From chemistry-request@www.ccl.net Thu Feb 11 06:22:48 1999 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA11455 Thu, 11 Feb 1999 06:22:40 -0500 (EST) Received: from xtallography.geol.ucl.ac.uk by mail-d.bcc.ac.uk with SMTP (XT-PP); Thu, 11 Feb 1999 11:22:01 +0000 Message-Id: <3.0.6.32.19990211112210.007bcb00@pop-server.ucl.ac.uk> X-Sender: ucfbaro@pop-server.ucl.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 11 Feb 1999 11:22:10 +0000 To: chemistry@www.ccl.net From: "Artem R. Oganov" Subject: CCL: Pseudopotentials Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, What is the difference in definitions between ultrasoft, soft, and hard pseudopotentials? Does any distinctive boundary exist between them? Thank you, Artem. From chemistry-request@www.ccl.net Thu Feb 11 06:40:42 1999 Received: from fikus.jh-inst.cas.cz (fikus.jh-inst.cas.cz [147.231.28.135]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA11533 Thu, 11 Feb 1999 06:40:32 -0500 (EST) Received: from tracy.jh-inst.cas.cz (tracy.jh-inst.cas.cz [147.231.29.251]) by fikus.jh-inst.cas.cz (8.7.6/8.7.3) with ESMTP id MAA20496 for ; Thu, 11 Feb 1999 12:39:58 +0100 Received: from TRACY/SpoolDir by tracy.jh-inst.cas.cz (Mercury 1.40); 11 Feb 99 12:39:59 +0200 Received: from SpoolDir by TRACY (Mercury 1.40); 11 Feb 99 12:39:46 +0200 Received: from pc8242.jh-inst.cas.cz (147.231.28.242) by tracy.jh-inst.cas.cz (Mercury 1.40); 11 Feb 99 12:39:41 +0200 Received: by pc8242.jh-inst.cas.cz with Microsoft Mail id <01BE55BB.83553F80@pc8242.jh-inst.cas.cz>; Thu, 11 Feb 1999 12:39:06 +0100 Message-ID: <01BE55BB.83553F80@pc8242.jh-inst.cas.cz> From: Jan Hrusak To: "'chemistry@www.ccl.net'" Subject: PA of Hydrocarbons Date: Thu, 11 Feb 1999 12:39:02 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit DEAR NETTERS IS SOMEONE IN THE COMMUNITY AVARE OF MEASURED ORE CALCULATED PROTONAFFINITIES OF SATURATED HYDROCARBONS ? MY SEARCHES IN VARIOUS DATABASES AND STANDARD TABLES INCLUDING THE MOST RECENT NIST COMPILATION WAS NOT VERY SUCCESSFUL. I KNOW LOCATED ONLY THE VALUES FOR C1 - C3 AND FOR ISO-BUTANE. THANX TO ALL WHO WILL REPLY JAN HRUSAK Hrusak@jh-inst.cas.cz From chemistry-request@www.ccl.net Thu Feb 11 08:28:15 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA12521 Thu, 11 Feb 1999 08:28:13 -0500 (EST) Received: from localhost by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id OAA27274; Thu, 11 Feb 1999 14:28:11 +0100 (MET) Date: Thu, 11 Feb 1999 14:28:10 +0100 (MET) From: Anik Peeters X-Sender: anik@inch.uia.ac.be To: chemistry@www.ccl.net Subject: colour of molecules in the solid state Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am studying molecular crystals using the supermolecule approach: a cluster of 10-15 molecules is described by the wave function and this cluster is surrounded by point charges simulating the other neighbours. The level of theory we are using is Hartree-Fock. The molecule I am studying right now has been observed in three different polymorphic forms. One has a white colour, another one is yellow and a third one is light yellow. I have been trying to relate the yellow and light yellow colour to the band gap between the HOMO and LUMO. However, the energy differences I obtained are too large. I was wondering whether there exists a cheap method (because of the size of the system) to get a better approximation of the band gap. Greetings, Anik. ************************************************************************* * Dr. Anik Peeters * * Quantum Chemistry Group, University of Antwerp (UIA) * * Universiteitsplein 1, B-2610 Wilrijk, Belgium * * phone: 32-3-8202366, fax: 32-3-8202310, e-mail: anik@uia.ac.be * ************************************************************************* From chemistry-request@www.ccl.net Wed Feb 10 02:33:52 1999 Received: from frederik.pml.tno.nl (frederik.pml.tno.nl [134.221.122.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA28655 Wed, 10 Feb 1999 02:33:50 -0500 (EST) Received: by frederik.pml.tno.nl; id IAA01987; Wed, 10 Feb 1999 08:33:34 +0100 Received: from postoffice.pml.tno.nl(134.203.134.74) by frederik.pml.tno.nl via smap (4.1) id xma001981; Wed, 10 Feb 99 08:33:34 +0100 Received: by postoffice.pml.tno.nl with Internet Mail Service (5.5.2232.9) id <14LB10TL>; Wed, 10 Feb 1999 08:32:57 +0100 Message-ID: <97C27A97BB05D211B37100805FE2A63814A3EB@postoffice.pml.tno.nl> From: "Gurp, Ron van" To: chemistry@www.ccl.net Cc: "Zelst, Michel van" Subject: Summary: Drawing Lewis structures Date: Wed, 10 Feb 1999 08:32:57 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain; charset="iso-8859-1" Dear Netters, Recently I posted the following question onto the list: > >We are looking for software (Linux/Windows95/98 or NT) that can draw Lewis >structures of organic molecules, depicting all electron lone pairs as well >as bonding pairs. Is there any computer program available that generates >such structures semi-automatically? > As promised, here's my summary of your replies. Thanks to Douglas E. Stack, Dr. Dragan Lj. Vuckovic, Allan Adler, Kenward Vaughan, Mark Forster and Dr. Wolf-D. Ihlenfeldt for your valuable remarks. We are currently pursuing your tips and comments. 1) I recall seeing a program called "Beaker" do what you describe. Unfortunately, all I remember is the name, I don't know who markets this program. It also provided nomenclature, reaction predictions and other handy calculations on organic structures. Perhaps an internet search engine could locate a seller. Douglas E. Stack Douglas_Stack@unomaha.edu 2) EduChem HS has a Molecule Viewer that can generate 3D Lewis structures automatically. Check our web page and our downloadable demo (Molecule Viewer plus some molecular files) at http://www.etci.on.ca. Dr. Dragan Lj. Vuckovic vuckovic@netaccess.on.ca ; info@etci.on.ca URL: http://www.etci.on.ca 3) I asked about this several years ago. At the time, people referred me to ChemTeX, which draws chemical formulas, but it doesn't seem to handle Lewis structures. In Latex, one could probably use the resident graphics capabilities to write macros or enhance the ones that come with ChemTeX. If I were to do it, I would probably write some programs directly in PostScript, but that is a matter of taste and endurance. Does "semi-automatically" imply that the program will figure out the Lewis structure as well as draw it? The problem with that, in my perception, is that, at least as it is described in textbooks, the procedures for determining Lewis structures are not consistent. There is an exception in the case of books which dumb down the rules to apply only to a small class of examples (the "This is a course on how to pass this course" approach), but let's not even mention that. People have been complaining about this all the way back to Lewis, who never intended that his innovation should be used to prop up the same kind of arbitrary rule-based pedagogy about bonding that he himself had to go through and which he had hoped to dispel by inventing Lewis structures. I have a list somewhere, guaranteed not to be complete, which I compiled when I was thinking of writing an article about how screwed up pedagogy seems to be on this point. I abandoned the project when I realized that people have long complained about this in print and it has had no effect whatsoever on pedagogical practice. Apart from such inconsistencies, different authors try to do different things with Lewis structures. For example, Wheland's book on resonance has much fancier versions of Lewis structures with different kinds of electrons, and if I remember correctly he refers to other literature that I was unable to obtain that takes it even further. At any rate, there seem to be a lot of versions of "Lewis structures" in the literature. Allan Adler adler@hera.wku.edu 4) You might look at Chem 4D Draw, by Cheminnovation. It does not automatically add lone pairs, but will generate Lewis structures from a IUPAC-correct name. Lone pairs can then be added where desired. Like other software, you can draw structures as well >from scratch, and add elemental symbols directly and fairly simply. Examples of drawings can be found at http://www.bc.cc.ca.us/programs/sea/chemist/kvaughan/structure.html (my Chime link in that page is broken for unknown reasons, but some of the early images are from Chem 4D). You can see if this is what you are looking for, and follow up on it. (The ball and stick models are from another package, which will also show lone pairs.) Kenward Vaughan kvaughan@bc.cc.ca.us 5) (See Also #6 below!) For a very inexpensive windows based package look at Molecules 3D from molecular arts corporation. Some contact information on them follows. Unfortunately their WWW page (http://www.molecules.com) does not seem to be functioning. Mark Forster mforster@nibsc.ac.uk 6) (In reply to Mark Forster's message) Yes , this package does have a Lewis structure drawing module. However, this company has a very dubious track record: a) They are the first chemistry software company I am aware of which was found guilty of email spamming by their ex-provider host4u.net (Host4u Abuse Team message dated 8 Sep 1998) after mass-mailing a typical spam mail (complete with their own private uncontrolled and unverifyable opt-out list and a reference to alleged compliance with federal bill 1619) advertising their 3D structure builder. b) They are selling for $199 apiece a 'Giant Library of 3D Molecular Models' and a 'Pharma CD'. These CDs are essentially unapproved copies of an old release of the NCI/NIH DTP structure database. The same structure data is freely available from various Internet sites (see for example http://www2.ccc.uni-erlangen.de/ncidb/, and the NCI DTP homepage http://dtp.nci.nih.gov/). They do not give (at least not on their Website) any credit for the origin of the data, or the coordinates of the structures (computed by the CORINA program, not their model builder) c) Compare that to their usage conditions of their WebMolecules(TM) online 3D structure display service usage conditions: This WebMolecules site contains copyrighted material, which is protected by US Federal Law and International Treaties. Unless you have our prior written agreement, all other uses, including but not limited to reverse engineering, repackaging, or any other reuse of the graphics, underlying data, or data manipulation source code is strictly prohibited. (The content of this service is not identical to the aforementioned data CDs, it contains only a few hundred structures) My personal opinion is that these business practices are deplorable and unethical. I would never consider to buy anything >from a proven spammer. Dr. Wolf-D. Ihlenfeldt Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE Ron A. Rumley- Van Gurp, M.Sc. TNO Prins Maurits Laboratory Chemical Toxicology E-mail: gurp@pml.tno.nl Tel: + 31 15 284 3532 Fax: + 31 15 284 3963 URL: http://www.tno.nl/instit/pml/ From chemistry-request@www.ccl.net Wed Feb 10 06:38:40 1999 Received: from bioem.ing.uniroma1.it (bioem.ing.uniroma1.it [151.100.8.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA29766 Wed, 10 Feb 1999 06:38:36 -0500 (EST) Received: from bioem.ing.uniroma1.it (bioem.ing.uniroma1.it [151.100.8.36]) by bioem.ing.uniroma1.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA13694 for ; Wed, 10 Feb 1999 12:44:49 -0800 Sender: daniele@bioem.ing.uniroma1.it Message-ID: <36C1EFC0.ACBF9D96@bioem.ing.uniroma1.it> Date: Wed, 10 Feb 1999 12:44:48 -0800 From: Daniele Spera X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: whole CCL Subject: CCL: G94 PCM and external field Content-Type: multipart/alternative; boundary="------------61538163D342205FE9DADAFA" --------------61538163D342205FE9DADAFA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am doing some particular work about biological solvated molecules exposed to external fields, static and dinamic, in order to comprehend the mechanism of interaction, specifically the belated complexation of protoporphirin IX with metallic ions due to an external microwave field. G94 does not provide either any procedure for dynamic external field, nor does G98: besides my molecular system's dimensions does not allow any calculation with the solvent (PCM model) within reasonable time, neither does it neglecting sidechains or substituing them by hydrogens. Has anyone worked with G94 implemented PCM model, or ever considered external fields, static and dinamic? Can anyone point to some references? Any suggestion will be appreciated and I willl summarize it. Daniele Spera -- _____________ Daniele Spera Universita' di Roma "La Sapienza", Italy E-mail: daniele@bioem.ing.uniroma1.it --------------61538163D342205FE9DADAFA Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I am doing some particular work about biological solvated molecules exposed to external fields, static and  dinamic, in order to comprehend the mechanism of interaction, specifically the belated complexation of protoporphirin IX with metallic ions due to an external microwave field.  G94 does not provide either any procedure for dynamic external field, nor does G98: besides my molecular system's dimensions does not allow any calculation with the solvent (PCM model) within reasonable time, neither does it neglecting sidechains or substituing them by hydrogens. Has anyone worked with G94 implemented PCM model, or ever considered external fields, static and dinamic? Can anyone point to some references? Any suggestion will be appreciated and I willl summarize it.
Daniele Spera 

-- 
_____________
Daniele Spera
Universita' di Roma "La Sapienza", Italy
E-mail: daniele@bioem.ing.uniroma1.it
  --------------61538163D342205FE9DADAFA-- From chemistry-request@www.ccl.net Wed Feb 10 07:59:12 1999 Received: from hotmail.com (law-f129.hotmail.com [209.185.131.192]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA00080 Wed, 10 Feb 1999 07:59:11 -0500 (EST) Received: (qmail 23289 invoked by uid 0); 10 Feb 1999 12:58:41 -0000 Message-ID: <19990210125841.23288.qmail@hotmail.com> Received: from 199.89.234.120 by www.hotmail.com with HTTP; Wed, 10 Feb 1999 04:58:41 PST X-Originating-IP: [199.89.234.120] From: "Gautham Nadig" To: chemistry@www.ccl.net Cc: gnadig@blr.vsnl.net.in Subject: Parameters for HYDROXYPROLINE Date: Wed, 10 Feb 1999 04:58:41 PST Mime-Version: 1.0 Content-type: text/plain Hi, I am searching for parameters for HYDROXYPROLINE [which occurs for ex. in collagen] . I am using amber. Any help is greatly appreciated. thanks gautham ----------------------------------------------------------- Consultant, Monsanto R&D Center, Bangalore, INDIA Internet: gautham_nadig@hotmail.com, gnadig@blr.vsnl.net.in ------------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@www.ccl.net Thu Feb 11 14:54:27 1999 Received: from chem.chem.rochester.edu (root@chem.chem.rochester.edu [128.151.176.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA16610 Thu, 11 Feb 1999 14:54:26 -0500 (EST) Received: from stc.chem.rochester.edu (stc.chem.rochester.edu [128.151.176.25]) by chem.chem.rochester.edu (8.8.5/8.8.5) with SMTP id OAA29221; Thu, 11 Feb 1999 14:54:23 -0500 (EST) Sender: jperl@chem.chem.rochester.edu Message-ID: <36C332EB.167E@chem.chem.rochester.edu> Date: Thu, 11 Feb 1999 14:43:39 -0500 From: Jerry Perlstein Organization: University of Rochester X-Mailer: Mozilla 2.01S (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: Anik Peeters CC: chemistry@www.ccl.net Subject: Re: CCL:colour of molecules in the solid state References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Anik Peeters wrote: > > Dear CCLers, > > I am studying molecular crystals using the supermolecule approach: > a cluster of 10-15 molecules is described by the wave function > and this cluster is surrounded by point charges simulating the other > neighbours. The level of theory we are using is Hartree-Fock. > > The molecule I am studying right now has been observed in three different > polymorphic forms. One has a white colour, another one is yellow and a > third one is light yellow. I have been trying to relate the yellow and > light yellow colour to the band gap between the HOMO and LUMO. Anik- I doubt whether the "band gap" has anything to do with the colors you observe. More likely they are either charge transfer transitions or possibly Davydov splittings of the exciton states. Before you do anything fancy why don't you visually looked at the structures to see if there are any molecular interactions which would suggest charge transfer transitions? JERRY -- ************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627-0216 Tel: (716)275-2511 FAX: (716)242-9485 perlstein@chem.chem.rochester.edu http://www.chem.rochester.edu/~stc/perlstein.html From chemistry-request@www.ccl.net Thu Feb 11 17:02:12 1999 Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu [146.96.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA18353 Thu, 11 Feb 1999 17:02:11 -0500 (EST) Received: by broadway.gc.cuny.edu id AA23321; Thu, 11 Feb 1999 17:01:58 -0500 Date: Thu, 11 Feb 1999 17:01:58 -0500 (EST) From: Artem Masunov X-Sender: amasunov@broadway.gc.cuny.edu Reply-To: Artem Masunov To: Jerry Perlstein Cc: chemistry@www.ccl.net Subject: More ?? :color of molecules in the solid state In-Reply-To: <36C332EB.167E@chem.chem.rochester.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Anik Peeters wrote: > > The molecule I am studying right now has been observed in three different > > polymorphic forms. One has a white colour, another one is yellow and a > > third one is light yellow. I have been trying to relate the yellow and > > light yellow colour to the band gap between the HOMO and LUMO. > On Thu, 11 Feb 1999, Jerry Perlstein wrote: > Before you do anything fancy why don't you visually looked at the > structures to see if there are any molecular interactions which would > suggest charge transfer transitions? I wonder what kind of interactions in homomolecular crystals (except conventional pi-pi stacking) could be considered as charge transfer? Are there CT spectra for sigma-interactions? I would appreciate if Jerry Perlstein (and all CCLers) give me some references for the examples and interpretations. Artem Masunov > __ _________ Artem.Masunov@usa.net;tel 212-772-5751;fax212-772-5332 > / \ / _ _ \ text pager: instantmessage@bigfoot.com (max. 120 char.) > / \\ \\ \\ \ Chemistry Department, Hunter College, City U. of NY > / /\ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 > / ____ \\ \\ \\ \ --------------------------------------------------- > /__/\__/\__\\__\\__\\__\ > \__\/ \/__//__//__//__/ From chemistry-request@www.ccl.net Thu Feb 11 20:41:28 1999 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 UAA19468 Thu, 11 Feb 1999 20:41:27 -0500 (EST) Received: from [150.46.162.71] ([150.46.162.71]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id KAA07518 for ; Fri, 12 Feb 1999 10:41:24 +0900 (JST) Message-Id: <199902120141.KAA07518@deews1.dent.okayama-u.ac.jp> Date: Fri, 12 Feb 1999 10:49:41 +0900 To: CHEMISTRY@www.ccl.net From: ep7@dent.okayama-u.ac.jp (masamura) Subject: CCL:HYDROGEN BOND MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: Please teach me recent comprehensive literature for hydrogen bond. Thank you. *********************************************************** Masao Masamura Okayama University ep7@dent.okayama-u.ac.jp FAX: 81-86-235-6714 TEL: 81-86-235-6712 ***********************************************************