A Practical Method for Calculating Relative Free Energies of Binding. Chiral Recognition of Peptidic Ammonium Ions by Synthetic Ionophores

Journal of Organic Chemistry

Volumn 62, Issue 26, 1997, Pages 9123-9127

  Senderowitz, Hanoch ^a   McDonald, D Quentin ^a   Still, W Clark ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000222509     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo9712106     Document Type: Article

References (21)

1. Examples of free energy-directed molecular design: (a) Mertz, K. M.; Kollman, P. A. J. Am. Chem. Soc. 1989, 111, 5649. (b) Burger, M. T.; Armstrong, A.; Guarnieri, F.; McDonald D. Q.; Still, W. C. J. Am. Chem. Soc. 1994, 116, 3593.
2. Examples of free energy-directed molecular design: (a) Mertz, K. M.; Kollman, P. A. J. Am. Chem. Soc. 1989, 111, 5649. (b) Burger, M. T.; Armstrong, A.; Guarnieri, F.; McDonald D. Q.; Still, W. C. J. Am. Chem. Soc. 1994, 116, 3593.
3. Dealing adequately with the sampling problem in necessary but insufficient to get accurate free energy results - one also needs an accurate potential energy force field which realistically includes effects of solvent.
4. For comments on the difficulty of the sampling problem with molecules, see: (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271. b) van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947. (c) van Gunsteren, W. F. J. Am. Chem. Soc. 1994, 116, 6293. (d) Balbes, L. M.; Mascarella, S. W.; Boyd, D. B. Rev. Comput. Chem. 1994, 5, 337. (e) Reference 4.
5. For comments on the difficulty of the sampling problem with molecules, see: (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271. b) van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947. (c) van Gunsteren, W. F. J. Am. Chem. Soc. 1994, 116, 6293. (d) Balbes, L. M.; Mascarella, S. W.; Boyd, D. B. Rev. Comput. Chem. 1994, 5, 337. (e) Reference 4.
6. For comments on the difficulty of the sampling problem with molecules, see: (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271. b) van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947. (c) van Gunsteren, W. F. J. Am. Chem. Soc. 1994, 116, 6293. (d) Balbes, L. M.; Mascarella, S. W.; Boyd, D. B. Rev. Comput. Chem. 1994, 5, 337. (e) Reference 4.
7. For comments on the difficulty of the sampling problem with molecules, see: (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271. b) van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947. (c) van Gunsteren, W. F. J. Am. Chem. Soc. 1994, 116, 6293. (d) Balbes, L. M.; Mascarella, S. W.; Boyd, D. B. Rev. Comput. Chem. 1994, 5, 337. (e) Reference 4.
8. For comments on the difficulty of the sampling problem with molecules, see: (a) Mitchell, M. J.; McCammon, J. A. J. Comput. Chem. 1991, 12, 271. b) van Gunsteren, W. F.; Mark, A. E. Eur. J. Biochem. 1992, 204, 947. (c) van Gunsteren, W. F. J. Am. Chem. Soc. 1994, 116, 6293. (d) Balbes, L. M.; Mascarella, S. W.; Boyd, D. B. Rev. Comput. Chem. 1994, 5, 337. (e) Reference 4.
9. Review: Kollman, P. Chem. Rev. (Washington, D.C) 1993, 93, 2395.
10. (a) Senderowitz, H.; Guarnieri, F.; Still, W. C. J. Am. Chem. Soc. 1995, 117, 8211.
11. (b) Senderowitz, H.; Still, W. C. J. Comput. Chem. 1997, submitted.
12. Tidor, B. J. Phys. Chem. 1993, 97, 1069.
13. Radmer, R. J.; Kollman, P. A. J. Comput. Chem. 1997, 18, 902.
14. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A.; Teller, E. J. Chem. Phys. 1953, 21, 1087.
15. Guarnieri, F.; Still, W. C. J. Comput. Chem. 1994, 15, 1302.
16. Kolossvary, I.; Guida, W. C. J. Am. Chem. Soc. 1996, 118, 5011.
17. While most of our simulations employed every minimum energy conformer located by the conformational searches, we found that virtually identical free energy results could be obtained when families of closely related conformations were replaced by a single representative example of the family. Closely related conformations are ones that are rapidly interconverted by standard simulation methods (e.g., simple MC or SD) at the temperature of the simulation. In practice, we distinguish such families by graphical examination of superimposed family candidates. Thus while it is important to include a representative example from each significantly populated conformational well as input to the JBW algorithm, it is not necessary to carry out extensive conformational searches to locate each minimum energy form.
18. Kabsh, W. Acta Crystallogr. 1976, A32, 944. Kabsch, W. Acta Crystallogr. 1978, A34, 837.
19. Kabsh, W. Acta Crystallogr. 1976, A32, 944. Kabsch, W. Acta Crystallogr. 1978, A34, 837.
20. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005.
21. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005.