From chemistry-request@ccl.net Tue May 27 05:31:41 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4R9VeKY004704 for ; Tue, 27 May 2003 05:31:40 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id B47F4C736D0; Tue, 27 May 2003 11:31:38 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 49E12C736C4; Tue, 27 May 2003 11:31:36 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 27 May 03 11:31:36 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 27 May 03 11:31:27 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "pop14848" Date: Tue, 27 May 2003 11:30:58 +0100 Subject: Re: CCL:HOMO/LUMO gap Reply-To: spanget/at/ruc.dk Cc: CHEMISTRY/at/ccl.net Message-ID: <3ED33E61.28734.769963@localhost> X-Confirm-Reading-To: spanget/at/ruc.dk X-pmrqc: 1 Priority: normal In-reply-to: <200305261833590671.0F6D9487/at/mailhub.uni-konstanz.de> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Status: No, hits=-6.5 required=5.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Eike Huebner: > I did some DFT calculations on transition metal complexes using the > 6-31G* basis set, Hay-Wadt effective core potential on the transition > metal (mainly Ru) and the BP86 functional. The HOMO-LUMO energy gaps > are too small (e.g. 1000nm instead of 460nm) in comparison to HF > calculations where the predicted HOMO-LUMO gaps are far too large. Can > someone point me to quotable papers where the reasons for the too > small gaps are discussed? I really need published papers and not a > list of reasons. Dear Eike: I am somewhat puzzled: What do you mean by too small or too large HOMO-LUMO energy gaps? Relative to some "experimental" values? But an electronic transition energy is not equal to an MO energy difference. And in principle, MOs are not physical quantities; they are model constructions, and as such they have no physical reality and they cannot be observed experimentally. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget/at/ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Tue May 27 07:56:17 2003 Received: from camdmail01.cam.accelrys.com (vpn.cam.accelrys.com [192.190.183.254]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RBuGKY009264 for ; Tue, 27 May 2003 07:56:17 -0400 To: chemistry(at)ccl.net Subject: HF and optical properties MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0 September 26, 2002 Message-ID: From: Victor Milman Date: Tue, 27 May 2003 12:56:15 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 6.0.1CF1|March 04, 2003) at 27/05/2003 11:56:16, Serialize complete at 27/05/2003 11:56:16 Content-Type: text/plain; charset="US-ASCII" Dear All, I would be grateful if you could give me some pointers - I am looking for the formalism that is used for the calculation of the optical matrix elements at the HF level. People in the solid state DFT world have long been doing optics, and found the way of treating nonlocality of the external (pseudo)potential. As far as I know, solid state HF (CRYSTAL code) does not do optics. What about molecular QC codes: is there any problem in getting optical properties at the HF level? Is this written up anywhere? Thanks! ============================================================= Victor Milman * Fellow Accelrys Inc * tel: (01223) 228500/228619 334 Science Park * fax: (01223) 228501 Cambridge CB4 0WN * tel. from abroad: +44 1223 228500 UK * e-mail: vmilman(at)accelrys.com ============================================================= From chemistry-request@ccl.net Tue May 27 06:00:00 2003 Received: from hpsv.pku.edu.cn ([162.105.153.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4R9xtKY005372 for ; Tue, 27 May 2003 05:59:55 -0400 Received: (from nobody@localhost) by hpsv.pku.edu.cn (8.9.3/8.9.3) id SAA30774; Tue, 27 May 2003 18:06:30 +0800 Date: Tue, 27 May 2003 18:06:30 +0800 Message-Id: <200305271006.SAA30774(at)hpsv.pku.edu.cn> X-Authentication-Warning: hpsv.pku.edu.cn: nobody set sender to wf(at)hpsv.pku.edu.cn using -f From: "Wang Fan" To: "Jens Spanget-Larsen" , "pop14848" , CHEMISTRY(at)ccl.net Subject: Re: CCL:HOMO/LUMO gap In-Reply-To: <3ED33E61.28734.769963@localhost> References: <200305261833590671.0F6D9487(at)mailhub.uni-konstanz.de> X-Mailer: Open WebMail 1.53 20011216 X-OriginatingIP: 162.105.22.62 (wf) MIME-Version: 1.0 Content-Type: text/plain; charset=GB2312 In DFT, LUMO energy level is normally lower than that in HF since the meaning of energy level of unoccupied orbitals is different in DFT and HF. So it is very normal that DFT HOMO-LUMO gap is smaller. I calculated some diatomics containing transition metals with G98 once. Sometimes the result HOMO-LUMO gap is very samll or even LUMO is lower, but it usually means that I did not find the lowest configuration. I don't know whether you got the lowest configuration or the gap for your system is indeed quite small. Fan Wang > Eike Huebner: > > > I did some DFT calculations on transition metal complexes using the > > 6-31G* basis set, Hay-Wadt effective core potential on the transition > > metal (mainly Ru) and the BP86 functional. The HOMO-LUMO energy gaps > > are too small (e.g. 1000nm instead of 460nm) in comparison to HF > > calculations where the predicted HOMO-LUMO gaps are far too large. Can > > someone point me to quotable papers where the reasons for the too > > small gaps are discussed? I really need published papers and not a > > list of reasons. > > Dear Eike: > I am somewhat puzzled: What do you mean by too small or too large > HOMO-LUMO energy gaps? Relative to some "experimental" values? But an > electronic transition energy is not equal to an MO energy difference. > And in principle, MOs are not physical quantities; they are model > constructions, and as such they have no physical reality and they > cannot be observed experimentally. > Yours, Jens >--< > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget(at)ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY- REQUEST(at)ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue May 27 04:00:24 2003 Received: from ns9.mmaweb.net ([64.71.146.31]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4R80NKY001827 for ; Tue, 27 May 2003 04:00:24 -0400 Received: from chemaxon.com (226.32-182-adsl-pool.axelero.hu [81.182.32.226]) by ns9.mmaweb.net (8.12.9/8.11.0) with ESMTP id h4R80KXS025992; Tue, 27 May 2003 04:00:21 -0400 (EDT) Message-ID: <3ED31B03.4000101-.at.-chemaxon.com> Date: Tue, 27 May 2003 10:00:03 +0200 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.3.1) Gecko/20030425 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: chemweb-.at.-ic.ac.uk, CHEMISTRY-.at.-ccl.net, CHMINF-L-.at.-LISTSERV.INDIANA.EDU, MOL-DIVERSITY-.at.-LISTSERV.ARIZONA.EDU, scitech-.at.-lists.apple.com Subject: Marvin 3.1.3 released Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Apologies for multiple postings. Marvin Applets and Marvin Beans 3.1.3 have been released. The packages contain software development tools and applications for chemistry. Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. FREE: - Marvin Applets are free for free web sites. - MarvinSketch and MarvinView applications accessed from ChemAxon's web site http://www.chemaxon.com/marvin/jnlp/index.html - Locally installed MarvinSketch, MarvinView, and MolConverter applications. Recent changes: - New installer of Marvin Beans for Windows and Mac OS X (Shortcuts for the MarvinSketch and MarvinView applications) - MarvinSketch can open 3D viewer windows. - Extended Molfile (V3) export. - Improved partial charge, pKa, logD predictions - Chart display for logD prediction - Atom polarizability plugin - Improved PDB support - Faster loading of applets The software can be tried/downloaded at http://www.chemaxon.com/products.html Online access: Applications (If you have Java installed): http://www.chemaxon.com/marvin/jnlp/index.html Applet demos: http://www.chemaxon.com/marvin/demos.html Examples for developers: http://www.chemaxon.com/marvin/doc/dev#examples Regards, Ferenc -- Dr. Ferenc Csizmadia CEO ChemAxon http://www.chemaxon.com From chemistry-request@ccl.net Tue May 27 10:59:00 2003 Received: from mail.cybermesa.com (mail.cybermesa.com [198.59.109.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4REwxKY016124 for ; Tue, 27 May 2003 10:58:59 -0400 Received: from dave (qwest210-dsl3.cybermesa.com [216.84.163.210]) by mail.cybermesa.com (8.11.6/8.11.6) with SMTP id h4REwtE01575 for ; Tue, 27 May 2003 08:58:55 -0600 (MDT) From: "David Miller" To: Subject: CCL: R tables added to ChemTK Date: Tue, 27 May 2003 09:00:48 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 ChemTK version 2.3 evaluation is now available for download > from http://www.chemtk.com New features include: - R table generation for any class of molecules - automatic alignment of molecules to any defined scaffold - multiple linear regression added to list of model types - scatter plots available in all views Visit http://www.chemtk.com to download the ChemTK product sheet, documentation, and release notes, and to learn more about the inexpensive licensing terms. Best regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller[at]sageinformatics.com From chemistry-request@ccl.net Tue May 27 11:57:25 2003 Received: from julesburg.uits.indiana.edu (julesburg.uits.indiana.edu [129.79.1.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RFvPKY017925 for ; Tue, 27 May 2003 11:57:25 -0400 Received: from auggiedoggie.uits.iupui.edu (auggiedoggie.uits.iupui.edu [134.68.220.202]) by julesburg.uits.indiana.edu (8.12.9/8.12.9/IUPO) with ESMTP id h4RFvOib004717 for ; Tue, 27 May 2003 10:57:24 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by auggiedoggie.uits.iupui.edu (8.12.9/8.12.9/IUPUIPO.20030331) with ESMTP id h4RFvO93008477 for ; Tue, 27 May 2003 10:57:24 -0500 (EST) Sender: qin|at|auggiedoggie.uits.iupui.edu Message-ID: <3ED38AF2.6F55454F|at|iupui.edu> Date: Tue, 27 May 2003 10:57:38 -0500 From: "Q." X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: CCL: chirality conversion Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Good day, I wonder if anyone knows some programs could convert a S-configuration into R-configuration for a simple small molecule and output a pdb format file. Thanks in advance. Q. From chemistry-request@ccl.net Tue May 27 11:14:38 2003 Received: from alcor.rede.usc.es (alcor.rede.usc.es [193.144.75.249]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RFEbKY016615 for ; Tue, 27 May 2003 11:14:37 -0400 Received: from localhost (localhost [127.0.0.1]) by alcor.rede.usc.es (Postfix) with ESMTP id DB7964911E for ; Tue, 27 May 2003 17:14:31 +0200 (CEST) Received: from qfcronos.usc.es (qfcronos.usc.es [193.144.74.154]) by alcor.rede.usc.es (Postfix) with ESMTP id E59F14909A for ; Tue, 27 May 2003 17:14:29 +0200 (CEST) Message-Id: <5.2.0.9.0.20030527170945.00a114a0/at/pop.usc.es> X-Sender: qftjesus/at/pop.usc.es X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 27 May 2003 17:15:34 +0200 To: chemistry/at/ccl.net From: Jesus Rodriguez-Otero Subject: UV spectrum calculation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: YES (by USC) Hi Is Zindo a good method to obtain lambda(max) of UV-visible spectrum of large molecules? Jesus Rodriguez-Otero Universidad de Santiago de Compostela qftjesus/at/usc.es From chemistry-request@ccl.net Tue May 27 13:32:09 2003 Received: from macbeth.if.usp.br (macbeth.if.usp.br [143.107.133.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RHW7KY020961 for ; Tue, 27 May 2003 13:32:08 -0400 Received: from localhost (rivelino@localhost) by macbeth.if.usp.br (8.9.3p2/8.9.3) with SMTP id OAA09153; Tue, 27 May 2003 14:31:58 -0300 (EST) Date: Tue, 27 May 2003 14:31:58 -0300 (EST) From: Roberto Rivelino To: "Q." cc: chemistry-.at.-ccl.net Subject: Re: CCL:chirality conversion In-Reply-To: <3ED38AF2.6F55454F-.at.-iupui.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hallo, WebLabViewer is a program able to convert optical isomers. Best wishes, Roberto On Tue, 27 May 2003, Q. wrote: > Good day, > I wonder if anyone knows some programs could convert a S-configuration > into R-configuration for a simple small molecule and output a pdb format > file. Thanks in advance. > > > Q. > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY-.at.-ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl-.at.-ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Tue May 27 13:55:04 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RHt4KY021584 for ; Tue, 27 May 2003 13:55:04 -0400 Received: from dgallagher.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h4RHrVI02123 for ; Tue, 27 May 2003 10:53:31 -0700 Message-Id: <5.2.0.9.0.20030527101629.03286120-.at.-wheresmymailserver.com> X-Sender: daveg-.at.-mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 27 May 2003 10:16:53 -0700 To: "CCL" From: David Gallagher Subject: CCL: MNDO/PM3/AM1 parameters for Transition metals Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_2083808==.ALT" --=====================_2083808==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Tapas, To calculate transition metals you would need a version of MOPAC that handles d-orbitals, such as MOPAC 2002 which currently includes parameters for Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zn, Zr, Mo, Pd, Ag, Cd, Pt, Hg. There is a table of accuracies by element for MNDO, AM1 PM3, and the new PM5 method at: http://www.cachesoftware.com/mopac/Mopac2002manual/Stats_for_heats.html You can get more information about MOPAC at http://www.cachesoftware.com/techsupport/mopac/ I hope this helps, David Gallagher, Fujitsu At 01:00 PM 5/23/2003 -0600, Tapas Kar wrote: >Dear Colleagues, >Where can I find MNDO/PM3/AM1 parameters for fist-row transition metals, >especially for Fe and Mn? >Tapas > >*********************************************** >"We owe a lot to the Indians, who taught us how to count, without >which no worthwhile scientific discovery could have been made." > - Albert Einstein - >-------------------------------------------------------------------------------- >Tapas Kar, Ph. D >Department of Chemistry & Biochemistry >Utah State University >Logan, UT 84322-0300 > >Tel: 435-797-7230 >Fax: 435-797-3390 >Email: tapaskar-.at.-cc.usu.edu >Web:http://www.chem.usu.edu/faculty/Tapas/index.html > ============================================== David A. Gallagher, C. Chem. Vice President, Sales and Marketing CAChe Group Fujitsu America, Inc. 15244 NW Greenbrier Parkway Beaverton, OR 97006-5733, USA Direct dial: 503 746 3607 Main Switchboard: 503 746 3600 Fax: 503 531 9966 email: dgallagher-.at.-cachesoftware.com http://www.cachesoftware.com http://www.cachesoftware.com/staff/dg.shtml ============================================== --=====================_2083808==.ALT Content-Type: text/html; charset="us-ascii" Hi Tapas,

