From owner-chemistry@ccl.net Wed Mar 8 03:17:00 2006 From: "Tamas E. Gunda tgunda2005#,#puma.unideb.hu" To: CCL Subject: CCL: ISIS format MDLSK Message-Id: <-31144-060308031550-3330-gzya+dlcXqwozYBaDCLQnQ,+,server.ccl.net> X-Original-From: "Tamas E. Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 8 Mar 2006 09:15:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas E. Gunda" [tgunda2005===puma.unideb.hu] You can download the description of mdl CT file formats from MDL's site: www.mdli.com Probably you have create an acoount and login to get to the download page. Tamas E. Gunda > Sent to CCL by: "Scott G Flicker" [sflicker2%x%earthlink.net] > I am looking for any information (reading/writing etc.) on the ISIS format MDLSK that is used by ISIS/Draw. > > Thanks > > > Scott Flicker > sflicker2[A]earthlink.net > > From owner-chemistry@ccl.net Wed Mar 8 06:05:01 2006 From: "Jacco van de Streek streek-.-ccdc.cam.ac.uk" To: CCL Subject: CCL: Cyclodextrins Message-Id: <-31145-060308060239-18193-duF2962qkoC5EMj4GI9nTw a server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 08 Mar 2006 10:18:25 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [streek[A]ccdc.cam.ac.uk] PankratovAN PankratovAN#,#chem.sgu.ru wrote: > Would you also advise on literature > references concerning X-ray diffraction > structure investigations of cyclodextrins? Dear Prof. Pankratov, you should be able to find these in the Cambridge Structural Database. http://www.ccdc.cam.ac.uk/products/csd/ I did a search for you, but there were too many hits to send to you (all of them hydrates), and it is better if you search the CSD for yourself, so that you can decide which entries are relevant for you. As far as I am aware, Russian academics have a licence for this database. Please contact support(-)ccdc.cam.ac.uk for further information. Best wishes, -- Dr Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom From owner-chemistry@ccl.net Wed Mar 8 09:07:00 2006 From: "Stefan Grimme grimmes..uni-muenster.de" To: CCL Subject: CCL:G: RI DFT approximation in G03 Message-Id: <-31146-060307093452-18936-Nw3lMYBxZGm/XS/b86tN0g(_)server.ccl.net> X-Original-From: Stefan Grimme Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 2 Mar 2006 15:00:46 +0100 MIME-Version: 1.0 Sent to CCL by: Stefan Grimme [grimmes---uni-muenster.de] Dear Pablo, for acetone PBE/SV(P) I get a RI-non-RI difference of 0.6 mEh with TURBOMOLE (old Coulomb aux-basis). Some time ago I did a RI-test with G03 that also produced a very, very big difference of some hundreds of mEh, so to me that sounds like a program bug. Regards Stefan ____________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes]|[uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ ____________________________________________________________ From owner-chemistry@ccl.net Wed Mar 8 09:56:01 2006 From: "Pablo Vitoria pablo.vitoria]![ehu.es" To: CCL Subject: CCL:G: RI DFT approximation in G03 Message-Id: <-31147-060308095401-27038-763Fwc+5a3NIk5Ahf+FWzQ[*]server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 8 Mar 2006 15:53:45 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria%%ehu.es] Dear Stefan, Thank you very much for your e-mail, which happens to be the first answer to my question. After sending the message to CCL I did some more testing, and I am quite sure that the problem happens with the normalization of the auxiliary density-fitting basis set, which G03 does wrong, probably a bug as you say since the other programs (ORCA, NWChem, ...) do it right. I asked Gaussian, Inc. about this but no answer yet. Thanks again Regards Pablo ----- Original Message ----- > From: "Stefan Grimme grimmes..uni-muenster.de" To: "Vitoria, Pablo " Sent: Wednesday, March 08, 2006 3:31 PM Subject: CCL:G: RI DFT approximation in G03 > Sent to CCL by: Stefan Grimme [grimmes---uni-muenster.de] > > Dear Pablo, > for acetone PBE/SV(P) I get a RI-non-RI difference of > 0.6 mEh with TURBOMOLE (old Coulomb aux-basis). > Some time ago I did a RI-test with G03 that also produced a very, very big > difference of some hundreds of mEh, so to me that sounds like a program > bug. > Regards > Stefan > ____________________________________________________________ > Prof. Dr. Stefan Grimme > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > Email:grimmes|a|uni-muenster.de > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > ____________________________________________________________> > From owner-chemistry@ccl.net Wed Mar 8 12:45:00 2006 From: "frisch%gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: [SPAM] CCL:G: RI DFT approximation in G03 Message-Id: <-31148-060308113727-9581-KGPirDs7pYFYj/qRh6cP8g|,|server.ccl.net> X-Original-From: frisch|a|gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 8 Mar 2006 10:40:18 -0500 Mime-Version: 1.0 Sent to CCL by: frisch[*]gaussian.com (Michael Frisch) On Wed, Mar 08, 2006 at 09:07:06AM -0500, Stefan Grimme grimmes..uni-muenster.de wrote: > Sent to CCL by: Stefan Grimme [grimmes---uni-muenster.de] > > Dear Pablo, > for acetone PBE/SV(P) I get a RI-non-RI difference of > 0.6 mEh with TURBOMOLE (old Coulomb aux-basis). > Some time ago I did a RI-test with G03 that also produced a very, very big > difference of some hundreds of mEh, so to me that sounds like a program bug. The way the coefficients for contracted fitting sets are specified in G03 is rather eccentric and accounts for this problem. You have to provide the coeficients of the unnormalized primitives, which is cumbersome. The easiest way to use density fitting in G03 is to use the option to automatically generate the fitting set from the AO basis, e.g. BLYP/6-31g*/Auto or HCTH/TZVP/Auto if you prefer the Alrichs basis sets. The automatically generated set gives similar accuracy to the Alrichs fittings sets for energies. Geometries and frequencies are virtually identical to the non-fitted results -- the differences are much, much smaller than the errors inherent in the method. So if you're doing a study using a pure DFT functional in G03, you should routinely use /Auto rather than doing the Coulomb problem without fitting. Fitting also speeds up TD-DFT with pure functionals. TD-DFT results are a lot better with hybrid functionals, but for medium to large molecules it's often faster to do the pure calculation first as a guess for the hybrid, e.g. BLYP/Aug-CC-pVTZ/Auto TD followed by B3LYP/Aug-CC-pVTZ TD=Read Geom=Check Guess=read Mike Frisch From owner-chemistry@ccl.net Wed Mar 8 13:19:01 2006 From: "Holger Gohlke gohlke++bioinformatik.uni-frankfurt.de" To: CCL Subject: CCL: 20th "Darmstadt" Molecular Modelling Workshop Message-Id: <-31149-060308105137-27156-554A4mNhGfU5d+v3ygu7tA * server.ccl.net> X-Original-From: Holger Gohlke Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 8 Mar 2006 15:39:06 +0100 MIME-Version: 1.0 Sent to CCL by: Holger Gohlke [gohlke%%bioinformatik.uni-frankfurt.de] We are pleased to announce the "20th Darmstadt Molecular Modelling Workshop" that will take place from 23rd to 24th May 2006 at the Computer-Chemie-Centrum in Erlangen, Germany. The workshop provides a forum particularly for young researchers to present and discuss recent results covering all aspects of molecular modelling - from life sciences to computational biology to computational chemistry to material sciences. For any further information regarding the program, registration, location, and accomodation, please refer to the following website: http://www.chemie.uni-erlangen.de/ccc/darmstadt.html The deadline for registration is 30th April 2006. Best regards Holger Gohlke -- ++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Holger Gohlke Juniorprofessur fuer Molekulare Bioinformatik J.W. Goethe-Universitaet Fachbereich Biowissenschaften Institut für Zellbiologie und Neurowissenschaft Marie-Curie-Str. 9 60439 Frankfurt/Main Germany Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29527 Email: gohlke ~~ bioinformatik.uni-frankfurt.de URL: http://www.uni-frankfurt.de/~hgohlke ++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Wed Mar 8 15:30:01 2006 From: "Pablo Vitoria pablo.vitoria-,-ehu.es" To: CCL Subject: CCL:G: [SPAM] CCL:G: RI DFT approximation in G03 Message-Id: <-31150-060308150633-25378-xMAc073BLlt/JhQDcnp/Gw---server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Wed, 8 Mar 2006 20:19:04 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria"[pablo.vitoria[A]ehu.es] Dear Mike, After my initial post to the list, I noticed that the problem was in the normalization of the coefficients. Since then I have run several single point and geometry optimization jobs using Auto, and as you say the error in the energies is very small and in the bond distances and angles negligible, with wall clock times 5 to 10 times faster (depends on problem size and computer characteristics). I guess the speedups will get even larger as the system size increases. Anyway, it would be nice if I could input the other fitting sets, very accurate and smaller in size since they have been optimized for a family (Ahlrichs') of basis sets, which I use quite a lot. Best regards Pablo > Sent to CCL by: frisch[*]gaussian.com (Michael Frisch) > On Wed, Mar 08, 2006 at 09:07:06AM -0500, Stefan Grimme grimmes..uni-muenster.de wrote: > > Sent to CCL by: Stefan Grimme [grimmes---uni-muenster.de] > > > > Dear Pablo, > > for acetone PBE/SV(P) I get a RI-non-RI difference of > > 0.6 mEh with TURBOMOLE (old Coulomb aux-basis). > > Some time ago I did a RI-test with G03 that also produced a very, very big > > difference of some hundreds of mEh, so to me that sounds like a program bug. > > The way the coefficients for contracted fitting sets are specified in > G03 is rather eccentric and accounts for this problem. You have to > provide the coeficients of the unnormalized primitives, which is > cumbersome. > > The easiest way to use density fitting in G03 is to use the option to > automatically generate the fitting set from the AO basis, e.g. > > BLYP/6-31g*/Auto > > or > > HCTH/TZVP/Auto if you prefer the Alrichs basis sets. > > The automatically generated set gives similar accuracy to the Alrichs > fittings sets for energies. Geometries and frequencies are virtually > identical to the non-fitted results -- the differences are much, much > smaller than the errors inherent in the method. So if you're doing a > study using a pure DFT functional in G03, you should routinely use > /Auto rather than doing the Coulomb problem without fitting. > > Fitting also speeds up TD-DFT with pure functionals. TD-DFT results are > a lot better with hybrid functionals, but for medium to large molecules > it's often faster to do the pure calculation first as a guess for the > hybrid, e.g. > > BLYP/Aug-CC-pVTZ/Auto TD > > followed by > > B3LYP/Aug-CC-pVTZ TD=Read Geom=Check Guess=read > > Mike Frisch> > > -- ******************************** Pablo Vitoria Garcia Dpto. Química Inorgánica, Fac. Ciencias Universidad del País Vasco (UPV/EHU) Aptdo. 644, 48080 Bilbao (Bizkaia) Tfno. +34 946015992 Fax +34 946013500 ******************************** From owner-chemistry@ccl.net Wed Mar 8 16:04:00 2006 From: "Boyd, D. boyd!=!chem.iupui.edu" To: CCL Subject: CCL: Gordon Conference on Computational Chemistry Message-Id: <-31151-060308151038-26379-a1pVawvH7YU+CIl96GLa3A]![server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 08 Mar 2006 14:08:56 -0500 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd],[chem.iupui.edu] Computational chemists of the world UNITE ... at the frontiers of science. The 2006 Gordon Research Conference on Computational Chemistry will be held 8-13 October 2006 in Les Diablerets, Switzerland. For more information, see http://chem.iupui.edu/rcc/grccc.html and www.grc.org Don From owner-chemistry@ccl.net Wed Mar 8 18:23:00 2006 From: "Changyong Qin changyong(-)wsu.edu" To: CCL Subject: CCL:G: Help with Geometry Opt for first singlet excited state usingTDDFT Message-Id: <-31152-060308182127-6637-zRDhu+S/BYBhzYHTE+Ufnw|-|server.ccl.net> X-Original-From: "Changyong Qin" Date: Wed, 8 Mar 2006 18:21:26 -0500 Sent to CCL by: "Changyong Qin" [changyong|-|wsu.edu] Dear All, Does anybody have experience in using TDDFT in Gaussian 03 to optimize the first singlet excited state? If yes, could you please share the input file ? Thanks. CY From owner-chemistry@ccl.net Wed Mar 8 19:21:00 2006 From: "Molsoft Training andy*molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-31153-060308182127-12345-+twsPgMAO3xzPHIG811jkg() server.ccl.net> X-Original-From: Molsoft Training Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 Mar 2006 11:39:36 -0800 MIME-Version: 1.0 Sent to CCL by: Molsoft Training [andy(-)molsoft.com] A two day workshop on the cutting-edge developments in crystallography and structure-based drug design will be held on May 25-26, 2006 in La Jolla California. The workshop will be conducted jointly by: Dr. Bernhard Rupp (Founder qed life science discoveries, inc) and Dr. Ruben Abagyan (Professor of Molecular Biology at The Scripps Research Institute and Founder of Molsoft LLC). The workshop entitled "Modern Drug Target Crystallography and Structure Based Drug Design" (http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm) is suitable for executives, scientists, and technicians in the field of biological sciences and drug discovery, who wish to expand their knowledge in the rapidly advancing field of high throughput drug target crystallography and structure guided drug discovery. The workshop is designed for those who are considering using crystallography and virtual ligand screening as a tool in their drug discovery research and wish to get an overview of the techniques as well as researchers already familiar with crystallography and in-silico, analysis, modeling and docking, who wish to learn more about the latest developments in this field. For more information please visit: http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm E mail andy .. molsoft.com or call (858 625 2000 x108). Places are limited (12 participants) so early enrollment is encouraged. -- From owner-chemistry@ccl.net Wed Mar 8 20:16:00 2006 From: "yang zhen na yangzn553,+,nenu.edu.cn" To: CCL Subject: CCL: PCM Message-Id: <-31154-060307055224-4720-EV16zmG/JrE6hstG/BVXJA(!)server.ccl.net> X-Original-From: "yang zhen na" Date: Tue, 7 Mar 2006 05:52:22 -0500 Sent to CCL by: "yang zhen na" [yangzn553]^[nenu.edu.cn] I use CIS method to optimize the geometry of a molecule in acetonitrile. The input file is as follows: P cis(direct)/3-21G** opt scf(maxcycl=150) scrf=(pcm,solvent=acetonitrile) gfinput iop(6/7=3) test The following are two parts of the output file: First, SCF Done: E(RHF) = -790.198795452 A.U. after 8 cycles Convg = 0.9854D-08 -V/T = 2.0028 S**2 = 0.0000 KE= 7.879538271323D+02 PE=-4.190314685897D+03 EE= 1.439311967412D+03 -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -790.167307 (a.u.) = -790.198795 Total free energy in solution: with all non electrostatic terms (a.u.) = -790.182049 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -19.76 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 26.61 Dispersion energy (kcal/mol) = -17.35 Repulsion energy (kcal/mol) = 1.25 Total non electrostatic (kcal/mol) = 10.51 -------------------------------------------------------------------- Second, Excitation energies and oscillator strengths: Excited State 1: Singlet-A' 3.9936 eV 310.45 nm f=0.5585 62 -> 63 0.66032 62 -> 64 -0.18256 This state for optimization and/or second-order correction. Total Energy, E(CIS) = -790.052032172 Copying the excited state density for this state as the 1-particle RhoCI density My question is that how to get the energy of the molecule in the first excited state in acetonitrile. Which one of the two data in bold is the result. Should I get the result in other way? For example, adding Total non electrostatic (kcal/mol) = 10.51 to Total Energy, E(CIS) = -790.052032172 to get the result. The last question is how to get the DG and DH values from the output file of frequence calculation in solution. Thanks for your help. I am waiting for your answer anxiously!!! From owner-chemistry@ccl.net Wed Mar 8 22:19:00 2006 From: "Roy Jensen rjensen^^^consol.ca" To: CCL Subject: CCL: Norming energies of different entities... Message-Id: <-31155-060308213539-4863-jJeaYDk1EF2KHbBnoRYBSw]_[server.ccl.net> X-Original-From: Roy Jensen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 08 Mar 2006 19:35:34 -0700 MIME-Version: 1.0 Sent to CCL by: Roy Jensen [rjensen]*[consol.ca] All A pedagogical question... Given calculations on a series of diatomic entities -- B2, C2, N2, O2, and F2 -- is there any way to know how the orbital energies relate between these species? I want to create a figure that accurately presents all the MO diagrams. On a second note, what does zero energy (E = 0.0000 Hartree) correspond to? Thanks, Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan College Edmonton, AB T5J 4S2 780.633.3915