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Volumn 105, Issue 40, 2001, Pages 9857-9871

Nature of the surface crossing process in bacteriorhodopsin: Computer simulations of the quantum dynamics of the primary photochemical event

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN;

EID: 0035846382     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp010704a     Document Type: Article
Times cited : (155)

References (84)
  • 1
    • 0025303725 scopus 로고
    • Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin
    • Birge, R.R. Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin. Biochim. Biophys. Acta 1990, 1016, 293-327.
    • (1990) Biochim. Biophys. Acta , vol.1016 , pp. 293-327
    • Birge, R.R.1
  • 3
    • 0024279842 scopus 로고
    • Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin
    • Mathies, R.A.; Brito Cruz, C.H.; Pollard, W.T.; Shank, C.V. Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin. Science 1988, 240, 777-779.
    • (1988) Science , vol.240 , pp. 777-779
    • Mathies, R.A.1    Brito Cruz, C.H.2    Pollard, W.T.3    Shank, C.V.4
  • 4
    • 0018504783 scopus 로고
    • Conversion of light energy to electrostatic energy in the proton pump of halobacterium halobium
    • Warshel, A. Conversion of Light Energy to Electrostatic Energy in the Proton Pump of Halobacterium halobium. Photochem. Photobiol. 1979, 30, 285-290.
    • (1979) Photochem. Photobiol. , vol.30 , pp. 285-290
    • Warshel, A.1
  • 5
    • 33845554105 scopus 로고
    • Energy storage and reaction pathways in the first step of the vision process
    • Warshel, A.; Barboy, N. Energy Storage and Reaction Pathways in the First Step of the Vision Process. J. Am. Chem. Soc. 1982, 104, 1469.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 1469
    • Warshel, A.1    Barboy, N.2
  • 6
    • 0017251977 scopus 로고
    • Bicycle-pedal model for the first step in the vision process
    • Warshel, A. Bicycle-Pedal Model for the First Step in the Vision Process. Nature 1976, 260, 679-683.
    • (1976) Nature , vol.260 , pp. 679-683
    • Warshel, A.1
  • 10
    • 0028519152 scopus 로고
    • Vibrationally coherent photochemistry in the femtosecond primary event of vision
    • Wang, Q.; Schoenlein, R.W.; Peteanu, L.A.; Mathies, R.A.; Shank, C.V. Vibrationally Coherent Photochemistry in the Femtosecond Primary Event of Vision. Science 1994, 266, 422.
    • (1994) Science , vol.266 , pp. 422
    • Wang, Q.1    Schoenlein, R.W.2    Peteanu, L.A.3    Mathies, R.A.4    Shank, C.V.5
  • 11
    • 20544447251 scopus 로고
    • Femtosecond spectroscopy of the 1st events of the photochemical cycle in bacteriorhodopsin
    • Nuss, M.C.; Zinth, W.; Kaiser, W.; Koelling, E.; Oesterhelt, D. Femtosecond spectroscopy of the 1st events of the photochemical cycle in bacteriorhodopsin. Chem. Phys. Lett. 1985, 117, 1-7.
    • (1985) Chem. Phys. Lett. , vol.117 , pp. 1-7
    • Nuss, M.C.1    Zinth, W.2    Kaiser, W.3    Koelling, E.4    Oesterhelt, D.5
  • 12
    • 0030299802 scopus 로고    scopus 로고
    • The photoisomerization of retinal in bacteriorhodopsin: Experimental evidence for a three-state model
    • Hasson, K.C.; Gal, F.; Anfinrud, P.A. The photoisomerization of retinal in bacteriorhodopsin: Experimental evidence for a three-state model. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 15124-15129.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 15124-15129
    • Hasson, K.C.1    Gal, F.2    Anfinrud, P.A.3
  • 13
    • 0001649161 scopus 로고
    • Excited-state reaction dynamics of bacteriorhodopsin studied by femtosecond spectroscopy
    • Dobler, J.; Zinth, W.; Kaiser, W.; Oesterhelt, D. Excited-state reaction dynamics of bacteriorhodopsin studied by femtosecond spectroscopy. Chem. Phys. Lett. 1988, 144, 214-220.
    • (1988) Chem. Phys. Lett. , vol.144 , pp. 214-220
    • Dobler, J.1    Zinth, W.2    Kaiser, W.3    Oesterhelt, D.4
  • 14
    • 0001078762 scopus 로고
    • Molecular dynamics of cis-trans isomerization in rhodopsin
    • Birge, R.R.; Hubbard, L.M. Molecular dynamics of cis-trans isomerization in rhodopsin. J. Am. Chem. Soc. 1980, 102, 2195-2205.
    • (1980) J. Am. Chem. Soc. , vol.102 , pp. 2195-2205
    • Birge, R.R.1    Hubbard, L.M.2
  • 16
    • 84961983828 scopus 로고    scopus 로고
    • Quantum chemistry: Molecular dynamics study of the dark-adaptation process in bacteriorhodopsin
    • Logunov, I.; Schulten, K. Quantum chemistry: Molecular dynamics study of the dark-adaptation process in bacteriorhodopsin. J. Am. Chem. Soc. 1996, 118, 9727-9737.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 9727-9737
    • Logunov, I.1    Schulten, K.2
  • 17
    • 0030058834 scopus 로고    scopus 로고
    • Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and the J, K intermediates
    • Xu, D.; Martin, C.; Schulten, K. Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling and the J, K intermediates. Biophys. J. 1996, 70, 453-460.
    • (1996) Biophys. J. , vol.70 , pp. 453-460
    • Xu, D.1    Martin, C.2    Schulten, K.3
  • 18
    • 0032228252 scopus 로고    scopus 로고
    • Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin
    • Ben-Nun, M.; Molnar, F.; Lu, H.; Philips, J.C.; Martinez, T.J.; Schulten, K. Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin. Faraday Discuss. 1998, 110, 447-462.
    • (1998) Faraday Discuss. , vol.110 , pp. 447-462
    • Ben-Nun, M.1    Molnar, F.2    Lu, H.3    Philips, J.C.4    Martinez, T.J.5    Schulten, K.6
  • 19
    • 0001604008 scopus 로고
    • The dynamics of the primary event in rhodopsins revisited
    • Warshel, A.; Chu, Z.T.; Hwang, J.-K. The Dynamics of the Primary Event in Rhodopsins Revisited. Chem. Phys. 1991, 158, 303-314.
    • (1991) Chem. Phys. , vol.158 , pp. 303-314
    • Warshel, A.1    Chu, Z.T.2    Hwang, J.-K.3
  • 20
    • 0019421990 scopus 로고
    • Molecular dynamics of trans-cis isomerization in bathorhodopsin
    • Birge, R.R.; Hubbard, L.M. Molecular dynamics of trans-cis isomerization in bathorhodopsin. Biophys. J. 1981, 34 (3), 517-34.
    • (1981) Biophys. J. , vol.34 , Issue.3 , pp. 517-534
    • Birge, R.R.1    Hubbard, L.M.2
  • 21
    • 0001628475 scopus 로고
    • A new view of the dynamics of singlet cis-trans photoisomerization
    • Weiss, R.M.; Warshel, A. A New View of the Dynamics of Singlet cis-trans Photoisomerization. J. Am. Chem. Soc. 1979, 101, 6131-6133.
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 6131-6133
    • Weiss, R.M.1    Warshel, A.2
  • 22
    • 33751130970 scopus 로고    scopus 로고
    • Photoisomerization quantum yield and apparent energy content of the K intermediate in the photocycles of bacteriorhodopsin, its mutants D85N, R82Q, and D212N, and deionized blue bacteriorhodopsin
    • Logunov, S.L.; El-Sayed, M.A.; Song, L.; Lanyi, J.K. Photoisomerization quantum yield and apparent energy content of the K intermediate in the photocycles of bacteriorhodopsin, its mutants D85N, R82Q, and D212N, and deionized blue bacteriorhodopsin. J. Phys. Chem. 1996, 100, 2391-2398.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2391-2398
    • Logunov, S.L.1    El-Sayed, M.A.2    Song, L.3    Lanyi, J.K.4
  • 23
    • 0001760699 scopus 로고    scopus 로고
    • Effects of changing the position and orientation of Asp85 relative to the protonated Schiff base within the retinal cavity on the rate of photoisomerization in bacteriorhodopsin
    • Song, L.; El-Sayed, M.A.; Lanyi, J.K. Effects of changing the position and orientation of Asp85 relative to the protonated Schiff base within the retinal cavity on the rate of photoisomerization in bacteriorhodopsin. J. Phys. Chem. 1996, 100, 10479-10481.
    • (1996) J. Phys. Chem. , vol.100 , pp. 10479-10481
    • Song, L.1    El-Sayed, M.A.2    Lanyi, J.K.3
  • 24
    • 0025327261 scopus 로고
    • The quantum yield of bacteriorhodopsin
    • Titor, J.; Oesterhelt, D. The quantum yield of bacteriorhodopsin. FEBS Lett. 1990, 263, 269-273.
    • (1990) FEBS Lett. , vol.263 , pp. 269-273
    • Titor, J.1    Oesterhelt, D.2
  • 26
    • 36749111955 scopus 로고
    • Nonadiabatic coupling between low lying singlet states of geometrically relaxed olefines: Ethylene and propylene
    • Persico, M.; Bonacic-Koutecky, V. Nonadiabatic coupling between low lying singlet states of geometrically relaxed olefines: Ethylene and propylene. J. Chem. Phys. 1982, 76, 6018.
    • (1982) J. Chem. Phys. , vol.76 , pp. 6018
    • Persico, M.1    Bonacic-Koutecky, V.2
  • 27
    • 0000488587 scopus 로고
    • Photochemical reactions of large molecules. I. A simple physical model of photochemical reactivity
    • Michl, J., Photochemical Reactions of Large Molecules. I. A Simple Physical Model of Photochemical Reactivity. Mol. Photochem. 1972, 4, 243, 257, 287.
    • (1972) Mol. Photochem. , vol.4 , pp. 243
    • Michl, J.1
  • 28
    • 4444254527 scopus 로고
    • A conical intersection mechanism for the photochemistry of butadiene
    • Olivucci, M.; Ragazos, I.N.; Bernardi, F.; Robb, M.A. A Conical Intersection Mechanism for the Photochemistry of Butadiene. J. Am. Chem. Soc. 1993, 115, 3710-3721.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3710-3721
    • Olivucci, M.1    Ragazos, I.N.2    Bernardi, F.3    Robb, M.A.4
  • 30
    • 84985512927 scopus 로고
    • Conical intersections and the mechanism of singlet photoreactions
    • Klessinger, M. Conical Intersections and the Mechanism of Singlet Photoreactions. Angew. Chem., Int. Ed. Engl. 1995, 34, 549-551.
    • (1995) Angew. Chem., Int. Ed. Engl. , vol.34 , pp. 549-551
    • Klessinger, M.1
  • 31
    • 0001294195 scopus 로고    scopus 로고
    • Conical intersections: Diabolical and often misunderstood
    • Yarkony, D.R. Conical Intersections: diabolical and often misunderstood. Acc. Chem. Res. 1998, 31, 511-518.
    • (1998) Acc. Chem. Res. , vol.31 , pp. 511-518
    • Yarkony, D.R.1
  • 32
    • 33947564300 scopus 로고
    • The crossing of potential surfaces
    • Teller, E. The crossing of potential surfaces. J. Phys. Chem. 1937, 41, 109-116.
    • (1937) J. Phys. Chem. , vol.41 , pp. 109-116
    • Teller, E.1
  • 34
    • 0032542573 scopus 로고    scopus 로고
    • Photoisomerization path for a realistic retinal chromophore model: The nonatetraeniminium cation
    • Garavelli, M.; Vreven, T.; Celani, P.; Bernardi, F.; Robb, M.A.; Olivucci, M. Photoisomerization path for a realistic retinal chromophore model: The nonatetraeniminium cation. J. Am. Chem. Soc. 1998, 120, 1285-1288.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 1285-1288
    • Garavelli, M.1    Vreven, T.2    Celani, P.3    Bernardi, F.4    Robb, M.A.5    Olivucci, M.6
  • 35
    • 0000464107 scopus 로고
    • Nonadiabatic interactions in unimolecular decay. V. Conical and Jahn-Teller intersections
    • Desouter-Lecomte, M.; Galloy, C.; Lorquet, J.C.; Vaz Pires, M. Nonadiabatic interactions in unimolecular decay. V. Conical and Jahn-Teller intersections. J. Chem. Phys. 1979, 71 (9), 3661-3672.
