From smori@utsc.s.u-tokyo.ac.jp Wed Jun 12 03:53:34 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@utsc.s.u-tokyo.ac.jp by www.ccl.net (8.7.5/950822.1) id DAA24314; Wed, 12 Jun 1996 03:29:05 -0400 (EDT) Received: by utsc.s.u-tokyo.ac.jp (8.7.5+2.6Wbeta6/TISN-1.3/R2) id QAA10084; Wed, 12 Jun 1996 16:28:29 +0900 (JST) Date: Wed, 12 Jun 1996 16:28:29 +0900 (JST) From: Seiji Mori Message-Id: <199606120728.QAA10084@utsc.s.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: First summary of plotting Laplacian Dear netters, Yesterday I posted a question about plotting contour of Laplacian of charge density. Today I have many responses. Now I feel that gnuplot program is free and use easily. That is easy to download from the famous FTP site. At first,I will try to use gnuplot program. I heard from Fernando Martin ,Prof.Bader's coworker, that Prof.Bader's group member uses Zeta plotters such as such as data-Explorer (IBM), info-Explorer , Irix-Explorer (SGI) , however, this costs high ($2000). I would like to convert from output to some graphical softwares in thw workstations and Mac, then save as TIFF, PICT, GIF images or scan the printted image with the scanner to store the Macintosh files. Macintosh plotter is the best for me. I think that MORPHY program is also useful program as the information from Ian Bytheway If you have any idea ,would you tell me? I also thank for the help of the other netters. This is a summary but I would like to continue this issue. If you give more detail,please send me your mail. Best wishes. Seiji Mori >From ANDRUNIO@Trurl.ch.uj.edu.pl Tue Jun 11 09:41 EDT 1996 Received: from nms.cyf-kr.edu.pl for ANDRUNIO@Trurl.ch.uj.edu.pl by www.ccl.net (8.7.5/950822.1) id JAA18100; Tue, 11 Jun 1996 09:41:10 -0400 (EDT) Received: from Trurl.ch.uj.edu.pl (trurl.ch.uj.edu.pl [149.156.72.6]) by nms.cyf-kr.edu.pl (8.6.11/8.6.11) with ESMTP id PAA13805 for ; Tue, 11 Jun 1996 15:46:57 +0200 Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.21); 11 Jun 96 15:39:17 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.21); 11 Jun 96 15:39:11 GMT+2 From: "Tadeusz Andruniow" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Tue, 11 Jun 1996 15:39:04 MET+2 Subject: g94 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <7846957D75@Trurl.ch.uj.edu.pl> Content-Type: text Content-Length: 2616 Status: RO Dear Netters, I have a big problems with Gaussian 94, which is installed on Exemplar SPP-1200 in our Computer Centre. I tried to calculate CASSCF for ethylen in a big basis set (AUG-cc-pVQZ) and turned up an error: "signal 11: segmentation violation". I calculated earlier the same task in different basis sets and occured that in all basis sets jobs were succesful exept basis sets: cc-pVDZ, cc-pVTZ, cc-pVQZ and cc-pV5Z. In all failed jobs, which used basis sets mentioned above (cc-...), I got the very strange message : " Unable to project orbital [...] (and here was the number of orbital depended on what basis sets I used, for example in AUG-cc-pVQZ there was 336)". Afterwards the message "Signal 11: segmentation violation". I should be very grateful if you send me any information about this problem. Tadeusz Andruniow Below there are last lines of output. ----------------------------------------------------------------------------------- HP-UX anna A.09.03 U 9000/735 65637 unlimited-user license The smallest eigenvalue of the overlap matrix is 2.525D-06 Projected INDO Guess. PAIRS OF ALPHA ORBITALS SWITCHED: 9 8 Unable to project orbital 336. ... Truncation Level= 99999 a= 1 b= 0 c= 1 a=N/2 - s b=2s c=n- (a+b) no. active orbitals (n) 2 no. active ELECTRONS (N)= 2 BOTTOM WEIGHT= 2 TOP WEIGHT= 4 PRIMARY BASIS FUNCTION= 1 1 2 SYMMETRY TYPE = 0 1 2 3 SYMMETRY TYPE = 0 2 2 NO OF BASIS FUNCTIONS = 3 NO TO BE DELETED = 0 CI Matrix Elements calculated here NO. OF CONFIGURATIONS IN REFERENCE SPACE = 1 SECONDARY SPACE = 3 TERTIARY SPACE = 3 NO. OF ORBITALS = 2 NO. OF ELECTRONS = 2 NO. OF WEIGHTS = 3 REFERENCE STATE CONFIGURATIONS ARE: 0 NO. OF CORE ORBITALS = 0 OPTION: NON-DIAGONAL HOLE LINE INTERACTIONS INCLUDED Len28= 81 LenMCI= 62. ENTER MCSCF PROGRAM NO. OF ORBITALS =344 NO. OF CORE-ORBITALS = 7 NO. OF VALENCE-ORBITALS = 2 NO. OF VIRTUAL-ORBITALS =335 USED ACCURACY IN CHECKING