Chem3D Users Manual - CambridgeSoft

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R*
The R* field is the van der Waals radius of the
particular atom. The larger the van der Waals radius
of an atom is, the larger that atom.
NOTE: Chem3D uses the van der Waals radius, R*, in
the MM2 Atom Types table for computation. It is not the
same as the van der Waals radius in the Atom Types table,
which is used for displaying the model.
Eps
The Eps or Epsilon field is a constant which is
proportional to the depth of the potential well. As
the value of epsilon increases, the depth of the
potential well increases, as does the strength of the
repulsive and attractive interactions between this
atom and other atoms.
NOTE: For specific VDW interactions, the R * and Eps
values from the VDW Interactions table are used instead of
values in the MM2 Atom Types table. See “VDW
Interactions” later in the chapter for more information.
Reduct
Reduct, the fourth field, is a constant used to orient
the center of the electron cloud on a hydrogen atom
toward the nucleus of the carbon atom to which it
is bonded by approximately 10% of the distance
between the two atoms.
Any atom in a van der Waals potential function
must possess a spherical electron cloud centered
about its nucleus. For most larger atoms this is a
reasonable assumption, but for smaller atoms such
as hydrogen it is not a good assumption. Molecular
mechanics calculations based on spherical electron
clouds centered about hydrogen nuclei do not give
accurate results.
However, it is a reasonable compromise to assume
that the electron cloud about hydrogen is still
spherical, but that it is no longer centered on the
hydrogen nucleus. The Reduct constant is
multiplied by the normal bond length to give a new
bond length which represents the center of the
repositioned electron cloud.
The value of the Reduct field for all non-hydrogen
atoms is zero.
Atomic Weight
The fifth field, Atomic Weight, is the atomic weight
of atoms represented by this atom type number.
NOTE: The atomic weight is for the isotopically pure
element, i.e. the atomic weight for atom type number 1 is
12.000, the atomic weight of 12 C.
Lone Pairs
The Lone Pairs field contains the number of lone
pairs around a particular atom type. Notice that an
amine nitrogen, atom type number 8, has one lone
pair and an ether oxygen, atom type number 6, has
two lone pairs. Lone pairs are treated explicitly for
atoms such as these, which have distinctly
non-spherical electron distributions. For atom
types such as O Carbonyl, which have more nearly
spherical electron distributions, no explicit lone
pairs are necessary.
NOTE: Lone pairs are added automatically to atoms
which require them at the beginning of an MM2
computation.
Torsional Parameters
The Torsional Parameters table (Torsional
Parameters.xml) contains parameters used to
compute the portions of the MM2 force field for
the torsional angles in your model. The 4-
284• Parameter Tables CambridgeSoft
Torsional Parameters