From chemistry-request@server.ccl.net Thu Aug 10 10:38:44 2000 Received: from rzcomm1.rz.tu-bs.de (root@rzcomm1.rz.tu-bs.de [134.169.9.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA13535 for ; Thu, 10 Aug 2000 10:38:42 -0400 Received: from chemistry.upatras.gr (beuys.thc.nat.tu-bs.de [134.169.41.56]) by rzcomm1.rz.tu-bs.de (8.9.3 (PHNE_18979)/8.9.3) with ESMTP id QAA03997 for ; Thu, 10 Aug 2000 16:38:29 +0200 (METDST) Message-ID: <3992C57A.95E0C1D0@chemistry.upatras.gr> Date: Thu, 10 Aug 2000 18:08:43 +0300 From: Demetrios Xenides X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: single linkage cluster analysis Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Hi all, I am looking for a software (freeware/shareware) that is able to produce the minimum spanning tree (MST) from the similarity matrix (Sij). Is there any chance to find something that fits my needs? Any suggestion is very wellcome! Cheers Demetrios From chemistry-request@server.ccl.net Thu Aug 10 11:09:06 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [199.245.177.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA13743 for ; Thu, 10 Aug 2000 11:09:06 -0400 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA19382; Thu, 10 Aug 2000 08:08:37 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id LAA06194; Thu, 10 Aug 2000 11:08:36 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Thu, 10 Aug 2000 11:08:36 -0400 (EDT) From: Peter Shenkin To: Demetrios Xenides cc: chemistry@ccl.net Subject: Re: CCL:single linkage cluster analysis In-Reply-To: <3992C57A.95E0C1D0@chemistry.upatras.gr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Well, it's not free, but our XCluster program does single-link. See Shenkin and McDonald, J. Comp. Chem. v15, pp899-916 (1994). -P. On Thu, 10 Aug 2000, Demetrios Xenides wrote: > Hi all, > > I am looking for a software (freeware/shareware) that is able to produce > the minimum spanning tree (MST) from the similarity matrix (Sij). > > Is there any chance to find something that fits my needs? > > Any suggestion is very wellcome! > > Cheers > Demetrios > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Aug 9 22:15:57 2000 Received: from hotmail.com (f6.law7.hotmail.com [216.33.237.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA09791 for ; Wed, 9 Aug 2000 22:15:57 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 9 Aug 2000 19:13:53 -0700 Received: from 200.17.23.122 by lw7fd.law7.hotmail.msn.com with HTTP; Thu, 10 Aug 2000 GMT X-Originating-IP: [200.17.23.122] From: "tek kno3" To: JOSE.DUCA@spcorp.com Cc: CHEMISTRY@ccl.net Subject: Re: CCL:pKa computation Date: Wed, 09 Aug 2000 23:13:53 EST Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 10 Aug 2000 02:13:53.0080 (UTC) FILETIME=[A1387B80:01C00270] > I have a few questions on pKa calculation methods: > 3. Any hints to use ab initio methods to obtain pKa's? Hi list, You can check: Nascimento M.A., "Ab Initio Calculations of Absolute pKa Values in Aqueous Solution I. Carboxilic Acids" et al. J.Phys.Chem. A, 103 (1999), 11194 Cheers, Guilherme Menegon IQUSP - BRasil ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Aug 10 01:00:59 2000 Received: from email.guomai.sh.cn (lcsfsradfv@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA10424 for ; Thu, 10 Aug 2000 01:00:58 -0400 Received: from guomai.sh.cn ([202.101.33.179]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0FZ2003NC971QM@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Thu, 10 Aug 2000 13:13:50 +0800 (CST) Date: Thu, 10 Aug 2000 13:01:04 +0800 From: Yubo Fan Subject: Agostic interaction To: CHEMISTRY@ccl.net Message-id: <39923710.F04644B0@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.73 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, All CCLers, I have met a keyword, agostic interaction, recently. It cannot be found in various dictionaries. To my knowledge, it means weak intermolecular interaction. I really don't understand it clearly. The problem is what types of intermolecular interactions can be regarded as agostic interaction. Could anybody give me the definition and examples? Thanks in advance Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Thu Aug 10 03:59:13 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA11013 for ; Thu, 10 Aug 2000 03:59:12 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id JAA10453; Thu, 10 Aug 2000 09:59:00 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id JAA20903; Thu, 10 Aug 2000 09:50:41 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 10 Aug 00 09:59:01 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 10 Aug 00 09:58:53 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Chris T. Middleton" Date: Thu, 10 Aug 2000 09:58:25 +0100 Subject: CCL:Z Matrix for [2.2]Paracyclophane CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Chris T. Middleton: > I am trying to create a Z Matrix for [2.2]Paracyclophane (two benzene > rings connected by two ethano bridges at the para positions). I have > tried a couple different ways of forming the matrix but have been able to get > Gaussian98 to recognize the D2 symmetry. It is a complex problem due to the > molecules low symmetry and large size. ... Dear Chris, I would not call cyclophane a molecule of particularly 'large size', nor do I consider D2 symmetry as 'low symmetry'. A couple of months ago I performed a calculation on D2 paracyclophane and Gaussian98 recognized the molecular symmetry with no problems at all. I prefer to work with input geometries in cartesian coordinates; below you find parts of my output file, containing the input atomic coordinates and the message 'Framework group D2[X(C16H16)]'. Yours, Jens >--< ********************************************* Gaussian 98: x86-Win32-G98RevA.7 11-Apr-1999 15-May-2000 ********************************************* -------------------------------------------- [2,2](1,4)Cyclophane = "Paracyclophane" (D2) -------------------------------------------- 6 1.41324 1.41357 -0.0015 6 0.69585 1.57437 1.19392 6 -0.69857 1.5745 1.19535 6 -1.41324 1.41357 0.0015 6 -0.69585 1.57437 -1.19392 6 0.69857 1.5745 -1.19535 6 -2.80085 0.80681 0.0035 6 -2.80085 -0.80681 -0.0035 6 1.41324 -1.41357 0.0015 6 0.69857 -1.5745 1.19535 6 -0.69585 -1.57437 1.19392 6 -1.41324 -1.41357 -0.0015 6 -0.69857 -1.5745 -1.19535 6 0.69585 -1.57437 -1.19392 6 2.80085 0.80681 -0.0035 6 2.80085 -0.80681 0.0035 1 1.22517 1.55289 2.14357 1 -1.22989 1.55316 2.1461 1 -1.22517 1.55289 -2.14357 1 1.22989 1.55316 -2.1461 1 -3.35807 1.13911 -0.87224 1 -3.3651 1.14647 0.8865 1 -3.3651 -1.14647 -0.8865 1 -3.35807 -1.13911 0.87224 1 1.22989 -1.55316 2.1461 1 -1.22517 -1.55289 2.14357 1 -1.22989 -1.55316 -2.1461 1 1.22517 -1.55289 -2.14357 1 3.35807 1.13911 0.87224 1 3.3651 1.14647 -0.8865 1 3.3651 -1.14647 0.8865 1 3.35807 -1.13911 -0.87224 Framework group D2[X(C16H16)] Deg. of freedom 24 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Aug 10 10:35:14 2000 Received: from sina.com ([202.106.187.156]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA13513 for ; Thu, 10 Aug 2000 10:35:12 -0400 Received: (qmail 68402 invoked from network); 10 Aug 2000 13:28:42 -0000 Received: from unknown (HELO pdc) (202.97.165.134) by 202.106.187.156 with SMTP; 10 Aug 2000 13:28:42 -0000 Message-ID: <001b01c002cf$5cb18ec0$41c809c0@pdc.domain> From: "Li Guo-Hui" To: Subject: Questions about ab-initio program MELD on Linux Date: Thu, 10 Aug 2000 21:31:53 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C00312.66F809C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C00312.66F809C0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear scientists: I am using ab-initio programs named MELD developped by Prof.E.R.Davidson = in Indiana Univ. I want to use it on PC with Linux platform, although i = had compiled and linked without any errors, i cannot make calculations = correctly. Do you make this job? i hope i can get some help from you, thanks in advance!!! =20 Sincerely yours ------=_NextPart_000_0018_01C00312.66F809C0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear scientists:
I am using ab-initio programs named = MELD=20 developped by Prof.E.R.Davidson in Indiana Univ. I want to use it on PC = with=20 Linux platform, although i had compiled and linked without any errors, i = cannot=20 make calculations correctly. Do you make this job?
i hope i can get some help from you, = thanks in=20 advance!!!
 
Sincerely = yours
------=_NextPart_000_0018_01C00312.66F809C0-- From chemistry-request@server.ccl.net Thu Aug 10 11:04:29 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA13709 for ; Thu, 10 Aug 2000 11:04:29 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id KAA32510 for ; Thu, 10 Aug 2000 10:04:16 -0500 (EST) Message-ID: Date: 10 Aug 2000 10:20:22 -0500 From: "Boyd" Subject: new book To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello All, We are pleased to announce the publication of Volume 15 of REVIEWS IN COMPUTATIONAL CHEMISTRY. The tutorials and reviews in this volume cover: o Understanding chemistry with Kohn-Sham density functional theory o Computational strategy for organic photochemistry o Predicting enthalpies of formation for gaseous compounds o Development of computational chemistry in Canada The featured authors are: Evert Jan Baerends, Fernando Bernardi, F. Matthias Bickelhaupt, Russell J. Boyd, Larry A. Curtiss, David J. Frurip, Marco Garavelli, Massimo Olivucci, Paul C. Redfern, and Michael A. Robb. Copies of this and other recent volumes may be obtained for inspection by ordering from Wiley http://www.wiley.com/. The ISBN of Vol. 15 is 0-471-36168-2. More information about the books can be found at http://chem.iupui.edu/rcc/rcc.html. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling (published in affiliation with the ACS Computers in Chemistry Division) Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Thu Aug 10 11:05:51 2000 Received: from sina.com ([202.106.187.156]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA13730 for ; Thu, 10 Aug 2000 11:05:50 -0400 Received: (qmail 75882 invoked from network); 10 Aug 2000 06:44:21 -0000 Received: from unknown (HELO pdc) (202.97.165.132) by 202.106.187.156 with SMTP; 10 Aug 2000 06:44:21 -0000 Message-ID: <001501c00296$e10190a0$41c809c0@pdc.domain> From: "Li Guo-Hui" To: Subject: help about MELD Programs Date: Thu, 10 Aug 2000 14:47:22 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C002D9.E4365A60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C002D9.E4365A60 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear scientists: I am using ab-initio programs named MELD developped by Prof.E.R.Davidson = in Indiana Univ. I want to use it on PC with Linux platform, although i = had compiled and linked without any errors, i cannot make calculations = correctly. Do you make this job? i hope i can get some help from you, thanks in advance!!! Sincerely yours ------=_NextPart_000_0012_01C002D9.E4365A60 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear scientists:
I am using ab-initio programs named = MELD=20 developped by Prof.E.R.Davidson in Indiana Univ. I want to use it on PC = with=20 Linux platform, although i had compiled and linked without any errors, i = cannot=20 make calculations correctly. Do you make this job?
i hope i can get some help from you, = thanks in=20 advance!!!
 
Sincerely = yours
------=_NextPart_000_0012_01C002D9.E4365A60-- From chemistry-request@server.ccl.net Thu Aug 10 11:59:24 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 LAA14312 for ; Thu, 10 Aug 2000 11:59:23 -0400 Received: from mail.chem.tamu.edu ([165.91.176.197]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu; Thu, 10 Aug 2000 11:08:48 -0500 Sender: fan@mail.chem.tamu.edu (Huajun Fan) Message-ID: <3992D06B.80695665@mail.chem.tamu.edu> Date: Thu, 10 Aug 2000 10:55:23 -0500 From: Huajun Fan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.net, fan@mail.chem.tamu.edu Subject: extrapolation in GAMESS(UK) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I was wondering if anyone understanding how the extrapolation techniques in Gamess (UK) is used to the final CI roots. The extrapolated results are present in the output files. However, there are several levels of extrapolation employed (standard extrapolation, Davidson, weighted Davidson 1, and weighted Davidson 2), and I'm trying explore exactly how they extrapolate the root energies. The only GAMESS documentation I can find is on the GAMESS UK homepage, which does not make readily available the cited references. Do you know of any other way to dig up the references? Thanks a lot, Huajun From chemistry-request@server.ccl.net Wed Aug 9 17:37:02 2000 Received: from sun1.phy.cuhk.edu.hk (sun1.phy.cuhk.edu.hk [137.189.40.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA08489 for ; Wed, 9 Aug 2000 17:37:00 -0400 Received: (from kyiwong@localhost) by sun1.phy.cuhk.edu.hk (8.9.3+Sun/8.9.1) id FAA05913; Thu, 10 Aug 2000 05:36:57 +0800 (HKT) Date: Thu, 10 Aug 2000 05:36:57 +0800 (HKT) From: "Wong Kin Yiu (cflo)" Subject: Summary: MO visualizied by contour plots with an ARBRITRARY plane To: chemistry@ccl.net cc: kiniu@cuhk.edu.hk Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, There are couples of reply about it. I would like to thank again to those who help me. So far, from all replies I don't know whether there are commercial softwares could visualize MO with an arbitrary plane, but at least a free software, MOLDEN, could do so (it seems IBM OpenDX could do also, but I haven't used it). However, MOLDEN only allow command interface to control the orientation of the plane, user could not rotate the plane by dragging a mouse. Anyway, only command interface is more than enough for my project. In the following, you could find my original quesiton and replies from others. Thanks a lot again! Best regards, Kiniu Undergraduate student Department of Physics The Chinese University of Hong Kong ----- Original Message ----- From: "Wong Kin Yiu (cflo)" To: Sent: Thursday, August 03, 2000 5:29 PM Subject: CCL:Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > Dear CCLers: > > Recently, I have downloaded two free molecular modeling softwares. One > is gOpenMol [1], another is MOLDEN [2]. Though both could visualise > molecular orbitals with contour plots by a cutplane, it seems I could not > rotate the plane arbitrarily with respect to the molecule. The plane is just > x-y plane, y-z plane or x-z plane of the system. I could not change its > orientation, such as the plane formed by any three atoms. Does anybody have > used either of these softwares to visualise contour plots by an arbitrary > plane? If so, would you mind teaching me how to do so? Thank you. > > Besides, are there other visualising softwares (either free or > comercial) could rotate the cutplane arbitrarily, such as GaussView [3] or > Chem3D [4]? Thanks in advance for any information about it. > > Anyway, I have tried another approach to rotate the plane. Since I > generated molecular orbitals by Gaussian [5] with keyword CUBE, so I have > tried whether I could transform the CUBE data to a new coordinate system > such that the orientations of cutplane is the one I wanted. However, after > reading the user's reference, I still do not understand the 'structure' of > CUBE data files. What I could do so far is only transform the positions of > atoms, the orbital values could not be transformed successfully. Does anyone > could help me to transform the CUBE data to a new coordinate system? Again, > thanks in advance. > > Finally, I will summarise any useful information to share with other > colleagues. > > References: > [1] http://www.csc.fi/~laaksone/gopenmol/gopenmol.html > [2] http://www.caos.kun.nl/~schaft/molden/molden.html > [3] http://www.gaussian.com/gvbroc.htm > [4] http://products.camsoft.com/chem3d/ > [5] http://www.gaussian.com > > Best regards, > Kiniu ----- Original Message ----- From: "Leif Laaksonen" To: "Kiniu ?o?P?O?l" Sent: Thursday, August 03, 2000 6:58 PM Subject: RE: gOpenMol: is it possible to visualise molecular orbitals with contour plots by an ARBITRARY plane?? > > Hi, > > No problem! I'm sorry but currently only the xy, xz and yz planes are > allowed. > > > Sorry to bother you again. I have a question. gOpenMol could visualise > > molecular orbitals with contour plots by a cutplane, it seems I could not > > rotate the plane arbitrarily with respect to the molecule. The plane is just > > x-y plane, y-z plane or x-z plane of the system. I could not change its > > orientation, such as the plane formed by any three atoms. Is it possible to > > visualise contour plots by an arbitrary plane? If so, would you mind > > teaching me how to do so? Thank you. > > > > The CUBE file format is described in the GaussianXX manual. That's > the text included with the CUBE programs. What I suggest is that > you rotate the molecule input coordinates for Gaussian, recalculate > it and display it using the three planes. > > > Anyway, I have tried another approach to rotate the plane. Since I > > generated molecular orbitals by Gaussian with keyword CUBE, so I have tried > > whether I could transform the CUBE data to a new coordinate system such that > > the orientations of cutplane is the one I wanted. However, after reading the > > user's reference, I still do not understand the 'structure' of CUBE data > > files. What I could do so far is only transform the positions of atoms, the > > orbital values could not be transformed successfully. Do you know how to > > transform the CUBE data to a new coordinate system? Again, thanks in > > advance. > > > > Go to the "Plot ==> Cutplane" widget. There are three buttons named > Animate "X - ===> +", "Y - ===> +" and "Z - ===> +". Click the one > you want. Remember to Click the tag at the beginning of the line > to actually show the plane! The animation you talk about is a > MPEG movie. > > > > Moreover, from the picture gallery of gOpenMol, I found it there are > > animations of moving cutplane. But I could not find this function in > > gOpenMol, what I found is only animating of trajectory. So, could gOpenMol > > animate moving plane? Or, you make the animations by other softwares? > > > > Regards, > > -leif laaksonen ----- Original Message ----- From: "Trohalaki Steven Contr AFRL/MLPJ" To: "'Wong Kin Yiu (cflo)'" Sent: Friday, August 04, 2000 3:42 AM Subject: RE: Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > in molden, you have to go into density mode. then click on plot plane and follow the instructions to define the atoms for the plane you want. > > be sure to include the keywords "gfinput IOP(6/7=3)" in your g98.com file. > > steve t ----- Original Message ----- From: "Matthias Mann" To: "Wong Kin Yiu (cflo)" Sent: Friday, August 04, 2000 3:56 PM Subject: Re: CCL: ... ARBITRARY plane?? > On Thu, 03 Aug 2000, you wrote: > > > Besides, are there other visualising softwares (either free or > >comercial) could rotate the cutplane arbitrarily, such as GaussView [3] or > >Chem3D [4]? Thanks in advance for any information about it. > > To move this plan ("slice") arbitrarily with the mouse, we using the > commercial software SPARTAN (http://www.wavefun.com) or > the IBM Open Visualization Data Explorer (now free available). > Example pictures I have under: > http://www.chm.tu-dresden.de/edv/spartan/spartan.html and > http://www.chm.tu-dresden.de/edv/dx/dx.html . > Spartan as an integrated quentum chemical package is more intuitive; > DataExplorer is an general 3D visualizing tool, but you will need longer > break-in period. > > Matthias > > -- > Dr. Matthias Mann > Institut fuer Organische Chemie, TU Dresden > D-01069 Dresden, Mommsenstr. 13 > Tel.: +49 (351) 463-4286 / Fax: -3162 > Email: Matthias.Mann@chemie.tu-dresden.de ----- Original Message ----- From: "BK Szefczyk" To: "Wong Kin Yiu (cflo)" Sent: Friday, August 04, 2000 5:36 PM Subject: Re: CCL:Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > Hi Kin Yiu, > > I am using Molden to visualise the molecular orbitals. I don't know > gOpenMol but I can tell you how to adjust the plane position in > Molden. When you choose the Density Mode, you can find in Miscellaneous > group button called PlotPlane. If you press this button you will > get a window in wich you can specify position of plot plane. > You just type in the text field, for example: > > Plane = (4,5,7) > > to visualise the plane formed by atoms 4, 5 and 7. > You can also rotate the plane with Rot and shift the plane > with Lift command. All the commands are described in the PlotPlane > window, under the text field. Remember that you have to specify > "gfinput" and "IOp(6/7=3)" keywords [1] in your input files for > gaussian. Otherwise you can't see the molecular orbitals in Molden. > > [1] http://www.cmbi.kun.nl/~schaft/molden/gauss.html > > Best regards, Borys. ----- Original Message ----- From: "Aldert Westra Hoekzema" To: "Wong Kin Yiu (cflo)" Sent: Friday, August 04, 2000 6:22 PM Subject: Re: CCL:Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > Hi Kiniu, > > Can't help you with the visualisation, but I can help you with > the CUBE files of gaussian. After the title line(s), in the > next 4 lines the coordinate system is defined as follows: > (no. atoms) Origin > (no. points) Axis 1 unit vector > (no. points) Axis 2 unit vector > (no. points) Axis 3 unit vector > So if you want a view from anaother direction, translate the > origin and/or rotate the axes (and of coarse don't forget the > atomic sites). Below you can find a simple program to expand > the CUBE files that may help you understand the structure, it > worked for g92/g94. > > Aldert > > ------------------------------------------- > A.J.A. Westra Hoekzema > Conformational Analysis (Organic Chemistry) > Leiden Institute of Chemistry, > Gorlaeus Laboraties, Leiden University > The Netherlands > ------------------------------------------- > > *-----fortran 77 > program g92cub > *---------------------------------------------------------------------- > * read formatted files produced with the g92 option cube and > * generate the implied grid that is written to a dump > *---------------------------------------------------------------------- > implicit double precision (a-h,o-z) > parameter (m3=6) > dimension pr(m3) > character ti*79,pr*13 > *---------------------------------------------------------------------- > 5000 format(a) > 5001 format(i5,4f12.6) > c5002 format(6g13.5) > 5002 format(6a13) > * ! manual mentions 6f12.6 ! > 6001 format(/1x,a:i12) > 6002 format(1x,a:3f12.6) > 6003 format(1x,a,2(i12:','),a12) > 6004 format(1x,i4,f7.1,3f12.6) > c6005 format(1x,i6,4g13.5) > 6005 format(1x,i6,3f12.6,a15) > *---------------------------------------------------------------------- > write(6,6002) 'Proces formatted output of g92 cube option' > > write(6,6001) 'Title and type of property on file :' > read(5,5000,end=13,err=13) ti > write(6,6002) ti > * the title may take 5 lines in g92!? > read(5,5000,end=13,err=13) ti > write(6,6002) ti > > read(5,5001,end=13,err=13) na,x0,y0,z0 > write(6,6001) 'No. atoms :',na > write(6,6002) 'Initial point grid :',x0,y0,z0 > read(5,5001,end=13,err=13) n1,x1,y1,z1 > write(6,6003) 'No. points 1st axis :',n1 > write(6,6002) 'Step vector :',x1,y1,z1 > read(5,5001,end=13,err=13) n2,x2,y2,z2 > write(6,6003) 'No. points 2nd axis :',n2 > write(6,6002) 'Step vector :',x2,y2,z2 > read(5,5001,end=13,err=13) n3,x3,y3,z3 > write(6,6003) 'No. points 3rd axis :',n3 > write(6,6002) 'Step vector :',x3,y3,z3 > > write(6,6001) 'Atomic numbers, nuclear charges, and coordinates' > do 111 i=1,na > read(5,5001,end=13,err=13) ni,qn,xi,yi,zi > write(6,6004) ni,qn,xi,yi,zi > 111 continue > > write(6,6001) 'Grid coordinates (generated), Property (read)' > do 222 i1=0,n1-1 > do 222 i2=0,n2-1 > write(6,6003) 'Points :',i1,i2,'*' > i3=0 > 22 continue > ni=min(n3-i3,m3) > read(5,5002,end=13,err=13) (pr(i),i=1,ni) > do 2 i=1,ni > xi=x0+i1*x1+i2*x2+i3*x3 > yi=y0+i1*y1+i2*y2+i3*y3 > zi=z0+i1*z1+i2*z2+i3*z3 > write(6,6005) i3,xi,yi,zi,pr(i) > i3=i3+1 > 2 continue > if(i3-n3) 22,222,222 > 222 continue > > read(5,5002,end=999,err=13) (pr(i),i=1,m3) > 13 continue > write(6,6001) '!! ERROR EXIT OF G92CUB !!' > stop 13 > 999 continue > write(6,6001) 'Normal completion of g92cub' > stop > *---------------------------------------------------------------------- > end ----- Original Message ----- From: "Stefan Konietzny" To: "Wong Kin Yiu (cflo)" Sent: Friday, August 04, 2000 6:55 PM Subject: Re: CCL:Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > Dear Wong Kin Yiu, > > i had the same problem, and sadly not solved it yet. I am also working > with > gopenmol and molden (by the way gopenmol is great). > I did not know that gaussview can display cutplanes and rotate them. I > will have a look at this.. on Monday :-) > > May i beg you to forward the replies you get to me. > > I would be very happy, > > thanks Stefan. > > P.S.: Maybe GNUplot is a good choice, but i have never worked with it. ----- Original Message ----- From: "Trohalaki Steven Contr AFRL/MLPJ" To: "'Wong Kin Yiu (cflo)'" Sent: Friday, August 04, 2000 8:16 PM Subject: RE: Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > sorry, i've never used cube in g98. the way i get contour plots is as follows: > > read g98.log file; go to density mode; define a plane; in the plot-function section, click on HOMO or orbital and then the particular orbital you want; then click on euclidean in the plot mode section. > > contour subcommands allow you to vary the step size and cutoffs of the contour plot. also, to get the orbital window (which displays the orbitals to select) to go away, click on the original orbital button on the molden control window. i have an older version of molden, so perhaps there is currently a close button on the orbital window. my version of molden doesn't have a read cube button, either. > > steve t > > steve t > > -----Original Message----- > From: Wong Kin Yiu (cflo) [mailto:kyiwong@sun1.phy.cuhk.edu.hk] > Sent: Thursday, August 03, 2000 8:26 PM > To: Steven.Trohalaki@wpafb.af.mil > Subject: Re: Molecular Orbitals: is it possible to visualise contour > plots by an ARBITRARY plane?? > > > Hi, > > Thanks for your quick reply first. I now could define the plot plane > with any three atoms. However, I am is a beginner to Molden, after > investigating for hours, I still don't know to how to plot a contour of a > molecular orbital. Take HOMO of a hydrogen molecule as an example. I > generate CUBE data file by the following input: > > #P RHF/6-31G(d) SCF=Tight Cube(orbitals) gfinput IOP(6/7=3) > > Hydrogen molecule > > 0 1 > H1 > H H1 R > Variables: > R=0.72965995 > > h2homo.data > HOMO > > And then I go to density mode of Molden, and click 'read cube'. However, > after reading h2homo.data, I couldn't get any contour plots even I have > tried all buttons. So, I go to read the manual, but I couldn't get any > useful instruction about it. Would you mind teaching me how to visualise the > contour plots by MOLDEN? Thank you very much. > > Best wishes, > Kiniu ----- Original Message ----- From: "Gijs Schaftenaar" To: Sent: Tuesday, August 08, 2000 5:53 PM Subject: Re: Molecular Orbitals: is it possible to visualise contour plots by an ARBITRARY plane?? > > Dear Kiniu, > > > > > Recently, I have downloaded MOLDEN (for X-Windows). Though it could > > visualise molecular orbitals with contour plots by a cutplane, it seems I > > could not rotate the plane arbitrarily with respect to the molecule. The > > plane is just x-y plane, y-z plane or x-z plane of the system. I could not > > change its orientation, such as the plane formed by any three atoms. Is it > > possible to visualise contour plots by an arbitrary plane? If so, would you > > mind teaching me how to do so in details? Thank you. > > > > Sorry for the somewhat late reply, i just returned from a two week holliday. > You can change the orientation of the plot plane, in the 'density mode' > click on the button 'PlotPlane'. Now there are two ways to change the > orientation of the plot plane. The 'center' and 'line' commands define > the center of the plot and the normal of the plane. Alternatively > you can use 'plane' and 'rot', which uses references to atoms to define > a plot. Lastly there is the 'lift' command which lift the plane along > the direction of its normal. > > Best Regards, > > Gijs Schaftenaar > > > -- > +----------------------------+-----------------------------------+ > Gijs Schaftenaar, Drs. | CMBI > Email: schaft@cmbi.kun.nl | University of Nijmegen > URL : http://www.cmbi.kun.nl/staff/schaft.html > Tel. : +31 24 3653369 | Toernooiveld 1 > Fax : +31 24 3652977 | 6525 ED Nijmegen, The Netherlands > +-------- The CMBI is the Dutch National Node in EMBnet ---------+ From chemistry-request@server.ccl.net Thu Aug 10 12:36:13 2000 Received: from mercury.chem.nwu.edu (hutchisn@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14626 for ; Thu, 10 Aug 2000 12:36:13 -0400 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id LAA13680; Thu, 10 Aug 2000 11:37:27 -0500 (CDT) Date: Thu, 10 Aug 2000 11:37:27 -0500 (CDT) From: Geoff Hutchison Reply-To: Geoff Hutchison To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:Agostic interaction In-Reply-To: <39923710.F04644B0@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The term "agostic interactions" is typically used in the context of inorganic and organometallic ligand systems. The term refers to an interaction between a metal center and usually a C-H bond and is typically indicated in diagrams with a dotted line or arrow from the H atom to the metal center. The M-H distance is usually close and the C-H (or other) bond is stretched somewhat. I imagine you can find the term in almost any textbook on inorganic chemistry along with some classic examples. However, a quick search for "agostic interaction" also turned up the following URL: Cheers, -Geoff Hutchison Northwestern Chemistry From chemistry-request@server.ccl.net Thu Aug 10 12:12:27 2000 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14434 for ; Thu, 10 Aug 2000 12:12:27 -0400 Received: from olymp.cup.uni-muenchen.de by mailrelay2.lrz-muenchen.de for CHEMISTRY@ccl.net; Thu, 10 Aug 2000 18:12:12 +0200 Received: by olymp.cup.uni-muenchen.de (AIX 3.2/UCB 5.64/4.03) id AA27624; Thu, 10 Aug 2000 18:12:09 +0200 Date: Thu, 10 Aug 2000 18:12:09 +0200 (MEST) From: Stefan Seidler To: CHEMISTRY@ccl.net Subject: single linkage cluster analysis / MST Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I am looking for a software (freeware/shareware) that is able to > produce the minimum spanning tree (MST) from the similarity matrix > (Sij). Have a look at the programm SPINNE (bin & src): http://www2.chemie.uni-erlangen.de/people/Bruno_Bienfait/Spinne/ Bruno Bienfait, Johann Gasteiger, Journal of Molecular Graphics & Modeling, 15 (1997) pages 203-215 & 254-258 Regards, Stefan Seidler Stefan.Seidler@cup.uni-muenchen.de From chemistry-request@server.ccl.net Thu Aug 10 11:41:28 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14179 for ; Thu, 10 Aug 2000 11:41:28 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id KAA08133 for ; Thu, 10 Aug 2000 10:41:15 -0500 (EST) Message-ID: Date: 10 Aug 2000 10:57:02 -0500 From: "Boyd" Subject: Emerging Technologies at Washington ACS To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 You are invited to attend the Emerging Technology Symposium of the Computers in Chemistry Division (COMP) at the American Chemical Society National Meeting, Washington, DC. Seven speakers will be competing for a cash prize of $1000, which is sponsored by Schroedinger, Inc. Tha seven talks will be judged by a Panel of Experts consisting of: Prof. Curt Breneman (Rensselaer Polytechnic Institute) Dr. George R. Famini (U.S. Army Edgewood RD&E Center) Dr. Charles H. Reynolds (R. W. Johnson Pharmaceutical Research Institute) Dr. Peter S. Shenkin (Schroedinger, Inc.) Dr. David C. Spellmeyer (DuPont Pharmaceuticals Research Laboratories) Dr. Terry R. Stouch (Bristol-Myers Squibb Pharmaceutical Research Institute) The symposium is on Tuesday, August 22 from 1:30 to 5:30 pm, in the Grand Hyatt Hotel, Constitution Ballroom B. See Chemical and Engineering News, July 24, page 82, for more information. Thanks, Don Donald B. Boyd, Ph.D. Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Indiana University-Purdue University at Indianapolis E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Thu Aug 10 16:06:18 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA16054 for ; Thu, 10 Aug 2000 16:06:18 -0400 Received: from localhost (gregori@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id NAA20132; Thu, 10 Aug 2000 13:06:15 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: gregori owned process doing -bs Date: Thu, 10 Aug 2000 13:06:15 -0700 (PDT) From: Gregori Ujaque Reply-To: Gregori Ujaque To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:Agostic interaction In-Reply-To: <39923710.F04644B0@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, The 'agostic' term was initially used for intramolecular covalent interactions between the metal center and the C-H group (in orgamometallic complexes). Nowadays, this term is used to design any interaction between the a sigma bond which belongs to a ligand already bonded to the metal center, and the metal center. You can take a look on the original papers, where the agostic term was first introduced: - Brookhart M, Green MLH J. Organomet. Chem. 1983, 250, 395. - Brookhart M, Green MLH, Wong L, Prog. Inorg. Chem. 1988, 36, 1. Some other interesting readings: - Ujaque G, Cooper AC, Maseras F, Eisenstein O, Caulton GC J. Am. Chem. Soc. 1998, 120, 361. - Koga N, Morokuma K, J. Am. Chem. Soc. J. Am. Chem. Soc. 1988, 110, 108. - Crantree RH, Hamilton DG, Adv. Organomet. Chem. 1988, 28, 299. I hope it helps, Gregori ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gregori Ujaque Department of Chemistry & Biochemistry gregori@chem.ucla.edu University of California, Los Angeles Phone: 1.310.825.0269 405 Hilgard Ave. LA, CA 90095-1569 Fax: 1.310.206.1843 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Thu, 10 Aug 2000, Yubo Fan wrote: > Hi, All CCLers, > > I have met a keyword, agostic interaction, recently. It cannot be found > in various dictionaries. To my knowledge, it means weak intermolecular > interaction. I really don't understand it clearly. The problem is what > types of intermolecular interactions can be regarded as agostic > interaction. Could anybody give me the definition and examples? > > Thanks in advance > > Y. Fan > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Aug 10 13:42:02 2000 Received: from compchem.dfh.dk (compchem.dfh.dk [130.225.225.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA15130 for ; Thu, 10 Aug 2000 13:42:01 -0400 Received: from [130.225.225.151] (dhcp225-151.dfh.dk [130.225.225.151]) by compchem.dfh.dk (SGI-8.9.3/8.9.3) with ESMTP id TAA47565 for ; Thu, 10 Aug 2000 19:39:50 +0200 (MEST) Mime-Version: 1.0 Message-Id: In-Reply-To: <3986FB1F.38006858@eeyore.cm.utexas.edu> References: <39823A46.37BBE83A@studentergaarden.dk> <3985A906.DF449838@eeyore.cm.utexas.edu> <00073114171305.29864@ice> <3986FB1F.38006858@eeyore.cm.utexas.edu> Date: Thu, 10 Aug 2000 19:39:26 +0200 To: chemistry@ccl.net From: Per-Ola Norrby Subject: Re: CCL:TM force fields Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi all, I'd like to take up this thread again. Also, I have a question at the end: Isaac B. Bersuker wrote: >The open (or quasi-open) d shell is the main reason of peculiar >properties of TM systems (TMS) >with regard to modeling: > >(1) 3D delocalization and hence strong mutual influence of the M-L >bonds on each other (e.g., >cis- and trans-effect), >(2) "back donation" and hence local excitation of the ligands >(chemical activation by >coordination), >(3) degeneracy and pseudodegeneracy and hence the strong Jahn-Teller >and pseudo JT effects. > >All this together makes imposible to get reasonable parametrization >of a force field (with >transferable parameters) that could be used in modeling similar to >that of organic and/or >non-TMS, in general. > >I am sorry that these important features of TMS remain unknown to >people engaged in their >investigation. I completely agree that these effects can make modelling of transition metals challenging. However, I disagree strongly with the word "impossible". We are still far from a force field that can do this for all conceivable complexes without parameterization, but wide transferability is not a requirement for force field modelling. Personally, I design force fields for specific problems (you can check my web page for examples, see below). Setting up the force field requires about the same time as doing e few QM/MM calculations, then I have access to a tool that allows rapid conformational searching. In the types of problems I'm working with (asymmetric catalysis), a good sampling of the conformational space is essential. The force fields are still 3-4 orders of magnitude faster than QM/MM calculations in this case, and seemingly almost as accurate. An attractive combination is to use the force field as a search tool, followed by refinement of a few selected structures by QM/MM. For the concerns listed above, we've only done simple things like introduction of specific cross terms to reproduce trans induction, but others have done a lot more. I'm aware of work by Landis, Comba, Deeth, and Carlsson, solving different aspects of these problems. I would like to see more. If you could send me references on how to treat the above problems, I'll summarize to the list. Best regards, Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * Tel. +45-35306506, fax +45-35306040 * Email: peo@dfh.dk (preferred), peo@compchem.dfh.dk * WWW: http://compchem.dfh.dk/PeO/ From chemistry-request@server.ccl.net Thu Aug 10 14:00:09 2000 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA15259 for ; Thu, 10 Aug 2000 14:00:09 -0400 Received: from euch4e.chem.emory.edu ([170.140.49.160]) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) with ESMTP id NAA32726; Thu, 10 Aug 2000 13:59:51 -0400 (EDT) Message-ID: <3992EEF7.D17C8A4@euch4e.chem.emory.edu> Date: Thu, 10 Aug 2000 14:05:47 -0400 From: Maricel Torrent Organization: Emory University X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: yubofan@guomai.sh.cn CC: CHEMISTRY@ccl.net Subject: Re: CCL:Agostic interaction Content-Type: multipart/alternative; boundary="------------16EFE7CC652DBE7729DE591D" --------------16EFE7CC652DBE7729DE591D Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hi Yubo, A couple of review articles with several examples 1. Zaera, F. Chem. Rev. 1995, 95, 2651. 2. Hall, C.; Perutz, R. N. Chem. Rev. 1996, 96, 3125. and an old (but very good) paper dealing with agostic interactions when they were not even termed 'agostic interactions' yet! Goddard, R. J.; Hoffmann, R.; Jemmis, E. D. J. Am. Chem. Soc. 1980, 102, 7667. Hope you find this material interesting and educational, Maricel On Thu, 10 Aug 2000 13:01:04 you wrote: > Hi, All CCLers, > > I have met a keyword, agostic interaction, recently. It cannot be found > in various dictionaries. To my knowledge, it means weak intermolecular > interaction. I really don't understand it clearly. The problem is what > types of intermolecular interactions can be regarded as agostic > interaction. Could anybody give me the definition and examples? > > Thanks in advance > > Y. Fan > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > **************************************************** Dr. Maricel Torrent, Postdoctoral Fellow Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atwood Hall, 1515 Pierce Drive, Atlanta, Georgia 30322, USA Phone: +1-404-727-6537 Fax: +1-404-727-7412 E-mail: maricel@euch4e.chem.emory.edu http://euch4m.chem.emory.edu/~maricel **************************************************** --------------16EFE7CC652DBE7729DE591D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
Hi Yubo,

A couple of review articles with several examples

1.  Zaera, F. Chem. Rev. 1995, 95, 2651.
2.  Hall, C.; Perutz, R. N. Chem. Rev. 1996, 96, 3125.

and an old (but very good) paper dealing with agostic interactions when they were not even termed 'agostic interactions' yet!

Goddard, R. J.; Hoffmann, R.; Jemmis, E. D. J. Am. Chem. Soc. 1980, 102, 7667.

Hope you find this material interesting and educational,

Maricel
 
 

On Thu, 10 Aug 2000 13:01:04 you wrote: 

Hi, All CCLers,

I have met a keyword, agostic interaction, recently. It cannot be found
in various dictionaries. To my knowledge, it means weak intermolecular
interaction. I really don't understand it clearly. The problem is what
types of intermolecular interactions can be regarded as agostic
interaction. Could anybody give me the definition and examples?

Thanks in advance

Y. Fan

--
=============================================================
Yubo Fan                         Email: yubofan@guomai.sh.cn
Organic Synthesis Lab
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641740
Shanghai, 200433
P. R. China
=============================================================

 
 

****************************************************

Dr. Maricel Torrent, Postdoctoral Fellow

Cherry L. Emerson Center for Scientific Computation
and Department of Chemistry, Emory University,
Atwood Hall, 1515 Pierce Drive,
Atlanta, Georgia 30322, USA
Phone:  +1-404-727-6537
Fax:      +1-404-727-7412
E-mail: maricel@euch4e.chem.emory.edu
http://euch4m.chem.emory.edu/~maricel

****************************************************
  --------------16EFE7CC652DBE7729DE591D-- From chemistry-request@server.ccl.net Thu Aug 10 17:27:29 2000 Received: from smtp10.nwnexus.com (smtp10.nwnexus.com [206.63.63.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA17797; Thu, 10 Aug 2000 17:27:28 -0400 Received: from m0w0m5 (blv-pm400-ip8.nwnexus.net [206.63.34.8]) by smtp10.nwnexus.com (8.8.8/8.8.8) with SMTP id OAA03547; Thu, 10 Aug 2000 14:27:24 -0700 (PDT) Message-ID: <00ab01c00313$12337cc0$08223fce@m0w0m5> From: "Gina Miller" To: Cc: Subject: Nanotechnology Industries Newsletter Issue 2 is now available! Date: Thu, 10 Aug 2000 14:36:39 -0700 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 5.00.2919.6600 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2919.6600 Nanotechnology Industries Newsletter Issue 2 is now available! This issue features an inside view on what is happening in Zyvex, the first company founded to develop molecular manufacturing technology. (interview with George Skidmore). Also read the thoughts of Robert Freitas, author of Nanomedicine, on what we might be spending after nanotechnology is developed. Will Ware (author of NanoCAD) provides a perspective on a simple approach to modeling some nanoscale devices. Charles Ostman (senior fellow, Institute for Global Futures) explores the convergence of breakthroughs in biotechnology as a progenitor to transformation of the world by nanotechnology. I have included a transcript of an interview I gave to journalist Max Block of Columbia University. Following the calendar of conferences and events is a collection of news shorts on significant nanotechnology milestones and issues since the last publication. Website: http://nanonews.homestead.com/issue2.html Thank you! Gina "Nanogirl" Miller Nanotechnology Industries http://www.nanoindustries.com Personal: http://www.nanogirl.com nanogirl@halcyon.com "Nanotechnology: Solutions for the future."