From chemistry-request@server.ccl.net Tue Apr 25 10:42:42 2000 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04344 for ; Tue, 25 Apr 2000 10:42:06 -0400 Received: from Alfredo ([150.161.5.112]) by npd.ufpe.br (PMDF V5.1-4 #20469) with SMTP id <01JONGSEV1WG0001VH@npd.ufpe.br> for CHEMISTRY@ccl.net; Tue, 25 Apr 2000 11:38:12 GMT-3 Date: Tue, 25 Apr 2000 11:33:52 -0300 From: Alfredo Mayall Simas Subject: RES: Semi empirical parameterisation for Transition elements In-reply-to: <10004191632.ZM17941@wavefun.com> To: yu@wavefun.com Cc: CHEMISTRY@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit Importance: Normal X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Yu, Please consider using our Sparkle model which is a simple and very cost effective way of determining the geometries of metal complexes. Our model was introduced in 1994 ("Sparkle model for the quantum chemical AM1 calculation of europium complexes", Chem. Phys. Lett., 227(3) 349-353, 1994) for the purpose of obtaining geometries of lanthanide complexes. At the time we observed it could also be used to determine the geometries of d element complexes as well. Since then it has been used for determining not only geometries, but also electronic spectra, for the design of luminescent complexes, etc. Cundari and Saunders have also extended it to other elements. More recently, Puchta and Hommes showed that it could be used for gallium, iron and lead complexes as well [J. Mol. Model. 6(2) 126-132, 2000]. The title of their paper is suggestive: "Exploring {2}-metallacryptands and {2}-metallacryptates with quantum chemical methods - When (not only) computer chemists' dreams come true" We are also in the proces of creating a site explaining how to use our sparkle model. Although it is still in construction it may be of some help. http://sites.netscape.net/SparkleMetals Sincerely, Alfredo Mayall Simas DQF/CCEN Universidade Federal de Pernambuco Recife, PE, Brazil -----Mensagem original----- De: Computational Chemistry List [mailto:chemistry-request@ccl.net]Em nome de yu@wavefun.com Enviada em: Quarta-feira, 19 de Abril de 2000 20:32 Para: scott.l.owens@bnfl.com Cc: CHEMISTRY@ccl.net Assunto: CCL:Semi empirical parameterisation for Transition elements On Apr 19, 2:45pm, scott.l.owens@bnfl.com wrote: > Subject: CCL:Semi empirical parameterisation for Transition elements > Hi there all, > > I am interested in modelling some transition metal complexes using > MOPAC2000, however the parameter set for these elements is pretty meagre. > Are there any resources for these semi-empirical parameters as there are > for the basis sets (as in the PNL database). If not is there anyone who has > parameters who would be willing to let them "go public". > Will summarise any responses for the list. > > Scott Owens > slo1@bnfl.com We, Wavefunction, do have semiempirical parameters covering almost all transition metels, and anybody can download them from our ftp side (ftp.wavefun.com). But I don't know whether our parameters match the methods used in MOPAC2000. If it doesn't, our SPARTAN series would be a natural choice. Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (949)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (949)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92612 | \/ | Lao-tzu (604-531 B.C.)| +----------------------http://www.wavefun.com------------------------+ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Apr 25 11:54:08 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04703 for ; Tue, 25 Apr 2000 11:53:55 -0400 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA00937 for ; Tue, 25 Apr 2000 11:49:20 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id LAA06198; Tue, 25 Apr 2000 11:48:48 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id LAA05317; Tue, 25 Apr 2000 11:30:30 -0400 (EDT) Date: Tue, 25 Apr 2000 11:30:30 -0400 (EDT) From: Steve Heller To: lists , amber@cgl.ucsf.edu, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.uwf.edu, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com, listserver@ic.ac.uk, mailbase@mailbase.ac.uk, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, molecular-dynamics-news@mailbase.ac.uk, NATODATA@CC1.KULEUVEN.AC.BE, pdb-l@rcsb.org, PHILCHEM@VM.SC.EDU, PLASMACHEM-L@LISTSERV.SYR.EDU, POLYMER@TECHUNIX.TECHNION.AC.IL, SAFETY@LIST.UVM.EDU, spectroscopy-group@mailbase.ac.uk, ToxList@esc.syrres.com, ucair-lib@twu.edu Subject: ChemInt2000 - Poster Submission Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is just a short note to remind eveyone that the web Abstract Submission deadline for papers to be considered for ChemInt2000 oral presentations is June 1, 2000. The web submission form is operational for the Chemistry and the Internet (ChemInt2000) meeting being held in at Georgetown University in Washington DC on September 23-26, 2000. The draft program of invited speakers, workshops, markup langauge tutorial, and panel sessions is available on the meeting web site: http://www.chemint.org You are urged to look at the program and to consider submitting a poster paper to the meeting. Some 8-10 of poster papers will be selected for oral presentation at the meeting. The main lecturers for the meeting will be: Rene DePlanque, FIZ - Berlin Jim Myers, Pacific Northwest Labs Glen Hopkinson, Synopsys Scientific Systems Wolf-Dietrich Ihlenfeldt, University of Erlangen-Nurenberg Jim Ostell, NIH/NLM/NCBI Engelbert Zass, ETH Henry Rzepa, Imperial College, London Peter Murray-Rust, Nottingham University Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC) Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: chem@feldmann.nist.gov From chemistry-request@server.ccl.net Tue Apr 25 13:38:06 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05382 for ; Tue, 25 Apr 2000 13:38:03 -0400 Received: from localhost (rkrocha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id OAA50171 for ; Tue, 25 Apr 2000 14:33:08 -0300 Date: Tue, 25 Apr 2000 14:33:07 -0300 (BSC) From: ramon kleber da rocha Reply-To: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: looking for a code Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, I am looking for a program able to perform free energy calculations based on Perturbation Method or Thermodynamic Integration or simular one. Our goal is to simulate the interaction between small organic molecules and DNA with water molecules explicity, because of it that program must support some requirements: 1) it should run within several processors (SP2 machines) 2) it should support amber force field 3) it should support particle mesh ewald summation (or derivated) on nonbond contribution in that kind of simulation. Does anybody knows any code that can do that? I'll be thankfull for any suggestions. I will summarize the replies. Thank you in advance. ________________________________________________________________________________ Ramon Kleber da Rocha, MSc. VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM - http://www.qui.ufmg.br/~nequim Departamento de Quimica - Universidade Federal de Minas Gerais - (DQ/ICEx/UFMG) --- The World is my Fatherland, Science is my Religion. Christiaan Huygens 1629-1695 ________________________________________________________________________________ From chemistry-request@server.ccl.net Tue Apr 25 13:42:05 2000 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05436 for ; Tue, 25 Apr 2000 13:41:57 -0400 Received: (from sjardino@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id OAA17731; Tue, 25 Apr 2000 14:22:19 -0300 (EST) Date: Tue, 25 Apr 2000 14:22:18 -0300 (EST) From: Sergio Augusto Jardino Filho To: CHEMISTRY@ccl.net Subject: Error in Gaussian`98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id NAA05440 Hi, Does anyone can help me with a error message from CBS-4M of Gaussian98? The message is the following: Initial guess read from the checkpoint file: sp1.chk4 Guess basis functions will be translated to current atomic coordinates. Logic error in ReDoC1: IndI= 284 but NBasI= 297. Error termination via Lnk1e in /usr/local/g98/l401.exe. I will be grateful with any help or advice. Thanks in advance. Sergio A. Jardino F¼ Instituto de Quimica Universidade de Sao Paulo Brazil From chemistry-request@server.ccl.net Tue Apr 25 17:19:45 2000 Received: from ncisun1-nf0.ncifcrf.gov (fcs280s.NCIFCRF.GOV [129.43.1.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06528 for ; Tue, 25 Apr 2000 17:19:44 -0400 Received: from fcindy5.NCIFCRF.GOV (fcindy5.NCIFCRF.GOV [129.43.50.12]) by ncisun1-nf0.ncifcrf.gov (8.10.0/8.10.0) with SMTP id e3PLJhu12062 for <@fcs280s.NCIFCRF.GOV:chemistry@ccl.net>; Tue, 25 Apr 2000 17:19:43 -0400 (EDT) Received: by fcindy5.NCIFCRF.GOV (950413.SGI.8.6.12/911001.SGI) for chemistry@ccl.net id RAA01827; Tue, 25 Apr 2000 17:17:15 -0400 Date: Tue, 25 Apr 2000 17:17:15 -0400 From: catfee@fcindy5.NCIFCRF.GOV (CATFEE) Message-Id: <200004252117.RAA01827@fcindy5.NCIFCRF.GOV> To: chemistry@ccl.net Subject: CATFEE: Drug Design Challenge Reply-To: catfee@fcindy5.NCIFCRF.GOV *** CATFEE *** CALL FOR TARGETS AND START OF THE PREDICTION SEASON Critical Assessment of Techniques for Free Energy Evaluation Asilomar, California, December 7-9, 2000 http://uqbar.ncifcrf.gov/~catfee/ CATFEE is a challenge and meeting designed to assess and discuss the techniques employed in computer assisted drug design efforts. Organized along the lines of previous challenges (CASP), CATFEE will provide the opportunity to modelers and experimentalists to test new algorithms and evaluate established techniques used for the prediction of binding free energies. We are building a database of previously unpublished binding affinities. If you have data you wish to make available to CATFEE you may use the auto- deposition form available at http://uqbar.ncifcrf.gov/~catfee/ or contact us for details. Pre-registration is open at http://uqbar.ncifcrf.gov/~catfee/ Raul E.Cachau (NCI-SAIC) Krzysztof Fidelis (LLNL) Adrian E.Roitberg (NIST-Geo Centers) Critical Assessment of Techniques for Free Energy Evaluation, CATFEE, Asilomar, California, USA; December 2000 e-Mail: catfee@uqbar.ncifcrf.gov; e-Fax/e-Voice: USA-(323)-9965699 WWW: http://uqbar.ncifcrf.gov/~catfee/ From chemistry-request@server.ccl.net Tue Apr 25 18:31:33 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06888 for ; Tue, 25 Apr 2000 18:31:32 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JONV7QRADK009FPP@trentu.ca> for chemistry@ccl.net; Tue, 25 Apr 2000 18:31:25 EDT Date: Tue, 25 Apr 2000 18:35:22 -0400 From: elewars Subject: van der Waals SURFACES/ELECTRON DEN To: chemistry@ccl.net Message-id: <39061DAA.E9D88A8D@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2000 April 25 Hello, I once read somewhere that an isosurface that encloses 97% of the total electron density of a molecule corresponds best to the experimental van der Waals surface. (1) Has anyone a reference to this, or to any percentage of the electron density? (2) Is it correct to say that the usual way to measure the "van der Waals size" of a molecule is by X-ray diffraction (the molecules in a crystal being considered to be in contact)? Thanks. E. Lewars ====== From chemistry-request@server.ccl.net Tue Apr 25 20:03:11 2000 Received: from mail.rpi.edu (root@mail.rpi.edu [128.113.100.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA07315 for ; Tue, 25 Apr 2000 20:03:11 -0400 Received: from brenemanP2.chem.rpi.edu (rts16p13.xyp.rpi.edu [128.113.30.142]) by mail.rpi.edu (8.9.3/8.9.3) with SMTP id UAA09716; Tue, 25 Apr 2000 20:03:04 -0400 Message-ID: <3906323D.52CD@rpi.edu> Date: Tue, 25 Apr 2000 20:03:09 -0400 From: "Prof. Curt M. Breneman" Organization: Rensselaer Polytechnic Institute X-Mailer: Mozilla 3.04 (Win95; I) MIME-Version: 1.0 To: elewars CC: chemistry@ccl.net Subject: Re: CCL:van der Waals SURFACES/ELECTRON DEN References: <39061DAA.E9D88A8D@trentu.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit elewars wrote: > > 2000 April 25 > > Hello, > > I once read somewhere that an isosurface that encloses 97% of the total > electron density of a molecule corresponds best to the experimental van > der Waals surface. > > (1) Has anyone a reference to this, or to any percentage of the electron > density? > (2) Is it correct to say that the usual way to measure the "van der > Waals size" of a molecule is by X-ray diffraction (the molecules in a > crystal being considered to be in contact)? > > Thanks. > > E. Lewars > ====== > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net There is one convention that says that for condensed phases, the Van der Waals surface is approximated by a 0.002 e/au3 isosurface, while the gas phase VdW surface is represented by the 0.001 e/au3 isosurface. Curt Breneman RPI Chemistry From chemistry-request@server.ccl.net Tue Apr 25 21:40:52 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA07792 for ; Tue, 25 Apr 2000 21:40:52 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id VAA27671; Tue, 25 Apr 2000 21:40:42 -0400 (EDT) Date: Tue, 25 Apr 2000 21:40:42 -0400 (EDT) From: "C.F. Matta" To: elewars cc: chemistry@ccl.net Subject: Re: CCL:van der Waals SURFACES/ELECTRON DEN In-Reply-To: <39061DAA.E9D88A8D@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Lewars In Prof. R.F.W.Bader's group, we integrate the properties densities of an atom in a molecule over the atomic basin. The basin is the region of space enclosed by the intersection of Inter-Atomic Surfaces (IAS) and and envelope of the density choosen at some value. I will explain HOW AND WHY we choose this value, with the hope of answering your question. The IASs are not arbitrary. They must satisfy a quantum condition that arises from the application of Swinger's principle of stationary action to a subsystem (e.g. an atom in a molecule). An IAS is the unique surface separating 2 atoms in a molecule so that the flux in the gradient vectror field of the density vanishes. If one integrates atomic properties up to the 0.001 a.u. isodensity envelope, these atomic values sum-up to the corresponding molecular (total system) values with reasonable accuracy. For example, summing atomic energies of medium-sized molecules such as the 20 naturally occuring amino acids recovers the SCF energy to within 1 kcal/mol (typically 0.5 kcal/mol). The sum of the atomic populations (or the corresponding atomic charges) is typically 0.001 e for a neutral molecule (or within 0.001 e of the molecular charge). The sum of the atomic volumes (molecular vol.) of the 20 amino acids integrated up to 0.001 a.u. envelope corrrelates highly with the experimental partial molar volumes (r^2=0.971). These results are not surprising given that the 0.001 a.u. envelope encloses over 98% of the electronic charge of H atoms in hydrocarbons, and over 99% of the electronic charge of atoms Carbon to Neon. The 0.001 a.u. isodensity envelope has been shown to yield values of molecular diameters of several gases in good agreement with the equilibrium diameters of these molecules determined experimentally (e.g. by viscosoity measurements fitted to a 6-12 potential). The 0.002 a.u. may be a more realistic measure of the molecular size in crystal, however. CONCLUSION ========== The 00.1-00.2 a.u. isodensity envelopes are good approximation to the experimentally determined van der Walls sizes of molecules. REFERENCES ========== [1] Bader RFW. Atoms in molecules: A quantum theory. Oxford, U.K.: Oxford University Press, (1990). pages 182,183,199,202. And references therein. (Radii of isolated ground-state atoms and ions is given in page 432, for both the 0.001 and 0.002 envelopes). [2] Matta CF, Bader RFW. Atoms-in-molecules study of the genetically-encoded amino acids. I. Effect of conformation on geometric,atomic, and bond properties. Proteins: Structure, Function and Genetics, (2000) [In Press]. ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. Member of the Board of Governors of the University ....................................................................... On Tue, 25 Apr 2000, elewars wrote: > 2000 April 25 > > Hello, > > I once read somewhere that an isosurface that encloses 97% of the total > electron density of a molecule corresponds best to the experimental van > der Waals surface. > > (1) Has anyone a reference to this, or to any percentage of the electron > density? > (2) Is it correct to say that the usual way to measure the "van der > Waals size" of a molecule is by X-ray diffraction (the molecules in a > crystal being considered to be in contact)? > > Thanks. > > E. Lewars > ====== > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > >