From owner-chemistry@ccl.net Thu Oct 9 05:30:00 2014 From: "Robin Shannon R.Shannon_+_leeds.ac.uk" To: CCL Subject: CCL: Kinetic Modeling Software Message-Id: <-50570-141009052805-8893-XE9JAWaPxR/RScLgsZTP2g[#]server.ccl.net> X-Original-From: Robin Shannon Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 9 Oct 2014 10:27:57 +0100 MIME-Version: 1.0 Sent to CCL by: Robin Shannon [R.Shannon%%leeds.ac.uk] Hi Fred Unless you can prove the system is high pressure limited, I think a Master equation is the way to go. We have been exploring the possibility of energy transfer in the Solid state in MESMER so there may be ways around this but I would suggest doing some tests with a relatively inefficient bath gas first and if you can show you are high pressure limiting in this case, then you can be confident that the same would be true of solid parahydrogen. Feel free to email me personally (chmrsh,leeds.ac.uk) with more details of your system and I will offer what advice I can. Best wishes Robin ________________________________________ > From: owner-chemistry+chmrsh==leeds.ac.uk,ccl.net [owner-chemistry+chmrsh==leeds.ac.uk,ccl.net] On Behalf Of Fredrick Mutunga fredrick.mutunga!A!gmail.com [owner-chemistry,ccl.net] Sent: 08 October 2014 19:58 To: Shannon, Robin J Subject: CCL: Kinetic Modeling Software Guys, I greatly appreciate your suggestions. I have started looking into the MESMER program and want to fit experimental data, I will also look into the Polyrate for comparison. Robin, I agree the Van der Waal complexes plays an important role in the reaction and I hope MESMER does a good job in accounting their effects. The only worry is as you said the extreme temp = 2K and pressure = 3Torr in which the experiment was done and the fact that the bath is solid parahydrogen (matrix isolation). Do you have an idea on how to circumvent any potential problems? Thanks, Fred On Tue, Oct 7, 2014 at 3:16 AM, Robin Shannon R.Shannon[a]leeds.ac.uk > wrote: Sent to CCL by: Robin Shannon [R.Shannon,,leeds.ac.uk] Hi Fred Assuming you are considering a bimolecular reaction, at such low temperatures even an extremely weak VdW complex (5 kJ mol-1 or less) will be key to the kinetic behavior. Such a complex a weak complex may be difficult to optimize using ab initio methods but there will undoubtedly be one and at 2 K even the weakest of complexes will have a significant lifetime and at 3 torr most systems will be close to capture controlled. Polyrate will do a very good job of each calculation step, capture step using variable reaction coordinate method, and unimolecular (tunneling step) using multi dimensional tunneling. However at such low temperatures, given the VdW complex considerations I have describe above, transition state theory is not really appropriate and a full master equation approach should be used. MESMER (http://www.chem.leeds.ac.uk/mesmer.html) could be used to treat the system and if you have very accurate data from Polyrate calculations, transition state sums of states and tunneling coefficients could be read in. There may be problems going quite as low as 2 K in MESMER though for most systems with a weak well, you could get down to 10 K or below. Best wishes Robin ________________________________________ > From: owner-chemistry+chmrsh==leeds.ac.uk,,ccl.net [owner-chemistry+chmrsh==leeds.ac.uk,,ccl.net] On Behalf Of Fredrick M Mutunga fredrick.mutunga**gmail.com [owner-chemistry,,ccl.net] Sent: 06 October 2014 23:41 To: Shannon, Robin J Subject: CCL: Kinetic Modeling Software Sent to CCL by: "Fredrick M Mutunga" [fredrick.mutunga-x-gmail.com] Hello Guys, Could anyone suggest a suitable program/software which can calculate rate constants for low temperature reactions (temperature ~ 2.0K and pressure ~3.0 Torr)with tunneling corrections. Thanks, Fredhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt or use:E-mail to administrators: CHEMISTRY-REQUEST ~~ ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Oct 9 06:36:01 2014 From: "Emilio Xavier Esposito emilio.esposito:+:gmail.com" To: CCL Subject: CCL: Call for COMP abstracts at the Denver ACS meeting (spring 2015) Message-Id: <-50571-141009063200-31372-CDrr+cI6SDPtCHYfQbUzqg/./server.ccl.net> X-Original-From: Emilio Xavier Esposito Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 9 Oct 2014 06:31:34 -0400 MIME-Version: 1.0 Sent to CCL by: Emilio Xavier Esposito [emilio.esposito^-^gmail.com] Hi You are invited to submit your abstract to COMP's technical program for the Denver ACS meeting (March 22 - 26, 2015). The abstract submission now uses Meeting Abstracts Programming System (MAPS; maps.acs.org ) by ScholarOne™ and while it will be different we believe it provides a better user experience. Because MAPS is new to all of us, we strongly encouraged you to submit your abstract early for the Denver meeting. By submitting your abstract early, any problems can be handled quickly and easily. COMP abstract submission is currently open via MAPS and closes for COMP division submissions at 11pm Eastern Time on Tuesday, October 28, 2014. Brief instructions to help you submit your abstract using MAPS ( maps.acs.org ) is provided here: http://www.acscomp.org/meetings/presenter-information#TOC-Abstract-Submissions Member Contributed Symposia The Computers in Chemistry (COMP) Division is a multidisciplinary organization with members from almost every ACS division. Please consider submitting an abstract to: - Computational Study of Water - Drug Discovery (ADME/Tox, Informatics, Ligand-based, Methodology, Structural Bioinformatics & Target-base) - Materials Science - Membranes - Molecular Mechanics (Applications, Electrostatics & Polarization, Force Field Development, Methodology, and Proteins) - Quantum Chemistry (Applications, Methodology, and Quantum Dynamics & Monte Carlo Simulations) - The COMP Poster Session COMP Awards The deadline to apply for the graduate student and junior faculty awards is 11:59pm EDT Friday, October 10, 2014. Please follow their respective links for information on how to apply. Chemical Computing Group Excellence Award for Graduate Students http://www.acscomp.org/awards/chemical-computing-group-excellence-award OpenEye Outstanding Junior Faculty Award in Computational Chemistry http://www.acscomp.org/awards/the-comp-acs-outstanding-junior-faculty-award NVIDIA GPU Award Please note that the submission deadline for the NVIDIA GPU Award is 11pm Eastern Time on Tuesday, October 28, 2014. http://www.acscomp.org/awards/nvidia-gpu-award We hope that you are able to present your work at the Denver ACS meeting and thank you for your time! The COMP Programming Board Emilio Xavier Esposito Maciej Haranczyk Eric V Patterson Daniel Sindhikara Yufeng Jane Tseng Scott A Wildman PS: Do you want to organize a symposium within COMP at the San Diego (spring 2016) or Philadelphia (fall 2016) ACS National Meeting? Let us know! We'd be happy to hear your idea for a symposium! From owner-chemistry@ccl.net Thu Oct 9 21:55:00 2014 From: "Gustavo L.C. Moura gustavo.moura*ufpe.br" To: CCL Subject: CCL: Gn Methods and PCM Message-Id: <-50572-141009184726-14724-QWU6x1Tvs+R6UKNCO20a9w^server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Thu, 9 Oct 2014 18:47:25 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura-#-ufpe.br] Dear CCL Community, I want to obtain the energies of the lowest conformers of a molecule, with the formula C18H19BrO2Se, in solution with the polarizable continuum model. My question is: Do the Gn methods give reliable results when combined with the PCM method? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura