to 333 K for various solvent-solute affinities and hydrogen bond energy alteration ratios. The predictions of our model for the effective width and average density of the transition layer are consistent with experiments and simulations. The small-to-large crossover lengthscale for hydrophobic hydration is expected to be about 3-5 nm. Remarkably, characterizing the transition layer with the average density, one can observe that for small hydrophobes, the transition layer becomes enriched with rather than depleted of fluid when the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of solvent-solute affinity and hb-energy alteration ratio, needed for the "depletion-to-enrichment" crossover (in the smoothed density sense), are predicted to decrease with increasing temperature.

Effect of Water Hydrogen Bonding on the Solvent-Mediated "Oscillatory" Repulsion of C60 Fullerenes in Water.

The solvent-mediated interaction of C60 fullerenes in liquid water is examined by using the combination of the probabilistic hydrogen bond model with the density functional theory. This combination allows one to take into account the effect of hydrogen bonding between water molecules on their interaction with fullerenes and to construct an approximation for the distribution of water molecules in the system, which provides an efficient foundation for studying hydrophobic phenomena. Our numerical evaluations predict the solvent-induced interaction of two C60 fullerenes in water at 293 K to have an oscillatory-repulsive character (previously observed in molecular dynamics simulations) only when the vicinal water-water hydrogen bonds are slightly weaker than bulk ones. Besides indicating the direction of the energetic alteration of water-water hydrogen bonds near C60 fullerenes, our model also suggests that the hydrogen bonding ability of water plays a defining role in the solvent-mediated C60-C60 repulsion.

Mechanical Model of Hydrogen Bonds in Protein Molecules

The unique properties of protein molecules have motivated researchers exploit them in the design and fabrication of bio-mimetic nano devices to perform a special task. Function of protein molecules is in turn dependent on their 3D structure and their ability to modify their shape for a specific task. To study and manipulate protein molecules we need to have knowledge of mechanical properties of these molecules. In this paper a multiscale model to predict stiffness of helical protein molecules has been developed. Hydrogen bonds as major contributing factor to proteins flexibility, are modeled as elastic springs based on their empirical potential energy. Such mechanical representation of hydrogen bonds enables us to obtain the stiffness ellipsoid of hydrogen bonds which leads to an understanding of the directional stiffness of protein molecules. The model has also been applied to three different protein molecules whose stiffness were reported in the literature. The comparison shows an agreement between the stiffness computed by the proposed model and that obtained through experiments and/or Molecular Dynamics (MD) simulations.

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.

Alternative hydrogen bond models of cellulose II and IIII based on molecular force-fields and density functional theory

Alternative hydrogen-bond structures were found for cellulose II and IIII based on molecular dynamics simulations using four force fields and energy optimization based on density functional theory. All the modeling results were in support to the new hydrogen-bonding network. The revised structures of cellulose II and IIII differ with the fiber diffraction models mainly in the orientation of two hydroxyl groups, namely, OH2 and OH6 forming hydrogen-bond chains perpendicular to the cellulose molecule. In the alternative structures, the sense of hydrogen bond is inversed but little difference can be seen in hydrogen bond geometries. The preference of these alternative hydrogen bond structures comes from the local stabilization of hydroxyl groups with respect to the β carbon. On the other hand when simulated fiber diffraction patterns were compared with experimental ones, the current structure of cellulose II with higher energy and the alternative structure of cellulose IIII with lower energy were in better agreement.

Investigation of cellulose supramolecular structure changes during conversion of waste paper in near-critical water on producing 5-hydroxymethyl furfural

Waste paper as a kind of biomass contains a great quantity of cellulose which is a renewable energy resource. However, complex cellulose supramolecular structure restricts the conversion of waste paper in near-critical water. This study aimed to investigate the change characteristics of cellulose supramolecular structure (hydrogen bond models and crystallinity) during hydrolysis and its effects on 5-HMF yield. Waste paper has been treated in near-critical water at 375 °C and 22.5 MPa for a reaction time (160–240 s) and correlation between 5-HMF yield and the supramolecular structure of cellulose residues has been built up. The 5-HMF yield was increased with the increase of intermolecular hydrogen bonds content in cellulose residues and was increased first and then decreased with the increase of crystallinity of cellulose residues. The rate of decrystallization was out of sync with that of depolymerization, which also influenced 5-HMF yield. Reaction time can be a macro method to adjust the supramolecular structure of cellulose during the conversion of waste paper to obtain more 5-HMF. It showed that 5-HMF yield reached maximum 9.41% ± 0.47% when the intermolecular hydrogen bonds content of cellulose in residue was 67.77% and the crystallinity of cellulose in residue was 57.14% at 200 s.

Temperature dependence of the evaporation lengthscale for water confined between two hydrophobic plates

Liquid water in a hydrophobic confinement is the object of high interest in physicochemical sciences. Confined between two macroscopic hydrophobic surfaces, liquid water transforms into vapor if the distance between surfaces is smaller than a critical separation, referred to as the evaporation lengthscale. To investigate the temperature dependence of the evaporation lengthscale of water confined between two hydrophobic parallel plates, we use the combination of the density functional theory (DFT) with the probabilistic hydrogen bond (PHB) model for water–water hydrogen bonding. The PHB model provides an analytic expression for the average number of hydrogen bonds per water molecule as a function of its distance to a hydrophobic surface and its curvature. Knowing this expression, one can implement the effect of hydrogen bonding between water molecules on their interaction with the hydrophobe into DFT, which is then employed to determine the distribution of water molecules between two macroscopic hydrophobic plates at various interplate distances and various temperatures. For water confined between hydrophobic plates, our results suggest the evaporation lengthscale to be of the order of several nanometers and a linearly increasing function of temperature from T=293K to T=333K, qualitatively consistent with previous results.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics. The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal structures. The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations and establishes a new standard energy function for Rosetta.

A new class of ion-ion interaction: Z-bond

The hydrogen-bond interactions in ionic liquids have been simply described by the conventional hydrogen-bond model of A-H…B. Coupling with the strong electrostatic force, however, hydrogen bond between the cation and anion shows particular features in the geometric, energetic, electronic, and dynamic aspects, which is inherently different from that of the conventional hydrogen bond. A general model could be expressed as +[A-H…B]-, in which A and B represent heavy atoms and + and - represent the charges of the cation containing A atom and anion containing B atom, respectively. Because the structure shows a zig-zag motif, this coupling interaction is defined here as the Z-bond. The new model could be generally used to describe the interactions in ionic liquids, as well as bio-systems involved in ions, ionic reaction, and ionic materials.

The solvent-induced interaction of spherical solutes in associated and non-associated liquids.

We propose an efficient method for studying the solvent-induced interaction of two solvophobic particles immersed in a liquid solvent. The method is based on the combination of the probabilistic hydrogen bond model with the density functional theory. An analytic expression for the number of hydrogen bonds per water molecule near two spherical hydrophobes is derived as a function of the molecule distance to both hydrophobes, distance between hydrophobes, and their radii. Using this expression, one can construct an approximation for the distribution of fluid (liquid water) molecules in the system which provides a reasonably good (much faster and accurate enough) alternative to a standard iteration procedure. Such an approximate density distribution constitutes an efficient foundation for studying the length-scale and temperature dependence of hydrophobic interactions. The model is applied to the interaction of solvophobic solutes in both associated and non-associated liquids. Of these two cases, the model predictions for the solvent-induced potential of mean force between two solutes in associated liquids are closer to the results of molecular dynamics simulation of hydrophobic interactions in the SPC/E model water. Our results suggest that the hydrogen bonding ability of water molecules may play a major role in hydrophobic phenomena.

Toward the development of the potential with angular distortion for halogen bond: a comparison of potential energy surfaces between halogen bond and hydrogen bond.

As noncovalent intermolecular interactions, hydrogen bond (HB) and halogen bond (XB) are attracting increasing attention. In this work, the potential energy surfaces (PESs) of hydrogen and halogen bonds are compared. Twelve halogen-bonded and three hydrogen-bonded models are scanned for analysis using the MP2 level of theory. This work indicates that potential energy surfaces of both HB and XB have angular distortion. The potential well of XB is narrower than that of HB. With the elongation of the bond length, the potential energy surfaces get flatter. The best fitting functions for angular distortion and the flattening character of angular terms are also combined into a modified Buckingham potential. The testing results show that the essential features of the PES, including angular distortion and flattening character, have been reproduced. These results provide a better understanding of halogen and hydrogen bonds and the optimization of halogen bond force fields.

Molecular interaction study of ethanol in non-polar solute using hydrogen-bonded model

The dielectric behaviour of binary mixture of ethanol with chlorobenzene and 1,2 dicholoroethane mixtures for various concentrations and temperatures have been studied using hydrogen-bonded model suggested by Luzar. The Luzar theory is applied to determine the molecular parameters and correlation terms for the mixture. The interaction of the chloro group molecules with ethanol hydrogen-bonded liquid is discussed. The calculation of the theoretical dielectric constant using Kirkwood correlation factor provides more precise theoretical model for the mixture.

Probing protein ensemble rigidity and hydrogen–deuterium exchange

Protein rigidity and flexibility can be analyzed accurately and efficiently using the program floppy inclusion and rigid substructure topography (FIRST). Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure. It is however well known that proteins can undergo spontaneous sub-molecular unfolding and refolding, or conformational dynamics, even under conditions that strongly favor a well-defined native structure. These (local) unfolding events result in a large number of conformers that differ from each other very slightly. In this context, proteins are better represented as a thermodynamic ensemble of ‘native-like’ structures, and not just as a single static low-energy structure. Working with this notion, we introduce a novel FIRST-based approach for predicting rigidity/flexibility of the protein ensemble by (i) averaging the hydrogen bonding strengths from the entire ensemble and (ii) by refining the mathematical model of hydrogen bonds. Furthermore, we combine our FIRST-ensemble rigidity predictions with the ensemble solvent accessibility data of the backbone amides and propose a novel computational method which uses both rigidity and solvent accessibility for predicting hydrogen–deuterium exchange (HDX). To validate our predictions, we report a novel site specific HDX experiment which characterizes the native structural ensemble of Acylphosphatase from hyperthermophile Sulfolobus solfataricus (Sso AcP). The sub-structural conformational dynamics that is observed by HDX data, is closely matched with the FIRST-ensemble rigidity predictions, which could not be attained using the traditional single ‘snapshot’ rigidity analysis. Moreover, the computational predictions of regions that are protected from HDX and those that undergo exchange are in very good agreement with the experimental HDX profile of Sso AcP.

Avoiding problems with hydrogen misplacement in reporting crystal structures

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one-, two- or three-dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space-group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H-atom electron densities associated with apparent D-H∙∙∙A trios, while some H-atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high-quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen-bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.

Vibrational Circular Dichroism Spectroscopy of Three Multidentate Nitrogen Donor Ligands: Conformational Flexibility and Solvent Effects

A series of multidentate nitrogen donor ligands have been synthesized and characterized and their conformational distributions in solution have been investigated. Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopy, complemented with DFT calculations, have been used to probe the conformations of these important ligands in solution directly. These three ligands demonstrate very different conformational flexibility; the pyridine subunits and amine groups may adopt a number of different conformations. Experimental VA and VCD data measured in CDCl3 have been compared to the theoretical spectra of all possible most stable conformers. Solvent effects have been taken into account by using the implicit polarizable continuum model and explicit solvation model. The explicit hydrogen-bonding solvation model is important for explaining the VCD sign-reverse phenomenon in the amide I region. Good agreement has been achieved between experimental and predicted spectra for all three ligands; thus allowing detailed examination of the related conformational structures and distributions in solution.

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode.This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

Structural and electronic aspects of hydrogen bonding in two polymorphs of butylene-N,N′-bis(O,O′-diarylphosphoramidate)

The bisphosphoramidate (C(6)H(5)O)(2)P(O)NH(CH(2))(4)NHP(O)(OC(6)H(5))(2) crystallizes in two polymorphs, one (ndl) with a needle habit from tetrahydrofuran (THF)/ethanol and another (prm) which forms prisms from H(2)O/ethanol. The molecules in the two forms differ from each other in some torsion angles and the orientation of the diaminobutane bridge, although the differences between the similar bond lengths are not significant for the two polymorphs. The geometry optimizations at the B3LYP/6-31+G* level for isolated molecules show that the two conformers which exist in the crystalline state also represent local gas-phase energy minima. The decrease in the N-H distance from the optimized to the crystal structures has been described in terms of the decrease in electron density (ρ) at the bond-critical point (b.c.p.) of the N-H bond path when the molecule participates in hydrogen bonding, comparing the results of atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses for fully optimized structures ndl and prm with their hydrogen-bonded model clusters.

Structural and electronic aspects of hydrogen bonding in two polymorphs of butylene-N,N′-bis(O,O′-diarylphosphoramidate)

The bisphosphoramidate (C(6)H(5)O)(2)P(O)NH(CH(2))(4)NHP(O)(OC(6)H(5))(2) crystallizes in two polymorphs, one (ndl) with a needle habit from tetrahydrofuran (THF)/ethanol and another (prm) which forms prisms from H(2)O/ethanol. The molecules in the two forms differ from each other in some torsion angles and the orientation of the diaminobutane bridge, although the differences between the similar bond lengths are not significant for the two polymorphs. The geometry optimizations at the B3LYP/6-31+G* level for isolated molecules show that the two conformers which exist in the crystalline state also represent local gas-phase energy minima. The decrease in the N-H distance from the optimized to the crystal structures has been described in terms of the decrease in electron density (ρ) at the bond-critical point (b.c.p.) of the N-H bond path when the molecule participates in hydrogen bonding, comparing the results of atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses for fully optimized structures ndl and prm with their hydrogen-bonded model clusters.