From Y0H8797@ACS.TAMU.EDU Tue Feb 18 00:23:52 1997 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.8.3/950822.1) id XAA21435; Mon, 17 Feb 1997 23:33:41 -0500 (EST) Date: Mon, 17 Feb 1997 22:33:40 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <970217223340.2041a581@ACS.TAMU.EDU> Subject: Summary & change of the question: simple way to measure delocalization I asked a question a few days ago. First, my original question: >A quick question. Is there any simple way to measure electronic delocaliza- >tion? We know tryptophan is probably the most delocalized in terms of >electron density among all the naturally occurring amino acids. Phenyl- >alanine may be second, glycine and proline very localized and so on. Any >quantitation has been done? Thanks for your help. > Dr. Dave Winkler (D.Winkler@chem.csiro.au) says: -------------------- I would be interested in the replies. In some QSAR studies, where delocalization is important (compounds active against electron transport systems) simply counting the length of the longest conjugated path worked quite well. -------------------- I'd like to know some references and/or tutorials on this, Dr. Winkler. No other responses except one saying "No", three saying "Please summarize". Let's see. The significance of this question lies in the fact that the more electronically delocalized, the less solvation stabilization you get when the molecule is put in solvent. A direct measurement in this regard is obviously a measurement of the actual solvation energy. Any work has been done, experimental or computational? This won't be a simple way of measuring delocalization. In fact it's not a way to quantitate it at all (unless the cause-effect relation is one-to-one and not many-to-one). A related property of molecules is polarizability, isn't it? Anybody knows any published work on polarizability of amino acids? Or refractive indeces? Or Raman spectroscopy work? I guess there must an answer to one of these questions. Thanks for any reply. Yong From taisung@chem.duke.edu Tue Feb 18 02:23:54 1997 Received: from chem.duke.edu for taisung@chem.duke.edu by www.ccl.net (8.8.3/950822.1) id BAA21885; Tue, 18 Feb 1997 01:29:12 -0500 (EST) Received: from huihui (annex-ppp15.med.unc.edu [152.2.169.15]) by chem.duke.edu (8.7.4/Duke-1.1) with ESMTP id BAA02652; Tue, 18 Feb 1997 01:29:10 -0500 (EST) Message-Id: <199702180629.BAA02652@chem.duke.edu> From: "Taisung Lee " To: Subject: Re: CCL:Summary & change of the question: simple way to measure delocalization Date: Tue, 18 Feb 1997 01:28:47 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit > Dr. Dave Winkler (D.Winkler@chem.csiro.au) says: > -------------------- > > Let's see. The significance of this question lies in the fact that the more > electronically delocalized, the less solvation stabilization you get when the > molecule is put in solvent. A direct measurement in this regard is obviously a > measurement of the actual solvation energy. Any work has been done, > experimental or computational? This won't be a simple way of measuring > delocalization. In fact it's not a way to quantitate it at all (unless the > cause-effect relation is one-to-one and not many-to-one). > > A related property of molecules is polarizability, isn't it? Anybody knows any > published work on polarizability of amino acids? Or refractive indeces? Or > Raman spectroscopy work? I guess there must an answer to one of these > questions. Thanks for any reply. > > Yong > Hi, I am little bit confused here. Maybe I need to read some basic text books again but, in my opinion, the solvation energy is nothing to do with the electron delocalizability (spell?). The solvation energy should depend on the electron density distribution. These two terms are quiet different. One can construct two artificial systems with similar electron density distribution but their degrees of delocalization are very different. (i.e., similar diagonal elements but very different off-diagonal elements in density matrix) Please point out if I am wrong. Taisung Lee From chpajt@bath.ac.uk Tue Feb 18 06:23:59 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA23450; Tue, 18 Feb 1997 05:24:10 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 18 Feb 1997 10:08:12 +0000 Date: Tue, 18 Feb 1997 10:07:38 +0000 (GMT) From: A J Turner To: Taisung Lee cc: CHEMISTRY Subject: Re: CCL:Summary & change of the question: simple way to measure delocalization In-Reply-To: <199702180629.BAA02652@chem.duke.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Solvation energy and delocalisation are connected. Systems _tend_ to be more stable if the delta positive and delta negative 'ness of regions of space are small. In gas phase, delocalisation alows this. In solution, the presence of solvent molecules acts to conpensate for partial charges on the molecule. Thus, if the molecule is well stablised in gas phase, the advantage (drop in heat) to go to solvent - is likely to less. Clearly - such a relationship is bound to be rather a vague guid though. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From waller@dur.mindspring.com Tue Feb 18 08:24:00 1997 Received: from mule1.mindspring.com for waller@dur.mindspring.com by www.ccl.net (8.8.3/950822.1) id HAA24042; Tue, 18 Feb 1997 07:53:31 -0500 (EST) Received: from waller (borg.mindspring.com [204.180.128.14]) by mule1.mindspring.com (8.8.4/8.8.4) with ESMTP id HAA159818 for ; Tue, 18 Feb 1997 07:53:30 -0500 Message-Id: <199702181253.HAA159818@mule1.mindspring.com> From: "Dr. Chris L. Waller" To: Subject: data quality again Date: Tue, 18 Feb 1997 07:47:14 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks to all those who have responded so far. I suppose I should try to refine the question just a little bit. I would like to do QSAR studies on high-throughput screening data. The quantity of data is not a problem here, but the quality does seem to suffer a bit. I would like to establish a set of acceptance criteria for modeling studies of this type. For instance, (1) all biological data values should be expressed relative to a positive, or maximal, control value. (2) all biological data values should be repeatable (n=3, SD < 10%), (3) and so on... Any ideas? **************************************************************** Chris L. Waller, Ph.D. (516) 222-0023 (NY) Oncogene (919) 489-4700 (NC) Science ///\\\ waller@mindspring.com \\\/// cwaller@oncogene.com **************************************************************** From roberta@popcsi.unian.it Tue Feb 18 10:24:00 1997 Received: from popcsi.unian.it for roberta@popcsi.unian.it by www.ccl.net (8.8.3/950822.1) id KAA25356; Tue, 18 Feb 1997 10:21:13 -0500 (EST) Received: from anvax1.unian.it ([193.205.128.183]) by popcsi.unian.it (8.6.12/8.6.12) with SMTP id QAA06900 for ; Tue, 18 Feb 1997 16:22:50 +0100 Message-Id: <3.0.32.19970218162207.006882c8@popcsi.unian.it> X-Sender: roberta@popcsi.unian.it X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 18 Feb 1997 16:22:08 +0100 To: chemistry@www.ccl.net From: Roberta Galeazzi Subject: looking for MM2 parameters Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all! I'm looking for MM2 parameters for sulfonammides, sulfonylureas and ureas (particularly ab initio derived parameters). Does anyone know where I can find any references? I'll summarize to the list. Thanks in advance for your help. Cheers Roberta ********************************************************************** Dr. Roberta Galeazzi Dipartimento di Scienze dei Materiali e della Terra Universit=E0 di Ancona via Brecce Bianche I-60131 Ancona- ITALY e-mail: roberta@popcsi.unian.it fax: 39-71-2204714 From M.E.Parker@surrey.ac.uk Tue Feb 18 10:31:57 1997 Received: from mailc.surrey.ac.uk for M.E.Parker@surrey.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA24761; Tue, 18 Feb 1997 09:26:32 -0500 (EST) Message-Id: <199702181426.JAA24761@www.ccl.net> Received: from surrey.ac.uk by mailc.surrey.ac.uk id <20146-0@mailc.surrey.ac.uk>; Tue, 18 Feb 1997 14:26:28 +0000 Subject: FTs of various ACFs To: chemistry@www.ccl.net Date: Tue, 18 Feb 1997 14:26:24 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Dr Malcolm E Parker Sender: M.E.Parker@surrey.ac.uk Hi. Hope someone here can help as I've had my colleagues scratching their heads all day.I have calculated the Fourier transforms of various ACFs obtained from MD simulations of water (bondlengths, angles, velocities etc). This has been done both by 'brute force' and via a FFT routine. The problem I am having is that there is a small constant baseline shift. Is this an error or a genuine effect? Also, some of the peaks are positive going, some negative going and some both. I am having poblems coming to terms with the concept of 'negative densities of states'. What do these signs physically represent, or is it just mathematical artifice ? The FORTRAN abs() function is not really an option here ;-) Thanks in advance for your help. -MAL -- Dr Malcolm Parker | email: m.e.parker@surrey.ac.uk Department of Chemistry, | www: http://www.chem.surrey.ac.uk/~chs1mp University of Surrey, | Guildford, Surrey. GU2 5XH. UK. | Tel: (01483) 300800x2580 Fax: (01483) 259514 |(International calls replace 01483 by +44 1483) From dsmith@CTCnet.Net Tue Feb 18 10:38:27 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id KAA25244; Tue, 18 Feb 1997 10:11:33 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id KAA25055; Tue, 18 Feb 1997 10:07:22 -0500 Date: Tue, 18 Feb 1997 10:07:22 -0500 Message-Id: <199702181507.KAA25055@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: Survey and Prize Cc: nteich@CTCnet.Net According to the report, Technology Vision 2020: The U.S. Chemical Industry, released last month by the American Chemical Society, the first two key steps in meeting challenges during the next 25 years requires = generation and use of new knowledge, and = capitalizing on information technology. Computational technologies were considered a key enabling technology area to achieve these goals. In particular, Technology Vision 2020 suggested that industry should "support further development of high-performance desktop workstations, large and fast vector-processor machines, and highly parallel processors." We agree, and would like to get the input of the computational chemistry, molecular modeling and simulation, and structural chemistry community. In order to get the views of the CCL community, I am requesting your participation in our survey, which The DASGroup, Inc. (DASGroup) is using to gain an understanding of current hardware and software utilization and future trends within the chemical industry. Feel free to tell a colleague about this survey as well. While a limited number of surveys were sent via U. S. mail to U. S. companies, I would appreciate it if you would take the time to fill in the survey on our web page at = www.dasgroup.com As an incentive, any company employee completing a survey will be entered into a drawing to win a Compaq PaC companion handheld computer with 4 Mb of RAM and running Windows CE. (Sorry, the drawing is not open to academics, students, or government employees.) We appreciate you taking the time to respond to our survey. Doug Smith -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From korkin@qtp.ufl.edu Tue Feb 18 11:24:00 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id KAA25473; Tue, 18 Feb 1997 10:27:35 -0500 (EST) Received: from red by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id KAA16301; Tue, 18 Feb 1997 10:26:30 -0500 Date: Tue, 18 Feb 1997 10:26:30 -0500 (EST) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:Summary & change of the question: simple way to measure delocalization To: chpajt@bath.ac.uk Cc: CHEMISTRY@www.ccl.net, rjbgroup@qtp.ufl.edu, christek@ple.af.mil, zerner@qtp.ufl.edu, boldyrev@iodide.chem.utah.edu, BOYD@AC.DAL.CA, FRENKING@ps1515.chemie.uni-marburg.de, hargittai@ch.bme.hu, houk@uclac1.chem.ucla.edu, katritzky@chem.ufl.edu, workman@coriolis.atms.purdue.edu, pvrs@organik.uni-erlangen.de, rivail@host11.lctn.u-nancy.fr, zefirov@synth.chem.msu.su, olah@ramoth.bitnet Message-ID: MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: YPkbPOS4MUSS9U+7gctkEg== X-Mailer: dtmail 1.2.0 CDE Version 1.2_14 SunOS 5.6 sun4d sparc > > Hi! > > Solvation energy and delocalisation are connected. Systems _tend_ to be > more stable if the delta positive and delta negative 'ness of regions of > space are small. In gas phase, delocalisation alows this. In solution, > the presence of solvent molecules acts to conpensate for partial charges > on the molecule. > > Thus, if the molecule is well stablised in gas phase, the advantage (drop > in heat) to go to solvent - is likely to less. > > Clearly - such a relationship is bound to be rather a vague guid though. > > Best wishes > > Alex Alex, I enjoyed your answer. I have not seen that stated so clearly, but probably it was said in this way somewhere. It is how mother nature turns all "crazy" delocalized bridged structures (in gas phase) into what organic chemists want them to be :-) (in solution). This is also a reason why many chemists were "unhappy" with quantum chemistry before they have turned into believers. I am not telling about the cases where different levels of approximation give different results. This is a separate story :-) Many qualitative concepts of organic chemistry are based on (quasi) orbital speculations (not computations!) with an IMPLICIT solvent effect. The history of SN2 reaction is probably the best documented story. I wish I would have time to write a review article on this topic, but may be someone did it already, and I have simply missed it :-) Anatoli Korkin From SMILLER@RARUSRAEXS1.prius.jnj.com Tue Feb 18 12:24:03 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id LAA26113; Tue, 18 Feb 1997 11:39:49 -0500 (EST) Received: by smtp-internet.jnj.com id AA16413 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Tue, 18 Feb 1997 11:39:48 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Tue, 18 Feb 1997 11:39:48 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Tue, 18 Feb 1997 11:39:48 -0500 Date: Tue, 18 Feb 1997 11:41:45 -0500 From: "Miller, Susan [PRI]" Subject: minimization in SYBYL To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers I've had the following problem with minimization in SYBYL and wonder what the implications for this problem are for further calculations: When I sketch a non-polar molecule (one containing no polar atoms) and then minimize, using electrostatics (Gasteiger-Hueckel charges) , I get clearly incorrect bond lengths and bond angles. If I turn off electrostatics, I get correct bond lengths and angles. What if I want to perform a minimization on a molecule that has a completely non-polar part and a highly polar part? Will I get a reasonable result if I do a minimization without electrostatics, followed by one with electrostatics or vice-versa? Thanks, Susan From parthi@aero.iisc.ernet.in Tue Feb 18 12:31:36 1997 Received: from naveen.ncst.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id MAA26318; Tue, 18 Feb 1997 12:09:49 -0500 (EST) Received: from iisc.ernet.in (iisc.ernet.in [144.16.64.3]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id WAA20972 for ; Tue, 18 Feb 1997 22:44:08 +0530 Received: from aero.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-8.6.5) id WAA03902; Tue, 18 Feb 1997 22:38:51 +0530 Received: by aero.iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA14949; Tue, 18 Feb 1997 22:36:10 -0500 Date: Tue, 18 Feb 1997 22:36:10 -0500 (GMT) From: S Parthiban To: chemistry@www.ccl.net Subject: Multimedia Problem- Summary Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: Recently I have asked a question on Multimedia Problem. Some CCLr's have interest in this problem and asked me to send the summary of replies to CCL. Here i have given my question, replies and finally i have given my feedback. Thank you very much for your timely replies. parthi ---------------- My original Question: I would like to capture the Inventor (involves rotation and translation of objects) files into a single movie file. I could able to make a movie file from various static images (rgb files). But I am still exploring the possibilities of importing a dynamic frames into a movie file. We have indycam.. Kindly advise me in making a movie file from the animation file. Any help is appreciated. Thanks parthi ---------------- From: Iraj Daizadeh To: S Parthiban Subject: Re: CCL:multimedia problem Hello. Would you mind sending a summary of responses back to the CCl. Thanks. Iraj Daizadeh ------------- From: "Victor M. Rosas Garcia" To: S Parthiban Subject: Re: CCL:multimedia problem I assume you have a Silicon Graphics box. If you have IRIX 5.3 ir higher there is a utility called "movieconvert". From the manpage: movieconvert(l) movieconvert(l) ...... ....... -----(manpage information on movieconvert)---- ------------------- From: "Salvador G. Medina" To: S Parthiban Subject: Re: CCL:multimedia problem Hi Parthi, What you need is an interphase, like those that use with projectors. Just be sure the frecuency is the same or you couldn't record the signal, is different for a MS-DOS (intel) machine than Mac. The software you need is QuickTime, I don't remember the exact addresse but you can find it and download from http://www.apple.com there is a version for Mac or Windows. Hope this help, if you need more information ask me. Best regards Salvador. ---------------- My feedback: From my own experience in these few days and the feed back from some of my other friends... i feel that the best way to capture the animation is to use "mediarecorder" which is available in O2 IRIX 6.3. But we do not have O2. So presently i have planned to manage with moviemaker and movieconvert. But this does not give me a freedom to choose the frame rate. As i have to complete this mini project in few days... i have used several frames of the same image...to get displayed for my required frame rate. (but i feel this may be crude method..) If anyone interested ..in more detail... may be u can mail me. If there are serveral requests...i can post it to CCL. Otherwise, I dont want to waste the bandwidth. Thank you again. ----end--- From genghis@darkwing.uoregon.edu Tue Feb 18 13:24:03 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id MAA26653; Tue, 18 Feb 1997 12:40:50 -0500 (EST) Received: (from genghis@localhost) by darkwing.uoregon.edu (8.8.5/8.8.5) id JAA06610; Tue, 18 Feb 1997 09:39:33 -0800 (PST) Date: Tue, 18 Feb 1997 09:39:33 -0800 (PST) From: Dale Braden To: cclpost Subject: calcn of ESR coupling constants Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Does anybody know how to get Gaussian 94 to calculate the ESR *anisotropic* coupling tensor elements? Or, given an LCAO-MO wavefunction and appropriate density matrices, does anybody have the equations (or a reference) for calculating the anisotropic tensor elements from this information? I'll summarize. Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From taisung@chem.duke.edu Tue Feb 18 14:24:11 1997 Received: from chem.duke.edu for taisung@chem.duke.edu by www.ccl.net (8.8.3/950822.1) id NAA27146; Tue, 18 Feb 1997 13:39:31 -0500 (EST) Received: from huihui (annex-ppp6.med.unc.edu [152.2.169.6]) by chem.duke.edu (8.7.4/Duke-1.1) with ESMTP id NAA11513; Tue, 18 Feb 1997 13:39:25 -0500 (EST) Message-Id: <199702181839.NAA11513@chem.duke.edu> From: "Taisung Lee " To: "CHEMISTRY" Subject: Re: CCL:Summary & change of the question: simple way to measure delocalization Date: Tue, 18 Feb 1997 13:39:10 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit > > Hi! > > Solvation energy and delocalisation are connected. Systems _tend_ to be > more stable if the delta positive and delta negative 'ness of regions of > space are small. In gas phase, delocalisation alows this. In solution, > the presence of solvent molecules acts to conpensate for partial charges > on the molecule. > > Thus, if the molecule is well stablised in gas phase, the advantage (drop > in heat) to go to solvent - is likely to less. > > Clearly - such a relationship is bound to be rather a vague guid though. > > Best wishes > > Alex Hi Alex & CCL, I totally agree with your words except you used 'delocalisation' not 'distribution'. Consider cyclohexane and benzene: both have very similar electron distribution (no net electron transfer between carbon atoms) if not considering geometries. However, the electrons in benzene are much more delocalized than in cyclohexane. I guess maybe the word 'delocalized' is not well defined here. It seems to me there are two means: 1. In quantum chemistry, electrons are delocalized means they occupy the molecular orbitals which are physically distributed over a large region. 2. In organic chemistry, it seems to me the word 'local' means the electron density distribution is concentrated in a small region. They look the same. However, they are different. Consider there are two cities A and B with population of 1,000,000 apiece. They are evenly distributed. Maybe you will call the people are delocalized over these two cities (according to the meaning #2). However, if people in one city never travel to another city, then the people are not delocalized according to meaning #1. Could any expert tell me how should I use the word 'delocalized' correctly? Taisung Lee From MARYJO@neu.edu Tue Feb 18 15:24:05 1997 Received: from NUHUB.DAC.NEU.EDU for MARYJO@neu.edu by www.ccl.net (8.8.3/950822.1) id OAA27671; Tue, 18 Feb 1997 14:50:43 -0500 (EST) From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01IFKCSVMGYS9LVXGJ@neu.edu>; Tue, 18 Feb 1997 14:50:19 EST Date: Tue, 18 Feb 1997 14:50:18 -0500 (EST) Subject: band gap calcs on WO3? To: chemistry@www.ccl.net Message-id: <01IFKCSVMGYU9LVXGJ@neu.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello netters! I am writing on behalf of a colleague who is interested in the UV-vis spectrum of WO3. He is working with the thin film, and wants to do band gap calculations. Does anybody have any suggestions about the best or easiest way to proceed? Thanks in advance for your wisdom. Mary j.o. From dsmith@CTCnet.Net Tue Feb 18 16:24:05 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id PAA28092; Tue, 18 Feb 1997 15:27:44 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id PAA26431; Tue, 18 Feb 1997 15:23:29 -0500 Date: Tue, 18 Feb 1997 15:23:29 -0500 Message-Id: <199702182023.PAA26431@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: Technology Vision 2020 Report For those with an interest, the Technology Vision 2020 report can be obtained by contacting Deitra Jackson of the American Chemical Society at 202-452-8917 or by email at d_jackson@acs.org. A press release is also available from the ACS News Service at 202-872-4371. The copies should be free (at least in the U.S.). Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From nash@chem.wisc.edu Tue Feb 18 16:28:43 1997 Received: from piggy.chem.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.8.3/950822.1) id QAA28299; Tue, 18 Feb 1997 16:09:27 -0500 (EST) Received: by piggy.chem.wisc.edu; id AA08856; 5.57/42; Tue, 18 Feb 97 15:09:16 -0600 Message-Id: <9702182109.AA08856@piggy.chem.wisc.edu> Date: Tue, 18 Feb 1997 15:09:23 -0600 To: CHEMISTRY@www.ccl.net From: nash@chem.wisc.edu (John R. Nash) X-Sender: jrnash@students.wisc.edu Subject: LINUX + G94 + RISC = ? Greetings all... I note with interest that GAUSSIAN is available for LINUX, although the release seems geared for Intel-based environments. With the rapid overtaking of computational number-crunching power by RISC-based desktop (and laptop!) machines, it seems to me that a PowerPC would be an attractive platform to run G94 under the newly-developed MkLinux for Macintosh. (As a side note, I'm sure a Dec Alpha would do veeeery nicely at the job as well.) Since LINUX is designed as a portable OS, it strikes me as very possible that this can be done, but I don't have the knowledge of how to do it myself. So, my question is... has anyone tried this? Anyone want to try it? (and then show us benchmarks if it works?) Thanks in advance. -john nash UW-Madison ----------------------------------------------- John Nash nash@chem.wisc.edu ----------------------------------------------- From jgilbert@du.edu Tue Feb 18 18:24:04 1997 Received: from odin.cair.du.edu for jgilbert@du.edu by www.ccl.net (8.8.3/950822.1) id RAA29224; Tue, 18 Feb 1997 17:49:57 -0500 (EST) Received: by odin.cair.du.edu; id AA30818; Tue, 18 Feb 1997 15:49:57 -0700 Date: Tue, 18 Feb 1997 15:49:56 -0700 (MST) From: JULANNA V GILBERT To: chemistry@www.ccl.net Subject: trajectory calculations (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We are planning a course in molecular dynamics/kinetics and want to find software (PC) that will allow visualization of trajectories for simple atom plus diatomic reactions over classical or quantum potential energy surfaces. A program that demonstrates trajectories for atomic scattering under various potential fields would also be useful. If anyone knows of such software (free or otherwise), please respond. Thank you, Julanna Gilbert From jgilbert@du.edu Tue Feb 18 18:28:56 1997 Received: from odin.cair.du.edu for jgilbert@du.edu by www.ccl.net (8.8.3/950822.1) id RAA29249; Tue, 18 Feb 1997 17:55:26 -0500 (EST) Received: by odin.cair.du.edu; id AA25816; Tue, 18 Feb 1997 15:55:26 -0700 Date: Tue, 18 Feb 1997 15:55:26 -0700 (MST) From: JULANNA V GILBERT To: CHEMISTRY@www.ccl.net Subject: trajectory calculations (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We are planning a graduatecourse in molecular dynamics/kinetics and want to find software (PC) that will allow visualization of trajectories for simple atom plus diatomic reactions over classical or quantum potential energy surfaces. A program that demonstrates trajectories for atomic scattering under various potential fields would also be useful. If anyone knows of such software (free or otherwise), please respond. Thank you, Julanna Gilbert From korkin@qtp.ufl.edu Tue Feb 18 18:31:55 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id RAA29176; Tue, 18 Feb 1997 17:31:35 -0500 (EST) Received: from red by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id RAA04224; Tue, 18 Feb 1997 17:31:18 -0500 Date: Tue, 18 Feb 1997 17:31:18 -0500 (EST) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:Summary & change of the question: simple way to measure delocalization To: taisung@chem.duke.edu Cc: prs@organik.uni-erlangen.de, pvrs@organik.uni-erlangen.de, CHEMISTRY@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: gCjCFyR+ydoXQiHHhTkMMQ== X-Mailer: dtmail 1.2.0 CDE Version 1.2_14 SunOS 5.6 sun4d sparc > > Hi Alex & CCL, > > I totally agree with your words except you used > 'delocalisation' not 'distribution'. Consider cyclohexane > and benzene: both have very similar electron distribution > (no net electron transfer between carbon atoms) if not > considering geometries. However, the electrons in benzene > are much more delocalized than in cyclohexane. > I guess maybe the word 'delocalized' is not well defined > here. It seems to me there are two means: > > 1. In quantum chemistry, electrons are delocalized means > they occupy the molecular orbitals which are physically > distributed over a large region. > Molecular orbitals are always delocalized, if species has a symmetry. Methane is a good example. Hardly, someone will call it as a "delocalized", it is rather used as an example of a "localized" system. And electrons are always delocalized by exchange interactions. > 2. In organic chemistry, it seems to me the word 'local' > means the electron density distribution is concentrated in > a small region. > > They look the same. However, they are different. > Consider there are two cities A and B with population of > 1,000,000 apiece. They are evenly distributed. Maybe you > will call the people are delocalized over these two cities > (according to the meaning #2). However, if people in one > city never travel to another city, then the people are not > delocalized according to meaning #1. > I like this example. The measure of delocalization in this case will be how much money (gas, time, etc) they spend for travelling among these cities. > Could any expert tell me how should I use the word > 'delocalized' correctly? > The same as with these cities, you need to agree with someone about the measure of "delocalization". It can be energy (which I consider as the best one), or bond lengths, or some more specific charactersitics, like diamagnetic susceptibility. There are a few books, where people discuss and argue about definition of aromaticity, for example. You may look over the last (?) one: Minkin, Glukhovtsev, Simkin, Aromaticity and antiaromaticity. Electronic and Structural Aspects, Wiley, 1994. Anatoli Korkin