From owner-chemistry@ccl.net Thu Jun 28 14:14:00 2007
From: "Shobe, David David.Shobe^sud-chemie.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: opt of aluminum complexes
Message-Id: <-34599-070628140730-760-8UBvoV/Hs7aRqAksO07kdA===server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe*sud-chemie.com>
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Date: Thu, 28 Jun 2007 20:07:04 +0200
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Sent to CCL by: "Shobe, David" [David.Shobe(a)sud-chemie.com]
Aleksandra,

Unless you're using a molecular mechanics method, the coordination
numbers shouldn't matter.  Perhaps the structure is tricky to draw, but
it should be possible with a decent front-end.  In particular there
should be an option to increase the valence of the selected atom; e.g.
this would change oxygen from divalent to trivalent.  

If that doesn't work, I suppose you can put in nitrogen for the oxygen
and a transition metal for the aluminium.  But you'd have to remember to
change them manually later to the correct atoms.  

Your structure probably has a number of unusual (for the organic
chemist) rings.  Again, your Gaussian front-end program should have a
means for adding a new bond between 2 selected elements.  For a
4-membered ring, create the chain A-B-C-D, paying attention to things
like dihedral angles, and then add a bond between A and D.   You can use
the "clean structure" option after that, but be prepared to go back to
the "uncleaned" structure if you don't like the results!

--David Shobe

-----Original Message-----
> From: owner-chemistry~!~ccl.net [mailto:owner-chemistry~!~ccl.net] 
Sent: Thursday, June 28, 2007 12:26 PM
To: Shobe, David
Subject: CCL:G: opt of aluminum complexes


Sent to CCL by: "Aleksandra N Rudnitskaya"
[Aleksandra.rudnit001=umb.edu]
Dear CCL members,

I have a problem with optimization of molecule that contains aluminum,
oxygen, hydrogen, and silicon. The main problem is that I have a lot of
doubly bridging oxygen sites. Those bridging bonds are different form
regular bonds and aluminum, for example, has coordination number 6
instead of expected 3, or oxygen has coordination number 3 instead of
usual 2. As fare as I can see, there are two problems, the first, how to
draw the structure with bridging bonds correctly and, the second, using
what basis set may I optimize this structure in Gaussian?

Thank you very much in advance. 

Aleksandrahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.