From qftramos@usc.es Sat Dec 14 06:09:32 1996 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.8.3/950822.1) id FAA03358; Sat, 14 Dec 1996 05:29:47 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA20271; Sat, 14 Dec 1996 11:29:29 +0100 Date: Sat, 14 Dec 1996 11:29:29 +0100 (MET) From: Antonio Fernandez Ramos To: Lista computacional Subject: Summary:Rate Constants Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII From hinsen@ibs.ibs.frSat Dec 14 11:25:23 1996 Date: Tue, 26 Nov 96 19:28:17 +0100 From: Konrad Hinsen To: qftramos@uscmail.usc.es Subject: Re: CCL:Rate constants > I am very interested in experimental rate constants in gas phase > for the intramolecular proton transfer in malonaldehyde and derivatives, > tropolone and derivatives etc. I did some research on that about a year ago, since I was working on numerical calculations of this rate constant in acetylacetone. I did not find anything on the rate constant itself, but some papers on related quantities (e.g. the tunneling splitting of the ground state). I'll check if I still have the output file of the database search somewhere. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- From ujita@cm.kyushu-u.ac.jpSat Dec 14 11:25:43 1996 Date: Mon, 2 Dec 96 10:02:02 JST From: Hiroki Ujita To: qftramos@uscmail.usc.es Subject: Re:CCL:Rate constants ------------------------------------------------------------------------- Dear Mr. Antonio Fernandez Ramos, I am a researcher in the Institute of advanced material study in Kyushu University. Dr. Takaaki Sonoda introduced you to me as a researcher of proton transfer. Dr. Hiroshi Sekiya and co-workers(including me) have investigated proton transfer and related phenomena of tropolone, 9-hydroxyphenalenone and their deriatives here. I have studied the electronic and vibrational structures of those molecules using Gaussian and GAMESS. Dr.Sekiya transferred to the Faculty of Science in this university as an associate professor and is continuing this research by electronic spectroscopy with the students there and here. Regards, Hiroki Ujita (E-Mail:ujita@cm.kyushu-u.ac.jp) From arilahti@ra.abo.fi Sat Dec 14 07:09:34 1996 Received: from ra.abo.fi for arilahti@ra.abo.fi by www.ccl.net (8.8.3/950822.1) id HAA03533; Sat, 14 Dec 1996 07:02:43 -0500 (EST) Received: from kirke.abo.fi (arilahti@kirke.abo.fi [130.232.80.238]) by ra.abo.fi (8.8.3/8.8.3) with ESMTP id OAA18040 for ; Sat, 14 Dec 1996 14:02:35 +0200 (EET) From: Ari Lahti IFK Received: (from arilahti@localhost) by kirke.abo.fi (8.8.3/8.8.3) id OAA28024 for chemistry@www.ccl.net; Sat, 14 Dec 1996 14:02:34 +0200 (EET) Message-Id: <199612141202.OAA28024@kirke.abo.fi> Subject: Summary: Intramolecular Hydrogen Bond and AIM To: chemistry@www.ccl.net Date: Sat, 14 Dec 1996 14:02:34 +0200 (EET) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Many thanks to all who responded to my query on Intramolecular Hydrogen Bond and AIM. According to the replies summerized below, the AIM theory really is applicable to the evaluation of the strength of intramolecular hydrogen bonds. It seems worthwhile trying AIMPAC, MORPHY, or EXTREME if Gaussian fails to identify the critical points. I also thank prof. Bader and dr Bayley, working in his group, for kindly delivering a copy of the AIMPAC program package. best wishes --ari lahti ----------------------------------------------------------------------------- * Ari Lahti, M.D., M.Sc. phone: +358 2 2654951 * * Dept. of Phys. Chem. fax: +358 2 2654706 * * Abo Akademi University email: arilahti@abo.fi * * Porthansg. 3-5 * * FIN - 20500 Abo * * Finland * ----------------------------------------------------------------------------- My original message: >I make calculations on a small molecule that has an imidazole ring and >another ring formed by an intramolecular hydrogen bond. I would like to >evaluate the strength of this intramolecular hydrogen bond, and I'm >wondering if the AIM theory might be useful in this respect. >The charge density at the critical point of a bond is supposed to correlate >with the strength of the bond. Is this correlation linear in the sense that >it lets one compare the strengths of intramolecular hydrogen bonds between >related molecules? Would this linearity make possible the evaluation of the >strength of an intramolecular hydrogen bond in absolute terms also, >through