Matthew R. Kennedy

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A largely unsolved problem in computational biochemistry is the accurate prediction of binding affinities of small ligands to protein receptors. We present a detailed analysis of the systematic and random errors present in computational methods through the use of error probability density functions, specifically for computed interaction energies between(More)
Diatoms are single-celled eukaryotic microalgae that are ubiquitously found in almost all aquatic ecosystems, and are characterized by their intricately structured SiO2 (silica)-based cell walls. Diatoms with a benthic life style are capable of attaching to any natural or man-made submerged surface, thus contributing substantially to both microbial biofilm(More)
With the fast-paced nature of technology, rapidly fielding systems has never been more important. Success depends on well-defined requirements and the ability to rapidly respond to change during and after deployment. The inability to rapidly respond may cause the system to become obsolete before initial fielding. Creating a structure where processes allow(More)
Density functional theory (DFT) has been applied to the proposed rate-limiting step of the hydrolytic kinetic resolution (HKR) of terminal epoxides as catalyzed by Co-salen-X (X = counterion) in order to resolve questions surrounding the mechanism. The present results indicate that the bimetallic mechanism proposed by Jacobsen shows nonadditive, cooperative(More)
π-π interactions are integral to many areas of chemistry, biochemistry, and materials science. Here we use electronic structure theory to analyze how π-π interactions change as the π-systems are curved in model complexes based on coronene and corannulene dimers. Curvature redistributes electronic charge in the π-cloud and creates a dipole moment in these(More)
Coupled-cluster theory including single, double, and perturbative triple excitations [CCSD(T)] has been applied to trimers that appear in crystalline benzene in order to resolve discrepancies in the literature about the magnitude of non-additive three-body contributions to the lattice energy. The present results indicate a non-additive three-body(More)
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