CONVEGERGENCE = 1.00D-05 Signal 11: segmentation violation PROCEDURE TRACEBACK: Signal 11: segmentation violation >From owner-chemistry@ccl.net Thu Jun 6 08:43 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id IAA21479; Thu, 6 Jun 1996 08:43:07 -0400 (EDT) Received: from gig.usda.gov for srheller@origin.gig.usda.gov by bedrock.ccl.net (8.7.5/950822.1) id IAA22111; Thu, 6 Jun 1996 08:43:06 -0400 (EDT) Received: by gig.usda.gov (5.x/SMI-SVR4) id AA00015; Thu, 6 Jun 1996 08:25:07 -0400 Date: Thu, 6 Jun 1996 08:25:07 -0400 (EDT) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software for review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2128 Status: RO 6 June, 1996 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have three (3) new software products. I am looking for people who are willing to review these software products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past four years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 8 June 1996 (Saturday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@GIG.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. ProCite for Windows 3.1 from PBS in Ann Arbor MI. 2. End Note2 Plus for Windows 3.1. 3. ASAP WordPower 1.0 for preparation of reports, handouts, and presentations. Runs under either Windows 3.1 or Windows95. Steve Heller, USDA, ARS, Plant Genome Project Bldg. 005, Room 337 Beltsville, MD 20705-2350 USA Phone: 301-504-6055 FAX: 301-504-6231 E-mail: srheller@gig.usda.gov WWW: www.hellers.com/~steve >From regina@lioness.cm.utexas.edu Fri Jun 7 12:27 EDT 1996 Received: from lioness.cm.utexas.edu for regina@lioness.cm.utexas.edu by www.ccl.net (8.7.5/950822.1) id MAA28729; Fri, 7 Jun 1996 12:27:42 -0400 (EDT) Received: by lioness.cm.utexas.edu (4.1/SMI-4.1) id AA14526; Fri, 7 Jun 96 11:28:03 CDT Date: Fri, 7 Jun 96 11:28:03 CDT From: regina@lioness.cm.utexas.edu (Regina Monaco) Message-Id: <9606071628.AA14526@lioness.cm.utexas.edu> To: CHEMISTRY@www.ccl.net Subject: Drug/DNA mailing List Cc: regina@lioness.cm.utexas.edu Content-Type: text Content-Length: 210 Status: RO Could someone repost the address of the Drug/DNA remailer? My computer went down for 10 days and evidentally I was removed from the list - and have no record of its address. Thanks in advance. Regina Monaco >From creyes@cgl.ucsf.EDU Tue Jun 11 14:27 EDT 1996 Received: from socrates.ucsf.EDU for creyes@cgl.ucsf.EDU by www.ccl.net (8.7.5/950822.1) id OAA21267; Tue, 11 Jun 1996 14:27:12 -0400 (EDT) Received: (from creyes@localhost) by socrates.ucsf.EDU (8.7.3/GSC4.25) id LAA04061 for chemistry-request@www.ccl.net; Tue, 11 Jun 1996 11:27:10 -0700 (PDT) From: Date: Tue, 11 Jun 1996 11:27:10 -0700 (PDT) Message-Id: <199606111827.LAA04061@socrates.ucsf.EDU> To: chemistry-request@www.ccl.net Subject: subscribe Content-Type: text Content-Length: 209 Status: R Does anybody have van der Waals parameters, R* and Epsilon, for Nickel(II), Copper(II), Cobalt(II)? Thanks, Carolina Reyes Pharmaceutical Chemistry University of California San Francisco creyes@cgl.ucsf.edu From gerwens@mbox.theochem.uni-hannover.de Wed Jun 12 05:53:36 1996 Received: from mgate.uni-hannover.de for gerwens@mbox.theochem.uni-hannover.de by www.ccl.net (8.7.5/950822.1) id FAA25007; Wed, 12 Jun 1996 05:29:23 -0400 (EDT) From: Received: from sun1.rrzn-user.uni-hannover.de (actually sun1.rrzn.uni-hannover.de) by mgate with SMTP (PP); Wed, 12 Jun 1996 11:29:11 +0200 Received: by sun1.rrzn-user.uni-hannover.de (SMI-8.6/SMI-SVR4) id LAA24940; Wed, 12 Jun 1996 11:28:57 +0200 Message-Id: <199606120928.LAA24940@sun1.rrzn-user.uni-hannover.de> Subject: Summary: Smallest rectangular Box To: chemistry@www.ccl.net (CCL CCL) Date: Wed, 12 Jun 1996 11:28:55 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text > Dear CCL'ers, > I've got the problem to find the smallest possible rectangular Box > around a set of points (atoms) in space. Any suggestions or ideas > are wellcome. I'll summerize the results. > > Heiko Gerwens ########################################################################## ########################################################################## I'd try this, and be prepared to be wrong. First off, simply do the usual inertial frame transformation on the points, ie: 1) Translate the points so their center of gravity coincides with the origin. 2) Rotate the points around the origin to align the inertial frame of the points. Now, minimize the volume of the axis aligned parallelpiped containing the points while rotating the points about the origin. Ie, minimize V = (max(x_i)-min(x_i))*(max(y_i)-min(y_i))*(max(z_i)-min(z_i)) It's possible that the inertial alignment will be the minimum. Finally, project the parallelpiped back into the original coordinate system. -- rec -- Return-Path: ########################################################################## ########################################################################## One approach is to do eigen analysis on the X'X matrix - the three eigen- vectors are the major axes of 'an' enclosing box - for a flat or a long molecule, this would be close to the smallest - for other shapes, it is necessary to either systematically rotate the box from the starting position, or use some optimization scheme (maybe GA?) to find the smallest enclosing box. There may be some way to take advantage of the molecule as a tree - I'm not sure... Return-Path: ########################################################################## ########################################################################## Assign unit mass to the points, and find the xyz-s that diagonlize the "momnet-of-inertia" tensor. the extrema should define the box you are looking for. If you need to preserve the original coordinates, save the transformation and apply its inverse. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ########################################################################## ########################################################################## 1) Transfrom your molecule into the principal axis coordinate system (i.e., the system in which the moment of inertia is diagonal) 2) Maximal and minimal values of atomic X, Y and Z should in principle define the smallest rectangular box Hope that helps, Robert Fraczkiewicz University of Texas Medical Branch Return-Path: From owner-chemistry@ccl.net Wed Jun 12 12:53:40 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id MAA25566; Wed, 12 Jun 1996 12:37:30 -0400 (EDT) Received: from netcomsv.netcom.com for uucp@netcom.com by bedrock.ccl.net (8.7.5/950822.1) id MAA18641; Wed, 12 Jun 1996 12:37:29 -0400 (EDT) Received: from hassan.UUCP by netcomsv.netcom.com with UUCP (8.6.12/SMI-4.1) id HAA22867; Wed, 12 Jun 1996 07:15:11 -0700 Received: by il-isb; Wed, 12 Jun 1996 10:40:39 +0500 Received: by network!hassan; Wed, 12 Jun 1996 09:29:31 X-Mailer: WinNET Mail, v2.20 Message-ID: <243@infolink.net.pk> Reply-To: hassan@infolink.net.pk (hassan iqbal) To: chemistry@ccl.net Date: Wed, 12 Jun 1996 09:29:30 Subject: INFORMATION. From: hassan@infolink.net.pk (hassan iqbal) I WANT TO HAVE THE INFORMATION ABOUT THE FOLLOWINF FACILITY. THANKS. HASSAN IQBAL. hassan@infolink.net.pk From mzim@mvax.cc.conncoll.edu Wed Jun 12 13:44:45 1996 Received: from oak.cc.conncoll.edu for mzim@mvax.cc.conncoll.edu by www.ccl.net (8.7.5/950822.1) id MAA25424; Wed, 12 Jun 1996 12:17:23 -0400 (EDT) Received: from dsys.cc.conncoll.edu by oak.cc.conncoll.edu; (5.65v3.2/1.1.8.2/18Mar96-1233PM) id AA26401; Wed, 12 Jun 1996 11:02:00 -0400 Date: Wed, 12 Jun 1996 11:02:00 -0400 (EDT) From: Marc Zimmer Subject: intermolecular distance in rasmol To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi I am using rasmol for the first time and would like to find the intermolecular distance between two residues. This seems fairly trivial yet I can't find out how to do it from the help manuals. If you know the solution, Please e-mail me directly as I am sure there is not much interest in the answer. Thanks Marc Zimmer From akinaga@qcl.t.u-tokyo.ac.jp Wed Jun 12 13:53:41 1996 Received: from hirao1.t.u-tokyo.ac.jp for akinaga@qcl.t.u-tokyo.ac.jp by www.ccl.net (8.7.5/950822.1) id MAA25584; Wed, 12 Jun 1996 12:38:28 -0400 (EDT) Received: from localhost (loopback [127.0.0.1]) by hirao1.t.u-tokyo.ac.jp (8.6.12+2.4W/3.4Wbeta3) with ESMTP id WAA18900 for ; Wed, 12 Jun 1996 22:01:33 +0900 Message-Id: <199606121301.WAA18900@hirao1.t.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: CCL:f polarization for Pt? Date: Wed, 12 Jun 1996 22:01:32 +0900 From: AKINAGA Yoshinobu Dear Netter I am calculating reaction of methane on Pt surface, and I want to use f polarization basis functions for Pt atoms, but I don't know the details(exponents,etc.) Does anyone know? Any references are welcome. Thanks Yoshinobu AKINAGA Graduate school Department of Engeneering University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo 113, JAPAN E-mail:akinaga@qcl.t.u-tokyo.ac.jp From csonka@brown.incm.u-nancy.fr Wed Jun 12 14:05:45 1996 Received: from brown.incm.u-nancy.fr for csonka@brown.incm.u-nancy.fr by www.ccl.net (8.7.5/950822.1) id MAA25429; Wed, 12 Jun 1996 12:17:40 -0400 (EDT) Received: by brown.incm.u-nancy.fr (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA26533; Wed, 12 Jun 1996 15:35:20 +0100 From: "Csonka Gabor" Message-Id: <9606121535.ZM26531@brown.incm.u-nancy.fr> Date: Wed, 12 Jun 1996 15:35:11 -0400 In-Reply-To: Seiji Mori "CCL:Contour map of Laplacian of raw" (Jun 11, 7:18pm) References: <199606111018.TAA04087@utsc.s.u-tokyo.ac.jp> X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Seiji Mori Subject: Re: CCL:Contour map of Laplacian of raw Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Seiji Mori, we have recently developed a a contour surface drawing software package, which works with Explorer. We published it at ECCC2. Now it is available at: http://www.ch.bme.hu/inc/ECCC2/paper5/lapl.html The idea was developed further. Sincerely, -- Gabor I. Csonka e-mail: csonka@web.inc.bme.hu Lab.Chimie Theorique Universite Henri Poincare B.P. 239 54506 Vandoeuvre-les-Nancy FRANCE tel: +33-83.91.25.29 fax: +33-83.91.25.30 http://www.ch.bme.hu/inc/csg.html From mikha001@maroon.tc.umn.edu Wed Jun 12 14:05:59 1996 Received: from mhub0.tc.umn.edu for mikha001@maroon.tc.umn.edu by www.ccl.net (8.7.5/950822.1) id NAA25822; Wed, 12 Jun 1996 13:23:10 -0400 (EDT) Received: from maroon.tc.umn.edu by mhub0.tc.umn.edu; Wed, 12 Jun 96 12:23:05 -0500 Received: by maroon.tc.umn.edu; Wed, 12 Jun 96 12:23:05 -0500 Date: Wed, 12 Jun 1996 12:23:04 -0500 (CDT) From: Dmitri V Mikhailov To: glycosci@net.bio.net cc: chemistry@www.ccl.net Subject: sulfate parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings everyone, We are looking for sulfate parameters for AMBER ff to model sulfated carbohydrates. Any references will be greatly appreciated. Regards, Dmitri Mikhailov ***************************************************** Univ. of Minnesota Medical School Department of Biochemistry Box 609, 420 Delaware St. SE Minneapolis MN 55455 tel. (612) 624-7107 fax. (612) 626-2325 e-mail: mikha001@maroon.tc.umn.edu ***************************************************** From owner-chemistry@ccl.net Wed Jun 12 14:17:45 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id MAA25545; Wed, 12 Jun 1996 12:35:28 -0400 (EDT) Received: from techfac.TechFak.Uni-Bielefeld.DE for friedric@TechFak.Uni-Bielefeld.DE by bedrock.ccl.net (8.7.5/950822.1) id MAA18594; Wed, 12 Jun 1996 12:35:24 -0400 (EDT) Received: from puccini.TechFak.Uni-Bielefeld.DE by techfac.TechFak.Uni-Bielefeld.DE id AA21837; Wed, 12 Jun 1996 13:59:47 +0200 Received: by puccini.TechFak.Uni-Bielefeld.DE (5.65/tp.29.08.90) id AA02921; Wed, 12 Jun 1996 13:59:46 +0200 Message-Id: <9606121159.AA02921@puccini.TechFak.Uni-Bielefeld.DE> Subject: Summary: Smallest rectangular Box To: chemistry@ccl.net Date: Wed, 12 Jun 1996 13:59:46 +0200 (MET DST) From: Friedrich Ackermann X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, sorry that I didn't answer the first time, but I am nearly sure that the posted answers concerning the question how to determine the smallest rectangular box containing a set of 3D points are w r o n g. E.g. it is obvious that the suggested "principal axis" algorithms can not work, because the principal axis are affected also by "interior" points that don't affect the correct position of the rectangular box searched for (only points at the "boundary" are important for this box). I'm no expert, but I would have a look at a book like @book{prepa85, author = {Preparata, F. P. and Shamos, M. I.}, title = {Computational Geometry. {A}n Introduction}, publisher = {New York: Springer}, year = {1985} } to get an idea of a correct answer. I think the faces of the rectangular box are related to the faces of the boundary of the convex hull of the point set. Hope that helps, Friedrich Ackermann ------------------------------------------- Friedrich Ackermann Applied Computer Science Bielefeld University P.O. 100131 D-33501 Bielefeld Phone: +49 521 106 2938 (2935) Fax: +49 521 106 2992 email: friedric@techfak.uni-bielefeld.de http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/friedric/ ------------------------------------------- From ncapron@ccr.jussieu.fr Wed Jun 12 14:23:35 1996 Received: from shiva.jussieu.fr for ncapron@ccr.jussieu.fr by www.ccl.net (8.7.5/950822.1) id NAA25862; Wed, 12 Jun 1996 13:36:40 -0400 (EDT) Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id MAA20525 for ; Wed, 12 Jun 1996 12:59:48 +0200 (METDST) Received: from (ncapron@localhost) by moka.ccr.jussieu.fr (8.7.5/jtpda-5.2) id MAA137650 for chemistry@www.ccl.net; Wed, 12 Jun 1996 12:59:44 +0200 Date: Wed, 12 Jun 1996 12:59:44 +0200 From: ncapron@ccr.jussieu.fr (Nathalie CAPRON) Message-Id: <199606121059.MAA137650@moka.ccr.jussieu.fr> To: chemistry@www.ccl.net Subject: CCL : Summary for beta-tin Dear all, Two weeks ago, I asked a question about beta-tin structure I send you the answers I get I am very grateful to these two persons who greatly helped me. QUESTION : > Subject: CCL:beta-tin structure > Dear All, > I should need more information about a crystallographic structure > It must be something very easy for a cristallographer but I have some > trouble with the beta tin structure. Indeed, I saw it is tetragonal > with a certain value of the ratio c/a, in the case of Sn. > But if this structure is applied to pure silicon do we have still > this structrure or does it become body-centered tetragonal ? > In one word : which is the beta tin structure for the silicon ? > Thanks for all your responses > > Nathalie Capron > Laboratoire de Chimie Physique > 11, rue Pierre et Marie Curie > 75005 Paris > France > ncapron@ccr.jussieu.fr *************************************************************************************** *************************************************************************************** ANSWER 1 : Dear Nathalie, if such a silicon polimorph exists, it will have exactly the same space group of beta-tin and, as a consequence, the same set of atomic positions. The values of the coordinates fixed by symmetry will be exactly the same, but the cell parameters, c/a ratio and symmetry free coordinates (if any) will be adapted to the new compound. You can look for the beta-tin structure in the A.F. Wells book: "structural inorganic chemistry", Clarendon Press ed. or in the literature... I hope this will help you, Gabriele -------------------------------------------------------------------------- Dr. Gabriele VALERIO Institut Francais du Petrole Division Informatique et Mathematiques Appliquees (RA60) Groupe de Modelisation Moleculaire 1 et 4 Avenue de Bois Preau BP 311 92506 Rueil-Malmaison Cedex France TEL. 33-1-47.52.68.97 Fax: 33-1-47.52.70.22 E-mail: gabriele.valerio@ifp.fr -------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** ANSWER 2 : Hi Nathalie, for the beta tin structure of silicon you can see for instance : J.Z. Hu et al., Phys.Rev. B 34, 4679(1986) R.J. Needs et al., Phys.Rev. B 30, 5390(1984) Good luck, -- Leonardo De Maria SISSA | Universita di Trieste Scuola Internazionale | Dipartimento di Fisica Teorica Superiore di Studi Avanzati | Strada Costiera 11 via Beirut 2-4, Grignano | Miramare-Grignano I-34014 - Trieste | I-34014 - Trieste tel: +39 40 3787506 | tel: +39 40 224265 fax: 3787528 | fax: 224601 e-mail:demaria@neumann.sissa.it | e-mail : demaria@vstst0.ts.infn.it From ibrahim@kimia.um.edu.my Wed Jun 12 14:53:42 1996 Received: from kimia.um.edu.my for ibrahim@kimia.um.edu.my by www.ccl.net (8.7.5/950822.1) id OAA26244; Wed, 12 Jun 1996 14:05:47 -0400 (EDT) Received: by kimia.kimia.um.edu.my (5.x/SMI-SVR4) id AA12743; Wed, 12 Jun 1996 19:29:01 +0800 Date: Wed, 12 Jun 1996 19:29:00 +0800 (MYT) From: "Dr. Ibrahim Noorbatcha" To: CHEMISTRY@www.ccl.net Subject: CCL:M: C.I. calculations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's, Recently I tried C.I. calculations using MOPAC for H2 molecule.(yes, I do not know about any other simpler neutral molecule). I got the following results for Delta_H (kcal/mol), using the key words PM3 C.I.=? NOANCI ROOT=1 SINGLET .... PM3 -13.39 C.I.=2 -15.98 C.I.=3 -22.45 C.I.=4 -19.31 C.I.=5 -19.31 My understanding is that if more orbitals of appropriate type are included then the energy should improve. I can understand why there is an increase in the |Delta_H|. But I don't know why the value decreases after C.I.=3. I hope there is a simple explanation other than to suggest not to do C.I. calculations with semi-empirical approx. I never thought that simple H2 molecule would give me so much of trouble. Can any body out there through some light on this?. Thanks Ibrahim ============================================================================ Dr. Ibrahim Noorbatcha Email: ibrahim@kimia.um.edu.my Department of Chemistry Phone: 603-759-4260 Universiti Malaya Fax : 603-759-4193 59100 Kuala Lumpur Malaysia ============================================================================= From hebant@ext.jussieu.fr Wed Jun 12 15:06:59 1996 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.5/950822.1) id NAA26123; Wed, 12 Jun 1996 13:57:36 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id OAA25380 ; Wed, 12 Jun 1996 14:18:55 +0200 (METDST) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 12 Jun 1996 14:18:51 +0200 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 12 Jun 1996 14:20:23 +0100 To: CHEMISTRY@www.ccl.net From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: NMR shielding calculations- Summary Cc: grzesb@asp.biogeo.uw.edu.pl Dear CCLers, I've posted the following the question : >I am performing NMR shielding calculations (of 7Li) but it seems to me >that the results are very dependant of the molecular geometry and that a >small change in the structure induces important changes for the chemical >shift. > >Have you more informations about this assumption? >More generally, what is the accuracy of such calculations? > Here are the messages I received on the topic : ---------------------------------------------------- A tutorial/review on this topic entitled "The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding" by D.B. Chesnut can be found in Reviews in Computational Chemistry, Volume 8, VCH Publishers, 1996, Chapter 5. It addresses the issue you raised. Kenny Lipkowitz ---------------------------------------------------- Pascal, Since the experimental NMR shielding tensor as expressed as a chemical shift is quite sensitive to geometries and even conformations (hence its utility as a diagnostic) the calculated is also dependant upon these influences. I expect vacume calculated NMR chemical shifts to be within 5 % of experimentallly obtained chemicals shifts from solid or liquid phase experiments for normal basis sets. In many cases one obtains considerably better agreement than this with values coming within 2 or 3 %. See the references here for examples and the references therein for background and further examples. 1. Journal of Chemical Physics. 104 (14), 8 April 1996. 2. International Journal of Quantum Chemistry, Vol. 57, 199-205 (1996) Thank-you Robert A. Kirby BioChem Therapeutiques Inc. 275 Armand-Frappier Blvd. Laval, Quebec, H7V 4A7 #514-978-7914 fax 514-978-7777 kirbyr@biochem-pharma.com ---------------------------------------------------- Hi! I saw your note on CCL, but wasn't quite sure if I had anything significant to contribute with. However, I guess that although the Bochum group has been investigating Li-compounds more than we have, they haven't looked too much into the geometry dependence (apart from a paper in which distinct conformers where distinguished by quantum chemical means). We did some work on C2H3Li a while ago (CPL 226, 1 (1994)), but there our goal was both the shieldings and spin-spin couplings. In general: As all shieldings also 7Li are dependent on geometry. The problem with Li-compounds is that whereas you normally can use an MP2 geometry optimization as a starting point, this might not be adequate for Li-compounds due the often very weak and long bonds. Experimental geometries are often troubled by the very large geometrical changes of Li-compounds in solvents (and it often polymerizes as well), making such geometries difficult to use. Thus, as I do not know the purpose of your investigation, it is difficult to make any clearcut recommendations. If purely theoretical, I would have done everything consistently, that is, optimize the geometry at the same level of theory as you calculate the shieldings. If comparison with experiment is the goal, use experimental geometries where available, although I haven't, sitting here thinking it through, decided quite what to do if the experiment has been performed in solvent. I dielectric continuum model might not be appropriate in such cases. Being a purist, I would go for internal consistency in the calculation (geometries and shieldings), but it is quite noteworthy that it actually was the shieldings that destroyed our spectrum the most compared to experiment in the CPL paper and not the spin-spin couplings as you would normally expect. It might be an idea to hear with Dr. Ulrich Fleischer or Prof. W.Kutzelnigg as well for some recommendations for prefered geometries. Good luck! Kenneth _______________________________________________________________________________ Kenneth Ruud, Ph.d.-student in Chemical Physics at the Department of Chemistry, University of Oslo, Norway. E-mail: kenneth@dalton.uio.no I don't know what the computer language of the year 2000 will look like, but I know it will be called FORTRAN. _______________________________________________________________________________ ---------------------------------------------------- Hi Pascal, there was a very similar question recently in the CCL, about the use of experimental vs. optimized geometries. So you might wish to search the CCL archives. About the sensitivity to the geometries: Yes, NMR shieldings are VERY sensitive to the geometries. In fact, I think that is part of why experimentalists like the method. I have seen something on shielding gradients recently in some review (the shielding gradient would be the geometry dependency taken in a quantitative manner). I can't exactly remember wish review it was, it might be in one of the annual reviews by C. Jameson, in Annual Reports on NMR Spectroscopy. Jameson has another review in Chem Rev 1991, 91, 1375 that contains, among other things, the temperature dependence of the (measured) shift/shielding. This temperature dependence is likely also due to the change of equilibrium geometry with T, at least to a large degree. > More generally, what is the accuracy of such calculations? This is indeed a VERY general question. The answer depends on what you are really doing. E.g., if you have one of the highly correlated methods, e.g. MPn or Coupled Cluster (the latter by Gauss et al.), then you get quantitative results with large enough basis sets. Else you might miss some correlation effects. Further, as mentioned, you need a good basis set, otherwise this gives you also an error. Finally, what you are probably calculating is the zero-pressure, zero-density limit of a gas-phase experiment. The experiment you are comparing to is likely done under finite pressures and temperatures, and in a condensed phase: all this can give considerable shifts. See one of the various reviews for more details on all of this. Yours, Georg -- ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== ---------------------------------------------------- Yes shielding is dependent on bond length. Use an optimised structure for gaseous molecules, experimental for solids. Take particular care if the bond length you are using is less than the equilibrium value and the molecule does not approach the combined atom smoothly. If there is a crossing of the ground and a repulsive state, the shielding values can go to very large positive and negative numbers.Shielding is also very dependent on basis set and gauge origin. Chemical shifts or relative shieldings are generally less sensitive. Cynthia Jameson and co-workers have done a lot of work on nmr shielding surfaces that is the change of shielding with geometry. Elaine A. Moore e.a.moore@open.ac.uk ---------------------------------------------------- Many thanks to all. Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html *****************************************************************************