How important is the refinement of transition state structures in enzymatic reactions?

Journal of Molecular Structure: THEOCHEM

Volumn 632, Issue 1-3, 2003, Pages 297-307

  Prat Resina, Xavier ^a   González Lafont, Àngels ^a   Lluch, José M ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Mandelate racemase reaction mechanisms; Micro iterative method; Quantum mechanical molecular mechanical transition state structures; Reaction coordinate approach; Second derivatives direct optimization method

Indexed keywords

ENZYME; RACEMASE;

ACCURACY; ALGORITHM; ARTICLE; ELECTRIC POTENTIAL; ENZYME ANALYSIS; ENZYME MECHANISM; GEOMETRY; PHASE TRANSITION; QUANTUM MECHANICS; REACTION ANALYSIS;

EID: 0242391070     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-1280(03)00307-5     Document Type: Article

References (38)

1. A. Warshel, M. Levitt, J. Mol. Biol. 103 (1976) 227.
2. M.J. Field, P.A. Bash, M. Karplus, J. Comput. Chem. 11 (1990) 700.
3. J. Gao, M.A. Thompson (Eds.), Combined Quantum Mechanical and Molecular Mechanical Methods, ACS Symposium Series 712, American Chemical Society, Washington, DC, 1998.
4. M.J. Field, J. Comput. Chem. 23 (2002) 48.
5. J. Gao, D. Truhlar, Annu. Rev. Phys. Chem. 53 (2002) 467.
6. D. Truhlar, B. Garrett, S. Klippenstein, J. Phys. Chem. 100 (1996) 12771.
7. A.R. Leach, Molecular Modelling. Principles and Applications, second ed., Pearson Education, England, 2001.
8. A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions, Wiley, New York, 1992.
9. J. Aqvist, A. Warshel, Chem. Rev. 93 (1993) 2523.
10. D.G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M.L. Sánchez, J. Villà, Acc. Chem. Res. 35 (2002) 341.
11. C. Alhambra, J. Corchado, M.L. Sánchez, M. Garcia-Viloca, J. Gao, D.G. Truhlar, J. Phys. Chem. B 105 (2001) 11326.
12. X. Prat-Resina, M. Garcia-Viloca, A. González-Lafont, J.M. Lluch, Phys. Chem. Chem. Phys. 4 (2002) 5365.
13. G. Monard, X. Prat-Resina, A. González-Lafont, J.M. Lluch, Int. J. Quantum Chem. 93 (2003) 229.
14. K. Németh, O. Coulaud, G. Monard, J.G. Ángyán, J. Chem. Phys. 113 (2000) 5598.
15. S.R. Billeter, A.J. Turner, W. Thiel, Phys. Chem. Chem. Phys. 2 (2000) 2177.
16. B. Paizs, J. Baker, S. Suhai, P. Pulay, J. Chem. Phys. 113 (2000) 6566.
17. D.C. Liu, J. Nocedal, Math. Programming (1989) 503.
18. G. Henkelman, G. Jóhannesson, H. Jónsson, Methods for finding saddle points and minimum energy path, in: S.D. Schwartz (Ed.), Progress on Theoretical Chemistry and Physics, 2000, p. 269.
19. S. Fischer, M. Karplus, Chem. Phys. Lett. 194 (1992) 252.
20. Q. Cui, M. Elstner, M. Karplus, J. Phys. Chem. B 106 (2002) 2721.
21. Q. Cui, M. Karplus, J. Am. Chem. Soc. 124 (2002) 3093.
22. R. Fletcher, Practical Methods of Optimization, second ed., Wiley, UK, 1987.
23. J. Simons, P. Jorgensen, H. Taylor, J. Ozment, J. Comput. Chem. 87 (1983) 2745.
24. A. Banerjee, N. Adams, J. Simons, R. Shepard, J. Comput. Chem. 89 (1985) 52.
25. E. Besalú, J.M. Bofill, Theor. Chem. Acc. 100 (1998) 265.
26. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 4 (1983) 187.
27. A.J. Turner, V. Moliner, I.H. Williams, Phys. Chem. Chem. Phys. 1 (1999) 1323.
28. R.J. Hall, S.A. Hindle, N.A. Burton, I.H. Hillier, J. Comput. Chem. 21 (2000) 1433.
29. Y. Zhang, H. Liu, W. Yang, J. Chem. Phys. 112 (2000) 3483.
30. T. Vreven, K. Morokuma, Ö. Farkas, H.B. Schlegel, M.J. Frisch, J. Comput. Chem. 24 (2003) 760.
31. X. Prat-Resina, M. Garcia-Viloca, G. Monard, A. González-Lafont, J.M. Lluch, J.M. Anglada, J.M. Bofill, Theor. Chem. Acc. 107 (2002) 147.
32. E. Anderson, Z. Bai, C. Bischof, S. Blackford, J. Demmel, J. Dongarra, J.D. Croz, A. Greenbaum, S. Hammarling, A. McKenney, D. Sorensen, LAPACK User's Guide, third ed., SIAM, 1999.
33. A. Cheng, R.S. Stanton, J.J. Vincent, A. van der Vaart, K.V. Damodaran, S.L. Dixon, D.S. Hartsough, M. Mori, S.A. Best, G. Monard, M. Garcia-Viloca, L.C.V. Zant, J.K.M. Merz, ROAR 2.0, The Pennsylvania State University, 1999.
34. D. Pearlman, D. Case, J. Caldwell, W. Ross, T. Cheatham, S. Debolt, D. Ferguson, G. Seibel, P. Kollman, Comput. Phys. Commun. 91 (1995) 1.
35. M. Garcia-Viloca, A. González-Lafont, J.M. Lluch, J. Am. Chem. Soc. 123 (2001) 709.
36. M.C. Hutter, J.M. Hughes, J.R. Reimers, N.S. Hus, J. Phys. Chem. B 103 (1999) 4906.
37. N. Reuter, A. Dejaegere, B. Maigret, M. Karplus, J. Phys. Chem. A 104 (1999) 1720.
38. S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Ghio, G.S. Alagona, J. Profeta, P. Weiner, J. Am. Chem. Soc. 106 (1984) 765.