From chemistry-request@server.ccl.net Mon Feb 14 21:19:06 2000 Received: from anusf.anu.edu.au (root@anusf.anu.edu.au [150.203.5.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA17368 for ; Mon, 14 Feb 2000 21:19:04 -0500 Received: from anu.edu.au (drifter.anu.edu.au [150.203.5.58]) by anusf.anu.edu.au (8.8.8+Sun/8.8.6) with ESMTP id MAA03050; Tue, 15 Feb 2000 12:14:05 +1100 (EST) Message-ID: <38A8A85F.4A77F6E2@anu.edu.au> Date: Tue, 15 Feb 2000 12:14:08 +1100 From: "Dr. Harold W. Schranz" X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: Alexei Khalizov CC: Computational Chemistry List Subject: CCL:How can one calculate reaction rate constant? References: <200002142351.SAA11552@sirocco.cc.mcgill.ca> Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 8bit Hi Alexi Alexei Khalizov wrote: > Dear CCLers, > > I would like to calculate rate constant k for bimolecular reaction A + B -> AB. I have found transition state and proved that it really connects reagents and products (G98w, GAMESS). According to RRKM the simplest expression for calculation of rate constant k is > > k = (kB*T/h)(Q’’/Qa*Qb) exp(-Eo/RT), > > where kB is Boltzmann’s constant; Q’’, Qa and Qb are partition functions for TS and reagents A and B; Eo ? difference in zero point energies of TS and reagents. > > Question: what units and what measure does this rate constant k have? Simple evaluation gives units of [s-1], but being a bimolecular it is expected to have units of [M-1s-1], [cm3 molecules-1 s-1] or such. How can we account for this? > > Sincerely, > Alexei Khalizov, > Balakrishnan Viswanathan Here is a very brief description. The expression you are looking for (e.g. see any reliable physical chemistry text e.g. Atkins) comes from Transition State Theory (TST) (sometimes called by the misleading name Activated Complex Theory (ACT) or Absolute Rate Theory (ART)) can be formulated in various units (e.g. as a molecular or as a molar rate constant). More specifically you are looking at canonical TST (as opposed to microcanonical TST which is essentially identical to RRKM theory). The expression you have is not entirely standard though it can still be correct in some formulations if there are units absorbed into the "partition functions". Strictly speaking though, molecular partition functions are dimensionless (sums over Boltzmann weights), though if one goes through a TST derivation one can see how a volume factor emerges in the bimolecular case (in the calculation of the concentration of transition state configurations). For a bimolecular reaction, (excuse the awful notation, being careful with parentheses): k = (kB*T/h) (RT/p0) NA ((Q'AB)/(QA*QB)) exp(-Eo/RT), where (kB*T/h) has units of inverse time (e.g. s-1) (RT/p0) has units of number density (n/V) (.e.g. cm-3) which can easily be converted to other concentration unit (be careful with units!). NA is Avogadro's number. The rest is dimensionless. QA, QB = partition functions for the reactants Q'AB = partition function for the transition state configuration A...B. (not a species!!!) Note that the degree of freedom which is the reaction coordinate is excluded in the calculation of Q'AB. (See derivation for details, though hard to find a good one! Most make an unecessarily strong (and incorrect) equilibrium assumption but still get the right expression. Better derivations involve a calculation of the flux through a dividing surface. So the above expression has units of, e.g., s-1 mol-1 cm-3 or s-1 M-1 depending on how the quantities are calculated (simple unit conversions). A similar expression applies for unimolecular reactions: k = (kB*T/h) (Q'/Q) exp(-Eo/RT), and has units of inverse time. Good luck with the application of these expressions (take care!!!) Regards Harry. -- ________________________________________________________________________ Dr. Harold W. Schranz, Office Ph.: +61 (02) 6249 5988 Computational Chemist, Dept Ph.: +61 (02) 6249 3437 ANU Supercomputer Facility, Fax: +61 (02) 6279 8199 Australian National University, Email: Harold.Schranz@anu.edu.au Canberra, ACT 0200, AUSTRALIA. WWW: http://anusf.anu.edu.au/~hws900 ________________________________________________________________________ From chemistry-request@server.ccl.net Mon Feb 14 21:39:40 2000 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA17447 for ; Mon, 14 Feb 2000 21:39:39 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id RAA01329 for chemistry@ccl.net; Mon, 14 Feb 2000 17:45:10 -0800 From: Schrodinger Info account Message-Id: <200002150145.RAA01329@canter-n-siegel.schrodinger.com> Subject: ANNC: Introductory Jaguar and MacroModel Wrokshops at Scripps To: chemistry@ccl.net Date: Mon, 14 Feb 2000 17:45:10 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Jaguar and MacroModel Introductory Workshops Providing tools for scientists in industry, government, and academia in the areas of life sciences, material sciences, and fundamental research, Schrödinger, Inc. is hosting Jaguar and MacroModel Introductory Workshops, to demonstrate to novice users how Jaguar and MacroModel are used in real-world applications. Where: The Scripps Research Institute, La Jolla, CA Dates: Maestro and MacroModel Wednesday, March 1, 2000 Jaguar Thursday, March 2, 2000 Lecture topics will include: Applications to drug discovery Applications to materials research Helpful hints and "tricks-of-the trade" to enhance productivity New features in Jaguar 4.0 and MacroModel 7.0 New unified graphical interface If you have any questions or comments, please see our website at http://www.schrodinger.com or contact Leo Brown (email: leobrown@schrodinger.com, phone: +1 630 752-9047). From chemistry-request@server.ccl.net Tue Feb 15 00:04:38 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA18052 for ; Tue, 15 Feb 2000 00:04:36 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id TAA26793; Mon, 14 Feb 2000 19:59:21 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14504.53014.537912.743810@lrz.uni-muenchen.de> Date: Mon, 14 Feb 2000 19:59:18 -0800 (PST) To: , Subject: Commodity Cluster Computing for Computational Chemistry X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid DHPC Technical Report DHPC-073: Commodity Cluster Computing for Computational Chemistry http://dhpc.adelaide.edu.au/reports/073/html/dhpc-073.html K.A. Hawick1, D.A. Grove1, P.D. Coddington1, M.A. Buntine2 1 Department of Computer Science, University of Adelaide, Adelaide, SA 5005, Australia 2 Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia khawick@cs.adelaide.edu.au, mark.buntine@adelaide.edu.au 21 January 2000 Keywords: Computational chemistry, Beowulf cluster, cluster computing, parallel computing, performance benchmarks Outline: Abstract 1. Introduction 2. Beowulf Clusters 3. System Requirements for Computational Chemistry 4. Designing a Beowulf Cluster 4.1. Processor Architecture 4.2. Network Infrastructure 4.3. Disk Configuration 4.4. Operating System 4.5. Cluster Management Software 4.6. Other Issues 5. Performance Benchmarks 6. Conclusions Acknowledgments References Abstract: Access to high-performance computing power remains crucial for many computational chemistry problems. Unfortunately, traditional supercomputers or cluster computing solutions from commercial vendors remain very expensive, even for entry level configurations, and are therefore often beyond the reach of many small to medium-sized research groups and universities. Clusters of networked commodity computers provide an alternative computing platform that can offer substantially better price/performance than commercial supercomputers. We have constructed a networked PC cluster, or Beowulf, dedicated to computational chemistry problems using standard ab initio molecular orbital software packages such as Gaussian and GAMESS-US. This paper introduces the concept of Beowulf computing clusters and outlines the requirements for running the ab initio software packages used by computational chemists at the University of Adelaide. We describe the economic and performance trade-offs and design choices made in constructing the Beowulf system, including the choice of processors, networking, storage systems, operating system and job queuing software. Other issues such as throughput, scalability, software support, maintenance, and future trends are also discussed. We present some benchmark results for the Gaussian 98 and GAMESS-US programs, in order to compare the processor performance (and price/performance) with other computing platforms. We also analyse the efficiency and scalability of the parallel versions of these programs on a commodity Beowulf cluster. We believe that the Beowulf cluster we have constructed offers the best price/performance ratio for our computational chemistry applications, and that commodity clusters can now provide dedicated supercomputer performance within the budget of most university departments. [ rest of paper snipped for brevity. consult above URL for the whole hog ] From chemistry-request@server.ccl.net Tue Feb 15 03:25:07 2000 Received: from rrzd1.rz.uni-regensburg.de (root@rrzd1.rz.uni-regensburg.de [132.199.1.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA18954 for ; Tue, 15 Feb 2000 03:25:06 -0500 Received: from kunz.chemie.ngate.uni-regensburg.de (rchnw3.chemie.uni-regensburg.de [132.199.48.203]) by rrzd1.rz.uni-regensburg.de (8.9.3/8.9.3-KLW-Linux-0.1) with ESMTP id IAA29892; Tue, 15 Feb 2000 08:20:05 +0100 Received: from RCHNW3/SpoolDir by kunz.chemie.ngate.uni-regensburg.de (Mercury 1.44); 15 Feb 00 08:20:16 +0100 Received: from SpoolDir by RCHNW3 (Mercury 1.44); 15 Feb 00 08:19:46 +0100 From: "Georg Schmeer" Organization: Universitaet Regensburg To: chemistry@ccl.net, "Alexei Khalizov" Date: Tue, 15 Feb 2000 08:19:45 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:How can one calculate reaction rate constant? Priority: normal In-reply-to: <200002142351.SAA11552@sirocco.cc.mcgill.ca> X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: <1999D67E2859@kunz.chemie.ngate.uni-regensburg.de> >From: "Alexei Khalizov" >Organization: Chemistry Dept., McGill University >To: chemistry@ccl.net >Date: Mon, 14 Feb 2000 18:51:16 -0500 >Subject: CCL:How can one calculate reaction rate constant? >Priority: normal >0100,0100,0100Times New RomanDear CCLers, > > >I would like to calculate rate constant k for bimolecular reaction >A + B -> AB. I have found transition state and proved that it >really connects reagents and products (G98w, GAMESS). >According to RRKM the simplest expression for calculation of >rate constant k is > > >k = (kB*T/h)(Q /Qa*Qb) exp(-Eo/RT), > > >where kB is Boltzmann s constant; Q , Qa and Qb are partition >functions for TS and reagents A and B; Eo difference in zero >point energies of TS and reagents. > > >Question: what units and what measure does this rate constant k >have? Simple evaluation gives units of [s-1], but being a >bimolecular it is expected to have units of [M-1s-1], [cm3 >molecules-1 s-1] or such. How can we account for this? > > >Sincerely, > >Alexei Khalizov, > >Balakrishnan Viswanathan > > > > >------------------------- >Dr. Alexei Khalizov >Departments of Chemistry >McGill University, >801 Sherbrooke St. W., >Montreal, Quebec, CANADA, >H3A 2K6 > >->MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > Dear Alexei Khalizov, this problem is a very universal one, because the equations for standard free energies and for equilibrium constants very often are not exactly formulated in the literature. Concerning the fundamental equation Delta(G-zero) = - R*T*ln(Equilibrium constant) the equilibrium constant must be a dimensionless magnitude. According to J.W.Moore, R.A.Pearson,"Kinetics and Mechanism", Wiley, New York, 1981, p.177-179 the equilibrium constant is related to a reference concentration eq.Constant = K^c*(c-ref)^(n-1), where n is the molecularity of the equilibrium reaction and K^c the ratio of the equilibrium concentrations with the same dimension as the reference concentration. Very often, the second factor of this equation is omitted: eq.Constant = K^c : and this is not true! Taking into account of the exact relation, the equations for rate constants yield always the right dimensions. I hope this is helpful for you Sincerely Georg Schmeer Prof. Dr. Georg Schmeer Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Georg.Schmeer@chemie.uni-regensburg.de Tel: 0941-943-4745 Fax: 0941-943-4532 From chemistry-request@server.ccl.net Tue Feb 15 08:03:09 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20966 for ; Tue, 15 Feb 2000 08:03:09 -0500 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id MAA16931; Tue, 15 Feb 2000 12:58:13 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id MAA17230; Tue, 15 Feb 2000 12:58:11 +0100 Date: Tue, 15 Feb 2000 12:58:07 +0100 (MET) From: Harald Svedung To: Alexei Khalizov cc: chemistry@ccl.net Subject: Re: CCL:How can one calculate reaction rate constant? In-Reply-To: <200002142351.SAA11552@sirocco.cc.mcgill.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id IAA20967 Hi Dr. Khalizov and all The first thing that comes to mind is to include the collision frequency, that is pressure (or conc.) dependent. Collision frequency and collisional energy transfer efficiency also becomes important in stabilizing the product at least in gas phase. for a further discussion se eg. : The theory of Unim. and Recomb. React., R. G. Gilbert and S. C. Smith, Blackwell Sci. Pub. (1990). and for energy transfer eg. : special issue Ber. Bunsenges. Phys. Chem., 101 (1997) :-) /Harald On Mon, 14 Feb 2000, Alexei Khalizov wrote: > > I would like to calculate rate constant k for bimolecular reaction > A + B -> AB. I have found transition state and proved that it > really connects reagents and products (G98w, GAMESS). > According to RRKM the simplest expression for calculation of > rate constant k is > > > k = (kB*T/h)(Q’’/Qa*Qb) exp(-Eo/RT), > > > where kB is Boltzmann’s constant; Q’’, Qa and Qb are partition > functions for TS and reagents A and B; Eo – difference in zero > point energies of TS and reagents. > > > Question: what units and what measure does this rate constant k > have? Simple evaluation gives units of [s-1], but being a > bimolecular it is expected to have units of [M-1s-1], [cm3 > molecules-1 s-1] or such. How can we account for this? > > > Sincerely, > > Alexei Khalizov, > > > > > > ------------------------- > Dr. Alexei Khalizov > Departments of Chemistry > McGill University, > 801 Sherbrooke St. W., > Montreal, Quebec, CANADA, > H3A 2K6 > > - Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Tue Feb 15 13:43:13 2000 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA22174 for ; Tue, 15 Feb 2000 13:43:13 -0500 Received: from tc.cornell.edu (LIGAND.TC.CORNELL.EDU [128.84.20.182]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id MAA15505 for ; Tue, 15 Feb 2000 12:38:15 -0500 Sender: richard@tc.cornell.edu Message-ID: <38A98E01.76582850@tc.cornell.edu> Date: Tue, 15 Feb 2000 12:33:53 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:ASSIGNMENT OF ATOM TYPES IN MMFF94 References: <38A8F1C8.D2BCD182@mahindrabt.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit First, the easy part: >2) Coordination no. (i.e. no of attached atoms) for all the 3 types (38)NPYD, > (39)NPYL and (79)N5 is [2]. How is this possible? e.g. in pyrrole, the > nitrogen atom gets atom type (39)NPYL, then how does (39)NPYL have > coordination no. [2]? If you are looking at table II of Halgren's first paper on MMFF94, the coordination number, [2], listed for NPYL is a typo. The properties table (I) in his paper V lists the coordination number as [3]. ----- now the hard part If you don't already know, it is very informative to look at the assigned structures in the free validation suite available on the osc web page. I tripped over this problem last summer, so it's not too fresh in my mind, but here goes: > The following questions arise from these facts: > 1) If ring is a hetero-aromatic 5-ring, with respect to the base atom, > only 4 atoms need to be addressed. Clearly 2 of them (the 2 atoms > directly connected to base atom) will be alpha to the base atom, > remaining 2 will be beta to the base atom. (If the hetero atom is N, it > would be of type (39)NPYL. Hence, any other N in the same 5-ring will > have the atom type (38)NPYD or (65)N5A or (66)N5B and C will have the > atom type (63)C5A or (64)C5B. Any other type of carbon can't exist if > 5-ring is an aromatic ring) >In this situation, where do the types (78)C5 and (79)N5 fit? Can any one >suggest me a structure in which atom types (78)C5 or (79)N5 would be >used? One example is GUANCH01 (protonated guanine) in the validation suite. The two carbons shared between the 5 and 6 membered rings are not part of the imidazolium resonance structure. Because of the imidazolium part, the position of the atoms relative to "the unique lone-pair heteroatom" is ambiguous and the L5 parameter in the aromatic substitution table gets a value of 4. At least, that's what works for me. The aromatic substitution table is a bit puzzling since several aromatic types (like C5A, for example) appear in the "OLD TYPE" column as if the substitution gets called more than once on a given structure. Perhaps now that Thomas Halgren is with another company, he can speak freely on the subject of implementation. There are many details like this that I have encountered and it makes me appreciate why he has requested that any implementation that does not pass the suite of 761 molecules be labeled as "partial". Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Tue Feb 15 20:59:05 2000 Received: from xx1.icas.ac.cn (zhangxd@[159.226.64.181]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA24874 for ; Tue, 15 Feb 2000 20:59:02 -0500 From: zhangxd@xx1.icas.ac.cn Received: from localhost (zhangxd@localhost) by xx1.icas.ac.cn (8.8.7/8.8.7) with SMTP id IAA20021; Tue, 15 Feb 2000 08:59:50 GMT Date: Tue, 15 Feb 2000 08:59:49 +0000 (GMT) To: "Prof. John D Goddard" cc: CHEMISTRY@ccl.net Subject: how to compile gaussian under linux In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CClneters Now I have a problem, i.e. how to compile the gaussian98 under Linux(redhat 5.0). Thanks in advance! with best regards, zhang, xiaoo dong From chemistry-request@server.ccl.net Wed Feb 16 15:12:39 2000 Received: from dalton.quimica.unlp.edu.ar (root@dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30563 for ; Wed, 16 Feb 2000 15:12:33 -0500 Received: from bilbo (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.9.0/8.9.0) with SMTP id PAA06916 for ; Wed, 16 Feb 2000 15:32:59 -0300 Message-Id: <3.0.1.32.20000216154931.006ac390@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 16 Feb 2000 15:49:31 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: G98 + Linda under Linux Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear ccl'ers, I want to run g98 using Linda on a couple of one-processor pentium/linux boxes. I wasn't able to find out about HOW to launch the program. I guess that ntsnet is involved but I'm not sure at all. I'd appreciate any hints. Regards, Reinaldo From chemistry-request@server.ccl.net Wed Feb 16 16:55:27 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA31054 for ; Wed, 16 Feb 2000 16:55:27 -0500 From: aileen.cheung@ic.ac.uk Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12LBOk-0000SP-00 for chemistry@ccl.net; Wed, 16 Feb 2000 20:50:10 +0000 Received: from sunfs1-gw.ps.ic.ac.uk ([155.198.164.2] helo=sunfs1.ps.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12LBOg-0006Im-00 for chemistry@ccl.net; Wed, 16 Feb 2000 20:50:06 +0000 Received: from indigo2.sunfs1.ps.ic.ac.uk by sunfs1.ps.ic.ac.uk (8.8.8+Sun/4.1) id UAA11439; Wed, 16 Feb 2000 20:50:09 GMT Date: Wed, 16 Feb 2000 20:50:09 GMT Message-Id: <10002162050.ZM11644@indigo2> In-Reply-To: Reinaldo Pis Diez "CCL:G98 + Linda under Linux" (Feb 16, 3:49pm) References: <3.0.1.32.20000216154931.006ac390@dalton.quimica.unlp.edu.ar> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: cartesian coordinates to internal coordinates Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, Can someone please point out either a C or a Fortran code which: i) converts cartesian coordinates to internal coordinates ii) transform gradients in cartesian coordinates to internal coordinates, if possible? Thank you for your help. Regards, Aileen -- Aileen Cheung CPSE Imperial College Tel: 0171-594 6612 From chemistry-request@server.ccl.net Wed Feb 16 18:21:18 2000 Received: from sdnt1.Acadia-SD (mail.acadia-pharm.com [209.77.18.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA31457 for ; Wed, 16 Feb 2000 18:21:17 -0500 Received: by sdnt1 with Internet Mail Service (5.5.2650.21) id <1YA34D1V>; Wed, 16 Feb 2000 14:13:13 -0800 Message-ID: <15189A4705A8D31189B700805F85410B05EADD@sdnt1> From: Daniel Severance To: "'chemistry@ccl.net'" Subject: GPCRs and other non-structural targets Date: Wed, 16 Feb 2000 14:13:12 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hi, Does anyone have a summary of what research groups are working on computational methods for dealing with things where no structures are known? I.e., given the structures of a series of small molecules and their activities, trying to infer something about what interactions must be important? Also, for those of you who may have hired people to work on these kinds of problems - what background have you found is best (assuming they did something different as a student). Thanks. Feel free to e-mail me directly and I'll summarize to the list. Dan ____________________________________________________ Daniel L. Severance Ph.D. phone (858) 558 2871 Computational Chemistry fax (858) 558 2872 ACADIA Pharmaceuticals 3911 Sorrento Valley Boulevard San Diego CA 92121-1402 USA dseverance@acadia-pharm.com www.acadia-pharm.com From chemistry-request@server.ccl.net Wed Feb 16 20:06:07 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA31912 for ; Wed, 16 Feb 2000 20:06:07 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JLZI4WYDRC0076NP@trentu.ca> for chemistry@ccl.net; Wed, 16 Feb 2000 19:00:28 EST Date: Wed, 16 Feb 2000 19:04:11 -0500 From: elewars Subject: PPP Method: status? To: chemistry@ccl.net Message-id: <38AB3AFB.54758889@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2000 Feb 16 Subject: the Pariser-Parr-Pople method Could someone with some familiarity with the PPP method please tell me: 1) is it still used at all? 2) was it used for calculation of UV spectra *at a given geometry* only, or could it perform realistic geometry optimizations on pi-systems? 2) what has it evolved into: what currently popular method or program for calculating electronic spectra is an offspring of the PPP method? Thank you. E. Lewars ===== From chemistry-request@server.ccl.net Wed Feb 16 12:18:02 2000 Received: from mail2.imation.com (mail2.imation.com [207.242.212.137]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA29958 for ; Wed, 16 Feb 2000 12:18:02 -0500 Received: by mail2.imation.com(Lotus SMTP MTA v4.6.6 (890.1 7-16-1999)) id 86256887.0058A29A ; Wed, 16 Feb 2000 10:08:07 -0600 X-Lotus-FromDomain: IMATION From: "Glen M. Robinson" To: CCL Message-ID: <86256887.0058A238.00@mail2.imation.com> Date: Wed, 16 Feb 2000 10:10:40 -0600 Subject: Gaussian and Windows 2000 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Does Gaussian 98W work with Windows 2000? Glen Robinson From chemistry-request@server.ccl.net Wed Feb 16 14:50:09 2000 Received: from VAX.PHR.UTEXAS.EDU (vax.phr.utexas.edu [128.83.164.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA30480 for ; Wed, 16 Feb 2000 14:50:09 -0500 From: PEARLMAN@VAX.PHR.UTEXAS.EDU Date: Wed, 16 Feb 2000 12:45:20 -0600 (CST) To: CHEMISTRY@ccl.net CC: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <000216124520.5102@VAX.PHR.UTEXAS.EDU> Subject: 4th Lake Tahoe Center Molecular Diversity Symposium - Mar 21-25, 2000 Hello everyone -- I've been asked to forward the following meeting announcement. First, I'd like to add a bit more information: 1. The Lake Tahoe Center is a *non-profit* corporation whose mission is to facilitate communication amongst scientists in the diverse disciplines loosely linked through the concept of chemical diversity. 2. The meeting is held at a particularly beautiful location and is conducted in a "Gordon Research Conference" format with lectures in the morning and evening, leaving afternoons free for discussion and/or recreation. I hope to see you there! -- Bob Pearlman > The organizers are pleased to announce the upcoming 4th Lake Tahoe > Symposium on MOLECULAR DIVERSITY, to be held March 21 - 25, 2000. > We hope that you make plans to attend our exciting program this year. > > You can view the latest program updates and register online by visiting > the Lake Tahoe Symposia web site: http://www.laketahoesymposia.org. > > Please forward this notice to colleagues who might also be interested > in our program - thank you! > > > Lake Tahoe Symposia > Lake Tahoe Center > 604 South Saltair Avenue > Los Angeles CA 90049-4135 > > Ph: 310 825-9329 (310 476-1147) > Fax: 310 206-1703 (310 476-7741) > Em: admin@laketahoesymposia.org > URL: http://www.laketahoesymposia.org From chemistry-request@server.ccl.net Wed Feb 16 19:20:35 2000 Received: from sandman.ucdavis.edu (root@sandman.ucdavis.edu [169.237.105.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA31719 for ; Wed, 16 Feb 2000 19:20:34 -0500 Received: from localhost (kylan@localhost [127.0.0.1]) by sandman.ucdavis.edu (8.9.3/8.9.3/IT4.3.1) with ESMTP id PAA05957 for ; Wed, 16 Feb 2000 15:15:17 -0800 (PST) Date: Wed, 16 Feb 2000 15:15:17 -0800 (PST) From: William Cope X-Sender: kylan@sandman.ucdavis.edu To: chemistry@ccl.net Subject: CCL: Gaussian Basis Sets for Tin Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, Does anyone know about a gaussian basis set for tin that is larger than 3-21G*? A 6-31G* basis set would be ideal. Feel free to e-mail me directly, replies will be summarized and posted here. Wil. From chemistry-request@server.ccl.net Wed Feb 16 22:00:29 2000 Received: from prserv.net (out5.prserv.net [32.97.166.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA32622 for ; Wed, 16 Feb 2000 22:00:29 -0500 From: jmmckel@attglobal.net Received: from attglobal.net ([166.72.87.103]) by prserv.net (out5) with SMTP id <2000021701550224303ikcmse>; Thu, 17 Feb 2000 01:55:03 +0000 Message-ID: <38AB1216.EEB17593@attglobal.net> Date: Wed, 16 Feb 2000 21:09:43 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:PPP Method: status? References: <38AB3AFB.54758889@trentu.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit PPP theory is still used. It can be quite accurate, and very fast, when parameterised carefully. It is best used for planar molecules in general. If nonplanar configurations are considered one must take care to avoid twists that bring components of localised lone pairs out of the plane. It works best at a frozen geometry. It can be used to optimize bond lengths by calibrating the expression R = a + b*P where P is the computed bond order for each nearest-neighbor bond type at experimental or high quality ab initio geometries. PPP theory is just the pi part of INDO/S and similar methodologies, and assumes a frozen sigma field that is incorporated into the one center parameters. Because INDO/S and related all valence electron methodologies treat sigma electrons explicitly it is superior to PPP theory for pnon-planar molecules. Geometry optimization for INDO/S spectroscopic methods are not very well developed because parameterizations for spectra give poor geometries, in general. John McKelvey elewars wrote: > 2000 Feb 16 > > Subject: the Pariser-Parr-Pople method > > Could someone with some familiarity with the PPP method please tell me: > 1) is it still used at all? > 2) was it used for calculation of UV spectra *at a given geometry* only, > or could it perform realistic geometry optimizations on pi-systems? > 2) what has it evolved into: what currently popular method or program > for calculating electronic spectra is an offspring of the PPP method? > > Thank you. > > E. Lewars > ===== > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Feb 16 23:54:22 2000 Received: from mail4.nycap.rr.com (mail4-1.nyroc.rr.com [24.92.33.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA00360 for ; Wed, 16 Feb 2000 23:54:21 -0500 Received: from claessen.nycap.rr.com ([24.161.16.156]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com for ; Wed, 16 Feb 2000 22:51:26 -0500 Reply-To: From: "Rolf Claessen" To: Subject: MOSOL Date: Wed, 16 Feb 2000 22:45:48 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Importance: Normal In-Reply-To: <38AB1216.EEB17593@attglobal.net> Dear Colleagues, did anyone here use MOSOL? Is it possible to calculate heats of formation in the solid state with it? Is it more accurate than the CRYSTAL or the WIEN code? Rolf