From rozas@pinar1.csic.es Wed Nov 26 04:37:26 1997 Received: from pinar.csic.es for rozas@pinar1.csic.es by www.ccl.net (8.8.3/950822.1) id DAA15919; Wed, 26 Nov 1997 03:56:55 -0500 (EST) Received: from pinar.csic.es by pinarvms.csic.es (PMDF V5.1-4 #13290) id <01IQGMJHD0QO001VWQ@pinarvms.csic.es> for CHEMISTRY@www.ccl.net; Wed, 26 Nov 1997 09:57:40 CE X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Wed, 26 Nov 1997 09:55:43 +0000 Date: Wed, 26 Nov 1997 09:55:43 +0000 From: Isabel Rozas Subject: SUMMARY of Sn basis sets To: CHEMISTRY@www.ccl.net Message-id: <925*rozas@pinar1.csic.es> Content-identifier: 925 MIME-version: 1.0 (Generated by Ean X.400 to MIME gateway) X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;971126095543] X400-Originator: rozas@pinar1.csic.es X400-Recipients: non-disclosure:; Thanks to everybody for your answers and advices about basis sets for Sn. In my question message I forgot to mention that I had checked the web place: http://www.emsl.pnl.gov:2080/forms/basisform.html but, in any case thanks to: Michael Hartmann, Stephan P.A. Sauer, Ole Swang, Reinaldo Pis Diez, and Pablo Vitoria Garcia, for suggesting it. Thanks also to Alexander Hofmann, Han Zuilhof, Carles Bo, Antonio Fernandez Ramos, and Jose Ignacio Garcia-Laureiro for suggesting: http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html And to Alexander Hofmann for suggesting: http://www.theochem.uni-stuttgart.de to Pablo Vitoria Garcia for suggesting: ftp://ftp.caos.kun.nl/pub/misc/deft/dgauss_bases ftp://ftp.caos.kun.nl/pub/misc/deft/deft_bases and http://tcpc.bham.ac.uk/molpro/basispe.html to John Waite for providing a whole contracted GTO basis set for Sn and spetial thanks to Michael Hartmann, Han Zuilhof, Christoph Widauer, Ole Swang, Pablo Vitoria Garcia, and Antonio M. Marquez, for their nice commentaries, explanations and advices and also for providing the following references: S. Huzinaga, J. Andzelm, M. Klobukowski, E. Radzio-Andzelm, Y. Sakai, H. Tatewaki, Gaussian Basis Sets for Molecular Calculations, Elsevier, Amsterdam, 1984. (Huzinaga basis sets). Str?mberg, A; Gropen, O; Wahlgren, U.: J. Comput. Chem. 4 (1983) 181 (VDZ basis sets). ----------------------------------------------------------------------- Isabel Rozas ROZAS@PINAR1.CSIC.ES Instituto de Quimica Medica (C.S.I.C.) Phone: 34-1-562 2900 c/ Juan de la Cierva 3 Fax: 34-1-564 4853 28003-Madrid (Spain) ----------------------------------------------------------------------- From simek@rudjer.irb.hr Wed Nov 26 06:37:26 1997 Received: from rudjer.irb.hr for simek@rudjer.irb.hr by www.ccl.net (8.8.3/950822.1) id FAA16268; Wed, 26 Nov 1997 05:48:02 -0500 (EST) Received: from tom (tom.irb.hr [161.53.129.102]) by rudjer.irb.hr (8.8.7/8.8.7) with SMTP id LAA30680; Wed, 26 Nov 1997 11:48:14 +0100 (MET) Message-ID: <347C8BDB.1E20@rudjer.irb.hr> Date: Wed, 26 Nov 1997 12:51:39 -0800 From: Visnja Simek Reply-To: simek@rudjer.irb.hr Organization: Rudjer Boskovic Institute X-Mailer: Mozilla 3.01 (Win16; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Literature about excited electronic states Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! I would appreciate if somebody point me to books, reviews or other sources dealing with the electronic excited states from theoretical(!) and experimental point of view. I would collect the answers and send them to the list. Thank you in advance, Visnja ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Visnja Simek Rudjer Boskovic Institute HR-10001 Zagreb, CROATIA phone:(385-1) 456 11 46 fax:(385-1) 27 26 48 e-mail:simek@rudjer.irb.hr; simek@faust.irb.hr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From doublet@gauss.lsd.univ-montp2.fr Wed Nov 26 08:37:37 1997 Received: from gauss.lsd.univ-montp2.fr for doublet@gauss.lsd.univ-montp2.fr by www.ccl.net (8.8.3/950822.1) id IAA16639; Wed, 26 Nov 1997 08:26:26 -0500 (EST) Received: (from doublet@localhost) by gauss.lsd.univ-montp2.fr (8.8.5/8.8.5) id OAA77380 for chemistry@www.ccl.net; Wed, 26 Nov 1997 14:27:02 +0100 Date: Wed, 26 Nov 1997 14:27:02 +0100 From: Marie-Liesse Doublet Message-Id: <199711261327.OAA77380@gauss.lsd.univ-montp2.fr> To: chemistry@www.ccl.net Subject: Bmtrx version2 Program Hi, I would like to know if someone knows something about the Bmtrx program from Komornicki (Palo Alto) that convert (apparently) the cartesian Hessian matrix in internal coordinates. Where can I find it ? Does it bring something more than Gamess for the transformation Cart. --> internal ? Thanks. (Could you please send the answers to pasfav@crit.univ-montp2.fr ?) Frederic ************************************************************************ Dr. Frederic Favier ----------- LAMMI (Laboratoire des Agregats Moleculaires et Materiaux Inorganiques) Universite des Sciences et Techniques du Languedoc Place Eugene Bataillon 34 095 Montpellier Cedex 05 e-mail : pasfav@crit.univ-montp2.fr ************************************************************************* From mckelvey@kodakr.kodak.com Wed Nov 26 08:43:22 1997 Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by www.ccl.net (8.8.3/950822.1) id IAA16570; Wed, 26 Nov 1997 08:07:35 -0500 (EST) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA14166 (5.67b/IDA-1.5 for ); Wed, 26 Nov 1997 08:04:55 -0500 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id IAA12324; Wed, 26 Nov 1997 08:20:11 -0500 (EST) Received: from kodak.com (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id IAA25013; Wed, 26 Nov 1997 08:08:18 -0500 Message-Id: <347B2FAA.9D9FA718@kodak.com> Date: Tue, 25 Nov 1997 20:06:02 +0000 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 4.02 [en] (WinNT; I) Mime-Version: 1.0 To: hou@agouron.com Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:LoBoS, a Beowulf cluster at NIH References: <199711252018.MAA11911@horton.agouron.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Comment: While the price of the more expensive 200Mhz PPRO chip may not get a lot cheaper, I would note that the price of the (only) 10% slower 180Mhz/256Kcache chip is available for ~40% of that of its faster brother/sister. They can be had for as little as $175. John Xinjun Hou wrote: > On Mon, 24 Nov 1997, Chris Harwell wrote: > >... > >3. Don't be taken in by the Intel Bunny people and automatically buy a > >PentiumII. The PentiumII is a PentiumPro with MMX (useless for > >floating point ops) and faster memory access. Unfortunately, the > >advantages are offset by an off-chip cache that runs at half the speed > >of the PentiumPro. Our benchmarks showed that the PentiumII performance > >improvements barely scale up with the faster clock rates. > > Another issue is the cost of processor in the future: PPro's architecture > (on-chip cache) makes it very costly in production. This is another reason > Intel came up with PentiumII with off-chip cache. The off-chip cache structure > is also cheaper to expand, both in terms of size and clock speed. > > So bottom line is that PPro with on-chip cache has a better architecture > than Pentium II for computional extensive work, but Intel might not lower > the price further or devepop it more (high clock speed or more cache). The > cost/performance ration of two CPU would change in the future. > > Xinjun > > C Xinjun J. Hou (hou@agouron.com) Agouron Pharmaceuticals, Inc. > C10110000110100101101110011010100111010101101110010010000110111101110101 > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: hou@Agouron.COM > -- Original Sender From: Address: hou@Agouron.COM > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html -- ************************************ * John McKelvey * * Computational Science Laboratory * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ From kharroub@cit.enscm.fr Wed Nov 26 10:37:28 1997 Received: from cit.enscm.fr for kharroub@cit.enscm.fr by www.ccl.net (8.8.3/950822.1) id KAA17202; Wed, 26 Nov 1997 10:21:02 -0500 (EST) Received: from [193.52.205.156] by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA18628; Wed, 26 Nov 1997 16:09:17 +0100 Message-Id: <3.0.2.32.19971126161844.00908d60@cit.enscm.fr> X-Sender: kharroub@cit.enscm.fr X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Wed, 26 Nov 1997 16:18:44 +0100 To: CHEMISTRY@www.ccl.net From: Kharroubi Mohamed Subject: Bond Dissociation Energies Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello! I would appreciate if somebody point me to books, reviews or other sources dealing with the calculation of bond dissociation energies (BDE) from theoretical (semi-empirical, ab initio or DFT) and experimental point of view. Thank you in advance. =================================== Mohamed KHARROUBI LCA UPRSA-5076 ENSCM 8, rue de l'Ecole Normale F-34296 MONTPELLIER CEDEX 5 FRANCE tel: 04.67.14.72.06 fax: 04.67.14.72.20 e-mail: kharroub@cit.enscm.fr ==================================== From glossman@overnet.com.ar Wed Nov 26 10:42:24 1997 Received: from carpincho.overnet.com.ar for glossman@overnet.com.ar by www.ccl.net (8.8.3/950822.1) id KAA17331; Wed, 26 Nov 1997 10:34:35 -0500 (EST) Received: from nppp157.overnet.com.ar (nppp157.overnet.com.ar [200.16.163.165]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id MAA19736 for ; Wed, 26 Nov 1997 12:35:03 -0300 Message-Id: <3.0.1.16.19971126122833.1a3f56e4@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: Windows Eudora Light Version 3.0.1 (16) Date: Wed, 26 Nov 1997 12:28:33 To: chemistry@www.ccl.net From: "Dr. M. Daniel Glossman" Subject: programs for plotting densities Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: I would like to receive information about any software (commercial or not) for the Windows NT environment that could be useful for plotting two and three dimensional electon densities and electrostatic potentials starting from Gaussian 94 computed wavefunctions ( .out and .chk files). I thank you in advance for your answers. Daniel Glossman ****************************************************************************** Dr. M. Daniel Glossman Universidad Nacional de Lujan e-mail: glossman@overnet.com.ar Departamento de Ciencias Basicas Phone: (+54) 323 23171 Casilla de Correo 221 FAX: (+54) 323 25795 (6700) Lujan Republica Argentina From widauer@inorg.chem.ethz.ch Wed Nov 26 12:37:31 1997 Received: from inorg.chem.ethz.ch for widauer@inorg.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id MAA17974; Wed, 26 Nov 1997 12:00:37 -0500 (EST) Received: from rosmarin (rosmarin.ethz.ch [129.132.65.132]) by inorg.chem.ethz.ch (8.8.8/8.8.8) with SMTP id SAA18970 for ; Wed, 26 Nov 1997 18:00:11 +0100 Message-Id: <3.0.32.19971126175958.00912100@elwood.ethz.ch> X-Sender: widauer@elwood.ethz.ch X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 26 Nov 1997 18:00:22 +0100 To: CHEMISTRY@www.ccl.net From: Christoph Widauer Subject: SUMMARY of As and Sb basis sets Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable dear netters Sorry that I summarize late. Here are the answers and advices for my question about all electron basis sets for As and Sb. Thanks a lot for all answers and advices. Special Thanks to Kerwin Dobbs and Cory.=20 Here is a list of the answers: 1.) Nathalie Goldbout wrote: I have optimized basis sets for these atoms.=20 PNL distributes them (http://www.emsl.pnl.gov:2080/forms/basisform.html). As you will find them, they are DZVP but you can make them=20 TZVP.=20 Nathalie 2.)Kerwin Dobbs suggests: They are not very large basis sets, but you could use my=20 3-21G* basis sets for these elements. They will get you=20 decent geometries (and frequencies) to be used in calculations with larger basis sets. If you have access to Gaussian 94, they are already in there.=20 -As 0 S 3 1.00 0.540761380E+04 0.626011000E-01 0.818174360E+03 0.372779000E+00 0.179265690E+03 0.685184200E+00 SP 3 1.00 0.237778288E+03 -.112838429E+00 0.149679775E+00 0.542566227E+02 0.872274379E-01 0.562322265E+00 0.163280291E+02 0.968188275E+00 0.459323497E+00 SP 3 1.00 0.171018532E+02 -.291453678E+00 0.256855918E-01 0.580514411E+01 0.296961892E+00 0.483396807E+00 0.190208419E+01 0.886579104E+00 0.588785396E+00 D 3 1.00 0.274372090E+02 0.154495200E+00=20 0.708404400E+01 0.511431800E+00=20 0.185582260E+01 0.582193500E+00=20 SP 2 1.00 0.167540361E+01 -.505760964E+00 0.252824660E-01 0.341655706E+00 0.125176452E+01 0.987432836E+00 SP 1 1.00 0.113630312E+00 0.100000000E+01 0.100000000E+01 D 1 1.00 0.293000000E+00 0.100000000E+01=20 **** -Sb 0 S 3 1.00 0.132893830E+05 0.609843000E-01 =20 0.201052180E+04 0.366848700E+00 =20 0.441698150E+03 0.691050100E+00 SP 3 1.00 0.598889050E+03 -.112720134E+00 0.153067117E+00 0.130038601E+03 0.826443261E-01 0.613597248E+00 0.421328602E+02 0.970257861E+00 0.391699015E+00 SP 3 1.00 0.515133288E+02 -.277043338E+00 -.137869858E+00 0.244359459E+02 0.575032340E-01 0.536354977E+00 0.742093080E+01 0.108470283E+01 0.650867638E+00 D 3 1.00 0.115809550E+03 0.116627900E+00=20 0.323058350E+02 0.483436300E+00=20 0.102503280E+02 0.590139500E+00=20 SP 3 1.00 0.731423541E+01 0.440381164E+00 0.153051809E-01 0.284405286E+01 -.473734095E+00 0.516083219E+00 0.110585467E+01 -.822134968E+00 0.538757047E+00 D 3 1.00 0.548621020E+01 0.248365600E+00=20 0.192161960E+01 0.574315400E+00=20 0.666062650E+00 0.364304400E+00=20 SP 2 1.00 0.127863729E+01 0.601695106E+00 -.222527566E-01 0.241232097E+00 -.125869202E+01 -.989643364E+00 SP 1 1.00 0.866296732E-01 0.100000000E+01 0.100000000E+01 D 1 1.00 0.211000000E+00 0.100000000E+01=20 **** 3.)Cory from University of calcgary wrote: The reference is: S. Huzinaga, J. Andzelm, M. Klobukowski, E. Radzio-Andzelm, Y. Sakai, H.=20 Tatewaki, Gaussian Basis Sets for Molecular Calculations, Elsevier,= Amsterdam, 1984.