Melting points and thermal expansivities of proton-disordered hexagonal ice with several model potentials

A method of free energy calculation is proposed, which enables to cover a wide range of pressure and temperature. The free energies of proton-disordered hexagonal ice (ice Ih) and liquid water are calculated for the TIP4P [J. Chem. Phys. 79, 926 (1983)] model and the TIP5P [J. Chem. Phys. 112, 8910 (2000)] model. From the calculated free energy curves, we determine the melting point of the proton-disordered hexagonal ice at 0.1 MPa (atmospheric pressure), 50 MPa, 100 MPa, and 200 MPa. The melting temperatures at atmospheric pressure for the TIP4P ice and the TIP5P ice are found to be about T(m)=229 K and T(m)=268 K, respectively. The melting temperatures decrease as the pressure is increased, a feature consistent with the pressure dependence of the melting point for realistic proton-disordered hexagonal ice. We also calculate the thermal expansivity of the model ices. Negative thermal expansivity is observed at the low temperature region for the TIP4P ice, but not for the TIP5P ice at the ambient pressure.     

An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model

The method of flexible constraints was implemented in a Monte Carlo code to perform numerical simulations of liquid water and ice Ih in the constant number of molecules, volume, and temperature and constant pressure, instead of volume ensembles, using the polarizable and flexible mobile charge densities in harmonic oscillators (MCDHO) model. The structural and energetic results for the liquid at T=298 K and rho=997 kg m(-3) were in good agreement with those obtained from molecular dynamics. The density obtained at P=1 atm with flexible constraints, rho=1008 kg m(-3), was slightly lower than with the classical sampling of the intramolecular vibrations, rho=1010 kg m(-3). The comparison of the structures and energies found for water hexamers and for ice Ih with six standard empirical models to those obtained with MCDHO, show this latter to perform better in describing water far from ambient conditions: the MCDHO minimum lattice energy, density, and lattice constants were in good agreement with experiment. The average angle HOH of the water molecule in ice was predicted to be slightly larger than in the liquid, yet 1.2% smaller than the experimental value.     

Structure and decompression melting of a novel, high-pressure nanoconfined 2-D ice

Molecular dynamics (MD) simulations of water confined in nanospaces between layers of talc (system composition Mg(3)Si(4)O(10)(OH)(2) + 2H(2)O) at 300 K and pressures of approximately 0.45 GPa show the presence of a novel 2-D ice structure, and the simulation results at lower pressures provide insight into the mechanisms of its decompression melting. Talc is hydrophobic at ambient pressure and temperature, but weak hydrogen bonding between the talc surface and the water molecules plays an important role in stabilizing the hydrated structure at high pressure. The simulation results suggest that experimentally accessible elevated pressures may cause formation of a wide range of previously unknown water structures in nanoconfinement. In the talc 2-D ice, each water molecule is coordinated by six O(b) atoms of one basal siloxane sheet and three water molecules. The water molecules are arranged in a buckled hexagonal array in the a-b crystallographic plane with two sublayers along [001]. Each H(2)O molecule has four H-bonds, accepting one from the talc OH group and one from another water molecule and donating one to an O(b) and one to another water molecule. In plan view, the molecules are arranged in six-member rings reflecting the substrate talc structure. Decompression melting occurs by migration of water molecules to interstitial sites in the centers of six-member rings and eventual formation of separate empty and water-filled regions.     

Comparison of the Dynamics of Water Molecules in Crystals of Proton-Ordered Ice IX and Its Proton-Disordered Analog III

A computer simulation of proton-ordered ice IX and its proton-disordered analog III (768 molecules, 90 K) was carried out by the molecular dynamics method using Poltev–Malenkov's potential. For ice IX, the differences in the dynamic characteristics of molecules with O(1) and O(2) are much wider than those in the case of ice III. The libration spectrum of ice IX has a number of distinct acute peaks, and the spectrum of ice III is strongly smoothed. These peculiarities are explained by the proton ordering of ice IX and disordering of ice III. The latter is responsible for the great differences in the short- and especially long-range environment of water molecules in ice crystals and hence for the presence of many molecules with different dynamic characteristics. Thus averaging over a large number of different vibrational spectra of molecules leads to a smoothed total spectrum in the case of the proton-disordered crystal modification of ice.     

