From chemistry-request@server.ccl.net Mon Apr 10 03:43:05 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 DAA32257 for ; Mon, 10 Apr 2000 03:43:05 -0400 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id DAA03208 for ; Mon, 10 Apr 2000 03:42:19 -0400 (EDT) Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id KAA13096 for ; Mon, 10 Apr 2000 10:04:20 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Mon, 10 Apr 2000 09:16:30 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Mon, 10 Apr 2000 09:16:10 +0200 From: "Krishna Bisetty" To: Subject: Cluster analysis Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA32258 Dear CCL'ers, I would appreciate any help in getting some references or review articles on hierarchical cluster analysis. Thanks Vincent Bisetty Dept of Chemistry ML Sultan Technikon Durban South Africa From chemistry-request@server.ccl.net Mon Apr 10 04:15:47 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA32582 for ; Mon, 10 Apr 2000 04:15:47 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP id KAA12141 (8.8.8/3.29); Mon, 10 Apr 2000 10:15:37 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost id KAA10732 (8.8.8/3.1); Mon, 10 Apr 2000 10:15:37 +0200 (MET DST) Date: Mon, 10 Apr 2000 10:15:37 +0200 (MET DST) Message-Id: <200004100815.KAA10732@studs3.sci.kun.nl> To: Bisettyk@wpogate.mlsultan.ac.za, CHEMISTRY@ccl.net Subject: re: Cluster analysis Have a look at the documentation for the 'R contributed code' at the website http://www.stat.math.ethz.ch/CRAN/src/contrib/PACKAGES.html. Especially look at the PDF's for cclust and clust. Each cluster procedure has references... Also a hclust procedure must be in some of these modules... that one is for hierarchical clustering. yours sincerely, Egon Willighagen From chemistry-request@server.ccl.net Mon Apr 10 07:54:35 2000 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA01715 for ; Mon, 10 Apr 2000 07:54:30 -0400 Received: from lgh ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id TAA24978 for ; Mon, 10 Apr 2000 19:52:45 +0800 (CST) Message-Id: <200004101152.TAA24978@ms.dicp.ac.cn> Date: Mon, 10 Apr 2000 19:56:8 -0800 From: Li Guohui Reply-To: chenhua@ms.dicp.ac.cn To: "CHEMISTRY@ccl.net" Subject: about DNA and RNA Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,CCLers: i want to get some papers about theoretical study on structures of DNA and RNA with MM,MD or other methods, and Is there a theoretical method which can give alpha and beta structures of DNA and RNA correctly? thanks in advance!!! From chemistry-request@server.ccl.net Mon Apr 10 05:53:34 2000 Received: from mauve.csi.cam.ac.uk (exim@mauve.csi.cam.ac.uk [131.111.8.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA00424 for ; Mon, 10 Apr 2000 05:53:34 -0400 Received: from su4.phar.cam.ac.uk ([131.111.156.196]) by mauve.csi.cam.ac.uk with smtp (Exim 3.13 #1) id 12eask-00015c-00 for CHEMISTRY@ccl.net; Mon, 10 Apr 2000 10:53:22 +0100 Received: from sg4.phar.cam.ac.uk by su4.phar.cam.ac.uk (SMI-8.6/CS-SUB) id KAA21330; Mon, 10 Apr 2000 10:52:52 +0100 Received: from localhost by sg4.phar.cam.ac.uk; Mon, 10 Apr 2000 10:52:51 +0100 (BST) Date: Mon, 10 Apr 2000 10:52:51 +0100 (BST) From: James Smith X-Sender: js252@sg4.phar.cam.ac.uk To: CHEMISTRY@ccl.net Subject: CCL:Cluster analysis (fwd) 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 FAA00425 Make sure that your chosen method doesn't violate the ultrametric inequality rule. I use Geometric (cluster centred), minimal variance, agglomerative clustering [1] can be applied to an rms difference-distance matrix and the number of significant clusters identified by Mojena's Stopping Rule No.1 (p < 0.05) [2]. 1 - Ward, J. H. (1963). Hierarchical Grouping for Evaluating Clustering Methods, Journal of the American Statistics Association, 58, 236-244. 2 -  Mojena, R. (1977). Hierarchical grouping methods and stopping rules: An evaluation, Computer Journal, 20 (4), 359-363. I hope this helps James _________________________________________________________________________ James Smith Drug Design Group +44 1223 338600 (College) St John's College Department of Pharmacology +44 1223 331985 (Office) Cambridge University of Cambridge +44 1223 331740 (Fax) CB2 1TP CB2 1QJ js252@cam.ac.uk United Kingdom United Kingdom http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ From chemistry-request@server.ccl.net Mon Apr 10 07:08:41 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA01563 for ; Mon, 10 Apr 2000 07:08:40 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id EAA06031; Mon, 10 Apr 2000 04:08:16 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14577.46622.456656.311124@lrz.uni-muenchen.de> Date: Mon, 10 Apr 2000 04:08:14 -0700 (PDT) Subject: VRML gallery of chiral Nano-Tubes X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid http://www.nirim.go.jp/~weber/gallery/NanoTubes/NanoTubes.html created with http://www.nirim.go.jp/~weber/JAVA/JSV/jsv.html More useful Java programs by Steffen Weber on http://members.xoom.com/_XOOM/steffenweber/index.html From chemistry-request@server.ccl.net Mon Apr 10 09:30:51 2000 Received: from szermierz.uni.wroc.pl (szermierz.uni.wroc.pl [156.17.93.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02363 for ; Mon, 10 Apr 2000 09:30:49 -0400 Received: from wchuwr.chem.uni.wroc.pl (wchuwr.chem.uni.wroc.pl [156.17.103.193]) by szermierz.uni.wroc.pl (8.9.1/8.9.3) with ESMTP id PAA22609 for ; Mon, 10 Apr 2000 15:29:50 +0200 (CET) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.44); 10 Apr 00 15:31:17 MET Received: from SpoolDir by WCHUWR (Mercury 1.44); 10 Apr 00 15:30:20 MET From: "Adrian Radomir Jaszewski" Organization: University of Wroclaw (Chemistry) To: chemistry@server.ccl.net Date: Mon, 10 Apr 2000 15:30:16 MET Subject: SOMO of the radical Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: Dear CCLers, From N linearly independent basis functions of the radical (S=1/2) one can construct N alpha and N beta orbitals: N alfa = (n-1) CORE + 1 SOMO occupied + (N-n) VIRTUAL N beta = (n-1) CORE + 1 SOMO unoccupied + (N-n) VIRTUAL where n denotes the number of electrons. Unrestricted DFT wavefunctions of the radicals are usually constructed using identical (or almost identical) spatial orbitals for different spins (alpha, beta) in the case of CORE and VIRTUAL MO. Lowest energy (occupied) alpha-spin SOMO and highest energy (unoccupied) beta-spin SOMO can be also very similar to each other but sometimes they are strongly asymmetrical. A knowledge of the SOMO contour can be helpful in the analysis of the spin density distribution as well as the values of the calculated hyperfine coupling constants for the radicals. My question is: When SOMO occupied (alpha) and SOMO unoccupied (beta) are dissimilar which of them (or what combination of these SOMOs) can be used to aid spin density analysis? In some cases I have observed that the spin density contours were similar to the highest energy beta-spin SOMO (unoccupied!!) contour rather than to the occupied alpha-spin SOMO; and what is the energy (in Hartree) of that SOMO when: E(lowest energy VMO)= -0.06916(alpha) -0.06008(beta) E(highest energy SOMO)= -0.12635(beta) E(lowest energy SOMO)= -0.26301(alpha) E(highest energy DOMO)= -0.24908(alpha) -0.24319(beta)? I will summarize. Thank you in advance. Adrian =============================================== Adrian R. Jaszewski Faculty of Chemistry UNIVERSITY OF WROCLAW 14 Joliot-Curie St. 50-383 Wroclaw Poland e-mail: adrian@wchuwr.chem.uni.wroc.pl ================================================ From chemistry-request@server.ccl.net Mon Apr 10 09:12:30 2000 Received: from joan.simmons.edu (joan.simmons.edu [134.140.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02264 for ; Mon, 10 Apr 2000 09:12:29 -0400 Received: from simmons.edu ([134.140.113.193]) by joan.simmons.edu (PMDF V5.2-31 #42187) with ESMTP id <0FSS009P1Y7HRT@joan.simmons.edu> for chemistry@ccl.net; Mon, 10 Apr 2000 09:16:30 -0400 (EDT) Date: Mon, 10 Apr 2000 08:33:05 -0500 From: Michael Kaplan Subject: XVth International Jahn-Teller Symposium To: chemistry@ccl.net Reply-to: mkaplan@simmons.edu Message-id: <38F1D810.1CF50515@simmons.edu> Organization: Simmons College MIME-version: 1.0 X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-transfer-encoding: 7bit To Whom It May Concern: I would like to announce that on Aug. 16-Aug.22 of 2000 in Boston a Symposium will take place. The title of the Meeting is: XVth INTERNATIONAL JAHN-TELLER SYMPOSIUM on Vibronic Interactions in Crystals and Molecules NATO ARW Colossal Magnetoresistance and Vibronic Interaction. Web page: http://www.physics.bu.edu/jts2000 Could you, please, put it on your net? Thank you in advance, Michael Kaplan. From chemistry-request@server.ccl.net Mon Apr 10 09:31:41 2000 Received: from linux2.ipc.pku.edu.cn (liangsd@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02387 for ; Mon, 10 Apr 2000 09:31:36 -0400 Received: from localhost (liangsd@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id VAA11601 for ; Mon, 10 Apr 2000 21:36:47 +0800 Date: Mon, 10 Apr 2000 21:36:47 +0800 (CST) From: Liang Shide To: chemistry@ccl.net Subject: Rotamer library Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear cclers, I'm doing the work of side chain construction at the protein-protein interface. The computational result was suffered from the incompleteness of the rotamer library, which is backbone independent and contains more than 300 elements. Can anyone tell me where can I get a more detailed library? Thanks in adance! Liang ---------------------------------------- Liang Shide Room 115,Building 30 Peking University Beijing, 100871 P.R.China Phone: 86-10-62756833 Fax: 86-10-62751725 E-mail: liangsd@linux2.ipc.pku.edu.cn ----------------------------------------- From chemistry-request@server.ccl.net Mon Apr 10 10:26:53 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA02733 for ; Mon, 10 Apr 2000 10:26:53 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id JAA30908 for ; Mon, 10 Apr 2000 09:26:40 -0500 (EST) Message-ID: Date: 10 Apr 2000 09:38:37 -0500 From: "Boyd" Subject: old computational chemists don't fade away To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear CCLers, I am curious if there are any subscribers to this list who are officially retired but are nevertheless still interested in staying involved in the field. If so, please contact me. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Indiana University-Purdue University at Indianapolis E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Mon Apr 10 11:41:38 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 LAA03451 for ; Mon, 10 Apr 2000 11:41:38 -0400 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA10351 for ; Mon, 10 Apr 2000 11:41:23 -0400 (EDT) Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA05687 for ; Mon, 10 Apr 2000 08:41:24 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id LAA28431 for ; Mon, 10 Apr 2000 11:41:23 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Mon, 10 Apr 2000 11:41:22 -0400 (EDT) From: Peter Shenkin To: chemistry@www.ccl.net Subject: Re: CCL:Cluster analysis In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, For the method we use in our xcluster program (single-link hierarchical clustering), see: Shenkin, P. S.; McDonald, D. Q., "Cluster Analysis of Molecular Conformations", J. Comput. Chem. 1994, 15, 899-916. There's a reference in this paper to an excellent book on cluster analysis; however, I don't have a copy of the paper with me at this moment, and I don't recall the author's name offhand. -P. On Mon, 10 Apr 2000, Krishna Bisetty wrote: > I would appreciate any help in getting some references or review > articles on hierarchical cluster analysis. -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Mon Apr 10 13:54:23 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA04515 for ; Mon, 10 Apr 2000 13:54:23 -0400 Received: from mail.chem.tamu.edu ([165.91.176.197]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu; Mon, 10 Apr 2000 13:02:31 -0500 Sender: fan@mail.chem.tamu.edu (Huajun Fan) Message-ID: <38F2149B.E58C8871@mail.chem.tamu.edu> Date: Mon, 10 Apr 2000 12:51:24 -0500 From: Huajun Fan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: Michael Kaplan CC: chemistry@ccl.net Subject: Re: CCL:XVth International Jahn-Teller Symposium References: <38F1D810.1CF50515@simmons.edu> Content-Type: multipart/alternative; boundary="------------E963410F9F85B17B5D56F9DD" --------------E963410F9F85B17B5D56F9DD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, It looks the address should be http://physics.bu.edu/jts2000/homepage.html Best regards. huajun Michael Kaplan wrote: > To Whom It May Concern: > > I would like to announce that on Aug. 16-Aug.22 of 2000 in Boston a > Symposium will take place. > The title of the Meeting is: > > XVth INTERNATIONAL JAHN-TELLER SYMPOSIUM on > Vibronic Interactions in Crystals and Molecules > NATO ARW Colossal Magnetoresistance and Vibronic Interaction. > > Web page: http://www.physics.bu.edu/jts2000 > > Could you, please, put it on your net? > Thank you in advance, > > Michael Kaplan. > > -= 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 -- Dr. Hua-Jun Fan Chemistry Department Texas A&M University 3255 TAMU College Station, TX 77843-3255 --------------E963410F9F85B17B5D56F9DD Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi,

It looks the address should be

http://physics.bu.edu/jts2000/homepage.html

Best regards.

huajun

Michael Kaplan wrote:

To Whom It May Concern:

I would like to announce that on Aug. 16-Aug.22 of 2000 in Boston a
Symposium will take place.
The title of the Meeting is:

XVth INTERNATIONAL JAHN-TELLER SYMPOSIUM on
Vibronic Interactions in Crystals and Molecules
NATO ARW Colossal Magnetoresistance and Vibronic Interaction.

Web page: http://www.physics.bu.edu/jts2000

Could you, please, put it on your net?
Thank you in advance,

Michael Kaplan.

-= 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

-- 
Dr. Hua-Jun Fan
Chemistry Department
Texas A&M University
3255 TAMU
College Station, TX 77843-3255
  --------------E963410F9F85B17B5D56F9DD-- From chemistry-request@server.ccl.net Mon Apr 10 14:14:20 2000 Received: from interlock.amoco.com (interlock.amoco.com [192.195.167.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA04651 for ; Mon, 10 Apr 2000 14:14:18 -0400 Received: by interlock.amoco.com id NAA16017 (InterLock SMTP Gateway 3.0 for CHEMISTRY@ccl.net); Mon, 10 Apr 2000 13:13:38 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Mon, 10 Apr 2000 13:13:38 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Mon, 10 Apr 2000 13:13:38 -0500 Message-Id: From: "Golab, Joseph T" To: "'ccl'" Subject: SUMMARY -- Refractive Index (4/00) Date: Mon, 10 Apr 2000 13:10:58 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: multipart/mixed; boundary="----_=_NextPart_000_01BFA318.1FDEE18A" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01BFA318.1FDEE18A Content-Type: text/plain Here is the summary for computational ways to calculate the refractive index of materials. As with other molecular properties, there are empirical (bond additivity) and "more" rigorous methods. Some have been incorporated into commercial code. There are also several recent, relevant articles on the topic. Thanks to all that replied. <> :Joe golabjt@bp.com +1 630 961-7878 (SOCON 231-7878) ------_=_NextPart_000_01BFA318.1FDEE18A Content-Type: text/plain; name="CCLrefractive index.txt" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="CCLrefractive index.txt" -----Original Message----- From: Golab, Joseph T [mailto:golabjt@bp.com] Sent: Wednesday, April 05, 2000 4:51 PM Subject: CCL:Refractive Index Is it possible to calculate the refractive index of a material using computational chemistry techniques either directly or indirectly? :Joe golabjt@bp.com +1 630 961-7878 (SOCON 231-7878) ---------- From: Mario Citra[SMTP:citra@syrres.com] Sent: Thursday, April 06, 2000 7:37 AM Subject: CCL:refractive index Try the SPARC program at the following website:=20 http://ibmlc2.chem.uga.edu/sparc Regards, Mario J. Citra Ph.D. Syracuse Research Corporation (315) 452-8406 citra@syrres.com ---------- From: Gregory Durst[SMTP:DURST_GREGORY@LILLY.COM] Sent: Thursday, April 06, 2000 7:44 AM Subject: Re: CCL:Refractive Index See: "Group contribution-additivity and quantum mechanical models for predicting the molar refractions, indexes of refraction, and boiling = points of fluorochemicals.", Le, Thao D.; Weers, Jeffry G., J. Phys. Chem. = 99(38), (1995), 13909-16. regards, Greg ---------- From: Bormann-Rochotte, Lynn M[SMTP:lbr92605@glaxowellcome.com] Sent: Thursday, April 06, 2000 7:37 AM Subject: RE: Refractive Index GULP lists refractive index calculations among its capabilities (http://www.ch.ic.ac.uk/gale/Research/gulp.html). GULP is commercially available through MSI. =20 Lynn Bormann-Rochotte ---------- From: Dr. Klaus Stark[SMTP:klaus@msi-eu.com] Sent: Thursday, April 06, 2000 6:47 AM Subject: Re: CCL:Refractive Index you can calculate the freqeuncy dependent refractive index with CASTEP = once you can the band gap correct (scissors operator!) Best regards Klaus Molecular Simulations Inc. Inselkammerstr. 1 82 008 Unterhaching-Muenchen Germany Phone : 0049-89-61459-420 Mobile : 0049-172-936-3380 Fax : 0049-89-61459-400 E-Mail : kstark@msi.de Web Page : http://www.msi.com ---------- From: David van der Spoel[SMTP:spoel@xray.bmc.uu.se] Sent: Thursday, April 06, 2000 1:03 AM Subject: CCL:Refractive Index On Thu, 6 Apr 2000, Ilfir R. Ramazanov wrote: The refractive index can be computed from the frequency dependent=20 dielectric constant, which in turn can be computed from molecular simulation. See my paper (and the 80 references therein): @Article{Spoel98a, author =3D {D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen}, title =3D {A systematic study of water models for molecular simulation}, year =3D 1998, journal =3D "J. Chem. Phys.", volume =3D 108, pages =3D {10220-10230} } an excellent review that covers this is Zhu et al. @Article{Zhu94, author =3D {S-B. Zhu and S. Singh and G. W. Robinson}, title =3D {Field-Perturbed Water}, journal =3D "Adv. Chem. Phys.", year =3D 1994, volume =3D 85, pages =3D {627-731} } Groeten, David. ________________________________________________________________________= Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ---------- From: Ilfir R. Ramazanov[SMTP:elf@anrb.ru] Sent: Thursday, April 06, 2000 1:42 AM Subject: CCL:Refractive Index ACD does calculate a refraction index but it has very poor results. And ACD is not a computational chemistry program. Ilfir. amdo> Package ACD calculates (Chem Sketch) refraction indexes. amdo> Andre Mauricio de Oliveira Best regards, Ilfir R. Ramazanov, Ph.D., Laboratory of Catalytic Synthesis Institute of Petrochemistry and Catalysis, pr. Oktyabrya, 141, Ufa, 450075, Russia. mailto:elf@anrb.ru Visit my homepage and find some QC software http://members.tripod.com/~ChemELF Visit our lab web page http://organomet.cjb.net 06.04.2000 11:37 ---------- From: Dr. Andreas Klamt[SMTP:andreas.klamt@cosmologic.de] Sent: Thursday, April 06, 2000 12:28 AM Subject: Re: CCL:Refractive Index isn't the MR (molar refraction) index calculated by the CLOGP program = (it did so in earlier versions, but I do not know about later version) some molar refraction index, which multiplied by molar = density gives the refractive index? Dr. Andreas Klamt COSMOlogic GmbH&Co.KG Burscheider Str. 515 51381 Leverkusen Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de ------------------------------------------------------------------------= -------- COSMOlogic Your Competent Partner for Computational Chemistry and Solvation ------------------------------------------------------------------------= -------- ---------- From: Andrew Rohl[SMTP:andrew@power.curtin.edu.au] Sent: Wednesday, April 05, 2000 8:19 PM Subject: Re: CCL:Refractive Index Almost every 3-D simulation code, both potentials and QM, can=20 calculate the dielectric constants of a material which in turn can be=20 used to calculate the refractive index (they are inverse related).=20 See for example: http://www.ch.ic.ac.uk/gale/Research/gulp.html Andrew Rohl Email: A.Rohl@curtin.edu.au School of Applied Chemistry Phone: +61 8 9266 7317 = (Office) Curtin University of Technology +61 8 9266 3780 (Lab) PO Box U 1987 FAX: +61 8 9266 2300 Perth, 6845 WESTERN AUSTRALIA WWW: http://chemistry.curtin.edu.au/staff/alr ---------- From: Joe Landman[SMTP:landman@sgi.com] Sent: Wednesday, April 05, 2000 8:14 PM Subject: RE: Refractive Index As the refractive index is a function of the dielectric function, as = long as you can calculate that, you should be ok. Most packages that do = H.F. or related calculations can give you the dielectric function (or close to = it). You can also do this via other methods (computational physics tools = that perform all electron calculations, or related levels of theory). Joseph Landman, Ph.D., | SGI Americas Technology Center email: landman@sgi.com | Bioinformatics, Linux, and Clusters voice: +1 248 848 4469 | fax: +1 248 848 5600 | =20 ---------- From: andre mauricio de oliveira[SMTP:amolive@dedalus.lcc.ufmg.br] Sent: Wednesday, April 05, 2000 5:30 PM Subject: CCL:Refractive Index Dear Joe, Package ACD calculates (Chem Sketch) refraction indexes. Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765=20 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil=20 ---------- From: Robert J. Doerksen[SMTP:rjd@bastille.cchem.berkeley.edu] Sent: Wednesday, April 05, 2000 6:20 PM Subject: RE: CCL:Refractive Index One more thing, the QSAR/QSPR approach (as in ACD ChemSketch) may give = a number accurate enough for your purposes (if you only need a ballpark figure), without bothering to do accurate calculations. That would presumably be based on atomic fragments of the sort calculated in my papers or Ratner's, or previously obtained from experimental data in = many sources. Note that the most ACD claims (on their website) is = 'estimation' molar refractivity, refractive index, molar volume, and density.=20 Cheers, =20 Robert ---------- From: Robert J. Doerksen[SMTP:rjd@bastille.cchem.berkeley.edu] Sent: Wednesday, April 05, 2000 6:09 PM Subject: RE: CCL:Refractive Index I did not work on refractive index itself, but I can comment briefly on the Ratner et al article. I think in general that the refractive index is accurately obtained from accurate polarizabilities. = My following comments are all on 'accuracy of polarizabilities' and thus = may be not exactly what you want to know about!=20 a. They calculate frequency-dependent polarizability for one non-zero freq. In my previous work I only calculated the static = (freq=3D0)=20 polarizability.=20 b. Neglect of e- correlation may work for benzene but is not accurate enough for many other molecules. c. the average polarizability is easier to get right than the anisotropy of the polarizability. d. Accurate geometries (rather than assumed model geometries) lead to more accurate polarizabilites. e. Additive models of polarizability were earlier a part of my papers, listed below (not mentioned by Ratner, et al.). For discussion of methods for polarizabilities of azoles, please refer to: > N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar > "Polarizabilities of aromatic five-membered rings: azoles," Journal = of > Physical Chemistry 99, 12790 (1995). in which we advocated using a specially optimized basis set for polarizabilities (labelled 'C') which had 5s3p2d basis functions for C = and N. We advocated using the MP2 level of theory to recover the bulk of electron correlation effects for such routine molecules. In subsequent work, we calculated polarizabilities for oxazoles, azines, and 87 boron-nitrogen containing monocycles, all using the MP2/C level in = order to obtain a consistent database of reasonably accurate = polarizabilities. The method used is 'finite field'. >From my webpage, the references are: R.J. Doerksen; A.J. Thakkar "Structures, vibrational frequencies and polarizabilities of diazaborinines, triazadiborinines, azaboroles, and oxazaboroles," Journal of Physical Chemistry A 103, = 2141 (1999).=20 R.J. Doerksen; A.J. Thakkar "Azaborinines: structures, vibrational frequencies and polarizabilities," Journal of Physical Chemistry A 102, 4679 (1998).=20 R. J. Doerksen; A.J. Thakkar "Polarizabilities of heteroaromatic molecules: azines revisited," International Journal of Quantum Chemistry 60, 421 (1996).=20 N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar "Polarizabilities of oxazoles: ab initio calculations and simple models," Journal of Physical Chemistry 100, 8752 (1996). (These references, with abstracts and links, can be found on my = webpage,=20 http://www.cchem.berkeley.edu/~mhggrp/doerksen/rjdhome.htm .) Oxidized purines (bicyclic) were considered by Kassimi and Thakkar, Polarizabilities of purine, allopurinol, hypoxanthine, xanthine and alloxanthine. N. El-Bakali Kassimi and A.J. Thakkar, J. Mol. Struct. (Theochem) 366, 185-193 (1996). Hinchliffe and Soscun published a set of polarizabilities in papers = >from 1993-96 (in Theochem and elsewhere) that included naphthalene (with somewhat less appropriate Pople basis sets).=20 Cheers, Robert ---------- From: kim[SMTP:kim@lowton.pnl.gov] Sent: Wednesday, April 05, 2000 5:47 PM Subject: RE: CCL:Refractive Index bond additivity should work. hyperchem uses a method (miller,jacs,112 = (1990)=20 8533) that they relate is an additivity scheme. they note that it is=20 insensitive to isomers. is that a concern of yours? somewhere there = must be a=20 ghose and crippen scheme. i've compared several methods, and they = generally=20 seem to be 'good students'. =20 kim ---------- From: kim[SMTP:kim@lowton.pnl.gov] Sent: Wednesday, April 05, 2000 5:33 PM Subject: Re: CCL:Refractive Index the answer would be yes on both accounts. one could calculate the=20 polarizability and go through the polarizability relationships or use a = structure-property approach. there are several useful and easy qsar=20 relationships out there for the polarizability and refractivity. the = next question is how accurate (in an absolute sense) do you want or need to = be? Kim F. Ferris =3D Pacific Northwest National Laboratory =3D Environmental and Health Sciences =3D P.O. Box 999; Mailstop K2-44 =3D Richland, WA 99352 =3D Voice (509) 375-3754 =3D Fax (509) 375-2186 =3D e-mail: kim@darter.pnl.gov =3D kim.ferris@pnl.gov =3D ---------- From: andre mauricio de oliveira[SMTP:amolive@dedalus.lcc.ufmg.br] Sent: Wednesday, April 05, 2000 5:30 PM Subject: Re: CCL:Refractive Index Package ACD calculates (Chem Sketch) refraction indexes. Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765=20 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil=20 ---------- From: PETERSON,BRIAN K.[SMTP:PETERSBK@apci.com] Sent: Wednesday, April 05, 2000 5:06 PM Subject: RE: Refractive Index The refractive index is directly related to the polarizability of a molecule. The Lorenz-Lorentz relation is R ("molar refraction") =3D = (n^2 - 1)/(n^2 + 2) * M/rho =3D 4/3 * N * pi * alpha=20 where n =3D refractive index, rho =3D density, M =3D molecular weight, = alpha =3D polarizability. To calculate accurate polarizabilities, I imagine you = need high-level basis sets because the "outer regions" are important. One = also needs to think about how to average the polarizability since it is, in general, a tensor. Cheaper, easier, and perhaps better is to use a bond-additivity type correlation for the molar refraction. Perhaps you could check out a = book like, "Dielectric Properties and Molecular Behavior," N. Hill, W.E. = Vaughan, A.H. Price, and M. Davies, Van Nostrand, 1969 or do some kind of search = on "molar refraction", "molar refractivity", and "correlation". I know = that there are some commercial codes that have a correlation like this built = in. Synthia probably does this for polymers and I think that there are PC = codes for small molecule systems. =20 Good luck, brian peterson Air Products and Chemicals, Inc. ---------- From: Robert J. Doerksen[SMTP:rjd@bastille.cchem.berkeley.edu] Sent: Wednesday, April 05, 2000 4:49 PM Subject: Re: CCL:Refractive Index Please look at: The Journal of Physical Chemistry A; 1999; 103(12); 1818-1821 for a simple demonstration of how to get the refractive index from the molecular polarizability. Accurate polarizabilities require inclusion = of electron correlation and a good basis set. Cheers, Dr. Robert J. Doerksen = ************************************************* Head-Gordon Group = * Department of Chemistry work phone (510) = 642-9304 University of California fax (510) = 643-6232 Berkeley, CA, USA 94720 e-mail: = rjd@bastille.cchem.berkeley.edu **** webpage: = http://www.cchem.berkeley.edu/~mhggrp/doerksen/rjdhome.htm ---------- From: Noppawan Tanpipat[SMTP:nxt@msi.com] Sent: Wednesday, April 05, 2000 4:26 PM Subject: Re: CCL:Refractive Index MSI's CASTEP can do this. Noppawan Tanpipat Product Manager, Quantum Chemistry Tel: (858) 799-5332 Molecular Simulations Inc. Fax: (858) = 458-0136 9685 Scranton Road Email: = nxt@msi.com San Diego, CA 92121 Web: = http://www.msi.com ---------- From: Michael J. Doyle[SMTP:mdoyle@msi.com] Sent: Wednesday, April 05, 2000 4:28 PM Subject: Re: CCL:Refractive Index try something like this MICHAEL DOYLE This is interesting stuff from rulequest.com. Basically they use = algorithms that are similar to our CSAR technology to analyze some interesting physical phenomena = of lattices and materials. Really its not ground breaking, but it is something we should do in the = formulations or a materials QSAR like series of tools. ".....The same rules were used to classify a further 10,000 unseen = cases (that is, substances that were not available to See5 when the theory was constructed). The = result -- 99.8% accuracy on these test cases! ...." =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D Predicting Magnetic Properties of Crystals This case study was carried out in collaboration with Dr John Rodgers = of National Research Council Canada. The aim is to develop rules that predict whether a = substance is magnetic or not; this would expedite the search for new synthetic compounds with = desirable magnetic behavior.=20 Each case describes over 120 properties of a substance, such as the = number of atoms of each element that it contains, the number of atoms belonging to each = periodic table family, density, crystal structure group, and so on. From 24,641 such cases that are = labeled pos and neg to indicate whether or not they are magnetic, See5 takes a little over a = minute on a 400MHz PC to construct a theory consisting of 23 rules. Magnetic substances are = described by 11 rules:=20 =A0=A0=A0 Rule 1: (110, lift 14.0) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 N > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.991] =A0=A0=A0 Rule 2: (342/3, lift 13.9) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Si <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Ba <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 6 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 4' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group =3D tI26 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.988] =A0=A0=A0 Rule 3: (1360/15, lift 13.9) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B <=3D 2 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 C <=3D 1 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Si <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 5 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 6 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 2' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 4' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.988] =A0=A0=A0 Rule 4: (63, lift 13.9) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3' > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP38, hR19, tI26} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Density > 5.23 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.985] =A0=A0=A0 Rule 5: (367/6, lift 13.8) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 6 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 4' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group =3D tI26 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.981] =A0=A0=A0 Rule 6: (43, lift 13.8) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B > 2 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B <=3D 9 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 > 10 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.978] =A0=A0=A0 Rule 7: (213/4, lift 13.8) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 10' > 1 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, tP68} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.977] =A0=A0=A0 Rule 8: (158/3, lift 13.7) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP38, hR19, tI26} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Density <=3D 5.23 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.975] =A0=A0=A0 Rule 9: (53/1, lift 13.6) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B <=3D 2 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Si > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 > 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 1' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.964] =A0=A0=A0 Rule 10: (1528/56, lift 13.6) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Si <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Ga <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 In <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Ba <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Tl <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 2 <=3D 9 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 5 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 6 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 4' <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.963] =A0=A0=A0 Rule 11: (15, lift 13.3) =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 2 > 9 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Family 3 <=3D 0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Group in {hP6, hP38, hR19, tI26, = tP68, hH6, hH38, tP88, tP92} =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ->=A0 class pos=A0 [0.941] Each rule is characterized by the statistics (N/E, lift L) where=20 =B7=A0=A0=A0=A0=A0=A0=A0N is the number of training cases covered by = the rule,=20 =B7=A0=A0=A0=A0=A0=A0=A0E (if shown) is the number of them that do not = belong to the rule's class, and=20 =B7=A0=A0=A0=A0=A0=A0=A0L is the estimated accuracy of the rule (the = figure in square brackets, e.g. [0.991]) divided by the prior probability of the rule's class.=20 The same rules were used to classify a further 10,000 unseen cases = (that is, substances that were not available to See5 when the theory was constructed). The result = -- 99.8% accuracy on these test cases!=20 This example demonstrates that See5 can speedily process large, = high-dimensional datasets to yield interpretable, accurate models.=20 Michael J. Doyle, PhD.=A0 mdoyle@msi.com=A0=20 Mail: 9685 Scranton Road, San Diego, CA 92121, USA Phone: 858 799 5358=A0=A0=A0=A0=A0=20 Fax: 858 458 0136 Home: 760 471 2910=A0=A0=A0=A0=A0=20 US-Cell: 760 809 1225 EU-Cell +44-411-88-6563 >----------END ------_=_NextPart_000_01BFA318.1FDEE18A-- From chemistry-request@server.ccl.net Mon Apr 10 14:47:28 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05040 for ; Mon, 10 Apr 2000 14:47:27 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id OAA00951; Mon, 10 Apr 2000 14:47:06 -0400 (EDT) Message-ID: <006401bfa31d$5ba062c0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "chinapong kritayakornupong" Cc: References: Subject: Re: CCL:about Schakal format Date: Mon, 10 Apr 2000 14:48:15 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi, the SCHAKAL format is quite easy: TITL some title, e.g. the name of the output that provided the geometry CELL 1 1 1 90 90 90 ### these are the unit cell dimensions, ### lengths and angles ATOM N1 -0.27637072297 1.13190217285 0 ATOM H2 0.5 2. -1 ### more lines for atoms with the ATOM keyword, an ### atom name and three fractional coordinates. (The ### program comes from crystallography.) If you use ### the cell dimensions as above, fractional and cartesian ### coordinates have identical values. END ### this marks the end of the file Stefan ______________________________________________________________________ Dr. Stefan Fau fau@qtp.ufl.edu Quantum Theory Project (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Mon Apr 10 14:53:51 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 OAA05101 for ; Mon, 10 Apr 2000 14:53:51 -0400 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA14759 for ; Mon, 10 Apr 2000 14:53:50 -0400 (EDT) Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id LAA08082; Mon, 10 Apr 2000 11:53:37 -0700 (PDT) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma008080; Mon, 10 Apr 00 11:53:35 -0700 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id LAA16788; Mon, 10 Apr 2000 11:53:35 -0700 (PDT) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2650.21) id <2GBX5J79>; Mon, 10 Apr 2000 11:53:35 -0700 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE5031C56E7@shepherd.mdli.com> From: Doug Henry To: "'Krishna Bisetty'" , chemistry@www.ccl.net Cc: Doug Henry Subject: RE: Cluster analysis Date: Mon, 10 Apr 2000 11:53:29 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" There is some fortran code for a variety of cluster methods, at http://win-www.uia.ac.be/u/statis/programs/clusfind_readme.html It supports the book Kaufman and Rousseeuw, Finding Groups in Data, Wiley, 1990. Doug Henry MDLI dough@mdli.com From chemistry-request@server.ccl.net Mon Apr 10 16:02:45 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 QAA05763 for ; Mon, 10 Apr 2000 16:02:45 -0400 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA16728 for ; Mon, 10 Apr 2000 16:02:43 -0400 (EDT) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se for ; Mon, 10 Apr 2000 22:03:56 +0200 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA17322; Mon, 10 Apr 2000 22:02:38 +0200 Date: Fri, 7 Jul 2000 21:51:27 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: chemistry@www.ccl.net Subject: Is CML dead? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Last year in May there was a vivid discussion on the CCL about using XML/CML for storing chemical information. I recently checked up the website http://www.xml-cml.org and it seems quite dead... The only software available is a bunch of java classes and the CML DTD (DocumentTypeDescription). If I would like to read or write CML/XML files from my programs written in C or Fortran do I have to write a complete library to do it? If I would do that, would others be interested to use it in their software? To extend the library? Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon Apr 10 16:48:18 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 QAA06172 for ; Mon, 10 Apr 2000 16:48:18 -0400 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA17723 for ; Mon, 10 Apr 2000 16:48:15 -0400 (EDT) Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP id WAA05751 (8.8.8/3.29); Mon, 10 Apr 2000 22:44:29 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost id WAA29861 (8.8.8/3.1); Mon, 10 Apr 2000 22:44:29 +0200 (MET DST) Date: Mon, 10 Apr 2000 22:44:29 +0200 (MET DST) Message-Id: <200004102044.WAA29861@studs3.sci.kun.nl> To: chemistry@www.ccl.net, spoel@xray.bmc.uu.se Subject: re: Is CML dead? > I recently checked up the website http://www.xml-cml.org and it seems quite dead... The website doesn't contain that much information indeed... their are several projects ongoing though... their is one about using CML in publications, one about storing NMR data in CML and ofcourse JChemPaint and Jmol that read and write CML (for 2D and 3D structures and 3D animations). Egon From chemistry-request@server.ccl.net Mon Apr 10 17:26:17 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06452 for ; Mon, 10 Apr 2000 17:26:12 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12elhO-0005ne-00 for CHEMISTRY@ccl.net; Mon, 10 Apr 2000 22:26:22 +0100 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12elhB-00066s-00 for CHEMISTRY@ccl.net; Mon, 10 Apr 2000 22:26:09 +0100 Received: from dialup-6-5.net.ic.ac.uk ([155.198.8.85]) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 12elhI-001tME-00; Mon, 10 Apr 2000 22:26:16 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: References: Date: Mon, 10 Apr 2000 22:26:05 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:Is CML dead? Content-Type: text/plain; charset="us-ascii" >Hi, > >Last year in May there was a vivid discussion on the CCL about using >XML/CML for storing chemical information. I recently checked up the >website http://www.xml-cml.org and it seems quite dead... >The only software available is a bunch of java classes and the CML DTD >(DocumentTypeDescription). > >If I would like to read or write CML/XML files from my programs written in >C or Fortran do I have to write a complete library to do it? If I would do >that, would others be interested to use it in their software? To extend >the library? The site is not dead! We will very shortly be mounting a CML schema, which can be used to validate CML documents, and we currently have an article in the process of being refereed. Once (if!) accepted, this will address several of the issues raised above -- Henry Rzepa. Imperial College, Chemistry Dept. +44 171 594 5774 (Office) +44 171 594 5804 (Fax) From chemistry-request@server.ccl.net Mon Apr 10 18:32:42 2000 Received: from mallard.duc.auburn.edu (mallard.duc.auburn.edu [131.204.2.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06855 for ; Mon, 10 Apr 2000 18:32:41 -0400 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id RAA11154 for ; Mon, 10 Apr 2000 17:32:24 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Mon, 10 Apr 2000 17:32:24 -0500 (CDT) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: triplet and singlet gap of C2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's; Could anybody give some information about C2? C2 can have triplet or singlet state and I would like to know which is more stable and what is the energy gap between two states? Thank you in advance. yours Ohyun Kwon, graduate Department of Chemistry Auburn University Auburn, AL 36849