Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations

Journal of Chemical Physics

Volumn 132, Issue 3, 2010, Pages

  Dieterich, Johannes M ^a   Werner, Hans Joachim ^a   Mata, Ricardo A ^b   Metz, Sebastian ^c   Thiel, Walter ^c  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; AB INITIO CALCULATIONS; BASIS SETS; COFACTORS; CONCERTED MECHANISM; COUPLED CLUSTERS; ENERGY PROFILE; FREE ENERGY PERTURBATION; HYDRIDE TRANSFERS; LEWIS BASE; LOCAL CORRELATIONS; METAL CENTERS; NUCLEOPHILIC ATTACK; OXIDOREDUCTASES; QM/MM CALCULATIONS; QUANTUM MECHANICAL/MOLECULAR MECHANICAL CALCULATIONS; RATE LIMITING; REACTION PATHS; REACTION STEPS; STATIONARY POINTS; TETRAHEDRAL INTERMEDIATES; THREE REACTION PATHWAYS;

ALDEHYDES; ENERGY BARRIERS; MOLECULAR DYNAMICS; REACTION KINETICS;

FREE ENERGY;

ACETALDEHYDE; ALDEHYDE DEHYDROGENASE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; QUANTUM THEORY; THERMODYNAMICS;

ACETALDEHYDE; ALDEHYDE OXIDOREDUCTASES; MODELS, CHEMICAL; MODELS, MOLECULAR; QUANTUM THEORY; THERMODYNAMICS;

EID: 77949881245     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3280164     Document Type: Article

References (75)

1. R. Hille, Chem. Rev. 96, 2757 (1996). 10.1021/cr950061t
2. C. Kisker, H. Schindelin, and D. C. Rees, Annu. Rev. Biochem. 0066-4154 66, 233 (1997). 10.1146/annurev.biochem.66.1.233 (Pubitemid 27274657)
3. C. J. Doonan, A. Stockert, R. Hille, and G. N. George, J. Am. Chem. Soc. 0002-7863 127, 4518 (2005). 10.1021/ja042500o (Pubitemid 40463078)
4. V. Massey and D. Edmondson, J. Biol. Chem. 0021-9258 245, 6595 (1970).
5. T. Santos-Silva, F. Ferroni, A. Thapper, J. Marangon, P. J. González, A. C. Rizzi, I. Moura, J. J. G. Moura, M. J. Romão, and C. D. Brondino, J. Am. Chem. Soc. 0002-7863 131, 7990 (2009). 10.1021/ja809448r
6. E. B. Skibo, J. G. Gilchrist, and C. H. Lee, Biochemistry 0006-2960 26, 3032 (1987). 10.1021/bi00385a013 (Pubitemid 17087833)
7. B. A. Barata, J. LeGall, and J. J. G. Moura, Biochemistry 0006-2960 32, 11559 (1993). 10.1021/bi00094a012 (Pubitemid 23341433)
8. S. L. Andrade, C. Brondino, M. J. Feio, I. Moura, and J. J. G. Moura, Eur. J. Biochem. 0014-2956 267, 2054 (2000). 10.1046/j.1432-1327.2000.01209.x (Pubitemid 30185292)
9. R. A. Torres, K. R. Korzekwa, D. R. McMasters, C. M. Fandozzi, and J. P. Jones, J. Med. Chem. 0022-2623 50, 4642 (2007). 10.1021/jm0703690 (Pubitemid 47463238)
10. E. Y. Choi, A. L. Stockert, S. Leimkühler, and R. Hille, J. Inorg. Biochem. 0162-0134 98, 841 (2004). 10.1016/j.jinorgbio.2003.11.010 (Pubitemid 38595285)
11. R. Hille, Eur. J. Inorg. Chem. 1434-1948 10, 1913 (2006). 10.1002/ejic.200600087
12. Y. Yamaguchi, T. Matsumura, K. Ichida, K. Okamoto, and T. Nishino, J. Biochem. 141, 513 (2007). 10.1093/jb/mvm053 0021-924X (Pubitemid 351455300)
13. S. E. Clarke, A. W. Harrell, and R. J. Chemery, Drug Metab. Dispos. 0090-9556 23, 251 (1995).
14. M. R. Rashidi, J. A. Smith, S. E. Clarke, and C. Beedham, Drug Metab. Dispos. 0090-9556 25, 805 (1997).
15. K. Kawashima, K. Hosoi, T. Naruke, T. Shiba, M. Kitamura, and T. Watabe, Drug Metab. Dispos. 0090-9556 27, 422 (1999).
16. B. G. Lake, S. E. Ball, J. Kao, A. B. Renwick, R. J. Price, and J. A. Scatina, Xenobiotica 0049-8254 32, 835 (2002). 10.1080/00498250210158915 (Pubitemid 35155519)
17. H. M. Senn and W. Thiel, Top. Curr. Chem. 0071-7894 268, 173 (2007). 10.1007/128-2006-084
18. H. M. Senn and W. Thiel, Angew. Chem., Int. Ed. 1433-7851 48, 1198 (2009). 10.1002/anie.200802019
19. S. Metz, D. Wang, and W. Thiel, J. Am. Chem. Soc. 0002-7863 131, 4628 (2009). 10.1021/ja805938w
20. S. Metz and W. Thiel, J. Am. Chem. Soc. 0002-7863 131, 14885 (2009). 10.1021/ja9045394
21. Y. Zhang, H. Liu, and W. Yang, J. Chem. Phys. 0021-9606 112, 3483 (2000). 10.1063/1.480503
22. J. Kästner, H. M. Senn, S. Thiel, N. Otte, and W. Thiel, J. Chem. Theory Comput. 1549-9618 2, 452 (2006). 10.1021/ct050252w
23. H. M. Senn, J. Kästner, J. Breidung, and W. Thiel, Can. J. Chem. 0008-4042 87, 1322 (2009). 10.1139/V09-092
24. J. M. Rebelo, J. M. Dias, R. Huber, J. J. G. Moura, and M. J. Romão, J. Biol. Inorg. Chem. 6, 791 (2001). 10.1007/s007750100255 (Pubitemid 33078033)
25. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 1089-5647 102, 3586 (1998).
26. J. C. Slater, Phys. Rev. 0096-8250 81, 385 (1951). 10.1103/PhysRev.81.385
27. S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 0008-4204 58, 1200 (1980).
28. A. D. Becke, Phys. Rev. A 1050-2947 38, 3098 (1988). 10.1103/PhysRevA.38. 3098
29. A. D. Becke, J. Chem. Phys. 0021-9606 98, 5648 (1993). 10.1063/1.464913
30. P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, J. Phys. Chem. 0022-3654 98, 11623 (1994). 10.1021/j100096a001
31. C. T. Lee, W. T. Yang, and R. G. Parr, Phys. Rev. B 0163-1829 37, 785 (1988). 10.1103/PhysRevB.37.785
32. R. Ahlrichs, M. Bär, M. Häser, H. Horn, and C. Kölmel, Chem. Phys. Lett. 0009-2614 162, 165 (1989). 10.1016/0009-2614(89)85118-8
33. W. Smith and T. R. Forester, J. Mol. Graphics 0263-7855 14, 136 (1996). 10.1016/S0263-7855(96)00043-4 (Pubitemid 26372493)
34. S. R. Billeter, A. J. Turner, and W. Thiel, Phys. Chem. Chem. Phys. 1463-9076 2, 2177 (2000). 10.1039/a909486e
35. P. Sherwood, A. H. de Vries, M. F. Guest, G. Schreckenbach, C. R. A. Catlow, S. A. French, A. A. Sokol, S. T. Bromley, W. Thiel, A. J. Turner, S. Billeter, F. Terstegen, S. Thiel, J. Kendrick, S. C. Rogers, J. Casci, M. Watson, F. King, E. Karlsen, M. Sjøvoll, A. Fahmi, A. Schäfer, and C. Lennartz, J. Mol. Struct.: THEOCHEM 0166-1280 632, 1 (2003). 10.1016/s0166-1280(03)00285-9
36. See: www.chemshell.org.
37. P. J. Hay and W. R. Wadt, J. Chem. Phys. 0021-9606 82, 270 (1985). 10.1063/1.448799
38. A. W. Ehlers, M. Böhme, S. Dapprich, A. Gobbi, A. Höllwarth, V. Jonas, K. F. Köhler, R. Stegmann, A. Veldkamp, and G. Frenking, Chem. Phys. Lett. 0009-2614 208, 111 (1993). 10.1016/0009-2614(93)80086-5
39. W. R. Wadt and P. J. Hay, J. Chem. Phys. 0021-9606 82, 284 (1985). 10.1063/1.448800
40. A. Höllwarth, M. Böhme, S. Dapprich, A. W. Ehlers, A. Gobbi, V. Jonas, K. F. Köhler, R. Stegmann, A. Veldkamp, and G. Frenking, Chem. Phys. Lett. 0009-2614 208, 237 (1993). 10.1016/0009-2614(93)89068-S
41. P. C. Hariharan and J. A. Pople, Theor. Chim. Acta 0040-5744 28, 213 (1973). 10.1007/BF00533485
42. T. Clark, J. Chandrasekhar, G. W. Spitznagel, and P. R. Schleyer, J. Comput. Chem. 0192-8651 4, 294 (1983). 10.1002/jcc.540040303
43. MOLPRO, a package of ab initio programs, version 2008.1, 2008, H. -J. Werner, P. J. Knowles, R. Lindh, see http://www.molpro.net.
44. P. Pulay, Chem. Phys. Lett. 0009-2614 100, 151 (1983). 10.1016/0009-2614(83)80703-9
45. S. Sbø and P. Pulay, Chem. Phys. Lett. 0009-2614 113, 13 (1985). 10.1016/0009-2614(85)85003-X
46. P. Pulay and S. Saebø, Theor. Chim. Acta 0040-5744 69, 357 (1986). 10.1007/BF00526697
47. M. Schütz, G. Hetzer, and H. -J. Werner, J. Chem. Phys. 0021-9606 111, 5691 (1999). 10.1063/1.479957
48. G. Hetzer, M. Schütz, H. Stoll, and H. -J. Werner, J. Chem. Phys. 0021-9606 113, 9443 (2000). 10.1063/1.1321295 (Pubitemid 32085123)
49. M. Schütz and H. -J. Werner, J. Chem. Phys. 0021-9606 114, 661 (2001). 10.1063/1.1330207 (Pubitemid 32138502)
50. M. Schütz, J. Chem. Phys. 0021-9606 113, 9986 (2000). 10.1063/1.1323265 (Pubitemid 32076893)
51. R. Polly, H. -J. Werner, F. R. Manby, and P. J. Knowles, Mol. Phys. 0026-8976 102, 2311 (2004). 10.1080/0026897042000274801 (Pubitemid 40002176)
52. H. -J. Werner, F. R. Manby, and P. Knowles, J. Chem. Phys. 0021-9606 118, 8149 (2003). 10.1063/1.1564816
53. H. -J. Werner and M. Schütz (to be published).
54. M. Schütz and F. R. Manby, Phys. Chem. Chem. Phys. 1463-9076 5, 3349 (2003). 10.1039/b304550a
55. T. H. Dunning, Jr., J. Chem. Phys. 0021-9606 90, 1007 (1989). 10.1063/1.456153
56. R. A. Kendall, T. H. Dunning, and R. J. Harrison, J. Chem. Phys. 0021-9606 96, 6796 (1992). 10.1063/1.462569
57. K. Peterson, D. Figgen, M. Dolg, and H. Stoll, J. Chem. Phys. 0021-9606 126, 124101 (2007). 10.1063/1.2647019 (Pubitemid 46522102)
58. F. Weigend, J. Comput. Chem. 29, 167 (2008). 10.1002/jcc.20702
59. F. Weigend, Phys. Chem. Chem. Phys. 1463-9076 4, 4285 (2002). 10.1039/b204199p
60. A. Hellweg, C. Hättig, S. Höfener, and W. Klopper, Theor. Chim. Acta 0040-5744 117, 587 (2007). 10.1007/s00214-007-0250-5
61. F. Weigend, A. Köhn, and C. Hättig, J. Chem. Phys. 0021-9606 116, 3175 (2002). 10.1063/1.1445115 (Pubitemid 34221281)
62. C. Hampel and H. -J. Werner, J. Chem. Phys. 0021-9606 104, 6286 (1996). 10.1063/1.471289
63. R. A. Mata, H. -J. Werner, S. Thiel, and W. Thiel, J. Chem. Phys. 0021-9606 128, 025104 (2008). 10.1063/1.2823055
64. F. Claeyssens, J. N. Harvey, F. R. Manby, R. A. Mata, A. J. Mulholland, K. E. Ranaghan, M. Schütz, S. Thiel, W. Thiel, and H. -J. Werner, Angew. Chem., Int. Ed. 1433-7851 45, 6856 (2006). 10.1002/anie.200602711 (Pubitemid 44654476)
65. A. E. Reed and F. Weinhold, J. Chem. Phys. 0021-9606 83, 1736 (1985). 10.1063/1.449360
66. R. Mata and H. -J. Werner, Mol. Phys. 0026-8976 105, 2753 (2007). 10.1080/00268970701628209 (Pubitemid 351194987)
67. J. W. Boughton and P. Pulay, J. Comput. Chem. 0192-8651 14, 736 (1993). 10.1002/jcc.540140615
68. J. Kaminsky, R. A. Mata, H. -J. Werner, and F. Jensen, Mol. Phys. 0026-8976 106, 1899 (2008). 10.1080/00268970802360355
69. M. Schütz, G. Rauhut, and H. -J. Werner, J. Phys. Chem. A 1089-5639 102, 5997 (1998). 10.1021/jp981168y
70. R. Mata and H. -J. Werner, J. Chem. Phys. 0021-9606 125, 184110 (2006). 10.1063/1.2364487 (Pubitemid 44749466)
71. See supplementary material at http://dx.doi.org/10.1063/1.3280164 E-JCPSA6-132-017002 for details of the QM/MM energies for the different QM methods, all correction terms included in the calculation of the free energy barriers, and additional graphical analysis of the FEP results.
72. S. Grimme, J. Chem. Phys. 0021-9606 118, 9095 (2003). 10.1063/1.1569242
73. P. Ilich and R. Hille, J. Phys. Chem. B 1089-5647 103, 5406 (1999). 10.1021/jp9904825
74. P. Ilich and R. Hille, J. Am. Chem. Soc. 0002-7863 124, 6796 (2002). 10.1021/ja011957k (Pubitemid 34633559)
75. T. Amano, N. Ochi, H. Sato, and S. Sakaki, J. Am. Chem. Soc. 0002-7863 129, 8131 (2007). 10.1021/ja068584d (Pubitemid 47035126)