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Reactive Processes with Molecular Simulations

  • Sabyashachi Mishra
  • Markus MeuwlyEmail author
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 12)

Abstract

Describing chemical reactions is one of the most challenging aspects of current computational approaches to chemistry. In this chapter established (EVB, ReaxFF) and novel (MMPT, ARMD) approaches are discussed that allow to study bond forming and bond breaking processes in a variety of chemical and biological environments. Particular emphasis is put on methods that enable investigating the dynamics of chemical reactions. For MMPT and ARMD methods, a number of model studies are discussed in more detail. They include the kinetics of NO rebinding to Myoglobin and the conformational transition in Neuroglobin which explores the full functionality of ARMD. The chapter closes with an outlook of possible generalizations of the methods discussed.

Keywords

Reactive Molecular Dynamics Proton Transfer Ligand Binding in Heme Proteins NO Detoxification 

References

  1. 1.
    London F (1929) Z Elektrochem 35:552–555Google Scholar
  2. 2.
    Eyring H, Polanyi M (1931) Z Phys Chem Abt B 12:279–311Google Scholar
  3. 3.
    Sato S (1955) J Chem Phys 23:592–593CrossRefGoogle Scholar
  4. 4.
    Sato S (1955) J Chem Phys 23:2465–2466CrossRefGoogle Scholar
  5. 5.
    Ellison FO (1963) J Am Chem Soc 85:3540–3544Google Scholar
  6. 6.
    Pauling L (1960) The nature of the chemical bond. Cornell University Press, Ithaca, NYGoogle Scholar
  7. 7.
    Pauling L (1932) J Am Chem Soc 54:3570–3582CrossRefGoogle Scholar
  8. 8.
    Johnston HS, Parr C (1963) J Am Chem Soc 85:2544–2551CrossRefGoogle Scholar
  9. 9.
    van Duin ACT, Dasgupta S, Lorant F, Goddard WA III (2001) J Phys Chem A 105:9396–9409CrossRefGoogle Scholar
  10. 10.
    Lifson S, Warshel A (1968) J Chem Phys 49:5116–5129CrossRefGoogle Scholar
  11. 11.
    Levitt M, Lifson S (1969) J Mol Biol 46:269–279CrossRefGoogle Scholar
  12. 12.
    Hwang MJ, Stockfisch TP, Hagler AT (1994) J Am Chem Soc 116:2515–2525CrossRefGoogle Scholar
  13. 13.
    Maple JR, Hwang MJ, Stockfisch TP, Dinur U, Waldman M, Ewig CS, Hagler AT (1994) J Comput Chem 15:162–182CrossRefGoogle Scholar
  14. 14.
    Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M (1983) J Comput Chem 4:18–217CrossRefGoogle Scholar
  15. 15.
    Weiner SJ, Kollman PA, Case DA, Singh U, Ghio C, Alagona G, Profeta S Jr, Weiner P (1984) J Am Chem Soc 106:765–784CrossRefGoogle Scholar
  16. 16.
    Jorgensen WL, Tirado-Rives J (1988) J Am Chem Soc 110:1657–1666CrossRefGoogle Scholar
  17. 17.
    Hermans J, Berendsen HJC, van Gunsteren WF, Postma JPM (1984) Biopolymers 23:1CrossRefGoogle Scholar
  18. 18.
    Deeth R, Anastasi A, Diedrich C, Randell K (2009) Coord Chem Rev 253:795–816CrossRefGoogle Scholar
  19. 19.
    Warshel A, Levitt M (1976) J Mol Biol 103:227–249CrossRefGoogle Scholar
  20. 20.
    Alagona G, Ghio C, Kollman PA (1986) J Mol Biol 191:23–27CrossRefGoogle Scholar
  21. 21.
    Bash PA, Field MJ, Karplus M (1987) J Am Chem Soc 109:8092–8094CrossRefGoogle Scholar
  22. 22.
    Claeyssens F, Ranaghan KE, Manby FR, Harvey JN, Mulholland AJ (2005) Chem Commun 40:5068–5070CrossRefGoogle Scholar
  23. 23.
    Zhou HY, Tajkhorshid E, Frauenheim T, Suhai S, Elstner M (2002) Chem Phys 277:91–103CrossRefGoogle Scholar
  24. 24.
    Konig PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, Cui Q (2006) J Phys Chem A 110:548–563CrossRefGoogle Scholar
  25. 25.
    Altun A, Guallar V, Friesner RA, Shaik S, Thiel W (2006) J Am Chem Soc 128:3924–3925CrossRefGoogle Scholar
  26. 26.
    Mei HS, Tuckerman ME, Sagnella DE, Klein ML (1998) J Phys Chem B 102:10446–10458CrossRefGoogle Scholar
  27. 27.
    Meuwly M, Karplus M (2002) J Chem Phys 116:2572–2585CrossRefGoogle Scholar
  28. 28.
    Cui Q, Elstner T, Karplus M (2003) J Phys Chem B 106:2721–2740CrossRefGoogle Scholar
  29. 29.
    Meuwly M, Müller A, Leutwyler S (2003) Phys Chem Chem Phys 5:2663–2672Google Scholar
  30. 30.
    Devi-Kesavan LS, Gao J (2003) J Am Chem Soc 125:1532–1540CrossRefGoogle Scholar
  31. 31.
    Zoete V, Meuwly M (2004) J Chem Phys 120:7085–7094CrossRefGoogle Scholar
  32. 32.
    Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J (2004) J Am Chem Soc 126:13649–13658CrossRefGoogle Scholar
  33. 33.
    Sauer J, Doebler J (2005) ChemPhysChem 6:1706–1710CrossRefGoogle Scholar
  34. 34.
    Li H, Elber R, Straub JE (1993) J Biol Chem 268:17908–17916Google Scholar
  35. 35.
    Zheng C, Makarov V, Wolynes PG (1996) J Am Chem Soc 118:2818–2824CrossRefGoogle Scholar
  36. 36.
    Meuwly M, Becker OM, Stone R, Karplus M (2002) Biophys Chem 98:183–207CrossRefGoogle Scholar
  37. 37.
    Nutt D, Meuwly M (2006) Biophys J 90:1191–1201CrossRefGoogle Scholar
  38. 38.
    Warshel A, Weiss RM (1980) J Am Chem Soc 102:6218–6226CrossRefGoogle Scholar
  39. 39.
    Grochowski P, Lesyng B, Bala P, McCammon JA (1996) Int J Quant Chem 60:1143–1164CrossRefGoogle Scholar
  40. 40.
    Kim Y, Corchado JC, Villa J, Xing J, Truhlar DG (2000) J Chem Phys 112:2718–2735CrossRefGoogle Scholar
  41. 41.
    Lammers S, Lutz S, Meuwly M (2008) J Comput Chem 29:1048–1063CrossRefGoogle Scholar
  42. 42.
    Lammers S (2006) Simulations of proton transfer processes using reactive force fields. Ph.D. thesis, University of BaselGoogle Scholar
  43. 43.
    Lammers S, Meuwly M (2004) Aust J Chem 57:1223–1228CrossRefGoogle Scholar
  44. 44.
    Meuwly M, Huston J (1999) J Chem Phys 110:8338–8347CrossRefGoogle Scholar
  45. 45.
    Danielsson J, Meuwly M (2008) J Chem Theory Comput 4:1083–1093CrossRefGoogle Scholar
  46. 46.
    Hong G, Rosta E, Warshel A (2006) J Phys Chem B 110:19570–19574CrossRefGoogle Scholar
  47. 47.
    Coulson CA, Danielsson U (1954) Ark Fys 8:239–244Google Scholar
  48. 48.
    Chang YT, Miller WH (1990) J Phys Chem 94:5884–5888CrossRefGoogle Scholar
  49. 49.
    Valero R, Song L, Gao J, Truhlar DG (2009) J Chem Theory Comput 5:1–22CrossRefGoogle Scholar
  50. 50.
    Valero R, Song L, Gao J, Truhlar DG (2009) J Chem Theory Comput 5:2191–2191CrossRefGoogle Scholar
  51. 51.
    Kamerlin SCL, Cao J, Rosta E, Warshel A (2009) J Phys Chem B 113:10905–10915CrossRefGoogle Scholar
  52. 52.
    Florian J (2002) J Phys Chem A 106:5046–5047CrossRefGoogle Scholar
  53. 53.
    Warshel A (1984) Proc Nat Acad Sci USA 81:444–448CrossRefGoogle Scholar
  54. 54.
    Strajbl M, Hong G, Warshel A (2002) J Phys Chem B 106:13333–13343CrossRefGoogle Scholar
  55. 55.
    Pauling L (1947) J Am Chem Soc 69:542–553CrossRefGoogle Scholar
  56. 56.
    Strachan A, van Duin ACT, Chakraborty D, Dasgupta S, Goddard WA III (2003) Phys Rev Lett 91:098301–1CrossRefGoogle Scholar
  57. 57.
    Ludwig J, Vlachos DG, van Duin ACT, Goddard WA III (2006) J Phys Chem B 110:4274–4282CrossRefGoogle Scholar
  58. 58.
    Vashishta P, Kalia RK, Nakano A (2006) J Phys Chem B 110:3727–3733CrossRefGoogle Scholar
  59. 59.
    Bala P, Grochowski P, Nowinski K, Lesyng B, McCammon JA (2000) Biophys J 79:1253–1262CrossRefGoogle Scholar
  60. 60.
    Marcus RA (1993) Angew Chem Int Ed 32:1111–1121CrossRefGoogle Scholar
  61. 61.
    Asmis KR, Pivonka NL, Santambrogio G, Bruemmer M, Kaposta C, Neumark DM, Woeste L (2003) Science 299:1375–1377CrossRefGoogle Scholar
  62. 62.
    Fridgen TD, McMahon GB, MacAleese L, Lemaire J, Maitre P (2004) J Phys Chem A 108:9008–9010CrossRefGoogle Scholar
  63. 63.
    Moore DR, Oomens J, van der Meer L, von Helden G, Meijer G, Valle J, Marshall AG, Eyler JR (2004) ChemPhysChem 5:740–743CrossRefGoogle Scholar
  64. 64.
    Hammer NI, Diken EG, Roscioli JR, Johnson MA, Myshakin EM, Jordan KD, McCoy AB, Huang X, Bowman JM, Carter S (2005) J Chem Phys 122:244301CrossRefGoogle Scholar
  65. 65.
    Dai J, Bacic Z, Huang X, Carter S, Bowman JM (2003) J Chem Phys 119:6571–6580CrossRefGoogle Scholar
  66. 66.
    Kaledin M, Kaledin AL, Bowman JM (2006) J Phys Chem A 110:2933–2939CrossRefGoogle Scholar
  67. 67.
    Lobaugh J, Voth GA (1996) J Chem Phys 104:2056–2059CrossRefGoogle Scholar
  68. 68.
    Cho HM, Singer SJ (2004) J Phys Chem A 108:8691–8702CrossRefGoogle Scholar
  69. 69.
    Lammers S, Meuwly M (2007) J Phys Chem A 111:1638–1647CrossRefGoogle Scholar
  70. 70.
    Huang S, Braams BJ, Bowman JM (2005) J Chem Phys 122:044308CrossRefGoogle Scholar
  71. 71.
    Asada T, Haraguchi H, Kitaura K (2001) J Phys Chem A 105:7423–7428CrossRefGoogle Scholar
  72. 72.
    Li GS, Costa MTCM, Millot C, Ruiz-Lopez MF (1999) Chem Phys 240:93–99CrossRefGoogle Scholar
  73. 73.
    Wang Y, Gunn JR (1999) Int J Quant Chem 73:357–367CrossRefGoogle Scholar
  74. 74.
    Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, Gunsalus IC (1975) Biochemistry 14:5355–5373CrossRefGoogle Scholar
  75. 75.
    Kim S, Jin G, Lim M (2004) J Phys Chem B 108:20366–20375CrossRefGoogle Scholar
  76. 76.
    Petrich JW, Lambry JC, Kuczera K, Karplus M, Poyart C, Martin JL (1991) Biochemistry 30:3975–3987CrossRefGoogle Scholar
  77. 77.
    Ouellet H, Ouellet Y, Richard C, Labarre M, Wittenberg B, Wittenberg J, Guertin M (2002) Proc Nat Acad Sci USA 99:5902–5907CrossRefGoogle Scholar
  78. 78.
    Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M (2004) J Biol Chem 279:21520–21525CrossRefGoogle Scholar
  79. 79.
    Bourassa JL, Ives EL, Marqueling AL, Shimanovich R, Groves JT (2001) J Am Chem Soc 123:5142–5143CrossRefGoogle Scholar
  80. 80.
    Mishra S, Meuwly M (2010) Peroxide bond cleavage versus rearrangement reaction in nitric oxide detoxification: a reactive molecular dynamics study of truncated hemoglobin J Am Chem Soc 132:2968Google Scholar
  81. 81.
    Blomberg LM, Blomberg MRA, Siegbahn PEM (2004) J Biol Inorg Chem 9:923–935CrossRefGoogle Scholar
  82. 82.
    Nauser T, Koppenol WH (2002) J Phys Chem A 106:4084–4086CrossRefGoogle Scholar
  83. 83.
    van Holde KE (2002) Biophys Chem 101:249–254CrossRefGoogle Scholar
  84. 84.
    Herold S, Exner M, Nauser T (2001) Biochemistry 40:3385–3395CrossRefGoogle Scholar
  85. 85.
    Herold S (1999) FEBS Lett 443:81–84CrossRefGoogle Scholar
  86. 86.
    Mishra S, Meuwly M (2009) Biophys J 96:2105–2118CrossRefGoogle Scholar
  87. 87.
    Burmester T, Weich B, Reinhardt S, Hankeln T (2000) Nature 407:520CrossRefGoogle Scholar
  88. 88.
    Vallone B, Nienhaus K, Brunori M, Nienhaus G (2004) Proteins 56:85CrossRefGoogle Scholar
  89. 89.
    Du W, Syvitski R, Dewilde S, Moens L, La Mar G (2003) J Am Chem Soc 125:8080Google Scholar
  90. 90.
    Price SL (1996) J Chem Soc Faraday Trans 92:2997CrossRefGoogle Scholar
  91. 91.
    Karamertzanis PG, Price SL (2006) J Chem Theory Comput 2:1184CrossRefGoogle Scholar
  92. 92.
    Plattner N, Meuwly M (2008) Biophys J 94:2505–2515CrossRefGoogle Scholar
  93. 93.
    Plattner N, Bandi T, Doll J, Freeman DL, Meuwly M (2008) Mol Phys 106:1675CrossRefGoogle Scholar
  94. 94.
    Plattner N, Meuwly M (2008) ChemPhysChem 9:1271CrossRefGoogle Scholar
  95. 95.
    Devereux M, Meuwly M (2009) J Phys Chem B 113:13061CrossRefGoogle Scholar
  96. 96.
    Schmid FFF, Meuwly M (2008) J Chem Theory Comput 4:1949CrossRefGoogle Scholar
  97. 97.
    Huang J, Meuwly M (2010) J Chem Theory Comput 6:467CrossRefGoogle Scholar
  98. 98.
    Ma A, Dinner AR (2005) J Phys Chem B 109:6769–6779CrossRefGoogle Scholar

Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of BaselBaselSwitzerland

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