From chemistry-request@server.ccl.net Wed May 9 03:22:23 2001 Received: from igc.phys.chem.ethz.ch ([129.132.102.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f497MNI02475 for ; Wed, 9 May 2001 03:22:23 -0400 Received: (from portmann@localhost) by igc.phys.chem.ethz.ch (8.11.1/8.11.1) id f497PMk20198 for chemistry@ccl.net; Wed, 9 May 2001 09:25:22 +0200 (MET DST) Date: Wed, 9 May 2001 09:25:22 +0200 (MET DST) From: chem-support@cscs.ch Message-Id: <200105090725.f497PMk20198@igc.phys.chem.ethz.ch> X-Authentication-Warning: igc.ethz.ch: portmann set sender to chem-support@cscs.ch using -r To: chemistry@ccl.net Subject: MOLEKEL: New Release Dear Computational Chemists CSCS (http://www.cscs.ch) is proud to announce the release of MOLEKEL version 4.1. Improvements compared to version 4.0beta are: - bugs fixed as far as reported to date - display of dipole moment as an arrow implemented - image export significantly improved: - inlimited image size (larger than screen) - image size can be set explicitly - automatic export of a series of images of a frequency animation or a series of structures to produce a movie or GIF animation with an external program - JPEG file format added MOLEKEL is an interactive molecular graphics program to visualize molecular and electronic structure data from a number of electronic structure program outputs (Gaussian, Gamess, ADF...) as well as from XYZ and PDB files. MOLEKEL is able to render the molecular structure in different styles, display orbitals, electron densities, map and color code properties on any surface, display and animate vibrational normal modes, animate a sequence of coordinates and produces great graphics... Look and see! More information, a precompiled binary for SGI, SUN, LINUX systems and WINDOWS PC's and detailed documentation is available from http://www.cscs.ch/molekel/. Best regards Stefan Portmann From chemistry-request@server.ccl.net Wed May 9 13:55:37 2001 Received: from judy.ic.ac.uk ([155.198.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f49HtaI17609 for ; Wed, 9 May 2001 13:55:36 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 14xYBO-0007Oj-00 for chemistry@ccl.net; Wed, 9 May 2001 18:55:30 +0100 Received: from icex9.cc.ic.ac.uk ([155.198.3.9]) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 14xYAz-0003vn-00 for chemistry@ccl.net; Wed, 9 May 2001 18:55:05 +0100 Received: from [155.198.234.86] (rzepa.ch.ic.ac.uk [155.198.234.86]) by icex9.cc.ic.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id KTFKRHGZ; Wed, 9 May 2001 17:44:37 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: Date: Wed, 9 May 2001 17:43:44 +0100 To: chemistry@ccl.net From: "Rzepa, Henry" Subject: shorter bond = Weaker/More reactive bond? Content-Type: text/plain; charset="us-ascii" I came across a claim last week that in a square planar Pd complex for which a structure had been determined, the shorter of two Pd-ligand bonds was also the more labile. Shorter of course cannot be formally equated with "more reactive", but in general we tend to assume that if a bond is to break, the "least motion" path is normally favoured. There are of course many examples of non-least-motion reactions, but does anyone know of any (other) clear cut cases of bonds where the shorter bond is the more reactive? -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0870) 132-3747 (eFax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Wed May 9 12:17:30 2001 Received: from web14002.mail.yahoo.com ([216.136.175.93]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f49GHUI16575 for ; Wed, 9 May 2001 12:17:30 -0400 Message-ID: <20010509161729.94417.qmail@web14002.mail.yahoo.com> Received: from [164.58.10.122] by web14002.mail.yahoo.com; Wed, 09 May 2001 09:17:29 PDT Date: Wed, 9 May 2001 09:17:29 -0700 (PDT) From: Adam Hixson Reply-To: chixson@chemdept.chem.ou.edu Subject: Silly question about entropy and MD. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii It would seem to my still immature scientific mind that calculating entropy differences in molecular dynamics simulations (while at the same time doing a free-energy perturbation calculation) ought to be fairly straight-foward. If I analytically do the required derivative (derv. of the free energy with respect to the temperature - I represent the free energy in terms of the natural log of the ratio of the partition functions of the initial and final states) I need two ensemble averages. One of these was calculated in the free-energy perturbation, the other is , where Delta H is the energy difference between the two states. Instead, AMBER, and apparently other packages, use a method where by they numerically calculate this derivative. See, for example, S. H. Fleischman and C. L. Brooks III J. Chem. Phys. "Thermodynamics of aqueous solvation: solution properties of alcohols and alkanes" 87.5 3029-3037 (1987). My question is simple. Either, what is the advantage in Fleischman and Brooks' method, or what is the disadvantage in doing what I consider the straight- foward method? Thanks. ===== ---- Adam Hixson Department of Chemistry and Biochemistry The University of Oklahoma chixson@chemdept.chem.ou.edu 620 Parrington Oval hixsonc@yahoo.com Norman, OK 73069 __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Wed May 9 14:46:15 2001 Received: from garnet.INS.cwru.edu (root@[129.22.8.233]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f49IkFI18340 for ; Wed, 9 May 2001 14:46:15 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by garnet.INS.cwru.edu with SMTP (8.11.2+cwru/CWRU-3.8) id f49IkE600768; Wed, 9 May 2001 14:46:14 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <00a301c0d8b8$ef22ef00$d9811681@cwru.edu> Reply-To: "Hui-Hsu \(Gavin\) Tsai" From: "Hui-Hsu \(Gavin\) Tsai" To: Subject: quality of basis set Date: Wed, 9 May 2001 14:50:36 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A0_01C0D897.67F8E500" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_00A0_01C0D897.67F8E500 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers: I posted a question about the basis set of second and third row = transition meta=20 (mainly focused on Zr and Ce) three weeks ago.=20 I received several responses. Most of them point to the site "http://www.emsl.pnl.gov:2080/forms/basisform.html" and the book "Gaussian Basis Sets for Molecular Calculations". I thank Dr. Arnold, Dr.Straka, Dr. Huniar, Dr. Schreckenbach, Dr. = Peralta for their responses and kindness. From the EMSL Basis Set Library, there are several basis sets = available for Zr: =20 WTBS Hay-Wadt MB (n+1) ECP Hay-Wadt VDZ (n+1) ECP LANL2DZ ECP SBKJC VDZ ECP CRENBL ECP CRENBS ECP Stuttgart RSC ECP DZVP (DFT Orbital) DeMon Coulomb Fitting DGauss A1 DFT Coulomb Fitting DGauss A1 DFT Exchange Fitting Ahlrichs Coulomb Fitting Can anyone share his/her experienence with me as how best to evaluate = the quality of those basis sets? And which one is theoretically equivalent with 6-31G** basis set=20 becasue I use 6-31G** basis set for the non-metal parts.=20 Any comment is welcome and appreciated. Gavin =20 ------=_NextPart_000_00A0_01C0D897.67F8E500 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CCLers:
 
   I posted a question about = the basis=20 set of second and third row transition meta
(mainly focused on Zr = and Ce)=20 three weeks ago.
 
   I received several = responses. Most of=20 them point to the site
"http://www.ems= l.pnl.gov:2080/forms/basisform.html"
and=20 the book "Gaussian Basis Sets for Molecular Calculations".
I thank = Dr.=20 Arnold, Dr.Straka, Dr. Huniar, Dr. Schreckenbach, Dr. Peralta
for = their=20 responses and kindness.
 
  From the EMSL Basis Set Library, = there are=20 several basis sets available for Zr:  =
 WTBS
 Hay-Wadt MB=20 (n+1) ECP
 Hay-Wadt VDZ (n+1) ECP
 LANL2DZ = ECP
 SBKJC=20 VDZ ECP
 CRENBL ECP
 CRENBS ECP
 Stuttgart RSC=20 ECP
 DZVP (DFT Orbital)
 DeMon Coulomb = Fitting
 DGauss=20 A1 DFT Coulomb Fitting
 DGauss A1 DFT Exchange = Fitting
 Ahlrichs=20 Coulomb Fitting
 
  Can anyone share his/her = experienence with=20 me as how best to evaluate the quality of those basis sets?
And which = one is=20 theoretically equivalent with 6-31G** basis set
becasue I use = 6-31G** basis=20 set for the non-metal parts.
 
  Any comment is welcome and=20 appreciated.
 
Gavin
  =
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