From qibvigap@lgdx02.lg.ehu.es Wed Jul 3 02:58:02 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lgdx02.lg.ehu.es by www.ccl.net (8.7.5/950822.1) id CAA03339; Wed, 3 Jul 1996 02:50:18 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA17141; Wed, 3 Jul 96 08:49:40 +0100 Received: from lcmx94.lc.ehu.es by lgdx02.lg.ehu.es (5.65/4.7) id AA24172; Wed, 3 Jul 1996 08:54:47 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 3 Jul 1996 08:51:02 +0000 To: chemistry@www.ccl.net From: qibvigap@lgdx02.lg.ehu.es (Pablo Vitoria) Subject: VALRAY program. Info requested. Hi everybody, When I was searching the literature, looking for applications to crystal charge densities of Bader's 'atoms in molecule' theory and topological description of bonding and structure, I came across the following reference: Destro, R., Bianchi, R., Gatti, C. and Merati, F., Chem. Phys. Lett., 1991, 186(1), 47 -52. In this study the experimental (as determined by X-ray diffraction) charge density and its Laplacian are evaluated for alanine, and their critical points located. The authors say that the calculations have been performed with a version of the VALRAy set of programs by R. F. Stewart and M. A. Spackman (at the Carnegie-Mellon University, Pittsburgh). Does anybody have some more information about this program? I'd like to know if it's available, and in that case, for which computers. And also if it calculates the critical points by itself. I'd like to get in touch with Prof. Stewart, but I don't have his address. Thank you very much for your information Best regards Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 ---------------------------------------------------------------------------- ---- From kessi@psizi1.psi.ch Wed Jul 3 04:58:02 1996 Received: from psizi1.psi.ch for kessi@psizi1.psi.ch by www.ccl.net (8.7.5/950822.1) id EAA03770; Wed, 3 Jul 1996 04:18:20 -0400 (EDT) Received: by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA18150; Wed, 3 Jul 1996 10:19:48 +0200 Date: Wed, 3 Jul 1996 10:19:48 +0200 From: kessi@psizi1.psi.ch (Alain Kessi) Message-Id: <9607030819.AA18150@psizi1.psi.ch> To: chemistry@www.ccl.net (Chemistry List) Subject: VALRAY and R F Stewart's address X-Mailer: [XMailTool v3.1.2b] Hi, a search on www.cmu.edu gave Robert F Stewart aeklund+@andrew.cmu.edu Chemistry as the address for the author of VALRAY. The two other authors of the VALRAY manual 1995, M A Spackman and C Flensburg, are unknown to the CMU finger server. Hope this helps, Alain -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zuerich, CH ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From mw@crystal.uwa.edu.au Wed Jul 3 05:58:02 1996 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.7.5/950822.1) id FAA04279; Wed, 3 Jul 1996 05:34:54 -0400 (EDT) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.6.11/8.6.9) with SMTP id RAA06453 for ; Wed, 3 Jul 1996 17:34:47 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA22127; Wed, 3 Jul 1996 19:27:13 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9607030930.AA26356@pack.crystal.uwa.edu.au> Subject: Van der Waals radii? To: CHEMISTRY@www.ccl.net Date: Wed, 3 Jul 96 17:30:06 WST Mailer: Elm [revision: 70.85] Dear All, I would like to ask if anyone knows the most recent reference which contains the expereimental values of Van der Waals radii of; H, O, Cl, F, N, Br, S, As, I, Se, & P ,elements. Thank you very much for your help. Magda Wajrak (email: mw@crystal.uwa.edu.au) From Steve.Bowlus@gwa.sandoz.com Wed Jul 3 11:58:06 1996 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@gwa.sandoz.com by www.ccl.net (8.7.5/950822.1) id LAA05818; Wed, 3 Jul 1996 11:05:26 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id AA19521; Wed, 3 Jul 1996 17:05:25 +0200 X400-Originator: Steve.Bowlus@gwa.sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-Mts-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700001957191000002] X400-Content-Type: P2-1988 (22) Message-Id: <0034700001957191000002*@MHS> To: Subject: Mopac93: Structure of excited states Date: Wed, 3 Jul 1996 17:07:39 +0200 I am interested in the relative energies and structures of the first excited states (triplet and singlet) of a series of compounds. I have obtained the energies relative to the ground state using the keywords: MECI C.I.=2. I now want to refine the structures of these states, but after 10 cpu-hr on an Indigo2, the gradients are still very large (> 20) and appear to be oscillating. I started the calculation with the optimized ground state structure, and used the keywords: AM1 EF MECI C.I.