Optimal site charge models for molecular electrostatic potentials

Molecular Simulation

Volumn 30, Issue 7, 2004, Pages 413-436

  Karamertzanis, Panagiotis G ^a   Pantelides, Constantinos C ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Confidence intervals; Cyclobutane; Electrostatic potentials; Global optimization; Site charges

Indexed keywords

CARRIER CONCENTRATION; GLOBAL OPTIMIZATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; OPTIMIZATION; PROBLEM SOLVING; QUANTUM THEORY;

CONFIDENCE INTERVALS; CYCLOBUTANE; ELECTROSTATIC POTENTIALS; SITE CHARGES;

ELECTRIC POTENTIAL;

EID: 10444287812     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/08927020410001680769     Document Type: Review

References (44)

1. Klooster, W.T. and Craven, B.M. (1992) "The electrostatic potential for the phosphodiester group determined from x-ray-diffraction", Biopolymers 32, 1141.
2. Ghermani, N.B., Bouhmaida, N. and Lecomte, C. (1993) "Modelling electrostatic potential from experimentally determined charge densities. 1. Spherical-atom approximation", Acta Cryst. A49, 781.
3. Cox, R.S. and Williams, D.E. (1981) "Representation of the molecular electrostatic potential by a net atomic charge model", J. Comp. Chem. 2, 304.
4. Singh, U.C. and Kollman, P.A. (1984) "An approach to computing electrostatic charges for molecules", J. Comp. Chem. 2, 129.
5. Chirlian, L.E. and Francl, M.M. (1987) "Atomic charges derived from electrostatic potentials", J. Comp. Chem. 8, 894.
6. Breneman, C.M. and Wiberg, K.B. (1990) "Determining atomcentered monopoles from molecular electrostatic potentials The need for high sampling density in formamide conformational-analysis", J. Comp. Chem. 11, 361.
7. Besler, B.H., Merz, K.M. and Kollman, P.A. (1990) "Atomic charges derived from semiempirical methods", J. Comp. Chem. 11, 431.
8. Spackman, M.A. (1996) "Potential derived charges using a geodesic point selection scheme", J. Comp. Chem. 17, 1.
9. Woods, R.J., Khalil, M., Pell, W., Moffat, S.H. and V.H.S., V.H.S. (1990) "Derivation of net atomic charges from molecular electrostatic potentials", J. Comp. Chem. 11, 297.
10. Sigfridsson, E. and Ryde, U. (1998) "Comparison of methods for deriving atomic charges from the electrostatic potential and moments", J. Comp. Chem. 19, 377.
11. Reynolds, C.A., Essex, J.W. and Richards, W.G. (1992) "Atomic charges for variable molecular conformations", J. Am. Chem. Soc. 114, 9075.
12. Francl, M.M. and Chirlian, L.E. (2000), "The pluses and minuses of mapping atomic charges to electrostatic potentials", chap 1, In: Lipkowitz, K.B. and Boyd, D.B., eds, Reviews In Computational Chemistry (John Wiley and Sons, New York), Vol. 14.
13. Bayly, C.I., Cieplak, P., Cornell, W.D. and Kollman, P.A. (1993) "A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges-the RESP model", J. Phys. Chem. 97, 10269.
14. Woods, R.J. and Chappelle, R. (2000) "Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates", J. Mol. Struct-Theochem. 527, 149.
15. Hinsen, K. and Roux, B. (1997) "A potential function for computer simulation studies of proton transfer in acetylacetone", J. Comp. Chem. 18, 368.
16. Levy, B. and Enescu, M. (1998) "Theoretical study of methylene blue: a new method to determine partial atomic charges; investigation of the interaction with guanine", J. Mol. Struct-Theochem. 432, 235.
17. Ridard, J. and Levy, B. (1998) "Effective atomic charges in alanine dipeptide", J. Comp. Chem. 20, 473.
18. Francl, M.M., Carey, C., Chirlian, L.E. and Gange, D.M. (1996) "Charges fit to electrostatic potentials.2. Can atomic charges be unambiguously fit to electrostatic potentials?", J. Comp. Chem. 17, 367.
19. Stouch, T.R. and Williams, D.E. (1993) "Conformational dependence of electrostatic potential-derived charges: Studies of the fitting procedure", J. Comp. Chem. 14, 858.
20. Willock, D.J., Price, S.L., Leslie, M. and Catlow, C.R. (1995) "The relaxation of molecular-crystal structures using a distributed multipole electrostatic model", Am. J. Comput. Chem. 16, 628.
21. Leach, A.R. (1999) Molecular Modelling (Pearson Education, Essex, England).
22. Williams, D.E. and Abraha, A. (1999) "Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane", J. Comp. Chem. 20, 579.
23. Dixon, R.W. and Kollman, P.A. (1997) "Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics", J. Comp. Chem. 13, 1632.
24. Williams, D.E. (1994) "Failure of net atomic charge models to represent the van-der-Waals envelope electric-potential of n-alkanes", J. Comp. Chem. 15, 719.
25. van Nes, G.J.H. and Vos, A. (1978) "Single-crystal structures and electron density distributions of ethane, ethylene and acetylene. I. Single-crystal X-ray structure determinations of two modifications of ethane", Acta Cryst. B34, 1947.
26. Stone, A.J. (1996) The Theory of Intermolecular Forces (Clarendon Press, Oxford).
27. Gelessus, A., Thiel, W. and Weber, W. (1995) "Multipoles and symmetry", J. Chem. Ed. 72, 505.
28. Bard, Y. (1974) Nonlinear Parameter Estimation (Academic Press, New York).
29. Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1984) Numerical Recipes (Cambridge University Press, New York).
30. Sobol', I.M. (1967) "On the distribution of points in a cube and the approximate evaluation of integrals", Comput. Math. Math. Phys. 7, 86.
31. Kucherenko S., and Sytsko Y (2002) "Application of deterministic low-discrepancy sequences to global optimisation problems", Submitted to J. Glob. Optim.
32. Rinnooy, K.A.H.G. and Timmer, G.T. (1987) "Stochastic global optimisation methods, part I: clustering methods", Math. Program. 39, 27.
33. Rinnooy, K.A.H.G. and Timmer, G.T. (1987) "Stochastic global optimisation methods, part II: multilevel methods", Math. Program. 39, 57.
34. Boender, C.G.E., "The generalized multinomial distribution: A Bayesian analysis and applications", Ph.D. thesis, Erasmus Universiteit Rotterdam, Centrum voor Wiskunde en Informatica (Amsterdam).
35. Almenningen, A., Bastiansen, O. and Skancke, P.N. (1961) "Preliminary results of an electron diffraction reinvestigation of cyclobutane and cyclopentane", Acta Chem. Scand. 15, 711.
36. Williams, D.E. (1999) "Improved intermolecular force field for crystalline hydrocarbons containing four-or three-coordinated carbon", J. Mol. Struct. 486, 321.
37. Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S.J., et al. (1993) "General atomic and molecular electronic-structure system", J. Comp. Chem. 14, 1347.
38. Motherwell, W.D.S., Ammon, H.L., Dunitz, J.D., Dzyabchenko, A., Erk, P., Gavezzotti, A., Hoffmann, D.W.M., Leusen, F.J.J., Lommerse, J.P.M., Mooij, W.T.M., et al. (2002) "Crystal structure prediction of small organic molecules: a second blind test", Acta Cryst. B58, 647.
39. Lommerse, J.P.M., Motherwall, W.D.S., Ammon, H.L., Dunitz, J.D., Gavezzotti, A., Hoffmann, D.W.M., Leusen, F.J.J., Mooij, W.T.M., Price, S.L., Schweizer, B., et al. (2000) "A test of crystal structure prediction of small organic molecules", Acta Cryst. B56, 697.
40. Karamertzanis, P.G. (2004) Crystal Structure Prediction of Molecular Solids, PhD Thesis (University of London).
41. Prusiner, P. and Sundaralingam, M. (1972) "Stereochemistry of nucleic acids and their constituents. XXIX. Crystal and molecular structure of allopurinol, a potent inhibitor of xanthine oxidase", Acta Cryst. B28, 2148.
42. Haisa, M., Kashino, S. and Maeda, H. (1974) "The orthorhombic form of p-hydroxyacetanilide", Acta Cryst. B30, 2510.
43. Swart, M., Duijnen, P.T.V. and Snijders, J.G. (2001) "A charge analysis derived from an atomic multipole expansion", J. Comp. Chem. 22, 79.
44. Haisa, M., Kashino, S. and Maeda, H. (1976) "The monoclinic form of p-hydroxyacetanilide", Acta Cryst. B32, 1283.