From owner-chemistry@ccl.net Thu Oct 27 13:21:00 2011 From: "=?ISO-8859-15?Q?Markus_Sch=FCtz?= schuhtib!A!physik.tu-berlin.de" To: CCL Subject: CCL: excited state TDDFT Message-Id: <-45749-111027130553-17902-XbMpU7owIELDtdQTjohdrw+/-server.ccl.net> X-Original-From: =?ISO-8859-15?Q?Markus_Sch=FCtz?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 27 Oct 2011 19:05:33 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-15?Q?Markus_Sch=FCtz?= [schuhtib::physik.tu-berlin.de] Hello, I tried to calculate the second excited state of adamantane cation (opt and freq) in TDDFT ( # TD(root=2,NStates=40) b3lyp/cc-pvtz opt sym=loose). Unfortunately the calculation ended with 'You need to solve for more vectors in order to follow this state.' So I set the keyword for NStates first to 10 then to 25 and finally also to 40, but the message is the same. I tried another way: From a cis calculation I wanted to get the force contants using them for the TDDFT calculation. But the cis calculation also ended with the message above (NStates=25). Is it useful to set NStates much higher or is there another way to do the TDDFT calculation? By the way, I also tried a cis calculation (# CIS=(Root=2, NStates=40) hf/cc-pvtz opt(calcFC) freq sym=loose). This delivers the message 'Tx not orthogonal to T.' I couldn't find any solution for this problem. Regards, Markus -- Markus Schütz Institut für Optik und Atomare Physik AG Dopfer Sekretariat EW 3-1 Technische Universität Berlin Hardenbergstraße 36 10623 Berlin Tel +49 (0)30 314 29808 Raum EW 337 From owner-chemistry@ccl.net Thu Oct 27 18:27:01 2011 From: "Arne Dieckmann adieckma|-|googlemail.com" To: CCL Subject: CCL:G: DFT and dispersion Message-Id: <-45750-111027182542-18148-bQVNL7jnqiiDfdA/hUKhvg^server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Oct 2011 15:25:32 -0700 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma()googlemail.com] Dear all, I am currently dealing with structures which require to compensate for the missing dispersion corrections in DFT. Therefore, I have optimized all geometries with M062X/6-31+G(d,p) as this functional already takes into account medium-ranged dispersion interactions (I know that a larger basis set would be desirable, but the systems size prevents this). However, my suspicion is that also long-ranged dispersion effects are not negligible for my structures. As a consequence, I would like to apply some kind of DFT-DX (X=2, 3) correction by Grimme. Can you tell by your experience if DFT-D2 would change M06-2X geometries significantly or if an additional single point correction to the energy is sufficient? Does it really make sense to add DFT-D3 corrections to M062X energies? Which other functional should I use (B97-D?)? Please note that I am limited to using Gaussian 09 which means I can only use DFT-D2 for optimizations. Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab University of California, Los Angeles email: adieckma#googlemail.com From owner-chemistry@ccl.net Thu Oct 27 19:02:01 2011 From: "=?UTF-8?B?VmxhZGltaXIgRWxpc2V2c2tpeQ==?= vladimir.elisevsky(-)mail.ru" To: CCL Subject: CCL: =?UTF-8?B?UHJlZGljdGluZyBiaW5kaW5nIHRvIG1vbGVjdWxlcyBhZHNvcmJlZCAgb24g?= =?UTF-8?B?YSBzbGlkZQ==?= Message-Id: <-45751-111027174538-9708-nsoB1ZKJYpcdSYSVns4vlQ||server.ccl.net> X-Original-From: =?UTF-8?B?VmxhZGltaXIgRWxpc2V2c2tpeQ==?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 28 Oct 2011 01:45:29 +0400 Mime-Version: 1.0 Sent to CCL by: =?UTF-8?B?VmxhZGltaXIgRWxpc2V2c2tpeQ==?= [vladimir.elisevsky]*[mail.ru] Hi, Is it possible to predict relative binding affinities of a small molecule to different RNA olygonucleotides that are bound (adsorbed) on a nitrocellulose slide? Can you share your thoughts or references? Thank you very much Vladimir From owner-chemistry@ccl.net Thu Oct 27 22:21:00 2011 From: "Dr. Lars Goerigk lars.goerigk{}chem.usyd.edu.au" To: CCL Subject: CCL:G: DFT and dispersion Message-Id: <-45752-111027202830-6322-gvYzmRPICXn7A6GVaHdnhA[A]server.ccl.net> X-Original-From: "Dr. Lars Goerigk" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Oct 2011 11:28:15 +1100 MIME-Version: 1.0 Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au] Dear Arne, M06-2X was fitted to noncovalently bound systems in their equilibrium geometries and due to that fit it somehow incorporates medium-range dispersion interactions. However, as also discussed in the literature, it is expected that the asymptotic long-range behavior is still not correct and that it can also benefit from dispersion corrections. On the issue DFT-D3 in combination with the Minnesota functionals you can refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those functionals were published and discussed. DFT-D2 parameters for the Minnesota functionals were published by the Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity, though, which still does not give the correct asymptotics, opposed to DFT-D3, where it was fixed to unity. If you have the Gaussian code available you could try to implement DFT-D3 (based on the code Stefan Grimme made available on his website). If you do not have the code, you would have to use DFT-D2. Please note that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D. That bug was fixed however and in Rev. B01 and higher you can now also use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2 paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86). You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you also get a printout to check, if the correct s6 value was applied. Other functionals are not supported and I do not know if it is possible to read in an s6 specified by the user (maybe you should contact the Gaussian support to find that out). IOp(3/124=1) adds the dispersion correction to any functional, but only with an s6=1, which is too large for the Minnesota functionals. If you can't use M06-2X, you could try TPSS in combination with D-corrections. Based on publications and my own experience, this gives very good structures. Another possibility would be to get ORCA, which is for free. I am not 100% sure if DFT-D3 is already implemented; have a look at the ORCA website for that. You could also check if other programs have already implemented DFT-D3. I hope these information could help you. With best wishes, Lars -- Dr. Lars Goerigk School of Chemistry The University of Sydney Sydney, New South Wales 2006 Australia