CCL:G: Transition state calculation

[Jean Jules FIFEN <julesfifen===gmail.com>]

If what suggest by Jan does not work, also try modifying the coordinates atom related to the last undesirable frequency mode and restart the computation. For that, you could use an atom editor from gausview, adding the opposite of amount of the higher deviations from zero on each coordinate.
If this does not also work, try doing the computation computing analytical hessian at the first point or at any point if the previous does not success.

J. Jules Fifen.

On 5 November 2010 07:37, Dillen, Jan jlmd(!)sun.ac.za JLMD(!)sun.ac.za <owner-chemistry .. ccl.net> wrote:

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


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Jean Jules FIFEN,
+237 75 21 61 39
+237 94 67 65 05
University of Ngaoundere,
PO.BOX 454 Ngaoundere