The MP/SOFT methodology for simulations of quantum dynamics: Model study of the photoisomerization of the retinyl chromophore in visual rhodopsin

Journal of Photochemistry and Photobiology A: Chemistry

Volumn 190, Issue 2-3, 2007, Pages 274-282

  Chen, Xin ^a   Batista, Victor S ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Nonadiabatic; Photoisomerization; Quantum dynamics; Retinal; Rhodopsin; Ultrafast phenomena

Indexed keywords

EID: 34447645652     PISSN: 10106030     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jphotochem.2007.05.015     Document Type: Article

References (110)

1. X. Chen, V.S. Batista. Matching-pursuit split operator Fourier transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine. J. Chem. Phys., 125:Art. No. 124313, 2006.
2. Wald G. Molecular basis of visual excitation. Science 162 (1968) 230-239
3. Goldschmidt C.R., Ottolenghi M., and Rosenfeld T. Primary processes in photochemistry of rhodopsin at room-temperature. Nature 263 (1976) 169
4. Rosenfeld T., Honig B., Ottolenghi M., Hurley J.B., and Ebrey T.G. cis-trans isomerization in photochemistry of vision. Pure Appl. Chem. 49 (1977) 341
5. Honig B., Ebrey T.G., Callender R.H., Dinur U., and Callender R.H. Photoisomerization, energy-storage, and charge separation-model for light energy transduction in visual pigments and bacteriorhodopsin. Proc. Natl. Acad. Sci. U.S.A. 76 (1979) 2503
6. Ebrey T., and Koutalos Y. Vertebrate photoreceptors. Prog. Retin. Eye Res. 20 (2001) 49
7. Menon S.T., Han M., and Sakmar T.P. Rhodopsin: structural basis of molecular physiology. Physiol. Rev. 81 (2001) 1659
8. Sakmar T.P., Franke R.R., and Khorana H.G. Glutamic acid-113 serves as the retinylidene schiff-base counterion in bovine rhodopsin. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 8309
9. Okada T., Ernst O.P., Palczewski K., and Hofmann K.P. Activation of rhodopsin: new insights from structural and biochemical studies. Trends Biochem. Sci. 26 (2001) 318
10. Wang Q., Schoenlein R.W., Peteanu L.A., Mathies R.A., and Shank C.V. Vibrationally coherent photochemistry in the femtosecond primary event of vision. Science 266 (1994) 422
11. Kochendoerfer G.G., and Mathies R.A. Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin. J. Phys. Chem. 100 (1996) 14526
12. Schoenlein R.W., Peteanu L.A., Mathies R.A., and Shank C.V. The 1st step in vision-femtosecond isomerization of rhodopsin. Science 254 (1991) 412
13. Warshel A., and Karplus M. Calculation of π-π* excited state conformations and vibronic structure of retinal and related molecules. J. Am. Chem. Soc. 96 (1974) 5677
14. Warshel A. Bicycle-pedal model for 1st step in vision process. Nature 260 (1976) 679
15. Weiss R.M., and Warshel A. A new view of the dynamics of singlet cis-trans photoisomerization. J. Am. Chem. Soc. 101 (1979) 6131
16. Warshel A., and Barboy N. Energy-storage and reaction pathways in the 1st step of the vision process. J. Am. Chem. Soc. 104 (1982) 1469
17. Birge R.R., and Hubbard L.M. Molecular dynamics of cis-trans isomerization in rhodopsin. J. Am. Chem. Soc. 102 (1980) 2195
18. Tallent J.R., Hyde E.W., Findsen L.A., Fox G.C., and Birge R.R. Molecular dynamics of the primary photochemical event in rhodopsin. J. Am. Chem. Soc. 114 (1992) 1581
19. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., and Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289 (2000) 739
20. Teller D.C., Okada T., Behnke C.A., Palczewki K., and Stenkamp R.E. Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry 40 (2001) 7761
21. Okada T., Yoshinori Y., Silow M., Navarro J., Landau J.N., and Schichida Y. Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc. Natl. Acad. Sci. 99 (2002) 5982
22. Sugihara M., Buss V., Entel P., Elstner M., and Frauenheim T. 11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry 41 (2002) 15259
23. Sugihara M., Entel P., and Buss V. A first-principles study of 11-cis-retinal: modelling the chromophore-protein interaction in rhodopsin. Phase Transit. 75 (2002) 11
24. Rohrig U.F., Guidoni L., and Rothlisberger U. Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations. Biochemistry 41 (2002) 10799
25. Yamada A., Kakitani T., Yamamoto S., and Yamato T. A computational study on the stability of the protonated Schiff base of retinal in rhodopsin. Chem. Phys. Lett. 366 (2002) 670
26. Ferre N., and Olivucci M. Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory. J. Am. Chem. Soc. 125 (2003) 6868
27. Gascon J.A., and Batista V.S. QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophys. J. 87 (2004) 2931-2941
28. Gascon J.A., Sproviero E.M., and Batista V.S. QM/MM study of the NMR spectroscopy of the retinylidene chromophore in visual rhodopsin. J. Chem. Theor. Comput. 1 (2005) 674-685
29. Gascon J.A., Sproviero E.M., and Batista V.S. Computational studies of the primary phototransduction event in visual rhodopsin. Acc. Chem. Res. 39 (2006) 184-193
30. Coto P.B., Sinicropi A., De Vico L., Ferre N., and Olivucci M. Characterization of the conical intersection of the visual pigment rhodopsin at the CASPT2//CASSCF/AMBER level of theory. Mol. Phys. 104 (2006) 983-991
31. Olivucci M., Lami A., and Santoro F. A tiny excited-state barrier can induce a multiexponential decay of the retinal chromophore: a quantum dynamics investigation. Ang. Chem. Int. 44 (2005) 5118-5121
32. Vreven T., Bernardi F., Garavelli M., Olivucci M., Robb M.A., and Schlegel H.B. Ab initio photoisomerization dynamics of a simple retinal chromophore model. J. Am. Chem. Soc. 119 (1997) 12687
33. Garavelli M., Vreven T., Celani P., Bernardi F., Robb M.A., and Olivucci M. Photoisomerization path for a realistic retinal chromophore model: the nonatetraeniminium cation. J. Am. Chem. Soc. 120 (1998) 1285
34. Ben-Nun M., and Martinez T.J. Electronic energy funnels in cis-trans photoisomerization of retinal protonated Schiff base. J. Phys. Chem. A 102 (1998) 9607
35. La Penna G., Buda F., Bifone A., de H.J.M., and Groot. The transition state in the isomerization of rhodopsin. Chem. Phys. Lett. 294 (1998) 447
36. Garavelli M., Bernardi F., Robb M.A., and Olivucci M. The shortchain acroleini-minium and pentadieniminium cations: towards a model for retinal photoisomerization. A CASSCF/PT2 study. J. Mol. Struc. Theochem. 463 (1999) 59
37. Molteni C., Frank I., and Parrinello M. An excited state density functional theory study of the rhodopsin chromophore. J. Am. Chem. Soc. 121 (1999) 12177
38. Hahn S., and Stock G. Quantum-mechanical modeling of the femtosecond isomerization in rhodopsin. J. Phys. Chem. B 104 (2000) 1146
39. Flores S.C., and Batista V.S. Model study of coherent-control of the femtosecond primary event of vision. J. Phys. Chem. B 108 (2004) 6745-6749
40. Burghardt I., Cederbaum L.S., and Hynes J.T. Environmental effects on a conical intersection: A model study. Faraday Discuss. 127 (2004) 395-411
