From owner-chemistry@ccl.net Fri Apr 28 01:40:01 2006 From: "Dipankar Roy dipankarroy---iitb.ac.in" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31615-060428004010-7735-xceIf6IsKGpvsqaPhK/SDQ#,#server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 28 Apr 2006 09:10:06 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy:-:iitb.ac.in] Hi, In my case 6-31G* and 6-31+G* gave nice results for CU-systems. But you can try (1)Wachters basis set (J. Phys. Chem. B 2002, 106, 7483); (2)TZV (J. Phys. Chem. B 2004, 108, 7495); (3)SDD hope these will work. -dipankar > Sent to CCL by: "Young Leh" [youngleh(_)gmail.com] > Dear CCLer, > > I am unfortunately working on transition metals on which the standard > basis sets give poor energies. Could somebody please recommend better > basis sets that works for transition metals like Cu?> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratoty Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Fri Apr 28 03:33:00 2006 From: "Rzepa, Henry h.rzepa%%imperial.ac.uk" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31616-060428022557-9176-j7cOgrO9jvniDVVet6Fa8A_-_server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Apr 2006 07:25:18 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa:+:imperial.ac.uk] Might I also suggest http://tyr0.chem.wsu.edu/~kipeters/basissets/basis.html which gives basis sets of aug-cc-pV5Z quality for Sc-Zn, (all electron) and aug-cc-pV5Z -pp for Cu, Ag, Au, Zn, Cd, Hg (pseudopotential) These were only published recently; N.B. Balabanov and K.A. Peterson, J. Chem. Phys. 123, 064107 (2005). >Sent to CCL by: "Dipankar Roy" [dipankarr >Hi, > In my case 6-31G* and 6-31+G* gave nice results for CU-systems. >But you can try >(1)Wachters basis set (J. Phys. Chem. B 2002, 106, 7483); >(2)TZV (J. Phys. Chem. B 2004, 108, 7495); >(3)SDD -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs+*+mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Fri Apr 28 06:42:00 2006 From: "Roger Kevin Robinson r.robinson/./imperial.ac.uk" To: CCL Subject: CCL:G: Gaussian Symmetry Number Message-Id: <-31617-060428063952-23852-sXSWC3dbpvxYvVTv4UH7+A^^server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Apr 2006 11:40:38 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson,imperial.ac.uk] Hi, As far as I am aware the symmetry number for acetone is 2. If I run acetone through a Gaussian geometry optimization then a frequency calculation (or a G3 or G3B3 method) I get a symmetry number of 1 and a point group of CS. If I use Gaussview to clean Acetone and then force the torsion angles to 0. Then run a frequency calculation without a geometry optimization I get a a symmetry number of 2 and a point group of C2V. So I assume the first method is coming up with a symmetry number of 1 because the molecule is not perfectly symmetrical after the optimization. Is there anyway round this ? ie to tell gaussian not to be so strict with the symmetry rules ? Is there any more information in a G3B3 output file which would tell me the symmetry number was really 2 ? I wanted to write a script which would harvest the symmetry number from the guassian output file and do some calculations so that someone else (not a chemist) could use it, but it would appear that I cant do this. Any help appreciated. Thanks Roger From owner-chemistry@ccl.net Fri Apr 28 07:23:00 2006 From: "Mikael Johansson mikael.johansson[]helsinki.fi" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31618-060428071655-11341-ypVT4zBISehoQe4g3/MdLQ() server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 28 Apr 2006 14:16:47 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson[a]helsinki.fi] Hello! On Thu, 27 Apr 2006, Young Leh youngleh*_*gmail.com wrote: > I am unfortunately working on transition metals on which the standard > basis sets give poor energies. Could somebody please recommend better > basis sets that works for transition metals like Cu? You already got good suggestions about basis sets, but I'd like to add the Karlsruhe sets, which I've found to work well. They go up to quadruple zeta and can be downloaded here: ftp://ftp.chemie.uni-karlsruhe.de/pub/basen/ On another note, is Cu considered to be a transition metal? Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Fri Apr 28 08:34:00 2006 From: "Bruce D Alexander glaikit_76%x%yahoo.co.uk" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31619-060428045529-15624-wsqHhLf0JCwkeWHKwZ2CXQ _ server.ccl.net> X-Original-From: Bruce D Alexander Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 28 Apr 2006 08:55:19 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Bruce D Alexander [glaikit_76*|*yahoo.co.uk] You might also want to try the DZVP and DZVP2 basis sets. Both very useful and can be found at http://www.emsl.pnl.gov/forms/basisform.html Bruce --- "Young Leh youngleh*_*gmail.com" wrote: > Sent to CCL by: "Young Leh" [youngleh(_)gmail.com] > Dear CCLer, > > I am unfortunately working on transition metals on > which the standard basis sets give poor energies. > Could somebody please recommend better basis sets > that works for transition metals like Cu? > > > > -= 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/> > > > ___________________________________________________________ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com From owner-chemistry@ccl.net Fri Apr 28 15:04:01 2006 From: "Shobe, David dshobe#,#sud-chemieinc.com" To: CCL Subject: CCL:G: Gaussian Symmetry Number Message-Id: <-31620-060428133844-14489-GVIAUuinoCohbJ/+hSItHA.@.server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 28 Apr 2006 19:38:24 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe()sud-chemieinc.com] Roger, Try "symm=loose". It's there for exactly the type of situation you mention. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] Sent: Friday, April 28, 2006 6:47 AM To: Shobe, David Subject: CCL:G: Gaussian Symmetry Number Sent to CCL by: Roger Kevin Robinson [r.robinson,imperial.ac.uk] Hi, As far as I am aware the symmetry number for acetone is 2. If I run acetone through a Gaussian geometry optimization then a frequency calculation (or a G3 or G3B3 method) I get a symmetry number of 1 and a point group of CS. If I use Gaussview to clean Acetone and then force the torsion angles to 0. Then run a frequency calculation without a geometry optimization I get a a symmetry number of 2 and a point group of C2V. So I assume the first method is coming up with a symmetry number of 1 because the molecule is not perfectly symmetrical after the optimization. Is there anyway round this ? ie to tell gaussian not to be so strict with the symmetry rules ? Is there any more information in a G3B3 output file which would tell me the symmetry number was really 2 ? I wanted to write a script which would harvest the symmetry number from the guassian output file and do some calculations so that someone else (not a chemist) could use it, but it would appear that I cant do this. Any help appreciated. Thanks Rogerhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Apr 28 15:39:01 2006 From: "Debasis Sengupta dxs%%cfdrc.com" To: CCL Subject: CCL:G: PQS ab initio Message-Id: <-31621-060428151021-29121-JrB0hFiQ1fzlkKD1xTTZGg|server.ccl.net> X-Original-From: Debasis Sengupta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 28 Apr 2006 14:10:15 -0500 MIME-Version: 1.0 Sent to CCL by: Debasis Sengupta [dxs]=[cfdrc.com] Hi, I was wondering if anybody has performed any benchmark test on the speed of Gaussian 03 and PQS ab initio software (both serial and parallel). Also I am interested in knowing the experience with PQS from those who have used it for a while. Thanks Debasis From owner-chemistry@ccl.net Fri Apr 28 16:14:01 2006 From: "Shobe, David dshobe() sud-chemieinc.com" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31622-060428143511-22541-r0WtUc0cu3KQJ0sCan23UQ(a)server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 28 Apr 2006 20:35:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe[*]sud-chemieinc.com] Mikael J. wrote: > On another note, is Cu considered to be a transition metal? I've seen some exclude Zn, Cd, and Hg from the transition metals, but Cu is always included AFAIK. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry||ccl.net [mailto:owner-chemistry||ccl.net] Sent: Friday, April 28, 2006 7:29 AM To: Shobe, David Subject: CCL: Basis Set for Transition Metals Sent to CCL by: Mikael Johansson [mikael.johansson[a]helsinki.fi] Hello! On Thu, 27 Apr 2006, Young Leh youngleh*_*gmail.com wrote: > I am unfortunately working on transition metals on which the standard > basis sets give poor energies. Could somebody please recommend better > basis sets that works for transition metals like Cu? You already got good suggestions about basis sets, but I'd like to add the Karlsruhe sets, which I've found to work well. They go up to quadruple zeta and can be downloaded here: ftp://ftp.chemie.uni-karlsruhe.de/pub/basen/ On another note, is Cu considered to be a transition metal? Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Apr 28 16:51:00 2006 From: "Mariusz Radon mariusz.radon]=[gmail.com" To: CCL Subject: CCL: Good review on Symmetry in Quantum Chemistry? Message-Id: <-31623-060428163145-5967-Gzu8soePLJnvShIiu/AS6g()server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Apr 2006 22:31:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon^gmail.com] On 4/24/06, Rick Muller rmuller]_[sandia.gov wrote: > Sent to CCL by: "Rick Muller" [rmuller..sandia.gov] > I would like to put symmetry into my program PyQuante (http:// > pyquante.sf.net). I know that the general idea is to form a symmetry- > adapted basis set and then compute the integrals in this basis. But I > was wondering whether anyone can recommend a good review with the > deeper details, since I'd prefer not to have to reinvent everything. Just a small remark from the beginner;): AFAIK computing 2el integrals in symmetry adapted basis is very bad idea, especially for direct SCF: prescreening, which normally eliminates very many small