A. Stuchebrukhov

发表

Proteins as strongly correlated protonic systems

Vernon A. Couch, A. Stuchebrukhov, 2012, FEBS letters.

Theory of coupled electron and proton transfer reactions.

S. Hammes-Schiffer, A. Stuchebrukhov, S. Hammes‐Schiffer, 2010, Chemical reviews.

Electronic continuum model for molecular dynamics simulations of biological molecules.

A. Stuchebrukhov, I. Leontyev, 2010, Journal of chemical theory and computation.

Accounting for electronic polarization in non-polarizable force fields.

A. Stuchebrukhov, I. Leontyev, 2011, Physical chemistry chemical physics : PCCP.

Combined DFT and electrostatic calculations of pK a s in proteins: study of cytochrome c oxidase

A. Stuchebrukhov, J. Quenneville, D. Popović, 2006 .

Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport.

A. Stuchebrukhov, Ryogo Sugitani, 2009, Biochimica et biophysica acta.

Dowser++, a new method of hydrating protein structures

A. Stuchebrukhov, A. Morozenko, 2016, Proteins.

Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome C Oxidase

A. Stuchebrukhov, J. Quenneville, D. Popović, 2009 .

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase.

A. Stuchebrukhov, J. Quenneville, D. Popović, 2006, Biochimica et biophysica acta.

Tunneling Time and the Breakdown of Born-Oppenheimer Approximation.

A. Stuchebrukhov, 2016, The journal of physical chemistry. B.

Effect of quantum modes in biological electron transfer reactions: A useful approximation for the harmonic model with frequency change and Duchinsky rotation

A. Stuchebrukhov, E. S. Medvedev, Eunjoo Lee, 2000 .

Breakdown of the Born-Oppenheimer-Condon-Marcus approximation in long distance electron transfer

A. Stuchebrukhov, E. S. Medvedev, 2004 .

Protein dynamics control of electron transfer in photosynthetic reaction centers from Rps. sulfoviridis.

A. Stuchebrukhov, A. Kotelnikov, D. Popović, 2008, The journal of physical chemistry. B.

Dispersion relations for electron and hole transfer in donor—bridge—acceptor systems

A. Stuchebrukhov, 1994 .

Long-distance electron tunneling in proteins

A. Stuchebrukhov, 2003 .

Mutations in NDUFS1 Cause Metabolic Reprogramming and Disruption of the Electron Transfer

Muhammad A. Hagras, D. Meierhofer, A. Stuchebrukhov, 2019, Cells.

Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I.

Muhammad A. Hagras, A. Stuchebrukhov, 2019, The journal of physical chemistry. B.

Internal switches modulating electron tunneling currents in respiratory complex III.

Muhammad A. Hagras, A. Stuchebrukhov, 2016, Biochimica et biophysica acta.

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

A. Stuchebrukhov, I. Leontyev, 2014, The Journal of chemical physics.

Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase.

A. Stuchebrukhov, M. Tashiro, 2005, The journal of physical chemistry. B.

Quantum electron tunneling in respiratory complex I.

A. Stuchebrukhov, Tomoyuki Hayashi, 2011, The journal of physical chemistry. B.

Electron tunneling pathways in respiratory complex I. The role of the internal water between the enzyme subunits.

A. Stuchebrukhov, Tomoyuki Hayashi, 2011, Journal of electroanalytical chemistry.

Electron tunneling in respiratory complex I

A. Stuchebrukhov, Tomoyuki Hayashi, 2010, Proceedings of the National Academy of Sciences.

Tunneling currents in electron transfer reaction in proteins. II. Calculation of electronic superexchange matrix element and tunneling currents using nonorthogonal basis sets

A. Stuchebrukhov, 1996 .

Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis

A. Stuchebrukhov, I. Leontyev, A. Morozenko, 2014, Journal of chemical theory and computation.

Theory of Coupled Electron and Proton Transfer Reactions

A. Stuchebrukhov, S. Hammes‐Schiffer, 2011 .

Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves.

Vernon A. Couch, A. Stuchebrukhov, E. S. Medvedev, 2010, Biochimica et biophysica acta.

Accounting for electronic polarization in non-polarizable force fields.

A. Stuchebrukhov, I. Leontyev, 2011, Physical chemistry chemical physics : PCCP.

Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields.

A. Stuchebrukhov, I. Leontyev, 2015, Journal of chemical theory and computation.

Pure dephasing of a nonlinear vibrational mode. Non‐Markovian line shape

A. Stuchebrukhov, Y. Georgievskii, 1990 .

Single-photon spectroscopy of singlet sulfur atoms and the autoionization lifetime measurements of the superexcited singlet states.

W. Jackson, A. Stuchebrukhov, Jianhua Huang, 2005, The Journal of chemical physics.

Long-distance electron tunneling in proteins: A new challenge for time-resolved spectroscopy

A. Stuchebrukhov, 2010, Laser physics.

Ab initio calculations of long‐distance electron tunneling in organometallic systems of biological origin

A. Stuchebrukhov, 2000 .

Calculation of electronic tunneling matrix element in proteins: Comparison of exact and approximate one-electron methods for Ru-modified azurin

A. Stuchebrukhov, I. Daizadeh, J. N. Gehlen, 1997 .

Kinetics of autoxidation of tartaric acid in presence of iron.

R. Coleman, R. Boulton, A. Stuchebrukhov, 2020, The Journal of chemical physics.

Using Proton Geminate Recombination as a Probe of Proton Migration on Biological Membranes.

N. Amdursky, A. Stuchebrukhov, Ambili Ramanthrikkovil Variyam, 2022, The journal of physical chemistry. B.

Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme.

A. Stuchebrukhov, E. S. Medvedev, Ryogo Sugitani, 2008, Biochimica et biophysica acta.

Proton exit channels in bovine cytochrome c oxidase.

A. Stuchebrukhov, D. Popović, 2005, The journal of physical chemistry. B.

Mechanism of long‐range proton translocation along biological membranes

A. Stuchebrukhov, E. S. Medvedev, Emile S. Medvedev, 2013, FEBS letters.

Kinetics of proton diffusion in the regimes of fast and slow exchange between the membrane surface and the bulk solution

A. Stuchebrukhov, E. S. Medvedev, 2006, Journal of mathematical biology.

Multiple photon dissociation of polyatomic molecules under vibrational deactivation by a buffer gas

A. Stuchebrukhov, M. Kuzmin, 1984 .

Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models.

A. Stuchebrukhov, I. Leontyev, 2009, The Journal of chemical physics.

Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I.

A. Stuchebrukhov, I. Leontyev, Panyue Wang, 2022, The journal of physical chemistry. B.

The homogeneous Lorentzian IR absorption spectrum of (CF3)3CI at twice the threshold vibrational energy

G. N. Makarov, V. Letokhov, V. Bagratashvili, 1988 .

Tunneling matrix element in Ru-modified blue copper proteins: Pruning the protein in search of electron transfer pathways

Iraj Daizadeh, Alexei A. Stuchebrukhov, Rudolph A. Marcus, 1996 .

Electrostatics of the FeS clusters in respiratory complex I.

Vernon A. Couch, A. Stuchebrukhov, Emile S Medvedev, 2009, Biochimica et biophysica acta.

Toward Ab Initio Theory of Longdistance Electron Tunneling in Proteins: Tunneling Currents Approach

A. Stuchebrukhov, 2007 .

Tunneling currents in long-distance electron transfer reactions. III. Many-electron formulation

A. Stuchebrukhov, 1998 .

ON THE NON-ORTHOGONAL BASIS SET CALCULATIONS OF THE BRIDGE-MEDIATED ELECTRONIC MATRIX ELEMENTS

A. Stuchebrukhov, 1997 .

Inelastic tunneling in long-distance biological electron transfer reactions

A. Stuchebrukhov, E. S. Medvedev, 1997 .

Proton transport via the membrane surface.

A. Stuchebrukhov, Y. Georgievskii, Yuri Georgievskii, 2002, Biophysical journal.

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

R. Marcus, A. Stuchebrukhov, 1993 .

Electronic Polarizability and the Effective Pair Potentials of Water.

A. Stuchebrukhov, I. Leontyev, I V Leontyev, 2010, Journal of chemical theory and computation.

Proton diffusion along biological membranes

A. Stuchebrukhov, E. S. Medvedev, 2011, Journal of physics. Condensed matter : an Institute of Physics journal.

Infrared spectroscopy and intramolecular vibrational relaxation of c-C6F12 excited above the dissociation threshold

V. Bagratashvili, A. Stuchebrukhov, A. Sviridov, 1987 .

Theory of multiple-photon IR excitation of polyatomic molecules in the model of active and passive modes of a vibrational reservoir

V. Letokhov, A. Stuchebrukhov, M. Kuzmin, 1985 .

Proton transport via coupled surface and bulk diffusion

A. Stuchebrukhov, Y. Georgievskii, E. S. Medvedev, 2002 .

Quantum Calculations of Electron Tunneling in Respiratory Complex III.

Muhammad A. Hagras, A. Stuchebrukhov, Tomoyuki Hayashi, 2015, The journal of physical chemistry. B.

Electron transfer in ferredoxin: are tunneling pathways evolutionarily conserved?

A. Stuchebrukhov, I. Daizadeh, D. Medvedev, 2002, Molecular biology and evolution.

Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH.

A. Stuchebrukhov, M. Cheung, I. Daizadeh, 1999, Biophysical journal.

Perturbation theory approach to dynamical tunneling splitting of local mode vibrational states in ABA molecules

R. Marcus, A. Stuchebrukhov, 1993 .

Mechanisms of proton transfer in proteins: localized charge transfer versus delocalized soliton transfer.

A. Stuchebrukhov, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

ELECTRON TRANSFER REACTIONS COUPLED TO PROTON TRANSLOCATION: CYTOCHROME OXIDASE, PROTON PUMPS, AND BIOLOGICAL ENERGY TRANSDUCTION

A. Stuchebrukhov, 2003 .

Effect of protein dynamics on biological electron transfer.

A. Stuchebrukhov, I. Daizadeh, E. S. Medvedev, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Electron tunneling in proteins program

Muhammad A. Hagras, Alexei A. Stuchebrukhov, A. Stuchebrukhov, 2016, J. Comput. Chem..

First principles studies of electron tunneling in proteins.

A. Stuchebrukhov, Tomoyuki Hayashi, 2011, Computational & theoretical chemistry.

Does internal water influence electron tunneling in proteins? Example of cytochrome c oxidase

A. Stuchebrukhov, Xuehe Zheng, D. Medvedev, 2005 .

Tunneling currents in long-distance electron transfer reactions. V. Effective one electron approximation

A. Stuchebrukhov, 2003 .

DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.

A. Stuchebrukhov, D. Medvedev, 2001, Journal of theoretical biology.

Concerted electron and proton transfer: Transition from nonadiabatic to adiabatic proton tunneling

A. Stuchebrukhov, Y. Georgievskii, 2000 .

VORTEX STRUCTURE OF THE TUNNELING FLOW IN LONG-RANGE ELECTRON TRANSFER REACTIONS

A. Stuchebrukhov, I. Daizadeh, Jian-xin Guo, 1999 .

New expression for the effective transfer matrix element in long-range electron transfer reactions

A. Stuchebrukhov, D. Katz, 1998 .

Tunneling currents in long-distance electron transfer reactions. IV. Many-electron formulation. Nonorthogonal atomic basis sets and Mulliken population analysis

A. Stuchebrukhov, 1998 .

Tunneling currents in proteins: Nonorthogonal atomic basis sets and Mulliken population analysis

A. Stuchebrukhov, 1997 .

Tunneling currents in electron transfer reactions in proteins

A. Stuchebrukhov, 1996 .

Quantum effects in electron transfer reactions with strong electronic coupling

A. Stuchebrukhov, Xueyu Song, 1994 .

Outer-sphere Electron Transfer in Polar Solvents: Quantum Scaling of Strongly Interacting Systems.

A. Stuchebrukhov, Xueyu Song, 1993 .

Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics.

A. Stuchebrukhov, S. Cramer, I. Leontyev, 2015, Biochemistry.

Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site

A. Stuchebrukhov, I. Leontyev, Panyue Wang, 2021, Photochemical & Photobiological Sciences.

Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening.

Muhammad A. Hagras, A. Stuchebrukhov, Panyue Wang, 2020, Biochimica et biophysica acta. Bioenergetics.

Electron Tunneling in Quasi-One-Dimensional Resonant Molecular Systems. Ab Initio Study

A. Stuchebrukhov, E. Heifets, I. Daizadeh, 1998 .

Calculation of Quantum Parameters for Nonadiabatic Redox Reactions. Application to Photoreduction of Flavin in DNA Photolyase

A. Stuchebrukhov, A. Medvedev, Eunjoo Lee, 2000 .

Watching DNA repair in real time

A. Stuchebrukhov, 2011, Proceedings of the National Academy of Sciences.

Theoretical Study of Electron Transfer between the Photolyase Catalytic Cofactor FADH- and DNA Thymine Dimer

Alexei A. Stuchebrukhov, J. Antony, A. Stuchebrukhov, 2000 .

Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase.

A. Stuchebrukhov, D. Popović, 2012, Biochimica et biophysica acta.

An accurate and efficient procedure of fitting electric field potential by point charges for QM/MM calculations

D. Makhov, A. Stuchebrukhov, 2006 .

Two conformational states of Glu242 and pK_as in bovine cytochrome c oxidase

A. Stuchebrukhov, D. Popović, 2006, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Kinetic advantage of forming respiratory supercomplexes.

A. Stuchebrukhov, P. Brzezinski, J. Berg, 2020, Biochimica et biophysica acta. Bioenergetics.

On the electron tunneling in molecules: a generalized orthogonalization procedure for finding tunneling orbitals.

A. Stuchebrukhov, Y. Georgievskii, Xuehe Zheng, 2004, The Journal of chemical physics.

Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating

A. Stuchebrukhov, D. Popović, 2004, FEBS letters.

A. Stuchebrukhov, I. Leontyev, D. Popović, 2010, Proteins.

Statistics of an ensemble of oscillators under excitation. V. Analysis of experiments on the absorption of CO2-laser radiation by SF6 based on a triply degenerate oscillator model

V. N. Sazonov, A. Stuchebrukhov, 1984 .

On statistics of an ensemble of oscillators under excitation. III. Quantum non-linear oscillators with fast phase relaxation in a non-monochromatic external field

V. N. Sazonov, A. Stuchebrukhov, S. V. Zatsepin, 1982 .

On statistics of the ensemble of oscillators under excitation. II. Parametric excitation of linear quantum oscillators

V. N. Sazonov, A. Stuchebrukhov, 1981 .

IR spectra of highly vibrationally excited large polyatomic molecules and intramolecular relaxation

V. Letokhov, A. Stuchebrukhov, S. Ionov, 1989 .

On the theory of intramolecular vibrational relaxation in highly excited polyatomic molecules: Quasi-harmonic versus random-phase approximation

A. Stuchebrukhov, 1988 .

Threshold energy dependence of intramolecular vibrational relaxation in polyatomic molecules

V. Letokhov, V. Bagratashvili, A. Stuchebrukhov, 1986 .

Measurement of the autoionization lifetime of the superexcited atomic sulfur S(3s23p3(2Do)4d) state using tunable vacuum ultraviolet (VUV) radiation

W. Jackson, A. Stuchebrukhov, Jianhua Huang, 2004 .

Vibrational Superexchange Mechanism of Intramolecular Vibrational Relaxation in (CH_3)_3CCCH Molecules

R. Marcus, A. Stuchebrukhov, A. Mehta, 1993 .

DFT calculation of electron tunneling currents: Real-space (grid) molecular orbitals vs. Gaussian-type molecular orbitals

A. Stuchebrukhov, Jian Wang, 2000 .

Electron Transfer Tunneling Pathways in Bovine Heart Cytochrome c Oxidase

Alexei A. Stuchebrukhov, Dmitry M. Medvedev, A. Stuchebrukhov, 2000 .

Theoretical Study of Electron Transfer in Ferrocytochromes

R. Marcus, A. Stuchebrukhov, 1995 .

IVR in Overtones of the Acetylenic C-H Stretch in Propyne

R. Marcus, A. Stuchebrukhov, A. Mehta, 1995 .

Green's functions in quantum transition state theory

A. Stuchebrukhov, 1991 .

Kinetics and Efficiency of Energy Transducing Enzymes.

A. Stuchebrukhov, 2019, The journal of physical chemistry. B.

Monte Carlo Simulations of Glu-242 in Cytochrome c Oxidase.

Vernon A. Couch, A. Stuchebrukhov, Benjamin M. Samudio, 2016, The journal of physical chemistry. B.

Transition Flux Formula for the Electronic Coupling Matrix Element.

Muhammad A. Hagras, A. Stuchebrukhov, 2015, The journal of physical chemistry. B.

Investigating the Many Roles of Internal Water in Cytochrome c Oxidase.

A. Farahvash, A. Stuchebrukhov, 2018, The journal of physical chemistry. B.

Decay and Recurrences of Wave Packets in Nonlinear Quantum Systems

R. Marcus, A. Stuchebrukhov, 1994 .

Mechanisms of generation of local ΔpH in mitochondria and bacteria

A. Stuchebrukhov, E. S. Medvedev, 2014, Biochemistry (Moscow).

A Theoretical Analysis of the Redox-Coupled Protonation of Heme a and CuA in the Cytochrome c Oxidase with CO-Inhibited Binuclear Center

A. Stuchebrukhov, Y. Georgievskii, E. S. Medvedev, 2004, Russian Journal of Bioorganic Chemistry.

Protein dynamics control of electron transfer in reaction centers from Rps. viridis

A. Stuchebrukhov, E. S. Medvedev, A. I. Kotel’nikov, 2006 .

Dynamic effects in long-distance biological electron transfer reactions

A. Stuchebrukhov, E. S. Medvedev, 1998 .

Theoretical study of excitation energy transfer in DNA photolyase.

A. Stuchebrukhov, Xuehe Zheng, Jorge García, 2008, The journal of physical chemistry. B.

Photoactivated excited states of DNA repair photolyase: Dynamical and semiempircal identification

A. Stuchebrukhov, Xuehe Zheng, Ngan M. Ly, 2007 .

Computer simulation of water in cytochrome c oxidase.

J. Swanson, A. Stuchebrukhov, Xuehe Zheng, 2003, Biochimica et biophysica acta.

Histidine in continuum electrostatics protonation state calculations

Vernon A. Couch, A. Stuchebrukhov, 2011, Proteins.

Single protonation of the reduced quinone in respiratory complex I drives four‐proton pumping

A. Stuchebrukhov, T. Hayashi, 2022, FEBS letters.

Redox-coupled protonation of respiratory complex I: the hydrophilic domain.

Vernon A. Couch, A. Stuchebrukhov, D. Popović, 2011, Biophysical journal.

Improved density functional theory/electrostatic calculation of the His291 protonation state in cytochrome C oxidase: self-consistent charges for solvation energy calculation.

D. Makhov, A. Stuchebrukhov, D. Popović, 2006, The journal of physical chemistry. B.

Electronic continuum model for molecular dynamics simulations.

A. Stuchebrukhov, I. Leontyev, I V Leontyev, 2009, The Journal of chemical physics.

Novel Inhibitors for a Novel Binding Site in Respiratory Complex III.

Muhammad A. Hagras, A. Stuchebrukhov, 2016, The journal of physical chemistry. B.

Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase.

A. Stuchebrukhov, D. Popović, 2004, Journal of the American Chemical Society.

Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection.

A. Stuchebrukhov, D. Medvedev, Emile S. Medvedev, 2005, Biochimica et biophysica acta.

Electron tunneling in respiratory complex I

A. Stuchebrukhov, Tomoyuki Hayashi, 2010, Proceedings of the National Academy of Sciences.

A. Stuchebrukhov, I. Leontyev, D. Popović, 2010, Proteins.

IR absorption spectroscopy of highly vibrationally excited polyatomic molecules

A. Stuchebrukhov, I. Khromov, 1987 .

Effect of inhomogeneity of absorption in collisionless multiple-proton dissociation

A. Stuchebrukhov, M. Kuzmin, 1984 .

Popović – Proton-Coupled Electron Transfer in CcO Supplementary Material Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase

A. Stuchebrukhov, D. Popovi, 2011 .

Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I

A. Stuchebrukhov, Panyue Wang, Jason Tae Yi, 2023, Scientific reports.

Kinetic Treatment of Coupled Electron and Proton Transfer in Flash-Photolysis Experiments on Carbon Monoxide-Inhibited Mixed-Valence Cytochrome c Oxidase

A. Stuchebrukhov, E. S. Medvedev, A. I. Kotel’nikov, 2001 .

Redox-Driven Proton Pumps of the Respiratory Chain.

A. Stuchebrukhov, 2018, Biophysical journal.