2. MM history: (a) References 1. (b) Engler EM, Andose JD, Schleyer PvR (1973) J Am Chem Soc 95:8005 and references therein. (c) Molecular mechanics up to the end of 1967 is reviewed in detail in: Williams JE, Stang PJ, Schleyer PvR (1968) Ann Rev Phys Chem 19:531 3. (a) Westheimer FH, Mayer JE (1946) J Chem Phys 14:733. (b) Hill TL (1946) J Chem Phys 14:465. (c) Dostrovsky I, Hughes ED, Ingold CK (1946) J Chem Soc 173. (d) Westheimer FH (1947) J Chem Phys 15:252 4. (a) Ma B, Lii J-H, Chen K, Allinger NL (1997) J Am Chem Soc 119:2570 and references therein. (b) In an MM4 study of amines, agreement with experiment was generally good: Chen K-H, Lii J-H, Allinger NL (2007) J Comp Chem 28:2391. (c) Five papers, using MM4, on Alcohols, ethers, carbohydrates, and related compounds. J Comp Chem 24 (2003): Allinger NL, Chen K-H, Lii J-H, Durkin KA, 1447; Lii J-H, Chen K-H, Durkin A, Allinger NL, 1473; Lii J-H, Chen K-H, Grindley TB, Allinger NL, 1490; Lii J-H, Chen K-H, Allinger NL, 1504; (2004) J Phys Chem A 108; Lii J-H, Chen K-H, Allinger NL, 3006 5. (a) Information on and references to molecular mechanics programs may be found in references 1 and the website of reference 1a. (b) For papers on the popular Merck Molecular Force Field and the MM4 forcefield (and information on some others) see the issue of J Comp Chem 17 (1996) 6. The force constant is defined as the proportionality constant in the equation force ¼ k x extension(of length or angle), so integrating force with respect to extension to get the energy ( ¼ force x extension) needed to stretch the bond gives E ¼ ( k /2)(extension) 2 , i.e. k ¼ force constant ¼ 2 k stretch (or 2 k bend ) 7. (a) A brief discussion and some parameters: Atkins PW (1994) Physical chemistry, 5th edn. Freeman, New York, pp 772, 773; it is pointed out here that e ± r/ s is actually a much better representation of the compressive potential than is r ± 12 . (b) Moore WJ (1972) Physical chemistry, 4th edn. Prentice-Hall, New Jersey, p 158 (From Hirschfelder JO, Curtis CF, Bird RB (1954) Molecular theory of gases and liquids. Wiley, New York). Note that our k nb is called 4 e here and must be multiplied by 8.31/1000 to convert it to our units of kJ mol ± 1 8. Infrared spectroscopy: Silverstein RM, Bassler GC, Morrill TC (1981) Spectrometric identifi- cation of organic compounds, 4th edn. Wiley, New York, Chapter 3 9. Different methods of structure determination give somewhat different results; this is discussed in reference 4(a) and in: (a) Ma B, Lii J-H, Schaefer HF, Allinger NL (1996) J Phys Chem 100:8763 and (b) Domenicano A, Hargittai I (eds) (1992) Accurate molecular structures. Oxford Science, New York 10. To properly parameterize a molecular mechanics forcefield by calculations only high-level ab initio (or density functional) calculations would actually be used, but this does not affect the principle being demonstrated 11. Reference 1b, section 4.8 12. MM3: Allinger NL, Yuh YH, Lii J-H (1989) J Am Chem Soc 111:8551. The calculation was performed with MM3 as implemented in Spartan (reference 15) 13. Eksterowicz JE, Houk KN (1993) Chem Rev 93:2439 14. Smith MB, March J (2000) March’s advanced organic chemistry. Wiley, New York, pp 284–285 15. Spartan is an integrated molecular mechanics, ab initio and semiempirical program with an input/output graphical interface. It is available in UNIX workstation and PC versions:
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