Steric and electrostatic effects on photoisomerization dynamics using QM/MM ab initio multiple spawning

Theoretical Chemistry Accounts

Volumn 133, Issue 7, 2014, Pages 1-11

  Virshup, Aaron M ^a   Levine, Benjamin G ^b   Martínez, Todd J ^c,d  

^a DUKE UNIVERSITY   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c STANFORD UNIVERSITY   (United States)

^d SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Isomerization; Nonadiabatic dynamics; Surface hopping

Indexed keywords

EID: 84901738534     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-014-1506-5     Document Type: Article

References (65)

1. Yarkony DR (1996) Diabolical conical intersections. Rev Mod Phys 68: 985.
2. Yarkony DR (1998) Conical intersections: diabolical and often misunderstood. Acc Chem Res 31: 511.
3. Bernardi F, Olivucci M, Robb MA (1996) Potential energy surface crossings in organic photochemistry. Chem Soc Rev 25: 321.
4. Klessinger M, Michl J (1995) Excited states and photochemistry of organic molecules. VCH Publishers Inc, New York.
5. Levine BG, Martinez TJ (2007) Isomerization through conical intersections. Ann Rev Phys Chem 58: 613.
6. Virshup AM, Punwong C, Pogorelov TV, Lindquist B, Ko C, Martínez TJ (2009) Photodynamics in complex environments: ab initio multiple spwaning quantum mechanical/molecular mechanical dynamics. J Phys Chem B 113: 3280.
7. Groenhof G, Schäfer LV, Boggio-Pasqua M, Grubmüller H, Robb MA (2008) Arginine52 controls the photoisomerization process in photoactive yellow protein. J Am Chem Soc 130: 3250.
8. Ko C, Virshup AM, Martínez TJ (2008) Electrostatic control of the photoisomerization in the photoactive yellow protein chromophore: hybrid QM/MM ab initio multiple spawning simulation. Chem Phys Lett 460: 272.
9. Cembran A, Bernardi F, Olivucci M, Garavelli M (2004) Counterion controlled photoisomerization of retinal chromophore models: a computational investigation. J Am Chem Soc 126: 16018.
10. Altoe P, Bernardi F, Garavelli M, Orlandi G, Negri F (2005) Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore: a quantum chemical study. J Am Chem Soc 127: 3952.
11. Cembran A, Bernardi F, Olivucci M, Garavelli M (2005) The retinal chromophore/chloride ion pair: structure of the photoisomerization path and interplay of charge transfer and covalent states. Proc Natl Acad Sci 102: 6255.
12. Olsen S, Toniolo A, Ko C, Manohar L, Lamothe K, Martinez TJ (2005) Computation of reaction mechanisms and dynamics in photobiology. In: Olivucci M (ed) Computational photochemistry. Elsevier, Amsterdam.
13. Toniolo A, Olsen S, Manohar L, Martinez TJ (2004) Conical intersection dynamics in solution: the chromophore of green fluorescent protein. Faraday Discus 127: 149.
14. Martínez TJ (2006) Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores. Acc Chem Res 39: 119.
15. Vallee BL, Williams RJP (1968) Metalloenzymes: the entatic nature of their active sites. Proc Natl Acad Sci 59: 498.
16. Lightstone FC, Bruice TC (1996) Ground state conformations and entropic and enthalpic factors in the efficiency of intramolecular and enzymatic reactions. 1. Cyclic anhydride formation by substituted glutarates, succinate, and 3, 6-Endoxo-Δ4-tetrahydrophthalate monophenyl ester. J Am Chem Soc 118: 2595.
17. Ford L, Johnson L, Machin P, Phillips D, Tijian R (1974) Crystal structure of lysozyme-tetrasaccharide lactone complex. J Mol Bio 88: 349.
18. Ryde U, Olsson MHM, Pierloot K, Roos BO (1996) The cupric geometry of blue copper proteins is not strained. J Mol Bio 261: 586.
19. Shurki A, Štrajbl M, Villa J, Warshel A (2002) How much do enzymes really gain by restraining fragments? J Am Chem Soc 124: 4097.
20. Warshel A (2003) Computer simulations of enzyme catalysis: methods, progress and insights. Ann Rev Biophys Biomol Struct 32: 425.
21. Warshel A, Sharma PK, Kato M, Parson WW (2006) Modeling electrostatic effects in proteins. Biochim Biophys Acta 1764: 1647.
22. Suydam IT, Snow CD, Pande VS, Boxer SG (2006) Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science 313: 200.
23. Ben-Nun M, Martínez TJ (2000) Photodynamics of ethylene: ab initio studies of conical intersections. Chem Phys 259: 237.
24. Quenneville J, Martínez T (2003) Ab initio study of cis-trans photoisomerization in stilbene and ethylene. J Phys Chem, 107A.
25. Barbatti M, Paier J, Lischka H (2004) Photochemistry of ethylene: a multireference configuration interaction investigation of the excited-state energy surfaces. J Chem Phys 121: 11614.
26. Barbatti M, Ruckenbauer M, Lischka H (2005) The photodynamics of ethylene: a surface-hopping study on structural aspects. J Chem Phys 122: 174307.
27. Tao H, Levine BG, Martinez TJ (2009) Ab initio multiple spawning dynamics using multi-state second-order perturbation theory. J Phys Chem A 113: 13656.
28. Mori T, Glover WJ, Schuurman MS, Martinez TJ (2012) Role of Rydberg States in the photochemical dynamics of ethylene. J Phys Chem A 116: 2808.
29. Mestdagh JM, Visticot JP, Elhanine M, Soep B (2000) Prereactive evolution of monoalkenes excited in the 6 eV region. J Chem Phys 113: 237.
30. Farmanara P, Stert V, Radloff W (1998) Ultrafast internal conversion and fragmentation in electronically excited C2H4 and C2H3Cl molecules. Chem Phys Lett 288: 518.
31. Tao H, Allison TK, Wright TW, Stooke AM, Khurmi C, Tilborg JV, Liu Y, Falcone RW, Belkacem A, Martinez TJ (2011) Ultrafast internal conversion in ethylene. I. The excited state lifetime. J Chem Phys 134: 244306.
32. Sension RJ, Hudson BS (1989) Vacuum ultraviolet resonance Raman studies of the excited electronic states of ethylene. J Chem Phys 90: 1377.
33. Brooks BR, Schaefer IHF (1979) Sudden polarization: pyramidalization of twisted ethylene. J Am Chem Soc 101: 307.
34. Bonacic-Koutecky V, Bruckmann P, Hiberty P, Koutecky J, Leforestier C, Salem L (1975) Sudden Polarization in the Zwitterionic Z1 excited states of organic intermediates Photochemical implications. Ang Chem 14: 575.
35. Bonacic-Koutecky V (1978) Sudden polarization in zwitterionic excited states of organic intermediates in photochemical reactions. On a possible mechanism for bicyclo[3. 1. 0]hex-2-ene formation. J Am Chem Soc 100: 396.
36. Bonacic-Koutecky V, Koutecky J, Michl J (1987) Neutral and charged Biradicals, Zwitterions, funnels in S1, and proton translocation: their role in photochemistry, photophysics, and vision. Ang Chem 26: 170.
37. Barbatti M, Granucci G, Persico M, Lischka H (2004) Semiempirical molecular dynamics investigation of the excited state lifetime of ethylene. Chem Phys Lett 401: 276.
38. Ben-Nun M, Martínez TJ (1998) Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene. Chem Phys Lett 298: 57.
39. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103: 227.
40. Hu H, Yang W (2008) Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Ann Rev Phys Chem 59: 573.
41. Zhang Y, Liu H, Yang W (2000) Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J Chem Phys 112: 3483.
42. Field M, Bash P, Karplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comp Chem 11: 700.
43. Friesner RA, Guallar V (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Ann Rev Phys Chem 56: 389.
44. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Ang Chem Int Ed 48: 1198.
45. Slavicek P, Martinez TJ (2006) Multicentered valence electron effective potentials: solution to the link atom problem for ground and excited electronic states. J Chem Phys 124: 084107.
46. Ben-Nun M, Martinez TJ (1998) Direct evaluation of the Pauli repulsion energy using 'classical' wavefunction in hybrid quantum/classical potential energy surfaces. Chem Phys Lett 290: 289.
47. Maitland GC, Smith EB (1971) The intermolecular pair potential of argon. Mol Phys 22: 861.
48. Cornell W, Cieplak P, Bayly C, Gould I, Merz JK, Ferguson D, Spellmeyer D, Fox T, Caldwell J, Kollman P (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179.
49. Roos BO (1987) The complete active space self-consistent field method and its applications in electronic structure calculations. In: Lawley KP (ed) Advances in chemical physics: ab initio methods in quantum chemistry II. Wiley, New York, p 399.
50. Docken K, Hinze J (1972) LiH potential curves and wave functions. J Chem Phys 57: 4928.
51. Werner H-J, Knowles PJ, Lindh R, Schuetz M, Celani P, Korona T, Manby FR, Rauhut G, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Hampel C, Hetzer G, Lloyd AW, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pitzer R, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T MOLPRO, version, a package of ab initio programs.
52. Frisch M, Pople J, Binkley J (1984) Self-consistent molecular orbital methods. J Chem Phys 80: 3265.
53. Ben-Nun M, Martínez T (2002) Ab initio quantum molecular dynamics. Adv Chem Phys, 121.
54. Ben-Nun M, Quenneville J, Martínez T (2000) Ab initio multiple spawning: photochemistry from first principles quantum molecular dynamics. J Phys Chem 104A: 5161.
55. Heller E (1981) Frozen gaussians: a very simple semiclassical approximation. J Chem Phys 75: 2923.
56. Levine BG, Coe JD, Virshup AM, Martínez TJ (2008) Implementation of ab initio multiple spawning in the MolPro quantum chemistry package. Chem Phys 347: 3.
57. Fernandez-Alberti S, Roitberg AE, Nelson T, Tretiak S (2012) Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules. J Chem Phys 137: 014512.
58. Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S (2013) Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules. Chem Phys Lett 590: 208.
59. Wang L, Prezhdo OV (2014) A simple solution to the trivial crossing problem in surface hopping. J Phys Chem Lett 5: 713.
60. Habershon S (2012) Linear dependence and energy conservation in Gaussian wave packet basis sets. J Chem Phys 136: 014109.
61. Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Oxford University Press, Oxford, p 385.
62. Kutteh R (1998) RATTLE recipe for general holonomic constraints angle and torsion constraints. CCP5 Newslett, 46: 9.
63. Hack MD, Wensmann AM, Truhlar DG, Ben-Nun M, Martinez TJ (2001) Comparison of full multiple spawning, trajectory surface hopping and converged quantum mechanics for electronically nonadiabatic dynamics. J Chem Phys 115: 1172.
64. Efron R, Tibshirani R (1986) Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat Sci 1: 54.
65. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709.