From chemistry-request@server.ccl.net Tue Sep 12 01:11:34 2000 Received: from chem_mail.chem.sc.edu (mail.chem.sc.edu [129.252.75.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA02331 for ; Tue, 12 Sep 2000 01:11:33 -0400 Received: from MOLETRONICS ([129.252.38.205]) by chem_mail.chem.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id Q9Z6H77Q; Tue, 12 Sep 2000 01:11:26 -0400 Message-ID: <000701c01c77$fe174e00$cd26fc81@psc.sc.edu> Reply-To: "derosa" From: "derosa" To: References: <14769.62702.739362.405188@lrz.uni-muenchen.de> <39B5150A.592A76AD@tera.com> Subject: Summary: Parallel Gaussian on Alpha platform Date: Tue, 12 Sep 2000 01:12:05 -0400 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello: Thank you very much to all of those who answer my question about running g98 in parallel in Alpha workstation. I received requests for a summary so here it is. G98 is parallelized using Linda. See below for my original question and the answers I received with some links and futher information that might be of some help. Pedro > > Hello everybody. > > > > Does anyone installed gaussian 98 in a cluster of Alpha workstations, > > running true64 Unix and parallelized using MPI. Can anyone give me a > > tip/detail instructions on how to compile or which libraries I should add in > > order to be able to run gaussian 98 in parallel in this cluster?. > > > > I'll summarized the answers if there is any interest. > > > > Thank you very much > > > > Pedro ******************************************************************** Hi, sorry but to the best of my knowledge G98 needs Linda ($1500) to run in parallel - unfortunately MPI is not an option. Peter -------------------------------- Peter Burger Anorg.-chem. Institut Universitaet Zuerich ******************************************************************** Hi, Gaussian98 runs using Tru64 with Linda software from SCA. See link below: http://www.gaussian.com/wp_linda.htm Jerry Lipchus ******************************************************************** I understood there to be only versions available using LINDA. There are optimized versions of this available for Memory Channel, AlphaServer Sc. LINDA over ethernet usese TCP/IP though. John ******************************************************************** Pedro; You can get something similar from Scientific Computing Associates, Jerry Lipchus 203-777 7442. It run under Linux and their package LINDA. Linux Networx (Formerly Alta Technology) is a supplier of Clusters based on the Intel, AMD and Alpha processors. We have arrangement in place with for both LINDA and Gaussion s/w products. When you are looking to add to your cluster, please keep us in mind Bill Harman Business Development Manager www.lnxi.com direct ph 801-304-0226 ******************************************************************** > > > > ****************************** > > Dr. Pedro Derosa > > Dept of Chemistry and Biochemistry > > University of South Carolina > > e-mail: derosa@mail.chem.sc.edu > > Ph: (803) 777-8401 > > Fax: (803) 777-9521 > > ****************************** From chemistry-request@server.ccl.net Tue Sep 12 01:27:37 2000 Received: from herald.cc.purdue.edu (herald.cc.purdue.edu [128.210.11.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA02393 for ; Tue, 12 Sep 2000 01:27:29 -0400 Received: from [209.178.160.81] by herald.cc.purdue.edu with ESMTP for chemistry@ccl.net; Tue, 12 Sep 2000 00:27:19 -0500 Mime-Version: 1.0 Message-Id: Date: Mon, 11 Sep 2000 22:34:17 -0800 To: chemistry@ccl.net From: Eric Scerri Subject: CCL. HYBRIDIZATION NOT "REAL";V. FOCK Content-Type: multipart/alternative; boundary="============_-1243382033==_ma============" --============_-1243382033==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Quantum Mechanics is a mathematical methodology which best (at this >time) reproduces existing knowledge. As such it is an approach that >we can use to understand our physical universe. While it describes >what we perceive as reality, it is no more "real" than the theory of >phlogiston nor are its constructs (i.e orbitals - hybridized or not) >any more real than the billiard ball representation of atomic >structure. While I agree with the jist of this statement I wonder whether you might be overstating the case? Phlogiston theory was long ago refuted and is therefore not even candidate for a true scientific entity. Not all the entities discussed by quantum mechanics have the same status surely? Most people would want to say that electrons and protons are real entities. Your statement could be taken to mean that QM is a theory (epistemology) and therefore may not give us direct access to real entities (ontology). But there is a problem that we can only get at the micoworld via quantum mechanics so the neat distinction between the world and our description of the world is blurred. I wonder whether you also intended the first sentence literally, namely that QM makes no true predictions? If so I think this is debateable although it is probably true that there are few genuine predictions, in the temporal sense, made by QM. To get back to the main issue we can distinguish between atomic orbitals (non real) and electron density (real). Each case can be dealt with separately whereas a general statement about quantum mechnics as a whole, as above, would suggest that all entities are lacking physical reality which to repeat is going too far. eric scerri > >These are all artificial constructs that help us humans find a frame >of reference in which we can understand the reality in which we are >immersed. They have no 'reality' beyond that we assign them to >enhance our understanding ... > Jim Kress ------------------------------------------------- Dr. Eric Scerri, Department of Chemistry & Biochemistry, Charles E. Young Drive, UCLA, Los Angeles, CA 90095 USA E-mail: scerri@chem.ucla.edu 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 --============_-1243382033==_ma============ Content-Type: text/enriched; charset="us-ascii" ArialQuantum Mechanics is a mathematical methodology which best (at this time) reproduces existing knowledge. As such it is an approach that we can use to understand our physical universe. While it describes what we perceive as reality, it is no more "real" than the theory of phlogiston nor are its constructs (i.e orbitals - hybridized or not) any more real than the billiard ball representation of atomic structure. Arial While I agree with the jist of this statement I wonder whether you might be overstating the case? Phlogiston theory was long ago refuted and is therefore not even candidate for a true scientific entity. Not all the entities discussed by quantum mechanics have the same status surely? Most people would want to say that electrons and protons are real entities. Your statement could be taken to mean that QM is a theory (epistemology) and therefore may not give us direct access to real entities (ontology). But there is a problem that we can only get at the micoworld via quantum mechanics so the neat distinction between the world and our description of the world is blurred. I wonder whether you also intended the first sentence literally, namely that QM makes no true predictions? If so I think this is debateable although it is probably true that there are few genuine predictions, in the temporal sense, made by QM. To get back to the main issue we can distinguish between atomic orbitals (non real) and electron density (real). Each case can be dealt with separately whereas a general statement about quantum mechnics as a whole, as above, would suggest that all entities are lacking physical reality which to repeat is going too far. eric scerri ArialThese are all artificial constructs that help us humans find a frame of reference in which we can understand the reality in which we are immersed. They have no 'reality' beyond that we assign them to enhance our understanding ... ArialJim Kress ------------------------------------------------- Dr. Eric Scerri, Department of Chemistry & Biochemistry, Charles E. Young Drive, UCLA, Los Angeles, CA 90095 USA E-mail: scerri@chem.ucla.edu 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 --============_-1243382033==_ma============-- From chemistry-request@server.ccl.net Tue Sep 12 01:29:29 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA02405 for ; Tue, 12 Sep 2000 01:29:28 -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 BAA10503; Tue, 12 Sep 2000 01:29:03 -0400 (EDT) Date: Tue, 12 Sep 2000 01:29:04 -0400 (EDT) From: Jan Labanowski To: vijay pargaonkar cc: "CHEMISTRY@ccl.net" Subject: Re: HYBRIDIZATION made easy In-Reply-To: <39BDA149.C2BD8915@mahindrabt.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mr. Pargaonkar Vijay What you are doing is quite questionable... You are reposting messages from CCL (Computational Chemistry List) on your board but you are REMOVING information about the original source of the messages and their original destination. You are also cleaning messages >from all reference to CCL (e.g., removing the footer, and quotes which contain original destination). In other words, you are IMPLYING that the messages were posted originally on your BOARD, not on CCL. While information posted on CCL is in public domain, modifying original messages and reposting them is unethical at best, and most likely illegal. Sooner or later someone may sue you for this practice: either one of the authors for modyfying his/her public statements, or my institution for routine (i.e., not fair use), distribution of copyrighted material. As you well know, collections are automatically copyrighted. This message is mostly intended for CCL subscribers to notify them that their postings are being modified and used without their permission to generate advertising income of http://www.science.domainvalet.com While I have nothing against advertising and generating income, I am quite opposed to modifying messages to collect undue credit. You may want to request the withdrawal of your messages from this site if you so desire. On Tue, 12 Sep 2000, vijay pargaonkar wrote: > Dear cclers, > > The topic discussed on hybridization is put on > > http://www.science.domainvalet.com > > Go to > > ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY > > The discussion so far is already put on the site. You can post your > arguments, comments, views, explainations on the discussion board. > > with regards > pargaonkar vijay > > 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 Tue Sep 12 07:27:40 2000 Received: from bilbo.edu.uy (bilbo.edu.uy [164.73.160.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA05092 for ; Tue, 12 Sep 2000 07:27:34 -0400 Received: from localhost (oscar@localhost) by bilbo.edu.uy (8.11.0/8.11.0) with SMTP id e8CBQu617985; Tue, 12 Sep 2000 08:26:57 -0300 Date: Tue, 12 Sep 2000 08:26:55 -0300 (GRNLNDST) From: "Oscar N. Ventura" To: Eric Scerri cc: chemistry@ccl.net Subject: Re: CCL:CCL. HYBRIDIZATION NOT "REAL";V. FOCK In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 11 Sep 2000, Eric Scerri wrote: > To get back to the main issue we can distinguish between atomic > orbitals (non real) and electron density (real). Each case can be > dealt with separately whereas a general statement about quantum > mechnics as a whole, as above, would suggest that all entities are > lacking physical reality which to repeat is going too far. It seems to me there's a confussion here. Atomic orbitals (or molecular, localized, canonical, Kohn-Sham, etc, etc....orbitals) are not less "real" than total, electron, differential, etc, etc....densities, provided we could arrive to an agreement of what "real" means. Both orbitals and densities can be obtained from the same theory and (to a point) even offer similar descriptions of the microworld. Physics tells us however that density is observable, i.e. that we can also construct some experimental devices which measure this property. So we should be talking about observability (i.e. the ability of an observer to obtain information >from an object which can be the subject of measurement) and not reality (which I would not dare to define, but seems to imply the object to exist independently of any observer and as such it is metaphysics, not physics). Total density (STM), differential density (X-ray), energies of single electrons within a molecule (photoelectron spectroscopy) are observable. Molecular or atomic orbitals, energies of the molecular orbitals, etc, are constructs of the theory and are not observable. Just my $ 0.015. Oscar ------------------------------------------------------------------------------- Prof.Dr.Oscar N. Ventura Tel.+(5982)9248396 Fax +(5982)9241906 MTC-Lab,Facultad de Quimica MTC-Lab http://bilbo.edu.uy/MTC-Lab.html Universidad de la Republica Gral.Flores 2124, C. C. 1157 All opinions are my own, and not Montevideo 11800, URUGUAY necessarily those of my employer "Violence is the last refuge of the incompetent." --- Salvor Hardin ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Sep 12 02:26:24 2000 Received: from shardagate.mahindrabt.com (root@[206.102.1.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA02814 for ; Tue, 12 Sep 2000 02:26:12 -0400 Received: (from uucp@localhost) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) id LAA29090; Tue, 12 Sep 2000 11:55:57 +0530 Received: from UNKNOWN(10.5.0.15), claiming to be "intranet.sharda.mahindrabt.com" via SMTP by shardagate, id smtpdnilbJ0; Tue Sep 12 11:55:53 2000 Received: from mahindrabt.com ([10.5.2.73]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id LAA10314; Tue, 12 Sep 2000 11:55:54 +0530 Message-ID: <39BDCA91.17A0B800@mahindrabt.com> Date: Tue, 12 Sep 2000 11:47:53 +0530 From: vijay pargaonkar X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: Jan Labanowski CC: "CHEMISTRY@ccl.net" Subject: Explaination for the Forum References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear jan, Wait a while. I am also a researcher in this field like you. And had received awards for my work in computational field. I am not after any income. The discussion forum is started on a free web site. The service is free. I want to contribute a lot to computational community. Also, I don't have any criminal record of breaking any rules or laws. The site is launched on a festival of lord ganesha ( ganesh chartuthi) who is god for all those who are after knowledge. Please notice the very first thread I have posted. It is to make the discussions easier. With mailing, what happens is everybody receives mails from different persons from different locations. Emails remain unsorted based on the topic of discussion. Furthure more it increases net traffic a lot. Discussion forum eliminates the above disadvantage. Please, Do not discourage me like this. I have good intentions in mind. There are different discussion boards for different fields eg, CFD online (computational fluid dynamics) etc. The site runs free of cost. Isn't it good if we start preparing such a board for our Computational Chemistry field. Now about posting the messages without informing the persons. The messages put here are just samples. I have quoted all the persons names correctly with there correct email ids. Why to repeat the same bottom lines in every message . It will just eat memory of the server. Neither the site reveals my original name nor this email. Becaus I believe in ************************************ WHERE EGO ASSERTS, LORD VANISHES. WHERE EGO VANISHES, LORD ENTERS. ************************************* Dear Jan, thank you so much for the caution you gave me. Will take care. With warm regards pargaonkar vijay Jan Labanowski wrote: > Dear Mr. Pargaonkar Vijay > > What you are doing is quite questionable... > You are reposting messages from CCL (Computational Chemistry List) > on your board but you are REMOVING information about the original source > of the messages and their original destination. You are also cleaning messages > from all reference to CCL (e.g., removing the footer, and quotes which > contain original destination). In other words, you are IMPLYING that the > messages were posted originally on your BOARD, not on CCL. > > While information posted on CCL is in public domain, modifying > original messages and reposting them is unethical at best, and most likely > illegal. > This message is mostly intended for CCL subscribers to notify them that > their postings are being modified and used without their permission > to generate advertising income of http://www.science.domainvalet.com > While I have nothing against advertising and generating income, I am > quite opposed to modifying messages to collect undue credit. > You may want to request the withdrawal of your messages from this site > if you so desire. > > On Tue, 12 Sep 2000, vijay pargaonkar wrote: > > > Dear cclers, > > > > The topic discussed on hybridization is put on > > > > http://www.science.domainvalet.com > > > > Go to > > > > ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY > > > > The discussion so far is already put on the site. You can post your > > arguments, comments, views, explainations on the discussion board. > > > > with regards > > pargaonkar vijay > > > > > > 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 Tue Sep 12 02:51:29 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA02914 for ; Tue, 12 Sep 2000 02:51:27 -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 CAA12314; Tue, 12 Sep 2000 02:51:07 -0400 (EDT) Date: Tue, 12 Sep 2000 02:51:07 -0400 (EDT) From: Jan Labanowski To: vijay pargaonkar cc: Jan Labanowski , "CHEMISTRY@ccl.net" Subject: Re: Explaination for the Forum In-Reply-To: <39BDCA91.17A0B800@mahindrabt.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Pargaonkar Vijay, Please understand that I do not care if you have a forum and I wish you best of luck to make it much better than mine, I may even join... I can sort messages by topic too, and I probably do it one day. Actually I had a more advanced similarity approach based on ngrams, but it needs more work, and one of my studens will have to continue it one day. And obviously, I can install hypermail and mimick what you do. At the same time, there is an hdig and regular expression search engine, so at this moment one can get to the material if one wants to. I agree with you that CCL can be better. You also have to understand that it is 2:45am in my place, and I have to waste my, and CCL subscribers time writing about it. However, what you are doing is taking messages from CCL, cutting ALL REFERENCES to CCL from within messages, and reposting those on your board in the format as if they were originally posted there. It is UNACCEPTABLE... Moreover, I want to make sure that people know that I have nothing to do with this... And beside, my institution may consider it a copyright violation, since they are supporting CCL and pay for students, network and computers. Last but not least, you are introducing confusion, since some people may respond to messages posted on your board, and those responses will not appear on CCL. So, I have to make it clear... You are doing it for quite some time and it is suprising that you did not contact me about the ramifications. We could have solved these issues off-line. I hope, I said enough about this issue... Sorry for taking the bandwidth... Jan Labanowski jkl@ccl.net On Tue, 12 Sep 2000, vijay pargaonkar wrote: > Dear jan, > > Wait a while. I am also a researcher in this field like you. And > had received awards for my work in computational field. > > I am not after any income. The discussion forum is started on a free web site. The > service is free. I want to contribute a lot to computational community. Also, I > don't have any criminal record of breaking any rules or laws. > > The site is launched on a festival of lord ganesha ( ganesh chartuthi) who is god > for all those who are after knowledge. Please notice the very first thread I have > posted. > > It is to make the discussions easier. With mailing, what happens is everybody > receives mails from different persons from different locations. Emails remain > unsorted based on the topic of discussion. Furthure more it increases net traffic > a lot. > > Discussion forum eliminates the above disadvantage. > > Please, Do not discourage me like this. I have good intentions in mind. There are > different discussion boards for different fields eg, CFD online (computational > fluid dynamics) etc. The site runs free of cost. Isn't it good if we start > preparing such a board for our Computational Chemistry field. > > Now about posting the messages without informing the persons. The messages put > here are just samples. I have quoted all the persons names correctly with there > correct email ids. Why to repeat the same bottom lines in every message . It will > just eat memory of the server. Neither the site reveals my original name nor > this email. Becaus I believe in > > ************************************ > WHERE EGO ASSERTS, LORD VANISHES. > WHERE EGO VANISHES, LORD ENTERS. > ************************************* > > > Dear Jan, thank you so much for the caution you gave me. Will take care. > > With warm regards > pargaonkar vijay > > > Jan Labanowski wrote: > > > Dear Mr. Pargaonkar Vijay > > > > What you are doing is quite questionable... > > You are reposting messages from CCL (Computational Chemistry List) > > on your board but you are REMOVING information about the original source > > of the messages and their original destination. You are also cleaning messages > > from all reference to CCL (e.g., removing the footer, and quotes which > > contain original destination). In other words, you are IMPLYING that the > > messages were posted originally on your BOARD, not on CCL. > > > > While information posted on CCL is in public domain, modifying > > original messages and reposting them is unethical at best, and most likely > > illegal. > > This message is mostly intended for CCL subscribers to notify them that > > their postings are being modified and used without their permission > > to generate advertising income of http://www.science.domainvalet.com > > While I have nothing against advertising and generating income, I am > > quite opposed to modifying messages to collect undue credit. > > You may want to request the withdrawal of your messages from this site > > if you so desire. > > > > On Tue, 12 Sep 2000, vijay pargaonkar wrote: > > > > > Dear cclers, > > > > > > The topic discussed on hybridization is put on > > > > > > http://www.science.domainvalet.com > > > > > > Go to > > > > > > ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY > > > > > > The discussion so far is already put on the site. You can post your > > > arguments, comments, views, explainations on the discussion board. > > > > > > with regards > > > pargaonkar vijay > > > > > > > > > > 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/ > 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 Tue Sep 12 06:06:52 2000 Received: from earth.ox.ac.uk (root@darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03901 for ; Tue, 12 Sep 2000 06:06:50 -0400 Received: from pauling.earth.ox.ac.uk (pauling [163.1.22.22]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id LAA12965 for ; Tue, 12 Sep 2000 11:06:37 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14781.65502.964778.456012@gargle.gargle.HOWL> Date: Tue, 12 Sep 2000 11:05:18 +0100 To: Subject: CCL:HYBRIDIZATION NOT "REAL";V. FOCK In-Reply-To: <001801c01c45$39ad6540$0300a8c0@quantumnt> References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> <39BD0F25.AA9F5F67@qta.qui.uc.pt> <39BD30E5.D6BC4D5C@eeyore.cm.utexas.edu> <39BD3554.404D072C@u.arizona.edu> <39BD4B04.4A8EB107@u.arizona.edu> <001801c01c45$39ad6540$0300a8c0@quantumnt> X-Mailer: VM 6.76.rf under 21.1 (patch 3) "Acadia" XEmacs Lucid The question of the "reality" of hybrid orbitals seems moot since even unhybridized orbitals are not physical observables. I would like to raise what seems to me to be a more pertinent question -- that of the usefulness of that concept. I ran up against this recently in teaching a course in quantum mechanics of mineral structures and bonding, and found myself questioning whether hybridization has any explanatory power at all. Here's my reasoning. "Hybridization" is not derivable from quantum mechanics. An sp2 or sp3 orbital is not an eigenstate of any Hamiltonian of which I am aware. One can certainly construct linear combinations of eigenstates in quantum mechanics, and a linear combination of eigenstates is also an eigenstate if its components are degenerate. But of course an s and a p state are non-degenerate in an isolated atom, so the hybrid is meaningless in the framework of quantum-mechanics. What QM *does* imply is that if we have a Hamiltonian with, for example C3 or Td symmetry then the eigenstates *will* be symmetry-adapted functions. These can be expressed as linear combinations of spherical harmonics which might look somewhat like (but are not) the sp2 and sp3 hybrid orbitals respectively. I can not find any sound argument in the textbooks to identify in what circumstances an sp2 hybrid might be "stable" over sp3 or vice versa or over unhybridized orbitals. The undergraduate physical chemistry texts I have read simply assert without evidence that hybridization can occur. ( Interestingly enough the small sample of "real" quantum mechanics books on my shelf do not mention hybridization at all!) The semi - implicit assumption in elementary discussions of hybridization is that the character of hybridization depends on the number of atoms to which bonds are being formed. To paraphrase the argument: An sp3 hybrid orbital has something of the character of an eigenstate of a Hamiltonian with Td symmetry. (I can not come up with a better justification for its existence than this. Anyone else?). Elements such as C and Si which form sp3 bonds tend to prefer tetrahedral co-ordination environments in molecules and solids. Electron-counting and valence arguments won't do either, as they can not explain why C can bond as either graphite or diamond. I can not see how to teach these concepts without resorting to unsubstantiated assertion or circular reasoning. I would really like to give my students some idea about the bonding "preferences" of Si and C which may be non-rigorous but can not be simply wrong. There is no way I am aware of to discuss energetics other than with full MO theory -- but the fact that a full HF or DFT calculation predicts this does not really count as an "explanation" either. I would appreciate any suggestions, especially those which can be treated at an elementary level. Keith Refson This message is copyright Keith Refson (2000), and is distributed with my permission by the Computational Chemistry email list (CCL) to its subscribers. Permission is also granted to reproduce this message on the official archives of the CCL list and authorised mirrors thereof. Any other reproduction is NOT authorised except where explicit permission is obtained from me. -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Tue Sep 12 06:27:18 2000 Received: from ICIL64.CILEA.IT (icil64.cilea.it [131.175.1.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03984 for ; Tue, 12 Sep 2000 06:27:16 -0400 Received: from dept.chem.polimi.it (dept.chem.polimi.it [131.175.68.1]) by ICIL64.CILEA.IT (PMDF V5.2-31 #32154) with ESMTP id <01JU339Z7Y9Y000G6U@ICIL64.CILEA.IT> for CHEMISTRY@ccl.net; Tue, 12 Sep 2000 12:26:47 MET-01DST Received: from Spooler by dept.chem.polimi.it (Mercury/32 v3.01a) ID MO002047; Tue, 12 Sep 2000 12:23:13 +0100 Received: from spooler by DEPT.CHEM.POLIMI.IT (Mercury/32 v3.01a); Tue, 12 Sep 2000 12:22:32 +0100 Received: from raos.chem.polimi.it (131.175.68.52) by DEPT.CHEM.POLIMI.IT (Mercury/32 v3.01a) ID MG002046; Tue, 12 Sep 2000 12:22:23 +0100 Date: Tue, 12 Sep 2000 12:27:47 +0000 From: Guido Raos Subject: HYBRIDIZATION NOT "REAL";V. FOCK In-reply-to: <12978376@isis.reed.edu> To: CHEMISTRY@ccl.net Cc: guido.raos@polimi.it Reply-to: guido.raos@polimi.it Message-id: <284DB94C7D54@DEPT.CHEM.POLIMI.IT> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v2.54) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Comments: Authenticated sender is The discussion about the reality of hybrid orbitals reminds me a lot of the one on the reality of molecular orbitals, which was on this list a few weeks ago. I believe we all agree that no orbitals can ever be observed. For this reason, some would then go on to argue that orbitals (of any kind: hybrids, canonical or localized MO's, natural orbitals, Kohn-Sham orbitals...) should be banned from our discussion of chemical phenomena. I do not share this view. The userfulness of the orbital concept should be judged from its "effectiveness" and "economy" in the explanation of particular phenomena. In particular, the canonical Hartree-Fock orbitals and energies help the discussion of photoelectron spectra and of a number of symmetry selection rules. However, hydrid orbitals do a much better job when it comes to chemical bonding. Incidentally, what "chemical" insights have been gained from "exact" quantum chemical calculations (full CI, diffusion Monte Carlo, and the like)? Often, approximate methods are much better at producing some understanding of particular chemical phenomenona. If I remember correctly, Dirac (quoted by Feynman) once said: "I understand an equation, if I don't have to solve it in order to know what the solution is going to look like". I think this applies also to our case: just replace "equation" with "molecular structure", and "solve it" with "run a Gaussian job". Coming back to the hydrids, I agree with Alan Shusterman that Coulson's discussion provides an excellent starting point: > "The previous discussion has brought out clearly the very wide > context in which hybridization seems to be relevant. We must not, > however, allow ourselves to believe that it represents any real > 'phenomenon', any more than resonance between different structures > such as the covalent and ionic ones of a polar bond may be called a > 'phenomenon'. But we can at least say: > > (a) that hybridization is the most efective way of preserving the > concept of a localized bond with perfect pairing of orbitals on the > two atoms of the bond; > > (b) that it is a restricted form of resonance, so that a residual > resonance, due to alternative schemes of pairing, still exists." Since then, one major advance has come from the applications of the GVB method of Goddard and the spin-coupled method of Gerratt, Cooper and Raimondi. Building on the Coulson-Fisher wavefunction for H_2, they both generalize and bridge the gap between MO and VB theories on a "one electron per orbital" basis. I shall not dwell on the differences between these methods. In simple cases, such as CH_4, they give very similar answers. The eight valence electrons turn out to be localized. Four of them are found on the hydrogens in distorted 1s H orbitals. The other four orbitals are centered on the carbon, and they are strikingly similar to Pauling's sp^3 hybrids. The point is that the shape of the orbitals in not given "a priori" (as in the classical VB treatment), but it is a _unique_ outcome of the energy minimization. The N-electron spin-coupled wavefunction is _not invariant_ under some unitary/linear transformation of the orbitals (as the Hartree-Fock wavefunction: a principle exploited in the construction of localized MO's). Sorry for the lengthy message. Thanks for the attention. Guido. ------------------------------------------------------ Dr. Guido Raos Dipartimento di Chimica, Politecnico di Milano Via L. Mancinelli 7, I-20131 Milano, Italy E-mail: guido.raos@polimi.it, raos@dept.chem.polimi.it phone: +39-02-2399-3051 fax: +39-02-2399-3080 From chemistry-request@server.ccl.net Tue Sep 12 06:44:47 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA04062 for ; Tue, 12 Sep 2000 06:44:44 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 12 Sep 2000 12:46:46 +0200 Sender: zhang@ccl.net Message-ID: <39BE0811.F8592BFE@mail.biokemi.su.se> Date: Tue, 12 Sep 2000 12:40:18 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: Trevor Kramer CC: chemistry@ccl.net Subject: Re: CCL:Reusing autogrid maps in autodock References: <968711513_PM_BeOS.tkramer@hampshire.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Trevor, If you run autogrid for your ligands against one macromolecule separately, you will get different map files for different ligands. As I understand, the map files should be ligand specific, otherwise the program may not discriminate good and bad ligand. Sincerely, Xiao-Ping Zhang > > Hello, > > I am currently using autodock3 for a research project and have a > question regarding its relation to autogrid. I have setup autodock to > automatically screen a large library of molecules by seting up the > parameter files for each ligand and then running autogrid3 and then > autodock3. Since autogrid takes a significant period of time I was > wandering of it was possible to reuse the grid maps it generates for all > the runs. The same macomolecule is used in each case and the size and > position of the grid is the same. I know I would have to run autogrid > once so it would generate grid maps for all supported atom types but > would this work? The dpf file also mentions the maps.fld file which may > need to be created for each run. Any help would be appreciated. Thank > you. > > Trevor Kramer > Hampshire College > > -= 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 -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Tue Sep 12 09:25:19 2000 Received: from aurora.balcab.ch (aurora.balcab.ch [213.200.1.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA06046 for ; Tue, 12 Sep 2000 09:25:18 -0400 Received: from sigma.balcab.ch (sigma.balcab.ch [213.200.1.125]) by aurora.balcab.ch (8.9.1/8.9.1) with ESMTP id PAA22612 for ; Tue, 12 Sep 2000 15:25:04 +0200 (MET DST) Received: from mdpi.org ([213.200.8.206]) by sigma.balcab.ch (Netscape Messaging Server 3.6) with ESMTP id AAA6743 for ; Tue, 12 Sep 2000 15:25:03 +0200 Message-ID: <39BE2F03.8D07B758@mdpi.org> Date: Tue, 12 Sep 2000 15:26:27 +0200 From: Shu-Kun Lin Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en-US,zh,zh-CN MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: CALL FOR PAPERS: Electronic Chemistry Publishing Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Division of Chemical Information (CINF) and the Chemical Structure Association will organize a joint symposium on "Electronic Chemistry Publishing" at the Spring ACS meeting in San Diego (April 1-5, 2001). The symposium will focus on two areas: Internet publication of chemistry journal and intranet publication and sharing of chemical information within an institute or a company. The internet publication of primary, secondary, and tertiary sources and their integration as searchable databases and electronic notebook are of particular interest. Papers regarding software or journal and online database publication projects are welcomed. For additional information regarding the ACS meeting in San Diego please see http://www.acs.org/meetings/sandiego2001/. If you would like submit a talk for this session please refer to the URL above and follow the links through the "Submitting a Paper" button and links to the Division of Chemical Information. The OASys system used for submitting abstracts for the meeting is open now until Nov. 30, 2000. If you have any questions regarding the symposium please send an email to the organizer, Shu-Kun Lin at lin@mdpi.org. (Excuse me for my sending to several mailing lists.) Best regards, Shu-Kun Lin -- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin@mdpi.org http://www.mdpi.org/lin/ From chemistry-request@server.ccl.net Tue Sep 12 10:23:51 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06457 for ; Tue, 12 Sep 2000 10:23:51 -0400 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id QAA04594; Tue, 12 Sep 2000 16:23:36 +0200 (MET DST) Message-Id: <4.3.2.7.0.20000912163032.00a94c20@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Tue, 12 Sep 2000 16:31:41 +0200 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: GOLPE for DOS/Win9x? Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues; Does anyone know whether the programme GOLPE has ever been compiled into a DOS and/or Win9x executable? Thanks, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Tue Sep 12 10:40:21 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06650 for ; Tue, 12 Sep 2000 10:40:21 -0400 Received: from eeyore.cm.utexas.edu (ne057.cm.utexas.edu [146.6.145.57]) by ne059.cm.utexas.edu (8.10.2/8.10.2) with ESMTP id e8CEXq509505; Tue, 12 Sep 2000 09:33:52 -0500 Message-ID: <39BE5AF3.21C6E4DC@eeyore.cm.utexas.edu> Date: Tue, 12 Sep 2000 09:33:55 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Eric Scerri CC: chemistry@ccl.net Subject: Re: CCL:CCL. HYBRIDIZATION NOT "REAL";V. FOCK References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I agree with your statement. I entered this discussion just to remind people that hybridization may be obtained from perturbation theory (mixing of s, p, d,... orbitals under the influence of the field of other atoms, bonding), and hence it is not just an arbitrary assumption (as it may appear at first sight). It leads to quite observable charge redistribution (s type admixture in different situations can be obtained also from spectroscopic data). This simple remark lead some people to global philosophycal deduction like "orbitals are not real", "quantum mechanics is not real", etc. I believe that such statements were of some interest 50 to 60 years ago, not now. It is well known that our knowledge is relative (not absolute) truth, but as a relative truth quantum mechanics is excelent with its predictions which are confirmed by experimental data. Isaac Bersuker Eric Scerri wrote: > Quantum Mechanics is a mathematical methodology which best (at this > time) reproduces existing knowledge. As such it is an approach that we can use > to understand our physical universe. While it describes what we perceive as > reality, it is no more "real" than the theory of phlogiston nor are its > constructs (i.e orbitals - hybridized or not) any more real than the billiard > ball representation of atomic structure. > > While I agree with the jist of this statement I wonder whether you might be > overstating the case? > > Phlogiston theory was long ago refuted and is therefore not even candidate for a true scientific entity. > > Not all the entities discussed by quantum mechanics have the same status surely? > Most people would want to say that electrons and protons are real entities. > > Your statement could be taken to mean that QM is a theory (epistemology) and > therefore may not give us direct access to real entities (ontology). > > But there is a problem that we can only get at the micoworld via quantum > mechanics so the neat distinction between the world and our description of the > world is blurred. > > I wonder whether you also intended the first sentence literally, namely that > QM makes no true predictions? If so I think this is debateable although it is > probably true that there are few genuine predictions, in the temporal sense, > made by QM. > > To get back to the main issue we can distinguish between atomic orbitals > (non real) and electron density (real). Each case can be dealt with separately > whereas a general statement about quantum mechnics as a whole, as above, would > suggest that all entities are lacking physical reality which to repeat is > going too far. > > eric scerri > > These are all artificial constructs > that help us humans find a frame of reference in which we can understand the > reality in which we are immersed. They have no 'reality' beyond that we assign > them to enhance our understanding ... > > Jim Kress > > ------------------------------------------------- > Dr. Eric Scerri, > Department of Chemistry & Biochemistry, > Charles E. Young Drive, > UCLA, > Los Angeles, CA 90095 > USA > > E-mail: scerri@chem.ucla.edu > > 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 -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Tue Sep 12 11:11:10 2000 Received: from arha.ciens.ula.ve (root@arha.ciens.ula.ve [150.185.128.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07061 for ; Tue, 12 Sep 2000 11:11:08 -0400 Received: from leviatan (leviatan.ciens.ula.ve [150.185.129.254]) by arha.ciens.ula.ve (8.9.1a/8.9.1) with ESMTP id LAA27279 for ; Tue, 12 Sep 2000 11:05:54 -0400 (GMT-0400) Date: Tue, 12 Sep 2000 11:16:20 -0400 (GMT) From: Javier Eduardo Cuervo Sanchez X-Sender: jcuervo@leviatan To: chemistry@ccl.net Subject: Problem with Gaussian 98 and AIM Calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I`ve had problems with some AIM calculations, The structure that I`am calculating have two rings, one of these is formed by hydrogen bonds. Gaussian can't find this critical Point and the output error is the following: 26 attractors - 27 bond point(s) + 1 ring point(s) - 0 cage point(s) = 0 The Hopf-Poincare condition cannot be satisfied. Apparently some critical points are missing. Abort! Error termination via Lnk1e in /usr/local/g98/l609.exe. Job cpu time: 0 days 2 hours 7 minutes 18.8 seconds. File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 2 Scr= 1 Could anyone help me please? Thanks in advanced Javier Cuervo CeCalCULA, Venezuela From chemistry-request@server.ccl.net Tue Sep 12 11:23:22 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07121 for ; Tue, 12 Sep 2000 11:23:21 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id IAA19138; Tue, 12 Sep 2000 08:22:09 -0700 (PDT) Message-ID: <004401c01ccd$37497bd0$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Yubo Fan" , References: <39BD802F.4C909AC9@guomai.sh.cn> Subject: Re: CCL:ECP basis set for Samarium Date: Tue, 12 Sep 2000 08:22:08 -0700 Hi! You must use the "GEN" and "Pseudo=Read" keywords in your route and append your Sm ECP and Basis functions to your input file. I have attached an example with rhodium. The Basis set goes first, terminated by a line containing "****" and is followed by a blank line and then the ECP. Let me know if this "explains by example" works for you. If I have been terse then I would be happy to explain in greater detail. Respectfully, Phillip Matz matz@wsunix.wsu.edu #P RHF/Gen Pseudo=Read Rh ecp28mhf 3 1 Rh RH 0 S 3 1.00 7.91774400 -2.41557750 6.84120700 3.09873820 2.95984000 0.28212560 S 1 1.00 1.33434100 1.00000000 S 1 1.00 0.59881000 1.00000000 S 1 1.00 0.12189400 1.00000000 S 1 1.00 0.04945200 1.00000000 S 1 1.00 0.01600000 1.00000000 P 2 1.00 4.13607900 -3.34435450 2.94628100 3.70374400 P 2 1.00 1.12230400 0.74622580 0.66617700 0.26988330 P 1 1.00 0.36574300 1.00000000 P 1 1.00 0.07668600 1.00000000 P 1 1.00 0.02417000 1.00000000 D 4 1.00 7.03289200 -0.01616040 2.30981900 0.27639870 0.99822800 0.48500260 0.41705700 0.39301990 D 1 1.00 0.16444700 1.00000000 D 1 1.00 0.05500000 1.00000000 **** RH 0 RH-ECP 4 28 G POTENTIAL 1 2 1.00000000 0.00000000 S-G POTENTIAL 2 2 11.72000000 225.34775400 2 5.82000000 32.82318900 P-G POTENTIAL 2 2 10.42000000 158.70941200 2 5.45000000 26.44410000 D-G POTENTIAL 2 2 8.82000000 62.75862600 2 3.87000000 10.97871900 F-G POTENTIAL 2 2 12.31000000 -30.09345600 2 6.16000000 -5.21848200 ----- Original Message ----- From: "Yubo Fan" To: Sent: Monday, September 11, 2000 6:00 PM Subject: CCL:ECP basis set for Samarium > Hi, Everyone, > > I have got an ECP basis set for Samarium recently. I don't know how to > use it in G98 input files. Could someone give me some help? Especially > the ECP part. > > The basis set is: > > Basis functions for Sm > > S 3 1.0 > 6.477588000 -.563323000 > 5.791813000 .961496000 > 2.412584000 -1.349481000 > S 1 1.0 > .606601000 1.000000000 > S 1 1.0 > .300832000 1.000000000 > S 1 1.0 > .055202000 1.000000000 > S 1 1.0 > .025731000 1.000000000 > P 3 1.0 > 4.026092000 .405992000 > 3.045263000 -.822491000 > .720567000 1.215545000 > P 1 1.0 > .313021000 1.000000000 > P 1 1.0 > .097310000 1.000000000 > P 1 1.0 > .033798000 1.000000000 > D 3 1.0 > 2.176192000 -.076284000 > .778621000 .385532000 > .323910000 .715687000 > D 1 1.0 > .131924000 1.000000000 > D 1 1.0 > .051322000 1.000000000 > **** > > ECP for Sm > > SM 4 51 > SM FIT G ECP > 1 > 1 1.0 0.0 > SM FIT S-G ECP > 2 > 2 4.4735 125.808087 > 2 2.2368 -6.169188 > SM FIT P-G ECP > 2 > 2 3.8294 86.294826 > 2 1.9147 -1.686917 > SM FIT D-G ECP > 2 > 2 2.6882 40.149862 > 2 1.3441 -0.140083 > SM FIT F-G ECP > 1 > 2 1.1741 8.925543 > > Sincerely > > 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 Tue Sep 12 12:23:56 2000 Received: from herald.cc.purdue.edu (herald.cc.purdue.edu [128.210.11.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07581 for ; Tue, 12 Sep 2000 12:23:55 -0400 Received: from [209.178.160.91] by herald.cc.purdue.edu with ESMTP for chemistry@ccl.net; Tue, 12 Sep 2000 11:23:39 -0500 Mime-Version: 1.0 Message-Id: In-Reply-To: <284DB94C7D54@DEPT.CHEM.POLIMI.IT> References: <284DB94C7D54@DEPT.CHEM.POLIMI.IT> Date: Tue, 12 Sep 2000 09:30:40 -0800 To: chemistry@ccl.net From: Eric Scerri Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK Content-Type: text/plain; charset="us-ascii" ; format="flowed" Guido Raos writes, >The discussion about the reality of hybrid orbitals reminds me a lot >of the one on the reality of molecular orbitals, which was on this >list a few weeks ago. > >I believe we all agree that no orbitals can ever be observed. For >this reason, some would then go on to argue that orbitals (of any >kind: hybrids, canonical or localized MO's, natural orbitals, >Kohn-Sham orbitals...) should be banned from our discussion of >chemical phenomena. I do not share this view. The userfulness of the >orbital concept should be judged from its "effectiveness" and >"economy" in the explanation of particular phenomena. In >particular, the canonical Hartree-Fock orbitals and energies help the >discussion of photoelectron spectra and of a number of symmetry >selection rules. However, hydrid orbitals do a much better job when >it comes to chemical bonding. etc. -------------------------- I am surprised to see this argument even needs to be presented to this forum given the prevalence of all kinds of very successful orbital methods in computational chemistry. Of course orbitals are supremely useful even though they are not 'real'. Did anyone seriously propose banning orbitals from discussion of chemical phenomena just on the grounds that they are not real? I should add that I am a relative newcomer to this list. * Does that someone not accept that the use of the square root of minus one is also very useful in many branches of mathematical physics, chemistry and engineering regardless of the lack of 'reality' of the square root of minus one as opposed to -1? I hope this will not lead to a discussion of whether numbers are 'real' although this might also prove interesting. The question has a long tradition in philosophy and philosophy of mathematics and many believe that numbers ARE real objects although not observable of course. This leads me to the earlier comment, by Oscar Ventura, who suggested that the whole discussion on orbitals etc. could be simplified by just taking "real" to mean observable. Such a 'Marxist' approach has some appeal but I believe is far too crude for the kinds of issues under discussion even without drifting off into philosophy of mathematics. For example quarks are considered to be 'real' particles in elementary particle physics but the theory itself now ensures that they cannot be directly observed. This may be a perverse aspect of modern particle theory but it cannot be swept aside too easily. eric scerri * I joined CCL after A. Hocquet mentioned my article "Have Orbitals Really Been Observed?' which is due to appear in Journal of Chemical Education. From chemistry-request@server.ccl.net Tue Sep 12 12:24:18 2000 Received: from efriedman.biomath.nyu.edu (EFRIEDMAN.BIOMATH.NYU.EDU [128.122.250.118]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07587 for ; Tue, 12 Sep 2000 12:24:17 -0400 Received: from localhost (strahs@localhost) by efriedman.biomath.nyu.edu (8.9.3/8.9.3) with ESMTP id MAA1956955 for ; Tue, 12 Sep 2000 12:24:12 -0400 (EDT) Date: Tue, 12 Sep 2000 12:24:12 -0400 From: Dan Strahs To: CHEMISTRY@ccl.net Subject: multiple alignment file format? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi: I apologize in advance for this slightly off-topic message... I am looking for definitions for the file formats used to store multiple sequence alignments. As you might imagine from the request, I'm writing some code to input this data. Can someone point me to a reference or a more relevant mailing list? Thanks! Dan Strahs From chemistry-request@server.ccl.net Tue Sep 12 11:27:30 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07163 for ; Tue, 12 Sep 2000 11:27:30 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA11654; Tue, 12 Sep 2000 11:27:15 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 12 Sep 2000 11:27:03 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com (lvlxch01.unitedcatalysts.com [10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G0S00CM15G26O@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 12 Sep 2000 11:24:02 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 12 Sep 2000 11:25:42 -0400 Content-return: allowed Date: Tue, 12 Sep 2000 11:25:41 -0400 From: "Shobe, Dave" Subject: more on AIM analysis when G98W fails To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D63854B@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA07164 A few more questions about options when G98W fails: #1. The AIMPAC download webpage http://www.chemistry.mcmaster.ca/aimpac/ describes the programs as being "vectorized". Will these run on my computer, which is not only a single-processor machine, but is Windows rather than Unix or Linux? #2. Is it possible to get bond orders, or has Cioslowski et al only made these available thru Gaussian? #3. It certainly would be easier to do this thru Gaussian. WHY does AIM=(charges,BO) fail so often? I couldn't even get pyrrole (HF/6-311++G**//CBS-4) to work. Has anyone had luck with changing to a different basis set, or anything like that?? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. From chemistry-request@server.ccl.net Tue Sep 12 13:25:21 2000 Received: from mcmail.cis.McMaster.CA (mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08449 for ; Tue, 12 Sep 2000 13:25:14 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id NAA13837; Tue, 12 Sep 2000 13:20:50 -0400 (EDT) Date: Tue, 12 Sep 2000 13:20:50 -0400 (EDT) From: "C.F. Matta" To: Javier Eduardo Cuervo Sanchez cc: chemistry@ccl.net Subject: Re: CCL:Problem with Gaussian 98 and AIM Calculations In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Try the program: Extreme of the aimpac program series, downloadable free at: http://www.chemistry.mcmaster.ca/aimpac/ Cheers, Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University _______________________ Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ On Tue, 12 Sep 2000, Javier Eduardo Cuervo Sanchez wrote: > > Hi, > > I`ve had problems with some AIM calculations, The structure that I`am > calculating have two rings, one of these is formed by hydrogen bonds. > Gaussian can't find this critical Point and the output error is the > following: > > 26 attractors - 27 bond point(s) + 1 ring point(s) - 0 cage point(s) > = 0 > > The Hopf-Poincare condition cannot be satisfied. > Apparently some critical points are missing. Abort! > Error termination via Lnk1e in /usr/local/g98/l609.exe. > Job cpu time: 0 days 2 hours 7 minutes 18.8 seconds. > File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 2 Scr= 1 > > Could anyone help me please? > > Thanks in advanced > > Javier Cuervo > CeCalCULA, Venezuela > > > -= 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 Tue Sep 12 12:01:48 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07455 for ; Tue, 12 Sep 2000 12:01:47 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id MAA13000; Tue, 12 Sep 2000 12:01:32 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 12 Sep 2000 12:01:20 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com (lvlxch01.unitedcatalysts.com [10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G0S00C2U717FS@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 12 Sep 2000 11:58:19 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 12 Sep 2000 11:59:59 -0400 Content-return: allowed Date: Tue, 12 Sep 2000 11:59:58 -0400 From: "Shobe, Dave" Subject: recommended visualization software? To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D63854C@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id MAA07456 Suppose I have a 3-dimensional array of data (commonly known as a cube file) about a molecule. For now I'm most interested in spin densities, transition densities, and electon density differences on ionization. I would like a way to visualize this data, both for my own understanding and for communication. I know that there are several commercial programs that do this, but I need to minimize my cost. :-( I alrady have GaussView (but if it has the ability to do this, I don't know how to activate it), and I have downloaded Casgen and Pgplot but can't get the Casgen examples to work. I am using a Windows PC and the languages I have are Salford Fortran95 and Perl, plus whatever version of Visual Basic comes with MS Office. Anyway, if someone out there can recommend cheap visualization software for this, I'd appreciate it. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. From chemistry-request@server.ccl.net Tue Sep 12 13:27:18 2000 Received: from hotmail.com (f122.law3.hotmail.com [209.185.241.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08471 for ; Tue, 12 Sep 2000 13:27:18 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 12 Sep 2000 10:27:03 -0700 Received: from 130.86.253.240 by lw3fd.law3.hotmail.msn.com with HTTP; Tue, 12 Sep 2000 17:27:02 GMT X-Originating-IP: [130.86.253.240] From: "narisara tanvirat" To: garrett@scrips.edu Cc: chemistry@ccl.net Subject: Problem with using addsol Date: Tue, 12 Sep 2000 17:27:02 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 12 Sep 2000 17:27:03.0039 (UTC) FILETIME=[AA3680F0:01C01CDE] Dear Sir, I have installed AutoDock 3.0.5 and everything seems to be fine. However, when I run addsol script with some example files, I couldn't convert pdbq to pdbqs. I'm just wandering if it's possible that the script has changed after execute it, sounds strange but it's only one thing I can think of. Thanks for your time Narisara Tanvirat _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Tue Sep 12 14:00:37 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08731 for ; Tue, 12 Sep 2000 14:00:37 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA17755; Tue, 12 Sep 2000 14:00:20 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 12 Sep 2000 14:00:08 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com (lvlxch01.unitedcatalysts.com [10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G0S00CKDCEMFS@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 12 Sep 2000 13:54:22 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 12 Sep 2000 13:56:02 -0400 Content-return: allowed Date: Tue, 12 Sep 2000 13:56:00 -0400 From: "Shobe, Dave" Subject: RE: CCL. HYBRIDIZATION NOT "REAL";V. FOCK To: chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D63854E@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA08732 I for one have been enjoying the philosophical discussion. Perhaps more useful(?) questions to discuss are: 1. Is hybridization a well-defined concept within quantum theory? (I suspect this is what the original posting "really" meant by "real")? 2. Is hybridization a useful concept in rationalizing or thinking about wave functions, or about the properties of molecules? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. -----Original Message----- From: Isaac B. Bersuker [mailto:bersuker@ne059.cm.utexas.edu] Sent: Tuesday, September 12, 2000 12:34 PM To: Eric Scerri Cc: chemistry@ccl.net Subject: CCL:CCL. HYBRIDIZATION NOT "REAL";V. FOCK I agree with your statement. I entered this discussion just to remind people that hybridization may be obtained from perturbation theory (mixing of s, p, d,... orbitals under the influence of the field of other atoms, bonding), and hence it is not just an arbitrary assumption (as it may appear at first sight). It leads to quite observable charge redistribution (s type admixture in different situations can be obtained also from spectroscopic data). This simple remark lead some people to global philosophycal deduction like "orbitals are not real", "quantum mechanics is not real", etc. I believe that such statements were of some interest 50 to 60 years ago, not now. It is well known that our knowledge is relative (not absolute) truth, but as a relative truth quantum mechanics is excelent with its predictions which are confirmed by experimental data. Isaac Bersuker Eric Scerri wrote: > Quantum Mechanics is a mathematical methodology which best (at this > time) reproduces existing knowledge. As such it is an approach that we can use > to understand our physical universe. While it describes what we perceive as > reality, it is no more "real" than the theory of phlogiston nor are its > constructs (i.e orbitals - hybridized or not) any more real than the billiard > ball representation of atomic structure. > > While I agree with the jist of this statement I wonder whether you might be > overstating the case? > > Phlogiston theory was long ago refuted and is therefore not even candidate for a true scientific entity. > > Not all the entities discussed by quantum mechanics have the same status surely? > Most people would want to say that electrons and protons are real entities. > > Your statement could be taken to mean that QM is a theory (epistemology) and > therefore may not give us direct access to real entities (ontology). > > But there is a problem that we can only get at the micoworld via quantum > mechanics so the neat distinction between the world and our description of the > world is blurred. > > I wonder whether you also intended the first sentence literally, namely that > QM makes no true predictions? If so I think this is debateable although it is > probably true that there are few genuine predictions, in the temporal sense, > made by QM. > > To get back to the main issue we can distinguish between atomic orbitals > (non real) and electron density (real). Each case can be dealt with separately > whereas a general statement about quantum mechnics as a whole, as above, would > suggest that all entities are lacking physical reality which to repeat is > going too far. > > eric scerri > > These are all artificial constructs > that help us humans find a frame of reference in which we can understand the > reality in which we are immersed. They have no 'reality' beyond that we assign > them to enhance our understanding ... > > Jim Kress > > ------------------------------------------------- > Dr. Eric Scerri, > Department of Chemistry & Biochemistry, > Charles E. Young Drive, > UCLA, > Los Angeles, CA 90095 > USA > > E-mail: scerri@chem.ucla.edu > > 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 -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu -= 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 Tue Sep 12 14:29:36 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08912 for ; Tue, 12 Sep 2000 14:29:36 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id LAA00162; Tue, 12 Sep 2000 11:29:20 -0700 (PDT) Message-ID: <001301c01ce7$5d32b040$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Phillip Matz" , "Yubo Fan" , References: <39BD802F.4C909AC9@guomai.sh.cn> <004401c01ccd$37497bd0$b4297986@chem.wsu.edu> Subject: Re: CCL:ECP basis set for Samarium Date: Tue, 12 Sep 2000 11:29:19 -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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 I'm not sure how my original post ended being changed, but my original post to the CCL list read "pseudo=read" with no "3D" in front of "Read". However the message posted states "3DRead"??? 3DRead is incorrect, it is also NOT in my post to CCL, how on earth did it get there? Does CCL use a message massager which accidentally edited my original posting? Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Phillip Matz" To: "Yubo Fan" ; Sent: Tuesday, September 12, 2000 8:22 AM Subject: CCL:ECP basis set for Samarium > Hi! > > You must use the "GEN" and "Pseudo=Read" keywords in your route and > append your Sm ECP and Basis functions to your input file. I have > attached an example with rhodium. > The Basis set goes first, terminated by a line containing "****" and is > followed by a blank line and then the ECP. Let me know if this > "explains by example" works for you. If I have been terse then I would > be happy to explain in greater detail. > > Respectfully, > Phillip Matz > matz@wsunix.wsu.edu > > #P RHF/Gen Pseudo=Read > > Rh ecp28mhf > > 3 1 > Rh > > RH 0 > S 3 1.00 > 7.91774400 -2.41557750 > 6.84120700 3.09873820 > 2.95984000 0.28212560 > S 1 1.00 > 1.33434100 1.00000000 > S 1 1.00 > 0.59881000 1.00000000 > S 1 1.00 > 0.12189400 1.00000000 > S 1 1.00 > 0.04945200 1.00000000 > S 1 1.00 > 0.01600000 1.00000000 > P 2 1.00 > 4.13607900 -3.34435450 > 2.94628100 3.70374400 > P 2 1.00 > 1.12230400 0.74622580 > 0.66617700 0.26988330 > P 1 1.00 > 0.36574300 1.00000000 > P 1 1.00 > 0.07668600 1.00000000 > P 1 1.00 > 0.02417000 1.00000000 > D 4 1.00 > 7.03289200 -0.01616040 > 2.30981900 0.27639870 > 0.99822800 0.48500260 > 0.41705700 0.39301990 > D 1 1.00 > 0.16444700 1.00000000 > D 1 1.00 > 0.05500000 1.00000000 > **** > > RH 0 > RH-ECP 4 28 > G POTENTIAL > 1 > 2 1.00000000 0.00000000 > S-G POTENTIAL > 2 > 2 11.72000000 225.34775400 > 2 5.82000000 32.82318900 > P-G POTENTIAL > 2 > 2 10.42000000 158.70941200 > 2 5.45000000 26.44410000 > D-G POTENTIAL > 2 > 2 8.82000000 62.75862600 > 2 3.87000000 10.97871900 > F-G POTENTIAL > 2 > 2 12.31000000 -30.09345600 > 2 6.16000000 -5.21848200 > > ----- Original Message ----- > From: "Yubo Fan" > To: > Sent: Monday, September 11, 2000 6:00 PM > Subject: CCL:ECP basis set for Samarium > > > > Hi, Everyone, > > > > I have got an ECP basis set for Samarium recently. I don't know how to > > use it in G98 input files. Could someone give me some help? Especially > > the ECP part. > > > > The basis set is: > > > > Basis functions for Sm > > > > S 3 1.0 > > 6.477588000 -.563323000 > > 5.791813000 .961496000 > > 2.412584000 -1.349481000 > > S 1 1.0 > > .606601000 1.000000000 > > S 1 1.0 > > .300832000 1.000000000 > > S 1 1.0 > > .055202000 1.000000000 > > S 1 1.0 > > .025731000 1.000000000 > > P 3 1.0 > > 4.026092000 .405992000 > > 3.045263000 -.822491000 > > .720567000 1.215545000 > > P 1 1.0 > > .313021000 1.000000000 > > P 1 1.0 > > .097310000 1.000000000 > > P 1 1.0 > > .033798000 1.000000000 > > D 3 1.0 > > 2.176192000 -.076284000 > > .778621000 .385532000 > > .323910000 .715687000 > > D 1 1.0 > > .131924000 1.000000000 > > D 1 1.0 > > .051322000 1.000000000 > > **** > > > > ECP for Sm > > > > SM 4 51 > > SM FIT G ECP > > 1 > > 1 1.0 0.0 > > SM FIT S-G ECP > > 2 > > 2 4.4735 125.808087 > > 2 2.2368 -6.169188 > > SM FIT P-G ECP > > 2 > > 2 3.8294 86.294826 > > 2 1.9147 -1.686917 > > SM FIT D-G ECP > > 2 > > 2 2.6882 40.149862 > > 2 1.3441 -0.140083 > > SM FIT F-G ECP > > 1 > > 2 1.1741 8.925543 > > > > Sincerely > > > > 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 Tue Sep 12 14:57:48 2000 Received: from facepe.dqf.ufpe.br (root@facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA09075 for ; Tue, 12 Sep 2000 14:51:28 -0400 Received: from npd.ufpe.br (hartree.dqf.ufpe.br [150.161.5.226]) by facepe.dqf.ufpe.br (8.9.3/8.8.7) with ESMTP id PAA03276 for ; Tue, 12 Sep 2000 15:53:54 -0300 Message-ID: <39BE7B1C.7B14BC3@npd.ufpe.br> Date: Tue, 12 Sep 2000 15:51:08 -0300 From: =?iso-8859-1?Q?Ot=E1vio=20Lu=EDs?= de Santana X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Compiling the NBO program. Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers: Recently I try to compile the NBO program with a number of atoms and orbitals grater than default (MAXATM = 99, MAXBAS = 500). When I make the modification in the parameters, the program don’t run properly. Certainly, the indexation of the natural bonds must be corrected, that implies in additional modification of the program... Anyone knows how to modify the NBO program conveniently, so that the program run with a different (grater than default) number of atoms and orbitals? How can a do it??!! Thanks in advance Otávio Luís de Santana From chemistry-request@server.ccl.net Tue Sep 12 14:41:13 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA09022 for ; Tue, 12 Sep 2000 14:41:13 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id LAA22070; Tue, 12 Sep 2000 11:41:13 -0700 (PDT) Message-ID: <000701c01ce9$066edb60$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Shobe, Dave" , "'CCL'" References: <157A51F55AAAD3119CD70008C7B1629D63854C@lvlxch01.unitedcatalysts.com> Subject: Re: CCL:recommended visualization software? Date: Tue, 12 Sep 2000 11:41:12 -0700 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello David! Try Molden3.6 for windows or linux, it reads Gaussian cube files just fine and the software is free. http://www.caos.kun.nl/~schaft/molden/windowsnt95.html http://www.caos.kun.nl/~schaft/molden/molden.html Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Shobe, Dave" To: "'CCL'" Sent: Tuesday, September 12, 2000 8:59 AM Subject: CCL:recommended visualization software? > Suppose I have a 3-dimensional array of data (commonly known as a > cube file) about a molecule. For now I'm most interested in spin densities, > > transition densities, and electon density differences on ionization. > > I would like a way to visualize this data, both for my own understanding > and for communication. I know that there are several commercial > programs that do this, but I need to minimize my cost. :-( > > I alrady have GaussView (but if it has the ability to do this, I don't know > how to activate it), and I have downloaded Casgen and Pgplot but > can't get the Casgen examples to work. I am using a Windows PC > and the languages I have are Salford Fortran95 and Perl, plus whatever > version of Visual Basic comes with MS Office. > > Anyway, if someone out there can recommend cheap visualization > software for this, I'd appreciate it. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Any opinions herein are not necessarily representative of Süd-Chemie. > > > > -= 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 Tue Sep 12 16:15:31 2000 Received: from mcmail.cis.McMaster.CA (mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA09653 for ; Tue, 12 Sep 2000 16:15:31 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id QAA06354; Tue, 12 Sep 2000 16:13:14 -0400 (EDT) Date: Tue, 12 Sep 2000 16:13:14 -0400 (EDT) From: "C.F. Matta" To: "Shobe, Dave" cc: "'CCL'" Subject: Re: CCL:more on AIM analysis when G98W fails In-Reply-To: <157A51F55AAAD3119CD70008C7B1629D63854B@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again, Please read my answers amongst your lines below: > #1. The AIMPAC download webpage > http://www.chemistry.mcmaster.ca/aimpac/ > describes the programs as being "vectorized". > Will these run on my computer, which is not only a single-processor machine, > but is Windows rather than Unix or Linux? Nope, AIPAC are designed for a UNIX or a LINUX platform. Nothing would prevent one to compile them using a FORTRAN77 compiler running under Windows, but one may have to do a few modifications. There is a Windows program that implements the Quantum Theory of Atoms-In-Molecules (AIM) , it is called AIM2000, and also available free of charge from: http://gauss.fh-bielefeld.de/aim2000/ > #2. Is it possible to get bond orders, or has Cioslowski et al only made > these available thru Gaussian? I wrote a shell scripts that calculates the delocalization/localization indeces using the integration files that AIMPAC produces. > #3. It certainly would be easier to do this thru Gaussian. > WHY does AIM=(charges,BO) fail so often? I couldn't even > get pyrrole (HF/6-311++G**//CBS-4) to work. Has anyone > had luck with changing to a different basis set, or anything > like that?? The GAUSSIAN implementation of AIM does indeed fails frequently. On the other hand, the AIMPAC software very rarely fails (Never happened to in five years since I started using it). AIMPAC is very reliable, but requires more user input (and thus more flexibility and more output) than the AIM-options in GUAUSSIAN. Hope the above helps. Cherif F. Matta ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ______________________ | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ From chemistry-request@server.ccl.net Tue Sep 12 22:57:41 2000 Received: from smtp.oz.nthu.edu.tw (smtp.Oz.nthu.edu.tw [140.114.63.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA11212 for ; Tue, 12 Sep 2000 22:57:39 -0400 Received: from oz.nthu.edu.tw (R214c.Chem.nthu.edu.tw [140.114.45.230]) by smtp.oz.nthu.edu.tw (8.9.3/8.9.3) with ESMTP id KAA08800 for ; Wed, 13 Sep 2000 10:57:32 +0800 (CST) Message-ID: <39BEED01.7FA9BF23@oz.nthu.edu.tw> Date: Wed, 13 Sep 2000 10:57:05 +0800 From: Chiu-Ling Lin X-Mailer: Mozilla 4.5 [zh-TW] (Win95; I) X-Accept-Language: zh-TW MIME-Version: 1.0 To: CHEMISTRY@server.ccl.net Subject: Basis Sets of Iodine ? Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Dear friends, Does anyone know where I can get the basis sets of iodine which contain diffusion functions, like 6-31+G* or 6-31++G*? Any reply will be appreciated and helpful. Best Regards, Anne Lin ********************************************** Anne Lin E-mail: d867403@oz.nthu.edu.tw Dept. of chemistry National Tsing Hua University Hsinchu 30043, Taiwan, R.O.C. ********************************************** From chemistry-request@server.ccl.net Tue Sep 12 23:17:00 2000 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA11331 for ; Tue, 12 Sep 2000 23:16:59 -0400 Received: from p17-78.dialup.UVic.CA (p17-78.dialup.UVic.CA [142.104.17.78]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id UAA83136 for ; Tue, 12 Sep 2000 20:16:52 -0700 From: Roy Jensen To: CHEMISTRY@ccl.net Subject: Deduction of electronic properties from Gaussian output. Date: Tue, 12 Sep 2000 20:18:06 -0700 Message-ID: X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id XAA11332 Thanks to those of you who have aided in my use of ab initio calculations thus far. With your help, I was able to get several transition metal cluster calculations running. Our lab uses mass spectrometry and spectroscopy to detect and characterize species. I was asked a question I cannot answer. That, of course led to more questions... 0. Many texts and manuals explain how to do quantum chemistry or use ab initio packages. Is there an introductory reference that explains how to extract information from the output, Gaussian in this case? 1. How can I tell if I need to use guess=alter? 2. Is it reasonable to run the same complex as a singlet, triplet, quintet, and septet and determine the ground state multiplicity as the job that has the lowest energy? 3. I generally run NBO analysis on these complexes. How do I determine the electronic angular momentum? 4. Is it reasonable to _estimate_ allowed and forbidden electronic transitions by using the orbital energy levels provided from the optimized geometries? I understand that CIS and CASSCF calculations would provide better results. I have been using the UB3LYP/LANL2DZ basis set for the calculations; MP2/anything takes too long to converge. Roy Jensen