From owner-chemistry@ccl.net Thu Aug 8 14:45:01 2013 From: "Johannes Johansson johjo76|*|gmail.com" To: CCL Subject: CCL:G: Large zero-point effect Message-Id: <-49067-130808095100-1523-hqU1GQ/Hoz+7RZoplGdmDQ:-:server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=e89a8f83937140fc6304e36ff2ed Date: Thu, 8 Aug 2013 15:50:52 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76[a]gmail.com] --e89a8f83937140fc6304e36ff2ed Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear all, how large can the zero point vibrational effect be for the activation energy of hydrogen atom transfer? In my experience it is a few (3-4) kcal/mol and in some cases, with rather activated substrates like dihydroanthracene, I found zero point effects of up to 6-7 kcal/mol, when the H-atom was transferred from a C-H bond to an iron-oxo group. Now I am calculating activation energies for hydrogen atom transfer reactions between hydrocarbons and polyaromatic systems containing a metal ion and Schr=C3=B6dingers Jaguar gives me zero point effects of nearly 20 kcal/mol (b3lyp/lacvp*)! (I always used Gaussian for ZPE before, does anyone have any experience in how Jaguar and Gaussian compares regarding ZPE?) The zero point effect on the reaction energy is small (2 kcal/mol), meaning that is is nearly the same for reactant and product. It is only in the transition state that it is much smaller, giving a large effect on the activation enthalpy. The stationary points are fully optimized and "confirmed", i.e. the reactant having no imaginary frequencies and the TS one. Maybe this is not unusual at all for this type of systems but in the ones I have worked with before ZPE were always much smaller. Therefore, I would like to hear how large ZPE you have seen for activation energies of (hydrogen) atom transfer reactions. Regards, Johannes --=20 Adam Johannes Johansson Ph.D., M.Sc. Linkedin: http://se.linkedin.com/pub/adam-johannes-johansson/22/209/395 ***************************************************************************= *********** Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish Pharmacist, Humanist and Pioneer Quantum Chemist: http://pubs.acs.org/doi/abs/10.1021/ed300024g ***************************************************************************= *********** --e89a8f83937140fc6304e36ff2ed Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear all, how large can the zero point vibrational effect = be for the activation energy of hydrogen atom transfer?

= In my experience it is a few (3-4) kcal/mol and in some cases, with rather = activated substrates like dihydroanthracene, I found zero point effects of = up to 6-7 kcal/mol, when the H-atom was transferred from a C-H bond to an i= ron-oxo group.

Now I am calculating activation energies for= hydrogen atom transfer reactions between hydrocarbons and polyaromatic sys= tems containing a metal ion and Schr=C3=B6dingers Jaguar gives me zero poin= t effects of nearly 20 kcal/mol (b3lyp/lacvp*)!

(I always used Gaussian for ZPE before, does anyone hav= e any experience in how Jaguar and Gaussian compares regarding ZPE?)
<= div>
The zero point effect on the reaction energy is small (2= kcal/mol), meaning that is is nearly the same for reactant and product. It= is only in the transition state that it is much smaller, giving a large ef= fect on the activation enthalpy.

The stationary points are fully optimized and "con= firmed", i.e. the reactant having no imaginary frequencies and the TS = one.

Maybe this is not unusual at all for this typ= e of systems but in the ones I have worked with before ZPE were always much= smaller. Therefore, I would like to hear how large ZPE you have seen for a= ctivation energies of (hydrogen) atom transfer reactions.=C2=A0

Regards, Johannes

--
Adam Johan= nes Johansson
Ph.D., M.Sc.
Linkedin: http://se.linke= din.com/pub/adam-johannes-johansson/22/209/395
***************************************************************************= ***********
Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swed= ish Pharmacist, Humanist and Pioneer Quantum Chemist: http://pubs.acs.org/= doi/abs/10.1021/ed300024g
***************************************************************************= ***********




--e89a8f83937140fc6304e36ff2ed-- From owner-chemistry@ccl.net Thu Aug 8 15:20:01 2013 From: "George Fitzgerald George.Fitzgerald]~[accelrys.com" To: CCL Subject: CCL: Amorphous Cells in Materials Studio Message-Id: <-49068-130808101029-3081-MRqZ3DPRKDgZdQBlh1DqpQ(_)server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 8 Aug 2013 07:10:13 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald^accelrys.com] Right-click on the background behind the structure to open the context menu. Select "Display style." Open the Lattice tab where you can set the display range. In future, I recommend sending Materials Studio questions to Accelrys.community.com. George Fitzgerald, Ph.D. George.Fitzgerald{=}accelrys.com Advisory Scientist Accelrys, Inc. 5005 Wateridge Vista Dr San Diego CA 92121 +1 858 799 5360 (office) +1 858 692 8722 (mobile) -----Original Message----- > From: owner-chemistry+gfitzgerald==accelrys.com{=}ccl.net [mailto:owner-chemistry+gfitzgerald==accelrys.com{=}ccl.net] On Behalf Of Jackeline Coelho Oliveira jacke_ufrj-*-hotmail.com Sent: Wednesday, August 07, 2013 8:49 AM To: George Fitzgerald Subject: CCL: Amorphous Cells in Materials Studio Sent to CCL by: "Jackeline Coelho Oliveira" [jacke_ufrj!A!hotmail.com] Dear researchers, I have a doubt in visualizing more than one unit cell in material studio. In my case I am studying a dimer, where each monomer goes to oposite sides of the box in the molecular dynamics calculation. It is clear to me that each monomer unit is interacting with the other, but not in the same cell unit. Because of this I need to know how can I visualize more than one cell unit. Kind Regards, Jackelinehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Aug 8 17:49:00 2013 From: "Laura Gonzalez lcgonzz7:-:tamu.edu" To: CCL Subject: CCL: Gaussview data to ro-vibrational plot Message-Id: <-49069-130808151349-26393-Usu0dEtqcuEEaU8x86m3Dw,server.ccl.net> X-Original-From: "Laura Gonzalez" Date: Thu, 8 Aug 2013 15:13:47 -0400 Sent to CCL by: "Laura Gonzalez" [lcgonzz7]~[tamu.edu] I have been working on taking data collected from Gaussview and creating Vibrational/Ro-vibrational plots. The data collected contains the Frequency data and the vibrot data. I have been trying to do this for about a week now and I have not been able to determine how to use the data to create these plots. Can anyone help with this?