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Subject: A Few Less Things To Worry About. . .
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From chemistry-request@server.ccl.net  Wed Dec 16 11:10:05 1998
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Date: Tue, 15 Dec 1998 16:54:33 -0500 (EST)
From: Qiang Cui <qiang@tammy.harvard.edu>
To: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
cc: CHEMISTRY@www.ccl.net
Subject: Re: CCL:G:CALCULATING A RATE COSTANT
In-Reply-To: <199812151757.MAA02387@alchemy.chem.utoronto.ca>
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On Tue, 15 Dec 1998, E. Lewars wrote:

> Tued 1998 Dec 15
> 
> Subject: Calculating rate constant
> 
> Hello,
> Has anyone any suggestions for a fairly easy way to calculate a rate constant
> using Gaussian? I want to avoid the intricacies of RRKM theory and just get
> a k_rate accurate to within a factor of, say, 10. For example, consider
> 
>                       HNC   --->   HCN
> 
> At some temp T  HNC in, say, the gas phase (or nonpolar solvent?) has a
> certain halflife (=ln2/k_r). It's easy to calculate a good number for the
> activation energy, but what's a simple way to estimate a realistic k_r (and
> thus t_1/2)?


	First of all, you will need a reasonably accurate barrier height
and reaction coordinate. I guess u will need to push your method a little
bit to get it right for the particular HNC/HCN system, 'cause you are
breaking the triple bond and electron correlation effect should be
significant. But there should be enough data in the literature, 'cause
it's one of the favorable system for people doing quantum dynamics. Read
some paper from Prof. J. Bowman, who did CCSD(T) level PES and some
complex L2 etc. as well. 

	As to the isomeration rate constant, I guess a decent approach is
VTST with semi-classical tunneling, 'cause tunneling should be significant
for your system. You can also try the approximate instaton approach, which
appear to be rather accurate as well for tunneling splittings and rate
constant etc. Any way, POLYRATE and DOIT are the program packages for the
above two approaches, respectively. Finally, as mentioned above, if you
want to push the limit, do the quantum mechanical calculations. The paper
by Bowman and co-workers should be very useful references. 

	Good luck.


> 
>   Thanks
>         E. Lewars
> ================
> 
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> 

___________________________________________________________________________	
Qiang Cui                   
Dept. of Chem.                   _ __..-;''`--/'/ /.',-`-.
Harvard Univ.                  (`/' ` |  \ \ \\ / / / / .-'/`,_
12 Oxford St.,                /'`\ \   |  \ | \| // // / -.,/_,'-,
Cambridge, MA 02138          /<7' ;  \ \  | ; ||/ /| | \/    |`-/,/-.,_,/')
(617)-495-8997              /  _.-, `,-\,__|  _-| / \ \/|_/  |    '-/.;.\'
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http://yuri.harvard.edu/~qiang         __/   /_..-' `  ),'  //
                                      ((__.-'((___..-'' \__.'
805 Mt. Auburn Street Apt. 35
Watertown, MA 02472
(617)-926-6027
__________________________________________________________________________
	


From chemistry-request@server.ccl.net  Wed Dec 16 11:10:08 1998
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From: Darren Andrews <darrena@chemistry.leeds.ac.uk>
Subject: DFT and intermolecular interactions


Dear all,

Has anybody published a definitive investigation of the accuracy of
intermolecular energies/geometries/properties using DFT?  I want to
calculate the energy of interaction and lowest energy geometry between two
relatively large molecules for which MP2 or higher is out of the question.

Darren Andrews.

PostGraduate Student,
School of Chemistry,
University of Leeds,
Leeds.
LS2 9JT.
England.

Darrena@chem.leeds.ac.uk

Tel: 0113 233 6594.
Fax: 0113 233 6565.

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From: Kim Takita <kmtakita@knowledgefoundation.com>
To: "'Computational Chemistry List (CCL)'" <chemistry@www.ccl.net>
Subject: Combinatorial Chemistry final announcement
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Final Announcement & Call for Posters
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------------------------------------------------------------------------  
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Kim Takita
Vice President
The Knowledge Foundation, Inc.
101 Merrimac Street
Boston, MA  02114
Phone: 617-367-7979 ext. 202
Fax: 617-367-7912
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end


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Arthur Wang recently posted a message to CCL announcing avaiability of
SPL programs which "improve" CoMFA analyses by exhaustively searching
the possible orientations and placements of molecules on the lattice and
using that which gives the highest q^2.  Users should be aware that when
this is done, that highest q^2 ceases to be a valid test statistic for
the significance of the model and no longer accurately reflects the
expected external predictivity, just as is the case for variable
selection methods in general( see U Norinder J. Chemonetrics 1996, 10,
95-105 and recent reports by other groups).  This is because compounds
are no longer completely "left out" of the analysis - each contributes
to identifying the highest q^2.

A lattice shift represents a random perturbation of the CoMFA
descriptors.  Though neither the highest nor the lowest q^2 value are of
interest in and of themselves, the AOS and APS programs may nonetheless
be useful for determining the distribution of values and hence how
robust a particular model (the scheme used to align each molecule with
the others) is.  When this is done, however, the appropriate test
statistic is the median or mode q^2 or, better, the mean cross-validated
standard error and the q^2 calculated therefrom. 

Lattice placements which give q^2 values at either extreme - high or low
- are misleading and therefore undesirable.  It turns out, however, that
good representative lattice orientations can reliably be obtained simply
by applying ORIENT BEST to a prototypical molecular (usually the most
extended of the more active compounds) and aligning other molecules in
the training set on that prototype (RD Clark, M Cline & TW Heritage
(1998) Making 3D QQSAR Both Simple and Robust, 215 ACS Natl Meeting,
Abstract COMP 057). In fact, this is now the default option in the
DATABASE ALIGNMENT dialog in SYBYL QSAR. 

Bob Clark
Tripos Inc.
1699 S. Hanley Road
St. Louis MO 63144

bclark@tripos.com

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From: John Wintersteen <johnw@msi.com>
To: "'chemistry@www.ccl.net'" <chemistry@www.ccl.net>
Subject: CCL: WebLab ViewerPro 3.2 from Molecular Simulations Inc.
Date: Wed, 16 Dec 1998 09:13:05 -0800
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Dear CCL,

Molecular Simulations Inc. is pleased to announce the release of the WebLab ViewerPro 3.2, the latest version of our popular desktop 3D visualization and molecular communication software.
 
In conjunction with this release, we would like to extend a special offer on purchases made through our on-line store.  Place your WebLab ViewerPro 3.2 web order before January 1, 1999 and receive a 15% discount off the list price. With your credit card you can order up to 10 copies and receive your software electronically.  To order your copy, please visit our web site at:
http://www.msi.com/viewer

Here is a list of some of the features new in version 3.2:
- OLE Automation (integrate your own applications with the ViewerPro) 
- Enhanced scripting capability (control the ViewerPro from a web page) 
- Data Table (spreadsheet like view of molecular data) 
- Chain Tool for drawing chains of atoms 
- Annotation Tool for inserting text 
- Fuse command for joining fragments 
- New clean options 
- Stereochemistry markers (relative, unknown) 
- Inversion of atom, bond, and molecule stereochemistry 
- Enhanced print quality control 
- Enhanced query editing

The implementation of OLE automation and the enhanced scripting capabilities has greatly improved the ViewerPro's usefulness.  The new Data Table has also been well received as a significant enhancement to usability.   

This is a limited time offer so place your WebLab ViewerPro order today.

Sincerely,

WebLab Viewer Team
Molecular Simulations Inc.
http://www.msi.com/viewer


From chemistry-request@server.ccl.net  Wed Dec 16 12:46:15 1998
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To: chemistry@www.ccl.net
Date: Wed, 16 Dec 98 11:52:20 EST
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From chemistry-request@server.ccl.net  Wed Dec 16 16:24:27 1998
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Date: Wed, 16 Dec 1998 16:21:32 -0500
From: jle@world.std.com (Joe M Leonard)
Message-Id: <199812162121.AA08609@world.std.com>
To: chemistry@ccl.net
Subject: Seeking references...


Folks,

What is/are the references for the Amber 4.0 forcefield -
the one which preceded the Cornell et al paper in 1995?
I'd appreciate any guidance/pointers!

Thanks in advance...

Joe Leonard
jle@world.std.com

