From chemistry-request@www.ccl.net Tue Sep 8 15:06:20 1998 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA00716 Tue, 8 Sep 1998 15:06:20 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id MAA10916 for ; Tue, 8 Sep 1998 12:06:20 -0700 (PDT) Date: Tue, 8 Sep 1998 12:06:19 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: summary: IR peak fitting Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Thank you to those who offered suggestions to my question about obtaining software for fitting a spectrum to a series of Lorentzian or Gaussian peaks. Unfortunately, it appears that one must either buy such a package ($495 academic price on PeakFit from SPSS), or modify existing nonlinear regression code. Sure would be nice if someone would write such a useful package and make it freely available...... Best wishes to all, Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@www.ccl.net Tue Sep 8 16:43:49 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA03916 Tue, 8 Sep 1998 16:43:43 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for jmnewsa@biff id AA13713; Tue, 8 Sep 98 13:14:23 -0700 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma013709; Tue, 8 Sep 98 13:14:01 -0700 Received: from newsam-pc.msi.com by biff.biosym.com (4.1/SMI-4.1) id AA07567; Tue, 8 Sep 98 13:11:46 PDT Message-Id: <3.0.2.32.19980908131628.007610c0@146.202.0.225> X-Sender: jmnewsa@146.202.0.225 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.2 (32) Date: Tue, 08 Sep 1998 13:16:28 -0700 To: chemistry@www.ccl.net From: John M Newsam Subject: MGMS meeting San Diego Dec 98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues, The deadline for submission of abstracts to the 17th International Meeting of the Molecular Graphics and Modelling Society is fast approaching. The meeting will take place at the Paradise Point Resort in San Diego, December 6-10, 1998 and has as a prime theme "Molecular Modelling in the Large". The program outline, further details, and abstract submission and registration forms are available on the conference Web site: http://www.mgmsoa.org/ It promises to be an interesting meeting to which we hope you will be able to contribute, with all best wishes, John M Newsam (on behalf of the program and local organizing committee) Prof. John M. Newsam, Chief Scientific Officer Molecular Simulations Inc., 9685 Scranton Road, San Diego CA 92121 http://www.msi.com/corp/science/index.html From chemistry-request@www.ccl.net Tue Sep 8 14:34:14 1998 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA29933 Tue, 8 Sep 1998 14:34:03 -0400 (EDT) Received: from danon (Danon.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01J1KHOQKEG00011SN@NPD.UFPE.BR> for chemistry@www.ccl.net; Tue, 8 Sep 1998 15:35:59 GMT-3 Date: Tue, 08 Sep 1998 15:46:10 -0300 From: Marcelo Zaldini Hernandes Subject: IGLO basis sets ? To: ccl-lista Message-id: <001801bddb58$f2f52900$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_0015_01BDDB3F.CD1FFC50" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_0015_01BDDB3F.CD1FFC50 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear colleagues, Anyone know where can I find IGLO basis sets for magnetic properties = calculations ? =20 Sincerely, = Marcelo Zaldini Hernandes =20 E-mail: zaldini@npd.ufpe.br =20 ------=_NextPart_000_0015_01BDDB3F.CD1FFC50 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
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------=_NextPart_000_0015_01BDDB3F.CD1FFC50-- From chemistry-request@www.ccl.net Tue Sep 8 14:31:01 1998 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA29867 Tue, 8 Sep 1998 14:31:00 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA29757 (5.65c/IDA-1.4.4 for ); Tue, 8 Sep 1998 14:29:36 -0400 Received: by zeus.cooper.edu id AA26398 (5.67b/IDA-1.5); Tue, 8 Sep 1998 14:30:16 -0400 From: TOPPER ROBERT Message-Id: <199809081830.AA26398@zeus.cooper.edu> Subject: Re: CCL:CCL: (1) Morse potential and (2) hindered rotations To: alexei@palladium.enscm.fr (Arbouznikov Alexei) Date: Tue, 8 Sep 1998 14:30:15 -0400 (EDT) Cc: topper@cooper.edu, CHEMISTRY@www.ccl.net In-Reply-To: from "Arbouznikov Alexei" at Sep 4, 98 10:56:24 am X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Alexei, I have done quite a bit of work with partition functions, and so I find myself able to answer your questions. (1) The Morse potential does indeed admit analytical solutions for rotationless motion. If you read Morse's original paper P.M. Morse, Phys. Rev. v.34, p.57 (1929) the eigenfunctions and eigenvalues are given. The eigenvalues are all that you need to get the partition function. Unfortunately, you will have to sum up the energy levels using a spreadsheet or small program, as the partition function is not analytically summable (Another example of this is the quantum rigid rotator, which has analytical eigenvalues but not a closed- form partition function). To summarize: the Morse potential is U = D{1-exp[-a(r-re)]}^2 where D= dissociation energy, re = equilibrium bond distance and a is a parameter used to fit the curvature to experiment. From Steinfeld's "Molecules and Radiation", 2nd ed. (1985), I read that to get the harmonic frequency exactly in agreement with experiment, one chooses a to be a = omega * sqrt [ pi*c*mu/(hbar * D)] with a, omega and D all in cm^-1 and r, re in cm. omega is the harmonic vibrational frequency, mu is the reduced mass in units appropriate to those used for hbar, and c is the speed of light in cm/sec. You may want to check that by evaluating the second derivative of the Morse potential at R = Re. The energy eigenvalues, again in cm^-1, are E = omega * (n + 0.5) - kappa * (n + 0.5)^2 with kappa = hbar* a^2 / 4*pi*c*mu Note that the energy eigenvalues are of the form E = E (harmonic oscillator) + correction, which is kind of cool. Spectroscopists have traditionally expanded vibrational energy levels in term series and this formula resembles the first 2 terms in such a series (sans rotations). (2) I believe you're thinking of a formula that Truhlar developed - although there is no truly exact solution this one comes close, and has good properties: D.G. Truhlar, J.Comp.Chem v12, p266 (1991) I hope this helps. Best, Robert Topper ***************************************************************************** Robert Q. Topper email: topper@cooper.edu Asst. Professor of Chemistry phone: (212) 353-4341 The Cooper Union fax: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 and you're there! http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** The Cooper Union for the Advancement of Science and Art is a tuition-free college in Greenwich Village, at Cooper Square and Astor Place. ***************************************************************************** > > Dear CCL'ers, > > Could anybody hint me (or give some reference) concerning the > energy levels for uni-dimensional motion in the Morse potential? (I read > that this problem has been solved exactly, but may be I confused something > and this is not the case). What I need in exactly is the partition > function for the vibrational motion just in this Morse potential. > > Secondly, I also heard (but not found anywhere) that there is an > exact expression of the partition function for the hindered internal > rotations. Does anybody know, where one could find it? > > Best regards, > > Alexei > From chemistry-request@www.ccl.net Tue Sep 8 05:42:00 1998 Received: from palladium.enscm.fr (palladium.enscm.fr [193.52.207.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA25633 Tue, 8 Sep 1998 05:41:59 -0400 (EDT) Received: from localhost (alexei@localhost) by palladium.enscm.fr (8.8.7/8.8.7) with SMTP id LAA27214 for ; Tue, 8 Sep 1998 11:35:54 +0200 (MDT) Date: Tue, 8 Sep 1998 11:35:54 +0200 (MDT) From: Arbouznikov Alexei X-Sender: alexei@palladium Reply-To: Arbouznikov Alexei To: CHEMISTRY@www.ccl.net Subject: partition functions - between vibration and translation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, 4 days ago, I have posted some questions associated with calculating partition functions. I need in some information more, concerning the following, may be, more general problem. Suppose, we have some weak interaction, e.g., physisorption, with the depth of the potential well about 2 - 3 kcal/mol, or even less. To calculate properly the vibrational partition function (for the motion of the adsorbed molecule, as a whole, against the surface) one has to keep in mind that: (1) traditional harmonic approximation may give a noticeable error; (2) just that I would like to discuss: since the dissociation limit is low-lying, then, probably, there could be some NON-NEGLIGIBLE contribution to the partition function from the states which lye ABOVE the dissociation limit. The latter could be treated in the manner similar to that for estimating the translational partition function. However, it is not so easy to do it analytically, without introducing approximations. The problems of this kind (even the simplest ones, e.g., rectangular potential well with finite-height walls) are known not to have closed solutions. Probably, such problems can be treated approximately, by, e.g., Wentzel-Kramers-Brillouin method. Speaking on the NON-NEGLIGIBILITY of the contribution from the states lying above the dissociation limit, I mean also that, if the latter tends to zero (no interaction), or if the temperature tends to infinity, our partition function should tend to the translational one which is usually HUGE with respect to any vibrational partition function (corresponding to the strong interaction) Thus, one needs to fill the gap between these two limiting cases by anything. There is an obvious similarity between that was discussed above, and hindered rotation. In the latter case, we have a contribution to the partition function form the vibrations (states below the rotational barrier) and more-or-less free rotations (above the barrier). At T ->inf, one can neglect the former; at T -> 0 - the latter. What to do for the moderate temperatures? I beleive, such problems arose (and, probably, were solved) in the past. I am grateful in advance to anybody for any discussion and references. Alexei ======================================================================== Dr. Alexei Arbouznikov Ecole Nationale Superieure de Chimie, Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula, 8, rue de l'Ecole Normale 34296 Montpellier, Cedex 5 FRANCE Telephone: (33) 4-67-14-72-68 Fax: (33) 4-67-14-43-49 E-mail: alexei@palladium.enscm.fr From chemistry-request@www.ccl.net Tue Sep 8 01:05:58 1998 Received: from Sun.Farlep.Net (Sun.Farlep.Net [195.145.102.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA24759 Tue, 8 Sep 1998 01:05:54 -0400 (EDT) Organization: Farlep-Internet Received: from farlep.net (L101.Farlep.Net [195.145.102.101]) by Sun.Farlep.Net (8.9.0/8.9.0/Farlep-Mail-2.0) with ESMTP id IAA04721; Tue, 8 Sep 1998 08:05:42 +0300 (EEST) Message-ID: <35F2588D.A44CE820@farlep.net> Date: Sun, 06 Sep 1998 12:40:30 +0300 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Diffusion within fractals-2 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit Dear Dr. X.Guo: You are studing a very spesial & interesting case. May I ask you any questions? 1. Are you simulating the diffusion of the fractal particles in the percolation clusters ? 2. Are theš clusters near the percolation threshold or more above ? 3. Did you tried to study & to compare to the case of the Knudsen diffusion & the case when "temperature" is very slowly and the pores size & the track length areš approximatly equals in the same clusters ? ššš Best regards. ššš A.Herega