Subject: Re: CCL:Spartan: MM2 parameters problems

From: "Robert K. Szilagyi" <[email-masked]>
Date: Wed, 21 May 1997 22:45:55 +0200

> SPARTAN MECHANICS (MM2) PROGRAM:  SGI/R4K  Release 4.1 a2
>   (Job run on ucmodl.che.uc.edu)
> 
> test
> 
> Missing angle parameter: 2 19 6  0 (2 1 13)
> 

Dear Jeffrey,

the bond angle parameter for an sp2 carbon - sp3 silicon - and an sp3
oxygen is missing. The zero means that this angle is not included in any
ring system. You have now two choices. 
You should check the bibliography, collect the available structural
information about the C-Si-O bond angle and then perform a parameter
optimisation which normally may take months.
The other way is to use the chemical analogy and you can try to guess
the missing parameters. (There was a paper published by Dr. Dora Schnurr
from the Monsanto Co. in the J. Comp. Chem. 1992 about the "quasi
quantitative" quess of missing parameters, but I think you do not have
to use this method due to a lucky situation.) The parameter set of the
Spartan can give some further information about the bonding for similar
silicon compounds:

	Atom type 	Force	Strain-free		MM2 
	mnemonic	Constant Angle		    numeric type
C sp2	Si sp3	C sp3	0.40	110.2		2	19	1
C sp2	Si sp3	C sp2	0.60	109.5		2	19	2
C sp2	Si sp3	H 	0.24	109.5		2	19	5
C sp2	Si sp3	Si sp3	0.40	110.2		2	19	19

Taking into account these figures, the force constant should be between
0.6 and 0.24 and the strain free bond angle should be about the ideal
sp3 hybrisisation state. If I were you, I choose the 0.60 and 109.5
deg., since the bonding between an sp3 Si and an sp3 O with lone pairs
is might be closest to the C sp2 Si sp3 Csp2 situation.

Technically, you should edit the params.MM2 file and insert somewhere
after the heading BEND (bond angle bending parameters) the line 2:

BEND
    2   19    6    0.60    109.50      0.0       0.0       0
    1    1    1    0.45    109.47    109.51    109.50      0
 ...
ENDBEND

Now, you can submit the MM2 job again and hopefully there will be no
further problem.

Good luck and let me know if you need further help!

Best wishes,
-- 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Robert K. Szilagyi                  Mueller Laboratory
      ph.d. student                     Dept. Organic Chemistry
                                        University of Veszprem
   [email-masked]                 Veszprem, H-8201
                                        POB. 158; Egyetem u. 10.
 Phone:  +36 88 422022 extn. 395        HUNGARY
 Mobile: +36 20 461413
 Fax:    +36 88 427492                  http://mm1.vein.hu/

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