From owner-chemistry@ccl.net Sun Oct 8 01:16:00 2006 From: "Sue L chsue2004]*[yahoo.com" To: CCL Subject: CCL: Software for Distance Measurement Between Molecules Message-Id: <-32735-061008010243-30464-OWGFSJWkKJqUag/aXVBI1Q||server.ccl.net> X-Original-From: "Sue L" Date: Sun, 8 Oct 2006 01:02:43 -0400 Sent to CCL by: "Sue L" [chsue2004##yahoo.com] Hi CCL users, Does anyone know any free software which can measure the distance between the center of two moleucles? Thanks, Sue From owner-chemistry@ccl.net Sun Oct 8 03:15:00 2006 From: "Tomasz Grabarkiewicz grabar:+:man.poznan.pl" To: CCL Subject: CCL: Software for Distance Measurement Between Molecules Message-Id: <-32736-061008031248-5613-vDpx8FKaL3zOS5txcu0HxQ[]server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Sun, 8 Oct 2006 08:27:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar[*]man.poznan.pl] Hi Sue, Mercury can do this for sure. http://www.ccdc.cam.ac.uk/products/csd_system/mercury/ Tomasz From owner-chemistry@ccl.net Sun Oct 8 04:20:01 2006 From: "Andreas Serr serr=theorie.physik.uni-muenchen.de" To: CCL Subject: CCL:G: static and dynamic polarizabilities Message-Id: <-32737-061007170826-16531-g8vFy990vEF5j1KFEbMYRA^^^server.ccl.net> X-Original-From: Andreas Serr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 07 Oct 2006 22:12:57 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Andreas Serr [serr-,-theorie.physik.uni-muenchen.de] Hi, the right polarizabilities done by Gaussian are the "exact" ones. The "approx" are done in an 'old fashion' and are for comparison only. The differences between "static" and "dynamic" pol. are described in electrodynamics literature, e.g. Böttcher, C. J. F. Theory of Electric Polarization: Dielectrics in Static Fields; Vol 1; Elsevier: Amsterdam, The Netherlands, 1973. Böttcher, C. J. F. Theory of Electric Polarization: Dielectrics in Time-Dependent Fields; Vol 2; Elsevier: Amsterdam, The Netherlands, 1978. static ones (experiment e.g. capacitor) include rotational, vibrational and electronic polarization (field fequency -> 0). dynamic ones (depending on the field frequency, experiment e.g. refraction/optical) only electronic polarization (field frequency >> 0). The Gaussian polarizability calculations are on the electronic part only. The standard pol. calc. is on a 'hypothetical' field: zero frequency, but frequency high enough not to include rotational & vibrational polarization. Note that you can also do the pol. calc. at an explicit frequency in Gaussian! Solvent effects on polarizability are complex & matter of current research. As a starting review on pol. of ions, you might want to look at our recent article: A. Serr and R.R. Netz Polarizabilities of hydrated and free ions derived from DFT calculations Int. J. Quant. Chem. 106 (12), 2409-2409 (2006) http://dx.doi.org/10.1002/qua.21121 Hope this helps, Andreas Quoting "Grigoriy Zhurko reg_zhurko(-)chemcraftprog.com" : > Sent to CCL by: Grigoriy Zhurko [reg_zhurko- -chemcraftprog.com] > Hello, > I have computed polarizabilities of some molecules using Gaussian98. > The question is, whether the printed values should be considered as > "static" or "dynamic" polarizabilities. These terms are unclear for me. > Besides that, I'd like to know what is the difference between "Exact > polarizability" and "Approx polarizability" printed by Gaussian98, and > what of these tensors should be used (I need to compare these > polarizabilities with experimental polarizabilities in solution). > > Sincerely, > Grigoriy Zhurko. > > > > -= 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)> > > Andreas Serr Biological Soft-Matter Theory Sektion Physik - Ludwig-Maximilians-Universitaet Theresienstr. 37, D-80333 Munich, Germany tel: +49-(0)89-2180-4603 / fax: +49-(0)89-2180-4517 room no: 304 / e-mail: serr]![theorie.physik.uni-muenchen.de http://www.theorie.physik.uni-muenchen.de/biophysics/ From owner-chemistry@ccl.net Sun Oct 8 05:28:00 2006 From: "Rafal A. Bachorz rafal.bachorz!=!chemie.uni-karlsruhe.de" To: CCL Subject: CCL: Software for Distance Measurement Between Molecules Message-Id: <-32738-061008051701-14111-NjyXNhFisoZ4mj4bzaBm8w_._server.ccl.net> X-Original-From: "Rafal A. Bachorz" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Sun, 08 Oct 2006 10:33:17 +0200 MIME-Version: 1.0 Sent to CCL by: "Rafal A. Bachorz" [rafal.bachorz%a%chemie.uni-karlsruhe.de] > Sent to CCL by: "Sue L" [chsue2004##yahoo.com] > Hi CCL users, > > Does anyone know any free software which can measure the distance > between the center of two moleucles? Dear Sue, Tomasz has probaly answered your question. From my site I can say that often you want to calculate the distance between the center of masses of two species. If you have XYZ coordinates of them, then you can write a simple code or even script which can do that for you. Have a good day, Rafal From owner-chemistry@ccl.net Sun Oct 8 13:39:00 2006 From: "Michel Petitjean ptitjean|a|itodys.jussieu.fr" To: CCL Subject: CCL: Software for Distance Measurement Between Molecules Message-Id: <-32739-061008133652-14659-mDvFBOEXVmT5zj6uaZrJJg^server.ccl.net> X-Original-From: Michel Petitjean Date: Sun, 8 Oct 2006 19:36:40 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean[]itodys.jussieu.fr] To: chemistry=-=ccl.net Subject: CCL: Re: Software for Distance Measurement Between Molecules I guess that calculating a distance between two points is not the problem. Rather, what is "the center" of a molecule: how do you define it ? Assuming n atoms, positions x1, ..., xn, some definitions are: - The mean of the atomic positions, i.e. (x1+..+xn)/n - The mass center: (M1*x1+...+Mn*xn)/(M1+...Mn) - The center of the minimal sphere containing the n atomic centers - The mean of the k vertices of the convex hull of the n atomic centers - Etc... Some of these calculations are performed by the freeware RADI: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean=-=itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean=-=ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: "Sue L" [chsue2004##yahoo.com] > Hi CCL users, > > Does anyone know any free software which can measure the distance between the center of two moleucles? > > Thanks, > Sue From owner-chemistry@ccl.net Sun Oct 8 15:06:00 2006 From: "ponnadurai ramasami ramchemi,,intnet.mu" To: CCL Subject: CCL: dielectric constant Message-Id: <-32740-061008085055-17368-Y5FpovULT7C86QAAoHOnMQ ~~ server.ccl.net> X-Original-From: "ponnadurai ramasami" Date: Sun, 8 Oct 2006 07:29:33 -0400 Sent to CCL by: "ponnadurai ramasami" [ramchemi .. intnet.mu] Does anyone know (with reference) about the dielectric constant of? 1-bromo-2-iodoethane 1-bromo-2-chloroethane Thanks