Spectroscopic and computational studies on [Ni(tmc)CH 3]OTf: Implications for Ni-methyl bonding in the a cluster of acetyl-CoA synthase

Inorganic Chemistry

Volumn 44, Issue 10, 2005, Pages 3605-3617

  Schenker, Ralph ^a   Mock, Michael T ^b   Kieber Emmons, Matthew T ^b   Riordan, Charles G ^b   Brunold, Thomas C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL COENZYME A SYNTHETASE; NICKEL; ORGANOMETALLIC COMPOUND;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METHYLATION; SPECTROSCOPY; THERMODYNAMICS;

ACETATE-COA LIGASE; METHYLATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NICKEL; ORGANOMETALLIC COMPOUNDS; SPECTRUM ANALYSIS; THERMODYNAMICS;

EID: 19944407939     PISSN: 00201669     EISSN: None     Source Type: Journal    
DOI: 10.1021/ic0483996     Document Type: Article

References (84)

1. (a) Ferry, J. G. Crit. Rev. Biochem. Mol. Biol. 1992, 27, 473-503.
2. (b) Lindahl, P. A. Biochemistry 2002, 41, 2097-2105.
3. Ragsdale, S. W.; Kumar, M. Chem. Rev. 1996, 96, 2515-2539.
4. Svetlitchnyi, V.; Dobbek, H.; Meyer-Klaucke, W.; Meins, T.; Thiele, B.; Römer, P.; Huber, R.; Meyer, O. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 446-451.
5. Ragsdale, S. W.; Wood, H. G. J. Biol Chem. 1985, 260, 3970-3977.
6. Doukov, T. I.; Iverson, T. M.; Seravalli, J.; Ragsdale, S. W.; Drennan, C. L. Science 2002, 298, 567-572.
7. Darnault, C.; Volbeda, A.; Kim, E. J.; Legrand, P.; Vernède, X.; Lindahl, P. A.; Fontecilla-Camps, J. C. Nat. Struct. Biol. 2003, 10, 271-279.
8. Bramlett, M. R.; Tan, X.; Lindahl, P. A. J. Am. Chem. Soc. 2003, 125, 9316-9317.
9. Seravalli, J.; Xiao, Y.; Gu, W.; Cramer, S. P.; Antholine, W. E.; Krymov, V.; Gerfen, G. J.; Ragsdale, S. W. Biochemistry 2004, 43, 3944-3955.
10. Chen, J.; Huang, S.; Seravalli, J.; Gutzman, H., Jr.; Swartz, D. J.; Ragsdale, S. W.; Bagley, K. A. Biochemistry 2003, 42, 14822-14830.
11. Schenker, R. P.; Brunold, T. C. J. Am. Chem. Soc. 2003, 125, 13962-13963.
12. Webster, C. E.; Darensbourg, M. Y.; Lindahl, P. A.; Hall, M. B. J. Am. Chem. Soc. 2004, 126, 3410-3411.
13. Russel, W. K.; Stålhandske, C. M. V.; Xia, J.; Scott, R. A.; Lindahl, P. A. J. Am. Chem. Soc. 1998, 120, 7502-7510.
14. Menon, S.; Ragsdale, S. W. J. Biol. Chem. 1999, 274, 11513-11518.
15. Kumar, M.; Qui, D.; Spiro, T. G.; Ragsdale, S. W. Science 1995, 270, 628-630.
16. Barondeau, D. P.; Lindahl, P. A. J. Am. Chem. Soc. 1997, 119, 3959-3970.
17. Seravalli, J.; Gu, W.; Tam, A.; Strauss, E.; Begley, T. P.; Cramer, S. P.; Ragsdale, S. W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3689-3694.
18. Grahame, D. A. Trends Biochem. Sci. 2003, 28, 221-224.
19. (a) Stavropoulos, P.; Carrié, M.; Muetterties, M. C.; Holm, R. H. J. Am. Chem. Soc. 1990, 112, 5385-5387.
20. (b) Stavropoulos, P.; Carrié, M.; Muetterties, M. C.; Holm, R. H. J. Am. Chem. Soc. 1991, 113, 8485-8492.
21. Tucci, G. C.; Holm, R. H. J. Am. Chem. Soc. 1995, 117, 6489-6496.
22. Ram, M. S.; Riordan, C. G.; Yap, G. P. A.; Liable-Sands, L.; Rheingold, A. L.; Marchaj, A.; Norton, J. R. J. Am. Chem. Soc. 1997, 119, 1648-1655.
23. -.
24. (a) Schachtschneider, J. H. Technical Report No. 57-65; Shell Development Company: Emeryville, CA, 1966.
25. (b) Fuhrer, H.; Kartha, V. B.; Kidd, K. G.; Krueger, P. J.; Manisch, H. H. Computer Programs for Infrared Spectroscopy; Bulletin No. 15; National Research Council of Canada: Ottawa, 1976.
26. (a) Baerends, E. J.; Ellis, D. E.; Ros, P. Chem. Phys. 1973, 2, 41-51.
27. (b) te Velde, G.; Baerends, E. J. Int. J. Comput. Phys. 1992, 99, 84-98.
28. (a) Fan, H.-J.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828-3829.
29. (b) Bruschi, M.; Fantucci, P.; De Gioia, L. Inorg. Chem. 2002, 41, 1421-1429.
30. (c) Liu, Z.-P.; Hu, P. J. Am. Chem. Soc. 2002, 124, 5175-5182.
31. (d) Georgakaki, I. P.; Thomson, L. M.; Lyon, E. J.; Hall, M. B.; Darensbourg, M. Y. Coord. Chem. Rev. 2003, 238-239, 255-266.
32. Stich, T. A.; Brooks, A. J.; Buan, N. R.; Brunold, T. C. J. Am. Chem. Soc. 2003, 125, 5897-5914.
33. Versluis, L.; Ziegler, T. J. Chem. Phys. 1988, 88, 322-329.
34. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200-1211.
35. Becke, A. D. J. Chem. Phys. 1986, 84, 4524-4529.
36. Perdew, J. P. Phys. Rev. B: Condens. Matter 1986, 33, 8822-8824.
37. Neese, F., Max Planck Institute for Bioinorganic Chemistry, D-45470 Miilheim/Ruhr, Germany. E-mail: neese@mpi-muelheim.mpg.de.
38. Perdew, J. P.; Wang, Y. Phys. Rev. B: Condens. Matter 1992, 45, 13244-13249.
39. (a) Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377.
40. (b) Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
41. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Condens. Matter 1988, 37, 785-789.
42. Schäfer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571-2577.
43. The Ahlrichs (2d, 2p, 2d2fg, and 3p2df) polarization functions were obtained from the TurboMole basis set library at ftp://ftp.chemie.uni-karlsruhe. de/pub/cbasen.
44. The Ahlrichs auxiliary basis sets were obtained from the TurboMole basis set library at ftp://ftp.chemie.uni-karlsruhe.de/pub/cbasen.
45. (a) Eichkorn, K.; Treutler, O.; Ohm, H.; Haser, M.; Ahlrichs, R. Chem. Phys. Lett. 1995, 240, 283-290.
46. (b) Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Theor. Chem. Acc. 1997, 97, 119-124.
47. The Ahlrichs auxiliary basis sets were obtained from the TurboMole basis set library at ftp://ftp.chemie.uni-karlsruhe.de/pub/cbasen. Weigend, F.; Häser, M. Theor. Chem. Acc. 1997, 97, 331-340.
48. (a) Bauernschmitt, R.; Ahlrichs, R. Chem. Phys. Lett. 1996, 256, 454-464.
49. (b) Casida, E. M.; Jamorski, C.; Casida, K. C.; Salahub, D. R. J. Chem. Phys. 1998, 108, 4439-4449.
50. (c) Stratman, R. E.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 1998, 109, 8218-8224.
51. (a) Hirata, S.; Head-Gordon, M. Chem. Phys. Lett. 1999, 302, 375-382.
52. (b) Hirata, S.; Head-Gordon, M. Chem. Phys. Lett. 1999, 314, 291-299.
53. Neese, F.; Olbrich, G. Chem. Phys. Lett. 2002, 362, 170-178.
54. (a) Laaksonen, L. J. Mol. Graphics 1992, 10, 33-34.
55. (b) Bergman, D. L.; Laaksonen, L.; Laaksonen, A. J. Mol. Graphics Modell. 1997, 15, 301-306.
56. (a) Ridley, J.; Zerner, M. C. Theor. Chim. Acta 1973, 32, 111.
57. (b) Zerner, M. C.; Loew, G. H.; Kirchner, R. F.; Mueller-Westerhof, U. T. J. Am. Chem. Soc. 1980, 102, 589-599.
58. Bacon, A. D.; Zerner, M. C. Theor. Chim. Acta 1979, 53, 21-54.
59. This conclusion is supported by the observation of a color change of the sample from light green to brown at the spot irradiated by the laser beam.
60. The ellipticity is defined as the rotation angle associated with the differential absorption of left and right circularly polarized light.
61. The MCD peak intensity and, hence, the |θ|/OD ratio for band F are somewhat inaccurate because of a sizable contribution from a paramagnetic impurity to this region of the MCD spectrum.
62. Johnson, M. K. In Physical Methods in Bioinorganic Chemistry: Spectroscopy and Magnetism; Que, L., Ed.; University Science Books: Sausalito, CA, 2000; pp 233-285.
63. The presence of a paramagnetic impurity precluded the analysis of VTVH data collected below 370 nm.
64. Bencini, A.; Gatteschi, D. Electron Paramagnetic Resonance of Exchange Coupled Systems; Springer-Verlag: Heidelberg, Germany, 1990.
65. Neese, F.; Solomon, E. I. Inorg. Chem. 1999, 38, 1847-1865.
66. Carlin, R. L. Magnetochemistry; Springer: Heidelberg, Germany, 1986; p 67.
67. 4C framework.
68. -1 that would be expected on the basis of this assignment lies within the experimental error of the frequencies determined from our rR data.
69. xy).
70. This contribution to transition 9 is not evident from the EDDM in Figure 9, but it becomes obvious if a lower isodensity value (0.002 a.u.) is employed.
71. -1 far exceeds the frequency of any resonance enhanced vibrational mode in the rR spectra obtained with laser excitation in this spectral region (Figure 3).
72. y orbital character of the principal acceptor MO (90β).
73. Because of the coordinate system chosen, the Ni xz and yz orbitals in 1 are strongly mixed; the designations xz and yz are, thus, used solely for labeling purposes.
74. -1, which is predicted to carry only little absorption intensity because of the vastly different compositions of the donor and acceptor MOs, in agreement with our experimental data.
75. 4] unit is in the diamagnetic +2 oxidation state before and after methylation of the A cluster.
76. With Ni - C bond lengths below 2.5 Å, model 2b failed to converge.
77. (a) Dong, S.; Padmakumar, R.; Banerjee, R.; Spiro, T. J. Am. Chem. Soc. 1996, 118, 9182-9183.
78. (b) Dong, S.; Padmakumar, R.; Banerjee, R.; Spiro, T. Inorg. Chim. Acta 1998, 270, 392-398.
79. The discrepancies between formal and DFT-computed bond orders mainly arise from the fact that the former neglect contributions from the Ni 4s and 4p orbitals to bonding.
80. 3 bond dissociation energy (BDE) for 1 is not available, it is useful to compare the M-C BDEs for the benzyl (Bn) derivative of 1 and benzylcobalamin (BnCbl). In BnCbI, the Co-C BDE is 23(1) kcal/mol (Brown, K. L.; Brooks, H. B. Inorg. Chem. 1991, 30, 3420-3430),
81. +, the Ni-C BDE is 19(1) kcal/mol (Schofield, M. H.; Halpern, J. Inorg. Chim. Acta 2003, 345, 353-358).
82. Smith, A. K. In Comprehensive Organometallic Chemistry II; Abel, E. W., Stone, F. G. A., Wilkinson, G., Eds.; Elsevier Science Ltd.: Tarrytown, NY, 1995; Vol. 9, pp 1-28.
83. (a) Tan, X. S.; Sewell, C.; Lindahl, P. A. J. Am. Chem. Soc. 2002, 124, 6277-6284.
84. (b) Tan, X. S.; Sewell, C.; Yang, Q.; Lindahl, P. A. J. Am. Chem. Soc. 2003, 125, 318-319.