Ice growth from supercooled aqueous solutions of benzene, naphthalene, and phenanthrene

Classical molecular dynamics (MD) were performed to investigate the growth of ice from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene. The main objective of this study is to explore the fate of those aromatic molecules after freezing of the supercooled aqueous solutions, i.e., if these molecules become trapped inside the ice lattice or if they are displaced to the QLL or to the interface with air. Ice growth from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene result in the formation of quasi-liquid layers (QLLs) at the air/ice interface that are thicker than those observed when pure supercooled water freezes. Naphthalene and phenanthrene molecules in the supercooled aqueous solutions are displaced to the air/ice interface during the freezing process at both 270 and 260 K; no incorporation of these aromatics into the ice lattice is observed throughout the freezing process. Similar trends were observed during freezing of supercooled aqueous solutions of benzene at 270 K. In contrast, a fraction of the benzene molecules become trapped inside the ice lattice during the freezing process at 260 K, with the rest of the benzene molecules being displaced to the air/ice interface. These results suggest that the size of the aromatic molecule in the supercooled aqueous solution is an important parameter in determining whether these molecules become trapped inside the ice crystals. Finally, we also report potential of mean force (PMF) calculations aimed at studying the adsorption of gas-phase benzene and phenanthrene on atmospheric air/ice interfaces. Our PMF calculations indicate the presence of deep free energy minima for both benzene and phenanthrene at the air/ice interface, with these molecules adopting a flat orientation at the air/ice interface.     

Energy relaxation of intermolecular motions in supercooled water and ice: a molecular dynamics study

We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed information on energy relaxation in condensed phases like two-color pump-probe spectroscopy. It is shown that the energy cascading in liquid water is characterized by four processes. The temperature dependences of the earlier three processes, the rotational-rotational, rotational-translational, and translational-translational energy transfers, are explained in terms of the density of states of the intermolecular motions. The last process is the slow energy transfer arising from the transitions between potential energy basins caused by the excitation of the low frequency translational motion. This process is absent in ice because the hydrogen bond network rearrangement, which accompanies the interbasin transitions in liquid water, cannot take place in the solid phase. We find that the last process in supercooled water is well approximated by a stretched exponential function. The stretching parameter, β, decreases from 1 to 0.72 with decreasing temperature. This result indicates that the dynamics of liquid water becomes heterogeneous at lower temperatures.     

Quantum effects in ice Ih

Quantum and classical simulations are carried out on ice Ih over a range of temperatures utilizing the TIP4P water model. The rigid-body centroid molecular dynamics method employed allows for the investigation of equilibrium and dynamical properties of the quantum system. The impact of quantization on the local structure, as measured by the radial and spatial distribution functions, as well as the energy is presented. The effects of quantization on the lattice vibrations, associated with the molecular translations and librations, are also reported. Comparison of quantum and classical simulation results indicates that shifts in the average potential energy are equivalent to rising the temperature about 80 K and are therefore non-negligible. The energy shifts due to quantization and the quantum mechanical uncertainties observed in ice are smaller than the values previously reported for liquid water. Additionally, we carry out a comparative study of melting in our classical and quantum simulations and show that there are significant differences between classical and quantum ice.     

