From owner-chemistry@ccl.net Wed Oct  6 02:18:01 2010
From: "klamt:-:cosmologic.de" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Experimental Solvation free energy
Message-Id: <-42910-101006021337-30448-qJrEoFBxocpog82paPG/BQ__server.ccl.net>
X-Original-From: klamt a cosmologic.de
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Date: Wed, 06 Oct 2010 08:13:30 +0200
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Sent to CCL by: klamt{}cosmologic.de
Hi William,

the data can be found in the suppl. mat. for
J. Chem. Theory Comput. 2007, 3, 2011-2033

Regarding the COSMO-RS method and our COSMOtherm software please find reference
and further information under www.cosmologic.de/publications.html

I do not know which method you used to get the 1.79 kcal/mol. COSMOtherm has an
RMSE in the order of 0.4-0.5 kcal/mol for dG_hydr. Most likely the method you
applied has a somewhat larger RMSE. Hence taking that into account we may
conclude that my value and your value are consistent within the expectable
uncertainty ranges.

Best regards

Andreas

Zitat von "William Flak williamflak.[#].yahoo.com" <owner-chemistry[#]ccl.net>:

>
> Sent to CCL by: William Flak [williamflak],[yahoo.com]
> Dear Prof Andreas
> Thanks so much for you reply.
> My calculation shows that dG(hyd) of Iodobenzene = -1.79 kcalmol
> So, I was wondering what level of calculation did you use to get -2.3, and
> which software.
> In addition, where can I find this Cramer database for 2343 molecule?
> Thanks in advance
> W. Flak
>
> --- On Tue, 10/5/10, klamt],[cosmologic.de <owner-chemistry(_)ccl.net> wrote:
>
> > From: klamt],[cosmologic.de <owner-chemistry(_)ccl.net>
> > Subject: CCL: Experimental Solvation free energy
> > To: "Flak, William " <williamflak(_)yahoo.com>
> > Date: Tuesday, October 5, 2010, 10:48 AM
> >
> > Sent to CCL by: klamt|-|cosmologic.de
> > Hi William,
> >
> > first of all, I guess you want dG_hydr, i.e. solvent beig
> > water.
> > Since it also was not in the 2343 dG_solv data set which
> > was collected by Cramer
> > and Truhlar for their SM8 fitting, I guess that there is no
> > published data
> > available.
> > If you should be interested in the COSMOtherm prediction:
> > dG_hydr(iodobenzene) =
> > -2.30 kcal/mol (reference system: 1 mol/l in gasphase and
> > solvent).
> >
> > Andreas
> >
> >
> > Am 04.10.2010 22:28, schrieb W Flak
> > williamflak::yahoo.com:
> > > Sent to CCL by: "W  Flak"
> > [williamflak*|*yahoo.com]
> > > Dear CCL
> > > It may be not the right place to post my question, so
> > I'd like to apologize
> > > firstly for that. I have been searching for the
> > experimental value of the
> > solvation free energy of iodobenzene, but I couldn't find
> > it. I used crossfire
> > > software, and many other databases.
> > > So, I was wondering if you know where I can find this
> > experimental value,
> > > please.
> > > Thanks in advance
> > > W. Flak
> >
> >
> >
> > -= This is automatically added to each message by the
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> > please change
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> >      >
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> > or use
> >      >      >      >
>
>


From owner-chemistry@ccl.net Wed Oct  6 09:00:00 2010
From: "Christopher Cramer cramer(0)umn.edu" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: MN-SOL Database
Message-Id: <-42911-101006075056-28702-TQG0Wh3ZoJEEHk3aykjpKw ~ server.ccl.net>
X-Original-From: Christopher Cramer <cramer^umn.edu>
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Sent to CCL by: Christopher Cramer [cramer-x-umn.edu]
> In addition, where can I find this Cramer database for 2343 molecule?
> Thanks in advance
> W. Flak

We (Don Truhlar and I) call it the Minnesota Solvation Database.

The Minnesota Solvation Database – version 2009 presents a collection of 2923 experimental solvation free energies for 
731 unique solutes in 91 solvents (water and 90 organic solvents) and gas-phase molecular geometries in Cartesian coordinates 
for the corresponding solutes. All of the 731 solutes in this database (482 neutrals in 91 solvents; 218 bare singly-charged ionic 
solutes in four solvents, and 31 singly-charged solutes clustered with one solvent molecule in water) contain at most the following 
elements: H, C, N, O, F, Si, P, S, Cl, and Br. 

The distributed version of the database is available for downloading (Web access only) at the University of Minnesota. 
The distributed version of the database includes unpublished licensed materials and requires a licence. To obtain the database, 
print, fill out, and sign the license below and either fax it to Donald G. Truhlar at 612-626-9390 or scan it and send it as 
an e-mail attachment to Software Manager (software at comp.chem.umn.edu). You will then receive the password required 
for downloading by email.

For non-profit organizations the license is free of charge. A commercial license is available for a fee of $6000.

All details/links are at:

http://comp.chem.umn.edu/mnsol/

Best regards,

Chris Cramer

P.S. Andreas Klamt was correct in noting that several of our papers, including the one that he cited, have included the full set of solvation free energies in the supporting information. The database goes beyond that to provide the additional information listed above.
--

Christopher J. Cramer
Elmore H. Northey Professor
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-7541
Mobile: (952) 297-2575
email:  cramer ~~ umn.edu
jabber:  cramer ~~ jabber.umn.edu
http://pollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
    of Computational Chemistry:  Theories and Models, 2nd Edition")


From owner-chemistry@ccl.net Wed Oct  6 09:35:00 2010
From: "nandhini nandhini#,#lgcpromochem.in" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry
Message-Id: <-42912-101006003515-28802-iISZevllvk+yX9Trnayj4w[]server.ccl.net>
X-Original-From: nandhini <nandhini^^^lgcpromochem.in>
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Date: Wed, 6 Oct 2010 10:04:50 +0530
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Sent to CCL by: nandhini [nandhini%%lgcpromochem.in]
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Dear Computational chemistry list

I am running  molecules for geometry optimization. I wanted to know how =
to do calculations for possibility of reactions between two reactants. =
Two reactants are known and a product is known. But how to do predictive =
reactions using MOPAC2009 OR ANY OTHER SOFTWARE AVAILABLE TO PREDICT =
REACTIONS. ANY THEORY AVAILABLE ON THIS METHODOLOGY ? I AM REGULAR VIEW =
OF CCL.NET AND I WAS A MEMBER TOO 6 YEARS BACK.

CAN YOU PLEASE GUIDE ME ?

yours sincerely,

Dr.Nandini.G
LGCPROMOCHEM
PEENYA IInd stage=20
Bangalore -560058
INDIA

EMAIL ID:nandhini,lgcpromochem.in
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<DIV><FONT size=3D2 face=3DArial>Dear Computational chemistry =
list</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2 face=3DArial>I am running&nbsp; molecules for =
geometry=20
optimization. I wanted to know how to do calculations for possibility of =

reactions between two reactants. Two reactants are known and a product =
is known.=20
But how to do predictive reactions using MOPAC2009 OR ANY OTHER SOFTWARE =

AVAILABLE TO PREDICT REACTIONS. ANY THEORY AVAILABLE ON THIS METHODOLOGY =
? I AM=20
REGULAR VIEW OF CCL.NET AND I WAS A MEMBER TOO 6 YEARS =
BACK.</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2 face=3DArial>CAN YOU PLEASE GUIDE ME ?</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2 face=3DArial>yours sincerely,</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2 face=3DArial>Dr.Nandini.G</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial>LGCPROMOCHEM</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial>PEENYA IInd stage </FONT></DIV>
<DIV><FONT size=3D2 face=3DArial>Bangalore -560058</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial>INDIA</FONT></DIV>
<DIV><FONT size=3D2 face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2 face=3DArial>EMAIL=20
ID:nandhini,lgcpromochem.in</DIV></FONT></BODY></HTML>

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From owner-chemistry@ccl.net Wed Oct  6 13:50:00 2010
From: "Sten Nilsson Lill stenil/./chalmers.se" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry
Message-Id: <-42913-101006114921-4438-qqGb/l9X8qiULCtcxl61fw/a\server.ccl.net>
X-Original-From: Sten Nilsson Lill <stenil . chalmers.se>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
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Date: Wed, 6 Oct 2010 17:45:23 +0200
MIME-Version: 1.0


Sent to CCL by: Sten Nilsson Lill [stenil+/-chalmers.se]
Dear Dr. Nandini,

how about reading some literature on the topic?

Hope that helps!

Best regards,

Sten 

Ph.D. Sten Nilsson Lill
Dep. of Chemistry
University of Gothenburg
SE-412 96 Gothenburg, Sweden
e-mail: stenil++chem.gu.se
Phone: +46-31 786 9103
Fax: +46-31-772 3840
________________________________________
> From: owner-chemistry+stenil==chem.gu.se++ccl.net [owner-chemistry+stenil==chem.gu.se++ccl.net] On Behalf Of nandhini nandhini#,#lgcpromochem.in [owner-chemistry++ccl.net]
Sent: Wednesday, October 06, 2010 6:34 AM
To: Nilsson Lill, Sten 
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry

[http://www.ccl.net/global_images/cclltd.gif]
[http://www.ccl.net/global_images/2715w.gif]
[http://www.ccl.net/global_images/colsoh.gif]
[http://www.ccl.net/global_images/telph.gif]
[http://www.ccl.net/global_images/emailccl.gif]
Dear Computational chemistry list

I am running  molecules for geometry optimization. I wanted to know how to do calculations for possibility of reactions between two reactants. Two reactants are known and a product is known. But how to do predictive reactions using MOPAC2009 OR ANY OTHER SOFTWARE AVAILABLE TO PREDICT REACTIONS. ANY THEORY AVAILABLE ON THIS METHODOLOGY ? I AM REGULAR VIEW OF CCL.NET AND I WAS A MEMBER TOO 6 YEARS BACK.

CAN YOU PLEASE GUIDE ME ?

yours sincerely,

Dr.Nandini.G
LGCPROMOCHEM
PEENYA IInd stage
Bangalore -560058
INDIA

EMAIL ID:nandhini/./lgcpromochem.in


From owner-chemistry@ccl.net Wed Oct  6 14:25:00 2010
From: "Van Dam, Hubertus J HubertusJJ.vanDam(!)pnl.gov" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry
Message-Id: <-42914-101006122230-14396-LcH2UfeSkpQHojA3zoxV8w%server.ccl.net>
X-Original-From: "Van Dam, Hubertus J" <HubertusJJ.vanDam*|*pnl.gov>
Content-Language: en-US
Content-Type: multipart/related;
	boundary="_008_FDD09CBD8676AE40957DCDAD24E9627A01889BEA7B21EMAIL04pnlg_";
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Date: Wed, 6 Oct 2010 09:22:20 -0700
MIME-Version: 1.0


Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam.:.pnl.gov]
--_008_FDD09CBD8676AE40957DCDAD24E9627A01889BEA7B21EMAIL04pnlg_
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Hi Dr. Nandini,

There are a number of options for looking at potential reactions, ranging f=
rom simple transition state theory all the way to running full blown dynami=
cs calculations. As a start you'll want to know the energy of the reactants=
 and the products, as well as the energy of the transition state (if there =
is one) on the reaction path between reactants and products. One way to fin=
d the transition state is to use Nudged Elastic Band (NEB) calculations. In=
 this approach you guess an initial pathway between reactant and product by=
 simple interpolation. Along this pathway you place a number of guess geome=
tries (the Nudges) and subsequently you minimize the total energy of all ge=
ometries while applying some constraints (e.g. the length of the reaction p=
athway between two adjacent geometries must be the same for each pair of ad=
jacent geometries). At the end of this procedure you should have a good ide=
a where the highest point along the pathway is and how high that is. From t=
his you can derive a guess for the reaction rates.

Among other codes the just released Open Source package NWChem 6.0 support =
NEB calculations. However, at present this functionality is undocumented bu=
t if you wish, I can provide you with some sample inputs that will help you=
 to get going. For more details about the code please look at http://www.nw=
chem-sw.org/ .

I hope this helps,

      Huub van Dam

> From: owner-chemistry+hubertus.vandam=3D=3Dpnl.gov-.-ccl.net [mailto:owner-ch=
emistry+hubertus.vandam=3D=3Dpnl.gov-.-ccl.net] On Behalf Of nandhini nandhin=
i#,#lgcpromochem.in
Sent: Tuesday, October 05, 2010 9:35 PM
To: Van Dam, Hubertus J
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry

[cid:image001.gif-.-01CB6535.FEA50210]
[cid:image002.gif-.-01CB6535.FEA50210]
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[cid:image004.gif-.-01CB6535.FEA50210]
[cid:image005.gif-.-01CB6535.FEA50210]
Dear Computational chemistry list

I am running  molecules for geometry optimization. I wanted to know how to =
do calculations for possibility of reactions between two reactants. Two rea=
ctants are known and a product is known. But how to do predictive reactions=
 using MOPAC2009 OR ANY OTHER SOFTWARE AVAILABLE TO PREDICT REACTIONS. ANY =
THEORY AVAILABLE ON THIS METHODOLOGY ? I AM REGULAR VIEW OF CCL.NET AND I W=
AS A MEMBER TOO 6 YEARS BACK.

CAN YOU PLEASE GUIDE ME ?

yours sincerely,

Dr.Nandini.G
LGCPROMOCHEM
PEENYA IInd stage
Bangalore -560058
INDIA

EMAIL ID:nandhini/./lgcpromochem.in

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<div class=3DWordSection1>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Hi Dr. Nandini,<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>There are a number of options for looking at potential
reactions, ranging from simple transition state theory all the way to runni=
ng
full blown dynamics calculations. As a start you&#8217;ll want to know the
energy of the reactants and the products, as well as the energy of the
transition state (if there is one) on the reaction path between reactants a=
nd
products. One way to find the transition state is to use Nudged Elastic Ban=
d
(NEB) calculations. In this approach you guess an initial pathway between
reactant and product by simple interpolation. Along this pathway you place =
a
number of guess geometries (the Nudges) and subsequently you minimize the t=
otal
energy of all geometries while applying some constraints (e.g. the length o=
f
the reaction pathway between two adjacent geometries must be the same for e=
ach
pair of adjacent geometries). At the end of this procedure you should have =
a
good idea where the highest point along the pathway is and how high that is=
.
> From this you can derive a guess for the reaction rates.<o:p></o:p></span><=
/p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Among other codes the just released Open Source package NWCh=
em
6.0 support NEB calculations. However, at present this functionality is
undocumented but if you wish, I can provide you with some sample inputs tha=
t will
help you to get going. For more details about the code please look at <a
href=3D"http://www.nwchem-sw.org/">http://www.nwchem-sw.org/</a> .<o:p></o:=
p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>I hope this helps,<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Huub van Dam<o:p></o:p></span=
></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in =
0in 0in'>

<p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-family:"Tahoma=
","sans-serif"'>From:</span></b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'> owner-chemist=
ry+hubertus.vandam=3D=3Dpnl.gov-.-ccl.net
[mailto:owner-chemistry+hubertus.vandam=3D=3Dpnl.gov-.-ccl.net] <b>On Behalf =
Of </b>nandhini
nandhini#,#lgcpromochem.in<br>
<b>Sent:</b> Tuesday, October 05, 2010 9:35 PM<br>
<b>To:</b> Van Dam, Hubertus J<br>
<b>Subject:</b> CCL: from Dr.Nandini.G, theoretical reaction chemistry<o:p>=
</o:p></span></p>

</div>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div>

<p class=3DMsoNormal><span style=3D'color:black'><img border=3D0 id=3D"_x00=
00_i1025"
src=3D"cid:image001.gif-.-01CB6535.FEA50210"><br>
<img border=3D0 id=3D"_x0000_i1026" src=3D"cid:image002.gif-.-01CB6535.FEA502=
10"><br>
<img border=3D0 id=3D"_x0000_i1027" src=3D"cid:image003.gif-.-01CB6535.FEA502=
10"><br>
<img border=3D0 id=3D"_x0000_i1028" src=3D"cid:image004.gif-.-01CB6535.FEA502=
10"><br>
<img border=3D0 id=3D"_x0000_i1029" src=3D"cid:image005.gif-.-01CB6535.FEA502=
10"></span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>Dear
Computational chemistry list</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>I
am running&nbsp; molecules for geometry optimization. I wanted to know how =
to
do calculations for possibility of reactions between two reactants. Two
reactants are known and a product is known. But how to do predictive reacti=
ons
using MOPAC2009 OR ANY OTHER SOFTWARE AVAILABLE TO PREDICT REACTIONS. ANY
THEORY AVAILABLE ON THIS METHODOLOGY ? I AM REGULAR VIEW OF CCL.NET AND I W=
AS A
MEMBER TOO 6 YEARS BACK.</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>CAN
YOU PLEASE GUIDE ME ?</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>yours
sincerely,</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>Dr.Nandini.G</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>LGCPROMOCHEM</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>PEENYA
IInd stage </span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>Bangalore
-560058</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>INDIA</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;font-family:"Arial","s=
ans-serif"'>EMAIL
ID:nandhini/./lgcpromochem.in<o:p></o:p></span></p>

</div>

</div>

</body>

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From owner-chemistry@ccl.net Wed Oct  6 16:48:01 2010
From: "David Gallagher gallagher.da#%#gmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: from Dr.Nandini.G, theoretical reaction chemistry
Message-Id: <-42915-101006144957-21568-ae/6tO0PX5kVwkFNoljqxg . server.ccl.net>
X-Original-From: David Gallagher <gallagher.da:+:gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_12476828==.ALT"
Date: Wed, 06 Oct 2010 11:49:11 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da=gmail.com]
--=====================_12476828==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

A quick answer is that you would start by calculating the 
thermodynamics (free energy of reaction) and kinetics (via the 
transition state) for each potential reaction path, then by comparing 
the results you could make a prediction on the most likely 
outcome.  There are a couple of introductory guides to modelling 
chemical reactivity: "Introduction to Reaction Modelling (Slides)" 
and "Stategies for finding transition states (overview)".

They are posted under "Re: CCL:G: problems with a transition state 
(22 April 2008)"
near the bottom of the page: 
<http://www.cacheresearch.com/presentations.html>http://cacheresearch.com/presentations.html 


Good luck,
David Gallagher
CACheResearch.com
(old chemists never die, they simply fail to react)


At 09:34 PM 10/5/2010, nandhini nandhini#,#lgcpromochem.in wrote:
>[]
>
>[]
>
>[]
>
>[]
>
>[]
>
>Dear Computational chemistry list
>
>I am running  molecules for geometry optimization. I wanted to know 
>how to do calculations for possibility of reactions between two 
>reactants. Two reactants are known and a product is known. But how 
>to do predictive reactions using MOPAC2009 OR ANY OTHER SOFTWARE 
>AVAILABLE TO PREDICT REACTIONS. ANY THEORY AVAILABLE ON THIS 
>METHODOLOGY ? I AM REGULAR VIEW OF CCL.NET AND I WAS A MEMBER TOO 6 YEARS BACK.
>
>CAN YOU PLEASE GUIDE ME ?
>
>yours sincerely,
>
>Dr.Nandini.G
>LGCPROMOCHEM
>PEENYA IInd stage
>Bangalore -560058
>INDIA
>
>EMAIL ID:nandhini/./lgcpromochem.in
>

--=====================_12476828==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
A quick answer is that you would start by calculating the thermodynamics
(free energy of reaction) and kinetics (via the transition state) for
each potential reaction path, then by comparing the results you could
make a prediction on the most likely outcome.&nbsp; There are a couple of
introductory guides to modelling chemical reactivity: &quot;Introduction
to Reaction Modelling (Slides)&quot; and &quot;Stategies for finding
transition states (overview)&quot;.<br><br>
They are posted under &quot;<b>Re: CCL:G: problems with a transition
state (22 April 2008)</b>&quot;<br>
near the bottom of the page:
<a href="http://www.cacheresearch.com/presentations.html">
http://cacheresearch.com/presentations.html</a> <br><br>
Good luck,<br>
David Gallagher<br>
CACheResearch.com<br>
<i>(old chemists never die, they simply fail to react)<br><br>
<br>
</i>At 09:34 PM 10/5/2010, nandhini nandhini#,#lgcpromochem.in
wrote:<br>
<blockquote type=cite class=cite cite="">
<img src="http://www.ccl.net/global_images/cclltd.gif" width=269 height=22 alt="[]">
<font face="Times New Roman, Times"><br>
<img src="http://www.ccl.net/global_images/2715w.gif" width=165 height=18 alt="[]">
<br>
<img src="http://www.ccl.net/global_images/colsoh.gif" width=250 height=21 alt="[]">
<br>
<img src="http://www.ccl.net/global_images/telph.gif" width=312 height=22 alt="[]">
<br>
<img src="http://www.ccl.net/global_images/emailccl.gif" width=103 height=18 alt="[]">
</font><font size=2><br>
Dear Computational chemistry list<br>
</font>&nbsp;<br>
<font size=2>I am running&nbsp; molecules for geometry optimization. I
wanted to know how to do calculations for possibility of reactions
between two reactants. Two reactants are known and a product is known.
But how to do predictive reactions using MOPAC2009 OR ANY OTHER SOFTWARE
AVAILABLE TO PREDICT REACTIONS. ANY THEORY AVAILABLE ON THIS METHODOLOGY
? I AM REGULAR VIEW OF CCL.NET AND I WAS A MEMBER TOO 6 YEARS BACK.<br>
</font>&nbsp;<br>
<font size=2>CAN YOU PLEASE GUIDE ME ?<br>
</font>&nbsp;<br>
<font size=2>yours sincerely,<br>
</font>&nbsp;<br>
<font size=2>Dr.Nandini.G<br>
LGCPROMOCHEM<br>
PEENYA IInd stage <br>
Bangalore -560058<br>
INDIA<br>
</font>&nbsp;<br>
<font size=2>EMAIL ID:nandhini/./lgcpromochem.in<br>
</font><br>
</blockquote></body>
</html>

--=====================_12476828==.ALT--


From owner-chemistry@ccl.net Wed Oct  6 20:32:00 2010
From: "Henry Martinez hmartine[-]gmail.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: CH3I ground state calculation
Message-Id: <-42916-101006203023-15291-JV2K6ikCeB3NLCLWdcfYlw- -server.ccl.net>
X-Original-From: "Henry  Martinez" <hmartine : gmail.com>
Date: Wed, 6 Oct 2010 20:30:15 -0400


Sent to CCL by: "Henry  Martinez" [hmartine!^!gmail.com]
I am trying to calculate the ground state of CH3I using LANL2DZ as a basis set, but I wan to use the Electron core potential (ECP) for the Iodine. However, I have no idea how to do it. The input should have some extras, even I read Gaussian manual, I do not really see how this input should go. Can anybody help me with this?

%chk=ch3i2.chk
%nproc=2
%mem=120MW
# opt freq b3lyp/LANL2DZ

ch3i

0 1
 c
 i   1 ic2
 h   1 hc3        2 hci3
 h   1 hc4        2 hci4         3 dih4
 h   1 hc5        2 hci5         4 dih5
variables
ic2         2.099967
hc3         1.070016
hci3        109.473
hc4         1.070016
hci4        109.473
dih4        120.011
hc5         1.070000
hci5        109.469
dih5        119.995