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1

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

Tomoyuki Hayashi, Alexei Stuchebrukhov

Journal:

Journal of Electroanalytical Chemistry

Year:

2011

Language:

english

File:

PDF, 608 KB

english, 2011

2

DNA Repair Mechanism by Photolyase: Electron Transfer Path from the Photolyase Catalytic Cofactor FADH−to DNA Thymine Dimer

DMITRY MEDVEDEV, ALEXEI A. STUCHEBRUKHOV

Journal:

Journal of Theoretical Biology

Year:

2001

Language:

english

File:

PDF, 416 KB

english, 2001

3

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

Stuchebrukhov, Alexei A.

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 532 KB

english, 1996

4

Proton Transport via the Membrane Surface

Georgievskii, Yuri, Medvedev, Emile S., Stuchebrukhov, Alexei A.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 170 KB

english, 2002

5

Accounting for electronic polarization in non-polarizable force fields

Leontyev, Igor, Stuchebrukhov, Alexei

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

6

Electron tunneling in respiratory complex I

Tomoyuki Hayashi, Alexei A. Stuchebrukhov and Harry B. Gray

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.62 MB

english, 2010

7

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

Alexei A. Stuchebrukhov

Journal:

International Journal of Quantum Chemistry

Year:

2000

Language:

english

File:

PDF, 508 KB

english, 2000

8

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

Jian Wang, Alexei A. Stuchebrukhov

Journal:

International Journal of Quantum Chemistry

Year:

2000

Language:

english

File:

PDF, 183 KB

english, 2000

9

ChemInform Abstract: Theory of Coupled Electron and Proton Transfer Reactions

Sharon Hammes-Schiffer, Alexei A. Stuchebrukhov

Journal:

Year:

2011

File:

PDF, 18 KB

2011

10

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

Alexei A. Stuchebrukhov

Journal:

Chemical Physics Letters

Year:

1994

Language:

english

File:

PDF, 591 KB

english, 1994

11

On the non-orthogonal basis set calculations of the bridge-mediated electronic matrix elements

Alexei A. Stuchebrukhov

Journal:

Chemical Physics Letters

Year:

1997

Language:

english

File:

PDF, 396 KB

english, 1997

12

Histidine in continuum electrostatics protonation state calculations

Vernon Couch, Alexei Stuchebrukhov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 252 KB

english, 2011

13

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

D. V. Makhov, Alexei A. Stuchebrukhov

Journal:

physica status solidi (b)

Year:

2006

Language:

english

File:

PDF, 552 KB

english, 2006

14

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

Xuehe Zheng, Dmitry M. Medvedev, Alexei A. Stuchebrukhov

Journal:

International Journal of Quantum Chemistry

Year:

2005

Language:

english

File:

PDF, 157 KB

english, 2005

15

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

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

Journal:

International Journal of Quantum Chemistry

Year:

2007

Language:

english

File:

PDF, 262 KB

english, 2007

16

Long-distance electron tunneling in proteins

Alexei A. Stuchebrukhov

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2003

Language:

english

File:

PDF, 557 KB

english, 2003

17

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

Ryogo Sugitani, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2009

Language:

english

File:

PDF, 1.37 MB

english, 2009

18

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

Stuchebrukhov, Alexei A.

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 472 KB

english, 1998

19

Tunneling currents in electron transfer reactions in proteins

Stuchebrukhov, Alexei A.

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 423 KB

english, 1996

20

Theory of Coupled Electron and Proton Transfer Reactions

Hammes-Schiffer, Sharon, Stuchebrukhov, Alexei A.

Journal:

Chemical Reviews

Year:

2010

Language:

english

File:

PDF, 1.09 MB

english, 2010

21

Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase

Stuchebrukhov, Alexei A., Popović, Dragan M.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 383 KB

english, 2004

22

Polarizable Mean-Field Model of Water for Biological Simulations with AMBER and CHARMM Force Fields

Leontyev, Igor V., Stuchebrukhov, Alexei A.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 625 KB

english, 2012

23

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

Ryogo Sugitani, Emile S. Medvedev, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2008

Language:

english

File:

PDF, 745 KB

english, 2008

24

Electrostatics of the FeS clusters in respiratory complex I

Vernon A. Couch, Emile S. Medvedev, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2009

Language:

english

File:

PDF, 335 KB

english, 2009

25

Statistical analysis of experimental data on titration of metal centers in respiratory complex I

Emile S. Medvedev, Vernon A. Couch, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2010

Language:

english

File:

PDF, 77 KB

english, 2010

26

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

Emile S. Medvedev, Vernon A. Couch, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2010

Language:

english

File:

PDF, 510 KB

english, 2010

27

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

Dragan M. Popović, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2012

Language:

english

File:

PDF, 980 KB

english, 2012

28

Proteins as strongly correlated protonic systems

Vernon Couch, Alexei Stuchebrukhov

Journal:

Year:

2012

Language:

english

File:

PDF, 573 KB

english, 2012

29

First principles studies of electron tunneling in proteins

Tomoyuki Hayashi, Alexei A. Stuchebrukhov

Journal:

Computational and Theoretical Chemistry

Year:

2011

Language:

english

File:

PDF, 1.17 MB

english, 2011

30

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

Dragan M. Popović, Alexei A. Stuchebrukhov

Journal:

Year:

2004

Language:

english

File:

PDF, 193 KB

english, 2004

31

Computer simulation of water in cytochrome c oxidase

Xuehe Zheng, Dmitry M Medvedev, Jessica Swanson, Alexei A Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2003

Language:

english

File:

PDF, 466 KB

english, 2003

32

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

Jason Quenneville, Dragan M. Popović, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2006

Language:

english

File:

PDF, 455 KB

english, 2006

33

C2.6 Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme and the identity of its proton pumping site

Ryogo Sugitani, Emile S. Medvedev, Alexei A. Stuchebrukhov

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2008

Language:

english

File:

PDF, 74 KB

english, 2008

34

Redox-Coupled Protonation of Respiratory Complex I: The Hydrophilic Domain

Couch, Vernon, Popovic, Dragan, Stuchebrukhov, Alexei

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 459 KB

english, 2011

35

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

Stuchebrukhov, Alexei A.

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 360 KB

english, 1997

36

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

Antony, Jens, Medvedev, Dmitry M., Stuchebrukhov, Alexei A.

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 244 KB

english, 2000

37

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

Lee, EunJoo, Medvedev, Emile S., Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 202 KB

english, 2000

38

Computational Studies of Electron Tunneling in Respiratory Complex III

Hagras, Muhammad A., Hayashi, Tomoyuki, Stuchebrukhov, Alexei A.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 48 KB

english, 2014

39

Coupled Electron and Proton Transfer in Complex I and Complex IV of the Respiratory Chain: Insights from Computer Simulations

Stuchebrukhov, Alexei

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

40

Electron Tunneling in Respiratory Complex I

Hayashi, Tomoyuki, Stuchebrukhov, Alexei A.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 77 KB

english, 2012

41

Mechanism of long-range proton translocation along biological membranes

Medvedev, Emile S., Stuchebrukhov, Alexei A.

Journal:

Year:

2013

Language:

english

File:

PDF, 377 KB

english, 2013

42

Effect of Protein Dynamics on Biological Electron Transfer

Iraj Daizadeh, Emile S. Medvedev and Alexei A. Stuchebrukhov

Journal:

Proceedings of the National Academy of Sciences

Year:

1997

Language:

english

File:

PDF, 1.47 MB

english, 1997

43

Thermodynamic Properties of Internal Water Molecules in the Hydrophobic Cavity around the Catalytic Center of Cytochrome c Oxidase

Tashiro, Motomichi, Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 259 KB

english, 2005

44

Ab Initio Study of Long-Distance Electron Tunneling in a Model Peptide System

Kim, Jongseob, Stuchebrukhov, Alexei

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 397 KB

english, 2000

45

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

Heifets, Eugene N., Daizadeh, Iraj, Guo, Jian-xin, Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry A

Year:

1998

Language:

english

File:

PDF, 154 KB

english, 1998

46

Improved Density Functional Theory/Electrostatic Calculation of the His291 Protonation State in Cytochrome c Oxidase: Self-Consistent Charges for Solvation Energy Calculation

Makhov, D. V., Popović, Dragan M., Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 128 KB

english, 2006

47

Electron Transfer Tunneling Pathways in Bovine Heart Cytochrome c Oxidase

Medvedev, Dmitry M., Daizadeh, Iraj, Stuchebrukhov, Alexei A.

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 421 KB

english, 2000

48

Redox-Dependent p K a of Cu B Histidine Ligand in Cytochrome c Oxidase

Quenneville, Jason, Popović, Dragan M., Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 217 KB

english, 2004

49

Quantum Electron Tunneling in Respiratory Complex I

Hayashi, Tomoyuki, Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 4.06 MB

english, 2011

50

Electron Tunneling in the His 126 Ru-Modified Azurin: Tunneling Jumps between Protein Strands via Hydrogen Bonds

Zheng, Xuehe, Stuchebrukhov, Alexei A.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 207 KB

english, 2003

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