Ward H. Thompson

Bio: Ward H. Thompson is an academic researcher from University of Kansas. The author has contributed to research in topics: Molecular dynamics & Diatomic molecule. The author has an hindex of 30, co-authored 113 publications receiving 2508 citations. Previous affiliations of Ward H. Thompson include University of Colorado Boulder & University of California, Berkeley.

Utilization of hydrogen bonds to stabilize M-O(H) units: synthesis and properties of monomeric iron and manganese complexes with terminal oxo and hydroxo ligands.

Abstract: Non-heme iron and manganese species with terminal oxo ligands are proposed to be key intermediates in a variety of biological and synthetic systems; however, the stabilization of these types of complexes has proven difficult because of the tendency to form oxo-bridged complexes. Described herein are the design, isolation, and properties for a series of mononuclear FeIII and MnIII complexes with terminal oxo or hydroxo ligands. Isolation of the complexes was facilitated by the tripodal ligand tris[(N‘-tert-butylureaylato)-N-ethyl]aminato ([H3 1]3-), which creates a protective hydrogen bond cavity around the MIII−O(H) units (MIII = Fe and Mn). The MIII−O(H) complexes are prepared by the activation of dioxygen and deprotonation of water. In addition, the MIII−O(H) complexes can be synthesized using oxygen atom transfer reagents such as N-oxides and hydroxylamines. The [FeIIIH3 1(O)]2- complex also can be made using sulfoxides. These findings support the proposal of a high valent MIV−oxo species as an interme...

Thermal rate constant calculation using flux–flux autocorrelation functions: Application to Cl+H2→HCl+H reaction

Abstract: An efficient method was recently introduced by Thompson and Miller [J. Chem. Phys. 106, 142 (1997)] for calculating thermal rate constants using the flux–flux autocorrelation function with absorbing boundary conditions. The method uses an iterative method to exploit the low rank feature of the Boltzmannized flux operator and subsequently only propagates the eigenvectors that have significant contributions to the rate constant. In the present article, this method is used to calculate the thermal rate constants of the Cl+H2→HCl+H reaction in the temperature range of 200–1500 °K. Total angular momentum is treated by employing the body-fixed axis frame, both exactly and also via various approximations. Comparisons with previous exact and approximate theoretical results are made.

On the “direct” calculation of thermal rate constants. II. The flux-flux autocorrelation function with absorbing potentials, with application to the O+HCl→OH+Cl reaction

Abstract: We present a method for obtaining the thermal rate constant directly (i.e., without first solving the state-to-state reactive scattering problem) from the time integral of the flux-flux autocorrelation function, Cff(t). The quantum mechanical trace involved in calculating Cff(t) is efficiently evaluated by taking advantage of the low rank of the Boltzmannized flux operator. The time propagation is carried out with a Hamiltonian which includes imaginary absorbing potentials in the reactant and product exit channels. These potentials eliminate reflection from the edge of the finite basis and ensure that Cff(t) goes to zero at long times. In addition, the basis can then be contracted to represent a smaller area around the interaction region. We present results of this method applied to the O+HCl reaction using the J-shifting and helicity conserving approximations to include nonzero total angular momentum. The calculated rate constants are compared to experimental and previous theoretical results. Finally, th...

Testing a two-state model of nanoconfined liquids: conformational equilibrium of ethylene glycol in amorphous silica pores.

Abstract: Molecular dynamics simulations of the conformational equilibrium of ethylene glycol in roughly cylindrical nanoscale amorphous silica pores are presented and analyzed in the context of a two-state model of confined liquids. This model assumes that an observable property of a confined liquid can be decomposed into a weighted average arising from two subensembles with distinct physical attributes: molecules at the surface and molecules in the interior of the pore. It is further assumed that the molecules in the interior exhibit behavior that is indistinguishable from that of the bulk liquid. However, the present simulation results are not consistent with this two-state model. Neither the assumption of two distinct subensembles nor the assumption that the interior molecules possess bulk-like behavior is supported.

Reorientation dynamics of nanoconfined water: power-law decay, hydrogen-bond jumps, and test of a two-state model.

Abstract: The reorientation dynamics of water confined within nanoscale, hydrophilic silica pores are investigated using molecular dynamics simulations. The effect of surface hydrogen-bonding and electrostatic interactions are examined by comparing with both a silica pore with no charges (representing hydrophobic confinement) and bulk water. The OH reorientation in water is found to slow significantly in hydrophilic confinement compared to bulk water, and is well-described by a power-law decay extending beyond one nanosecond. In contrast, the dynamics of water in the hydrophobic pore are more modestly affected. A two-state model, commonly used to interpret confined liquid properties, is tested by analysis of the position-dependence of the water dynamics. While the two-state model provides a good fit of the orientational decay, our molecular-level analysis evidences that it relies on an over-simplified picture of water dynamics. In contrast with the two-state model assumptions, the interface dynamics is markedly heterogeneous, especially in the hydrophilic pore and there is no single interfacial state with a common dynamics.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Transition Metal-Catalyzed Decarboxylative Allylation and Benzylation Reactions

Abstract: A review. Transition metal catalyzed decarboxylative allylations, benzylations, and interceptive allylations are reviewed.

Substrates for gallium nitride epitaxy

Abstract: In this review, the structural, mechanical, thermal, and chemical properties of substrates used for gallium nitride (GaN) epitaxy are compiled, and the properties of GaN films deposited on these substrates are reviewed. Among semiconductors, GaN is unique; most of its applications uses thin GaN films deposited on foreign substrates (materials other than GaN); that is, heteroepitaxial thin films. As a consequence of heteroepitaxy, the quality of the GaN films is very dependent on the properties of the substrate—both the inherent properties such as lattice constants and thermal expansion coefficients, and process induced properties such as surface roughness, step height and terrace width, and wetting behavior. The consequences of heteroepitaxy are discussed, including the crystallographic orientation and polarity, surface morphology, and inherent and thermally induced stress in the GaN films. Defects such as threading dislocations, inversion domains, and the unintentional incorporation of impurities into the epitaxial GaN layer resulting from heteroepitaxy are presented along with their effect on device processing and performance. A summary of the structure and lattice constants for many semiconductors, metals, metal nitrides, and oxides used or considered for GaN epitaxy is presented. The properties, synthesis, advantages and disadvantages of the six most commonly employed substrates (sapphire, 6H-SiC, Si, GaAs, LiGaO 2 , and AlN) are presented. Useful substrate properties such as lattice constants, defect densities, elastic moduli, thermal expansion coefficients, thermal conductivities, etching characteristics, and reactivities under deposition conditions are presented. Efforts to reduce the defect densities and to optimize the electrical and optical properties of the GaN epitaxial film by substrate etching, nitridation, and slight misorientation from the (0 0 0 1) crystal plane are reviewed. The requirements, the obstacles, and the results to date to produce zincblende GaN on 3C-SiC/Si(0 0 1) and GaAs are discussed. Tables summarizing measures of the GaN quality such as XRD rocking curve FWHM, photoluminescence peak position and FWHM, and electron mobilities for GaN epitaxial layers produced by MOCVD, MBE, and HVPE for each substrate are given. The initial results using GaN substrates, prepared as bulk crystals and as free-standing epitaxial films, are reviewed. Finally, the promise and the directions of research on new potential substrates, such as compliant and porous substrates are described.