Computational Chemistry

(Steven Felgate) #1

  1. The Merck force field (ref. [18]) often gives geometries that are satisfactory for energy
    calculations (i.e. for single-point energies, no geometry optimization with the quantum
    mechanical method) with quantum mechanical methods; this could be very useful for large
    molecules: Hehre WJ, Yu J, Klunzinger PE (1997) A guide to molecular mechanics and
    molecular orbital calculations in Spartan. Wavefunction Inc., Irvine, CA, chapter 4

  2. Halgren TA (1996) J Comp Chem 17:490

  3. Nicklaus MC (1997) J Comp Chem 18:1056; the difference between CHARMM and
    CHARMm is explained here

  4. (a)www.amber.ucsf.edu/amber/amber.html(b) Cornell WD, Cieplak P, Bayly CI, Gould IR,
    Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am
    Chem Soc 117:5179 (c) Barone V, Capecchi G, Brunel Y, Andries M-LD, Subra R (1997)
    J Comp Chem 18:1720

  5. (a) Field MJ, Bash PA, Karplus M (1990) J Comp Chem 11:700. (b) Bash PA, Field MJ,
    Karplus M (1987) J Am Chem Soc 109: 8092

  6. Singh UC, Kollman P (1986) J Comp Chem 7:718

  7. (a) Reference 1b, chapter 10. (b) H€oltje H-D, Folkers G (1996) Molecular modelling,
    applications in medicinal chemistry. VCH, Weinheim, Germany. (c) van de Waterbeemd H,
    Testa B, Folkers G (eds) (1997) Computer-assisted lead finding and optimization. VCH,
    Weinheim, Germany

  8. (a) Reference 1b, chapter 6. (b) Karplus M, Putsch GA (1990) Nature 347:631. (c) Brooks III CL,
    Case DA (1993) Chem Rev 93:2487. (d) Eichinger M, Grubm€uller H, Heller H, Tavan P (1997)
    J Comp Chem 18:1729. (e) Marlow GE, Perkyns JS, Pettitt BM (1993) Chem Rev 93:2503.
    (f) Aqvist J, Warshel A (1993) Chem Rev 93:2523

  9. Reference 1b, pp 410–456

  10. Lipkowitz KB, Peterson MA (1993) Chem Rev 93:2463

  11. (a) Saunders M (1991) Science 253:330. (b) See too Dodziuk H, Lukin O, Nowinski KS
    (1999) Polish J Chem 73:299

  12. (a) Hehre WJ, Radom L, Schleyer pvR, Pople JA (1986) Ab initio Molecular Orbital Theory.
    Wiley, New York (b) M.D. Harmony, V.W. Laurie, R.L. Kuczkowski, R.H. Schwenderman,
    D.A. Ramsay, F.J. Lovas, W.H. Lafferty, A.G. Makai, Molecular Structures of Gas-Phase
    Polyatomic Molecules Determined by Spectroscopic Methods”, J. Physical and Chemical
    Reference Data, 1979 , 8 , 619–721 (c) Huang J, Hedberg K (1989) J Am Chem Soc 111:6909

  13. Lii J-H, Allinger NL (1992) J Comp Chem 13:1138. The MM3 program can be bought from
    Tripos Associates of St. Louis, Missouri

  14. Nevins N, Allinger NL (1996) J Comp Chem 17:730 and references therein

  15. Lipkowitz KB (1995) J Chem Ed 72:1070

  16. (a) Wiberg K (1996) Angew Chem Int Ed Engl 25:312. (b) Issue no. 5 of Chem Rev, 1989, 89.
    (c) Inagaki S, Ishitani Y, Kakefu T (1994) J Am Chem Soc 116:5954. (d) Nagase S (1995) Acc
    Chem Res 28:469. (e) Gronert S, Lee JM (1995) J Org Chem 60:6731. (f) Sella A, Basch H,
    Hoz S (1996) J Am Chem Soc 118:416. (g) Grime S (1996) J Am Chem Soc 118:1529. (h)
    Balaji V, Michl J (1988) Pure Appl Chem 60:189. (i) Wiberg KB, Ochterski JW (1997)
    J Comp Chem 18:108

  17. Seeman JI (1983) Chem Rev 83:83


Added in press:



  1. Handley CM, Popelier PLA (2010) The use of neural networks used to devise forcefields.
    J Phys Chem A 114:3371


References 81

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