From wall@phys.chem.ethz.ch Fri Jun 14 05:54:04 1996 Received: from bernina.ethz.ch for wall@phys.chem.ethz.ch by www.ccl.net (8.7.5/950822.1) id FAA07839; Fri, 14 Jun 1996 05:35:59 -0400 (EDT) Received: from helios (actually helios-chem.ethz.ch) by bernina.ethz.ch with SMTP inbound; Fri, 14 Jun 1996 11:35:39 +0200 Received: from jetson.ppc-sun by helios.ethz.ch id AA26531; Fri, 14 Jun 1996 11:35:38 +0200 Received: by jetson.ppc-sun (5.x/SMI-SVR4) id AA07451; Fri, 14 Jun 1996 11:35:37 +0200 Date: Fri, 14 Jun 1996 11:35:37 +0200 From: wall@phys.chem.ethz.ch (Ernst U. Wallenborn) Message-Id: <9606140935.AA07451@jetson.ppc-sun> To: chemistry@www.ccl.net Subject: [R] G94 Excited States X-Sun-Charset: US-ASCII Hi there, A while ago (May 20th) i posted a question concerning the ab-initio calculation of electronic spectra. I got a couple of answers and posted a summary of these (May 29th). I tested the methods recommended to me on a toy problem (formaldehyde) and thought it might be an idea to make the data available to you, in case someone is interested to see them. Just have a look at http://www.chem.ethz.ch/~wall/form.html where a link to a Postscript document containing the details of the calculation is also available. Thanks again for helping me with that. -- Ernst-Udo Wallenborn Laboratorium fuer Physikalische Chemie ETH Zentrum CH-8092 Zuerich From toukie@zui.unizh.ch Fri Jun 14 06:21:01 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id FAA07823; Fri, 14 Jun 1996 05:33:52 -0400 (EDT) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA13809; Fri, 14 Jun 96 11:33:48 +0200 X-Nupop-Charset: Swiss Date: Fri, 14 Jun 1996 11:34:45 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <41685.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Seeking references ... Dear Colleagues; I am seeking published references giving neutron diffraction-derived structural details for phenolic compounds containing an oxygen or sulphur atom ortho the the -OH group; or a carbonyl moiety (C=O), nitro moiety (NO2), amino moiety (NH2, RHR), or amido moiety (NHCOR) ortho to the -OH group. So far the _only_ reference I have come across is Bacon & Jude, Z. Kristallogr. Kristallgeom. Kristallphys. Kristallchem. 138: 19-40 (1973), which is for salicylic acid. If anyone can recommend additional references, I would be very grateful to hear from you. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 ZH 7 Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From Jeffrey.Gosper@brunel.ac.uk Fri Jun 14 06:43:14 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id FAA07661; Fri, 14 Jun 1996 05:01:04 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Fri, 14 Jun 1996 10:00:56 +0100 Date: Fri, 14 Jun 1996 10:00:53 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Summary: IUPAC colors for atoms To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Original Message: 'I was told the other day that the color used to represent atoms have been defined by IUPAC. Does anyone know a source of information on this topic?' There question seemed to generate quite a bit of interest and I had a number of requests to forward any information I received on the topic. The explicit answer was provided by Jeff Williams (Information Officer, IUPAC) how stated the following as a response: 'No, IUPAC has not made recommendations about the colours used to represent different atoms.' As IUPAC has not provided standards what are people actual using in this respect? Also given that we all have an interest in computational chemistry, which largely depends on the visualization of molecules, maybe there should be a standard setup by the IUPAC. Just a thought. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From smillefiori@dipchi.unict.it Fri Jun 14 07:54:07 1996 Received: from ns.dipchi.unict.it for smillefiori@dipchi.unict.it by www.ccl.net (8.7.5/950822.1) id HAA08293; Fri, 14 Jun 1996 07:07:14 -0400 (EDT) Received: from millefiori.dipchi.unict.it ([151.97.236.168]) by ns.dipchi.unict.it (post.office MTA v1.9.3 ID# 0-11335) with SMTP id AAA184 for ; Fri, 14 Jun 1996 13:06:11 +0100 X-Sender: smillefiori@dipchi.unict.it X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry@www.ccl.net From: "Millefiori Salvatore" Subject: software for PED Date: Fri, 14 Jun 1996 13:06:11 +0100 Message-ID: <19960614120611337.AAA184@millefiori.dipchi.unict.it> Hi, I am looking for free PC-software to get the Potential Energy Distribution (PED) for description of vibrations which involve mixtures of internal coordinates of molecules. Thanks, Andrea Alparone.