From chemistry-request@server.ccl.net Tue Jul 25 19:33:12 2000 Received: from hotmail.com (f39.law9.hotmail.com [64.4.9.39]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA12300 for ; Tue, 25 Jul 2000 19:33:11 -0400 Received: (qmail 71510 invoked by uid 0); 25 Jul 2000 23:31:09 -0000 Message-ID: <20000725233109.71509.qmail@hotmail.com> Received: from 138.80.128.19 by www.hotmail.com with HTTP; Tue, 25 Jul 2000 16:31:09 PDT X-Originating-IP: [138.80.128.19] From: "Henry Pang" To: hakalad@ameritech.net, CHEMISTRY@ccl.net Cc: mab@fcindy13.ncifcrf.gov, b_duke@lacebark.ntu.edu.au Subject: Towards a Philosophy of Computational Chemistry Date: Tue, 25 Jul 2000 23:31:09 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Hi David, greetings to Dr Buyong Ma You said You discern correctly. Buyong Ma (1995), is refreshing because addressing the wider nature of CC within the environment of science, but different to my concern. My point of departure is me. The most vital concern in my life is me. I want to survive so I can address other things. To survive in real terms, I want to develop a holistic integrated view of of reality. The basic unit is the system of the infinity of universes beyond our home Universe. In hierarchal form, all the fields we know as disciplines, are not isolated things but are linked otherwise they would disintegrate. I mean the Milky Way, solar system, planet earth, biosphere, living things, homo sapiens and so on. The key instruments which explore reality at this time, include cosmology, quantum theory, relativity and higher dimensions theory. Astronomy appears to merely catalogue the celestial bodies. I have yet to see an astronomer discuss why these bodies exist in the heavens? When I was introduced to CC, I was delighted because I naively thought the precision, the 3D and the associated computational power would produce essential data for my Universe model? Alas, like the astronomers, CC seems only concerned with the means and not the ends. CC is intensely focussed on computer programs and delights in addressing techniques. There are a few bold warriors apart from Buyong Ma (1995). Stephen Mason(1991), Chemical Evolution - Origins of the Elements, Molecules and Living Systems, Clarendon Press Oxford, but closer to my vision - Pierre Teilhard de Chardin (1955), The Phenomenon of Man, Fontana Books. Review by Arnold Toynee Observer - I believe computational chemistry is more than mere mensuration and rotating images. I am sure molecules were created as the essential building blocks of the infinite universe system. I want to set out the physical, mental, social and spiritual nature of living things and our Universe. I am intensely interested in Origins? I am sure the findings of CC form an important part of this unfolding story. Dr Henry Pang Postgraduate Student, Computational Chemistry Faculty of Science, Information Technology and Education Northern Territory University PO Box U273 NT University 0815 Australia Mobile 0419 682121 Fax 61 8 8946 6847 hpangaus@hotmail.com >From: "David Hakala" >To: "Henry Pang" >Subject: Re: CCL:Seeing molecular orbitals? >Date: Tue, 25 Jul 2000 06:26:34 -0500 > >This is my attempt to try again....all I have to do is click on the link >and >it goes directly to site,,,,I am using IE5 for a browser. > > >http://alphanla.chem.uga.edu/~buyong/philo/philo.html >----- Original Message ----- >From: "Henry Pang" >To: >Sent: Sunday, July 23, 2000 11:39 PM >Subject: Re: CCL:Seeing molecular orbitals? > > > > Hi David > > > > I would love to see it. Unfortunately I cannot raise after several ways. > > Could you sent it again? Thanks > > > > Henry > > > > > > >From: "David Hakala" > > >To: "Henry Pang" , > > >CC: , , > > >, , > > > > > >Subject: Re: CCL:Seeing molecular orbitals? > > >Date: Sun, 23 Jul 2000 23:35:27 -0500 > > > > > >Henry are you familiar with the following link: > > >http://alphanla.chem.uga.edu/~buyong/philo/philo.html > > >This is a summary of a thesis on the Philosophy of Computational >Quantum > > >Chemistry by Dr. Buyong Ma done at the University of Georgia, which may >be > > >of some interest to you, although from your comments I sense that you >are > > >taking a significantly different approach than Ma. > > > Dave Hakala > > >----- Original Message ----- > > >From: "Henry Pang" > > >To: > > >Cc: ; ; > > >; ; > > > > > >Sent: Thursday, July 20, 2000 7:05 PM > > >Subject: CCL:Seeing molecular orbitals? > > > > > > > > > > Hi Jens (Denmark) > > > > > > > > You said > > > >observable quantities; MOs have no physical existence> > > > > > > > > I am new to computational chemistry. My background is medicine and >human > > > > ecology in Australia. Your post is the first indicator I have seen >over > > >a > > > > wide range of CCL and books which signals caution. I am overwhelmed >by > > >the > > > > volume and intensity of work on the methodology and mensuration of > > > > molecules, as if that were the end in itself. No where do I see any > > >concern > > > > for a Philosophy of Computational Chemistry, which addresses just >what > > >is > > > > computational chemistry and what its purpose might be in our >Universe. >I > > > > cannot believe the objective is merely to measure everything and >simply > > > > document these data? > > > > > > > > Even at my early stage, I am seriously pondering writing material > > >jointly > > > > with my academic supervisor who is a computational chemist, which >sets > > >out > > > > the link (as I see it) between cosmology, quantum theory, relativity >and > > > > higher dimensions theory on the one hand and computational chemistry >on > > >the > > > > other. I think molecules are the beautiful building blocks of our > > >Universe > > > > and created for a purpose. I decline the view molecules are just >chance > > > > particles. I suspect from my reading of CCL, my intention may be >seen >as > > > > revolutionary if not outrageous and could well cause an uproar? > > > > > > > > Best wishes from Australia > > > > > > > > Dr Henry Pang > > > > Postgraduate Student, Computational Chemistry > > > > Faculty of Science, Information Technology and Education > > > > Northern Territory University > > > > PO Box U273 NT University 0815 Australia > > > > Mobile 61 419 682121 Fax 61 8 8946 6847 hpangaus@hotmail.com > > > > > > > > >---------------------------------------------------------------------- > > > > > > > > >From: "Jens Spanget-Larsen" > > > > >To: CHEMISTRY@ccl.net > > > > >Subject: CCL:Seeing molecular orbitals? > > > > >Date: Thu, 20 Jul 2000 10:43:01 +0100 > > > > > > > > > >Dear CCL: > > > > > > > > > >In a recent, most interesting publication ('Seeing molecular >orbitals', > > > > >Chem.Phys.Letters 321, 78-82 [2000]) scanning tunneling microscopy >is > > >used > > > > >to > > > > >observe the shapes of single molecular orbitals of the fullerene >C60: > > > > > > > > > > "..the scanning tunneling microscope (STM) is probing a single > > >molecular > > > > > orbital (MO)." > > > > > > > > > >However, this reminds me of previous statements in the literature >some > > >time > > > > >ago, associated with the advent of molecular photoelectron > > >spectroscopy, > > > > >f.i. > > > > > > > > > > "Chemists can see the orbital structure of even fairly large > > >molecules > > > > >and no > > > > > longer have to rely on the predictions of theoreticians" > > > > > > > > > > "Photoelectron spectroscopy has demonstrated experimentally to > > >chemists, > > > > > physicists and other sceptics that molecular orbitals really do > > >exist" > > > > > > > > > >I wonder whether this is acceptable terminology, considering the >fact > > > > >that molecular orbitals are model constructs; they are not physical > > > > >observables. By using approximations, such as Koopmans' >approximation, > > >many > > > > >experimental observations can be conveniently interpreted in terms >of > > > > >theoretical MO data. But strictly speaking, this does not turn MOs >into > > > > >observable quantities; MOs have no physical existence. > > > > > > > > > >Any comments? > > > > > > > > > >Yours, Jens >--< > > > > > > > > > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > > > >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/ > > > > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Wed Jul 26 07:19:11 2000 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA15864 for ; Wed, 26 Jul 2000 07:19:10 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Wed, 26 Jul 2000 12:18:58 +0100 Sender: mb@ucl.ac.uk Message-ID: <397ED6A6.82071BB9@ucl.ac.uk> Date: Wed, 26 Jul 2000 13:16:38 +0100 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Force field for amino acids/crystal morphology Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, * i'm calculating some crystal morphologies of small organic molecules. As force field i used the one by Lifson and Hager. Since this set of parameters is rather old I wonder, whether there'd be another, more recently developed (and possibly more accurate) and preferably non-commercial set of LJ-parameters and partial charges ... * is anyone aware of recent developements of new methods/algorithms for crystal morphology prediction ?? thanx for any hints! cheers mic ========================================================== Writing software is more fun than working. ---------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London 20 Gordon Street, London WC1H 0AJ, U.K. mailto:m.brunsteiner@ucl.ac.uk http://www.unet.univie.ac.at/~a8805193 ---------------------------------------- From chemistry-request@server.ccl.net Wed Jul 26 08:42:02 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 IAA16158 for ; Wed, 26 Jul 2000 08:42:01 -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 OAA00307 for ; Wed, 26 Jul 2000 14:41:48 +0200 (METDST) Message-ID: <397EE34E.B472C3C6@chemistry.upatras.gr> Date: Wed, 26 Jul 2000 16:10:38 +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: strange (?) behaviour of G98 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Hi outhere, I am trying to "run" a job with the command line %nproc=4 %chk=dv_0030 %nosave #p rhf/gen scfcon=10 polar scf=direct then after ~10s the job stops and when the following appears in the end of the file Two-electron integral symmetry is turned on. 440 basis functions 632 primitive gaussians 38 alpha electrons 38 beta electrons nuclear repulsion energy 597.5471427395 Hartrees. Leave Link 301 at Wed Jul 26 12:23:13 2000, MaxMem= 16777216 cpu: 0.6 (Enter /opt/rzsoft/g98/l302.exe) One-electron integrals computed using PRISM. One-electron integral symmetry used in STVInt MDFork failed with status -1. MDFork failed. Error termination via Lnk1e in /opt/rzsoft/g98/l302.exe. Job cpu time: 0 days 0 hours 0 minutes 10.7 seconds. File lengths (MBytes): RWF= 16 Int= 0 D2E= 0 Chk= 4 Scr= 1 any suggestions? Cheers DX From chemistry-request@server.ccl.net Wed Jul 26 11:36:46 2000 Received: from arbornet.org (m-net.arbornet.org [209.142.209.161]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16946 for ; Wed, 26 Jul 2000 11:36:46 -0400 Received: from localhost (mrdonkey@localhost) by arbornet.org (8.10.2/8.10.2) with ESMTP id e6QFB1q90971 for ; Wed, 26 Jul 2000 11:11:01 -0400 (EDT) Date: Wed, 26 Jul 2000 11:11:01 -0400 (EDT) From: Mr Donkey To: chemistry@ccl.net Subject: DelPhi on linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCLers, Have any of you succesfully compiled DelPhi for linux? If so, could you please send me the makefile you used. (I am using GNU compilers on a dual Pentium II running RedHat 6.2) The web page (http://trantor.bioc.columbia.edu/delphi/) states that it does run on Linux. But the package does not include a makefile for Linux. I tried changing the flags for the UNIX-specific compilers into ones that the GNU compilers would understand, but I haven't gotten it to work. The only flags in the RS/6000 makefile is "-O -qintlog". Is there a comparable one for GNU compilers? Thanks for any help. - Don Key mrdonkey@m-net.arbornet.org From chemistry-request@server.ccl.net Wed Jul 26 09:46:07 2000 Received: from pdchfi.chfi.unipd.it (root@pdchfi.chfi.unipd.it [147.162.53.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA16492 for ; Wed, 26 Jul 2000 09:46:06 -0400 Received: from chfi.unipd.it (gtw2.chfi.unipd.it [147.162.53.202]) by pdchfi.chfi.unipd.it (8.8.8/8.8.8) with ESMTP id PAA11481 for ; Wed, 26 Jul 2000 15:46:43 +0200 Posted-Date: Wed, 26 Jul 2000 15:46:43 +0200 Message-ID: <397EEA98.A9704CC4@chfi.unipd.it> Date: Wed, 26 Jul 2000 15:41:44 +0200 From: Gabriella Severin X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: answer to scipcm problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, last week I posted a question on a problem I had in using SCIPCM with Gaussian98. > #P B3LYP/6-31G(d) SCRF=scipcm Pop=Reg Opt Nosymm Test > > WARNING! Serious error in surface integrals. > It is probable that some of the solute is outside the cavity and/or > parts of the cavity surface cannot be reached from the origin. > Try more integration points or a different set of integration origins. > > Surface Problems in SciFoc > Error termination via Lnk1e in /usr/local/g98/l502.exe. > Since some of you wished to get the the latest news, here they are. I got the answer from Gaussian (I thank D.J. Fox), and it was as predicted by Patrik Johansson, Han Zuilhof and Richard Wang (many thanks to all of you!): SCIPCM doesn't work well in gaussian98. SCRF calculations can be done either with gaussian94 (and scipcm) or with the other options dpcm, cpcm and iefpcm. Answer from Gaussian: We are aware of some problem with the SCIPCM option in G98 related to our attempt to fix problems with anionic systems which has unfortunately destabilized all calculations with SCIPCM. We are evaluating where to go next but currently we are happy to report that the implementation of SCRF=PCM in G98 is an excellent alternative to the SCIPCM model. This version is a contribution from Tomasi and co-workers and include gradients so that geometry optimizations and frequencies can be computed as with SCIPCM. Also the input has been streamlines so that a number of common solvents can be named on the route, SCRF=(PCM,Solvent=water), and this includes parameters for estimating cavitation and dispersion contributions to the solvation energy. We apologies for the inconvenience if you have a previous study started with SCIPCM but G94 can still be used. If you are starting a new study then you should find PCM, including the CPCM and IEFPCM options, are excellent ways to go. Best wishes Gabriella Maria Gabriella Severin Dipartimento di Chimica Fisica University of Padua 35131 Padova- Italy From chemistry-request@server.ccl.net Wed Jul 26 02:08:14 2000 Received: from iisc.ernet.in (iisc.ernet.in [144.16.64.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA13711 for ; Wed, 26 Jul 2000 02:08:10 -0400 Received: from helix.orgchem.iisc.ernet.in (IDENT:srb@orgchem.iisc.ernet.in [144.16.77.3]) by iisc.ernet.in (8.9.2/8.9.0) with ESMTP id LAA02460 for ; Wed, 26 Jul 2000 11:39:37 +0530 (IST) Received: from localhost (srb@localhost) by helix.orgchem.iisc.ernet.in (8.8.7/8.8.7) with ESMTP id LAA06136 for ; Wed, 26 Jul 2000 11:40:42 +0530 Date: Wed, 26 Jul 2000 11:40:42 +0530 (IST) From: "R.B.Sunoj" To: chemistry@ccl.net Subject: Molecular Orbitals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL friends, Is there any website or books/papers containing pictorial representation of Molecular orbitals of a wide range of compounds (particulary organic compounds)?. I would be happy if there is any such collection similar to 'The Organic Chemists Book of Orbitals' by Jorgensen and Salem (AP, 1973). (Where they have plotted the frontier MOs of a variety of molecules). with regards, Sunoj ========================= R.B.Sunoj Dept of Organic Chemistry IISc Bangalore, India 560 012 ========================= From chemistry-request@server.ccl.net Wed Jul 26 16:58:15 2000 Received: from chem.ufl.edu (server.chem.ufl.edu [128.227.16.141]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA18242 for ; Wed, 26 Jul 2000 16:58:14 -0400 Received: from chem.ufl.edu (biochem45.chem.ufl.edu [128.227.16.32]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id QAA22404 for ; Wed, 26 Jul 2000 16:58:14 -0400 (EDT) Message-ID: <397F537A.6C76C8CD@chem.ufl.edu> Date: Wed, 26 Jul 2000 17:09:14 -0400 From: "Xiang(Simon) Wang" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Dielectric in Charmm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, When setting up the dielectric constant in charmm, what's the difference between [ EPS real ] and [ E14Factor real ]? Thank you very much. Simon Wang