Biomedical subjects

Dmitry M Medvedev

Publications and source records attributed to Dmitry M Medvedev.

5 recordsLinked to original sources

PubMed2006

Quantum dynamics study of the dissociative photodetachment of HOCO-.

Six-dimensional wave packet calculations are carried out to study the behavior of HOCO subsequent to the photodetachment of an electron from the negative anion, HOCO-. It is possible to form stable and/or long-lived HOCO complexes, as well as the dissociative products OH+CO and H+CO2. A variety of observables are determined: the electron kinetic energy (eKE) distributions associated with the OH+CO and H+CO2 channels, the correlated eKE and product translational energy distribution for the OH+CO channel, and product branching ratios. Most of our results are in good accord with the experimental results of Clements, Continetti, and Francisco [J. Chem. Phys. 117, 6478 (2002)], except that the calculated eKE distribution for the H+CO2 channel is noticeably colder than experiment. Reasons for this discrepancy are suggested.

Journal Article↗

PubMed2004

A new expression for the direct quantum mechanical evaluation of the thermal rate constant.

Based on the formalism of Miller, Schwartz, and Tromp [J. Chem. Phys. 79, 4889(1983)], we derive a new expression for the thermal rate constant for a chemical reaction. The expression involves an unperturbed, i.e., reactant or product channel Boltzmann operator for the imaginary time propagation, making it possible to compute efficiently the rate constant for a range of temperatures. We illustrate numerical aspects with an extensive study of the one-dimensional Eckart barrier problem, as well as a study of the three-dimensional (J = 0) D + H2 problem.

Journal Article↗

PubMed2004

Quantum wave packet and quasiclassical trajectory studies of OH+CO: influence of the reactant channel well on thermal rate constants.

We study the OH+CO-->H+CO2 reaction with both six-dimensional quantum wave packets (QM) and quasiclassical trajectories (QCT), determining reaction probabilities and thermal rate constants (or coefficients), and studying the influence of the reactant channel hydrogen-bonded complex well on the reaction dynamics. The calculations use the recently developed Lakin-Troya-Schatz-Harding (LTSH) ground electronic state potential energy surface, along with a modified surface developed for this study (mod-LTSH), in which the reactant channel well is removed. Our results show that there can be significant differences between the QM and QCT descriptions of the reaction for ground-state reactants and for energies important to the thermal rate constants. Zero-point energy violation plays an important role in the QCT results, and as a result, the QCT reaction probability (for ground-state reactants and zero impact parameter) is much higher than its QM counterpart at moderate to low reagent translational energies. The influence of the reactant channel well in the QCT results is to enhance reactivity at moderate energies and to suppress reactivity at the very lowest collision energies. The QM results also show the enhancement at moderate energies but, while the very lowest translational energies cannot be adequately converged, they do not indicate any tendency toward suppression as energy is reduced. QCT calculations for excited rotational states of the reactants show that the suppression of reactivity associated with the reactant channel well is less important when the reactants are rotating, and as a result, the influence of the reactant channel well on the thermal rate coefficients is relatively small, being important below 200 K. Our results indicate that there still remain important discrepancies between experiment and theory in this low temperature regime and that further improvements of the potential are needed.

Journal Article↗

PubMed2003

Computer simulation of water in cytochrome c oxidase.

Statistical mechanics and molecular dynamics simulations have been carried out to study the distribution and dynamics of internal water molecules in bovine heart cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of water, which in subunit I alone amounts to about 165 molecules. The dynamic characterization of these water molecules is carried out. The nascent water molecules produced in the redox reaction at the heme a(3)-CuB binuclear site form an intriguing chain structure. The chain begins at the position of Glu242 at the end of the D channel, and has a fork structure, one branch of which leads to the binuclear center, and the other to the propionate d of heme a(3). The branch that leads to the binuclear center has dynamic access both to the site where the formation of water occurs, and to delta-nitrogen of His291. From the binuclear center, the chain continues to run into the K channel. The stability of this hydrogen bond network is examined dynamically. The catalytic site is located at the hydrophobic region, and the nascent water molecules are produced at the top of the energy hill. The energy gradient is utilized as the mechanism of water removal from the protein. The water exit channels are explored using high-temperature dynamics simulations. Two putative channels for water exit from the catalytic site have been identified. One is leading directly toward Mg(2+) site. However, this channel is only open when His291 is dissociated from CuB. If His291 is bound to CuB, the only channel for water exit is the one that originates at E242 and leads toward the middle of the membrane. This is the same channel that is presumably used for oxygen supply.

Animals↗

PubMed2002

Electron transfer in ferredoxin: are tunneling pathways evolutionarily conserved?

A theoretical study of electron transfer (ET) pathways in a recently crystallized Clostridium acidurici ferredoxin is reported. The electronic structure of the protein complex is treated at the semiempirical extended Hückel level, and the tunneling pathways are calculated with the rigorous quantum mechanical method of tunneling currents. The model predicts two pathways between the two [4Fe-4S] cubanes: a strong one running directly from Cys(14) to Cys(43) and a weaker one from Cys(14) via Ile(23) to Cys(18), whereas other amino acids do not play a significant role in the electron tunneling. The cysteine ligands conduct almost all of the current when Ile(23) is mutated to valine in silico, so that there is no appreciable change in the ET rate. The calculated value of the transfer matrix element is consistent with the experimentally determined rate of transfer. Results of the sequence analysis performed on this ferredoxin reveal that Ile(23) is a highly variable amino acid compared with the cubane-ligating cysteine amino acids, even though Ile(23) lies directly between the donor and acceptor complexes. We further argue that the homologous proteins with a [3Fe-4S] cofactor, which does not have one of the four cysteine ligands, use the same tunneling pathways as those in this ferredoxin, on the basis of the high homology as well as the absolute conservation of Cys(14) and Cys(43) which serve as the main tunneling conduit. Our results explain why mutation of amino acids around and between the donor and acceptor cubane clusters, including that of Ile(23), does not appreciably affect the rate of transfer and add support to the proposal that there exist evolutionarily conserved electron tunneling pathways in biological ET reactions.

Amino Acid Sequence↗