From aiba@ir.phys.chem.ethz.ch Mon Apr 22 11:42 EDT 1996 Received: from volta for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.7.1/950822.1) id LAA15217; Mon, 22 Apr 1996 11:40:58 -0400 (EDT) Date: Mon, 22 Apr 1996 17:39:59 +0200 Message-Id: <96042217395960@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zuerich (Zentrum)) To: chemistry@www.ccl.net Subject: tensor components X-VMS-To: SMTP%"chemistry@www.ccl.net" X-VMS-Cc: AIBA Content-Type: text Content-Length: 2341 Status: RO Dear Marc, you might look for the answers to your question (specifically for molecules) "..how to obtain quadrupole or octupole moment values from their tensor components ?" in two (to get started) books: 1. Chapter 8 and for octupole -- Exercise 8-1, in R.K.Wangness "Electromagnetic fields", John Wiley & Sons, Inc, 1979; 2. M. Rigby et al., "The forces between molecules", Oxford, Clarendon Press, 1986. More generally speaking, the way you posed the question is a bit off the actual status of things in electrostatics. I mean the following. Majority of multipole components (tensor components) of an ARBITRARY charge distribution are INDEPENDENT physical quantities and IN GENERAL there are very few conditions which allow to determine one component through some other components. Let's take an example of quadrupole moment. It's a 3 by 3 tensor of rank 2, which has 9 components. Since it's symmetric, only 6 components are left, and since it's traceless, only 5 independent components survive. So, in case WHEN ALL 5 COMPONENTS ARE INDEPENDENT ONE CANNOT SPEAK OF JUST SINGLE QUADRUPOLE MOMENT VALUE. There are 5 of them - the whole lot! However, if the system is axially symmetric, then indeed, only one component (normally Q_ZZ) is independent, and people speak of a unique quadrupole moment value. In case of octupole moment the situation is worse, and it will take some effort from you to get simple expressions even for particular symmetries. I certainly cannot cover it in email (I might get it wrong). Thus, I wanted you to notice that only in case of particular symmetries there is "single" (i.e. independent) N-pole moment, like in above example when for an axially symmetric system one gets: 1) single "quadrupole" moment Q = Q_ZZ, 2) which determines Q_XX=Q_YY=-1/2*Q=-1/2*Q_ZZ; 3) all off-diagonal components must be zeros. If you don't know the symmetry but are left with "some quadrupole moment matrix" which is: -- real; -- symmetric; -- traceless; then just diagonalize it and put Q=Q_ZZ, and name it quadrupole moment, and here you are BUT ONLY if Q_XX=Q_YY=-1/2*Q_ZZ !!! If the above doesn't hold, then you have more independent components then just one. [Some authors take apart factor 1/2, so take care of definitions] I hope I put it all correctly. The best wishes, Ayaz Bakasov. From owner-chemistry@ccl.net Tue Apr 23 07:39 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id HAA28818; Tue, 23 Apr 1996 07:39:11 -0400 (EDT) Received: from arwen.unibe.ch for bennett@ubeclu.unibe.ch by bedrock.ccl.net (8.7.1/950822.1) id HAA17169; Tue, 23 Apr 1996 07:39:01 -0400 (EDT) Message-ID: Date: Tue, 23 Apr 96 13:37:11 +0100 From: Frederick Bennett Subject: G94:splitting scratch files To: chemistry@ccl.net X-Mailer: VersaTerm Link v1.1 Content-Type: text Content-Length: 872 Status: RO Hello, I have found the facility to split scratch files across file systems very useful. The have one query however. If I have very long path names defining filesystems the specification for how to handle the scratch files becomes far to long to fit on an 80 column line. Is it possible to somehow continue the specification onto further lines of the input file? Frederick Bennett =============================================================================== Namenet Address: Frederick R. Bennett Papernet Address: Institut fuer anorg. anal. und phys. Chemie Freiestrasse 3 CH-300 Bern 9 Switzerland Mouthnet Address: [41] (31) 631 4231 Internet Address: bennett@ubeclu.unibe.ch =============================================================================== From owner-chemistry@ccl.net Sun Apr 21 15:21 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id PAA05603; Sun, 21 Apr 1996 15:21:18 -0400 (EDT) Received: from volta for aiba@ir.phys.chem.ethz.ch by bedrock.ccl.net (8.7.1/950822.1) id PAA26862; Sun, 21 Apr 1996 15:21:15 -0400 (EDT) Date: Sun, 21 Apr 1996 21:21:14 +0200 Message-Id: <96042121211400@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zuerich (Zentrum)) To: chemistry@ccl.net Subject: SUMMARY - small CHIRAL molecules X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA Content-Type: text Content-Length: 9334 Status: RO Dear CCLers, this is summary of responses to the posting, which asked for examples of small chiral molecules. I think enough time has passed so it's safe to summarize what arrived but MORE EXAMPLES WOULD STILL BE WELCOMED, and I am poised ( ;-) ) to summarize again. I wanted to thank the following people (list is arranged in message arrival ordering): -- Alan Shusterman Department of Chemistry Reed College Portland, OR 97212; -- I.Novak, Dept.of Chemistry, National University of Singapore, Singapore 119260; -- Alain Kessi (alain.kessi@psi.ch) at Paul Scherrer Institut, Zuerich, Switzerland; -- John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada E1A 3E9; -- Rene Fournier fournier@physics.unlv.edu; -- Dr. Robert B. Funchess bobf@msi.com Senior Support Scientist Voice (619) 458-9990 x738 Molecular Simulations Inc.; -- Frank Jensen ; -- Marvin Waldman, Ph.D. Director, Rational Drug Design Molecular Simulations Inc. -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431; Now, there will be an excerpt from original posting and then, with very little ommisions (of copies of my posting), the texts of responses (altogether 12 - quite a chiral number). Note, that posting by Alain Kessi (No.3) on how to trace references not only backwards but also forwards, would be very interesting to almost everyone. Thank you all once more, Ayaz Bakasov. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Original posting: &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dear CCLers, ............. Desired stuff is that a molecule is not only CHIRAL (or has CHIRAL geometry in some of electronic states) but also that it is relatively stable, has volatile phase (i.e. it is in principle suitable for spectroscopy). I look for SMALL molecules - then ab initio calculations on them are, in principle, more reliable. Lastly, references (fresh ones to trace work back) on the molecule-example would be most welcome. Ayaz Bakasov. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.1 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Almost any (every?) molecule that contains a carbon atom with four different substituents is chiral. For example, CHDTF (where H, D, T are three isotopes of hydrogen). Less esoteric, CFClBrI, CH3CHFCl. And so on. Alan Shusterman &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.2 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dear Dr Bakasov, there is a whole series of chiral 5-atomic halomethanes of general formula CXYWZ (where X,Y,W,Z= F, Cl , Br, I). Here are some references: Chem.Phys.Lett. vol. 215 (1993) 561. Bull.Chem.Soc.Jpn. vol. 63 (1990) 1278. J.Chem.Educ. vol. 70 (1993) 548. Regards, I.Novak &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.3 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& In case the references you get are not so recent: Just thought I'd call your attention to the Science Citation Index, available at the ETH library on CD-ROM. If you have older references, you can find all the papers that cite that given reference, so you can not only trace back but also trace forward. Greetings from Zuerich to Zuerich, Alain Kessi (also a theoretical physicist working in chemistry) &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.4 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& I would suggest reading the section on "optical isomers" in an introductory organic chemistry book. The classic example in organic chemistry is a carbon with 4 different substituents such as CHFClBr. Simple examples relevant to biology include 1. lactic acid CH_3_CH(OH)COOH (the central C has 4 different substituents) 2. alanine CH_3_CH(NH2)COOH (a simple component of proteins) John-M. Sichel &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.5 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& How about these two with 7 and 9 atoms from the 1st and 2d row? 1. 