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Simulations of hydride and deuteride transfer catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) are presented using ensemble-averaged variational transition theory with multidimensional tunneling. The results suggest that quantum mechanical tunneling makes a significant contribution to the reaction rate at all temperatures and dimerization is important for thermal stability of TmDHFR and its catalytic activity.

The solvent-dependent transition states for decarboxylations are interpreted.

The characterization of alternative mechanisms for the reductive dechlorination of hexachloroethane (HCA) to perchloroethylene is discussed. It was possible to obtain theoretical predictions accurate to within 23 mV for four aqueous reduction potentials relevant to HCA.

Research is presented on the computation of kinetic isotope effects and Swain-Schaad exponents in enzymatic reactions by using combined quantum mechanical and molecular mechanical potential energy function in quantum dynamics simulations.

The reaction rate and kinetic isotope effects (KIE) during the conversion of 2-phospho-D-glycerate (2-PGA) to phosphoenolpyruvate (PEP) by the yeast enolase during glucose fermentation have been calculated using semiclassical variational transition state theory. Enolase is a glycolytic enzyme that catalyzes the reversible dehydration of 2-PGA to PEP. Primary and secondary KIEs strongly point to the presence of a stepwise carbanionic mechanism in the early formation of a carbanion intermediate.

The effects of para substitution on the electronic properties of phenylnitrenium ions in the gas phase and aqueous solution were investigated via quantum chemical computations. Linear free energy relationships between phenylnitrenium ion S-T gaps and three model substituents for para-substitution effects were also examined. Experimental results revealed trends in singlet-triplet splittings, singlet aromatic stretching frequencies and singlet C-N+ bond lengths, which are associated with linear free energy relationships.

A study based on variational transition state theory was conducted on the temperature dependence of the dynamical bottleneck location for the prototype olefin addition process H + C2H4. A method called variable scaling of external correlation which uses a scale factor was developed. The findings indicate that tunneling effects are quantitatively responsible for the curvature of the Arrhenius plots.

Carbenes occur widely as reactive intermediates in many organic reactions and they are extensively studied. The isoelectronic analog of a carbene with a negative charge is a borenide anion. A study has been undertakent to characterize how a charge on a divalent atom affects reactivity, through the calculation of barrier heights to 1,2-hydrogen migration, for single states of methylphenylborenide, methylphenylnitrenium and methylphenylcarbene. Energy splittings are also examined.

The reaction rate constant of the trans-Rh(PHsub3)sub3C1(etasuper2-CHsub4) to RH(PHsub3)sub2-CIH(CHsub3) rearrangement, where the C-H bond of methane is activated, is calaculated. Density functional theory based on the direct dynamics approach was used to obtain Born-Oppenheimer potential energies, reaction-path geometries and vibrational frequences.

The rate constants and deuterium kinetic isotope effects (KIEs) for the competing SN2 and E2 reactions of ClO- and C2H5Cl were determined. Dual-level generalized transition state theory and statistical calculations based on correlated electronic calculation were used in the study. The results showed that the KIEs at room temperature were normal for the E2 reaction and inverse for the SN2 reaction. The temperature dependences of the KIEs were also observed.

The calculated kinetic isotopic effect (KIE) and their temperature dependence for gas-phase S(sub N)2 reactions X(super -) + CH3Y gives CH3X + Y(super -)(X, Y = Cl, Br, I) are consistent with the experimentally established data. Small alterations of the transition state theory from conventional transition state occurs. The KIE is susceptible to vibrational frequencies. Anharmonicity have substantial effect on the experimental results. Rate constants exhibit negative correlation below 500 K.

Theoretical studies help develop a quantum mechanical solvation model to evaluate solvation free energies in the nonpolar solvent n-hexadecane. Transferable parameters of the solvation model are Hamiltonian-independent. This model utilizes the CM1 charge models and a set of both short and long-range surface tensions. Solvation effect significantly influences the size of the primary solvation shell. Application of this model to 306 compounds produces an rms errors of 0.41 kcal mol.

Theoretical studies help examine gas-phase S(N)2 reactions between F(-)(H2O) and CH3Cl, and the deuterium substituted analogs. Electronic structure calculations help define geometries and evaluate energies and vibrational frequencies of reactants, products and saddle points of the reactions. The data helps determine transition state theory rate constants and secondary kinetic isotope effects for CD3 and D2O substitution.

Aqueous solvation of all possible conformers of 1,2-ethanediol are analyzed by the combination of correlated, extended basis set, gas-phase free energies with the quantum statistical SMx models. Aqueous equilibrium population and free energy of solvation for the solute are determined and are in agreement with the experimental results. Free energies of solvation between conformers with and without hydrogen bonds are calculated and show increased trans C-C conformations in aqueous solutions compared to the gas phase.

Extended-basis-set electronic structure computations with high levels of electron correlation for heterocyclic tautomerizations were reinforced by an elaborate study of the aqueous solvation of free energy differences, including electronic and geometric relaxation in aqueous solution. The Austin Model 1-solvation model 2 (AM1-SM2) formed the basis of the attempts.

A study used a semiclassical technique to estimate the kinetic isotope effect of the reaction Fe3 + CD3H to understand the tunneling paths for hydrogen atom transfer. The neglect of diatomic differential overlap (NDDO) molecular orbital theory with semiempirical specific-reaction parameters (SRP) are used. With variational transition state theory and multidimensional semiclassical tunneling computations including corner cutting, this technique can be used to model to intricate quantum mechanical dynamics of organic reactions.

Researchers used a quantum chemical solvation model drawn from a continuum treatment of dielectric polarization and solvent accessible surface area to assess the aqueous solvation influences on the anomeric and conformational equilibria of D-glucopyranose. The solvation model places the comparative sequencing of the hydroxymethyl conformers in accordance with the experimentally identified sequencing of populations. The study offers proof of intra-glucose hydrogen bond conjugation in aqueous solution.

The kinetic isotope effect for the (1,5) sigmatropic rearrangement reaction of cis-1,3-pentadiene was studied. The direct dynamics method was employed in conjunction with a new computer program to simulate the reaction process. All dynamic calculations were performed based on the cannonical variational transition-state theory. The results show excellent agreement with available experimental data.

Analyses of Claisen rearrangement of carboxymethylated derivative, possible methoxy-substituted derivatives, a pair of alkylated derivatives and allyl vinyl ether confirm that electric polarization and first hydration shell hydrophilic effects are responsible for the aqueous acceleration of the rearrangement. Responsiveness to substitution pattern is very high.

Several liquid-phase density functional theory calculations are conducted to explain the different concerted and nonconcerted [alpha],[beta]-elimination reactions of esters, as well as thioesters. The compounds are shown to prefer the anti transition state more, as compared to the syn state.

A new model is described for predicting branching ratios of chemical reactions when a branching of the reaction path occurs after the dynamical bottleneck, including the case where it occurs after an intermediate. The new model is based on combining nonstatistical phase space theory for the direct component of a reaction with variational transition-state theory for an indirect component of reaction and the competition between direct and indirect processes is treated by the unified statistical model.

4-Oxalocrotonate tautomerase enzyme (4-OT) has catalyzed the isomerization of 2-oxo-4-hexenedioate and the isomerization is studied by using the combined quantum mechanical and molecular mechanical method. The studies have shown that proton transfer process is coupled to a conformational change of the substrate and the conformation change is promoted by the changes in the electron distribution of the substrate taking place as the proton transfer has occurred.

The melting transition of metal nanoparticles is examined with a realistic many-body potential developed from quantum mechanical calculations on nanoparticles. The studies have shown that [Al.sub.n] nanoparticles have a wide temperature window of coexistence of solid and liquid states and this coexistence regime is called the slush state.

The multiconfigurational electronic structure calculations are employed to study the relation between the hydrogen atom transfer (HAT) and proton-coupled electron transfer (PCET) mechanisms. The conical intersection seam is shown to be a major topographical feature, which affects the reaction between phenol and radicals.

The characterization of thermodynamic properties of neural [Al.sub.n] (2 (less than or equal to) n (less than or equal to) 65) particles which provide insight into size-selective reactivity and catalytic activity of metal nanoparticles is reported.

An intramolecular proton-transfer mechanism is described for the carbocationic cyclization of farnesyl pyrophosphate (FPP) to (+)-aristolochene catalyzed by aristolochene synthase. The results have shown that the mutations of either residue have led to pronounced generation of aborted cyclization products.

The rate constants for the OH + [H.sub.2]S -> [H.sub.2]O + HS reaction are calculated by direct dynamics with the M06-2X density functional theory. The rate constants are important for both atmospheric chemistry and combustion, while the temperature dependence is accounted for even in the context of a simple abstraction reaction.

Density functionals that provide an accurate description of noncovalent pi interactions is developed. The density functional results in the present study are in agreement with experiments and a present ab initio study for hexamethyd HMB@[6]CPPA , which along with validation studies in Supporting Information lends credibility to the predictions for larger scale complexes for which ab initio calculations are prohibitively resource consuming.

A theoretical study designed to examine the reliability of inferring the transition state structure for an enzyme-catalyzed hydride transfer reaction on the basis of an empirical criterion is presented. Results reveal that the donor carbon at the hydride transfer transition state resembles the reactant state more than the product state, whereas the acceptor carbon is more productlike, which is a symptom of transition state imbalance.

An investigation using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiemperical Hamiltonian is described for the wild-type ornithine decarboxylase reaction with orthinine and lysine and for mutant E274A with orthinine substrate. The dynamical method is variational transition state theory with quantized vibrations.

The (super 12)C/(super 13)C kinetic isotope effect (KIE) and its T dependence for the reaction of methane with OH radical are studied. It is found that and advanced level of dynamical theory, variational transition state theory with multidimensional tunneling contributions (VTST/MT), is necessary for quantitative prediction of the T dependence, and the inclusion of torsion anharmonicity is critical even for qualitative prediction of the KIE magnitude.