Using the computer to understand the chemistry of conical intersections

Photochemical and Photobiological Sciences

Volumn 10, Issue 6, 2011, Pages 867-886

  Schapiro, Igor ^a   Melaccio, Federico ^a,b   Laricheva, Elena N ^a   Olivucci, Massimo ^a,b  

^a BOWLING GREEN STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SIENA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79958064739     PISSN: 1474905X     EISSN: 14749092     Source Type: Journal    
DOI: 10.1039/c0pp00290a     Document Type: Review

References (182)

1. M. Venturi, V. Balzani and M. T. Gandolfi, Fuels from solar energy, Proceedings of the 2005 Solar World Congress, 2005
2. P. Hamm S. M. Ohline W. Zinth Vibrational cooling after ultrafast photoisomerization of azobenzene measured by femtosecond infrared spectroscopy J. Chem. Phys. 1997 106 519
3. M. Rini A. Kummrow J. Dreyer E. T. J. Nibbering T. Elsaesser Femtosecond mid-infrared spectroscopy of condensed phase hydrogen-bonded systems as a probe of structural dynamics Faraday Discuss. 2003 122 27
4. Nobel Lectures, Chemistry 1963-1970, Elsevier Publishing Company, 1972
5. H. Kandori Y. Shichida T. Yoshizawa Photoisomerization in Rhodopsin Biochemistry (Moscow) 2001 66 1197
6. R. N. Day M. W. Davidson The fluorescent protein palette: tools for cellular imaging Chem. Soc. Rev. 2009 38 2887
7. A. Sinicropi E. Martin M. Ryasantsev J. Helbing J. Briand D. Sharma J. Léonard S. Haacke A. Cannizzo M. Chergui V. Zanirato S. Fusi F. Santoro R. Basosi N. Ferré M. Olivucci An Artificial Molecular Switch that Mimics the Visual Pigment and Completes its Photocycle in Picoseconds Proc. Natl. Acad. Sci. U. S. A. 2008 105 17642
8. A. Melloni R. Rossi Paccani D. Donati V. Zanirato A. Sinicropi M. L. Parisi E. Martin M. Ryazantsev W. J. Ding L. M. Frutos R. Basosi S. Fusi L. Latterini N. Ferré M. Olivucci Modeling, Preparation and Characterization of a Dipole Moment Switch Driven by Z/E Photoisomerization J. Am. Chem. Soc. 2010 132 9310
9. F. Bernardi M. Olivucci M. A. Robb Potential energy surface crossings in organic photochemistry Chem. Soc. Rev. 1996 25 321
10. F. Bernardi M. Olivucci J. Michl M. A. Robb Conical Intersections in the Theory of Organic Singlet Photochemistry The Spectrum 1996 9 1
11. F. Bernardi M. Olivucci M. A. Robb The role of conical intersections and excited state reaction paths in photochemical pericyclic reactions J. Photochem. Photobiol., A 1997 105 365
12. M. Garavelli F. Bernardi M. Olivucci T. Vreven S. Klein P. Celani M. A. Robb Potential-energy surfaces for ultrafast photochemistry - Static and dynamic aspects Faraday Discuss. 1998 110 51
13. M. Garavelli F. Bernardi M. A. Robb M. Olivucci The short-chain acroleiniminium and pentadieniminium cations: towards a model for retinal photoisomerization. A CASSCF/PT2 study THEOCHEM 1999 463 59
14. M. A. Robb, M. Garavelli, M. Olivucci and F. Bernardi, in Reviews in Computational Chemistry, Wiley-Vch, Inc, New York, 2000, pp. 87-46
15. M. Olivucci and A. Sinicropi, in Computational Chemistry, Elsevier, 2005
16. D. G. Truhlar M. S. Gordon From Force Fields to Dynamics: Classical and Quantal Paths Science 1990 249 491
17. K. F. Freed Radiationless transitions in molecules Acc. Chem. Res. 1978 11 74
18. G. J. Atchity S. S. Xantheas K. Ruedenberg Potential-energy surfaces near intersections J. Chem. Phys. 1991 95 1862
19. D. R. Yarkony Diabolical conical intersections Rev. Mod. Phys. 1996 68 985
20. 2 photochemical reactions of benzene J. Am. Chem. Soc. 1993 115 673
21. R. S. Minns D. S. Parker T. J. Penfold G. A. Worth H. H. Fielding Competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene Phys. Chem. Chem. Phys. 2010 12 15607
