From owner-chemistry -8 at 8- ccl.net Fri Nov 5 04:30:01 2010 From: "Dillen, Jan jlmd(!)sun.ac.za JLMD(!)sun.ac.za" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-43079-101105023753-19823-VkVgULrYi8DiPPf+RZ0e8A^^^server.ccl.net> X-Original-From: "Dillen, Jan " Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Nov 2010 08:37:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" Henry, 1. Animate the vibrations associated with the negative frequencies. 2. Decide from the movements of the atoms which modes have nothing to do with the reaction coordinate that you associate with the SN2 reaction. 3. Distort the atoms with the eigenvectors of the unwanted negative frequencies (meaning that you add the eigenvector times a constant [0.5 usually works fine] to the coordinates). Alternatively, if these movements are e.g. rotations of alkyl groups, you can give them a kick by changing the torsion angles with e.g. MOLDEN. 4. Re-optimize with Opt(TS, NoEigenTest). Jan -----Original Message----- > From: owner-chemistry+jlmd==sun.ac.za/./ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za/./ccl.net] On Behalf Of Henry Martinez hmartine * gmail.com Sent: 04 November 2010 22:00 To: Dillen, Jan Subject: CCL:G: Transition state calculation Sent to CCL by: "Henry Martinez" [hmartine###gmail.com] Hi everyone, I am running a Transition state calculation in Gaussian 03, using a b3lyp/ 3-21g freq opt:(ts, qst3,noigentest) for a simple SN2 over a primary alkyl halide (so I can start with something small then move to my systems). I am getting 2, some times 3 negative frequencies. I supposed to get only one. The transition state looks fine, I mean, it makes senses for this simple rx. But I would like to know how can I fix this problem of having more than one negative frequency. Thanks a lot for the help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt