From mattacf@mcmail.CIS.McMaster.CA Sun Jul 12 01:44:45 1998 Received: from mcmail.CIS.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.20.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA20715 Sun, 12 Jul 1998 01:44:45 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.8/8.8.8) with SMTP id BAA18403; Sun, 12 Jul 1998 01:44:32 -0400 (EDT) Date: Sun, 12 Jul 1998 01:44:32 -0400 (EDT) From: "C.F. Matta" To: Romano Kroemer cc: chemistry@www.ccl.net Subject: Re: CCL:partial charges for large molecules In-Reply-To: <199807091119.LAA23721@bellatrix.pcl.ox.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Kroemer, The only theoretically sound partitioning of ANY molecular property (including atomic populations) into a sum of atomic contributions is the Bader (or virial) partitioning [2]. Bader and his coworkers generalized quantum mechanics to "subsystem" quantum mechanics in which parts of a system are treated on the same footing as the total system. However, the total system cannot be arbitrarily partitioned. It can be rigorously proved that the total molecular system can ONLY be partitioned at the so called zero-flux surfaces which satisfy the quantum boundary condition [2]: grad rho (r) . n(r) = 0 for all r belonging to the surface. These surfaces always enclose regions of the molecular space with only one nucleus and fall between neighboring atom, which justify their identification as "inter-atomic surfaces". An atomic population is computed by integrating the electron density bounded by all the interatomic surfaces of the atom and an exterior envelope in the electron density. The resulting population can then be easily translated to an atomic charge.[2] The atomic charges computed in this way retain a remarkable stability and transferability among different molecules. These charges are independent of basis functions centered on neighboring atoms and retain the characteristic signature of the "atoms of wet chemistry" even when bonded to dissimilar neighboring atoms. With this transferability in mind, we have just completed a study (to be submitted to publication soon) of the atomic properties of the genetically-coded amino acids, which will become our electron density building blocks (exactly what nature does!).[1] All the atomic properties (including the populations) retain a remarkable stability on going from amino acids to dipeptides to tripeptides etc. which justifies the approach of building a polypeptide density by sticking amino acid fragments together at their common inter-atomic surface.[1] I suggest you have a look at: [1] C. Chang and R. F. W. Bader "Theoretical Construction of a Polypeptide", J. Phys. Chem. Vol. 96, No.4 (1992), p.1654. [2] R. F. W. Bader "Atoms in Molecules: A Quantum Theory", Clarendon Press, (Oxford, 1990). Or visit the web site (where you can also download all the software related to the theory): http://www.chemistry.mcmaster.ca/faculty/bader/aim/ Sincerely, Cherif Matta Graduate student Department of Chemistry McMaster University Hamilton, Ontario Canada L8S 4M1 On Thu, 9 Jul 1998, Romano Kroemer wrote: > > Dear all, > > could somebody point me to references for the following problem/method: > > I have a large molecule and want to calculate partial charges with a fairly > sophisticated method. As the molecule is too large, I divide it into > moderately sized _overlapping_ pieces, calculate the partial charges for > each of these chunks, and derive then the charges for the whole molecule. > The "overlapping pieces" procedure is necessary in order to avoid > "boundary problems". > > Comments on the advantages and drawbacks of such an approach (such as the > perturbations of the charges on one end of the molecule by the charges > on the other end when the molecule is not linear) are of course > welcome. > > Thank you very much in advance for your input. I will post a summary to the > list. > > Yours sincerely, > Romano Kroemer > > -- > =============================================================================== > Dr. Romano T. Kroemer > Phys. & Theoret. Chem. Lab. > University of Oxford > South Parks Rd. | Tel: ++44-1865-275475 > Oxford OX1 3QZ | Fax: ++44-1865-275410 > England, U.K. | Email: romano@bellatrix.pcl.ox.ac.uk > =============================================================================== > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From michener@echuca.net.au Sun Jul 12 07:30:40 1998 Received: from users.mcmedia.com.au (users.mcmedia.com.au [203.7.198.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA23876 Sun, 12 Jul 1998 07:30:22 -0400 (EDT) Received: (qmail 20543 invoked from network); 12 Jul 1998 11:47:17 -0000 Received: from echuca-dialup16.echuca.net.au (HELO 203.17.151.116) (203.17.151.116) by users.mcmedia.com.au with SMTP; 12 Jul 1998 11:47:17 -0000 Message-ID: <35A88F9D.302F@echuca.net.au> Date: Sun, 12 Jul 1998 21:27:47 +1100 From: Michener Reply-To: sus25@hotmail.com X-Mailer: Mozilla 3.02Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: chemchat@uafsysb.uark.edu, chemclub@umslvma.bitnet, chemcom@listserv.acsu.buffalo.edu, chemconf@umdd.umd.edu, chemcord@umdd.umd.edu, CHEME-L@PSUVM.PSU.EDU, CHEMED-L@UWF.CC.UWF.EDU, CHEMIND-L@DERWENT.CO.UK, chemistry@www.ccl.net, CHMINF-L@IUBVM@BITNET, hilliard@deakin.edu.au, HYDROGEN@URIACC.URI.EDU, iearnoz@peg.apc.org, iecc@stolaf.edu, jceonline@chem.wisc.edu, jwalter@ams.greenpeace.org, kim@chem.umu.se, michener@echuca.net.au, NAPRONET@bilkent.edu.tr, orgchem@extreme.chem.rpi.edu, scied@bootes.astro.washington.edu, sus25@hotmail.com, tissue@vt.edu, toyota@spike.com.au, twsnews@peg.apc.org, vic_teachers@srl.rmit.edu.au, wmcic-l@qucdn.queensu.ca, ysn@crow-t-robot.stanford.edu Subject: Future Vehicle Fuels Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am interested in obtaining information concerning the future of vehicle fuels, namely petrol, ethanol/methanol, hydrogen and electricity. For each fuel, I am researching: 1. What are the chemical reactions involved when used in the engine? 2. How much energy is contained per unit mass/volume? 3. How efficient is energy conversion when using the fuel? 4. Where does the fuel come from? 5. How safe is production and use of the fuel? 6. What waste materials does use of the fuel produce? 7. What are other environmental considerations? 8. What are the economic considerations? (eg. cost of production, cost per unit energy, impact on current fuel organisations) If you have any information that would help with my research, please email me A.S.A.P. with details (eg. URL, reference, or means by which I can recieve the information, eg. fax). This information is for a Year 12 Chemistry Project and will be used and acknowledged appropriately. Any help would be greatly appreciated :) Regards, Sarah Michener P.S. This message was mailed to several mailing lists. I appologise to those who receive it more than once. ---------------------------- Sarah Michener Email: sus25@hotmail.com URL: http://users.mcmedia.com.au/~michener/sarah.html Year 12 (Senior), Rochester Secondary College Edward St., Rochester, Victoria, Australia, 3561 Phone (RSC) 03 5484 1844, Fax (RSC) 03 5484 2348 From pueyo@pinon.ccu.uniovi.es Sun Jul 12 11:17:09 1998 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA26065; Sun, 12 Jul 1998 11:17:08 -0400 (EDT) Received: from pinon.ccu.uniovi.es by aleph.net.uniovi.es (PMDF V5.1-10 #4541) with ESMTP id <01IZBK95Q3IM00RXGX@aleph.net.uniovi.es>; Sun, 12 Jul 1998 17:14:46 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.8.8/8.7.3) id RAA12851; Sun, 12 Jul 1998 17:17:08 +0200 (METDST) Date: Sun, 12 Jul 1998 17:17:08 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:basis functions in LaTeX To: CHEMISTRY@www.ccl.net, chemistry-request@www.ccl.net Message-id: <199807121517.RAA12851@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=X-roman8 Content-transfer-encoding: 7bit >Krzysztof Radacki wrote: > .... >I'm trying to formate table with some basis fuctions in first column. >When I type: >{\centering \begin{tabular}{|c|c|c|c|c|c|c|} >\hline >&$^1$H&$^{11}$B&$^{13}$C&$^{19}$F&$^{29}$Si &$^{31}$P\\ >\hline >\hline >RHF/6$-$31G(d)&32.9017&106.750&201.7315&&450.1988&\\ > .... >\end{tabular}\par} > .... >What should I write to obtain output with '/' in the same position in >cell? You can try to split the first column into three parts: \begin{tabular}{|r@{0pt}c@{0pt}l|c ....} .... RHF & / & 6--31G(d) & .... Note the use of @{0pt} to avoid the standard separation between columns inserted by TeX. Best regards, Victor Lua~na -- HomePage %%http://www3.uniovi.es/~quimica.fisica/qcg/vlc/luana.html%% +----------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember +----------------------------------------------+ | / where Oviedo ! fax: (34)-8-5103125 ! |____ ___/ is ;-) +----------------------------------------------+ \/ From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Sun Jul 12 14:06:07 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA27930 Sun, 12 Jul 1998 14:06:06 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id DAA27115; Mon, 13 Jul 1998 03:07:26 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9807122007.ZM27113@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Sun, 12 Jul 1998 20:07:16 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: linear molecule optimization Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues Locating a transition state, I have to optimize a molecule in a linear conformation. I tried to use redundant coordinate as well as cartesian coordinnates to optimize the system. However, always the job (G94) stops because of the very large RMS in the change in the internal coordinates during the geometry optimization. I decided to first look at another (standard) linear molecule, namely allene molecule (H2C=C=CH2). G94 automatically assigns the following bond angles by calling them "L" and proceeds successfully to optimize the system. ! A4 L(1,2,5) 180. estimate D2E/DX2 ! ! A5 L(1,2,5) 180. estimate D2E/DX2 ! First of all, I would like to know whether it is possible to define such coordinates in the input file. And ... My main problem is to optimize the linear system. Any comment and/or suggestion with regard to the linear system optimization is highly appreciated. Thanx in advance -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * *********************************************************************