Selected References for Molecular Mechanics

This listing is intended to be representative, rather than comprehensive.

Section 1. General References

  1. Burkert, U.; Allinger, N. L. Molecular Mechanics, American Chemical Society, Washington, DC, 1982.

  2. Rappe, A. K; Casewit, C. J. Molecular Mechanics Across Chemistry, University Science Books, Sausalito, CA, 1997.

  3. Cramer, C. J., Essentials of Computational Chemistry, Wiley, New York, 2002; Chapters 2 and 3.

  4. Holtje, H.-D.; Sippl, W.; Rognan, D.; Folkers, G., Molecular Modeling: Basic Principles and Applications, 2nd ed,, Wiley-VCH, Darmstadt, 2003 (emphasis is largely on biomolecules and drug design).

  5. Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. "Molecular Mechanics. The MM3 Force Field for Hydrocarbons", J. Am. Chem. Soc., 1989, 111, 8551.

  6. Extensions of MM3:

    1. Allinger, N. L.; Li, F.; Yan, L. "The MM3 Force Field for Alkenes", J. Comput. Chem., 1990, 11, 848.

    2. Lii, J.-H.; Allinger, N. L. "MM3 Parameters for Amides, Polypeptides and Proteins", J. Comput. Chelm., 1991, 12, 186.

    3. Allinger, N. L.; Chen, K.; Rahman, M.; Pathiaseril, A. "MM3 Parameters for Aldehydes and Ketones", J. Am. Chem. Soc., 1991, 113, 4505.

    4. Allinger, N. L.; Zhu, Z.-q. S.; Chen, K. "Application of MM3 to Carboxylic Acids and Esters", J. Am. Chem. Soc., 1992, 114, 6120.

  7. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caulfield, C.; Chang, G.; Hendrickson, T.; Still, W. C. "Molecular Mechanics with MacroModel", J. Comput. Chem., 1990, 11, 440.

  8. Still, W. C.; Tempczyk, A.; Hawlely, R. C.; Hendrickson, T. "A General Treatment of Solvation for Molecular Mechanics", J. Am. Chem. Soc., 1990, 112, 6127.

  9. Gundertofte, K.; Palm, J.; Petterson, I.; Stamvik, A. "A Comparision of Molecular Mechanics Force Fields", J. Comput. Chem., 1991, 12, 200.

Section 2. Specialized Force Fields

  1. OPLS (general purpose, proteins): Jorgenson, W. L.; Tirado-Rives, J., J. Am. Chem. Soc., 1988, 110, 1657.

  2. AMBER (proteins, nucleic acids): Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A., J. Comput. Chem., 1986, 7, 230.

  3. CHARMM (a) nuclei acids: Brooks, B. R.; Bruccoleri, R. E., Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M., J. Comput. Chem., 1983, 4, 187; (b) sugars: Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W., Carbohydr. Res., 1988, 180, 207; (c) proteins: Clark, M. Cramer, R. D.; Opdenbosch, N. V., J. Comput. Chem., 1989, 10, 982.

  4. ECEPP (proteins): Momany, A.; McGuire, R. F.; Burgess, A. W.; Scheraga, H. A., J. Phys. Chem., 1975, 79, 2361.

Section 3. The Global Minimum Problem

  1. Saunders, M. "A Stochastic Method for Searching Conformation Space", J. Comput. Chem., 1991, 12, 645.

  2. Saunders, M.; Houk, K. N.; Wu, Y.-D.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. "Conformations of Cycloheptadecane. A Comparison of Methods for Conformational Searching", J. Am. Chem. Soc., 1990, 112, 1419.

  3. Goodman, J. M.; Still, W. C. "Searching Conformation Space", J. Comput. Chem., 1991, 12, 1110

Section 4. Comparison of Force fields

  1. Pettersson, I.; Liljefors, T., Rev. Comput. Chem, 1996, 9, 167

  2. Gundertofte, K.; Liljefors, T.; Norby, P.-O.; Pettersson, I.; J. Comput. Chem., 1996, 17, 429.

  3. Corness, W. D.; Ha, M. P.; Sun, Y.; Kollman, P. A. J. Comput. Chem., 1996, 17, 1541

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