From chemistry-request@server.ccl.net Sun Sep 17 18:32:45 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 SAA12435 for ; Sun, 17 Sep 2000 18:32:45 -0400 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id SAA03021 for ; Sun, 17 Sep 2000 18:32:39 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au [138.194.46.107]) by mercury.chem.csiro.au (8.9.3/8.9.3) with ESMTP id JAA01353; Mon, 18 Sep 2000 09:32:22 +1100 (EST) X-Sender: win097@clex1.vic.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 18 Sep 2000 09:32:19 +1100 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Symposium on Mathematical and Computational Aspects of Molecular Design at Pacifichem 2000 Dec 14-19 2000 in Honolulu Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id SAA12436 Pacifichem is on in December. Further details can be found at http://www.acs.org/meetings/pacific2000/ The conference will contain over 8600 research presentations by individuals from more than 50 countries! SYMPOSIUM 140 Co-organizers: Gerry Maggiora, Glen Kellogg, Toshimasa Takahashi, David Winkler 7.00-10.30pm Friday Session 1 Similarity, Diversity and Libraries (7 x 30 minutes) ------------------------------------------------------------------------ Pearlman Evolving Roles for Combichem and Diversity Software Maggiora An Information-Theoretic Approach to Cell-Based mappings in Chemistry Spaces Agrafiotis Multidimensional Scaling of Massive Similarity Tables Gussio Use of Pharmacophore Analysis in Mining Biological Data at the National Cancer Institute Gottfries ChemGPS: A Chemical Space Navigation Tool Shi R-group Feature Vector Representation and its Application in the Rapid Lead Optimization of Glucagon Antagonists Fujita Characteristic-monomial method for enumeration of isomers. Comparison with unit-subduced-cycle-index methods 9.00-12.30 Saturday Session 2 Novel QSAR Paradigms (7 x 30 minutes) ----------------------------------------------------------------- Crippen A Simple, Continuous Chirality Measure Labute A Widely-Applicable Set of Molecular Descriptors Chuman A Novel Three-dimensional QSAR Procedure: Voronoi Fields Winkler Robust QSAR using Automatic Relevance Determination and Bayesian Neural Nets Burden SAR using Gaussian Processes Okada SAR Discovery using the Cascade Model Mezey Quantum Holography as a Computational Tool for Molecular Design 2.00-5.30pm Saturday Session 3 Modelling Molecular interactions (7 x 30 minutes) ----------------------------------------------------------------------------- Nicholls Rapid Structure Generation, Shape Classification, Docking, and Scoring Takahashi Representation of Hydrophobic Profile of Chemical Compounds Based on The TFS Method Kellogg Empirical Free Energy Scoring of Biological Interactions. Understanding the Effects of Site-Directed Mutations on Protein-Protein Associations Nakazawa Alpha Helix Folding in Isolated S-Peptide of RNase A by Monte carlo Simulated Annealing Karuso Design and Synthesis of Novel Peptidyl Prolyl Isomerase (PPI) Inhibitors Vercauteren Molecular Docking Using a GA Approach Based on Graphs of Critical Points of Electron Density Meurice Simultaneous Superimposition of Several Rigid and Flexible Benzodiazepine-Like Ligands Using a Specific GA Strategy Total talks 21 x 30 minutes Speaker origin: USA, Canada, Japan, Australia, Europe, South America POSTERS Sunday evening ------------------------ 1. Shimazaki The Relationships Betwen Structural/Electronic Properties And Odour Activities Of Pyrazine Derivatives 2. Güner Recent Developments in Pharmacophore Perception in Drug Design 3. Martin OSPPREYS: an Oriented Substituent Pharmacophore PRopErtY Space 4. Svensson Combinatorial Library Design: An Integrated Approach Based on Interactive Visualization, Property and Structure-based Selection of Reagents and Products. 5. Kato An Approach to Automated Identification of Three-Dimensional Protein Motifs 6. Pogliani Modelling with Molecular Pseudo-Connectivity Descriptors 7. Embrechts GA Approaches for Successful QSAR Modelling 8. Wheelock 3D QSAR Analysis of Inhibition of Murine Soluble Epoxide Hydrolase (MsEH) by Benzoylureas, aryl ethers and their Analogues 9. Yasri Towards and Optimal Procedure for Variable Selection and QSAR Model Building 10. Bradley Informative Library Design as an Efficient Tool for Lead Generation and Optimization. Method and Applications 11. Vargyas Finding Guarenteed Global Energy Minimas for Conformationally Flexible Molecules 12. Galvao Electronic Indices Methodology (EIM) Applied to the Study of Taxol and Derivatives 13. Galvao New Methodology to Classify Active and Inactive Organic Molecules using Quantum Mechanical Descriptors 14. Barone On the Electronic Structure of Antitumour Drugs Ellipticines 15. Wang Harness the Power of Computers in Drug Design for Lead Discovery and Optimization 16. Wang Computational Approaches for Structure-Based Rational design of HIV-1 Protease Inhibitors: 2-D and 3-D Molecular Modelling 17. Griffith New Computer-Aided Drug Design Methodologies 18. Trinajstic CROMRsel-s: Efficient Algorithms for the Selection of Most Important Variables in QSAR/QSPR Modelling 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 From chemistry-request@server.ccl.net Mon Sep 18 00:46:15 2000 Received: from sunflare.ccs.yorku.ca (sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA13734 for ; Mon, 18 Sep 2000 00:46:14 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id AAA29684 for ; Mon, 18 Sep 2000 00:45:53 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id e8I4jro04300 for chemistry@ccl.net; Mon, 18 Sep 2000 00:45:53 -0400 (EDT) From: Wai-To Chan Message-Id: <200009180445.e8I4jro04300@curl.gkcl.yorku.ca> Subject: Pauling and orbitals To: chemistry@ccl.net Date: Mon, 18 Sep 2000 00:45:53 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I don't see how Pauling's statement, when considered in the context of his J Chem Ed article, can be viewed as naive philosophicaly or scientificaly. Consider what you think how Gilbert Lewis should respond when asked if electron-pairs exist. Granted that Lewis could be excused for not knowing quantum mechanics which preclude spatial localization of two electrons he must have known the coulomb's law for repulsion between electrons. Yet we have been using Lewis model to explain much of descriptive chemistry to this day. We also use aufbau principle to rationalize the periodic table when we know that these K, L, M and N shells and S, P, D and F wavefunctions don't exist; or at least they don't exist for all elements beyond hydrogen. But then our concept of valence shells/orbitals based on aufbau principle is very much in line with the chemical periodicity of elements. The Lewis electron-pair model has a validity that seem to transcend our understanding of QM. Hence, in spite of its not being a physical entity we continue to apply it to interpretation of chemical reactivity in such a manner as to imply its 'existence'. In light of this I think it is not unreasonable to say that electron-pairs/orbitals exist. Wai-To Chan Eric Scerri (scerri@chem.ucla.edu) wrote: <<<<<<<<<<<<<<<<<<<<<<<<< THe original question which started this thread was partly about Pauling's OWN views about hybridization and orbitals. I think Pauling was surprisingly naive philosophically when it came to interpretation of what he was doing. I base this on the following personal anecdote. When the debate with Ogilvie was taking place in J. Chem. Ed. the same issue that carried the Pauling response also included three other reponses including a brief piece by myself. I used this as an excuse to get in touch with Pauling to try to explore his view further. In his reply he said almost verbatim, "Orbitals clearly exist since Mulliken and I have been writing about them for the past 60 years" I could not resist replying that storytellers have also been writing about unicorns for many years. Dr. Eric R. Scerri >>>>>>>>>>>>>>>>>>>> From chemistry-request@server.ccl.net Mon Sep 18 03:08:02 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 DAA14254 for ; Mon, 18 Sep 2000 03:08:01 -0400 Received: from p17-29.dialup.UVic.CA (p17-29.dialup.UVic.CA [142.104.17.29]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id AAA74470; Mon, 18 Sep 2000 00:07:49 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: SUMMARY: Deduction of electronic properties from Gaussian output. Date: Mon, 18 Sep 2000 00:09:08 -0700 Message-ID: References: In-Reply-To: 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 DAA14255 Thanks to those who responded. I have summarized the answers below. Question 3 may not have been phrased well; I may have figured it out and will let you know shortly... Roy Jensen ***************************************************************** 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? "Phillip Matz" > 0. Absolutely. Try the paperback titled "Exploring Chemistry with > Electronic Structure Methods, 2nd Ed." It was written by Foresman and > Frisch for Gaussian Inc. Foresman works with Gaussian Inc. as you may well > already know. The ISBN is 0-9636769-3-8 and is $42 US at amazon.com - try > this link: > http://www.amazon.com/exec/obidos/ASIN/0963676938/qid%3D/104-4973463-2525537 > > This book is good, it is by far the best you can buy but it still won't > explain exactly how to do some things - but it is far more verbose than the > G98 manual! elewars > Two introductory refs on using gaussian output are: > (1) "Exploring chemistry with Electronic Structure Methods", Second Ed., J. B. > Foresman and A. Frisch, Gaussian Inc., Pittsburgh, PA, 1996. This is guide to using > and interpreting the results of G94, but it's good for G98 too. The first ed., was > for G92. A third Ed. is being prepared. > (2) Out of date but still of some value is the first Ed. of "A Handbook of > computational chemistry", Tim Clark, Wiley, 1985. I hear that a new edition is, or > soon will be, out. The new edition should be very useful. 1. How can I tell if I need to use guess=alter? "Shobe, Dave" > I don't know of a way to test a "stable" wavefunction to see if it's the > lowest energy state, anymore than I know of a way to test if a particular > geometry is the lowest energy for the system. It's the "a local minimum is > not necessarily the global minimum" problem. You could try switching the > HOMO and LUMO (especially if they have different symmetries) and seeing what > happens. > > One thing I haven't tried but might work: if you do a CIS calculation, maybe > it will show a negative excitation energy if you don't start with a ground > state. (Reading below, it sounds like you'd like to do a CIS calc. anyway > if you can afford it). > > Also, if you're calculating a series of similar complexes, you might see > whether the orbitals (especially the SOMOs) are similar. You wouldn't > expect NiCl2(NH3)2 and NiCl2(ethylenediamine) to have wildly different > electron configurations for example. "Phillip Matz" > 1. guess=alter is really only important if you are going to be using the > unoccupied ground state orbitals in a post-scf calculation. An > excited-state calculation (CIS) will use unoccupied orbitals, as will a > CASSCF calc. The only time I have encountered the need for guess=alter on a > ground state electronic calculation is if they are having problems getting > the wavefunction to converge. In that case the initial guess (Extended > Huckel for 3rd row and beyond) is usually so bad that the virtual annealing > algorithms cannot overcome the inverted orbital assignment and the > wavefunction fails to converge. I can help you with performing both types > of calculations if you like/need to. Otherwise you do not need to use this > route command. Valentina Vetere > I'm doing in this way. I'm first performing a calculation with guess=only > Pop=Reg with big distance between the transition metal and ligands. > Looking to the output you have all the occupations and because of the big > distance between ligands and metal the `orbitals'on metals looks like atomic > one . After I'm going to see the number of electrons described with the RECP > basis set on my transition metal. As example immagine this number is 16, and > that my metal is Fe(II). So I have 16-2=14 electrons in the valence basis set > of FeII. > I'm go to see on the periodic table the valence configuration of Fe(2) for 14 > electrons ( In our example is 3s2, 3p6, 3d6). Now, looking to my output I have > to find this occupations on FeII. If it is different I need an alter. John Bushnell > For transition metal systems in general, you can't. Trying every > "reasonable" possibility seems to be the safest bet. 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? "Shobe, Dave" > That's basically what you have to do, although you may be able to rule some > of these out by chemical intuition. Be careful, though: the HF method > heavily favors high-spin states. (I.e. there's more correlation energy > within electron pairs than between unpaired electrons). > I don't know if that applies to B3LYP or not. "Phillip Matz" > 2. Absolutely. This is a routine procedure for determining the lowest > electronic configuration of a molecule for which the configuration is not > experimentally known. And since you are performing an ab initio > calculation, you truly should not be required to predetermine what the > spin-multiplicity is for the sake of the computational program. It is an > option in G98 purely to reduce the computation time by reducing the total > number of variables with which the algorithms must minimize the energy with > respect to. In fact, using the stable=opt command in your route should > result in G98 telling you (essentially, it gives you S^2 from which you can > deduce S and hence the multiplicity) what is the energetically lowest > electronic configuration for your system regardless of what you place in the > route line (singlet, triplet, etc.). John Bushnell > If you can get them all to converge to a good spin state, yes. > By a good spin state, I mean that the value of S**2 is close to > the correct value. Since you are using B3LYP, the spin contamination > should be small (even before annihilation). You should ALWAYS check > S**2. As Dave Shobe pointed out, HF calculations will tend to favor > higher spin states due to the free correlation energy. Similarly, > HF will tend to favor 4s3dn-1 states over 3dn states of the same > multiplicity. However, B3LYP tends to favor the 3dn states over > 4s3dn-1 of the same multiplicity. In any case, be more cautious in > making firm conclusions about relative stabilities of different spin > states. 3. I generally run NBO analysis on these complexes. How do I determine the electronic angular momentum? John Bushnell > Real (spatial) orbitals can be written as linear combinations of > angular momentum orbitals. It is not usually that straightforward to > say that a particular spatial occupation has a particular 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. "Shobe, Dave" > I imagine the trends within a series of similar complexes would be useful > information. "Phillip Matz" > 4. Sometimes... If (and only if) your system has symmetry and Gaussian > has taken advantage of that symmetry in determining what your orbitals are > and it uses those orbitals to form SALC molecular orbitals then those > molecular orbitals will be symmetry labeled (i.e. you will see a B1g or an > A1 or any other symmetry label). From these symmetry labels you can > determine if the electronic transition moment is forbidden or not. Are you > Group Theory savvy? It is quite easy to do the above even if you are not > familiar with chemical group theory. Let me know and I would be more than > happy to explain how the molecular orbital symmetry labels and your > molecule's assigned geometry will tell you exactly what orbital electronic > transitions will be forbidden. > > CIS and CASSCF will do three major things for you in this regard. a) they > will attempt to quantify the extent to which the transition is allowed, b) > they will do this even when your system has no symmetry (i.e. C1), and c) > they will attempt to quantify the transition energy to a better > approximation than simply subtracting the ground state orbital energies > involved in the transition. > > Roy, I'm sorry for the length of this message... If you want to pursue > discussion on any of my responses above I would be honored. If you want to > ask the CCL list about any of the above (as to whether it is true or not) I > would not be insulted. And if you feel that this message should be posted > on CCL, go for it - that is fine by me. Like I said before, I hope this > helps you in some form or another! "Samuel A. Abrash" > If the level of theory you're using is HF, then definitely no. The reason > is that all virtual orbitals in an HF calculation are not energy levels of > the neutral but of the corresponding anion. > > One of the weaknesses of CIS is that it uses these virtual orbitals as the > basis for it's 1st order CI, and so must involve many orbitals to get > energies approaching accuracy. > > CASSCF is somewhat better, but still a relatively low level of theory. > > The real challenge you face in estimating excited state energies is that > your systems tend to have fairly close lying excited states of the same > symmetry so that extensive mixing can occur. Single refernce state methods > won'd deal well with this problem. Accurate determination of the excited > state energies requires a multiple reference state approach like MRD CI. From chemistry-request@server.ccl.net Mon Sep 18 04:12:17 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA14754 for ; Mon, 18 Sep 2000 04:12:16 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id KAA05809 for ; Mon, 18 Sep 2000 10:12:07 +0200 (MET DST) Date: Mon, 18 Sep 2000 10:12:07 +0200 (MET DST) Message-Id: <200009180812.KAA05809@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: archives to mgep or avi Hi, is there any way to convert Tinker or XMol archives into a 'movie' format that is readible for a powerpoint presentation ? Any suggestions are welcome ! Thanks Serge Kwasniewski ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Sep 18 08:07:56 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 IAA16471 for ; Mon, 18 Sep 2000 08:07:56 -0400 Received: from physics.msuiit.edu.ph (root@physics.msuiit.edu.ph [202.78.82.11]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id IAA10411 for ; Mon, 18 Sep 2000 08:07:40 -0400 (EDT) Received: from localhost (alguno@localhost) by physics.msuiit.edu.ph (8.9.3/8.9.3) with ESMTP id UAA19880 for ; Mon, 18 Sep 2000 20:06:46 +0800 Date: Mon, 18 Sep 2000 20:06:46 +0800 (PHT) From: Arnold Alguno To: chemistry@ccl.net Subject: Inquiry! In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: Anybody here who have a result on the energy band gap of intrinsic polythiophene, lithium doped polythiophene, Na-doped polythiophene and BF4-doped poltythiophene. please send your response to my email address. Thank you! _________ Very truly yours, ARNOLD C. ALGUNO IITHEP, Department of Physics MSU-IIT, Iligan City Philippines alguno@physics.msuiit.edu.ph From chemistry-request@server.ccl.net Mon Sep 18 08:24:47 2000 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA16560 for ; Mon, 18 Sep 2000 08:24:42 -0400 Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by aleph.net.uniovi.es (PMDF V6.0-24 #45227) with ESMTP id <01JUBL4WXKWE00RLSR@aleph.net.uniovi.es> for chemistry@ccl.net; Mon, 18 Sep 2000 14:24:24 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id OAA07031; Mon, 18 Sep 2000 14:24:13 +0200 (METDST) Date: Mon, 18 Sep 2000 14:24:13 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:Pauling and orbitals To: chemistry@ccl.net, owner-chemistry@server.ccl.net Cc: pueyo@pinon.ccu.uniovi.es Message-id: <200009181224.OAA07031@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT ] Date: Mon, 18 Sep 2000 00:45:53 -0400 (EDT) ] From: Wai-To Chan ] Subject: CCL:Pauling and orbitals ] ] Eric Scerri (scerri@chem.ucla.edu) wrote: ]> I think Pauling was surprisingly naive philosophically when it came to ]> interpretation of what he was doing. I base this on the following personal ]> anecdote. When the debate with Ogilvie was taking place in J. Chem. Ed. ]> the same issue that carried the Pauling response also included three other ]> reponses including a brief piece by myself. I used this as an excuse to ]> get in touch with Pauling to try to explore his view further. In his reply ]> he said almost verbatim, ]> "Orbitals clearly exist since Mulliken and I have been writing about them ]> for the past 60 years" ] ] I don't see how Pauling's statement, when considered in the context ] of his J Chem Ed article, can be viewed as naive philosophicaly or ] scientificaly. Certainly, it look more like the annoyed answer of someone not very willing to discuss the concept at that time or in that circumstances. Pauling's books and articles, usually written with great care and in a very pedagogical way, emphasize the usefulness of sound but simple concepts able to explain and predict very general trends. I don't think Pauling was interested in the 'ultimate truth' behind chemistry, whatever such a thing may be. Implying naivety from such an answer of a genius that made ground-breaking contributions to structural chemistry, crystallography or biochemistry is, perhaps, a too strong statement. ] Consider what you think how Gilbert Lewis should respond when asked ] if electron-pairs exist. ] Granted that Lewis could be excused for not knowing quantum ] mechanics which preclude spatial localization of two electrons ] he must have known the coulomb's law for repulsion between ] electrons. Yet we have been using Lewis model to explain much of ] descriptive chemistry to this day. We also use aufbau principle ] to rationalize the periodic table when we know that these ] K, L, M and N shells and S, P, D and F wavefunctions ] don't exist; or at least they don't exist for all elements ] beyond hydrogen. But then our concept of valence shells/orbitals ] based on aufbau principle is very much in line with the ] chemical periodicity of elements. The Lewis electron-pair model ] has a validity that seem to transcend our understanding ] of QM. Hence, in spite of its not being a physical entity ] we continue to apply it to interpretation of chemical reactivity ] in such a manner as to imply its 'existence'. ] In light of this I think it is not unreasonable to ] say that electron-pairs/orbitals exist. Lewis neglected, at first, that Coulomb's law could be at work in chemistry, such was his 'faith' in the explanatory power of pairs and octaves. The interesting thing is that Lewis's concept of electron pairs is essentially recovered within the framework of Quantum Mechanically rigorous Atoms in Molecules theory, even though in a form which departs from the naive orbital ideas propagated by most General Chemistry manuals. The same can be said of the shell structure of atoms. Both can be determined from the rigorous analysis of the experimental or theoretical electron densities. Pauli's principle and the fermionic nature of electrons provide the origin of Lewis's pairing. Two recent references on this subject can help any interested reader: @Article{ BDR-FAB99, author = { X. Fradera and M. A. Austen and R. F. W. Bader }, title = { The Lewis Model and Beyond }, journal = { J. Phys. Chem. A }, year = { 1999 }, volume = { 103 }, pages = { 304--314 }, } @Article{ BDR-BH99, author = { R. F. W. Bader and G. L. Heard }, title = { The mapping of the conditional pair density onto the electron density }, journal = { J. Chem. Phys. }, year = { 1999 }, volume = { 111 }, pages = { 8789--8798 }, } Regards, Victor Lua~na victor@carbono.quimica.uniovi.es From chemistry-request@server.ccl.net Mon Sep 18 06:15:54 2000 Received: from tibre.ujf-grenoble.fr (tibre.ujf-grenoble.fr [193.54.238.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA15227 for ; Mon, 18 Sep 2000 06:15:54 -0400 Received: from corot.ujf-grenoble.fr (corot.ujf-grenoble.fr [193.54.242.2]) by tibre.ujf-grenoble.fr (Pro-8.9.3/8.9.3/Configured by AD & JE 25/10/1999) with ESMTP id MAA03214 for ; Mon, 18 Sep 2000 12:15:35 +0200 (MET DST) Received: from [193.54.244.187] (poulbot [193.54.244.187]) by corot.ujf-grenoble.fr (AIX4.3/UCB 8.8.8/8.8.5) with ESMTP id MAA29594 for ; Mon, 18 Sep 2000 12:11:20 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Sender: tdbruin@chimie Message-Id: Date: Mon, 18 Sep 2000 12:15:29 +0000 To: chemistry@ccl.net From: Theo de Bruin Subject: Summary: wavefunction instability vs. spin contamination Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA15228 Dear CCL'ers Some time ago I posted a question about a wavefunction instabiltiy versus spin contamination problem. Although I received some replies, I was not able to solve the problem: i.e. to find a stable wavefunction that yields good geometries (with respect to crystal data structures). I can add that the use of a larger basis set does not make the instability disappear (as was suggested by one the repliers). Apart from using d-functions on C and O atoms, we now also added f-functions on the Co atoms (these atoms contain the highest spin density using UB3LYP) but this had no influence on the (in)stability of the wavefunction. Anyway, I would like to thank Joe Harrison, Robert Szilagyi and John McKelvey for their help. Here is the orginal question, followed by the replies: ********* QUESTION ********* At the moment we are performing calculations on several (relatively large) di-cobalt complexes using the B3LYP functional and LanL2DZ basis set. Restricted B3LYP calculations yield geometries that fit quite well the corresponding crystal structures. However, from computations with the G98 keyword STABLE it was clear that wavefunctions showed a RHF --> UHF instability. For example: Eigenvector 1: Triplet-?Sym Eigenvalue = -0.0067007 (it seems that the negative eigenvalue is rather small....?) Performing the same calculations with the UNrestricted B3LYP (using guess=mix and changing the DIIS for the QC algorithm) does yield stable wavefunctions, which are about 0.1 to 0.2 kcal/mol lower in energy. However, the obtained geometries with the unrestricted wavefunctions deviate substantially from the crystal structures (delta r(Co-Co) > 0.2 angstrom!), and moreover there is a large spin contamination (S**2 is up to 0.74 for a singlet ground state), which probably results from the (too) large Co-Co distance. We have calculated that the triplet electron configuration has a much higher energy (> 50 kcal/mol). Unfortunately, we were not able to perform successful CASSCF calculations to find out if there was contribution of the triplet in the ground state, since the necessary number of electrons and orbitals in the active space was far too large. Since MP2 calculations on 1st row transition metals are unreliable, higher (than HF or DFT) correlations methods are completely impractical for this size of systems, and the instability seems to be very small (small neg. eigenvalue and small energy difference between restr. and unrestr. wavefunctions), it is very tempting to continue the work with the restricted B3LYP method. Especially, because we are mostly interested in the geometries and their relative energies. Does anybody have some tips or advice how to continue? ******** ANSWERS ******** Joe Harrison wrote: I'm not sure if you are using a package that would allow you to look at the spin densities graphically, but if so, I would recommend looking at the difference in spin densities for outer atoms of your complex. I suspect that your UHF result allows for "surface" spin density to build up whereas your RHF result suppresses that. That would seem to be consistent with the increase in Co-Co distance (movement of the electron density from between the atoms to the "surface"). If your objective is to use your RHF calculation as a paradigm for simulating a crystal, then >from that perspective, the use of UHF would be analogous to allowing surface states to arise. If this were a cluster simulation of a covalent crystal, the effect you describe would be like the problem of "dangling bonds" in those applications. Perhaps there would be something analogous to hydrogen terminators that could be used to suppress the tendency for the spin density to migrate to the outside of the complex. However, hydrogen terminators can result in a monumental explosion of the size of the calculation, so whatever the analog might be, it would probably suffer the same drawback. If nothing else, if what I have suggested is in fact what you find, you could use it as partial justi- fication for the continued use of RHF. BTW if you don't have the ability to look at the spin density, the spin populations in the G98 output might also give such information with the usual caveat in regard to basis sets with diffuse orbitals. Robert K Szilagyi wrote: my guess would be carefully check the wavefunctions. You can easily analyse the gross population analyses, spin density of each orbitals. Also you might consider different spin-coupling schemes (ferromagnetic, antiferromagnetic) and try to calculate the broken symmetry wavefunction where you mix the singlet and triplet wavefunctions. I don't know your system, whether it is feasible or not! I strongly recommend to correlate these data with experimental values of excitation energies, ground state spin densities, etc. Once you have the right wavefunction, the geometry of the complex should be okay as well and not other way around! John McKelvey wrote: While Post-Docing with Prof Berthier someww time ago (> 20 years) I discovered that UHF triplet spin contamination of singlet molecules seems to disappear as the quality of the basis set is improved. Later someone else reported that the contamination decreases even further if the geometry is simultaneously optimized... ----------------------------------------------------------------------- Dr. Theodorus J.M. de Bruin Phone +33 4 76 63 56 28 Université Joseph Fourier Fax +33 4 76 51 43 82 LEDSS VII Chimie Théorique E-mail theo.de-bruin@ujf-grenoble.fr UMR CNRS 5616 Bâtiment 52 - Chimie Recherche DU BP 53 38041 Grenoble Cedex 9 FRANCE ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Sep 18 06:16:27 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 GAA15257 for ; Mon, 18 Sep 2000 06:16:27 -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 MAA02006; Mon, 18 Sep 2000 12:16:16 +0200 (MET DST) Message-Id: <4.3.2.7.0.20000918122238.00a912a0@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Mon, 18 Sep 2000 12:24:21 +0200 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: SAS for DOS/Win95 Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues; Is anyone aware of freeware/shareware programmes executable under DOS/Win9x that will calculate solvent-accessible volumes for small molecular-weight species (like enzyme substrates) -> macromolecules? If so, kindly provide details. Thanks, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Mon Sep 18 13:45:11 2000 Received: from chemistry.mps.ohio-state.edu (chemistry.mps.ohio-state.edu [128.146.33.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA18058 for ; Mon, 18 Sep 2000 13:45:11 -0400 Received: (from rzellmer@localhost) by chemistry.mps.ohio-state.edu (8.9.3+Sun/8.9.3) id NAA05310; Mon, 18 Sep 2000 13:44:57 -0400 (EDT) Date: Mon, 18 Sep 2000 13:44:57 -0400 (EDT) From: Robert Zellmer Message-Id: <200009181744.NAA05310@chemistry.mps.ohio-state.edu> To: chemistry@ccl.net Subject: GAMESS on Alpha using Quadrics switch Has anyone compiled the May 6 1998 MPI version of GAMESS on a Compaq (Dec) Alpha using a Quadrics switch (or for that matter any more recent version using MPI)? We previously had the "same" Alpha machine w/o this switch and the MPI version compiled and worked quite well using `mpich`. However, since we put in this switch and recompiled we can only get the serial version to run. We are using the "prun" command and the parallel version will not run and produce output. It will not run interactively or in our batch system (PBS). We can get the parallel compiled version to run by asking for only 1 cpu. Any help will be greatly appreciated. Thanks, Robert J. Zellmer CSC/Nichols, WPAFB ASC MSRC ASC MSRC URL: http://www.asc.hpc.mil/ Commercial: (937)255-4064 x253 FAX: (937)656-9538 DSN: 785-4064 x253 Toll Free: 1-888-MSRC ASC (1-888-677-2272) Email: zellmerj@asc.hpc.mil, rzellmer@chemistry.ohio-state.edu From chemistry-request@server.ccl.net Mon Sep 18 14:14:18 2000 Received: from mercury.chem.nwu.edu (hutchisn@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA18229 for ; Mon, 18 Sep 2000 14:14:18 -0400 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id NAA11078 for ; Mon, 18 Sep 2000 13:16:09 -0500 (CDT) Date: Mon, 18 Sep 2000 13:16:08 -0500 (CDT) From: Geoff Hutchison Reply-To: Geoff Hutchison To: chemistry@ccl.net Subject: Re: Babel authors and/or OpenBabel Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I'm wondering if anyone knows how to contact the authors of the program 'babel'--Patrick Walters and Matthew T. Stahl. The addresses in the README file no longer work. The latest version I can find is v.1.6 from 1996 and I'd like very much to improve some aspects of the code (and add some additional translators). However, the copyright says "All Rights Reserved" which worries me to some degree. My hope is that either the code can be brought back under the GPL or LGPL license (or similar) or a new "OpenBabel" project can be started for similar purpose. Thanks very much for any help you can provide, -Geoff Hutchison Northwestern Chemistry From chemistry-request@server.ccl.net Mon Sep 18 16:36:56 2000 Received: from castor.rice.edu (castor.rice.edu [128.42.81.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA18909 for ; Mon, 18 Sep 2000 16:36:56 -0400 Received: from localhost (knk@localhost) by castor.rice.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id PAA18976 for ; Mon, 18 Sep 2000 15:36:07 -0500 Date: Mon, 18 Sep 2000 15:36:07 -0500 (CDT) From: News user To: chemistry@ccl.net Subject: Geometry optimization of periodic systems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear collegues I am looking for references that describe geometry optimization methods for periodic systems, and their applications. Specifically, I would like to know about any algorithm that employs something more complicated than the usual Cartesian coordinates for atomic positions and lattice vectors. An example of such more elaborate method would be a variable-cell-shape (VCS) algorithm which optimizes the dot products between the lattice vectors instead of the Cartesian components of these vectors. {I. Souza and J.L. Martins, Phys. Rev. B, 55, 8733 (1997).} Regards, Konstantin Kudin