From chemistry-request@www.ccl.net Thu Sep 3 02:02:25 1998 Received: from beryl.kapatel.gr (mail@beryl.kapatel.gr [193.92.133.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA27242 Thu, 3 Sep 1998 02:02:22 -0400 (EDT) Received: (from mail@localhost) by beryl.kapatel.gr (8.6.12/8.6.9) id JAA05993 for ; Thu, 3 Sep 1998 09:03:07 +0200 Received: from agate.kapatel.gr(193.92.133.34) by beryl.kapatel.gr via smap (V2.0) id xma005984; Thu, 3 Sep 98 09:02:49 +0200 Message-ID: <35EEBD5A.62E0@beryl.kapatel.gr> Date: Thu, 03 Sep 1998 09:01:30 -0700 From: Nicholas Harkiolakis Organization: Agricultural University of Athens X-Mailer: Mozilla 2.0 (Win95; I; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Benchmark Functions for Minimization Algorithms References: <35ECDAAA.40E0@beryl.kapatel.gr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings all, I'm developing a new method for locating Global and Local minima and interested to compare it with other methods in a mathematical sense initialy. I would appreciate any recomentations - functions (single and multi variable) with well defined global and local minima, that will be widely accepted as benchmark functions for messuring the efficiency of an algorithm. Also I would wellcome any relevant data - refferences anyone wishes to share or recomend. My goal is to apply the algorithm for the refinement of protein models using the AMBER forcefield. Thanks in advance, Nick Harkiolakis e-mail : nick@beryl.kapatel.gr From chemistry-request@www.ccl.net Thu Sep 3 06:16:01 1998 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA27881 Thu, 3 Sep 1998 06:16:01 -0400 (EDT) Received: from matthieu.saclay.cea.fr (matthieu.saclay.cea.fr [132.166.52.157]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0) with SMTP id MAA27347 for ; Thu, 3 Sep 1998 12:16:02 +0200 (MET DST) Received: by matthieu.saclay.cea.fr (940816.SGI.8.6.9/SGI+CEANET.2.0.1) (for chemistry@www.ccl.net) id MAA13202; Thu, 3 Sep 1998 12:16:02 +0200 From: "BOULARD" Message-Id: <9809031216.ZM13200@matthieu> Date: Thu, 3 Sep 1998 12:16:01 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: HP converter Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleaques, I am looking for a program which could convert HPplotter format (HP7550A) into any other format. Thanks for your help. Yves Boulard -- ```` ( @ @ ) +------------------------oOOo-(_)-oOOo-------------------------------+ | Dr BOULARD Yves | | | CEA SACLAY | Tel: (0033) 01 69 08 35 84 | | DSV DBCM SBGM Bat. 142 | Fax: (0033) 01 69 08 47 12 | | 91191 GIF-SUR-YVETTE CEDEX | | | FRANCE | e-mail: ybou@matthieu.saclay.cea.fr | +------------------------------+-------------------------------------+ From chemistry-request@www.ccl.net Thu Sep 3 10:01:29 1998 Received: from xx1.icas.ac.cn (root@[159.226.64.181]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA28829 Thu, 3 Sep 1998 10:01:21 -0400 (EDT) Received: from zhangxd ([192.168.2.32]) by xx1.icas.ac.cn (8.8.7/8.8.7) with ESMTP id JAA14869; Mon, 4 Sep 1995 09:28:30 GMT Message-ID: <000901bdd744$63767ee0$2002a8c0@zhangxd.xx1.icas.ac.cn> From: "zhangxd" To: "Steven Creve" , "Computational Chemistry List" Subject: =?gb2312?B?u9i4tDogQ0NMOm1vZGVsbGluZyBzdW1tYXJ5?= Date: Thu, 3 Sep 1998 22:08:47 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 hi,netters please excuse me to ask one question: how to control the degree of polymerization of a polymer with MOPAC program? what is the degree of polymerization when Tv is used?ThanX in advance. with good lucky1 zhangxd From chemistry-request@www.ccl.net Thu Sep 3 10:11:20 1998 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA28935 Thu, 3 Sep 1998 10:11:19 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id HAA25833 for ; Thu, 3 Sep 1998 07:11:20 -0700 (PDT) Date: Thu, 3 Sep 1998 07:11:19 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: computer fitting of IR spectra Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Does anyone know of a freeware program for Unix or Windows that will enable one to fit an IR spectrum to a series of Lorentzian peaks? Ideally, it should accept data as ascii x,y pairs (position, amplitude) and automatically generate an initial guess for band positions by doing some kind of peak pick. Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@www.ccl.net Thu Sep 3 11:42:02 1998 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA29654 Thu, 3 Sep 1998 11:42:01 -0400 (EDT) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.1/8.9.1) with ESMTP id QAA27870 for ; Thu, 3 Sep 1998 16:42:51 +0100 (BST) From: Michael Nolan Received: (mnolan@localhost) by cashel.nmrc.ucc.ie (8.6.8.1/8.6.6) id QAA07929 for chemistry@www.ccl.net; Thu, 3 Sep 1998 16:40:16 +0100 Message-Id: <199809031540.QAA07929@cashel.nmrc.ucc.ie> Subject: EMRS Symposium To: chemistry@www.ccl.net (ccl) Date: Thu, 3 Sep 1998 16:40:16 +0100 (BST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Call for papers. The European Materials Research Society (EMRS) invites submissions to the following symposium "Ab-initio approaches to Microelectronics Materials and Process Modelling" which will be held in Strasbourg, France on June 1 - 4 1999. Information may be found at the following URL: http://nmrc.ucc.ie/groups/AMT/SympMain.html. Contact J. Greer for more information at jgreer@nmrc.ucc.ie Michael ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND Email: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/Modelling.html http://nmrc.ucc.ie/groups/AMT/ModellingRes.html **************************************************************************** From chemistry-request@www.ccl.net Thu Sep 3 13:02:06 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA00186 Thu, 3 Sep 1998 13:02:05 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA24251; Thu, 3 Sep 98 09:37:05 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma024247; Thu, 3 Sep 98 09:36:35 -0700 Sender: osman@msi.com Message-Id: <35EEC592.AB4C22AA@msi.com> Date: Thu, 03 Sep 1998 09:36:34 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Call for Papers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit MODELING AND ANALYSIS THROUGH THE INTERNET to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Chemical Informatics As Internet is rapidly becoming and essential part of our day-to-day concerns, more and more modeling and analysis tools are also becoming available through the Internet. This symposium will show off the current developments in this area: modeling and analysis tools through the Internet, corporate-intranet applications, on-line modeling services, educational intiatives on the Internet, and others. If you are interested in contributing to this symposium, the due date for 150 word abstracts is November 15, 1998. Electronic version of ACS abstract forms are prefered and can be obtained from http://www.acs.org/meetings/abstract/absdown.html Thx...osman -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Thu Sep 3 13:08:22 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA00215 Thu, 3 Sep 1998 13:08:15 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA23896; Thu, 3 Sep 98 09:21:43 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma023893; Thu, 3 Sep 98 09:21:25 -0700 Sender: osman@msi.com Message-Id: <35EEC204.11F9EAC9@msi.com> Date: Thu, 03 Sep 1998 09:21:24 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, catalyst-l@msi.com Subject: Call for Papers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit TECHNIQUES IN PHARMACOPHORE DEVELOPMENT to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Chemical Informatics Co-sponsored by Division of Computers in Chemistry While "3D Searching" has established itself as one of the essential tools in Computer-Aided Drug Design, the ability to ask better questions to retrieve better answers from 3D databases is still a challenging task. The better questions in 3D Searching involve development of search queries that represent "pharmacophores." Pharmacophore development may involve anywhere from a simple visual pattern recognition, to fully automated model generation tools, to receptor-based methods. In this symposium, we will try to cover new developments in the area of pharmacophore development as well as validation studies on the existing methods, experimental prototypes, and in short, full spectrum of techniques in pharmacophore development. If you are interested in contributing to this symposium, the due date for 150 word abstracts is November 15, 1998. Electronic version of ACS abstract forms are preferred and can be obtained from http://www.acs.org/meetings/abstract/absdown.html Thx...Osman -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Thu Sep 3 15:00:38 1998 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA01703 Thu, 3 Sep 1998 15:00:37 -0400 (EDT) Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id PAA08916 for ; Thu, 3 Sep 1998 15:00:40 -0400 (EDT) Received: from localhost (proynov@localhost) by esi21.ESI.UMontreal.CA with SMTP id PAA27903 (8.8.7/IDA-1.6 for ); Thu, 3 Sep 1998 15:00:39 -0400 (EDT) X-Authentication-Warning: esi21.ESI.UMontreal.CA: proynov owned process doing -bs Date: Thu, 3 Sep 1998 15:00:39 -0400 (EDT) From: Proynov Emil X-Sender: proynov@esi21.ESI.UMontreal.CA To: chemistry@www.ccl.net Subject: How to cite the LAP Ec functionals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, In response to several inquiries directed to me I am enclosing below the way the LAP Ec density functional should be properly cited in case it comes to it: Example: "...The kinetic-energy-density (tkin) and Laplacian dependent correlation functional of the LAP family developed by Proynov et al. [1-4]..." where the references read (I enclose a brief description of each of them for a guide): [1]. E.I. Proynov and D.R. Salahub, Phys.Rev.vol. B49, 7874 (1994) ; Erratum, ibid, in press. (The basic formalism and the main formulae are derived for the gradientless form of the Ec functional in question) [2] E. Proynov, A. Vela and D. R. Salahub, Chem.Phys.Lett. vol.230, 419 (1994); Erratum, ibid., vol 234, 462 (1995). (A way of how to incorporate explicit tkin dependence into the model [1] is proposed leading to the LAP1 Ec) [3] E.I. Proynov, E. Ruiz, A. Vela, and D.R. Salahub, Int. J. Quant. Chem.(Symp.) vol 29, 61 (1995); (The derivation and the parametrization of the LAP1 functional is refined and the BLAP1 and PLAP1 schemes are validated with extensive tests) [4] E. I. Proynov, S. Sirois and D. R. Salahub, Int. J. Quant. Chem.vol.64, 427, (1997). (The LAP1 functional is developed further to include the missing parallel spin part of the Ec, the LAP3 functional. The BLAP3 and PLAP3 Exc schemes are parametrized and validated in this work). These functionals are programmed so far (to my knowledge) only in the code deMon-KS, but separate transferable routines are available upon request. Emil Proynov +-----------------------------+ | Dr Emil Proynov | | Montreal University | | Department of Chemistry | | proynov@chimie.umontreal.ca | +-----------------------------+ +-----------------------------+ | Emil Proynov | | proynov@chimie.umontreal.ca | +-----------------------------+ From chemistry-request@www.ccl.net Thu Sep 3 18:20:53 1998 Received: from ns-mx.uiowa.edu (ns-mx.uiowa.edu [128.255.1.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA03665 Thu, 3 Sep 1998 18:20:53 -0400 (EDT) Received: from [128.255.138.237] (his.chem.uiowa.edu [128.255.138.237]) by ns-mx.uiowa.edu (8.8.8/8.8.5) with ESMTP id RAA135776 for ; Thu, 3 Sep 1998 17:20:55 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Date: Thu, 3 Sep 1998 17:23:37 -0500 To: chemistry@www.ccl.net From: "Jan H. Jensen" Subject: Multideterminantal DFT The possible need for multideterminantal DFT has been most interesting and seems to me to be of fundamental importance. I would like to add my (current) view on this and get other people's opinions on it. In so far as the exchange-correlation functional used is correct, the main consideration should be whether the density from a single determinant wavefunction can accurately describe the exact density. Handy has discussed this issue for a two-electron case (J.Chem.Phys. 105, 9202, 1996) and states that only within an infinite basis set is that rigorously possible. Thus, the need for several configurations in DFT calculations is likely to be very basis set dependent. Depending on the rate of basis set convergence (and the form of the empirical functional?), it may be more computationally efficient to include a few more determinants to get a better description of the density. However, from a purely formalistic point of view (exact functional, infinite basis set) one determinant should be sufficient for any system. Best regards, Jan Jensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@www.ccl.net Thu Sep 3 20:24:00 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA05205 Thu, 3 Sep 1998 20:23:53 -0400 (EDT) Received: from [150.46.162.70] ([150.46.162.70]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id JAA03883 for ; Fri, 4 Sep 1998 09:24:54 +0900 (JST) Message-Id: <199809040024.JAA03883@deews1.dent.okayama-u.ac.jp> Date: Fri, 4 Sep 1998 09:32:25 +0900 To: CHEMISTRY@www.ccl.net From: ep7@dent.okayama-u.ac.jp (masamura) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) I sent CCL some questions. However, you did not adopt my questions. Please help me. I am good member of CCL. Thank you. *********************************************************** Masao Masamura Okayama University ep7@dent.okayama-u.ac.jp FAX: 81-86-235-6714 TEL: 81-86-235-6712 *********************************************************** From chemistry-request@www.ccl.net Thu Sep 3 21:26:42 1998 Received: from xray0.chem.arizona.edu (xray0.chem.Arizona.EDU [128.196.200.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA05730 Thu, 3 Sep 1998 21:26:41 -0400 (EDT) Date: Thu, 3 Sep 1998 18:16:22 MDT From: MCARDUCCI@xray0.chem.arizona.edu Message-Id: <980903181622.202009b1@XRAY0.CHEM.ARIZONA.EDU> Subject: RE: CCL:charges from X-ray Data To: chemistry@www.ccl.net, laidig@pg.com X-Vmsmail-To: SMTP%"chemistry@www.ccl.net",SMTP%"laidig@pg.com" Bill Laidig (and other interested parties), There is a lively community of scientists studying atomic charges (and other properties) derived from experimentally determined charge densities by small molecule X-ray diffraction. I have appended below an "Introduction to Charge Density Literature" that will give you lots of good starting points. I picked them to emphasize the experimental side of things, but theory gets a good coverage too. That question about defining a charge partitioning scheme is a tough one. Lecomte has the only group that I am aware of that is working on using derived charges in quantum mechanical programs, though I am sure there are others. As for the software used in these experiments, the most up-to-date, complete and widely used package available is XD. You can find more information about it at http://www.chem.gla.ac.uk/~paul/xd.html. The XDPROP portion I hope this helps you out, ---Michael Carducci Molecular Structure Laboratory Department of Chemistry University of Arizona Tucson, AZ 85721 USA Email: carducci@u.arizona.edu Phone: (520)621-4168 Fax : (520)621-8407 <--------------------------------------------------------------------------> Introduction to Charge Density Literature X-ray Charge Densities and Chemical Bonding by Philip Coppens IUCR Book Series, Oxfor University Press 1997 The Application of Charge Density Research to Chemistry and Drug Design Edited by George Jeffrey and Juan Piniella NATO ASI Series B Volume#250 Plenum Press 1991 Studies of Electron Distributions in Molecules and Crystals Edited by Robert Blessing Transactions of the ACA Vol.#26 1990 Electron Density from X-Ray Diffraction by P. Coppens Annu. Rev. Phys. Chem. 1992. 43:663- 692 Chasing the Elusive d Electron with X-rays by Philip Coppens Chapter 4 in Computational Chemistry: The challenge of d and f electrons; Salahub, D.R.; Zerner,M.C., Editors;ACS Symposium Series No.394 1989 Israel Journal of Chemistry (entire Symposium Issue) Vol.16 1977 Papers on Individual Compounds can be found by searches with the following authors (I just pulled out a few papers from my files): P.R. Mallinson, et. al. J. Chem. Phy. 97(8), 15 Oct. 1992 T. Koritsanszky, et al. JACS 1991, 113,9148-9154 C. Lecomte, et.al. Acta Cryst. (1991) B47, 253-266 B. Craven, et.al. Acta Cryst. (1984). B40, 511-518 Yu Wang, et.al. Acta Cryst. (1992). B48, 319-324 From chemistry-request@www.ccl.net Thu Sep 3 21:42:32 1998 Received: from xplain.com ([131.161.38.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA05819 Thu, 3 Sep 1998 21:42:30 -0400 (EDT) Received: from [131.161.38.102] by xplain.com with ESMTP (Eudora Internet Mail Server 2.1); Thu, 3 Sep 1998 18:41:49 -0700 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: nick@mail.mactech.com Message-Id: Date: Thu, 3 Sep 1998 18:44:57 -0800 To: computational chemistry mailing list From: Nick DeMello Subject: Oxford Molecular Reports Surge in Sales for the Macintosh I came by this in a totally non-chemistry related manner, but --as a computational chemist and Mac enthusiast--I thought some folks here might appreciate the info. Oxford Molecular Reports Surge in Sales for the Macintosh FYI, I have no relationship at all with Oxford Molecular, just thought folks might like to book mark this page for the next time a co-worker makes some comment about the "shrinking Macintosh platform" :-) ____Nicholas C. DeMello, Ph.D.________________________________________ Editor of MacTech Magazine, for Macintosh Developers and Programmers http://www.mactech.com/ _/ _/ _/ _/_/_/ _/ _/ _/_/ _/ _/ _/ _/ _/_/_/ mailto:editor@mactech.com _/ _/_/ _/ _/ _/ _/ http://www.nick.demello.com/ _/ _/ _/ _/_/_/ _/ _/