comparison of the charge density at the critical point of the >system under investigation to that of a known model system? >I have made some preliminary calculations using the AIM card of >Gaussian94. My calculations always end up with 'Hopf-Poincare condition not >satisfied', possibly because the program cannot handle the ring structures >of my molecule. The ring points are thus not given. However, the critical >points of the covalent bonds and the intramolecular hydrogen bond are >indicated. Are these results useful, or does the Hopf-Poincare error >message mean that even data concerning these bond critical points are >corrupted? The replies: _____________________________________________________________________________ From sctbythe@kraken.itc.gu.edu.au Tue Dec 10 04:19 EET 1996 Dear Ari There is a paper by Koch & Popelier, in JPC last year which you will find useful, as it deals with AIM and H-bonding. (sorry I don't have the full reference in front of me, only a preprint) It also has references to other AIM studies of H-bonding. A strong correlation between rho at the X--H (hydrogen bond) bond critical point and the bond strength is evident from these studies. For an AIM study of intramolecular H-bonding see: D.K. Taylor, I. Bytheway, D.H.R. Barton, C.A. Bayse, M.B. Hall "Toward the Generation of NO in Biological Systems: Theoretical Studies of the N2O2 Grouping" Journal of Organic Chemistry, 1995, 60, 435-444. As for your output, I'd suggest running either MORPHY or EXTREME on the molecule to see if they find the ring critical point - you might need to search "by hand" although MORPHY is usually good at picking up these rogue critical points. If that fails you might need to look at the basis set and check that your total charge density is ok. Hope this is of some use. Ian Bytheway _____________________________________________________________________________ _____________________________________________________________________________ From laidig@u.washington.edu Tue Dec 10 02:01 EET 1996 Ari: You can find examples of the use of properties of the total charge density to characterize intermolecular interactions in Bader's book R. F. W. Bader, Atoms in Molecules - A Quantum Theory, Oxford University Press, Oxford, 1990. [http://www.chemistry.mcmaster.ca/faculty/bader] and the work of Bader and M. T. Carroll. For the studies of the relationship between the properties of critical points and bonding strength, you might want to look at the work of R. J. Boyd. The topology of the charge density in the systems you discussed should be relatively straightforward. I don't know why you had difficulty with Gaussian, but you might want to look into getting the latest versions of Bader's AIMPAC program suite. Write Bader at bader@mcmail.cis.mcmaster.ca You might also want to investigate P. L. A. Popelier's program MORPHY which provides a very nice and automated procedure for searching the topology. MORPHY, a program for an automatic Atoms in Molecules Analysis, PLA Popelier, Comp.Phys.Comm, 1996 93, 212. [http://uchsg11.ch.umist.ac.uk/popelier.htm] Good Luck... Keith +-| Keith E. Laidig, Ph.D., Research Associate +-| Department of Medicinal Chemistry +-| University of Washington, Seattle, WA 98195-7610 +-| E-Mail: laidig@u.washington.edu Phone#: (206) 616-2780 +-| WWW: http://weber.u.washington.edu/~laidig FAX #: (206) 685-3252 _____________________________________________________________________________ _____________________________________________________________________________ From dudisds@Picard.ml.wpafb.af.mil Tue Dec 10 15:11 EET 1996 Dear Ari, We did some semiempirical and ab initio calcs on similar systems a year or so ago (see "Modeling the Hydrogen Bond", ACS Symposium Series 569, Doug Smith, editor, 1994, pages 269-276). Actually, the whole volume is a good summary of H-bond modeling. For our imidazole/oxazole type systems, we found that AM1 gave really poor results. In some cases, it even missed some H-bonds altogether as I recall. When we did ab initio calcs, even including correlation, we found these H-bonds to be very strong indeed (among the strongest H-bonds), and this correlated well with experiment. Good luck. Doug Dudis Polymer Branch Wright Laboratory - Materials Directorate Dayton, Ohio USA _____________________________________________________________________________ _____________________________________________________________________________ From alcami@idefix.qui.uam.es Thu Dec 12 14:20 EET 1996 Dear Ari Lahti In our Department O. Mo and M. Yanez have made calculation of hydrogen bonds and related the streghth of the bond with properties of the bond critical points. Have a look at: O.Mo, M. Yanez and J. Elguero J. Chem. Phys. 97, 6628 (1992) Theochem 314, 73 (1994) We have found sometimes problems with gaussian94 when locating the critical points because the Hopf-poincare condition was not satisfied, I suggest you to use Baderīs programs instead. Hope this help Manuel Alcami Departamento de Quimica Facultad de Ciencias C-9 Universidad Autonoma de Madrid 28049-Madrid (Spain) Phone: 397-38-57 Fax: 397-41-87 _____________________________________________________________________________ _____________________________________________________________________________ From bader@mcmaster.ca Wed Dec 11 18:27 EET 1996 dear dr. lahti, i just returned from europe and found your ,message. yes, we will send you a copy of aimpac and you have no trouble finding cps . the gaussian 94 version of aimpac has problems. use outr program. we have used the theory to study h-bonds in a large number of systems. some refeeeeernces are Mol. Phys. 1988, vol 65, 695: Chem. Phys. Letts. 189, 542, 1992. mol phy. 1988, 63, 387. you will find in these papaers and in other references given there, results which show a linear corel;ation of h-bpond strength with density at cp and with other properteis obtained from the thoery. best regards, richard bader. _____________________________________________________________________________ From friedric@TechFak.Uni-Bielefeld.DE Sat Dec 14 11:09:36 1996 Received: from techfac.TechFak.Uni-Bielefeld.DE for friedric@TechFak.Uni-Bielefeld.DE by www.ccl.net (8.8.3/950822.1) id KAA04453; Sat, 14 Dec 1996 10:50:35 -0500 (EST) Received: from puccini.TechFak.Uni-Bielefeld.DE by techfac.TechFak.Uni-Bielefeld.DE id AA09172; Sat, 14 Dec 1996 16:50:25 +0100 Received: by puccini.TechFak.Uni-Bielefeld.DE (5.65/tp.29.08.90) id AA13656; Sat, 14 Dec 1996 16:50:24 +0100 Message-Id: <9612141550.AA13656@puccini.TechFak.Uni-Bielefeld.DE> Subject: docking blind test To: CHEMISTRY@www.ccl.net Date: Sat, 14 Dec 1996 16:50:24 +0100 (GMT) From: Friedrich Ackermann X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear netters, in a pair of recently published articles the results of a blind test of PROTEIN DOCKING ALGORITHMS were published: @article{stryn96, author = {Strynadka, N. C. J. and Eisenstein, M. and Katchalski--Katzir, E. and Shoichet, B. K. and Kuntz, I. D. and Abagyan, R. and Totrov, M. and Janin, J. and Cherfils, J. and Zimmerman, F. and Olson, A. and Duncan, B. and Rao, M. and Jackson, R. and Sternberg, M. and James, M. N. G.}, title = {Molecular docking programs successfully predict the binding of a $\beta$--lactamase inhibitory protein to TEM--1 $\beta$--lactamase}, journal = {Nature Structural Biology}, year = {1996}, volume = {3}, pages = {233-239}} @article{shoic96, author = {Shoichet, B. K. and Kuntz, I. D.}, title = {Predicting the structure of protein complexes: a step in the right direction}, journal = {Chemistry \& Biology}, year = {1996}, volume = {3}, pages = {151-156}} The paper reporting on the discussed protein complex itself was @article{stryn96a, author = {Strynadka, N. C. J. and Jensen, S. E. and Alzari, P. M. and James, M. N. G.}, title = {A potent new mode of $\beta$--lactamase inhibition revealed by the 1.7{\AA} X--ray crystallographic structure of the TEM--1--BLIP complex}, journal = {Nature Structural Biology}, year = {1996}, volume = {3}, pages = {290-297}} My questions are: - Are the structures discussed in these papers already deposited in the PDB? - What are the relevant PDB-Id codes? I was able to extract some lactamase related PDB-entries, but I'm not sure whether they are the structures discussed in the papers quoted above. Any hint is appreciated! Best wishes, Friedrich Ackermann ------------------------------------------- Friedrich Ackermann Technical Faculty Applied Computer Science Bielefeld University P.O. 100131 D-33501 Bielefeld Phone: +49 521 106 2938 (2935) Fax: +49 521 106 2992 email: friedric@techfak.uni-bielefeld.de http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/friedric/ -------------------------------------------