41. Thoss M., and Wang H.B. Quantum dynamical simulation of ultrafast molecular processes in the condensed phase. Mol. Phys. 322 (2006) 210-222
42. Lin S.M., Groesbeek M., van-der Hoef I., Verdegem P., Lugtenburg J., and Mathies R.A. Vibrational assignment of torsional normal modes of rhodops Probing excited-state isomerization dynamics along the reactive c - 11 = c - 12 torsion coordinate. J. Phys. Chem. B 102 (1998) 2787-2806
43. 2O. J. Chem. Phys. 100 (1994) 9272
44. 2 + CN reaction. Chem. Phys. Lett. 292 (1998) 46
45. 2. Faraday Discuss. 84 (1987) 359
46. Clary D.C. 4-atom reaction dynamics. J. Phys. Chem. 98 (1994) 10678
47. Kosloff R. Propagation methods for quantum molecular dynamics. Annu. Rev. Phys. Chem. 45 (1994) 145
48. 2O. J. Chem. Phys. 116 (2002) 1406
49. Echave J., and Clary D.C. Quantum-theory of planar 4-atom reactions. J. Chem. Phys. 100 (1994) 402
50. Yu H.G., and Muckerman J.T. Quantum dynamics of the photoinitiated unimolecular dissociation of HOCO. J. Chem. Phys. 117 (2002) 11139
51. 2 + H reaction. J. Chem. Phys. 101 (1994) 2779
52. Charlo D., and Clary D.C. Quantum-mechanical calculations on termolecular association reactions XY + Z + M → XYZ + M: application to ozone formation. J. Chem. Phys. 117 (2002) 1660
53. Bowman J.M. Resonances: bridge between spectroscopy and dynamics. J. Phys. Chem. A 102 (1998) 3006
54. Xie D.Q., Chen R.Q., and Guo H. Comparison of Chebyshev, Faber, and Lanczos propagation-based methods for calculating resonances. J. Chem. Phys. 112 (2000) 5263
55. Anderson S.M., Park T.J., and Neuhauser D. Local propagating Gaussians: flexible vs. frozen widths. Phys. Chem. Chem. Phys. 1 (1999) 1343
56. Feit M.D., Fleck Jr. J.A., and Steiger A. Solution of the Schrödinger-equation by a spectral method. J. Comput. Phys. 47 (1982) 412
57. Feit M.D., Fleck Jr. J.A., and Steiger A. Solution of the Schrödinger equation by a spectral method. II. Vibrational energy levels of triatomic molecules. J. Chem. Phys. 78 (1983) 301
58. Kosloff D., and Kosloff R. A Fourier method solution for the time-dependent Schrödinger-equation as a tool in molecular-dynamics. J. Comput. Phys. 52 (1983) 35
59. Tal-Ezer H., and Kosloff R. An accurate and efficient scheme for propagating the time-dependent Schrödinger equation. J. Chem. Phys. 81 (1984) 3967-3971
60. Park T.J., and Light J.C. Unitary quantum time evolution by iterative Lanczos reduction. J. Chem. Phys. 85 (1986) 5870-5876
61. + system. J. Chem. Phys. 54 (1971) 4297
62. Tully J.C. Molecular dynamics with electronic transitions. J. Chem. Phys. 93 (1990) 1061
63. Gerber R.B., Buch V., and Ratner M.A. Time-dependent self-consistent field approximation for intramolecular energy transfer. 1. Formulation and application to dissociation and Van-der-Waals molecules. J. Chem. Phys. 77 (1982) 3022-3030
64. Meyer H.D., and Miller W.H. A classical analog for electronic degrees of freedom in non-adiabatic collision processes. J. Chem. Phys. 70 (1979) 3214-3223
65. Sun X., and Miller W.H. Semiclassical initial value representation for electronically non-adiabatic molecular dynamics. J. Chem. Phys. 106 (1997) 6346-6353
66. Thoss M., and Stock G. Mapping approach to the semiclassical description of non-adiabatic quantum dynamics. Phys. Rev. A 59 (1999) 64
67. Herman M.F., and Kluk E. A semiclassical justification for the use of non-spreading wavepackets in dynamics calculations. Chem. Phys. 91 (1984) 27
68. Kluk E., Herman M.F., and Davis H.L. Comparison of the propagation of semiclassical frozen Gaussian wave-functions with quantum propagation for a highly excited anharmonic-oscillator. J. Chem. Phys. 84 (1986) 326-334
69. Yang G., and Herman M.F. Semiclassical surface hopping h-k propagator: application to two-dimensional, two-surface problems. J. Phys. Chem. B 105 (2001) 6562
70. Webster F., Rossky P.J., and Friesner R.A. Nonadiabatic processes in condensed matter: semi-classical theory and implementation. Comput. Phys. Commun. 63 (1991) 494
71. Prezhdo O.V., and Rossky P.J. Mean-field molecular dynamics with surface hopping. J. Chem. Phys. 107 (1997) 825
72. Coker D.F. Computer simulation of nonadiabatic dynamics in condensed systems. In: Allen M.P., and Tildesley D.J. (Eds). Computer Simulation in Chemical Physics (1993), Kluwer Academic Publishers, Dordrecht 315-377
73. Hammes-Schiffer S. Multiconfigurational molecular-dynamics with quantum transitions: multiple proton-transfer reactions. J. Chem. Phys. 105 (1996) 2236
74. Hammes-Schiffer S., and Tully J.C. Nonadiabatic infrequent events. J. Chem. Phys. 103 (1995) 8528
75. Makri N., and Miller W.H. A semiclassical tunneling model for use in classical trajectory simulations. J. Chem. Phys. 91 (1989) 4026
76. 2 electronic state using a realistic 24-mode model Hamiltonian. J. Chem. Phys. 110 (1999) 936-946
77. Thoss M., Miller W.H., and Stock G. Semiclassical description of nonadiabatic quantum dynamics: application to the S1-S2 conical intersection in pyrazine. J. Chem. Phys. 112 (2000) 10282-10292
78. Ben-Nun M., and Martinez T.J. Nonadiabatic molecular dynamics validation of the multiple spawning method for a multi-dimensional problem. J. Chem. Phys. 108 (1998) 7244
79. Ben-Nun M., and Martinez T.J. Ab initio quantum molecular dynamics. Adv. Chem. Phys. 121 (2002) 439
80. Coletti C., and Billing G.D. Quantum dressed classical mechanics: application to the photo-absorption of pyrazine. Chem. Phys. Lett. 368 (2003) 289-298
81. Shalashilin D.V., and Child M.S. Real time quantum propagation on a Monte Carlo trajectory guided grids of coupled coherent states: 26d simulation of pyrazine absorption spectrum. J. Chem. Phys. 121 (2004) 3563-3568
82. Wu Y., and Batista V.S. Matching pursuit for simulations of quantum processes. J. Chem. Phys. 118 (2003) 6720
83. Wu Y., and Batista V.S. Erratum: Matching pursuit for simulations of quantum processes [J. Chem. Phys.118, 6720, 2003], by yinghua wu and victor s. batista. J. Chem. Phys. 119 (2003) 7606
84. Wu Y., and Batista V.S. Quantum tunneling dynamics in multidimensional systems: a matching-pursuit description. J. Chem. Phys. 121 (2004) 1676
85. Chen X., Wu Y., and Batista V.S. Matching-pursuit split operator Fourier transform computations of thermal correlation functions. J. Chem. Phys. 122 (2005) 64102
86. Wu Y., Herman M.F., and Batista V.S. Matching-pursuit split operator Fourier transform simulations of nonadiabatic quantum dynamics. J. Chem. Phys. 122 (2005) 114114
87. Wu Y., and Batista V.S. Matching pursuit split operator Fourier transform simulations of excited-state intramolecular proton transfer in 2-(2′-hydroxyphenyl)-oxazole. J. Chem. Phys. 124 (2006) Art. No. 224305
88. Press W.H., Flannery B.P., Teukolsky S.A., and Vetterling W.T. In Numerical Recipes (1986), Cambridge University Press, Cambridge (Chapter 12)
89. Burghardt I., Meyer H.D., and Cederbaum L.S. Approaches to the approximate treatment of complex molecular systems by the multiconfiguration time-dependent hartree method. J. Chem. Phys. 111 (1999) 2927-2939
90. Beck M.H., Jackle A., Worth G.A., and Meyer H.D. The multiconfiguration time-dependent Hartree (MCTDH) method: a highly efficient algorithm for propagating wavepackets. Phys. Rep. Rev. Sec. Phys. Lett. 324 (2000) 1
91. Heller E.J. Wavepacket path integral formation of semiclassical dynamics. Chem. Phys. Lett. 34 (1975) 321-325
92. Davis M.J., and Heller E.J. Semi-classical Gaussian-basis set method for molecular vibrational wave-functions. J. Chem. Phys. 71 (1979) 3383
93. Heller E.J. Frozen Gaussians: a very simple semiclassical approximation. J. Chem. Phys. 75 (1981) 2923-2931
94. Coalson R.D., and Karplus M. Extended wave packet dynamics; exact solution for collinear atom, diatomic molecule scattering. Chem. Phys. Lett. 90 (1982) 301
95. Sawada S.I., Heather R., Jackson B., and Metiu H. A strategy for time-dependent quantum-mechanical calculations using a Gaussian wave packet representation of the wave-function. Chem. Phys. Lett. 83 (1985) 3009
96. Kay K.G. Improved semiclassical propagation of wave packets. J. Chem. Phys. 91 (1989) 107
97. Thompson K., and Martinez T.J. Ab initio/interpolated quantum dynamics on coupled electronic states with full configuration interaction wavefunctions. J. Chem. Phys. 110 (1999) 1376
98. Coe J.D., and Martinez T.J. Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer. J. Am. Chem. Soc. 127 (2005) 4560-4561
99. Coe J.D., and Martinez T.J. Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde. J. Chem. Phys. 110 (2006) 618-630
100. Shalashilin D.V., and Jackson B. Initial value representation for the classical propagator and S-matrix with the help of coherent states. Chem. Phys. Lett. 291 (1998) 143
101. Andersson L.M. Quantum dynamics using a discretized coherent state representation: an adaptive phase space method. J. Chem. Phys. 115 (2001) 1158-1165
102. Shalashilin D.V., and Child M.S. Time dependent quantum propagation in phase space. J. Chem. Phys. 113 (2000) 10028
103. Shalashilin D.V., and Child M.S. Multidimensional quantum propagation with the help of coupled coherent states. J. Chem. Phys. 115 (2001) 5367
104. Worth G.A., and Burghardt I. Full quantum mechanical molecular dynamics using Gaussian wavepackets. Chem. Phys. Lett. 368 (2003) 502-508
105. Worth G.A., Robb M.A., and Burghardt I. A novel algorithm for non-adiabatic direct dynamics using variational Gaussian wavepackets. Faraday Discuss. 127 (2004) 307-323
106. Mallat S.G., and Zhang Z.F. Matching pursuits with time-frequency dictionaries. IEEE T. Signal Process. 41 (1993) 3397
107. http://www-unix.mcs.anl.gov/mpi/http://www-unix.mcs.anl.gov/mpi/tutorial/gropp/talk.html.
108. Seidner L., and Domcke W. Microscopic modelling of photoisomerization and internal-conversion dynamics. Chem. Phys. 186 (1994) 27-40
109. Seidner L., Stock G., and Domcke W. Nonperturbative approach to femtosecond spectroscopy: general theory and application to multidimensional nonadiabatic photoisomerization processes. J. Chem. Phys. 103 (1995) 3998-4011
110. Hahn S., and Stock G. Femtosecond secondary emission arising from the nonadiabatic photoisomerization in rhodopsin. Chem. Phys. 259 297 (2000)