22. A. Migani and M. Olivucci, in Conical Intersections: Electronic Structure, Dynamics and Spectroscopy, ed., W. Domcke, D. R. Yarkony, and, H. Köppel, World Scientific, Singapore, 2004, pp. 271-20
23. M. J. Bearpark M. A. Robb H. B. Schlegel A direct method for the location of the lowest energy point on a potential surface crossing Chem. Phys. Lett. 1994 223 269
24. N. Koga K. Morokuma Determination of the lowest energy point on the crossing seam between two potential surfaces using the energy gradient Chem. Phys. Lett. 1985 119 371
25. M. R. Manaa D. R. Yarkony On the intersection of potential energy surfaces of the same symmetry: Systematic characterization using a Lagrange multiplier constrained procedure J. Chem. Phys. 1993 99 5251
26. J. M. Anglada J. M. Bofill A reduced-restricted-quasi-Newton-Raphson method for locating and optimizing energy crossing points between two potential energy surfaces J. Comput. Chem. 1997 18 992
27. F. Sicilia L. Blancafort M. J. Bearpark M. A. Robb New Algorithms for Optimizing and Linking Conical Intersection Points J. Chem. Theory Comput. 2008 4 257
28. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.,. J. A. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N. J. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Gaussian, Inc., Wallingford, CT, 2009
29. F. Aquilante L. De Vico N. Ferré G. Ghigo P. A. Malmqvist P. Neogrady T. B. Pedersen M. Pitonak M. Reiher B. O. Roos L. Serrano-Andres M. Urban V. Veryazov R. Lindh MOLCAS 7: The Next Generation J. Comput. Chem. 2010 31 224
30. M. S. Gordon, M. W. Schmidt, Advances in electronic structure theory GAMESS a decade later, in Theory and Applications of Computational Chemistry: The First Forty Years, ed., C. E. Dykstra, G. Frenking, K. S. Kim, and, G. E. Scuseria, Elsevier, Amsterdam, 2005, pp. 1167-1189
31. H. Lischka, R. Shepard, I. Shavitt, R. M. Pitzer, M. Dallos, T. Müller, P. G. Szalay, F. B. Brown, R. Ahlrichs, H. J. Böhm, A. Chang, D. C. Comeau, R. Gdanitz, H. Dachsel, C. Ehrhardt, M. Ernzerhof, P. Höchtl, S. Irle, G. Kedziora, T. Kovar, V. Parasuk, M. J. M. Pepper, P. Scharf, H. Schiffer, M. Schindler, M. Schüler, M. Seth, E. A. Stahlberg, J. - Zhao, S. Yabushita, Z. Zhang, M. Barbatti, S. Matsika, M. Schuurmann, D. R. Yarkony, S. R. Brozell and J. - Blaudeau, Columbus, an ab initio electronic structure program, release 5.9.1, 2006
32. A. A. Granovsky, Firefly version 7.1.G, http://classic.chem.msu.su/gran/ firefly/index.html
33. L. M. Frutos T. Andruniów F. Santoro N. Ferré M. Olivucci Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry Proc. Natl. Acad. Sci. U. S. A. 2007 104 7764
34. J. C. Tully R. K. Preston Trajectory surface hopping approach to nonadiabatic molecular collisions: the reaction of H+ with D2 J. Chem. Phys. 1971 55 562
35. J. C. Tully Molecular dynamics with electronic transitions J. Chem. Phys. 1990 93 1061
36. B. R. Smith M. J. Bearpark M. A. Robb F. Bernardi M. Olivucci 'Classical wavepacket dynamics through a conical intersection. Application to the S1/S0 photochemistry of benzene Chem. Phys. Lett. 1995 242 27
37. G. A. Worth M. A. Robb B. Lasorne Solving the time-dependent Schrödinger equation for nuclear motion in one step: direct dynamics of non-adiabatic systems Mol. Phys. 2008 106 2077
38. W. H. Miller Electronically Nonadiabatic Dynamics via Semiclassical Initial Value Methods J. Phys. Chem. A. 2009 114 1405
39. C. Gonzalez H. B. Schlegel Improved algorithms for reaction path following: Higher-order implicit algorithms J. Chem. Phys. 1991 95 5853
40. F. Jolibois M. J. Bearpark M. A. Robb Potential energy surfaces and dynamical behavior of two rigidly linked bichromophoric molecules studied by CASSCF computations and ab initio classical trajectory simulations J. Phys. Chem. A 2002 106 4358
41. B. G. Levine T. J. Martínez Isomerization through conical intersections Annu. Rev. Phys. Chem. 2007 58 613
42. M. Ruckenbauer M. Barbatti T. Muller H. Lischka Nonadiabatic Excited-State Dynamics with Hybrid ab Initio Quantum-Mechanical/Molecular- Mechanical Methods: Solvation of the Pentadieniminium Cation in Apolar Media J. Phys. Chem. A 2010 114 6757
43. O. Weingart A. Migani M. Olivucci M. A. Robb V. Buss P. Hunt Probing the Photochemical Funnel of a Retinal Chromophore Model via Zero-Point Energy Sampling Semiclassical Dynamics J. Phys. Chem. A 2004 108 4685
44. O. Weingart I. Schapiro V. Buss Photochemistry of Visual Pigment Chromophore Models by Ab Initio Molecular Dynamics J. Phys. Chem. B 2007 111 3782
45. M. Boggio-Pasqua M. Ravaglia M. J. Bearpark M. Garavelli M. A. Robb Can diarylethene photochromism be explained by a reaction path alone? A CASSCF study with model MMVB dynamics J. Phys. Chem. A 2003 107 11139
46. M. Ben-Nun T. J. Martínez Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene Chem. Phys. Lett. 1998 298 57
47. M. Garavelli F. Bernardi M. Olivucci M. J. Bearpark S. Klein M. A. Robb Product distribution in the photolysis of s-cis butadiene: A dynamics simulation J. Phys. Chem. A 2001 105 11496
48. S. Hayashi E. Tajkhorshid K. Schulten Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore Biophys. J. 2003 85 1440
49. S. Hayashi E. Taikhorshid K. Schulten Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation Biophys. J. 2009 96 403
50. T. J. Martínez R. D. Levine First-principles molecular dynamics on multiple electronic states: A case study of NaI J. Chem. Phys. 1996 105 6334
51. A. L. Kaledin J. Seong K. Morokuma Predominance of nonequilibrium dynamics in the photodissociation of ketene in the triplet state, J. Phys. Chem. A 2001 105 2731
52. A. M. Virshup C. Punwong T. V. Pogorelov B. A. Lindquist C. Ko T. J. Martínez Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics J. Phys. Chem. B 2009 113 3280
53. G. Zechmann M. Barbatti H. Lischka J. Pittner V. Bonaić- Koutecký Multiple pathways in the photodynamics of a polar [pi]-bond: A case study of silaethylene Chem. Phys. Lett. 2006 418 377
54. D. Polli P. Altoè O. Weingart K. M. Spillane C. Manzoni D. Brida G. Tomasello P. Kukura R. Mathies M. Garavelli G. Cerullo Conical Intersection Dynamics of the Primary Photoisomerization Event in Vision Nature 2010 467 440
55. K. Drukker Basics of Surface Hopping in Mixed Quantum/Classical Simulations J. Comput. Phys. 1999 153 225
56. J. R. Schmidt P. V. Parandekar J. C. Tully Mixed quantum-classical equilibrium: Surface hopping J. Chem. Phys. 2008 129 6
57. W. T. A. M. Van der Lugt L. J. Oosterhoff Symmetry control and photoinduced reactions J. Am. Chem. Soc. 1969 91 6042
58. D. Grimbert G. Segal A. Devaquet Ab initio SCF study of the photochemical disrotatory closure of butadiene to cyclobutene J. Am. Chem. Soc. 1975 97 6629
59. P. Celani M. Garavelli S. Ottani F. Bernardi M. A. Robb M. Olivucci Molecular "Trigger" for the Radiationless Deactivation of Photoexcited Conjugated Hydrocarbons J. Am. Chem. Soc. 1995 117 11584
60. K. R. Naqvi On the non-crossing rule for potential energy surfaces of polyatomic molecules Chem. Phys. Lett. 1972 15 634
61. A. Gilbert and J. Baggott, Essentials of Molecular Photochemistry, CRC Press, 1991
62. N. J. Turro, Modern Molecular Photochemistry, University Science Books, 1991
63. L. R. Khundkar A. H. Zewail Ultrafast Molecular Reaction Dynamics in Real-Time: Progress Over a Decade Annu. Rev. Phys. Chem. 1990 41 15
64. A. H. Zewail Femtochemistry: Atomic-Scale Dynamics of the Chemical bond using ultrafast lasers - (Nobel lecture) Angew. Chem. Int. Ed. Engl. 2000 39 2587
65. M. Bixon J. Jortner Intramolecular Radiationless Transitions J. Chem. Phys. 1968 48 715
66. W. M. Gelbart K. F. Freed S. A. Rice Internal Rotation and the Breakdown of the Adiabatic Approximation: Many-Phonon Radiationless Transitions J. Chem. Phys. 1970 52 2460
67. H. E. Zimmerman Molecular Orbital Correlation Diagrams, Mobius Systems, and Factors Controlling Ground- and Excited-State Reactions. II J. Am. Chem. Soc. 1966 88 1566
68. J. Michl Mol. Photochem. 1972 4 243
69. L. Salem Surface crossings and surface touchings in photochemistry J. Am. Chem. Soc. 1974 96 3486
70. J. von Neumann E. P. Wigner Eigenwerte bei adiabatischen prozessen Phys. Z. 1929 30 465
71. E. Teller The Crossing of Potential Surfaces J. Phys. Chem. 1937 41 109
72. G. Herzberg H. C. Longuet-Higgins Intersection of potential energy surfaces in polyatomic molecules Discuss. Faraday Soc. 1963 35 77
73. E. Teller Internal Conversion In Polyatomic Molecules Isr. J. Chem. 1969 7 227
74. P. Celani F. Bernardi M. Olivucci M. A. Robb Excited-state reaction pathways for s-cis buta-1, 3-diene J. Chem. Phys. 1995 102 5733
75. M. Garavelli F. Ruggeri F. Ogliaro M. J. Bearpark F. Bernardi M. Olivucci M. A. Robb A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s-cis butadiene J. Comput. Chem. 2003 24 1357
76. P.-O. Löwdin Quantum Theory of Many-Particle Systems. III. Extension, of the Hartree-Fock Scheme to Include Degenerate Systems and Correlation Effects Phys. Rev. 1955 97 1509
77. K. Ruedenberg and K. Sundberg, in Quantum Science, ed., J. L. Calais, O. Goscinski, J. Linderberg, and, Y. Öhrn, Plenum Publ. Co., New York, 1976, pp. 505-15
78. 2 J. Am. Chem. Soc. 1983 105 1459
79. F. Bernardi S. De M. Olivucci M. A. Robb The mechanism of ground-state-forbidden photochemical pericyclic reactions: evidence for real conical intersections J. Am. Chem. Soc. 1990 112 1737
80. E. Runge E. K. U. Gross Density-Functional Theory for Time-Dependent Systems Phys. Rev. Lett. 1984 52 997
81. E. Tapavicza I. Tavernelli U. Rothlisberger C. Filippi M. E. Casida Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry J. Chem. Phys. 2008 129 19
82. E. J. Baerends G. Ricciardi A. Rosa S. J. A. van Gisbergen A DFT/TDDFT interpretation of the ground and excited states of porphyrin and porphyrazine complexes Coord. Chem. Rev. 2002 230 5
83. O. Cramariuc T. I. Hukka T. T. Rantala H. Lemmetyinen TD-DFT Description of Photoabsorption and Electron Transfer in a Covalently Bonded Porphyrin-Fullerene Dyad J. Phys. Chem. A 2006 110 12470
84. K. A. Nguyen R. Pachter Ground state electronic structures and spectra of zinc complexes of porphyrin, tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study J. Chem. Phys. 2001 114 10757
85. B. G. Levine C. Ko J. Quenneville T. J. Martínez Conical intersections and double excitations in time-dependent density functional theory Mol. Phys. 2006 104 1039
86. K. Andersson P. A. Malmqvist B. O. Roos A. J. Sadlej K. Wolinski Second-order perturbation theory with a CASSCF reference function J. Phys. Chem. 1990 94 5483
87. V. Bonaić-Koutecký On Avoided Crossings Between Molecular Excited States; Photochemical Implications Pure Appl. Chem. 1988 55 213
88. V. Bonaić-Koutecký J. Köhler J. Michl Prediction of structural and environmental effects on the S1 - S0 energy gap and jump probability in double-bond cis-trans photoisomeriz Chem. Phys. Lett. 1984 104 440
89. V. Bonaić-Koutecký J. Michl Photochemical syn-anti Isomerization of a Schiff Base: A two-dimensional Description of a Conical Intersection in Formaldimine Theor. Chim. Acta 1985 68 45
90. 1, and proton translocation - Their role in photochemistry, photophysics, and vision Angew. Chem., Int. Ed. Engl. 1987 26 170
91. V. Bonaić-Koutecký K. Schöffel J. Michl Critically heterosymmetric biradicaloid geometries of of protonated Schiff bases Theor. Chim. Acta 1987 72 459
92. J. Michl and V. Bonaić-Koutecký, Electronic Aspects of Organic Photochemistry, J. Wiley, and Sons inc., New York, 1990
93. S. Xantheas S. T. Elbert K. Ruedenberg An Intersection Seam Between Ground-State of Ozone and an Excited-State of Like Symmetry J. Chem. Phys. 1990 93 7519
94. S. Xantheas S. T. Elbert K. Ruedenberg The Ring-Opening of Cyclopropilidene to Allene - Key Features of the Accurate Reaction Surface Theor. Chim. Acta 1991 78 365
95. G. J. Atchity K. Ruedenberg A. Nanayakkara The intersection seam between the 1(1)A' and 2(1)A' states of ozone Theor. Chim. Acta 1997 96 195
96. F. Molnar M. Ben-Nun T. J. Martinez K. Schulten Characterization of a conical intersection between the ground and first excited state for a retinal analog THEOCHEM 2000 506 169
97. L. Seidner G. Stock A. L. Sobolewski W. Domcke Ab initio Characterization of the S1-S2 Conical Intersection in Pyrazine and Calculation of Spectra J. Chem. Phys. 1992 96 5298
98. A. L. Sobolewski C. Woywod W. Domcke Ab initio investigation of Potential-energy Surfaces Involved in the Photophysics of Benzene and Pyrazine J. Chem. Phys. 1993 98 5627
99. C. Woywod W. Domcke A. L. Sobolewski H. J. Werner Characterization of the S1-S2 Conical Intersection in Pyrazine Using ab initio Multiconfigurational Self-Consistent-Field and Multireference Configuration-Interaction Methods J. Chem. Phys. 1994 100 1400
100. C. Woywod M. Stengle W. Domcke H. Flothmann R. Schinke Photodissociation of ozone in the Chappuis band.1. Electronic structure calculations J. Chem. Phys. 1997 107 7282
101. A. L. Sobolewski W. Domcke Ab initio investigations on the photophysics of indole Chem. Phys. Lett. 1999 315 293
102. A. L. Sobolewski W. Domcke Conical intersections induced by repulsive (1)pi sigma* states in planar organic molecules: malonaldehyde, pyrrole and chlorobenzene as photochemical model systems Chem. Phys. 2000 259 181
103. H. Muller H. Köppel L. S. Cederbaum Topology and Dynamics of Vibrationally Coupled Potential-Energy Surface. General-Aspects and Applications to the Ozone Cation New J. Chem. 1993 17 7
104. S. Mahapatra H. Köppel L. S. Cederbaum Impact of nonadiabatic coupling between the conically intersecting (X)over-tilde(2)A(1) and (A)over-tilde(2)B(2) states of NO2 on the negative ion photoelectron spectra of NO2 J. Chem. Phys. 1999 110 5691
105. D. R. Yarkony On the Role of Conical Intersections of Two Potential-Energy Surfaces of the Same Symmetry in Photodissociation.1. CH3SH->CH3S+H and CH3+SH J. Chem. Phys. 1994 100 3639
106. M. R. Manaa D. R. Yarkony On the Role of Conical Intersections of Two Potential energy surfaces of the Same Symmetry in Photodissociation. 2. CH3SCH3->CH3S+CH3 J. Am. Chem. Soc. 1994 116 11444
107. H. Hettema D. R. Yarkony On the Role of Conical Intersections in Photodissociation.3. The Case of Hydroxylamine J. Chem. Phys. 1995 102 8431
108. M. Doscher H. Köppel Multiple surface intersections and strong nonadiabatic coupling effects between the (D)over-tilde(2)E(1u) and (E)over-tilde(2)B(2u) states of C6H6+ Chem. Phys. 1997 225 93
109. D. R. Yarkony S1-S0 internal conversion in ketene. 1. The role of conical intersections J. Phys. Chem. A 1999 103 6658
110. J. Dreyer M. Klessinger Excited-States and Photochemical Reactivity of Fulvene - A Theoretical-Study J. Chem. Phys. 1994 101 10655
111. J. Bentzien M. Klessinger Theoretical Investigations on the Regiochemistry and Stereochemistry of the Photochemical [2+2]-Cycloaddition of Propene J. Org. Chem. 1994 59 4887
112. J. Dreyer M. Klessinger The photochemical formation of fulvene from benzene via prefulvene - A theoretical study Chem.-Eur. J. 1996 2 335
113. H. M. Steuhl C. Bornemann M. Klessinger The mechanism of the photochemical hydrogen migration in 1,3,5-cycloheptatriene: A theoretical study Chem.-Eur. J. 1999 5 2404
114. I. N. Ragazos M. A. Robb F. Bernardi M. Olivucci Optimization and characterization of the lowest energy point on a conical intersection using an MC-SCF Lagrangian Chem. Phys. Lett. 1992 197 217
115. S. Matsika D. R. Yarkony Conical Intersections of Three Electronic States Affect the Ground State of Radical Species with Little or No Symmetry: Pyrazolyl J. Am. Chem. Soc. 2003 125 12428
116. B. G. Levine J. D. Coe T. J. Martinez Optimizing Conical Intersections without Derivative Coupling Vectors: Application to Multistate Multireference Second-Order Perturbation Theory (MS-CASPT2) J. Phys. Chem. B 2007 112 405
117. S. Maeda K. Ohno K. Morokuma Updated Branching Plane for Finding Conical Intersections without Coupling Derivative Vectors J. Chem. Theory Comput. 2010 6 1538
118. M. Klessinger Conical Intersections and the Mechanism of Singlet Photoreactions Angew. Chem., Int. Ed. Engl. 1995 34 549
119. 2 Pathways for the Cyclohexadiene/Hexatriene Photochemical Interconversion J. Phys. Chem. 1996 100 19364
120. F. Bernardi M. Olivucci M. A. Robb G. Tonachini Can a photochemical reaction be concerted? A theoretical study of the photochemical sigmatropic rearrangement of but-1-ene J. Am. Chem. Soc. 1992 114 5805
121. M. Garavelli P. Celani M. Fato M. J. Bearpark B. R. Smith M. Olivucci M. A. Robb Relaxation Paths from a Conical Intersection: The Mechanism of Product Formation in the Cyclohexadiene/Hexatriene Photochemical Interconversion J. Phys. Chem. A 1997 101 2023
122. A. Migani A. Sinicropi N. Ferré A. Cembran M. Garavelli M. Olivucci Structure of the intersection space associated with Z/E photoisomerization of retinal in rhodopsin proteins Faraday Discuss. 2004 127 179
123. C. Sannen G. Raeev C. Galloy G. Fauville J. C. Lorquet Unimolecular decay paths of electronically excited species. II. The, C2H4+ ion J. Chem. Phys. 1981 74 2402
124. H. Köppel L. S. Cederbaum W. Domcke Strong nonadiabatic effects and conical intersections in molecular spectroscopy and unimolecular decay: C2H4+ J. Chem. Phys. 1982 77 2014
125. H. Köppel L. S. Cederbaum W. Domcke S. S. Shaik Symmetry Breaking and Non-Born-Oppenheimer Effects in Radical Cations Angew. Chem., Int. Ed. Engl. 1983 22 210
126. H. Köppel L. S. Cederbaum W. Domcke Interplay of Jahn-Teller and pseudo-Jahn-Teller vibronic dynamics in the benzene cation J. Chem. Phys. 1988 89 2023
127. H. Köppel M. Döscher I. Bâldea H. D. Meyer P. G. Szalay Multistate vibronic interactions in the benzene radical cation. II. Quantum, dynamical simulations J. Chem. Phys. 2002 117 2657 (Pubitemid 34945453)
128. I. Bäldea J. Franz H. Köppel Jahn-Teller and related conical intersections in the benzene radical cation and the monofluoro derivate J. Mol. Struct. (THEOCHEM) 2007 838 94
129. T. Bally S. Matzinger P. Bednarek The Dewar benzene radical cation and its ring-opening reaction. J. Am. Chem. Soc. 2006 128 7828
130. V. Hrouda T. Bally P. Carsky P. Jungwirth The C4H4+ Potential Energy Surface. 2. The Jahn- Teller Stabilization of Ionized Tetrahedrane and Its Rearrangement to Cyclobutadiene Radical Cation J. Phys. Chem. A 1997 101 3918
131. E. Laricheva, M. Olivucci, J. Grilj and E. Vauthey, The Fluorescence of the Wurster's Blue Radical Cation is Controlled by a Conical Intersection, 64th International Symposium On Molecular Spectroscopy, 2009
132. J. Grilj E. N. Laricheva M. Olivucci E. Vauthey Fluorescence of Radical Ions in Liquid Solution: A Case Study Angew. Chem., Int. Ed.
133. A. C. Albrecht W. T. Simpson Spectroscopic study of Wurster's Blue and tetramethyl-p-phenylenediamine with assignments of electronic transitions J. Am. Chem. Soc. 1955 77 4454
134. K. H. Hausser Reinterpretation of Wursters Blue ESR Spectrum Mol. Phys. 1964 7 195
135. Z. R. Grabowski K. Rotkiewicz A. Siemiarczuk D. J. Cowley W. Baumann Twisted Intramolecular Charge Transfer States (TICT)-New Class Of Excited-States With A Full Charge Separation New J. Chem. 1979 3 443
136. Z. R. Grabowski J. Dobkowski Twisted intramolecular charge transfer (tict) excited states: energy and molecular structure Pure Appl. Chem. 1988 55 245
137. M. Garavelli P. Celani F. Bernardi M. A. Robb M. Olivucci The C5H6NH2+ Protonated Shiff Base: An ab Initio Minimal Model for Retinal Photoisomerization J. Am. Chem. Soc. 1997 119 6891
138. D. S. Ruiz A. Cembran M. Garavelli M. Olivucci W. Fuss Structure of the conical intersections driving the cis-trans photoisomerization of conjugated molecules Photochem. Photobiol. 2002 76 622
139. M. Olivucci F. Santoro Chemical selectivity through control of excited-state dynamics Angew. Chem., Int. Ed. 2008 47 6322
140. U. Manthe H. Köppel Dynamics on potential energy surfaces with a conical intersection - Adiabatic, intermediate, and diabatic behavior J. Chem. Phys. 1990 93 1658
141. W. Siebrand Radiationless Transitions in Polyatomic Molecules. I. Calculation, of Franck-Condon Factors J. Chem. Phys. 1967 46 440
142. M. Bixon J. Jortner Radiationless Transitions in Polyatomic Molecules Isr. J. Chem. 1969 7 189
143. G. W. Robinson C. A. Langhoff Theory of radiationless transitions in polyatomic molecules. The intermediate case Chem. Phys. 1974 5 1
144. H. M. Senn W. Thiel QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009 48 1198
145. A. Warshel M. Levitt Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 1976 103 227
146. A. Warshel Bicycle-pedal model for the first step in the vision process Nature 1976 260 679
147. D. Bakowies W. Thiel Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches J. Phys. Chem. 1996 100 10580
148. B. Brooks R. Bruccoleri B. Olafson D. States S. Swaminathan M. Karplus CHARMM: A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 1983 4 187
149. W. D. Cornell P. Cieplak C. I. Bayly I. R. Gould K. M. Merz D. M. Ferguson D. C. Spellmeyer T. Fox J. W. Caldwell P. A. Kollman A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995 117 5179
150. M. J. Field P. A. Bash M. Karplus A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 1990 11 700
151. U. C. Singh P. A. Kollman A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl- exchange reaction and gas phase protonation of polyethers J. Comput. Chem. 1986 7 718
152. P. B. Coto A. Strambi N. Ferre M. Olivucci The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution Proc. Natl. Acad. Sci. U. S. A. 2006 103 17154
153. P. Altoè A. Cembran M. Olivucci M. Garavelli An aborted double bicycle-pedal isomerization with hydrogen bond-breaking is the primary event in the Bacteriorhodopsin proton-pumping Proc. Natl. Acad. Sci. U. S. A. 2010 107 20172
154. A. Strambi B. Durbeij N. Ferré M. Olivucci Anabaena sensory rhodopsin is a light-driven unidirectional rotor Proc. Natl. Acad. Sci. U. S. A. 2010 10.1073/pnas.1015085107
155. A. Sinicropi T. Andruniow N. Ferre R. Basosi M. Olivucci Properties of the Emitting State of the Green Fluorescent Protein Resolved at the CASPT2//CASSCF/CHARMM Level J. Am. Chem. Soc. 2005 127 11534
156. P. B. Coto S. Martí M. Oliva M. Olivucci M. Merchán J. Andrés Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods J. Phys. Chem. B 2008 112 7153
157. S. Pistolesi A. Sinicropi R. Pogni R. Basosi N. Ferré M. Olivucci Modeling the Fluorescence of Protein-Embedded Tryptophans with ab Initio Multiconfigurational Quantum Chemistry: The Limiting Cases of Parvalbumin and Monellin J. Phys. Chem. B 2009 113 16082
158. I. Schapiro M. N. Ryazantsev W. J. Ding M. H. Huntress F. Melaccio T. Andruniow M. Olivucci Computational Photobiology and Beyond Aust. J. Chem. 2010 63 413
