Computational Modeling of Human Paraoxonase 1: Preparation of Protein Models, Binding Studies, and Mechanistic Insights.

The enzyme human paraoxonase 1 (huPON1) has demonstrated significant potential for use as a bioscavenger for treatment of exposure to organophosphorus (OP) nerve agents. Herein we report the development of protein models for the human isoform derived from a crystal structure of a chimeric version of the protein (pdb ID: 1V04) and a homology model derived from the related enzyme diisopropylfluorophosphatase (pdb ID: 1XHR). From these structural models, binding modes for OP substrates are predicted, and these poses are found to orient substrates in proximity to residues known to modulate specificity of the enzyme. Predictions are made with regard to the role that residues play in altering substrate binding and turnover, in particular with regard to the stereoselectivity of the enzyme, and the known differences in activity related to a natural polymorphism in the enzyme. Potential mechanisms of action of the protein for catalytic hydrolysis of OP substrates are also evaluated in light of the proposed binding modes.

Combustion pathways of the alkylated heteroaromatics: bond dissociation enthalpies and alkyl group fragmentations.

The bond dissociation enthalpies (BDEs) of the alkyl groups of the alkyl-substituted heterocycles have been studied and compiled using DFT methodology, with the intent of modeling the larger heterocyclic functionalities found in coal. DFT results were calibrated against CBS-QB3 calculations, and qualitative trends were reproduced between these methods. Loss of hydrogen at the benzylic position provided the most favorable route to radical formation, for both the azabenzenes and five-membered heterocycles. The ethyl derivatives had lower BDE values than the methyl derivatives due to increased stabilization of the corresponding radicals. Calculated spin densities correlated well with bond dissociation enthalpies for these compounds, while geometric effects were minimal with respect to the heterocycles themselves. Temperature effects on the bond dissociation enthalpies were minor, ranging by about 5 kcal/mol from 298 to 2000 K; the free energies of reaction dropped significantly over the same range due to entropic effects. Monocyclic heteroaromatic rings were seen to replicate the chemistry of multicyclic heteroaromatic systems.

Kinetic barriers of H-atom transfer reactions in alkyl, allylic, and oxoallylic radicals as calculated by composite ab initio methods.

Composite ab initio and density functional theory (DFT) methods were used to explore internal hydrogen-atom transfers in a variety of primary, secondary, and tertiary alkyl and functionalized radicals with implications for combustion environments. The composite ab initio method G3MP2B3 was found to achieve the most reasonable balance between accuracy and economy in modeling the energetics of these reactions. Increased alkyl substitution reduced barriers to isomerization by about 10 and 20 kJ mol(-1) for secondary and tertiary radical formation, respectively, relative to primary radical reactions and was relatively insensitive to the transition-state ring size (extent of H-atom internal shift). Reactions involving alkenyl and alkanoyl radicals were also explored. Hydrogen-atom transfers involving allylic radical formation demonstrated barrier heights that were 15-20 kJ mol(-1) lower than those in corresponding alkyl radicals, whereas those involving oxoallylic species (alpha-site radicals of aldehydes and ketones) were 20-40 kJ mol(-1) lower. In the cases of the alkyl radicals, enthalpies of activation were seen to scale with enthalpies of reaction. This correlation was not seen, however, in the cases of the allylic and oxoallylic radicals; this fact has significant implications in combustion chemistry and mechanism development, considering that such Evans-Polanyi correlations are widely used in estimating barrier heights for rate expressions.

Non-aqueous solvation of n-octanol and ethanol: spectroscopic and computational studies.

Raman spectroscopy was used to examine the interactions of the free O-H bonds in n-octanol and ethanol with the organic solvents carbon tetrachloride (CCl(4)), cyclohexane, and benzene. These spectra reveal that the solvents CCl(4) and cyclohexane have a small effect on the free O-H peak of alcohols, whereas benzene as a solvent significantly red-shifts the free O-H band. Calculated spectra were generated via MP2/6-31G* calculations and the B3LYP/6-31+G**//MP2/6-31G*-derived Boltzmann populations of each ethanol complex and are consistent with the experimental results. Additional spectra were calculated using Boltzmann populations derived from single-point energies at the polarizable continuum model (PCM) level with the B3LYP/6-31+G** level of theory to take overall solvent effects into account, and these simulated spectra are also largely consistent with the experimental results. Analysis of the computational results reveals a lengthening of the O-H bond from the O-H interaction with the delocalized electronic structure of benzene as well as a bimodal distribution of the free O-H peak of the alcohol/benzene mixtures due to two distinctly different types of alcohol/benzene complexes.

Theoretical determinations of the ambient conformational distribution and unimolecular decomposition of n-propylperoxy radical.

The conformational distribution and unimolecular decomposition pathways for the n-propylperoxy radical have been generated at the CBS-QB3, B3LYP/6-31+G and mPW1K/6-31+G levels of theory. At each of the theoretical levels, the 298 K Boltzmann distributions and rotational profiles indicate that all five unique rotamers of the n-propylperoxy radical can be expected to be present in significant concentrations at thermal equilibrium. At the CBS-QB3 level, the 298 K distribution of rotamers is predicted to be 28.1, 26.4, 19.6, 14.0, and 11.9% for the gG, tG, gT, gG', and tT conformations, respectively. The CBS-QB3 C-OO bond dissociation energy (DeltaH298 K) for the n-propylperoxy radical has been calculated to be 36.1 kcal/mol. The detailed CBS-QB3 potential energy surface for the unimolecular decomposition of the n-propylperoxy radical indicates that important bimolecular products could be derived from two 1,4-H transfer mechanisms available at T < 500 K, primarily via an activated n-propylperoxy adduct.