From chemistry-request@server.ccl.net Fri May 26 02:40:58 2000 Received: from uni-paderborn.de (uni-paderborn.de [131.234.22.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA08232 for ; Fri, 26 May 2000 02:40:58 -0400 Received: from oc24 ([131.234.240.84]:62876 "EHLO upb.de") by mail.uni-paderborn.de with ESMTP id ; Fri, 26 May 2000 08:40:42 +0200 Message-ID: <392E1C56.C2543618@upb.de> Date: Fri, 26 May 2000 08:40:22 +0200 From: edgar X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: DOCK 4 problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Users, I'm new to DOCK 4 and I have a problem even before running dock. Unfortunately I don't have access to MS or QCPE_MS but I do have access to a similar program. Therefore I tried to convert the molcular surface output to the format required by SPHGEN. I tried all the three different formats which are documented in the manual but none worked. So I would be very happy if someone could provide me with the correct format or even a fragment of a correct molecular surface file. I found the following three formats: 1.) (A3, I5, 2X, A3, 3(F8.3, X), X, A3, 4F7.3) This is from the manual page 95 and this is supposed to be the format that SPHGEN reads. 2.) (A3, I5, X, A4, X, 2F8.3, F9.3, X, A3, 7X, 3F7.3) Is written on page 84 as the format expected by SPHGEN. 3.) (A3,I3,A1,2X,A4,1X,F7.3,2F9.3,1X,A3,7X,3F7.3) Is produced by SPHGEN as an error message if started with an incorrect file format. Thanks in advance for any help. Edgar -- Edgar Luttmann University of Paderborn, Germany Department of organic chemistry office: J6.302 Warburger Str. 100 phone: (+49) 5251 60-2498 33098 Paderborn mobile: (+49) 171 7406386 eMail: edgar@upb.de From chemistry-request@server.ccl.net Fri May 26 04:44:49 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA08842 for ; Fri, 26 May 2000 04:44:48 -0400 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 12vFij-0001BO-00 for chemistry@ccl.net; Fri, 26 May 2000 09:43:53 +0100 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.11 #2) id 12vFjS-0003Gg-00 for chemistry@ccl.net; Fri, 26 May 2000 09:44:38 +0100 Date: Fri, 26 May 2000 09:43:49 +0100 (BST) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: chemistry@ccl.net Subject: Antibody Modelling/Autodock Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Given that antibody crystal structures represent a static form of a dynamic structure, does anybody know a decent method to change the bite angle between the light and heavy chains? This would allow the binding pocket to become more accessible for docking using Autodock 3.0. At present the docking structures I've obtained show that the ligand (co-crystallised with the antibody) does not have complete access to the pocket once removed from it. Any ideas would be much appreciated. ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Thu May 25 17:07:53 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05946 for ; Thu, 25 May 2000 17:07:53 -0400 Received: from mail.chem.tamu.edu ([165.91.176.63]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Thu, 25 May 2000 16:16:53 -0500 Sender: jshen@ccl.net Message-ID: <392D964A.B99049A1@mail.chem.tamu.edu> Date: Thu, 25 May 2000 14:08:26 -0700 From: Jingyi Shen Organization: TAMU To: CHEMISTRY@ccl.net Subject: How to make Gaussian recognize symmetry of [ZR6Cl12B.6PH3](+) cluster? Dear CCLer, I have been doing calculation on [ZR6Cl12B.6PH3](+) cluster using Gaussian 98. The six Zirconium atoms in the molecule form an octahedral cage which is centered by a boron atom. Twelve chlorides bridge every of the twelve edges each. PH3 (in C3v symmetry) molecule axially binds to zirconium atom. The binding of PH3 to the zirconium and halide cage (Oh) lowered the total symmetry. By rotating PH3 along Zr-P bond, D3d symmetry is achieved for the molecule. Now comes the problem. Gaussian can not recognize symmetry of the molecule if the input is exactly D3d. I tried cartesian coordinate, z-matirx and mixed coordinate, But none of them worked. Listed below are one set of geometry inputs I tried and error message I always got. Interestingly, if Hx1(x=1,6) atoms are removed without changing the symmetry, gaussian did recognize D3d symmetry. My question are: (1)What caused the problem? (2)Could it be solved by improving the z-matrix? And how? Are there any other solutions ? Any suggestions from you would be highly appreciated! Jingyi Shen Dept of Chemistry TAMU ******** INPUT ******** X1 B1 X1 RBX CL01 B1 RCLB1 X1 90.0 CL02 B1 RCLB1 X1 90.0 CL01 60.0 CL03 B1 RCLB1 X1 90.0 CL01 -60.0 CL04 B1 RCLB1 X1 90.0 CL01 120.0 CL05 B1 RCLB1 X1 90.0 CL01 -120.0 CL06 B1 RCLB1 X1 90.0 CL01 180.0 X2 B1 RBX CL01 90.0 X1 180.0 ZR1 X2 RZX B1 90.0 CL01 -150.0 ZR2 X2 RZX B1 90.0 ZR1 120.0 ZR3 X2 RZX B1 90.0 ZR1 -120.0 ZR4 X1 RZX B1 90.0 ZR1 180.0 ZR5 X1 RZX B1 90.0 ZR2 180.0 ZR6 X1 RZX B1 90.0 ZR3 180.0 CL11 B1 RCLB1 X2 ACLBX ZR3 dc CL12 B1 RCLB1 X2 ACLBX ZR1 dc CL13 B1 RCLB1 X2 ACLBX ZR2 dc CL21 B1 RCLB1 X1 ACLBX ZR5 dc CL22 B1 RCLB1 X1 ACLBX ZR6 dc CL23 B1 RCLB1 X1 ACLBX ZR4 dc P11 ZR1 RZP X2 APZX ZR3 -90.0 P12 ZR2 RZP X2 APZX ZR1 -90.0 P13 ZR3 RZP X2 APZX ZR2 -90.0 P21 ZR4 RZP X1 APZX ZR5 -90.0 P22 ZR5 RZP X1 APZX ZR6 -90.0 P23 ZR6 RZP X1 APZX ZR4 -90.0 H11 P11 1.41500000 ZR1 114.000000 Zr3 -45.0 H21 P12 1.41500000 ZR2 114.000000 Zr1 -45.0 H31 P13 1.41500000 ZR3 114.000000 Zr2 -45.0 H41 P21 1.41500000 ZR4 114.000000 Zr5 -45.0 H51 P22 1.41500000 ZR5 114.000000 Zr6 -45.0 H61 P23 1.41500000 ZR6 114.000000 Zr4 -45.0 H12 P11 1.41500000 ZR1 114.000000 Zr3 75.0 H22 P12 1.41500000 ZR2 114.000000 Zr1 75.0 H32 P13 1.41500000 ZR3 114.000000 Zr2 75.0 H42 P21 1.41500000 ZR4 114.000000 Zr5 75.0 H52 P22 1.41500000 ZR5 114.000000 Zr6 75.0 H62 P23 1.41500000 ZR6 114.000000 Zr4 75.0 H13 P11 1.41500000 ZR1 114.000000 Zr2 -75.0 H23 P12 1.41500000 ZR2 114.000000 Zr3 -75.0 H33 P13 1.41500000 ZR3 114.000000 Zr1 -75.0 H43 P21 1.41500000 ZR4 114.000000 Zr6 -75.0 H53 P22 1.41500000 ZR5 114.000000 Zr4 -75.0 H63 P23 1.41500000 ZR6 114.000000 Zr5 -75.0 RBX=1.3273283 RCLB1=3.6076588 RZX=1.8771256 ACLBX=35.26439 RZP=2.8000000 APZX=144.73561 dc=-60.00 ************ Error Message ************ Error permuting atoms in Fill, LPerm: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Symmetry turned off: Internal error in symmetry package. ****************************** From chemistry-request@server.ccl.net Thu May 25 23:50:42 2000 Received: from mx1.ustc.edu.cn ([202.102.223.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA07611 for ; Thu, 25 May 2000 23:50:39 -0400 Received: from ustc.edu.cn (hpe25.nic.ustc.edu.cn [202.38.64.1]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id MAA00480 for ; Fri, 26 May 2000 12:06:14 -0800 Received: from mail.ustc.edu.cn by ustc.edu.cn with SMTP (8.6.10/16.2) id LAA04857; Fri, 26 May 2000 11:55:57 +0800 Received: (qmail 22102 invoked by uid 4742); 26 May 2000 03:47:24 -0000 Date: Fri, 26 May 2000 11:47:24 +0800 (CST) From: TingWei Mu To: CHEMISTRY@ccl.net Subject: Viewing the process of optimization of G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sir or Madam, I have a problem in viewing the process of the optimization of G98. That is to say, when I performed the optimization by G94, I can use MOLDEN to see each optimization step to get some information about how the molecule change. But for G98, MOLDEN cannot give the function when the moleule is big enough. Which software can give the function? You can e-mail to mtw@mail.ustc.edu.cn Sincerely yours, Tingwei Mu 320-313, East Campus, USTC Hefei, Anhui, 230026, P. R. China Tel: 86-551-3664161(Dorm) 86-551-3606640(Lab) E-mail: mtw@mail.ustc.edu.cn From chemistry-request@server.ccl.net Fri May 26 02:08:47 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA08054 for ; Fri, 26 May 2000 02:08:47 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id XAA12592; Thu, 25 May 2000 23:06:08 -0700 Resent-From: Eugene Leitl Resent-Message-ID: <14638.5200.698443.303283@lrz.uni-muenchen.de> Resent-Date: Thu, 25 May 2000 23:06:08 -0700 (PDT) Resent-To: , Delivered-To: all-eugene.leitl@lrz.uni-muenchen.de Message-Id: References: <392CDA7F.511DBCEE@medchem.dfh.dk> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by bw150zhb.bluewin.ch id LAA06927 X-SLUIDL: 58286947-325511D4-9E43004F-4908FE7D X-UID: 63 From: To: Multiple recipients of list orglist Subject: ORGLIST: Cost of Knowledge, Scientific Information? Date: Thu, 25 May 2000 10:41:06 +0200 (((reformatted))) From: "Paul Thind" Dear Friends, Henry Rezepa has raised the profile of a topic which has been of general concern to educators, scientists and our community of chemist for sometime. This phenomena of the global economy moving to a more capitalist model has been going on for sometime in all aspects of economic life and informatio n (in particular scientific information - high value added content) is no exception. As a community we can do something about it. But I disagree wi th some of the suggestions put forward, in particular that perhaps individua ls should start selling their manuscripts (presumably to the highest bidder). Most Scientists in the world are employees of companies or public institutions. One can argue that they are