Nonadiabatic ab initio dynamics of two models of schiff base retinal

Journal of Physical Chemistry A

Volumn 113, Issue 16, 2009, Pages 4356-4366

  Ishida, Toshimasa ^a   Nanbu, Shinkoh ^b   Nakamura, Hiroki ^c  

^a KYOTO UNIVERSITY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

^c INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; AB INITIO DYNAMICS; BASIS SETS; BRANCHING RATIO; C-C BONDS; CAS-SCF; CLASSICAL DYNAMICS; DIHEDRAL ANGLES; ELECTRONIC GROUND STATE; ENERGY RELAXATION; FINAL STATE; FOURIER TRANSFORMATIONS; GASPHASE; INTERMEDIATE STATE; METASTABLE INTERMEDIATE; METHYL GROUP; NON-ADIABATIC; NON-ADIABATIC TRANSITIONS; ON-THE-FLY; PROTONATED SCHIFF BASE; QUANTUM CHEMICAL; QUANTUM CHEMICAL COMPUTATIONS; SCHIFF-BASE; SHAFT MOTION; SWITCHING SCHEME; TIME EVOLUTIONS; TRANSITION MECHANISM; VIBRATIONAL FREQUENCIES;

ALGORITHMS; BOND LENGTH; DYNAMICS; FOURIER ANALYSIS; GROUND STATE; HYDROCARBONS; ISOMERIZATION; MINING; PHOTOEXCITATION; POTENTIAL ENERGY; POTENTIAL ENERGY SURFACES; QUANTUM CHEMISTRY;

OPHTHALMOLOGY;

RETINAL; SCHIFF BASE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; FOURIER ANALYSIS; ISOMERISM; MOTION; QUANTUM THEORY; TIME;

FOURIER ANALYSIS; ISOMERISM; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOTION; QUANTUM THEORY; RETINALDEHYDE; SCHIFF BASES; TIME FACTORS;

EID: 65749102124     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8110315     Document Type: Article

References (52)

1. Okada, T.; Ernst, O. P.; Palczewski, K.; Hofmann, K. P. Trends Biochem. Sci. 2001, 26, 318-324.
2. Sakmar, T. P.; Menon, S. T.; Marin, E. P.; Awad, E. S. Annu. Rev. Biophys. Biomol. Struct. 2002, 31, 443-484.
3. Burns, M. E.; Baylor, D. A. Annu. Rev. Neurosci. 2001, 24, 779-805.
4. Hubbell, W. L.; Altenbach, C.; Hubbell, C. M.; Khorana, H. G. Adv. Protein Chem. 2003, 63, 243-290.
5. Wanko, M.; Hoffmann, M.; Frauenheim, T. J.; Elstner, M. J. Comput. Aided Mol. Des. 2006, 20, 511-518.
6. Vreven, T.; Morokuma, K. J. Chem. Phys. 2000, 113, 2969-2975.
7. Frutos, L. M.; Andruniow, T.; Santoro, F.; Ferroee, N.; Olivucci, M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7764-7769.
8. Weingart, O. J. Am. Chem. Soc. 2007, 129, 10618-10619.
9. Schapiro, I.; Weingart, O.; Buss, V. J. Am. Chem. Soc. 2009, 131, 16-17.
10. Nakamura H. Nonadiabatic Transitions, Concepts, Basic Theories and Applications; World Scientific: Singapore, 2002.
11. Zhu, C.; Nakamura, H. J. Chem. Phys. 1994, 101, 4855-4866.
12. Zhu, C.; Nakamura, H. J. Chem. Phys. 1994, 101, 10630-10647.
13. Zhu, C.; Nakamura, H. J. Chem. Phys. 1995, 102, 7448-7461.
14. Nakamura, H. J. Theor. Comput. Chem. 2005, 4, 127-137.
15. Nakamura, H. Adv. Chem. Phys. 2008, 138, 95-212.
16. Landau, L. Phys. Z. Soviet. 1932, 2, 46-51.
17. Zener, C. Proc. R. Soc. London A 1932,137, 696-702.
18. Stiickelberg, E. C. G. Helv. Phys. Acta 1932, 5, 369.
19. Kakitani, T.; Kakitani H., J. Phys. Soc. Jpn. 1975, 38, 1455-1463.
20. Warshel, A. Nature 1976, 260, 679-683.
21. Liu, R. S. H.; Asato, A. E. Proc. Natl. Acad. Sic. U.S.A. 1985, 82, 259-263.
22. Liu, R. S. H.; Browne, D. T. Acc. Chem. Res. 1986, 19, 42-48.
23. Liu, R. S. H.; Hammond, G. S. Proc. Natl. Acad. Sic. U.S.A. 2000, 97, 11153-11158.
24. Yamada, Y.; Yamato, T.; Kakitani, T.; Yamamoto, S. J. Photo-science 2002, 9, 51-54.
25. Strambi, A.; Coto, P. B.; Frutos, L. M.; Ferre, N.; Olivucci, M. J. Am. Chem. Soc. 2008, 130, 3382-3388.
26. MOLPRO, version 2006.1, a package of ab initio programs designed by:Werner, H.-J.; Knowles, P. J.; Lindh, R.; Manby, F. R.; Schutz, M.; Celani, P.; Korona, T.; Rauhut, G.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Cooper, D. L.; Deegan, M. J. O.; Dobbyn, A. J.; Eckert, F.; Hampel, C.; Hetzer, G.; Lloyd, A. W.; McNicholas, S. J.; Meyer, W.; Mura, M. E.; Nicklass, A.; Palmieri, P.; Pitzer, R.; Schumann, U.; Stoll, H.; Stone, A. J.; Tarroni, R.; Thorsteinsson, T.; 2006; http://www.molpro.net.
27. MOLPRO, version 2002.6, a package of ab initio programs designed by: Werner, H.-J.; Knowles, P. J.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Celani, P.; Cooper, D. L.; Deegan, M. J. O.; Dobbyn, A. J.; Eckert, F.; Hampel, C.; Hetzer, G.; Knowles, P. J.; Korona, T.; Lindh, R.; Lloyd, A. W.; McNicholas, S. J.; Manby, F. R.; Meyer, W.; Mura, M. E.; Nicklass, A.; Palmieri, P.; Pitzer, R.; Rauhut, G.; Schutz, M.; Schumann, U.; Stoll, H.; Stone, A. J.;Tarroni, R.; Thorsteinsson, T.; Werner, H.-J., 2003; www.molpro.net.
28. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; Gaussian, Inc., Wallingford, CT, 2004.
29. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649.
30. Zhu, C.; Nobusada, K.; Nakamura, H. J. Chem. Phys. 2001, 115. 3031-3044.
31. Li, B.; Han, K.-L. J. Chem. Phys. 2008, 128, 114116/1-7.
32. Zhu, C.; Kamisaka, H.; Nakamura, H. J. Chem. Phys. 2001, 115, 11036-11039.
33. Zhu, C.; Kamisaka, H.; Nakamura, H. J. Chem. Phys. 2002, 116, 3234-3247.
34. Oloyede, P.; Mil'nikov, G.; Nakamura, H. J. Chem. Phys. 2006, 124, 144110/1-11.
35. Photodissociation of BrCH2COCl: Zhang, F.; Ding, W-J.; Fang, W.-H. J. Chem. Phys. 2006, 125, 184305/1-7.
36. Hubbard, R.; Kropf, A. Proc. Natl. Acad. Sci. U.S.A. 1958, 44, 130-139.
37. Kochendoerfer, G. G.; Mathies, R. A. J. Phys. Chem. 1996, 100, 14526-14532.
38. Vreven, T.; Bernardi, F.; Graveilli, M.; Olivucci, M.; Robb, A. A.; Schlegel, H. B. J. Am. Chem. Soc. 1997, 119, 12687-12688.
39. Atkins, P. W. Physical Chemistry, 6th ed.; Oxford University Press: Oxford, UK, 1998.
40. Gonzalez-Luque, R; Garavelli, M; Bernardi, F.; Merchan, M.; Robb, M. A.; Olivucci, M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9379-9384.
41. BlackmanR. B.; TukeyJ. W. The Measurement of Power Spectra; Dover: New York, 1958; Appendix B.5, pp 95-100.
42. Harris, F. J. Proc. IEEE 1978, 66, 51.
43. Miller W. H. Classical-Limit Quantum Mechanics and the Theory of Molecular Collisions. In Advances in Chemical Physics; Prigogine, I., Rice, S. A., Eds.; Wiley: New York, 1974; Vol XXVpp. 69177.
44. Hutchinson, J. S.; Wyatt, R. E. Phys. Rev.A 1981, 23, 1567-1584.
45. Hurley, J. B.; Ebrey, T. G.; Ilonig, B.; Ottolenghi, M. Nature 1977, 270, 540-542.
46. Koyama, Y.; Kubo, K.; Komori, M.; Yasuda, H.; Mukai, Y. Photochem. Photobiol. 1991, 54, 433-443.
47. Mayne H. R. The Classical Trajectory Approach to Reaction Dynamics In Dynamics of Molecules and Chemical Reactions; Wyatt R. E., Zhang J. Z. H., Eds.; Marcel Dekker, Inc.: New York, 1996; Chapter 15, p 589.
48. Weingart, O.; Migani, A.; Olivucci, M.; Robb, M. A.; Buss, V.; Hunt, P. J. Phys. Chem. A 2004, 108, 4685-4693.
49. Barbatti, M.; Ruckenbauer, M.; Szymczak, J. J.; Aquino Adelia, J. A.; Lischka, H. Phys. Chem. Chem. Phys. 2008, 10, 482-494.
50. Groenhof, G.; Bouxin-Cademartory, M.; Hess, B.; De Visser, S. P.; Berendsen, H. J. C.; Olivucci, M.; Mark, A. E.; Robb, M. A. J. Am. Chem. Soc. 2004, 126, 4228-4233.
51. Klein, S.; Bearpark, M. J.; Smith, B. R.; Robb, M. A.; Olivucci, M.; Bernardi, F. Chem. Phys. Lett. 1981, 292, 259-266.
52. Barbatti, M.; Granucci, G.; Persico, M.; Ruckenbauer, M.; Vazdar, M.; Eckert-Maksic, M.; Lischka, H. J. Photochem. Photobiol. A 2007, 190, 228-240.