Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: Models of the iron-iron hydrogenase enzyme active site

Journal of Computational Chemistry

Volumn 27, Issue 12, 2006, Pages 1454-1462

  Tye, Jesse W ^a   Darensbourg, Marcetta Y ^a   Hall, Michael B ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Infrared spectroscopy; Iron carbonyl complexes; Iron iron hydrogenase model complexes; Prediction of infrared spectra; Simulation of infrared spectra

Indexed keywords

IRON-CARBONYL COMPLEXES; IRON-IRON HYDROGENASE MODEL COMPLEXES; PREDICTION OF INFRARED SPECTRA; SIMULATION OF INFRARED SPECTRA;

COMPLEXATION; ENZYMES; MATHEMATICAL MODELS; NATURAL FREQUENCIES; ORGANIC SOLVENTS; POLARIZATION; PROBABILITY DENSITY FUNCTION;

INFRARED SPECTROSCOPY;

HYDROGENASE; IRON;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GAS; INFRARED SPECTROPHOTOMETRY; METABOLISM; PROTEIN CONFORMATION; SOLUTION AND SOLUBILITY;

BINDING SITES; COMPUTER SIMULATION; GASES; HYDROGENASE; IRON; MODELS, MOLECULAR; PROTEIN CONFORMATION; SOLUTIONS; SPECTROPHOTOMETRY, INFRARED;

EID: 33747178665     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20456     Document Type: Article

References (61)

1. Nakamoto, K. IR and Raman Spectra of Inorganic and Coordination Compounds; Wiley-Interscience: New York, 1997, 5th ed.
2. Momenteau, M.; Reed, C. A. Chem Rev 1994, 94, 659.
3. Lukin, J. A.; Ho, C. Chem Rev 2004, 104, 1219.
4. Nicolet, Y.; Cavazza, C.; Fontecilla-Camps, J. C. J Inorg Biochem 2002, 91, 1.
5. Tamagnini, P.; Axelsson, R.; Lindberg, P.; Oxelfelt, F.; Wunschiers, R.; Lindblad, P. Microbiol Mol Biol Rev 2002, 66, 1.
6. Volbeda, A.; Charon, M.-H.; Piras, C.; Hatchikian, E. C.; Frey, M.; Fontecilla-Camps. J. C. Nature 1995, 373, 580.
7. Volbeda, A.; Garcia, E.; Piras, C.; de Lacey, A. L.; Fernéndez, V. M.; Hatchikian, E. C.; Frey, M.; Fontecilla-Camps J. C. J Am Chem Soc 1996, 118, 12989.
8. Volbeda, A.; Montet, Y.; Vernede, X.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Int J Hydrogen Res 2002, 27, 1449.
9. Nicolet, Y.; Lemon, B. J.; Fontecilla-Camps, J. C.; Peters J. W. Trends Biochem Sci 2000, 25, 138.
10. Peters, J. W.; Lanzilotta, W. N.; Lemon, B. J.; Seefedt L. C. Science 1998, 282, 1853 (Errata: 283, 35; 283, 2102; Protein Data Bank code 1FEH).
11. Lemon, B. J.; Peters J. W. Biochemistry 1999, 39, 12969 (Protein Data Bank codes 1C4A and 1C4C).
12. Nicolet, Y.; de Lacey, A. L.; Vemede, X.; Femandez, V. M.; Hatchikian, E. C.; Fontecilla-Camps, J. C. J Am Chem Soc 2001, 123, 1596.
13. Nicolet, Y.; Piras, C.; Legrand, P.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Structure, 1999, 7, 13 (Protein Data Bank code 1HFE).
14. Nicolet, Y.; de Lacey, A. L.; Vernede, X.; Fernandez, V. M.; Hatchikian, E. C.; Fontecilla-Camps, J. C. J Am Chem Soc 2001, 123, 1596.
15. de Lacey, A. L.; Stadler, C.; Fernandez, V. M.; Hatchikian, E. C.; Fan, H.-J.; Li, S.; Hall, M. B. J Biol Inorg Chem 2002, 7, 318.
16. Ogata, H.; Mizoguchi, Y.; Mizuno, N.; Miki, K.; Adachi, S.-I.; Yasuoka, N.; Yagi, T.; Yamauchi, O.; Hirota, S.; Higuchi Y. J Am Chem Soc 2002, 124, 11628.
17. Popescu, C. V.; Münck, E. J Am Chem Soc 1999, 121, 7877.
18. Pereira, A. S.; Tavares P.; Moura, I.; Moura J. J. G.; Huynh B. H. J Am Chem Soc 2001, 123, 2771.
19. Volbeda, A.; Martin, L.; Cavazza, C.; Matho, M.; Faber, B. W.; Roseboom, W.; Albracht, S. P. J.; Garcin, E.; Rousset, M.; Fontecilla-Camps, J. C. J Biol Inorg Chem 2005, 10, 239.
20. Pardo, A.; De Lacey, A. L.; Fernandez, V. M.; Fan, H.-J.; Fan Y.; Hall, M. B. J Biol Inorg Chem 2006, 11, 286.
21. Becke, A. D. J Chem Phys 1993, 98, 5648.
22. Lee, C.; Yang, W.; Parr, R. G. Phys Rev 1988, 37, 785.
23. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A. Gaussian 03, Revision B.05; Gaussian, Inc.: Wallingford, CT, 2004.
24. Hay, P. J.; Wadt, W. R. J Chem Phys 1985, 82, 284.
25. Hay, P. J.; Wadt, W. R. J Chem Phys 1985, 82, 270.
26. Couty, M.; Hall, M. B. J Comp Chem 1996, 17, 1359.
27. Ehlers, A. W.; Böhme, M.; Dapprich, S.; Gobbi, A.; Höllwarth, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Veldkamp, A.; Frenking, G. Chem Phys Lett 1993, 208, 111.
28. Höllwarth, A.; Böhme, M.; Dapprich, S.; Ehlers, A. W.; Gobbi, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Frenking, G. Chem Phys Lett 1993, 208, 237.
29. Hariharan, P. C.; Pople, J. A. Theor Chim Acta 1973, 28, 213.
30. Petersson, G. A.; Bennett, A.; Tensfeldt, T. G.; Al-Laham, M. A.; Shirley, W. A.; Mantzaris, J. J Chem Phys 1988, 89, 2193.
31. Petersson, G. A.; Al-Laham, M. A. J Chem Phys 1991, 94, 6081.
32. Hehre, W. J.; Ditchfield, R. Pople, J. A. J Chem Phys 1972, 56, 2257.
33. Wong, M. W.; Wiberg, K. B.; Frisch, M. J Chem Phys 1991, 95, 8991.
34. Wong, M. W.; Frisch, M. J.; Wiberg, K. J Am Chem Soc 1991, 113, 4776.
35. Wong, M. W.; Wiberg, K. B.; Frisch, M. J. J Am Chem Soc 1992, 114, 523.
36. Wong, M. W.; Wiberg, K. B.; Frisch, M. J. J Am Chem Soc 1992, 114, 1645.
37. Onsager, L. J Am Chem Soc 1936, 58, 1486.
38. Kirkwood, J. G. J Chem Phys 1934, 2, 351.
39. Le Cloirec, A.; Davies, S. C.; Evans, D. J.; Hughes, D. L.; Pickett, C. J.; Best, S. P.; Borg, S. Chem Commun 1999, 22, 2285.
40. Razavet, M.; Davies, S. C.; Hughes, D. L.; Barclay, J. E.; Evans, D. J.; Fairhurst, S. A.; Liu, X.; Pickett C. J. Dalton Trans 2003, 586.
41. Gloaguen, F.; Lawrence, J. D.; Schmidt, M.; Wilson, S. R.; Rauchfuss, T. B. J Am Chem Soc 2001, 123, 12518.
42. Lyon, E. J.; Georgakaki, I. P.; Reibenspies, J. H.; Darensbourg, M. Y. Angew Chem Int Ed 1999, 38, 3178.
43. Zhao, X.; Georgakaki, I. P.; Miller, M. L.; Mejia-Rodriguez, R.; Chiang, C.-Y.; Darensbourg, M. Y. Inorg Chem 2002, 41, 3917.
44. Hasan, M. M.; Hursthouse, M. B.; Kabir, S. E.; Malik, K. M. A. Polyhedron 2001, 20, 97.
45. Li, H.; Rauchfuss, T. B. J Am Chem Soc 2002, 124, 726.
46. Lawrence, J. D.; Li, H.; Rauchfuss, T. B.; Bénard, M.; Rohmer, M.-M. Angew Chem Int Ed 2001, 40, 1768.
47. Mejia-Rodriguez, R.; Chong, D.; Reibenspies, J. H.; Soriaga, M. P.; Darensbourg, M. Y. J Am Chem Soc 2004, 126, 12004.
48. Gloaguen, F.; Lawrence, J. D.; Rauchfuss, T. B.; Bénard, M.; Rohmer, M.-M. Inorg Chem 2002, 41, 6573.
49. Georgakaki, I. P.; Miller, M. L.; Darensbourg, M. Y. Inorg Chem 2003, 42, 2489.
50. Pople, J. A.; Scott, A. P.; Wong, M. W.; Radom, L. Israel J Chem 1993, 33, 345.
51. Fast, P. L.; Corchado, J.; Sänchez, M.; Truhlar, D. G. J Phys Chem A 1999, 103, 3139.
52. Zhao, Y.; Lynch, B. J.; Truhlar D. G. J Phys Chem A 2004, 108, 4786.
53. Lide, D. R., Ed. CRC Handbook of Chemistry and Physics, Internet Version 2005 (http://www.hbcpnetbase.com); CRC Press: Boca Raton, FL, 2005.
54. Boyke, C. A.; Rauchfuss, T. B.; Wilson, S. R.; Rohmer, M.-M.; Bénard, M. J Am Chem Soc 2004, 126, 15151.
55. Chong, D.; Georgakaki, I. P.; Mejia-Rodriguez, R.; Sanabria-Chinchilla, J.; Soriaga, M. P.; Darensbourg, M. Y. Dalton Trans 2003, 21, 4158.
56. Ott, S.; Kritikos, M.; Akermark, B.; Sun, L.; Lomoth, R. Angew Chem Int Ed Engl 2004, 43, 1006.
57. Capon, J.-F.; Gloaguen, F.; Schollhammer, P.; Talarmin, J. J Electroanal Chem 2004, 566, 241.
58. Liu, T.; Wang, M.; Shi, Z.; Cui, H.; Dong, W.; Chen, J.; Äkermark, B.; Sun, L. Chem Eur J 2004, 10, 4474.
59. Borg, S. J.; Behrsing, T.; Best, S. P.; Razavet, M.; Liu, X.; Pickett C. J. J Am Chem Soc 2004, 126, 16988.
60. Darchen, A.; Mousser, H.; Patin, H. Chem Commun 1988, 968.
61. Fiedler, A. T.; Brunold, T. C. Inorg Chem 2005, 44, 9322.