From owner-chemistry@ccl.net Mon Mar 2 15:10:02 2009 From: "Richard Tia richtiagh a gmail.com" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38727-090302150508-17721-2RDTRT2msSiDENvGEGjzDA(a)server.ccl.net> X-Original-From: "Richard Tia" Date: Mon, 2 Mar 2009 15:05:03 -0500 Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com] Hi everybody, To those who have some experience in computing reaction pathways, how would you rationalize a situation where the 'transition state' is lower in energy than the reactants? Is this a common occurrence? Could it be that the located TS is for a side reaction? Could the 'TS' just be an artifact? I would be very grateful if someone could offer some suggestions as to the chemistry involved here. Thanks in advance. Richard Tia KNUST Kumasi Ghana From owner-chemistry@ccl.net Mon Mar 2 15:44:01 2009 From: "Grady Scott Weston weston[]uiwtx.edu" To: CCL Subject: CCL: Call for Speakers -- ACS Fall National Meeting Message-Id: <-38728-090302150156-17207-up8sq4Sww+3xLge/1mgXww|server.ccl.net> X-Original-From: "Grady Scott Weston" Date: Mon, 2 Mar 2009 15:01:52 -0500 Sent to CCL by: "Grady Scott Weston" [weston%%uiwtx.edu] To all, We are organizing a COMP division symposium entitled Computational Chemistry in the Discovery & Development of Novel Anti-Infective Agents for the upcoming fall ACS National Meeting in Washington, DC (August 16-20, 2009). We invite those of you who work in the anti-infective area (antiviral, antibiotic, antifungal, etc.) to submit oral presentations for this symposium online at http://oasys.acs.org/ (under the COMP division link). Please note: the deadline for online abstract submissions is midnight (CST), Monday, March 16. Please feel free to contact either myself or one of the other symposium co-organizers, Dr. Ryszard Czerminski (ryszard.czerminski!^!astrazeneca.com) or Dr. John Manchester (John.Manchester!^!astrazeneca.com) if you have any questions or need any additional information. Thanks, gsw G. Scott Weston, R.Ph., Ph.D. Assistant Professor Dept. of Pharmaceutical Sciences Feik School of Pharmacy University of the Incarnate Word 4301 Broadway CPO #99 San Antonio, Texas 78209 210-883-1072 phone <-- NOTE: new phone # 210-822-1516 FAX <-- NOTE: new fax # weston!^!uiwtx.edu gscottweston!^!hotmail.com (external email for problems sending to campus email account) From owner-chemistry@ccl.net Mon Mar 2 16:21:01 2009 From: "David Gallagher gallagher.da_-_gmail.com" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38729-090302155203-12634-Y43T7QKpP4tzckOQKIuedQ..server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 02 Mar 2009 12:51:54 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da]~[gmail.com] Hi Richard, Assuming your reactants are kinetically stable (at a minimum on the potential energy surface), the likelihood is that an 'overlooked' intermediate(s) (minimum) lies between the reactants and the transition state you have found, i.e. it is a multi-step reaction. You would need to follow the intrinsic reaction coordinate (IRC) down each side of your transition state to find the 'missing' intermediate, then you would need to locate the other transition state(s) between the reactants and the intermediate. There are some notes on transition state modelling "Stategies for finding transition states (overview)" that discuss this issue, posted near the bottom of the following page http://www.cacheresearch.com/presentations.html . Although, the notes were based on using MOPAC with CAChe, the principles should apply to any quantum chemistry method. Good luck, David Gallagher CACheResearch.com At 12:05 PM 3/2/2009, Richard Tia richtiagh a gmail.com wrote: >Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com] >Hi everybody, > >To those who have some experience in computing reaction pathways, >how would you rationalize a situation where the 'transition state' >is lower in energy than the reactants? Is this a common occurrence? >Could it be that the located TS is for a side reaction? Could the >'TS' just be an artifact? > >I would be very grateful if someone could offer some suggestions as >to the chemistry involved here. Thanks in advance. > >Richard Tia >KNUST >Kumasi >Ghana From owner-chemistry@ccl.net Mon Mar 2 17:43:01 2009 From: "Roland Stote rstote^^^chimie.u-strasbg.fr" To: CCL Subject: CCL: Meeting of the GGMM May 5-7, 2009 Mittelwihr, Alsace France Message-Id: <-38730-090302172000-12169-pkzWBnxFKWBjKsteaQJt3w::server.ccl.net> X-Original-From: "Roland Stote" Date: Mon, 2 Mar 2009 17:19:57 -0500 Sent to CCL by: "Roland Stote" [rstote-$-chimie.u-strasbg.fr] Dear Colleagues, The thematic Group of Graphics and Molecular Modeling (GGMM) is organizing its 16th congress from May 5 to 7, 2009 in Mittelwihr (Alsace), France. The program is accessible online at http://ggmm2009.u-strasbg.fr/conference/program.html ** PLEASE NOTE THAT THIS CONFERENCE IS CONDUCTED IN FRENCH ** This meeting is oriented toward the international French speaking computational community and it brings together between 100 and 150 researchers from the public and industrial domains. The program includes plenary lectures, oral communications and poster presentations. The objective of the meeting is the address advances in the area of molecular simulations and their applications to complex systems. The themes covered in this year's meeting concern simulations of nucleic acids, proteins, sugars, membranes, as well as molecular interactions applied to pharmacology and supramolecular systems. The organizing committee, Annick Dejaegere, Pascal Auffinger, Joerg Baschnagel, Martin Spichty, Roland Stote and Antoine Taly