Classical Interaction Potentials Research Articles

The bend angle of water in ice Ih and liquid water: The significance of implementing the nonlinear monomer dipole moment surface in classical interaction potentials

The implementation of the physically accurate nonlinear dipole moment surface of the water monomer in the context of the Thole-type, polarizable, flexible interaction potential results in the only classical potential, which, starting from the gas phase value for the bend angle (104.52 degrees), reproduces its experimentally observed increase in the ice Ih lattice and in liquid water. This is in contrast to all other classical potentials to date, which predict a decrease of the monomer bend angle in ice Ih and in liquid water with respect to the gas phase monomer value. Simulations under periodic boundary conditions of several supercells consisting of up to 288 molecules of water used to sample the proton disorder in the ice Ih lattice yield an average value of vartheta(HOH)(I(h))=108.4 degrees +/-0.2 degrees for the minimized structures (T=0 K) and 108.1 degrees +/-2.8 degrees at T=100 K. Analogous simulations for liquid water predict an average value of vartheta(HOH)(liquid)=106.3 degrees +/-4.9 degrees at T=300 K. The increase of the monomer bend angle of water in condensed environments is attributed to the use of geometry-dependent charges that are used to describe the nonlinear character of the monomer's dipole moment surface. Our results suggest a new paradigm in the development of classical interaction potential models of water that can be used to describe condensed aqueous environments.

Structure and Dynamics of the Aqueous Liquid−Vapor Interface: A Comprehensive Particle-Based Simulation Study

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.

Ab initio molecular dynamics of liquid hydrogen chloride

We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (l-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)(2) dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in [script-l]-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.

Partition of protein solvation into group contributions from molecular dynamics simulations

Linear response theory coupled to molecular dynamics simulations with an explicit solvent representation is used to derive fractional contributions of amino acid residues to the solvation of proteins. The new fractional methods developed here are compared with standard approaches based on empirical 1D and 3D statistical potentials, as well as with estimates obtained from the analysis of classical molecular interaction potentials. The new fractional methods, which have a clear physical basis and explicitly account for the effects due to protein structure and flexibility, provide an accurate picture of the contribution to solvation of different regions of the protein.

Ab initio based force field and molecular dynamics simulations of crystalline TATB.

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.

A fully polarizable and dissociable potential for water

A new classical interaction potential for water simulations is presented. Water is modeled as a fully dissociable set of atoms with a point dipole, determined self-consistently, on every oxygen atom. The oxygen polarizability is not fixed but depends on the geometry of the system. We show that, in spite of the limited number of free parameters, the model reproduces the geometrical and vibrational properties of microclusters in a satisfactory way.

Understanding the sensitivity of nucleation kinetics: A case study on water

Small atomic or molecular clusters provide the bridge between vapor and liquid phases. Nucleation is a rare event process by which clusters of a new phase are produced. This process is inherently dynamic and as such the new phase cannot exist until an activation barrier is surmounted. Dynamical nucleation theory (DNT) utilizes variational transition state theory to provide a framework in which cluster evaporation and condensation rate constants can be determined directly. To date, the fundamental nature regarding the intrinsic instability of the kinetics of the nucleation process has eluded theoretical efforts. In this paper we present a sensitivity analysis of the homogeneous nucleation rate on kinetic parameters used in DNT. Moreover, several classical interaction potentials for water exist, most of which have been parametrized to reproduce some bulk properties of water at ambient conditions. Thus, an analysis was undertaken to explore what effects different water potentials have on the dynamical quantities relevant to nucleation. The implication of these results on future work will be discussed.

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.

The latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories.

Theoretical study of the mechanisms of substrate recognition by catalase.

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.

Simulation of thermal conductivity and heat transport in solids

Using molecular dynamics (MD) with classical interaction potentials we present calculations of thermal conductivity and heat transport in crystals and glasses. Inducing shock waves and heat pulses into the systems we study the spreading of energy and temperature over the configurations. Phonon decay is investigated by exciting single modes in the structures and monitoring the time evolution of the amplitude using MD in a microcanonical ensemble. As examples, crystalline and amorphous modifications of Selenium and $\rm{SiO_2}$ are considered.

Quantum chemistry based force fields for soft matter

We describe the use of ab initio electronic structure calculations in the development of high-quality classical interaction potentials for liquid crystal modeling. Our focus is on methods for the rapid, on-demand creation of force fields for use in mean field theory based calculations of materials properties, employed for routine pre-synthesis evaluation of novel liquid crystalline materials. The role of quantum chemistry in the development of intermolecular interaction potentials for large-scale simulations of soft matter is also discussed, and directions for future work are outlined. The utility of quantum chemistry derived force fields for liquid crystal modeling is illustrated by two example applications: mean field theory based prediction of the spontaneous polarization density P of ferroelectric liquid crystals, and large-scale simulation studies of the nanosegregation of polymer precursors in smectic liquid crystal hosts.

Calculation of vibrational properties of selenium

Using molecular dynamics with a classical interaction potential we present methods for calculating both vibrational properties and thermodynamic quantities for solids and estimating their temperature dependence. The density of states is given by the Fourier transformation of the displacement autocorrelation function. Applying the harmonic approximation we calculate the specific heat . Elastic constants are determined from the response of the structures to external pressures and volume changes. As an example, crystalline and amorphous modifications of selenium are considered.

Theoretical modeling of a weak correlation effect in a nonideal plasma

Weak correlation effect in a nonideal plasma system has been modeled within a fluid description by an average classical Coulomb interaction potential in dynamic momentum equation of the electrons. This is the lowest order correction and models the small deviation from the ideal gas behavior of the plasma. Numerical solution of the Poisson equation shows a reasonably good agreement with the earlier calculation based on the statistical formulation of the particle correlation in plasmas. Effects of the particle correlation may be displayed through the modification in the dispersion characteristics of the plasma waves/sheath potential at a surface in contact with the nonideal plasma.

Anharmonic effects at metal surfaces

We present here results of temperature-dependent studies of the dynamics of several fcc metal surfaces using classical molecular dynamic simulations and interaction potentials from the embedded atom method. At room temperature, the mean square vibrational amplitudes of the (100) surface of Ag, Cu and Ni are found to be isotropic, while on (111) the out-of-plane vibration is larger and on the (110) surface the in-plane motion along <001 > is the dominant one. Beyond room temperature, anharmonic effects at the surface become noticeable and at a temperature somewhat larger than half the melting temperature the in-plane, anharmonic vibrational amplitudes on the (110) surface become so larger that adatoms and vacancies are created. This leads the surface to disorder and eventually to premelt. On the (100) surface, however, adatoms and vacancies do not appear until close to the melting temperature, while Cu(110) is found to premelt at about 1200K and Ag(110) at about 1050K. The surface thermal expansion of Ag(110) is also found to be significantly larger than for the bulk. The phonon frequency shifts and line-width broadening are calculated as a function of surface temperature. These characteristics on Ag(110) are compared with those on Cu(110).

Evaluation of the Stillinger-Weber classical interaction potential for tetragonal semiconductors in nonideal atomic configurations.

A classical potential incorporating two- and three-body interaction terms has recently been introduced by Stillinger and Weber (SW) for simulation of the liquefaction transition of silicon. The equilibrium mechanical properties of this potential are determined and found to agree well with experimental values. The potential also seems to be adequate for problems involving computation of defect energies, such as the stability of strained-layer superlattice interfaces. However, inadequate treatment of configurations with low coordination number makes modeling of the epitaxial growth of (111) silicon impossible. Simple modifications of the SW potential form do allow for (111) epitaxial growth, but the earliest stages of growth then become unphysical.

Equilibrium properties of a one-dimensional kinetic system

One-dimensional systems of N = 500 and 250 particles in equilibrium are numerically simulated utilizing the method of molecular dynamics. Periodic boundary conditions are imposed. The classical two-body interaction potential is short range, repulsive and has a corresponding finite force. The equations of state are determined for densities both less and greater than one. Corresponding theoretical isochores are determined from models based on nearest-neighbor interactions and on a truncated virial expansion, and a comparison is made with the experimental isochores. Time independent radial distributions are constructed numerically and discussed. A change of state from a solidlike state to a fluid-gas state based on the penetrability of the particles is predicted. The transition temperatures are estimated from the radial distribution functions and the nearest-neighbor model. Self-diffusion is observed and the corresponding constants are determined from the velocity autocorrelation functions.