Subject: summary of the pi stacking area calculation

From: <[email-masked]>
Date: Wed, 08 Nov 1995 20:49:09 MET-DST

Dear CCL Netters, 

here is the summary about the pi stacking area calculation. Those interested 
generally in pi stacking calculations can find an older CCL summary by  Mirko
Kranenburg on  21 Jul 1995 (e-mail:[email-masked]).

--------------------------------------------------

My question:
------------

Dear CCL Netters,

Does anybody know for some program applicable to crystals or molecules with pi
stacking interactions, that calculate area of the aromatic molecule or fragment
covered by the neighbour aromatic molecule or fragment? I shall summarize the
replies. Thanks in advance.

Rudolf
-------------

Rudolf Kiralj
Department of Materials Science and Electronics
Rudjer Boskovic Institute
Bijenicka 54
10 000 Zagreb
Croatia
e-mail: [email-masked]

Replies:
--------

1)

Dear Rudolf,
I'm interested to know what sort of calculations you're doing
involving pi-stacking interactions. I will presently be studying the packing of 
conducting polymer chains after I build and optimise some oligomer
molecules of polyaniline with AM1. The pi-interactions will have to be taken
into account. Maybe you may have some expertise or ideas in this area ?

Keep in touch.> 
:
Dr. Aidan Boyle
Instituto de Quimica
UNICAMP

CP 6154
13.081-970 Campinas SP
Brazil

Tel:    00-55-192-397266
Fax:    00-55-192-393805
e-mail: [email-masked]

2)

Dear Dr. Rudolf Kiralj

Could you please tell me if you got any
responses to your query?

Thanks for your help

pavan

please send your mail to
[email-masked]

3)

Please send me a copy of responses you  receive for pi-stacking /area//
Thanks in advance
Satyam

[email-masked]

4)

Dear Rudolf,

When you summarize the CCL replies, could you join some
bibliographic references about pi stacking interactions?
Thanks in advance,

Nathalie

[email-masked]

My repeated question:
--------------------

Dear CCL Netters,

Last week I posted to the CCL inquiring with the following problem:

Does anybody know for some program applicable to crystals or molecules with pi
stacking interactions, that calculate area of the aromatic molecule or fragment
covered by the neighbour aromatic molecule or fragment?

Since I have no answers to summarize the subject, and supposing my question 
was not precise enough, I am asking for help on the pi stacking area 
calculations:

   Suppose one have several solved crystal structures or extracted from 
Cambridge Structural Database, or molecules are built and optimized by
molecular mechanics or quantum mechanics programs. If these molecules are 
partially or completely aromatic, then it is possible that
neighbour molecules or aromatic fragments are mutually parallel and on the
distance approximately 3.5 A. If one can find a suitable view normal to the 
aromatic planes, stacking could be observed as covering of one aromatic system
by one or two neighbour system. By changing the relative positional parameters
of the neighbour aromatic systems this covering is changed. In the first 
approximation it could be taken that measure of this covering is area of the
observed aromatic system (the system is taken as planar hexagons) or surface
area (the system is supposed to be three-dimensional in pi interactions, 
and the interacting surface is not a plane containing the hexagons).
The question is: 
Is there any program or appropriate reference dealing with such or similar 
calculations of the covering (pi stacking) areas or surface areas for a
specified set of relative positional parameters?
Any information or suggestion is welcome. Thanks in advance.

Rudolf
-------------

Rudolf Kiralj
Department of Materials Science and Electronics
Rudjer Boskovic Institute
Bijenicka 54
10 000 Zagreb
Croatia
e-mail: [email-masked]

Replies:
--------

1)

Rudolf,
I have also wondered about the quantitative treatment of pi stacking
interactions.  But I have no info/references on it. I would be interested to
hear from someone who could shed some light on the topic.

Jeanne

***************************************

Jeanne Siemion, MS
Academic Computing Services
Advanced Technology Laboratory for Molecular Development
Enrico Fermi Institute
5640 S. Ellis Ave. 
U of Chicago, Chicago, IL, USA
phone: 312-702-7825
fax: 312-702-8038
e-mail: [email-masked]
office: EFI 184

***************************************

2)

I have a program designed primarily to look at steric effects in terms 
of cone angles and solid angles in organometallics, but which has been 
expanded to include molecular volumes in crystals.  I am now adding a 
feature to calculate the area of a molecules projection onto a plane 
analytically.  It would not be very difficult to enhance this to include 
the area of overlap of two molecules onto that plane, which seems to be 
what you are after (at least one possible solution).  The resulting 
calculation would do several things:
 - find the l.s. plane through predefined groups of atoms (eg. phenyl 

groups)
 - projection all atoms, or selected atoms, onto plane
 - calculate the area of that region due to projection of atoms from two 
groups of interest.

If this is what you are interested in, I'm sure I could add the 
calculation after I've completed the normal molecular projection area 
code.

Cheers, Craig

"If God had meant us to be naked, we would have been born that way."

Craig Taverner
Structural Chemistry, University of the Witwatersrand, South Africa
[email-masked]