From chemistry-request@server.ccl.net Fri Jul 7 15:22:28 2000 Received: from mail.bucknell.edu (marge.bucknell.edu [134.82.9.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA15136 for ; Fri, 7 Jul 2000 15:22:28 -0400 Received: from williams.bucknell.edu (williams.bucknell.edu [134.82.59.42]) by mail.bucknell.edu (8.10.1/8.10.1) with SMTP id e67JMSW32176 for ; Fri, 7 Jul 2000 15:22:28 -0400 (EDT) Date: Fri, 7 Jul 2000 15:22:28 -0400 (EDT) Message-Id: <200007071922.e67JMSW32176@mail.bucknell.edu> X-Sender: williams@mail.bucknell.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Brian Williams Subject: QSAR This is probably a FAQ, but an organic colleague of mine is interested in knowing more about what packages or code might be available to do QSAR. We are a PUI ("Primarily Undergraduate Institution") and are looking to this in as cost-effective manner as possible. I myself have used molecular modelling/computational chemistry at very basic levels with packages such as Spartan and HyperChem, but know little about QSAR. Thanks for any advice. Brian Williams Dept. Chemistry Bucknell University From chemistry-request@server.ccl.net Fri Jul 7 16:27:01 2000 Received: from firewall2.cfdrc.com (root@host-208-166-121-13.cfdrc.com [208.166.121.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA15707 for ; Fri, 7 Jul 2000 16:27:00 -0400 Received: from cfdrc.com (dxspc.cfdrc.com [192.77.87.143]) by firewall2.cfdrc.com (8.9.3/8.9.3) with ESMTP id PAA13694 for ; Fri, 7 Jul 2000 15:27:00 -0500 Message-ID: <39663D71.ED5BB51B@cfdrc.com> Date: Fri, 07 Jul 2000 15:28:33 -0500 From: Debasis Sengupta To: chemistry@ccl.net Subject: cc-pVDZ for DFT ?? Can correlation consistent basis sets (such as cc-pVDZ, cc-pVTZ etc etc) be used with DFT? -- -------- Debasis ------------ ==================================================== Debasis Sengupta, Ph.D (Computational Chemistry) CFD Research Corporation 215, Wynn Drive, Huntsville, AL-35805 Ph: 256-726-4944 Fax: 256-7264806 ==================================================== From chemistry-request@server.ccl.net Fri Jul 7 16:48:31 2000 Received: from shiva.hunter.cuny.edu (shiva.hunter.cuny.edu [146.95.128.96]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA15963 for ; Fri, 7 Jul 2000 16:48:30 -0400 Received: from shiva (shiva [146.95.128.96]) by shiva.hunter.cuny.edu (8.9.3/8.9.3) with ESMTP id QAA05718; Fri, 7 Jul 2000 16:48:42 -0400 (EDT) Date: Fri, 7 Jul 2000 16:48:41 -0400 (EDT) From: AM To: chemistry@ccl.net cc: Artem Masunov , =?X-UNKNOWN?Q?Eldbj=F8rg_Sofie_Heimstad?= , Kristy Mardis , Flemming Steen Jorgensen , Dave , Anita Ilze Zvaigzne Subject: Summary: water/cyclohexane partition database Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id QAA15964 The original question: > We need data on solvation free energies for as many organic compounds as > possible, especially for non-polar solvent. > Does anyone know of such a database (preferably, on-line, preferably, > free)? ====================================================================== I know of ACD labs database and prediction tool for octanol/water partition coefficient (and its pH dependence for charged structures) http://www.acdlabs.com/products/phys_chem_lab/compare.html Unfortunately, you have to buy it or pay monthly fee for Internet access. ====================================================================== The replies I got: From: "Eldbjørg Sofie Heimstad" Rolf Claessen's Chemistry Index: http://www.claessen.net/chemistry/soft_en.html & http://www-fbsc.ncifcrf.gov/compenv/app_soft/index.html (for instance AMSOL software) From: "Dave" You'll find a considerable amount of data at: http://comp.chem.umn.edu/amsol/AlkaneSuppTables.html which is supplementary material for a paper published in J. Phys. Chem. Journal of Physical Chemistry, 99, 7137-7146 (1995) From: Kristy Mardis You might want to look at: D. J. Giesen, C. J. Cramer, and D. G. Truhlar J. Phys. Chem vol 99, p. 7137, 1995 They provide tables (in supplemental material) of a number of experimental solvation free energies in nonpolar solvents. From: Flemming Steen Jorgensen The following reference contains a lot of free energy of solvation data: S. Cabani, P. Gianni, V. Mollica and L. Lepori, Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution, Journal of Solution Chemistry, 1981, vol. 10, number 8, pp. 563-595. ====================================================================== Thank you all who replied! Artem __ ___________ Artem.Masunov@usa.net;tel 212-650-7792;fax877-280-5146 / \ / __ __ \ Ph.D., Research Associate, Comput. Biophys. Chemistry / \/\ \ \ \ \ \ Chemistry Department, City College, City U. of NY / /\ \ \ \ \ \ \ \ J-1325, Convent Ave at 138 Str, New York, NY 10038 / ____ \ \ \ \ \ \ \ --------------------------------------------------- /__/\ _/\ _\ \ _\ \ _\ \ _\ FORGIVE MY NONSENSE AS I ALSO FORGIVE THOSE \ _\/ \/__/\ __/\ __/\ __/ WHO THINK THEY TALK SENSE -- ROBERT FROST From chemistry-request@server.ccl.net Sat Jul 8 08:22:09 2000 Received: from gate.ggr.co.uk (gate.ggr.co.uk [193.128.25.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20363 for ; Sat, 8 Jul 2000 08:22:08 -0400 Received: (uucp@localhost) by gate.ggr.co.uk; Sat, 8 Jul 2000 13:22:50 +0100 (BST) Received: from uk-stv-mhub1.ggr.co.uk(147.184.212.132) by gb-stv-fw2.ggr.co.uk via smap (V4.2) id xma000392; Sat, 8 Jul 00 13:22:16 +0100 Received: from ukz590.ggr.co.uk (ukz590.ggr.co.uk [147.184.226.247]) by mailhub.ggr.co.uk; Sat, 8 Jul 2000 13:18:23 +0100 (BST) Received: from ukz582.ggr.co.uk (unverified) by ukz590.ggr.co.uk (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Sat, 08 Jul 2000 13:19:16 +0100 Received: by ukz582.ggr.co.uk with Internet Mail Service (5.5.2448.0) id <3333GVY2>; Sat, 8 Jul 2000 13:18:07 +0100 Message-Id: From: "Zuccotto, Fabio" To: "'chemistry@ccl.net'" Subject: DOCK chem.defn file Date: Fri, 7 Jul 2000 13:54:47 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain Dear CCL users, the atom labelling parameters used by DOCK (chemical matching option) are contained in the file chem.defn.There, a set of atom definition rules (based on .mol2 atom types) is used to define acceptor, donor, polar hydrophobic atoms. For instance a carboxylate carbon is defined as C.2 (2 O.co2) where ( ) specify atoms that must be bounded to the parent atom. Similarly [ ] specify atoms that must not be bound to the parent atom. (*) specify any atom type (page 96 of the manual). Looking at the chem.defn file (page 98 of the manual) it contains, for instance, entries such as: F [*] for polar C.3 [*] for hydrophobic O. [H] [N.] (*) for acceptor The way I read these entries is: F [*] = a fluorine atom with nothing attached to it C.3 [*] = an sp3 carbon with nothing attached to it O. [H] [N.] (*) = any kind of oxygen with any atom attached to it but H or N Clearly it is not possible that DOCK is defining the labels as isolated fluorine or carbon atoms as it is not possible that the definition of acceptor does not include -OH. Any better way to interpret these definitions? Thank you very much. fabio From chemistry-request@server.ccl.net Sat Jul 8 15:14:58 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA21731 for ; Sat, 8 Jul 2000 15:14:58 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id PAA19353; Sat, 8 Jul 2000 15:14:29 -0400 (EDT) Message-ID: <021f01bfe911$0c005f10$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Debasis Sengupta" Cc: "CCL - all" References: <39663D71.ED5BB51B@cfdrc.com> Subject: Re: CCL:cc-pVDZ for DFT ?? Date: Sat, 8 Jul 2000 15:16:32 -0400 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 Hi Debasis, the cc basis sets can be used with DFT, although there are basis sets that are explicitly optimized for use with DFT. The cc basis sets are designed specifically for the classical correlation treatment and the functions that are new in the next bigger basis set contribute similar amounts of energy. I have heard that DFT has a stronger dependency on the radial parts and a weaker dependency on the angular components of the basis set. Therefore the bigger cc basis sets (cc-pVTZ, cc-pVQZ) might carry unneeded f or even g functions together with the actually used radial parts of the basis set. If anybody is aware of a paper that treats this topic in depth, I'd like to hear about it. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Sat Jul 8 15:28:27 2000 Received: from mail5.svr.pol.co.uk (mail5.svr.pol.co.uk [195.92.193.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA21818 for ; Sat, 8 Jul 2000 15:28:26 -0400 Received: from modem-40.titanium.dialup.pol.co.uk ([62.136.21.40] helo=chmibm275) by mail5.svr.pol.co.uk with smtp (Exim 3.13 #0) id 13B0Gm-0006SV-00 for chemistry@ccl.net; Sat, 08 Jul 2000 20:28:09 +0100 Message-Id: <3.0.6.32.20000708202944.00804b20@chmsun1.leeds.ac.uk> X-Sender: wolfgang@chmsun1.leeds.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Sat, 08 Jul 2000 20:29:44 +0100 To: chemistry@ccl.net From: Wolfgang Roth Subject: CCL:cc-pVDZ for DFT ?? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Debasis Sengupta wrote: > Can correlation consistent basis sets (such as cc-pVDZ, cc-pVTZ etc >etc) be used with DFT? They certainly CAN be used if they are available to your favourite ab initio program. I assume the correct question is more like "Does it make sense to use (Dunnings) correlation consistent basis sets in DFT calculation?" To my experience they give very similar results to Poples 6-31G(d,p) [cc-pVDZ] and 6-311G(d,p) [cc-pVTZ] concerning molecular geometry and vibrational frequencies but lower SCF energies. I'd like to see some more theoretically founded answer(s) ;-) Regards Wolfgang ==W=R==========================W=o=l=f=g=a=n=g==R=o=t=h== University of Leeds School of Chemistry Leeds LS2 9JT UK ========== http://home.germany.net/100-500777/ ==========