Development of the flexible effective fragment QM/MM method for modeling properties of biomolecules 

B.L. Grigorenko, I.A. Kaliman, S.S. Konyukhov, A.A. Moskovsky, A.V. Nemukhin

An approach to the hybrid quantum mechanical and molecular mechanical (QM/MM) theory based on the effective fragment potential (EFP) technique (M. Gordon and co-authors) for modeling properties and reactivity of large molecular systems of biochemical significance is being developed. Currently we are preparing a novel version of the computer program based on the most recent variant of the PC GAMESS quantum chemistry package (A. A. Granovsky) and the TINKER molecular modeling package (J. Ponder). A new QM/MM program will allow us to employ the density function theory methods in the quantum part.

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Modeling mechanisms of enzymatic reactions of nucleoside triphosphate hydrolysis

B.L. Grigorenko, M.S. Shadrina, I.V. Kupchenko, A.V. Nemukhin

We continue studies of the mechanisms of guanosine triphosphate (GTP) hydrolysis in G-proteins by using the flexible effective fragment QM/MM method. The current projects include analysis of the hydrolysis reactions by the EF-Tu and transducin proteins. We are planning to create a new Data Base for the computed reaction energy profiles for hydrolysis of nucleoside triphosphates.

Modeling mechanisms of dioxygen activation by non-heme iron-containing enzymes

B.L. Grigorenko, A.V. Nemukhin

The flexible effective fragment QM/MM method is used to simulate the mechanism of dioxygen activation by the factor-inhibiting hypoxia-inducible factor (FIH) enzymes.

Modeling properties of the kindling fluorescent protein asFP595

B.L. Grigorenko, I.V. Polyakov, A.V. Nemukhin, in collaboration

with Prof. A.P. Savitsky (A. N. Bach Institute of Biochemistry, RAS) 

We model properties the member of the Green Fluorescent Protein family, the kindling protein asFP595. The current project attempts to understand the mechanism of kindling.

Modeling photo-absorption of the retinal molecule in the Rhodopsin protein, in solution and in the gas phase

M.G Khrenova, A.V. Bochenkova, A.V. Nemukhin 

A variety of combined QM/MM levels along with an efficient algorithms for the large-scale nonlinear optimization problem are used to locate the stationary points and estimate S0-S1 excitation energy of the protonated Shiff-base of retinal in water and rhodopsin environment. It is shown that the key factor contributing tothe observed opsin shift is traced to the conformational changes of the retinal chromophore due to formation of the specific hydrogen bond network in the protein environment.

Modeling properties and spectra of photoreceptor proteins with the BLUF domains

B. L. Grigorenko, M.G. Khrenova, A. V. Nemukhin,  in collaboration

with Dr. T. Domratcheva (Max-Plank Institute of

Medical Studies, Heidelberg, Germany)

QM/MM and quantum chemistry tools are used to characterize species formed in the photoexcitation of the BLUF containing photoreceptors.

Studies of the enzymatic catalysis by acetylcholinesterase and butyrylcholineserase

S.V. Lushchekina, B.L. Grigorenko, A.V. Nemukhin,

in collaboration with Prof. S.D. Varfolomeev

(N. M. Emanuel Institute of Biochemcal Physics, RAS)

Different QM/MM methods are used to understand mechanisms of enzymatic catalysis by acetylcholinesterase and butyrylcholinesterase.

Development and applications of rigid-body molecular dynamics

A.A. Moskovsky, A.V. Akimov, I.A. Kaliman, S.S. Konyukhov, A.V. Nemukhin

We are developing a version of the computer program of the rigid-body molecular dynamics to be used in future for the mixed quantum-classical molecular dynamics. Modeling movements of a nanocar is a part of the project.

Modeling vibrational spectra of HArF in argon matrices

A.V. Bochenkova, A.V. Nemukhin,

in collaboration with L.Yu. Khriachtchev, M. RÄsÄnen

(Laboratory of Physical Chemistry, University of

 Helsinki, P. O. Box 55, FIN-00014 Helsinki, Finland)

Features in the vibrational spectra of the "exotic" molecule HArF in argon matrices are being studied by using a newly developed hybrid quantum mechanical - diatomics-in-molecules (QM/DIM) potential for the Ar_n-HArF clusters.

Photochemistry of hydrogen peroxide in low-temperature matrices

B.L. Grigorenko, A.V. Nemukhin, in collaboration with

L.Yu. Khriachtchev, M. RÄsÄnen (Laboratory of Physical Chemistry,

University of Helsinki, P. O. Box 55, FIN-00014 Helsinki, Finland) 

Creation of hydrogen peroxide in photochemical reactions in low-temperature matrices is studied by quantum chemistry tools.