159. I. Navizet Y.-J. Liu N. Ferré H.-Y. Xiao W.-H. Fang R. Lindh J. Am. Chem. Soc. 2009 132 706 712
160. X. Li L. W. Chung H. Mizuno A. Miyawaki K. Morokuma J. Phys. Chem. B 2009 114 1114 1126
161. P. Altoè T. Climent G. C. De Fusco M. Stenta A. Bottoni L. Serrano-Andrès M. Merchàn G. Orlandi M. Garavelli J. Phys. Chem. B 2009 113 15067 10573
162. I. Schapiro M. N. Ryazantsev L. M. Frutos N. Ferré R. Lindh M. Olivucci The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin are Modulated by Bond Alternation and HOOP driven Electronic Effects J. Am. Chem. Soc. 2011 10.1021/ja1056196
163. A. Strambi P. B. Coto L. M. Frutos N. Ferré M. Olivucci Relationship between the Excited State Relaxation Paths of Rhodopsin and Isorhodopsin J. Am. Chem. Soc. 2008 130 3382
164. M. Boggio-Pasqua M. A. Robb G. Groenhof Hydrogen Bonding Controls Excited-State Decay of the Photoactive Yellow Protein Chromophore J. Am. Chem. Soc. 2009 131 13580
165. G. Groenhof M. Bouxin-Cademartory B. Hess S. P. de Visser H. J. C. Berendsen M. Olivucci A. E. Mark M. A. Robb Photoactivation of the Photoactive yellow Protein: Why Protein Absorption Triggers a Trans-to-Cis Isomerization of the Chromophore in the Protein J. Am. Chem. Soc. 2004 126 4228
166. I. V. Polyakov B. L. Grigorenko E. M. Epifanovsky A. I. Krylov A. V. Nemukhin Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections J. Chem. Theory Comput. 2010 6 2377
167. L. V. Schäfer G. Groenhof M. Boggio-Pasqua M. A. Robb H. Grubmüller Chromophore protonation state controls photoswitching of the fluoroprotein asFP595 PLoS Comput. Biol. 2008 4 e1000034
168. L. W. Chung S. Hayashi M. Lundberg T. Nakatsu H. Kato K. Morokuma Mechanism of Efficient Firefly Bioluminescence via Adiabatic Transition State and Seam of Sloped Conical Intersection J. Am. Chem. Soc. 2008 130 12880
169. J. Finley P. Malmqvist B. O. Roos L. Serrano-Andrés The multi-state CASPT2 method Chem. Phys. Lett. 1998 288 299
170. H. Lischka M. Dallos P. G. Szalay D. R. Yarkony R. Shepard Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. I. Formalism J. Chem. Phys. 2004 120 7322
171. R. J. Cave F. Zhang N. T. Maitra K. Burke A dressed TDDFT treatment of the 21Ag states of butadiene and hexatriene Chem. Phys. Lett. 2004 389 39
172. M. Hellgren U. Von Barth Correlation energy functional and potential from time-dependent exact-exchange theory J. Chem. Phys. 2010 132 044101
173. H. Tao B. G. Levine T. J. Martínez Ab Initio Multiple Spawning Dynamics Using Multi-State Second-Order Perturbation Theory J. Phys. Chem. A 2009 113 13656
174. M. Barbatti H. Lischka Nonadiabatic Deactivation of 9H-Adenine: A Comprehensive Picture Based on Mixed Quantum-Classical Dynamics J. Am. Chem. Soc. 2008 130 6831
175. J. J. Szymczak M. Barbatti J. T. S. Hoo J. A. Adkins T. L. Windus D. Nachtigallova H. Lischka Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State J. Phys. Chem. A 2009 113 12686
176. C. Filippi M. Ziccheddu F. Buda Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods? J. Chem. Theory Comput. 2009 5 2074
177. V. Balzani E. Marchi M. Semeraro From the periodic table to photochemical molecular devices and machines Rend. Lincei 2010 21 91
178. I. S. Ufimtsev T. J. Martínez Graphical Processing Units for Quantum Chemistry Comput. Sci. Eng. 2008 10 26
179. I. S. Ufimtsev T. J. Martinez Quantum chemistry on graphical processing units. 1. strategies for two-electron integral evaluation J. Chem. Theory Comput. 2008 4 222
180. M. Watson R. Olivares-Amaya R. G. Edgar A. Aspuru-Guzik Accelerating correlated quantum chemistry calculations using graphical processing units Comput. Sci. Eng. 2010 12 40
181. L. Vogt R. Olivares-Amaya S. Kermes Y. Shao C. Amador-Bedolla A. Aspuru-Guzik Accelerating resolution-of-the-identity second-order Møller-Plesset quantum chemistry calculations with graphical processing units J. Phys. Chem. A 2008 112 2049
182. K. Yasuda Two-electron integral evaluation on the graphics processor unit J. Comput. Chem. 2008 29 334