Chem3D Users Manual - CambridgeSoft

• Cutoffs for electrostatic and van der Waals
terms with 5th order polynomial switching
function
• Automatic pi system calculations when
necessary
• Torsional and non-bonded constraints
Chem3D stores the parameters used for each of the
terms in the potential energy function in tables.
These tables are controlled by the Table Editor
application, which allows viewing and editing of the
parameters.
Each parameter is classified by a Quality number.
This number indicates the reliability of the data.
The quality ranges from 4, where the data are
derived completely from experimental data (or ab
initio data), to 1, where the data are guessed by
Chem3D.
The parameter table, MM2 Constants, contains
adjustable parameters that correct for failings of the
potential functions in outlying situations.
NOTE: Editing of MM2 parameters in the Table Editor
should only be done with the greatest of caution by expert
users. Within a force-field equation, parameters operate
interdependently; changing one normally requires that others
be changed to compensate for its effects.
Bond Stretching Energy
E Stretch
=71.94K ∑(r−r
Bonds s o
) 2
The bond stretching energy equation is based on
Hooke's law. The K s parameter controls the
stiffness of the spring’s stretching (bond stretching
force constant), while r o defines its equilibrium
length (the standard measurement used in building
models). Unique K s and r o parameters are assigned
to each pair of bonded atoms based on their atom
types (C-C, C-H, O-C). The parameters are stored
in the Bond Stretching parameter table. The
constant, 71.94, is a conversion factor to obtain the
final units as kcal/mole.
The result of this equation is the energy
contribution associated with the deformation of a
bond from its equilibrium bond length.
This simple parabolic model fails when bonds are
stretched toward the point of dissociation. The
Morse function would be the best correction for
this problem. However, the Morse Function leads
to a large increase in computation time. As an
alternative, cubic stretch and quartic stretch
constants are added to provide a result approaching
a Morse-function correction.
The cubic stretch term allows for an asymmetric
shape of the potential well, allowing these long
bonds to be handled. However, the cubic stretch
term is not sufficient to handle abnormally long
bonds. A quartic stretch term is used to correct
problems caused by these very long bonds. With
the addition of the cubic and quartic stretch term,
the equation for bond stretching becomes:
E Stretch
=71.94 ∑[(r K−r Bonds s o
) 2 +CS (r−r o
) 3 +QS (r−r o
) 4 ]
Both the cubic and quartic stretch constants are
defined in the MM2 Constants table.
To precisely reproduce the energies obtained with
Allinger’s force field: set the cubic and quartic
stretching constant to “0” in the MM2 Constants
tables.
Angle Bending Energy
E Bend
=0.02191418 K ∑(θ−θ b o
) 2
Angles
The bending energy equation is also based on
Hooke’s law. The K b parameter controls the
stiffness of the spring’s bending (angular force
ChemOffice 2005/Chem3D Computation Concepts • 137
Molecular Mechanics Theory in Brief