From owner-chemistry@ccl.net Sat Jul 20 02:56:00 2013 From: "meishway linkon meishwaylinkon- -yahoo.com" To: CCL Subject: CCL: natural transition orbital analysis Message-Id: <-48975-130720025503-15342-cvYiJ7aWccdwdqqKbekdeA]_[server.ccl.net> X-Original-From: "meishway linkon" Date: Sat, 20 Jul 2013 02:55:02 -0400 Sent to CCL by: "meishway linkon" [meishwaylinkon()yahoo.com] hello everybody: actually i want to do natural transition orbital (NTO)analysis, can anybody guide me quickly hoe to perform it, how to write its route section,and how can i get finals figs for orbitals etc. please tell me in detail.which kind of information i get from it? is there any need to solve some equation after doing calculations? what about method and basis set? should it be same as we used for excited state properties calculation before? please help me as soon possible , i need it, i will be really grateful to you all. From owner-chemistry@ccl.net Sat Jul 20 03:31:00 2013 From: "meishway linkon meishwaylinkon###yahoo.com" To: CCL Subject: CCL: natural transition orbital analysis Message-Id: <-48976-130720031854-25521-bBbNVY0lrjEARmZSWNQiIQ~~server.ccl.net> X-Original-From: "meishway linkon" Date: Sat, 20 Jul 2013 03:18:53 -0400 Sent to CCL by: "meishway linkon" [meishwaylinkon[-]yahoo.com] hello, before i sent a question about NTO analysis, i got information from some CCl past questions. i found its route section # opt td=(root=1,nstates=6) b3lyp/6-31g(d) density=transition=1 pop(NTO,saveNTO) am wondering why the word opt is used? is it necessary to carry NTO analysis, as structure is already ground state optimized. secondly, what does mean "density=transition=1" why it is written 1 here? thanks From owner-chemistry@ccl.net Sat Jul 20 17:39:00 2013 From: "Adel Reisi areisi%%kashanu.ac.ir" To: CCL Subject: CCL:G: Using of Partition Functions for Rate constant Calculation Message-Id: <-48977-130720173651-10165-nHCzSi2HiWVWoDdFG5ufgA-.-server.ccl.net> X-Original-From: "Adel Reisi" Date: Sat, 20 Jul 2013 17:36:50 -0400 Sent to CCL by: "Adel Reisi" [areisi]*[kashanu.ac.ir] For calculation of rate constants, partition function is necessary, but I doubt what partition function in Gaussian output (Total (Bot)or Total (V=0))must be used? Please help to me. Thanks From owner-chemistry@ccl.net Sat Jul 20 18:35:01 2013 From: "Radoslaw Kaminski rkaminski.rk() gmail.com" To: CCL Subject: CCL: Generating neighboring molecule Message-Id: <-48978-130720012659-8392-5vKyCiQ684sKE273CwxLpQ:+:server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=001a1132f610ce15c004e1eab0b9 Date: Sat, 20 Jul 2013 01:26:11 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk*o*gmail.com] --001a1132f610ce15c004e1eab0b9 Content-Type: text/plain; charset=ISO-8859-1 Hi Bradley, You could also use our very simple CLUSTERGEN program. It reads CIF files and produces various input files. I did also implemented a new feature that automatically find dimers in the crystal and produces XYZ files. I will update the version on the web where is it available. Here is the link: http://www.chem.uw.edu.pl/people/RKaminski/software.html Regards, Radek On 17 July 2013 21:56, Bradley K Welch bwelch5 .. slu.edu < owner-chemistry]=[ccl.net> wrote: > > Sent to CCL by: "Bradley K Welch" [bwelch5]-[slu.edu] > Dear All, > > I have a .cif of a molecule from the literature. I want to do a > calculation on > its dimer. The authors give the transformation to generate the neighboring > molecule (the .cif does not include the dimer). What software could I use > to > help me generate the molecule? I have chemcraft and jmol but any other > program > suggested works would be fine as well. > > Bradley Welch> > > -- Radoslaw Kaminski, Ph.D. Eng. Postdoctoral Research Associate Department of Chemistry, University at Buffalo The State University of New York 747 Natural Sciences Complex Buffalo, NY 14260-3000, USA http://www.chem.uw.edu.pl/people/RKaminski/ --001a1132f610ce15c004e1eab0b9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Bradley,

You could also use our very simple CLUSTERGEN program. I= t reads CIF files and produces various input files. I did also implemented = a new feature that automatically find dimers in the crystal and produces XY= Z files. I will update the version on the web where is it available. Here i= s the link:

ht= tp://www.chem.uw.edu.pl/people/RKaminski/software.html

Regards,<= br>
Radek


On 17 July 2013 21:56, B= radley K Welch bwelch5 .. slu.edu <o= wner-chemistry]=[ccl.net> wrote:

Sent to CCL by: "Bradley =A0K Welch" [bwelch5]-[slu.edu]
Dear All,

I have a .cif of a molecule from the literature. I want to do a calculation= on
its dimer. The authors give the transformation to generate the neighboring<= br> molecule (the .cif does not include the dimer). What software could I use t= o
help me generate the molecule? I have chemcraft and jmol but any other prog= ram
suggested works would be fine as well.

Bradley Welch



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--
Radosl= aw Kaminski, Ph.D. Eng.
Postdoctoral Research Associate
Department of= Chemistry, University at Buffalo
The State University of New York
74= 7 Natural Sciences Complex
Buffalo, NY 14260-3000, USA
http://www.chem.uw.edu.pl/people/RKaminski/
--001a1132f610ce15c004e1eab0b9-- From owner-chemistry@ccl.net Sat Jul 20 19:19:00 2013 From: "Bradley Welch bwelch5-*-slu.edu" To: CCL Subject: CCL:G: Using of Partition Functions for Rate constant Calculation Message-Id: <-48979-130720191731-21747-Zv9rANGh3iGFFqKRrWpOxQ-*-server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=089e0141a1fc45931304e1f9a562 Date: Sat, 20 Jul 2013 18:17:22 -0500 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5.{}.slu.edu] --089e0141a1fc45931304e1f9a562 Content-Type: text/plain; charset=ISO-8859-1 Adel, Read the Gaussian whitepaper on thermochemistry with the program. They have a section on rate constants. http://www.gaussian.com/g_whitepap/thermo.htm On Sat, Jul 20, 2013 at 4:36 PM, Adel Reisi areisi%%kashanu.ac.ir < owner-chemistry{}ccl.net> wrote: > > Sent to CCL by: "Adel Reisi" [areisi]*[kashanu.ac.ir] > For calculation of rate constants, partition function is necessary, but I > doubt > what partition function in Gaussian output (Total (Bot)or Total > (V=0))must be > used? Please help to me. Thanks> > > -- Bradley Welch Saint Louis University Monsanto Hall Room 218 --089e0141a1fc45931304e1f9a562 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


On Sat, Jul 20, 2013 at 4:36 PM= , Adel Reisi areisi%%kashanu.ac.ir <owner-chemistry{}ccl.net> wrote:

Sent to CCL by: "Adel =A0Reisi" [areisi]*[kashanu.ac.ir]
For calculation of rate constants, partition function is necessary, but I d= oubt
=A0what partition function in Gaussian output (Total (Bot)or Total (V=3D0))= must be
=A0used? Please help to me. Thanks



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--
Bradley Welc= h
Saint Louis University
Monsanto Hall Room 218
--089e0141a1fc45931304e1f9a562--