Free energy of liquid water from a computer simulation via cell theory

A method to calculate the free energy of water from computer simulation is presented. Based on cell theory, it approximates the potential energy surface sampled in the simulation by an anisotropic six-dimensional harmonic potential to model the three hindered translations and three hindered rotations of a single rigid water molecule. The potential is parametrized from the magnitude of the forces and torques measured in the simulation. The entropy of these six harmonic oscillators is calculated and summed with a conformational term to give the total entropy. Combining this with the simulation enthalpy yields the free energy. The six water models examined are TIP3P, SPC, TIP4P, SPC/E, TIP5P, and TIP4P-Ew. The results reproduce experiment well: free energies for all models are within 1.6 kJ mol(-1) and entropies are within 3.6 J K(-1) mol(-1). Approximately two-thirds of the entropy comes from translation, a third from rotation, and 5% from conformation. Vibrational frequencies match those in the experimental infrared spectrum and assist in their assignment. Intermolecular quantum effects are found to be small, with free energies for the classical oscillator lying 0.5-0.7 kJ mol(-1) higher than in the quantum case. Molecular displacements and vibrational and zero point energies are also calculated. Altogether, these results validate the harmonic oscillator as a quantitative model for the liquid state.     

Stability of molecular form of HCl in water vapor: A computer simulation

The free energy and entropy of the dissociation of HCl molecule into ions in water vapor, HCl(H₂O) _n + mH₂O → H₃O + (H₂O) _n+m -1Cl^?, were calculated. The dependences of various parameters on the interionic distance at 273 K and various vapor pressures were obtained. A detailed model taking into account unpaired covalent-type interactions, polarization interactions, charge transfer effect, and hydrogen bonds was applied. The numerical values of the parameters were reconstructed from the experimental data on the free energy and enthalpy of the first reactions of addition of vapor molecules to ions, and also from the results of quantum-chemical calculations of the energy and geometry of locally stable configurations of clusters HCl(H₂O) _n . Despite lower internal energy of the dissociated state, the molecular form is absolutely stable in clusters of water molecules. The dissociated state is relatively stable. Accumulation of unrecombined ion pairs in clusters is possible with a decrease in the temperature to 200 K.     

A computer simulation study of water drying at the interface of protein chains

This study investigated the water drying (cavitation) in the interfacial region of two chains of a dimeric protein by nanosecond molecular dynamics simulations using explicit water representation. Separation-induced cavity of water was directly observed in the region. We evaluated the separation length scale of two chains on which the drying transition occurs, and the average number of water molecules that are expelled from the interfacial region during the transition. The obtained values can be rationalized by Kelvin equation for finite lateral size of confinement [K. Lum and A. Luzar, Phys. Rev. E 56, R6283 (1997)]. Also, we found that the drying transition is accompanied by an exponential reduction in the average hydrogen-bond number per interfacial water molecule. The results of this study may deepen the understanding of how hydrophobic interaction drives the assembly of protein chains.     

On the dielectric theory and computer simulation of water

The static dielectric properties of ST2 water are carefully examined by means of a computer-adapted Kirkwood theory. “Experimental” data are provided by various molecular dynamics simulations involving 216. 500 and 1000 water molecules and corresponding to a variety of boundary conditions. It is shown that the integral of the respective modified T tensor plays the central role in matching different boundary conditions. Thus a unique dielectric constant σ = 82 ± 15 is obtained for a density p = 1 g/cm³ and a temperature T = 120°C. Furthermore, it is found that the constitutive relation P = [(σ - 1)/4 – is already fulfilled in a sample of a few hundred molecules. Finally, R-dependent Kirkwood g factors are discussed, which give a vivid picture, how different boundary conditions influence orientational correlations between water dipoles.     

A computer simulation of trapping electrophoresis

The gel electrophoretic migration of streptavidin-DNA complexes is severely altered by the phenomenon known as “trapping electrophoresis.” We present a first computer simulation study of this process. Our simulations use the very efficient biased reptation algorithm. The steady state is characterized by a large increase in band broadening and interband separation. However, we also find that for a narrow range of molecular sizes, the separation power of gel electrophoresis is greatly increased. We discuss the implications of our findings for the possible improvement of DNA sequencing technologies. © 1992 John Wiley & Sons, Inc.     

A plastic columnar discotic phase Dp

A plastic columnar discotic phase is reported for an asymmetrically substituted triphenylene. It is characterized by a three-dimensional crystal-like registry of ordered columns in a hexagonal lattice while the disc molecules within the columns are able to rotate. At the phase transition from the normal discotic hexagonal phase to the new phase only very minute changes in structure and dynamics occur.     

Sodium chloride ion pair interaction in water: computer simulation

The thermodynamics and structure of a sodium chloride ion pair in liquid water are studied as a function of the ion pair separation. Distinct minima in the free energy of the system are found for contact and solvent separated ion geometries.     

A computer simulation of model discotic dimers

We set up a model for discotic liquid crystal dimers and study, by means of Monte Carlo simulations, their phase behaviour and self–assembling properties, in comparison with the simpler monomeric case. Each discotic dimer is described by two oblate Gay–Berne ellipsoids connected by a flexible spacer, modelled by a harmonic “spring” of three different lengths. We find that dimerization in general yields produces a significant change on the phase behaviour, with an increase of the columnar–nematic transition temperature, a widening of the nematic region and the apparent suppression of the crystalline phase in favour of the columnar phase up to very low temperatures. Longer spacers prove to ease the formation of columns and to increase the orientational order. Contribution to the Fernando Bernardi memorial issue.     

Liquid-liquid phase transitions in supercooled water studied by computer simulations of various water models

Liquid-liquid and liquid-vapor coexistence regions of various water models were determined by Monte Carlo (MC) simulations of isotherms of density fluctuation-restricted systems and by Gibbs ensemble MC simulations. All studied water models show multiple liquid-liquid phase transitions in the supercooled region: we observe two transitions of the TIP4P, TIP5P, and SPCE models and three transitions of the ST2 model. The location of these phase transitions with respect to the liquid-vapor coexistence curve and the glass temperature is highly sensitive to the water model and its implementation. We suggest that the apparent thermodynamic singularity of real liquid water in the supercooled region at about 228 K is caused by an approach to the spinodal of the first (lowest density) liquid-liquid phase transition. The well-known density maximum of liquid water at 277 K is related to the second liquid-liquid phase transition, which is located at positive pressures with a critical point close to the maximum. A possible order parameter and the universality class of liquid-liquid phase transitions in one-component fluids are discussed.     

Collective effects in diffusional motion of water molecules: computer simulation

Structural Chemistry - Molecular dynamics simulation of the system containing 3,456 water molecules in the cubic periodic box was performed. Virtual temperatures were 261 and 297&;nbsp;K....     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.     

Plasma sputtering of water molecules from the liquid phase by low-energy ions: Molecular dynamics simulation

The ion bombardment-assisted transfer of the components of a solution to the plasma zone in an atmospheric-pressure glow discharge with a liquid cathode plays an important role. The dynamics of the impact of a 50–500 eV ion on the surface of liquid water was studied by molecular dynamics simulation. Data on the amount of water molecules transferred by ion impact to the gas phase are presented. It was shown that the sputtering yield of water can reach 450 molecules per ion at an energy consumption of 0.75 eV for sputtering. Structural changes occurring in the liquid phase under ion bombardment were analyzed on the basis of the dynamics of degradation of hydrogen bonds.     

A computer simulation of the iodine molecule dissociation reaction

The iodine dissociation reaction has been studied using a many-body classical trajectory technique. A qualitative analysis of the results shows that most of the molecules are both vibrationally and rotationally excited when they dissociate.     

Properties of liquid crystal molecules from first principles computer simulation

We explore the valence charge distribution, equilibrium geometry and harmonic force fields of the 4-pentyl-4-cyanobiphenyl (5CB) molecule and the benzene (C6H6) molecule, which provides an important mesogenic fragment, using first principles techniques adapted from large scale electronic structure calculations of periodic solids. We present for the first time accurate structural data for the isolated 5CB molecule and observe subtle broken symmetries relative to the constituent mesogenic fragments. The dynamic properties of these molecules are determined by diagonalization of dynamical matrices, the elements of which are obtained directly from quantum mechanical Hellmann-Feynman forces. Results for both molecules are in excellent agreement with available spectroscopic data, and for benzene are comparable to the most accurate quantum chemistry calculations to date. For 5CB we also present values for the molecular dipole and quadrupole moments.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Molecular orientation of monododecyl pentaethylene glycol at water/air and water/oil interfaces. A molecular dynamics computer simulation study

With a molecular dynamics computer simulation we investigated the dynamic properties of a monododecyl pentaethylene glycol (C₁₂E₅) molecule adsorbed at air/water and oil/water interfaces. In these simulations we investigated the molecular orientation of the surfactant molecules in detail. At the air/water interface the maximum of the C₁₂ chain tilt angle distribution measured with respect to the water surface is about 50°. This result is in fairly good agreement with neutron reflection experiments of monododecyl glycol ethers at the air/water interface. At the oil/water interface no significant changes were detected in the molecular orientation. We found that at equilibrium oil molecules penetrate into the hydrophobic monododecyl layer, this was also found by neutron reflection studies of the interactions between C₁₂E₅ and dodecane. The observed oil penetration results in an increase in the surface area per surfactant molecule. Received: 16 July 1999/Accepted in revised form: 28 August 1999     

A computer simulation study of the formation of liquid crystal nanodroplets from a homogeneous solution

The aggregation of liquid crystal nanodroplets from a homogeneous solution is an important but not well understood step in the preparation of various advanced photonic materials. Here, the authors performed molecular dynamics computer simulations of the formation of liquid crystalline nanodroplets, starting from an isotropic and uniform binary solution of spherical Lennard-Jones (solvent) and elongated ellipsoidal Gay-Berne (solute) rigid particles in low (<10%) concentration. They studied the dynamics of demixing and the mesogen ordering process and characterized the resulting nanodroplets assessing the effect of temperature, composition, and specific solute-solvent interaction on the morphology, structure, and anisotropy. They find that the specific solute-solvent interaction, composition, and temperature can be adjusted to tune the nanodroplet growth and size.     

Partial enthalpies and related quantities in mixtures from computer simulation

We report a method of calculating partial molar quantities in mixtures by computer simulation. The method is based on an extension of Widom's potential distribution theorem and provides an alternative way of computing partial enthalpies and volumes.