Biomedical subjects

György Lendvay

Publications and source records attributed to György Lendvay.

5 recordsLinked to original sources

PubMed2006

Theoretical study of the reaction of H atoms with vibrationally highly excited HF molecules.

Vibrationally highly excited molecules react extremely fast with atoms and probably with radicals. The phenomenon can be utilized for selectively enhancing the rate of reactions of specific bonds. On the basis of quasiclassical trajectory calculations, the paper analyzes mechanistic details of a prototype reaction, H + HF(v). At vibrational quantum numbers v above 2, the reaction exhibits capture-type behavior, that is, the reactive cross section diverges as the relative translational energy of the partners decreases, both for the abstraction and for the exchange channel. The mechanism of the reaction for both channels is different at low and at high translational energy. At low vibrational energy, the reaction is activated, which is switched to capture-type at high excitation. The reason is an attractive potential that acts on the attacking H atom when the HF molecule is stretched. In contrast to the 6-SEC potential surface of Mielke et al., the switch cannot be observed on the Stark-Werner potential surface, due to a small artificial barrier at high H-HF separation, preventing the reactants from obeying the attractive potential and also proving the importance of the latter. The exchange reaction can be observed even when the total energy available for the partners is below the exchange barrier, because at low translational energies the product F atom of a successful abstraction step can re-abstract that H atom from the intermediate product H2 molecule that was originally the attacker.

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PubMed2006

H + CD4 abstraction reaction dynamics: product energy partitioning.

This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.

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PubMed2006

H + CD4 abstraction reaction dynamics: excitation function and angular distributions.

We compare experimental photoloc measurements and quasi-classical trajectory calculations of the integral cross sections, lab-frame speed distributions, and angular distributions associated with the CD3 products of the H + CD4(nu = 0) --> CD3 + HD reaction at collision energies ranging from 0.5 to 3.0 eV. Of the potential energy surfaces (PES) we explored, the direct dynamics calculations using the B3LYP/6-31G** density functional theory PES provide the best agreement with the experimental measurements. This agreement is likely due to the better overall description that B3LYP provides for geometries well removed from the minimum energy path, even though its barrier height is low by approximately 0.2 eV. In contrast to previous theoretical calculations, the angular distributions on this surface show behavior associated with a stripping mechanism, even at collision energies only approximately 0.1 eV above the reaction barrier. Other potential energy surfaces, which include an analytical potential energy surface from Espinosa-García and a direct dynamics calculation based on the MSINDO semiempirical Hamiltonian, are less accurate and predict more rebound dynamics at these energies than is observed. Reparametrization of the MSINDO surface, though yielding better agreement with the experiment, is not sufficient to capture the observed dynamics. The differences between these surfaces are interpreted using an analysis of the opacity functions, where we find that the wider cone of acceptance on the B3LYP surface plays a crucial role in determining the integral cross sections and angular distributions.

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PubMed2005

Dynamics of bimolecular reactions of vibrationally highly excited molecules: quasiclassical trajectory studies.

Excitation functions from quasiclassical trajectory calculations on the H + H2O --> OH + H2, H + HF --> F + H2, and H + H'F --> H' + HF reactions indicate a different behavior at low and high vibrational excitation of the breaking bond. When the reactant tri- or diatomic molecule is in vibrational ground state or in a low vibrationally excited state, all these reactions are activated; i.e., there is a nonzero threshold energy below which there is no reaction. In contrast, at high-stretch excited-states capture-type behavior is observed; i.e., with decreasing translational energy the reactive cross-section diverges. The latter induces extreme vibrational enhancement of the thermal rate consistent with the experiments. The results indicate that the speed-up observed at high vibrational excitation is beyond the applicability of Polanyi's rules in their common form; instead, it can be interpreted in terms of an attractive potential acting on the attacking H atom when it approaches the reactant with a stretched X-H bond.

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PubMed2005

A reinterpretation of the mechanism of the simplest reaction at an sp3-hybridized carbon atom: H + CD4 --> CD3 + HD.

A comparison between theory and experiment for the benchmark H + CD4 --> HD + CD3 abstraction reaction yields a reinterpretation of the reaction mechanism and highlights the unexpected contribution of a stripping mechanism. Whereas the best analytic surface fails to reproduce experiment, a first-principles direct-dynamics (on the fly) treatment is in good agreement, showing that the H + CD4 reaction exhibits extreme sensitivity to modest differences in the potential energy surface. We find that bent H-D-C transition state geometries play an important role in the dynamics. A simple model that relates the scattering angle impact parameter and cone of acceptance accounts well for the overall reaction dynamics.

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