Biomedical subjects

Oksana Tishchenko

Publications and source records attributed to Oksana Tishchenko.

4 recordsLinked to original sources

PubMed2006

Optimizing the performance of the multiconfiguration molecular mechanics method.

Multiconfiguration molecular mechanics (MCMM) is a general algorithm for constructing potential energy surfaces for reactive systems (Kim, Y.; Corchado, J. C.; Villà, J.; Xing, J.; Truhlar, D. G. J. Chem. Phys. 2000, 112, 2718). This paper illustrates how the performance of the MCMM method can be improved by adopting improved molecular mechanics parameters. We carry out calculations of reaction rate constants using variational transition state theory with optimized multidimensional tunneling on the MCMM PESs for three hydrogen transfer reactions, and we compare the results to direct dynamics. We find that the MCMM method with as little as one electronic structure Hessian can describe the dynamically important regions of the ground-electronic state PES, including the corner-cutting-tunneling region of the reaction swath, with practical accuracy.

Journal Article↗

PubMed2005

How well can density functional methods describe hydrogen bonds to pi acceptors?

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.

Letter↗

PubMed2005

Theoretical study on the group 2 atoms + N2O reactions.

The electronic structure aspects of the M (1S,3P) + N2O(X 1sigma+) (M = Be, Mg, Ca) reactions are investigated using the CASSCF/MRMP2 (complete active space SCF and the multireference Møller-Plesset perturbation theory of the second order) computational methodology. The lowest adiabatic 1 1A' and 1 3A' potential energy surfaces (PESs) favor the bending dissociation mechanism of N2O in all studied cases. The rate-limiting channels are determined by the classical barriers that decrease in the series Be (8.9) > Mg (7.0) > Ca (1.2) kcal/mol, whereas the spin-forbidden reaction channels are found to be less important. A comparison with elaborated kinetic results (Plane et al. J. Phys. Chem. 1990, 94, 5255; Gas-Phase Metal Reactions; Elsevier: Amsterdam, 1992; Vinckier et al. J. Phys. Chem. A 1999, 103, 5328) on the Ca (1S) + N2O(X 1sigma+) reaction is presented, and the differences in the kinetic behavior of the title reactions are discussed. Our results also indicate that the techniques based on the multiconfigurational wave functions are unavoidable if a correct topology of the PESs governing these reactions is needed.

Journal Article↗

PubMed2002

Theoretical vibrational analysis of monohalogenated phenols.

Harmonic vibrational frequencies of a representative series of X-phenols (X = F, Cl, Br) in ortho, meta and para positions are determined using density functional theory (B3LYP) in conjunction with 6-311 + + G(d,p), 6-311 + + G(2d,2p), and 6-311 + + G(2df,2p) basis sets. Their complete and clear-cut vibrational assignment based on the concept of the potential energy distribution is carried out. Such assignment allows to resolve a number of uncertainties appeared in the previous studies and to propose a new explanation of frequency alterations of particular vibrational modes in this series.

Computer Simulation↗