From owner-chemistry@ccl.net Sat Jan 22 00:08:00 2011 From: "baljinder baljinder7-x-gmail.com" To: CCL Subject: CCL:G: optimisation Message-Id: <-43730-110121230742-3591-my73Je21t6eP4e5xM0fHQA*server.ccl.net> X-Original-From: baljinder Content-Type: multipart/alternative; boundary=000e0cd4887043222e049a6781d9 Date: Sat, 22 Jan 2011 09:37:27 +0530 MIME-Version: 1.0 Sent to CCL by: baljinder [baljinder7[a]gmail.com] --000e0cd4887043222e049a6781d9 Content-Type: text/plain; charset=ISO-8859-1 Dear all, I am trying to optimise my reaction pathway in aqueous medium using gaussian03. In transition state water molecule is expected to form six-membered ring and hence stabilise the structure. Is using cpcm model and water as solvent is sufficient or i have to draw water molecule with my structure showing stable TS. If yes kindly suggest additional keyword i have to use and whether for reactant and product also i should draw water molecule. Thanks in advance. Baljinder --000e0cd4887043222e049a6781d9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all,
I am trying to optimise my reaction pathway i= n aqueous medium using gaussian03. In transition state water molecule is ex= pected to form six-membered ring and hence stabilise the structure. Is usin= g cpcm model and water as solvent is sufficient or i have to draw water mol= ecule with=A0 my structure showing stable TS. If yes kindly suggest additio= nal keyword i have to use and whether for reactant and product also i shoul= d draw water molecule.

Thanks in advance.
Baljinder

--000e0cd4887043222e049a6781d9-- From owner-chemistry@ccl.net Sat Jan 22 07:14:01 2011 From: "Alexander Bagaturyants bagaturyants()gmail.com" To: CCL Subject: CCL: IC-MAST 2011 Session/Symposium on "Multiscale Predictive Simulation of Sensing Materials" Message-Id: <-43731-110122070837-3583-paY6gcVysXxAI8wHTs2ZNw..server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: ru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 22 Jan 2011 15:08:10 +0300 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [bagaturyants(a)gmail.com] Dear CCLers, I would like to draw your attention to the International Conference for Materials and Applications for Sensors and Transducers, ICMAST-2011 (http://www.icmast.net/index.php ), which will be held at the Kos Island, Greece during May 13-17, 2011. The conference aims at creating a forum in the field of materials research and their applications, especially for those materials that are used for sensors and devices that transduce physical properties. A Session or Symposium (depending on the number of participants) devoted to Multiscale Predictive Simulation of Sensing Materials will be organized within this Conference. I would be happy to meet you or your colleagues at this Symposium. Please, feel free to send this invitation to your colleagues who might be interested in this field. Best regards Prof. Alexander A. Bagaturyants Photochemistry Center Russian Academy of Sciences ul. Novatorov 7a, b. 1 Moscow 119421 Russia Phone: +7(495)9362588 (office) +7(916)5317022 (mobile) Fax: +7(495)9361255 e-mail: sasha_+_photonics.ru bagaturyants_+_gmail.com From owner-chemistry@ccl.net Sat Jan 22 11:59:00 2011 From: "Angela Bruneau amb458-x-cornell.edu" To: CCL Subject: CCL:G: optimisation Message-Id: <-43732-110122081449-23905-GAkO2TZPdmq8JLVMbkpAOQ||server.ccl.net> X-Original-From: Angela Bruneau Content-Type: multipart/alternative; boundary=000e0cd32840cf88ea049a6f25ee Date: Sat, 22 Jan 2011 08:14:33 -0500 MIME-Version: 1.0 Sent to CCL by: Angela Bruneau [amb458*cornell.edu] --000e0cd32840cf88ea049a6f25ee Content-Type: text/plain; charset=ISO-8859-1 Dear Baljinder, First I will disclose that I have not used the solvent selection within gaussian. Either way, In your case it sounds like specific coordination sites exist that affect the structure and stabilization of the ts. I would coordinate the solvent molecules explicitly for your ts. For the ground state of reactants and products you can also coordinate water if you know that coordination exists. If a difference in the number of coordinated water molecules between the ground and ts exists, then run a calc on water molecule itself so that you have stoichiometric balance when you calculate energy barriers. As to keywords, nothing specific from other successful ts calcs you have run. You will have to wait to hear from someone else about the use of solvent functionality in Gaussian. hth. gl. On Fri, Jan 21, 2011 at 11:07 PM, baljinder baljinder7-x-gmail.com wrote: > Dear all, > I am trying to optimise my reaction pathway in aqueous medium using > gaussian03. In transition state water molecule is expected to form > six-membered ring and hence stabilise the structure. Is using cpcm model and > water as solvent is sufficient or i have to draw water molecule with my > structure showing stable TS. If yes kindly suggest additional keyword i have > to use and whether for reactant and product also i should draw water > molecule. > > Thanks in advance. > Baljinder > > -- Angela M. Bruneau Ph.D. Candidate Cornell University Department of Chemistry and Chemical Biology --000e0cd32840cf88ea049a6f25ee Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Baljinder,=A0

First I will disclose that I have not= used the solvent selection within gaussian. Either way, In your case it so= unds like specific coordination sites exist that affect the structure and s= tabilization of the ts. I would coordinate the solvent molecules explicitly= for your ts.=A0

For the ground state of reactants and products you can = also coordinate water if you know that coordination exists. If a difference= in the number of coordinated water molecules between the ground and ts exi= sts, then run a calc on water molecule itself so that you have stoichiometr= ic balance when you calculate energy barriers.

As to keywords, nothing specific from other successful = ts calcs you have run.=A0

You will have to wait to= hear from someone else about the use of solvent functionality in Gaussian.=

hth. gl.

On Fr= i, Jan 21, 2011 at 11:07 PM, baljinder baljinder7-x-gmail.com <owner- chemistry/a\ccl.net> wrote:
Dear all,
I am trying to optimise my reaction pathway i= n aqueous medium using gaussian03. In transition state water molecule is ex= pected to form six-membered ring and hence stabilise the structure. Is usin= g cpcm model and water as solvent is sufficient or i have to draw water mol= ecule with=A0 my structure showing stable TS. If yes kindly suggest additio= nal keyword i have to use and whether for reactant and product also i shoul= d draw water molecule.

Thanks in advance.
Baljinder




--
Angela M. Bruneau
Ph= .D. Candidate
Cornell University
Department of Chemistry and Chemica= l Biology

--000e0cd32840cf88ea049a6f25ee-- From owner-chemistry@ccl.net Sat Jan 22 12:34:00 2011 From: "Adam Kubas ad.kubas-$-gmail.com" To: CCL Subject: CCL: Zero-point energy calculations between two species Message-Id: <-43733-110122034136-32279-Ar+5wkegaBH8qwMO+FLgoA%%server.ccl.net> X-Original-From: Adam Kubas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 22 Jan 2011 09:41:21 +0100 MIME-Version: 1.0 Sent to CCL by: Adam Kubas [ad.kubas-#-gmail.com] Dear Yanbin, I think you should use ZPE(A+B)-ZPE(A)-ZPE(B). Moreover you have to remember that ZPE(A) and ZPE(B) have to be calculated on relaxed A and B geometries. Best regards, Adam -- Adam Kubas Karlsruher Institut für Technologie (KIT) From owner-chemistry@ccl.net Sat Jan 22 21:24:00 2011 From: "Herbert Fruchtl herbert.fruchtl-$-st-andrews.ac.uk" To: CCL Subject: CCL:G: Gaussian on Centos? Message-Id: <-43734-110122094014-7149-gSlq1Z5AIowg+fgLKvNiNw-.-server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 22 Jan 2011 14:39:49 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl(_)st-andrews.ac.uk] I'm not speaking for Gaussian, but I don't think it's a licensing issue. They officially support it on Red Hat. If you install it on something different, they won't send the lawyers; they will just not help you with it. At least they are not contractually obliged to (they might anyway, if you ask nicely). Herbert Quoting "Jason Swails swails||qtp.ufl.edu" : > Hi (myself? :), > > I'm sure you tried, and I'm by no means implying it would be easy (or that > I'd be able to do it when all's said and done). I'd certainly like to try. > I'll dig around here and see if we don't have some kind of site license that > will let me attempt it. Without it, Gaussian and GaussView are much to > expensive to expect an individual to swallow the cost (especially for a > graduate student). > > I merely remarked that it must be POSSIBLE to install GaussView on any Linux > flavor, since at the end of the day Linux is Linux. However, all flavors of > Linux are different, and different groups decide that different components > are "essential", so the likelihood that it'll work out-of-the-box on > all/most distributions is slim-to-none. Not having access to the source code > and being able to compile it on-site means that we have to pick and guess > about the ones that GaussView was linked to at the time it was built, or any > of the other dependencies that it may have. > > Furthermore, Gaussian is faced with one of 2 options: 1) Work to make > GaussView as compatible as possible with as many platforms as possible. 2) > Make it work well with 1 platform and make that a prerequisite. Based on > the relative difficulty of the two, you can hardly be surprised they went > with the latter. > > All the best, > Jason > > On Fri, Jan 21, 2011 at 12:54 PM, Jason DAcchioli jdacchio * gmail.com < > owner-chemistry,,ccl.net> wrote: > > > Hi Jason, > > > > I did try. Honest, I did, but with no luck (I took a look at the link you > > sent a few months ago, but again, no dice). If anyone else out there has a > > good recipe, please let me know! Thanks again for the info. > > > > Be well, > > > > Jason > > > > On Thu, Jan 20, 2011 at 5:06 PM, Jason Swails swails%qtp.ufl.edu < > > owner-chemistry{:}ccl.net > wrote: > > > >> > >> > >> On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com < > >> owner-chemistry(_)ccl.net > wrote: > >> > >>> Hi Daniel, > >>> > >>> Both Gaussian and Gaussview will run on CentOS; I've got it working on an > >>> Altix XE310 in my lab. A word of warning, though; if you get Gaussview, > it > >>> will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other > >>> open-source Linux flavor (easily, at least). > >> > >> > >> ooh! A challenge! Were it not for the hefty price tag I'd give it a go. > >> An ubuntu thread that may be helpful: > >> http://ubuntuforums.org/showthread.php?t=634578 > >> > >> In any case, Linux is Linux, so I can't imagine it's completely > >> incompatible with other flavors. It may be necessary to install > additional > >> packages with the proper library versions. > >> > >> As a side-note, SUSE 10 is listed as a supported platform if an additional > >> package is installed. > >> > >> All the best, > >> Jason > >> > >> > >>> > >>> Be well, > >>> > >>> Jason > >>> > >>> Jason S. D'Acchioli > >>> Assistant Professor of Chemistry > >>> University of Wisconsin-Stevens Point > >>> > >>> On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu < > >>> owner-chemistry],[ccl.net> wrote: > >>> > >>>> > >>>> Sent to CCL by: Daniel Strahs [dstrahs**pace.edu] > >>>> Hello colleagues: > >>>> > >>>> Has any one had any experience installing Gaussian for Linux/Red Hat > >>>> Enterprise on the Centos OS? The binary compatibility with RedHat > >>>> interests us. > >>>> > >>>> Thanks for any responses! > >>>> > >>>> -- > >>>> Daniel B. Strahs > >>>> Associate Professor > >>>> Biology and Health Sciences Department > >>>> Pace University, New York>>>> E-mail to subscribers: CHEMISTRY],[ccl.net > or use:>>>> > >>>> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use>>>> > >>>> > >>>> > >>> > >> > >> > >> -- > >> Jason M. Swails > >> Quantum Theory Project, > >> University of Florida > >> Ph.D. Graduate Student > >> 352-392-4032 > >> > > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk