Steven J. Stuart

A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons

A second-generation potential energy function for solid carbon and hydrocarbon molecules that is based on an empirical bond order formalism is presented. This potential allows for covalent bond breaking and forming with associated changes in atomic hybridization within a classical potential, producing a powerful method for modelling complex chemistry in large many-atom systems. This revised potential contains improved analytic functions and an extended database relative to an earlier version (Brenner D W 1990 Phys. Rev. B 42 9458). These lead to a significantly better description of bond energies, lengths, and force constants for hydrocarbon molecules, as well as elastic properties, interstitial defect energies, and surface energies for diamond.

A reactive potential for hydrocarbons with intermolecular interactions

A potential function is presented that can be used to model both chemical reactions and intermolecular interactions in condensed-phase hydrocarbon systems such as liquids, graphite, and polymers. This potential is derived from a well-known dissociable hydrocarbon force field, the reactive empirical bond-order potential. The extensions include an adaptive treatment of the nonbonded and dihedral-angle interactions, which still allows for covalent bonding interactions. Torsional potentials are introduced via a novel interaction potential that does not require a fixed hybridization state. The resulting model is intended as a first step towards a transferable, empirical potential capable of simulating chemical reactions in a variety of environments. The current implementation has been validated against structural and energetic properties of both gaseous and liquid hydrocarbons, and is expected to prove useful in simulations of hydrocarbon liquids, thin films, and other saturated hydrocarbon systems.

Dynamical fluctuating charge force fields: Application to liquid water

A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of electronegativity equalization according to which: (a) the electronegativity of an atomic site is dependent on the atom’s type and charge and is perturbed by the electrostatic potential it experiences from its neighbors and (b) charge is transferred between atomic sites in such a way that electronegativities are equalized. The charges are treated as dynamical variables using an extended Lagrangian method in which the charges are given a fictitious mass, velocities, and kinetic energy and then propagated according to Newtonian mechanics along with the atomic degrees of freedom. Models for water with fluctuating charges are developed using the geometries of two common fixed‐charge water potentials: the simple point charge (SPC) and the four‐point transferable intermolecular po...

Fluctuating charge force fields for aqueous solutions

Abstract A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment has been developed in a previous work (J. Chem. Phys., 101:6151 (1994)). The model and its application to liquid water are briefly reviewed. Various properties of the model are calculated, with emphasis on the bonding characteristics. The water model is also used to investigate the aqueous solvation of formaldehyde.

Molecular dynamics with multiple time scales: The selection of efficient reference system propagators

Several heuristic rules are developed to assist in the implementation of the reversible reference system propagator algorithm (rRESPA). This is done through the use of examples, illustrating the use of properly chosen rRESPA splits of various types, as well as the dangers associated with improperly chosen ones. It is concluded that a particle‐based rRESPA split should be used only when there is a great disparity in particle masses, and that a force‐based split should be used only when there is no persisting opposition between forces in the system which are integrated with different time steps.

Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions

In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (DeltaG(ads)) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. DeltaG(ads) was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent DeltaG(ads) within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results clearly show that improvements in force field parameterization are needed in order to accurately represent interactions between amino acid residues and functional groups of a surface and they provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.

Chemical sputtering from amorphous carbon under bombardment by deuterium atoms and molecules

We perform classical molecular dynamics simulations of the chemical sputtering of deuterated amorphous carbon surfaces by D and D2, at energies of 7.5–30 eV D−1. Particular attention is paid to the preparation of the target surfaces for varying impact projectile fluence, energy and species, to the vibrational state of D2 projectiles, as well as to the variation in sputtering yields with target surface and impact projectile. The methane and acetylene sputtering yields per deuteron, obtained with atomic and molecular projectiles, agree quantitatively with recent experimental values. We study the distribution of sputtered species, as well as their kinetic energy and angular spectra.

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na+) as the solute positioned over a surface functionalized with one negatively charged group (COO-) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions.

Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results.

Understanding collision cascades in molecular solids

Abstract This paper describes simulations of the sputtering of a molecular solid that uses a reactive potential with both covalent bonding and van der Waals interactions. Recently, the adaptive intermolecular REBO (AIREBO) potential has been developed, which incorporates intermolecular interactions in a manner that maintains the reactivity of the original reactive empirical bond-order (REBO) potential. Preliminary simulations of the keV bombardment of a molecular solid have been performed using the AIREBO potential. Molecules that are initially struck by the bombarding particle break into fragments. The fragments initiate molecular collision cascades leading to the ejection of intact molecules and molecular fragments from the surface.