CCL:G: Transition state calculation

 Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]"
 <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 <jlmd/./sun.ac.za>
 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