c19 JWBS043-Rogers September 13, 2010 11:29 Printer Name: Yet to Come
310 CLASSICAL MOLECULAR MODELINGIntramolecular interactions are not independent of one another. For example, bending
of a stretched bond is not the same as bending of a bond at its equilibrium length
r 0. Conversely, stretching of a bent bond is not the same as stretching of a bond at
θ=θ 0. A stretch-bend termVs-b, called across term, is added. Other terms, especially
electrostatic terms, have been added (somewhat reluctantly) as necessary to achieve
closer and closer agreement with known experimental data. The collection of terms
and the parameters that produce them is called aforce field. The MM force field has
become larger as new experimental evidence has been added to the basis set and as
a larger set of molecular problems has been attempted. Allinger et al. (1996, 2010)
have augmented the strainless energy by an 11-term equation in his programs MM3
and MM4.19.5 MOLECULAR MODELING
The termmolecular modelincludes ball-and-stick physical models used as visual
aids to facilitate thinking about the invisible world of the molecule. In contemporary
usage, however, the term usually denotes a mathematical model, possibly generating
a computer output set of Cartesian triples, each of which specifies the position of an
atom in the model.
The most fundamental molecular property obtained from a molecular model is its
geometry. Geometry is found by optimization of an estimated input geometry. One
of many possible geometry optimization procedures is shown in Example 19.1.19.6 THE GUI
Input files for more complicated molecules can be constructed using a point-and-click
graphical user interface(GUI)—for example, PCModel©C. Having the optimized
model in mathematical form permits use of the coordinate set to draw two- orFIGURE 19.4 Visualization of the output for the ethane molecule (PCModel 8.0©C).