From owner-chemistry@ccl.net Thu May 28 01:08:00 2009 From: "Dipankar Roy dipankarroy++iitb.ac.in" To: CCL Subject: CCL:G: simple butane calculation. Rotation energy barrier. Gaussian Message-Id: <-39393-090528000715-23940-e5ohgswvS9bgfK0Plpc8jw-.-server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Thu, 28 May 2009 09:36:59 +0530 MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy:-:iitb.ac.in] Hi, Scan along PES will generate energy profile along variable(s) of your choice. Additionally you can use OPT=MODREDUNDANT option in Gaussion03. Please check G03 manual for further details on modredundant card. Hope this may work, Dipankar *********************************************** Dipankar Roy Computational Chemistry Group Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** On Thu, May 28, 2009 8:28 am, Henry Martinez hmartine\a/gmail.com wrote: > > Sent to CCL by: "Henry Martinez" [hmartine*gmail.com] > I would like to calculate with a good aprox. the Rotation energy barrier > for butane. So, I have to calculate the structure with the two methyl anti > (180), then 120 (eclipse), then 60 (Gauche), and finally 0 degrees > (eclipse). The question is: For each geometry I should calculate the > OPTIMIZATION using a keyword to do not change the geometry so much (I > think that at some point it will try to go to the anti geometry, dont?) or > I just calculate the energy for that particular geometry (I alredy tried > that but the results were not close, so may be I am missing something) . I > am using Gaussian 03, HF/6-31g*. Is there any other way to do it. Can > anyone explain me how to do it? > Thanks a lot> > > From owner-chemistry@ccl.net Thu May 28 06:09:01 2009 From: "Anindita De de.anindita++gmail.com" To: CCL Subject: CCL:G: questions about TDDFT calculation Message-Id: <-39394-090528055942-26589-cMw7IeFldX/VvJnlzQbL5w##server.ccl.net> X-Original-From: "Anindita De" Date: Thu, 28 May 2009 05:59:38 -0400 Sent to CCL by: "Anindita De" [de.anindita],[gmail.com] Hello, I am a beginner in TDDFT calculation. I want to generate a UV-visible spectram and I am using Gaussian 03 for the calculation. I have following question (i) how to calculate the percentage contribution of each transition in UV-Vis spectra ? (ii) right now I am using GaussSum programme to plot the spectra. Some time it gives contribution more that 100%. Is it correct? (iii)I want to do calculation for a dimeric system having two unpaired electron in each metal center. Is it better to do calculation considering closed shell system? I am really confused about these things. Please someone help me. Regards, Anindita From owner-chemistry@ccl.net Thu May 28 09:52:01 2009 From: "Noel M O Boyle baoilleach::gmail.com" To: CCL Subject: CCL:G: questions about TDDFT calculation Message-Id: <-39395-090528094719-21022-XSdmh3DlMr8UpzK6pPCMzA(0)server.ccl.net> X-Original-From: "Noel M O Boyle" Date: Thu, 28 May 2009 09:47:16 -0400 Sent to CCL by: "Noel M O Boyle" [baoilleach^gmail.com] Hello Anindita, You should probably use the latest version of GaussSum (2.1.6) to see whether the problem has been fixed. Regarding the general problem, it is not possible to accurately calculate the % contribution of each singly-excited configuration to a particular transition from the output of a Gaussian TDDFT calculation. As a result, the sum of the squares of the contributions will not add to 1.0 exactly. Note that this is not the case for the TDDFT implementations in several other QM programs (I don't recall the details). BTW, like many (but not all) software discussed on this list, GaussSum provides a mailing list for questions: gausssum-help::lists.sf.net Regards, Noel (developer of GaussSum) > "Anindita De de.anindita++gmail.com" wrote: > > Sent to CCL by: "Anindita De" [de.anindita],[gmail.com] > Hello, > > I am a beginner in TDDFT calculation. I want to generate a UV-visible spectram and I am using Gaussian 03 for the calculation. I have following question > > (i) how to calculate the percentage contribution of each transition in UV-Vis spectra ? > > (ii) right now I am using GaussSum programme to plot the spectra. Some time it gives contribution more that 100%. Is it correct? > > (iii)I want to do calculation for a dimeric system having two unpaired electron in each metal center. Is it better to do calculation considering closed shell system? > > I am really confused about these things. Please someone help me. > > Regards, > > Anindita > > From owner-chemistry@ccl.net Thu May 28 11:06:00 2009 From: "Jens Spanget-Larsen spanget---ruc.dk" To: CCL Subject: CCL:G: questions about TDDFT calculation Message-Id: <-39396-090528110327-20534-GIGYuCzkC9DeCGTO9S4Nrw%%server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 28 May 2009 17:03:29 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget%ruc.dk] Hello Noel and Anindita! Regarding Gaussian TD-DFT output: In case the TD calculation is based on a closed shell ground state representation, computation of the percentages is straight forward. If the printed coefficient is given by C, then the percentage is twice the square of C, i.e., 2*C^2. The factor 2 is due to the circumstance that Gaussian prints the coefficients of microstates, not spin-adapted configurations (if I understand correctly!). I use a small utility program to add the percentages, if larger than 10%, to the output file, see below. The situation is more complicated in the case of an unrestricted open-shell calculation, where this procedure will not work. Yours, Jens >--< ___________ Excitation energies and oscillator strengths: Excited State 1: Singlet-B1U 28.31005 1000/cm 353.23 nm f=1.9822 73 -> 74 0.64930 84% [ 1,-1 ] Excited State 2: Singlet-AG 35.42708 1000/cm 282.27 nm f=0.0000 72 -> 74 0.61806 76% [ 2,-1 ] 73 -> 75 -0.32572 21% [ 1,-2 ] Excited State 3: Singlet-B2U 36.18604 1000/cm 276.35 nm f=0.0002 69 -> 74 0.43019 37% [ 5,-1 ] 73 -> 76 0.51753 54% [ 1,-3 ] 73 -> 78 -0.21135 ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget=-=ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Noel M O Boyle baoilleach::gmail.com wrote: > Sent to CCL by: "Noel M O Boyle" [baoilleach^gmail.com] > Hello Anindita, > > You should probably use the latest version of GaussSum (2.1.6) to see whether the problem has been fixed. > > Regarding the general problem, it is not possible to accurately calculate the % contribution of each singly-excited configuration to a particular transition from the output of a Gaussian TDDFT calculation. As a result, the sum of the squares of the contributions will not add to 1.0 exactly. Note that this is not the case for the TDDFT implementations in several other QM programs (I don't recall the details). > > BTW, like many (but not all) software discussed on this list, GaussSum provides a mailing list for questions: gausssum-help[a]lists.sf.net > > Regards, > Noel (developer of GaussSum) > > > >> "Anindita De de.anindita++gmail.com" wrote: >> >> Sent to CCL by: "Anindita De" [de.anindita],[gmail.com] >> Hello, >> >> I am a beginner in TDDFT calculation. I want to generate a UV-visible spectram and I am using Gaussian 03 for the calculation. I have following question >> >> (i) how to calculate the percentage contribution of each transition in UV-Vis spectra ? >> >> (ii) right now I am using GaussSum programme to plot the spectra. Some time it gives contribution more that 100%. Is it correct? >> >> (iii)I want to do calculation for a dimeric system having two unpaired electron in each metal center. Is it better to do calculation considering closed shell system? >> >> I am really confused about these things. Please someone help me. >> >> Regards, >> >> Anindita >> >> >> > > > From owner-chemistry@ccl.net Thu May 28 12:10:01 2009 From: "aa aa|a|chemaxon.hu" To: CCL Subject: CCL: First call for papers: ChemAxon's 2009 US UGM and Training Day, September 15-16 and September 14, San Diego, California Message-Id: <-39397-090528120846-17505-djHQ9ISeOlAZ8QJvKJTNnQ()server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------080106060406020007060007" Date: Thu, 28 May 2009 18:08:32 +0200 MIME-Version: 1.0 Sent to CCL by: aa [aa|,|chemaxon.hu] This is a multi-part message in MIME format. --------------080106060406020007060007 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse cross postings Good day, ChemAxon's 2009 US User Group Meeting will be held on Tuesday and Wednesday, September 15 - 16th at the Catamaran Resort Hotel, San Diego. The meeting will preceded by a training day on September 14th. The User Group Meeting will feature oral and poster presentations from ChemAxon users, scientists, developers and partners as well as our usual range of social events to mix, speak and enjoy with staff and peers. We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is June 26th. To find out more and submit your abstract please visit: http://www.chemaxon.com/UGM/09/US/. The presentations archive, including previous meeting reports from Yvonne Martin and Wendy Warr is here: http://www.chemaxon.com/UGM/ugm_land.html. The Developer Workshop and End User Training day on June 2nd (2 tracks) will give hands on experience with ChemAxon functionality and best practices, for topics see : http://www.chemaxon.com/training/UGM0914.html We hope you can join us for what has proven to be a most interesting and enjoyable cheminformatics event. See you there. Alex -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------080106060406020007060007 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 
Excuse cross postings

Good day,

ChemAxon's 2009 US User Group Meeting will be held on Tuesday and Wednesday, September 15 - 16th at the Catamaran Resort Hotel, San Diego. The meeting will preceded by a training day on September 14th.

The User Group Meeting will feature oral and poster presentations from ChemAxon users, scientists, developers and partners as well as our usual range of social events to mix, speak and enjoy with staff and peers. 

We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is June 26th. To find out more and submit your abstract please visit: http://www.chemaxon.com/UGM/09/US/. The presentations archive, including previous meeting reports from Yvonne Martin and Wendy Warr is here: http://www.chemaxon.com/UGM/ugm_land.html.

The Developer Workshop and End User Training day on June 2nd (2 tracks) will give hands on experience with ChemAxon functionality and best practices, for topics see : http://www.chemaxon.com/training/UGM0914.html

We hope you can join us for what has proven to be a most interesting and enjoyable cheminformatics event.

See you there.

Alex
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce
--------------080106060406020007060007--