PEN2 — Activate conformational penalty function.
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.
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