Subject: Molecular Mechanics

From: Paddy Kane <[email-masked]>
Date: Mon, 20 Nov 1995 23:23:07 +0000 (GMT)

Hi,

 I am a HyperChem user and I have two questions about molecular 
mechanics (MM):

 I recently asked the following question 
>  While I know that the energies obtained in an MM calculation have
> no absolute  meaning, would the difference in energies of two 
> optimized conformations of the same complex have any meaning? If 
> so, what kind of energy are we talking about?

 What I wanted to know but did not specifically ask (typical of the 
way I ask questions!!!!!) is that if I have two different 
complexes where the ligand is the same but the ion is different what 
is the significance of the difference in energy resulting from an 
(MM) optimization?

 The reason that I ask is that I obtained the following energies from 
MM optimizations for complexes of the same ligand but with different 
ions:
		Energy/ (kcal / mol)
Li+		-190.6
Na+		-171.2
K+		-150.8

 We have found experimentally that the ligand is selective for 
sodium over magnesium; so I would have expected to have obtained a 
lower energy for the sodium complex. So *IF* MM optimization 
energies are not a reliable indicator of selectively what exactly is 
the significance of the above difference of 63 kcal / mol?

 The above optimizations were carried out by assigning the atom types 
to the metals published by Grootenhuis and Kollman, JACS., 1989, 111, 
2152-2158. However I am not aware of the existence of atom types in 
the case of Group 2 metals and so I propose to use Noble Gas atoms as 
substitutes with charges of 2+ but I am not certain as to what atom 
types to use. Should I use the Noble Gas atom types that are part of 
the MM+ force field or should I leave the atom type as **.

Regards,
Paddy

Paddy Kane
E.mail: [email-masked]
School of Chemical Sciences
Dublin City University
Dublin
Ireland