Hydrogen Bond Lifetimes Research Articles

Dynamics of hydrogen bonds in water and consequences for the unusual behaviour of supercooled water

The dynamics of liquid water is evaluated by the coherent quasi-elastic scattering at two different momentum transfers, in order to discriminate hydrogen bond lifetime from molecular dynamics. The results indicate a possible issue for the puzzle of the behaviour of supercooled water.

Vibrational Spectral Diffusion and Hydrogen Bond Dynamics in Heavy Water from First Principles

We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.

Single particle and pair dynamics in water–formic acid mixtures containing ionic and neutral solutes: Nonideality in dynamical properties

A series of molecular dynamics simulations of water-formic acid mixtures containing either an ionic solute or a neutral hydrophobic solute has been performed to study the extent of nonideality in the dynamics of these solutes for varying composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to show nonideal behavior with variation of composition, and similar nonideality is also observed for the diffusion and orientational relaxation of solvent molecules in these mixtures. The diffusion coefficient of a neutral hydrophobic solute, however, decreases monotonically with increase in water concentration. We have also investigated some of the pair dynamical properties such as water-water and water-formic acid hydrogen bond relaxation and residence dynamics of water molecules in water and formic acid hydration shells. The lifetimes of water-water hydrogen bonds are found to be longer than those between formic acid carbonyl oxygen-water hydrogen bonds, whereas the lifetimes of formic acid hydroxyl hydrogen-water hydrogen bonds are longer than those of water-water hydrogen bonds. In general, the hydrogen bond lifetimes for both water-water and water-formic acid hydrogen bonds are found to decrease with increase in water concentration. Residence times of water molecules also show the same trend with increase in formic acid concentration. Interestingly, these pair dynamical properties show a monotonic dependence on composition without any maximum or minimum and behave almost ideally with respect to changes in the composition of the mixtures. The present calculations are performed with fixed-charge nonpolarizable models of the solvent and solute molecules without taking into account many-body polarization effects in an explicit manner.

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra

We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.

Effect of Anions on Static Orientational Correlations, Hydrogen Bonds, and Dynamics in Ionic Liquids: A Simulational Study

Three different ionic liquids are investigated via atomistic molecular dynamics simulations using the force field of Lopes and PAdua (J. Phys. Chem. B 2006, 110, 19586). In particular, the 1-ethyl-3-methylimidazolium cation EMIM+ is studied in the presence of three different anions, namely, chloride Cl-, tetrafluoroborate BF(4)(-), and bis((trifluoromethyl)sulfonyly)imide TF2N-. In the focus of the present study are the static distributions of anions and cations around a cation as a function of anion size. It is found that the preferred positions of the anions change from being close to the imidazolium hydrogens to being above and below the imidazolium rings. Lifetimes of hydrogen bonds are calculated and found to be of the same order of magnitude as those of pure liquid water and of some small primary alcohols. Three kinds of short-range cation-cation orderings are studied, among which the offset stacking dominates in all of the investigated ionic liquids. The offset stacking becomes weaker from [EMIM][Cl] to [EMIM][BF4] to [EMIM][TF2N]. Further investigation of the dynamical behavior reveals that cations in [EMIM][TF2N] have a slower tumbling motion compared with those in [EMIM][Cl] and [EMIM][BF4] and that pure diffusive behavior can be observed after 1.5 ns for all three systems at temperatures 90 K above the corresponding melting temperatures.

Temperature dependence of the two-dimensional infrared spectrum of liquid H2O.

Two-dimensional infrared photon-echo measurements of the OH stretching vibration in liquid H2O are performed at various temperatures. Spectral diffusion and resonant energy transfer occur on a time scale much shorter than the average hydrogen bond lifetime of approximately 1 ps. Room temperature measurements show a loss of frequency and, thus, structural correlations on a 50-fs time scale. Weakly hydrogen-bonded OH stretching oscillators absorbing at high frequencies undergo slower spectral diffusion than strongly bonded oscillators. In the temperature range from 340 to 274 K, the loss in memory slows down with decreasing temperature. At 274 K, frequency correlations in the OH stretch vibration persist beyond approximately 200 fs, pointing to a reduction in dephasing by librational excitations. Polarization-resolved pump-probe studies give a resonant intermolecular energy transfer time of 80 fs, which is unaffected by temperature. At low temperature, structural correlations persist longer than the energy transfer time, suggesting a delocalization of OH stretching excitations over several water molecules.

Structure and stability of water chain in a carbon nanotube

Water molecules form a single-file chain structure in a (6, 6) carbon nanotube (CNT), andthis stability is different from that of water molecules confined in CNTs with largerdiameters, let alone the bulk. Using the molecular dynamics (MD) method and quantummechanical (QM) calculations, we investigate the characteristics in the context of densitydependence of the collective structure and hydrogen bond behavior. The results obtainedfrom MD show that high water density leads to substantially longer hydrogen bondlifetimes. On the other hand, the hydrogen bond lifetime does not noticeablydecrease with decreasing density but remains roughly the same when the density islower than a certain critical value. The mean molecular orientation angle of thewater molecule, defined by the angle that comprises the water dipole momentand the CNT axis, is smaller for higher densities, and asymptotically approaches33° on the low density side. Such an asymptotic nature of the structure and stability stemsfrom non-uniform distribution of water molecules. The mean orientation angle obtainedfrom QM calculations using density functional theory coincides with the MD result. QManalysis also suggests that the charge distribution of water in the CNT originates from themolecular configuration due to spatial confinement rather than strong electronic interactionbetween water and the CNT.

Evaluation of the criteria of hydrogen bonding in highly associated liquids

Evaluation of the geometric and energetic definitions of a hydrogen bond have been performed for the liquid water under ambient ( T = 298 K, ρ = 0.998 kg dm −3) and sub-critical ( T = 573 K, ρ = 0.72 kg dm −3) conditions using the flexible BJH model. It has been shown that single-condition geometric definitions only controlling the intermolecular separation are not capable to reject molecular pairs having repulsive interaction energy and are inapplicable at any temperature. The geometric definitions which additionally account for the allowable orientation of the H-donor molecule are reliable under ambient conditions. They are, however, not sufficient to exclude pairs which are unbound or weakly bound in the physical sense at elevated temperatures. The deficiency of the simple energetic and the mixed energy-distance definition consists in the inability to distinguish pairs having improper relative orientation. The extended energetic definition controlling the interaction energy, intermolecular O⋯H separation and orientation of the H-donating partner seems the most reliable. The purely geometric and energetic definitions have been shown to overestimate the connectivity, statistics and lifetime of hydrogen bonds. The overestimation of the connectivity and statistics is substantial in the sub-critical region whereas more significant differences in the dynamics of hydrogen bonds have been found for ambient water.

Ab initio molecular dynamics study of aqueous formaldehyde and methanediol

The solvation shell of aqueous formaldehyde has been studied by ab initio molecular dynamics. Two different DFT approaches using BLYP and PBE functionals were explored. The results show only a slightly different mobility in the solvation shells and allow characterization of the hydrogen bonded structure with a H2C = O··HOH hydrogen bond lifetime of ca. 3 ps. Formaldehyde hydrolysis was studied by following the reverse process, methanediol decomposition, by Blue Moon constrained MD showing that four water molecules are directly involved in the reaction and assisted by the whole hydration shell. The total energy of the aqueous methanediol to formaldehyde inter-conversion process is calculated with a barrier height of ca. 95 kJ mol−1 while the corresponding free energy barrier is only ΔG‡ = 46 kJ mol−1 at 300 K.

The impact of kosmotropes and chaotropes on bulk and hydration shell water dynamics in a model peptide solution

Kosmotropic (order-making) and chaotropic (order-breaking) co-solvents influence stability and biochemical equilibrium in aqueous solutions of proteins, acting indirectly through the structure and dynamics of the hydration water that surrounds the protein molecules. We have investigated the influence of kosmotropic and chaotropic co-solvents on the hydrogen bonding network dynamics of both bulk water and hydration water. To this end the evolution of bulk water and hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), has been studied by quasielastic neutron scattering as a function of solvent composition. The results show that bulk water and hydration water dynamics, apart from a dynamical suppression that depends on the NALMA solute, exhibit the same dependence on addition of co-solvent for all of the co-solvents studied (urea, glycerol, MgSO 4, and dimethyl sulfoxide). The hydrophobic solute and the high concentration water-structuring additive have the same effect on the water hydrogen bonding network. Water remains the preferential hydration of the hydrophobic side chain and backbone. We also find that the reorganization of the bulk water hydrogen bond network, upon addition of kosmotrope and chaotrope additives, is not dynamically perturbed, and that the hydrogen bond lifetime is maintained at 1 ps as in pure bulk water. On the other hand the addition of NALMA to the water/co-solvent binary system causes reorganization of the hydrogen bonds, resulting in an increased hydrogen bond lifetime. Furthermore, the solute’s side chain dynamics is not affected by high concentrations of co-solvent. We shall discuss the hydration dynamics results in the context of protein folding and protein–solvent interactions.

Hydrogen bond dynamics and water structure in glucose-water solutions by depolarized Rayleigh scattering and low-frequency Raman spectroscopy

The effect of glucose on the relaxation process of water at picosecond time scales has been investigated by depolarized Rayleigh scattering (DRS) experiments. The process is assigned to the fast hydrogen bonding dynamics of the water network. In DRS spectra this contribution can be safely separated from the slower relaxation process due to the sugar. The detected relaxation time is studied at different glucose concentrations and modeled considering bulk and hydrating water contributions. As a result, it is found that in diluted conditions the hydrogen bond lifetime of proximal water molecules becomes about three times slower than that of the bulk. The effect of the sugar on the hydrogen bond water structure is investigated by analyzing the low-frequency Raman (LFR) spectrum sensitive to intermolecular modes. The addition of glucose strongly reduces the intensity of the band at 170 cm(-1) assigned to a collective stretching mode of water molecules arranged in cooperative tetrahedral domains. These findings indicate that proximal water molecules partially lose the tetrahedral ordering typical of the bulk leading to the formation of high density environments around the sugar. Thus the glucose imposes a new local order among water molecules localized in its hydration shell in which the hydrogen bond breaking dynamics is sensitively retarded. This work provides new experimental evidences that support recent molecular dynamics simulation and thermodynamics results.

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.

How strongly can calcium ion influence the hydrogen-bond dynamics at complex aqueous interfaces?

The author has performed three independent molecular dynamics computer simulations to examine the effects of counterion identity on hydrogen-bond dynamics in the enclosed water pool of anionic surfactant-based reverse micelles. The water-water hydrogen-bond lifetime in the reverse micelle (RM) with calcium ions is found to be longer than that in the RM with sodium or ammonium ions. The hydrogen bond between a polar head group and a water molecule, on the other hand, breaks but reforms most rapidly in the RM with calcium ions, indicating that there exists a strong competition between head group-counterion and head group-water interactions at such complex interfaces.

Hydrogen bond lifetimes and energetics for solute/solvent complexes studied with 2D-IR vibrational echo spectroscopy.

Weak pi hydrogen-bonded solute/solvent complexes are studied with ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature-dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute/solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen-bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory.

Hydrogen-bond dynamics of interior and surface molecules in a water nanocluster: temperature and size effects

Molecular dynamics simulations are employed to investigate the effects of temperature and size on the hydrogen-bond dynamics of interior molecules and surface molecules in a water nanocluster. The flexible three-centred (F3C) water model is invoked in the simulations. To inspect the dynamics of the interior hydrogen bonds and the surface hydrogen bonds, a spherical water nanocluster is modelled and then divided into interior molecules and surface molecules according to the density profile of the water nanocluster. It is observed that at higher temperatures the average number of hydrogen bonds decreases and yields faster hydrogen-bond relaxation for both interior molecules and surface molecules of the water nanocluster. Furthermore, the surface molecules have a lower average number of hydrogen bonds than the interior molecules. The lifetime of the surface hydrogen bonds is slightly longer than that of the interior hydrogen bonds, whereas the hydrogen-bond structural relaxation time of the surface molecules is more obviously slower than that of the interior molecules. Regarding the size effect, a larger water nanocluster is seen to have a larger average number of hydrogen bonds and a longer hydrogen-bond structural relaxation time.

Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation

Dynamics of water molecules in the grooves of DNA are of great interest both for practical (functionality of DNA) and fundamental (as examples of confined systems) interest. Here the authors employ atomistic molecular dynamics simulations to understand varying water dynamics at the minor and the major grooves of a 38 base-pair long DNA duplex in water. In order to understand and quantify the diversity in the nature of hydrogen bond due to many hydrogen bond donors and acceptors present in the four bases, they have undertaken study of hydrogen bond lifetime (HBLT) correlation functions of all the specific hydrogen bonds between the base atoms and water molecules. They find that the HBLT correlation functions are in general multiexponential, with the average lifetime depending significantly on the specificity and may thus be biologically relevant. The average hydrogen bond lifetime is longer in the minor groove than that in the major groove by almost a factor of 2. Analysis further shows that water hydrogen bonds with phosphate oxygen have substantially shorter lifetimes than those with the groove atoms. They also compute two different orientational time correlation functions (OTCFs) of the water molecules present at the major and the minor grooves and attempt to correlate OTCF with HBLT correlation function. The OTCFs in the minor groove exhibit three time scales, with the time constant of the slowest component one to two orders of magnitude longer than what is observed for bulk water. A slow component is also present for the major groove water but with shorter time constant. Interestingly, correlation between reformations allowed HBLT correlation function [C(HB)(t)] and the OTCF markedly deviates from each other in the grooves, indicating enhanced rigidity of water molecules in the grooves.

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.

Computational study of structural and dynamical properties of formamide-water mixtures

A molecular dynamics simulation study of structural and dynamical properties in liquid mixtures of formamide and water is presented. Site-site radial pair distribution functions, local mole fractions, pair energy distributions, and tetrahedral orientational order are the quantities analyzed to investigate the local structure in the simulated mixtures, along with a review of the intermolecular structure in terms of the distribution of hydrogen bonds. Our results indicate that there is a substitution of formamide molecules by water in the hydrogen bonds and a formation of a common hydrogen bond network. By analyzing the extent of tetrahedral order in the liquid as a function of composition, it is observed that whereas the tetrahedral network of liquid water is progressively lost by increasing the formamide concentration, the water structure within the first coordination shell is preserved and somewhat enhanced. The hydrogen-bond mean lifetimes were estimated by performing a time integration of the autocorrelation functions of bond occupation numbers. The lifetimes associated with hydrogen bonds between water, formamide, and interspecies pairs are found to increase with increasing formamide concentration. The lifetimes of the water hydrogen bonds show the largest variations, supporting the picture of an enhancement of the water structure among the nearest neighbors within the first coordination shell. We have used two different force field models for water, SPC/E [J. C. Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] and TIP4P/2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)]. Our results for structural and dynamical properties yield very small differences between those models, the TIP4P/2005 predicting a slightly more structured liquid and, consequently, exhibiting a slightly slower translational and librational dynamics.

Hydrogen Bond Lifetime Dynamics at the Interface of a Surfactant Monolayer

The dynamics of water near the polar headgroups of surfactants in a monolayer adsorbed at the air/water interface is likely to play a decisive role in determining the physical behavior of such organized assemblies. We have carried out an atomistic molecular dynamics (MD) simulation of a monolayer of the anionic surfactant sodium bis(2-ethyl-1-hexyl) sulfosuccinate (aerosol-OT or AOT) adsorbed at the air/water interface. The simulation is performed at room temperature with a surface coverage of that at the critical micelle concentration (78 Angstrom(2)/molecule). Detailed analyses of the lifetime dynamics of surfactant-water (SW) and water-water (WW) hydrogen bonds at the interface have been carried out. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the bound states at the interface and quantification of the dynamic equilibrium between bound and quasi-free water molecules, in terms of time-dependent relaxation rates. It is observed that the water molecules present in the first hydration layer form strong hydrogen bonds with the surfactant headgroups and hence have longer lifetimes. Importantly, it is found that the overall relaxation of the SW hydrogen bonds is faster for those water molecules which form two hydrogen bonds with the surfactant headgroups than those forming one such hydrogen bond. Equally interestingly, it is further noticed that water molecules beyond the first hydration layer form weaker hydrogen bonds than pure bulk water.

Structure and dynamics of liquid water

A review of recent studies on the structure and dynamics of water (in liquid and amorphous states) by physical methods and computer experiment is presented together with a brief summary of historical background. Basic concepts offered for describing the structure and dynamics of water are considered. The structure of water is currently viewed as having a uniform three-dimensional network formed by hydrogen-bonded molecules. The arrangement of this network is dissimilar from that found in any crystal structures; it is dynamically and structurally inhomogeneous. The network is rather labile; water molecules continuously change their neighbors, so that the average lifetime of hydrogen bonds is about a few picoseconds.