From owner-chemistry@ccl.net Wed Nov 15 01:46:00 2006 From: "Wai-To Chan chan#curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: CC and CI excited states Message-Id: <-33033-061115011711-19733-5EvX2NUUqLaAoDv/Z6NmZw]^[server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 15 Nov 2006 00:34:08 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan-#-curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<< What is the best way to calculated excited states using couple cluster or configuration interaction methods (on Gaussian)? I've been using the TD(Root=n) keyword, but I was wondering if there was a better way. Thanks in advance for your help, >>>>>>>>>>>>>>>>>>>>>> What kind of excited states you want to calculate? If you have a closed shell ground state and it is the lowest triplet state you are interested in then any of the DFT or HF-based methods like MPn and CCSD would serve your puprose? If your system is a doublet radical with a ground state of 2-A' and you want to calculate the lowest 2-A" state CASSCF should be the appropriate choice. In principle you can still use DFT or the CCSD type of methods. But you have to teach the program to generate a 2-A" wavefunction. This is not always easy and from my limited experience the excited state HF solution could be incorrect. For the case of the lowest open-shell singlet state of a ground state closed-shell singlet you may use either GVB(OSS) or CCSD type of methods based on a broken-spin-symmetry HF wavefunction (if it exists). If you want to calculate a series of higher states with the same spin-multiplicity and spatial symmetry then you have to use either CIS or the TDDFT type of methods (or CASSCF if it works). I am not familiar with G03. As far as I remember CIS and TDDFT with G98 can only give you either triplet or singlet excited states of a closed-shell singlet. I am not sure if you can carry out geometry optimization with TDDFT with G03. Other posters may point out cases where TDDFT and CIS would fail very badly. Wai-To Chan From owner-chemistry@ccl.net Wed Nov 15 03:54:00 2006 From: "Roger Kevin Robinson r.robinson:imperial.ac.uk" To: CCL Subject: CCL:G: Vibrational Frequencies of Adsorbed species Message-Id: <-33034-061114134655-17340-tZcOuntb3vVg6RwthIMQog:-:server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Nov 2006 17:41:34 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson : imperial.ac.uk] Hi, I've been using G3 to calculate Vibration Frequencies of molecules in the gas phase. Presumably these would be different if a species had been adsorbed to some surface. Would it be possible to calculate vibration frequencies for an adsorbed species. I've looked through the Gaussian manual but I cant find much on surface science. Thanks Roger -- Dr. R.Robinson Research Associate Department of Mechanical Engineering Imperial College London - South Kensington Campus London SW7 2AZ UK Tel: +44 20 7589 5111 Ext.57112 Email: r.robinson:imperial.ac.uk From owner-chemistry@ccl.net Wed Nov 15 06:58:01 2006 From: "Orlin Blajiev blajiev=vub.ac.be" To: CCL Subject: CCL:G: Vibrational Frequencies of Adsorbed species Message-Id: <-33035-061115045607-16749-4QDIMzy0U5mzk0ei7W94hQ(!)server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 15 Nov 2006 10:56:02 +0100 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev|vub.ac.be] Roger Kevin Robinson r.robinson:imperial.ac.uk wrote: > Sent to CCL by: Roger Kevin Robinson [r.robinson : imperial.ac.uk] > Hi, > > I've been using G3 to calculate Vibration Frequencies of molecules in > the gas phase. Presumably these would be different if a species had been > adsorbed to some surface. Would it be possible to calculate vibration > frequencies for an adsorbed species. I've looked through the Gaussian > manual but I cant find much on surface science. > > Thanks Roger > > Hi Roger, This is being done in connection with Raman and SERS spectroscopy for example. In those cases usually one or several atoms serve as "substrate". We have used this approach, but there are many problems because (1) the limited number (especially one) of substrate atoms do not convey well the interaction of the molecular dipole moment with a real metal surface. A solution for this problem might be the use of periodic boundary conditions codes instead of Gaussian-Gamess-etc. They might not calculate the vibration properties, though; (2) if the molecule possibly dissociates, there is the problem of which ionization state to use (especially with one atom as a substrate). Besides, as you know, hydrogen dissociation can completely change such factors as electrostatic potentials and HOMO-LUMO morphology. (3) if the molecule has more that one adsorption centre present, it is usually difficult to decide which is the actual one base on calculations only. Best regards, Orlin -- ECASIA '07 will take place in Brussels > From 9th to 14th September 2007 http://www.ecasia07.be/ Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Wed Nov 15 11:03:01 2006 From: "Simon Bloxham simon.bloxham,+,rca.ac.uk" To: CCL Subject: CCL:G: Vibrational Frequencies of Adsorbed species Message-Id: <-33036-061115071814-123456-xjzmDL7/S1jO0TH0++ZsCA- -server.ccl.net> X-Original-From: "Simon Bloxham" Date: Wed, 15 Nov 2006 12:03:46 -0000 Sent to CCL by: "Simon Bloxham" [simon.bloxham . rca.ac.uk] [-- winmail.dat attachment removed by CCL administrator --] Roger, This is an excellent example of the "old" problem of accuracy versus computational cost. In theory, the best way to accomplish this is to attach the adosrbates to an infinitely long surface and then carry out your calculation (remembering that the surface should be a few atoms thick and that any model should allow for surface relaxation). I looked at SAMs (self-assembled monolyaers) of simple alkyl thiols (ethanethiol and cysteamine) on copper. Using G98W I then tried to model the adsorbtion but used the adsorbates on Cu clusters (up to 9 atoms) and obtained promising calculated results that compared well to experimental Raman spectra. Simon -----Original Message----- From: Roger Kevin Robinson r.robinson:imperial.ac.uk [mailto:owner-chemistry]*[ccl.net] Sent: Wed 15-Nov-06 9:08 AM To: Simon Bloxham Subject: CCL:G: Vibrational Frequencies of Adsorbed species Sent to CCL by: Roger Kevin Robinson [r.robinson : imperial.ac.uk] Hi, I've been using G3 to calculate Vibration Frequencies of molecules in the gas phase. Presumably these would be different if a species had been = adsorbed to some surface. Would it be possible to calculate vibration frequencies for an adsorbed species. I've looked through the Gaussian manual but I cant find much on surface science. Thanks Roger Dr. R.Robinson Research Associate Department of Mechanical Engineering Imperial College London - South Kensington Campus London SW7 2AZ UK Tel: +44 20 7589 5111 Ext.57112 Email: r.robinson+/-imperial.ac.uk From owner-chemistry@ccl.net Wed Nov 15 14:45:01 2006 From: "Kalju Kahn kalju^_^chem.ucsb.edu" To: CCL Subject: CCL: intra-molecular H-Bonds Message-Id: <-33037-061115144220-28694-CjtN56m9N97NzNqATpDw2w]-[server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 15 Nov 2006 11:41:51 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju*|*chem.ucsb.edu] Dear Arturo, You could test this with a Monte Carlo simulation using explicit water if you had force field parameters ... Jorgensen's group has shown that in succinate monoanion, an internal H-bond or approximately 15 kcal/mol will not survive in water but will survive in THF. Water solvates well both the donor and acceptor atoms in succinate, which may not be the case in your rhutenium complex. See: Daniel J. Price, John D. Roberts, and William L. Jorgensen Conformational Complexity of Succinic Acid and Its Monoanion in the Gas Phase and in Solution: Ab Initio Calculations and Monte Carlo Simulations, J. Am. Chem. Soc. 1998, 120, 9672-9679 Best regards, Kalju ------------------- > Sent to CCL by: Arturo Robertazzi [robertaz_._sissa.it] > Dear all, > > I am currently working on the hydrolysis of some ruthenium complexes. In one of > the steps, I see the formation of a very strong intra-molecular OH...O hydrogen > bond. > H...O distance is 1.8A and OHO angle 155 degrees. Also, The Atoms in Molecules > analysis (along with other data) would indicate that the energy is roughly 6-8 > kcal/mol in solution (estimated with the PCM model). > > My questions are the following: > 1) do you think this H-Bond could survive (weaken or even strengthen) in > solution as it would interact with a large number of external water molecules? > 2) Can you indicate any paper/review on the topic? > > Thank you very much, > > Arturo Robertazzi > > > -- > Dr. Arturo Robertazzi > INFM Democritos Center > and > International School for Advanced Studies (SISSA/ISAS) > via Beirut 2-4 Trieste, 34014 Italy > e-mail: robertaz_._sissa.it > phone: 040-3787-571 > Home-Page: www.arturorobertazzi.blogspot.com> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Wed Nov 15 15:19:00 2006 From: "Dr. Raphael Berger rberg_01|a|uni-muenster.de" To: CCL Subject: CCL: coordinative bonds => multi refence ? Message-Id: <-33038-061115133650-18103-8/D/dF8hDclIKDUE5T3HnA_-_server.ccl.net> X-Original-From: "Dr. Raphael Berger" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 15 Nov 2006 18:35:27 +0100 (MEZ) MIME-Version: 1.0 Sent to CCL by: "Dr. Raphael Berger" [rberg_01 ~ uni-muenster.de] Hello (a)all, considering the equlibrium geometry of a complex compound, like for example Cl_nM..NH3 for some n valent metal or other electropositve element (maybe SiCl4). Usually RHF will describe this kind of interaction at least very rough if not wrong. Applying MP2 may yield much better results. One of my questions is: Could non-dynamic correlation, namely the use of MCSCF with a proper choice of (a couple of) active orbitals, substantially improve the description of the N..M interaction? Another (closely related) question is: Must the chemically intuitive interaction of the NH3 HOMO (lone pair) with the LUMO of the (distorted) MCln fragment be already governed somehow by a HF calculation? Or can this interaction only be described by multireference calculations? Is a general answer possible? Are there substantial differences between p- and d-block elemts in this respect? Thank You in advance for any hints!! From owner-chemistry@ccl.net Wed Nov 15 16:54:00 2006 From: "Pradeep Indrakanti vxi103 ~ psu.edu" To: CCL Subject: CCL: request: MSINDO Lowdin charges and band gap Message-Id: <-33039-061115151119-12280-lFz5rIvY5Yc2UhtpVY6OjQ]^[server.ccl.net> X-Original-From: "Pradeep Indrakanti" Date: Wed, 15 Nov 2006 15:11:18 -0500 Sent to CCL by: "Pradeep Indrakanti" [vxi103 ~ psu.edu] Hi All, I am using MSINDO (source code from Dr. Bredow's group) v.3.1 to calcualate the ground state geometries of CO2 on TiO2 crystallites. I started with a stoichiometric cluster (Ti20O40) having 4 singly coordinated oxygen atoms. MSINDO can predict the homo-lumo band gap in this cluster (4.00 eV) to a rough approximation. But, when I tried to satured the singly coordinated oxygens by adding 4H (and adding 4 OH groups to make the cluster neutral),and tried optimizing the OH, H atoms alone, I get a homo-lumo gap of 6.9 eV. Can anyone kindly tell me ideas to overcome this problem? Also, when I do a geometry optimization in MSINDO using LCHARGE as a keyword (to print the Lowdin atomic charges), all I get is a table to orthogonal valence densities for the atoms. Lowdin charges work ok for smaller molecules (CO2, H2O etc.). Is there a variable somewhere in the source code that needs to be changed to enable the Lowdin population analysis for larger clusters in MSINDO ? Thanks, Pradeep Ph.D. student, Department of Energy and GeoEnvironmental Eng, Penn State University. From owner-chemistry@ccl.net Wed Nov 15 17:29:00 2006 From: "Prema latha Mallipeddi plmallip.:.mail.uh.edu" To: CCL Subject: CCL: sdf file (with stereoisomers) to catalyst (accelrys software) bdb file Message-Id: <-33040-061115155847-13002-8jw26Kxcgumhn/98xH6KSQ..server.ccl.net> X-Original-From: "Prema latha Mallipeddi" Date: Wed, 15 Nov 2006 15:58:46 -0500 Sent to CCL by: "Prema latha Mallipeddi" [plmallip[*]mail.uh.edu] Hi, When I am trying to convert "sdf file" with stereoisomers into "bdb file" using catDB of catalyst, I am unable to retrieve the stereomers. The command is deleting stereoisomers as duplicate structures. Is there any other way I can convert the "sdf file" to "bdb file" without lose of the stereoisomers? I would be grateful if someone can help me in this regard. Thanks in advance. latha, E-mail:plmallip{:}mail.uh.edu From owner-chemistry@ccl.net Wed Nov 15 23:33:00 2006 From: "Jimmy Lawrence jlawrence%%slb.com" To: CCL Subject: CCL: OH radical attack to aromatic compounds Message-Id: <-33041-061115220830-7959-BtDTh5VEM6DS1zO811ALQw{=}server.ccl.net> X-Original-From: Jimmy Lawrence Content-transfer-encoding: 7BIT Content-type: text/plain; charset=iso-2022-jp Date: Thu, 16 Nov 2006 11:21:41 +0900 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [jlawrence~!~slb.com] Dear all, I would like to do some calculations regarding free radical attack (e.g. OH free radical ) to aromatic compounds to find its preference and easiness to attack on aromatic ring (attack location). Right now I think IRC calculation might help this. Can you share any experiences/ suggest methods for this kind of calculation ? Since calculating system with free radical might be tricky, should I start > from H2O2, for example ? Thank you in advance, Jimmy Lawrence