From chemistry-request@www.ccl.net Mon Feb 1 04:44:11 1999 Received: from sauer.ethz.ch (sauer.ethz.ch [129.132.17.91]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA07811 Mon, 1 Feb 1999 04:44:09 -0500 (EST) Received: from igc.phys.chem.ethz.ch (localhost [127.0.0.1]) by sauer.ethz.ch (8.8.8/8.8.8) with ESMTP id KAA18708 for ; Mon, 1 Feb 1999 10:42:03 +0100 (CET) Sender: portmann@scsc.ethz.ch Message-ID: <36B576EA.26F3AE85@igc.phys.chem.ethz.ch> Date: Mon, 01 Feb 1999 10:42:02 +0100 From: Stefan Portmann X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL CCL Subject: meldf-x Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello is anybody out there using meldf-x? Where are reaching the filesize limit of 4.29GB on a HP-Exemplar for scratch files. We also figured out how to split them in sint but we don't see any way to use them further in symtrn. Does anybody have experience with that kind of problems? Thanks for your help in advance! Stefan -- Dr. Stefan Portmann Physical Chemistry Institute ETH-Zentrum, RZ F15 Clausiusstrasse 59 CH-8092 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 11 04 e-mail: portmann@igc.phys.chem.ethz.ch From chemistry-request@www.ccl.net Mon Feb 1 09:29:33 1999 Received: from uldns2.unil.ch (uldns2.unil.ch [130.223.4.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA10319 Mon, 1 Feb 1999 09:29:32 -0500 (EST) Received: from pcbch3207a.unil.ch ([130.223.143.43]) by uldns2.unil.ch with smtp (Exim 2.10 #1) for chemistry@www.ccl.net id 107KLl-0004dR-00; Mon, 1 Feb 1999 15:29:17 +0100 Message-Id: <3.0.3.32.19990201152935.008c8ce0@pop-server.unil.ch> X-Sender: aporquet@pop-server.unil.ch X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 01 Feb 1999 15:29:35 +0100 To: chemistry@www.ccl.net From: Alain Porquet Subject: CCL: Gaussian98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers! I wonder to known if G94 and G98 output files are identical Thank you for your attention. From chemistry-request@www.ccl.net Mon Feb 1 10:03:50 1999 Received: from sun.rhrk.uni-kl.de (sun.rhrk.uni-kl.de [131.246.137.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA11040 Mon, 1 Feb 1999 10:03:43 -0500 (EST) Received: from aix12.rhrk.uni-kl.de ( aix12.rhrk.uni-kl.de [131.246.137.12] ) by sun.rhrk.uni-kl.de id aa28690 ; 1 Feb 99 16:04 MET Received: from aixd1.rhrk.uni-kl.de(really [131.246.137.210]) by aix12.rhrk.uni-kl.de via smtpd with smtp id for ; Mon, 1 Feb 1999 16:03:32 +0100 (MEZ) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Received: by aixd1.rhrk.uni-kl.de via send-mail with stdio id for gerwalin@rhrk.uni-kl.de; Mon, 1 Feb 1999 16:03:25 +0100 (MEZ) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Message-Id: Date: Mon, 1 Feb 1999 16:03:25 +0100 (MEZ) From: Elmar Gerwalin To: chemistry@www.ccl.net Subject: Gavezotti-Programm ? Cc: gerwalin@rhrk.uni-kl.de Hi ! I heard that Mr. Gavezotti has developped a program to calculate (resp. predict) Crystal strcutures of molecular systems. Is that true ? Can you give me a hint where to get that program (if it exists) ? Thank you for your help (in advance) Bye Elmar gerwalin@rhrk.uni-kl.de From chemistry-request@www.ccl.net Mon Feb 1 12:24:51 1999 Received: from hermes.fju.edu.tw (hermes.ch.fju.edu.tw [140.136.196.150]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA18464 Mon, 1 Feb 1999 12:24:47 -0500 (EST) Received: by hermes.fju.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA13267; Tue, 2 Feb 1999 01:18:29 +0800 Date: Tue, 2 Feb 1999 01:18:29 +0800 From: shin@hermes.fju.edu.tw (Shin-Inn Chen) Message-Id: <9902011718.AA13267@hermes.fju.edu.tw> To: chemistry@www.ccl.net Subject: initial guess method dear netters: does any one know any references about applying initial guess method on calculations of electronic excited states? any suggestions will be appreciated and i will summarize it. e-mail: shin@hermes.fju.edu.tw shin 1999/2/2 From chemistry-request@www.ccl.net Mon Feb 1 13:07:34 1999 Received: from sun.rhrk.uni-kl.de (sun.rhrk.uni-kl.de [131.246.137.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA22871 Mon, 1 Feb 1999 13:07:32 -0500 (EST) Received: from aix12.rhrk.uni-kl.de ( aix12.rhrk.uni-kl.de [131.246.137.12] ) by sun.rhrk.uni-kl.de id aa16514 ; 1 Feb 99 19:08 MET Received: from aixd1.rhrk.uni-kl.de(really [131.246.137.210]) by aix12.rhrk.uni-kl.de via smtpd with smtp id for ; Mon, 1 Feb 1999 19:07:29 +0100 (MEZ) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Received: by aixd1.rhrk.uni-kl.de via send-mail with stdio id for gerwalin@rhrk.uni-kl.de; Mon, 1 Feb 1999 19:07:27 +0100 (MEZ) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Message-Id: Date: Mon, 1 Feb 1999 19:07:27 +0100 (MEZ) From: Elmar Gerwalin To: chemistry@www.ccl.net Subject: Program to calc. Crystals(Gavezotti?) Cc: gerwalin@rhrk.uni-kl.de Hi ! I heard that Mr. Gavezotti has developped a program to calculate (resp. predict) Crystal strcutures of molecular systems. Is that true ? Can you give me a hint where to get that program (if it exists) ? Thank you for your help (in advance) Bye Elmar gerwalin@rhrk.uni-kl.de From chemistry-request@www.ccl.net Thu Jan 28 13:25:13 1999 Received: from mail-relay.ubc.ca (mail-relay.ubc.ca [137.82.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA21617 Thu, 28 Jan 1999 13:25:12 -0500 (EST) Received: from byron.biochem.ubc.ca (byron.biochem.ubc.ca [137.82.133.119]) by mail-relay.ubc.ca [137.82.1.2] (8.8.8/8.8.8) with SMTP id KAA14325; Thu, 28 Jan 1999 10:25:13 -0800 (PST) Received: (from sness@localhost) by byron.biochem.ubc.ca (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA07141; Thu, 28 Jan 1999 10:24:17 -0800 Date: Thu, 28 Jan 1999 10:24:17 -0800 (PST) From: Steven Ness To: chemistry@www.ccl.net Subject: Re: CCL:academic docking software In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 26 Jan 1999, Jan De Kerpel wrote: > Dear CCL's, > > > I am looking for receptor/ligand protein docking software > (flexible and/or rigid) like FlexiDock or Affinity (provided > by some commercial groups) but for low/free prices (academic > usage). > To be run on sgi R10000, IBM RS6000 or pc. > > Thanks, > Jan De Kerpel > email : jan.dekerpel@chem.kuleuven.ac.be Dr. De Kerpel, We have a program DockVision that might be what you are looking for. DockVision is a new docking package created by scientists for scientists. By including Monte Carlo, Genetic Algorithm, and database screening docking algorithms in one complete docking package, DockVision increases your capability to generate laudable results. Moreover, access to multiple algorithms is not the only advantage DockVision gives you; you also have access to a full suite of powerful tools at your disposal. Instead of waiting for the full docking run to be completed before you can check RMS deviation and other data, access them at any time from within the same interface. With it's companion visualization program DockCam, you can quickly look at docking results, Dockvision currently runs on SGI, RS6000 and Linux. For more information, go to www.dockvision.com Steven Ness sness@byron.biochem.ubc.ca Strynadka Lab Department of Biochemistry University of British Columbia Canada From chemistry-request@www.ccl.net Thu Jan 28 15:41:26 1999 Received: from matahari.spi.nd.edu (matahari.spi.nd.edu [129.74.38.105]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA22714 Thu, 28 Jan 1999 15:41:26 -0500 (EST) Received: (from owiest@localhost) by matahari.spi.nd.edu (8.8.5/8.8.5) id PAA19410 for chemistry@www.ccl.net; Thu, 28 Jan 1999 15:41:29 -0500 Date: Thu, 28 Jan 1999 15:41:29 -0500 From: Olaf Wiest Message-Id: <199901282041.PAA19410@matahari.spi.nd.edu> To: chemistry@www.ccl.net Subject: 32. MWTCC at Notre Dame, May 20-22 +++++++++++++++++++++++++++++++++++++++++++++ FIRST ANNOUNCEMENT 32nd Midwest Theoretical Chemistry Conference University of Notre Dame Notre Dame, IN May 20-22, 1999 +++++++++++++++++++++++++++++++++++++++++++++ Please mark your calendar and plan to attend the 32nd Midwest Theoretical Chemistry Conference to be held May 20-22, 1999, at the University of Notre Dame and hosted jointly by the Department of Chemistry and Biochemistry and by the Radiation Laboratory. The conference covers all areas of theoretical and computational chemistry. Contributions are invited from all researchers, including undergraduate students, graduate students, postdocs, faculty, corporate scientists, and government researchers. A broad cross section of theoretical and computational topics is expected to be represented in both the oral and poster sessions. Traditionally, this meeting has served as a unique opportunity for students and postdocs to give short oral presentations on their current research. As more information on the conference becomes available it can be obtained at the WWW site http://www.nd.edu/~mwtcc. This site is currently under construction and significant material will be added in the coming weeks. We look forward to seeing you this May. The Organizing Committee: Daniel M. Chipman Sharon Hammes-Schiffer Olaf Wiest From chemistry-request@www.ccl.net Thu Jan 28 16:09:35 1999 Received: from chemvx.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA23020 Thu, 28 Jan 1999 16:09:34 -0500 (EST) Received: from biosym.chem.tamu.edu ([165.91.176.9]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with SMTP id AAA154 for ; Thu, 28 Jan 1999 15:11:37 -0600 Sender: plin@mail.chem.tamu.edu (Ping Lin) Message-ID: <36B0D20D.167E@mail.chem.tamu.edu> Date: Thu, 28 Jan 1999 13:09:33 -0800 From: ping lin Organization: Texas A&M University X-Mailer: Mozilla 2.0S (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL: references and suggestions on theoretical ET study X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I want to investigate some systems involving electron transfer (ET) reactions, theoretically. As I am still at the beginning stage, I am looking for some good references (reviews, books, papers, etc) and suggestions about the theoretical electran transfer study, specifically, the most recent articles applying quantum mechanical methods. I know that there have been many models in this area, among them, I am most interested in those using ab initio methods. Thanks, Ping Lin plin@mail.chem.tamu.edu From chemistry-request@www.ccl.net Fri Jan 29 06:40:14 1999 Received: from dirc.bris.ac.uk (dirc.bris.ac.uk [137.222.10.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA27150 Fri, 29 Jan 1999 06:40:13 -0500 (EST) Received: from mole.chm.bris.ac.uk by dirc.bris.ac.uk with SMTP-PRIV (PP) with ESMTP; Fri, 29 Jan 1999 11:39:48 +0000 Received: from chth044.chm.bris.ac.uk (chth044.chm.bris.ac.uk [137.222.40.38]) by mole.chm.bris.ac.uk (8.9.1/8.9.1) with SMTP id LAA25285 for ; Fri, 29 Jan 1999 11:36:40 GMT From: Adrian Mulholland Sender: Adrian.Mulholland@bristol.ac.uk Reply-To: Adrian.Mulholland@bristol.ac.uk To: chemistry@www.ccl.net Subject: MGMS meeting "QM/MM Methods and Applications" Message-ID: Date: Fri, 29 Jan 1999 11:31:12 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers, I have been asked to send on this meeting announcement. My apologies if you have received it before. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ MEETING ANNOUNCEMENT The Molecular Graphics and Modelling Society presents MM/QM METHODS AND APPLICATIONS The first MM/QM meeting in the UK 14-16 April, 1999 University of Southampton, United Kingdom +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A two day meeting covering the development and application of combined Molecular Mechanics/Quantum Mechanics methods. Invited speakers: Tim Clark University of Erlangen, Germany Ian Hillier University of Manchester, UK Paul Lyne University of Oxford, UK Adrian Mullholland University of Bristol, UK Jean-Louis Rivail Universite Henri Poincare-Nancy, France Walter Thiel University of Zurich, Switzerland Ian Williams University of Bath, UK The meeting will begin after lunch on Wednesday, 14 April, 1999, and finish before lunch on Friday, 16 April, 1999. Oral contributions and poster presentations are invited; abstracts should be submitted for consideration to Dr Frank Blaney by 1 February, 1999. A limited number of student bursaries are available; students should indicate that they wish to be considered for a bursary when they submit their abstract. For further information about the meeting, see: http://www.soton.ac.uk/~chemphys/jessex/mgms To register, send a completed registration form obtainable from the above web page to Dr Frank Blaney by 1 March, 1999. EARLY REGISTRATION IS RECOMMENDED AS PLACES ARE LIMITED The 1999 Annual General Meeting of the Molecular Graphics and Modelling Society will take place on Thursday, 15 April, 1999, at 5 pm at this conference. Dr FE Blaney SmithKline Beecham Pharmaceuticals New Frontiers Science Park (North) Third Avenue Harlow Essex CM19 5AW email: frank_e_blaney@sbphrd.com +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ---------------------- Adrian Mulholland School of Chemistry Phone: 0117-928-9097 University of Bristol Fax: 0117-925-1295 Bristol BS8 1TS Adrian.Mulholland@bris.ac.uk From chemistry-request@www.ccl.net Fri Jan 29 09:18:58 1999 Received: from bbhm.na.pg.com (bbhm.na.pg.com [192.44.184.159]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA13095 Fri, 29 Jan 1999 09:18:57 -0500 (EST) From: shelley.jc@pg.com Received: from bhh5.na.pg.com (root@bhh5.na.pg.com [192.44.184.129]) by bbhm.na.pg.com (8.8.8/8.8.8) with ESMTP id JAA05531 for ; Fri, 29 Jan 1999 09:15:46 -0500 (EST) Received: from bdc-notes003.na.pg.com (bdc-notes003.na.pg.com [155.125.116.11]) by bhh5.na.pg.com (8.8.8/8.8.8) with SMTP id JAA10657 for ; Fri, 29 Jan 1999 09:18:09 -0500 (EST) Received: by bdc-notes003.na.pg.com(Lotus SMTP MTA v4.6.2 (693.3 8-11-1998)) id 85256708.004E9556 ; Fri, 29 Jan 1999 09:18:20 -0500 X-Lotus-FromDomain: PGI To: chemistry@www.ccl.net Message-ID: <85256708.004BD21D.00@bdc-notes003.na.pg.com> Date: Fri, 29 Jan 1999 08:48:02 -0500 Subject: Alpha based computers in computational chemistry Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hello, In the context of individual research laboratories looking for workstations or low to mid-range compute servers, are alpha based computers used much in computational chemistry laboratories and if so how? (For this question please regard Alpha based Cray computers as upper-range compute servers.) On paper these machines seem quite powerful. I would appreciate hearing what people think of such machines, particularly people who have used them. John Shelley From chemistry-request@www.ccl.net Fri Jan 29 09:54:36 1999 Received: from catios.udea.edu.co ([200.24.20.180]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA15527 Fri, 29 Jan 1999 09:54:04 -0500 (EST) Received: from catios.udea.edu.co (lab-carb2-059.udea.edu.co [200.24.16.227]) by catios.udea.edu.co (8.8.7/8.8.7) with ESMTP id JAA32523 for ; Fri, 29 Jan 1999 09:55:42 -0500 Message-ID: <36B1CB17.50FA9F77@catios.udea.edu.co> Date: Fri, 29 Jan 1999 09:52:07 -0500 From: Alejandro Montoya X-Mailer: Mozilla 4.08 [en] (Win95; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: Chemisorption Content-Type: multipart/alternative; boundary="------------CEE03D3695ABDDE80E628A8B" --------------CEE03D3695ABDDE80E628A8B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Readers: I am studying gas chemisorption on solid surface and I am interested in knowing how the CO2 can be chemisorbed ( Different states of energy, any mechanical theory about that or whatever, and calculus ab initio) . If someone can help me whit any kind of information (publications/refrences) about this topic I will be very grateful. Thanks in advance. Alejandro Montoya E. Ph.D student University of Antioquia --------------CEE03D3695ABDDE80E628A8B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  Dear CCL Readers:

 I am studying  gas chemisorption  on  solid surface and I am interested  in knowing how the CO2 can be chemisorbed ( Different states of energy, any mechanical theory about that or whatever, and calculus ab initio)  . If someone can help me whit any kind of information  (publications/refrences) about  this topic I will be very grateful.

Thanks in advance.

Alejandro Montoya E.
Ph.D student
University of Antioquia --------------CEE03D3695ABDDE80E628A8B-- From chemistry-request@www.ccl.net Fri Jan 29 11:42:24 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA17119 Fri, 29 Jan 1999 11:42:24 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id LAA29251; Fri, 29 Jan 1999 11:42:23 -0500 (EST) Date: Fri, 29 Jan 1999 11:42:21 -0500 (EST) From: Jan Labanowski To: chemistry@www.ccl.net Subject: 99.06.21 31st ACS Central Regional Meeting in Columbus Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I did not see it advertized on CCL, but it probably should have had been. I am not in anyway involved in organization, so I am not working for myself here. 31st Central Regional Meeting of American Chemical Society will be held at: June 21 - 23 1999 The Ohio State University Fawcett Center Hotel-Restaurant-Conference Center 2400 Olentangy River Road Columbus OH 43210 For program, calls for papers, details, session chairpeople, etc, etc. look at: http://chemistry.ohio-state.edu/acs-crm31/ The motto is "Chemistry in Space", but/and we CompChem geeks fit anywhere, so you may want to speak there. In short, the deadline to give a talk or whatever is March 1, 1999. Get your ACS forms ready... Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | From chemistry-request@www.ccl.net Fri Jan 29 12:52:32 1999 Received: from imo12.mx.aol.com (imo12.mx.aol.com [198.81.17.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA18150 Fri, 29 Jan 1999 12:52:31 -0500 (EST) From: Mmgerhardt@aol.com Received: from Mmgerhardt@aol.com by imo12.mx.aol.com (IMOv18.1) id FXPJa04795 for ; Fri, 29 Jan 1999 12:51:52 -0500 (EST) Message-ID: Date: Fri, 29 Jan 1999 12:51:52 EST To: chemistry@www.ccl.net Mime-Version: 1.0 Subject: SBS 5th Annual Conference and Exhibition Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Windows 95 sub 64 SBS will host its 5th Annual Conference and Exhibition at the Edinburgh International Conference Center, September 13-16, 1999. This meeting will address all aspects of High Throughput Screening including combinatorial chemistry, lead generation, assay design, automation, software and information handling. For additional information please contact the Society for Biomolecular Screening at 203-743-1336, email: sbsemail@aol.com or visit our website at www.sbsonline.org. From chemistry-request@www.ccl.net Sat Jan 30 03:49:15 1999 Received: from mailrelay1.lrz-muenchen.de (mailrelay1.lrz-muenchen.de [129.187.254.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA27986 Sat, 30 Jan 1999 03:49:14 -0500 (EST) Received: from [129.187.26.12] by mailout.lrz-muenchen.de with ESMTP; Sat, 30 Jan 1999 09:49:12 +0100 Received: from pet.localnet.hh (pet [192.17.5.9]) by localnet.hh (8.9.1/8.9.1) with SMTP id HAA19942; Sat, 30 Jan 1999 07:37:32 +0100 (CET) Message-Id: <199901300637.HAA19942@localnet.hh> Received: by pet.localnet.hh (NX5.67g/NX3.0X) id AA01520; Sat, 30 Jan 1999 07:14:29 +0100 Mime-Version: 1.0 (NeXT Mail 4.2mach v148) Content-Type: text/enriched; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline X-Image-Url: http://www.lrz.de/~heller/hheller.tiff X-Face: #K8+M!=vK|\bQ[&P:z)d$Q:i(@36P1!7if~nI%OB\9I>;p5Vs<_YkU;].K(chZJ,k8X96t ]!d?;H/|Jc:Hr-hhbBow![@FkT0xNOVXK|TO%Jg@Xz X-Nextstep-Mailer: Mail 4.2mach (Enhance 2.2p1) Received: by NeXT.Mailer (1.148) From: Helmut Heller Date: Sat, 30 Jan 1999 07:14:28 +0100 Subject: Re: CCL:HELP WITH TINKER To: chemistry@www.ccl.net Reply-To: hheller@gmx.de References: <19990127124952.9468.qmail@hotmail.com> X-Url: http://www.lrz.de/~heller Status: RO Content-Length: 1426 <= nofill>040b73747265616d747970656481a203840163c4840373737381dadb81070781161684= 012584067f411b312d36 You wrote: > I am trying to implement TINKER to run MD on biomolecules. I am unable=20 > to do a minimization of a tripeptide in solution. the energy blows up. > is there an example file where i could look into? [it is a tripeptide=20 > immersed in a 15A cube of tip3p waters]. the minimization in vaccum runs=20= > fine. minimization/md of water alone runs fine too. Most likely you were not carefull enough when you immersed the peptide into the water cube and you ended up with vdW overlaps. Check the INITIAL vdW energy! If it is high (several powers of 10) then your initial setup is bad. Helmut --- HelveticaServus, Helmut (DH0MAD) =20 ___________ NeXT-mail welcome ________________ FAX: +49-8671Symbol- Helvetica881 665 " Knowledge must be gathered and cannot be given " hheller@gmx.de ZEN, one of BLAKES7 Phone: +49-8671Symbol- Helvetica881665 =20 --------------------------------------------------------------------------- Dr. Helmut Heller, M=FChldorfer Str. 72, 84503 Alt=F6tting, GERMANY From chemistry-request@www.ccl.net Fri Jan 29 11:02:37 1999 Sender: mathieu@ripault.cea.fr Date: Fri, 29 Jan 1999 16:02:11 +0000 From: Didier MATHIEU To: chemistry@www.ccl.net Subject: [Fwd: PACK of replies: DFT/H-bonds] [Edited by CCL Administrator -- long headers and repeats removed Dear all, In reply to requests, here are the replies I got to my question about DFT description of H-bonds. Regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 Here are the replies I got to my answer. -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 -------------- Subject: Date: Mon, 25 Jan 1999 10:17:27 -0600 (CST) From: Carlo Adamo To: mathieu@ripault.cea.fr Ciao Didier, I did some works about DFT & H-bond. Please give a look at these papers: Chem. Phys. Lett. 224 (1994) 432 Chem. Phys. Lett. 231 (1994) 295 J. Chem. Phys. 102 (1995) 364 Int. J. Quantum. Chem. 56 (1995) 697 J. Phys. Chem. 99 (1995) 15062 J. Chem. Phys. 105 (1996) 11007 Int. J. Quantum. Chem. 61 (1997) 429 J. Comp. Chem. 18 (1997) 1993 a review was published in: Recent Advances in Density Functional Methods, Part II, Edited by D.P. Chong, World Scientific Press, Singapore (1997). Furthermore the computation of H-bond strength in small complexes, as water dimer, is one of the tests to check the performances of new functionals. So you might find some informations also in J. Chem. Phys. 108 (1998) 664 J. Comp. Chem. 19 (1998) 418 Carlo ******************************************************************* ** * H** O Dr Carlo ADAMO * phone +1-713-5278101 O**^||} Rice University * ext. 3734 T***-| Depart. of Chemistry MS60 * ****_| P.O. Box 1892 * e-mail: I*** Houston TX 77251-1892 * carlo@celaeno.rice.edu C** USA * E** * ******************************************************************* -------------- >From pudziana@bms.com Tue Jan 26 16:03:35 1999 Date: Tue, 26 Jan 1999 09:59:46 -0500 From: Andrew T Pudzianowski Subject: Re: CCL:Hydrogen Bonds with DFT / GGA To: Didier MATHIEU Didier MATHIEU wrote: > > Hello everybody, > > I have carried out some calculations of energetic data for molecules > including nitroaromatics with gradient-corrected DFT functionals, > especially Becke-Perdew86. > The results are satisfactory excepted for tri-amino-trinitro-benzene, > the only molecule in my dataset showing intramolecular hydrogen bond. > I read somewhere that DFT was not very good at describing hydrogen > bonds. > I wonder if anybody can provide me some details about this subject, i.e. > performance of DFT with regard to hydrogen bonds. > > Thank you. > Regards > > -- > Didier MATHIEU > CEA - Le Ripault, BP 16 > 37260 Monts (France) > Tel. 33(0)2.47.34.41.85 > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: mathieu@ripault.cea.fr > 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 Dear Dr. Mathieu - I have done some work myself on this subject. There are two publications you might find informative, as follows: A. T. Pudzianowski, "A Systematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100, 4781-4789 (1996) A. T. Pudzianowski, "Current Computational Approaches to the Strong Hydrogen Bond," in "Recent Research Developments in Physical Chemistry," vol. 1, Transworld Research Network, Trivandrum, India (1997), pp. 81-97. The second is a review with lots of references; unfortunately, the book may be hard to find but I can send a reprint if you wish. Both of these can serve as an effective introduction to the subject and the newer literature. With best wishes, Andrew Pudzianowski >From rozas@pinar1.csic.es Tue Jan 26 09:35:20 1999 Date: Tue, 26 Jan 1999 10:33:38 +0000 From: Isabel Rozas Subject: HB with DFT To: mathieu@ripault.cea.fr Hello there! I don't know if you remember me, it was many many years ago that we met in some of this french-spanish conferences. I did my PhD with Pilar Goya and now I work with her and with Prof. Elguero in Madrid in the Medicinal Chemistry Institute. I am also subscribe to the computational chemistry list so I saw your question this morning. Enough of presentations and let's go with the question. Latetly we have work quite a lot in hydrogen bonding. We have used >from HF/6-31G till MP2 (and more)/6-311++G**. Also we have used DFT but not the Becke-Perdew86 but the B3LYP. I do not too much about the Perdew but I can tell you that the Becke3LYP works very well for hydrogen bonds. We have even found out that using B3LYP/6-311++G** (or even with a little smaller base like 6-31+G*) you get results similar to those obtained with MP2/6-311++G**. Some of our work is gathered in: I. Alkorta, I. Rozas and J. Elguero. "Non-conventional hydrogen bonds" Chem. Soc. Rev., 163-170, 27 (1998). but if you want more information we have just create a web page with all the theoretical work we are doing and maybe can be of some utility for you. The address of that web page is as follows: http://www.iqm.csic.es/are/main.htm So trying to answer your question, I don't beleive is a problem of DFT but maybe can be a problem of the method you chose (BeckePerdew86 vs. Becke3LYP). I do not know either which program are you using byt this B3LYP is included in Gaussian94 and 98. I hope everything is fine with you and I sent you my regards Isabel Rozas >From jsl@virgil.ruc.dk Tue Jan 26 10:18:48 1999 From: "Jens Spanget-Larsen" To: Didier MATHIEU Date: Tue, 26 Jan 1999 10:21:49 +0100 Subject: Re: CCL:Hydrogen Bonds with DFT / GGA Didier MATHIEU: > I have carried out some calculations of energetic data for molecules > including nitroaromatics with gradient-corrected DFT functionals, > especially Becke-Perdew86. > The results are satisfactory excepted for tri-amino-trinitro-benzene, > the only molecule in my dataset showing intramolecular hydrogen bond. > I read somewhere that DFT was not very good at describing hydrogen > bonds. > I wonder if anybody can provide me some details about this subject, i.e. > performance of DFT with regard to hydrogen bonds. We obtained satisfactory results with B3LYP/6-31G* for molecular and vibrational structures of intramolecularly H-bonded beta-hydroxy carbonyl compounds like malonaldehyde enol and anthralin: Chem. Phys. 240, 51-61 (1999) J. Mol. Struct. 475, 131-140 (1999) Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >From brauer@al.bundy.uni-jena.de Tue Jan 26 09:09:35 1999 From: Michael Braeuer Subject: Re: CCL:Hydrogen Bonds with DFT / GGA To: mathieu@ripault.cea.fr (Didier MATHIEU) Date: Tue, 26 Jan 99 9:13:41 MET > > Hello everybody, > > I have carried out some calculations of energetic data for molecules > including nitroaromatics with gradient-corrected DFT functionals, > especially Becke-Perdew86. > The results are satisfactory excepted for tri-amino-trinitro-benzene, > the only molecule in my dataset showing intramolecular hydrogen bond. > I read somewhere that DFT was not very good at describing hydrogen > bonds. > I wonder if anybody can provide me some details about this subject, i.e. > performance of DFT with regard to hydrogen bonds. Hi, the Montreal group around Prof. Salahub developed a functional called LAP3 which is able to handle hydrogen bonds correctly (even transition states for hydrogen transfer). This work is conected mainly to E. Proynov after whom the functional is named. If you contact them they surely provide you with their program DeMon. Best regards Michael -- Michael Braeuer http://www.uni-jena.de/chemie/anders/micha.htm PhD Student E-mail: brauer@al.bundy.uni-jena.de IOMC FSU Jena Tel: ++49/3641/948217 Humboldtstrasse 10 Fax: ++49/3641/948212 07743 Jena Germany >From gerwalin@rhrk.uni-kl.de Mon Jan 25 23:06:59 1999 Date: Mon, 25 Jan 1999 23:07:14 +0100 (MEZ) From: Elmar Gerwalin To: mathieu@ripault.cea.fr Subject: Second (and last) list of articles Hi Didier Here comes the second (and last) list of articles I have about H-bonded systems. It#s from Thomas Steiner from Berlin, who does crystallisation experiments and is not a theretical chemist. Hope that helps you, nevertheless. Bye Elmar (the part from the original mail, that was in german:) Umezawa et al., Bull.Chem.Soc.Jpn, 71, 1998, 1207. Uebersichtsartikel: Nishio et al., Tetrahedron, 51, 1989, 7201 und Tetrahedron, 51, 1995, 8665. for organic chemists mainly (collections of structures from databases) (a book:) M.Nishio, M.Hirota and Y. Umezawa. The CH/pi interaction. Evidence, nature and consequences. Wiley, New York, 1998. Ich selbst habe ueber CH-pi mit aciden CH Gruppen publiziert, z.B. Steiner et al., Acta Cryst. B53, 1997, 843, J.Chem.Soc., Perkin Trans, 2, 1995, 1312 und 1996, 2441. Theoretical articles !: Rozas et al., J.Phys.Chem.A, 101, 1997, 9457, Review: Alkorta et al., Chem.Soc.Rev., 27, 1998, 163. (author:Thomas Steiner , Berlin) >From dima@euch4e.chem.emory.edu Mon Jan 25 22:56:46 1999 From: Dmitry Khoroshun Subject: Re: CCL:Hydrogen Bonds with DFT / GGA To: mathieu@ripault.cea.fr (Didier MATHIEU) Date: Mon, 25 Jan 1999 16:56:47 -0500 (EST) Hello! Some people think that the quality of description of hydrogen bonds by density functional methods is very sensitive to the quality of the basis set used. One of the suggestions is that the convergence of DFT methods with respect to basis set is much slower than that of, for example, MP2. You may want to check CPL 1995, 245, 129 CPL 1995, 247, 112 Canadian J. Chem. 1995, 73, 710 JPC 1995, 99, 5899 JPC 1995, 99, 15837 JPC 1996, 100, 3942 Usually, gradient-corrected functionals are reliable with large basis sets CPL 1996, 254, 135 CPL 1996, 263, 345 JPC 1995, 99, 592 Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu >From gerwalin@rhrk.uni-kl.de Mon Jan 25 22:55:19 1999 Date: Mon, 25 Jan 1999 22:55:18 +0100 (MEZ) From: Elmar Gerwalin To: mathieu@ripault.cea.fr Subject: List of articles on DFT+HBOND Hi Didier Here's the first list of articles I found on your theme. It's a summary from the CCL from a while ago: Hope it helps. >From chemie.uni-kl.de!elg Mon Jan 25 22:50:14 1999 Date: Mon, 25 Jan 1999 22:50:11 +0100 From: elg@chemie.uni-kl.de (Elmar Gerwalin) To: gerwalin@rhrk >From chemistry-request@www.ccl.net Wed Aug 13 21:35:52 1997 Date: Wed, 13 Aug 1997 14:09:07 -0400 (EDT) From: Anatoli Korkin Subject: CCL:G:Summary - B3LYP for H-bonded systems To: chemistry@www.ccl.net >Does any one know references on comparative ab initio and DFT (preferably >B3LYP) studies of H-bonded systems and proton transfer? Any reviews on >this topic? Dear CCLers, CCLers, Thanks to everybody who responded on my question. I have received as much answers as requests for summary. It was also fun to hear from and about my old friends and to make new contacts. H-boding seems to be a nice topic for a chat, although I was surprized it is still so popular :-) We have decided to extend our introduction a bit to cite and to discuss some recent results. Have a good day, everybody! Anatoli P.S. Sorry, I have no time to clean up messages properly. Please, substract what you need yourself. I also keep the addresses to let H-bonding community to have some local talks among them :-) Summary: -------- Dear Anatoli, Dennis Salahub has worked on this extensively; several imporatant papers were published recently, also with repsect to developing new functionals for these purposes (BLap.. functionals). What systems are you interested in? Please summarize the responses, I'm curious. Hope all is well at your end. It's finally HOT here (for German standards). All the best, Peter -- //// ___|--00___________________________________________________________________ C ^ Dr. Peter R. Schreiner \ ~/ Institut fuer Organische Chemie <><> Georg-August Universitaet Goettingen Tammannstr. 2 Phone: +49-(0)551-393287 D-37077 Goettingen, Germany FAX: +49-(0)551-399475 http://www.gwdg.de/~ucoc/schreiner ___________________________________________________________________________ HI, ANATOLI - I can certainly give you one. J. E. Del Bene, W. B. Person, and K. Szczepaniak, J. Phys. Chem. 99, 10705 (1995). DFT/B3LYP can be quite erratic. What's up????? Janet hi Anatoli, I've been working for a while in H-bonded systems comparing dft (b3lyp is included) and ab-initio methods. Maybe this can help: "Cooperative effects in water trimers. The performance of density functional approaches" L. Gonzalez et al. J. Molec. Struct. (Theochem) 371 (1996) 1 "High level ab initio versus DFT calculations on (H2O2)2 and H2O2-H2O complexes as prototypes of multiple h-bonded systems" L. Gonzalez et al. J. Comput. Chem. 18 (1997) 1124. Best wishes, Leticia Gonzalez ********************************* * Leticia Gonzalez * * Dept. of Chemistry * * Dalhousie University * * Halifax, NS B3H 4J3 * * Canada * * * * Phone: 902-494 7021 * * e-mail: gonzalez@is.dal.ca * ********************************* Hi Anatoli, I assumed you already received a message from Leti Gonzales about her work done on water dimers (she sits next door in Boyd's lab). I also can add to that list a paper J.Chem.Soc., Faraday Trans., 1997, 93(2), 333. Best regards, Vladimir ********************************************************************** Vladimir V. Murashov Department of Chemistry tel : +1-902-494-6538 Dalhousie University fax : +1-902-494-1310 Halifax, NS E-mail: murashov@is2.dal.ca Canada B3H 4J3 ********************************************************************** I hope you find the following references useful. Sim et al. JACS 1992, 114, 4391 "Gaussian density functional calculations on h bonded systems" Kovacs et al J. Comp. Chem. 1996, 17(16), 1804 "Theoretical study of intramolecular hydrogen bonding ... " Gonzalez et al J. Comp. Chem. 1997, 18, 1124 " High level ab initio versus dft calculations on ... " Hobza et al J. Comp. Chem. 1995, 16(11), 1315 " density functional theory and molecular clusters" Kind Regards, Damian Moran email: damian.moran@mq.edu.au voice:(+61) 2 9850 8278 fax:(+61) 2 9850 8313 www:http://www.chem.mq.edu.au/~dmoran School of Chemistry,Macquarie University,NSW 2109 Australia H-bonded, i don't know, but you might find @ARTICLE{Jursic1996a, AUTHOR = {Branko S. Jursic}, JOURNAL = CPL, PAGES = {603-608}, TITLE = {Density functional theory study of radical hydrogen abstraction with hydrogen and hydroxyl radicals}, VOLUME = {256}, YEAR = {1996} } interesting anyway. --------------------------- Dear Anatoli, a comparison between HF, MP2, different DFT methods and experimental data for the water dimer and hydrogen bonded base pairs is given in: A. St-Amant, Density functional methods in biomolecular modeling, Reviews in Computational Chemistry 7, chapter 5, VCH 1996. We have carried out some calculations of hydrogen bonded nucleic acid base pairs at MP2/6-31G**//HF/6-31G** and B3LYP/6-31G** level. The B3LYP- intermolecular distances seem to be somewhat better than the HF- distances and the interaction energies from single point MP2 and B3LYP are in reasonable agreement. Michael Meyer -- ---------------------------------------------------------------------------- Michael Meyer Institut fuer Molekulare Biotechnologie (IMB) Biocomputing E-mail: mmeyer@imb-jena.de Beutenbergstrasse 11, Jena Tel.: +49-3641-65-6203 Postfach 100 813, D-07708 Jena, Germany Fax: +49-3641-65-6210 ---------------------------------------------------------------------------- Anatoli, in response to your question about proton transfer and DFT methods, we have been doing alot of calcs on the effectiveness of various DFT methods for the study of short, strong (or low-barrier) hyrogen bonds. One of these studies will come out this month in JACS, watch for it! If I had to summarize, I would say that in general the B3LYP functional gives geomtries and energies of reactions almost identical to MP2 in all cases. BLYP itself often gives hydrogen bond energies a little larger than either MP2 or B3LYP. For the hydrogen bifluoride system (coming out in Theochem shortly) the B3LYP, BLYP, MP2, MP3, MP4, QCISD,and CCSD results are almost identical. The SVWN and HF results are somewhat different than the other correlated methods. If you are interested in more specifics just contact me. Mike M. ************************************************************************** Michael A. McAllister Assistant Professor of Chemistry voice: 940-565-4584 University of North Texas fax: 940-565-4318 P.O. Box 305070 email: McAllister@unt.edu Denton, TX 76203 www: http://people.unt.edu/~mam0008 ************************************************************************** hese may be of some use: Proton affinity and DFT Phys Chem (jpc) 100 (1996) 11595 Deprotonation (E2 reactions) jpc 100 (1996) 16892 Gas-phase acidity jpc 100 (1996) 17465 C-H...O hydrogen bonds, MP2 cf. B-LYP Chem Phys Letters 266(1,2) (1997) 23 ---------- Your friend Igor Svishchev has just joined our Department. Best Wishes, E. Lewars ================= Dr. Korkin - Forgive me if I recommend a couple of my own publications: A. T. Pudzianowski, "A Systematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100 (12), 4781-4789 (1996) and A. T. Pudzianowski, "Current computational approaches to the strong hydrogen bond," Recent Res. Devel. in Physical Chem., 1, 81-97 (1997). The first deals with the strong H-bond and has a lot to say about comparisons of B3-LYP and B-LYP with MP2, mostly with the 6-311++ G(d,p) basis set. The second is a review of the whole area of com- putational descriptions of the strong H-bond. The reference is a bit obscure, so if you're interested please let me know and I'll send you a reprint. Hoping this will be helpful, Andrew Pudzianowski *********************************************************************** Andrew T. Pudzianowski,Ph.D. Bristol-Myers Squibb PRI Box 4000 * "There are two ways to do things. Princeton NJ 08543-4000 * There's the scientific way, and (609) 252-4248 * there's the disgusting way." (609) 252-6030: fax * pudzianowski@bms.com * "Beakman's World", 1994 *********************************************************************** Perhaps J. M. L. Martin, V. Aviyente, and C. Lifshitz, ``The insertion of amines and alcohols into proton bound dimers. A density functional study'', Journal of Physical Chemistry A 101, 2597-2606 (1997) might interest you. JM --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitfached k'lal --- See for a very recent review : Carlo Adamo, Vincenzo Barone Structural and Dynamical Features of Hydrogen Bonds from Conventional and Hybrid Density Functional Methods in : Recent Advances in Density Functional Meythods, Part II, Ed.: Delano P. Chong, World Scientific, 1997, Chap. 5, pp. 115-164 ( Recent Advances in Computational Chemistry, Vol.1 ) -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com Hi Anatoli, try 1. P. Hobza, J. Sponer, T. Reschel: "Density Functional Theory and Molecular Clusters", J. Comput. Chem. 16 (1995) 1315 2. M. Planas, C. Lee, J. Novoa: "Kinetic of the Proton Transfer in X-(H2O)4 Clusters (X=H2O, NH3, H2S, and HCl): Evidence for a Concerted Mechanism", J. Phys. Chem. 100 (1996) 16495 3. J. Del Bene, W. Person, K. Szczepaniak: "Properties of Hydrogen-Bonded Complexes Obtained from the B3LYP Functional with 6-31G(d,p) and 6-31+G(d,p) Basis Sets: Comparison with MP2/6-31+G(d,p) Results and Experimental Data", J. Phys. Chem. 99 (1995) 10705 4. Z. Latajka, Y. Boutellier, S. Scheiner: "Critical assessment of density functional methods for study of proton transfer processes. (FHF)-", Chem. Phys. Lett. 234 (1995) 159 5. Z. Latajka, S. Berski: "Density functional study of the H3N-Cl2 system - the importance of Hartree-Fock exchange in density function methods", J. Mol. Struct. (Theochem) 371 (1996) 11 6. J. Lundell, Z. Latajka: "Density Functional Study of Hydrogen-Bonded Systems: The Water-Carbon Monoxide Complex", J. Phys. Chem. A 101 (1997) in press. Sincerely yours, Bernd ----------------------------------------------------- Dr. Bernd Kallies Institut fuer Physikalische und Theoretische Chemie Universitaet Potsdam Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm Tel : [+49] (0)331 / 977-1313 Fax : [+49] (0)331 / 977-1315 ----------------------------------------------------- ======================================================== Elmar Gerwalin , University of Kaiserslautern Dept. of Theoretical Chemistry Erwin-Schroedinger-Str. 67663 Kaiserslautern, Germany http://iris2.chemie.uni-kl.de elg@chemie.uni-kl.de ======================================================== >From echamot@chamotlabs.com Mon Jan 25 19:37:13 1999 Date: Mon, 25 Jan 1999 12:37:12 -0600 To: Didier MATHIEU From: Ernest Chamot Subject: Re: CCL:Hydrogen Bonds with DFT / GGA Hi Didier, You asked: >I read somewhere that DFT was not very good at describing hydrogen >bonds. >I wonder if anybody can provide me some details about this subject, i.e. >performance of DFT with regard to hydrogen bonds. I use DFT a fair amount, and try to keep track of its strengths and weaknesses. The ability of DFT to describe hydrogen bonds (like so many other properties) has been improved by the use of gradient corrections, so that earlier generalizations of whether DFT is or isn't good at describing H-bonds are no longer appropriate. Sim, St-Amant, Papai, & Salahub, J. Am. Chem. Soc., 114, 4391-400 (1992). The accuracy will depend on the GGA used. Here are some estimates (and sources) of the accuracy of DFT calculations (including BP calculations, since you stated that you had been using that GGA) on H-bonded systems: 1) Earlier, bond lengths for a couple of H-bond systems were found accurate only to within ~ 0.1 and 0.3 A respectively with BP and VWN: See "Density Functional Methods in Chemistry," Labanowski & Andzelm Ed., Springer-Verlag (1991). 2) The B88P92 combination was supposed to be better for H-bonds: Perez-Jorda & Becke, Chem. Phys. Lett., 233, 134-7 (1995). 3) A comparison of BLYP & B3-LYP/ACM GGA's with several ionic H-bonds was reported to this list to calculate bond lengths within ~ 0.02-0.04 A and energies within ~ 2 kcal: See posting to CCL by A. T. Pudzianowski, 5/3/95. 4) A related calculation, would be to compare the accuracy of proton affinities. These have been found to be accurate within ~ 4 kcal for BP and VWN, and ranging from ~ 0.1 to 2 kcal for B3LYP/ACM: Fitzgerald & Andzelm, J. Phys. Chem., 95, 10531-4 (1991). Reported by A. Becke, San Francisco ACS Meeting, PHYS248, April, 1997. P. Redfern, J-P Blaudeau, & L. Curtiss, J. Phys. Chem. A, 101(46), 8701-5 (1997). Finally, you mentioned that you saw a problem with an amino-nitro aromatic: >I have carried out some calculations of energetic data for molecules >including nitroaromatics with gradient-corrected DFT functionals, >especially Becke-Perdew86. >The results are satisfactory excepted for tri-amino-trinitro-benzene, >the only molecule in my dataset showing intramolecular hydrogen bond. Out of curiosity, when you say the results are unsatisfactory, are you comparing against experimental data measured in the presence of a solvent? And if so, are you including solvent effects in your calculations? Nitroaromatics (specifically their radical anions) can show some subtle changes in geometry that can significantly change the energies. Cramer et. al. have reported some dramatic differences accurately reproduced with their semiempirical solvation model calculations (SM2 etc.): Initially in ECTOC-1, paper #46, 6/12/95; http://www.ch.ic.ac.uk/ectoc/ectoc-1.html And I have seen this in my own calculations using the COSMO solvation model, which has since been implemented in combination with DFT: J. Andzelm, C. Kolmel, & A. Klamt, J. Chem. Phys., 103(21), 9312-20 (1995). I hope this helps. EC --- Ernest Chamot Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, IL 60540 (630) 637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl >From gautier@and.mpi-stuttgart.mpg.de Mon Jan 25 18:07:10 1999 Date: Mon, 25 Jan 1999 18:07:10 +0100 From: Regis Gautier To: Didier MATHIEU Subject: Re: CCL:Hydrogen Bonds with DFT / GGA Bonjour, Il s'avere que le cas des liaisons faibles comme les liaisons hydrogene n'est pas maitrise par les fonctionelles GGA comme BP86. Il apparait que les fonctionelles hybrides conduisent a de meilleurs resultats comme B3LYP. Voir : H. Chermette, L'Actualite Chimique 1996, 7 ,10-15 et ref citees Cordialement, R. Gautier > Hello everybody, > > I have carried out some calculations of energetic data for molecules > including nitroaromatics with gradient-corrected DFT functionals, > especially Becke-Perdew86. > The results are satisfactory excepted for tri-amino-trinitro-benzene, > the only molecule in my dataset showing intramolecular hydrogen bond. > I read somewhere that DFT was not very good at describing hydrogen > bonds. > I wonder if anybody can provide me some details about this subject, i.e. > performance of DFT with regard to hydrogen bonds. > > Thank you. > Regards > ------------------------------------------------------------- Regis GAUTIER Max-Planck-Institut fur Festkorperforschung Heisenbergstr. 1, 70569 Stuttgart, Germany E-mail: gautier@and.mpi-stuttgart.mpg.de Tel: +49 711 689-1566 ; Fax: +49 711 689-1632 ------------------------------------------------------------- >From carlo@celaeno.rice.edu Mon Jan 25 17:19:24 1999 Date: Mon, 25 Jan 1999 10:17:27 -0600 (CST) From: Carlo Adamo To: mathieu@ripault.cea.fr Ciao Didier, I did some works about DFT & H-bond. Please give a look at these papers: Chem. Phys. Lett. 224 (1994) 432 Chem. Phys. Lett. 231 (1994) 295 J. Chem. Phys. 102 (1995) 364 Int. J. Quantum. Chem. 56 (1995) 697 J. Phys. Chem. 99 (1995) 15062 J. Chem. Phys. 105 (1996) 11007 Int. J. Quantum. Chem. 61 (1997) 429 J. Comp. Chem. 18 (1997) 1993 a review was published in: Recent Advances in Density Functional Methods, Part II, Edited by D.P. Chong, World Scientific Press, Singapore (1997). Furthermore the computation of H-bond strength in small complexes, as water dimer, is one of the tests to check the performances of new functionals. So you might find some informations also in J. Chem. Phys. 108 (1998) 664 J. Comp. Chem. 19 (1998) 418 Carlo ******************************************************************* ** * H** O Dr Carlo ADAMO * phone +1-713-5278101 O**^||} Rice University * ext. 3734 T***-| Depart. of Chemistry MS60 * ****_| P.O. Box 1892 * e-mail: I*** Houston TX 77251-1892 * carlo@celaeno.rice.edu C** USA * E** * ******************************************************************* From chemistry-request@www.ccl.net Mon Feb 1 16:52:50 1999 Received: from chem2.usc.edu (chem2.usc.edu [128.125.253.153]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA03490 Mon, 1 Feb 1999 16:52:49 -0500 (EST) Received: from localhost (devlin@localhost) by chem2.usc.edu (8.8.4/8.7) with SMTP id NAA53862; Mon, 1 Feb 1999 13:52:46 -0800 X-Authentication-Warning: chem2.usc.edu: devlin owned process doing -bs Date: Mon, 1 Feb 1999 13:52:46 -0800 (PST) From: "Frank J. Devlin" To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:optical activity prediction In-Reply-To: <199901291711.AA09473@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Robert, Take a look at Beratan's article in Science, 282, 2247 (1998). Regards, Frank Devlin. On Fri, 29 Jan 1999, TOPPER ROBERT wrote: > Hello all, > > An organic chemists with whom I collaborate has asked me > whether it is possible to predict the optical activity > of a mixture of enantiomers, even semiquantitatively. > (i.e., is the optical activity "big" or "small" for > a given enantiomeric excess, or e.e.). > > My own search of the Internet has failed to turn up anything. > Can anyone give us any suggestions? > > Thanks very much! > > best, > rqt > > ***************************************************************************** > Prof. Robert Q. Topper email: topper@cooper.edu > Department of Chemistry phone: (212) 353-4378 > The Cooper Union fax: (212) 353-4341 > 51 Astor Place subway: take the 6 to Astor Place > New York, NY 10003 and you're there! > http://www.cooper.edu/engineering/chemechem/ > ***************************************************************************** > The Cooper Union for the Advancement of Science and Art is a tuition-free > college in Greenwich Village, at Cooper Square and Astor Place. > ***************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: topper@cooper.edu > 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 1 17:59:09 1999 Received: from mailbox1.ucsd.edu (mailbox1.ucsd.edu [132.239.1.53]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA04503 Mon, 1 Feb 1999 17:59:09 -0500 (EST) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox1.ucsd.edu (8.9.1a/8.9.1) with ESMTP id OAA28733 for <@mailbox.UCSD.EDU:chemistry@www.ccl.net>; Mon, 1 Feb 1999 14:59:10 -0800 (PST) Received: from chemcca10 (localhost [127.0.0.1]) by chemcca10.ucsd.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id OAA23225 for ; Mon, 1 Feb 1999 14:59:09 -0800 (PST) Sender: wriggers@chemcca10.ucsd.edu Message-ID: <36B631BD.167E@chemcca10.ucsd.edu> Date: Mon, 01 Feb 1999 14:59:09 -0800 From: Willy Wriggers Organization: University of California, San Diego, Dept. of Chemistry and Biochemistry X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Xtal / EM docking with Situs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Dear all: I hereby announce the official release of Situs, a program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy. The program package has been developed to provide a robust and quantitative method for the localization of biomolecular subunits in low-resolution data. The package makes use of single-molecule density maps that can be obtained by subtraction of maps from specimens of variable subunit composition. The central algorithm is a topology-representing neural network to correlate features within the structural data sets. Version 1.0 is available at http://chemcca10.ucsd.edu/~situs/ Willy Wriggers, Ph.D. - http://chemcca10.ucsd.edu/~wriggers -- wriggers@ucsd.edu - Dept. of Chemistry and Biochemistry 0365, University of California, San Diego -- La Jolla, CA 92093. (619)534-2913 (tel), (619)534-7042 (fax). - Dept. of Cell Biology MB25, The Scripps Research Institute -- La Jolla, CA 92037. (619)784-2701 (tel), (619)784-2749 (fax). From chemistry-request@www.ccl.net Mon Feb 1 21:56:54 1999 Received: from chemvx.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA05753 Mon, 1 Feb 1999 21:56:54 -0500 (EST) Received: from mail.chem.tamu.edu ([165.91.68.230]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with ESMTP id AAA83; Mon, 1 Feb 1999 20:59:00 -0600 Message-ID: <36B66A1C.54D3C837@mail.chem.tamu.edu> Date: Mon, 01 Feb 1999 20:59:41 -0600 From: plin@mail.chem.tamu.edu (Ping Lin) X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Chemistry , Giovanni Scalmani , Jaouad El Bahroui Subject: CCL: Summary:programs for electron transfer theory Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Here is the summary of my question about the programs for ET theory. There were much less responses than I expected. I received quite some responses showing they are interested to see the summary. I do hope someone work in this area can provide some help in leading me and those who are interested to enter this area. The orginal question: > Hello, everyone, > > I am looking for any programs or softwares that is used in electron > transfer study. There have been many models developed in electron > transfer theory. I want to do some quantum mechanical study in some > systems. > Any suggestion is welcomed. Reply one: - From: Motohiro NAKANO I think you may be interested in the following paper by Prof. Nancy Makri: "Filtered propagator functional for iterative dynamics of quantum dissipative systems", which appeared in Comp. Phys. Commun. 99, 335-354 (1997). The source code (fortran) is available from cpc archive. Reply 2: -- >From : Jian-Xin Guo Department of Chemistry, University of California, Davis,CA95616 E-mail: guo@indigo.ucdavis.edu whick kind of calculations do you expect? most of them need you to make yourself code. Depend on what you want.