EXPERTISE AND SKILLS

Ab Initio

DFT

QM/MM

Improved semiempirical methods

Force Field methods

Genetic Algorithm (method developement)

Free Energy Perturbation method

Monte Carlo

Molecular Dynamics

Gaussian, MOLPRO, NWChem, GAMESS, MCPRO, BOSS, MOPAC, Glide

Chimera, PyMol, Molden, WebLabViewer, Midas, GaussView

C++, Python, Perl, FORTRAN, CSH, BASH, HTML

English, Russian, basics of Spanish

Electronic structure calculations

Multiconfigurational and relativistic methods

Small molecules and clusters: structure, spectroscopic properties (e.g. IR, UV Vis, Photoelectron)

Analysis of chemical bonding

Monte Carlo simulations for proteins, mechanistic studies of enzymes

Docking studies

Protein structure manipulation and analysis

Simulations for reaction mechainsms in explicit and implicit solvents

Programming



Comprehensive web design for science and other uses

RESEARCH INTERESTS

1. COMPUTATIONAL BIOCHEMISTRY AND ENZYMOLOGY.

I am interested in the design of artificial enzymes, and development of new strategies for it; understanding mechanisms of enzymatic catalysis; and understanding Nature's reasons for protein structure.

2. PHOTO-INDUCED DAMAGE OF DNA, SKIN CANCER.

UV damage of DNA leads to the accumulation of errors in the genome and ultimately results in skin cancer. Non-adiabatic processes occuring in DNA after the excitation by UV light have a highly complex nature. These processes involve many ultra-short lived intermediate states, some of which are "dark" and cannot be detected experimentally. I am interested in unraveling the mechanism of mutagenesis and non-radiative decay of the excited states in DNA.

3. GENERAL THEORY OF CHEMICAL BONDING.

Engineering of new species (clusters, ligands, building blocks of desired properties), manipulating and re-landscaping PES of chemical systems.

4. PROOBLEMS OF ALTERNATIVE ENERGETICS.

Hydrogen storage materials, new heterogeneous catalysts for the synthesis of hydrogen from the biomass.

5. MEDICINAL MATERIALS.

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I received my Ph.D. in Physical Chemistry. The Dissertation was entitled: "Multiply-Aromatic Clusters vi Ab Initio Genetic Algorithm". We worked in collaboration with experimental photoelectron spectroscopy, finding the shape of the hetherto unknown species observed in the experiment and describing the chemical bonding in them, i. e. finding the reason for their shape and stability. My Ph.D. work resulted in 18 articles, one of which was featured on the cover of J. Phys. Cem., and numerous conference presentations. It has been recognized via many awards at the Department, College, Univeristy, and National levels, and a highlight article in C&E New magazine.
For finding the global minima shapes of clusters, I have written a unique new software, the abinitio Gradient Embedded Genetic Algorithm (GEGA). GEGA uses conventional genetic algorith methodology, plus gradient following, second derivative analysis (frequencies), specific mulation procedure, and an level of theory. It converges substantially faster than most GAs, and results in a global minimum of a high-quality geometry. The Figure below depicts the two major GEGA-operators "at play".



Using high-level abinitio techniques, I studied small cluster systems, primarely of boron, lithium, magnesium and copper. We discovered that the shape and stability of small clusters of main-group elements are often governed by the multiply-aromatic or multiply-antiaromatic character of the chemical.
We found that small pure-boron cluster from B₃ to B₉ are planar, which at first seemed very unusual for the mostly three-dimensioanl vast chemistry of boranes and bulk boron. The key to this phenomenon was found in multiple aromaticity and antiaromaticity of these species. One of the most astonishing results was the unpesedented perfectly symmetric molecular wheels: charges and neutral B₈ and B₉. The central B-atoms possessed extreme coordination numbers of seven and eight.





The reason was identified as a doubly-aromatic character of the chemical bonding in both systems. Below the picture of the delocalized molecular orbitals of the clusters are shown. Both π and σ-subsystems of molecular orbitals contain six electrons occupying these MOs. The 4n+2 rule for aromaticity is thus obeued for both subsystems, and the wheels are both π- and σ- aromatic.

A new class of inorganic compounds: planar, aromatic, highly-charged boranes, were further discovered. B₆H₆^2- is a well-known borane, forming a stable salt, Li₂B₆H₆. If to add four electrons to this system and stabilize it by six additional Li⁺-cations, a surprizingly stable planar aromatic species will result. The theoretically evaluated enthalpy of its formation from Li₂B₆H₆ and Li₄ is -53 kcal/mol (B3LYP/6-311++G** level). The molecular orbital constitution of the B₆H₆^6- core of Li₆B₆H₆ is identical to that of benzene (Figure below shows the π-MOs systems of the highly-charged borane and benzene). B₆H₆^6- is π-aromatic, which makes it so stable, despite the high concentration of the negative charge on the borane core. A whole new family of such stable planar π-aromatic boranes, isoelectronic to various planat aromatic hydrocarbons, was discovered.

Our work on boron was highlighted in the "Chemical & Engineering New" magazine.

In our joint theoretical and photoelectron spectroscopic study we discoved a new sandwich molecule with two revolving propellers: Cu₃C₄^-. The key to its shape was found in the aromaticity of the Cu₃³⁺ core. We made it on the cover of J. Phys. Chem..