Stereoelectronic requirements for optimal hydrogen-bond-catalyzed enolization

Chemistry - A European Journal

Volumn 17, Issue 10, 2011, Pages 2859-2866

  Pápai, Imre ^a   Hamza, Andrea ^a   Pihko, Petri M ^b   Wierenga, Rik K ^c  

^a CHEMICAL RESEARCH CENTER   (Hungary)

^b UNIVERSITY OF JYVÄSKYLÄ   (Finland)

^c UNIVERSITY OF OULU   (Finland)

Author keywords

catalyst design; density functional theory; enolization; hydrogen bonds; oxyanion hole

Indexed keywords

CARBONYL COMPOUNDS; CHEMICAL ANALYSIS; COMPLEXATION; COMPUTATION THEORY; CRYSTAL ORIENTATION; DENSITY FUNCTIONAL THEORY; ENZYMES; POSITIVE IONS; QUANTUM CHEMISTRY; THERMODYNAMICS;

CATALYST DESIGNS; COMPUTATIONAL RESULTS; CRYSTALLOGRAPHIC ANALYSIS; ENOLIZATION; KINETICS AND THERMODYNAMICS; OUT-OF-PLANE ORIENTATION; OXYANION HOLE; QUANTUM CHEMICAL CALCULATIONS;

HYDROGEN BONDS;

EID: 79951994097     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201002943     Document Type: Article

References (56)

1. For reviews on enolizing enzymes, see
2. P. A. Frey, A. D. Hegeman, Enzymatic Reaction Mechanisms, Oxford University Press, Oxford, 2007
3. H. M. Holden, M. M. Benning, T. Haller, J. A. Gerlt, Acc. Chem. Res. 2001, 34, 145
4. P. M. Pihko, S. Rapakko, R. K. Wierenga, Oxyanion Holes and their Mimics in Hydrogen Bonding in Organic Synthesis (Ed.:, P. M. Pihko,), Wiley-VCH, Weinheim, 2009.
5. E. J. Corey, R. A. Sneen, J. Am. Chem. Soc. 1956, 78, 6269.
6. See, for example
7. A. F. Bell, J. Wu, Y. Feng, P. J. Tonge, Biochemistry 2001, 40, 1725
8. D. A. Kraut, P. A. Sigala, B. Pybus, C. W. Liu, D. Ringe, G. A. Petsko, D. Herschlag, PLoS Biol. 2006, 4, e 99
9. G. Merilainen, V. Poikela, P. Kursula, R. K. Wierenga, Biochemistry 2009, 48, 11011.
10. For previous structural analyses demonstrating the lone-pair directionality of Cï£O-H hydrogen bonding, see
11. B. A. Grzybowski, A. V. Ischienko, R. DeWitte, G. M. Whitesides, E. I. Shakhnovich, J. Phys. Chem. B 2000, 104, 7293
12. R. Taylor, O. Kennard, W. Vershiche, J. Am. Chem. Soc. 1983, 105, 5761
13. P. Murray-Rust, J. P. Glusker, J. Am. Chem. Soc. 1983, 105, 1018
14. T. Steiner, Angew. Chem. 2002, 114, 50
15. Angew. Chem. Int. Ed. 2002, 41, 48.
16. L. Simón, J. M. Goodman, J. Org. Chem. 2010, 75, 1831.
17. T. S. Snowden, A. P. Bisson, E. V. Anslyn, J. Am. Chem. Soc. 1999, 121, 6324
18. Z. Zhong, T. S. Snowden, M. Best, E. V. Anslyn, J. Am. Chem. Soc. 2004, 126, 3488
19. R. J. T. Houk, E. V. Anslyn, J. F. Stanton, Org. Lett. 2006, 8, 3461
20. R. J. T. Houk, A. Monzingo, E. V. Anslyn, Acc. Chem. Res. 2008, 41, 401.
21. R. Amstutz, W. B. Schweizer, D. Seebach, J. D. Dunitz, Helv. Chim. Acta 1981, 64, 2617
22. P. G. Williard, G. B. Carpenter, J. Am. Chem. Soc. 1986, 108, 462.
23. J. A. Gerlt, P. G. Gassman, J. Am. Chem. Soc. 1992, 114, 5928
24. J. A. Gerlt, P. G. Gassman, J. Am. Chem. Soc. 1993, 115, 11552.
25. For a review on the importance of electrostatic activation in enzyme catalysis, see:, A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, M. H. M. Olsson, Chem. Rev. 2006, 106, 3210.
26. The X-ray crystallographic data for enolizing enzymes were collected from the following references (for further details, see the Supporting Information)
27. S. A. Partanen, D. K. Novikov, A. N. Popov, A. M. Mursula, J. K. Hiltunen, R. K. Wierenga, J. Mol. Biol. 2004, 342, 1197
28. C. K. Engel, M. Mathieu, J. Ph. Zeelen, J. K. Hiltunen, R. K. Wierenga, EMBO J. 1996, 15, 5135
29. Y. Modis, R. K. Wierenga, J. Mol. Biol. 2000, 297, 1171
30. J. J. Kim, M. Wang, R. Paschke, Proc. Natl. Acad. Sci. USA 1993, 90, 7523
31. M. Karpusas, D. Holland, S. J. Remington, Biochemistry 1991, 30, 6024
32. G. Jogl, S. Rozovsky, A. E. McDermott, L Tong, Proc. Natl. Acad. Sci. USA 2003, 100, 50
33. D. Arsenieva, R. Hardre, L. Salmon, C. J. Jeffery, Proc. Natl. Acad. Sci. USA 2002, 99, 5872
34. A. Roos, E. Burgos, D. J. Ericsson, L. Salmon, S. L. Mowbray, J. Biol. Chem. 2005, 280, 6416
35. N. C. Ha, M. S. Kim, W. Lee, K. Y. Choi, B. H. Oh, J. Biol. Chem. 2000, 275, 41100.
36. The data for functional groups represents the combined data for OH and NH hydrogen bonds, with an O/N-H-Oï£C distance of 2.0 à or less. The "lone-pair cones" were defined by a Cï£O-H angle of 100-160° and an X-Cï£O-H torsion angle of 0°Â± 30° or 180°Â±30°. See the Supporting Information for details and further data at different hydrogen-bond length cutoffs.
37. 3 enolate disappears when a solvated lithium enolate is considered. See:, E. E. Kwan, D. A. Evans, Org. Lett. 2010, 12, 5124.
38. A similar model has been used by Bach et al. to investigate substrate activation by Acyl-CoA dehydrogenases:, R. D. Bach, C. Thorpe, O. Dmitrenko, J. Phys. Chem. B 2002, 106, 4325.
39. We note that in a recent paper (, S. C. L. Kamerlin, Z. T. Chu, A. Warshel, J. Org. Chem. 2010, 75, 6391) the authors criticize the use of constrained gas-phase models for understanding enzyme mechanisms. We agree with this concern and we do not think that the stereoelectronic effects addressed in our studies are sufficient to explain the catalytic power of enzymes. However, it appears that directional preference of HBDs in oxyanion holes does not correspond to the fully optimal configuration for substrate binding; therefore, we believe that the positions of the HBDs are interesting and important. If the positions are important, the only computationally meaningful way to understand their effects is to constrain the positions of the HBDs in the calculations.
40. F. M. Menger, Biochemistry 1992, 31, 5368
41. A. R. Fersht, Structure and Mechanism in Protein Science, Freeman and Company, New York, 1999.
42. See, for example
43. O. Herzberg, J. Moult, Proteins 1991, 11, 223
44. I. Kursula, R. K. Wierenga, J. Biol. Chem. 2003, 278, 9544.
45. J. E. Carpenter, F. Weinhold, THEOCHEM 1988, 41, 169.
46. Details are provided in the Supporting Information.
47. For the introduction of PNS, see:, C. F. Bernasconi, Acc. Chem. Res. 1992, 25, 9.
48. 2O system are given in the Supporting Information.
49. Y. Zhao, N. E. Schultz, D. G. Truhlar, J. Chem. Theory Comput. 2006, 2, 364.
50. For the 6-311++G(d,p) basis set, see
51. R. Krishnan, J. S. Binkley, R. Seeger, J. A. Pople, J. Chem. Phys. 1980, 72, 650
52. A. D. McLean, G. S. Chandler, J. Chem. Phys. 1980, 72, 5639
53. T. Clark, J. Chandrasekhar, G. W. Spitznagel, P. v. R. Schleyer, J. Comput. Chem. 1983, 4, 294.
54. Y. Zhao, D. G. Truhlar, Acc. Chem. Res. 2008, 41, 157.
55. Gaussian 03 Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., J. T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, J. A. Pople, Gaussian, Inc., Wallingford CT, 2004.
56. Gaussian 09 Revision A.02, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.