From chemistry-request@www.ccl.net Fri Oct 16 04:15:59 1998 Received: from mercury.ukc.ac.uk (mercury.ukc.ac.uk [129.12.21.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA18581 Fri, 16 Oct 1998 04:15:59 -0400 (EDT) Received: from kiwi.ukc.ac.uk ([129.12.200.20] ident=root) by mercury.ukc.ac.uk with smtp (Exim 2.02 #1) id 0zU52m-0006Z0-00; Fri, 16 Oct 1998 09:15:28 +0100 Received: from localhost by kiwi.ukc.ac.uk (SMI-8.6/UKC-2.14) id JAA23440; Fri, 16 Oct 1998 09:15:26 +0100 Date: Fri, 16 Oct 1998 09:15:26 +0100 (BST) From: Manuel Melle Franco X-Sender: mm29@kiwi To: pascal boulet cc: ccl Subject: Re: CCL:Look for potential parameters for ZrO2 In-Reply-To: <01bdf759$b9e3b560$7134c281@PC-Pascal.unige.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear CCL'ers, > > > I am looking for references where I could find the parameters for ZrO2 for > the following potentials: > > 1- Buckingham > 2- Lennard-Jones > 3- Morse > 4- Harmonic > > Thank you very much for your help, > One of my friends was doing part of his Ph.D. simulating doped ZrO2 systems with Buckingham pots. He was working for Saiful Islam. If you cannot find the references E-mail and I will look for them. Cheers Manu From chemistry-request@www.ccl.net Fri Oct 16 10:17:43 1998 Received: from ganimedes.overnet.com.ar (ns1.overnet.com.ar [200.10.96.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23951 Fri, 16 Oct 1998 10:17:41 -0400 (EDT) Received: from carpincho.overnet.com.ar (carpincho.overnet.com.ar [200.10.96.19]) by ganimedes.overnet.com.ar (8.8.7/8.8.3) with ESMTP id LAA01073 for ; Fri, 16 Oct 1998 11:34:24 -0300 Received: from nppp157.overnet.com.ar (nppp157.overnet.com.ar [200.16.162.165]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id LAA08170 for ; Fri, 16 Oct 1998 11:33:55 -0300 Message-Id: <3.0.5.16.19981016110550.27cf35fe@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (16) Date: Fri, 16 Oct 1998 11:05:50 To: chemistry@www.ccl.net From: "Dr. Daniel Glossman" Subject: CCL:Recommendations for textbooks and teaching software Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" This is slightly off-topic for CCL, but I'm guessing there might be some people on the list who will be able to help. I'm in the position of having to teach an elementary undergraduate course on chemical bonding and structure of solids. It will be a short course (12 teaching hours) and the students will not have had any quantum mechanics or atomic structure beyond (high-)school level. I am having trouble finding a decent textbook at the right level (ie very introductory) and I'd appreciate any recommendations you may have. I also wish to make heavy use of computer-assisted learning so I'm also looking for recommendations of teaching software -- perhaps for visualization of atomic orbitals and bonding. The students will be Earth scientists, not chemists or physicists and I don't want to take too a rigorous approach. So though I may display the 3D solutions of the Schroedinger equation for the H atom I won't do the solution. I hope to rely on computer graphics to illustrate wavefunctions orbitals and hopefully bonding. I'd like to cover at least some of the following topics from a solid-state point of view using mineralogical examples. * the schroedinger equation and QM in 1 dimension - quantization. * The H atom. Atomic structure, orbitals, the aufbau principle and the periodic table. * Ionic bonding. Ionization energies, electronegativities. Ionic radii and mineral crystal structures. * covalent bonding, H2, sp2, sp3 bonding in molecules and solids using the LCAO approach. * Structural trends and polymorphism in the solid state. Silicate structures. * Substitutional defects. So if anyone knows of a textbook which covers this material at an introductory level and/or any educational software (Windows 95 or Linux) which could be used in support of such a course I'd like to hear from you. (I'd also welcome any comments from anyone who has taught a similar course on the amount of material given the 12 hours teaching time!) I'll summarize if requested. Thanks in advance. Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ --- Administrivia: This message is automatically appended by the mail exploder: 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 --- From chemistry-request@www.ccl.net Fri Oct 16 10:43:51 1998 Received: from listserv.oit.unc.edu (listserv.oit.unc.edu [152.2.25.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA25157 Fri, 16 Oct 1998 10:43:51 -0400 (EDT) Received: from root@login4.isis.unc.edu (port 1178 [152.2.25.134]) by listserv.oit.unc.edu with ESMTP id <222586-13605>; Fri, 16 Oct 1998 10:42:25 -0400 Received: by email.unc.edu id <61514-45982>; Fri, 16 Oct 1998 10:43:20 -0400 Date: Fri, 16 Oct 1998 10:43:18 -0400 (EDT) Sender: Ganesh Ethiraj From: Ganesh Ethiraj X-Sender: viggan@login4.isis.unc.edu To: "Dr. Daniel Glossman" cc: chemistry@www.ccl.net Subject: Re: CCL:Recommendations for textbooks and teaching software In-Reply-To: <3.0.5.16.19981016110550.27cf35fe@pop.overnet.com.ar> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Glossman: In my Grad school I was introduced to a book in solid state chemistry which I still try to recollect. The book is: Seven solid states: An introduction to the chemistry and Physics of solids----BY- Walter J.Moore. NY, W.A., Benjamin, 1967 . This book should be apt for the course and the background of the students. Ganesh On Fri, 16 Oct 1998, Dr. Daniel Glossman wrote: > > This is slightly off-topic for CCL, but I'm guessing there might be > some people on the list who will be able to help. > > I'm in the position of having to teach an elementary undergraduate > course on chemical bonding and structure of solids. It will be a > short course (12 teaching hours) and the students will not have had > any quantum mechanics or atomic structure beyond (high-)school level. > > I am having trouble finding a decent textbook at the right level (ie > very introductory) and I'd appreciate any recommendations you may > have. I also wish to make heavy use of computer-assisted learning so > I'm also looking for recommendations of teaching software -- perhaps > for visualization of atomic orbitals and bonding. > > The students will be Earth scientists, not chemists or physicists > and I don't want to take too a rigorous approach. So though I may > display the 3D solutions of the Schroedinger equation for the H atom > I won't do the solution. I hope to rely on computer graphics to > illustrate wavefunctions orbitals and hopefully bonding. > > I'd like to cover at least some of the following topics from a > solid-state point of view using mineralogical examples. > > * the schroedinger equation and QM in 1 dimension - quantization. > * The H atom. Atomic structure, orbitals, the aufbau principle > and the periodic table. > * Ionic bonding. Ionization energies, electronegativities. > Ionic radii and mineral crystal structures. > * covalent bonding, H2, sp2, sp3 bonding in molecules and solids > using the LCAO approach. > * Structural trends and polymorphism in the solid state. Silicate > structures. > * Substitutional defects. > > So if anyone knows of a textbook which covers this material at an > introductory level and/or any educational software (Windows 95 or > Linux) which could be used in support of such a course I'd like to > hear from you. (I'd also welcome any comments from anyone who has > taught a similar course on the amount of material given the 12 hours > teaching time!) > > I'll summarize if requested. > > Thanks in advance. > > Keith Refson > -- > ------------------------------------------------------------------------------ > Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | > earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | > Spam: root@cyberpromo.com | Parks Road, Oxford OX1 3PR, UK| > ------------------------------------------------------------------------------ > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: glossman@overnet.com.ar > 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 > > From chemistry-request@www.ccl.net Fri Oct 16 12:17:43 1998 Received: from mx2.cso.uiuc.edu (mx2.cso.uiuc.edu [128.174.5.