From owner-chemistry@ccl.net Thu Nov 12 07:04:01 2015 From: "John M. Simmie john.simmie[-]nuigalway.ie" To: CCL Subject: CCL:G: Transition state location Message-Id: <-51875-151112070313-7299-WX+Gj2xr7YtQDCsHIKW0fQ|*|server.ccl.net> X-Original-From: "John M. Simmie" Date: Thu, 12 Nov 2015 07:03:12 -0500 Sent to CCL by: "John M. Simmie" [john.simmie^^nuigalway.ie] Saied: If A + B ==> C + D + E is a genuine termolecular reaction then yes you have to include all products in the QST2 calculation, appropriately numbered otherwise Gaussian gets confused. But are you sure that your reaction is termolecular? These are quite rare. John M. Simmie::School of Chemistry::NUI Galway, Ireland H91 TK33 From owner-chemistry@ccl.net Thu Nov 12 11:03:01 2015 From: "Fedor Goumans goumans|scm.com" To: CCL Subject: CCL: Transition state location Message-Id: <-51876-151112033838-13027-v+EhYrnItyNRa4bBgdWFlg|,|server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 12 Nov 2015 09:38:35 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans],[scm.com] Dear Saied, It may be that A + B -> P1 + P2 + P3 is not a one-step mechanism. I.e. in your case, CO2 and H2O would be split off later. In that case you should try to map out the entire reaction pathway and find out the rate-limiting step. E.g. A + B -> I(1) -> I(2) + CO2 -> P + CO2 + H2O. You should try to locate the TS for each of these steps. For a synchronous transfer (or string-based method) you should indeed define the atom mapping between the reactants and the (intermediate) product(s), for each step. Hope this helps, Best wishes, Fedor On 11/11/2015 11:13 PM, Saied Mohammed Soliman saied11soliman[]gmail.com wrote: > Sent to CCL by: "Saied Mohammed Soliman" [saied11soliman- -gmail.com] > I need to know the possibility of doing QST2 calculations to locate the > transition state for reaction between two reactants system that produce one > product + side products? > As usual in QST2, the reactants and product should be defined and they must > have the same atom numbering sequence. my reactions is > > A + B-------- product + CO2 + H2O > > so I had to draw the reactants and product to keep all atoms with the same > sequence in the input. My question, Is the presence of these side products > affect the accuracy of the transition state calculation? > Should I ignore them in the calculations (I doubt)? > > Could any one help me ? > > Thanks > > Saied> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam