Kim K. Baldridge

General atomic and molecular electronic structure system

A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines.

First principles implementation of solvent effects without outlying charge error

In this work, we present a sound modified implementation of the noniterative approach for the inclusion of solvent effects for molecular-shaped cavities in conventional ab initio gas phase computations. This model will serve as the starting point from which to add additional influences such as nonelectrostatic and correlation effects, as well as optimization of cavity radii. The improvement over recent dielectric continuum models is (a) the utilization of distributed multipoles up to hexadecapoles for the generation of the potential on the cavity boundary to the dielectric and the calculation of surface charges, and (b) an accurate assessment of outlying charge effects. The new method is tested in calculations of solvation energies and geometries for a number of neutral and charged molecules.

A framework for the design and reuse of grid workflows

Grid workflows can be seen as special scientific workflows involving high performance and/or high throughput computational tasks. Much work in grid workflows has focused on improving application performance through schedulers that optimize the use of computational resources and bandwidth. As high-end computing resources are becoming more of a commodity that is available to new scientific communities, there is an increasing need to also improve the design and reusability “performance” of scientific workflow systems. To this end, we are developing a framework that supports the design and reuse of grid workflows. Individual workflow components (e.g., for data movement, database querying, job scheduling, remote execution etc.) are abstracted into a set of generic, reusable tasks. Instantiations of these common tasks can be functionally equivalent atomic components (called actors) or composite components (so-called composite actors or subworkflows). In this way, a grid workflow designer does not have to commit to a particular Grid technology when developing a scientific workflow; instead different technologies (e.g. GridFTP, SRB, and scp) can be used interchangeably and in concert. We illustrate the application of our framework using two real-world Grid workflows from different scientific domains, i.e., cheminformatics and bioinformatics, respectively.

Through-space interactions between face-to-face, center-to-edge oriented arenes: importance of polar-π effects

Two series of conformationally restricted polycyclic compounds (1-3 and 4-7) have been synthesized as model systems for studying the through-space interactions between face-to-face, center-to-edge (parallel-offset) oriented arenes. These compounds feature different X substituents on one of the interacting rings. By monitoring the variation of the delta Gz for the rotation around the aryl-aryl bond in 1-7 as a function of X by 2D [1H,1H] EXSY NMR spectroscopy, it was found that the barriers increase on passing from electron-donating to electron-withdrawing substituted derivatives. Quantum mechanical calculations [MP2/DVZ (2d,p)//B3LYP/DVZ(2d,p)] gave barrier values and variations in agreement with the experimental data. The results are consistent with a repulsive arene-arene interaction dominated by electrostatic effects.

Transition state structure, barrier height, and vibrational frequencies for the reaction Cl+CH4→CH3+HCl

We have carried out ab initio calculations using second‐ and fourth‐order Mo/ller–Plesset perturbation theory, scaled electron correlation, and several basis sets for the reaction Cl+CH4→CH3+HCl. We found that including electron correlation is essential for obtaining accurate barrier heights and vibrational frequencies. Furthermore, scaling the correlation energy further improves the barrier height predictions provided that the basis set being used is correlation balanced for both bonds involved in the reaction. Geometries and transition state frequencies calculated at the MP2 and MP‐SAC2 levels with the most extensive and best balanced basis set are in good agreement with one another for all bound modes, but the unbound‐mode frequency changes by 214i cm−1.

Uncatalyzed peptide bond formation in the gas phase

Several levels of electronic structure theory are used to analyze the formation of a peptide bond between two glycine molecules. Both a stepwise and concerted mechanism were considered. The energetic requirements for the stepwise and concerted mechanisms are essentially the same within the expected accuracy of the methods used. A simpler model system comprised of formic acid and ammonia is found to provide a good representation of the essential features of dipeptide formation. Total electron demities and localized molecular orbitals are used to interpret the mechanisms

Long CC single bonds in anthracene dimers: The structure of bi(anthracene-9,10-dimethylene) photodimer is redetermined

Abstract Ab Initio HF and DF Theory computations are performed on anthracene dimers 1–3 Crystal structures are redetermined at low temperature for 2 and 3. The 1.77 A central bond length previously reported for 3 is shown to be only 1.648 A. Through-bond coupling as a primary cause of bond lengthening in 1–3 is questioned.

QMView: a computational chemistry three-dimensional visualization tool at the interface between molecules and mankind.

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, PostScript files, slide, and/or video. These and other original features discussed in this article provide a graphic interface that is unique compared to others that are currently available. Examples of images produced by QMView are presented.

Ionization of corannulene and 1,6-dimethylcorannulene: photoelectron spectra, electrochemistry, charge transfer bands and ab initio computations

Abstract The ionization energies of corannulene and 1,6-dimethylcorannulene are measured by PES, voltammetry and UV charge transfer bands and are compared to values predicted by ab initio calculations and Koopmans theorem.

Ground state gas and solution phase conformational dynamics of polar processes: Furfural systems

The conductorlike continuum solvation model, modified for ab initio in the quantum chemistry program GAMESS, implemented at the Moller–Plesset Order 2 (MP2) level of theory has been applied to a group of push–pull pyrrole systems to illustrate the effects of donor/acceptor and solvation on the stability and energetics of such systems. The most accurate theoretical gas and solution phase data to date has been presented for the parent furan-2-carbaldehyde (furfural) system, and predictions made for three additional analogues, thiophene-2-carbaldehyde, pyrrole2-carbaldehyde, and, cyclopentadiene-1-carbaldehyde. Solvent effects on internal rotational barriers in all systems were evaluated over six different values of dielectric, using the new method. Calculated electrostatic energies are shown to be highly sensitive to level of theory incorporated.