From slee@ccl.net Thu Dec 9 10:54:31 1993 Received: from mail.uunet.ca for slee@ccl.net by www.ccl.net (8.6.4/930601.1506) id KAA23634; Thu, 9 Dec 1993 10:41:55 -0500 Received: from hyper by mail.uunet.ca with UUCP id <54389(6)>; Thu, 9 Dec 1993 10:41:37 -0500 Received: by hyper.hyper.com (920330.SGI/890607.SGI) (for ccl.net!chemistry) id AA26769; Thu, 9 Dec 93 10:40:05 -0500 From: slee@ccl.net (Thomas Slee) Message-Id: <9312091540.AA26769@hyper.hyper.com> Subject: Hypercube announces ChemPlus. To: chemistry@ccl.net Date: Thu, 9 Dec 1993 10:40:02 -0500 X-Mailer: ELM [version 2.3 PL9] aterloo, December 8, 1993 Hypercube is pleased to announce the release of ChemPlus, a set of extensions for HyperChem. ChemPlus requires HyperChem Release 3 for Windows, and has an introductory price of $395 US. ChemPlus brings many new capabilities to HyperChem users. Some of the major features include high-quality ball-and-stick images, 3D renderings of molecular orbitals, conformational searching, evaluation of Log P, of surface areas and of other indicators, automated building of sugars and crystals, amino acid sequence editing, and RMS overlay. ChemPlus is closely integrated with HyperChem: it adds the individual modules into the HyperChem menus for easy access and all programs use Dynamic Data Exchange for smooth communication with HyperChem. For more information, including a detailed description of ChemPlus's features, contact us on Internet at info@hyper.com. Hypercube, Inc. 419 Phillip Street, Waterloo, Ontario, N2L 3X2. Phone: (519) 725-4040 FAX: (519) 725-5193 From AZHARI@FRCU.EUN.EG Thu Dec 9 11:54:36 1993 Received: from FRCU.EUN.EG for AZHARI@FRCU.EUN.EG by www.ccl.net (8.6.4/930601.1506) id LAA24036; Thu, 9 Dec 1993 11:04:39 -0500 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01H6A9J1ETCG000Y12@FRCU.EUN.EG>; Thu, 9 Dec 1993 18:04:12 O Date: Thu, 09 Dec 1993 18:04:12 +0000 (O) Subject: on-line CADPAC manual To: chemistry@ccl.net Message-id: <01H6A9J1H85U000Y12@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters: Would you please if someone have an online manual for CADPAC VERSION 5.0 to send it to me by e-mail. Thanks a lot. Adel From mercie@med.cornell.edu Thu Dec 9 13:42:41 1993 Received: from cumc.cornell.edu for mercie@med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id NAA25649; Thu, 9 Dec 1993 13:27:47 -0500 Received: from localhost (mercie@localhost) by cumc.cornell.edu (8.6.4/ECH1.13) id NAA07478; Thu, 9 Dec 1993 13:26:09 -0500 Date: Thu, 9 Dec 1993 13:26:08 -0500 (EST) From: Gustavo Mercier Subject: ADF/DFT and 1st row d-d transitions To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Netters! May be somebody could shed some light in a simple test of DFT and transition metal complexes with rather poor results. I am puzzled by the results obtained using ADF v. 1.0.2 (Aug. 1993): I am attempting to reproduce calculations on the spectroscopy of M(H2O)6 (+n), where M is a first row transition metal, and n varies >from 2 to 3. The geometry is Th (although, the highest compatible symmetry available in ADF is D2h). This leaves the M-O, O-H, and M-O-H as the only internal coordinates necessary to specify the whole system. Th symmetry is forced through proper construction of the Z-mat. The density is symmetry constrained up to D2h symmetry.The excited states are computed at the optimized ground state geometry. I am using the II basis set (double zeta Slater functions with triple zeta for 3d orbitals in the metal), and the default xc functional (implementaion of VWN parameterization of CA MC simulations of an electron gas). All computations are unrestricted, including those with singlet states for the purpose of proper comparison with the excited states. The frozen core approximation is used with the core of the Metal corresponding to [Ne], so the 3s,3p electrons are also part of the valence shell. To speeds things: integration = 2.5 (lowest adequate accuracy for integrals), scfconvergence 0.001, gconv = 0.01 with M-O and H2O geometries as initial input corresponding to standard H2O geometry and M-O 1.95 - 2.15 Angstroms. This is what I get: M Configuration (&) State Energy (x 1000 cm-1) ---------------------------------------------------------------------------- Cr+3 d3 t2g(3) 4A1.g 0 t2g(2) eg 4Tx.g(?) 16.9 (17.4, 17.6)* Mn+2 d5 t2g(3) eg(2) 6A1.g 0 d5 t2g(4) eg 4Tx.g(?) 12.1 (18.9) Fe+3 d5 t2g(3) eg(2) 6A1.g 0 t2g(4) eg 4Tx.g(?) 9.7 (12.6) Co+3 d6 t2g(6) 1A1.g 0 t2g(5) eg 1Tx.g(?) 9.7 (16.6, 18.9) (&) In Th symmetry the nomenclature Eg/u Tg/u is retained, but in D2h symmetry is reduced and Eg -> A1.g, with T2g -> B1.g + B2.g + B3.g. The ground state orbital energies do show BX.g to have proper degeneracies. Similarly, the two HOMO's in A1.g symmetry are degenerate. (?) x=1 or 2 the exact definition of the state is unclear to me. See below for the orbital occupation numbers. (*) values in parenthesis are from Anderson et.al. Inorg. Chem. 1986, 25, 2728-2732. These are experimental results that a new version of INDO/S is able to reproduce. I am surprised that not even a qualitative trend is reproduced. Extensions to include Stoll's correction or increase the basis set to add polarization functions in the light atoms (Basis Set III) do not appear to improve the situation. Could you comment on these results? Are DFT methods inadequate to address spectroscopy questions such as the levels of d-d transitions? Do any HF based methods be adequate (e.g. HF/MP2, MCSCF etc)? We are doing this work as a test of the reliability of computations we intend to do on the spin density of metalloporphyrins and some Lanthanide complexes that have not been parameterized within the INDO/S formalism. Below I have reproduced the occupation numbers used in my calculations as specified in ADF. spin 1 // spin 2 Cr A1.G 7 // 7 A1.G 8 // 7 B1.G 3 // 2 B1.G 3 // 2 B2.G 3 // 2 B2.G 2 // 2 B3.G 3 // 2 B3.G 3 // 2 A1.U 0 // 0 A1.U 0 // 0 B1.U 5 // 5 B1.U 5 // 5 B2.U 5 // 5 B2.U 5 // 5 B3.U 5 // 5 B3.U 5 // 5 Mn A1.G 9 // 7 A1.G 8 // 7 B1.G 3 // 2 B1.G 3 // 2 B2.G 3 // 2 B2.G 3 // 3 B3.G 3 // 2 B3.G 3 // 2 A1.U 0 // 0 A1.U 0 // 0 B1.U 5 // 5 B1.U 5 // 5 B2.U 5 // 5 B2.U 5 // 5 B3.U 5 // 5 B3.U 5 // 5 Fe A1.G 9 // 7 A1.G 8 // 7 B1.G 3 // 2 B1.G 3 // 2 B2.G 3 // 2 B2.G 3 // 3 B3.G 3 // 2 B3.G 3 // 2 A1.U 0 // 0 A1.U 0 // 0 B1.U 5 // 5 B1.U 5 // 5 B2.U 5 // 5 B2.U 5 // 5 B3.U 5 // 5 B3.U 5 // 5 Co A1.G 7 // 7 A1.G 8 // 7 B1.G 3 // 3 B1.G 3 // 3 B2.G 3 // 3 B2.G 2 // 3 B3.G 3 // 3 B3.G 3 // 3 A1.U 0 // 0 A1.U 0 // 0 B1.U 5 // 5 B1.U 5 // 5 B2.U 5 // 5 B2.U 5 // 5 B3.U 5 // 5 B3.U 5 // 5 Gus Mercier mercie@cumc.cornell.edu From PEARLMAN@VAX.PHR.UTEXAS.EDU Thu Dec 9 14:54:26 1993 Received: from VAX.PHR.UTEXAS.EDU for PEARLMAN@VAX.PHR.UTEXAS.EDU by www.ccl.net (8.6.4/930601.1506) id OAA26430; Thu, 9 Dec 1993 14:33:46 -0500 Date: Thu, 9 Dec 1993 13:34:13 -0600 (CST) From: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <931209133413.508@VAX.PHR.UTEXAS.EDU> Subject: how-to book on writing code for parallel platforms To: CHEMISTRY@ccl.net X-Vmsmail-To: SMTP%"CHEMISTRY@ccl.net" In response to a recent inquiry: A *very* good book discussing coding for parallel platforms is: B. Bauer, "Practical Parallel Programming," Academic Press, 1992. It includes clear discussions of both introductory and advanced concepts. It provides numerous examples of both FORTRAN and C code (not pseudo-code but actual code which the user could compile and execute). The book will be useful regardless of hardware platform but will be particularly useful to programmers working on Silicon Graphics hardware. --- Bob Pearlman From ross@cgl.ucsf.EDU Thu Dec 9 15:01:47 1993 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.4/930601.1506) id OAA26998; Thu, 9 Dec 1993 14:53:31 -0500 Received: from localhost by socrates.ucsf.EDU (8.6.4/GSC4.24) id LAA03495; Thu, 9 Dec 1993 11:53:29 -0800 Date: Thu, 9 Dec 1993 11:53:29 -0800 Message-Id: <199312091953.LAA03495@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: Re: van der Waals parameters Date: Thu, 09 Dec 1993 08:12:32 -0500 From: nauss@ucmodl.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: van der Waals parameters To: ross@cgl.ucsf.EDU (Bill Ross ) Message-id: <9312091312.AA19486@ucmodl.che.uc.edu> Content-transfer-encoding: 7BIT Bill - I disagree with your explanation of R and sigma. Acoording to Moore in his book "Physical Chemistry" (4th edition) page 128, sigma for the Lennard- Jones potential is the value of r (distance) where the potential energy equals zero, i.e. where the curve crosses the x-axis other than where r approaches infinity. On the other hand, according to Hill in "Introduction to Statistical Thermodynamics", Appendix IV, pg 484, r* is the distance at the potential minimum. Thus r* = sigma * 2^(1/6). Jeff Nauss ************************************************************************ * Dr. Jeffrey L. Nauss * Telephone: 513-556-0148 * * Department of Chemistry * Fax: 513-556-9239 * * University of Cincinnati * e-mail: nauss@ucmodl.che.uc.edu * * Cincinnati, OH 45221-0172 * * ************************************************************************ Since the combining rule for sigma is the same as it would be for 2 * R*, and the sigmas in Allen & Tildesly p 21 look like 2 * R*'s, I apparently made a wrong assumption. Thanks to Jeff Nauss for the correction. Bill Ross