Reactive Processes with Molecular Simulations

Challenges and Advances in Computational Chemistry and Physics

Volumn 12, Issue , 2010, Pages 137-155

  Mishra, Sabyashachi ^a   Meuwly, Markus ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Ligand binding in heme proteins; NO detoxification; Proton transfer; Reactive molecular dynamics

Indexed keywords

EID: 85073242691     PISSN: 25424491     EISSN: 25424483     Source Type: Book Series    
DOI: 10.1007/978-90-481-3034-4_5     Document Type: Chapter

References (98)

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