already being compensated for their output. This approach will not solve any problems facing the majority of students and scientists from around the world and may create new problems. What needs to happen is quite the reverse. The Scientific community needs to organize itself through not-for-profit organizations in order to publish research results at cost or for free. However our experience shows that at least our own community of organic chemists is very poorly organized and not yet sufficiently motivated to t ake advantage of some existing initiatives which can benefit everyone. Almost a year ago we established the not-for-profit ARKAT Foundation. Its sole aim is to publish a free online journal of organic chemistry which i s available to the global community. The project is being funded by an init ial donation of a substantial sum of money from Alan Katritzky & Linde Katritzky. The funding level is sufficient for us to make this service available for at least 3-5 years during which time we are confident in generating other revenue streams to make it secure for ever. The details are on www.arkat.org . One might have assumed that authors would be knocking on our doors wishin g to publish and share their results, with the widest possible distribution , and at no cost to themselves or the user. This has not been the case. We are publishing. Two Issues of the Journal are now online. Third is on the way. But we could be publishing ten to twenty times as many manuscripts as we are presently receiving. Not even all Professors on our Board of Refer ees have submitted a manuscript! We can help authors in publishing their books. We can help the chemistry community to have its own cost effective databases. We could be publishing other educational material free or at no or very low cost in accordance with the author's wishes. I can only challege all of you. We have a solution to these problem. Anyo ne who is concerned about the high cost of journals, books, databases is encouraged to join us in this project. I would like to hear about reasons for not publishing in Arkivoc! Please forgive me if I seem to be pouring cold water on a very important debate! Best wishes, Paul Thind CEO ARKAT Foundation Schanzeneggstrasse 1 8002 Zurich Tel: 411 201 9700 ----- Original Message ----- From: Eva Horn Moeller To: Multiple recipients of list orglist Sent: Thursday, May 25, 2000 9:47 AM Subject: ORGLIST: Information - Revolution? Dear all, this is indeed a very important and critical issue, and I am wholly surprised that I haven=B4t thought of this or have heard a discussion of this kind yet. It is in fact absurd that the scientific habit of sharing information globally is taken advantage of by the publishers. Many libraries cannot lift the economic burden of keeping e.g. CAS, and many departments, as some of you mention, end up choosing between very slow and difficult - or very expensive access to chemical info. Now, the publishers can set the price at any level they choose, and the libraries just have to pay. Maybe we have been too naive. Especially because we, the researchers, in theory have the power to shut off the commercial scientific publishing at very short notice. I really feel that something should be done about this, and the discussion ought to be taken to a higher level. What are the opinions of e.g. the Royal Chemical Society and the American Chemical Society on this issue? Best regards, Eva Horn Moeller (MSc, PhD) The Royal Danish School of Pharmacy __________________ ORGLIST - Organic Chemistry Mailing List Website / Archive / FAQ: http://www.dq.fct.unl.pt/orglist/ To post a message (TO EVERYBODY) send to orglist@dq.fct.unl.pt To unsubscribe, send to listserver@dq.fct.unl.pt the message: unsubscribe orglist List coordinator: Joao Aires de Sousa (jas@mail.fct.unl.pt) __________________ ORGLIST - Organic Chemistry Mailing List Website / Archive / FAQ: http://www.dq.fct.unl.pt/orglist/ To post a message (TO EVERYBODY) send to orglist@dq.fct.unl.pt To unsubscribe, send to listserver@dq.fct.unl.pt the message: unsubscribe orglist List coordinator: Joao Aires de Sousa (jas@mail.fct.unl.pt) From chemistry-request@server.ccl.net Fri May 26 02:12:17 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA08074 for ; Fri, 26 May 2000 02:12:16 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id XAA12604; Thu, 25 May 2000 23:09:38 -0700 Resent-From: Eugene Leitl Resent-Message-ID: <14638.5405.248355.845722@lrz.uni-muenchen.de> Resent-Date: Thu, 25 May 2000 23:09:33 -0700 (PDT) Resent-To: , , , , Delivered-To: all-eugene.leitl@lrz.uni-muenchen.de Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: <14636.56680.445595.488059@lrz.uni-muenchen.de> References: <392CDA7F.511DBCEE@medchem.dfh.dk> <14636.56680.445595.488059@lrz.uni-muenchen.de> Content-Type: text/plain; charset="us-ascii" X-SLUIDL: 582868A8-325511D4-9E43004F-4908FE7D X-UID: 60 From: To: Multiple recipients of list orglist Subject: Re: ORGLIST: Information - Revolution? Date: Thu, 25 May 2000 09:32:26 +0100 (((reformatted))) From: "Rzepa, Henry" >To counteract electronical publishing standard erosion as pushed by >the marketplace, a globally accepted open/noncommercial expandable >document publishing standard has to be defined (inasmuch chemical XML >doesn't qualify already), which has to have means of intelligent full >text, structure (unique SMILES or graphs) and (IR, MS, NMR) spectre >searching. These standards have to be implemented in OpenSource >software, putting the development into the hands of the users. All >this is not exactly rocket science so far. > >This is all very doable, and in fact being partly done already, but is >being habitually ignored by the chemical community. Apart from >occasional laments, the comminity seems to like things just fine as >they are. Watching this happening for years is incredibly frustrating. I totally agree that the retention of semantic meanings in the data is something of a holy grail amongst some of us. Our own contribution for example is at http://www.ch.ic.ac.uk/chimeral/ which shows how XML and CML can be used to create an electronic article where IR, MS, NMR, structures, etc are all "re-usable" information components, presented (using XSLT stylesheets) in the "way the user wants" and in the context of appropriate tools. By the way, all this and much more will be discussed at the Chemint2000 conference (http://www.chemint.org/ ) if anyone wants to participate) There have been brave experiments with electronic journals that offer this to users; J Mol Mod was one of the first, the Internet J of Chemistry offers perhaps the most developed integration, and projects such as PhysChemComm from the Royal Society of Chemistry and the Arkivoc organic chemistry journal (http://arkat.org/arkat/ ) show one way forward. But not enough authors (yet) submit articles to such journals! When this is analysed, one common reason is that such "new" journals do not (yet) have an "impact" factor, a chicken and egg situation if ever I saw one. Ah, impact factors. What HAVE they done to our subject!! But if all chemistry journals were of this type (and in particular expressed in XML, so I feel) then the cost of creation of a CAS, or a Beilstein, or an ISI or a Cambridge Crystal structure database would (should!) drop dramatically. The only people preventing this from happening, is US, ie the authors and readers of the chemical heritage! (Hope this did not sound too pompous! Is there an Internet equivalent of a soap box?) -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ __________________ ORGLIST - Organic Chemistry Mailing List Website / Archive / FAQ: http://www.dq.fct.unl.pt/orglist/ To post a message (TO EVERYBODY) send to orglist@dq.fct.unl.pt To unsubscribe, send to listserver@dq.fct.unl.pt the message: unsubscribe orglist List coordinator: Joao Aires de Sousa (jas@mail.fct.unl.pt) From chemistry-request@server.ccl.net Fri May 26 10:05:55 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11402 for ; Fri, 26 May 2000 10:05:53 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id SAA01506 for ; Fri, 26 May 2000 18:05:19 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <392E849E.2338EC3F@cacr.ioc.ac.ru> Date: Fri, 26 May 2000 18:05:18 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: SUMMARY 1,3,5-cyclohexatriene Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL, Below is my original message and replies I've got. In summary the following references were suggested: J. Mol. Struct. (THEOCHEM) 1994, 398-399 155-167 J.Am.Chem.Soc., 1996, 118: (31) 7381-7385 Chem.Ber., 1994, 127: (9) 1765-1779 J.Am.Chem.Soc., 1993, 115: (23) 10952-10957 J.Am.Chem.Soc., 1992, 114: (21) 8263-8268 and I thank to Xavier Assfeld, Chaitanya Wannere, E. Lewars, Adam Matzger, and Alan Shusterman for the contribution! best regards, Valentin. ---------- Dear List Members, Does anybody have an information about predicted structure and stability for 1,3,5-cyclohexatriene? I mean a six-membered ring with alternating single and double C-C bonds, but without aromatic pi-electrons delocalization due to non-planar conformation (i.e. non-planar benzene isomer). Would such structure exist in principle? Thanks! Valentin. ----------- +++++++++++ Hi, have a look at: "a different story of benzene" S. Shaik, A. Shurki, D. Danovich, P. Hiberty J. Mol. Struct. (THEOCHEM) 398-399 (1997) 155-167. Hope this helps. ...Xav Ast. Pr. Xavier Assfeld +++++++++++++ +++++++++++++ Hi Valentine, This is the geometry of the 1,3,5-cyclohexatriene that I got from our archive. C 1.2263000 0.6748000 0.0000000 C 1.2263000 -0.6748000 -0.0000001 C -1.1975440 0.7246069 0.0000001 C -0.0287562 1.3994070 -0.0000001 C -0.0287562 -1.3994070 0.0000001 C -1.1975440 -0.7246069 0.0000000 H 2.1548711 1.2347514 -0.0000001 H 2.1548711 -1.2347514 -0.0000000 H -2.1467617 1.2487973 0.0000000 H -0.0081096 2.4835488 -0.0000001 H -0.0081096 -2.4835488 0.0000001 H -2.1467617 -1.2487973 0.0000001 1. Johnson RP, Daoust KJ Electrocyclic ring opening modes of Dewar benzenes: Ab initio predictions for Mobius benzene and trans-Dewar benzene as new C6H6 isomers J AM CHEM SOC 118: (31) 7381-7385 AUG 7 1996 2. ROTH WR, HOPF H, HORN C THE ENERGY WELL OF DIRADICALS .5. 1,3,5-CYCLOHEXATRIENE-1,4-DIYL AND 2,4-CYCLOHEXADIENE-1,4-DIYL CHEM BER 127: (9) 1765-1779 SEP 1994 3. GILLARD JR, NEWLANDS MJ, BRIDSON JN, et al. PI-FACIAL STEREOSELECTIVITY IN THE DIELS-ALDER REACTIONS OF BENZENE OXIDES CAN J CHEM 69: (9) 1337-1343 SEP 1991 4. KREITER CG, MICHELS E, KURZ H PHOTOCHEMICAL-REACTIONS OF TRANSITION-METAL OLEFIN COMPLEXES .4. PHOTOCHEMICAL CYCLOADDITION OF CYCLIC DIENES ON TRICARBONYL-ETA-6-1,3,5-CYCLOHEXATRIENE-CHROMIUM(O) J ORGANOMET CHEM 232: (3) 249-260 1982 These are the references that I know of, additionally the back references included in this paper might help you in tracing what you are exactly looking for. Best Wishes, Chait Chaitanya S. Wannere ++++++++++++ ++++++++++++ Hello, The answer to your question (below), phrased as a general problem, is not as quite simple as one may think. The conventional response would be that cyclohexatrine structures are resonance structures (canonical structures) contributing to the actual structure, a resonance hybrid, and so can't have any real existence: they are just bond-stretching vibrational extremes with benzene vibrating about a geometry of mean (average) hexagonal symmetry (think of a Morse curve). the energy of the purely hypothetical 1,3,5-cyclohexatriene has been evaluted in connection with its use as areference molecule in assigning a resonance energy to benzene (e.g. work by M. J. S. Dewar--treated in some org chem textbooks). So much for benzene, but for cyclobutadiene the alternating C-C/C=C structures are real: the potential energy surface has two minima separated by a transition state. Predicting the results for simple polyene cases requires, usually, only knowing about aromaticity and antiaromaticity and the Hueckel rule, but _generally_ distinguishing between resonance (as in benzene) and valence tautomerism (as in cyclobutadiene) requires actual calculation. The problem of "the thin line" (quoting Paquette) between the two was discussedby L. Paquette in J Am Chem Soc in a paper on homoaromaticity about 10-15 years ago. E. Lewars ++++++++++ ++++++++++ These references will get you started: THE ROLE OF DELOCALIZATION IN BENZENE GLENDENING ED, FAUST R, STREITWIESER A, VOLLHARDT KPC, WEINHOLD F JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 115: (23) 10952-10957 NOV 17 1993 ABINITIO STUDY OF SIGMA-EFFECTS AND PI-EFFECTS IN BENZENES FUSED TO 4-MEMBERED RINGS - REHYBRIDIZATION, DELOCALIZATION, AND ANTIAROMATICITY FAUST R, GLENDENING ED, STREITWIESER A, VOLLHARDT KPC JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 114: (21) 8263-8268 OCT 7 1992 You should also check science citation index for opposing viewpoints. Adam Matzger ++++++++++ ++++++++++ Dear Valentin, Your question is almost impossible to answer because 1,3,5-cyclohexatriene does not exist, and all quantum calculations will allow electrons to delocalize. There are some ways to restrict the degree of localization during the calculation, but calling any of the resulting molecules "1,3,5-cyclohexatriene" is very arbitrary (and different localization schemes will give you different results). I tried using Jaguar to do a GVB-PP/6-31G** calculation on "1,3,5-cyclohexatriene". There were 9 GVB electron pairs in my calculation, the 6 CC sigma bond pairs and the 3 CC pi bond pairs. The other electron pairs were all treated using Hartree-Fock-type orbitals. The CC bond distances finished at 1.367 and 1.458 Å, so that is one estimate of the structure of this fictional molecule. -Alan ==== Alan Shusterman +++++++++++ ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Fri May 26 10:33:48 2000 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11599 for ; Fri, 26 May 2000 10:33:47 -0400 Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id PAA19831 for ; Fri, 26 May 2000 15:33:32 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14638.35650.87579.57216@gargle.gargle.HOWL> Date: Fri, 26 May 2000 15:33:38 +0100 (BST) To: "CCL, Computational Chemistry List" Subject: PDB format with 100000 atoms X-Mailer: VM 6.75 under 21.1 (patch 3) "Acadia" XEmacs Lucid According to the Brookhaven PDB format website it seems that only a 5 digit field is allowed for the atom sequence number, so there is no way of generating a correct PDB file containing 100000 atoms or more. Has anyone else come up against this limit and found any workaround? sincerely Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Fri May 26 10:15:04 2000 Received: from mail1.mclink.it (net128-007.mclink.it [195.110.128.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11451 for ; Fri, 26 May 2000 10:15:02 -0400 Received: from Attila (net138-149.mclink.it [195.110.138.149]) by mail1.mclink.it (8.9.1/8.9.0) with SMTP id QAA19284 for ; Fri, 26 May 2000 16:14:44 +0200 (CEST) Message-ID: <023201bfc71d$22376d20$070000c0@CADD> From: "Elena Fioravanzo" To: "ccl" Subject: molecular diversity Date: Fri, 26 May 2000 15:00:18 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear collegues, please excuse me if I send this message again, but I was asked to re-send it in text format (I did not notice the former one was in HTML format) to allow everybody to read it. Thanks again. Elena Hi, there are many methods and indices to estimate molecular similarity, but it is quite difficult to estimate-calculate molecular diversity. Could someone give me, please, references (articles, web-site, softwares) about this point? Thanks in advance, I will sumarize if someone is interested. Elena --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ From chemistry-request@server.ccl.net Fri May 26 10:26:44 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11535 for ; Fri, 26 May 2000 10:26:43 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id SAA01523 for ; Fri, 26 May 2000 18:26:05 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <392E897D.A3C23528@cacr.ioc.ac.ru> Date: Fri, 26 May 2000 18:26:05 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: SUMMARY - MP2/UMP2 vs B3LYP/UB3LYP Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCl members, Please find my original question and replies on the subject topic below. To summarize, the following references were suggested: 1) Cramer, C. J.; Worthington, S. E., J.Phys.Chem. 1995, 99, 1462. 2) Lim, M. H.; Worthington, S. E.; Dulles, F. J.; Cramer, C. J. "Density Functional Calculations of Radicals and Diradicals" in Density-Functional Methods in Chemistry, ACS Symposium Series, Volume 629, Laird, B. B., Ross, R. B. Ziegler, T., Eds.; American Chemical Society: WashingtonDC, 1996; 402. 3) Worthington, S. E.; Cramer, C. J., J. Phys. Org. Chem. 1997, 10, 755. 4) Cramer, C. J.; Dulles, F. J.; Giesen, D. J.; Alml÷f, J., Chem. Phys. Lett. 1995, 245, 165. 5) Holger F. Bettinger,Paul von Rague Schleyer, Peter R. Schreiner, and Henry F. Schaefer III, J. Org.Chem. 1997, 62, 9267-9275. 6) Yaoming Xie, Peter R. Schreiner, Paul von Rague Schleyer, and Henry F. Schaefer III, J. Am.Chem.Soc. 1997, 119, 1370-1377. 7) Holger F. Bettinger, Peter R. Schreiner, Paul von Rague Schleyer, and Henry F. Schaefer III, J. Phys. Chem. 1996, 100, 16147-16154. 8) Peter R. Schreiner, William L. Karney, Paul von Rague Schleyer, Weston T. Borden, Tracy P. Hamilton, and Henry F. Schaefer III, J. Org. Chem. 1996, 61, 7030-7039. 9) Sulzbach, et al . JACS, 1997, 119, 5682. and I really thank to Christopher Cramer, Alexander Bagatur'yants, Seiji Mori, Stefan Grimme, Xavier Assfeld and Peter Schreiner for the contribution and helpful discussion. regards, Valentin. --------------- Dear CCL, I am a little surprised with the following problem and would be grateful for helpful comments. On a substituted carbene compound MP2/UMP2 optimization of singlet and triplet states respectively leads to energy gap of about 9 kcl/mol and low lying singlet state. However, in the case of B3LYP/UB3LYP optimized structures triplet state is more stable by approximately the same value. Geometry parameters are also different. Unfortunately, experimental data for this compound is not available. Is this a known thing ? any precedents ? Does anybody have an idea on the possible explanation and what accuracy one would expect from MP2 and B3LYP calculated s/t gaps? Thank you! best regards, Valentin. --------------- +++++++++++++++ Dear Valentine, to my experience, B3LYP is quite good for S-T gaps if both states are single reference and spin-contamination is not a problem. For CH2, B3LYP gives a good value, a little bit too low for the triplet. I think MP2 has problems here because it is known to be more sensitive to the multi-reference character and small spin-contamination may also be a problem. I would suggest to use MR-MP or MR-CI. stefan _________________________________________________________ Prof. Dr. Stefan Grimme +++++++++++++++ +++++++++++++++ MP2 is a disaster for most carbenes, unless they are very stable singlets. The bottom line is that the singlets tend to be two-configurational (e.g., psi = c1 * |...HOMO^2> + c2 * |...LUMO^2> where ... refers to double occupation of all HF orbitals 1 to HOMO-1 and c1 > c2 but not necessarily by all that much) and the extent of the non-dynamical correlation is such that perturbation theory is not a good way to estimate the energy. DFT tends to be MUCH more reliable, although it too ultimately fails if c1 and c2 come closer to being equal. There is a vast literature on this topic, particularly with the carbene focus. My group has contributed a bit. Cramer, C. J.; Worthington, S. E. "The Electronic Structures of Aziridenium and Cyclopropylidene. Hypovalent Atoms in Three-Membered Rings" J. Phys. Chem. 1995, 99, 1462. and Lim, M. H.; Worthington, S. E.; Dulles, F. J.; Cramer, C. J. "Density Functional Calculations of Radicals and Diradicals" in Density-Functional Methods in Chemistry, ACS Symposium Series, Volume 629, Laird, B. B., Ross, R. B. Ziegler, T., Eds.; American Chemical Society: Washington DC, 1996; 402. provide some discussion, and also point to other excellent references. Chris Cramer +++++++++++++++ +++++++++++++++ Dear Valentin, This is a well-known problem, closely associated with the Kohn-Sham formalism. Relative stabilization of the singlet state in a carbenoid system is due to the (nondynamic!) correlation effect of the mixing between the ground state [sigma]2[pi]0 configuration and the doubly excited [sigma]0[pi]2 configuration. This mixing gives rise to some electron density transfer to the region of p[pi] orbital. However, one cannot reproduce this electron density pattern within the Kohn-Sham formalism simply because of symmetry restrictions. Even if the symmetry restrictions are removed, the one-electron orbital mixing between the [sigma] and [pi] orbitals will be negligible. Best regards, Prof. Alexander Bagatur'yants +++++++++++++++ +++++++++++++++ Hi, have a look at : 1) Worthington, S. E.; Cramer, C. J. "Density Functional Calculations of the Influence of Substitution on Singlet-Triplet Gaps in Carbenes and Vinylidenes" J. Phys. Org. Chem. 1997, 10, 755. 2) Cramer, C. J.; Dulles, F. J.; Giesen, D. J.; Alml÷f, J. "Density Functional Theory: Excited States and Spin Annihilation" Chem. Phys. Lett. 1995, 245, 165. hope this helps. ...Xav Ast. Pr. Xavier Assfeld +++++++++++++++ +++++++++++++++ Hi Valentin, you may take carbenes as prime examples for computing S/T-gaps - DFT is clearly superior due to a better description of the singlet (not necessarily for a good reason). Have a look at: Carbenes: A Test Ground for Electronic Structure Methods. Holger F. Bettinger, Peter R. Schreiner, Paul von Rague Schleyer, and Henry F. Schaefer III; in "The Encyclopedia of Computational Chemistry" Paul v. Ragué Schleyer, Norman L. Allinger, Tim Clark, Johann Gasteiger, Peter A. Kollman, Henry F. Schaefer III, and Peter R. Schreiner (Eds.), John Wiley & Sons Inc.; Chichester, 1998, 183-196. Substituted Cyclopropylidenes and Cyclic Allenes. Holger F. Bettinger, Paul von Rague Schleyer, Peter R. Schreiner, and Henry F. Schaefer III J. Org. Chem. 1997, 62, 9267-9275. The Naphthylcarbene Potential Energy Hypersurface. Yaoming Xie, Peter R. Schreiner, Paul von Rague Schleyer, and Henry F. Schaefer III J. Am. Chem. Soc. 1997, 119, 1370-1377. The Ring Opening of Cycopropylidene and the Internal Rotation of Allene. Holger F. Bettinger, Peter R. Schreiner, Paul von Rague Schleyer, and Henry F. Schaefer III J. Phys. Chem. 1996, 100, 16147-16154. Carbene Rearrangements Unsurpassed: The C7H6 Potential Energy Surface Revealed. Peter R. Schreiner, William L. Karney, Paul von Rague Schleyer, Weston T. Borden, Tracy P. Hamilton, and Henry F. Schaefer III J. Org. Chem. 1996, 61, 7030-7039. Hope this provides some input - Peter -- Prof. Dr. Peter R. Schreiner +++++++++++++++ +++++++++++++++ Hi. Valentine: ... You may find hints from a paper at Sulzbach, et al . JACS, 1997, 119, 5682. With hyperconjugation of a p orbital of substituents into empty p orbital of singlet carbene, S/T gap is smaller or sometimes a singlet state could be more stable than the triplet. although that of methylene carbene is 9.0 kcal/mol experimentally (triplet ground state). And is of UMP2 result of triplet carbene fine? Is that close to 0.75? Sulzbach, et al .used BHandHLYP. Hope it helps. Seiji ************************************************** Seiji Mori, Ph.D. +++++++++++++++ ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Fri May 26 12:00:51 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12554 for ; Fri, 26 May 2000 12:00:50 -0400 Received: from iaf.uquebec.ca ([198.168.44.40]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 262 for ; Fri, 26 May 2000 11:57:21 -0400 Message-ID: <392EA1CD.8CBC1595@iaf.uquebec.ca> Date: Fri, 26 May 2000 12:09:49 -0400 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Large loop + Binding site Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, A couple days ago, I asked question about modelling large loop. I received several request for the summary. Sorry folks, I have not got any useful response yet. Maybe my question is too broad. Let me try it again. To model a large flexible loop in the protein modelling is risky. However, if the loop is found to involve with ligand binding (it happens!), then the key step is to get a good model of the loop. Moreover, the loop conformation usually will change on the binding of ligand. In my case, the loop contains about 55 residues. What is the state of the art in modelling this kind of loop? Do you know any successful case? I got several models of this large loop, most of them point away from the protein surface! Any suggestion will be greatly appreciated. Sincerely, Jian Hui Wu Institute Armand-Frappier Laval, QC From chemistry-request@server.ccl.net Fri May 26 13:19:01 2000 Received: from CPWSCA.PSC.EDU (a-73.psc.edu [128.182.73.105]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA13058 for ; Fri, 26 May 2000 13:19:01 -0400 Received: from armada ([128.182.62.170]) by d.psc.edu with SMTP for chemistry@ccl.net; Fri, 26 May 2000 13:18:46 -0400 From: "Nick Nystrom" To: Subject: Workshop: Structure Determination Using NMR, July 26-29, 2000 Date: Fri, 26 May 2000 13:18:45 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 ********************************************************************** PSC Biomedical Initiative Workshops 2000 Structure Determination Using NMR Pittsburgh Supercomputing Center July 26-29, 2000 Application Deadline: June 14, 2000 The objective of this workshop is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The programs AMBER and MORASS will be discussed. In addition to lectures, there will be extensive hands-on sessions. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#NMR If you have any questions, please contact Nancy Blankenstein at blankens@psc.edu or 412/268-4960 (FAX). Many thanks for your interest and help. ********************************************************************** From chemistry-request@server.ccl.net Fri May 26 12:35:07 2000 Received: from tech.chem.ethz.ch (ltcmail.ethz.ch [129.132.124.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12808 for ; Fri, 26 May 2000 12:35:06 -0400 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id SAA14334; Fri, 26 May 2000 18:33:21 +0200 (CEST) Message-ID: <392EA871.637188A5@tech.chem.ethz.ch> Date: Fri, 26 May 2000 18:38:09 +0200 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: TingWei Mu , chemistry@ccl.net Subject: Re: CCL:Viewing the process of optimization of G98 References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit TingWei Mu wrote: > Dear Sir or Madam, > > I have a problem in viewing the process of the optimization of G98. > That is to say, when I performed the optimization by G94, I can use > MOLDEN to see each optimization step to get some information about > how the molecule change. But for G98, MOLDEN cannot give the function > when the moleule is big enough. > > Which software can give the function? > > You can e-mail to > mtw@mail.ustc.edu.cn > Your problem may be the MOLDEN version you are using. Try to install MOLDEN 3.6, you should have no problems with Gaussian 98 movies then. Hope this helps Angelo _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54, Room CNB B98.3 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/HOMEPAGE/members/vargas/vargas.html ________________________________________________________________________