Model Systems for Dynamics of π-Conjugated Biomolecules in Excited States

  • Mario Barbatti
  • Matthias Ruckenbauer
  • Jaroslaw J Szymczak
  • Bernhard Sellner
  • Mario Vazdar
  • Ivana Antol
  • Mirjana Eckert-Maksić
  • Hans Lischka
Reference work entry


Mixed-quantum classical dynamics simulations have recently become an important tool for investigations of time-dependent properties of electronically excited molecules, including non-adiabatic effects occurring during internal conversion processes. The high computational costs involved in such simulations have often led to simulation of model compounds instead of the full biochemical system. This chapter reviews recent dynamics results obtained for models of three classes of biologically relevant systems: protonated Schiff base chains as models for the chromophore of rhodopsin proteins; nucleobases and heteroaromatic rings as models for UV-excited nucleic acids; and formamide as a model for photoexcited peptide bonds.


Dynamic Simulation Conical Intersection Dissociation Channel Complete Active Space Bond Length Alternation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors gratefully acknowledge computer time at the Vienna Scientific Cluster (project nos. 70019 and 70151). This work was supported by the Austrian Science Fund within the framework of the Special Research Program F41 Vienna Computational Materials Laboratory (ViCoM). The work in Zagreb (M.E.-M., I.A., and M.V.) is supported by the Ministry of Science, Education and Sport of Croatia through the project. No. 098-0982933-2920. The support by the COST D37 action, WG0001-06 and the WTZ treaty between Austria and Croatia (Project No. HR17/2008) is also acknowledged. This work was also performed as part of research supported by the National Science Foundation Partnership in International Research and Education (PIRE) Grant No. OISE-0730114; support was also provided by the Robert A. Welch Foundation under Grant No. D-0005.


  1. Abouaf, R., Pommier, J., & Dunet, H. (2003). Electronic and vibrational excitation in gas phase thymine and 5-bromouracil by electron impact. Chemical Physics Letters, 381(3–4), 486–494. doi:10.1016/j.cplett.2003.09.121.Google Scholar
  2. Alexandrova, A. N., Tully, J. C., & Granucci, G. (2010). Photochemistry of DNA fragments via semiclassical nonadiabatic dynamics. The Journal of Physical Chemistry B, 114(37), 12116–12128. doi:10.1021/jp103322c.Google Scholar
  3. Andruniow, T., Ferre, N., & Olivucci, M. (2004). Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level. Proceedings of the National Academy of Sciences of the United States of America, 101(52), 17908–17913. doi:10.1073/pnas.0407997101.Google Scholar
  4. Antol, I., Eckert-Maksić, M., Barbatti, M., & Lischka, H. (2007). Simulation of the photodeactivation of formamide in the n\({}_{\mathrm{o}}{\pi }^{{\ast}}\) and \(\pi {\pi }^{{\ast}}\) states: An ab initio on-the-fly surface-hopping dynamics study. Journal of Chemical Physics, 127(23), 234303–234308. doi:10.1063/1.2804862.Google Scholar
  5. Antol, I., Barbatti, M., Eckert-Maksić, M., & Lischka, H. (2008a). Quantum chemical calculations of electronically excited states: Formamide, its protonated form and alkali cation complexes as case studies. Monatshefte für Chemie/Chemical Monthly, 139(4), 319–328. doi:10.1007/s00706-007-0803-2.Google Scholar
  6. Antol, I., Vazdar, M., Barbatti, M., & Eckert-Maksić, M. (2008b). The effect of protonation on the photodissociation processes in formamide – An ab initio surface hopping dynamics study. Chemical Physics, 349(1–3), 308–318. doi:10.1016/j.chemphys.2008.01.026.Google Scholar
  7. Araujo, M., Lasorne, B., Bearpark, M. J., & Robb, M. A. (2008). The photochemistry of formaldehyde: Internal conversion and molecular dissociation in a single step? The Journal of Physical Chemistry A, 112(33), 7489–7491.Google Scholar
  8. Asturiol, D., Lasorne, B., Robb, M. A., & Blancafort, L. (2009). Photophysics of the \(\pi {\pi }^{{\ast}}\) and n,\({\pi }^{{\ast}}\) states of thymine: MS-CASPT2 minimum energy paths and CASSCF on-the-fly dynamics. The Journal of Physical Chemistry A, 113(38), 10211–10218. doi:10.1021/jp905303g.Google Scholar
  9. Back, R. A., & Boden, J. C. (1971). High-temperature photolysis and pyrolysis of formamide vapour, and thermal decomposition of carbamyl radical. Transactions of the Faraday Society67(577), 88–96.Google Scholar
  10. Barbatti, M., & Lischka, H. (2007). Can the nonadiabatic photodynamics of aminopyrimidine be a model for the ultrafast deactivation of adenine? The Journal of Physical Chemistry A, 111(15), 2852–2858. doi:10.1021/jp070089w.Google Scholar
  11. Barbatti, M., & Lischka, H. (2008). Nonadiabatic deactivation of 9H-adenine: A comprehensive picture based on mixed quantum-classical dynamics. Journal of the American Chemical Society, 130(21), 6831–6839. doi: 10.1021/ja800589p.Google Scholar
  12. Barbatti, M., Vazdar, M., Aquino, A. J. A., Eckert-Maksić, M., & Lischka, H. (2006). The nonadiabatic deactivation paths of pyrrole. Journal of Chemical Physics, 125(16), 164323. doi:10.1063/1.2363376.Google Scholar
  13. Barbatti, M., Granucci, G., Persico, M., Ruckenbauer, M., Vazdar, M., Eckert-Maksić, M., & Lischka, H. (2007a). The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems. Journal of Photochemistry and Photobiology A, 190(2–3), 228–240. doi:10.1016/j.jphotochem.2006.12.008.Google Scholar
  14. Barbatti, M., Granucci, G., Ruckenbauer, M., Pittner, J., Persico, M., & Lischka, H. (2007b). NEWTON-X: A package for Newtonian dynamics close to the crossing seam.
  15. Barbatti, M., Ruckenbauer, M., Szymczak, J. J., Aquino, A. J. A., & Lischka, H. (2008). Nonadiabatic excited-state dynamics of polar p-systems and related model compounds of biological relevance. Physical Chemistry Chemical Physics, 10, 482. doi:10.1039/b709315m.Google Scholar
  16. Barbatti, M., Aquino, A. J. A., Szymczak, J. J., Nachtigallová, D., Hobza, P., & Lischka, H. (2010a). Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases. Proceedings of the National Academy of Sciences of the United States of America, 107(50), 21453–21458. doi:10.1073/pnas.1014982107.Google Scholar
  17. Barbatti, M., Pittner, J., Pederzoli, M., Werner, U., Mitric, R., Bonacic-Koutecký, V., & Lischka, H. (2010b). Non-adiabatic dynamics of pyrrole: Dependence of deactivation mechanisms on the excitation energy. Chemical Physics, 375(1), 26–34.Google Scholar
  18. Barbatti, M., Aquino, A. J. A., Szymczak, J. J., Nachtigallová, D., & Lischka, H. (2011a).Photodynamics simulations of cytosine: Characterization of the ultra fast bi-exponential UV deactivation. Physical Chemistry Chemical Physics, 13, 6145–6155. doi:10.1039/C1030CP02142C.Google Scholar
  19. Barbatti, M., Szymczak, J. J., Aquino, A. J. A., Nachtigallova, D., & Lischka, H. (2011b). The decay mechanism of photoexcited guanine – A nonadiabatic dynamics study. Journal of Chemical Physics, 134(1), 014304.Google Scholar
  20. Ben-Nun, M., Molnar, F., Lu, H., Phillips, J. C., Martinez, T. J., & Schulten, K. (1998). Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin. Faraday Discuss, 110, 447–462.Google Scholar
  21. Ben-Nun, M., Quenneville, J., & Martínez, T. J. (2000). Ab initio multiple spawning: Photochemistry from first principles quantum molecular dynamics. The Journal of Physical Chemistry A, 104(22), 5161–5175.Google Scholar
  22. Birge, R. R. (1981). Photophysics of light transduction in rhodopsin and bacteriorhodopsin. Annual Review of Biophysics & Bioengineering, 10, 315–354.Google Scholar
  23. Birge, R. R. (1990). Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin. Biochimica et Biophysica Acta, 1016(3), 293–327.Google Scholar
  24. Blank, D. A., North, S. W., & Lee, Y. T. (1994). The ultraviolet photodissociation dynamics of pyrrole. Chemical Physics, 187(1–2), 35–47.Google Scholar
  25. Boden, J. C., & Back, R. A. (1970). Photochemistry and free-radical reactions in formamide vapour. Transactions of the Faraday Society66, 175–182.Google Scholar
  26. Boeyens, J. C. A. (1978). The conformation of six-membered rings. Journal of Chemical Crystallography, 8, 317–320.Google Scholar
  27. Burghardt, I., & Hynes, J. T. (2006). Excited-state charge transfer at a conical intersection: Effects of an environment. The Journal of Physical Chemistry A, 110(40), 11411–11423.Google Scholar
  28. Cadet, J., & Berger, M. (1985). Radiation-induced decomposition of the purine-bases within DNA and related model compounds. International Journal of Radiation Biology, 47(2), 127–143.Google Scholar
  29. Canuel, C., Mons, M., Piuzzi, F., Tardivel, B., Dimicoli, I., & Elhanine, M. (2005). Excited states dynamics of DNA and RNA bases: Characterization of a stepwise deactivation pathway in the gas phase. Journal of Chemical Physics, 122(7), 074316.Google Scholar
  30. Chen, X.-B., & Fang, W.-H. (2004). Insights into photodissociation dynamics of benzamide and formanilide from ab initio calculations. Journal of the American Chemical Society, 126(29), 8976–8980.Google Scholar
  31. Chen, X.-B., Fang, W.-H., & Fang, D. C. (2003). An ab initio study toward understanding the mechanistic photochemistry of acetamide. Journal of the American Chemical Society, 125(32), 9689–9698.Google Scholar
  32. Chin, C. H., Mebel, A. M., Kim, G. S., Baek, K. Y., Hayashi, M., Liang, K. K., & Lin, S. H. (2007). Theoretical investigations of spectroscopy and excited state dynamics of adenine. Chemical Physics Letters, 445(4–6), 361–369.Google Scholar
  33. Ciminelli, C., Granucci, G., & Persico, M. (2008). The photoisomerization of a peptidic derivative of azobenzene: A nonadiabatic dynamics simulation of a supramolecular system. Chemical Physics, 349(1–3), 325-333. doi:10.1016/j.chemphys.2008.01.030.Google Scholar
  34. Clark, L. B., & Tinoco, I. (1965). Correlations in ultraviolet spectra of purine and pyrimidine bases. Journal of the American Chemical Society, 87(1), 11.Google Scholar
  35. Clark, L. B., Peschel, G. G., & Tinoco, I. (1965). Vapor spectra and heats of vaporization of some purine and pyrimidine bases. The Journal of Physical Chemistry, 69(10), 3615–3618.Google Scholar
  36. Cremer, D., & Pople, J. A. (1975). General definition of ring puckering coordinates. Journal of the American Chemical Society, 97(6), 1354–1358.Google Scholar
  37. Crespo-Hernández, C. E., Cohen, B., Hare, P. M., & Kohler, B. (2004). Ultrafast excited-state dynamics in nucleic acids. Chemical Reviews, 104(4), 1977–2019.Google Scholar
  38. Crespo-Hernandez, C. E., Cohen, B., & Kohler, B. (2005). Base stacking controls excited-state dynamics in A-T DNA. Nature, 436(7054), 1141–1144. doi:10.1038/Nature03933.Google Scholar
  39. Cui, W., Thompson, M. S., & Reilly, J. P. (2005). Pathways of peptide ion fragmentation induced by vacuum ultraviolet light. Journal of The American Society for Mass Spectrometry, 16(8), 1384–1398.Google Scholar
  40. Dallos, M., Lischka, H., Shepard, R., Yarkony, D. R., & Szalay, P. G. (2004). Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. II. Minima on the crossing seam: Formaldehyde and the photodimerization of ethylene. Journal of Chemical Physics, 120(16), 7330–7339.Google Scholar
  41. Daura, X., Antes, I., van Gunsteren, W. F., Thiel, W., & Mark, A. E. (1999). The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins-Structure Function and Genetics, 36(4), 542–555.Google Scholar
