From tamasgunda@tigris.klte.hu Sun Nov 2 04:34:43 1997 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id DAA21177; Sun, 2 Nov 1997 03:35:14 -0500 (EST) Message-Id: <199711020835.DAA21177@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Sun, 02 Nov 1997 09:29:50 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@www.ccl.net Date: Sun, 2 Nov 1997 09:29:55 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Mol2mol 3.2 Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) MOL2MOL 3.2 -- an easy-to-use file conversion program for the chemist. Mol2Mol automatically converts many of the widely used file formats in chemistry. Running under Windows, Mol2Mol helps you with the conversion, manipulation and inspection of different molecular structure files. Currently thirty different molecule file formats are supported, as well as your own free format ASCII files. Mol2Mol automatically recognizes the format of most of these files. The program also helps in capturing co-ordinates from the big output files of quantum chemistry programs. It possesses some chemical intelligence for recognizing extended atom and bond types, chemical environments, or adding hydrogens, which is necessary for converting simpler formats to SYBYL, HyperChem, MacroModel, Cache, PCMODEL etc files. Mol2Mol is more than just a file conversion system. It has a number of features which offer outstanding ease-of-use to a researcher who needs different tools for molecule inspection. * Simple graphical window to inspect the input molecule with standard manipulations (translation, rotation, stereo modes etc.) * Quick calculation of basic geometrical data (distances, angles, planes, pyramidality, proton-proton and proton-methyl centroid distances, distance from fitted planes, dihedral angle of planes/rings etc) * Ring puckering data of 5-9 membered rings * Simple correction of atom or bond types * Adding of hydrogens to X-ray or PDB files * In the case of problems manual corrections of the input or output file with an ASCII editor * Phi-Psi data of proteins + Ramachandran plot * Conversion of a peptide to "backbone molecule" * Splitting of multiple structures (e.g. peptides with more than one strands) to the individual molecules * Calculation of sterimol parameters * Batch calculation of geometric data from multiple (e.g. Macromodel) files and compering them with e.g. NOE data * Batch conversion for files to similar type * Text window to follow the conversion process. For the time being, MOL2MOL can automatically recognize (R) and write (W) the following co-ordinate file formats: ALCHEMY I-III *RW SYBYL MOL and MOL2 *RW MDL mol *RW MOLIDEA *RW Desktop Molecular Modeller *RW PCMODEL *RW HyperChem *RW Macromodel *RW Cache *RW Insight *RW MOBY (Cartesian) *RW CACAO *RW Beilstein Rosdal *R ChemDraft (Cartesian) *RW Xmol *RW ChemWindow (mol) *RW Brookhaven PDB *RW Z matrix, free format #*RW AMPAC #*RW MOPAC #*RW Gaussian #*RW X-ray fractional CIF *R Cambridge FDAT *R Cambridge MODEL *R user's free format R Cartesian free format RW ChemDraw ct *RW PLUTO W PLT W WIMP (.ftr) W Schakal W MolPic3 *RW PovRay W * recognized automatically # insertion of a marker is necessary when capturing co-ordinates Since many of the above programs are also capable of communicating with others or accepting different database formats (e.g. Protein Data Bank, CSSR files), the effective range of MOL2MOL is even wider. Several other programs not included in the above table use common formats. System requirements: IBM PC with Windows 3.1/95, 8 MB RAM Demo version will be available soon from the CompuChem homepage. For more information contact: CompuChem Software Chemie Vogtherrstr. 10 74676 Niedernhall - Germany Tel: +49 (0)7940-4328 Fax: (0)7940-4304 e-mail: compuchem@compuchem.com Or have a look: Internet: http://www.compuchem.com/neu.htm ------------------------------------------------------- From elewars@alchemy.chem.utoronto.ca Sun Nov 2 17:34:47 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id QAA22707; Sun, 2 Nov 1997 16:54:21 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id QAA26919 for chemistry@www.ccl.net; Sun, 2 Nov 1997 16:54:11 -0500 (EST) Date: Sun, 2 Nov 1997 16:54:11 -0500 (EST) From: "E. Lewars" Message-Id: <199711022154.QAA26919@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: OVERLAP INTEGRAL AND SLATER FUNNC 1997 Nov 2 SLATER OVERLAP INTEGRALS >From E. Lewars To CCL Hello, There is some info' about overlap integrals and Slater functions that I am finding it hard to dig out of the literature. I should state at the outset that _I know_: that there are programs for calculating overlap integrals that in most molecular quantum chem Gaussian functions, not Slater functions, are used that Mulliken et al published a long paper (J Chem Phys, 17 (1949) 1248-1267)) with recipes for calculating overlap integrals that all kinds of tricks exist for "simplifying" the calculation of overlap integrals --------- OK, but what I want is simply this: (1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), where the coordinates are in Angstroms (_not_ atomic units or Bohrs) and if we write for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} (usually a is expressed in terms of zeta and pi, b = -zeta, and the variable is a radius vector r) QUESTION: what are a_1 and b_1, as numbers, not Greek letters? what are a_2,and b_2 as numbers, not Greek letters? (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz must = the correct overlap, if the six Cartesian coordinates are in Angstroms. And of course integral of S_11 = S_22 = 1. (2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? (3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), is there a simple function S_12 = f(d) ? (for H, He? for any two 1s orbitals)? Of course f will depend parametrically on the a's and b's. ------------- Thanks E. Lewars =============== From psa@star.le.ac.uk Thu Oct 23 14:22 EDT 1997 Received: from venus.le.ac.uk for psa@star.le.ac.uk by bedrock.ccl.net (8.8.6/950822.1) id OAA18994; Thu, 23 Oct 1997 14:22:22 -0400 (EDT) Received: from ltsun0.le.ac.uk (actually host ltsun0.star.le.ac.uk) by venus.le.ac.uk with SMTP (PP); Thu, 23 Oct 1997 19:18:27 +0100 Date: Thu, 23 Oct 1997 19:23:33 +0100 (BST) From: Peter Sarre X-Sender: psa@ltsun0 Reply-To: Peter Sarre To: jkl@ccl.net Subject: 98.04.15 CHEMISTRY AND PHYSICS OF MOLECULES AND GRAINS IN SPACE Message-ID: MIME-Version: 1.0 Content-Transfer-Encoding: QUOTED-PRINTABLE Content-Type: TEXT/PLAIN; charset=US-ASCII Royal Society of Chemistry Faraday Discussion 109,=20 The University of Nottingham, UK, 15-17 April 1998 "CHEMISTRY AND PHYSICS OF MOLECULES AND GRAINS IN SPACE" The preliminary programme and other information are now available: * on the WWW at http://www.nottingham.ac.uk/faraday.html, or.... * by ftp from brian.chem.nottingham.ac.uk, log on as ftp, use your E-mail address as the password to get faraday.txt, or.... * by post; please write requesting the First Circular to: Ms S Riaz, The Royal Society of Chemistry, Burlington House, Piccadilly, London W1V 0BN This Faraday Discussion of the Royal Society of Chemistry is sponsored by the Astrophysical Chemistry Group which is affiliated to the Royal Astronomical Society. It is limited =20 Faraday Discussion no. 109 CHEMISTRY AND PHYSICS OF MOLECULES AND GRAINS IN SPACE Preliminary Programme INTRODUCTORY LECTURE: Frontiers of Astrochemistry D A Williams, University College London Chemical Processes in Astrophysical Radiation Fields A Dalgarno, Harvard-Smithsonian Center for Astrophysics, Cambridge, USA,=20 and P C Stancil, Oak Ridge National Laboratory, USA Chemical Models of Hot Molecular Cores T J Millar and J Hatchell, UMIST, UK Molecules in Harsh Environments J H Black, Onsala Space Observatory, Sweden Observational and Theoretical Constraints on the Chemistry of Pre-Stellar= =20 Nebulae R Plume, E A Bergin, P Myers and J Williams, Harvard-Smithsonian Center=20 for Astrophysics, Cambridge, USA =20 The Calculation of Molecular Opacities for Stellar Atmospheres D W Schwenke, NASA Ames Research Center, California, USA Inorganic Dust Formation in Astrophysical Environments H-P Gail, University of Heidelberg, Germany, and E Sedlmayr, TU Berlin,=20 Germany The Role of Molecules and Dust in Shells Around Carbon Stars B Gustafsson and K Eriksson, Uppsala Astronomical Observatory, and H=20 Olofsson, Stockholm Observatory, Sweden Neutral-neutral reactions at the temperatures of interstellar clouds:=20 rate coefficients for reactions of C2H and C atoms D Chastaing, P L James, I R Sims and I W M Smith, University of=20 Birmingham, UK Low Temperature Electron Attachment to Polycyclic Aromatic Hydrocarbons T Moustefaoui, C Rebrion-Rowe, J L Le Garrec, B R Rowe and J B A=20 Mitchell, Universit=E9 de Rennes, France Circumstellar Molecular Absorption Lines from the Ultraviolet to the Infrar= ed E J Bakker and D L Lambert, University of Texas, Austin, USA New Carbon Chains in the Laboratory and in Interstellar Space P Thaddeus, Harvard-Smithsonian Center for Astrophysics, Cambridge, USA Crossed Molecular Beam Investigations on the Formation of Carbon-bearing=20 Molecules in the ISM via Neutral-Neutral Reactions R I Kaiser, D Stranges, C Ochsenfeld, M Head-Gordon and Y T Lee,=20 University of California, Berkeley, USA What ISO tells us about Gas-Grain Chemistry E F van Dishoeck, Leiden Observatory, The Netherlands Some Striking New Spectral Evidence Supporting the H2 DIBs Theory P P Sorokin and J H Glownia, IBM Research Division, Yorktown Heights, USA Electronic Spectroscopy of Carbon Chains and Relevance to Astrophysics J P Maier, University of Basel, Switzerland=20 Excitation Processes for the Emission of UIR Bands O Guillois, G Ledoux, I Nenner, R Papoular and C Reynaud, SPAM CE Saclay,= =20 France Infrared Molecular Astronomy P F Bernath, University of Waterloo, Canada Apolar Ices P Ehrenfreund, Leiden Observatory, The Netherlands, A C A Boogert,=20 Kapteyn Astronomical Institute, The Netherlands, P A Gerakines,=20 Rensselaer Polytechnic, USA, and A G G M Tielens, NASA Ames Research=20 Center, USA Probing the Connection between PAH's and Carbonaceous Grains C Joblin, CESR, Toulouse, France From=20the Interstellar Medium to Planetary Atmospheres via Comets=20 T Owen, Institute for Astronomy, Hawaii, USA=20 Molecular Evolution in Planet-forming Circumstellar Disks Y Aikawa and S M Miyama, National Astronomical Observatory of Japan, T=20 Nakano, Nobeyama Radio Observatory, and T Umebayashi, Yamagata=20 University, Japan Evidence for Extraterrestrial Origin of PAHs in the Martian Meteorite=20 ALH84001 S J Clemett, X D F Chillier, J S Gillette and R N Zare, Stanford=20 University, USA Exploring Grains and Molecules on Earth Using Stable Isotope Techniques C T Pillinger, The Open University, UK Interstellar and Cometary Ices: Molecular Emission From Recent Comets' W M Irvine, C H DeVries, J E Dickens, A J Lovell, F P Schloerb and M=20 Senay, University of Massachusetts, Amherst, D Jewitt, Institute for=20 Astronomy, Hawaii, and H E Matthews, Joint Astronomy Centre, Hilo,=20 USA =20 Physics and Chemistry of Comets: Recent Results From Comets Hyakutake and= =20 Hale-Bopp J Crovisier, Observatoire de Paris-Meudon, France