From chemistry-request@ccl.net Wed Dec 10 10:46:57 2003 Received: from hellmouth4.gatech.edu (hellmouth4.gatech.edu [130.207.165.164]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAFkQJO001554 for ; Wed, 10 Dec 2003 10:46:26 -0500 Received: from hellmouth4.gatech.edu (localhost [127.0.0.1]) by hellmouth4.gatech.edu (Postfix) with SMTP id C24A0A85E for ; Wed, 10 Dec 2003 10:45:39 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Received: from acmey.gatech.edu (acmey.prism.gatech.edu [130.207.171.27]) by hellmouth4.gatech.edu (Postfix) with ESMTP id 64E83A847 for ; Wed, 10 Dec 2003 10:45:39 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Received: by acmey.gatech.edu (Postfix, from userid 11564) id 218DC31F25; Wed, 10 Dec 2003 10:45:38 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by acmey.gatech.edu (Postfix) with ESMTP id F243E330FB for ; Wed, 10 Dec 2003 10:45:38 -0500 (EST) (envelope-from ok16!at!mail.gatech.edu) Date: Wed, 10 Dec 2003 10:45:38 -0500 (EST) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: 5d and 6d functions in basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers; According to Gaussian and other program manuals, some basis sets employ 6d, and others do 5d. For example, 6-31G* basis set use 6d (Cartesian d function) but 6-311G* basis set use 5d (pure d function). And in GaussianXX program, when the keyword of "Gen" is applied, using 5d is default. Is any particular reason for that? I would appreciate it if anyone could kindly give some advice on this maater. Thank you very much for your attention. Best wishes, Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon!at!chemistry.gatech.edu From chemistry-request@ccl.net Tue Dec 9 12:01:36 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB9H14JO003216 for ; Tue, 9 Dec 2003 12:01:04 -0500 Received: from moline.ks.uiuc.edu (moline.ks.uiuc.edu [130.126.120.60]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hB9H13u5016981; Tue, 9 Dec 2003 11:01:03 -0600 (CST) Received: (from johns@localhost) by moline.ks.uiuc.edu (8.11.6+Sun/8.9.1) id hB9H13A08328; Tue, 9 Dec 2003 11:01:03 -0600 (CST) Date: Tue, 9 Dec 2003 11:01:02 -0600 From: John Stone To: chemistry=at=ccl.net Subject: VMD 1.8.2 is available Message-ID: <20031209110102.C8172=at=moline.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i X-Spam-Status: No, hits=-2.5 required=7.0 tests=USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, We've released a new version of VMD, a free OpenGL-based molecular visualization tool for MacOS X, Unix, and Windows: http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.2/ The release notes for the new version are available here: http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.2/README.html Thanks for your time, John Stone vmd=at=ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns=at=ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@ccl.net Tue Dec 9 06:10:02 2003 Received: from web1.ulb.ac.be (resulb.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB9B9UJO023715 for ; Tue, 9 Dec 2003 06:09:31 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id MAA14265; Tue, 9 Dec 2003 12:09:28 +0100 (MET) for chemistry(at)ccl.net Date: Tue, 9 Dec 2003 12:09:28 +0100 (MET) Message-Id: <200312091109.MAA14265(at)web1.ulb.ac.be> From: Giju Kalathingal To: chemistry(at)ccl.net Subject: Calculations without Born-Oppenheimer approximation X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL-all, Could you please give me some info on programs that let me to do quantum chemical calculations (geometry optimzations and vibrational frequencies) without Born-Oppenheimer approximation? Thanks in advance. With best wishes, Giju Kalathingal Department of General Chemistry (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium. Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 E-mail: Giju.Kalathingal(at)vub.ac.be ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Tue Dec 9 07:16:36 2003 Received: from guppy.vub.ac.be (www.vub.ac.be [134.184.129.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB9CG3JO025947 for ; Tue, 9 Dec 2003 07:16:04 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id NAA26766; Tue, 9 Dec 2003 13:16:03 +0100 (MET) for Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.5.aejp (mach)) id NAA08425; Tue, 9 Dec 2003 13:16:02 +0100 (MET) for Message-ID: <3FD5DEC4.3080105(at)ulb.ac.be> Date: Tue, 09 Dec 2003 15:40:04 +0100 From: Christophe Biot Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: fr, en-us MIME-Version: 1.0 To: Liste CCL Subject: LUMO HF level Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I'd like to perform computationial estimations of the energy levels for the frontier orbitals (HOMO, LUMO). What is the accuracy of performing such calculations at the HF level?? More precisely, are the LUMO orbitals correctly described at this level of calculation? Best regards. C Biot From chemistry-request@ccl.net Tue Dec 9 06:35:30 2003 Received: from outbound.kcl.ac.uk (elder.kcl.ac.uk [137.73.2.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB9BYtJO024615 for ; Tue, 9 Dec 2003 06:34:58 -0500 Received: from outbound.kcl.ac.uk ([137.73.2.214] helo=elder) by outbound.kcl.ac.uk outbound-standard with esmtp (TLSv1:DHE-RSA-AES256-SHA:256) id 1ATg8l-0001Pv-AT for chemistry*at*ccl.net; Tue, 09 Dec 2003 11:34:55 +0000 Received: from fwb249-41.paws.kcl.ac.uk ([137.73.202.101] helo=fwb249-00.paws.kcl.ac.uk) by elder ib2-received with esmtp id 1ATg8M-0000lO-Hb for chemistry*at*ccl.net; Tue, 09 Dec 2003 11:34:30 +0000 From: Nikeel Patel Sender: nikeel.patel*at*kcl.ac.uk Date: Tue, 9 Dec 2003 11:34:30 +0000 To: chemistry*at*ccl.net Subject: Code for chirality Message-ID: Priority: NORMAL X-Mailer: Execmail for Win32 5.1 Build (9) MIME-Version: 1.0 Content-Type: Text/Plain; charset="us-ascii" X-KCLSpamScore: -49 X-KCLRealSpamScore: -4.9 X-KCLSpamReport: BAYES_00=-4.9 X-KCL-MailScanner: Found to be clean X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello I am a 4th year pharmacy student at King's College London. I am currently undertaking a project which looks at the reactivity between enantiomers in their solid state using computer simulations. I was wondering if anyone knows where I could obtain a computer code for determining the chirality of an atom. Any help with this request would be greatly appreciated and acknowledged as such. Thanking you in advance. ---------------------- Nikeel Patel nikeel.patel*at*kcl.ac.uk From chemistry-request@ccl.net Tue Dec 9 09:23:22 2003 Received: from bute.st-andrews.ac.uk (bute.st-and.ac.uk [138.251.12.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB9EMoJO029451 for ; Tue, 9 Dec 2003 09:22:51 -0500 Received: from Babydesign.st-andrews.ac.uk (bmspc-glt2-18 [138.251.94.166]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id OAA16603 for ; Tue, 9 Dec 2003 14:17:23 GMT Message-Id: <6.0.0.22.0.20031209141952.01f26098*at*bute.st-andrews.ac.uk> X-Sender: im17*at*bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Tue, 09 Dec 2003 14:22:47 +0000 To: chemistry*at*ccl.net From: "Ibrahim M.Moustafa" Subject: Carbohydrate stereochemistry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=1.1 required=7.0 tests=FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCl users, Could someone help me and explain what is meant by the following terms used in the description of the stereochemistry of carbohydrates: gg, tg, gt, anti, syn. I'd really be grateful for your help. regards, Ibrahim Ibrahim M.Moustafa Centre for Biomolecular Sciences St-Andrews University North Haugh, St-Andrews Fife KY16 9ST Scotland, U.K. Tel. +44 (0)1334 467257 Fax +44 (0)1334 462595 e-mail: im17*at*st-andrews.ac.uk From chemistry-request@ccl.net Wed Dec 10 12:07:07 2003 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAH6ZJO005361 for ; Wed, 10 Dec 2003 12:06:35 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id hBAH6YcD001258; Wed, 10 Dec 2003 12:06:35 -0500 (EST) Date: Wed, 10 Dec 2003 11:59:37 -0500 From: Rick Venable To: "Ibrahim M.Moustafa" cc: chemistry~at~ccl.net Subject: Re: CCL:Carbohydrate stereochemistry In-Reply-To: <6.0.0.22.0.20031209141952.01f26098~at~bute.st-andrews.ac.uk> Message-ID: References: <6.0.0.22.0.20031209141952.01f26098~at~bute.st-andrews.ac.uk> ReplyTo: Rick_Venable~at~nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, 9 Dec 2003, Ibrahim M.Moustafa wrote: > Could someone help me and explain what is meant by the following > terms used in the description of the stereochemistry of carbohydrates: > gg, tg, gt, anti, syn. > > I'd really be grateful for your help. > > Ibrahim M.Moustafa > Centre for Biomolecular Sciences > St-Andrews University > North Haugh, St-Andrews > Fife KY16 9ST > Scotland, U.K. They aren't really sterechemistry terms, but configurational descriptors of the 2 torsions between 2 sugar rings in a typical di- or poly-saccharide. The gg, tg, gt etc. terms are simple shorthand for trans (180 deg) and gauche (+/- 60 deg); you have to very careful about stating which 4 atoms define the torsion, as there are multiple choices. The syn and anti terms refer more explicitly to the conformation wrt. to the aliphatic protons at either end of the linkage, e.g. H1 and H4' for a typcial 1,4 linkage. If the the protons are on the same side of the linkage, i.e. the C-H bonds point in roughly parallel directions, they are 'syn'. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable~at~nih.gov ALT email: rvenable~at~speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Wed Dec 10 12:36:11 2003 Received: from smtp4.server.rpi.edu (smtp4.server.rpi.edu [128.113.2.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAHZeJO006496 for ; Wed, 10 Dec 2003 12:35:40 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp4.server.rpi.edu (8.12.10/8.12.9) with ESMTP id hBAHZdto024445 for ; Wed, 10 Dec 2003 12:35:39 -0500 Message-Id: <200312101735.hBAHZdto024445:at:smtp4.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: CHEMISTRY:at:ccl.net From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Wed, 10 Dec 2003 12:35:39 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:Molecular Complexes X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Thu, 04 Dec 2003 18:33:16 +0100 Anton Feenstra wrote: > Tarek M. El-Gogary wrote: > > > I am looking for an accurate definition for the term, Molecular > Complexes. > [...] > > This would, I'm afraid, be somewhat context dependent. There is a wide, > and > fairly continues scale of complexes, both terms of affinity (i.e. > strength > of binding of the partners in the comples) and in lifetime (i.e. > persistence > times of the binding). In other words, it would depend on the time-window > you are interested in, and on the relative affinity with respect to other > processes/binding partners/etc. in your sysem of interest. > > > -- > Groetjes, > > Anton Good point. I am reminded of something one of my physics teachers once said: "From the point of view of a physicist, a molecule is just a collision that takes too long." Sukumar From chemistry-request@ccl.net Wed Dec 10 11:27:58 2003 Received: from bmbpcu21.leeds.ac.uk (bmbpcu21.leeds.ac.uk [129.11.110.201]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAGRQJO003341 for ; Wed, 10 Dec 2003 11:27:27 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by bmbpcu21.leeds.ac.uk (8.11.3/8.11.3/SuSE Linux 8.11.1-0.5) id hBAGOVj10289 for chemistry_at_ccl.net; Wed, 10 Dec 2003 16:24:31 GMT Content-Type: text/plain; charset="iso-8859-15" From: Peter Oledzki Reply-To: peter_at_bioinformatics.leeds.ac.uk To: chemistry_at_ccl.net Subject: Chemistry Resources for Ligands? Date: Wed, 10 Dec 2003 16:24:31 +0000 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <03121016243100.10214@bmbpcu21> Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello CCLers, I was wondering if anybody knew of any resources which could help me in identifying ligand chemotypes. I'm using a docking method that converts functional groups/ligand atoms into certain types of empirical probes. Seeing that I'm from a molecular biology/genetics background my medicinal chemistry is too bad to talk about. Does anybody know of any websites that show the major types of functional groups with the chemical structures of known ligands. Anything along these lines will be very helpful. Cheers Pete -- *********************************************************** Peter Oledzki PhD Bioinformatics Research Student School of Biochemistry and Molecular Biology University of Leeds LS2 9JT 0113 34334447 From chemistry-request@ccl.net Wed Dec 10 12:28:22 2003 Received: from bohr.quimica.ufpr.br ([200.17.215.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAHRoJO006229 for ; Wed, 10 Dec 2003 12:27:51 -0500 Received: from laplace.quimica.ufpr.br ([200.17.215.88] helo=quimica.ufpr.br) by bohr.quimica.ufpr.br with esmtp (Exim 3.36 #1 (Debian)) id 1AU87n-00038R-00 for ; Wed, 10 Dec 2003 15:27:47 -0200 Message-ID: <3FD75792.4070601_at_quimica.ufpr.br> Date: Wed, 10 Dec 2003 15:27:46 -0200 From: Eduardo User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:1.4) Gecko/20031105 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: anti-ferromagnectic Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Sirs and Madams I am studying complex compounds (built with Fe centers) that show anti-ferromagenectic behaviour. Could you, please, point to me any software that can handle these compounds or which is the best approach for this study. Thanks a lot in advance yours Eduardo -- Eduardo Lemos de Sa - edulsa_at_quimica.ufpr.br Dep. Quimica - Universidade Federal do Parana Curitiba - PR - Brazil Box: 19081 - Zip: 81531-990 - Phone: +55(41)361-3300 From chemistry-request@ccl.net Wed Dec 10 12:11:44 2003 Received: from rwcrmhc12.comcast.net (rwcrmhc12.comcast.net [216.148.227.85]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAHBDJO005532 for ; Wed, 10 Dec 2003 12:11:13 -0500 Received: from YOURBD32B012D4 (pcp02630529pcs.univde01.de.comcast.net[68.82.79.253]) by comcast.net (rwcrmhc12) with SMTP id <20031210171112014008ks66e>; Wed, 10 Dec 2003 17:11:12 +0000 Message-ID: <01a301c3bf40$9fc44c80$6400a8c0@YOURBD32B012D4> From: "Matthew Schlecht" To: References: <6.0.0.22.0.20031209141952.01f26098_at_bute.st-andrews.ac.uk> Subject: Re: CCL:Carbohydrate stereochemistry Date: Wed, 10 Dec 2003 12:11:16 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-0.6 required=7.0 tests=MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) In carbohydrate nomenclature: gg - gauche, gauche tg - trans, gauche gt - gauche, trans Definitions for these, as well as for the terms anti and syn, can be found at the excellent IUPAC stereochemical nomenclature site, the index for which can be found at: http://www.chem.qmul.ac.uk/iupac/stereo/cont.html Basically these are descriptors for the relative stereochemistry in polycyclic compounds, such as oligo- and polysaccharides. HTH, Matthew Schlecht ********************************************************* ----- Original Message ----- From: "Ibrahim M.Moustafa" To: Sent: Tuesday, December 09, 2003 9:22 AM Subject: CCL:Carbohydrate stereochemistry > Dear CCl users, > > Could someone help me and explain what is meant by the following terms > used in the description of the stereochemistry of carbohydrates: gg, tg, > gt, anti, syn. > > I'd really be grateful for your help. > > regards, > Ibrahim > > Ibrahim M.Moustafa > Centre for Biomolecular Sciences > St-Andrews University > North Haugh, St-Andrews > Fife KY16 9ST > Scotland, U.K. > > Tel. +44 (0)1334 467257 > Fax +44 (0)1334 462595 > e-mail: im17_at_st-andrews.ac.uk > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl_at_ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > From chemistry-request@ccl.net Wed Dec 10 12:53:03 2003 Received: from crunch.qtp.ufl.edu (crunch.qtp.ufl.edu [128.227.192.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAHqWJO007259 for ; Wed, 10 Dec 2003 12:52:32 -0500 Received: from pc1 (dred1 [192.168.4.129]) by crunch.qtp.ufl.edu (8.12.8p1/8.12.8/Server/deumens) with SMTP id hBAHqU6N024912; Wed, 10 Dec 2003 12:52:30 -0500 (EST) Message-ID: <018801c3bf48$2a8f97f0$8104a8c0_at_qtp.ufl.edu> From: "Stefan Fau" To: "Ohyun Kwon" Cc: "CCL - all" References: Subject: CCL: Re: 5d and 6d functions in basis set Date: Wed, 10 Dec 2003 13:05:16 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Scanned-By: MIMEDefang 2.36 X-Spam-Status: No, hits=-0.5 required=7.0 tests=REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Ohyun, my speculation on this is as follows: cartesian d-functions are linear combinations of the five "pure" d-functions and an s-function of the same exponent. Therefore, using cartesian d-functions introduces an additional s-function into the basis set. This may lead to near linear dependence problems in larger basis sets. Since many smaller basis sets are part of Gaussians basis set library, it is probably more likely that the GEN keyword is used to specify large basis sets. Hence the 5D default. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau_at_qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 From chemistry-request@ccl.net Wed Dec 10 13:49:28 2003 Received: from freyr.chem.washington.edu (freyr.chem.washington.edu [128.95.128.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBAImvJO028559 for ; Wed, 10 Dec 2003 13:48:57 -0500 Received: from freyr.chem.washington.edu (localhost [127.0.0.1]) by freyr.chem.washington.edu (8.12.8/8.12.8) with ESMTP id hBAIm21c020144 for ; Wed, 10 Dec 2003 10:48:02 -0800 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.12.8/8.12.8/Submit) with ESMTP id hBAIm2uF020140 for ; Wed, 10 Dec 2003 10:48:02 -0800 Date: Wed, 10 Dec 2003 10:48:01 -0800 (PST) From: "Fernando D. Vila" To: Computational Chemistry List Subject: Simple implementation of DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi.. I was wondering if anybody knows of a simple implementation of DFT. For example, a simple program that does LDA in atomic systems and would be useful to test some simple ideas. It could be in any language, I'm not very picky, but should fairly well commented to make changes easier. Cheers and thanks in advance, Fer. ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206)685-8665 University of Washington E-mail fdv$at$u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv ******************************************************************************* From chemistry-request@ccl.net Wed Dec 10 16:46:58 2003 Received: from f04n01.cac.psu.edu (f04s01.cac.psu.edu [128.118.141.31]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBALkR8a031737 for ; Wed, 10 Dec 2003 16:46:27 -0500 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n01.cac.psu.edu (8.9.3p2.1/8.9.3) with ESMTP id QAA79016 for ; Wed, 10 Dec 2003 16:46:26 -0500 Subject: problem calculating Fukui indices with Mopac From: Rajarshi Guha Reply-To: rxg218^at^psu.edu To: chemistry^at^ccl.net Content-Type: text/plain Organization: Message-Id: <1071092914.2714.5.camel^at^ra.chem.psu.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.2 (1.2.2-5) Date: 10 Dec 2003 16:48:34 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.3 required=7.0 tests=FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR,USER_AGENT_XIMIAN version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, I'm trying to calculate condensed Fukui indices. I am using Mopac 7.01 and I am doing the calculations with the PM3 hamiltonian. My problem occurs when I try and calculate mulliken charges for the molecule with N+1 and N-1 electrons (where N is the number of electrons in the neutral molecules). For the N+1 case my keyword line is PM3 doublet charge=1 mullik However though the calculation for the neutral molecule takes less than a minute for the above case the calculation does not end after 5 minutes. Is this to be expected or am I doing something wrong? I tried adding mmok and geo-ok since the structures are already geometry optimized but that does'nt help. Is it correct to be using a PM3 hamiltonian for such systems? Any pointers would be appreciated. Thanks, ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- How I wish I were what I was when I wished I were what I am.