From owner-chemistry@ccl.net Wed Aug 9 04:21:00 2006 From: "Jens Spanget-Larsen spanget[#]ruc.dk" To: CCL Subject: CCL:G: MP2 HOMO-LUMO gap with G03 Message-Id: <-32360-060809042014-28654-VuoLzDvpiTG3C5WXY7inMQ[A]server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 09 Aug 2006 10:20:01 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget:-:ruc.dk] Dear Herbert, the MP2 procedure uses the orbitals produced by a HF calculation so the HOMO-LUMO gap should be excactly the same (provided the same basis set is used). The orbitals of a DFT calculation are the so-called Kohn-Sham orbitals, and they are conceptually different from HF orbitals. - Yes, a better way to predict electronic excitation energies would be to use CIS or TD-DFT. In particular, TD-DFT frequently works beautifully. See f.inst. J. Fabian et al., J. Mol. Struct. (Theochem) 594, 41-53 (2002). Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget%ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Herbert Fruchtl herbert.fruchtl*_*st-andrews.ac.uk wrote: > Sent to CCL by: "Herbert Fruchtl" [herbert.fruchtl!^!st-andrews.ac.uk] > Something I should probably know, but... > > I am calculating the HOMO-LUMO gap of small organic molecules with HF, DFT and MP2 using Gaussian 03. For MP2, I use the keywords "Density=MP2 Pop=Regular", and the output says that the MP2 density is used. The numbers for HF and MP2 are extremely close (at least 3 digits). Is this to be expected, or is there something I am missing? > > I assume a better way to get vertical excitation energies would be to calculate the first roots with CIS or TDDFT. Is this correct? > > Herbert> > > From owner-chemistry@ccl.net Wed Aug 9 07:29:00 2006 From: "Michael Shokhen shokhen^^^mail.biu.ac.il" To: CCL Subject: CCL: CCL SCRF solvation energy structure-additivity decomposition Message-Id: <-32361-060809072531-30047-IpOVAZDRk4bD9b62xXC1Jw(a)server.ccl.net> X-Original-From: "Michael Shokhen" Date: Wed, 9 Aug 2006 07:25:31 -0400 Sent to CCL by: "Michael Shokhen" [shokhen\a/mail.biu.ac.il] Dear colleagues, My question concerns a SCRF continuum solvation model in frames of Poisson-Bolzmann equation implemented in quantum mechanical calculations. The molecular cluster, S (solute), solvated in a polar solvent can contain several charged groups. The total structure of solute, S, can be formally decomposed on substructures, s(i), where every s(i) contains only one charged group. In such a way the total solvation energy, Gsolv, in principle can be represented as a sum of contributions of solvation energies, Gsolv(i), corresponding to solute substructures: Gsolv = SUM[ Gsolv(i)] + B, where B accounts all cross interactions to correct the additivity approximation. I would appreciate, if somebody could address me to theoretical works considering principal algorithms of such kind structure-additivity decomposition of the reaction field solvation energy. All the best, Michael All the best, Michael From owner-chemistry@ccl.net Wed Aug 9 09:00:00 2006 From: "Andreas Klamt klamt()cosmologic.de" To: CCL Subject: CCL: CCL SCRF solvation energy structure-additivity decomposition Message-Id: <-32362-060809085606-25202-yaS/2tjI1lIOl7hYGCP5Qg[]server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 09 Aug 2006 14:55:58 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt- -cosmologic.de] Dear Michael, in some way my COSMO-RS method (see e.g. Klamt: COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design, Elsevier 2005) is using such kind of additivity. Starting from the solvation energy of the molecules in a conductor all differences of the solvation energies in real solvents to the conductor (and between different solvents) are calculated as surface integrals, and hence each substructure s(i) would thus contribute additive to the solvation free energy difference. Thus differences of the solvation free energy between different solvents can be considered as rather additive, but the solvation energy from the vacuum to the conductor is much less additive, especially for charged species. But most likely you are not interested in the charged species in the gasphase or vacuum, but just in differences between diferent solvents, right? Andreas Michael Shokhen shokhen^^^mail.biu.ac.il schrieb: > Sent to CCL by: "Michael Shokhen" [shokhen\a/mail.biu.ac.il] > Dear colleagues, > > My question concerns a SCRF continuum solvation model > in frames of Poisson-Bolzmann equation implemented in quantum mechanical > calculations. > > The molecular cluster, S (solute), solvated in a polar solvent can contain several charged groups. The total structure of solute, S, can be formally decomposed on substructures, s(i), where every s(i) contains only one charged group. In such a way the total solvation energy, Gsolv, in principle can be represented as a sum of contributions of > solvation energies, Gsolv(i), corresponding to solute substructures: > > > Gsolv = SUM[ Gsolv(i)] + B, > > > where B accounts all cross interactions to correct the additivity approximation. > I would appreciate, if somebody could address me to theoretical works > considering principal algorithms of such kind structure-additivity decomposition of the reaction field solvation energy. > > All the best, > Michael > > All the best, > > Michael> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt-*-cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Aug 9 09:55:00 2006 From: "Steve Gwaltney drg51^-^ra.msstate.edu" To: CCL Subject: CCL:G: MP2 HOMO-LUMO gap with G03 Message-Id: <-32363-060808220333-1414-i40jeT/OX3HJDJdG3YscMw(-)server.ccl.net> X-Original-From: Steve Gwaltney Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 8 Aug 2006 20:20:19 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Steve Gwaltney [drg51 .. ra.msstate.edu] On Tue, 8 Aug 2006, Herbert Fruchtl herbert.fruchtl*_*st-andrews.ac.uk wrote: > Sent to CCL by: "Herbert Fruchtl" [herbert.fruchtl!^!st-andrews.ac.uk] > Something I should probably know, but... > > I am calculating the HOMO-LUMO gap of small organic molecules with HF, DFT and MP2 using Gaussian 03. For MP2, I use the keywords "Density=MP2 Pop=Regular", and the output says that the MP2 density is used. The numbers for HF and MP2 are extremely close (at least 3 digits). Is this to be expected, or is there something I am missing? > > I assume a better way to get vertical excitation energies would be to calculate the first roots with CIS or TDDFT. Is this correct? > > Herbert > There appear to be a couple of misconceptions here. First, the HOMO-LUMO gap has little to do with excitation energies. Specifically, the LUMO calculated using most basis sets is not the "LUMO" most chemists think of. This is especially true when using very diffuse basis sets, where the LUMO often becomes an approximation to a free electron. Second, MP2 will not change the orbital energies, since the orbital energies are the eigenvalues of the Fock matrix. If you want the vertical excitation energies, you need an excited state method. For HF the corresponding method is CIS, which can have an error of up to 2 eV. Just like with HF, CIS energies are bad, but the geometries are decent. The corresponding method to DFT is TDDFT. This is normally pretty reliable for excited states well below the first Rydberg state. If you want an excited state method that corresponds to MP2, you should use CIS(D). Steve Dr. Steven Gwaltney Phone: 662-325-7602 Assistant Professor Fax: 662-325-1618 Department of Chemistry, Mail: Box 9573 Center for Environmental Health Sciences, Mississippi State University and HPCC Center for Computational Sciences ississippi State, MS 39762 From owner-chemistry@ccl.net Wed Aug 9 11:42:00 2006 From: "Eric Scerri scerri _ chem.ucla.edu" To: CCL Subject: CCL: Latest issue Foundations of Chemistry Message-Id: <-32364-060808082329-9374-VQuVDNvbAkjrLb6/gfNpGA() server.ccl.net> X-Original-From: "Eric Scerri" Date: Tue, 8 Aug 2006 10:54:14 -0000 Sent to CCL by: "Eric Scerri" [scerri=chem.ucla.edu] FOUNDATIONS OF CHEMISTRY/ VOLUME 8 / NUMBER 1 Editorial 22 pp. 1 - 2 Eric Scerri A Process Theory of Enzyme Catalytic Power – the Interplay of Science and Metaphysics pp. 3 - 29 Ross L. Stein Concerning the Position of Hydrogen in the Periodic Table pp. 31 - 35 Lawrence J. Sacks The Role of Observables and Non-observables in Chemistry: A Critique of Chemical Language pp. 37 - 52 Shant Shahbazian and Mansour Zahedi Gestalt Switch in Molecular Image Perception: The Aesthetic Origin of Molecular Nanotechnology in Supramolecular Chemistry pp. 53 - 72 Joachim Schummer Ontological Reduction: A Comment on Lombardi and LaBarca pp. 73 - 80 Paul Needham The ontological autonomy of the chemical world: a response to Needham pp. 81 - 92 Olimpia Lombardi and Martín Labarca -------------------------------------------------------------- THE PERIODIC TABLE: ITS STORY AND ITS SIGNIFICANCE, by Eric Scerri Published by Oxford University Press on Sept 10th, 2006. see OUP website or Amazon.com for placing advance orders. -------------------------------------------------------- Dr. Eric Scerri, Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, UCLA web page, http://chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257 From owner-chemistry@ccl.net Wed Aug 9 15:31:01 2006 From: "Christian Pilger christian.pilger%a%gmx.net" To: CCL Subject: CCL: CHIME string conversion Message-Id: <-32365-060809152852-17222-P6w8PqPFoUYI0c9538dorQ%a%server.ccl.net> X-Original-From: "Christian Pilger" Date: Wed, 9 Aug 2006 15:28:52 -0400 Sent to CCL by: "Christian Pilger" [christian.pilger^^^gmx.net] Dear CCLers, are you aware of software allowing for the conversion of the MDL CHIME string format into something other like SMILES, Tripos-mol2, MDL-mol etc. ? I checked openbabel but it does not seem to be suited for this task. Regards, Christian