For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.

Interaction Models for Water in Relation to Protein Hydration

https://is.muni.cz/el/1431/podzim2006/C7780/um/Read/2711172/SAM_str_grwth_ProgSurfSci00_151.pdf

Structure and growth of self-assembling monolayers

HYDROGEN bonds play a crucial role in the behaviour of water1–4; their spatial patterns and fluctuations characterize the structure and dynamics of the liquid5–7. The processes of breaking and making hydrogen bonds in the condensed phase can be probed indirectly by a variety of experimental techniques8, and more quantitative information can be obtained from computer simulations9. In particular, simulations have revealed that on long timescales the relaxation behaviour of hydrogen bonds in liquid water exhibit non-exponential kinetics7,10–13, suggesting that bond making and breaking are not simple processes characterized by well defined rate constants. Here we show that these kinetics can be understood in terms of an interplay between diffusion and hydrogen-bond dynamics. In our model, which can be extended to other hydrogen-bonded liquids, diffusion governs whether a specific pair of water molecules are near neighbours, and hydrogen bonds between such pairs form and persist at random with average lifetimes determined by rate constants for bond making and breaking.

Hydrogen-bond kinetics in liquid water

New force fields for carbon dioxide and nitrogen are introduced that quantitatively reproduce the vapor–liquid equilibria (VLE) of the neat systems and their mixtures with alkanes. In addition to the usual VLE calculations for pure CO2 and N2, calculations of the binary mixtures with propane were used in the force-field development to achieve a good balance between dispersive and electrostatic (quadrupole–quadrupole) interactions. The transferability of the force fields was then assessed from calculations of the VLE for the binary mixtures with n-hexane, the binary mixture of CO2/N2, and the ternary mixture of CO2 /N2/propane. The VLE calculations were carried out using configurational-bias Monte Carlo simulations in either the grand canonical ensemble with histogram–reweighting or in the Gibbs ensemble.

Vapor–liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen

Molecular dynamics simulations of ionic systems require the inclusion of long‐range electrostatic forces. We propose an expression for the long‐range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost.

A generalized reaction field method for molecular dynamics simulations

Hydration and mobility of ions in solution

Four recently proposed intermolecular-potential models have been used in molecular-dynamics simulations of liquid methanol over a temperature range of approximately 70 K. Results are reported for thermodynamic and structural properties, self-diffusion coefficients, and reorientational correlation times. Two of the models are shown to give results in fair agreement with a wide variety of experimental data. The pattern of hydrogen bonding and the distribution of hydrogen-bond lifetimes in the simulated liquids have been investigated. The structure in each case is found to be dominated by winding chains, in agreement with earlier work. For the more realistic models, the mean hydrogen-bond lifetime at room temperature is approximately 1 to 2 ps, which is several times larger than the corresponding time for liquid water.

Molecular-dynamics simulation of liquid methanol

Effective pair‐potential models, parametrized to the properties of the pure liquids, have been used in molecular‐dynamics simulations of aqueous (binary) mixtures containing methanol, ammonia, or acetone. Results are reported for thermodynamic and structural properties, self‐diffusion coefficients, and reorientational correlation times. There is fair agreement with a wide variety of experimental data. The pattern of hydrogen bonding and the distribution of hydrogen‐bond lifetimes in the simulated mixtures have been investigated. The observed anomalous behavior of methanol and acetone solutions appears to be related to specific features of the hydrogen bonding—namely, the ability of these molecules to exhibit enhanced acceptor character. As a consequence of the assumed intermolecular potentials, the balance between the competing effects of hydrophobic hydration of methyl groups and hydrogen bonding to oxygen atoms is tipped towards the latter. A number of interesting structural effects have been noted. In ...

Molecular-dynamics simulation of aqueous mixtures : methanol, acetone, and ammonia

Comprehensive coverage of topics in the theory of classical liquids
Widely regarded as the standard text in its field, Theory of Simple Liquids gives an advanced but self-contained account of liquid state theory within the unifying framework provided by classical statistical mechanics. The structure of this revised and updated Fourth Edition is similar to that of the previous one but there are significant shifts in emphasis and much new material has been added.
Major changes and Key Features in content include:

Expansion of existing sections on simulation methods, liquid-vapour coexistence, the hierarchical reference theory of criticality, and the dynamics of super-cooled liquids.
New sections on binary fluid mixtures, surface tension, wetting, the asymptotic decay of pair correlations, fluids in porous media, the thermodynamics of glasses, and fluid flow at solid surfaces.
An entirely new chapter on applications to 'soft matter' of a combination of liquid state theory and coarse graining strategies, with sections on polymer solutions and polymer melts, colloidal dispersions, colloid-polymer mixtures, lyotropic liquid crystals, colloidal dynamics, and on clustering and gelation.



Expansion of existing sections on simulation methods, liquid-vapour coexistence, the hierarchian reference of criticality, and the dynamics of super-cooled liquids.
New sections on binary fluid mixtures, surface tension, wetting, the asymptotic decay of pair correlations, fluids in porous media, the thermodynamics of glasses, and fluid flow at solid surfaces.
An entirely new chapter on applications to 'soft matter' of a combination of liquid state theory and coarse graining strategies, with sections on polymer solutions and polymer melts, colloidal dispersions, colloid-polymer mixtures, lyotropic liquid crystals, colloidal dynamics, and on clustering and gelation.

Theory of Simple Liquids: with Applications to Soft Matter

The adequacy of simple potential models to describe the properties of carbon dioxide in its different phases is explored. The molecules are assumed to interact through two or three Lennard-Jones n-6 centres and a point quadrupole moment placed at the molecular centre of mass. Good agreement with a wide range of properties is obtained for a three-centre model with n=12 and a value of the quadrupole moment which is somewhat smaller than the experimental one.

Ian R. McDonald

Papers

Hydration and mobility of ions in solution

Molecular-dynamics simulation of liquid methanol

Molecular-dynamics simulation of aqueous mixtures : methanol, acetone, and ammonia

Theory of Simple Liquids: with Applications to Soft Matter

Interaction site models for carbon dioxide