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Charge-Dipole Interaction
Term
Allinger’s potential function includes one of two
possible electrostatic terms: one based on bond
dipoles, or one based on partial atomic charges. The
addition of a charge-dipole interaction term allows
for a combined approach, where partial charges are
represented as bond dipoles, and charged groups,
such as ammonium or phosphate, are treated as
point charges.
Quartic Stretching Term
With the addition of a quartic bond stretching term,
troublesome negative bond stretching energies
which appear when long bonds are treated by
Allinger’s force field are eliminated.
The quartic bond stretching term is required
primarily for molecular dynamics; it has little or no
effect on low energy conformations.
To precisely reproduce energies obtained with
Allinger’s force field:
• Set the quartic stretching constant in the MM2
Constants table window to zero.
The quartic term is eliminated.
Electrostatic and van der
Waals Cutoff Terms
The cutoffs for electrostatic and van der Waals
terms greatly improve the computation speed for
large molecules by eliminating long range
interactions from the computation.
To precisely reproduce energies obtained with
Allinger’s force field:
• Set the cutoff distances to large values (greater
than the diameter of the model).
Every interaction is then computed.
The cutoff is implemented gradually, beginning at
50% of the specified cutoff distance for charge and
charge-dipole interactions, 75% for dipole-dipole
interactions, and 90% for van der Waals
interactions. Chem3D uses a fifth-order polynomial
switching function so that the resulting force field
is second-order continuous.
Because the charge-charge interaction energy
between two point charges separated by a distance
r is proportional to 1/r, the charge-charge cutoff
must be rather large, typically 30 or 40Å. The
charge-dipole, dipole-dipole, and van der Waals
energies, which fall off as 1/r 2 , 1/r 3 , and 1/r 6 ,
respectively, can be cut off at much shorter
distances, for example, 25Å, 18Å, and 10Å,
respectively. Fortunately, since the van der Waals
interactions are by far the most numerous, this
cutoff speeds the computation significantly, even
for relatively small molecules.
Pi Orbital SCF Computation
Chem3D determines whether the model contains
any pi systems, and performs a Pariser-Parr-Pople
pi orbital SCF computation for each system. A pi
system is defined as a sequence of three or more
atoms of types which appear in the Pi Atoms table
window (PIATOMS.xml).
The method used is that of D.H. Lo and M.A.
Whitehead, Can. J. Chem., 46, 2027 (1968), with
heterocycle parameters according to G.D. Zeiss
and M.A. Whitehead, J. Chem. Soc. (A), 1727 (1971).
The SCF computation yields bond orders which are
used to scale the bond stretching force constants,
standard bond lengths, and twofold torsional
barriers.
A step-wise overview of the process used to do pi
system calculations is as follows:
5. A matrix called the Fock matrix is initialized to
represent the favorability of sharing electrons
between pairs of atoms in a pi system.
Appendices
ChemOffice 2005/Appendix MM2 • 673
Chem3D Changes to Allinger’s Force Field