From owner-chemistry@ccl.net Mon Aug 13 03:49:01 2007 From: "Andreas Klamt klamt:-:cosmologic.de" To: CCL Subject: CCL: solvent calc. Message-Id: <-34921-070813030404-10928-I2y4EO06zp0fYAceLc81kg|*|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1250; format=flowed Date: Mon, 13 Aug 2007 09:03:36 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt###cosmologic.de] Dear Aleksandra, sorry to tell you that even in the case of neutral reactions it does not make much sense to apply the standard gasphase methods. All the vibrational free energy contributions are not meaningful in the solvent. The change in vibrational free energy from gasphase to the solvent is already parameterized into the solvent models (see e.g. my CCL contribution from 17.05.2007 ). In my opinion, the only reasonable way to do this in the solvent is to calculate the gasphase reaction and to apply dG_solvation (from a good, quantitative solvation model) to educts and products., i.e. use the thermodynamic cycle Educts, solv ---> Educts, gas --> Products,gas --> Products, solv Andreas Aleksandra Rudnitskaya aleksandra.rudnit001#umb.edu schrieb: > Sent to CCL by: "Aleksandra Rudnitskaya" [aleksandra.rudnit001##umb.edu] > Thanks a lot to everyone who sent his answer. I realized I took a wrong example. What if I choose the other system with benzene as a solvent? The questions are the same - > what should I write in input file for optimization, and TS? > > > Thank you > > Aleksandra > > >> Dear CCL members, >> >> Ive just started calculations with solvent. I decided to start from reaction of neutralization NaOH+HCl=H2O+NaCl. As I understand I should calculate >> 1) optimization sodium hydroxide in solvent (water); >> 2) optimization hydrochloric acid in solvent; >> 3) optimization sodium chloride in solvent; >> 4) transition state again in solvent. >> Idea is very similar to that when I calculate rxns in gas phase. Is it correct? >> When I calculate stable species without any solvent I use >> opt freq=noraman RHF/6-31G(d) >> For TS calculations I use >> RHF/6-31G(d) Opt(TS,CalcFC,noeigentest) Freq=noraman >> >> and then charge and multiplicity, and simple Z-matrix in specification part. How should input files look for optimization and searching TS? I know I have to use keyword SCRF, and one of those (SCRF=Dipole, PCM, DPCM, CPCM or IEFPCM), then specify solvent, and probably, dielectric constant somewhere in specification part after matrix. If you may guide me how to create input file itll help a lot. >> >> Thank you very much.> > > > > -- ----------------------------------------------------------------------------- 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 Mon Aug 13 04:24:01 2007 From: "andras.borosy++givaudan.com" To: CCL Subject: CCL: runtime libraries of IRIX 6.5.18 Message-Id: <-34922-070813041309-28413-ytYN9rCGH/VvO0KHajJZhA[]server.ccl.net> X-Original-From: andras.borosy-,-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002D173BC1257336_=" Date: Mon, 13 Aug 2007 10:12:27 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy~~givaudan.com This is a multipart message in MIME format. --=_alternative 002D173BC1257336_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, I have IRIX 6.5.18 at our Octanes containing 7.3.1 version of the runtime libraries. I have an application that needs 7.4.2. What shall I do? =20 Many thank, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 002D173BC1257336_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

I have IRIX 6.5.18 at our Octanes containing 7.3.1 version of the runtime
libraries. I have an application that needs 7.4.2. What shall I do?

Many thank,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com --=_alternative 002D173BC1257336_=-- From owner-chemistry@ccl.net Mon Aug 13 11:53:01 2007 From: "Oellien, F (Frank) Frank.Oellien#%#Intervet.com" To: CCL Subject: CCL: Final Call for paper: German Conference on Chemoinformatics+- Message-Id: <-34923-070813103615-21140-1mOhaR9xRJlXPGuIauOYwQ---server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 13 Aug 2007 15:38:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [Frank.Oellien^Intervet.com] Dear Colleagues, This is the final call for papers for the 3. German Conference on Chemoinformatics (http://www.gdch.de/gcc2007) to be held in Goslar, Germany, November 11-13, 2007. You can still submit your abstract for oral or poster contribution until August, 15. 2007. The international symposium will address a broad range of modern research topics in the field of Computers and Chemistry. Focus will be on recent developments and trends in the fields of * Chemoinformatics and Drug Development * Chemical Information * Molecular Modelling * Computational Material Science and Nanotechnology and other highlights in the field of Computational Chemistry. The scientific program will include plenary lectures, short lectures as well as poster presentations. Invited Speakers are J. Bajorath, T. Frauenheim, S. Heller, A. Hillisch, T. Oprea, A. Tropsha A special highlight of the conference will be the awarding of the Gmelin-Beilstein-Denkmünze to Dr. Olga Kennard and the handover of the FIZ BERLIN Chemie awards. We will also award the three best poster submissions. Abstracts for oral contributions and posters can still be submitted until July 31. The conference website at http://www.gdch.de/gcc2007 has links to the abstract submission interface, a PDF version of the first circular as well as additional information. Please distribute this call to all interested parties. Feel free to contact me if you have questions. Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien!A!intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com Intervet Innovation GmbH is an Akzo Nobel company Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. --------------------------------------