Name
PEN2 — Activate conformational penalty function.
Description
This keyword activates a penalty function that attempts to maintain the bonding pattern
of the original input molecule. For an atom pair that is bonded in the input molecule, any
conformation in the annealing search that does not maintain this bond within certain limits
will be penalized. (See TOL for specifying
these distances.) This effectively enforces indestructible bonds. For an atom pair that is not
bonded in the input molecule, any conformation where the distance becomes short enough to be
considered bonded will be penalized. This effectively prevents non-bonded atoms from becoming
bonded. A diagram showing which atom pairs will be considered as bonded (marked as a “*”) and
which are non-bonded pairs (marked as “.”) is given in the output file. The primary use of
PEN2 is to prescribe implicit ring closure conditions for cyclical molecules. For example, in
cyclohexane only 5 of the 6 carbon-carbon bonds are explicitly defined in internal coordinates
and the remaining bond is only defined implicitly. So, cyclohexane will naturally fragment
into a linear chain during the simulated annealing search even if strong limits are placed on
bond lengths (such as by LIMIT or
AUTOLIMIT). PEN2 applies a
penalty based
on the bonding in the initial molecule rather than using internal coordinates and so can
properly constrain the system to maintain ring closure. PEN2 was defined to be general enough
to apply to any type of ring system.