integrals in large system is no longer effective, since basis you're working in is now strongly delocalized. Better approach is so called skeleton Fock matrix [Dupuis and King] -- you generate skeleton of the Fock matrix using only symmetry unique integrals (in AO basis, not symmetry adapted) and, after all, this skeleton gives real Fock matrix during the process of symmetrization. Then, final Fock matrix can be transformed to symmetry adapted basis (very cheap in comparison with transforming 2e integrals). But I don't have much experience in this topic. Also don't know good book:( Best regards, Mariusz -- Mariusz Rado\'n e-mail: mradon/at/chemia.uj.edu.pl e-mail & im: mariusz.radon/at/gmail.com From owner-chemistry@ccl.net Fri Apr 28 17:26:03 2006 From: "Jim Kress ccl_nospam++kressworks.com" To: CCL Subject: CCL:G: PQS ab initio Message-Id: <-31624-060428165244-29203-ffvouW64MN7TXm0qGrrflA(~)server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Apr 2006 16:52:27 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%%kressworks.com] It's a violation of the (absurd) Gaussian license to perform such a comparison. If one does such a comparison they will be banned by Gaussian > from using their software. http://www.bannedbygaussian.org/ Jim > -----Original Message----- > From: Debasis Sengupta dxs%%cfdrc.com > [mailto:owner-chemistry-,-ccl.net] > Sent: Friday, April 28, 2006 3:49 PM > To: Kress, Jim > Subject: CCL:G: PQS ab initio > > Sent to CCL by: Debasis Sengupta [dxs]=[cfdrc.com] Hi, I was > wondering if anybody has performed any benchmark test on the > speed of Gaussian 03 and PQS ab initio software (both serial > and parallel). > Also I am interested in knowing the experience with PQS from > those who have used it for a while. > Thanks > Debasis > > > > -= 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.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Fri Apr 28 18:20:01 2006 From: "Robinson, James James.Robinson%x%evotec.com" To: CCL Subject: CCL:G: Gaussian problems Message-Id: <-31625-060426125811-26960-LNCNgr0bDlYURJXp41Dztw++server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Apr 2006 17:57:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson-x-evotec.com] Hi, You Gaussian input needs a blank line between title and charge/multipilicity. Also add a few blank lines after the input of the second z-matrix, this does help sometimes. If you have Molden, check that the atom ordering are the same and if problems persist I suggest you try a saddle calculation using MOPAC and use cartesian coordinates for the two input structures in your mopac saddle calculation. I cannot immediately recall how the out from NMR jobs compare to TMS. Some calculation often need to be compared to TMS to compare calculations, you may need the difference between TMS and your calculated molecule. I also suspect that the basis set for your NMR calculation maybe too small, daft I know, but perhaps 6-311+(2d,p) may be more adequate. Also I think the NOSYMM keyword is useful Hope this helps or at least causes some thought. Dr James J Robinson Evotec, Oxford. -----Original Message----- > From: owner-chemistry^^^ccl.net [mailto:owner-chemistry^^^ccl.net] Sent: 26 April 2006 16:42 To: Robinson, James Subject: CCL:G: Gaussian problems Sent to CCL by: "Melanie Trusselle" [mt237]|[bath.ac.uk] Dear All, I am a new user of Gaussian and have encountered two problems that I have been unable to resolve. The first problem is the calculation of the energy barrier between two conformers. I am using QST2 for this and my input is below. %chk=QST2.chk %mem=500MB %nproc=1 pm3 Opt=QST2 find barrier for chair-boat interconversion 1 1 zmatrix of first structure 1 1 zmatrix of second structure This input gives the error message shown below: Symbolic Z-matrix: End of file in GetChg. Error termination via Lnk1e in /usr/local/g03/l101.exe at Tue Apr 25 14:53:45 2006. Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1 I believe it relates to a lack of memory so I have tried changing %mem and have specifed extra memory when submitting the job but this has not solved the problem. I an aware that this question has been asked previously, and appologies for asking it again but there is no answer available. I am also interested in obtaining the J coupling constants for a molecule. I have used the following commands: nmr=SpinSpin b3lyp/6-31g(d) geom=connectivity An section of the output is: Total nuclear spin-spin coupling J (Hz): 1 2 3 4 5 1 0.000000D+00 2 0.482568D+02 0.000000D+00 3 0.581831D+02 0.557526D+01 0.000000D+00 4 0.167946D+03 -0.143914D+00 -0.160153D+01 0.000000D+00 5 0.107532D+01 0.576884D+02 -0.428170D+00 0.621590D+01 0.000000D+00 This is different from what I was expecting and I do not know how to relate it to my NMR specra or even if I have given the correct input. If anyone can advise me on these matters I would be most grateful. Thank you in advance. Melanie Trusselle mt237#,#bath.ac.uk University of Bath, UKhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt