>From ccl@www.ccl.net Thu Jan 2 15:30 EST 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA09766; Thu, 2 Jan 1997 15:30:24 -0500 (EST) Received: from lists.Princeton.EDU for jimreho@phoenix.Princeton.EDU by bedrock.ccl.net (8.8.3/950822.1) id PAA07023; Thu, 2 Jan 1997 15:30:23 -0500 (EST) Received: from ponyexpress.Princeton.EDU ([128.112.129.131]) by lists.Princeton.EDU with ESMTP id <370273.s1-2>; Thu, 2 Jan 1997 15:30:17 -0500 Received: from phoenix.Princeton.EDU (phoenix.Princeton.EDU [128.112.128.43]) by ponyexpress.Princeton.EDU (8.6.12/8.6.12) with ESMTP id PAA11135 for ; Thu, 2 Jan 1997 15:30:00 -0500 Received: (jimreho@localhost) by phoenix.Princeton.EDU (8.6.12/8.6.12) id PAA15291; Thu, 2 Jan 1997 15:29:35 -0500 Date: Thu, 2 Jan 1997 15:29:35 -0500 (EST) From: "James H. Reho" Subject: Triplet states of alkali dimers To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! I am a novice user of Gaussian '92 and was wondering if anyone could offer me advice in the calculation of upper triplet states of alkali dimers. I need to do HF calculations of Li2 and Na2, etc. I have calculated the lowest triplet states of these molecules using 6-311G** basis and now need to do the upper states. If anyone has a user-friendly methodology, I would certainly appreciate the advice! Thanks, James Hughes Reho jimreho@phoenix.princeton.edu Frick 10 D Frick Laboratories, Princeton U phone 258-5189 / 4975 fax 258-6665 >From watts@gwinn.medc.umn.edu Fri Jan 3 14:09 EST 1997 Received: from chet.medc.umn.edu for watts@gwinn.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id OAA01748; Fri, 3 Jan 1997 14:09:03 -0500 (EST) Received: from gwinn.medc.umn.edu (root@gwinn.medc.umn.edu [134.84.172.12]) by chet.medc.umn.edu (8.8.3/8.6.9) with ESMTP id NAA08140 for ; Fri, 3 Jan 1997 13:09:03 -0600 (CST) Received: from localhost (watts@localhost) by gwinn.medc.umn.edu (8.8.3/8.6.9) with SMTP id NAA00993 for ; Fri, 3 Jan 1997 13:09:01 -0600 (CST) Date: Fri, 3 Jan 1997 13:09:01 -0600 (CST) From: Chuck Watts To: The Computational Chemistry List Subject: Protein Hydration and Spectral Density Functions. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL: I have a small queation for you that is not completely computational in nature although it does pertain to the investigation of biomolecular dynamics using NMR and I know that many NMR spectroscopists subscribe to this list. I was recently reading the papers Otting, G.; Liepinsh, E.; Wutrich, K. (1991) "Protein Hydration in Aqueous Solution" Science 254, 974-980. and Kubinec, M. G.; Wemmer, D. E. (1992) "NMR Evidence for DNA Bound Water in Solution" JACS 114, 8739-8740. In these papers combined NOESY and ROESY experiments are used to measure the lifetimes of waters bound to BPTI and DNA as interpreted by a Random Diffusion model. The model consists of a protein molecule with a radius rp, a proton spin displaced from the protein center by pp, and a rotational correlation time of tp, a water molecule with a radius rw, a proton spin displaced from the water center by pw, and a rotational correlation time of tw, the protein and water are related to each other via the diffusion coefficient D which can then be translated into a correlation time for the interaction using the Einstein-Smoluchowski relation. The NOE and ROE rates dependency on the spectral density function are then given as k(NOE) = 6J(2wo) - J(0) k(ROE) = 3J(wo) + 2J(0) and it is stated that the spectral density is related to the rate processes that govern the modulation of the dipole-dipole coupling of the system. My question is as follows, I can easily find the generic treatment of the spectral density function that relates its dependency on a single correlation time with the assumption of isotropic tumbling, how is the spectral density function used in these studies different from this and how specifically did they generate the NOE/ROE vs. 1/D curves for this paper given the data above. Sorry, I know this pobably isn'y a short queation but I thought someone on the list might have some insight as to the solution. Best Wishes, Charles R. Watts ************************************ Department of Medicinal Chemistry * * College of Pharmacy * An appeaser is one who feeds * University of Minnesota * a crocodile, hoping it will eat * 8-101 HSUF * him last. * 308 Harvard St. SE. * * Minneapolis, MN 55455 * -Winston Churchill * Phone: (612) 624-5486 * * Fax: (612) 626-4429 * * E-Mail: watts004@128.101.118.21 ************************************ >From cfisher@strubix.com Fri Jan 3 14:41 EST 1997 Received: from alpha.strubix.com for cfisher@strubix.com by www.ccl.net (8.8.3/950822.1) id OAA02997; Fri, 3 Jan 1997 14:41:05 -0500 (EST) Received: from alpha.strubix.com ([127.0.0.1]) by alpha.strubix.com (Netscape Mail Server v1.1) with SMTP id AAA14813 for ; Fri, 3 Jan 1997 11:40:59 -0800 From: cfisher@strubix.com (Cindy Fisher) Message-Id: <9701031140.ZM14810@alpha.strubix.com> Date: Fri, 3 Jan 1997 11:40:59 -0800 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry-request@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Length: 90 Status: R subscribe ccl -- Cindy Fisher Structural Bioinformatics, Inc. cfisher@alpha.strubix.com >From stevef@myst.mbt.com Fri Jan 3 16:34 EST 1997 Received: from myst.mbt.com for stevef@myst.mbt.com by www.ccl.net (8.8.3/950822.1) id QAA03534; Fri, 3 Jan 1997 16:34:40 -0500 (EST) Received: by myst.mbt.com (940816.SGI.8.6.9/940406.SGI.AUTO) id QAA09982; Fri, 3 Jan 1997 16:36:48 -0500 Date: Fri, 3 Jan 1997 16:36:38 -0500 (EST) From: "Stephen A. Farrington" Subject: Forwarded mail.... To: CHEMISTRY-REQUEST@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 209 Status: R unsubscribe ---------- Forwarded message ---------- Date: Fri, 3 Jan 1997 16:35:04 -0500 (EST) From: Stephen A. Farrington To: CHEMISTRY-REQUEST@ccl.osu.edu Subject: unsubscribe >From ccl@www.ccl.net Thu Jan 2 14:28 EST 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA09393; Thu, 2 Jan 1997 14:28:09 -0500 (EST) Received: from unexexch.unex.ucla.edu for bgoodin@unex.ucla.edu by bedrock.ccl.net (8.8.3/950822.1) id OAA04619; Thu, 2 Jan 1997 14:28:07 -0500 (EST) Received: by unexexch.unex.ucla.edu with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63) id <01BBF89F.90AA9ED0@unexexch.unex.ucla.edu>; Thu, 2 Jan 1997 11:24:49 -0800 Message-ID: From: "Goodin, Bill" To: "'List-Computational chem2'" , List-Chemistry modeling , List-Computational chemistry Subject: UCLA short course on "Java/JavaScript for Science and Engineering Problems" Date: Thu, 2 Jan 1997 11:26:00 -0800 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" On March 10-14, 1997, UCLA Extension will present the short course, "Java/JavaScript Applied to Scientific and Engineering Problems", on the UCLA campus in Los Angeles. The instructors are Bruce Chapman, PhD, Member Technical Staff, Jet Propulsion Laboratory (http://southport.jpl.nasa.gov), and Victor B. Taylor, MSEE, Member Technical Staff, Jet Propulsion Laboratory (http://airsar.jpl.nasa.gov). Course topics include: Java: objects, primitives, classes; simple I/O, AWT, GUI; applets vs. applications; file management; streams and threads; networking; graphics, animation, audio; databases. JavaScript: arrays, loops, debugging, interfaces/plugins; Security, net-based operating systems. This course features extensive lab time which is devoted to exercises to demonstrate functionality and usage of the Java and JavaScript languages for science and engineering applications. The course should enable participants to: o Develop their own Java applets and applications o Develop their own JavaScript enhanced web pages o Develop an understanding of how Java and JavaScript may be applied to a variety of science and engineering problems. Prerequisite C and/or C++ programming experience is required, as well as a familiarity with the World Wide Web. The course fee is $1495, which includes extensive course materials. These materials are for participants only and are not for sale. For additional information and a complete course description, please contact Marcus Hennessy at: (310) 825-1047 (310) 206-2815 fax mhenness@unex.ucla.edu http://www.unex.ucla.edu/shortcourses This course may also be presented on-site at company locations. From giovanni@sg2.csrsrc.mi.cnr.it Tue Jan 7 13:14:45 1997 Received: from sg2.csrsrc.mi.cnr.it for giovanni@sg2.csrsrc.mi.cnr.it by www.ccl.net (8.8.3/950822.1) id MAA23279; Tue, 7 Jan 1997 12:42:31 -0500 (EST) Received: by sg2.csrsrc.mi.cnr.it (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for chemistry@www.ccl.net id JAA13792; Tue, 7 Jan 1997 09:42:44 -0800 Date: Tue, 7 Jan 1997 09:42:44 -0800 From: giovanni@sg2.csrsrc.mi.cnr.it (Giovanni Scalmani) Message-Id: <199701071742.JAA13792@sg2.csrsrc.mi.cnr.it> To: chemistry@www.ccl.net Subject: Electrostatic_effects_in_molecular_crystals Dear friends, I am wondering about the following problem: I would like to model - by means of ab-initio calculations - the electrostatic effects on a single molecule due to the crystalline environment within a molecular crystal, i.e. I would like to perform a (possibly high level) calculation of a single molecule's electronic structure under the influence of a neighbouring molecules' charge distribution. An iterative procedure should be necessary to attain self-consistency between the ab-initio charge distribution of the reference molecule and the neighbouring molecules' charge distribution, which will be in turn derived from the reference molecule's wavefunction. Since I have no deep knowledge of crystallography, I will appreciate advises about two issues: 1) Widely speaking: Is such an approach correct? Can you give me some references in the literature? If I have more than one molecule (or even different molecular species) in the cell a similar approach on more than one molecule is still feasible, but is it worth while? How should I model the neighbouring molecules' charge distribution (Mulliken charges, charges fitted to the molecular electrostatic potential, Atom-In-Molecule-derived charges, orientable atomic dipoles, ... ) ? 2) More technically: do you know a program which reads the crystalline structure (for example from the Cambridge Database) and performs all coordinates manipulation I will need ? In particular to obtain cartesian coordinates of any specified molecule in the cell surrounded by all the neighbouring molecules whose centers of mass are within a certain radius from the reference molecule's center of mass ? Thank you in advance for all suggestions, Giovanni. ---------------------------------------------------------------------- ^^^ | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it o o | Universita' degli Studi di Milano | | Dipartimento di Chimica Fisica ed Elettrochimica \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- From giovanni@sg2.csrsrc.mi.cnr.it Tue Jan 7 13:44:53 1997 Received: from sg2.csrsrc.mi.cnr.it for giovanni@sg2.csrsrc.mi.cnr.it by www.ccl.net (8.8.3/950822.1) id MAA23320; Tue, 7 Jan 1997 12:44:03 -0500 (EST) Received: by sg2.csrsrc.mi.cnr.it (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for chemistry@www.ccl.net id JAA13855; Tue, 7 Jan 1997 09:45:35 -0800 Date: Tue, 7 Jan 1997 09:45:35 -0800 From: giovanni@sg2.csrsrc.mi.cnr.it (Giovanni Scalmani) Message-Id: <199701071745.JAA13855@sg2.csrsrc.mi.cnr.it> To: chemistry@www.ccl.net Subject: Electrostatic_effects_in_molecular_crystals Dear friends, I am wondering about the following problem: I would like to model - by means of ab-initio calculations - the electrostatic effects on a single molecule due to the crystalline environment within a molecular crystal, i.e. I would like to perform a (possibly high level) calculation of a single molecule's electronic structure under the influence of a neighbouring molecules' charge distribution. An iterative procedure should be necessary to attain self-consistency between the ab-initio charge distribution of the reference molecule and the neighbouring molecules' charge distribution, which will be in turn derived from the reference molecule's wavefunction. Since I have no deep knowledge of crystallography, I will appreciate advises about two issues: 1) Widely speaking: Is such an approach correct? Can you give me some references in the literature? If I have more than one molecule (or even different molecular species) in the cell a similar approach on more than one molecule is still feasible, but is it worth while? How should I model the neighbouring molecules' charge distribution (Mulliken charges, charges fitted to the molecular electrostatic potential, Atom-In-Molecule-derived charges, orientable atomic dipoles, ... ) ? 2) More technically: do you know a program which reads the crystalline structure (for example from the Cambridge Database) and performs all coordinates manipulation I will need ? In particular to obtain cartesian coordinates of any specified molecule in the cell surrounded by all the neighbouring molecules whose centers of mass are within a certain radius from the reference molecule's center of mass ? Thank you in advance for all suggestions, Giovanni. ---------------------------------------------------------------------- ^^^ | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it o o | Universita' degli Studi di Milano | | Dipartimento di Chimica Fisica ed Elettrochimica \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- From boyd@chem.iupui.edu Tue Jan 7 16:14:47 1997 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.8.3/950822.1) id PAA24475; Tue, 7 Jan 1997 15:49:53 -0500 (EST) Received: from macgw.chem.iupui.edu (134.68.137.71) by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01IDXQRLM8G000985D@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Tue, 07 Jan 1997 15:51:29 -0500 Date: Tue, 07 Jan 1997 15:49:01 -0500 From: Boyd Subject: Reviews in Computational Chemistry To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT CCLers, We wish to announce the publication of Volume 10 of REVIEWS IN COMPUTATIONAL CHEMISTRY. This volume contains tutorials and timely reviews of genetic algorithms, nonlinear dynamics, and the role of computational chemistry in this era of combinatorial chemistry. In addition, the history of computational chemistry in the UK is chronicled. The preface tracks the direction of journals in the field. The authors and chapters are: 1. Richard Judson, Genetic Algorithms and Their Use in Chemistry. 2. Eric J. Martin, David C. Spellmeyer, Roger E. Critchlow Jr., and Jeffrey M. Blaney, Does Combinatorial Chemistry Obviate Computer-Aided Drug Design? 3. Robert Q. Topper, Visualizing Molecular Phase Space: Non-Statistical Effects in Reaction Dynamics. 4. Raima Larter and Kenneth Showalter, Computational Studies in Nonlinear Dynamics. 5. Stephen J. Smith and Brian T. Sutcliffe, The Development of Computational Chemistry in the United Kingdom. Since John Wiley and Sons acquired VCH Publishers last year, our volumes are now available through Wiley. Volume 10 (xxii + 334 pp) has ISBN 1-56081-957-X. The price is $110 for single copies and only $90 with standing orders. Inquires can be directed to custserv@wiley.com or visit http://chem.iupui.edu/~boyd/rcc.html Thanks, Don Donald B. Boyd, Ph.D. Co-editor, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Internet boyd@chem.iupui.edu From watts@gwinn.medc.umn.edu Tue Jan 7 16:26:34 1997 Received: from chet.medc.umn.edu for watts@gwinn.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id PAA24423; Tue, 7 Jan 1997 15:33:45 -0500 (EST) Received: from gwinn.medc.umn.edu (root@gwinn.medc.umn.edu [134.84.172.12]) by chet.medc.umn.edu (8.8.3/8.6.9) with ESMTP id OAA23075; Tue, 7 Jan 1997 14:32:04 -0600 (CST) Received: from localhost (watts@localhost) by gwinn.medc.umn.edu (8.8.3/8.6.9) with SMTP id OAA08900; Tue, 7 Jan 1997 14:32:01 -0600 (CST) Date: Tue, 7 Jan 1997 14:32:00 -0600 (CST) From: Chuck Watts To: The Computational Chemistry List cc: bruno@antas.agraria.uniss.it Subject: CCL:Order Parameters In-Reply-To: <199701032002.VAA21256@rugmd2> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL: Thanks to Dr. Ir. David van der Spoel, Dr. David Case and Dr. Tom Hendrickson for answering my questions regarding the the calculation of order parameters from molecular dynamics trajectories and the availability of code. The references are given below and code is available for both the AMBER and Charmm packages. Thanks, Charles R. Watts ************************************ Department of Medicinal Chemistry * * College of Pharmacy * An appeaser is one who feeds * University of Minnesota * a crocodile, hoping it will eat * 8-101 HSUF * him last. * 308 Harvard St. SE. * * Minneapolis, MN 55455 * -Winston Churchill * Phone: (612) 624-5486 * * Fax: (612) 626-4429 * * E-Mail: watts004@128.101.118.21 ************************************ On Fri, 3 Jan 1997 D.van.der.Spoel@chem.rug.nl wrote: > Chuck Watts writes: > : > : > :Dear CCL: > : > : Would anyone know of a good reference pertaining to the extraction > :of order parameters from molecular dynamics simulations of bioploymers, > :and the availability of code to do so. I would also be interested in any > :references comparing these to one obtained by NMR. > : > check out: > > @Article{Palmer92, > author = {A. G. {Palmer III} and D. A. Case}, > title = {Molecular Dynamics Analysis of {NMR} Relaxation in a > Zinc-Finger Peptide}, > journal = jacs, > year = 1992, > volume = 114, > pages = {9059-9067} > } > > @Article{PSmith95a, > author = {P. E. Smith and R. C. van Schaik and T. Szyperski > and K. W{\"u}thrich and W. F. van Gunsteren}, > title = {Internal Mobility of the Basic Pancreatic Trypsin > Inhibitor in Solution: A Comparison of {NMR} SPin > Relaxation Measurements and Molecular Dynamics Simulations}, > journal = jmb, > year = 1995, > volume = 246, > pages = {356-365} > } > > > > > David > ________________________________________________________________________ > Dr. Ir. David van der Spoel > e-mail: spoel@chem.rug.nl www: http://rugmd0.chem.rug.nl/~spoel > phone: 31-50-3634327 fax: 31-50-3634800 > s-mail: Nijenborgh 4, 9747 AG Groningen, The Netherlands. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > From ahocquet@tamarugo.cec.uchile.cl Tue Jan 7 17:14:48 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id RAA25059; Tue, 7 Jan 1997 17:06:52 -0500 (EST) Received: from [146.83.10.50] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA22663; Tue, 7 Jan 1997 19:05:46 +0400 Date: Tue, 7 Jan 1997 19:05:46 +0400 Message-Id: <9701072205.AA22663@tamarugo.cec.uchile.cl> To: peon@medchem.dfh.dk (Per-Ola Norrby) From: ahocquet@tamarugo.cec.uchile.cl (Alexandre Hocquet) Subject: Diphenylamine and rules of thumbs Cc: gertvh@sci.kun.nl >>I would be interested if there is a 'rule of thumb' about differences >>in bond length (and angles) between solid and gase phase organic >>molecules. > > We can actually do better than a rule of thumb. MM3 (that is, >Allingers original MM3, none of the copies, this is the Mac version) can >calculate the difference between bond lengths from different determination >methods > (I'm not entirely sure how much >the nitrogen lone pair will affect the position in the X-ray though). >>Specifically, we are interested in diphenylamine and would >>like to know if one can use the solid state (x-ray) data and somehow >>scale it to a gas phase value. > > One problem here, the usual with MM3. We don't have all >parameters. However, using an "amide" (sp2) nitrogen and guessing a single >parameter, I calculated the following table for diphenyl amine: > > Per-Ola Norrby > Dear Gert and Per-Ola, dear cclers, The problem with diphenylamine is the status of the nitrogen. Should we consider it as trigonal or tetrahedral ? Per-Ola took an amide N because it was the case that minimised parameter guessing. I suppose a tetrahedral amine would have been more convenient to this kind of molecule, guessing the potential energy surface would look like the diphenylmethane or phenoxybenzene ones. Obviously, the lack of parameters did not allow that. Why is it so annoying ? As Per-Ola pointed out, the position of the N lone pair could have influence upon the the measurement of bonds distances based on Xray techniques. Actually, Allinger et al. (Theochem, 312 (1994), p69-83) do give a rule of thumb (Aaaah ! at last, he comes to the point) for converting bonds from electron diffraction into microwave or Xray . It is quite different for a C-Nsp3 and a C-Nsp2 bond : Xray (298K) Xray (100K) MW C-Nsp3 +0,002 -0,002 +0,004 C-Nsp2 +0,007 +0,003 +0,004 (in Angstroms) Hope this helps... Alexandre Hocquet Laboratorio de Cristalografia Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago CHILE fax : 56 2 696 73 59 From MARYJO@neu.edu Tue Jan 7 22:14:50 1997 Received: from NUHUB.DAC.NEU.EDU for MARYJO@neu.edu by www.ccl.net (8.8.3/950822.1) id VAA26156; Tue, 7 Jan 1997 21:22:13 -0500 (EST) From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01IDY2A2VM5C99DS4T@neu.edu>; Tue, 7 Jan 1997 21:22:01 EST Date: Tue, 07 Jan 1997 21:22:01 -0500 (EST) Subject: vitamin B6? To: chemistry@www.ccl.net Message-id: <01IDY2A3064I99DS4T@neu.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi! Has anybody out there done computation on derivatives of vitamin B6 (pyridoxal phosphate)? I would appreciate your references. Thanks, Mary j.o.