Progress in Force-Field Calculations of Molecular Interaction Fields and Intermolecular Interactions

Perspectives in Drug Discovery and Design

Volumn 9, Issue , 1998, Pages 3-17

  Liljefors, Tommy ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 1542739415     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1027224402069     Document Type: Article

References (50)

1. Burkert, U. and Allinger, N.L., Molecular mechanics, ACS Monograph 177, American Chemical Society, Washington D.C., 1982.
2. Siebel, G.L. and Kollman, P.A., Molecular mechanics and the Modeling of drug structures, In Comprehensive medicinal chemistry, Vol. 4, Hansch C., Sammes P.G., Taylor, J.B. and Ramsden, C.A. (Eds.), Pergamon Press, Oxford, 1990, pp. 125-138.
3. Goodford, P., The properties of force fields, In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, Prous Science Publishers, Barcelona, 1995, pp. 199-205.
4. Hehre, W.J., Radom, L., v.R. Schleyer, P. and Pople, J.A., Ab initio molecular orbital theory, John Wiley & Sons, New York, 1986.
5. (a) Gundertofte, K., Liljefors, T., Norrby, P.-O. and Pettersson, I., A comparison of conformational energies calculated by several molecular mechanics methods, J. Comput. Chem., 17 (1996) 429-449.
6. (b) Pettersson, I. and Liljefors, T., Molecular mechanics calculated conformational energies of organic molecules, In Lipkowitz, K.B. and Boyd, D.B. (Eds.) Reviews in Computational Chemistry, Vol. 9, VCH Publishers, Inc., New York, 1996, pp. 167-189.
7. Cramer, III, R.D., Patterson, D.E. and Bunce, J.D., Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steriods to carrier proteins, J. Am. Chem. Soc., 110 (1988) 5959-5967.
8. Goodford, P.J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28 (1985) 849-857.
9. Boobbyer, D.N.A., Goodford, P.J., McWhinnie, P.M. and Wade, R.C., New hydrogen-bond potentials for use in determining energetically favourable binding sites on molecules of known structure, J. Med. Chem., 32 (1989) 1083-1094.
10. Wade, R.C., Clark, K. and Goodford, P.J., Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure: 1. Ligand probe groups with the ability to form two hydrogen bonds, J. Med. Chem., 36 (1993) 140-147.
11. Wade, R.C., Clark, K. and Goodford, P.J., Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure: 2. Ligand probe groups with the ability to form more than two hydrogen bonds, J. Med. Chem., 36 (1993) 148-156.
12. Goodford, P., Multivariate characterization of molecules for QSAR analysis, J. Chemometrics, 10 (1996) 107-111.
13. Cramer, III, R.D., DePriest, S.A., Patterson, D.E. and Hecht, P., The developing practice of comparative molecular field analysis. In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 443-485.
14. Folkers, G., Merz, A. and Rognan, D., CoMFA: Scope and limitations, In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 583-618.
15. Kroemer, R.T. and Hecht, P. Replacement of steric 6-12 potential-derived interaction energies by atombased indicator variables in CoMFA leads to models of higher consistency, J. Comput.-Aided Mol. Design, 9 (1995) 205-212.
16. Floersheim, P., Nozulak, J. and Weber, H.P., Experience with comparative molecular fields analysis, In Wermuth, C.G. (Ed.) Trends in QSAR and molecular modelling 92 (Proceedings of the 9th European Symposium on Structure-Activity Relationships: QSAR and Molecular Modeling), ESCOM Science Publishers, Leiden, 1993, pp. 227-232.
17. Berendsen, H.J.C., Electrostatic interactions, In van Gunsteren, W.F., Weiner, P.K. and Wilkinson, A.J. (Eds.) Computer simulation of biomolecular systems: Theoretical and experimental applications, Vol. 2, ESCOM Science Publishers, Leiden, 1993. pp. 161-181.
18. Kim, K. H. and Martin, Y.C. Direct prediction of linear free energy substituent effects from 3D structures using comparative molecular field analysis: 1. Electronic effects of substituted benzoic acids, J. Org. Chem., 34 (1991) 2723-2729.
19. Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges, Tetrahedron, 36 (1980) 3219-3228.
20. (a) Chirlian, L.E. and Francl, M.M., Atomic charges derived from electrostatic potentials: A detailed study, J. Comput. Chem., (1987) 894-905.
21. (b) Besler, B.H., Merz, Jr., K.M. and Kollman, P.A., Atomic charges derived from semiempirical methods. J. Comput. Chem., 11 (1990) 431-439
22. Kroemer, R.T., Hecht, P. and Liedl, K.R., Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials, J. Comput. Chem., 11 (1996) 1296-1308.
23. Wade, R.C., Molecular interaction fields, In Kubinyi, H. (Ed.) 3D QSAR in drug design, Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 486-505.
24. Goodford, P., GRID user guide, Edition 15, Molecular Discovery Ltd., Oxford, UK, 1997.
25. Liljefors, T. and Norrby, P.-O., unpublished results.
26. Mills, J.E.J. and Dean, P.M., Three-dimensional hydrogen-bond geometry and probablity information from a crystal survey, J. Comput.-Aided Mol. Design, 10 (1996) 607-622.
27. Clementi, S., Cruciani G., Riganelli, D. and Valigi, R., GOLPE: Merits and drawbacks in 3D-QSAR, In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and molecular modelling: Concepts, computational tools and biological applications, Prous Science Publishers, Barcelona, 1996, pp. 408-414.
28. Goodford, P., personal communication.
29. Bemis, G.W. and Murcko, M.A., The properties of known drugs: 1. Molecular frameworks, J. Med. Chem., 39 (1996) 2887-2983.
30. Dougherty, D.A., Cation-π interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp, Science, 271 (1996) 163-168.
31. Dougherty, D.A., and Stauffer, D.A., Acetycholine binding by a synthetic receptor: Implications for biological recognition, Science, 250 (1990) 1558-1560.
32. (a) Sussman, J.L., Harel, M., Frolow. F., Oefner, C., Goldman, A., Toker, L. and Silman, I., Atomic structure of acetylcholinesterase from Torpedo californica: A prototypic acetycholine-binding protein, Science, 253 (1991) 872-879.
33. (b) Harel, M., Quinn, D.M., Nair, H. K., Silman, I. and Sussman, J.L., The X-ray structure of a transition state analog complex reveals the molecular origin of the catalytic power and substrate specificity of acetylcholinesterase, J. Am. Chem. Soc., 118 (1996) 2340-2346.
34. Caldwell, J.W. and Kollman, P.A., Cation-π interactions: Nonadditive effects are critical in their accurate representation, J. Am. Chem. Soc., 117 (1995) 4177-4178.
35. Kim, K.S., Lee, J.Y., Lee, S.J., Ha, T.-K. and Kim, D.H., On binding forces between aromatic ring and quaternary ammonium compound, J. Am. Chem. Soc., 116 (1994) 7399-7400.
36. Caldwell, J., Dang, L.X. and Kollman, P.A., Implementation of nonadditive intermolecular potentials by use of molecular dynamics: Development of a water-water potential and water-ion cluster interactions, J. Am. Chem. Soc., 112 (1990) 9144-9147.
37. Meng, E.C., Cieplak, P., Caldwell, J. W. and Kollman, P.A., Accurate solvation free energies of acetate and methylammonium ions calculated with a polarizable water model J. Am. Chem. Soc., 119 (1994) 12061-12062.
38. Mecozzi, S., West, Jr., A.P. and Dougherty, D.A., Cation-π interactions in simple aromatics: Electrostatics provide a predictive tool, J. Am. Chem. Soc., 118 (1996) 2307-2308.
39. Cheney, B.V., Schultz, M.W., Cheney, J. and Richards, W.G., Hydrogen-bonded complexes involving benzene as an H-acceptor, J. Am. Chem. Soc. 110 (1988) 4295-4198.
40. Rodham, D.A., Suzuki, S., Suenram, R.D., Lovas, F.J., Dasgupta, S., Goddard, III, W.A. and Blake, G.A., Hydrogen bonding in the benzene-ammonia dimer, Nature, 363 (1993) 735-737.
41. Trumpp-Kallmeyer, S., Hoflack, J., Bruinvels, A. and Hibert, M., Modeling of G-protein-coupled receptors: Application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors, J. Med. Chem., 35 (1992) 3448-62.
42. Liljefors, T. and Norrby, P.-O., Ab initio quantum chemical model calculations on the interactions between monoamine neurotransmitters and their receptors, In Schwartz, T.W., Hjort, S.A. and Sandholm Kastrup, J. (Eds.) Structure and function of 7TM receptors, Alfred Benzon Symposium 39, Munksgaard, Copenhagen, 1996, pp. 194-207,
43. Liljefors, T. and Norrby, P.-O., An ab initio study of the trimethylamine-formic acid and the trimethylammonium-formate anion complexes, their monohydrates and continuum salvation, J. Am. Chem. Soc., 119 (1997) 1052-1058.
44. Williams, D.E., Coulombic interaction in crystalline hydrocarbons, Acta Cryst., A30 (1974) 71-77.
45. Pettersson, I. and Liljefors, T., Benzene-benzene (phenyl-phenyl) interactions in MM2/MMP2 molecular mechanics calculations, J. Comput. Chem., 8 (1987) 139-145.
46. Burley, S.K. and Petsko, G.A., Aromatic-aromatic interaction: A mechanism of protein structure stabilization, Science, 229 (1985) 23-28.
47. Burley, S.K. and Petsko, G.A., Dimerization energetics of benzene and aromatic amino acid side chains, J. Am. Chem. Soc., 108 (1986) 7995-8001.
48. Singh, J. and Thornton, J.M., The interaction between phenylalanine rings in proteins, FEBS Lett., 191 (1985) 1-6.
49. Chipot, C., Jaffe, R., Maigret, B., Pearlman, D.A. and Kollman, P.A., Benzene dimer: A good model for π-π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in aqueous solution, J. Am. Chem. Soc., 118 (1996) 11217-11224.
50. Schauer, M. and Bernstein, E.R., Calculations of the geometry and binding energy of aromatic dimers: benzene, toluene, and toluene-benzene, J. Chem. Phys., 82 (1985) 3722-3727.