Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules

Journal of Computational Chemistry

Volumn 17, Issue 5-6, 1996, Pages 616-641

  Halgren, Thomas A ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 5244268272     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X     Document Type: Article

References (54)

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2. Part II: T. A. Halgren, J. Comput. Chem. (this issue).
3. Part III: T. A. Halgren, J. Comput. Chem. (this issue).
4. Part IV: T. A. Halgren and R. B. Nachbar, J. Comput. Chem. (this issue).
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7. AMF is the proprietary Advanced Modeling Facility developed at the Merck Research Laboratories by J. D. Andose, R. A. Blevins E. M. Fluder, J. Shpungin, and others in the Scientific Computing Group of the Department of Molecular Design and Diversity.
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11. PROBE is a computer program used to derive molecular-mechanics parameters in least-squares fits to data obtained from ab initio calculations. PROBE was created for the Biosym Consortium on Potential Energy Functions by Biosym Technologies, Inc. (San Diego, CA); cf. J. R. Maple, M.-J. Hwang, T. P. Stockfish, U. Dinur, M. Waldman, C. S. Ewig, and A. T. Hagler, J. Comput. Chem., 15, 161-182 (1994).
12. In addition to the 27 values constrained in the PROBE fit to CHELPG-based values, the "#X94" bond charge increments also include parameters for homopolar bonds (having zero bond charge increments) and parameters for bonds to bromine and iodine from carbons of MMFF atom types 1 and 2. Owing to the unavailability of 6-31G* basis sets for Br and I in Gaussian 92, we estimated these quantities from scaled values (increased by 20%) of observed dipole moments for the methyl and vinyl halides.
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15. L. Pauling, The Nature of the Chemical Bond, 3rd ed., Cornell University Press, Ithaca, NY, 1960, Chapter 3.
16. The MMFF94 parameters are included in Appendix B (Supplementary Material) for Part I (ref. 1) and are available in computer-readable ASCII format.
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19. Eq. (18) was developed by Joseph D. Andose of the Merck Research Laboratories for use with the predecessor MM2X force field (cf. ref. 1). The parameters and the adjustments for hybridization and bond-order described in the subsection "Empirical Rule For Reference Bond Lengths" include modifications to parameters and procedures he developed.
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29. Badger's rule (cf. ref. 28) also performed reasonably well, but gave a somewhat higher rms deviation of 1.06 md/Å.
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32. These calculations used the MM2X force field and the sulfonamide-based supplementary parameter file "SULF.PAR" described in: M. K. Holloway, J. M. Wai, T. A. Halgren, P. M. D. Fitzgerald, J. P. Vacca, B. D. Dorsey, R. B. Levin, W. J. Thompson, L. J. Chen, S. J. deSolms, N. Gaffin, A. K. Ghosh, E. A. Giuliani, S. L. Graham, J. P. Guare, R. W. Hungate, T. A. Lyle, W. M. Sanders, T. J. Tucker, M. Wiggins, C. M. Wiscount, O. W. Woltersdorf, S. D. Young, P. L. Darke, and J. A. Zugay, J. Med. Chem., 38, 305-317 (1995).
33. In a few cases, information on crystal-structure geometries was used to modify the empirical-rule values for delocalized single bonds. Such torsion parameters are identified by the label "#E94."
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42. The same assumption was previously employed in the core MMFF94 parameterization of polar intermolecular interactions (ref. 2). It presumes that additional polarization in the condensed phase should strengthen favorable electrostatic interactions.
43. See, for example: R. F. Frey, J. Coffin, S. Q. Newton, M. Ramek, V. K. W. Cheng, F. A. Momany, and L. Schafer, J. Am. Chem. Soc., 114, 5369-5377 (1992).
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47. B. D. Olafson, personal communication.
48. R. Fletcher, Practical Methods of Optimization: Unconstrained Optimization, Vol. 1, Wiley, New York, 1980, Chapter 3.
49. M. C. Nicklaus, S. Wang, J. S. Driscoll, and G. W. A. Milne, Biorganic & Medicinal Chemistry, 3, 411-428 (1995).
50. Current intentions are to release OPTIMOL/MMFF94 through the Quantum Chemistry Program Exchange (Indiana University) under terms that would permit its unrestricted usage but prohibit its commercialization.
51. R. Czerminski, T. A. Halgren, and J. L. Banks, unpublished research. Currently, a version CHARMm that includes the earlier and less widely parameterized MMFF93 force field (refs. 3, 4; see also "Extension of the Parameterization for van der Waals Interactions" section of this study) is available from Molecular Simulations, Inc. (San Diego, CA). However, while the local Merck code employs MMFF94, arrangements for including MMFF94 in the distributed MSI version have not yet been concluded.
52. R. Czerminski, T. A. Halgren, and J. L. Banks, unpublished research. Currently, a version CHARMm that includes the earlier and less widely parameterized MMFF93 force field (refs. 3, 4; see also "Extension of the Parameterization for van der Waals Interactions" section of this study) is available from Molecular Simulations, Inc. (San Diego, CA). However, while the local Merck code employs MMFF94, arrangements for including MMFF94 in the distributed MSI version have not yet been concluded.
53. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187-217 (1983).
54. P. S. Shenkin and T. A. Halgren, work in progress. The MacroModel program suite, developed in the laboratories of Professor Clark Still, is available from Columbia University.