Biomedical subjects

Yuri Georgievskii

Publications and source records attributed to Yuri Georgievskii.

6 recordsLinked to original sources

PubMed2006

Predictive theory for the combination kinetics of two alkyl radicals.

An ab initio transition state theory based procedure for accurately predicting the combination kinetics of two alkyl radicals is described. This procedure employs direct evaluations of the orientation dependent interaction energies at the CASPT2/cc-pvdz level within variable reaction coordinate transition state theory (VRC-TST). One-dimensional corrections to these energies are obtained from CAS+1+2/aug-cc-pvtz calculations for CH3 + CH3 along its combination reaction path. Direct CAS+1+2/aug-cc-pvtz calculations demonstrate that, at least for the purpose of predicting the kinetics, the corrected CASPT2/cc-pvdz potential energy surface is an accurate approximation to the CAS+1+2/aug-cc-pvtz surface. Furthermore, direct trajectory simulations, performed at the B3LYP/6-31G* level, indicate that there is little local recrossing of the optimal VRC transition state dividing surface. The corrected CASPT2/cc-pvdz potential is employed in obtaining direct VRC-TST kinetic predictions for the self and cross combinations of methyl, ethyl, iso-propyl, and tert-butyl radicals. Comparisons with experiment suggest that the present dynamically corrected VRC-TST approach provides quantitatively accurate predictions for the capture rate. Each additional methyl substituent adjacent to a radical site is found to reduce the rate coefficient by about a factor of two. In each instance, the rate coefficients are predicted to decrease quite substantially with increasing temperature, with the more sterically hindered reactants having a more rapid decrease. The simple geometric mean rule, relating the capture rate for the cross reaction to those for the self-reactions, is in remarkably good agreement with the more detailed predictions. With suitable generalizations the present approach should be applicable to a wide array of radical-radical combination reactions.

Journal Article↗

PubMed2005

A two transition state model for radical-molecule reactions: a case study of the addition of OH to C2H4.

A two transition state model is applied to the study of the addition of hydroxyl radical to ethylene. This reaction serves as a prototypical example of a radical-molecule reaction with a negative activation energy in the high-pressure limit. The model incorporates variational treatments of both inner and outer transition states. The outer transition state is treated with a recently derived long-range transition state theory approach focusing on the longest-ranged term in the potential. High-level quantum chemical estimates are incorporated in a variational transition state theory treatment of the inner transition state. Anharmonic effects in the inner transition state region are explored with direct phase space integration. A two-dimensional master equation is employed in treating the pressure dependence of the addition process. An accurate treatment of the two separate transition state regions at the energy and angular momentum resolved level is essential to the prediction of the temperature dependence of the addition rate. The transition from a dominant outer transition state to a dominant inner transition state is predicted to occur at about 130 K, with significant effects from both transition states over the 10 to 400 K temperature range. Modest adjustment in the ab initio predicted inner saddle point energy yields theoretical predictions which are in quantitative agreement with the available experimental observations. The theoretically predicted capture rate is reproduced to within 10% by the expression [4.93 x 10(-12) (T/298)(-2.488) exp(-107.9/RT) + 3.33 x 10(-12) (T/298)(0.451) exp(117.6/RT); with R = 1.987 and T in K] cm3 molecules(-1) s(-1) over the 10-600 K range.

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PubMed2005

Predictive theory for hydrogen atom-hydrocarbon radical association kinetics.

Procedures for accurately predicting the kinetics of hydrogen atom associations with hydrocarbon radicals are described and applied to a series of reactions. The approach is based on CASPT2/cc-pvdz evaluations of the orientation-dependent interaction energies within variable reaction coordinate transition state theory. One-dimensional corrections to the interaction energies are estimated from CAS+1+2/aug-cc-pvtz evaluations for the H + CH3 reaction, and a dynamical correction factor of 0.9 is applied. This corrected CASPT2 approach yields results that are within 10% of those obtained with the full CAS+1+2/aug-cc-pvtz potential for the H + CH3, H + C2H5, H + C2H3, and H + C2H reactions. New predictions are made for the H + iso-C3H7, H + tert-C4H9, H + C6H5, and H + C10H7 reactions. For the H + CH3 and H + C2H3 reactions, where the experimental values appear to be the most well-determined, theory and experiment essentially agree to within their error bars. For the other reactions, the agreement is reasonably satisfactory given the often large dispersion in the experimental results. For the reactions with saturated alkyl radicals, the theory predicts that each additional CH3 group increases the steric factor by approximately a factor of 2. In contrast, for the unsaturated radicals, the H + C6H5 and H + C10H7 high-pressure association rate coefficients are nearly identical to that for H + C2H3.

Journal Article↗

PubMed2005

Long-range transition state theory.

The implementation of variational transition state theory (VTST) for long-range asymptotic potential forms is considered, with particular emphasis on the energy and total angular momentum resolved (microJ-VTST) implementation. A long-range transition state approximation yields a remarkably simple and universal description of the kinetics of reactions governed by long-range interactions. The resulting (microJ-VTST) implementation is shown to yield capture-rate coefficients that compare favorably with those from trajectory simulations (deviating by less than 10%) for a wide variety of neutral and ionic long-range potential forms. Simple analytic results are derived for many of these cases. A brief comparison with a variety of low-temperature experimental studies illustrates the power of this approach as an analysis tool. The present VTST approach allows for a simple analysis of the applicability conditions for some related theoretical approaches. It also provides an estimate of the temperature or energy at which the "long-range transition state" moves to such short separations that short-range effects, such as chemical bonding, steric repulsion, and electronic state selectivity, must be considered.

Journal Article↗

PubMed2004

On the electron tunneling in molecules: a generalized orthogonalization procedure for finding tunneling orbitals.

A simple method for finding tunneling orbitals of a long-distance electron transfer system is described. The procedure is an approximate biorthogonalization of many-electron donor and acceptor states in which the corresponding orbitals of the system are obtained; one pair of such corresponding orbitals describes the tunneling electron. Usually, the biorthogonalization is performed on the states that describe simultaneously both donor and acceptor complexes and the bridge connecting them, which make the procedure computationally demanding. In this paper a significant simplification of the procedure is proposed. In the procedure, to identify the tunneling orbitals roughly one half of the system is needed--only donor complex, or acceptor complex, plus part of the bridge. The procedure is practically equivalent to biorthogonalization, but computationally much simpler. Applications are illustrated with the results for a model of biological long-distance electron transfer in Ru-modified azurin, and electron transfer involving heme a of cytochrome c oxidase.

Journal Article↗

PubMed2002

Proton transport via the membrane surface.

Some proton pumps, such as cytochrome c oxidase (C(c)O), translocate protons across biological membranes at a rate that considerably exceeds the rate of proton transport to the entrance of the proton-conducting channel via bulk diffusion. This effect is usually ascribed to a proton-collecting antenna surrounding the channel entrance. In this paper, we consider a realistic phenomenological model of such an antenna. In our model, a homogeneous membrane surface, which can mediate proton diffusion toward the channel entrance, is populated with protolytic groups that are in dynamic equilibrium with the solution. Equations that describe coupled surface-bulk proton diffusion are derived and analyzed. A general expression for the rate constant of proton transport via such a coupled surface-bulk diffusion mechanism is obtained. A rigorous criterion is formulated of when proton diffusion along the surface enhances the transport. The enhancement factor is found to depend on the ratio of the surface and bulk diffusional constants, pK(a) values of surface protolytic groups, and their concentration. A capture radius for a proton on the surface and an effective size of the antenna are found. The theory also predicts the effective distance that a proton can migrate on the membrane surface between a source (such as CcO) and a sink (such as ATP synthase) without fully equilibrating with the bulk. In pure aqueous solutions, protons can travel over long distances (microns). In buffered solutions, the travel distance is much shorter (nanometers); still the enhancement effect of the surface diffusion on the proton flow to a target on the surface can be tens to hundreds at physiological buffer concentrations. These results are discussed in a general context of chemiosmotic theory.

Biophysical Phenomena↗