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Accelerating QM/MM Calculations by Using the Mean Field Approximation

  • M. Elena Martín
  • M. Luz Sánchez
  • Aurora Muñoz-Losa
  • Ignacio Fdez. Galván
  • Manuel A. AguilarEmail author
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 21)

Abstract

It is well known that solvents can modify the frequency and intensity of the solute spectral bands, the thermodynamics and kinetics of chemical reactions, the strength of molecular interactions or the fate of solute excited states. The theoretical study of solvent effects is quite complicated since the presence of the solvent introduces additional difficulties with respect to the study of analogous problems in gas phase. The mean field approximation (MFA) is used for many of the most employed solvent effect theories as it permits to reduce the computational cost associated to the study of processes in solution. In this chapter we revise the performance of ASEP/MD, a quantum mechanics/molecular mechanics method developed in our laboratory that makes use of this approximation. It permits to combine state of the art calculations of the solute electron distribution with a detailed, microscopic, description of the solvent. As examples of application of the method we study solvent effects on the absorption spectra of some molecules involved in photoisomerization processes of biological systems.

Keywords

Excited State Oscillator Strength Phenolic Oxygen Bright State Classical Molecular Dynamic Simulation 
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.

References

  1. 1.
    Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation methods. Chem Rev 105:2999–3093CrossRefGoogle Scholar
  2. 2.
    Cramer CJ, Truhlar DG (1999) Chem Rev 99:2161Google Scholar
  3. 3.
    Rivail JL, Rinaldi D (1976) Chem Phys 18:233–242CrossRefGoogle Scholar
  4. 4.
    Ruiz-López MF (2008) In: solvation effects on molecules and biomolecules: computational methods and applications. In: Canuto S (ed) Springer series: Challenges and advances in computational chemistry and physics, SpringerGoogle Scholar
  5. 5.
    Warshel A, Levitt M (1976) J Mol Biol 103:227–249CrossRefGoogle Scholar
  6. 6.
    Singh UC, Kollman PA (1986) J Comput Chem 7:718–730CrossRefGoogle Scholar
  7. 7.
    Field M J, Bash PA, Karplus M (1990) J Comput Chem 11(6):700–733Google Scholar
  8. 8.
    Sánchez ML, Martín ME, Galván IF, Olivares del Valle FJ, Aguilar MA (2002) J Phys Chem B 106:4813CrossRefGoogle Scholar
  9. 9.
    Martín ME, Sánchez ML, Corchado JC, Muñoz-Losa A, Galván IF, Olivares del Valle FJ, Aguilar MA (2011) Theor Chem Acc 128:783–793CrossRefGoogle Scholar
  10. 10.
    Yamamoto T (2008) J Chem Phys 129:244104CrossRefGoogle Scholar
  11. 11.
    Warshel A (1991) Computer modelling of chemical reactions in enzymes and solutions. Wiley Interscience Publication, New YorkGoogle Scholar
  12. 12.
    Ten-no S, Hirata F, Kato S (1993) Chem Phys Lett 214:391CrossRefGoogle Scholar
  13. 13.
    Sato H, Hirata F, Kato S (1996) J Chem Phys 105:1546CrossRefGoogle Scholar
  14. 14.
    Hirata F (ed) (2003) Molecular theory of solvation (understanding chemical reactivity). Springer, BerlinGoogle Scholar
  15. 15.
    Nakano H, Yamamoto T (2013) J Chem Theory Comput 9:188–203CrossRefGoogle Scholar
  16. 16.
    Kaminski JW, Gusarov S, Kovalenko A, Wesolowski TA (2010) J Phys Chem A 114:6082CrossRefGoogle Scholar
  17. 17.
    Sánchez ML, Aguilar MA (1997) Olivares del Valle FJ. J Comput Chem 18:313CrossRefGoogle Scholar
  18. 18.
    Sánchez ML, Martín ME, Aguilar MA (2000) Olivares del Valle FJ J Comput Chem 21:705CrossRefGoogle Scholar
  19. 19.
    Galván IF, Sánchez ML, Martín ME, Olivares del Valle FJ (2003) Aguilar MA Comput Phys Commun 155:244Google Scholar
  20. 20.
    Tapia O (1991) In: Maksic ZB (ed) Theoretical treatment of large molecules and their interactions, vol 4. Springer, Berlin, p 435CrossRefGoogle Scholar
  21. 21.
    Angyán JG (1992) J Math Chem 10:93CrossRefGoogle Scholar
  22. 22.
    Sánchez ML, Aguilar MA, Olivares del Valle FJ (1997) J Comput Chem 18:313CrossRefGoogle Scholar
  23. 23.
    Canuto S, Coutinho K (1997) Avd Quantum Chem 28:89Google Scholar
  24. 24.
    Coutinho K, Oliveira MJ et al (1998) Int J Quantum Chem 66:249CrossRefGoogle Scholar
  25. 25.
    Martín ME, Sánchez ML, Olivares del Valle FJ, Aguilar MA (2002) J Chem Phys 116:1613CrossRefGoogle Scholar
  26. 26.
    Martín ME, Muñoz Losa A, Galván IF, Aguilar MA (2003) J Chem Phys 118:255CrossRefGoogle Scholar
  27. 27.
    Galván IF, Martín ME, Aguilar MA (2004) J Comput Chem 25:1227CrossRefGoogle Scholar
  28. 28.
    Galván IF, Sánchez ML, Martín ME, Olivares del Valle FJ, Aguilar MA (2003) J Chem Phys 118:255CrossRefGoogle Scholar
  29. 29.
    Okuyama-Yoshida N, Nagaoka M, Yamabe T (1998) Int J Quantum Chem 70:95CrossRefGoogle Scholar
  30. 30.
    Okuyama-Yoshida N, Kataoka K, Nagaoka M, Yamabe T (2000) J Chem Phys 113:3519CrossRefGoogle Scholar
  31. 31.
    Hirao H, Nagae Y, Nagaoka M (2001) Chem Phys Lett 348:350CrossRefGoogle Scholar
  32. 32.
    Banerjee A, Adams N, Simons J, Shepard R (1985) J Phys Chem 89:52CrossRefGoogle Scholar
  33. 33.
    Lippert E, Lüder W, Moll F, Nägele W, Boos H, Prigge H, Seibold-Blankenstein I (1961) Angew Chem 73:695–706CrossRefGoogle Scholar
  34. 34.
    Rotkiewicz K, Grellmann KH, Grabowski ZR (1973) Chem Phys Lett 19:315–318CrossRefGoogle Scholar
  35. 35.
    Grabowski ZR, Rotkiewicz K, Rettig W (2003) Chem Rev 103:3899–4032CrossRefGoogle Scholar
  36. 36.
    Kukura P, McCamant DW, Yoon S, Wandschneider DB, Mathies RA (2005) Science 310:1006CrossRefGoogle Scholar
  37. 37.
    Muñoz Losa A, Martin ME, Galván IF, Sánchez ML, Aguilar MA (2011) J Chem Theory Comput 7:4050–4059CrossRefGoogle Scholar
  38. 38.
    Meyer TE (1985) Biochim Biophys Acta 806:175CrossRefGoogle Scholar
  39. 39.
    Muñoz-Losa A, Galván IF, Aguilar MA, Martín ME (2007) J Phys Chem B 111:9864–9870CrossRefGoogle Scholar
  40. 40.
    Muñoz-Losa A, Martín ME, Galván I, Sánchez ML, Aguilar MA (2011) J Chem Theory Comput 7:4050–4059CrossRefGoogle Scholar
  41. 41.
    Muñoz-Losa A, Galván IF, Aguilar MA, Martín ME (2013) J Chem Theory Comput 9:1548–1556CrossRefGoogle Scholar
  42. 42.
    García-Prieto FF, Galván IF, Muñoz-Losa A, Aguilar MA, Martín ME (2013) J Chem Theory Comput 9:4481–4494CrossRefGoogle Scholar
  43. 43.
    Kort R, Vonk H, Xu X, Hoff WD, Crielaard W, Hellingwerf K (1996) J FEBS Lett 382:73CrossRefGoogle Scholar
  44. 44.
    Xie A, Hoff WD, Kroon AR, Hellingwerf K (1996) J Biochem 35:14671CrossRefGoogle Scholar
  45. 45.
    Unno M, Kumauchi M, Sasaki J, Tokunaga F, Yamaguchi S (2000) J Am Chem Soc 122:4233CrossRefGoogle Scholar
  46. 46.
    Genik UK, Soltis SM, Kuhn P, Canestrelli IL, Getzoff ED (1998) Nature 392:206CrossRefGoogle Scholar
  47. 47.
    Rocha-Rinza T, Christiansen O, Rajput J, Gopalan A, Rahbek DB, Andersen LH, Bochenkova AV, Granovsky AA, Bravaya KB, Nemukhim AV, Chistiansen KL, Nielsen MB (2009) J Phys Chem A 113:9442CrossRefGoogle Scholar
  48. 48.
    Nielsen IB, Boyé-Péronne S, El Ghazaly MOA, Kristensen MB, Nielsen SB, Andersen LH (2005) Biophys J 89:2597CrossRefGoogle Scholar
  49. 49.
    Putschögl M, Zirak P, Penzkofer A (2008) Chem Phys 343:107CrossRefGoogle Scholar
  50. 50.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, revision A11.3. Gaussian, Inc., PittsburghGoogle Scholar
  51. 51.
    Andersson K, Barysz M, Bernhardsson A, Blomberg MRA, Carissan Y, Cooper DL, Cossi M, Fleig T, Fu¨lscher MP, Gagliardi L, de Graaf C, Hess BA, Karlström G, Lindh R, Malmqvist P-Å, Neogrády P, Olsen J, Roos BO, Schimmelpfennig B, Schütz M, Seijo L, Serrano-Andrés L, Siegbahn PEM, Stalring J, Thorsteinsson T, Veryazov V, Wierzbowska M, Widmark P-O (2003) MOLCAS Version 5.2, University of Lund, Lund, SwedenGoogle Scholar
  52. 52.
    Refson K (2000) Comput Phys Commun 126:310CrossRefGoogle Scholar
  53. 53.
    Berendsen HJC, van der Spoel D, van Drunen R (1995) Comp Phys Comm 91:43–56CrossRefGoogle Scholar
  54. 54.
    Jorgensen W, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225CrossRefGoogle Scholar
  55. 55.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926CrossRefGoogle Scholar
  56. 56.
    Chirlian LE, Francl MM (1987) J Comput Chem 8:894CrossRefGoogle Scholar
  57. 57.
    Breneman M, Wiberg KB (1990) J Comput Chem 11:316CrossRefGoogle Scholar
  58. 58.
    Zuev D, Bravaya KB, Crawford TD, Lindh R, Krilov AI (2011) J Chem Phys 134:034310CrossRefGoogle Scholar
  59. 59.
    Gromov E, Burghardt I, Hynes I, Köppel H, Cederbaum LS (2007) J Photochem Photobiol A 190:241CrossRefGoogle Scholar
  60. 60.
    Gromov E, Burghardt I, Köppel H, Cederbaum LS (2007) J Am Chem Soc 129:6798CrossRefGoogle Scholar
  61. 61.
    Boggio-Pasqua M, Groenhof G (2012) J Phys Chem B 115:7021CrossRefGoogle Scholar
  62. 62.
    Putschögl M, Zirak P, Penzkofer A (2008) Chem Phys 343:107CrossRefGoogle Scholar
  63. 63.
    Rocha-Rinza T, Christiansenm O, Rajput H, Gopalan A, Rahbek DB, Andersen LH, Bochenkova AV, Granovsky AA, Bravaya KB, Nemukhin AV, Christiansen KL, Nielsen MB (2009) J Phys Chem A 113:9442CrossRefGoogle Scholar
  64. 64.
    Nielsen IB, Boye-Peronne S, El Ghazaly MOA, Kristensen MB, Nielsen SB (2005) Anderson LH. Biophys J 89:2597CrossRefGoogle Scholar
  65. 65.
    Zuev D, Bravaya KB, Crawford TD, Lindh R, Krylov AI (2011) J Chem Phys 134:034310CrossRefGoogle Scholar
  66. 66.
    Gromov EV, Burghardt I, Hynes JT, Köppel H, Cederbaum LS (2007) J Photochem Photobiol A Chem 190:241CrossRefGoogle Scholar
  67. 67.
    Muguruza González E, Guidoni L, Molteni C (2009) Phys Chem Chem Phys 11:4556CrossRefGoogle Scholar
  68. 68.
    Sergi A, Crüting M, Ferrario M (2001) F Buda J Phys Chem B 105:4386CrossRefGoogle Scholar
  69. 69.
    Naseem S, Laurent AD, Carroll EC, Vengris M, Kumauchi, Hoff MWD, Krylov AI, Larsen DS (2013) J Photochem Photobiol A Chem 270:43CrossRefGoogle Scholar
  70. 70.
    Wang Y, Li H (2010) J Chem Phys 133:034108CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • M. Elena Martín
    • 1
  • M. Luz Sánchez
    • 1
  • Aurora Muñoz-Losa
    • 1
  • Ignacio Fdez. Galván
    • 2
  • Manuel A. Aguilar
    • 1
    Email author
  1. 1.Área de Química FísicaUniversity of ExtremaduraBadajozSpain
  2. 2.Department of Chemistry–Ångström, The Theoretical Chemistry ProgrammeUppsala UniversityUppsalaSweden

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