  42. Devine, A. L., Cronin, B., Nix, M. G. D., & Ashfold, M. N. R. (2006). High resolution photofragment translational spectroscopy studies of the near ultraviolet photolysis of imidazole. Journal of Chemical Physics, 125(18), 184302, doi:Artn184302, 10.1063/1.2364504.Google Scholar
  43. Duggan, D. E., Bowman, R. L., Brodie, B. B., & Udenfriend, S. (1957). A spectrophotofluorometric study of compounds of biological interest. Archives of Biochemistry and Biophysics, 68(1), 1–14.Google Scholar
  44. Eckert-Maksić, M., & Antol, I. (2009). Study of the mechanism of the N-CO photodissociation in N,N-Dimethylformamide by direct trajectory surface hopping simulations. The Journal of Physical Chemistry A, 113(45):12582–12590. doi:10.1021/jp9046177.Google Scholar
  45. Eckert-Maksić, M., Antol, I., Vazdar, M., Barbatti, M., & Lischka, H. (2010a). Formamide as the model compound for photodissociation studies of the peptide bond. In P. Paneth & A. Dybala-Defratyka (Eds.), Kinetics and dynamics: Challenges and advances in coutational chemistry and physics (pp. 77–106). Netherlands: Springer.Google Scholar
  46. Eckert-Maksić, M., Vazdar, M., Ruckenbauer, M., Barbatti, M., Muller, T., & Lischka, H. (2010b). Matrix-controlled photofragmentation of formamide: Dynamics simulation in argon by nonadiabatic QM/MM method. Physical Chemistry Chemical Physics, 12(39), 12719–12726.Google Scholar
  47. Fabiano, E., & Thiel, W. (2008). Nonradiative deexcitation dynamics of 9H-adenine: An OM2 surface hopping study. The Journal of Physical Chemistry A, 112(30), 6859–6863. doi:10.1021/Jp8033402.Google Scholar
  48. Fabiano, E., Groenhof, G., & Thiel, W. (2008a). Approximate switching algorithms for trajectory surface hopping. Chemical Physics, 351(1–3), 111–116.Google Scholar
  49. Fabiano, E., Keal, T. W., & Thiel, W. (2008b). Implementation of surface hopping molecular dynamics using semiempirical methods. Chemical Physics, 349(1–3), 334–347. doi:10.1016/j.chemphys.2008.01.044.Google Scholar
  50. Ferretti, A., Granucci, G., Lami, A., Persico, M., & Villani, G. (1996). Quantum mechanical and semiclassical dynamics at a conical intersection. Journal of Chemical Physics, 104(14), 5517–5527.Google Scholar
  51. Frutos, L. M., Andruniow, T., Santoro, F., Ferre, N., & Olivucci, M. (2007). Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry. Proceedings of the National Academy of Sciences of the United States of America, 104(19), 7764–7769.Google Scholar
  52. Garavelli, M., Celani, P., Bernardi, F., Robb, M. A., & Olivucci, M. (1997). The C5H6NH2+ protonated Shiff base: An ab initio minimal model for retinal photoisomerization. Journal of the American Chemical Society, 119(29), 6891–6901.Google Scholar
  53. Garavelli, M., Bernardi, F., Robb, M. A., & Olivucci, M. (1999a). The short-chain acroleiniminium and pentadieniminium cations: Towards a model for retinal photoisomerization. A CASSCF/PT2 study. Journal of Molecular Structure: THEOCHEM, 463(1–2), 59–64.Google Scholar
  54. Garavelli, M., Negri, F., & Olivucci, M. (1999b). Initial excited-state relaxation of the isolated 11-cis protonated Schiff base of retinal: Evidence for in-plane motion from ab initio quantum chemical simulation of the resonance Raman spectrum. Journal of the American Chemical Society, 121(5), 1023–1029.Google Scholar
  55. Gascon, J. A., & Batista, V. S. (2004). QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophysical Journal, 87(5), 2931–2941. doi:10.1529/biophysj.104.048264.Google Scholar
  56. Gingell, J. M., Mason, N. J., Zhao, H., Walker, I. C., & Siggel, M. R. F. (1997). VUV optical-absorption and electron-energy-loss spectroscopy of formamide. Chemical Physics, 220(1–2), 191–205Google Scholar
  57. González-Luque, R., Garavelli, M., Bernardi, F., Merchán, M., Robb, M. A., & Olivucci, M. (2000). Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization. Proceedings of the National Academy of Sciences of the United States of America, 97(17), 9379–9384.Google Scholar
  58. González-Vázquez, J., & González, L. (2010). A time-dependent picture of the ultrafast deactivation of keto-cytosine including three-state conical intersections. A European Journal of Chemical Physics and Physical Chemistry, 11(17), 3617–3624.Google Scholar
  59. Granucci, G., & Persico, M. (2007). Critical appraisal of the fewest switches algorithm for surface hopping. Journal of Chemical Physics, 126(13), 134114–134111.Google Scholar
  60. Granucci, G., Persico, M., & Toniolo, A. (2001). Direct semiclassical simulation of photochemical processes with semiempirical wave functions. Journal of Chemical Physics, 114(24), 10608–10615.Google Scholar
  61. Grégoire, G., Lucas, B., Barat, M., Fayeton, J. A., Dedonder-Lardeux, C. & Jouvet, C. (2009). UV photoinduced dynamics in protonated aromatic amino acid. European Physical Journal D, 51(1), 109–116.Google Scholar
  62. Grégoire, G., Dedonder-Lardeux, C., Jouvet, C., Desfrançois, C., & Fayeton, J. A. (2007). Ultrafast excited state dynamics in protonated GWG and GYG tripeptides. Physical Chemistry Chemical Physics, 9(1), 78–82.Google Scholar
  63. Grégoire, G., Kang, H., Dedonder-Lardeux, C., Jouvet, C., Desfrançois, C., Onidas, D., Lepere, V., & Fayeton, J. A. (2006). Statistical vs. non-statistical deactivation pathways in the UV photo-fragmentation of protonated tryptophan-leucine dipeptide. Physical Chemistry Chemical Physics, 8(1), 122–128.Google Scholar
  64. Greenberg, A., Breneman, C. M., & Liebman, J. F. (2002). The amide linkage: Selected structural aspects in Chemistry, Biochemistry, and Materials Science. The amide linkage: Structural significance in Chemistry, Biochemistry, and Materials Science. New York: WileyGoogle Scholar
  65. Gustavsson, T., Sarkar, N., Lazzarotto, E., Markovitsi, D., & Improta, R. (2006). Singlet excited state dynamics of uracil and thymine derivatives: A femtosecond fluorescence upconversion study in acetonitrile. Chemical Physics Letters, 429(4–6), 551–557. doi:10.1016/j.cplett.2006.08.058.Google Scholar
  66. Hack, M. D., Wensmann, A. M., Truhlar, D. G., Ben-Nun, M., & Martínez, T. J. (2001). Comparison of full multiple spawning, trajectory surface hopping, and converged quantum mechanics for electronically nonadiabatic dynamics. Journal of Chemical Physics, 115(3), 1172–1186.Google Scholar
  67. Hammes-Schiffer, S., & Tully, J. C. (1994). Proton-transfer in solution–Molecular-dynamics with quantum transitions. Journal of Chemical Physics, 101(6), 4657–4667.Google Scholar
  68. Hayashi, S., Taikhorshid, E., & Schulten, K. (2009). Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophysical Journal, 96(2), 403–416. doi:10.1016/j.bpj.2008.09.049.Google Scholar
  69. He, Y., Wu, C., & Kong, W. (2003). Decay pathways of thymine and methyl-substituted uracil and thymine in the gas phase. The Journal of Physical Chemistry A, 107(26), 5145–5148. doi:10.1021/jp034733sGoogle Scholar
  70. Hudock, H. R., & Martinez, T. J. (2008). Excited-state dynamics of cytosine reveal multiple intrinsic subpicosecond pathways. A European Journal of Chemical Physics and Physical Chemistry, 9(17), 2486–2490. doi:10.1002/cphc.200800649.Google Scholar
  71. Hudock, H. R., Levine, B. G., Thompson, A. L., Satzger, H., Townsend, D., Gador, N., Ullrich, S., Stolow, A., & Martinez, T. J. (2007). Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine. The Journal of Physical Chemistry A, 111(34), 8500–8508.Google Scholar
  72. Improta, R., Barone, V., Lami, A., & Santoro, F. (2009). Quantum dynamics of the ultrafast \(\pi {\pi }^{{\ast}}/n{\pi }^{{\ast}}\) population transfer in uracil and 5-fluoro-uracil in water and acetonitrile. The Journal of Physical Chemistry B, 113(43), 14491–14503Google Scholar
  73. Ishida, T., Nanbu, S., & Nakamura, H. (2009). Nonadiabatic ab initio dynamics of two models of schiff base retinal. The Journal of Physical Chemistry A, 113(16), 4356–4366. doi:10.1021/Jp8110315.Google Scholar
  74. Jasper, A. W., Stechmann, S. N., & Truhlar, D. G. (2002). Fewest-switches with time uncertainty: A modified trajectory surface-hopping algorithm with better accuracy for classically forbidden electronic transitions. Journal of Chemical Physics, 116(13), 5424–5431.Google Scholar
  75. Jeong, H. M., Young, S. S., Hyun, J. C., & Myung, S. K. (2007). Photodissociation at 193 nm of some singly protonated peptides and proteins with m/z 2000–9000 using a tandem time-of-flight mass spectrometer equipped with a second source for delayed extraction/post-acceleration of product ions. Rapid Communications in Mass Spectrometry, 21(3), 359–368Google Scholar
  76. Jeong, H. M., So, H. Y., & Myung, S. K. (2005). Photodissociation of singly protonated peptides at 193 nm investigated with tandem time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry, 19(22), 3248–3252Google Scholar
  77. Jones, G. A., Acocella, A., & Zerbetto, F. (2008). On-the-fly, electric-field-driven, coupled electron-nuclear dynamics. The Journal of Physical Chemistry A, 112(40), 9650–9656. doi:10.1021/Jp805360v.Google Scholar
  78. Jorgensen, W. L., & McDonald, N. A. (1998). Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes. Journal of Molecular Structure: Theochem, 424(1–2), 145–155.Google Scholar
  79. Kang, T. Y., & Kim, H. L. (2006). Photodissociation of formamide at 205 nm: The H atom channels. Chemical Physics Letters, 431(1–3), 24–27.Google Scholar
  80. Kang, H., Jouvet, C., Dedonder-Lardeux, C., Martrenchard, S., Grégoire, G., Desfrançois, C., Schermann, J. P., Barat, M., & Fayeton, J. A. (2005). Ultrafast deactivation mechanisms of protonated aromatic amino acids following UV excitation. Physical Chemistry Chemical Physics, 7(2), 394–398.Google Scholar
  81. Kang, H., Dedonder-Lardeux, C., Jouvet, C., Martrenchard, S., Grégoire, G., Desfrançois, C., Schermann, J. P., Barat, M., & Fayeton, J. A. (2004). Photo-induced dissociation of protonated tryptophan TrpH+: A direct states dissociation channel in the excited controls the hydrogen atom loss. Physical Chemistry Chemical Physics, 6(10), 2628–2632.Google Scholar
  82. Kang, H., Lee, K. T., Jung, B., Ko, Y. J., & Kim, S. K. (2002). Intrinsic lifetimes of the excited state of DNA and RNA bases. Journal of the American Chemical Society, 124(44), 12958–12959.Google Scholar
  83. Keal, T., Wanko, M., & Thiel, W. (2009). Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 123(1), 145–156.Google Scholar
  84. Kochendoerfer, G. G., & Mathies, R. A. (1996). Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin. The Journal of Physical Chemistry, 100(34), 14526– 14532.Google Scholar
  85. Köppel, H., Gromov, E. V., & Trofimov, A. B. (2004). Multi-mode-multi-state quantum dynamics of key five-membered heterocycles: Spectroscopy and ultrafast internal conversion. Chemical Physics, 304(1–2), 35–49.Google Scholar
  86. Kukura, P., McCamant, D. W., Yoon, S., Wandschneider, D. B., & Mathies, R. A. (2005). Structural observation of the primary isomerization in vision with femtosecond-stimulated Raman. Science, 310(5750), 1006–1009.Google Scholar
  87. Lan, Z., & Domcke, W. (2008). Role of vibrational energy relaxation in the photoinduced nonadiabatic dynamics of pyrrole at the \({}^{1}\pi {\sigma }^{{\ast}}-{\mathrm{S}}_{\mathrm{o}}\) conical intersection. Chemical Physics, 350(1–3), 125–138.Google Scholar
  88. Lan, Z., Fabiano, E., & Thiel, W. (2009). Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: On-the-fly surface-hopping study with semiempirical methods. The Journal of Physical Chemistry B, 113(11), 3548–3555. doi:10.1021/jp809085h.Google Scholar
  89. Langer, H., Doltsinis, N. L., & Marx, D. (2005). Excited-state dynamics and coupled proton–electron transfer of guanine. A European Journal of Chemical Physics and Physical Chemistry, 6(9), 1734–1737.Google Scholar
