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References
General references to MM: (a) A. K. Rappe, C. L. Casewit, “Molecular mechanics across chemistry,” University Science Books, Sausalito, CA, 1997, website http://www.chm.colostate.edu/mmac; (b) A. R. Leach, “Molecular Modelling, Principles and Applications,” Addison Wesley Longman, Essex (UK), 1996, chapter 3; (c) U. Burkert, N. L. Allinger, “Molecular Mechanics”, ACS Monograph 177, American Chemical Society, Washington, DC, 1982; (d) N. L. Allinger, “Calculation of Molecular Structures and Energy by Force Methods”, in Advances in Physical Organic Chemistry, 13, V. Gold and D. Bethell, Eds., Academic Press, New York, 1976; (e) T. Clark, “A Handbook of Computational Chemistry” Wiley, New York, 1985; (f) I. N. Levine, “Quantum Chemistry,” 4th edn, Prentice Hall, Engelwood Cliffs, New Jersey, 1991, pp. 583–587; (g) Issue No. 7 of Chem. Rev., 1993, 93; (h) Conformational energies: I. Pettersson, T. Liljefors, in Reviews in Computational Chemistry, 1996, 9; (i) Inorganic and organometallic compounds: C. R. Landis, D. M. Root, T. Cleveland, in Reviews in Computational Chemistry, 1995, 6; (j) Parameterization: J. P. Bowen, N. L. Allinger, Reviews in Computational Chemistry, 1991, 2.
MM history: (a) Ref. C. L. Casewit, “Molecular mechanics across chemistry,” University Science Books, Sausalito, CA, 1997, website http://www.chm.colostate.edu/mmac [1]; (b) E. M. Engler, J. D. Andose, P. von R. Schleyer, J. Am. Chem. Soc., 1973, 95, 8005 and references therein; (c) MM up to the end of 1967 is reviewed in detail in: J. E. Williams, P. J. Stang, P. von R. Schleyer, Annu. Rev. Phys. Chem., 1968, 19, 531.
F. H. Westheimer, J. E. Mayer, J. Chem. Phys., 1946, 14, 733; (b) T. L. Hill, J. Chem. Phys., 1946, 14, 465; (c) I. Dostrovsky, E. D. Hughes, C. K. Ingold, J. Chem. Soc., 1946, 173; (d) F. H. Westheimer, J. Chem. Phys., 1947, 15, 252.
B. Ma, J-H Lii, K. Chen, N. L. Allinger, J. Am. Chem. Soc., 1997, 119, 2570 and references therein.
Information on and references to MM programs may be found in Ref. C. L. Casewit, “Molecular mechanics across chemistry,” University Science Books, Sausalito, CA, 1997, website http://www.chm.colostate.edu/mmac [1] and the website of Ref. [1a]; (b) For papers on the popular MMFF and the MM4 forcefield (and information on some others) see the issue of J. Comp. Chem., 1996, 17.
A brief discussion and some parameters: P. W. Atkins, “Physical Chemistry,” 5th edn, Freeman New York, 1994, pp.772, 773; it is pointed out here that e−r/σ is actually a much better representation of the compressive potential than is r−12; (b) W. J. Moore, “Physical Chemistry,” 4th edn, Prentice-Hall, New Jersey, 1972, p. 158 (from J. O. Hirschfelder, C. F. Curtis and R. B. Bird, “Molecular Theory of Gases and Liquids,” Wiley, New York, 1954). Note that our knb is called 4ε here and must be multiplied by 8.31/1000 to convert it to our units of kJ mol−1.
Infra red spectroscopy: R. M. Silverstein, G. C. Bassler and T. C. Morrill, “Spectrometric Identification of Organic Compounds,” 4th edn, Wiley, New York, 1981, chapter 3.
Different methods of structure determination give some what different results; this is discussed in Ref. J-H Lii, K. Chen, N. L. Allinger, J. Am. Chem. Soc., 1997, 119, 2570 and references therein. [4] and in: (a) B. Ma, J-H Lii, H. F. Schaefer, N. L. Allinger, J. Phys. Chem., 1996, 100, 8763; (b) A. Domenicano, I. Hargittai, Eds., “Accurate Molecular Structures,” Oxford Science Publications, New York, 1992.
Ref. Ref.[1b, pp. 148–181].
MM3: N. L. Allinger, Y. H. Yuh, J-H Lii, J. Am. Chem Soc., 1989, 111, 8551. The calculation was performed with MM3 as implemented in Spartan (Ref.[13]).
Ref. N. L. Allinger, “Molecular Mechanics”, ACS Monograph 177, American Chemical Society, Washington, DC, 1982 [1c, pp. 182–184].
K. Gundertofte, T. Liljefors, P.-O. Norby, I. Pettersson, J. Comp. Chem., 1996, 17, 429.
Comparison of various force fields for geometry (and vibrational frequencies): T. A. Halgren, J. Comp. Chem., 1996, 17, 553.
The Merck force field (Ref. [18]) often gives geometries that are satisfactory for energy calculations (i.e. for single-point energies) with quantum mechanical methods; this could be very useful for large molecules: W. J. Hehre, J. Yu, P. E. Klunzinger, “A Guide to Molecular Mechanics and Molecular Orbital calculations in Spartan,” Wavefunction Inc., Irvine CA, 1997, chapter 4.
T. A. Halgren, J. Comp. Chem., 1996, 17, 490.
M. C. Nicklaus, J. Comp. Chem., 1997, 18, 1056; the difference between CHARMM and CHARMm is explained here.
www.amber.ucsf.edu/amber/amber.html; (b) W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M Ferguson, D. C Sellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc., 1995, 117, 5179; (c) V. Barone, G. Capecchi, Y. Brunei, M.-L. D. Andries, R. Subra, J. Comp. Chem., 1997, 18, 1720.
M. J. Field, P. A. Bash, M. Karplus, J. Comp. Chem., 1990, 11, 700; (b) P. A. Bash. M. J. Field, M. Karplus, J. Am. Chem. Soc., 1987, 109, 8092.
U. C. Singh, P. Kollman, J. Comp Chem., 1986, 7, 718.
Reference [1b, chapter 10]; (b) H.-D. Höltje, G. Folkers “Molecular Modelling, Applications in Medicinal Chemistry,” VCH, Weinheim, Germany, 1996; (c) “Computer-Assisted Lead Finding and Optimization,” H. van de Waterbeemd, B. Testa, G. Folkers, Eds., VCH, Weinheim, Germany, 1997.
J. E. Eksterowicz and K. N. Houk, Chem. Rev., 1993, 93, 2439.
M. B. Smith and J. March, “March’s Advanced Organic Chemistry,” Wiley, New York, 2000, pp.284–285.
K. B. Lipkowitz, M. A. Peterson, Chem Rev., 1993, 93, 2463.
M. Saunders, Science, 1991, 253, 330.
Ref. [1b, chapter 6]; (b) M. Karplus, G. A. Putsch, Nature, 1990, 347, 631; (c) C. L. Brooks III, D. A. Case, Chem. Rev., 1993, 93, 2487; (d) M. Eichinger, H. Grubmüller, H. Heller, P. Tavan, J. Comp. Chem., 1997, 18, 1729; (e) G. E. Marlow, J. S. Perkyns, B. M. Pettitt, Chem. Rev., 1993, 93, 2503; (f) J. Aqvist, A. Warshel, Chem. Rev., 1993, 93, 2523.
Ref. [1b, chapter 7].
W. J. Hehre, L. Radom, P. V. R. Schleyer, J. A. Pople, “Ab initio Molecular Orbital Theory,” Wiley, New York, 1986.
J.-H. Lii and N. L. Allinger, J. Comp. Chem., 1992, 13, 1138. The MM3 program with the ability to calculate IR intensities can be bought by academic users from QCPE (the Quantum Chemistry Exchange Program of the University of Indiana) and by commercial users from Tripos Associates of St. Louis, Missouri.
N. Nevins, N. L. Allinger, J. Comp. Chem., 1996, 17, 730 and references therein.
K. B. Lipkowitz, J. Chem. Ed., 1995, 72, 1070.
K. Wiberg, Angew. Chem., Int. Ed. Engl., 1986, 25, 312; (b) Issue No. 5 of Chem. Rev., 1989, 89; (c) S. Inagaki, Y. Ishitani, T. Kakefu, J. Am. Chem. Soc., 1994, 116, 5954; (d) S. Nagase, Acc. Chem. Res., 1995, 28, 469; (e) S. Gronert, J. M. Lee, J. Org. Chem., 1995, 60, 6731; (f) A. Sella, H. Basch, S. Hoz, J. Am. Chem. Soc., 1996, 118, 416; (g) S. Grime, J. Am. Chem. Soc., 1996, 118, 1529; (h) V. Balaji, J. Michl, Pure Appl. Chem., 1988, 60, 189; (i) K. B. Wiberg, J. W. Ochterski, J. Comp. Chem., 1997, 18, 108.
J. I. Seeman, Chem. Rev., 1983, 83, 83.
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(2004). Molecular Mechanics. In: Computational Chemistry. Springer, Boston, MA. https://doi.org/10.1007/0-306-48391-2_3
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