Journal of Computer-Aided Molecular Design

, Volume 20, Issue 7–8, pp 511–518 | Cite as

Computational photochemistry of retinal proteins

  • Marius Wanko
  • Michael Hoffmann
  • Thomas Frauenheim
  • Marcus Elstner


High spectral tunability and quantum yield are the striking features of rhodopsin photochemistry. They rely on a strong and complex interaction of their chromophore, the protonated Schiff base of retinal, with its protein environment. In this article, we review the progress in the computational modeling of these systems, focusing on the optical properties and the excited state dynamics. While the earlier success of atomistic theoretical models was based on the breakthrough in X-ray crystallography and combined quantum mechanical molecular mechanical (QM/MM) methodology, recent advances point out the importance of high-level QM methods and the incorporation of effects that are neglected in conventional QM/MM or ONIOM schemes, like polarization and charge transfer.


Retinal Rhodopsin Color tuning Opsin shift Photoisomerization QM/MM MRCI TDDFT OM2 SORCI 



Becke-3-parameter hybrid exchange and Lee–Yang–Parr correlation functional


Bond length alternation




Complete active space self consistent field method


Complete active space method with second order perturbation correction


Coupled cluster singles doubles


Chemistry at HArvard molecular mechanics


(Time-dependent) density functional theory


Generalized gradient approximation


Hydrogen bonded network


Hartree–Fock method


Local density approximation


Second order Møller–Plesset perturbation theory


Multi-reference configuration interaction


Orthogonalization method 2


Proton affinity


Pharaonis phoborhodopsin (also called sensory rhodopsin II)


Protonated Schiff base


Combined quantum mechanical molecular mechanical method


Self-consistent charge density functional based tight binding method


Spectroscopy oriented configuration interaction


  1. 1.
    Logunov SL, Song L, El-Sayed MA (1996) J Phys Chem 100:18586CrossRefGoogle Scholar
  2. 2.
    Kochendoerfer GG, Lin SW, Sakmar TT, Mathies RA (1999). TIBS 24:300Google Scholar
  3. 3.
    Nakanishi K, Balogh-Nair Y, Arnaboldi M, Tsujimoto K, Honig B (1980) J Am Chem Soc 102:7945CrossRefGoogle Scholar
  4. 4.
    Van der Steen R, Biesheuvel BL, Lugtenburg J (1986) J Am Chem Soc 108:6410CrossRefGoogle Scholar
  5. 5.
    Harbison GS, Mulder PPJ, Pardoen JA (1985) Biochemistry 24:6955CrossRefGoogle Scholar
  6. 6.
    Harbison GS, Mulder PPJ, Pardoen JA (1985) J Am Chem Soc 107:4810Google Scholar
  7. 7.
    Wada M, Sakutai M, Inoue Y, Tamura Y, Watanabe Y (1994) J Am Chem Soc 116:1537CrossRefGoogle Scholar
  8. 8.
    Kakitani H, Kakitani T, Rodman H, Honig B (1985) Photochem Photobiol 41:471Google Scholar
  9. 9.
    Kochendoerfer G, Wang Z, Oprian DD, Mathies RA (1997) Biochemistry 36:6577CrossRefGoogle Scholar
  10. 10.
    Irving CS, Byers GW, Leermake PA (1969) J Am Chem Soc 91:2141CrossRefGoogle Scholar
  11. 11.
    Irving CS, Byers GW, Leermake PA (1970) Biochemistry 9:858CrossRefGoogle Scholar
  12. 12.
    Beppu Y, Kakitani T (1994) Photochem Photobiol 59:660Google Scholar
  13. 13.
    Birge RR, Murray LM, Pierce BM, Akita H, Balogh-Nair V, Findsen LA, Nakanishi K (1985) Proc Natl Acad Sci USA 82:4117CrossRefGoogle Scholar
  14. 14.
    Baasov T, Friedman N, Sheves M (1987) Biochemistry 26:3210CrossRefGoogle Scholar
  15. 15.
    Hu J, Griffin RG, Herzfeld J (1994) Proc Natl Acad Sci USA 91:8880CrossRefGoogle Scholar
  16. 16.
    Ren L, Martin CH, Wise KJ, Gillespie NB, Luecke H, Lanyi JK, Spudich JL, Birge RR (2001) Biochemistry 40:13906CrossRefGoogle Scholar
  17. 17.
    Rajamani R, Gao J (2002) J Comp Chem 23(1):96CrossRefGoogle Scholar
  18. 18.
    Dinner AR, Lopez X, Karplus M (2003) Theor Chem Acc 109:118Google Scholar
  19. 19.
    Vreven T, Morokuma K (2003) Theor Chem Acc 109:125Google Scholar
  20. 20.
    Hayashi S, Ohmine I (2000) J Phys Chem B 104:10678CrossRefGoogle Scholar
  21. 21.
    Houjou H, Koyama K, Wada M, Sameshima K, Inoue Y, Sakurai M (1998) Chem Phys Lett 294:162CrossRefGoogle Scholar
  22. 22.
    Warshel A, Chu ZT (2001) J Phys Chem B 105:9857CrossRefGoogle Scholar
  23. 23.
    Zhou H, Tajkhorshid E, Frauenheim Th, Suhai S, Elstner M (2002) Chem Phys 277:91CrossRefGoogle Scholar
  24. 24.
    Wanko M, Hoffmann M, Strodel P, Koslowski A, Thiel W, Neese F, Frauenheim T, Elstner M (2005) J Phys Chem B 109:3606CrossRefGoogle Scholar
  25. 25.
    Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim Th, Suhai S, Seifert G (1998) Phys Rev B 58:7260CrossRefGoogle Scholar
  26. 26.
    Okada T, Sugihara M, Bondar A, Elstner M, Entel P, Buss V (2004) J Mol Biol 342:571CrossRefGoogle Scholar
  27. 27.
    Champagne B, Perpète EA, Jacquemin D, van Gisbergen SJA, Baerends E-J, Soubra-Ghaoui C, Robins KA, Kirtman B (2000) J Phys Chem A 104(20):4755CrossRefGoogle Scholar
  28. 28.
    Van Gisbergen SJA, Fonseca Guerra C, Baerends EJ (2000) J Comp Chem 21(16):1511CrossRefGoogle Scholar
  29. 29.
    Martin JML (1996) Chem Phys Lett 259(3):669CrossRefGoogle Scholar
  30. 30.
    N. Bondar et al. (2007) (to be published)Google Scholar
  31. 31.
    Bondar A, Fischer S, Smith JC, Elstner M, Suhai S (2004) J Am Chem Soc 126:14668CrossRefGoogle Scholar
  32. 32.
    Bondar A, Elstner M, Suhai S, Smith JC, Fischer S (2004) Structure 12:1281CrossRefGoogle Scholar
  33. 33.
    Koslowski A, Beck ME, Thiel W (2003) J Comput Chem 24:714CrossRefGoogle Scholar
  34. 34.
    Neese F (2003) J Chem Phys 119:9428CrossRefGoogle Scholar
  35. 35.
    Hoffmann M, Wanko M, Strodel P, König PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M (2006) J Am Chem Soc 128:10808CrossRefGoogle Scholar
  36. 36.
    Birge RR, Zhang C (1990) J Chem Phys 92:7178CrossRefGoogle Scholar
  37. 37.
    Chizhov I, Schmies G, Seidel R, Sydor JR, Lüttenberg B, Engelhard M (1998) Biophys J 75:999Google Scholar
  38. 38.
    Shimono K, Iwamoto M, Sumi M, Kamo N (2000) Photochem Photobiol 72:141CrossRefGoogle Scholar
  39. 39.
    Shimono K, Kitami M, Iwamoto M, Kamo N (2000) Biophys Chem 87:225CrossRefGoogle Scholar
  40. 40.
    Shimono K, Furutani Y, Kandori H, Kamo N (2002) Biochemistry 41:6504CrossRefGoogle Scholar
  41. 41.
    Shimono K, Iwamoto M, Sumi M, Kamo N (2001) Biochim Biophys Acta 1515:92CrossRefGoogle Scholar
  42. 42.
    Shimono K, Hayashi T, Ikeura Y, Sudo Y, Iwamoto M, Kamo N (2003) J Biol Chem 278:23882CrossRefGoogle Scholar
  43. 43.
    Kandori H, Furutani Y, Shimono K, Shichida Y, Kamo N (2001) Biochemistry 40:15693CrossRefGoogle Scholar
  44. 44.
    Houjou H, Inoue Y, Sakurai M (2001) J Phys Chem B 105:867CrossRefGoogle Scholar
  45. 45.
    Wang Q, Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1994) Science 266:422CrossRefGoogle Scholar
  46. 46.
    Atkinson GH, Ujj L, Zhou YD (2000) J Phys Chem A 104:413CrossRefGoogle Scholar
  47. 47.
    Herbst J, Heyne K, Diller R (2002) Science 294:822CrossRefGoogle Scholar
  48. 48.
    Terentis AC, Zhou Y, Atkinson GH (2003) J Phys Chem A 107:10787CrossRefGoogle Scholar
  49. 49.
    Schenkl S, van Mourik F, Friedman N, Sheves M, Schlesinger R, Haacke S, Chergui M (2006) Proc Natl Acad Sci USA 103(11):4101CrossRefGoogle Scholar
  50. 50.
    Wanko M, Garavelli M, Bernardi F, Niehaus TA, Frauenheim Th, Elstner M (2004) J Chem Phys 120:1674CrossRefGoogle Scholar
  51. 51.
    Garavelli M, Celani P, Bernardi F, Robb MA, Olivucci M (1997) J Am Chem Soc 119:6891CrossRefGoogle Scholar
  52. 52.
    Vreven T, Bernardi F, Garavelli M, Olivucci M, Robb MA, Schlegel HB (1997) J Am Chem Soc 119:12687CrossRefGoogle Scholar
  53. 53.
    Cembran A, Bernardi F, Olivucci M, Garavelli M (2003) J Am Chem Soc 125:12509CrossRefGoogle Scholar
  54. 54.
    Cembran A, Bernardi F, Olivucci M, Garavelli M (2005) Proc Natl Acad Sci USA 102(18):6255CrossRefGoogle Scholar
  55. 55.
    Garavelli M, Vreven T, Celani P, Bernardi F, Robb M, Olivucci M (1998) J Am Chem Soc 120:1285CrossRefGoogle Scholar
  56. 56.
    Garavelli M, Bernardi F, Robb MA, Olivucci M (1999) J Mol Struct 463:59CrossRefGoogle Scholar
  57. 57.
    Tsiper EV, Chernyak V, Tretiak S, Mukamel S (1999) J Chem Phys 110(17):8328CrossRefGoogle Scholar
  58. 58.
    González-Luque R, Garavelli M, Bernardi F, Merchán M, Robb MA, Olivucci M (2000) Proc Natl Acad Sci USA 97(17):9379CrossRefGoogle Scholar
  59. 59.
    Migani A, Robb MA, Olivucci M (2003) J Am Chem Soc 125:2804CrossRefGoogle Scholar
  60. 60.
    Weingart O, Migani A, Olivucci M, Robb MA, Buss V, Hunt P (2004) J Phys Chem A 108:4685CrossRefGoogle Scholar
  61. 61.
    Hayashi S, Tajkhorshid E, Schulten K (2003) Biophys J 85:1440CrossRefGoogle Scholar
  62. 62.
    Page CS, Olivucci M (2003) J Comput Chem 24:298CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2006

Authors and Affiliations

  • Marius Wanko
    • 1
  • Michael Hoffmann
    • 1
  • Thomas Frauenheim
    • 1
  • Marcus Elstner
    • 2
    • 3
  1. 1.BCCMSUniversität BremenBremenGermany
  2. 2.Theoretische Chemie, TU BraunschweigBraunschweigGermany
  3. 3.Department of Molecular BiophysicsGerman Cancer Research CenterHeidelbergGermany

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