162 COMPUTER HARDWARE, SOFTWARE
structure. The visualization and analysis of such structures, their molecular
properties, and their molecular interactions are based on some theoretical
means for predicting the structures and properties of molecules and com-
plexes. If an algorithm can be developed to calculate a structure with a given
stoichiometry and connectivity, one can then attempt to compute properties
based on calculated molecular structure and vice versa.
Molecular mechanics is defi ned as the calculation of the molecular structure
and corresponding strain energy by minimization of the total energy. The ener-
gies of various minima are calculated using functions that relate internal
coordinates to energy values. Molecular mechanics methods can provide excel-
lent descriptions of equilibrium geometries and conformations, but do not
supply thermochemical information. They cannot yield acceptable results
outside the range of their parameterization. This important point, repeated
and amplifi ed below, says that a force fi eld parameter set (also defi ned below),
assembled for one coordination complex or bioinorganic molecule, may not
be applied to other molecules unless some means of testing the parameter set
(comparison of calculated bond distances and bond angles to those known
experimentally from an X - ray crystallographic structure, for instance) is
applied.
An excellent introduction to molecular modeling of inorganic compounds
has been provided by Comba and Hambley in their 1995 bookMolecular
Modeling of Inorganic Compounds. 3a The book has been updated by a new
enlarged edition containing an interactive tutorial on CD - ROM. The newer
edition includes descriptions of calculations of stereoselective interactions of
metal complexes with biomolecules. 3b Additionally, the authors have devel-
oped a inorganic compound - oriented molecular modeling system called
MOMEC, which has been designed as an add - on to the HyperChem TM drawing
and modeling program discussed below in Section 4.5. The reference 3 authors
discuss the application of molecular mechanics to coordination and organo-
metallic compounds, to inorganic compounds involved in catalysis (including
stereospecifi c catalysts), to design of new metal - based drugs, and to the inter-
action of metal ions with biological macromolecules such as proteins or DNA.
In all cases, modeling of transition metal species is complicated by the number
of different metals of interest as well as the variety of coordination numbers,
geometries, and electronic states they may adopt. Other pitfalls abound. If a
calculation is performed on the wrong electronic state of a molecule (singlet
rather than triplet oxygen for example), any energy minimization result will
be incorrect as well. An incorrect starting geometry (the wrong conformer for
instance) may yield the wrong energy minimum. The geometry optimization
method defi ned may not produce an accurate geometric result.
In spite of its limitations, molecular mechanics (MM) is a technique that is
widely used for the computation of molecular structures and relative stabili-
ties. The advantage of MM over quantum mechanical methods is mainly based
on the computational simplicity of empirical force fi eld calculations, leading
to a comparatively small computational effort for MM calculations. Therefore,