=20 These are all minimal basis sets. What we did was split the outermost shell and add a d-polarization function accordind to Huzinaga's suggestions. For example, the arsenic minimal basis set is (4333/433/4). We split the= outer most s and p shell (since the d shell is not participating in the bonding, we left it as a single-zeta), and added a d-polarization function to obtain (43321/4321/41*) - note that the 1* at the end stands for a polarization fn,= =20 some authors just use the *, so be careful. The resulting basis set (in MUNGAUSS/MONSTERGAUSS format) is: 1S 1.000000 15860.364 0.0171048 2391.2232 0.1200249 542.23120 0.4378747 146.00269 0.5576566 2S 1.000000 219.08007 -.1096535 24.437631 0.6475717 10.206970 0.4248194 3S 1.000000 18.744848 -.2334702 3.1047892 0.7294911 1.2970598 0.4044278 4S 1.000000 1.8301844 -.1924620 0.28147770 0.6866084 5S 1.000000 0.10437810 1.000000 2P 1.000000 670.45052 0.000000 0.0275156 157.17065 0.000000 0.1794001 48.639537 0.000000 0.5052466 16.532308 0.000000 0.4576592 3P 1.000000 7.4556466 0.000000 0.3248901 2.9185276 0.000000 0.5568808 1.1701325 0.000000 0.2280292 4P 1.000000 0.17189969 0.000000 0.5495546 0.44648872 0.000000 0.3297273 5P 1.000000 0.06621832 0.000000 1.000000 3D 1.000000 49.802186 0.0618851 13.722924 0.2858504 4.3622725 0.5264330 1.3044304 0.4103582 4D 1.000000 0.2930000 1.000000 **** For antimony, the minimal basis set is (43333/4333/43), this becomes (433321/43321/431*) , giving 1S 1.000000 39022.365 0.0166099 5882.7978 0.1168445 1336.0527 0.4316276 360.85938 0.5658267 2S 1.000000 537.93220 -.1140683 62.500390 0.6463407 27.197858 0.4259875 3S 1.000000 50.167831 -.2738817 9.1496108 0.8622209 4.1385594 0.2916257 4S 1.000000 7.9705964 0.3451482 1.8315322 -.8192352 .83166100 -.3885285 5S 1.000000 1.2644570 0.2282069 .20413637 -.7343321 .07938248 -.4004066 2P 1.000000 1824.8261 0.000000 0.0243008 429.63172 0.000000 0.1658149 134.35726 0.000000 0.4934148 47.067397 0.000000 0.4764640 3P 1.000000 146.26897 0.000000 -.0249529 19.176344 0.000000 0.4788591 7.5448193 0.000000 0.5894057 4P 1.000000 3.1351377 0.000000 0.4330085 1.3685954 0.000000 0.5296693 .59068398 0.000000 0.1168509 5P 1.000000 .30628842 0.000000 -.3619153 .12718587 0.000000 -.5374627 .05241622 0.000000 -.2013450 3D 1.000000 213.55477 0.0392992 62.116599 0.2241339 21.914940 0.5229188 7.9902814 0.4250002 4D 1.000000 5.0718312 0.2751370 1.8456173 0.5677492 .64518169 0.3414352 5D 1.000000 .21100000 1.0000000 **** Note that the format is the same for both P shells above and for SP shells. (exponent s-contraction p-contraction). This explains the 0.0000 in the=20 P shells in the s-contraction coefficient column. Gaussian XX wouldn't have this. -COry 4.) Doug Fox wrote: For As the 6-311G basis set is defined and is roughly triple zeta in quality. Also we have adopted Curtiss's 6-41G basis set for As=20 as a double zeta quality basis which you can select as 6-31G. There are no comparable basis sets built in for Sb nor do I have a suggestion that I could support for such a basis. Again, thanks to all who answered. The next time I will summrize earlier for sure. christoph ---- Christoph Widauer Laboratorium f. Anorganische Chemie ETH-Zentrum CAB C8 Universit=E4tsstrasse 6 CH-8092 Zuerich=20 Phone (Zurich): +41 (1) 632 61 19 Fax (Zurich): +41 (1) 632 10 90 e-mail: widauer@inorg.chem.ethz.ch From ryszard@lisa.moldyn.com Mon Nov 24 13:35:14 1997 Received: from worf.moldyn.com for ryszard@lisa.moldyn.com by www.ccl.net (8.8.3/950822.1) id MAA05974; Mon, 24 Nov 1997 12:55:13 -0500 (EST) Received: from lisa.moldyn.com by worf.moldyn.com via ESMTP (950413.SGI.8.6.12/950213.SGI.AUTOCF) for <@worf.moldyn.com:CHEMISTRY@www.ccl.net> id MAA12997; Mon, 24 Nov 1997 12:55:01 -0500 Received: by lisa.moldyn.com (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) id MAA26328; Mon, 24 Nov 1997 12:54:59 -0500 Date: Mon, 24 Nov 1997 12:54:57 -0500 (EST) From: Ryszard Czerminski To: CHEMISTRY@www.ccl.net Subject: tRNA modelling: summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---- Original question: Dear All, I am looking for information about tRNA modelling. In particular for MD simulations and parametrization of rare nucleotides (pseudo-uracil etc...) Ryszard Czerminski phone : (617)354-3124 x 13 Moldyn, Inc. fax : (617)491-4522 955 Massachusetts Avenue e-mail: ryszard@moldyn.com Cambridge MA, 02139-3180 or ryszard@photon.com SUMMARY: If anybody has information about charges (preferably published) used for rare nucleotides either with amber or charmm ff I would appreciate to hear from you... RC. ---- Thank you to all who responded (in chronological order) Darrell R. Davis Christoph Schneider Thomas Hermann John E. Reissner Kevin J. Mcconnell Pascal Auffinger ---- useful RNA links http://www.imb-jena.de/RNA.html http://www.ibc.wustl.edu/~zucker/ma (does not work ?) http://algodones.unm.edu/~phraber/ma.html (does not work ?) ---- and recent references ---- (biased by my interests and by no means complete) % % tRNA structure and dynamics % @INCOLLECTION{Auffinger98, AUTHOR = "Pascal Auffinger and Eric Westhof", BOOKTITLE = "Modification and Editing of RNA: The alternation of RNA Structure and Function", chapter = 6, title = "Effects of Pseudouridylation on tRNA Hydration and Dynamics: A Theoretical Approach", PUBLISHER = {Americal Society for Microbiology}, ADDRESS = {Washington, DC 20005}, YEAR = 1998 } @INCOLLECTION{Auffinger97a, AUTHOR = "Pascal Auffinger and Eric Westhof", BOOKTITLE = "Enclyclopedia of computational chemistry", title = "Molecular Dynamics Simulations of Nucleic Acids", PUBLISHER = {Wiley \& Sons}, ADDRESS = {NY}, YEAR = 1997 } @ARTICLE{Hermann97, author = "Thomas Hermann and Pascal Auffinger and William G. Scott and Eric Westhof", title = {Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme}, journal = {Nucl. Acid Res.}, year = 1997, volume = 25, number 17, pages = {3421-3427}, abstract = {In the presence of magnesium ions cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash- freezing of crystals under conditions where the ribozyme is active, provide evidence that a $\mu$-bridging OH$^-$ ion is located between the two Mg$^{+2}$ ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'-endo to the C2'-endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorus atom and the $\mu$-bridging OH$^-$ ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a $\mu$-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH$^-$ ion that is able to activate the 2'-hydroxyl nucleophile after a minor conformational change in the RNA.}} @ARTICLE{Auffinger97b, author = "Pascal Auffinger and Eric Westhof", title = {{RNA} Hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated {tRNA$^{Asp}$} anticodon hairpin.}, journal = {J. Mol. Biol.}, year = 1997, volume = 269, pages = "326-341", abstract = {The hydration of the tRNA$^{Asp}$ anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the PME method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the ``theoretical'' conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as G-U base pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine [...] No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-R$_P$ phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusions reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggest that RNA and water together constitute the biologically relevant functional entity}} @ARTICLE{Auffinger97c, AUTHOR = {Pascal Auffinger and Shirley Louise-May and Eric Westhof}, TITLE = {Hydration of C-H groups in tRNA}, JOURNAL = {Faraday Discuss.}, YEAR = 1997, VOLUME = 103, PAGES = {151-174}, abstract = {MD simulations of the anticodon hairpin of tRNA$^Asp$ and of full tRNA, both in a solvent bath with neutralizing NH$_4^+$ counter ions, have been produced with the particle mesh ewald (PME) method and multiple molecular dynamics (MMD) strategy [...]}} @ARTICLE{Auffinger97d, author = "Pascal Auffinger and Eric Westhof", title = {{RNA} Hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated {tRNA$^{Asp}$} anticodon hairpin.}, journal = {J. Mol. Biol.}, year = 1997, volume = 274, pages = "54-63", abstract = {MD simulations reveal that, in C$_{3'}$-endo sugar puckers, only three orientations are accessible to the 2'-hydroxyl groups distinctive of RNA molecules: towards (i) the O$_{3'}$, (ii) the O$_{4'}$ of the same sugar, and (iii) the shallow groove base atoms. In the rarer C$_{2'}$-endo sugar puckers, orientations towards the O$_{3'}$ atom of the same sugar are strongly favoured. Surprisingly, in helical regions, the frequently suggested intra-strand O$_{2'}$ - H(n)...O$_{2'}$(n+1) interaction is not found. This observation led to the detection of an axial C-H...O interaction between the C$_{2'}H(n) group and the O$_{4'}$(n+1) atom contributing to the stabilization of RNA helical regions. Subsequent analysis of crystallographic structures of both RNA and A-DNA helices fully supports this finding. Specific hydration patterns are also thought to play a significant role in the stabilization of RNA structures. In the shallow groove of RNA, known as a favorable RNA or protein binding region, three well defined hydration sites are located around the O$_{2'}$ atoms. These hydration sites, occupied by water molecules exchanging with a bulk, constitute after dehydration, anchor points for specific interactions between RNA and nucleic acids, proteins or drugs. Therefore, the fact that the 2'-hydroxyl group is not monopolised by axial stabilization, together with its water like behavior, facilitates complex formation involving RNA helical regions.}} @ARTICLE{Jia97, author = {Yiwei Jia, Alexander Sytnik, Liangquan Li, Serguei Vladimirov, Barry S. Cooperman, and Robin M. Hochstrasser}, title = {Nonexponential kinetics of a single {tRNA$^{Phe}$} molecule under physiological conditions}, journal = {Proc. Natl. Acad. Sci. USA, Biophysics}, year = 1997, volume = 94, pages = "7932-7936", abstract = {The fluorescence decay functions of individual, specifically labeled tRNAPhe molecules exhibit nonexponential character as a result of conformational dynamics occurring during the measurement on a single molecule. tRNAPhe conformational states that interchange much more slowly are evidenced by the distribution of lifetimes observed for many individual molecules. A structural model for the nonexponential decay indicates that the tRNAPhe-probe adduct fluctuates between two states, one of which provides conditions that quench the probe fluorescence.} } @MISC{Lahiri97, author = "Ansuman Lahiri and Lennart Nilsson", title = {Molecular dynamics study of the anticodon loop of Yeast tRNAphe}, howpublished = "http://hackberry.chem.niu.edu/ECCC4/articles/article41" year = 1997, month = November, abstract = {Molecular dynamics simulations of the aqueous solution of Yeast tRNAphe anticodon loop with counterions were carried out. We looked at the stability of the system and the simulation protocol by a long simulation (over 1 ns) and a set of shorter simulations (duration 300 ps each) which differed only in the initial velocity assignments. In all the cases, the structure remains close to the starting crystal structure with a 3'-stacked conformation nicely maintained. We have also investigated the dynamics of the anticodon loop interacting with UUU and UUC ribotrinucleotide diphosphates, codons for the amino acid phenylalanine.}, note = {CHARMM22 all atom parameter set + modified parameters for rare nucleotides}} @ARTICLE{Auffinger96a, author = {P. Auffinger and E. Westhof}, title = {H-bond stability in the {tRNA$^{Asp}$} anticodon hairpin: 3 ns of multiple molecular dynamics simulation}, journal = "Biophys. J.", year = 1996, volume = 71, pages = "940-954", abstract = { Multiple MD trajectories of the solvated and neutralized 17-residue tRNS$^{Asp}$ anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base-pairs, the noncanonical G30-U40 ``wobble'' base pair, and the $\Psi$32-C38 pseudo-baise pair is presented as well as that of two C-H...O hydrogen bonds found to contribute to array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biologocal function. The set of multiple molecular dynamics trajectories does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.}} @ARTICLE{Auffinger96b, author = "P. Auffinger and E. Westhof", title = {Molecular dynamics simulations of the anticodon hairpin of tRNA$^{Asp}$: Structuring effects of C-H...O hydrogen bonds and of long-range hydration forces}, journal = JACS, year = 1996, volume = 118, pages = "1181-1189", abstract = {The inclusion of long-range sovent interactions out to 16A in a molecular dynamics study of the anticodon loop of tRNA$^{Asp}$ led to an overall structural stabilization of the RNA hairpin tertiary interactions in a set of six independent fully solvated and neutralized 100ps MD trajectories as compared to a shorter-ranged solvent interaction electrostatic model (8A). The increased structural stabilization allowed for the emegence of non-classical C-H...O hydrogen bonds in the MD trajectories. The presence of the C-H...O hydrogen bonds in the crystal structure was subsequently verified and dynamically characterized and their contribution to the preservation of the tertiary native conformation was assessed [...]} } @ARTICLE{Louise96, AUTHOR = {Shirley Louise-May and Pascal Auffinger and Eric Westhof}, TITLE = {Calculations of nucleic acid conformations}, JOURNAL = {Curr. Opin. Struct. Biol.}, YEAR = 1996, VOLUME = 6, PAGES = {289-298}, abstract = {The present computational power and sophistication of theoretical approaches to nucleic acid structural investigation are sufficient for the realization of static and dynamic models that correlate accurately with current crystallographic, NMR and solution-probing structural data, and consequently are able to provide valuable insights and predictions for a variety of nucleic acid conformational families. In molecular dynamics simulations, the year 1995 was marked by the foray of fast Ewald methods, an accomplishment resulting from several years' work in the search for an adequate treatment of the electrostatic long-range forces so primordial in nucleis acids behavior. In very large systems, and particularly in the RNA-folding field, techniques originating from artificial intelligence research, like constraint satisfaction programming or genetic algorithms, have established their utility and potential.}} @ARTICLE{Westhof96a, author = "E. Westhof et al.", title = {}, journal = Science, year = 1996, volume = 272, pages = "1343", abstract = {} } @ARTICLE{Auffinger95, AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof}, TITLE = {Multiple molecular dynamics simulations of the anticodon loop of tRNA$^Asp$ in aqueous solution with counterions}, JOURNAL = JACS, YEAR = 1995, VOLUME = 117, PAGES = {6720-6726}, abstract = {In a systematic search for a stable protocol with which to extend our dynamical investigations, a nanosecond of MD simulations of the solvated anticodon loop of tRNA$^Asp$ consisting of ten unique trajectories was obtained by slight modifications to the starting conditions. These changes produced divergent trajectories which varied widely in structural and dynamical characteristics. However, the properties of these trajectories could not be directly correlated to the slight modifications introduced in the system, and thus, questions were raised regarding the probity of the standard protocol we utilized. Instead of a detailed analysis of the results, the multiple molecular dynamics approach was used as a diagnostic for estimating the reliability of the set of trajectories generated and the extent of relevant biochemical information which cen be extracted from it. We address here issues concerning critical evaluation of molecular dynamics methodology and detection of protocol instabilities. We infer that an ensemble of initial uncorrelated trajectories should be generated in order to investigate the constancy of structural and dynamical properties of the system under study}} @ARTICLE{Nakamura94, author = {Shugo Nakamura and Junta Doi}, title = {Dynamics of transfer RNAs analyzed by normal mode calculation}, journal = {Nucl. Acids Res.}, year = 1994, volume = 22, number = 3, pages = {514-521}, abstract = {Normal mode calculation is applied to tRNA$^{Phe}$ and tRNA$^{Asp}$, and their structural and vibrational aspects are analyzed. Dihedral angles along the phosphate-riboze backbone ($\alpha, \beta, \gamma, \epsilon, \ksi$) and dihedral angles of glycosyl bonds ($\chi$) are selected as movable parameters. The calculated displacement of each atom agrees with experimental data In modes with frequencies higher then 130cm$^{-1}$, the motions are localized around each stem and the elbow region of the L-shape. On the other hand, collective motions such as bending and twisting of arms are seen in modes with lower frequencies. Hinge axes and bend angles are calculated without prior knowledge. Movements in modes with very low frequencies are combinations of hinge bending motions with various hinge axes and and bend angles. The thermal fluctuations of dihedral angles well reflect the structural changes of transfer RNAs. There are some dihedral angles of nucleotides located around the elbow region of L-shape, which fluctuate about five to six time more than the average value. Nucleotides in the position seem to be influential in the dynamics of the entire structure. The normal mode calculation seems to provide much information for the study of conformational changes of transfer RNAs induced by aminoacyl-tRNA synthetase or codon during molecular recognition}} @ARTICLE{Nardi94, author = {F. Nardi and W. Doster and B. Tidor and M. Karplus and S. Cusack and J. C. Smith}, title = {Dynamics of tRNA: Experimental Neutron Spectra Compared with Normal Mode Analysis}, journal = {Israel J. Chem.}, year = 1994, volume = 34, pages = {233-238}, abstract = {A comparison is made of experimental inelastic neutron scattering spectra from tRNA with spectra calculated from a normal mode analysis. The experimental data indicate that a dynamic transition occurs with temperature, as is seen in proteins. At low temperatures a broad peak is seen in the dynamic structure factor, due to the lowest frequency collective modes. This peak is centered at ~40cm$^{-1}$, somewhat higher than that observed in small globular proteins. The vibrational frequency distribution calculated from the normal mode analysis rises to a broad maximum at ~50cm$^{-1}$, in general accord with the experiment. However the lowest frequency vibrations in the harmonic model (<40cm$^{-1}$) are nor present in experimental sample. Possible reasons for this are discussed.}, note = {in calculations tRNA-Phe was used}} @ARTICLE{Harvey93, author = "Harvey, S. C.; Gabb, H. A.", title = {Conformational transitions using molecular dynamics with minimum biasing}, journal = Biopolymers, year = 1993, volume = 33, pages = "1167-1172", abstract = {The molecular dynamics algorithm (MD), which simulates intramolecular motions on the subnanosecond timescale, has been modified to allow the investigation of slow conformational transitions that do not necessarily occur spontaneously in MD simulations. The method is designated CONTRA MD (CONformational TRAnsitions by Molecular Dynamics with minimum biasing). The method requires the prior definition of a single conformational variable that is required to vary monotonically from an initial conformation to a final target conformation. The simulation is broken up into a series of short free MD segments, and we determine, after each segment of MD, whether or not the system has evolved toward the final conformation. Those segments that do not move the system in that direction are deleted. Those that do move it toward the final conformation are patched together sequentially to generate a single representative trajectory along the transition pathway. The CONTRA MD method is demonstrated first by application to the simultaneous C2'-endo to C3'-endo repucker and anti to syn N-glycosidic torsion transitions in 2'-deoxyadenosine and then to the large-scale bending in phenylalanine transfer RNA.}} From glossman@overnet.com.ar Mon Nov 24 16:37:08 1997 Received: from carpincho.overnet.com.ar for glossman@overnet.com.ar by www.ccl.net (8.8.3/950822.1) id QAA07435; Mon, 24 Nov 1997 16:09:03 -0500 (EST) Received: from nppp239.overnet.com.ar (nppp239.overnet.com.ar [200.16.164.252]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id SAA04163 for ; Mon, 24 Nov 1997 18:10:11 -0300 Message-Id: <3.0.1.16.19971124180255.1c8f8ee6@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar (Unverified) X-Mailer: Windows Eudora Light Version 3.0.1 (16) Date: Mon, 24 Nov 1997 18:02:55 To: chemistry@www.ccl.net From: "Dr. M. Daniel Glossman" Subject: using Molden with NT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: I am looking for somebody in the net who has been succesfull in using the Molden program in a Windows NT environment. I need some advice. Thanks in advance Daniel Glossman *************************************************************************** Dr. M. Daniel Glossman Universidad Nacional de Lujan e-mail: glossman@overnet.com.ar Departamento de Ciencias Basicas Phone: (+54) 323 - 23171 Casilla de Correo 221 Fax: (+54) 323 - 25795 6700 - Lujan Republica Argentina **************************************************************************** From kristyan@euch4e.chem.emory.edu Mon Nov 24 16:55:23 1997 Received: from euch4e.chem.emory.edu for kristyan@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id PAA07314; Mon, 24 Nov 1997 15:45:31 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA29755; Mon, 24 Nov 1997 15:45:32 -0500 Date: Mon, 24 Nov 1997 15:45:32 -0500 Message-Id: <9711242045.AA29755@euch4e.chem.emory.edu> To: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit Dear Collagues Dear Isabel Rozas & Han Zuilhof >A more substantial double zeta DFT basis set is available for Sn on the >EMSL website, from which it can be downloaded. >http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html I did not have too much time to check, but after a few