From owner-chemistry@ccl.net Sat Aug  9 11:13:01 2008
From: "alexandre()cermm.concordia.ca (Alexandre Foisy-Geoffroy Undergraduate Student)" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: How to find reaction intermediates with Gaussian
Message-Id: <-37527-080808185852-5558-M06FoeRtByuK1KE8PN7+GQ*o*server.ccl.net>
X-Original-From: alexandre::cermm.concordia.ca (Alexandre Foisy-Geoffroy Undergraduate Student)
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Date: Fri, 08 Aug 2008 17:54:26 -0400
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Sent to CCL by: alexandre/a\cermm.concordia.ca (Alexandre Foisy-Geoffroy Undergraduate Student)
Hello!

I'm working with a reaction between VxOy clusters and small organic molecules, and I have problems finding good guesses for the intermediate minima between the reactants and products. The only idea I have right now that hasn't failed yet is to take one vibration mode from the pre-reaction complexes ot try to find the following steps. How would I go to do that?

Are there other, better ways to start from a pre-reaction complex and go to a guess for the next minimum in the reaction mechanism? 

We know from experiment that the specific cluster I'm studying does not do the reaction, while smaller clusters do. We basically want to support that observation with a theoretical study. The reaction mechanism for the smaller cluster has been identified, but applying it to the larger cluster has yielded no result, possibly because of the geomtery difference between the two.

Thank you for your time and consideration.

Alexandre foisy-Geoffroy.


From owner-chemistry@ccl.net Sat Aug  9 11:49:01 2008
From: "Derek J. Cashman derek.cashman===gmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: SAR predictions for this paticular question
Message-Id: <-37528-080808185354-2641-4yVHu+cSPQDrW797eniqQw%x%server.ccl.net>
X-Original-From: "Derek J. Cashman" <derek.cashman(-)gmail.com>
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Date: Fri, 8 Aug 2008 17:59:02 -0400
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Sent to CCL by: "Derek J. Cashman" [derek.cashman%gmail.com]
On Fri, Aug 8, 2008 at 4:12 PM, Nancy Ann Neale nealen!A!mail.nih.gov
<owner-chemistry+*+ccl.net> wrote:
>
> Sent to CCL by: "Nancy Ann Neale" [nealen#,#mail.nih.gov]
> I am looking for recommendations for SAR softawre for a specific problem.
>
> What we have at this point is approximately 50 compounds that have bee qualitately analyzed for activity in a certain cell.  We haven't structural data on the surface protein that shuttles substrates accross the membrane, but that is only the first step in detrmining what a good canddiate is.
>
> We have 'downstream' data on these compounds with respect to activity, IC50, and a selectivity ratio.
>
> My first thought is AutoDock, but am concerned that may not do the trick because of our lack of structural data of that protein.
>
> My goal is to train some program with the good amount of data we have to recognize adn ultimately predict reasonable candidates in the future for this application.
>
> Any suggestions are most welcome.

Looks like this data set would be ideal for running a CoMFA study
(Comparative Molecular Field Analysis) in SYBYL (www.tripos.com).
Assuming that SYBYL is available or within your budget (it's a
commercial package).


Derek J. Cashman, Ph.D.
derek.cashman+*+gmail.com

"A Drug is any substance which, when injected into a rat, produces a
publishable, scientific paper."


From owner-chemistry@ccl.net Sat Aug  9 12:24:01 2008
From: "Raphael Ribeiro raphaelri^-^hotmail.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: ZPEs and thermal corrections HF/post-HF
Message-Id: <-37529-080809003435-765-d/wH0Lt4Jgjp6vwyQeVkaw ~~ server.ccl.net>
X-Original-From: "Raphael  Ribeiro" <raphaelri]*[hotmail.com>
Date: Sat, 9 Aug 2008 00:34:32 -0400


Sent to CCL by: "Raphael  Ribeiro" [raphaelri---hotmail.com]
Dear all,

I am working on the thermodynamics of an organic reaction.
My focus at this point is the relative stability of the products in the gas phase. I am calculating the electronic energy of the compounds and also ZPE besides doing thermal corrections. Initially, I did RHF calculations with several basis and now I'm working on post-HF methods.

My question  is if it is a good approximation to introduce the ZPEs and thermal corrections obtained in the  RHF-only calculations in my post-HF results without any change, or if the results obtained by doing that wouldn't be reliable?? I mean, would i have to calculate the HESSIANS again? Is it a very poor approximation? I've already tried looking for references about that, but I couldn't find.

Thanks in advance
Raphael


From owner-chemistry@ccl.net Sat Aug  9 12:58:00 2008
From: "Raphael Ribeiro raphaelri*o*hotmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: ZPEs and thermal corrections HF/post-HF
Message-Id: <-37530-080809010018-2726-Zbt/rYkIoXpbperNZJy7bQ%a%server.ccl.net>
X-Original-From: Raphael Ribeiro <raphaelri]~[hotmail.com>
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Date: Sat, 9 Aug 2008 04:27:28 +0000
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Sent to CCL by: Raphael Ribeiro [raphaelri[a]hotmail.com]

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Dear all=2C

I am working on the thermodynamics of an organic reaction.
My focus at this point is the relative stability of the products in the gas=
 phase. I am calculating the electronic energy of the compounds and also ZP=
E besides doing thermal corrections. Initially=2C I did RHF calculations wi=
th several basis and now I'm working on post-HF methods.=20
My question  is if it is a good approximation to introduce the ZPEs and the=
rmal corrections obtained in the  RHF-only calculations in my post-HF resul=
ts without any change=2C or if the results obtained by doing that wouldn't =
be reliable?? I mean=2C would i have to calculate the HESSIANS again? Is it=
 a very poor approximation? I've already tried looking for references about=
 that=2C but I couldn't find.

Thanks in advance
Raphael

_________________________________________________________________
Receba GR=C1TIS as mensagens do Messenger no seu celular quando voc=EA esti=
ver offline. Conhe=E7a  o MSN Mobile!
http://mobile.live.com/signup/signup2.aspx?lc=3Dpt-br=

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<body class=3D'hmmessage'>Dear all=2C<br><br>I am working on the thermodyna=
mics of an organic reaction.<br>My focus at this point is the relative stab=
ility of the products in the gas phase. I am calculating the electronic ene=
rgy of the compounds and also ZPE besides doing thermal corrections. Initia=
lly=2C I did RHF calculations with several basis and now I'm working on pos=
t-HF methods. <br>My question&nbsp=3B is if it is a good approximation to i=
ntroduce the ZPEs and thermal corrections obtained in the&nbsp=3B RHF-only =
calculations in my post-HF results without any change=2C or if the results =
obtained by doing that wouldn't be reliable?? I mean=2C would i have to cal=
culate the HESSIANS again? Is it a very poor approximation? I've already tr=
ied looking for references about that=2C but I couldn't find.<br><br>Thanks=
 in advance<br>Raphael<br><br /><hr />Receba GR=C1TIS as mensagens do Messe=
nger no seu celular quando voc=EA estiver offline. Conhe=E7a  o MSN Mobile!=
 <a href=3D'http://mobile.live.com/signup/signup2.aspx?lc=3Dpt-br' target=
=3D'_new'>Crie j=E1 o seu!</a></body>
</html>=

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