Vibrational analysis of the chorismate rearrangement: Relaxed force constants, isotope effects and activation entropies calculated for reaction in vacuum, water and the active site of chorismate mutase

Journal of Physical Organic Chemistry

Volumn 17, Issue 6-7 SPEC.ISS., 2004, Pages 592-601

  Ruggiero, Giuseppe D ^a   Guy, Sara J ^a   Marti, Sergio ^b   Moliner, Vicent ^b   Williams, Ian H ^a  

^a University of Bath Claverton Down   (United Kingdom)

^b UNIVERSITAT JAUME I   (Spain)

Author keywords

Cut off rule; Enzyme catalysis; Isotope effects; QM MM Hessian; Relaxed force constants; Solvation; Transition state; Vibrational entropy

Indexed keywords

ACTIVATION ENERGY; CATALYSIS; CHEMICAL BONDS; COMPUTATIONAL METHODS; ENTROPY; ISOTOPES; PHASE TRANSITIONS; REACTION KINETICS; SUBSTRATES; VACUUM;

ENZYME CATALYSIS; ISOTOPE EFFECTS; RELAXED FORCE CONSTANTS; SOLVATION; TRANSITION STATES; VIBRATIONAL ENTROPY;

ENZYMES;

EID: 2942717103     PISSN: 08943230     EISSN: None     Source Type: Journal    
DOI: 10.1002/poc.781     Document Type: Article

References (51)

1. Page MI, Jencks WP. Proc. Natl Acad. Sci. USA 1971; 68: 1678-1683.
2. Jencks WP. Adv. Enzymol. 1975; 43: 219-410.
3. Blow D. Struct. Fold. Des. 2000; 8: R77-R81.
4. Menger FM. Acc. Chem. Res. 1993; 26: 206-212.
5. (a) Brown KG, Erfurth SC, Small EW, Peticolas WL. Proc. Natl Acad. Sci. USA 1972; 69: 1467;
6. (b) Chou KC. Biophys. J. 1988; 30: 3-48;
7. (c) Britt BM. Biophys. J. 1997; 69: 63-70.
8. Cook DB, McKenna J. J. Chem. Soc., Perkin Trans. 2 1974; 1223-1225.
9. Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J, Field MJ. J. Am. Chem. Soc. 2001; 123: 1709-1712.
10. Martí S, Moliner V, Tuñón I, Williams IH. Org. Biomol Chem. 2003; 1: 483-487.
11. (a) Wolfsberg M, Stern MJ. Pure Appl. Chem. 1964; 8: 325;
12. (b) Stern MJ, Wolfsberg M. J. Phys. Chem. 1966; 45: 4105.
13. Thornton EK, Thornton ER. In Isotope Effects in Chemical Reactions, Collins CJ, Bowman NS (eds). Van Nostrand Reinhold: New York, 1970; 225.
14. Melander L, Saunders WH. Reaction Rates of Isotopic Molecules. Wiley: New York, 1980; 71-73.
15. Gandour RD, Schowen RL (eds). Transition States of Biochemical Processes. Plenum Press: New York, 1978.
16. Page M, Williams A. Organic and Bioorganic Mechanisms. Longman: Harlow, 1997; 94-95.
17. Gajewski JJ. Acc. Chem. Res. 1997; 30: 219-225.
18. Glad SS, Jensen F. J. Am. Chem. Soc. 1994; 116: 9302-9310; J. Phys. Chem. 1996; 100: 16892-16898; J. Org. Chem. 1997; 62: 253-260; Nielsen PA, Glad SS, Jensen F. J. Am. Chem. Soc. 1996; 118: 10577-10583.
19. Glad SS, Jensen F. J. Am. Chem. Soc. 1994; 116: 9302-9310; J. Phys. Chem. 1996; 100: 16892-16898; J. Org. Chem. 1997; 62: 253-260; Nielsen PA, Glad SS, Jensen F. J. Am. Chem. Soc. 1996; 118: 10577-10583.
20. Glad SS, Jensen F. J. Am. Chem. Soc. 1994; 116: 9302-9310; J. Phys. Chem. 1996; 100: 16892-16898; J. Org. Chem. 1997; 62: 253-260; Nielsen PA, Glad SS, Jensen F. J. Am. Chem. Soc. 1996; 118: 10577-10583.
21. Glad SS, Jensen F. J. Am. Chem. Soc. 1994; 116: 9302-9310; J. Phys. Chem. 1996; 100: 16892-16898; J. Org. Chem. 1997; 62: 253-260; Nielsen PA, Glad SS, Jensen F. J. Am. Chem. Soc. 1996; 118: 10577-10583.
22. Saunders WH. Croat. Chem. Acta 2001; 74: 575-591.
23. Meyer MP, DelMonte AJ, Singleton DA. J. Am. Chem. Soc. 1999; 121: 10865-10874.
24. Williams IH. Chem. Phys. Lett. 1982; 88: 462-466.
25. Francisco JS, Williams IH. Chem. Phys. 1985; 95: 373-383.
26. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. J. Am. Chem. Soc. 1985; 107: 3902-3909.
27. (a) Becke AD. Phys. Rev. A 1988; 38: 3098-3100; J. Chem. Phys. 1993; 98: 5648;
28. (a) Becke AD. Phys. Rev. A 1988; 38: 3098-3100; J. Chem. Phys. 1993; 98: 5648;
29. (b) Lee C, Yang W, Parr RG. Phys. Rev. B 1988; 37: 785-789;
30. (c) Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ. J. Phys. Chem. 1994; 98: 11623-11627.
31. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA. Gaussian 98, Revision A. 6. Gaussian: Pittsburgh, PA, 1998.
32. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. J. Comput. Chem. 1983; 4: 187-217.
33. (a) Moliner V, Turner AJ, Williams IH. J. Chem. Soc., Chem. Commun. 1997; 1271-1272;
34. (b) Turner AJ, Moliner V, Williams IH. Phys. Chem. Chem. Phys. 1999; 1: 1323-1331.
35. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. J. Chem. Phys. 1983; 79: 926-935.
36. Chook YM, Ke H, Lipscomb WN. Proc. Natl Acad. Sci. USA 1993; 90: 8600-8603.
37. Williams IH. J. Mol. Struct. (THEOCHEM) 1983; 94: 275-284.
38. Wilkie J, Williams IH. J. Chem. Soc., Perkin Trans. 2 1995; 1559-1567.
39. Houk KH, Gustafson SM, Black KA. J. Am. Chem. Soc. 1992; 114: 8565-8572.
40. Li H, Jensen JH. Theor. Chem. Acc. 2002; 107: 211-219.
41. (a) Jencks WP. Chem. Rev. 1985; 85:511-527;
42. (b) More O'Ferrall RA. J. Chem. Soc. B 1970; 274-277.
43. (a) Burton GW, Sims LB, Wilson JC, Fry A. J. Am. Chem. Soc. 1977; 99: 3371-3379;
44. (b) Johnston HS. Gas Phase Reaction Rate Theory. Ronald Press: New York, 1966; 72-77.
45. Burrows CJ, Carpenter BK. J. Am. Chem. Soc. 1981; 103: 6984-6986.
46. Kast P, Tewari YB, Wiest O, Hilvert D, Houk KN, Goldberg RN. J. Phys. Chem. B 1997; 101: 10976-10982.
47. Andrews PR, Smith GD, Young IG. Biochemistry 1973; 12: 3492-3498.
48. Galopin CC, Zhang S, Wilson DB, Ganem B. Tetrahedron Lett. 1996; 37: 8675-8678.
49. Kast P, Asif-Ullah M, Hilvert D. Tetrahedron Lett. 1996; 37: 2691-2694.
50. Mattei P, Kast P, Hilvert D. Eur. J. Biochem. 1999; 261: 25-32.
51. Villa J, Štrajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A. Proc. Natl Acad. Sci. USA 2000; 97: 11899-11904.