Prof. Dr. Nemukhin Alexander Vladimirovich

Laboratory of Chemical Cybernetics,
Physical Chemistry Division,
Department of Chemistry,
M.V.Lomonosov Moscow State University,
Moscow 119991 Russian Federation

 

Phone:

Fax:

E-mail:

+7(495)939-10-96

+7(495)939-02-83

anemukhin@yahoo.com

anem@lcc.chem.msu.ru

 

Education:

  • M.Sc. in Chemistry (Physical Chemistry), 1969, Department of Chemistry, M.V.Lomonosov Moscow State University
  • Ph.D. in Physical Chemistry, 1975, Department of Chemistry, M.V.Lomonosov Moscow State University, Thesis "Diatomic potential curves in molecular spectroscopy and atomic scattering"
  • Doctor of Sciences in Physical Chemistry, 1989, Department of Chemistry, M.V.Lomonosov Moscow State University, Thesis "Multiconfigurational wavefunction expansions in the electronic structure theory"

 

Positions held:

  • 1991 - present : Professor, Physical Chemistry Division, Department of Chemistry, M. V. Lomonosov Moscow State University. The Head of Laboratory of Chemical Cybernetics (since 1993)
  • 1985 - 1991: Docent, Physical Chemistry Division, Department of Chemistry, M.V.Lomonosov Moscow State University
  • 1975 - 1985: Senior Researcher, Physical Chemistry Division, Department of Chemistry, M.V.Lomonosov Moscow State University
  • 1969 - 1975: Junior Researcher, Physical Chemistry Division, Department of Chemistry, M.V.Lomonosov Moscow State University


Fields of Specialization:

  • Quantum Chemistry and Computational Chemistry
  • Molecular Spectroscopy
  • Molecular Dynamics
  • Computer Programming

 

Teaching Experience:

Lectures:

  • Quantum Mechanics and Molecular Structure
  • Solid State Physical Chemistry
  • Molecular Modeling
  • Classical Mechanics and Field Theory
  • Quantum Chemistry
  • Mathematical Methods in Chemistry

Supervisor of 9 Ph.D. theses on quantum chemistry.

Supervisor of the specialized student group of computational chemistry at the Chemistry Department of Moscow State University.


Honors:

  • State Fellowship for Russian Scientists - 1997-1999, 2000-2003
  • Soros Professor - 1997 - 2000
  • Moscow-City Grant in Natural Sciences - 2001-2004

 

Most recent publications:

 

1 Rocha-Rinza T.
Christiansen O.
Rajput J.
Gopalan A.
Rahbek D.B.
Andersen L.H.
Bochenkova A.V.
Granovsky A.A.
Bravaya K.B.
Nemukhin A.V.
Christiansen K.L.
Nielsen M.B.
Gas phase absorption studies of photoactive yellow protein chromophore derivatives J. Phys. Chem. A 2009, Articles ASAP
2 Khriachtchev L.
Domanskaya A.
Marushkevich K.
Rasanen M.
Grigorenko B.L.
Ermilov A.Y.
Andrijchenko N.
Nemukhin A.V.
Conformation-dependent chemical reaction of formic acid with an oxygen atom J. Phys. Chem. A 2009, V.113, #29, P.8143-8146
3 Kaliman I.A.
Grigorenko B.L.
Shadrina M.S.
Nemukhin A.V.
Opening the Arg-Glu salt bridge in myosin: computational study Phys. Chem. Chem. Phys. 2009, V.11, #24, P.4804-4807
4 Nemukhin A.V.
Kaliman I.A.
Moskovsky A.A.
Modeling negative ion defect migration through the gramicidin A channel J. Mol. Model. 2009, V.15, #8, P.1009-1012
5 Polyakov I.V.
Epifanovsky E.
Grigorenko B.L.
Krylov A.I.
Nemukhin A.V.
Quantum chemical benchmark studies of the electronic properties of the green fluorescent protein chromophore: 2. Cis-trans isomerization in water J. Chem. Theory Comput. 2009, V.5, #7, P.1907-1914
6 Epifanovsky E.
Polyakov I.V.
Grigorenko B.L.
Krylov A.I.
Nemukhin A.V.
Quantum chemical benchmark studies of the electronic properties of the green fluorescent protein chromophore: 1. Electronically excited and ionized states of the anionic chromophore in the gas phase J. Chem. Theory Comput. 2009, V.5, #7, P.1895-1906
7 Grigorenko B.L.
Shadrina M.S.
Topol I.A.
Collins J.R.
Nemukhin A.V.
Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu Biochim. Biophys. Acta 2008, V.1784, #12, P.1908-1917
8 Bravaya K.B.
Bochenkova A.V.
Granovsky A.A.
Savitsky A.P.
Nemukhin A.V.
Modeling photoabsorption of the asFP595 chromophore J. Phys. Chem. A 2008, V.112, #37, P.8804-8810
9 Nemukhin A.V.
Lushchekina S.V.
Bochenkova A.V.
Golubeva A.A.
Varfolomeev S.D.
Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling J. Mol. Model. 2008, V.14, #5, P.409-416
10 Akimov A.V.
Nemukhin A.V.
Moskovsky A.A.
Kolomeisky A.B.
Tour J.M.
Molecular dynamics of surface-moving thermally driven nanocars J. Chem. Theory Comput. 2008, V.4, #4, P.652-656
11 Domratcheva T.M.
Grigorenko B.L.
Schlichting I.
Nemukhin A.V.
Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors Biophys. J. 2008, V.94, #10, P.3872-3879
12 Grigorenko B.L.
Rogov A.V.
Topol I.A.
Burt S.K.
Martinez H.M.
Nemukhin A.V.
Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling  Proc. Natl. Acad. Sci. USA 2007, V.104, #17, P.7057-7061
13 Rogacheva M.V.
Bochenkova A.V.
Kuznetsova S.A.
Sarabaev M.K.
Nemukhin A.V.
Impact of pyrophosphate and o-ethyl-substituted pyrophosphate groups on DNA structure J. Phys. Chem. B 2007 ,V.111, P.432-438
14 Grigorenko B.L.
Nemukhin A.V.
Shadrina M.S.
Topol I.A.
Burt S.K.
Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations Proteins: Structure, Function, and Bioinformatics 2007, V.66, P.456-466
15 Topol I.A.
Nemukhin A.V.
Salnikow K.
Cachau R.E.
Abashkin Yu.G.
Kasprzak K.S.
Burt S.K.
Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: Effect of substitution of iron by nickel and cobalt J. Phys. Chem. A 2006 ,V.110, P.4223-4228
16 Nemukhin A.V.
Topol I.A.
Cachau R.E.
Burt S.K.
On the nature of oxoiron (IV) intermediate in dioxygen activation by non-heme enzymes Theoretical Chemistry Accounts 2006, V.115, P.348-353
17 Nemukhin A.V.
Grigorenko B.L.
Topol I.A.
Burt S.K.
Modeling dioxygen binding to the non-heme iron-containing enzymes Intern. J. Quantum Chem. 2006, V.106, P.2184-2190
18 Nemukhin A.V.
Gariev I.A.
Rogov A.V.
Varfolomeev S.D.
Serine hydrolase catalytic sites: Geometry invariants and modeling catalytic activity Mendeleev Communications 2006, V.16, #6, P.290-292
19 Grigorenko B.L.
Savitsky A.P.
Topol I.A.
Burt S.K.
Nemukhin A.V.
Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595  J. Phys. Chem. B 2006 ,V.110, P.18635-18640
20 Bravaya K.B.
Bochenkova A.V.
Grigorenko B.L.
Topol I.A.
Burt S.K.
Nemukhin A.V.
Molecular modeling the reaction mechanism of serine-carboxyl peptidases J. Chem. Theory and Computation 2006, V.2, P.1168-1175
21 Nemukhin A.V.
Topol I.A.
Burt S.K.
Electronic excitations of the chromophore from the fluorescent protein asFP595 in solutions J. Chem. Theory and Computation 2006, V.2, P.292-299
22 Grigorenko B.L.
Rogov A.V.
Nemukhin A.V.
Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters J. Phys. Chem. B 2006 ,V.110, P.4407-4412
23 Moskovsky A.A.
Vanovschi V.V.
Konyukhov S.S.
Nemukhin A.V.
Implementation of the replica-exchange molecular dynamics method for rigid bodies Intern. J. Quantum Chem. 2006, V.106, #10, P.2208-2213

 

Most cited previous publications:

 

1 Nemukhin A.V.
Grigorenko B.L.
Khriachtchev L.Yu.
Tanskanen H.
Pettersson M.
Rasanen M.
Intermolecular complexes of HXeOH with water: Stabilization and destabilization effects  J. Amer. Chem. Soc. 2002, V.124, P.10706-10711
2 Grigorenko B.L.
Nemukhin A.V.
Buchachenko A.A.
Stepanov N.F.
Umanskii S.Ya.
Diatomics-in-molecules description of the Rg-Hal2 rare gas-halogen van der Waals complexes with applications to He-Cl2 J.Chem. Phys., 1997, V.106, P.4575
3 Nemukhin A.V.
Grigorenko B.L.
Topol I.A.
Burt S.K.
Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments J. Phys. Chem. A 2002 ,V.106, P.10663-10672
4 Topol I.A.
Nemukhin A.V.
Ming Chao
Iyer L.K.
Tawa G.J.
Burt S.K.
Quantum chemical studies of reactions of the cyclic disulfides with the zinc finger domains in the HIV-1 nucleocapsid protein (NCp7)   J. Amer. Chem. Soc. 2000, V.122, P.7087-7094
5 Grigorenko B.L.
Nemukhin A.V.
Apkarian V.A.
Many-body potentials and dynamics based on diatomics-in-molecules: Vibrational frequency shifts in ArnHF (n=1-12,62) clusters J.Chem. Phys., 1996, V.104, P.5510
6 Buchachenko A.A.
Stepanov N.F.
Grigorenko B.L.
Nemukhin A.V.
ArHF vibrational predissociation dynamics using the diatomics-in-molecules potential energy surface J. Chem. Phys. 1999, V.111, P.2470-2477
7 Nemukhin A.V.
Grigorenko B.L.
Topol I.A.
Burt S.K.
Flexible effective fragment QM/MM method: Validation through the challenging tests J. Comput. Chem. 2003 ,V.24, P.1410-1420