Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water

Molecular-dynamics simulations were carried out for the SPC, SPCE, TIP4P, and TIP5P models of water at 298 K. From these results we determine the following quantities: the absolute entropy using the two-particle approximation, the mean lifetime of the hydrogen bond, the mean number of hydrogen bonds per molecule, and the mean energy of the hydrogen bond. From the entropy calculations we find that nearly all contributions to the total entropy originates from the orientation effects. Moreover, we determine the contributions to the total entropy which originate from the first, second, and higher solvation shells. It is interesting that the limits between solvation shells are clearly visible. The first solvation shell (0.22 < r < 0.36 nm) contributes approximately 43 J mol K to the total entropy; the second solvation shell (0.36 < r < 0.60 nm) contributes approximately 12 J mol K, while contributions from the third and other solvation shells are very small, approximately 2 J mol K in summary. This indicates that water molecules are strongly ordered up to 0.55-0.6 nm around the central water molecule, and beyond this limit the ordering diminishes. The results of calculations (entropy and hydrogen bonds) are compared with the experimental data for the choosing of the best water model. We find that the SPC and TIP4P models reproduce the best experimental values, and we recommend these models for computer simulations of the aqueous solution of biomolecules.     

Hydrogen bond lifetime in supercritical water

Molecular dynamics simulations of water were performed in a wide range of supercritical temperatures and pressures with using TIP4P-HB model potential. The effect of state parameters on microdynamics of hydrogen bonds was studied. Isobaric (P = 30, 50, 80, 100 MPa) and isothermal (T = 673 K) dependencies of average hydrogen bond lifetime were calculated.     

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

We report extensive replica exchange molecular dynamics (REMD) simulations on the folding/unfolding equilibrium of Trp-cage miniprotein using the Amber ff99SB all atom forcefield and TIP3P and TIP4P-Ew explicit water solvent models. REMD simulation-lengths in the 500 ns to the microsecond regime per replica are required to adequately sample the folding/unfolding equilibrium. We observe that this equilibrium is significantly affected by the choice of the water model. Compared with experimental data, simulations using the TIP3P solvent describe the stability of the Trp-cage quite realistically, providing a melting point which is just a few Kelvins above the experimental transition temperature of 317 K. The TIP4P-Ew model shifts the equilibrium towards the unfolded state and lowers the free energy of unfolding by about 3 kJ mol(-1) at 280 K, demonstrating the need to fine-tune the protein-forcefield depending on the chosen water model. We report evidence that the main difference between the two water models is mostly due to the different solvation of polar groups of the peptide. The unfolded state of the Trp-cage is stabilized by an increasing number of hydrogen bonds, destabilizing the α-helical part of the molecule and opening the R-D salt bridge. By reweighting the strength of solvent-peptide hydrogen bonds by adding a hydrogen bond square well potential, we can fully recover the effect of the different water models and estimate the shift in population as due to a difference in hydrogen bond-strength of about 0.4 kJ mol(-1) per hydrogen bond.     

Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models

Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.     

Structural properties and thermodynamics of water clusters: a Wang-Landau study

The temperature dependence of structural properties and thermodynamic behavior of water clusters has been studied using Wang-Landau sampling. Four potential models, simple point charge/extended (SPC/E), transferable intermolecular potential 3 point (TIP3P), transferable intermolecular potential 4 point (TIP4P), and Gaussian charge polarizable (GCP), are compared for ground states and properties at finite temperatures. Although the hydrogen bond energy and the distance of the nearest-neighbor oxygen pair are significantly different for TIP4P and GCP models, they approach to similar ground state structures and melting transition temperatures in cluster sizes we considered. Comparing with TIP3P, SPC/E model provides properties closer to that of TIP4P and GCP.     

All-Atom Molecular Dynamics of Pure Water–Methane Gas Hydrate Systems under Pre-Nucleation Conditions: A Direct Comparison between Experiments and Simulations of Transport Properties for the Tip4p/Ice Water Model

(1) Background: New technologies involving gas hydrates under pre-nucleation conditions such as gas separations and storage have become more prominent. This has necessitated the characterization and modeling of the transport properties of such systems. (2) Methodology: This work explored methane hydrate systems under pre-nucleation conditions. All-atom molecular dynamics simulations were used to quantify the performance of the TIP4P/2005 and TIP4P/Ice water models to predict the viscosity, diffusivity, and thermal conductivity using various formulations. (3) Results: Molecular simulation equilibrium was robustly demonstrated using various measures. The Green–Kubo estimation of viscosity outperformed other formulations when combined with TIP4P/Ice, and the same combination outperformed all TIP4P/2005 formulations. The Green–Kubo TIP4P/Ice estimation of viscosity overestimates (by 84% on average) the viscosity of methane hydrate systems under pre-nucleation conditions across all pressures considered (0–5 MPag). The presence of methane was found to increase the average number of hydrogen bonds over time (6.7–7.8%). TIP4P/Ice methane systems were also found to have 16–19% longer hydrogen bond lifetimes over pure water systems. (4) Conclusion: An inherent limitation in the current water force field for its application in the context of transport properties estimations for methane gas hydrate systems. A re-parametrization of the current force field is suggested as a starting point. Until then, this work may serve as a characterization of the deviance in viscosity prediction.     

Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model

Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a "lone-pair" orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the "dipole" orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars.     

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 for water in classic and quantum molecular dynamics

The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.     

On the Problem of Criteria for Phase Transitions in Water Clusters (A Hexamer and Octamer Example)

The study concerns the dynamics of a network of hydrogen bonds in small water clusters (on the example of hexamer and octamer clusters). The numerical experiment is carried out with the molecular dynamics method using two analytical rigid potentials TIP4P and TIP5P. According to the obtained results, the criteria of phase transitions provided by the cluster theory are not reliable enough in the case of small water clusters. This is testified by the distributions of potential energies of individual molecules in the clusters. It is shown that the appearance of several peaks in these distributions reflects the number of hydrogen bonds between the molecule and other molecules of the cluster.     

Proper and improper hydrogen bonds in liquid water

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.     

A flexible model for water based on TIP4P/2005

A new flexible water model, TIP4P/2005f, is developed. The idea was to add intramolecular degrees of freedom to the successful rigid model TIP4P/2005 in order to try to improve the predictions for some properties, and to enable the calculation of new ones. The new model incorporates flexibility by means of a Morse potential for the bond stretching and a harmonic term for the angle bending. The parameters have been fitted to account for the peaks of the infrared spectrum of liquid water and to produce an averaged geometry close to that of TIP4P/2005. As for the intermolecular interactions, only a small change in the σ parameter of the Lennard-Jones potential has been introduced. The overall predictions are very close to those of TIP4P/2005. This ensures that the new model may be used with the same confidence as its predecessor in studies where a flexible model is advisable.     

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.     

Spectral characterization of hydrogen bond network dynamics in water

Some computational aspects of the characterization of the complex hydrogen bond network dynamics using power spectral analysis are discussed. In the case of hydrogen-bonded liquids, the tagged molecule potential energy is shown to be a useful quantity for capturing the behavior of the networked liquid on different lengths and time scales. The computation of the tagged potential energy for rigid-body effective pair potentials, such as the TIP5P-E and SPC-E models, is discussed. The more structured nature of the TIP5P-E potential, compared to the SPC/E potential, shows up as differences in the high-frequency librational band of the power spectra of the tagged molecule potential energies. The static distributions of the tagged molecule potential energies are also more structured in the case of TIP5P-E, rather than SPC/E, water. The overall behavior of the key power spectral features remains the same in both the models. The possibility of detailed characterization of the power spectrum, and therefore of the underlying dynamics, using a model-based parametric fitting procedure for the power spectra is also discussed. We show that a parametric fitting can allow one to test alternative models of the dynamics underlying the liquid state dynamics.     

Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent

The atomic-level mechanisms of protein regulation by post-translational phosphorylation remain poorly understood, except in a few well-studied systems. Molecular mechanics simulations can in principle be used to help understand and predict the effects of protein phosphorylation, but the accuracy of the results will of course depend on the quality of the force field parameters for the phosphorylated residues as well as the quality of the solvent model. The phosphorylated residues typically carry a -2 charge at physiological pH; however, the effects of phosphorylation can sometimes be mimicked by substituting Asp or Glu for the phosphorylated residue. Here we examine the suitability of explicit and implicit solvent models for simulating phospho-serine in both the -1 and -2 charge states. Specifically, we simulate a capped phosphorylated peptide, Ace-Gly-Ser-pSer-Ser-Nme, and compare the results to each other and to experimental observables from an NMR experiment. The first major conclusion is that explicit water models (TIP3P, TIP4P and SPC/E) and a Generalized Born implicit solvent model provide reasonable agreement with the experimental observables, given appropriate partial charges for the phosphate group. The Generalized Born results, however, show greater hydrogen bonding propensity than the explicit solvent results. Distance dependent dielectric treatments perform poorly. The second major conclusion is that many ensemble-averaged properties obtained for the phosphopeptide in the -1 and -2 charge states are strikingly similar; the -1 species has a slightly higher propensity to form internal hydrogen bonds. All of the results can be rationalized by quantifying the strength of the P-O/H-N hydrogen bond, which depends on a sensitive balance between strongly favorable charge/dipole and dipole/dipole interactions and strongly unfavorable desolvation.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

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.     

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.     

Resonant 2-photon ionization study of the conformation and the binding of water molecules to 2-phenylethanethiol (PhCH2CH2SH)

The structures of 2-phenylethanethiol (PET, PhCH(2)CH(2)SH) and its 1:1 water clusters have been studied using resonant two-photon ionization spectroscopy including band contour analysis and UV-UV holeburning, combined with extensive ab initio calculations on ground and excited states. The most populated conformer, labeled Ggpi, has a gauche arrangement about the SCCC and HSCC bonds that permits a stabilizing SH...dpi type of hydrogen bond. The other observed conformer, Ag, is anti with respect to the SCCC bond. In the dominant 1:1 water cluster, a water molecule binds to the Ggpi conformer via an OH...S hydrogen bond and two significant CH...O interactions. There is also evidence for water binding to conformer Ag with a similar arrangement, and for a second Ggpi cluster where water inserts between the SH and the aromatic ring. The additional interactions to the water molecules result in net D(e) binding energies approximately double those resulting from a single thiol-water hydrogen bond. The (1)(pi,pi(*)) excited state lifetimes in the bare molecules are very short because of internal conversion to a dissociative (1)(n,pi(*)) state related to the thiol. In the dominant Gw(1) cluster, the lifetime is significantly increased from <1 to approximately 4 ns. Hydrogen bonding to the thiol, which raises the energy of the dissociative (1)(n,pi(*)) state, accounts for this behavior.