From owner-chemistry@ccl.net Wed Jun 21 07:22:00 2006 From: "Jens Spanget-Larsen spanget|*|ruc.dk" To: CCL Subject: CCL: DipoleDeriv Message-Id: <-31972-060621072015-31331-1oayn+DcuXTPNn4vRaCnRg[-]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, 21 Jun 2006 13:20:06 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget-x-ruc.dk] Shobe, David dshobe.:.sud-chemieinc.com wrote: > Sent to CCL by: "Shobe, David" [dshobe++sud-chemieinc.com] > OK here's a physics question for the list. Is there a reason that the off-diagonal elements of this matrix should be zero? In other words, can the motion of a nucleus perpendicular to the dipole affect the dipole? > > --David Shobe, Ph.D., M.L.S. Sure, the motion of a nucleus in a direction perpendicular to the molecular dipole moment will affect the dipole moment, in particular its direction. 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 ------------------------------------------------------ From owner-chemistry@ccl.net Wed Jun 21 08:00:01 2006 From: "Jim Kress ccl_nospam^^^kressworks.com" To: CCL Subject: CCL:G: computation of franck condon factors for O2 cation Message-Id: <-31973-060620214845-31410-YdOqV4te+VtptlPd8MRnUg#%#server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Jun 2006 21:48:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam^kressworks.com] Why not use a MCSCF calculation that includes the proper separation states? That way the PES will accurately represent the process of bond dissociation. In many cases, correlated methods based on a single state reference will not separate properly. Your MP2 result is a good example. Jim > -----Original Message----- > From: Steve Williams willsd_+_appstate.edu > [mailto:owner-chemistry=-=ccl.net] > Sent: Tuesday, June 20, 2006 5:48 PM > To: Kress, Jim > Subject: CCL:G: computation of franck condon factors for O2 cation > > Sent to CCL by: Steve Williams [willsd,,appstate.edu] I am > looking at a problem that seemed simple but looks more > complicated. I'd like to compute Franck Condon factors for > the lowest 5 or so vibrational states of the quartet pi > excited state of O2+ going to the lowest 10 or so vibrational > states of the doublet pi ground state (of O2+). I have what > I think will be a useful method (Thanks to Russell Johnson > for his fgh1d code) for computing vibrational wavefunctions > and energies from a discrete set representation of the PES > for a given state. > > My problem is computing the PES... I know that I can get > excellent minima (experiment is 1.1164 A and computation > gives 1.11637 A) and pretty good frequencies for both states > using ccsd(t) with the aug-cc-pvtz basis set. I have done > some PES scans (for the ground state only so far) with > ACESII, QCHEM 3, and G03, and all show problems. At very > short bond lengths (say 0.8 A) down to the minimum the energy > drops smoothly then rises in a way that looks quite like a > Morse function, but at longer distances bad things happen. > The ccsd(t) reaches a maximum at about 1.9 A, falls smoothly > to about 2.2 A, then drops very rapidly. In ACESII the cc > equations will not converge at bond lengths greater than > 2.263 A. In QCHEM 3 the MP2/aug-cc-pvqz PES is similar: a > maximum at about 1.5 A; by 1.9 A the energy is well below the > "minimum". > > I think what I am seeing is interaction between the doublet > pi ground state surface and the quartet pi excited state (or > maybe some other excited state). Fig 2 in J. Phys. Chem. > Ref. Data, Vol 1, No2, 1972 implies a crossing of these > surfaces near 2 A. > > Does anyone have suggestions of better ways to generate the > potential energy surfaces I need for these states? I suspect > that something like EOM-CCSD may be better, but I am unsure > how to use such methods. I have access to Gaussian, ACESII > and QCHEM 3 (at least for a while on the latter two). > > Thanks, > Steve Williams > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the =-= sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Wed Jun 21 08:35:02 2006 From: "Greg Sigalov sigalov..uiuc.edu" To: CCL Subject: CCL: using MCLite to solve Poisson-Boltzman equation Message-Id: <-31974-060621012702-2985-rwbWIatBll1nH9WbQnS8bA..server.ccl.net> X-Original-From: "Greg Sigalov" Date: Wed, 21 Jun 2006 01:27:00 -0400 Sent to CCL by: "Greg Sigalov" [sigalov . uiuc.edu] Hello, have anyone used MCLite to solve Poisson-Boltzman equation, or any other equation, for that matter? I really need some advice on setting up the calculations. In particular, could you tell me what exactly are "natural boundary conditions" in files fu_v.m and dfu_wv.m and where the form to estimate them arises from? Thanks, Greg. From owner-chemistry@ccl.net Wed Jun 21 09:10:01 2006 From: "Temur Kutsia kutsia++risc.uni-linz.ac.at" To: CCL Subject: CCL: Transnational Access Program at RISC Message-Id: <-31975-060621064544-27644-z5416we8AKZrGd2PVZhJXA,+,server.ccl.net> X-Original-From: "Temur Kutsia" Date: Wed, 21 Jun 2006 06:45:37 -0400 Sent to CCL by: "Temur Kutsia" [kutsia a risc.uni-linz.ac.at] [Apologies if you receive multiple copies] ******************************************************** * European Commission Framework 6 Programme * * Integrated Infrastructures Initiatives * * * * Symbolic Computation in Europe (SCIEnce) * * * * TRANSNATIONAL ACCESS PROGRAM * * * * * * Research Institute for Symbolic Computation (RISC) * * Johannes Kepler University of Linz, Austria * * * ******************************************************** RISC-Linz, a research institute at the Johannes Kepler University, Austria, offers opportunities to researchers to obtain access to its infrastructure and facilities. Access is free of charge and is provided through the project SCIEnce within the 6th Framework Programme of the European Commission. What we offer ============= Free access to the infrastructure, facilities, and expertise of a world-leading center in symbolic computation. Scientific, technical, administrative, and logistic support, including travel and living expenses. Who can benefit =============== Researchers from any field of sciences who use or would like to use symbolic computation in their research. For more information and the application procedure please visit the program web page: http://www.risc.uni-linz.ac.at/research/projects/science/access/ From owner-chemistry@ccl.net Wed Jun 21 10:09:01 2006 From: "Shobe, David dshobe---sud-chemieinc.com" To: CCL Subject: CCL:G: How to calculate excited states of Cu(II) complexes by G98? Message-Id: <-31976-060621091656-5633-DfGmdcsIzmVEJPGdxcv0kA..server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 21 Jun 2006 15:15:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe/a\sud-chemieinc.com] You don't need a "doublet" keyword. When you use CIS, TDDFT and Zindo to calculate excited states, the default is that the excited states have the same spin multiplicity as indicated in the line just before the z-matrix. So you can study doublet->doublet transitions. With a singlet ground state you can study both singlet->triplet transitions using the "triplet" keyword, but otherwise you are limited to transitions in which the spin multiplicity remains constant. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry]=[ccl.net [mailto:owner-chemistry]=[ccl.net] Sent: Tuesday, June 20, 2006 10:00 PM To: Shobe, David Subject: CCL:G: How to calculate excited states of Cu(II) complexes by G98? Sent to CCL by: "Yi wen Dong" [yyyy2469[-]163.com] Would anybody likes to tell me how to calculate the excited states of Cu(II) complexes? The Cu(II) complexes have a Cu-d9 configuretion, so the multiplicities for these complexes are 2, not 1 and 3. The CIS, TDDFT and Zindo levels of G98 have no option, Doublet, therefore it is concluded that the excited states for these complexes would be impossible for calculation by G98. Is it Ok? If not, how to calculate them? I will be very appreciated if you can send me a calculating example input file for such complexes or give some comments or suggestion. Dr. Yi-wen Dong yyyy2469 . 163.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jun 21 10:44:00 2006 From: "Shobe, David dshobe/./sud-chemieinc.com" To: CCL Subject: CCL: DipoleDeriv Message-Id: <-31977-060621100741-5767-aJ3b1Kzn/JWkWMhslnYQwA,,server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Jun 2006 16:06:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe_._sud-chemieinc.com] OK, the two questions I asked are not quite equivalent: my mistake. But it's the first question that I was interested: Is there a reason that the off-diagonal elements of this matrix should be zero? --David Shobe -----Original Message----- > From: owner-chemistry|*|ccl.net [mailto:owner-chemistry|*|ccl.net] Sent: Wednesday, June 21, 2006 7:31 AM To: Shobe, David Subject: CCL: DipoleDeriv Sent to CCL by: Jens Spanget-Larsen [spanget-x-ruc.dk] Shobe, David dshobe.:.sud-chemieinc.com wrote: > Sent to CCL by: "Shobe, David" [dshobe++sud-chemieinc.com] OK here's a > physics question for the list. Is there a reason that the off-diagonal elements of this matrix should be zero? In other words, can the motion of a nucleus perpendicular to the dipole affect the dipole? > > --David Shobe, Ph.D., M.L.S. Sure, the motion of a nucleus in a direction perpendicular to the molecular dipole moment will affect the dipole moment, in particular its direction. 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 ------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jun 21 13:35:01 2006 From: "Nathan Baker nathan.baker],[wustl.edu" To: CCL Subject: CCL: using MCLite to solve Poisson-Boltzman equation Message-Id: <-31978-060621125730-5671-/sJF2B0kYRkqBwnBe+4mmQ,+,server.ccl.net> X-Original-From: Nathan Baker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 21 Jun 2006 11:00:52 -0500 Mime-Version: 1.0 (Apple Message framework v750) Sent to CCL by: Nathan Baker [nathan.baker . wustl.edu] Yes, we have. It was the basis for APBS's interface with the Holst group's FEtk software. Many of the details to the implementation are provided in: Holst M, Baker N, Wang F. Adaptive multilevel finite element solution of the poisson-boltzmann equation i. Algorithms and examples. Journal of Computational Chemistry. 21 (15), 1319-42, 2000. http://www3.interscience.wiley.com/cgi-bin/abstract/73503240/ ABSTRACT Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the poisson-boltzmann equation ii. Refinement at solvent- accessible surfaces in biomolecular systems. Journal of Computational Chemistry. 21 (15), 1343-52, 2000. http:// www.interscience.wiley.com/jpages/0192-8651 Please let me know if these papers answer your questions. We'd be happy to help with additional information. Thanks, Nathan On Jun 21, 2006, at 8:07 AM, Greg Sigalov sigalov..uiuc.edu wrote: > Sent to CCL by: "Greg Sigalov" [sigalov . uiuc.edu] > Hello, > > have anyone used MCLite to solve Poisson-Boltzman equation, or any > other equation, for that matter? I really need some advice on > setting up the calculations. In particular, could you tell me what > exactly are "natural boundary conditions" in files fu_v.m and > dfu_wv.m and where the form to estimate them arises from? > > Thanks, > > Greg. > > > > -= 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)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ From owner-chemistry@ccl.net Wed Jun 21 17:23:00 2006 From: "Carol Parish cparish{}richmond.edu" To: CCL Subject: CCL: 5th MERCURY Conference in Undergraduate Computational Chemistry Message-Id: <-31979-060621172157-22626-XunOmlIblBAHoklGfeC3+g a server.ccl.net> X-Original-From: "Carol Parish" Date: Wed, 21 Jun 2006 17:21:50 -0400 Sent to CCL by: "Carol Parish" [cparish!^!richmond.edu] Dear Colleagues: We are pleased to announce the Fifth MERCURY Conference for Undergraduate Computational Chemistry. The Conference will be held July 26-28th, 2006, at Hamilton College, in Clinton, NY. The conference will feature plenary lectures by Dagmar Ringe, Brandis University; Andras Fiser, Albert Einstein College of Medicine; Heather Gordon, Brock University; Yvonne Martin, Abbott Laboratories; Hugh Nymeyer, Florida State University; and Jeff Saven, University of Pennsylvania. In addition mainstays of the conference include an Undergraduate Poster Session and evening social sessions. This conference represents an excellent forum for undergraduates to present their work and to learn from experts in the field, allowing them to put their own research in perspective. It is equally valuable as a network for faculty working with undergraduates. Undergraduates from all institutions are invited to come present their work. Conference Fees are 210 for faculty, postdocs, or graduate students, and 105 for undergraduates, and include registration, housing, and meals. Details of the conference and information on registration and submission of Abstracts can be found on our web site: http://mercury.chem.hamilton.edu/conference/2006 George Shields, on behalf of MERCURY, the Molecular Education and Research Consortium in Undergraduate computational chemistRY