From owner-chemistry@ccl.net Thu Oct 23 03:50:00 2008 From: "andras.borosy:givaudan.com" To: CCL Subject: CCL: dielectric constants Message-Id: <-37968-081023034918-16588-WCEfqx7TYwjIc6ieQoo9kg(0)server.ccl.net> X-Original-From: andras.borosy|a|givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002AF1DCC12574EB_=" Date: Thu, 23 Oct 2008 09:49:04 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy^^givaudan.com This is a multipart message in MIME format. --=_alternative 002AF1DCC12574EB_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable - Dear Colleagues, How can dielectric constants of small organic molecules be estimated by=20 any computational method? Regards, 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 002AF1DCC12574EB_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
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Dear Colleagues,

How can  dielectric constants of small organic molecules be estimated by any computational method?

Regards,

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 002AF1DCC12574EB_=-- From owner-chemistry@ccl.net Thu Oct 23 09:16:00 2008 From: "Thomas Mitterfellner thomas.mitterfellner*o*tugraz.at" To: CCL Subject: CCL:G: Questions about excited state optimizations/excited states Message-Id: <-37969-081023070512-26940-zwxlylMK3b9sGGL1b1pDJA!A!server.ccl.net> X-Original-From: "Thomas Mitterfellner" Date: Thu, 23 Oct 2008 07:05:09 -0400 Sent to CCL by: "Thomas Mitterfellner" [thomas.mitterfellner-,-tugraz.at] Hello! I am trying to optimize the geometry of the excited state of a molecule. I tried to use Turbomole 5.7.1 and Gaussian 03 but I'd also appreciate hints to other computational chemistry packages which can do this (especially if they are non-commercial). About the molecule: In the ground state, the molecule is of c3v symmetry. The HOMO and the LUMO are non-degenerate and belong to the irreps a2 and a1, respectively, and this excitation is symmetry forbidden. The (HOMO-1), however is twofold degenerate (irrep e) and the (HOMO-1) -> LUMO transition has appreciable oscillator strengths. irrep occupation LUMO a1 0 HOMO a2 2 HOMO-1 e 4 This is what I also observe in the experimental UV absorption spectrum: a band of very little intensity at the wavelength calculated (TDDFT) for the HOMO -> LUMO transition, and a much stronger band located at the wavelength calculated for the (HOMO-1) -> LUMO transition. Now, some practical and theoretical questions arose: 1.) If I look at a plot of the frontier orbitals, can I qualitatively say something like: the HOMO consists mainly of bonding X-X orbitals, whereas the LUMO consists of antibonding X-Y orbitals, so the excited state geometry will probably contain elongated X-X bonds (missing electron density in the bonding orbital) and elongated X-Y bonds (populated antibonding orbitals)? If so, a) Wouldn't an excited state geometry resulting from a HOMO->LUMO transition look different from one that results from a (HOMO-1)->LUMO transition? b) Should I modify the starting geometry with slightly elongated bonds (or whatever hint the qualitative view of the frontier orbitals gave), or should I start the excited state optimization from the ground state geometry? c) Can I, with any excited state optimization method select to optimize a certain occupation, eg: alpha beta LUMO: 1 0 HOMO: 1 1 (HOMO-1): 0 1 2.) What about symmetry? My ground state is of c3v symmetry, but since I don't exactly know what the excited state will look like, should I rather not use symmetry? 3.) Are there some general guidelines when to use RPA (TDDFT), and when to use TDA (CIS)? What advantages does each one have over the other in describing real-life problems and in computational performance? What other methods are tractable for excited state optimizations of a medium to big sized molecule of, say, ~20 non-hydrogen atoms of second and third period and about 30 hydrogens? Please feel free reply on any of my questions and assumptions. Thank you in advance! From owner-chemistry@ccl.net Thu Oct 23 09:50:01 2008 From: "John Edward jeedward^yahoo.com" To: CCL Subject: CCL: BCBGC-09 call for papers Message-Id: <-37970-081023090600-6838-BkHH/lMjD7Z4aERGWsahEg^server.ccl.net> X-Original-From: John Edward Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Thu, 23 Oct 2008 05:10:01 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: John Edward [jeedward]~[yahoo.com] BCBGC-09 call for papers The 2009 International Conference on Bioinformatics, Computational Biology,= Genomics and Chemoinformatics (BCBGC-09) (website: www.PromoteResearch.org= ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft= paper submissions. The conference will take place at the same time and ven= ue where several other international conferences are taking place. The othe= r conferences include: =E2=80=A2=09International Conference on Artificial Intelligence and Pattern= Recognition (AIPR-09)=20 =E2=80=A2=09International Conference on Automation, Robotics and Control Sy= stems (ARCS-09) =E2=80=A2=09International Conference on Enterprise Information Systems and = Web Technologies (EISWT-09) =E2=80=A2=09International Conference on High Performance Computing, Network= ing and Communication Systems (HPCNCS-09)=20 =E2=80=A2=09International Conference on Information Security and Privacy (I= SP-09) =E2=80=A2=09International Conference on Recent Advances in Information Tech= nology and Applications (RAITA-09) =E2=80=A2=09International Conference on Software Engineering Theory and Pra= ctice (SETP-09)=20 =E2=80=A2=09International Conference on Theory and Applications of Computat= ional Science (TACS-09) =E2=80=A2=09International Conference on Theoretical and Mathematical Founda= tions of Computer Science (TMFCS-09) The website www.PromoteResearch.org contains more details. Sincerely John Edward Publicity committee =0A=0A=0A From owner-chemistry@ccl.net Thu Oct 23 11:32:00 2008 From: "Zork Zou zorkzou^^gmail.com" To: CCL Subject: CCL: Questions about excited state optimizations/excited states Message-Id: <-37971-081023112932-2360-71PbPOnRvbArXKVTXhle1w : server.ccl.net> X-Original-From: "Zork Zou" Content-Type: multipart/alternative; boundary="----=_Part_36799_13659169.1224775760449" Date: Thu, 23 Oct 2008 10:29:20 -0500 MIME-Version: 1.0 Sent to CCL by: "Zork Zou" [zorkzou . gmail.com] ------=_Part_36799_13659169.1224775760449 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Among the free softwares, I think GAMESS-US, PC-GAMESS, and NWChem are suitable for you. GAMESS-US TDDFT can optimize the excited states of both closed-shell and open-shell molecules. For siglet excited states, you can also use analytical gradient. PC-GAMESS TDDFT can only optimize the singlet and triplet excited states of closed-shell molecules, and the gradient is numerical. You can also pick up some states with special irre., including non-Abelian symmetry. Moreover, it supports both RPA and TDA. NWChem TDDFT has similar capabilities to that of PC-GAMESS, except it supports open-shell molecules and LB94/CS00 asymptotic correction. Unfortunately, since revision 4.7, the non-Abelian point group is not supported in TDDFT calculation. ------=_Part_36799_13659169.1224775760449 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Among the free softwares, I think GAMESS-US, PC-GAMESS, and NWChem are suitable for you.

GAMESS-US TDDFT can optimize the excited states of both closed-shell and open-shell molecules. For siglet excited states, you can also use analytical gradient.

PC-GAMESS TDDFT can only optimize the singlet and triplet excited states of closed-shell molecules, and the gradient is numerical. You can also pick up some states with special irre., including non-Abelian symmetry. Moreover, it supports both RPA and TDA.

NWChem TDDFT has similar capabilities to that of PC-GAMESS, except it supports open-shell molecules and LB94/CS00 asymptotic correction. Unfortunately, since revision 4.7, the non-Abelian point group is not supported in TDDFT calculation.
------=_Part_36799_13659169.1224775760449-- From owner-chemistry@ccl.net Thu Oct 23 16:33:01 2008 From: "Kalju Kahn kalju[a]chem.ucsb.edu" To: CCL Subject: CCL: dielectric constants Message-Id: <-37972-081023162909-17053-4X4PxMtV4LHfK0NH/45eaA(!)server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 23 Oct 2008 13:28:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju*|*chem.ucsb.edu] András, For atoms and nonpolar (dipole moment = 0) molecules in the gas phase, use Clausius-Mossotti equation, which when solved for dielectric, reads: eps = 1 - (3*N_avg*polarizability /(N_avg*polarizability - 3*V_molar*eps_0)) For polar molecules, Debye-Langevin form should be used. After some trouble with unit conversions, you can arrive to formula that calculates dielectric from polarizability (and dipole moment for polar molecules. But in the gas phase, the result is very close to 1. For liquids, the answer is much more complex ... Kirkwood–Fröhlich theory with MD or MC sampling. Kalju > - > Dear Colleagues, > > How can dielectric constants of small organic molecules be estimated by > any computational method? > > Regards, > > Dr. András Péter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - > Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Thu Oct 23 18:21:01 2008 From: "Kadir Diri kadir**visual1.chem.pitt.edu" To: CCL Subject: CCL: GRC and GRS on Molecular Energy Transfer: 3rd circular and deadlines extension (fwd) Message-Id: <-37973-081023181806-27481-+gEolFXpKDC4Q7iroNOiTg*server.ccl.net> X-Original-From: Kadir Diri Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Oct 2008 15:17:40 -0700 MIME-version: 1.0 Sent to CCL by: Kadir Diri [kadir##visual1.chem.pitt.edu] Please note the extended deadlines: kadir > Dear Colleagues, > > This is the third announcement of the upcoming Gordon Research > Conference on Molecular Energy Transfer > (http://www-rcf.usc.edu/~krylov/grcomet2009), to be held at the Four > Points Sheraton Harbortown, in Ventura California, January 18-22, > 2009. In keeping with the tradition of this meeting, which > alternates between the MET Gordon Conference in the US and the COMET > meeting in Europe, we are organizing sessions to cover all areas of > molecular energy transfer: > > * Chemical reactivity and reaction dynamics. > * Ionized and electronically excited species. > * Clusters, interfaces and the condensed phases. > * Photochemistry, spectroscopy, and imaging. > * Non-adiabatic, spin-forbidden, and vibronic ET. > > Confirmed Speakers: Confirmed Session Chairs: > > Millard Alexander Ara Apkarian > Joel Bowman Mark Johnson > Steve Bradforth Ken Jordan > Piero Casavecchia Marsha Lester > Robert Continetti Carl Lineberger > Bob Field Anne McCoy > George Flynn David Perry > Benny Gerber Scott Reid > Wei Kong Alec Wodtke > Kevin Lehmann > Kopin Liu > David Nesbitt > Hanna Reisler > Andrei Sanov > George Schatz > Reinhard Schinke > David Sherrill > Albert Stolow > Arthur Suits > Arthur Utz > Curt Wittig > David Yarkony > > The conference will be preceded by a graduate and post-doctoral > research seminar (GRS), a 2-day satellite meeting on January 17-18 > for PhD students and post-doctoral researchers, to amplify their > participation in this Gordon conference. The GRS, first initiated > at the 2005 meeting in Buellton, CA, has proven to be a great > success. > > Professors Daniel Neumark and Alexander Benderskii have agreed to be > Faculty Mentors for the GRS meeting which will be co-chaired by > Anton Zadorozhny and Sarandis Marinakis. The full program, location > information, history of the meeting, application instructions, and > other details are available on the conference website: > > http://www-rcf.usc.edu/~krylov/grcomet2009/ > > Limited travel support for graduate students is available. Students > are strongly encouraged to apply as early as possible. Earlier > applications can facilitate the funding decisions and. Note that > participation in the GRS requires separate application! > > > We are grateful to the following organizations for their financial support: > Department of Energy, Office of Basic Energy Sciences > Molecular Physics/Taylor & Francis Group > Del Mar Photonics > Q-Chem > PCCP > > We are looking forward for the exciting meeting and hope to see you in Ventura! > > Sincerely, > > H. Floyd Davis Anna I. Krylov > Professor of Chemistry Professor of Chemistry > Cornell University University of Southern California > http://www.chem.cornell.edu/hfd1 http://www-rcf.usc.edu/~krylov > > > Anton Zadorozhny Sarantos Marinakis > Department of Chemistry School of Engineering and Physical Sciences > University of Southern California Heriot-Watt University, Edinburgh > From owner-chemistry@ccl.net Thu Oct 23 20:25:00 2008 From: "Gustavo Seabra gustavo.seabra|-|gmail.com" To: CCL Subject: CCL:G: Gaussian 03W for Windows Message-Id: <-37974-081023201407-4954-3d0AhYMvX31ssJgmAuocqw!=!server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 23 Oct 2008 20:13:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra : gmail.com] Have you tried to contact Gaussian about this? They should be the best qualified ones to answer your question. Gustavo. On Wed, Oct 22, 2008 at 9:32 AM, Carmela Bonaccorso wrote: > Hello > > I'm a beginner in the field of Computational Chemistry. > I would like to know what version of Gaussian 03 should > I use on a machine with the following cpu: INTEL CORE > 2 QUAD Q8200. I need the Parallel version: Single multiprocessor > machine license or the Serial (Single CPU) Version: Single Windows machine license? > Now I'm working with Gaussian 03 Rev.B03 and obtain olny > 25% of cpu usage on the quad core machine and 50% on a dual > core machine and never reached 100%. > I have no problem of Ram or disk space... > The problem is related to the older version that I'm using or I > neglect some Link0 commands? (I usually specify only nprocshared=4) > Thanks a lot.