tries a gave up on this web site. (But there may be some, and this www is definitely useful.) I have one on file, available below. See the definition of this rep. of basis (very simple) in Sandor Kristyan.: Note on the choice of basis set in density functional theory calculations for electronic structure of molecules (test on the atoms from the first three rows of the periodic table (2 ² N ² Z ² 18), water, ammonia and pyrrole) Chemical Physics Letters, 256, 1996, 229-240 (This article has no info about Sn.) kristyan@euch4e.chem.emory.edu Sandor Kristyan November 21, 1997 FOR SN S 1 12741.6740 0.061135 2 1928.46920 0.367293 3 423.807970 0.690545 S 4 564.682200 -0.109749 5 55.241831 0.718112 6 23.121421 0.349097 P 7 816.773230 0.082073 8 191.127720 0.426433 9 56.771595 0.635902 S 10 48.493098 -0.270898 11 8.770315 0.840906 12 4.037810 0.310103 P 13 121.244870 -0.031564 14 19.577904 0.415167 15 7.571713 0.654993 D 16 108.056300 0.119824 17 30.131576 0.487591 18 9.530036 0.584987 S 19 7.615495 -0.347566 20 1.729893 0.793758 21 0.771888 0.413201 P 22 3.047403 0.398267 23 1.302218 0.555779 24 0.544629 0.130139 D 25 4.962610 0.252949 26 1.712083 0.572761 27 0.577195 0.369039 S 28 1.197655 -0.238559 29 0.173037 0.705986 P 30 0.267529 0.321091 31 0.104183 0.565904 S 32 0.066960 0.423612 P 33 0.041626 0.221811 ****** From arthur@csb0.IPC.PKU.EDU.CN Mon Nov 24 21:37:08 1997 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id UAA08924; Mon, 24 Nov 1997 20:53:57 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA04702; Tue, 25 Nov 97 09:53:53 -0800 Date: Tue, 25 Nov 1997 09:53:53 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Summary: logP for amino acids Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Two weeks ago, I posted such a question: "We are currently on a project of de novo protein design. A set of scales which describe the hydrophobicities of the natural amino acids is what we badly need. So, would you please kindly provide any clue for the following issues: (1) Any paper describing such a set of scales (2) LogP values for the 20 natural amino acids and oligopeptides (up to buta- or pentapeptides). (3) Solubilities for these amino acids and oligopeptides." And the answers I have received are: -------------------------------------------------------------------------- From: Thomas Scior NI HOW Arthur ! Please, do apologize I do not speak Chinese ! But conerning your question : there is a book called Introduciiton to LIPOPHILICITY from VCH Verlagsgesellschaft Weinheim Germany maybe there is a home page http://vch.de or .com If you can not find this book , please mail me in December again, then I can give you the exact reference. Also, I am doeing the same kind of project with small molecules see http://link.springer.de/link/service/journals/00894/bibs/7003008/70030332.htm Best wishes Tom Scior, Pharmacy Molecular Modeling germany ------------------------------------------------------------------------------ From: Wayne Steinmetz You will probably find the data and discussion in the following paper useful: W. E. Steinmetz, "A CoMFA Analysis of Selected Physical Properties of Amino Acids in Water", Quant. Struct.-Act. Relat., 14, 19-23 (1995). There is a medicinal chemistry institute headed by Professor Ren Li in Beijing. Thje institute should have a subscription to this journal. ------------------------------------------------------------------------------- From: Richard Gillilan Andrew Karplus' latest paper on that subject is well worth looking at: "Hydrophobicity regained" P.A. Karplus Protein Science (1997) 6:1-6 ------------------------------------------------------------------------------- From: A literature search concerning Z-scales and Svante Wold (spelling?) should provide some leading references for (1), and probably references relating to (2), since the scales include that information, if I recall correctly. Several years ago (1991-1994?), Tripos did an application note on this topic. You might try contacting them. The presentation was given by Wally Reiher (are you out there, Wally?). sb ------------------------------------------------------------------------------ From: victoria@acdlabs.com (Victoria Barclay) Advanced Chemistry Development has software to calculate LogP (and as of this fall, LogD and Solubility) for peptides (and oligopeptides) in zwitterionic form. Literature values for 3600 structures with known LogP and the conditions of determination can also be automatically looked up. Our algorithm is based on well-characterized logP contributions of separate atoms, structural fragments, and intramolecular interactions between different fragments. If you would like to receive a copy of our demo CD, which contains a demo version of the software and more detailed product information, please let me know. Best regards, Victoria ------------------- Victoria Barclay, Ph.D. Manager, Scientific Support Advanced Chemistry Development, Inc. Suite 605, 133 Richmond St. W., Toronto, Canada M5H 2L3 Voice: (416) 368-3435 Fax: (416) 368-5596 Toll-free: 800-304-3988 e-mail: victoria@acdlabs.com web: http://www.acdlabs.com ------------------------------------------------------------------------------ From: Willie Cui Authur, For the hydro. scale, try HINT by Kelloge of Virgina Common Wealth Univ. I do not quite remember the web address. If you have difficulty locate it,let me know I will find it out for you. -- Willie Cui voice: 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Road email: info@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com ----------------------------------------------------------------------------- From: Kapi Rosenfeld a good paper to look at (although a little bit old) is the analysis performed by J. Cornette et al published in the late 80's or early 90's in the Journal of Molecular Biology. These authors analyze about 40 different hydrophobicity scales. (if i remember correctly the last author on this paper is C. DeLisi. R. Rosenfeld ----------------------------------------------------------------------------- From: shaun@uthct.edu (Shaun D. Black) Dear Arthur, I have developed and published parameters for about 60 amino acid side chains (native, post-translational, co-translational, and artificial). You can check them out at: http://pegasus.uthct.edu/ResUTHCT/Investigators/SBlack/aagrease.html (parameters for native 20 amino acids, molecular weights, refs., etc.) http://pegasus.uthct.edu/ResUTHCT/Investigators/SBlack/aamodgre.html (parameters etc. for many modified amino acids) I hope this helps! Best regards, Shaun Black =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet e-mail address: shaun@uthct.edu = = Dept. of Biochemistry | University of Texas Health Center at Tyler = = Tyler, TX 75710 | World Wide Web: http://www.uthct.edu = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ----------------------------------------------------------------------------- From: Tomoko Niwa Please check the following papers: Tomoko Sotomatsu-Niwa, Akio Ogino, Evaluation of the hydrophobic parameters of the amino acid side chains of peptides and their application in QSAR and conformational studies, THEOCHEM (1997), 392, 43-54. We statistically analyzed the experimentally determined 1-octanol/water partition coefficient, log P, of a wide variety of N-acetyl-di- and tripeptide amides and unblocked di- and tripeptides to evaluated the hydrophobic parameters of the amino acid side chains of peptides. For blocked peptides, hydrophobic parameters were defined for amino acids having un-ionizable and ionizable side chains. For unblocked peptides, hydrophobic parameters were evaluated for 12 amino acids with un-ionizable side chains. In order to estimate the hydrophobic parameters for unnatural and ionizable amino acids, a procedure was developed based on the relationship between our hydrophobic parameters and the log P values of model amino acids calculated by the fragment constant method. Use of the hydrophobic parameters in quantitative structure-activity relationship (QSAR) studies of bioactive peptides and conformational studies of proteins have also been presented. (Our method is valid for the log P values for buta- or pentapeptides. ) Table 4 Hydrophobic parameters for the amino acid side chains of unblocked peptides amino acid pa(N) pa(MC) pa(N) a pa(MC) a CLOGP-R A Ala 0.24 0.12 0.19 0.24 2.680 G Gly 0.00 0.00 0.00 0.00 2.281 I Ile 0.99 1.10 0.72 1.17 4.137 L Leu 1.03 1.24 0.92 1.28 4.137 M Met 0.64 0.89 0.67 0.93 2.828 F Phe 1.36 1.55 1.35 1.57 4.248 P Pro 0.19 b c c 3.314 S Ser 0.02 -0.20 -0.08 0.04 0.693 T Thr 0.47 0.06 0.07 0.25 1.002 W Trp 1.76 1.78 1.72 1.93 4.248 Y Tyr 0.94 0.90 0.78 1.01 3.581 V Val 0.42 0.68 0.49 0.82 3.608 a Taken from Ref. 10. b pa(M): 0.64, pa(C): 0.92 c pa(location, number of residues); pa(N,2): 0.35, pa(MC,2): 1.16, pa(N,3): 0.00, pa(MC,3): 0.81, pa(N,4): -0.34, pa(MC,4): 0.46. Abraham, Donald J.; Leo, Albert J., Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients, Proteins: Struct., Funct., Genet. (1987), 2(2), 130-52 Leo, A. J., Computer calculation of peptide hydrophobicity, Pharmacochem. Libr. (1991), 16(QSAR: Ration. Approaches Des. Bioact. Compd.), 349-52 Fauchere, Jean Luc; Charton, Marvin; Kier, Lemont B.; Verloop, Arie; Pliska, Vladimir, Amino acid side chain parameters for correlation studies in biology and pharmacology, Int. J. Pept. Protein Res. DATE: 1988 VOLUME: 32 NUMBER: 4 PAGES: 269-78 Akamatsu, Miki; Fujita, Toshio, Quantitative analyses of hydrophobicity of di- to pentapeptides having unionizable side chains with substituent and structural parameters, J. Pharm. Sci. (1992), 81(2), 164-74 Akamatsu, Miki; Okutani, Shinichi; Nakao, Kazuya; Hong, Nam Joo; Fujita, Toshio, Hydrophobicity of N-acetyl-di- and tripeptide amides having unionizable side chains and correlation with substituent and structural parameters, Quant. Struct.-Act. Relat. DATE: 1990 VOLUME: 9 NUMBER: Akamatsu, Miki; Yoshida, Yohji; Nakamura, Hideaki; Asao, Masaaki; Iwamura, Hajime; Fujita, Toshio, Hydrophobicity of di- and tripeptides having unionizable side chains and correlation with substituent and structural parameters, Quant. Struct.-Act. Relat. DATE: 1989 VOLUME: 8 NUMBER: 3 [8] R.-S. Tsai, B. Testa, N. El Tayar, P.-A. Carrupt, J. Chem. Soc. Parkin Trans. 2, (1991), 1797. [9] P. Vallat, P. Gaillard, P.-A. Carrupt, R.-S. Tsai, B. Testa, Helv. Chim. Acta, 78 (1995), 471. [11] W. E. Steinmetz, Quant. Struct.-Act. Relat., 14 (1995), 19. [12] N. El Tayar, H. Karajiannis, H. van de Waterbeemd, Amino Acids, 8 (1995), 125. Best Regards =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Tomoko Sotomatsu Niwa, Ph.D. Research Lab. Nippon Shinyaku Co., Ltd. Nishiohji Hachijo Minami-ku Kyoto, 601 Japan tel 075-321-9047, fax 075-321-9038 t.niwa@nippon-shinyaku.co.jp =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ----------------------------------------------------------------------------- God bless all of you! Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From tgakrh@sg10.chem.tue.nl Tue Nov 25 04:37:14 1997 Received: from mailhost.tue.nl for tgakrh@sg10.chem.tue.nl by www.ccl.net (8.8.3/950822.1) id EAA10313; Tue, 25 Nov 1997 04:05:53 -0500 (EST) Received: from sg10.chem.tue.nl [131.155.80.53] by mailhost.tue.nl (8.8.5) for id KAA03511 (ESMTP). Tue, 25 Nov 1997 10:05:47 +0100 (MET) Received: from tgakrh@localhost by sg10.chem.tue.nl (8.8.5) for chemistry@www.ccl.net id KAA16031. Tue, 25 Nov 1997 10:05:45 +0100 (MET) From: Roelant Harmsen Message-Id: <199711250905.KAA16031@sg10.chem.tue.nl> Subject: Basis Set for Pd To: chemistry@www.ccl.net (Computational Chemistry List) Date: Tue, 25 Nov 1997 10:05:45 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi Everyone, Does anyone know of a good gaussian type basis set for palladium optimised for DFT? Thanks, Roelant ********************************************************************** Roelant Harmsen |tel: ++31 40 2473575/5032 University of Technology Eindhoven |fax: ++31 40 2455054 Laboratory of Inorganic |e-mail : tgakrh@chem.tue.nl Chemistry and Catalysis (TAK) |www: http://www.tak.chem.tue.nl/ P.O. box 513 |personal/rharmsen 5600 MB Eindhoven | The Netherlands |AD&D: Xahnar (Wild Mage) ********************************************************************** From yubofan@guomai.sh.cn Tue Nov 25 06:37:14 1997 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id GAA11108; Tue, 25 Nov 1997 06:28:35 -0500 (EST) Received: from default (Email-39 [210.0.0.7]) by guomai.sh.cn (8.8.7/8.8.7) with ESMTP id TAA08613 for ; Tue, 25 Nov 1997 19:25:58 +0800 (CST) Message-Id: <199711251125.TAA08613@guomai.sh.cn> From: "Yubo Fan" To: Subject: Need some reference about molecular geometry optimization. Date: Tue, 25 Nov 1997 19:28:39 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1157 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 7bit Hi, I am doing geometry optimization of a big molecule. I think it is impossible for me to do these jobs for the whole molecule which contains over 40 C atoms, so I want to split it into several parts and calculate each of them respectively. Then I will put them together. Is this thought possible? If possible, could you please give me some advice or reference with the same kind of work. With best regards Y. Fan ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641470 Shanghai, 200433 P. R. China ============================================================= From metz@phindigo.oci.uni-heidelberg.de Tue Nov 25 11:37:16 1997 Received: from phindigo.oci.uni-heidelberg.de for metz@phindigo.oci.uni-heidelberg.de by www.ccl.net (8.8.3/950822.1) id LAA12811; Tue, 25 Nov 1997 11:34:26 -0500 (EST) Received: by phindigo.oci.uni-heidelberg.de (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA20001; Tue, 25 Nov 1997 17:35:49 -0100 From: "Markus Metz" Message-Id: <9711251735.ZM19999@phindigo.oci.uni-heidelberg.de> Date: Tue, 25 Nov 1997 17:35:34 +0000 In-Reply-To: Steven Creve "Re: CCL:G:atom in molecules" (Nov 24, 10:05am) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Steven Creve Subject: Summary AIM-Visualization Programs Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Summary of the responses to visualize Atom in Molecules. On the following mail ... > > I am using GAUSSIAN 94 to calculate the properties of atoms in molecules (1) > using the SCF density.