From owner-chemistry@ccl.net Mon Jan 22 04:50:02 2007 From: "Marcel Swart marcel.swart..icrea.es" To: CCL Subject: CCL:G: polarizability of organometallic Re(I) compounds Message-Id: <-33420-070122041311-8276-5w+s0xifrfNnE3Dm1cPUYw]![server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Date: Mon, 22 Jan 2007 10:13:00 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart|a|icrea.es] Hello Filipe, the polarizability is defined as the second order response of the energy (U) with respect to the electric field (E), i.e. U = Uzero + Mu*E + 1/2 * E*Alfa*E + 1/6 * E*Beta*E*E + 1/24 *E*E*Gamma*E*E + .. So if you use small electric fields (1e-4 a.u.) you can get the polarizability tensor from taking the numerical derivative of the dipole moment w.r.t. to the applied electric fields. See for instance: J.Phys.Chem.A 1998, 102, 2399. On Jan 19, 2007, at 6:56 PM, Filipe Duarte filipe.duarte-x- dq.fct.unl.pt wrote: > > Sent to CCL by: "Filipe Duarte" [filipe.duarte[A]dq.fct.unl.pt] > Hello everyone, > > I am using DFT methods and polar=enonly input Gaussian_03 for > polarizability calculation of ground-state of a series of > organometallic Re(I) compounds > In the output I get the polarizability and the energies of the > orbitals HOMO and LUMO. > To confirm the variation of the polarizability of a series > organometallic Re(I) compounds, I am using the relation between > polarizability and 1/DE (LUMO-HOMO). > > polarizability is proportional to 1/deltaE (LUMO-HOMO). > > The results that I got are in disagreement of this relation > > polarizability 1/deltaE (LUMO-HOMO) > 31.70 0.3472 > 34.64 0.2968 > 49.19 0.2829 > > The results show, that the polarizability increase when 1/E > decreases, this is the opposite of the relation between > polarizability and 1/E described in the literature. > What does that mean its not clear to me. > To trying understanding these results I performed the some > calculations for a small compounds, methanol, ethanol and 1- > propanol. The results achieved are in agreement with the relation > between polarizability and 1/deltaE. > > I would like to know if is possible/correctly use this method to > calculate the polarizability. > If you have a suggestion please email me directly. > > > Thanks and warm regards, > Filipe Duarte > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > –––––––––––––––––––––––––––––––––––––––––––– dr. Marcel Swart ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart*icrea.es marcel.swart*udg.es web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.es/~marcel –––––––––––––––––––––––––––––––––––––––––––– From owner-chemistry@ccl.net Mon Jan 22 04:56:00 2007 From: "Val Gillet v.gillet!^!sheffield.ac.uk" To: CCL Subject: CCL: Second Call for Papers: Sheffield Chemoinformatics Conf, June 2007 Message-Id: <-33421-070122045259-11925-5dy6Gz/VurkND9XyadKnkQ^-^server.ccl.net> X-Original-From: "Val Gillet" Date: Mon, 22 Jan 2007 04:52:56 -0500 Sent to CCL by: "Val Gillet" [v.gillet{=}sheffield.ac.uk] Fourth Joint Sheffield Conference on Chemoinformatics: Second Call for Papers The Chemical Structure Association Trust and the Molecular Graphics and Modelling Society announce their Fourth Joint Sheffield Conference on Chemoinformatics. The conference will be held in The Octagon Centre and the Stephenson and Tapton Halls of Residence, University of Sheffield, UK, from 18th-20th June 2007. Offers of papers are welcomed in all aspects of chemoinformatics. Possible topics include (but are not limited to): * High-Throughput Screening, including: assay quality control; design of screening collections; systems based design * Virtual Screening including, including: docking and pharmacophore analysis, similarity and clustering methods; machine learning * Computational Methods for Lead Identification and Optimisation including: modelling and structure-activity methods; structure-based design; ADMET prediction * New Algorithms and Technologies including: data mining; searching methods; distributed processing; data handling and visualisation; * Case Histories, incorporating practical experience of any of the above The programme will have space for ca. two dozen oral presentations, and there will also be extensive opportunities for poster presentations. Authors wishing to submit a paper should send a title and abstract by 31st January 2007 to cheminf2007.^-^.sheffield.ac.uk, stating whether they wish to be considered for an oral or for a poster presentation. Submissions will be selected as either oral contributions or posters by the Organising Committee, with notification of acceptance by 28th February 2007. In selecting papers for oral presentation, the Committee will seek to achieve a balance between the various areas of the subject and between new methodologies and successful applications of existing techniques. Preliminary details of the conference are available at http://cisrg.shef.ac.uk/shef2007/. Registration and programme information will appear there shortly. Val Gillet, v.gillet.^-^.sheffield.ac.uk From owner-chemistry@ccl.net Mon Jan 22 08:53:00 2007 From: "T. Daniel Crawford crawdad(!)exchange.vt.edu" To: CCL Subject: CCL:G: question regarding comparison of Jaguar and Gaussian03 programs Message-Id: <-33422-070121233150-27283-tcVvgveEkyQWMrPBBYS+vQ:_:server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Sun, 21 Jan 2007 22:59:16 -0500 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad]_[exchange.vt.edu] It is perfectly reasonable to expect to reproduce absolute energies between computer programs for a given model, assuming that sufficient details are given (and within control of the user's input) and that the model is not bound by statistical sampling restrictions (as is the case for quantum chemical models). Comparisons between programs or published absolute energies are common for developers trying to ensure that their code is correct. For example, users should be able to match Hartree-Fock energies to very high precision (at least 12 decimal places) between programs like Jaguar and Gaussian. It is somewhat more problematic to match B3LYP energies because of the use of numerical integration grids and pseudospectral methods, but if sufficient high-density integration grids and tight convergence parameters are used, then different programs should give essentially identical results. (Note that some differences exist in B3LYP "definitions" -- such as between Turbomole and G03 -- but these have been published in the open literature, and so careful users should be able to discern the differences.) -Daniel On 1/21/07 7:13 PM, "Sengen Sun sengensun++yahoo.com" wrote: > > Sent to CCL by: Sengen Sun [sengensun++yahoo.com] > I would emphasize that you can only use relative > energies (e.g., rotational barrier, activation > energy...) for the comparison of different programs. >> > It is meaningless to compare the total energies of a > molecule from different programs as we all know that > absolute value of potential energy does not exist. >> > I have some experience with Titan that uses the Jaguar > code. It repeats well the data (e.g., activation > energies of Diels-Alder reactions) from other major > programs with errors less than 0.1 kcal/mol. >> > Sengen > -- T. Daniel Crawford Department of Chemistry crawdad_+_vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Mon Jan 22 09:38:00 2007 From: "Pierre Archirel pierre.archirel*lcp.u-psud.fr" To: CCL Subject: CCL: polarizability of organometallic Re(I) compounds Message-Id: <-33423-070122091708-9537-QkydiDkdwd0P1TOfSW8Q2w**server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 Jan 2007 15:04:07 +0100 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel|-|lcp.u-psud.fr] Dear collegues, About polarisability and Homo-Lumo gap: Low lying Rydberg state are not expected to contribute to the static polarisability. The CO molecule is a good example, in which one half of the polarisability is due to the 6th excited state: see M. Rerat, C. Pouchan et al. Physical Review A vol. 42(11) p. 5832 (1991) __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel^lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Mon Jan 22 22:17:00 2007 From: "Richard Huhn huhnra[#]mit.edu" To: CCL Subject: CCL:G: Orbitals and (de)contractions Message-Id: <-33424-070122213138-20503-qLfbNN4OCaxhuNP1SAf9nA#%#server.ccl.net> X-Original-From: "Richard Huhn" Date: Mon, 22 Jan 2007 21:31:34 -0500 Sent to CCL by: "Richard Huhn" [huhnra]|[mit.edu] I would like to know the method by which gaussian-type orbitals are contracted and decontracted. I have read an excellent "Basis set intro" found on this list, but the mathematics has not worked out for me. In particular, I would like to know how to modify a basis set when a publication says, for example, that a valence p-orbital was decontracted. The reverse is of interest to me, as well: If I were given a set of exponents for an uncontracted basis set, what is done to contract it? If possible, perhaps you could explain by example: below is the output from Gaussian 03 for two situations, one simple case which I hope will be generally instructive, and another which is of particular interest to me at the moment. 6-31G basis set for H atom: S 3 1.00 0.000000000000 0.1873113696D+02 0.3349460434D-01 0.2825394365D+01 0.2347269535D+00 0.6401216923D+00 0.8137573261D+00 S 1 1.00 0.000000000000 0.1612777588D+00 0.1000000000D+01 LANL2DZ basis set for Pd atom: S 3 1.00 0.000000000000 0.2787000000D+01 -0.1610239066D+01 0.1965000000D+01 0.1848984076D+01 0.6243000000D+00 0.6037492248D+00 S 4 1.00 0.000000000000 0.2787000000D+01 0.1354078141D+01 0.1965000000D+01 -0.1678085175D+01 0.6243000000D+00 -0.8559381894D+00 0.1496000000D+00 0.1020030107D+01 S 1 1.00 0.000000000000 0.4360000000D-01 0.1000000000D+01 P 3 1.00 0.000000000000 0.5999000000D+01 -0.1034909945D+00 0.1443000000D+01 0.7456951606D+00 0.5264000000D+00 0.3656493807D+00 P 2 1.00 0.000000000000 0.7368000000D+00 0.7632850274D-01 0.8990000000D-01 0.9740065349D+00 P 1 1.00 0.000000000000 0.2620000000D-01 0.1000000000D+01 D 3 1.00 0.000000000000 0.6091000000D+01 0.3761460071D-01 0.1719000000D+01 0.5200479099D+00 0.6056000000D+00 0.5706071108D+00 D 1 1.00 0.000000000000 0.1883000000D+00 0.1000000000D+01 For the H case, for example, how might I decontract the basis set, or how might I contract all four primitives into a single basis function? For the Pd case, I have read (e.g. J. Chem. Phys. 2004, 121(20), 9982-9992 (see pg 9984), and Chem. Rev. 2000, 100, 439-493 (see pg 483)) that the LANL2TZ basis set contains the same primitives as the double-zeta version, but is decontracted. My goal is to have the triple-zeta basis set in hand in a format suitable for input to Gaussian, but it also to learn how to get from one basis set to the other. Thank you for any and all help! Rich