1,3-difluoroallene (HCF=C=CHF). The two C=CHF systems are in perpendicular planes. 2. 1,2-trans-difluorocyclopropane CH2 H / \ F C-------C F H John-M. Sichel &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.6 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& I have thought of a third example related to the other two. 3. 1,3-difluorocyclopropene CHF / \ FC======CH In this molecule the F and H bonded to the doubly-bonded carbons are in the plane of the carbons, while the CHF carbon is tetrahedral with H and F above and below the plane. So now you have a series of three related molecules. John Sichel &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.7 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dear Ayaz Bakasov; As you said, there is a huge number of chiral molecules; depending how small you want them, you can narrow down the field. The prototypical small chiral molecule that we learn in undergrad. chemistry is C(WXYZ), where C is a tetrahedrally bonded sp3 carbon atom and W, X, Y, Z are four different monovalent ligands. If you want to keep the molecule small, you can pick W, X, Y, Z among the following: H, F, Cl, Br, I, OH, SH, NH2, CH3. That already makes 126 possibilities (all combinations of 4 among 9) and I *guess* that many of them are stable and volatile. I cannot tell if any one of these was indeed studied by spectroscopy or theory, but I would start my search of the literature by keywords among those 126 possibilities. Regards, Rene Fournier &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.8 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dear Ayaz, Many sugars are chiral, but I don't know if something with a dozen heavy atoms fits a theoretical physicist's definition of "small". Most (but not all) molecules which contain a carbon atom which has four different substituent groups are chiral. Any Organic Chemistry text should give you a lot of examples; look for the chapter on stereochemistry or enantiomers. Regards, Bob Funchess &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.9 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The simplest chiral molecule is probably NHDT (isotopomer of NH3), but it is not very "stable" in term of chirality since the inversion barrier is very low. The smallest stable molecule is probably something like XCHDT, with X being any group other than H/D/T (like F for example). Frank &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.10 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dear Ayaz, If you are interested in the calculation of the parity violating energy differences, then you may want to take a look at the following article (in case you were not already aware of it): "The Parity-Violating Energy Difference Between Enantiomeric Molecules", S.F. Mason and G.E. Tranter, Chemical Physics Letters, Volume 94, pp. 34-37 (1983). The energy differences are believed to be exceedingly small and to have no practical consequences to chemistry at this time. Whether or not this energy difference is believed to have any role in the choice of chiral state found in organic molecules in living beings, I do not know. Regards, Marvin Waldman &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& No.11 &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Ayaz Bakasov, ........... Your request is mildly amusing. Chirality is implicit in any structure possessing C1 symmetry, and clearly ANY molecule of four or more atoms can be distorted to C1 symmetry at negligible energetic cost. So, if it is only STRUCTURES you are interested in, you can construct almost any molecule you like. It seems, however, that you would like chiral structures that are local minima on the molecular potential energy surface and moreover in reasonably deep wells. I might suggest NHFCl (i.e., ammonia with two hydrogens replaced, one by F, the other by Cl). A cheaper alternative is NHDT (i.e., ammonia with one deuterium and one tritium), but the inversion barrier of the latter will be tiny, while that for the former will be considerably more substantial. PHFCl would be a higher inversion barrier still. As for molecules having chiral (and enantiomeric) rotamers, an obvious choice would be HOOH. Another cheap (computationally, that is) chiral molecule with a VERY high barrier to racemization would be CHDTF (deuterotritiofluoromethane). Finally, if you would like to add a more amusing form of chirality to your list--one that does not derive from the presence of a stereogenic center-- you might consider CHF=C=CHF. 1,3-Difluoroallene has a screw axis chirality. (As does HOOH mentioned above, but there the barrier to racemization is small, since it is only a single bond that must rotate). Best regards, Christopher J. Cramer &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& &&&& End of summary &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& From John_Beckerle@quickmail.clemson.edu Wed Apr 24 12:50 EDT 1996 Received: from CLEMSON.EDU for John_Beckerle@quickmail.clemson.edu by www.ccl.net (8.7.1/950822.1) id MAA18538; Wed, 24 Apr 1996 12:50:36 -0400 (EDT) Received: from quickmail.clemson.edu (quickmail.clemson.edu [130.127.8.57]) by CLEMSON.EDU (8.7.5/8.7.3) with SMTP id MAA08077 for ; Wed, 24 Apr 1996 12:50:31 -0400 (EDT) Message-ID: Date: 24 Apr 1996 12:46:56 -0500 From: "John Beckerle" Subject: ECP Second Derivatives? To: "List CCL" X-Mailer: Mail*Link SMTP-QM 3.0.2 Content-Type: text Content-Length: 1083 Status: RO Subject: Time:12:30 PM OFFICE MEMO ECP Second Derivatives? Date:4/24/96 I am trying to calculate the force constants for a Rhodium carbonyl by DFT using the LANL2DZ basis set within Gaussian 94. According to Gaussian, G94 does not have analytic second derivatives for the LANL2DZ basis (with ECP for Rhodium), so the second derivatives are being numerically evaluated. This is taking a long time. Gaussian is working on analytic second derivatives for bases with ECPs for the next major release. I have 3 questions: 1) Is there a rule of thumb for the speed/accuracy differential between numerical and analytic evaluation of derivatives? 2) Does anyone know of an existing package/software/program for analytic second derivatives for LANL2DZ with ECPs? 3) Is there another similar/equivalent basis with ECPs for which analytic second derivatives can be calculated? 4) Any other suggested basis set/theory/package combinations to approach this problem? Thanks, John Beckerle beckerj@clemson.edu From qibsawea@lgdx02.lg.ehu.es Wed Apr 24 13:27 EDT 1996 Received: from lgsx01.lg.ehu.es for qibsawea@lgdx02.lg.ehu.es by www.ccl.net (8.7.1/950822.1) id NAA19096; Wed, 24 Apr 1996 13:27:20 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA16153; Wed, 24 Apr 96 19:26:53 +0100 Received: from lcmx94.lc.ehu.es by lgdx02.lg.ehu.es (5.65/4.7) id AA28527; Wed, 24 Apr 1996 19:30:12 +0100 X-Sender: qibsawea@lgdx02.lg.ehu.es (Unverified) Message-Id: Mime-Version: 1.0 Date: Wed, 24 Apr 1996 19:29:47 +0000 To: chemistry@www.ccl.net From: qibsawea@lgdx02.lg.ehu.es (Pablo Vitoria) Subject: Volume calculation for small molecules Content-Type: text/plain; charset="us-ascii" Content-Length: 637 Status: RO Does someone know (or has) a program to calculate the volume of small molecules using as input atomic coordinates, e.g. from CSD data? I'd prefer versions for Mac or PC, although any information about programs for other systems is welcome. Thank you very much for any help Pablo Vitoria -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN Phone: +34 4 4647700 Ext. 2450 ---------------------------------------------------------------------------- ---- From hrusak@zeus1.ims.ac.jp Wed Apr 24 08:41 EDT 1996 Received: from zeus1.ims.ac.jp for hrusak@zeus1.ims.ac.jp by www.ccl.net (8.7.1/950822.1) id IAA12637; Wed, 24 Apr 1996 08:41:06 -0400 (EDT) Received: by zeus1.ims.ac.jp (4.2/Sony4.2MX) id AA19874; Wed, 24 Apr 96 21:37:58 JST From: Date: Wed, 24 Apr 96 21:37:58 JST Message-Id: <9604241238.AA19874@zeus1.ims.ac.jp> To: CHEMISTRY@www.ccl.net Content-Type: text Content-Length: 774 Status: RO Dear Netters, Just today I learned, that Gaussian94 versions C and below has some error in the frequency part (at least for the CRAY PLATFORMS). I do not know any details but it seems to be serious, since the computer center in Berlin deleted the the program and is waiting for the revision D. The error seems to show up in the frequency calculations if some point groups were used (C3h etc.). I could not get any details about the failures and thus I would like to ask the broad community, if some body is aware of discrepancies between the calculated (G94) frequencies and numbers obtained by other programs. It was claimed that the RS6000 results are corect and CRAY computers posses wrong (even imaginary) frequencies in the output. Jan Hrusak IMS Okazaki Japan From mattijs@xs4all.nl Tue Apr 23 14:03 EDT 1996 Received: from toutatis.xs4all.nl for mattijs@xs4all.nl by www.ccl.net (8.7.1/950822.1) id OAA05071; Tue, 23 Apr 1996 14:03:45 -0400 (EDT) Received: from xs1.xs4all.nl (root@xs1.xs4all.nl [193.78.33.42]) by toutatis.xs4all.nl (8.7.5/8.7.2) with SMTP id TAA13751 for ; Tue, 23 Apr 1996 19:58:14 +0200 (MET DST) Received: from [194.109.7.103] (asd05-11.dial.xs4all.nl) by xs1.xs4all.nl with SMTP id AA19178 (5.67b/IDA-1.5 for ); Tue, 23 Apr 1996 19:58:05 +0200 Date: Tue, 23 Apr 1996 19:58:05 +0200 Message-Id: Mime-Version: 1.0 X-Motd: Not young enough to know everything To: CHEMISTRY@www.ccl.net From: mattijs@xs4all.nl (Mattijs Koeberg) Subject: photophysics, photochemistry and photobiology discussion list Content-Type: text/plain; charset="us-ascii" Content-Length: 1255 Status: RO [This message is cross posted to other lists. Excuses for any duplicates.] Dear members of CHEMISTRY, I'm pleased to announce the phocet-l discussion-list. The purpose of this discussion-list is to serve as a forum for discussion about and information concerning the interesting fields of Photochemistry, Photophysics and Photobiology and in particular Photoinduced Charge and Energy Transfer. People interested in these fields are invited to join and share their information or questions with others on the list. Announcements of - Meetings - Conferences - Lectures - Courses - Books - Articles - Internet sources are very welcome. Subscription is open to everyone interested. To subscribe send an e-mail message to: Majordomo@uva.nl and put the following in the body of your message: subscribe phocet-l With a growing number of participants this discussion-list will get more valuable, so please forward this message to your colleagues! For more information send an e-mail message to owner-phocet-l@uva.nl. *==========================================================================* What do we live for if not to make the world less difficult for each other *==========================================================================* From rino@ibc.wustl.edu Wed Apr 24 17:03 EDT 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.1/950822.1) id RAA20948; Wed, 24 Apr 1996 17:03:58 -0400 (EDT) Received: from ibc.wustl.edu by wugate.wustl.edu (8.6.12/8.6.11) with ESMTP id QAA10731 for ; Wed, 24 Apr 1996 16:03:58 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id QAA20112; Wed, 24 Apr 1996 16:03:56 -0500 Date: Wed, 24 Apr 1996 16:03:55 -0500 (CDT) From: Rino Ragno To: Computational Chemistry List Subject: MOZYME Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 3160 Status: RO Dear netters, I have read about a program called MOZYME, by James J. P. Stewart and I would like to try it. Any of you out there does know anything about it? Thank you Rino <><><><><><><><><><><><><><><><><><><><><><><><><>><><><><><><><><><><><><><><> /\ /\ \/ \/ [] Dr. Rino Ragno E-mail: ragno@kea.caspur.it [] /\ Dip. di Studi di Chimica e Tecnologia or: ragno@axcasp.caspur.it /\ \/ delle Sostanze Biologicamente Attive tel.: 39 6 49913814 \/ [] Universita' degli Studi di Roma FAX: 39 6 49913888 [] [] "La Sapienza" [] /\ Piazzale Aldo Moro, 5 /\ \/ 00185 - ROMA \/ [] I T A L I A [] /\ /\ \/ \/ <><><><><><><><><><><><><><><><><><><><><><><><><>><><><><><><><><><><><><><><> || || \||/ \||/ \/ \/ *************************************************************************** | \ /| | \ N.B. fino al 1 marzo 1997 rivolgersi al seguente indirizzo grazie / | | / (please mail to the following address untill the 1st of March) \ | | / \| *************************************************************************** || || \||/ \||/ \/ \/ ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From amir@genie.terra.co.il Thu Apr 25 02:48:51 1996 Received: from genie.terra.co.il for amir@genie.terra.co.il by www.ccl.net (8.7.1/950822.1) id BAA23966; Thu, 25 Apr 1996 01:51:25 -0400 (EDT) Received: from cool.terra.co.il (cool.terra.co.il [194.90.101.35]) by genie.terra.co.il (8.6.12/8.6.12) with SMTP id FAA16324 for ; Thu, 25 Apr 1996 05:41:38 GMT Date: Thu, 25 Apr 1996 08:41:32 +0300 (IST) From: Amir Gil X-Sender: amir@cool.terra.co.il To: list CC Subject: Force Field distribution method for parallel computation-references Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all! We, as developers of parallel computer for computational chemistry, are intersted in the method of force field method for parallel calculations. Can anybody give me some good updated references for this method? As the good tradition of this list works, I'll summarize your responses. Thanks Amir !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Amir Gil ! ! Chemical and Application engineer ! ! Terra Computers ! ! Ashuah 6 st. ! ! Omer ! ! ISRAEL 84965 ! ! Tel. 07-467502 ! ! Fax. 07-467475 ! ! E-Mail amir@genie.terra.co.il ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From owner-chemistry@ccl.net Thu Apr 25 03:07:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id CAA24343; Thu, 25 Apr 1996 02:21:40 -0400 (EDT) Received: from riker.ac1.uni-duesseldorf.de for kay@riker.ac1.uni-duesseldorf.de by bedrock.ccl.net (8.7.1/950822.1) id CAA15494; Thu, 25 Apr 1996 02:21:35 -0400 (EDT) Received: from deanna by riker.ac1.uni-duesseldorf.de via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id IAA05863; Thu, 25 Apr 1996 08:20:17 +0200 Message-Id: <1.5.4b13.32.19960425062131.002c1850@riker.ac1.uni-duesseldorf.de> X-Sender: kay@riker.ac1.uni-duesseldorf.de X-Mailer: Windows Eudora Light Version 1.5.4b13 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 25 Apr 1996 08:21:31 +0200 To: chemistry@ccl.net From: Kay Kreidler Subject: Intramolecular Hydrogen Bridges Dear Netters! I am investigating the structure of 1,2-Dicarboxylic acids, 1,2-Phosphonocarboxylic acids and 1,2-Diphosphonic acids in aqueous solution using molecular modeling methods. For the 1,2-Dicarboxylic acids there is an excellent review of Eberson: "The Chemistry of Carboxylic Acids and Esters" (Editor S.Patai) p.272-284. Interscience. New York (1969). In this article, Eberson described the influence of intramolecular hydrogen bridges on the structure of these compounds. As the review is nearly 30 years old, maybe there is anything newer available? More importent to me is the question, if similar papers dealing with the 1,2-Phosphonocarboxylic or 1,2-Diphosphonic acids exist. Any suggestions are welcome, I will summarise the answers to the mailing list. Thanks Kay Kreidler Kay Kreidler Institut fuer Anorganische Chemie und Strukturchemie I Heinrich-Heine-Universitaet Duesseldorf 40225 Duesseldorf Germany From rachelle@picard.niehs.nih.gov Thu Apr 25 11:48:54 1996 Received: from kamakazi.niehs.nih.gov for rachelle@picard.niehs.nih.gov by www.ccl.net (8.7.1/950822.1) id LAA29823; Thu, 25 Apr 1996 11:47:51 -0400 (EDT) Received: from picard.niehs.nih.gov by kamakazi.niehs.nih.gov via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@kamakazi.niehs.nih.gov:chemistry@www.ccl.net> id LAA05851; Thu, 25 Apr 1996 11:30:17 -0400 Received: from picard by picard.niehs.nih.gov via SMTP (950413.SGI.8.6.12/930416.SGI.AUTO) for id LAA26131; Thu, 25 Apr 1996 11:45:27 -0400 Sender: rachelle@picard.niehs.nih.gov Message-ID: <317F9E16.167E@picard.niehs.nih.gov> Date: Thu, 25 Apr 1996 11:45:26 -0400 From: "Rachelle J. Bienstock" X-Mailer: Mozilla 2.0 (X11; I; IRIX64 6.1 IP26) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Human Serum Albumin x-ray crystal coordinates X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit For all of those of you interested in the Human Serum Albumin x-ray crystal coordinates, initially published by Xe Min He and Daniel Carter in Nature, 358 (209-215), 1992, I received the following response from Dr. Carter: Hello Dr. Bienstock, As you have ascertained, the coordinates of albumin are not yet publicly available. We hope to begin deposition of some of the structures this year, pending completion of the high resolution refinements and accompanying manuscripts. While we have generally answered most of the questions that various colleagues have concerning specific aspects of the structure, I do not see a simple answer in your case. We have made it a policy not to distribute the coordinates prior to finishing the final refinements and the public deposition. I apologize for any inconvenience to you. Sincerely, Daniel C. Carter Senior Scientist for Biophysics So, after 4 years from initially publishing the coordinates, they are STILL being refined and are unavailable.... Rachelle From heather@ramana.chem.yale.edu Thu Apr 25 12:49:02 1996 Received: from ramana.chem.yale.edu for heather@ramana.chem.yale.edu by www.ccl.net (8.7.1/950822.1) id MAA00093; Thu, 25 Apr 1996 12:29:37 -0400 (EDT) Received: by ramana.chem.yale.edu; Thu, 25 Apr 96 12:29:08 -0400 Date: Thu, 25 Apr 96 12:29:08 -0400 From: Heather Carlson Message-Id: <9604251629.AA12733@ramana.chem.yale.edu> To: CHEMISTRY@www.ccl.net Subject: vancomycin Hello All- I am looking for protein crystal structures of the enzymes in the vancomycin resistance cascade (VanA, VanH, VanX, and VanR). I've been in contact with Chris Walsh and Jim Knox; both have been very helpful. I was just wondering who else out there is trying to solve/grow crystals of the Van proteins... so far, none are available. Thanks- Heather Carlson heather@ramana.chem.yale.edu From craig@occam.gh.wits.ac.za Thu Apr 25 13:48:59 1996 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.7.1/950822.1) id MAA00367; Thu, 25 Apr 1996 12:54:50 -0400 (EDT) Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id SAA20553; Thu, 25 Apr 1996 18:46:59 +0200 Date: Thu, 25 Apr 1996 18:46:58 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Pablo Vitoria cc: chemistry@www.ccl.net Subject: Re: CCL:Volume calculation for small molecules In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Does someone know (or has) a program to calculate the volume of small > molecules using as input atomic coordinates, e.g. from CSD data? > I'd prefer versions for Mac or PC, although any information about programs > for other systems is welcome. Steric (ftp://hobbes.gh.wits.ac.za/pub/steric/) has a very simple monte carlo volume calculation for any size molecules and can read a variety of formats (that babel can convert CSD data to). It is primarily for Unix platforms, but a DOS port is available. Cheers, Craig "Imagine if every Thursday your shoes exploded if you tied them the usual way. This happens to us all the time with computers, and nobody thinks of complaining." -- Jeff Raskin, interviewed in Doctor Dobb's Journal Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig