Subject: Re: CCL:M:(1)Koopman's Theorem and (2)BondingREAD/NEW

From: </G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com>
Date: Mon, 4 Dec 1995 09:53:00 -0500

>(2) I use CAChe MOAPC to calculate the distances and bond orders 
             between the 3 
             >hydrogens of a NH3 right above the pai ring of ferulic acid 
             (4-OH-3-OCH3- 
             >cinnamic acid). After geometry optimization, NH3 shifts to the 
             edge of the 
             >pai-ring. I did this calculation in 3 ways: 1) no bonding is 
             specified between 
             >H's of NH3 and pai-ring; 2) 1 H of NH3 hydrogen-bonded to carbons 
             #1,3,5 (if 
             >the 6 C's are numbered 1 to 6); 3) 3 H's of NH3 hydrogen-bonded to 
             C's #1,3,5, 
             >respectively. My question is: Does the calculation take into 
             account whether I 
             >specified the bonding at all? It seems it doesn't. The results 
             always show 
             >small bond order between H's of NH3 and substituents of the ring 
             AND EVEN 
             >SMALLER bond order between those H's of NH3 and C's of the ring, 
             regardless of 
             >whether I draw hydrogen bond lines in the CAChe Editor (Graphic 
             Interface for 
             >MOPAC). Seems MOPAC Input doesn't have bond information. I guess 
             specifying 
             >bonds in Editor doesn't do anything at all. Can someone clarify 
             this for me?
             
             One of the big flaws of a graphical interface is the thinking that 
             the graphics themselves have meaning. This is especially true for 
             semiempirical and ab-initio schemes.
             
             Unless you do something to lock a particular conformation, risking 
             locking it into a non-minimum conformation, all the atoms are 
             'free' to do whatever they want in a minimization. There's no such 
             thing as a bond, especially a hydrogen bond, outside of the 
             'bonding state' generated by a particular agreeable overlap of 
             orbitals. Try drawing a molecule with every atom bonded to every 
             other atom, and you'll get the same result as bonding no atoms to 
             any other atom in the graphical interface for MOPAC. 
             
             Molecular mechanics, on the other hand, is a whole different story.
             
             matt