  90. Lasser, C., & Swart, T. (2008). Single switch surface hopping for a model of pyrazine. Journal of Chemical Physics, 129(3), 034302–034308.Google Scholar
  91. Lei, Y., Yuan, S., Dou, Y., Wang, Y., & Wen, Z. (2008). Detailed dynamics of the nonradiative deactivation of adenine: A semiclassical dynamics study. The Journal of Physical Chemistry A, 112(37), 8497–8504. doi:10.1021/jp802483b.Google Scholar
  92. Levine, B. G., Ko, C., Quenneville, J., & Martínez, T. J. (2006). Conical intersections and double excitations in time-dependent density functional theory. Molecular Physics, 104(5–7), 1039–1051.Google Scholar
  93. Levine, B. G., Coe, J. D., Virshup, A. M., & Martinez, T. J. (2008). Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package. Chemical Physics, 347(1–3), 3–16. doi:10.1016/j.chemphys.2008.01.014.Google Scholar
  94. Li, X. S., Tully, J. C., Schlegel, H. B., & Frisch, M. J. (2005). Ab initio Ehrenfest dynamics. Journal of Chemical Physics, 123(8), 084106.Google Scholar
  95. Lin, H., & Truhlar, D. G. (2007). QM/MM: What have we learned, where are we, and where do we go from here? Theoretical Chemistry Accounts, 117(2), 185–199.Google Scholar
  96. Lippert, H., Ritze, H. H., Hertel, I. V., & Radloff, W. (2004). Femtosecond time-resolved hydrogen-atom elimination from photoexcited pyrrole molecules. A European Journal of Chemical Physics and Physical Chemistry, 5(9), 1423–1427.Google Scholar
  97. Lischka, H., Shepard, R., Brown, F. B., & Shavitt, I. (1981). New implementation of the graphical unitary-group approach for multi-reference direct configuration-interaction calculations. International Journal of Quantum Chemistry, S.15, 91–100.Google Scholar
  98. Lischka, H., Shepard, R., Pitzer, R. M., Shavitt, I., Dallos, M., Müller, T., Szalay, P. G., Seth, M., Kedziora, G. S., Yabushita, S., & Zhang, Z. Y. (2001). High-level multireference methods in the quantum-chemistry program system COLUMBUS: Analytic MR-CISD and MR-AQCC gradients and MR-AQCC-LRT for excited states, GUGA spin-orbit CI and parallel CI density. Physical Chemistry Chemical Physics, 3(5), 664–673.Google Scholar
  99. Lischka, H., Dallos, M., & Shepard, R. (2002). Analytic MRCI gradient for excited states: Formalism and application to the n-\({\pi }^{{\ast}}\) valence- and n-(3s,3p) Rydberg states of formaldehyde. Molecular Physics, 100(11), 1647–1658.Google Scholar
  100. Lischka, H., Dallos, M., Szalay, P. G., Yarkony, D. R., & Shepard, R. (2004). Analytic evaluation of nonadiabatic coupling terms at the MR-CI level. I. Formalism. Journal of Chemical Physics, 120(16), 7322–7329.Google Scholar
  101. Lischka, H., Shepard, R., Shavitt, I., Pitzer, R. M., Dallos, M., Mueller, T., Szalay, P. G., Brown, F. B., Ahlrichs, R., Boehm, H. J., Chang, A., Comeau, D. C., Gdanitz, R., Dachsel, H., Ehrhardt, C., Ernzerhof, M., Hoechtl, P., Irle, S., Kedziora, G., Kovar, T., Parasuk, V., Pepper, M. J. M., Scharf, P., Schiffer, H., Schindler, M., Schueler, M., Seth, M., Stahlberg, E. A., Zhao, J.-G., Yabushita, S., Zhang, Z., Barbatti, M., Matsika, S., Schuurmann, M., Yarkony, D. R., Brozell, S. R., Beck, E. V., & Blaudeau, J.-P. (2006). COLUMBUS, an ab initio electronic structure program, release 5.9.1.
  102. Liu, R. S. H., & Asato, A. E. (1985). Photochemistry of polyenes. 22. The primary process of vision and the structure of bathorhodopsin – A mechanism for photoisomerization of polyenes. Proceedings of the National Academy of Sciences of the United States of America, 82(2), 259–263.Google Scholar
  103. Liu, R. S. H. (2002). Introduction to the symposium-in-print: Photoisomerization pathways, torsional relaxation and the Hula Twist & para. Photochemistry and Photobiology, 76(6), 580–583.Google Scholar
  104. Liu, D., Fang, W. H., & Fu, X. Y. (2000). Ab initio molecular orbital study of the mechanism of photodissociation of formamide. Chemical Physics Letters, 318(4–5), 291–297.Google Scholar
  105. Logunov, I., & Schulten, K. (1996). Quantum chemistry: Molecular dynamics study of the dark-adaptation process in bacteriorhodopsin. Journal of the American Chemical Society, 118(40), 9727–9735.Google Scholar
  106. Longworth, J. W., Rahn, R. O., & Shulman, R. G. (1966). Luminescence of pyrimidines purines nucleosides and nucleotides at 77 degrees K. Effect of ionization and tautomerization. Journal of Chemical Physics, 45(8), 2930.Google Scholar
  107. Lundell, J., Krajewska, M., & Räsänen, M. (1998). Matrix isolation Fourier transform infrared and ab initio studies of the 193-nm-induced photodecomposition of formamide. The Journal of Physical Chemistry A, 102(33), 6643–6650.Google Scholar
  108. Malone, R. J., Miller, A. M., & Kohler, B. (2003). Singlet excited-state lifetimes of cytosine derivatives measured by femtosecond transient absorption. Photochemistry and Photobiology, 77(2), 158–164.Google Scholar
  109. Marian, C. M. (2005). A new pathway for the rapid decay of electronically excited adenine. Journal of Chemical Physics, 122(10), 104314.Google Scholar
  110. Matsika, S. (2004). Radiationless decay of excited states of uracil through conical intersections. The Journal of Physical Chemistry A, 108(37), 7584–7590.Google Scholar
  111. Merchan, M., Gonzalez-Luque, R., Climent, T., Serrano-Andres, L., Rodriuguez, E., Reguero, M., & Pelaez, D. (2006). Unified model for the ultrafast decay of pyrimidine nucleobases. The Journal of Physical Chemistry B, 110(51), 26471–26476. doi:10.1021/Jp066874a.Google Scholar
  112. Middleton, C. T., de La Harpe, K., Su, C., Law, Y. K., Crespo-Hernandez, C. E., & Kohler, B. (2009). DNA excited-state dynamics: From single bases to the double helix. Annual Review of Physical Chemistry, 60(1), 217–239. doi:10.1146/annurev.physchem.59.032607.093719.Google Scholar
  113. Migani, A., Robb, M. A., & Olivucci, M. (2003). Relationship between photoisomerization path and intersection space in a retinal chromophore model. Journal of the American Chemical Society, 125(9), 2804–2808.Google Scholar
  114. Mitric, R., Petersen, J., & Bonacic-Koutecky, V. (2009a). Laser-field-induced surface-hopping method for the simulation and control of ultrafast photodynamics. Physical Review A, 79(5), 053416.Google Scholar
  115. Mitric, R., Werner, U., Wohlgemuth, M., Seifert, G., & Bonacic-Koutecky, V. (2009b). Nonadiabatic dynamics within time-dependent density functional tight binding method. The Journal of Physical Chemistry A, 113(45), 12700–12705. doi: 10.1021/Jp905600w.Google Scholar
  116. Mulcahy, M., McInerney, J. G., Nikogosyan, D. N., & Görner, H. (2000). 193 Nm photolysis of aromatic and aliphatic dipeptides in aqueous solution: Dependence of decomposition quantum yield on the amino acid sequence. Biological Chemistry, 381(12), 1259–1262.Google Scholar
  117. Muller, U., & Stock, G. (1997). Surface-hopping modeling of photoinduced relaxation dynamics on coupled potential-energy surfaces. Journal of Chemical Physics, 107(16), 6230–6245.Google Scholar
  118. Nachtigallova, D., Zeleny, T., Ruckenbauer, M., Muller, T., Barbatti, M., Hobza, P., & Lischka, H. (2010). Does stacking restrain the photodynamics of individual nucleobases? Journal of the American Chemical Society, 132(24), 8261–8263. doi:10.1021/ja1029705.Google Scholar
  119. Nieber, H., & Doltsinis, N. L. (2008). Elucidating ultrafast nonradiative decay of photoexcited uracil in aqueous solution by ab initio molecular dynamics. Chemical Physics, 347(1–3), 405–412. doi:10.1016/j.chemphys.2007.09.056.Google Scholar
  120. Nolting, D., Schultz, T., Hertel, I. V., & Weinkauf, R. (2006). Excited state dynamics and fragmentation channels of the protonated dipeptide H2N-Leu-Trp-COOH. Physical Chemistry Chemical Physics, 8(44), 5247–5254. doi:10.1039/B609726.Google Scholar
  121. Palings, I., Pardoen, J. A., Vandenberg, E., Winkel, C., Lugtenburg, J., & Mathies, R. A. (1987). Assignment of fingerprint vibrations in the resonance Raman-spectra of rhodopsin, isorhodopsin, and bathorhodopsin – Implications for chromophore structure and environment. Biochemistry (Mosc), 26(9), 2544–2556.Google Scholar
  122. Pei, K.-M., Ma, Y., & Zheng, X. (2008). Resonance Raman and theoretical investigation of the photodissociation dynamics of benzamide in S\({}_{3}\) state. The Journal of Chemical Physics, 128(22), 224310–224310.Google Scholar
  123. Perun, S., Sobolewski, A. L., & Domcke, W. (2005a). Ab initio studies on the radiationless decay mechanisms of the lowest excited singlet states of 9H-adenine. Journal of the American Chemical Society, 127(17), 6257–6265.Google Scholar
  124. Perun, S., Sobolewski, A. L., & Domcke, W. (2005b). Photostability of 9H-adenine: Mechanisms of the radiationless deactivation of the lowest excited singlet states. Chemical Physics, 313(1–3), 107–112.Google Scholar
  125. Peteanu, L. A., Schoenlein, R. W., Wang, Q., Mathies, R. A., & Shank, C. V. (1993). The 1st Step in vision occurs in femtoseconds – Complete blue and red spectral studies. Proceedings of the National Academy of Sciences of the United States of America, 90(24), 11762–11766.Google Scholar
  126. Petersen, C., Dahl, N. H., Jensen, S. K., Poulsen, J. A., Thøgersen, J., & Keiding, S. R. (2008). Femtosecond Photolysis of Aqueous Formamide. The Journal of Physical Chemistry A, 112(15), 3339–3344.Google Scholar
  127. Pittner, J., Lischka, H., & Barbatti, M. (2009). Optimization of mixed quantum-classical dynamics: Time-derivative coupling terms and selected couplings. Chemical Physics, 356(1–3), 147–152. doi:10.1016/j.chemphys.2008.10.013.Google Scholar
  128. Polli, D., Altoe, P., Weingart, O., Spillane, K. M., Manzoni, C., Brida, D., Tomasello, G., Orlandi, G., Kukura, P., Mathies, R. A., Garavelli, M., & Cerullo, G. (2010). Conical intersection dynamics of the primary photoisomerization event in vision. Nature, 467(7314), 440–443. doi:10.1038/nature09346.Google Scholar
  129. Poterya, V., Profant, V., Farnik, M., Slavicek, P., & Buck, U. (2007). Experimental and theoretical study of the pyrrole cluster photochemistry: Closing the \(\pi {\sigma }^{{\ast}}\) dissociation pathway by complexation. Journal of Chemical Physics, 127(6), 064307. doi:10.1063/1.2754687.Google Scholar
  130. Powner, M. W., Gerland, B., & Sutherland, J. D. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459(7244), 239–242. doi:10.1038/Nature08013.Google Scholar
  131. Rohrig, U. F., Guidoni, L., Laio, A., Frank, I., & Rothlisberger, U. (2004). A molecular spring for vision. Journal of the American Chemical Society, 126(47), 15328–15329. doi:10.1021/ja048265r.Google Scholar
  132. Rohrig, U. F., Guidoni, L., & Rothlisberger, U. (2005). Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore. A European Journal of Chemical Physics and Physical Chemistry, 6(9), 1836–1847. doi:10.1002/cphc.200500066.Google Scholar
  133. Ruckenbauer, M., Barbatti, M., Muller, T., & Lischka, H. (2010). Nonadiabatic excited-state dynamics with hybrid ab initio quantum-mechanical/molecular-mechanical methods: Solvation of the pentadieniminium cation in Apolar media. The Journal of Physical Chemistry A, 114(25), 6757–6765. doi:10.1021/jp103101t.Google Scholar
  134. Saam, J., Tajkhorshid, E., Hayashi, S., & Schulten, K. (2002). Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophysical Journal, 83(6), 3097–3112.Google Scholar
  135. Santoro, F., Barone, V., & Improta, R. (2007a). Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. Proceedings of the National Academy of Sciences of the United States of America, 104(24), 9931–9936. doi:10.1073/pnas.0703298104.Google Scholar
  136. Santoro, F., Lami, A., & Olivucci, M. (2007b). Complex excited dynamics around a plateau on a retinal-like potential surface: Chaos, multi-exponential decays and quantum/classical differences. Theoretical Chemistry Accounts, 117(5–6), 1061–1072. doi:10.1007/s00214-006-0220-3.Google Scholar
  137. Schapiro, I., Weingart, O., & Buss, V. (2009). Bicycle-pedal isomerization in a rhodopsin chromophore model. Journal of the American Chemical Society, 131(1), 16. doi:10.1021/Ja805586z.Google Scholar
  138. Schoenlein, R. W., Peteanu, L. A., Mathies, R. A., & Shank, C. V. (1991). The 1st step in vision – Femtosecond isomerization of rhodopsin. Science, 254(5030), 412–415.Google Scholar
  139. Schultz, T., Samoylova, E., Radloff, W., Hertel, I. V., Sobolewski, A. L., & Domcke, W. (2004). Efficient deactivation of a model base pair via excited-state hydrogen transfer. Science, 306(5702), 1765–1768.Google Scholar
  140. Sellner, B., Barbatti, M., & Lischka, H. (2009). Dynamics starting at a conical intersection: Application to the photochemistry of pyrrole. Journal of Chemical Physics, 131(2), 024312. doi:10.1063/1.3175799.Google Scholar
  141. Send, R., & Sundholm, D. (2007). Stairway to the conical intersection: A computational study of the retinal isomerization. The Journal of Physical Chemistry A, 111(36), 8766–8773.Google Scholar
  142. Serrano-Andres, L., & Merchan, M. (2009). Are the five natural DNA/RNA base monomers a good choice from natural selection? A photochemical perspective. Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 10(1), 21–32. doi:10.1016/j.jphotochemrev.2008.12.001.Google Scholar
  143. Shepard, R. (1995). The analytic gradient method for configuration interaction wave functions. In D. R. Yarkony (Ed.), Modern electronic structure theory. Advanced series in physical chemistry (Vol. 1, p. 345). Singapore: World Scientific.Google Scholar
  144. Shepard, R., Lischka, H., Szalay, P. G., Kovar, T., & Ernzerhof, M. (1992). A general multireference configuration-interaction gradient program. Journal of Chemical Physics, 96(3), 2085–2098.Google Scholar
  145. Shin, E. J. (2004). Photochemistry of anthrylethene derivatives containing heteroaromatic ring: Pyrrole and indole derivatives. Bulletin of the Korean Chemical Society, 25(6), 907–909.Google Scholar
  146. Sobolewski, A. L., & Domcke, W. (2000). Conical intersections induced by repulsive \({}^{1}\pi {\sigma }^{{\ast}}\) states in planar organic molecules: Malonaldehyde, pyrrole and chlorobenzene as photochemical model systems. Chemical Physics, 259(2–3), 181–191.Google Scholar
  147. Sobolewski, A. L., Domcke, W., & Hättig, C. (2005). Tautomeric selectivity of the excited-state lifetime of guanine/cytosine base pairs: The role of electron-driven proton-transfer processes. Proceedings of the National Academy of Sciences of teh United States of America, 102(50), 17903–17906.Google Scholar
  148. Szymczak, J. J., Barbatti, M., & Lischka, H. (2008). Mechanism of ultrafast photodecay in restricted motions in protonated Schiff bases: The pentadieniminium cation. Journal of Chemical Theory and Computation, 4(8), 1189–1199. doi:10.1021/Ct800148n.Google Scholar
  149. Szymczak, J. J., Barbatti, M., & Lischka, H. (2009). Is the photoinduced isomerization in retinal protonated schiff bases a single- or double-torsional process? The Journal of Physical Chemistry A, 113(43), 11907–11918. doi:10.1021/jp903329j.Google Scholar
  150. Szymczak, J. J., Barbatti, M., & Lischka, H. (2011). Influence of the active space on CASSCF nonadiabatic dynamics simulations. International Journal of Quantum Chemistry, 111(13), 3307–3315. doi:10.1002/qua.22978.Google Scholar
  151. Tapavicza, E., Tavernelli, I., & Rothlisberger, U. (2007). Trajectory surface hopping within linear response time-dependent density-functional theory. Physical Review Letters, 98(2), 023001.Google Scholar
  152. Thompson, M. S., Cui, W., & Reilly, J. P. (2007). Factors that impact the vacuum ultraviolet photofragmentation of peptide ions. Journal of The American Society for Mass Spectrometry, 18(8), 1439–1452.Google Scholar
  153. Thompson, M. S., Cui, W., & Reilly, J. P. (2004). Fragmentation of singly charged peptide ions by photodissociation at î= 157 nm. Angewandte Chemie-International Edition,43(36), 4791–4794Google Scholar
  154. Torikai, A., & Shibata, H. (1999) Effect of ultraviolet radiation on photodegradation of collagen. Journal of Applied Polymer Science, 73(7), 1259–1265.Google Scholar
  155. Tully, J. C. (1990). Molecular-dynamics with electronic-transitions. Journal of Chemical Physics, 93(2), 1061–1071.Google Scholar
  156. Tully, J. C. (1998). Mixed quantum-classical dynamics. Faraday Discussions, 110, 407–419.Google Scholar
  157. Ullrich, S., Schultz, T., Zgierski, M. Z., & Stolow, A. (2004). Electronic relaxation dynamics in DNA and RNA bases studied by time-resolved photoelectron spectroscopy. Physical Chemistry Chemical Physics, 6(10), 2796–2801.Google Scholar
  158. Vallet, V., Lan, Z. G., Mahapatra, S., Sobolewski, A. L.,& Domcke, W. (2004). Time-dependent quantum wave-packet description ofthe \({}^{1}\pi {\sigma }^{{\ast}}\) photochemistry of pyrrole. Faraday Discussions, 127, 283–293.Google Scholar
  159. Vallet, V., Lan, Z. G., Mahapatra, S., Sobolewski, A. L.,& Domcke, W. (2005). Photochemistry of pyrrole: Time-dependent quantum wave-packet description of the dynamics at the \({}^{1}{\mathrm{GREEK(ps)}}^{{\ast}}-{\mathrm{S}}_{\mathrm{o}}\) conical intersections. Journal of Chemical Physics, 123(14), 144307.Google Scholar
  160. van den Brom, A. J., Kapelios, M., Kitsopoulos, T. N., Nahler, N. H., Cronin, B., & Ashfold, M. N. R. (2005). Photodissociation and photoionization of pyrrole following the multiphoton excitation at 243 and 364.7 nm. Physical Chemistry Chemical Physics, 7(5), 892–899.Google Scholar
  161. Vazdar, M., Eckert-Maksić, M., Barbatti, M., & Lischka, H. (2009). Excited-state non-adiabatic dynamics simulations of pyrrole. Molecular Physics, 107(8), 845–854. doi:10.1080/00268970802665639.Google Scholar
