Accurate Description of Spin States and its Implications for Catalysis

Quantum Biochemistry

Volumn , Issue , 2010, Pages 551-583

  Swart, Marcel ^a,b   Güell, Mireia ^b   Solá, Miquel ^b  

^a INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^b UNIVERSITY OF GIRONA   (Spain)

Author keywords

Benchmark data; Biocomputational chemistry; Catalysis; DFT functional; Spin state

Indexed keywords

EID: 84885501663     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629213.ch19     Document Type: Chapter

References (127)

1. Harvey, J.N., Poli, R., and Smith, K.M. (2003) Coord. Chem. Rev., 238-239, 347-361.
2. Harvey, J.N. (2004) Struct. Bond., 112, 151-183.
3. Ortiz de Montellano, P.R. (1995) Cytochrome P450 Structure, Mechanism and Biochemistry, Plenum, New York.
4. Tyson, C.A., Lipscomb, J.D., and Gunsalus, I.C. (1972) J. Biol. Chem., 247, 5777-5784.
5. Loew, G.H. and Harris, D.L. (2000) Chem. Rev., 100, 407-419.
6. Harris, D. and Loew, G. (1993) J. Am. Chem. Soc., 115, 8775-8779.
7. Poulos, T.L., Finzel, B.C., and Howard, A.J. (1986) Biochem., 25, 5314-5322.
8. Poulos, T.L., Finzel, B.C., and Howard, A.J. (1987) J. Mol. Biol., 195, 687-700.
9. Green, M.T. (2000) J. Am. Chem. Soc., 120, 10772-10773.
10. Dawson, J.H. and Sono, M. (1987) Chem. Rev., 87, 1255-1276.
11. Di Primo, C., Hui Bon Hoa, G., Douzou, P., and Sligar, S.G. (1990) J. Biol. Chem., 265, 5361-5363.
12. Swart, M., Groenhof, A.R., Ehlers, A.W., and Lammertsma, K. (2005) Chem. Phys. Lett., 403, 35-41.
13. Schlichting, I., Jung, C., and Schulz, H. (1997) FEBS Lett., 415, 253-257.
14. Raag, R. and Poulos, T.L. (1991) Biochemistry, 30, 2674-2684.
15. Hintz, M.J., Mock, D.M., Peterson, L.L., Tuttle, K., and Peterson, J.A. (1982) J. Biol. Chem., 257, 14324-14332.
16. Shimada, H., Nagano, S., Ariga, Y, Unno, M., Egawa, T., Hishiki, T., Ishimura, Y., Masuya, F., Obata, T., and Hori, H. (1999) J. Biol. Chem., 274, 9363-9369.
17. Parr, R.G. and Yang, W. (1989) Density Functional Theory of Atoms and Molecules, Oxford University Press, New York.
18. Koch, W. and Holthausen, M.C. (2000) A Chemist's Guide to Density Functional Theory, Wiley-VCH Verlag GmbH, Weinheim.
19. Dreizler, R. and Gross, E. (1995) Density Functional Theory, Plenum Press, New York.
20. Becke, A.D. (1993) J. Chem. Phys., 98, 5648-5652.
21. Stephens, P.J., Devlin, F.J., Chabalowski, C.F., and Frisch, M.J. (1994) J. Phys. Chem., 45, 11623-11627.
22. Becke, A.D. (1988) Phys. Rev. A, 38, 3098-3100
23. Perdew, J.P. (1986) Phys. Rev. B, 33, 8822-8824; Erratum: (1986) Phys. Rev. B, 34, 7406.
24. Swart, M., Groenhof, A.R., Ehlers, A.W., and Lammertsma, K. (2004) J. Phys. Chem. A, 108, 5479-5483.
25. Swart, M. (2008) J. Chem. Theory Comput., 4, 2057-2066.
26. Reiher, M., Salomon, O., and Hess, B.A. (2001) Theor. Chem. Acc., 107, 48-55.
27. Sproviero, E.M., Gascon, J.A., McEvoy, J.P., Brudvig, G.W., and Batista, V.S. (2006) J. Inorg. Biochem., 100, 786-800.
28. Bruschi, M., De Gioia, L., Zampella, G., Reiher, M., Fantucci, P., and Stein, M. (2004) J. Biol. Inorg. Chem., 9, 873-884.
29. Swart, M. (2007) Inorg. Chim. Acta, 360, 179-189.
30. Perdew, J.P. (1991), in Electronic Structure of Solids (eds P. Ziesche and H. Eschrig), Akademie, Berlin, p. 11.
31. Perdew, J.P., Chevary, J.A., Vosko, S.H., Jackson, K.A., Pederson, M.R., Singh, D.J., and Fiolhais, C. (1992) Phys. Rev. B, 46, 6671-6687; Erratum (1993) Phys. Rev. B, 48, 4978.
32. Xu, X. and Goddard, W.A. III. (2004) Proc. Natl. Acad. Sci. U.S.A., 101, 2673-2677.
33. Scherlis, D.A., Cococcioni, M., Sit, P., and Marzari, N. (2007) J. Phys. Chem. B, 111, 7384-7391.
34. Handy, N.C. and Cohen, A.J. (2001) Mol. Phys., 99, 403-412.
35. Swart, M., Ehlers, A.W., and Lammertsma, K. (2004) Mol. Phys., 102, 2467-2474.
36. Lee, C., Yang, W., and Parr, R.G. (1988) Phys. Rev B, 37, 785-789.
37. Baker, J. and Pulay, P. (2002) J. Chem. Phys., 117, 1441-1449.
38. Baker, J. and Pulay, P. (2003) J. Comput. Chem., 24, 1184-1191.
39. Hoe, W.M., Cohen, A.J., and Handy, N.C. (2001) Chem. Phys. Lett., 341, 319-328.
40. Bento, A.P., Sola, M., and Bickelhaupt, F.M. (2005) J. Comput. Chem., 26, 1497-1504.
41. Xu, X. and Goddard, W.A. III. (2004) J. Phys. Chem. A, 108, 8495-8504.
42. Conradie, J. and Ghosh, A. (2007) J. Phys. Chem. B, 111, 12621-12624.
43. Zhao, Y., Schultz, N.E., and Truhlar, D.G. (2006) J. Chem. Theory Comput., 2, 364-382.
44. Zhao, Y. and Truhlar, D.G. (2008) Theory Chem. Acc., 120, 215-241.
45. Tao, J.M., Perdew, J.P., Staroverov, V.N., and Scuseria, G.E. (2003) Phys. Rev. Lett., 91, 146401.
46. Staroverov, V.N., Scuseria, G.E., Tao, J., and Perdew, J.P. (2003) J. Chem. Phys., 119, 12129-12137.
47. Hirao, H., Kumar, D., Que, L. Jr., and Shaik, S. (2006) J. Am. Chem. Soc., 128, 8590-8606.
48. Lepetit, C., Chermette, H., Gicquel, M., Heully, J.-L., and Chauvin, R. (2007) J. Phys. Chem. A, 111, 136-149.
49. Zein, S., Borshch, S.A., Fleurat-Lessard, P., Casida, M.E., and Chermette, H. (2007) J. Chem. Phys., 126, 014105.
50. Liao, M.-S., Watts, J.D., and Huang, M.-J. (2006) J. Comput. Chem., 27, 1577-1592.
51. Jensen, F. (1998) Introduction to Computational Chemistry, John Wiley & Sons, Inc., New York.
52. Kamachi, T. and Yoshizawa, K. (2003) J. Am. Chem. Soc., 125, 4652-4661.
53. Guell, M., Luis, J.M., Sola, M., and Swart, M. (2008) J. Phys. Chem. A, 112, 6384-6391.
54. Mitin, A.V., Baker, J., and Pulay, P. (2003) J. Chem. Phys., 118, 7775-7782.
55. Martin, J., Baker, J., and Pulay, P. (2009) J. Comput. Chem., 30; 881-883.
56. Szabo, A. and Ostlund, N.S. (1982) Modern Quantum Chemistry- Introduction to Advanced Electronic Structure Theory, Macmillan Publishing Co.
57. Feixas, F., Sola, M., and Swart, M. (2009) Can. J. Chem., 87, 1063-1073.
58. Cohen, A.J., Tozer, D.J., and Handy, N.C. (2007) J. Chem. Phys., 126, 214104.
59. Swart, M. and Bickelhaupt, F.M. (2008) J. Comput. Chem., 29, 724-734.
60. Swart, M., Sola, M., and Bickelhaupt, F.M. (2007) J. Comput. Chem., 28, 1551-1560.
61. Swart, M. and Bickelhaupt, F.M. (2006) J. Chem. Theory Comp., 2, 281-287.
62. de Jong, G.T., Geerke, D.P., Diefenbach, A., and Bickelhaupt, F.M. (2005) Chem. Phys., 313, 261-270.
63. te Velde, G., Bickelhaupt, F.M., Baerends, E.J., Fonseca Guerra, C., van Gisbergen, S.J.A., Snijders, J.G., and Ziegler, T. (2001) J. Comput. Chem., 22, 931-967.
64. Stewart, J.J. (2007) J. Mol. Model., 13, 1173-1213.
65. Lovell, T., Himo, F., Han, W.-G., and Noodleman, L. (2003) Coord. Chem. Rev., 238-239, 211-232.
66. Himo, F. and Siegbahn, P.E.M. (2003) Chem. Rev., 103, 2421-2456.
67. Siegbahn, P.E.M. and Blomberg, M.R.A. (2000) Chem. Rev., 100, 421-437.
68. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. (1995) J. Am. Chem. Soc., 117, 5179-5197.
69. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S.J., and Karplus, M. (1983) J. Comput. Chem., 4, 187-217.
70. Groenhof, A.R., Swart, M., Ehlers, A.W., and Lammertsma, K. (2005) J. Phys. Chem. A, 109, 3411-3417.
71. Jones, D.H., Hinman, A.S., and Ziegler, T. (1993) Inorg. Chem., 32, 2092-2095.
72. Rydberg, P., Sigfridsson, E., and Ryde, U. (2004) J. Biol. Inorg. Chem., 9, 203-223.
73. Liao, M.-S., Watts, J.D., and Huang, M.-J. (2007) J. Phys. Chem. A, 111, 5927-5935.
74. Liao, M.-S. and Scheiner, S. (2002) J. Chem. Phys., 117, 205-219.
75. Rosa, A., Ricciardi, G., and Baerends, E.J. (2006) J. Phys. Chem. A, 110, 5180-5190.
76. Reiher, M. (2002) Inorg. Chem., 41, 6928-6935.
77. Pierloot, K. and Vancoillie, S. (2006) J. Chem. Phys., 125, 124303.
78. Malassa, A., Görls, H., Buchholz, A., Plass, W., and Westerhausen, M. (2006) Z. Anorg. Allg. Chem., 632, 2355-2362.
79. Güell, M., Sola, M., and Swart, M. (2009) Polyhedron, in press, Doi: 10.1016/j.poly.2009.06.006.
80. Siegbahn, P.E.M. and Haeffner, F. (2004) J. Am. Chem. Soc., 126, 8919-8932.
81. Schoneboom, J.C., Cohen, S., Lin, H., Shaik, S., and Thiel, W. (2004) J. Am. Chem. Soc., 126, 4017-4034.
82. Jayapal, P., Sundararajan, M., Hillier, I.H., and Burton, N.A. (2006) Phys. Chem. Chem. Phys., 8, 4086-4094.
83. Bruschi, M., Zampella, G., Fantucci, P., and De Gioia, L. (2005) Coord. Chem. Rev., 249, 1620-1640.
84. Ortiz de Montellano, P.R. and De Voss, J.J. (2002) Nat. Prod. Rep., 19, 477-493.
85. Denisov, I.G., Makris, T.M., Sligar, S.G., and Schlichting, I. (2005) Chem. Rev., 105, 2253-2278.
86. Limberg, C. (2003) Angew. Chem. Int. Ed., 42, 5932-5954.
87. Harris, D.L. and Loew, G.H. (1998) J. Am. Chem. Soc., 120, 8941-8948.
88. Meunier, B., de Visser, S.P., and Shaik, S. (2004) Chem. Rev., 104, 3947-3980.
89. Guallar, V., Gherman, B.F., Lippard, S.J., and Friesner, R.A. (2002) Curr. Opin. Chem. Biol., 6, 236-242.
90. Shaik, S., Cohen, S., de Visser, S.P., Sharma, P.K., Kumar, D., Kozuch, S., Ogliaro, F., and Danovich, D. (2004) Eur. J. Inorg. Chem., 207-226.
91. Shaik, S., Kumar, D., de Visser, S.P., Altun, A., and Thiel, W. (2005) Chem. Rev., 105, 2279-2328.
92. Schoneboom, J.C. and Thiel, W. (2004) J. Phys. Chem. B, 108, 7468-7478.
93. Fisher, M.T. and Sligar, S.G. (1987) Biochemistry, 26, 4797-4803.
94. Schulze, H., Hui Bon Hoa, G., and Jung, C. (1997) Biochim. Biophys. Acta, 1338, 77-92.
95. Bach, R.D. and Dmitrenko, O. (2006) J. Am. Chem. Soc., 128, 1474-1488.
96. Groenhof, A.R., Ehlers, A.W., and Lammertsma, K. (2007) J. Am. Chem. Soc., 129, 6204-6209.
97. Harris, D.L. (2001) Curr. Opin. Chem. Biol., 5, 724-735.
98. Yoshioka, S., Tosha, T., Takahashi, S., Ishimori, K., Hori, H., and Morishima, I. (2002) J. Am. Chem. Soc., 124, 14571-14579.
99. Guallar, V., Baik, M.-H., Lippard, S.J., and Friesner, R.A. (2003) Proc. Nati. Acad. Sci. U.S.A., 100, 6998-7002.
100. Guallar, V. and Olsen, B. (2006) J. Inorg. Biochem., 100, 755-760.
101. Guallar, V. (2008) J. Phys. Chem. B, 112, 13460-13464.
102. Chen, Z., Ost, T.W.B., and Schelvis, J.P.M. (2004) Biochemisty, 43, 1798-1808.
103. Schlichting, I., Berendzen, J., Chu, K., Stock, A.M., Maves, S.A., Benson, D.E., Sweet, B.M., Ringe, D., Petsko, G.A., and Sligar, S.G. (2000) Science, 287, 1615-1622.
104. Zurek, J., Foloppe, N., Harvey, J.N., and Mulholland, A.J. (2006) Org. Biomol. Chem., 4, 3931-3937.
105. Altun, A., Guallar, V., Friesner, R.A., Shaik, S., and Thiel, W. (2006) J. Am. Chem. Soc., 128, 3924-3925.
106. Hu, C., Roth, A., Ellison, M.K., An, J., Ellis, C.M., Schulz, C.E., and Scheidt, W.R. (2005) J. Am. Chem. Soc., 127, 5675-5688.
107. Rovira, C., Kunc, K., Hutter, J., Ballone, P., and Parrinello, M. (1997) J. Phys. Chem . A, 101, 8914-8925.
108. Strickland, N. and Harvey, J.N. (2007) J. Phys. Chem. B, 111, 841-852.
109. Ghosh, A., Vangberg, T., Gonzalez, E., and Taylor, P. (2001) J. Porphyrins Phthalocyanines, 5, 345-356.
110. Ghosh, A., Tangen, E., Ryeng, H., and Taylor, P.R. (2004) Eur. J. Inorg. Chem., 4555-4560.
111. Ghosh, A., Persson, B.J., and Taylor, P.R. (2003) J. Biol. Inorg. Chem., 8, 507-511.
112. Liao, M.-S. and Scheiner, S. (2002) J. Comput. Chem., 23, 1391-1403.
113. Fraústo do Silva, J.J.R. and Williams, R.J.P. (1991) The Biological Chemistry of the Elements. The Inorganic Chemistry of Life, Oxford University Press, Oxford.
114. Siegbahn, P.E.M., Tye, J.W., and Hall, M.B. (2007) Chem. Rev., 107, 4414-4435.
115. Wang, H., Ralston, C.Y, Patil, D.S., Jones, R.M. et al.. (2000) J. Am. Chem. Soc., 122, 10544-10552.
116. Fan, H.-J. and Hall, M.B. (2002) J. Am. Chem. Soc., 124, 394-395.
117. van Lenthe, E. and Baerends, E.J. (2003) J. Comput. Chem., 24, 1142-1156.
118. Baerends, E.J., Autschbach, J., Bérces, A., Berger, J.A. et al.. (2007) ADF version 2007.01,SCM, Amsterdam.
119. Frisch, M.J.,Trucks, G.W., Schlegel, H.B., Scuseria, G.E. et al.. (2004) Gaussian 03, Revision B.02, Gaussian Inc., Pittsburgh PA, USA.
120. Bylaska, E.J., de Jong, W.A., Kowalski, K., Straatsma, T.P. et al.. (2006) NWChem version 5.1, Pacific Northwest National Laboratory, Richland, Washington, USA.
121. Neese, F. (2007) ORCA, Bonn.
122. Vosko, S.H., Wilk, L., and Nusair, M. (1980) Can.J. Phys., 58, 1200-1211.
123. Perdew, J.P., Burke, K., and Ernzerhof, M. (1996) Phys. Rev. Lett., 77, 3865-3868; Erratum (1997) Phys. Rev. Lett., 78, 1396.
124. Perdew, J.P. and Wang, Y. (1992) Phys. Rev. B, 45, 13244-13249.
125. Perdew, J.P. and Zunger, A. (1981) Phys. Rev. B, 23, 5048-5079.
126. Swart, M. and Bickelhaupt, F.M. (2006) Int. J. Quantum Chem., 106, 2536-2544.
127. Wittbrodt, J.M. and Schlegel, H.B. (1996) J. Chem. Phys., 105, 6574-6577.