(keywords: AIM=ALL, DENSITY=LAPLACIAN) > For example the attractors, critical points on attractor interaction lines, > zero flux surfaces, bond paths and the second derivative of the electron > density of cyclopropane were calculated. > What I am interested in are the bent bonds in this molecule. > Does anybody know, how to visualize this data? > (1) R. F. W. Bader, Atoms in Molecules: a quantum theory, Clarendon Press, > Oxford, 1990. ... I got the responses: ------------------------------------------------------------ Keith E. Laidig wrote: You can get all of Bader's code directly from him. There are postscript generating routine within the package (I think). Anyway, you can build easily upon these programs to produce pictures in most graphic environments. Bader's email address is: bader@mcmail.cis.mcmaster.ca and his WWW page is: http://www.chemistry.mcmaster.ca/faculty/bader/bader.html. -------------------------------------------------------------------------------- Hi, there are some persons here working on that. They are using a sofware called AVS (Advanced Visual System) to visualize all the needed quantities. AVS however is expensive but as far as they told me it is very good. You can find more info about it on: http://www.avs.com Good luck, Leonardo -------------------------------------------------------------------------------- Dr. Paul L. A. Popelier hat ein Programm namens MORPHY, welches er gern zur Verfuegung stellt (zusammen mit einigen seiner Artikel). MORPHY erlaubt es, die vollstaendige AIM Analyse durchzufuehren, wenn man ein Gaussian-94 WFN File bereitstellt. Das Programm erzeugt Postscript-Output. Ich habe es im Rahmen meiner Dissertation verwendet und bin sehr zufrieden mit der Darstellung. Dr Popeliers Email ist: pla@umist.ac.uk. Eine weitere Visualisierung ist in Chem. Eur. J. 1997, 3, No. 8, 1244ff. zu finden. Die Autoren (R. Glaser und D. Farmer) benutzen ein eigenes Programm namens CCGVF. Ich weiss leider nicht, ob sie es herausgeben. Vielleicht hilft dies ein bisschen weiter, Magnus -- ======================================================================== Magnus Kessler kessler@mpi-muelheim.mpg.de PhD Student MPI fuer Kohlenforschung Lembkestrasse 5 Strukturchemie D-45470 Muelheim / Germany ======================================================================== -------------------------------------------------------------------------------- I wrote Dr. Propelier and he sent me the program. Best regards, Markus. -- -------------------------------------------------------------------------------- Markus Metz Universitaet Heidelberg Tel.: 06221-54-6066 Organ.-Chem. Institut Lehrstuhl III Fax: 06221-54-4885 Im Neuenheimer Feld 270 69120 Heidelberg -------------------------------------------------------------------------------- From hp003@THEORY.dra.hmg.gb Tue Nov 25 12:37:23 1997 Received: from relay.mod.uk for hp003@THEORY.dra.hmg.gb by www.ccl.net (8.8.3/950822.1) id MAA12935; Tue, 25 Nov 1997 12:13:33 -0500 (EST) Received: from hermes.dra.hmg.gb by relay.mod.uk with local SMTP id ; Tue, 25 Nov 1997 17:13:26 +0000 Received: from THEORY.dra.hmg.gb by hermes.dra.hmg.gb (MX V4.2 VAX) with SMTP; Tue, 25 Nov 1997 17:13:20 GMT Received: (from hp003@localhost) by THEORY.dra.hmg.gb (8.7.6/8.7.3) id RAA18114 for CHEMISTRY@www.ccl.net; Tue, 25 Nov 1997 17:13:01 GMT From: Mike Fearn Message-ID: <199711251713.RAA18114@THEORY.dra.hmg.gb> Subject: Two centre coulomb integral evaluation. To: CHEMISTRY@www.ccl.net Date: Tue, 25 Nov 1997 17:13:00 GMT X-Mailer: Elm [revision: 212.4] Dear all, As part of the development of a new semi-empirical method, I'd be most grateful if anyone can point me to (ideally freely available) code which can evaluate two-center two-electron integrals using slater orbitals (s,p type) for a given nuclear separation. Many thanks in advance. Mike Fearn. hp003@dra.hmg.gb From yu@infiniti.wavefun.com Tue Nov 25 14:37:18 1997 Received: from volvo.wavefun.com for yu@infiniti.wavefun.com by www.ccl.net (8.8.3/950822.1) id OAA13629; Tue, 25 Nov 1997 14:03:22 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA04909; Tue, 25 Nov 97 11:06:18 -0800 Received: from infiniti.wavefun.com(198.147.95.4) by volvo.wavefun.com via smap (V1.3) id sma004905; Tue Nov 25 11:05:24 1997 Received: from ) by infiniti.wavefun.com (931110.SGI/950213.SGI.AUTOCF) id AA15843 for @volvo.wavefun.com:CHEMISTRY@www.ccl.net; Tue, 25 Nov 97 11:01:28 -0800 From: "Jianguo Yu" Message-Id: <9711251101.ZM15841@infiniti.wavefun.com> Date: Tue, 25 Nov 1997 11:01:27 -0800 Reply-To: yu@wavefun.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Spring-1998 Computational Chemistry Workshops Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues, A brief note to announce the upcoming Spring 1998 Computational Chemistry workshops schedule held in Wavefunction, Inc., Irvine, California: _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Format: 3-day intensive workshop on electronic structure _/ _/ methods and applications, and hands-on molecular _/ _/ modeling laboratory on individual workstations. _/ _/ _/ _/ Schedule: January 14-16, March 18-20, May 13-15, 1998 _/ _/ _/ _/ Instructors: Warren Hehre & Wayne Huang _/ _/ _/ _/ Textbooks: o "Chemistry with Computation", Warren Hehre & _/ _/ Wayne Huang, 1995. _/ _/ o "A Laboratory Book of Computational Organic _/ _/ Chemistry", Warren Hehre, Alan Shusterman & _/ _/ Wayne Huang, 1996. _/ _/ o "A Short Course in Modern Electronic Structure _/ _/ Methods", Warren Hehre, 1993-1997. _/ _/ _/ _/ For complete brochure, drop me a note to workshop@wavefun.com _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemistry | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ From iguana@one.net Wed Nov 26 21:37:36 1997 Received: from mail.one.net for iguana@one.net by www.ccl.net (8.8.3/950822.1) id UAA20873; Wed, 26 Nov 1997 20:50:14 -0500 (EST) Received: from port-38-31.access.one.net ([209.50.100.93] HELO default ident: IDENT-NOT-QUERIED [port 12292]) by mail.one.net with SMTP id <16797-11506>; Wed, 26 Nov 1997 20:48:37 -0500 Message-Id: <3.0.5.32.19971126205536.007a5650@mail.one.net> X-Sender: iguana@mail.one.net X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 26 Nov 1997 20:55:36 +0000 To: CHEMISTRY@www.ccl.net From: Ray Crawford Subject: CCL:cyclodextrin inclusion complexes Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, Could someone give me any references or suggestions of the most appropriate force field for calculations of cyclodextrin inclusion complexes ? Thank you very much in advance! -- *********************************************************************** Universidade Federal de Pernambuco Centro de Ciencias Exatas e da Natureza Departamento de Quimica Fundamental http://www.dqf.ufpe.br Recife - PE - Brazil Gerd Bruno da Rocha E-Mail : gbr@npd.ufpe.br : gerd@dqf.ufpe.br MSc Student in Computational Chemistry *********************************************************************** -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: gbr@NPD.UFPE.BR -- Original Sender From: Address: gbr@NPD.UFPE.BR CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html