  162. Venkatesan, T. S., Mahapatra, S., Meyer, H. D., Koppel, H., & Cederbaum, L. S. (2007). Multimode Jahn-Teller and pseudo-Jahn-Teller interactions in the cyclopropane radical cation: Complex vibronic spectra and nonradiative decay dynamics. The Journal of Physical Chemistry A, 111(10), 1746–1761.Google Scholar
  163. Virshup, A. M., Punwong, C., Pogorelov, T. V., Lindquist, B. A., Ko, C., & Martinez, T. J. (2009). Photodynamics in complex environments: Ab initio multiple spawning quantum mechanical/molecular mechanical dynamics. The Journal of Physical Chemistry B, 113(11), 3280–3291. doi:10.1021/Jp8073464Google Scholar
  164. Vreven, T., Bernardi, F., Garavelli, M., Olivucci, M., Robb, M. A., & Schlegel, H. B. (1997). Ab initio photoisomerization dynamics of a simple retinal chromophore model. Journal of the American Chemical Society, 119(51), 12687–12688.Google Scholar
  165. Wald, G. (1968). Molecular basis of visual excitation. Science, 162(3850), 230.Google Scholar
  166. Wang, Q., Schoenlein, R. W., Peteanu, L. A., Mathies, R. A., & Shank, C. V. (1994). Vibrationally coherent photochemistry in the femtosecond primary event of vision. Science, 266(5184), 422–424.Google Scholar
  167. Wanko, M., Hoffmann, M., Strodet, P., Koslowski, A., Thiel, W., Neese, F., Frauenheim, T., & Elstner, M. (2005). Calculating absorption shifts for retinal proteins: Computational challenges. The Journal of Physical Chemistry B, 109(8), 3606–3615.Google Scholar
  168. Warshel, A. (1976). Bicycle-pedal model for 1st step in vision process. Nature, 260(5553), 679–683.Google Scholar
  169. Warshel, A., & Barboy, N. (1982). Energy-storage and reaction pathways in the 1st step of the vision process. Journal of the American Chemical Society, 104(6), 1469–1476.Google Scholar
  170. Warshel, A., & Chu, Z. T. (2001). Nature of the surface crossing process in bacteriorhodopsin: Computer simulations of the quantum dynamics of the primary photochemical event. The Journal of Physical Chemistry B, 105(40), 9857–9871.Google Scholar
  171. Wei, J., Riedel, J., Kuczmann, A., Renth, F., & Temps, F. (2004). Photodissociation dynamics of pyrrole: Evidence for mode specific dynamics from conical intersections. Faraday Discussions, 127, 267–282.Google Scholar
  172. Weingart, O., Buss, V., & Robb, M.A. (2005). Excited state molecular dynamics of retinal model chromophores. Phase Transitions78(1–3), 17–24.Google Scholar
  173. Weingart, O., Migani, A., Olivucci, M., Robb, M. A., Buss, V., & Hunt, P. (2004). Probing the photochemical funnel of a retinal chromophore model via zero-point energy sampling semiclassical dynamics. The Journal of Physical Chemistry A,108(21), 4685–4693.Google Scholar
  174. Weingart, O., Schapiro, I., & Buss, V. (2006). Bond torsion affects the product distribution in the photoreaction of retinal model chromophores. Journal of Molecular Modeling, 12(5), 713–721.Google Scholar
  175. Weingart, O., Schapiro, I., & Buss, V. (2007). Photochemistry of visual pigment chromophore models by ab initio molecular dynamics. The Journal of Physical Chemistry B, 111(14), 3782–3788.Google Scholar
  176. Werner, U., Mitric, R., Suzuki, T., & Bonacic-Koutecký, V. (2008). Nonadiabatic dynamics within the time dependent density functional theory: Ultrafast photodynamics in pyrazine. Chemical Physics, 349(1–3), 319–324.Google Scholar
  177. Worth, G. A., & Cederbaum, L. S. (2004). Beyond Born-Oppenheimer: Molecular dynamics through a conical intersection. Annual Review of Physical Chemistry, 55, 127–158.Google Scholar
  178. Worth, G. A., Hunt, P., & Robb, M. A. (2003). Nonadiabatic dynamics: A comparison of surface hopping direct dynamics with quantum wavepacket calculations. The Journal of Physical Chemistry A, 107(5), 621–631.Google Scholar
  179. Yagi, K., & Takatsuka, K. (2005). Nonadiabatic chemical dynamics in an intense laser field: Electronic wave packet coupled with classical nuclear motions. Journal of Chemical Physics, 123(22), 224103. doi:Artn224103. doi:10.1063/1.2130335.Google Scholar
  180. Zechmann, G., & Barbatti, M. (2008). Photophysics and deactivation pathways of thymine. The Journal of Physical Chemistry A, 112(36), 8273–8279. doi:10.1021/jp804309x.Google Scholar
  181. Zewail, A. H. (2000). Femtochemistry: Atomic-scale dynamics of the chemical bond. The Journal of Physical Chemistry A, 104(24), 5660–5694. doi:10.1021/Jp001460h.Google Scholar
  182. Zhu, C. Y., Nangia, S., Jasper, A. W., & Truhlar, D. G. (2004). Coherent switching with decay of mixing: An improved treatment of electronic coherence for non-Born-Oppenheimer trajectories. Journal of Chemical Physics, 121(16), 7658–7670.Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Mario Barbatti
    • 1
  • Matthias Ruckenbauer
    • 2
  • Jaroslaw J Szymczak
    • 3
  • Bernhard Sellner
    • 4
  • Mario Vazdar
    • 5
  • Ivana Antol
    • 6
  • Mirjana Eckert-Maksić
    • 7
  • Hans Lischka
    • 8
  1. 1.Institute for Theoretical ChemistryUniversity of ViennaViennaAustria
  2. 2.Max-Planck-Institut für KohlenforschungMülheim an der RuhrGermany
  3. 3.Research Lab Computational Technologies and ApplicationsUniversity of ViennaViennaAustria
  4. 4.Laboratory for Physical-Organic Chemistry – Division of Organic Chemistry and BiochemistryRudjer Bošković InstituteZagrebCroatia
  5. 5.Department of Chemistry and BiochemistryTexas Tech UniversityLubbockUSA
  6. 6.Laboratory for Physical-Organic Chemistry – Division of Organic Chemistry and BiochemistryRudjer Bošković InstituteZagrebCroatia
  7. 7.Laboratory for Physical-Organic Chemistry – Division of Organic Chemistry and BiochemistryRudjer Bošković InstituteZagrebCroatia
  8. 8.Department of Chemistry and BiochemistryTexas Tech UniversityLubbockUSA

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