Dynamical properties of hydrogen sulphide motion in its clathrate hydrate from ab initio and classical isobaric-isothermal molecular dynamics

Equilibrium ab initio (AI) and classical constant pressure-constant temperature molecular dynamics (MD) simulations have been performed to investigate the dynamical properties in (type I) hydrogen sulphide hydrate at 150 and 300 K and 1 bar, and also lower temperatures, with particular scrutiny of guest motion. The rattling motions of the guests in the large and small cavities were around 45 and 75-80 cm(-1), respectively, from AIMD, with the corresponding classical MD modes being 10-12 cm(-1) less at 150 K and around 5 cm(-1) lower at 300 K. The rattling motion in the small cavity overlapped somewhat with the translational motion of the host lattice (with modes at circa 85 and 110 cm(-1)), due in part to a smaller cage radius and more frequent occurrences of guest-host hydrogen bonding leading to greater coupling in the motion. The experimentally determined H-S stretch and H-S-H bending frequencies, in the vicinity of 2550-2620 and 1175 cm(-1) [H.R. Richardson et al., J. Chem. Phys.1985, 83, 4387] were reproduced successfully in the AIMD simulations. Consideration of Kubic harmonics for the guest molecules from AIMD revealed that a preferred orientation of the dipole-vector (or C(2)-axis) exists at 150 K vis--vis the [100] cube axis in both the small and large cavities, but is markedly more significant for the small cavity, while there is no preferred orientation at 300 K. In comparison, classical MD did not reveal any preferred orientation at either temperature, or at 75 K (closer to the AIMD simulation at 150 K vis-à-vis that approach's estimated melting point). Probing rotational dynamics of the guests reinforced this temperature effect, revealing more rapid rotational time scales at 300 K with faster decay times of dipole-vector (C(2)) and H-H-vector (C(2)(y)) being similar for each cage, at around 0.25 and 0.2 ps, respectively, versus approximately 0.45 and 0.5 ps (large) and 0.8 ps (small) at 150 K. It was found that the origin of the observed preferred orientations, especially in the small cages, at 150 K via AIMD was attributable to optimization of the dipolar interaction between the guest and outward-pointing water dipoles in the cavity, with guests "flitting" rotationally between various such configurations, forming occasionally hydrogen bonds with the host molecules.     

Protein boson peak originated from hydration-related multiple minima energy landscape

The boson peak is a broad peak found in the low-frequency region of inelastic neutron and Raman scattering spectra in many glassy materials, including biopolymers below approximately 200 K. Here, we give a novel insight into the origins of the protein boson peak, which may also be valid for materials other than proteins. Molecular simulation reveals that the structured water molecules around a protein molecule increase the number of local minima in the protein energy landscape, which plays a key role in the origin of the boson peak. The peak appears when the protein dynamics are trapped within a local energy minimum at cryogenic temperatures. This trapping causes very low frequency collective motions to shift to higher frequencies. We demonstrate that the characteristic frequency of such systems shifts higher as the temperature decreases also in model one-dimensional energy surfaces with multiple minima.     

NMR investigation of the porosity of hypercrosslinked polystyrene and the properties of water confined in its nanopores

The melting of water frozen preliminarily at 180 K in a free internal volume of water-swollen hypercrosslinked polystyrene networks with degrees of crosslinking ranging from 43 to 500% is studied by NMR. It is found that ice melts within a narrow range of low temperatures, 195?C225 K, demonstrating that the pores in the networks are small and uniform in size. It is, however, impossible to calculate the pore size via the Gibbs-Thomson equation, since the structure of water (and hence its properties) depend on a sample??s rate of freezing. We conclude that the activation of the orientational motions of water molecules starts to manifest itself already at 200 K; upon reaching 220?C230 K, the total mobility of water molecules is due largely to translational motions with an activation energy of 27?C28 kJ/mol.     

Vibrational density of states of hydration water at biomolecular sites: hydrophobicity promotes low density amorphous ice behavior

Inelastic neutron scattering experiments and molecular dynamics simulations have been used to investigate the low frequency modes, in the region between 0 and 100 meV, of hydration water in selected hydrophilic and hydrophobic biomolecules. The results show changes in the plasticity of the hydrogen-bond network of hydration water molecules depending on the biomolecular site. At 200 K, the measured low frequency density of states of hydration water molecules of hydrophilic peptides is remarkably similar to that of high density amorphous ice, whereas, for hydrophobic biomolecules, it is comparable to that of low density amorphous ice behavior. In both hydrophilic and hydrophobic biomolecules, the high frequency modes show a blue shift of the libration mode as compared to the room temperature data. These results can be related to the density of water molecules around the biological interface, suggesting that the apparent local density of water is larger in a hydrophilic environment.     

A facet of recent ice sciences

Of prime interest in the numerous studies on water, an important substance to mankind and all other living systems, may be its chemical, physical, biological or geological characteristics but underlying all these is a basic structural problem. One of the important questions that still remains unanswered in this field is: why ordinary ice keep its proton-disordered state down to the lowest temperature. We found that the slowing down of water re-orientational motion at low temperatures leads to freezing of the disordered state in the ice crystal at around 110 K. This was the origin of the deviation of the crystal from the third law of thermodynamics. Doping by a particular kind of impurity recovered the mobility of the molecule to exhibit a long-awaited ordering transition at 72 K. The dopant dramatically accelerated the motion of water molecules to change the crystal from a non-equilibrium frozen-in disordered state to the equilibrium one within our experimental time. New steps in ice sciences and procedures used in these experiments are reviewed briefly. The structure and some properties of the low-temperature ordered phase, designated as ice XI, are described.     

Hydration dynamics and time scales of coupled water-protein fluctuations

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.     

Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion

Water expulsion from the protein core is a key step in protein folding. Nevertheless, unusually large water clusters confined into the nonpolar cavities have been observed in the X-ray crystal structures of tetrabrachion, a bacterial protein that is thermostable up to at least 403 K (130 degrees C). Here, we use molecular dynamics (MD) simulations to investigate the structure and thermodynamics of water filling the largest cavity of the right-handed coiled-coil stalk of tetrabrachion at 365 K (92 degrees C), the temperature of optimal bacterial growth, and at room temperature (298 K). Hydrogen-bonded water clusters of seven to nine water molecules are found to be thermodynamically stable in this cavity at both temperatures, confirming the X-ray studies. Stability, as measured by the transfer free energy of the optimal size cluster, decreases with increasing temperature. Water filling is thus driven by the energy of transfer and opposed by the transfer entropy, both depending only weakly on temperature. Our calculations suggest that cluster formation becomes unfavorable at approximately 384 K (110 degrees C), signaling the onset of drying just slightly above the temperature of optimal growth. "Drying" thus precedes protein denaturation. At room temperature, the second largest cavity in tetrabrachion accommodates a five water molecule cluster, as reported in the X-ray studies. However, the simulations show that at 365 K the cluster is unstable and breaks up. We suggest that the large hydrophobic cavities may act as binding sites for two proteases, possibly explaining the unusual thermostability of the resulting protease-stalk complexes (up to approximately 393 K, 120 degrees C).     

A powerful computational crystallography method to study ice polymorphism

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction potential for oxygen and hydrogen in bulk water, derived from neutron scattering data, able to successfully describe complex phenomena such as proton hopping and bond formation/breaking. The present study demonstrates the ability of the interaction potential model to well describe most ice structures found in the phase diagram of water and to estimate the relative stability of 16 known phases through a cluster analysis of simulated powder diagrams of polymorphs obtained from MD simulations. The proposed computational protocol is suited for automated crystal structure identification.     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.     

