T. Hayashi, A. A. Stuchebrukhov
Electron Tunneling in Respiratory Complex I.
Proc.Natl. Acad. Sci. USA 107, 19157-19162 (2010).
A. A. Stuchebrukhov
Long-distance electron tunneling in proteins: a new challenge for time-resolved spectroscopy.
Laser Physics 19: 1-14 (2009).
V. Couch, Emile S. Medvedev, A. A. Stuchebrukhov
Electrostatics of the FeS clusters in respiratory complex I.
Biochim. Biophys. Acta 1787: 1266-71 (2009).
R. Sugitani, A. A. Stuchebrukhov
Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways
and the mechanism of its transport.
Biophys. Acta 1787 (9):1140-50 (2009).
A. A. Stuchebrukhov
Mechanisms of proton transfer in proteins. Localized charge transfer versus delocalized soliton transfer.
Phys. Rev. E 79, 031927 (2009).
A. A. Stuchebrukhov
Electron transfer reactions coupled to proton translocation in proteins. Computational studies of redox driven proton pumps, cytochrome c oxidase and biological energy transduction.
in: Energy Flows in Proteins, D. Leitner and J. Straub Eds., Taylor and Francis/CRC Press (2009).
A. A. Stuchebrukhov, J. Quenneville, D. Popovic
First principles studies of proton pumping mechanism in cytochrome c oxidase.
in: Computational Inorganic and Bioinorganic Chemistry, Edward I. Solomon, R. Bruce King, Robert A. Scott Eds., Wiley (2009).
A. A. Stuchebrukhov
Long-distance electron tunneling in proteins.
in: Quantum Tunneling in Enzyme-Catalysed Reactions, R. K. Allemann, N. S. Scrutton Eds., pp. 314-342 (2009).
I. Leontyev, A. A. Stuchebrukhov
Dielectric relaxation of cytochrome c oxidase: Comparison of microscopic and continuum models.
J. Chem. Phys. 130, 085103 (2009).
I. Leontyev, A. A. Stuchebrukhov
Electronic continuum model for molecular dynamics simulations.
J. Chem. Phys. 130, 085102 (2009).
E. S. Medvedev, A. I. Kotelnikov, A. V. Barinov , B. L. Psikha, J. M. Ortega, D. M. Popovic, and A. A. Stuchebrukhov
Protein dynamics control of electron transfer in photosynthetic reaction centers from Rps. Sulfoviridis.
J. Phys. Chem. 112, 3208-3216 (2008).
R. Sugitani, E. S. Medvedev, and A. A. Stuchebrukhov
Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme.
Biochim. Biophys. Acta 1777, 1129-1139 (2008).
X. Zheng, G. Garcia, and A.A. Stuchebrukhov
Theoretical Study of Excitation Energy Transfer in DNA Photolyase.
J. Phys. Chem. B 112, 8724- 8729 (2008).
A.A. Stuchebrukhov
Coupled electron and proton transfer reactions in proteins and computational challenges of membrane redox pumps.
Review in Computational Chemistry, Tom Cundari Ed., Wiley-VCH, 2007 (Invited Review Article).
A.A. Stuchebrukhov and D.M. Popovic
Comment on "Acidity of Cu-bound histidine in the binuclear center of cytochrome oxidase".
J. Phys. Chem. B 110 (2006) 17286-17287.
D.M. Popovic and A.A. Stuchebrukhov
Two conformational states of Glu242 and pKa's in bovine cytochrome oxidase.
Photochem. Photobiol. Sci. (PPS) 5 (2006) 611-620.
E.S. Medvedev, A.I. Kotelnikov, N.S. Goryachev, B.L. Psikha, J.M. Ortega and A.A. Stuchebrukhov
Protein dynamics control of electron transfer in reaction centers from RPS. VIRIDIS.
Molecular Simulations, 32, 735, 2006.
A.A. Stuchebrukhov
Biological electron transfer.
Encyclopedia for Molecular Medicine. Invited Paper (in preparation).
D.V. Makhov, A.A. Stuchebrukhov
An accurate and efficient procedure of fitting electric field potential by point charges
for QM/MM calculations.
Phys. Stat. Sol. (b), 243, 2030-2037, (2006).
D.M. Popovic, J. Quenneville, A.A. Stuchebrukhov
Combined DFT and Electrostatic Calculations of pKa’s in proteins: Study of Cytochrome c Oxidase.
Review article in: "Modern Methods for Theoretical Physical Chemistry of Biopolymers"
Editors: E.B. Starikow, J.P. Lewis, S. Tanaka, Elsevier 2006, [ISBN:0-444-52220-4].
(Chapter 3, pp 53-78)
A.A. Stuchebrukhov, D.M. Popovic
Comment on “Acidity of a Cu-bound Histidine in
the Binuclear Center of Cytochrome c Oxidase?.
J.
Phys. Chem. B, 110, 17286-17287, (2006).
D.V. Makhov, D.M. Popovic, A.A. Stuchebrukhov
Improved Density Functional Theory/Electrostatic Calculation of the His291 Protonation State in Cytochrome c Oxidase:
Self-Consistent Charges for Solvation Energy Calculation.
J.
Phys. Chem. B, 110, 12162-12166, (2006).
E.S. Medvedev, A.A. Stuchebrukhov
Kinetics of proton diffusion in the regimes of fast and slow exchange between
the membrane surface and bulk solution.
J. Math. Biology, 52, 209-239, (2006).
D.M. Popovic, A.A. Stuchebrukhov
Two Conformational States of Glu242 and pKa’s in Bovine Cytochrome c Oxidase.
Photochemical & Photobiological Sciences, 5, 611-620, (2006).
J. Quenneville, D.M. Popovic,
A.A. Stuchebrukhov
Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase.
Biochem.
Biophys. Acta - Bioenerg., 1757, 1035-1046, (2006).
D.M. Medvedev, E. Medvedev, A.A. Stuchebrukhov
Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase
upon single electron injection.
Biophys.Biochem.Acta, 1710, 47-56, (2005).
D.M. Popovic, J. Quenneville,
A.A. Stuchebrukhov
DFT/electrostatic calculations of pKa values in
cytochrome c oxidase.
J.
Phys. Chem. B, 109, 3616-3626, (2005).
D.M. Popovic, A.A.
Stuchebrukhov
Proton Exit Channels in Bovine Cytochrome c Oxidase.
J.
Phys. Chem. B, 109, 1999-2006, (2005).
M. Tashiro, A.A.
Stuchebrukhov
Thermodynamic Properties of Internal Water Molecules in the
Hydrophobic Cavity around the Catalytic Center of Cytochrome c Oxidase.
J.
Phys. Chem. B, 109, 1015-1022, (2005).
J. Huang, D. Xu, A.A. Stuchebrukhov, and W.M. Jackson
Single photon spectroscopy of autoionizating levels of atomic sulfur and the measurements of their life-time.
J. Chem. Phys., Accepted Jan. 2005.
J. Huang, D. Xu, A.A. Stuchebrukhov, and W.M. Jackson
Auto-ionization lifetime of super-excited atomic sulfur atoms.
Canadian J. Chem., the Herzberg Issue, 82, 885, (2004).
J. Quenneville, D.M. Popovic,
A.A. Stuchebrukhov
Redox-Dependent pKa of CuB Histidine Ligand in Cytochrome
c Oxidase.
J.
Phys. Chem. B, 108, 18383-18389, (2004).
D.M. Popovic, A.A. Stuchebrukhov
Proton pumping mechanism and catalytic cycle of cytochrome c oxidase:
Coulomb pump model with kinetic gating.
FEBS Lett., 566,
126-130, (2004).
D.M. Popovic, A.A. Stuchebrukhov
Electrostatic study of proton pumping mechanism in cytochrome oxidase.
J.
Am. Chem. Soc., 126, 1858-1871, (2004).
J. Kim, X. Zheng, Y. Georgievskii, A. Stuchebrukhov
On the mechanism of proton transfer in proton conducting channels in proteins.
Localized charge hopping vs delocalized soliton-like transfer.
J. Chem. Phys., 2004.
Emile Medvedev and A.A.
Stuchebrukhov
Breakdown of Born-Oppenheimer approximation for long-distance
electronic tunneling.
Chem.Phys., 296, 181-192, (2003).
X. Zheng, D.M. Medvedev,
J.Swanson, A.A. Stuchebrukhov
Computer simulations of internal water in
cytochrome oxidase.
Biophys.Biochem.Acta, 1557, 99-107, (2003).
A.A. Stuchebrukhov
Coupled electron and proton transfer reactions. Proton pumps, cytochrome
oxidase, and biological energy transduction.
J.Theor.Comp.Chem.,
1, 91-118, (2003), Review Article.
A.A. Stuchebrukhov
Electron tunneling in many-electron systems. Correlation, polarization,
quantization, and other effects.
Theor.Chem.Acc., 110, 291-306, (2003),
Feature Article.
A.A. Stuchebrukhov
Electron tunneling in many-electron systems.Effective one-electron
approximation.
J.Chem.Phys., 118, 7898-7906, (2003).
Yu. Georgievskii, E.S.
Medvedev, and A.A. Stuchebrukhov
Oxidoreduction of heme a in cytochrome
oxidase with CO-inhibited binuclear center.
BioOrg. Chem. (Russ),
29, 21-29, (2003).
X.Zheng, A.A. Stuchebrukhov
Electron tunneling in Ru-modified azurin. Tunneling jumps between protein
strands via hydrogen bonds.
J.Phys.Chem., 107, 9579-9584, (2003).
X. Zheng, A.A. Stuchebrukhov
INDO calculations of electron tunneling in proteins.
J.Phys.Chem., 107,
6621-6628, (2003).
Yu. Georgievskii, Emile S.
Medvedev, and A.A. Stuchebrukhov
Proton transport along the biomembrane
surfaces.
Biophys.J., 82, 2833-2846, (2002).
Yu. Georgievskii, Emile S.
Medvedev, and A.A. Stuchebrukhov,
Proton migration via coupled surface and
bulk diffusion.
J. Chem. Phys., 116, 1692-1699, (2002).
I. Daizadeh, D.M. Medvedev,
and A.A. Stuchebrukhov,
Electron Transfer in Ferredoxin: Are Tunneling
Pathways Evolutionarily Conserved?
Molecular Biology and Evolution, 19, 406-415,
(2002).
D.M. Medvedev and A.A.
Stuchebrukhov
DNA repair mechanism by photolyase: electron transfer path
from FADH to DNA thymine dimer.
J. Theor.
Biology 210, 237-248, (2001).
A.I. Kotelnikov, E.S.
Medvedev, D.M. Medvedev, and A.A. Stuchebrukhov
Kinetic treatment of coupled
electron and proton transfer in flash-photolysis experiments on carbon
monoxide-inhibited mixed-valence cytochrome c oxidase.
J.
Phys. Chem. B, 105, 5789-5796, (2001).
A.A. Stuchebrukhov
Toward
ab initio theory of long-distance electron tunneling in proteins: tunneling
currents approach.
Advances in Chemical Physics 118, 1-44, (2001).
Yu. Georgievskii, A.A.
Stuchebrukhov,
Concerted electron and proton transfer. Transition from
nonadiabatic to adiabatic proton tunneling.
J.
Chem. Phys., 113, 10438, (2000).
J. Kim, A. Stuchebrukhov, Ab
initio study of long-distance electron tunneling in a model peptide system.
J.
Phys. Chem. B, 104, 8606, (2000).
Jian Wang, A. Stuchebrukhov
DFT calculations of tunneling current in molecules.
Int. J. Quant. Chem., 80(4), 591, (2000).
EunJoo Lee, E.S. Medvedev,
and A.A. Stuchebrukhov
Calculation of quantum parameters for nonadiabatic
redox reactions. Application to photoreduction of flavin in DNA photolyase.
J.
Phys. Chem. B, 104, 6894-6902, (2000).
D.M. Medvedev, I. Daizadeh,
and A.A. Stuchebrukhov,
Electron transfer tunneling pathways in bovine heart
cytochrome c oxidase.
JACS
122, 6571, (2000).
Eun Joo Lee, E.S. Medvedev,
and A.A. Stuchebrukhov
Effect of Quantum modes in biological electron
transfer reactions. A useful approximation for the harmonic model with frequency
change and Duchinsky rotation.
J.
Chem. Phys., 112, 9015, (2000).
Jens Antony, Dmitry M.
Medvedev, and Alexei Stuchebrukhov
Theoretical Study of Electron Transfer
between the Photolyase Catalytic Cofactor FADH- and DNA Thymine Dimer.
JACS
122, 1057, (2000).
A.A. Stuchebrukhov
Ab
initio calculations of long-distance electron tunneling in organometallic
systems of biological origin.
Int.
J. Quant. Chem., 77, 16, (2000).
Margaret Chung, Iraj
Daizadeh, Alexei Stuchebrukhov and Paul Heelis
Electron transfer pathways in
E. coli DNA Photolyase: Trp306 to FADH.
Biophys. J., 76, 1241,
(1999).
Iraj Daizadeh, Jian-xin Guo,
and Alexei Stuchebrukhov
Vortex structure of the tunneling flow in
long-range electron transfer reactions.
J.
Chem. Phys., 110, 8865, (1999).
Emile Medvedev and Alexei
Stuchebrukhov.
Dynamic effects in long- distance biological electron
transfer reactions.
IUPAC Journal, 70(11), 2201-2210, (1998).
Katz, D. J.; Stuchebrukhov,
A.A.
A new expression for superexchange matrix element in long-distance
electron transfer reactions.
J.
Chem. Phys., 109, 4960, (1998).
Heifets, E. N.; Daizadeh, I.;
Guo, J. X.; Stuchebrukhov, A. A.
Electron tunneling in quasi-one-dimensional
resonant molecular systems. Ab initio study.
J.
Phys. Chem. A., 102, 2847, (1998).
Stuchebrukhov, A. A.
Tunneling currents in long-distance electron transfer reactions.IV.
Many-electron formulation. Interatomic Currents and Mulliken population
analysis.
J.
Chem. Phys., 108, 8510, (1998).
Stuchebrukhov, A. A.
Tunneling currents in long-distance electron transfer reactions.III.
Many-electron formulation.
J.
Chem. Phys., 108, 8499, (1998).
Medvedev, E. S.;
Stuchebrukhov, A. A.
Inelastic tunneling in long- distance electron transfer
reactions.
J.
Chem. Phys., 107, 3821, (1997).
Stuchebrukhov, A.A.
Tunneling currents in proteins: non-orthogonal atomic basis sets and
Mulliken population analysis.
J.
Chem. Phys., 107, 6495, (1997).
Daizadeh, I.; Medvedev, E.
S.; Stuchebrukhov, A. A.
Effect of Protein Dynamics on Biological Electron
Transfer.
Proc. Natl. Acad. Sci. USA,
94, 3703, (1997).
Daizadeh, I.; Gehlen, J. N.;
Stuchebrukhov, A. A.
Calculation of Electronic Tunneling Matrix Elements in
Proteins. Comparison of Exact and Approximate One-electron Methods for
Ru-modified Proteins.
J.
Chem. Phys., 106, 5658, (1997).
Stuchebrukhov, A. A.
On
the non-orhtogonal Basis Set Calculation of the Bridge-mediated Electronic
Matrix Elements.
Chem.
Phys. Lett., 265, 643, (1997).
Stuchebrukhov, A. A.
Tunneling Currents in Electron Transfer Reactions in Proteins.II.
Calculation of Tunneling Matrix Element and Tunneling Currents Using
Non-Orthogonal Basis Sets.
J.
Chem. Phys., 105, 10819, (1996).
Stuchebrukhov, A. A.
Tunneling Currents in Electron Transfer Reactions in Proteins.
J.
Chem. Phys., 104, 8424, (1996).
Gehlen, J. N.; Daizadeh, I.;
Stuchebrukhov, A.A.; Marcus, R.A.
Tunneling Matrix Element in Ru-Modified
Blue Copper Proteins: Pruning the Protein in Search of Electron Transfer
Pathways.
Inorganica
Chimica Acta, 243, 271, (1996).
Stuchebrukhov, A.A.; Marcus,
R.A.
Theoretical Study of Electron Transfer in Ferrocytochromes.
J.
Phys. Chem., 99, 7581, (1995).
Stuchebrukhov, A.A.
Dispersion Relations for Electron and Hole Transfer in Donor-Bridge-Acceptor
systems.
Chem. Phys. Lett., 225, 55, (1994).
Stuchebrukhov, A.A.; Song, X.
Electron Transfer in Strongly Interacting Systems: Quantum Effects and the
Inverted Region.
J.
Chem. Phys., 101, 9354, (1994).
Stuchebrukhov, A.A.; Marcus,
R.A.
Decay and Recurrences of Wave Packets in Nonlinear Quantum Systems.
J. Phys. Chem., 98, 3285, (1994).
Stuchebrukhov, A.A., Mehta,
A.; Marcus, R.A. Vibrational Superexchange Mechanism of Intramolecular
Vibrational Relaxation in (CH3)3CCCH Molecules.
J. Phys. Chem., 97, 12491, (1994).
Stuchebrukhov, A.A.; Marcus,
R.A.
Theoretical Study of Intramolecular Vibrational Relaxation of
Acetylenic CH Vibration for v=1 and 2 in Large Polyatomic Molecules (CX3)3YCCH,
where X=H or D and Y=C or Si.
J.
Chem. Phys., 98, 6044, (1993).
Kuzmin, M.V.; Stuchebrukhov,
A.A.
Dynamical Chaos, Intramolecular Vibrational Relaxation and Spectroscopy
of Vibrationally Excited Polyatomic Molecules.
Laser Spectroscopy of
Vibrationally Excited Polyatomic Molecules, edited by V.S. Letokhov (Adam
Hilger, N.Y. Bristol, 1989) Chapter 4.
COMPLETE LIST OF PUBLICATIONS (1981-...)