Constrained spin-density dynamics of an iron-sulfur complex: Ferredoxin cofactor

Journal of Chemical Physics

Volumn 136, Issue 22, 2012, Pages

  Ali, Md Ehesan ^a   Nair, Nisanth N ^b   Staemmler, Volker ^a   Marx, Dominik ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO MOLECULAR DYNAMICS; ANTIFERROMAGNETIC COUPLING; ANTIFERROMAGNETIC EXCHANGE COUPLING; COFACTORS; COUPLING CONSTANTS; DENSITY-BASED APPROACHES; GEOMETRICAL STRUCTURE; MAGNETIC ORBITALS; ON-THE-FLY; ROOM TEMPERATURE; SPIN DENSITIES; SPIN GROUND STATE; SPIN PROJECTIONS; TRANSITION-METAL CENTERS;

IRON COMPOUNDS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; SULFUR; TRANSITION METALS;

SPIN DYNAMICS;

FERREDOXIN; IRON SULFUR PROTEIN;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; QUANTUM THEORY;

ANIMALS; FERREDOXINS; IRON-SULFUR PROTEINS; MODELS, MOLECULAR; QUANTUM THEORY;

EID: 84866904101     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4722552     Document Type: Article

References (75)

1. R. Martin and F. Illas, Phys. Rev. Lett. 79, 1539 (1997). 10.1103/PhysRevLett.79.1539
2. C. Adamo, V. Barone, A. Bencini, F. Totti, and I. Ciofini, Inorg. Chem. 38, 1996 (1999). 10.1021/ic9812306
3. M. Mitani, H. Mori, Y. Takano, D. Yamaki, Y. Yoshioka, and K. Yamaguchi, J. Chem. Phys. 113, 4035 (2000). 10.1063/1.1286418
4. I. Ciofini and C. A. Daul, Coord. Chem. Rev. 238, 187 (2003). 10.1016/S0010-8545(02)00330-2
5. C. Calzado, J. Cabrero, J. Malrieu, and R. Caballol, J. Chem. Phys. 116, 2728 (2002). 10.1063/1.1430740
6. B. Wang and Z. Chen, Chem. Phys. Lett. 387, 395 (2004). 10.1016/j.cplett.2004.02.057
7. I. Ciofini, C. Adamo, and V. Barone, J. Chem. Phys. 121, 6710 (2004). 10.1063/1.1791031
8. I. Moreira and F. Illas, Phys. Chem. Chem. Phys. 8, 1645 (2006). 10.1039/b515732c
9. E. Schreiner, N. N. Nair, R. Pollet, V. Staemmler, and D. Marx, Proc. Natl. Acad. Sci. U.S.A. 104, 20725 (2007). 10.1073/pnas.0706740104
10. N. N. Nair, E. Schreiner, R. Pollet, V. Staemmler, and D. Marx, J. Chem. Theory Comput. 4, 1174 (2008). 10.1021/ct800089x
11. C. J. Calzado, C. Angeli, D. Taratiel, R. Caballol, and J. P. Malrieu, J. Chem. Phys. 131, 044327 (2009). 10.1063/1.3185506
12. V. Barone, I. Cacelli, and A. Ferretti, J. Chem. Phys. 130, 094306 (2009). 10.1063/1.3077029
13. N. N. Nair, J. Ribas-Arino, V. Staemmler, and D. Marx, J. Chem. Theory Comput. 6, 569 (2010). 10.1021/ct900547w
14. S. A. Fiethen, V. Staemmler, N. N. Nair, J. Ribas-Arino, E. Schreiner, and D. Marx, J. Phys. Chem. B 114, 11612 (2010). 10.1021/jp1014912
15. V. Barone, I. Cacelli, A. Ferretti, S. Monti, and G. Prampolini, J. Chem. Theory. Comput. 7, 699 (2011). 10.1021/ct100602y
16. L. Noodleman, J. Chem. Phys. 74, 5737 (1981). 10.1063/1.440939
17. L. Noodleman, D. A. Case, and A. Aizman, J. Am. Chem. Soc. 110, 1001 (1988). 10.1021/ja00212a003
18. F. Neese, J. Phys. Chem. Solids 65, 781 (2004). 10.1016/j.jpcs.2003.11. 015
19. D. Marx and J. Hutter, Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods (Cambridge University Press, Cambridge, 2009).
20. E. Ruiz, S. Alvarez, J. Cano, and V. Polo, J. Chem. Phys. 123, 164110 (2005). 10.1063/1.2085171
21. C. Adamo, V. Barone, A. Bencini, R. Broer, M. Filatov, N. Harrison, F. Illas, J. Malrieu, and I. de PR Moreira, J. Chem. Phys. 124, 107101 (2006). 10.1063/1.2178791
22. A. Cohen, P. Mori-Sánchez, and W. Yang, J. Chem. Phys. 126, 191109 (2007). 10.1063/1.2741248
23. V. I. Anisimov, J. Zaanen, and O. K. Andersen, Phys. Rev. B 44, 943 (1991). 10.1103/PhysRevB.44.943
24. A. I. Liechtenstein and J. Zaanen, Phys. Rev. B 52, R5467 (1995). 10.1103/PhysRevB.52.R5467
25. P. Rivero, C. Loschen, I. Moreira, and F. Illas, J. Comput. Chem. 30, 2316 (2009). 10.1002/jcc.21221
26. Y. Zhang and H. Jiang, J. Chem. Theory Comput. 7, 2795 (2011). 10.1021/ct200299s
27. M. Cococcioni and S. de Gironcoli, Phys. Rev. B 71, 035105 (2005). 10.1103/PhysRevB.71.035105
28. H. J. Kulik, M. Cococcioni, D. A. Scherlis, and N. Marzari, Phys. Rev. Lett. 97, 103001 (2006). 10.1103/PhysRevLett.97.103001
29. F. Illas, Chem. Eng. Commun. 195, 1465 (2008). 10.1080/00986440801967338
30. R. Valero, F. Illas, and D. G. Truhlar, J. Chem. Theory Comput. 7, 3523 (2011). 10.1021/ct200393s
31. J. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981). 10.1103/PhysRevB.23.5048
32. C. Herrmann, L. Yu, and M. Reiher, J. Comput. Chem. 27, 1223 (2006). 10.1002/jcc.20409
33. P. H. Dederichs, S. Blügel, R. Zeller, and H. Akai, Phys. Rev. Lett. 53, 2512 (1984). 10.1103/PhysRevLett.53.2512
34. H. Akai, S. Blügel, R. Zeller, and P. Dederichs, Phys. Rev. Lett. 56, 2407 (1986). 10.1103/PhysRevLett.56.2407
35. J. Behler, B. Delley, S. Lorenz, K. Reuter, and M. Scheffler, Phys. Rev. Lett. 94, 36104 (2005). 10.1103/PhysRevLett.94.036104
36. Q. Wu and T. V. Voorhis, Phys. Rev. A 72, 024502 (2005). 10.1103/PhysRevA.72.024502
37. Q. Wu and T. V. Voorhis, J. Chem. Theory Comput. 2, 765 (2006). 10.1021/ct0503163
38. I. Rudra, Q. Wu, and T. V. Voorhis, J. Chem. Phys. 124, 024103 (2006). 10.1063/1.2145878
39. J. R. Schmidt, N. Shenvi, and J. C. Tully, J. Chem. Phys. 129, 114110 (2008). 10.1063/1.2978168
40. Q. Wu, B. Kaduk, and T. V. Voorhis, J. Chem. Phys. 130, 034109 (2009). 10.1063/1.3059784
41. H. Oberhofer and J. Blumberger, J. Chem. Phys. 131, 064101 (2009). 10.1063/1.3190169
42. H. Oberhofer and J. Blumberger, J. Chem. Phys. 133, 244105 (2010). 10.1063/1.3507878
43. J. J. Phillips and J. E. Peralta, J. Chem. Phys. 135, 184108 (2011). 10.1063/1.3660351
44. B. Kaduk, T. Kowalczyk, and T. V. Voorhis, Chem. Rev. 112, 321 (2012). 10.1021/cr200148b
45. Q. Wu and T. V. Voorhis, J. Chem. Phys. 125, 164105 (2006). 10.1063/1.2360263
46. T. Voorhis, T. Kowalczyk, B. Kaduk, L. Wang, C. Cheng, and Q. Wu, Annu. Rev. Phys. Chem. 61, 149 (2010). 10.1146/annurev.physchem.012809.103324
47. Z. Zhang and S. Satpathy, Phys. Rev. B 44, 13319 (1991). 10.1103/PhysRevB.44.13319
48. M. S. Hybertsen, M. Schlüter, and N. E. Christensen, Phys. Rev. B 39, 9028 (1989). 10.1103/PhysRevB.39.9028
49. B. Ujfalussy, X. Wang, D. M.C. Nicholson, W. A. Shelton, and G. M. Stocks, J. Appl. Phys. 85, 4824 (1999). 10.1063/1.370494
50. I. Rudra, Q. Wu, and T. V. Voorhis, Inorg. Chem. 46, 10539 (2007). 10.1021/ic700871f
51. CPMD, Version 3.12, Copyright IBM Corp. 1990-2008, MPI für Festkörperforschung Stuttgart, 1997-2001.
52. D. O. Hall, R. Cammack, and K. K. Rao, Nature 233, 136 (1971). 10.1038/233136a0
53. G. Palmer, W. Dunham, J. Fee, R. Sands, T. Iizuka, and T. Yonetani, BBA-Bioenergetics 245, 201 (1971). 10.1016/0005-2728(71)90022-3
54. L. Petersson, R. Cammack, and K. Rao, Biochim. Biophys. Acta 622, 18 (1980). 10.1016/0005-2795(80)90154-3
55. O. Kahn, Molecular Magnetism (Wiley-VCH, New York, 1993).
56. L. Noodleman and E. R. Davidson, Chem. Phys. 109, 131 (1986). 10.1016/0301-0104(86)80192-6
57. L. Noodleman, J. G. Norman Jr., J. H. Osborne, A. Aizman, and D. A. Case, J. Am. Chem. Soc. 107, 3418 (1985). 10.1021/ja00298a004
58. L. Noodleman, C. Peng, D. Case, and J.-M. Mouesca, Coord. Chem. Rev. 144, 199 (1995). 10.1016/0010-8545(95)07011-L
59. R. Caballol, O. Castell, F. Illas, I. de P. R. Moreira, and J. P. Malrieu, J. Phys. Chem. A 101, 7860 (1997). 10.1021/jp9711757
60. D. Vanderbilt, Phys. Rev. B 41, 7892 (1990). 10.1103/PhysRevB.41.7892
61. J. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996). 10.1103/PhysRevLett.77.3865
62. P.-O. Löwdin, J. Chem. Phys. 18, 365 (1950). 10.1063/1.1747632
63. P.-O. Löwdin, Adv. Quantum Chem. 5, 185 (1970). 10.1016/S0065- 3276(08)60339-1
64. F. L. Hirshfeld, Theor. Chim. Acta 44, 129 (1977). 10.1007/BF00549096
65. R. F. W. Bader, Atoms in Molecules: A Quantum Theory (Oxford University Press, 1994).
66. A. Becke, Phys. Rev. A 38, 3098 (1988). 10.1103/PhysRevA.38.3098
67. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988). 10.1103/PhysRevB.37.785
68. C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999). 10.1063/1.478522
69. Y. Zhao and D. Truhlar, J. Chem. Phys. 128, 184109 (2008). 10.1063/1.2912068
70. Y. Zhao and D. Truhlar, Theor. Chem. Acc. 120, 215 (2008). 10.1007/s00214-007-0310-x
71. R. Morales, M. Charon, G. Hudry-Clergeon, Y. Pétillot, S. Norager, M. Medina, and M. Frey, Biochemistry 38, 15764 (1999). 10.1021/bi991578s
72. M. Antonio, B. Averill, I. Moura, J. Moura, W. Orme-Johnson, B. Teo, and A. Xavier, J. Biol. Chem 257, 6646 (1982).
73. M. Shoji, K. Koizumi, T. Taniguchi, Y. Kitagawa, S. Yamanaka, M. Okumura, and K. Yamaguchi, Int. J. Quantum Chem. 107, 116 (2006). 10.1002/qua.21016
74. E. Anxolabehere-Mallart, T. Glaser, P. Frank, A. Aliverti, G. Zanetti, B. Hedman, K. Hodgson, and E. Solomon, J. Am. Chem. Soc. 123, 5444 (2001). 10.1021/ja010472t
75. P. Jorgensen and J. Simons, J. Chem. Phys. 79, 334 (1983). 10.1063/1.445528