Molecular dynamics simulations of ice nucleation by electric fields

Molecular dynamics simulations are used to investigate heterogeneous ice nucleation in model systems where an electric field acts on water molecules within 10-20 ? of a surface. Two different water models (the six-site and TIP4P/Ice models) are considered, and in both cases, it is shown that a surface field can serve as a very effective ice nucleation catalyst in supercooled water. Ice with a ferroelectric cubic structure nucleates near the surface, and dipole disordered cubic ice grows outward from the surface layer. We examine the influences of temperature and two important field parameters, the field strength and distance from the surface over which it acts, on the ice nucleation process. For the six-site model, the highest temperature where we observe field-induced ice nucleation is 280 K, and for TIP4P/Ice 270 K (note that the estimated normal freezing points of the six-site and TIP4P/Ice models are ～289 and ～270 K, respectively). The minimum electric field strength required to nucleate ice depends a little on how far the field extends from the surface. If it extends 20 ?, then a field strength of 1.5 × 10(9) V/m is effective for both models. If the field extent is 10 ?, then stronger fields are required (2.5 × 10(9) V/m for TIP4P/Ice and 3.5 × 10(9) V/m for the six-site model). Our results demonstrate that fields of realistic strength, that act only over a narrow surface region, can effectively nucleate ice at temperatures not far below the freezing point. This further supports the possibility that local electric fields can be a significant factor influencing heterogeneous ice nucleation in physical situations. We would expect this to be especially relevant for ice nuclei with very rough surfaces where one would expect local fields of varying strength and direction.     

X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations

Full potential x-ray spectroscopy simulations of hexagonal ice and liquid water are performed by means of the newly implemented methodology based on the Gaussian augmented plane waves formalism. The computed spectra obtained within the supercell approach are compared to experimental data. The variations of the spectral distribution determined by the quality of the basis set, the size of the sample, and the choice of the core-hole potential are extensively discussed. The second part of this work is focused on the understanding of the connections between specific configurations of the hydrogen bond network and the corresponding contributions to the x-ray absorption spectrum in liquid water. Our results confirm that asymmetrically coordinated molecules, in particular, those donating only one or no hydrogen bond, are associated with well identified spectral signatures that differ significantly from the ice spectral profile. However, transient local structures, with half formed hydrogen bonds, may still give rise to spectra with dominant postedge contributions and relatively weaker oscillator strengths at lower energy. This explains why by averaging the spectra over all the O atoms of liquid instantaneous configurations extracted from ab initio molecular dynamics trajectories, the spectral features indicating the presence of weak or broken hydrogen bonds turn out to be attenuated and sometimes not clearly distinguishable.     

Molecular dynamics study of tryptophylglycine: a dipeptide nanotube with confined water

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG.H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules. The details of the structural behavior with temperature are investigated for the entire simulated temperature range. Phase transitions were obtained at 115, 245, 270, 310, and 385 K, due to the contributions of both the peptide and the confined water subsystems. The crystalline, amorphous, liquidlike, liquid, and superheated phases of water were observed in the temperature ranges 40-115, 115-245, 245-310, 310-385, and >385 K, respectively. At 300 K, the diffusion constant of the confined water is 0.46 x 10-5 cm2 s-1, a value comparable to that of other peptide nanotubes. The empty peptide system melts at 440 K. Mechanisms of the negative thermal expansion (NTE) along the tube axis were investigated for different temperature ranges. The contraction of the crystalline water (or amorphous water) draws also the tube walls in and leads to NTE below 245 K. The other NTEs appear to be connected to the collapse of the ice network or the solid peptide network between 245 K and room temperature or from 310 to 440 K, respectively.     

First-principles study of fluoroform adsorption on a hexagonal ice (0001) surface: weak hydrogen bonds-strong structural effects

For isolated fluoroform (F(3)CH) molecules adsorbed on a hexagonal ice (0001) surface the properties of blue- and red-shifting hydrogen bonds were studied using static density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CP-MD) simulations. A systematic search by starting from many initial configurations was performed to determine the lowest-energy structures of F(3)CH on the ice surface, and for the optimized geometries the vibrational frequencies were calculated. The local minima structures are analyzed in terms of their coordination to the surface, with special focus on identifying blue-shifting hydrogen bonds via their spectroscopic signature of an increased frequency of the C-H fundamental stretching vibration. Subsequently, by CP-MD simulations the stability of the lowest-energy configurations at finite temperatures was verified and possible transformation pathways connecting the local minima structures were explored.