=20 =20 __________________________________________________________________________ =20 Dr. Andrea Giovanni Alparone ________ ___ (c/o Prof. Salvatore Millefiori) \___ \_____/ / Dottorato di Ricerca Scienze Chimiche, \ _/ Universit=E0 di Catania. \______ CT\ Address: Dipartimento Scienze Chimiche, \___\ Viale A. Doria,6- 95125 Catania, ITALY. Phone: 39-95-330319 (334) E-mail: smillefiori@dipchi.unict.it __________________________________________________________________________ From gever@ruca.ua.ac.be Fri Jun 14 09:54:05 1996 Received: from maze.ruca.ua.ac.be for gever@ruca.ua.ac.be by www.ccl.net (8.7.5/950822.1) id JAA08797; Fri, 14 Jun 1996 09:06:22 -0400 (EDT) Received: by maze.ruca.ua.ac.be (1.37.109.4/16.2) id AA00937; Fri, 14 Jun 96 15:04:16 +0200 Date: Fri, 14 Jun 1996 15:04:16 +0200 (METDST) From: Gert Everaert Sender: Gert Everaert Reply-To: Gert Everaert Subject: Re: CCL:software for PED To: Millefiori Salvatore Cc: chemistry@www.ccl.net In-Reply-To: <19960614120611337.AAA184@millefiori.dipchi.unict.it> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII This may be of interest : gar2ped is a utility program for post-processing the archive records of GAUSSIAN 94 frequency calculations. Features include isotopic shifts, potential energy distribution, APT population analysis, and vibrational mode animation. It was written by C. Van Alsenoy and J.M.L. Martin and is available by anonymous ftp from the Computational Chemistry Archives at ftp://ftp.ccl.net/pub/chemistry Sincerely, Gert _______________________________________________________________________________ Gert Everaert RUCA, Department of Chemistry Tel: + 32 3 218 03 63 Groenenborgerlaan 171 Fax: + 32 3 218 02 33 B 2020 Antwerpen E-mail gever@ruca.ua.ac.be Belgium _______________________________________________________________________________ From owner-chemistry@ccl.net Fri Jun 14 10:54:06 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id KAA09142; Fri, 14 Jun 1996 10:27:16 -0400 (EDT) Received: from phy.mtu.edu for kxiang@mtu.edu by bedrock.ccl.net (8.7.5/950822.1) id KAA12497; Fri, 14 Jun 1996 10:27:15 -0400 (EDT) Received: from phyfac1.phy.mtu.edu (phyfac1.phy.mtu.edu [141.219.151.67]) by phy.mtu.edu (8.6.10/8.6.9) with SMTP id KAA17434 for ; Fri, 14 Jun 1996 10:27:15 -0400 From: Kai-hua Xiang Received: (from kxiang@localhost) by phyfac1.phy.mtu.edu (8.6.10/MTU-1.2) id KAA02844 for chemistry@ccl.net; Fri, 14 Jun 1996 10:28:43 -0400 Message-Id: <199606141428.KAA02844@phyfac1.phy.mtu.edu> Subject: molecules absorbed on porous activated carbon To: chemistry@ccl.net Date: Fri, 14 Jun 1996 10:28:42 -0400 (EDT) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear Friends, Are there any softwares that can quantitatively compare the interactions of different molecules, such as mercury,nitrogen, alcohol, etc. with the porous activated carbon? Any suggestions are welcome. Thanks in advance! Kai-hua Xiang kxiang@mtu.edu From dsmith@debye.dasgroup.com Fri Jun 14 11:54:09 1996 Received: from cool95.third-wave.com for dsmith@debye.dasgroup.com by www.ccl.net (8.7.5/950822.1) id LAA09513; Fri, 14 Jun 1996 11:08:39 -0400 (EDT) Received: from dirac ([206.31.47.72]) by cool95.third-wave.com (Netscape Mail Server v1.1) with SMTP id AAA104 for ; Fri, 14 Jun 1996 11:08:29 +0000 X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) To: CHEMISTRY@www.ccl.net From: dsmith@dasgroup.com (Douglas A. Smith Ph.D.) Subject: need dielectric constant for THF Date: Fri, 14 Jun 1996 11:08:29 +0000 Message-ID: <19960614110828955.AAA104@dirac> We are doing some MOPAC 93/COSMO calculations and need the following information, if anyone has it. (1) Dielectric constant for THF (tetrahydrofuran) (2) Solvent radius for THF (the value used for RSOLV) Thanks in advance. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology. From owner-chemistry@ccl.net Fri Jun 14 13:54:08 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id NAA10390; Fri, 14 Jun 1996 13:11:51 -0400 (EDT) Received: from bioc1.msi.com for marvin@bioc1.msi.com by bedrock.ccl.net (8.7.5/950822.1) id NAA20987; Fri, 14 Jun 1996 13:11:48 -0400 (EDT) Received: from iris147.biosym.com by bioc1.msi.com (5.64/0.0) id AA20986; Fri, 14 Jun 96 10:10:35 -0700 Received: by iris147.msi.com (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id KAA09077; Fri, 14 Jun 1996 10:11:10 -0700 Date: Fri, 14 Jun 1996 10:11:10 -0700 From: marvin@msi.com (Marvin Waldman) Message-Id: <199606141711.KAA09077@iris147.msi.com> To: chemistry@ccl.net Subject: SMALLEST BOUNDING BOX - THE PROBLEM THAT WOULD NOT DIE Before some clever computational geometrist(?) flames me, I thought I would flame myself. My previous "analytical" solution does not even work for the simple case of a tetrahedron! Cory C. Pye wrote: >the likelihood that any two faces opposite to each other would be parallel is >small, and given any face A, B, C, and the point P farthest from the plane >containing it, a slight rotation of the normal of the plane toward >avg(A,B,C)-P would shorten the distance from the plane to P, and thus the >most likely scenario would entail a vertex pair as being on the two planes. This appears to be correct for the case of a tetrahedron. If one constructs a tetrahedron of edge length 1, then I calculate its height to be sqrt(2/3). So, constructing a plane containing one face and another plane parallel and intersecting the opposite point has the two planes a distance of sqrt(2/3) apart. Projecting the 4 points onto one of the planes produces a triangle with a base of 1 and a height of sqrt(3)/2. The fourth point (from the opposite plane) is inside the triangle. The minimum bounding rectangle for this triangle is then adjacent to one edge and intersects the opposite point. So, the bounding box for the construction I originally proposed has a volume of: sqrt(2/3) * 1 * sqrt(3)/2 = 1/sqrt(2) Now, consider the following construction. Construct a plane intersecting one edge of the tetrahedron and parallel to the opposite (non-adjacent) edge. Construct a plane for the opposite edge parallel to the first plane. The two planes are a distance 1/sqrt(2) apart (proof is left to the reader - have fun). Projecting the four points onto one of these planes produces a square with diagonals equal to 1 and edges equal to 1/sqrt(2). So the bounding box for this construction has a volume of: 1/sqrt(2) * 1/sqrt(2) * 1/sqrt(2) = 1/( 2*sqrt(2) ) which is clearly smaller than the original "solution". The paper of Martin and Stephenson that I referred to in my earlier posting mentions that the bounding rectangle of minimum area (and I think minimum perimeter) must be adjacent to one of the edges of the 2D convex hull. I had incorrectly assumed that this property could be extended to 3 dimensions and would work for any metric! The extension to any metric was clearly a case of faulty (stupid!) reasoning on my part. However, it was somewhat surprising that the metrics that do work for 2 dimensions using the convex hull approach (rectangle adjacent to one of the edges works for minimum area and maybe perimeter) don't work analogously in 3 dimensions (box adjacent to one of the faces doesn't work for minimum volume or area). It was only after reading Cory Pye's posting that I began to think harder about the problem, and discovered the alternate solution for the tetrahedron. With all this in mind, I would now like to propose an addendum to my original solution. I will not claim it works all the time, as I don't have a proof, and I would be interested if anyone can find a counter-example. Consider all the bounding boxes formed from planes adjacent to one face of the 3D convex hull as before. In addition, consider the following set of bounding boxes. For each pair of non-adjacent edges of the 3D convex hull, form the pair of planes going through one edge and parallel to the other edge. If either of these planes penetrates the convex hull, reject this pair. Otherwise, project all the points onto one of the planes and form the 2D bounding rectangle for these points using the 2D convex hull as before. Consider all the bounding boxes formed >from this approach (planes coincident with pairs of edges) and the bounding boxes from the original approach (planes coincident with a face and its furthest point) and select the box of minimum volume (or maybe area). Once again, many improvements may be envisioned to the above algorithm to improve its efficiency. A solution for the VDW surface of the molecule may be similarly constructed (I think) by constructing the convex hull of the VDW surface by generating planes which are tangent to triplets of the VDW spheres and for which all the remaining spheres lie on one side of the plane. The intersections of these planes defining the convex hull for the VDW surface define a new set of points, faces, and edges to which we can apply the above algorithm. Two more special cases need to be considered. For a planar molecule such as benzene, we need to construct additional planes to define the VDW convex hull by constructing pairs of planes tangent to 2 of the spheres and which are perpendicular to the parallel bounding planes above and below the plane of the atoms. For a linear molecule, the problem has the trivial solution of 2 planes tangent to the 2 spheres at the ends of the molecule and perpendicular to the line going through the atoms. The 4 remaining planes are chosen to be tangent to the largest VDW sphere of the atoms, perpendicular to the first 2 planes, and perpendicular to each other. Regards, Marvin Waldman, Ph.D. Director, Rational Drug Design Molecular Simulations Inc. e-mail: marvin@msi.com Web: http://www.msi.com