giving actual numbers to the constants in the forcefield constitutes parameterizing
the field. An example is given of the devising and parameterization of an MM
forcefield.
MM is widely used to create reasonable geometries for input to other calculations.
Such calculations are fast and can be very accurate, provided that the forcefield has
been carefully parameterized for the types of molecules under study. Calculations on
biomolecules is a very important application of MM; the pharmaceutical industry
designs new drugs with the aid of MM: for example, examining how various
candidate drugs fit into the active sites of biomolecules (docking) and the related
aspect of QSAR are of major importance. MM is of some limited use in calculating
the geometries and energies of transition states. Organic synthesis now makes
considerable use of MM, which enables chemists to estimate which products are
likely to be favored and to devise more realistic routes to a target molecule than was
hitherto possible. In molecular dynamics MM is used to generate the forces acting on
molecules and hence to calculate their motions, and in Monte Carlo simulations MM
is used to calculate the energies of the many randomly generated states.
MM is fast, it can be accurate, it is undemanding of computer power, and it
provides reasonable starting geometries for quantum mechanical calculations. It
ignores electrons, and so can provide parameters like dipole moment only by
analogy. One must be cautious about the applicability of MM parameters to the
problem at hand. Stationary points from MM, even when they are relative minima,
may not be global minima. Ignoring solvent effects can give erroneous results for
polar molecules. MM gives strain energies, the difference of which for structurally
similar isomers represent enthalpy differences; parameterization to give enthalpies
of formation is possible. Strictly speaking, relative amounts of isomers depend on
free energy differences. The major conformation (even when correctly identified) is
not necessarily the reactive one.
References
- General references to molecular mechanics: (a) Rappe AK, Casewit CL (1997) Molecular
mechanics across chemistry. University Science Books, Sausalito, CA; websitehttp://www.
chm.colostate.edu/mmac. (b) Leach AR (2001) Molecular modelling, principles and applica-
tions, 2nd edn. Prentice Hall, Essex (UK), chapter 4. (c) Burkert U, Allinger NL (1982)
Molecular mechanics, ACS Monograph 177. American Chemical Society, Washington, DC.
(d) Allinger NL (1976) Calculation of molecular structures and energy by force methods.
In: Gold V, Bethell D (eds) Advances in physical organic chemistry, vol 13. Academic,
New York. (e) Clark T (1985) A handbook of computational chemistry. Wiley, New York.
(f) Levine IN (2000) Quantum chemistry, 5th edn. Prentice-Hall, Engelwood Cliffs,
NJ, pp 664–680. (g) Issue no. 7 of Chem Rev (1993), 93. (h) Conformational energies:
Pettersson I, Liljefors T (1996) In: Reviews in Computational Chemistry, vol 9, Lipkowitz
KB, Boyd DB (eds) VCH Weinheim. (i) Inorganic and organometallic compounds: Landis
CR, Root DM, Cleveland T (1995) In: Reviews in Computational Chemistry, vol 6, Lipkowitz
KB, Boyd DB (eds) VCH Weinheim. (j) Parameterization: Bowen JP, Allinger NL (1991)
Reviews in Computational Chemistry, vol 6, Lipkowitz KB, Boyd DB (eds) VCH Weinheim
References 79