From chemistry-request@www.ccl.net Fri Feb 12 05:45:17 1999 Received: from ds.cesga.es (ds.cesga.es [193.144.33.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA20852 Fri, 12 Feb 1999 05:44:51 -0500 (EST) Received: (from uviqplco@localhost) by ds.cesga.es (8.9.1b+Sun/8.9.1) id LAA14016; Fri, 12 Feb 1999 11:44:45 +0100 (MET) Date: Fri, 12 Feb 1999 11:44:45 +0100 (MET) From: Luis Carballeira Oca~na To: chemistry@www.ccl.net Subject: P and As basis sets? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am interested in making COMPARATIVE conformational analysis ( full geometrical optimization, HF and MP2, using GAUSSIAN 94 ) of compounds with five carbons and two phosphorus atoms and compounds with five carbons and two arsenic atoms. I have a medium/high capacity of calculation. Which would be the basis sets best adapted for phosphorous and arsenic? Thank you. Luis Carballeira Physical Chemistry Lab. University of Vigo, Spain e-mail: uviqplco@ds.cesga.es From chemistry-request@www.ccl.net Fri Feb 12 06:58:20 1999 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA21063 Fri, 12 Feb 1999 06:57:37 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.3/8.9.3) with ESMTP id LAA01260 for ; Fri, 12 Feb 1999 11:56:31 GMT Date: Fri, 12 Feb 1999 11:56:34 +0000 From: Michael Nolan To: ccl Subject: density matrix renormalisation group methods Message-ID: <19990212115632.A1705@rennes.nmrc.ucc.ie> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.1i Hello all, I posted this question about a week ago ************************************************************* Dear CCLers... We are looking at studying conjugated polymers for application in photvoltaic devices. I have seen the density matrix renormalisation group (DMRG) method used for calculation of excitations and non-linear optical properties. Does anyone have (i) any experience with using DMRG and (ii) knowledge as to where there might be an available code? (A web search is none too useful...) Thank you in advance Michael **************************************************************** Unfortunately, because there were no answers, it seems that nobody uses this method in mainstream comp. chem. regards Micheal -- ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html **************************************************************************** From chemistry-request@www.ccl.net Fri Feb 12 09:30:34 1999 Received: from mgw2.merck.com (mgw2.merck.com [155.91.4.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA22225 Fri, 12 Feb 1999 09:30:33 -0500 (EST) Message-Id: <199902121430.JAA22225@www.ccl.net> Date: Fri, 12 Feb 1999 09:27:50 -0500 From: "Halgren, Thomas" Subject: An evaluation suite for conformatonal energies, intermolecular in teraction energies and geometries, and molecular geometries To: "'Computational Chemistry List'" Cc: "Halgren, Thomas" MIME-version: 1.0 Content-type: text/plain Content-transfer-encoding: 7BIT Dear CCLers, Jan Labanowski has kindly posted on the Computational Chemistry List archives a force-field evaluation suite that is geared to assessing performance for reproducing conformational energies and for producing reasonable values and trends for intermolecular-interaction energies and geometries. This evaluation suite provides the input data and a summary of principal results for the following manuscript: T. A. Halgren, "MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries," J. Comput. Chem., in press (expected out in April 1999). As most of the reference ab initio structures are MP2(FULL)/6-31G*-optimized structures, the suite can also be used for testing or parameterizing force-field geometries. Input data are provided for three sets of conformational energy comparisons. The first uses the 37 comparisons to experiment employed in the original MMFF94 paper on this subject (T. A. Halgren and R. B. Nachbar, J. Comput. Chem., 17, 587-615 (1996)); reference "MP4SDQ/TZP" and GVB-LMP2/cc-pVTZ(-f) energies are also provided. The second set consists of 19 comparisons to experiment taken from K. Gundertofte, T. Liljefors, P.-O. Norrby, and I. Petterssen, J. Comput. Chem., 17, 429-449 (1996) for which neither ab initio nor experimental data were used in the development of MMFF94. The third set consists of 147 comparisons to ab initio values obtained at the composite "MP4SDQ/TZP" level. For Sets 1 and 3, the input structures provided are MP2(FULL)/6-31G*-optimized structures; for Set 2, MMFF94-optimized structures that can serve as a useful starting place for optimizations using other methods are provided. Input data are also provided for comparisons of intermolecular-interaction energies and geometries to scaled HF/6-31G* results for the 66 small-molecule dimers used in the nonbonded parameterization of MMFF94 (T. A. Halgren, J. Comput. Chem., 17, 520-552 (1996)). Two postscript files provide tables that summarize the overall success of the fits to experimental or ab initio data for the various theoretical methods. In all, the evaluation suite contains 25 files. A README file (or, for Web browsers, its html equivalent) explains the role of each. Please note also that a revised and updated MMFF94 validation suite has been posted elsewhere on the CCL archives. The force-field evaluation suite can be accessed at: ftp://www.ccl.net/pub/chemistry/data/ff_evaluation_suite or at: http://www.ccl.net/cca/data/ff_evaluation_suite I would be pleased to hear of any uses made of this data. Best regards, Tom Halgren voice: 732-594-7735 fax: 732-594-4224 halgren@merck.com From chemistry-request@www.ccl.net Fri Feb 12 09:51:07 1999 Received: from mgw2.merck.com (mgw2.merck.com [155.91.4.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA22443 Fri, 12 Feb 1999 09:51:07 -0500 (EST) Message-Id: <199902121451.JAA22443@www.ccl.net> Date: Fri, 12 Feb 1999 09:44:44 -0500 From: "Halgren, Thomas" Subject: Revised and extended MMFF94 Validation Suite To: "'Computational Chemistry List'" Cc: "Halgren, Thomas" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear CCLers, Jan Labanowski has kindly posted on the Computational Chemistry List archives a revised and extended version of the MMFF94 Validation Suite that was first released in May 1998. The new suite corrects MMFF94 results for eight structures for which the atom typing has been found to be erroneous, and adds eight additional structures geared to more fully test the empirical-rule parameter generation procedures defined in the published MMFF94 papers. The suite contains a README file (or, for Web browsers, its html equivalent) that defines the files in the validation suite. The most important are: MMFF94_dative.mol2 mol2-format input, using dative bonds for certain sulfur and phosphorous compounds MMFF94_hypervalent.mol2 SYBYL mol2 input, using "hypervalent" representations MMFF94.mmd BatchMin/MacroModel dat-format input MMFF94.energies list of BatchMin and Merck-OPTIMOL total energies MMFF94_bmin.log BatchMin output log file MMFF94_opti.log OPTIMOL output file with detailed interaction analyses MMFF94.changed-or-new_results Energies for new structures and for structures affected by corections to the MMFF94 atom-typing procedures MMFF94.empirical_rule_parameters Listing of structures and interactions for which empirical-rule parameters are generated These input and output files provide data for the validation suite, which now consists of 761 molecules. Also provided are auxiliary files that list the names of molecules that have alternative dative and hypervalent representations (MMFF94.dative_molecules); that specify the formal atomic charges used in the dative and hypervalent representations (MMFF94.fc_dative and MMFF94.fc_hypervalent); and that list the molecule names and titles (MMFF94.titles). Most of the input data is derived from CSD structures. I wish to thank Steve Salisbury and the Cambridge Crystallographic Data Center for graciously consenting to the use of this data. I also wish to thank Jan Labanowski for his encouragement in the posting of this validation suite and for his role in providing CCL and its archives to the community. My hope is that this data will assist members of the community who have independently implemented MMFF94, or who are in the process of doing so, to validate their efforts (I am aware of five such initiatives, in addition to the BatchMin and CHARMm implementations to which Merck has contributed). Those who have already implemented MMFF94 should obtain and compare results for the corrected and added members of the validation suite, and should insure that any modifications they need to make do not affect the other members of the suite. This validation suite is also intended allow individuals who use an independently developed commercial implementation of MMFF94 to carry out their own validation and to satisfy themselves as to its authenticity. Those who are not interested in pursuing MMFF94 per se might view the suite as a source of input data that could be useful in developing and testing other force fields. A force-field evaluation suite comprised of ab initio and/or experimental data on conformational energies and on intermolecular interactions together with input molecular structure data is being posted elsewhere on the CCL archives. This suite may be even more useful for this purpose. The MMFF94 validation suite can be accessed at: ftp://www.ccl.net/pub/chemistry/data/MMFF94 or at: http://www.ccl.net/cca/data/MMFF94 I would be pleased to hear of any use made of this data. Best regards, Tom Halgren voice: 732-594-7735 fax: 732-594-4224 halgren@merck.com From chemistry-request@www.ccl.net Fri Feb 12 10:55:07 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23187 Fri, 12 Feb 1999 10:55:02 -0500 (EST) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id HAA26179 for ; Fri, 12 Feb 1999 07:55:03 -0800 (PST) Date: Fri, 12 Feb 1999 07:55:03 -0800 (PST) From: "Dale A. Braden" Reply-To: "Dale A. Braden" To: cclpost Subject: Summary: vib. PED program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, A few days ago I asked about a program that could decompose vibrational normal modes into a potential energy distribution based on internal coordinates. Thanks to all who responded, and here is the list: GAMESS-US: set DECOMP=.TRUE. in the $FORCE section REDONG: contact Alain Allouche (Marseilles, France) allouche@piimsdm11.univ-mrs.fr (this program will read G94 output files directly) SVIB: see http://spiro.princeton.edu/~arka/info but this link has been broken for a few days, so I don't really know that this program does what I want. One could contact the authors Arka Mukherjee and Thomas Spiro at Princeton. NMODES: contact Siva Umapathy at uma@ims.ac.jp (this program will read G94 files directly) Best wishes to all, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@www.ccl.net Fri Feb 12 11:30:36 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 LAA23640 Fri, 12 Feb 1999 11:30:33 -0500 (EST) Received: from nppp204.overnet.com.ar (nppp204.overnet.com.ar [200.16.162.217]) by carpincho.overnet.com.ar (8.9.3/8.9.3) with SMTP id NAA22570 for ; Fri, 12 Feb 1999 13:35:13 -0300 Message-Id: <3.0.6.16.19990212132538.130738de@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (16) Date: Fri, 12 Feb 1999 13:25:38 To: chemistry@www.ccl.net From: "Dr. Daniel Glossman" Subject: PC version of AIMPAC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: Is there any available PC (Windows) version of the AIMPAC series of programs? Thanks in advance Daniel Glossman From chemistry-request@www.ccl.net Fri Feb 12 13:07:11 1999 Received: from relay.stjohns.edu (relay.stjohns.edu [149.68.16.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA25519 Fri, 12 Feb 1999 13:07:05 -0500 (EST) Received: from mail.stjohns.edu ([149.68.17.15]) by relay.stjohns.edu (Post.Office MTA v3.5.3 release 223 ID# 576-55350U23000L23000S0V35) with ESMTP id edu; Fri, 12 Feb 1999 13:07:40 -0500 Received: from w-qsal1107b001 ([149.68.97.193]) by mail.stjohns.edu (Post.Office MTA v3.5.3 release 223 ID# 576-55350U23000L23000S0V35) with SMTP id edu; Fri, 12 Feb 1999 12:58:16 -0500 Received: by localhost with Microsoft MAPI; Fri, 12 Feb 1999 13:08:08 -0500 Message-ID: <01BE5688.BC4C4A90.korlipav@stjohns.edu> From: korlipav@stjohns.edu (Korlipara Vijaya) Reply-To: "korlipav@stjohns.edu" To: "'masamura'" Cc: "'CHEMISTRY@www.ccl.net'" Subject: RE: HYDROGEN BOND Date: Fri, 12 Feb 1999 13:08:07 -0500 Organization: sju X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 46 TEXT You may wish to look into the following article that appeared in the Perspectives section of "Science" recently. A New Type of Hydrogen Bond, by Robert H. Crabtree, Science, Vol.282, 2000-2001, 1998. It is not a review article, but a report on a newly discovered "third type of H-bond". Vijaya Korlipara, Ph.D. Associate Professor of Medicinal Chemistry College of Pharmacy St. John's University Jamaica, NY 11439 -----Original Message----- From: masamura [SMTP:ep7@dent.okayama-u.ac.jp] Sent: Thursday, February 11, 1999 8:50 PM To: CHEMISTRY@www.ccl.net Subject: CCL:HYDROGEN BOND Dear Sir: Please teach me recent comprehensive literature for hydrogen bond. Thank you. *********************************************************** Masao Masamura Okayama University ep7@dent.okayama-u.ac.jp FAX: 81-86-235-6714 TEL: 81-86-235-6712 *********************************************************** -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: chemistry-request@www.ccl.net -- Original Sender From: Address: ep7@dent.okayama-u.ac.jp 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 Fri Feb 12 16:54:57 1999 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA10014 Fri, 12 Feb 1999 16:54:55 -0500 (EST) Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id WAA21021; Fri, 12 Feb 1999 22:51:17 +0100 (MET) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id VAA01797; Fri, 12 Feb 1999 21:51:18 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9902122251.ZM1795@torvs.ccc.uni-erlangen.de> Date: Fri, 12 Feb 1999 22:51:17 +0000 Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Chemistry Web Service Abuse Cc: ak@organik.uni-erlangen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit In the night of Feb 10th, our chemical structure GIF image generator service (http://www2.ccc.uni-erlangen.de/services/gifcreator/) was under attack. The unidentifyable host 134.192.72.194 posted several ten thousand image generation requests, which all failed, probably due to some programming error in the requester script. Some hours before that and again later a few requests from the same source were successfully processed, probably the result of manual experimental submission. We do not appreciate this kind of exploitation. Since this is a pretty special Web service, the originator of this attack may be listening. The conditions of this service explicitly forbid the use of the images for a commercial application, which given the number of requests looks likely. They contain copyright information embedded in the image data. Even if the intended use was for another, non-commercial purpose, we definitely prefer to be informed beforehand if such a massive number of structures is going to be processed. In such cases, send us an email. We are willing to help and process your structures as a batch job without going through the Web interface. If this incidence is not resolved, the domain 134.192.72.xxx will be locked out. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu