Thomas A. Halgren

Bio: Thomas A. Halgren is an academic researcher from California Institute of Technology. The author has contributed to research in topics: Molecular orbital & Localized molecular orbitals. The author has an hindex of 14, co-authored 27 publications receiving 1279 citations.

The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters

Abstract: This paper explores the premise that insights gained from studying the well-characterized van der Waals (vdW) interactions of rare-gas atoms can be used advantageneoulsy in formulating the representation of vdW nonbonded interactions in molecular mechanics force fields, a subject to which little attention has been givin to date

Kinetics and Equilibrium Constants for Reactions of α-Phenyl-Substituted Cyclopropylcarbinyl Radicals

Abstract: Laser-flash photolysis methods were used to determine Arrhenius functions for cyclizations of the 4,4-diphenyl-3-butenyl (2) and trans-4-phenyl-3-butenyl (5) radicals to the 1,1-diphenylcyclopropylcarbinyl (1) and 1-phenylcyclopropylcarbinyl (4) radicals, respectively. At 20 °C, the cyclization rate constants are 1.7 × 107 and 5.4 × 106 s-1. Equilibrium constants for the two processes were estimated and evaluated with thermochemical data and via computational methods, and Arrhenius functions for the ring-opening reactions of the cyclopropylcarbinyl radicals were calculated. The cyclization reactions of 2 and 5 are strongly enthalpy controlled. Production of radicals 1 and 2 from the corresponding tert-butylperoxy esters in the presence of Et3SnH gave diphenylcyclopropylmethane and 1,1-diphenyl-1-butene from H-atom trapping of radicals 1 and 2 and 4-phenyl-1,2-dihydronaphthalene which derives from the product radical formed by addition of the radical moiety in 2 to the cis-phenyl group. Rate constants for ...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

Abstract: A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

Abstract: This article introduces MMFF94, the initial published version of the Merck molecular force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodology employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and experimental data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in molecular-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small molecules in a combined “organic/protein” force field that is equally applicable to proteins and other systems of biological significance. A second distinguishing feature is that the core portion of MMFF94 has primarily been derived from high-quality computational data—ca. 500 molecular structures optimized at the HF/6-31G* level, 475 structures optimized at the MP2/6-31G* level, 380 MP2/6-31G* structures evaluated at a defined approximation to the MP4SDQ/TZP level, and 1450 structures partly derived from MP2/6-31G* geometries and evaluated at the MP2/TZP level. A third distinguishing feature is that MMFF94 has been parameterized for a wide variety of chemical systems of interest to organic and medicial chemists, including many that feature frequently occurring combinations of functional groups for which little, if any, useful experimental data are available. The methodology used in parameterizing MMFF94 represents a fourth distinguishing feature. Rather than using the common “functional group” approach, nearly all MMFF parameters have been determined in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addition, MMFF94 reproduces experimental bond lengths (0.014 A root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm−1 rms), conformational energies (0.38 kcal/mol/rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermolecular interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field. © 1996 John Wiley & Sons, Inc.

Molecular Models of Hydroxide, Oxyhydroxide, and Clay Phases and the Development of a General Force Field

Abstract: The fate of chemical and radioactive wastes in the environment is related to the ability of natural phases to attenuate and immobilize contaminants through chemical sorption and precipitation processes. Our understanding of these complex processes at the atomic level is provided by a few experimental and analytical methods such as X-ray absorption and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental atomic-level understanding, interpretation, and prediction of these phenomena. In this effort, we have developed a general force field, CLAYFF, suitable for the simulation of hydrated and multicomponent mineral systems and their interfaces with aqueous solutions. Interatomic potentials were derived from parametrizations incorporating structural and spectroscopic data for a variety of simple hydrated compounds. A...

Force fields for protein simulations

Abstract: Publisher Summary The chapter focuses on a general description of the force fields that are most commonly used at present, and it gives an indication of the directions of current research that may yield better functions in the near future. After a brief survey of current models, mostly generated during the 1990s, the focus of the chapter is on the general directions the field is taking in developing new models. The most commonly used protein force fields incorporate a relatively simple potential energy function: The emphasis is on the use of continuum methods to model the electrostatic effects of hydration and the introduction of polarizability to model the electronic response to changes in the environment. Some of the history and performance of widely used protein force fields based on an equation on simplest potential energy function or closely related equations are reviewed. The chapter outlines some promising developments that go beyond this, primarily by altering the way electrostatic interactions are treated. The use of atomic multipoles and off-center charge distributions, as well as attempts to incorporate electronic polarizability, are also discussed in the chapter.