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA29717 Fri, 16 Oct 1998 12:17:42 -0400 (EDT) Received: from london.ks.uiuc.edu (london.ks.uiuc.edu [128.174.214.2]) by mx2.cso.uiuc.edu (8.8.8/8.8.8) with ESMTP id LAA26189 for ; Fri, 16 Oct 1998 11:17:12 -0500 (CDT) Received: from istanbul.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2) id AA048804631; Fri, 16 Oct 1998 11:17:11 -0500 Received: from localhost (jim@localhost) by istanbul.ks.uiuc.edu (8.8.7/8.6.9) with SMTPid LAA02508 for ; Fri, 16 Oct 1998 11:17:16 -0500 X-Authentication-Warning: istanbul.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 16 Oct 1998 11:17:16 -0500 (CDT) From: Jim Phillips X-Sender: jim@istanbul To: chemistry@www.ccl.net Subject: Parallel MD Program NAMD 2.0b2 Available Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of the parallel molecular dynamics simulation program NAMD. NAMD2 is a major improvement over its predecessor, NAMD 1.5, in both computation speed and simulation features. This release is a binary-only beta version of NAMD2. It has already received extensive testing inside our group, but we still have some additional testing and code cleanup before releasing the source. Nevertheless, we believe it to be stable, and think you will find it a significant improvement over NAMD 1.5. NAMD2 binaries for Linux, HP-UX, Solaris, SGI Origin and the T3E are available at ftp://ftp.ks.uiuc.edu/pub/mdscope/namd2/bin/. For more information see http://www.ks.uiuc.edu/Research/namd/Namd2.html and direct questions or comments to namd@ks.uiuc.edu. ---------------------------------------------------------------------- NAMD 2.0 New Features - Supports periodic and non-periodic MD simulations. - Can use DPME for full electrostatics for periodic simulations, and DPMTA for non-periodic simulations. Cutoff simulations are also supported. - Triple timestepping. - Rigid bonds to hydrogen atoms. - Fixed atoms (Atoms which are constrained not to move do not have forces calculated for them). - Berendsen and Langevin piston constant pressure methods. - Steered Molecular Dynamics (SMD). ---------------------------------------------------------------------- Problems? For problems or questions, send email to namd@ks.uiuc.edu. If you think you have found a bug, please include what machine you are running on, and, if possible, a dump of the program output and/or a copy of your input files. As a beta release, we expect you will find a few rough edges in the program or documentation. Your feedback will help us to fix these. ---------------------------------------------------------------------- NAMD2 Known Deficiencies - NAMD2 will currently not run if the number of processors exceeds the number of patches in the system. This typically only results when you use a large number of processors and a large cutoff. - Do not use constant-pressure with multiple timestepping or rigid bonds. - DPME has not yet received extensive testing. - NAMD2 requires the X-PLOR package to produce the .psf and .par input files. If you don't have X-PLOR, you probably can't use NAMD2 yet. See http://xplor.csb.yale.edu/xplor-info/xplor-info.html for information. ---------------------------------------------------------------------- From chemistry-request@www.ccl.net Fri Oct 16 12:50:28 1998 Received: from hecky.acns.nwu.edu (hecky.acns.nwu.edu [129.105.16.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA00618 Fri, 16 Oct 1998 12:50:28 -0400 (EDT) Received: (from mailnull@localhost) by hecky.acns.nwu.edu (8.8.7/8.8.7) id LAA01291 for ; Fri, 16 Oct 1998 11:50:18 -0500 (CDT) Received: from beluga.cqe.nwu.edu(129.105.122.27) by hecky.acns.nwu.edu via smap (V2.0) id xma000987; Fri, 16 Oct 98 11:49:41 -0500 Message-Id: <3.0.1.32.19981016114854.008edb10@hecky.acns.nwu.edu> X-Sender: kfc828@hecky.acns.nwu.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Fri, 16 Oct 1998 11:48:54 -0500 To: chemistry@www.ccl.net From: Ken Czaplewski Subject: Summary Re Parameters for MMx Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, Several weeks back I inquired about Re(VI) parameters for forcefield calculations. The following is the summary of replies I received. " Two sources come to mind: 1) AK (Tony) Rappe's Universal ForceField (UFF) 2) Tom Halgren's Merck Molecular ForceField (MMFF) Of these two, MMFF is probably more accurate than UFF. There are others, of course, but they may not have rhenium parameters. Others which may have either explicit parameters or a function generator: 3) Allinger's MM3/MM4 4) Clark Landis' VALBOND (?) 5) Kevin Gilbert's MMX If you are using Hyperchem, then you might be able to use MMX or MM3/MM4 parameters (if they are available). UFF uses a Lennard-Jones 12-6, and MMFF uses a buffered LJ 14-7 potential. Hope this helps, Craig cburkhart@goodyear.com " What I have found in the meantime is that MSI's esff force field has 16 different Re parameters for different coordination and symmetry. This info can be found in the file esff.frc in the BioSymm forcefield library of their software. The package PCMODEL from Serena software is based on the MM2 forcefield. Two related articles are J Comput Chem 19:1167-1178,1998 which gives the parameters, and J Phys Chem B 1997, 101, 3174-3180 about the use of this software to model organmetalic compounds containing Re. Hope this is helpful to those who replied stating a similar interest in Re parameters. Ken From chemistry-request@www.ccl.net Fri Oct 16 18:22:11 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA27709 Fri, 16 Oct 1998 18:22:11 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id SAA08278 for chemistry@www.ccl.net; Fri, 16 Oct 1998 18:22:09 -0400 (EDT) Date: Fri, 16 Oct 1998 18:22:09 -0400 (EDT) From: "E. Lewars" Message-Id: <199810162222.SAA08278@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: EXPERIMENTAL DIHEDRALS? Friday 1998 Oct 16 From E. Lewars To CCL Hello, I need the *experimental* gas-phase dihedral angles for a set of small molecules A-X-Y-B, like say: Me-CH2-CH2-Me H-O-O-H, Me-O-O-H Me-O-O-Me F-CH2-CH2-H F-O-O-F Cl-CH2-CH2-Cl HO-CH2-CH2-OH Me-CH2-CH2-F Me-CH2 CH2-OH for example. I would appreciate it if any one could give me a reference to such experimental dihedral angles. Exp. bond lengths and angles are not hard to find, but there seems to be a dearth of dihedrals in the literature. Thanks E. Lewars =========================== From chemistry-request@www.ccl.net Fri Oct 16 21:57:34 1998 Received: from listserv.oit.unc.edu (listserv.oit.unc.edu [152.2.25.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA28561 Fri, 16 Oct 1998 21:57:34 -0400 (EDT) Received: from root@login3.isis.unc.edu (port 4886 [152.2.25.133]) by listserv.oit.unc.edu with ESMTP id <222538-13596>; Fri, 16 Oct 1998 21:56:08 -0400 Received: by email.unc.edu id <65634-98434>; Fri, 16 Oct 1998 21:57:10 -0400 Date: Fri, 16 Oct 1998 21:57:02 -0400 (EDT) Sender: Ganesh Ethiraj From: Ganesh Ethiraj X-Sender: viggan@login3.isis.unc.edu To: Inge Muszynski cc: chemistry@www.ccl.net Subject: Re: CCL:bioisosterism In-Reply-To: <199810131622.SAA23172@mx02.uni-tuebingen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi: I was talking to one of the Grad students( David Vanvilet) about your problem and immediately he pointed out a reference which might be useful for your problem. The Ref: Bioisosterism: A Rational Approach in Drug Design. GeorgeA.Patani and Edmond J.LaVoie. Chem Rev 1996, 96, 3147-3176. David's emails is: vanvlid@isis.unc.edu Ganesh On Tue, 13 Oct 1998, Inge Muszynski wrote: > > Dear CCl'lers, > > does anybody has an idea how the bioisosteric groups Ester and > 1,2,4-Oxadiazole could be aligned in biological targets. I am looking > forward to any references or crystallographic data. > > Inge Muszynski > University of Tuebingen > Auf der Morgenstelle 8 > > 72076 Tuebingen > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > >