Building molecular charge distributions from fragments: application to HIV-1 protease inhibitors

Journal of Computational Chemistry

Volumn 18, Issue 4, 1997, Pages 522-532

  Young, L ^a   Topol, I A ^a   Rashin, A A ^b   Burt, S K ^b  

^a SAIC FREDERICK INC   (United States)

^b BioChemComp Inc New Jersey   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0037571292     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199703)18:4<522::AID-JCC6>3.0.CO;2-V     Document Type: Article

References (21)

1. B. H. Besler, K. M. Merz, Jr., and P. A. Kollman, J. Comput. Chem., 11, 431 (1990).
2. A. A. Rashin, M. A. Bukatin, J. Andzelm, and A. T. Hagler, Biophys. Chem., 51, 375 (1994).
3. A. A. Rashin, L. Young, I. A. Topol, and S. K. Burt, Chem. Phys. Lett., 230, 182 (1994).
4. A. A. Rashin, L. Young, and I. A. Topol, Biophys. Chem., 51, 359 (1994).
5. M. N. Bellido and J. A. C. Rullmann, J. Comput. Chem., 10, 479 (1989).
6. U. C. Singh and P. A. Kollman, J. Comput. Chem., 5, 129 (1984).
7. K. M. Merz, Jr., J. Comput. Chem., 13, 749 (1992).
8. Averaging the partial charges of the overlapping atoms yields an excess charge on the molecule on the order of hundredths of atomic units. Thus, the partial charges of all the atoms in the molecule must be altered by the amount of excess charge divided by the number of atoms-a value on the order of 10~4 atomic units.
9. P. Cieplak, W. D. Cornell, C. Bayly, and P. A. Kollman, J. Cimput. Chem., 16, 1357 (1995).
10. M. J. Frisch, C. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. W. Wong, J. B. Foresman, M. A. Robb, M. Head-Gordon, E. S. Replogle, R. Gomperts, J. L. Andres, K. Raghavachari, J. S. Binkley, C. Gonzalez, R. L. Martin, D. ]. Fox, D. J. Defrees, J. Baker, J. J. P. Stewart, and J. A. Pople, Gaussian 92/DFT, revision G.2, Gaussian, Inc., Pittsburgh, PA, 1993.
11. A. D. Becke, J. Chem. Phys., 93, 5648 (1993).
12. J. P. Perdew, Phys. Rev. B, 33, 8822 (1986), erratum in J. P. Perdew, Phys. Rev. B, 38, 7406 (1986).
13. The diffuse d-exponent for the sulphur atom was obtained using simple sulfur-containing molecules. Only the diffuse d-exponent in the DZVPD basis set of sulfur was varied to obtain the minimum energy for H2S. Dipole moments for H2S, CH4S, and (CH3)2SO calculated with this optimal DZVPD basis set were within 0.1 Debye from experimental vacuum dipole moments.
14. J. Brady, B. R. Brooks, R. E. Bruccoleri, A. Brunger, M. J. Field, T. Ichiye, L. Nilsson, B. D. Olafson, D. Perahya, C. B. Post, W. E. Reiher II, D. J. States, S. Swaminathan, B. Tidor, and M. Karplus, CHARMm, version 22, Copyright 1984, 1987, 1991, President and Fellows of Harvard College.
15. B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983).
16. D. A. Pearlman, D. A. Case, J. C. Caldwell, G. L. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman, AMBER 4.0, University of California, San Francisco, 1991.
17. M. V. Hosur, T. N. Bhat, D. J. Kempf, E. T. Baldwin, B. Liu, S. Gulnik, N. E. Wideburg, D. W. Norbeck, K. Appelt, and J. W. Erickson, J. Am. Chem. Soc., 116, 847 (1994).
18. E. T. Baldwin, T. N. Bhat, S. Gulnik, B. Liu, I. A. Topol, Y. Kiso, T. Mimoto, H. Mitsuya, and J. W. Erickson, Structure, 3, 581 (1995).
19. A. L. Swain, M. M. Miller, J. Green, D. H. Rich, J. Schneider, S. B. H. Kent, and A. Wlodawer, Proc. Natl. Acad. Set. USA, 87, 8805 (1990).
20. Per unit charge is assumed.
21. Based on the evaluations for molecules A, B, and C, -CH3 neutralization was not tested on molecules D and E. Thus, the average is for three molecules.