=2 ROOT=2 (for the triplet, ROOT=3 for the singlet). I have also done the calculation adding SHIFT=15, in an attempt to damp the oscillation. This is my first attempt at working with excited state structures. . .is this typical behavior, and I just need to be patient (sigh!), or have I missed something? If there is interest, I will summarize useful replies, for which I thank the authors in advance. =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From nteich@dasgroup.com Wed Jul 3 14:58:05 1996 Received: from pop.third-wave.com for nteich@dasgroup.com by www.ccl.net (8.7.5/950822.1) id OAA07487; Wed, 3 Jul 1996 14:37:03 -0400 (EDT) Received: from dirac ([206.31.47.72]) by pop.third-wave.com (Netscape Mail Server v1.1) with SMTP id AAA6681 for ; Wed, 3 Jul 1996 14:34:39 -0400 X-Sender: nteich@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: nteich@dasgroup.com (Nancy Teich) Subject: Mopac93 and ground state with neg. frequency? Date: Wed, 3 Jul 1996 14:34:39 -0400 Message-ID: <19960703183438.AAA6681@dirac> We recently ran Mopac93 using the following keywords: PM3 NODIIS GEO-OK GNORM=0.01 PRECISE LET DDMIN=0.0 FORCE THERMO(273,1273). The output tells me that the system is at ground state and yet the first root is negative. Can anyone elighten me... Also, is there an arbitrary cut-off such that vibrations with frequencies below a specific value are not printed out? Thanks in advance. nteich@dasgroup.com NORMAL COORDINATE ANALYSIS Root No. 1 2 3 4 5 6 7 8 1 A" 2 A" 3 A" 1 A' 2 A' 4 A" 5 A" 3 A' -19.3 22.3 46.6 47.0 84.2 85.4 90.7 102.6 DESCRIPTION OF VIBRATIONS (this was the first vibration printed) VIBRATION 5 2A' ATOM PAIR ENERGY CONTRIBUTION RADIAL FREQ. 84.25 O13 -- O14 11.7% (305.6%) .0% T-DIPOLE .1555 C 7 -- N12 11.5% .0% TRAVEL .2133 N12 -- O13 8.9% .6% RED. MASS 1.4084 N12 -- O14 8.0% .7% SYSTEM IS A GROUND STATE -- Nancy Teich | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: nteich@dasgroup.com Johnstown, PA 15904-5428 | From cliang@amati.curagen.com Wed Jul 3 17:58:07 1996 Received: from guarneri.curagen.com for cliang@amati.curagen.com by www.ccl.net (8.7.5/950822.1) id RAA08344; Wed, 3 Jul 1996 17:47:36 -0400 (EDT) Received: from amati.curagen.com by guarneri.curagen.com via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA11140; Wed, 3 Jul 96 17:47:06 -0400 Received: by amati.curagen.com (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA25545; Wed, 3 Jul 1996 17:47:03 -0400 From: "Charlene Liang" Message-Id: <9607031746.ZM25543@amati.curagen.com> Date: Wed, 3 Jul 1996 17:46:57 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: mjrothberg@laticrete.com Subject: Help! Cc: amilosav@guarneri.curagen.com, chemistry@www.ccl.net, ewhaylan@guarneri.curagen.com, fottens@guarneri.curagen.com, jrothberg@guarneri.curagen.com, cliang@guarneri.curagen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Michael, This is Charlene Liang from CuraGen Corp. We need your help on getting a good price on an Oracle product. We need this product badly! Please, please help us as soon as you can. Here is the product information: Vendor: Oracle Corporation Product name: Oracle Designer 2000 for NT system Price: $3995.00 1 year of silver technical support and service Price: $1800.00 Telephone: 415-506-7000 ( California ) fax: 415-506-7133 Please let me or Frank know if you need more information. Thanks a lot! Charlene -- Charlene Liang | (203) 481-1104 ext. 287 CuraGen Corporation | 322 E. Main St. | Branford, CT 06405 | cliang@curagen.com | (FAX) (203) 481-1102 From Steve.Bowlus@gwa.sandoz.com Wed Jul 3 20:58:09 1996 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@gwa.sandoz.com by www.ccl.net (8.7.5/950822.1) id UAA09019; Wed, 3 Jul 1996 20:00:06 -0400 (EDT) From: Received: by gatekeeper.sandoz.att.nl; id AA20318; Thu, 4 Jul 1996 01:59:56 +0200 X400-Originator: Steve.Bowlus@gwa.sandoz.com X400-Recipients: non-disclosure:; X400-Mts-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700001960140000002] X400-Content-Type: P2-1988 (22) Message-Id: <0034700001960140000002*@MHS> To: Cc: Subject: Mopac: Negative frequencies Date: Thu, 4 Jul 1996 02:02:09 +0200 Sorry to put this up to the list, but our server doesn't seem to know about DASgroup. . .Earlier today, nteich@dasgroup.com wrote, querying the meaning of the small, negative frequencies reported in the force calculation of a ground state. My $0.02: There seems to be some question or perhaps even controversy over the meaning of the negative frequencies (actually, imaginary roots) in Mopac calculations. In the case where one is calculating a _transition state_, one expects to get exactly one imaginary root. What one frequently observes, however, is one root which is large and negative (say -450) and one (or more!) imaginary roots which are small, along the order of the root you report. The large, negative root is "real", i.e. corresponds to the reaction coordinate; the small ones seem to be spurious. While some investigators interpret them as "higher order" saddle points (whatever these may be), Hehre has attributed them to mixing in of roto- vibrational states (or some such bumpf -- you can tell I'm not a theoretician), which can be safely ignored. I expect that you are running into the same phenomenon, but for a mimimum at which exactly zero imaginary roots should be observed. As a practical matter, you can ignore them, or you can try to get rid of them. To get rid of them, a reasonably sure, but painful way, is to follow Stewart's recipe for "escaping >from a hilltop" in the Mopac documentation. Alternatively, you can do the computational equivalent of "purification by resubmission": simply rerefine the structure, starting with the coordinates from the .arc file, or (perhaps better) >from something like a Sybyl .mol2 file. _Don't_ use the restart file of the previous calculation. . .the rounding and truncation errors introduced in the other results files is frequently a sufficient perturbation of the structure to get rid of the nuisance frequency. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ===========================================================================