From chemistry-request@www.ccl.net Mon Feb 8 06:10:31 1999 Received: from mail.matav.hu (mail.matav.hu [145.236.224.244]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA07445 Mon, 8 Feb 1999 06:10:27 -0500 (EST) Received: (qmail 20782 invoked from network); 8 Feb 1999 11:55:07 +0100 Received: from comnet1.comgenex.hu (HELO compudrug.hu) (195.228.105.146) by mail.matav.hu with SMTP; 8 Feb 1999 11:55:07 +0100 Message-ID: <36BED798.29D466C@compudrug.hu> Date: Mon, 08 Feb 1999 13:24:56 +0100 From: Akos Papp Organization: CompuDrug International Inc. X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Steven Creve , CHEMISTRY-list at OSC CC: Aida Citti Subject: pKa and pKb calculation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Steven, There is a software available on the market for acidic and basic pKa-values of organic compounds. It estimates pKa using Hammett and Taft equations. It contains of approximately 1400 fragments (including ~600 ionizable center types). If you need more info, please contact Ms. Aida Citti (e-mail address above; I've carbon-copied this message to her). Sincerely, Akos Papp From chemistry-request@www.ccl.net Mon Feb 8 08:55:06 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA08554 Mon, 8 Feb 1999 08:55:04 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA16908; Mon, 8 Feb 99 05:53:55 -0800 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma016904; Mon, 8 Feb 99 05:53:27 -0800 Received: by news.msi.com (4.1/SMI-4.1) id AA13241; Mon, 8 Feb 99 05:31:51 PST Newsgroups: msi.comp-chem-list Path: uucp From: Victor Milman Subject: Re: CCL:G:Scanning Probe Microscopy X-Nntp-Posting-Host: 192.190.183.137 Content-Type: text/plain; charset=us-ascii To: "C.F. Matta" Message-Id: <36BEEC73.AD24603B@msi.com> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. References: Mime-Version: 1.0 Date: Mon, 8 Feb 1999 13:53:55 GMT X-Mailer: Mozilla 4.03 [en] (WinNT; I) Hello, Here are some recent papers based on the plane-wave technology: R. Perez, I. Stich, M. C. Payne, K. Terakura, Surface-Tip Interactions in Noncontact Atomic-Force Microscopy on Reactive Surfaces: Si(111), Phys. Rev. B58 (1998) 10835. http://www.msi.com/science/online/references/CASTEP_list/Abs/Perez.PRB_1998_58_10835.html R. Perez, M. C. Payne, I. Stich, K. Terakura, Contrast Mechanism in Non-Contact AFM on Reactive Surfaces, Appl. Surf. Sci. 123 (1998) 249. http://www.msi.com/science/online/references/CASTEP_list/Abs/Perez.ASS_1998_123_249.html R. Perez, M. C. Payne, I. Stich, K. Terakura, Role of Covalent Tip-Surface Interactions in Noncontact Atomic Force Microscopy on Reactive Surfaces, Phys. Rev. Lett. 78 (1997) 678. http://www.msi.com/science/online/references/CASTEP_list/Abs/Perez.PRL_1997_78_678.html R. Perez, M. C. Payne, A. D. Simpson, First Principles Simulations of Silicon Nanoindentation, Phys. Rev. Lett. 75 (1995) 4748. http://www.msi.com/science/online/references/CASTEP_list/Abs/Perez.PRL_1995_75_4748.html (a reasonably complete list of CASTEP publications is at http://www.msi.com/science/online/references/CASTEP_list/CASTEP_pubs.html) Udo Becker has done a lot of AFM/STM modeling for surfaces of minerals, using CRYSTAL (HF) (ubecker@uni-muenster.de), see http://www.uni-muenster.de/Chemie/MI/people/becker/beckerpubl-e.html Hope this helps C.F. Matta wrote: > > Hi everybody, > > First: > I would much appreciate if you could point to me recent publications > about modeling/computational studies of the interaction of the tip with > the substrate in Atomic Force Microscopy (AFM) or/and Scanning Tunneling > Microscopy (STM). > > Second: > In STM, a typical separation from the tip to the substarte is 3-10 A, > i.e. the tails of the wavefunctions of the tip and of the substrate are > crucial. Gaussian functions are not behaving physically at long distances. > Moreover, if the substrate consists of different atoms described with > basis functions decaying at different rates, this will overemphasize the > peacks due to the one decaying slower (the true wavefunction decays > at a single rate). The Linearized Augmented PlaneWave method (LAPW), due > to Tersoff & Hamann, is supposed to remedy for this. > (1) Is there other methods better than LAPWD? > (2) Can one implement LAPWD in, say GAUSSIAN or GAMESS? > (3) If the answer to (2) is YES, then HOW? > (4) If NO, then what program(s) implements this method? > (5) Other suggestions? > > Thank you all very much. I will summarize. > > Cherif > ....................................................................... > Cherif F. Matta tel. (905) 525-9140 ext. 22502 > Chemistry Department fax (905) 522-2509 > McMaster University > Hamilton, Ontario, CANADA L8S 4M1. > ....................................................................... > > -------This is added Automatically by the Software-------- > > ****Posts to this newsgroup leave MSI's network**** -- =================================================================== Victor Milman * Project Leader, Quantum Mechanics Molecular Simulations Inc * tel: (01223) 413300 The Quorum * fax: (01223) 413301 Barnwell Road * tel. from abroad: +44 1223 413301 Cambridge CB5 8RE, UK * e-mail: vmilman@msicam.co.uk =================================================================== From chemistry-request@www.ccl.net Mon Feb 8 12:47:17 1999 Received: from cucbs.chem.columbia.edu (cucbs.chem.columbia.edu [128.59.112.96]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA16828 Mon, 8 Feb 1999 12:47:15 -0500 (EST) Received: from localhost (jasna@localhost) by cucbs.chem.columbia.edu (8.9.1a/8.9.1) with SMTP id MAA13436; Mon, 8 Feb 1999 12:47:02 -0500 (EST) Date: Mon, 8 Feb 1999 12:47:01 -0500 (EST) From: Jasna Klicic To: Yongxing Liu cc: chemistry@www.ccl.net Subject: Re: CCL:Metal ion-water complex calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Date: Fri, 05 Feb 1999 13:47:05 -0500 > From: Yongxing Liu > To: chemistry@www.ccl.net > Subject: CCL:Metal ion-water complex calculations > > Dear CCLers, > > Would any one please point to me any references of ab initio, > semiempirical, DFT calculations on metal ion-water complexes? The metal > ions I am interested in are Na+, K+, Mg2+, Zn2+, Cl-, etc. > > Thanks a lot in advance. > > Sincerely, > > Yongxing Liu > Dear Yongxing Liu, There is an ab initio study of Zn(II)dithiophosphate by W. Goddard you might be interested to see. The reference is: Whaoyi Jiang et al, J. Phys. Chem. 1996, (100), p15760 Best regards, Jasna =============================================================== Jasna J. Klicic, Ph.D. Schrodinger, Inc. One Exchange Place jasna@schrodinger.com Suite 604 tel. (201) 433-2014 x104 Jersey City, NJ 07302 fax. (201) 433-2065 http://www.schrodinger.com =============================================================== From chemistry-request@www.ccl.net Mon Feb 8 17:14:28 1999 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA25404 Mon, 8 Feb 1999 17:14:28 -0500 (EST) From: luojun@ne059.cm.utexas.edu Received: from ne056.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA14711; Mon, 8 Feb 1999 16:05:47 -0600 Message-Id: <3.0.1.32.19990208161236.0090a880@eeyore.cm.utexas.edu> X-Sender: luojun@eeyore.cm.utexas.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 08 Feb 1999 16:12:36 -0600 To: chemistry@www.ccl.net Subject: parameters for platinum Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all: I am looking for the software which includes the parameters of platinum(Pt) for semiemperical calculations. Could you give me any suggestion? Thank you very much. Sincerely, Jun Luo From chemistry-request@www.ccl.net Mon Feb 8 20:30:26 1999 Received: from karplus0.harvard.edu (tammy.harvard.edu [128.103.92.198]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA26789 Mon, 8 Feb 1999 20:30:26 -0500 (EST) Received: from usagi.harvard.edu (leclerc@usagi [128.103.92.19]) by karplus0.harvard.edu (8.8.2/8.8.2) with ESMTP id UAA01753; Mon, 8 Feb 1999 20:43:12 -0500 (EST) Received: (from leclerc@localhost) by usagi.harvard.edu (8.8.5/8.8.2) id UAA12618; Mon, 8 Feb 1999 20:31:01 -0500 Date: Mon, 8 Feb 1999 20:31:01 -0500 Message-Id: <199902090131.UAA12618@usagi.harvard.edu> From: Fabrice Leclerc To: Rissers-C@BATTELLE.ORG CC: chemistry@www.ccl.net In-reply-to: <5913080CA46DD111A98200A0C9960C10967C7B@ns-bco-mse7.im.battelle.org> (Rissers-C@BATTELLE.ORG) Subject: Re: CCL:periodic boundary conditions with DFT Date: Fri, 05 Feb 1999 09:38:14 -0500 From: "Risser, Steve" X-Mailer: Internet Mail Service (5.5.1960.3) Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Content-Type: text Content-Length: 1044 Hi All Does anyone know of any existing DFT code that can perform calculations on periodic systems, explicitly including symmetry? Thanks. Steve Hi Steve, You can do that with NWCHEM. I'm not sure there is any other code available with this feature. (see: http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html) From chemistry-request@www.ccl.net Mon Feb 8 21:03:55 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA26868 Mon, 8 Feb 1999 21:03:54 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA01648; Mon, 8 Feb 99 18:02:45 -0800 Received: from nxt-pc.msi.com(146.202.7.237) by bioc1.msi.com via smap (V2.0) id xma001644; Mon, 8 Feb 99 18:02:34 -0800 Message-Id: <3.0.3.32.19990208180206.0073d428@146.202.6.218> X-Sender: nxt@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 08 Feb 1999 18:02:06 -0800 To: "Risser, Steve" , "'chemistry@www.ccl.net'" From: Noppawan Tanpipat Subject: Re: CCL:periodic boundary conditions with DFT In-Reply-To: <5913080CA46DD111A98200A0C9960C10967C7B@ns-bco-mse7.im.batt elle.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Steve, You could do this with CASTEP (with symmetry) See http://www.msi.com/solutions/products/cerius2/modules/castep.html#info and DMol3 (with P1) See http://www.msi.com/solutions/products/cerius2/modules/dmol3.html#info Cheers, Noppawan At 09:38 AM 2/5/99 -0500, Risser, Steve wrote: >Hi All > >Does anyone know of any existing DFT code that can perform calculations on >periodic systems, explicitly including symmetry? >Thanks. > >Steve > >---------------------------------------------------------------------------- >------------------------ >Dr. Steven M Risser > >Current Year >Associate Professor of Physics Polymer Center >Texas A&M University-Commerce Battelle Memorial Institute >Commerce TX 75429 505 King Avenue > >Columbus, OH 43201-2693 > >(614) 424-3715 >---------------------------------------------------------------------------- >----------------------- > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: Rissers-C@BATTELLE.ORG >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > > ************************************* Noppawan Tanpipat, Ph.D. Product Specialist, Quantum Chemistry Molecular Simulations Inc. 9685 Scranton Road San Diego, CA 92121 Tel: (619) 799-5332 Fax: (619) 458-0136 Email: nxt@msi.com From chemistry-request@www.ccl.net Mon Feb 8 21:18:39 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA26951 Mon, 8 Feb 1999 21:18:38 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA01930; Mon, 8 Feb 99 18:17:28 -0800 Received: from nxt-pc.msi.com(146.202.7.237) by bioc1.msi.com via smap (V2.0) id xma001925; Mon, 8 Feb 99 18:17:11 -0800 Message-Id: <3.0.3.32.19990208181642.006c6e90@146.202.6.218> X-Sender: nxt@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 08 Feb 1999 18:16:42 -0800 To: chemistry@www.ccl.net From: Noppawan Tanpipat Subject: Re: CCL:periodic boundary conditions with DFT Cc: Rissers-C@BATTELLE.ORG Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Steve, You could do this with CASTEP (with symmetry) See http://www.msi.com/solutions/products/cerius2/modules/castep.html#info and DMol3 (with P1) See http://www.msi.com/solutions/products/cerius2/modules/dmol3.html#info Cheers, Noppawan At 09:38 AM 2/5/99 -0500, Risser, Steve wrote: >Hi All > >Does anyone know of any existing DFT code that can perform calculations on >periodic systems, explicitly including symmetry? >Thanks. > >Steve > >---------------------------------------------------------------------------- >------------------------ >Dr. Steven M Risser > >Current Year >Associate Professor of Physics Polymer Center >Texas A&M University-Commerce Battelle Memorial Institute >Commerce TX 75429 505 King Avenue > >Columbus, OH 43201-2693 > >(614) 424-3715 >---------------------------------------------------------------------------- >----------------------- > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: Rissers-C@BATTELLE.ORG >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Mon Feb 8 22:53:28 1999 Received: from carpincho.overnet.com.ar (carpincho.overnet.com.ar [200.10.96.19]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA27564 Mon, 8 Feb 1999 22:53:25 -0500 (EST) Received: from nppp184.overnet.com.ar (nppp184.overnet.com.ar [200.16.162.197]) by carpincho.overnet.com.ar (8.9.1/8.9.1) with SMTP id AAA17751 for ; Tue, 9 Feb 1999 00:58:10 -0300 Message-Id: <3.0.6.16.19990209004847.2c3746a6@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (16) Date: Tue, 09 Feb 1999 00:48:47 To: chemistry@www.ccl.net From: "Dr. Daniel Glossman" Subject: Bader's population analysis Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: Is there any program which is able to calculate (separately) the sigma and pi contributions to the total electronic charge within the context of a Bader's population analysis? Thamks in advance Daniel Glossman glossman@overnet.com.ar From chemistry-request@www.ccl.net Mon Feb 8 22:53:31 1999 Received: from carpincho.overnet.com.ar (carpincho.overnet.com.ar [200.10.96.19]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA27565 Mon, 8 Feb 1999 22:53:28 -0500 (EST) Received: from nppp184.overnet.com.ar (nppp184.overnet.com.ar [200.16.162.197]) by carpincho.overnet.com.ar (8.9.1/8.9.1) with SMTP id AAA17754 for ; Tue, 9 Feb 1999 00:58:13 -0300 Message-Id: <3.0.6.16.19990209004927.2c37fd9a@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (16) Date: Tue, 09 Feb 1999 00:49:27 To: chemistry@www.ccl.net From: "Dr. Daniel Glossman" Subject: Pop=Bonding calculation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear sirs: I have been doing some G94W calculations on several molecules with the POP=Bonding keyword, but I don't know how to do an interpretation of the results and the Gaussian 94 manual is not very informative in this respect. For example, after the title "... Condensed to atoms (all electrons..." I got a symmetric matrix with diagonal elements equal to zero. 1) What do the numbers mean? 2) Where do they come from? 3) Are they related to the so called bond order analysis? 4) Are there any bibliographic references for the calculation of these numbers? After that I got the total atomic charges. These charges are different from those coming from a traditional Mulliken population analysis in that they are not summed up to the charge of the molecule under study. Again, 1) What do these charges mean? 2) What's the meaning of the summation? 3) Where do these numbers come from? 4) which are the bibliographic references? Thanks in advance for a kind consideration of this request. Best regards Dr. Daniel Glossman ***************************************************************************** Universidad Nacional de Lujan Departamento de Ciencias Basicas e-mail: glossman@overnet.com.ar Casilla de Correo 221 phone: (+54) 1 5533797 (6700) Lujan fax: (+54) 1 5539824 Republica Argentina **************************************************************************** **