From owner-chemistry@ccl.net Sat Jul 29 03:54:00 2006 From: "Neeraj Misra misraneeraj]*[gmail.com" To: CCL Subject: CCL:G: vibrational frequencies Message-Id: <-32295-060729034443-15080-qAqr/j2YqMV0PfJ8v0t9Ng|server.ccl.net> X-Original-From: "Neeraj Misra" Date: Sat, 29 Jul 2006 03:44:43 -0400 Sent to CCL by: "Neeraj Misra" [misraneeraj~~gmail.com] I want Help in the folowing case. HOW TO READ THE GAUSSIAN VIBRATIONAL FREQUENCY OUTPUT WHICH WE GET AFTER RUNNING A CALCULATION GIVING THE OPTION OPT+FREQ .THE PROBLEM IS HOW TO IDENTIFY THE CORRESPONDING MODE AT THAT PARTICULAR FREQUENCY IN THE GAUSSIAN OUTPUT. Any help in this regard would be acknowleged. Thanks in advance. neeraj From owner-chemistry@ccl.net Sat Jul 29 11:09:00 2006 From: "Vincent Xianlong Wang xloongw+*+yahoo.com" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32296-060729110757-31953-UeiMiEo8EMuEkxIrnAwoQA::server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 29 Jul 2006 08:07:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw|yahoo.com] Hi Daria, Why not do potential energy surface scan with respect to the rotation? To do this, use the Geom=ModRedundant to fix the dihedral of the rotation and optimize the rest of moleucles. Once you have the PES, you may perform a normal mode analysis at its transition state. Hope this helps. Best regards, Vincent --- "Daria Khvostichenko dkhvosti%x%uiuc.edu" wrote: > Sent to CCL by: "Daria Khvostichenko" > [dkhvosti|,|uiuc.edu] > Dear CCL subscribers, > > Does anybody know how to obtain a transition state > structure for ethylene rotation about the double > bond? I have tried QST2 and QST3 optimizations; they > converge to the same structure, but frequency > analysis of the output structure does not show any > imaginary frequencies. Berny TS optimization does > not converge (it runs into structures with two > imaginary frequencies). When I used > opt=(ts,noeigentest,calcfc,EF) it converged to the > same structure as QST2 and QST3. I did calculations > with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) methods; > the results are more or less identical for both > basis sets. > > Thank you in advance, > > Daria > > dkhvosti-.-uiuc.edu > > Daria Khvostichenko > Postdoctoral Research Associate > Department of Chemistry > Roger Adams Laboratory, 23-5 > 600 S. Mathews ave., MC-712 > University of Illinois > Urbana, IL 61801 > 217-244-2102; 217-244-3186 (fax) > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the {} > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Jul 29 12:18:00 2006 From: "Sergio Emanuel Galembeck segalemb\a/usp.br" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32297-060729121707-28050-7dTr0ypoI29Ksm/XxS3uXg(!)server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 29 Jul 2006 13:17:02 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb!A!usp.br] Dear Daria, The transition state of the rotation of ethylene is a biradical, one single electron in each p(pi) orbital of a carbon. Best regards, Sergio Citando "Daria Khvostichenko dkhvosti%x%uiuc.edu" : > Sent to CCL by: "Daria Khvostichenko" [dkhvosti|,|uiuc.edu] > Dear CCL subscribers, > > Does anybody know how to obtain a transition state structure for ethylene > rotation about the double bond? I have tried QST2 and QST3 optimizations; > they converge to the same structure, but frequency analysis of the output > structure does not show any imaginary frequencies. Berny TS optimization does > not converge (it runs into structures with two imaginary frequencies). When I > used opt=(ts,noeigentest,calcfc,EF) it converged to the same structure as > QST2 and QST3. I did calculations with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) > methods; the results are more or less identical for both basis sets. > > Thank you in advance, > > Daria > > dkhvosti-.-uiuc.edu > > Daria Khvostichenko > Postdoctoral Research Associate > Department of Chemistry > Roger Adams Laboratory, 23-5 > 600 S. Mathews ave., MC-712 > University of Illinois > Urbana, IL 61801 > 217-244-2102; 217-244-3186 (fax)> > > > From owner-chemistry@ccl.net Sat Jul 29 14:03:00 2006 From: "Tapas Kar tapaskar*cc.usu.edu" To: CCL Subject: CCL:G: vibrational frequencies Message-Id: <-32298-060729135207-17388-z0lVAhkLMUy769J+MWtl3g]_[server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Sat, 29 Jul 2006 11:52:04 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar~~cc.usu.edu] Hello, Use Molden to visualize modes. Gaussview, Xvibs etc are other options. Thanks Tapas -----Original Message----- > From: owner-chemistry^_^ccl.net [mailto:owner-chemistry^_^ccl.net] Sent: Saturday, July 29, 2006 2:01 AM To: Kar, Tapas Subject: CCL:G: vibrational frequencies Sent to CCL by: "Neeraj Misra" [misraneeraj~~gmail.com] I want Help in the folowing case. HOW TO READ THE GAUSSIAN VIBRATIONAL FREQUENCY OUTPUT WHICH WE GET AFTER RUNNING A CALCULATION GIVING THE OPTION OPT+FREQ .THE PROBLEM IS HOW TO IDENTIFY THE CORRESPONDING MODE AT THAT PARTICULAR FREQUENCY IN THE GAUSSIAN OUTPUT. Any help in this regard would be acknowleged. Thanks in advance. neerajhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Jul 29 23:55:00 2006 From: "Wai-To Chan chan.:.curl.gkcl.yorku.ca" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32299-060729235043-17468-hdmZkoUux/sNt3uqlXp7mw-*-server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sat, 29 Jul 2006 23:53:48 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan]![curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<<<<<<<, Does anybody know how to obtain a transition state structure for ethylene rotation about the double bond? I have tried QST2 and QST3 optimizations; they converge to the same structure, but frequency analysis of the output structure does not show any imaginary frequencies. Berny TS optimization does not converge (it runs into structures with two imaginary frequencies). When I used opt=(ts,noeigentest,calcfc,EF) it converged to the same structure as QST2 and QST3. I did calculations with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) methods; the results are more or less identical for both basis sets. >>>>>>>>>>>> I assume the correct TS geometry is in the middle of the minimum potential energy pathway for the twisting of the CH2 group from the equilibrium planar structure. In that case there is no need to use any of the TS search methods. To obtain the TS structure I will first optimize the equilibrium geometry of C2H2. I will then twist one of the CH2 group by 90 deg in the Z-Matrix input. Optimization (NOT opt=ts) of the twisted strcuture withing the symmetry constraint will give you the correct TS. Without trying out the calculation I can't tell if the ub3lyp method you used would give a second imaginary frequency at the correct geometry. Chance is that the spin contamination could distort the geometry from the correct symmetry. I would compare the results from optimization using UB3LYP on a broken-symmetry wavefunction (one obtained from guess=mix stable=opt NOSYMM) to the geometry from RB3LYP which is unstable toward spin symmetry breaking for the TS. Potential surface of the twisting of ethylene is one of the study cases described in this recent study: "The spin-flip approach within time-dependent density functional theory: Theory and applications to diradicals" Shao, Head-Gordon and Krylov, J. Chem. Phys. vol 118 pg 4807 (2003)" You will find a comparison of the ethylene twisting potential obtained from RDFT, UDFT and SF-DFT. It is an interesting paper to check out. Wai-To Chan