To calculate transition metals you would need a version of MOPAC that handles d-orbitals, such as MOPAC 2002 which currently includes parameters for Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zn, Zr, Mo, Pd, Ag, Cd, Pt, Hg. There is a table of accuracies by element for MNDO, AM1 PM3, and the new PM5 method at: http://www.cachesoftware.com/mopac/Mopac2002manual/Stats_for_heats.html
 
You can get more information about MOPAC at http://www.cachesoftware.com/techsupport/mopac/

I hope this helps,
David Gallagher, Fujitsu


At 01:00 PM 5/23/2003 -0600, Tapas Kar wrote:
Dear Colleagues,
Where can I find  MNDO/PM3/AM1 parameters for fist-row transition metals, especially for Fe and Mn?
Tapas

***********************************************
"We owe a lot to the Indians, who taught us how to count, without
which no worthwhile scientific discovery could have been made."
                                           - Albert Einstein -
--------------------------------------------------------------------------------
Tapas Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax: 435-797-3390
Email: tapaskar-.at.-cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html
 

==============================================
  David A. Gallagher, C. Chem.
  Vice President, Sales and Marketing
  CAChe Group
  Fujitsu America, Inc.
  15244 NW Greenbrier Parkway
  Beaverton, OR 97006-5733, USA
  Direct dial:          503 746 3607
  Main Switchboard:     503 746 3600
  Fax:                  503 531 9966
  email: dgallagher-.at.-cachesoftware.com
  http://www.cachesoftware.com
  http://www.cachesoftware.com/staff/dg.shtml
============================================== --=====================_2083808==.ALT-- From chemistry-request@ccl.net Tue May 27 15:01:58 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RJ1uKY023294 for ; Tue, 27 May 2003 15:01:57 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) with ESMTP id WAA333706; Tue, 27 May 2003 22:01:51 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Tue, 27 May 2003 22:01:51 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans_at_soul.helsinki.fi To: Jens Spanget-Larsen cc: pop14848 , CHEMISTRY_at_ccl.net Subject: Re: CCL:HOMO/LUMO gap In-Reply-To: <3ED33E61.28734.769963@localhost> Message-ID: References: <3ED33E61.28734.769963@localhost> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Jens and All! On Tue, 27 May 2003, Jens Spanget-Larsen wrote: > And in principle, MOs are not physical quantities; they are model > constructions, and as such they have no physical reality and they > cannot be observed experimentally. Well, there is a lot of discussion in the literature on this topic. A few good examples, biased towards my thinking, could be: [1] Stowasser and Hoffmann, "What Do the Kohn-Sham Orbitals and Eigenvalues Mean?", J.Am.Chem.Soc. 121 (1999) 3414-3420. [2] Baerends, Theor.Chem.Acc. 103 (2000) 265-269. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry@ccl.net Tue Apr 15 16:08:54 2003 -0400 Return-Path: Received: from rwcrmhc52.attbi.com (rwcrmhc52.attbi.com [216.148.227.88]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h3FK8rt03510 for ; Tue, 15 Apr 2003 16:08:54 -0400 (EDT) Received: from c1353359a (12-207-198-103.client.attbi.com[12.207.198.103]) by rwcrmhc52.attbi.com (rwcrmhc52) with SMTP id <2003041520085205200lkbg2e>; Tue, 15 Apr 2003 20:08:52 +0000 Reply-To: From: "Mark Thompson" To: Subject: CCL: UV spectrum calculation Date: Tue, 15 Apr 2003 13:06:52 -0700 Message-ID: <000501c3038a$8e52ff40$0300a8c0:at:attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 We've posted an updated set of INDO/s parameters on the ArgusLab website. These include parameters for Si and P. (click on the downloads button on the homepage). Please send email to info:at:arguslab.com for any questions or problems with this download. ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= > -----Original Message----- > From: Mark Thompson [mailto:mark:at:planaria-software.com] > Sent: Tuesday, May 27, 2003 1:47 PM > To: Jesus Rodriguez-Otero; chemistry:at:ccl.net > Subject: CCL: UV spectrum calculation Dear Jesus, ZINDO does indeed give good results for large organic systems, mainly those with low-energy pi-pi* excitations. As with many semi-empirical methods, it works best on a series of related molecules where you might be interested in the effects of certain substitutents. Also, the effects of solvent can be very important and several solvent models have been applied to the ZINDO method with good results. Here are a couple of my publications where I applied ZINDO to studies of photosynthetic pigments: "Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization" J. Phys. Chem. 1995, 99, 6374-6386. Mark Thompson and Gregory Schenter "Effect of a Polarizable Medium on the Charge-Transfer States of the Photosynthetic Reaction Center from Rhodopseudomonas viridis. " I. Am. Chem. Soc. 1990, 112, 7828. Mark Thompson and Michael Zerner ZINDO is available in the ArgusLab 3.1 program. In addition to the normal ZINDO method (based on singles-CI description of the excited state), ArgusLab also implements the ZINDO-RPA method which includes contributions > from certain low-lying doubles and is particularly good at describing rotational spectra and giving good agreement between dipole length and dipole velocity transition moments. ArgusLab also implements the Self-Consistent Reaction Field model of Zerner and Karlsson. You can obtain ArgusLab at http:://www.arguslab.com Mark Thompson ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= From chemistry@ccl.net Tue May 27 03:10:42 2003 -0400 Return-Path: Received: from imeil.udg.es (imeil.udg.es [130.206.45.97]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h4R7Aet18910 for ; Tue, 27 May 2003 03:10:41 -0400 (EDT) Received: from imeil.udg.es (localhost.localdomain [127.0.0.1]) by imeil.udg.es (8.11.6/out/otb) with ESMTP id h4RE8g606816 for ; Tue, 27 May 2003 09:08:42 -0500 Received: from manol.udg.es (manol.udg.es [130.206.127.227]) by imeil.udg.es (8.11.6/in/otb) with ESMTP id h4RE8go06810 for ; Tue, 27 May 2003 09:08:42 -0500 Received: from udg.es (portiqc.udg.es [130.206.124.218]) by manol.udg.es (Postfix) with ESMTP id 4EFF9F2AEC for ; Tue, 27 May 2003 09:10:33 +0200 (CEST) Message-ID: <3ED30F68.5050904..at..udg.es> Date: Tue, 27 May 2003 09:10:32 +0200 From: =?ISO-8859-1?Q?Miquel_Sol=E0?= User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry..at..ccl.net Subject: CCL:Summary, Chemistry & Architecture Content-Type: multipart/alternative; boundary="------------050809010902060207030406" --------------050809010902060207030406 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear CCLers, Thanks to Carlos Silva, Anselm Horn, Doug Henry, Luigi Cavallo, Egon W., David Shobe, David Reichert, Brian K. Peterson, Ralph Puchta, Bartolomeo Civalleri, Kieran F Lim, Francis T. Marchese, Pete Gannett, Charles Woodbury, Richard Gililan and E. Lewars who responded to my question on the relationship between Chemistry and Architecture. It turns out that there a lot of relations between the two disciplines, most of them will be useful for my introduction to the subject. Thank you very much!! I give a summary of the responses below. Best regards, Miquel ************* I highly recommend you to browse the literarure authored by Leo Paquette, he is an organic chemist who has built some "structuraly fair" molecules. Look Figure 4 in his website: http://www.chemistry.ohio-state.edu/cgi/brochure?Faculty=Paquette More complicated simmetrical structures within his publications. Hope it helps _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_ ************* Hello, the names "pagodane" and "housane" come into my mind. Regards, Anselm -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn..at..chemie.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | 91052 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/ __ ************* >From Doug Henry: Google search "nanotubes" and "mile high": (space elevator, mile-high skyscrapers) http://flightprojects.msfc.nasa.gov/pdf_files/usrp.pdf http://www.nature.com/nsu/021007/021007-13.html popularmechanics.com/science/space/ 2002/7/going_up/print.phtml www.discover.com/feb_01/feattech.html www.manufacturing.net/esec/Article_108499.htm ************* E.g. the double helix of DNA... Also a number of organic ring systems like for example benzene (6 ring) can be found in architecture too... kind regards, Egon ************* There should be sort of a review that was published recently on Chemistry - A European Journal. The author should be Vincenzo Balzani. luigi ************* You might want to look at "supramolecular" chemistry, where molecules are used as "building blocks" to make more complicated structures. Typically these are held together by hydrogen bonds or similar interactions. There are also articles on molecular versions of the construction toys, "Tinkertoys" and "Meccano", perhaps others. (These are analogies used by the authors of the papers, but do are not meant to imply any connection to the companies that manufacture these toys or own the trademarks thereto). These are typically rigid molecules which react, forming covalently bonded structures. Hope this helps, --David Shobe S|d-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe..at..sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. ************* I don't know if this is entirely applicable but Jerry Atwood at University of Missouri - Columbia has been publishing on large self-assembled molecules that represent the Platonic and Aristolean solids which might interest Architecture students. Can't recall the references off the top of my head though. -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd..at..mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 ************* >From Brian K. Peterson Random thoughts: If your intended use of a relationship between chemistry and architecture includes higher levels of abstraction, chemistry and architecture are related via their use of a hierarchy of structures. Molecules are built out of atoms and functional groups. Buildings are built out of struts, beams, bricks, floors, exteriors, interiors, etc. Molecules exhibit function and form. They have symmetry. They must be somehow compatible or commensurate with nearby molecules. A dense layer of single chain surfactant molecules on a liquid surface looks something like the high-rise region of a large city. An ion channel in a cell wall is somewhat like a door or a hallway. Carbon nanotubes are cylindrical columns. Some zeolites include extended frameworks with interior regions that could function as a buidling with rooms. ************* Dear Miquel, what about C20H20 isomer Pagodane and the coresponding japanese houses? Greetings Ralph ************* Dear Miquel Sola', you can have a look at the zeolite frameworks which are very similar to Romanesque and Islamic decorations. You can find more information on zeolite topochemistry in a review by J.V. Smith published on Chem. Rev. in 1988: J.V. Smith Topochemistry of zeolites and related materials. 1. Topology and geometry Chem. Rev. 1988, 88, 149-182 I hope this could be useful to your talk. All the best Mimmo Dr. Bartolomeo Civalleri Dipartimento di Chimica IFM - Universita' di Torino Via P. Giuria 7, 10125 Torino (Italy) Phone: +39-011-6707564; Fax: +39-011-6707855 E-mail: bartolomeo.civalleri..at..unito.it ************* Another example is cubane -- a (multi)cyclic alkane molecule consisting of 8 carbon atoms in the form of a cube. Another example are the zeolytes Another example is from the lab of Dainis Dakternieks (Australia) and his collaborators in Germany. They synthesize "ladders" of tin-containing compounds ... something like R - Sn - O - Cl - Sn - R | | | | R - O - Cl - Sn - O if the R groups are chosen carefully, then each "ladder" can form a "floor" and the R groups can form "columns" joining and holding the ladders/floors at fixed distances ... I have also heard of two "Lego" examples. The first is from the lab of Ilo Hansen (Spelling?) in Denmark where actual Lego blocks are used to construct robotic modular automated sampling handling instruments for analytical chemistry. The second is the construction of larger rigid molecules > from smaller ones by Richard Russell and Ron Warrener (both Australia) using the term molecular "Lego" -- along the lines of Dave Shobe's e-mail -- without implying any connection to real Lego blocks. Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mobile phone: 0438 350 259 (within Australia) mailto:lim..at..deakin.edu.au http://www.deakin.edu.au/~lim ------------------------------------------------------------ ************ Hi Miquel, Some things you may want to talk about: 1. Architecture defines space. So do molecules. For example, cage compounds, zeolites, many proteins define spaces for other molecules to inhabit. (keywords: host-guest compounds, cages, cryptands, protein active site) 2. Form follows function. For example, the "shapes" of proteins have evoled to perform a specific function. 3. Architectural orders. There is a systematic way in which atoms are combined to create spatial structure. Models such as VSEPR are easy heuristic models to look at this. Correlations could be made with Palladian motifs. Mitchell's book "The Logic of Architecture" talks about "a Palladian grammar." The periodic table and rules of chemical combination are a more complex 3D grammar. Another example... Proteins are built from a set of architectural "motifs" (e.g. "greek key"). A good place to look is "Introduction to Protein Structure" by Carl Branden and John Tooze. Finally, molecules crystallize in regular patterns, very much like "wall paper" patterns. 4. Inorganic vs organic architecture. Inorganic substances have highly regular structures (e.g. salt (NaCl)). But most organic molecules are less-so. There is a whole class of molecules called "dendritic molecules" that have branching patterns much like trees or bushes. 5. Positive vs Negative space. The Seagram building in NYC is my favorite example of this. Mies van der Rohe's monolithic structure defines a complmentary rectangular volume. Many atomic arrangements create these types of spatial relationships. For example, the packing arrangement of Cl- ions in the NaCl lattice defines spaces for the smaller Na+ ions to occupy. Enough for now. Hope this is useful. Regards Frank Dr. Francis T. Marchese Professor Dept. of Computer Science Pace University 163 William Street, 2nd Floor NY, NY 10038 and Director Center for Advanced Media http://csis.pace.edu/~cam and Director Pace Digital Gallery http://www.pace.edu/DigitalGallery ************* Miquel: Sounds like a tough audience. Here are a few that come to mind and might help. Hydrocarbons: Tetrahedran, housane, basketane, cubane (just search on the names to get structures for but you can get a good idea of what they look like from their names). There are also the catenanes (two rings, one passing through the other). Others come to mind but need a bit of imagination, for example, DNA looks like a spiral staircase. Hope this helps. Pete Gannett ************* Dear Miquel: Here at the University of Illinois at Chicago, we have a new building (the Molecular Biology Research Building or MBRB) in which the main staircase is a double helix. This was of course designed deliberately for this building. Take a look at it: http://www.uic.edu/orgs/mbrb/staircas.htm Hope this helps. Chuck Woodbury ************* I once gave an invited lecture on molecular graphics at a conference on oil and gas discovery. They invited a variety of speakers from different fields to get a perspective on visualization methods and technology. One of the things molecular graphics has to offer is the ways in which various simplified representations are used to bring out different aspects of a more complex data set. Ribbon representation for example, removes the complexity of sidechains and focuses on the underlying architectural structure of the protein. Molecular surface focuses on the shape and surface form without regard to interior. Biochemists may have some of the most complex geometric data to deal with in any field. Architects are only recently getting into 3D (stereo and VR) display technology, while chemists have used it for decades. Although architects are quite good at photorealism now (more so than chemists I think), it always surprises me that so little use is made of depth-cuing (fade to black with distance) and stereo in geometric modeling programs (geometric modelers in film/animation fall in this category too). Could be that man-made structures are (have been) easier to visualize with simple orthographic (front/back/side) projections than natural 3D objects. Molecular building programs in chemistry & crystallography contain integrated physical simulations (structure minimization for example). The analogy would be designing a building using real-time load-bearing simulations or something of that type. If you are interested, I could probably dig up some old slides. Richard Gillilan MacCHESS, Cornell ************* 2003 April 24 Hello, Don't forget pyramidane (the pyramids are the only architectural wonder of the ancient world still standing; may the molecule be as stable! THEOCHEM, 1998, _423_, 173 THEOCHEM, 2000, _507_, 165 E. Lewars ==== ***** -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Miquel Sol` Institut de Qummica Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola..at..udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- --------------050809010902060207030406 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Dear Jan,

I want to send this e-mail to CCL but it gets bounced. Could you please
send it? Thanks in advance.

Miquel

*****
Dear CCLers,

Thanks to Carlos Silva, Anselm Horn, Doug Henry, Luigi Cavallo, Egon W., David Shobe,
David Reichert, Brian K. Peterson, Ralph Puchta, Bartolomeo Civalleri, Kieran F Lim,
Francis T. Marchese, Pete Gannett, Charles Woodbury, Richard Gililan and E. Lewars
who responded to my question on the relationship between Chemistry and Architecture.
It turns out that there a lot of relations between the two disciplines, most of them will be
useful for my introduction to the subject. Thank you very much!!
I give a summary of the responses below.

Best regards,

Miquel

*************
I highly recommend you to browse the literarure authored by Leo Paquette,
he is an organic chemist who has built some "structuraly fair" molecules.
Look Figure 4 in his website:
http://www.chemistry.ohio-state.edu/cgi/brochure?Faculty=Paquette
More complicated simmetrical structures within his publications.
Hope it helps

_-_-_-_-_-_-_-_-_-_-_-_-

   Carlos Silva López
 Dept. Química Orgánica
  Universidade de Vigo
  Phone:0034 986812226
-_-_-_-_-_-_-_-_-_-_-_-_

*************
Hello,

the names "pagodane" and "housane" come into my mind.

Regards,

Anselm



--
_______________________________________________________________________
Anselm Horn, Dipl. Chem. Univ.       Anselm.Horn..at..chemie.uni-erlangen.de
  ___
 / __|        ___                               Computer Chemie Centrum
| /     ___  / __|
| |    / __|| /                                   Naegelsbachstrasse 25
\ \__ | /   | |                                          91052 Erlangen
 \___|| |   \ \__                                 Deutschland / Germany
      \ \__  \___|    Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565
       \___|                 http://www.ccc.uni-erlangen.de/clark/horn/
__

*************

>From Doug Henry:
Google search "nanotubes" and "mile high": (space elevator, mile-high skyscrapers)
 
*************

E.g. the double helix of DNA... Also a number of organic ring systems like
for example benzene (6 ring) can be found in architecture too...

kind regards,

Egon

*************

There should be sort of a review
that was published recently on Chemistry - A European Journal. The author
should be Vincenzo Balzani.

luigi

*************
You might want to look at "supramolecular" chemistry, where molecules are used as "building blocks" to make more complicated structures.  Typically these are held together by hydrogen bonds or similar interactions.
 
There are also articles on molecular versions of the construction toys, "Tinkertoys" and "Meccano", perhaps others.  (These are analogies used by the authors of the papers, but do are not meant to imply any connection to the companies that manufacture these toys or own the trademarks thereto).  These are typically rigid molecules which react, forming covalently bonded structures.
 
Hope this helps,

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe..at..sud-chemieinc.com

Don't bother flaming me: I'm behind a firewall.

 
*************


 
I don't know if this is entirely applicable but Jerry Atwood at University
of Missouri - Columbia has been publishing on large self-assembled
molecules that represent the Platonic and Aristolean solids which might
interest Architecture students. Can't recall the references off the top of
my head though.
-david
David Reichert, Ph.D.
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd..at..mir.wustl.edu
voice: (314) 362-8461
fax: (314) 362-9940

*************

>From Brian K. Peterson
Random thoughts:
 
If your intended use of a relationship between chemistry and architecture includes higher levels of abstraction, chemistry and architecture are related via their use of a hierarchy of structures.  Molecules are built out of atoms and functional groups.  Buildings are built out of struts, beams, bricks, floors, exteriors, interiors, etc.  Molecules exhibit function and form.  They have symmetry.  They must be somehow compatible or commensurate with nearby molecules.
 
A dense layer of single chain surfactant molecules on a liquid surface looks something like the high-rise region of a large city.  An ion channel in a cell wall is somewhat like a door or a hallway.  Carbon nanotubes are cylindrical columns. Some zeolites include extended frameworks with interior regions that could function as a buidling with rooms.  
*************

Dear Miquel, 

what about C20H20 isomer Pagodane and the coresponding japanese houses?

Greetings

Ralph

*************
Dear Miquel Sola',
you can have a look at the zeolite frameworks
which are very similar to Romanesque and Islamic decorations.

You can find more information on zeolite topochemistry
in a review by J.V. Smith published on Chem. Rev. in 1988:

J.V. Smith
Topochemistry of zeolites and related materials. 1. Topology and
geometry
Chem. Rev. 1988, 88, 149-182

I hope this could be useful to your talk.
All the best

Mimmo

Dr. Bartolomeo Civalleri
Dipartimento di Chimica IFM - Universita' di Torino
Via P. Giuria 7, 10125 Torino (Italy)
Phone: +39-011-6707564; Fax: +39-011-6707855
E-mail: bartolomeo.civalleri..at..unito.it
*************

Another example is cubane -- a (multi)cyclic alkane molecule

consisting of 8 carbon atoms in the form of a cube.



Another example are the zeolytes



Another example is from the lab of Dainis Dakternieks (Australia)

and his collaborators in Germany. They synthesize "ladders" of tin-containing

compounds ... something like



    R - Sn - O - Cl - Sn - R

        |    |   |    |

    R - O - Cl - Sn - O



if the R groups are chosen carefully, then each "ladder" can form a "floor"

and the R groups can form "columns" joining and holding the ladders/floors

at fixed distances ...



I have also heard of two "Lego" examples.



The first is from the lab of Ilo Hansen (Spelling?) in Denmark where actual

Lego blocks are used to construct robotic modular automated sampling

handling instruments for analytical chemistry.



The second is the construction of larger rigid molecules

> from smaller ones by Richard Russell and Ron Warrener (both Australia)

using the term molecular "Lego"

-- along the lines of Dave Shobe's e-mail --

without implying any connection to real Lego blocks.



Kieran



------------------------------------------------------------

 Dr Kieran F Lim              Biol. and Chemical Sciences

   (Lim Pak Kwan)             Deakin University

 ph:  + [61] (3) 5227-2146    Geelong          VIC   3217

 fax: + [61] (3) 5227-1040    AUSTRALIA

 mobile phone: 0438 350 259 (within Australia)

 mailto:lim..at..deakin.edu.au     http://www.deakin.edu.au/~lim

------------------------------------------------------------

************
Hi Miquel,

Some things you may want to talk about:

1. Architecture defines space. 
So do molecules. For example, cage compounds, zeolites, many 
proteins define spaces for other molecules to inhabit. 
(keywords: host-guest compounds, cages, cryptands, protein active site) 

2. Form follows function. 
For example, the "shapes" of proteins have evoled to perform a specific
function.

3. Architectural orders. 
There is a systematic way in which atoms are combined to create spatial
structure. Models such as VSEPR are easy heuristic models to look at this. 
Correlations could be made with Palladian motifs. Mitchell's book "The Logic
of Architecture" talks about "a Palladian grammar." The periodic
table and rules of chemical combination are a more complex 3D grammar.

Another example... Proteins are built from a set of architectural "motifs" 
(e.g. "greek key"). A good place to look is "Introduction to Protein Structure" 
by Carl Branden and John Tooze.

Finally, molecules crystallize in regular patterns, very much like 
"wall paper" patterns. 

4. Inorganic vs organic architecture. 
Inorganic substances have highly regular structures (e.g. salt (NaCl)). But 
most organic molecules are less-so. There is a whole class of molecules
called "dendritic molecules" that have branching patterns much like 
trees or bushes.

5. Positive vs Negative space. 
The Seagram building in NYC is my favorite example of this. Mies van der Rohe's 
monolithic structure defines a complmentary rectangular volume.  Many atomic
arrangements create these types of  spatial relationships. For example, the packing
arrangement of Cl- ions in the NaCl lattice defines spaces for the smaller Na+ ions
to occupy.


Enough for now. Hope this is useful.

Regards
Frank

Dr. Francis T. Marchese
Professor
Dept. of Computer Science
Pace University
163 William Street, 2nd Floor
NY, NY 10038

and

Director
Center for Advanced Media
http://csis.pace.edu/~cam

and 

Director
Pace Digital Gallery
http://www.pace.edu/DigitalGallery


*************
Miquel:

Sounds like a tough audience.  Here are a few that come to mind and might help. 

Hydrocarbons:  Tetrahedran, housane, basketane, cubane (just search on the names to get structures for but you can get a good idea of what they look like from their names).  There are also the catenanes (two rings, one passing through the other).  

Others come to mind but need a bit of imagination, for example, DNA looks like a spiral staircase.

Hope this helps.

Pete Gannett

*************
Dear Miquel:


Here at the University of Illinois at Chicago, we have a new building (the 
Molecular Biology Research Building or MBRB) in which the main staircase is 
a double helix.  This was of course designed deliberately for this 
building.  Take a look at it:



http://www.uic.edu/orgs/mbrb/staircas.htm



Hope this helps.



Chuck Woodbury




*************
I once gave an invited lecture on molecular graphics at a conference on  
oil and

gas discovery. They invited a variety of speakers from different fields  
to get

a perspective on visualization methods and technology. One of the  
things molecular

graphics has to offer is the ways in which various simplified  
representations are

used to bring out different aspects of a more complex data set. Ribbon  
representation

for example, removes the complexity of sidechains and focuses on the  
underlying architectural structure of the protein. Molecular surface  
focuses on the shape and

surface form without regard to interior. Biochemists may have some of  
the most complex

geometric data to deal with in any field. Architects are only recently  
getting into

3D (stereo and VR) display technology, while chemists have used it for  
decades.

Although architects are quite good at photorealism now (more so than  
chemists I think),

it always surprises me that so little use is made of depth-cuing (fade  
to black with

distance) and stereo in geometric modeling programs (geometric modelers  
in

film/animation fall in this category too). Could be that man-made  
structures are

(have been) easier to visualize with simple orthographic  
(front/back/side)

projections than natural 3D objects. Molecular building programs in  
chemistry & crystallography contain integrated physical simulations  
(structure

minimization for example).  The analogy would be designing a building  
using

real-time load-bearing simulations or something of that type.

If you are interested, I could probably

dig up some old slides.



Richard Gillilan

MacCHESS, Cornell


*************

2003 April 24

Hello,

Don't forget pyramidane (the pyramids are the only architectural wonder of the ancient world still standing; may the molecule be as stable!

THEOCHEM, 1998, _423_, 173
THEOCHEM, 2000, _507_, 165

E. Lewars
====

*****

 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
 Miquel Solà                           
 Institut de Química Computacional         
 Universitat de Girona                   
 Campus Montilivi
 17071 Girona, CATALONIA (Spain)          
 Phone +34.972.41.89.12
 Cellular-Phone:  +34.626.163.580
 FAX   +34.972.41.83.56                               
 World Wide Web: http://iqc.udg.es/~miquel/mike.html   
 e-mail: miquel.sola..at..udg.es                         
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--------------050809010902060207030406-- From chemistry-request@ccl.net Tue May 27 16:14:57 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RKEuKY024952 for ; Tue, 27 May 2003 16:14:57 -0400 Received: from dgallagher.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h4RKDII04239; Tue, 27 May 2003 13:13:18 -0700 Message-Id: <5.2.0.9.0.20030527130429.04a4ce60^at^mail.cachesoftware.com> X-Sender: daveg^at^mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 27 May 2003 13:13:53 -0700 To: "Q." From: David Gallagher Subject: Re: CCL:chirality conversion Cc: chemistry^at^ccl.net In-Reply-To: <3ED38AF2.6F55454F^at^iupui.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed All versions of CAChe can convert chirality, either on selected individual chiral centers or the complete molecule. CAChe can also read and write a range of formats including PDB. More information at www.cachesoftware.com David Gallagher, Fujitsu At 10:57 AM 5/27/2003 -0500, Q. wrote: >Good day, > I wonder if anyone knows some programs could convert a S-configuration >into R-configuration for a simple small molecule and output a pdb format >file. Thanks in advance. > > >Q. > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY^at^ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl^at^ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue May 27 18:49:40 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4RMndKY029650 for ; Tue, 27 May 2003 18:49:40 -0400 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h4RMnW4m027069 for ; Wed, 28 May 2003 00:49:32 +0200 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h4RMnWZk027064 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 28 May 2003 00:49:32 +0200 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id h4RMnVR5023814; Wed, 28 May 2003 00:49:31 +0200 Date: Wed, 28 May 2003 00:49:31 +0200 (CEST) From: Carlos Silva Lopez X-X-Sender: To: Roy Jensen cc: Subject: Re: CCL:'electron density' vs 'electronic configurations'... In-Reply-To: <1vc5dvsgb9me1hhadkauvah18q291sjst4^at^4ax.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h4RMneKY029651 Hello, I have enjoyed a lot this question you have conveyed to the list. I am not very proficient with the mathematics of ab initio and DFT methods but, let's move towards the phylosophy of these methods, let's say towards the "meaning" of these aproaches. I would say that the variational principle, though it has given us the better possibility to construct theoretical methods to describe the electronic structure, is the virus in the development of the quantum chemistry. We now know that, just obeying the border conditions, we will never have a lower than the exact energy. This is great because it simplifies the wark dramatically, but we are now more interested in the development of methods with more and more determinants and with the widest basis set available than in looking for the "nature" of the electronic structure. I mean, if we calculate the average weight of a doubly excited configuration by means of thermostatistics we will conclude that the energy gap between the ground state and the excited state is so large at work temperatures that this weight should be neglected. The use of multiconfigurational methods is justified just because there are more variational parameters to optimize; then the work out could be a lower energy (better approximated to the real), there are uniquely mathematical reasons to do that. If you want a method based on physical meaning consider pertubations. Obviously this is just an opinion, and could be as far from reality as the ab initio phylosophy is from the DFT's. _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_