From chemistry-request@server.ccl.net Wed Jun 13 08:46:43 2001 Received: from mr1.wpafb.af.mil ([198.97.67.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DCkg508365 for ; Wed, 13 Jun 2001 08:46:42 -0400 Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.26.202]) by mr1.wpafb.af.mil (8.11.3/8.11.3) with ESMTP id f5DCkfl32627 for ; Wed, 13 Jun 2001 08:46:42 -0400 (EDT) Received: by fszhtv02.wpafb.af.mil with Internet Mail Service (5.5.2653.19) id ; Wed, 13 Jun 2001 08:42:42 -0400 Message-ID: <53A10F824E50D511820800508BDF3F2214CADD@fszhtv12.wpafb.af.mil> From: Dudis Douglas S Civ AFRL/MLBP To: "'chemistry@ccl.net'" Subject: quotation Date: Wed, 13 Jun 2001 08:42:37 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Simple request. I am looking for the exact quotation (preferably with a reference) for the quote that goes along the lines: '... the laws governing most of physics, and all of chemistry, are now known ...' Help much appreciated. Doug Dudis ------------------------------- Douglas S. Dudis, Ph.D. Research Leader - Polymers Air Force Research Laboratory Materials and Manufacturing Directorate 2941 P St., Bldg. 654, Ste. 347 Wright-Patterson AFB, OH 45433-7750 Phone: (937) 255-9148 FAX: (937) 255-9157 e-mail:Douglas.Dudis@afrl.af.mil From chemistry-request@server.ccl.net Wed Jun 13 09:14:17 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DDEH508871 for ; Wed, 13 Jun 2001 09:14:17 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id JAA14339; Wed, 13 Jun 2001 09:14:16 -0400 (EDT) Date: Wed, 13 Jun 2001 09:14:14 -0400 (EDT) From: Jan Labanowski To: Dudis Douglas S Civ AFRL/MLBP cc: Jan Labanowski , "'chemistry@ccl.net'" Subject: Re: quotation In-Reply-To: <53A10F824E50D511820800508BDF3F2214CADD@fszhtv12.wpafb.af.mil> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try CCL archive search: http://server.ccl.net/htdig/ and try dirac citation or http://server.ccl.net/cgi-bin/ccl/message.cgi?2001+03+15+013 Jan (I am abroad, please do not send me e-mail unless you have to). On Wed, 13 Jun 2001, Dudis Douglas S Civ AFRL/MLBP wrote: > Simple request. I am looking for the exact quotation (preferably with a reference) for > the quote that goes along the lines: > > '... the laws governing most of physics, and all of chemistry, are now known ...' > > Help much appreciated. > Doug Dudis > > ------------------------------- > Douglas S. Dudis, Ph.D. > Research Leader - Polymers > Air Force Research Laboratory > Materials and Manufacturing Directorate > 2941 P St., Bldg. 654, Ste. 347 > Wright-Patterson AFB, OH 45433-7750 > Phone: (937) 255-9148 > FAX: (937) 255-9157 > e-mail:Douglas.Dudis@afrl.af.mil > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Wed Jun 13 06:53:16 2001 Received: from mailhub.usp.br ([143.107.253.61]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5DArG506334 for ; Wed, 13 Jun 2001 06:53:16 -0400 Received: (qmail 21440 invoked from network); 13 Jun 2001 10:53:14 -0000 Received: from unknown (HELO sergio) (143.107.194.151) by 143.107.253.60 with SMTP; 13 Jun 2001 10:53:14 -0000 Message-ID: <000301c0f3f6$91514260$97c26b8f@ligquim.ffclrp.usp.br> Reply-To: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= From: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= To: Subject: compilation error on G98 Date: Tue, 12 Jun 2001 17:52:05 -0300 Organization: =?iso-8859-1?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear G98 gurus, I am trying to install G98 Rev A.7 in an athlon 800MHz with RedHat 7.1 and pgf77, but I had a compilation error in a C routine: ---------------------------------------------------------------------------- -------------------------------------------------- uname -a Linux athlon 2.4.2-2 #1 Sun Apr 8 20:41:30 EDT 2001 i686 unknown make -f ../bsd/g98.make JUNK1=JUNK mdutil.o cc -g -I/usr/g98 -I/usr/g98s -DGAUSS_PAR -DGAUSS_THPAR -DDEFMAXSHL=20000 -D DEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE_LOO PS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAXCHR= 1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXLECP= 10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200 -DD EFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_CORE_ - DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -DDEFM XBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 -mali gn-double -m486 -fexpensive-optimizations -O3 -ffast-math -funroll-loops -c bsd/mdutil.c bsd/mdutil.c: In function `etime_': bsd/mdutil.c:2319: `CLK_TCK' undeclared (first use in this function) bsd/mdutil.c:2319: (Each undeclared identifier is reported only once bsd/mdutil.c:2319: for each function it appears in.) bsd/mdutil.c: In function `fdate_': bsd/mdutil.c:2332: warning: assignment makes pointer from integer without a cast make: *** [mdutil.o] Error 1 ---------------------------------------------------------------------------- -------------------------------------------------- Thank you for any advice, Best regards, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratório de Modelagem Molecular Departamento de Química Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Av Bandeirantes, 3900 Ribeirão Preto, SP Brasil phone: +55-16-602-37-65 fax: +55-16-633-81-51 e-mail: segalemb@usp.br ============================================================== From chemistry-request@server.ccl.net Wed Jun 13 08:06:24 2001 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DC6N507506 for ; Wed, 13 Jun 2001 08:06:23 -0400 Received: from b159504364 (PPP301.fukuoka-ip.dti.ne.jp [211.132.93.51]) by smtp1.dti.ne.jp (8.9.3/3.7W) with SMTP id VAA08462 for ; Wed, 13 Jun 2001 21:06:21 +0900 (JST) Message-ID: <004101c0f400$74661b80$335d84d3@b159504364> From: "TELKUNI" To: Subject: Summary - How to find the molecular multiplicity? Date: Wed, 13 Jun 2001 21:00:34 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit 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 Hello! CCLers Earlier this week, I posted a question about molecular multiplicity. Original question: > I am using Gaussian98W and have basic question of quantum chemistry. > > Starting with the G98 calculation, we must set the Charge and Multiplicity, > but I don't know the practical method to find the each molecular multiplicity. > > I have read books and chemical articles which are describing the multiplicity > and its numerical expression. But I can't find the other methods except the > numerical expression. > > Does any chemical researcher always calculate the molecular multiplicity with > such numerical expression in his brain? Or is there any other method? > > I will summarize the answers for novice quantum chemistry researcher, just like me! I have received very useful replies and summarize them. Reading these replies, I aware that there are something easy rules to find the molecular multiplicity. If you like to get in touch with replyers, please let me know. I hope this summary will be helpful to some others. Thanks a lot! **** 1) from Alan Shusterman **** In most cases the multiplicity can be set according to the following rules: All electrons in pairs --> singlet (multiplicity = 1) One unpaired electron (free radical) --> doublet (multiplicity = 2) Two unpaired electrons (diradical) --> and unpaired electrons have opposite spin --> singlet (multiplicity = 1) or and unpaired electrons have same spin --> triplet (multiplicity = 3) Multiplicity is the number of degenerate spin eigenfunctions that can be attached to the spatial part of the wavefunction. **** 2) from David Shobe **** First of all, for closed shell molecules--including most of the isolable organic molecules--the multiplicity is 1, no further questions needed. Essentially "closed shell" means that the molecule follows the octet rule. Molecular fragments such as radicals and carbenes may have multiplicity >1. Organic radicals can be assumed to have multiplicity 2 (with very rare exceptions). Carbenes can be either 1 or 3 (singlet or triplet), as can biradicals such as tetramethylene and "trimethylenemethane" (2-methylene-1,3-propanediyl). If the multiplicity is unknown, you have to try both. The d-block elements and some of the f-block elements are trickiest. You may recall the "high-spin" and "low-spin" states from ligand field theory. Even worse, the multiplicity tends to become blurred when relativistic effects (spin-orbit coupling) are taken into account. Again, in cases of unknown multiplicity, one has to try two or more options, each of which is a separate calculation. Generally, instead of using the formula in the quantum textbooks, I just add 1 to the number of unpaired electrons (singly-occupied orbitals). The textbook formula is very useful, however, in determining what S**2 should be. This is important as a multiplicity=3 calculation is not guaranteed to yield the correct S**2 value of 2.000. This is known as spin contamination, as it involves mixing-in of higher spin states. **** 3) from Mary O'Connor **** Hello-- A general guideline (or so I have read), is that most organic molecules in the ground states are closed shells, and thus, have a multiplicity of one and no charge. Since multiplicity only means the number of ways that an electron can orient itself to a magnetic field, no unpaired electrons means it can only be in one orientation. I thonk the formula is 2J + 1 for spin states, where J is +/- 1/2. For closed shells this sums to 1. Then feed any unpaired electrons into the formula. I suppose this could be done by drawing Lewis structures to find the number of unshared electrons. Sometimes, knowing the charge will preset your options for multiplicity in Gaussian. My first instinct is to go with the lowest multiplicity choice offered to you, as this will probably be either the correct one, or the first excited state. I'm fairly new with Gaussian myself, but these are the ideas I keep in mind. I will be interested in the other replies that you get. Good luck! **** 4) from Wang Dongqi **** Dear Telkuni, There is an easy way to find the multiplicity. Just to find the number of the unpair electron, so you will get the multiplicity=2S+1.(S=n*1/2, n is the number of unpair electron), that is, to molecules and ions, S=0, while to radical, S=n*1/2. OK? Wish this is useful for you. --------------------------------------------------- Telkuni Tsuru telkuni@venus.dti.ne.jp From chemistry-request@server.ccl.net Tue Jun 12 23:39:17 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5D3dG518764 for ; Tue, 12 Jun 2001 23:39:16 -0400 Received: from [128.97.147.206] (ch-06.psnet.ucla.edu [128.97.147.206]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id UAA16317 for ; Tue, 12 Jun 2001 20:39:15 -0700 (PDT) Mime-Version: 1.0 Message-Id: Date: Tue, 12 Jun 2001 20:39:10 -0700 To: chemistry@ccl.net From: Eric Scerri Subject: phase/orbitals (alleged earlier posting) Content-Type: text/plain; charset="us-ascii" ; format="flowed" Apologies for the confusion. In fact I failed to send my earlier posting which I have now corrected. Here it is (or was). >Dr. Richard L. Wood: > >> I think he means that the idea of an orbital is NOT a mathematical >> concept, but a "physical", i.e. from a physics point of view, >> concept. > >Well, we apparently disagree. To me, the idea of "orbitals" in the >case of a many electron system is basically a mathematical concept, >since these "orbitals" have no physical reality. But they do of >course have physical significance, in so far as they are excellent >approximate models in the rationalization of many kinds of physical >and chemical behaviour. > >Yours, Jens >--< > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >JENS SPANGET-LARSEN ----------------------------------------------------- I agree with Jens regarding the mathematical nature of orbitals although when I recently gave a talk on this topic and presented a very similar position to the above I was urged to consider the experiments which purport to reveal phase information. The implication was that I was incorrect in ruling out the possibility of ever observing orbitals. This troubled me and this is what led to my posting. So far the many responses I have received seem to suggest that phase information may be obtainable but that this still does not imply that individual atomic/molecular orbitals have been or ever will be observed in many-electron systems. But I wonder whether the approximate nature of orbitals in many-electron systems might be a separate issue from whether they might be observable in general. Orbitals are presumably not observable in H atoms either although within a non-relativistic Schrodinger treatment they are defined exactly. Should we perhaps separate the approximate nature of orbitals in N electron systems from the more categorical aspect that an orbital is not an actual electron path, even in H, or He+, or Li2+ etc although the term "orbital" wrongly suggests that it might be. So until somebody observes phase information in any one-electron system I think I can continue to insist that orbitals cannot be observed. eric scerri -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Wed Jun 13 10:37:13 2001 Received: from mailx.chem.wisc.edu ([128.104.68.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DEb9511381 for ; Wed, 13 Jun 2001 10:37:13 -0400 Received: from chem.wisc.edu (bert.chem.wisc.edu [128.104.70.10]) by mailx.chem.wisc.edu (8.9.3/8.9.3) with SMTP id JAA06781 for ; Wed, 13 Jun 2001 09:37:00 -0500 Received: from fozzie by chem.wisc.edu; Wed, 13 Jun 01 09:33 CST Received: from localhost (uddin@localhost) by chem.wisc.edu (8.8.7/8.8.5) with SMTP id IAA25263; Wed, 13 Jun 2001 08:37:47 -0500 Message-Id: Date: Wed, 13 Jun 2001 08:37:47 -0500 (CDT) From: Jamal Uddin Subject: Re: CCL:quotation To: Dudis Douglas S Civ AFRL/MLBP CC: "'chemistry@ccl.net'" In-Reply-To: <53A10F824E50D511820800508BDF3F2214CADD@fszhtv12.wpafb.af.mil> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Dudis, This was written by P. A. M. Dirac: "The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble." - P. A. M. Dirac, Proc. Roy. Soc. 123, 714 (1929) (Note: This is not taken from the original reference) Cheers, Jamal Uddin On Wed, 13 Jun 2001, Dudis Douglas S Civ AFRL/MLBP wrote: > Simple request. I am looking for the exact quotation (preferably with a reference) for > the quote that goes along the lines: > > '... the laws governing most of physics, and all of chemistry, are now known ...' > > Help much appreciated. > Doug Dudis > > ------------------------------- > Douglas S. Dudis, Ph.D. > Research Leader - Polymers > Air Force Research Laboratory > Materials and Manufacturing Directorate > 2941 P St., Bldg. 654, Ste. 347 > Wright-Patterson AFB, OH 45433-7750 > Phone: (937) 255-9148 > FAX: (937) 255-9157 > e-mail:Douglas.Dudis@afrl.af.mil > > > > -= 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 Jun 13 10:46:58 2001 Received: from univ-mlv.fr ([193.55.61.191]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DEku511764 for ; Wed, 13 Jun 2001 10:46:57 -0400 Received: from pclav107.univmlv.fr (pclav107.univ-mlv.fr [193.55.62.231]) by univ-mlv.fr (8.9.3 (PHNE_18979)/8.9.3) with SMTP id QAA22247; Wed, 13 Jun 2001 16:47:17 +0200 (METDST) Message-ID: <002401c0f417$747f5160$e73e37c1@univmlv.fr> Reply-To: "Alexandre Hocquet" From: "Alexandre Hocquet" To: "Dudis Douglas S Civ AFRL/MLBP" , References: <53A10F824E50D511820800508BDF3F2214CADD@fszhtv12.wpafb.af.mil> Subject: Re: CCL:quotation Date: Wed, 13 Jun 2001 16:45:06 +0200 Organization: UMLV 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 > '... the laws governing most of physics, and all of chemistry, are now known ...' Hi Doug, Your quotation might be "The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the application of these laws leads to equations much too complicated to be soluble". It has been extracted from : "Quantum mechanics of many-electron systems" Dirac PAM (1929) Proc R Soc Lond Ser A 123: 714 It has been commented in : Kutzelnigg W, Theoretical Chemistry Accounts, 103, (2000), 182-186 And also : Hocquet, A ECCC7 Poster #10: "The Epistemological Status of Computational Chemistry: A Tentative Sociological Study" at http://eccc7.cooper.edu/ You may also have a look at : Simoes A and Gavroglu K : " the Americans, the Germans, and the beginnings of quantum chemistry : the confluence of diverging traditions ", Historical Studies in the Physical and Biological Sciences, 25 (1994), 47-110 Hope this helps, Alexandre Hocquet From chemistry-request@server.ccl.net Wed Jun 13 12:38:24 2001 Received: from smtp4-cm.mail.eni.net ([216.133.226.137]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DGcN514419 for ; Wed, 13 Jun 2001 12:38:23 -0400 Received: from meta.home.dix (node-cffba4d6.powerinter.net [207.251.164.214]) by smtp4-cm.mail.eni.net (8.9.3/8.9.3) with ESMTP id JAA04488 for ; Wed, 13 Jun 2001 09:38:22 -0700 Subject: Re: Summary: Docking of Covalently Bound ligands From: Scott Dixon To: chemistry@ccl.net Content-Type: text/plain X-Mailer: Evolution/0.10 (Preview Release) Date: 13 Jun 2001 09:38:21 -0700 Message-Id: <992450302.3971.0.camel@meta> Mime-Version: 1.0 Hi, Just a follow up on Suzie Byum's message, quoted yesterday by David Turner. DockIt is a program currently being marketed by Metaphorics, LLC. It uses a novel distance geometry based approach to the computation of ligand conformation and placement. Thus, it can handle covalent bonding between receptor and ligand by allowing for user specified distance constraints. These constraints can also be useful in specifying other interactions like particular hydrogen bonds, etc. DockIt is aimed at hight throughput virtual screening applications and for further information, or to arrange a test, you can send email to info@metaphorics.com. Scott Dixon Chief Scientific Officer Metaphorics, LLC From chemistry-request@server.ccl.net Wed Jun 13 12:57:21 2001 Received: from post2.inre.asu.edu ([129.219.110.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DGvL514809 for ; Wed, 13 Jun 2001 12:57:21 -0400 Received: from conversion.post2.inre.asu.edu by asu.edu (PMDF V6.0-24 #47347) id <0GEV00B01OF6XJ@asu.edu> for chemistry@ccl.net; Wed, 13 Jun 2001 09:57:06 -0700 (MST) Received: from webmail2.asu.edu (webmail2.asu.edu [129.219.10.28]) by asu.edu (PMDF V6.0-24 #47347) with ESMTP id <0GEV00AJBOF6TB@asu.edu> for chemistry@ccl.net; Wed, 13 Jun 2001 09:57:06 -0700 (MST) Received: (from nobody@localhost) by webmail2.asu.edu (8.9.3/8.9.3) id JAA22086 for chemistry@ccl.net; Wed, 13 Jun 2001 09:57:05 -0700 Date: Wed, 13 Jun 2001 09:57:05 -0700 (MST) From: Benjamin.Moritz@asu.edu Subject: Large Mass Atoms X-Originating-IP: 149.169.26.88 To: chemistry@ccl.net Message-id: <992451425.3b279b61df089@webmail2.asu.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 Dear All, I was wondering if anyone can help me out with an isotope problem in G98. I want to set the value of some of my atoms to a very large mass, but I'm not sure how the input file should look. Do I need two seperate jobs to do this? Any help will be greatful. Thank you. ******************************************************************************** Benjamin J. Moritz Work: 480-965-8509 College of Engineering and Applied Sciences Mailto:bmoritz@asu.edu Dept. of Chemical & Materials Engineering PO Box 876006 Tempe, AZ 85287-6006 ******************************************************************************** From chemistry-request@server.ccl.net Wed Jun 13 12:57:23 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DGvN514817 for ; Wed, 13 Jun 2001 12:57:23 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA20267; Wed, 13 Jun 2001 12:57:22 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B279720.BDF45088@cornell.edu> Date: Wed, 13 Jun 2001 12:38:56 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:phase/orbitals (alleged earlier posting) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Eric Scerri wrote: > Apologies for the confusion. In fact I failed to send my earlier > posting which I have now corrected. Here it is (or was). > But isn't the actual "orbital" the result of taking a MATHEMATICAL function and squaring it to get a "probability density"? And, as such, isn't this "probability density" also a MTHEMATICAL construct? Later, someone related the "probability density" with the concept of an "orbital". And wasn't this someone a physicist? Please correct me if I'm incocrrect. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Jun 13 16:06:02 2001 Received: from baton.phys.lsu.edu ([130.39.182.71]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DK61519073 for ; Wed, 13 Jun 2001 16:06:01 -0400 Received: (from vani@localhost) by baton.phys.lsu.edu (8.9.2/8.9.2) id PAA09730; Wed, 13 Jun 2001 15:02:36 -0500 (CDT) Date: Wed, 13 Jun 2001 15:02:36 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: how to simulate water Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, what is the best way to get an initial state(coordinates) for simulating water? What is the best way to have a minimization run on water? Thanks vani From chemistry-request@server.ccl.net Wed Jun 13 16:11:20 2001 Received: from lambda.inrs.uquebec.ca ([207.162.3.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DKBK519204 for ; Wed, 13 Jun 2001 16:11:20 -0400 Received: from iaf.Uquebec.ca ([198.168.44.100]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 127 for ; Wed, 13 Jun 2001 16:05:12 -0400 Sender: wujih@ccl.net Message-ID: <3B27C890.40EB11E6@iaf.Uquebec.ca> Date: Wed, 13 Jun 2001 16:09:52 -0400 From: JianHui Wu Reply-To: jianhui_Wu@iaf.Uquebec.ca Organization: Institut Armand-Frappier X-Mailer: Mozilla 4.72 [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en, Chinese/China, zh-CN MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dock, two substrates in one binding site Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I work on a protein which catalyzes substrates A and B into a peptide AB. Obviously, these two substrates have to bind with the protein before the catalytic reaction can take place. I like to dock these two substates into the putative binding site and wonder how to dock two substrates into one binding site at the same time. To dock them one by one is probably not a good way. One way I like to try is to dock the peptide AB instead and split AB into A and B followed by some MM/MD refinement. The purpose of this study is to build a model for the catalytic reaction. After substrates A and B in the reasonable binding mode, QM perhaps can be applied to the binding site to search for tansition state (?). Any comment or suggestion will be greatly appreciated. Yours sincerely, Jian Hui Wu McGill Translational Research in Cancer Lady Davis Institute Jewish General Hospital Montreal, QC From chemistry-request@server.ccl.net Wed Jun 13 15:51:54 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5DJps518486 for ; Wed, 13 Jun 2001 15:51:54 -0400 Received: from u.arizona.edu (128.196.184.158) by deimos.email.Arizona.EDU (5.1.056) (authenticated as mcafiero@email.arizona.edu) id 3B2669E400017452; Wed, 13 Jun 2001 12:51:34 -0700 Sender: mcafiero@ccl.net Message-ID: <3B27C443.1FB0E20F@u.arizona.edu> Date: Wed, 13 Jun 2001 19:51:31 +0000 From: Maurice Cafiero X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: Eric Scerri CC: chemistry@ccl.net Subject: Re: CCL:phase/orbitals (alleged earlier posting) References: Content-Type: multipart/alternative; boundary="------------F9CDE0F5E36BBDA4E6ADC730" --------------F9CDE0F5E36BBDA4E6ADC730 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello: I apologize for dragging this out, but I would like to add someting to this discussion. I attribute the widely accepted yet *wrong* idea that orbitals are real to the fact that within HF theory, a physical property can be attributed to the orbital enegies (IP, EA). But just because the enegies have a (weak) predictive power does not mean that orbitals are real. How "physical" or "mathematical" is it to take one multiplicative term out of a wavefunction and square it and expect to get something meaningful? Lewis dot structures have a somewhat predictive power, but are we going to start looking for experimental evidence for lewis dots? -- Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona --------------F9CDE0F5E36BBDA4E6ADC730 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit hello:
    I apologize for dragging this out, but I would like to add someting to this discussion.
I attribute the widely accepted yet *wrong* idea that orbitals are real to the fact that within HF theory,
a physical property can be attributed to the orbital enegies (IP, EA). But just because the enegies have a
(weak) predictive power does not mean that orbitals are real.  How "physical" or "mathematical" is it
to take one multiplicative term out of a wavefunction and square it and expect to get something meaningful?

Lewis dot structures have a somewhat predictive power, but are we going to start looking for experimental evidence
for lewis dots? 




-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona

 

--------------F9CDE0F5E36BBDA4E6ADC730--



From chemistry-request@server.ccl.net Wed Jun 13 17:40:08 2001
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From: Vemparala Satyavani 
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Hi all,
 i posted a question regarding simulation of water. The problem i have is 
this:
I am using AMBER potential parameters to simulate water. I have file with 
216 water molecules at experimental density(~1g/cc). when iam 
equilibriating the system, a hydrogen atom is coming close to oxygen(as 
the LJ potential is only between oxygen atoms), and the huge coulomb 
potential takes over(iam using ewald method) and there are these huge 
fluctuations in energy. What do i do about it?

i tried placing the same system in a large box(with half density) and 
tried equilibriating.. but i still have the same problem. How to prevent 
this?

thanks
vani

From chemistry-request@server.ccl.net Wed Jun 13 21:26:10 2001
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From: "N. Sukumar" 
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The approximate nature of orbitals in many-electron systems is indeed a very
different issue from the question of "observability" or "physical reality".

LCAO orbitals do not "exist" in many-electron atoms and pi-electron density
is an approximation in polyatomic molecules, but natural orbitals are
well-defined as functions that diagonalize the many-electron density matrix.
Does this mean that natural orbitals are observable?

Electronic phase is certainly not an "observable" in the sense of being an
expectation value of a Hermitian operator, but experimental manifestations of
phase differences can be observed as e.g. the interference of electrons in
the molecular Aharonov-Bohm effect and the Berry phase (Mead and Truhlar, JCP
70, 2284, 1979, exptl.cofirmation by Delacretaz et al. PRL 56, 2598, 1986)

It has been argued likewise that bond lengths and bond angles in polyatomic
molecules are equally "unobservable", being defined only within the
Born-Oppenheimer approximation and ignoring indistinguishability of protons
(extensive discussion by many authors in Israel J. Chem, vol.19, 1980). The
fact that bond distances obtained from quantum calculations performed within
the nonrelativistic B.O. approximation in a finite basis correspond
approximately to distances obtained from an X-ray structure is analogous to
the approximate correspondence between Hartree-Fock orbital energies and
experimental ionization potentials.

For a one-electron system the gradient of the electronic phase has a direct
interpretation as the velocity field, which when multiplied by the electron
density, gives the current density. Madelung (Z. Phys. 40, 332) in 1926
established the fluid dynamical analogy of quantum mechanics by transforming
the Shroedinger equation into a pair of fluid dynamical equations (one of
which is the familiar continuity equation: d/dt(rho) + del.j = 0

So are natural orbitals observable? Well, the total one-electron density is
observable; experimental manifestations of electronic phase differences are
observable. The total current density can now be constructed from the natural
orbital densities and gradients of the orbital phases (orbital velocity
fields). More discussion can be found in my paper "Phase associated with the
single-particle density of many-electron systems", Int. J. Quantum. Chem. 40,
501-510 (1991). If a mathematical construct is suitably defined to correspond
to an experimental situation, it is to me a physical concept.

Dr. N. Sukumar
Rennselaer Department of Chemistry

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/  Dr. N. SUKUMAR		     /
/  Department of Chemistry           /
/  Rensselaer Polytechnic Institute  /
/  Troy, NY 12180-3590               /
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From chemistry-request@server.ccl.net Wed Jun 13 23:40:27 2001
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>From: "N. Sukumar" 
>Date: Wed, 13 Jun 2001 21:26:05 -0400
>To: chemistry@ccl.net
>Subject: CCL:phase/orbitals
>Sender: "Computational Chemistry List" 
>
>The approximate nature of orbitals in many-electron systems is indeed a very
>different issue from the question of "observability" or "physical reality".
>

Note that physical methods such as electron momentum spectroscopy 
(EMS) can probe the momentum distributions of orbitals (especially 
valence orbitals) and in that sense allows one to 'visualize' them. 
It is possible to get extremely nice agreement between the 
theoretical momentum distributions from DFT calculations, for 
example, and the experimentally observed MDs.


-- 
Cheers,

Dave

Dr. David A. Winkler                    Email: dave.winkler@molsci.csiro.au  
Senior Principal Research Scientist     Voice: 61-3-9545-2477     
CSIRO Molecular Science			Fax:   61-3-9545-2446
Private Bag 10,Clayton South MDC 3169   http://www.csiro.au
Australia	       		http://www.molsci.csiro.au

For the World Chemical Congress in Brisbane, July 2001 check the details at
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