From owner-chemistry@ccl.net Tue Dec 30 00:18:01 2008 From: "Marco Zimmer-De Iuliis miuliis^chem.utoronto.ca" To: CCL Subject: CCL:G: NBO questions using Gaussian03 Message-Id: <-38376-081229151852-27158-hSeqCdGRdtsQeb5E4Ov3nw|-|server.ccl.net> X-Original-From: "Marco Zimmer-De Iuliis" Date: Mon, 29 Dec 2008 15:18:48 -0500 Sent to CCL by: "Marco Zimmer-De Iuliis" [miuliis * chem.utoronto.ca] Hello. I am starting to use the NBO package that comes with Gaussian03 and I have some questions. There is a section in the output file under "NATURAL BOND ORBITAL ANALYSIS" where it shuffles electrons around between BD/LP (CR remains the same), and it stops at "0.21 deviation". I believe that this is the point where the program decides where it may change things with the structure. My questions are as follows: 1. What determines this value of "0.21"? 2. Why did it decide this was the best Lewis structure? 3. Is a deviation of 0.21 good enough? That is, what is an acceptable value for the deviation? Thank you in advance and I am looking forward to hearing any input as I am eager to understand this. Marco Ph. D Candidate University of Toronto From owner-chemistry@ccl.net Tue Dec 30 13:12:01 2008 From: "Mihaly Mezei Mihaly.Mezei===mssm.edu" To: CCL Subject: CCL: Looking for a Monte Carlo simulation package for... Message-Id: <-38377-081229220121-28642-lFz5rIvY5Yc2UhtpVY6OjQ.:.server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 29 Dec 2008 22:01:03 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei^^^mssm.edu] Have a look at MMC: http://inka.mssm.edu/~mezei/mmc Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Tue Dec 30 16:49:00 2008 From: "Roman D Gorbunov rgorbuno|a|aecom.yu.edu" To: CCL Subject: CCL:G: Transition Dipole Moments in Gaussian Message-Id: <-38378-081230164732-4723-SrDqcA0DjTO4zHRbnOO8ag**server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Tue, 30 Dec 2008 16:47:29 -0500 Sent to CCL by: "Roman D Gorbunov" [rgorbuno**aecom.yu.edu] Dear CCL Subscribers, I calculate transition dipole moments by Gaussian. I take the transition dipole moments from the following part of the Gaussian output: Dipole derivatives wrt mode 1: -1.63752D-01 7.85856D-01 -1.21676D+00 Dipole derivatives wrt mode 2: 1.93037D-02 -2.30767D-01 -5.74025D-01 Dipole derivatives wrt mode 3: 1.43907D-01 8.46225D-01 1.16777D+00 .... Then I plot these vectors together with the atoms of the system, given in the "Standard orientation" frame. When I compare this picture with those obtained by the Gaussian viewer (gview) I have a disagreement in the orientations of the transition dipoles. Does anybody know the possible reason of that disagreement? I heard that the components of the transition dipole moments are given in the standard orientation frame. But it is in a contradiction with what I observe. I also tried to use the input orientation and I still have the disagreement with the picture given by the gview. Thank you in advance for any help, Roman From owner-chemistry@ccl.net Tue Dec 30 18:57:00 2008 From: "Jianping Wang jwang . iccas.ac.cn" To: CCL Subject: CCL:G: Transition Dipole Moments in Gaussian Message-Id: <-38379-081230184430-7922-r1xM0PObESvsYnftDmXmiw_-_server.ccl.net> X-Original-From: Jianping Wang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 31 Dec 2008 07:13:23 +0800 MIME-Version: 1.0 Sent to CCL by: Jianping Wang [jwang::iccas.ac.cn] It is the electric components that you should use (a few lines below dipole derivatives). They are similar, but different. Roman D Gorbunov rgorbuno|a|aecom.yu.edu wrote: > Sent to CCL by: "Roman D Gorbunov" [rgorbuno**aecom.yu.edu] > Dear CCL Subscribers, > > I calculate transition dipole moments by Gaussian. I take the transition dipole moments from the following part of the Gaussian output: > Dipole derivatives wrt mode 1: -1.63752D-01 7.85856D-01 -1.21676D+00 > Dipole derivatives wrt mode 2: 1.93037D-02 -2.30767D-01 -5.74025D-01 > Dipole derivatives wrt mode 3: 1.43907D-01 8.46225D-01 1.16777D+00 > .... > > Then I plot these vectors together with the atoms of the system, given in the "Standard orientation" frame. When I compare this picture with those obtained by the Gaussian viewer (gview) I have a disagreement in the orientations of the transition dipoles. > > Does anybody know the possible reason of that disagreement? I heard that the components of the transition dipole moments are given in the standard orientation frame. But it is in a contradiction with what I observe. I also tried to use the input orientation and I still have the disagreement with the picture given by the gview. > > Thank you in advance for any help, > > Roman> > > > >