PEN2GRP 

Description

PEN2GRP is identical to PEN2 except that the molecule is divided into distinct fragments and penalties are only applied between atoms in the same fragment. (See PEN2 for general details.) This penalty may be useful when there are two or more distinct fragments, each of which should be preserved independently. PEN2GRP, unlike PEN2, requires additional data to be read in from the extra input section. The beginning of this extra input section should be marked with

$$ pen2grp - pen2 group assignments

which can be abbreviated as

$$ pen2grp

The data must contain a list of positive integers, one for each atom in the molecule, in free format. The n^th integer represents fragment group to which the n^th atom is to be assigned. The group number may range from 1 to the total number of atoms. This input can be further simplified by grouping consecutive identical indices using the “n*m” abbreviation. For example, a sequence of 10 atoms all belonging to group 2 can be abbreviated as “10*2”.

To illustrate the usefulness of PEN2GRP, let us consider the Diels-Alder reaction of butadiene and ethylene to give cyclohexene. This is a bimolecular reaction, so we naturally want to divide the system into two fragment groups corresponding to each of the reactants. This will preserve bonding within each of the reactants but allow the forming and breaking of bonds between them. A simple example of this case, where all of the butadiene atoms appear first followed by the ethylene atoms is given for illustration.

  am1 rhf singlet t=auto anneal truste pen1 pen2grp tol=0.25 filter=0.6 +
temp=300 print=1 pena=1.05
Butadiene + ethylene --> cyclohexene (diels-alder rxn)
Annealing on bimolecular rxn: PEN1, PEN2GRP, PENA
 C              0.000000  0    0.000000  0    0.000000  0    0    0    0
 C              1.337782  1    0.000000  0    0.000000  0    1    0    0
 C              1.483289  1  119.934174  1    0.000000  0    2    1    0
 C              1.483189  1  120.016987  1   -0.202915  1    1    2    3
 H              1.098298  1  122.734039  1  179.289735  1    2    1    3
 H              1.098366  1  122.709460  1 -179.295139  1    1    2    3
 H              1.125038  1  108.427700  1   81.269478  1    3    2    1
 H              1.121728  1  110.447160  1 -161.655787  1    3    2    1
 H              1.125194  1  108.315952  1  -81.709901  1    4    1    2
 H              1.121845  1  110.388121  1  161.370024  1    4    1    2
 C              1.518471  1  112.234312  1  -39.611502  1    3    2    1
 C              1.518408  1  115.303050  1   38.578780  1   11    3    2
 H              1.122252  1  108.401962  1  161.441043  1   11    3    2
 H              1.123114  1  108.297786  1  -83.229242  1   11    3    2
 H              1.122357  1  109.299728  1  120.881335  1   12   11    3
 H              1.123137  1  108.482906  1 -123.240802  1   12   11    3
 0              0.000000  0    0.000000  0    0.000000  0    0    0    0
$$ pen2grp - pen2 group assignments
  1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
$$ end of extra data

This assigns the butadiene atoms to group 1 and the ethylene atoms to group 2. Using the “n*m” abbreviation, the extra data section can be simplified to:

$$ pen2grp - pen2 group assignments
  10*1 6*2
$$ end of extra data

See also:

PEN1, PENA, PEN2, TOL