    • (1979) J. Chem. Phys. , vol.71 , Issue.9 , pp. 3661-3672
    • Desouter-Lecomte, M.1    Galloy, C.2    Lorquet, J.C.3    Vaz Pires, M.4
  • 36
    • 0025292355 scopus 로고
    • Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
    • Henderson, R.; Baldwin, J.M.; Ceska, T.A.; Zemlin, F.; Beckman, E.; Downing, K.H. Model for the Structure of Bacteriorhodopsin Based on High-resolution Electron Cryo-microscopy. J. Mol. Biol. 1990, 213, 899-929.
    • (1990) J. Mol. Biol. , vol.213 , pp. 899-929
    • Henderson, R.1    Baldwin, J.M.2    Ceska, T.A.3    Zemlin, F.4    Beckman, E.5    Downing, K.H.6
  • 38
    • 0033536594 scopus 로고    scopus 로고
    • Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution
    • Luecke, H.; Schobert, B.; Richter, H.-T.; Cartailler, J.-P.; Lanyi, J.K. Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science 1999, 286, 255-260.
    • (1999) Science , vol.286 , pp. 255-260
    • Luecke, H.1    Schobert, B.2    Richter, H.-T.3    Cartailler, J.-P.4    Lanyi, J.K.5
  • 40
    • 36849103764 scopus 로고
    • Semiclassical theory of electronic transitions in low energy atomic and molecular collisions involving several nuclear degrees of freedom
    • Miller, W.H.; George, T.F. Semiclassical Theory of Electronic Transitions in Low Energy Atomic and Molecular Collisions Involving Several Nuclear Degrees of Freedom. J. Chem. Phys. 1972, 56, 5637-5652.
    • (1972) J. Chem. Phys. , vol.56 , pp. 5637-5652
    • Miller, W.H.1    George, T.F.2
  • 42
    • 0000374857 scopus 로고    scopus 로고
    • Microscopic based density matrix treatments of electron-transfer reactions in condensed phases
    • Jen, C.F.; Warshel, A. Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases. J. Phys. Chem. A. 1999, 103, 11378-11386.
    • (1999) J. Phys. Chem. A. , vol.103 , pp. 11378-11386
    • Jen, C.F.1    Warshel, A.2
  • 43
    • 0002772685 scopus 로고
    • Semiclassical trajectory approach to photoisomerization
    • Warshel, A.; Karplus, M. Semiclassical Trajectory Approach to Photoisomerization. Chem. Phys. Lett. 1975, 32, 11.
    • (1975) Chem. Phys. Lett. , vol.32 , pp. 11
    • Warshel, A.1    Karplus, M.2
  • 44
    • 0007836334 scopus 로고
    • Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions
    • Warshel, A. Dynamics of Reactions in Polar Solvents. Semiclassical Trajectory Studies of Electron-Transfer and Proton-Transfer Reactions. J. Phys. Chem. 1982, 86 (12), 2218-2224.
    • (1982) J. Phys. Chem. , vol.86 , Issue.12 , pp. 2218-2224
    • Warshel, A.1
  • 45
    • 1542382717 scopus 로고
    • Simulation of the dynamics of electron-transfer reactions in polar solvents: Semiclassical trajectories and dispersed polaron approaches
    • Warshel, A.; Hwang, J.-K. Simulation of the Dynamics of Electron-Transfer Reactions in Polar Solvents: Semiclassical Trajectories and Dispersed Polaron Approaches. J. Chem. Phys. 1986, 84, 4938-4957.
    • (1986) J. Chem. Phys. , vol.84 , pp. 4938-4957
    • Warshel, A.1    Hwang, J.-K.2
  • 46
    • 0026103656 scopus 로고
    • Nonadiabatic processes in condensed matter: Semiclassical theory and implementation
    • Webster, F.; Rossky, P.J.; Friesner, R.A. Nonadiabatic Processes in Condensed Matter: Semiclassical Theory and Implementation. Comput. Phys. Comm. 1991, 63, 494-522.
    • (1991) Comput. Phys. Comm. , vol.63 , pp. 494-522
    • Webster, F.1    Rossky, P.J.2    Friesner, R.A.3
  • 47
    • 36049058156 scopus 로고
    • Time-dependent semiclassical scattering theory. I. Potential scattering
    • Pechukas, P. Time-Dependent Semiclassical Scattering Theory. I. Potential Scattering. Phys. Rev. 1969, 181, 161-185.
    • (1969) Phys. Rev. , vol.181 , pp. 161-185
    • Pechukas, P.1
  • 49
    • 36849105325 scopus 로고
    • Internal rotation and the breakdown of the adiabatic approximation: Many-phonon radiationless transititons
    • Gelbart, W.M.; Freed, K.F.; Rice, S.A. Internal rotation and the breakdown of the adiabatic approximation: many-phonon radiationless transititons. J. Chem. Phys. 1970, 52, 2460-2473.
    • (1970) J. Chem. Phys. , vol.52 , pp. 2460-2473
    • Gelbart, W.M.1    Freed, K.F.2    Rice, S.A.3
  • 50
    • 20844446886 scopus 로고
    • Intramolecular radiationless transitions
    • Bixon, M.; Jortner, J. Intramolecular radiationless transitions. J. Chem. Phys. 1968, 48, 715-726.
    • (1968) J. Chem. Phys. , vol.48 , pp. 715-726
    • Bixon, M.1    Jortner, J.2
  • 51
    • 36849100924 scopus 로고
    • Radiationless transitions in polyatomic molecules. I. Calculations of franck-condon factors
    • Siebrand, W. Radiationless transitions in polyatomic molecules. I. Calculations of Franck-Condon factors. J. Chem. Phys. 1967, 46, 440-447.
    • (1967) J. Chem. Phys. , vol.46 , pp. 440-447
    • Siebrand, W.1
  • 52
    • 36849114379 scopus 로고
    • Radiationless transitions in polyatomic molecules. II. Triplet-ground-state transitions in hydrocarbons
    • Siebrand, W. Radiationless transitions in polyatomic molecules. II. Triplet-ground-state transitions in hydrocarbons. J. Chem. Phys. 1967, 47, 2411-2422.
    • (1967) J. Chem. Phys. , vol.47 , pp. 2411-2422
    • Siebrand, W.1
  • 53
    • 2242435790 scopus 로고
    • The electronic structure of naphthalene
    • Ito, H.; I'Haya, Y. The Electronic Structure of Naphthalene. Theor. Chim. Acta, 1964, 2, 247-257.
    • (1964) Theor. Chim. Acta , vol.2 , pp. 247-257
    • Ito, H.1    I'Haya, Y.2
  • 54
    • 0000187309 scopus 로고
    • The role of nonadiabatic coupling and sudden polarization in the photoisomerization of olefins
    • Persico, M. The Role of Nonadiabatic Coupling and Sudden Polarization in the Photoisomerization of Olefins. J. Am. Chem. Soc. 1980, 102, 7839-7545.
    • (1980) J. Am. Chem. Soc. , vol.102 , pp. 7839-7545
    • Persico, M.1
  • 55
    • 0000100702 scopus 로고
    • A quantum chemical study on the mechanism of cis trans isomerization in retinal-like protonated Schiff bases
    • Dormans, G.J.M.; Groenenboom, G.C.; van Dorst, W.C.A.; Buck, H.M. A quantum chemical study on the mechanism of cis trans isomerization in retinal-like protonated Schiff bases. J. Am. Chem. Soc. 1988, 110, 1406-1415.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1406-1415
    • Dormans, G.J.M.1    Groenenboom, G.C.2    Van Dorst, W.C.A.3    Buck, H.M.4
  • 56
    • 0031176370 scopus 로고    scopus 로고
    • Dynamical theory of photoisomerization of the rhodopsin chromophore: Generation of a transient electric field during photoisomerization
    • Kikuchi, H.; Suzuki, H. Dynamical theory of photoisomerization of the rhodopsin chromophore: generation of a transient electric field during photoisomerization. J. Phys. Chem. B 1997, 101, 6050-6056.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 6050-6056
    • Kikuchi, H.1    Suzuki, H.2
  • 57
    • 0001385748 scopus 로고
    • Calculations of ground-and excited-state potential surfaces for conjugated heteroatomic molecules
    • Warshel, A.; Lappicirella, A. Calculations of Ground-and Excited-State Potential Surfaces for Conjugated Heteroatomic Molecules. J. Am. Chem. Soc. 1981, 103, 4664.
    • (1981) J. Am. Chem. Soc. , vol.103 , pp. 4664
    • Warshel, A.1    Lappicirella, A.2
  • 58
    • 0016384497 scopus 로고
    • Calculation of π π* excited state conformations and vibronic structure of retinal and related molecules
    • Warshel, A.; Karplus, M. Calculation of π π* Excited State Conformations and Vibronic Structure of Retinal and Related Molecules. J. Am. Chem. Soc. 1974, 96, 5677.
    • (1974) J. Am. Chem. Soc. , vol.96 , pp. 5677
    • Warshel, A.1    Karplus, M.2
  • 59
    • 0000728542 scopus 로고
    • Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
    • Lee, F.S.; Chu, Z.T.; Warshel, A. Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the POLARIS and ENZYMIX Programs. J. Comput. Chem. 1993, 14, 161-185.
    • (1993) J. Comput. Chem. , vol.14 , pp. 161-185
    • Lee, F.S.1    Chu, Z.T.2    Warshel, A.3
  • 60
    • 0000420301 scopus 로고
    • Microscopic calculations of solvent effects on absorption spectra of conjugated molecules
    • Luzhkov, V.; Warshel, A. Microscopic Calculations of Solvent Effects on Absorption Spectra of Conjugated Molecules. J. Am. Chem. Soc. 1991, 113, 4491-4499.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4491-4499
    • Luzhkov, V.1    Warshel, A.2
  • 61
    • 0004316256 scopus 로고
    • QCFF/PI: A program for the consistent force field evaluation of equilibrium geometries and vibrational frequencies of molecules
    • Quantum Chemistry Program Exchange; Indiana University: Bloomington, IN
    • Warshel, A.; Levitt, M. QCFF/PI: A Program for the Consistent Force Field Evaluation of Equilibrium Geometries and Vibrational Frequencies of Molecules. QCPE 247, Quantum Chemistry Program Exchange; Indiana University: Bloomington, IN, 1974.
    • (1974) QCPE , vol.247
    • Warshel, A.1    Levitt, M.2
  • 62
    • 0025262197 scopus 로고
    • Prediction by AM1 of more reasonable geometries for 1,2-diphenylcycloalkenes than by other semiempirical MO methods
    • Muller, M.G.; Hohlneicher, G. Prediction by AM1 of More Reasonable Geometries for 1,2-Diphenylcycloalkenes Than by Other Semiempirical MO Methods. J. Am. Chem. Soc. 1990, 112, 1273-1274.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 1273-1274
    • Muller, M.G.1    Hohlneicher, G.2
  • 63
    • 2242428487 scopus 로고    scopus 로고
    • note
    • Reference 62 has compared the performance of the QCFF/PI to that of other methods including AM1. The results presented (which appear to be in contrast with the authors conclusions) indicate that the QCFF/PI provides the most reliable structures for sterically hindered conjugated molecules. This is apparent from examination of the calculated and observed values of the angles Ω and θ, while noting that the calculated potential minima must correspond to θ values which are smaller than the corresponding observed values (that reflect thermal average over a very flat and anharmonic potential).
  • 64
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King, G.; Warshel, A. A Surface Constrained All-Atom Solvent Model for Effective Simulations of Polar Solutions. J. Chem. Phys. 1989, 91 (6), 3647-3661.
    • (1989) J. Chem. Phys. , vol.91 , Issue.6 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 65
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee, F.S.; Warshel, A. A Local Reaction Field Method for Fast Evaluation of Long-Range Electrostatic Interactions in Molecular Simulations. J. Chem. Phys. 1992, 97, 3100-3107.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 66
    • 0032054517 scopus 로고    scopus 로고
    • Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
    • Warshel, A.; Papazyan, A. Electrostatic Effects in Macromolecules: Fundamental Concepts and Practical Modeling. Curr. Opinion Struct. Biol. 1998, 8, 211-217.
    • (1998) Curr. Opinion Struct. Biol. , vol.8 , pp. 211-217
    • Warshel, A.1    Papazyan, A.2
  • 67
    • 0034315814 scopus 로고    scopus 로고
    • Electrostatic protein-chromophore interactions promote the all-trans-13-cis isomerization of the protonated retinal schiff base in bacteriorhodopsin: An ab initio CASSCF/MRCI study
    • Nonella, M. Electrostatic Protein-Chromophore Interactions Promote the all-trans-13-cis Isomerization of the Protonated Retinal Schiff Base in Bacteriorhodopsin: An ab Initio CASSCF/MRCI Study. J. Phys. Chem. B 2000, 104, 11379-11388.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 11379-11388
    • Nonella, M.1
  • 68
    • 2242469818 scopus 로고    scopus 로고
    • note
    • 15 used 1-D surfaces and represented the protein by the Lys residue that forms the Schiff base and by an external point charge. The steric effects of the Lys residue would have relaxed in more realistic calculations and the effect of the counterion would have been drastically reduced by protein dielectric effect. This effect is introduced and treated consistently in our QM/MM treatment, which includes the protein-solvent electrostatic interactions and the proper microscopic dielectric effect.
  • 69
    • 84985091477 scopus 로고
    • On the absorption maxima of protonated retinal schiff bases. An interaction with external charges
    • Baasov, T.; Sheves, M. On the Absorption Maxima of Protonated Retinal Schiff Bases. An Interaction with External Charges. Isr. J. Chem. 1985, 25, 53-55.
    • (1985) Isr. J. Chem. , vol.25 , pp. 53-55
    • Baasov, T.1    Sheves, M.2
  • 70
    • 33845378460 scopus 로고
    • Model compounds for the study of spectroscopic properties of visual pigments and bacteriorhodopsin
    • Baasov, T.; Sheves, M. Model Compounds for the Study of Spectroscopic Properties of Visual Pigments and Bacteriorhodopsin. J. Am. Chem. Soc. 1985, 107, 7524-7533.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 7524-7533
    • Baasov, T.1    Sheves, M.2
  • 71
    • 2242449327 scopus 로고
    • Quantum chemistry of in sim retinal: Study of the spectral properties and dark adaptation of bacteriorhodopsin
    • Bicout, D., Field, M., Eds.; Springer: Berlin, Germany
    • Logunov, I.; Schulten, K. Quantum Chemistry of in sim Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin. In Quantum Mechanical Simulation Methods for Studying Biological Systems; Bicout, D., Field, M., Eds.; Springer: Berlin, Germany, 1995.
    • (1995) Quantum Mechanical Simulation Methods for Studying Biological Systems
    • Logunov, I.1    Schulten, K.2
  • 72
    • 33847086787 scopus 로고
    • An external point-charge model for bacteriorhodopsin to account for its purple color
    • Nakanishi, K.; Balogh-Nair, V.; Arnadboldi, M.; Tsujimoto, K.; Honig, B. An External Point-Charge Model for Bacteriorhodopsin To Account for Its Purple Color. J. Am Chem. Soc. 1980, 102, 7945-7947.
    • (1980) J. Am Chem. Soc. , vol.102 , pp. 7945-7947
    • Nakanishi, K.1    Balogh-Nair, V.2    Arnadboldi, M.3    Tsujimoto, K.4    Honig, B.5
  • 73
    • 0018504832 scopus 로고
    • Kinetic and spectroscopic effects of protein-chromophore electrostatic interactions in bacteriorhodopsin
    • Warshel, A.; Ottolenghi, M. Kinetic and Spectroscopic Effects of Protein-Chromophore Electrostatic Interactions in Bacteriorhodopsin. Photochem. Photobiol. 1979, 30, 291.
    • (1979) Photochem. Photobiol. , vol.30 , pp. 291
    • Warshel, A.1    Ottolenghi, M.2
  • 74
    • 0021476470 scopus 로고
    • Calculations of electrostatic interactions in biological systems and in solutions
    • Warshel, A.; Russell, S.T. Calculations of Electrostatic Interactions in Biological Systems and in Solutions. Q. Rev. Biophys. 1984, 17, 283-421.
    • (1984) Q. Rev. Biophys. , vol.17 , pp. 283-421
    • Warshel, A.1    Russell, S.T.2
  • 75
    • 0000357781 scopus 로고
    • Calculations of chemical processes in solutions
    • Warshel, A. Calculations of Chemical Processes in Solutions. J. Phys. Chem. 1979, 83, 1640-1650.
    • (1979) J. Phys. Chem. , vol.83 , pp. 1640-1650
    • Warshel, A.1
  • 76
    • 36549092428 scopus 로고
    • Quantized semiclassical trajectory approach for evaluation of vibronic transitions in anharmonic molecules
    • Warshel, A.; Hwang, J.-K. Quantized Semiclassical Trajectory Approach for Evaluation of Vibronic Transitions in Anharmonic Molecules. J. Chem. Phys. 1985, 82, 1756.
    • (1985) J. Chem. Phys. , vol.82 , pp. 1756
    • Warshel, A.1    Hwang, J.-K.2
  • 77
    • 36149027699 scopus 로고
    • On the theory of the Brownian motion II
    • Wang, M.C.; Uhlenbeck, G.E. On the theory of the Brownian motion II. Rev. Mod. Phys. 1945, 17, 323-342.
    • (1945) Rev. Mod. Phys. , vol.17 , pp. 323-342
    • Wang, M.C.1    Uhlenbeck, G.E.2
  • 78
    • 0001435437 scopus 로고
    • Charge stabilization mechanism in the visual and purple membrane pigments
    • Warshel, A. Charge Stabilization Mechanism in the Visual and Purple Membrane Pigments. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 2558.
    • (1978) Proc. Natl. Acad. Sci. U.S.A. , vol.75 , pp. 2558
    • Warshel, A.1
  • 80
    • 33748878838 scopus 로고    scopus 로고
    • Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin
    • Kochendoerfer, G.G.; Mathies, R.A. Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin. J. Phys. Chem. 1996, 100, 14526-14532.
    • (1996) J. Phys. Chem. , vol.100 , pp. 14526-14532
    • Kochendoerfer, G.G.1    Mathies, R.A.2
  • 81
    • 0001149659 scopus 로고    scopus 로고
    • Femtosecond polarized pump-probe and stimulated emission spectroscopy of the isomerization reaction of rhodopsin
    • Haran, G.; Morlino, E.A.; Matthes, J.; Callender, R.H.; Hochstrasser, R.M. Femtosecond polarized pump-probe and stimulated emission spectroscopy of the isomerization reaction of rhodopsin. J. Phys. Chem. A 1999, 103, 2202-2207.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 2202-2207
    • Haran, G.1    Morlino, E.A.2    Matthes, J.3    Callender, R.H.4    Hochstrasser, R.M.5
  • 82
    • 0032475417 scopus 로고    scopus 로고
    • Primary step in bacteriorhodopsin photosynthesis: Bond stretch rather than angle twist of its retinal excited-state structure
    • Song, L.; El-Sayed, M.A. Primary step in bacteriorhodopsin photosynthesis: Bond stretch rather than angle twist of its retinal excited-state structure. J. Am. Chem. Soc. 1998, 120, 8889-8890.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 8889-8890
    • Song, L.1    El-Sayed, M.A.2
  • 84
    • 33748595259 scopus 로고    scopus 로고
    • Excited-state dynamics of a protonated retinal schiff base in solution
    • Logunov, S.; Song, L.; El-Sayed, M. Excited-state dynamics of a protonated retinal schiff base in solution. J. Phys. Chem. 1996, 100, 18586-18591.
    • (1996) J. Phys. Chem. , vol.100 , pp. 18586-18591
    • Logunov, S.1    Song, L.2    El-Sayed, M.3


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