From makula #at# bisance.citi2.fr Wed Sep 28 05:10:47 1994 Received: from FRMOP11.CNUSC.FR for makula _-at-_)bisance.citi2.fr by www.ccl.net (8.6.9/930601.1506) id EAA27060; Wed, 28 Sep 1994 04:22:13 -0400 Received: from galaad.citi2.fr by FRMOP11.CNUSC.FR (IBM VM SMTP V2R2) with TCP; Wed, 28 Sep 94 09:21:15 EST Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA01699; Wed, 28 Sep 1994 09:12:57 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA05377; Wed, 28 Sep 1994 09:21:57 --100 From: makula # - at - # bisance.citi2.fr (makula-bisance) Message-Id: <9409280821.AA05377-: at :-bisance.citi2.fr> Subject: Sparkles in Mopac : summary To: chemistry %-% at %-% ccl.net Date: Wed, 28 Sep 1994 09:21:56 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 7381 Dear Netters, here is a summary of the messages I received after my original posting about the use of sparkles in Mopac. --------------------------------------------------- Original posting : Dear Netters, I would like to calculate with MOPAC the geometry of an organic anion. I am not sure that the calculation of an ion alone in the gas-phase would be very realistic (mainly because of intramolecular electrostatic repulsion), so I tried to use the so-called "sparkles" which are defined in the MOPAC manual as "pure ionic charges" or more precisely as an "integer charge at the center of a repulsion sphere of form exp(-alpha*r)". The manual explains further that the sparkles can be used as counterions. Unfortunately, my MOPAC calculation with a positive sparkle "+" ended up with the positive charge almost superimposed on the atom of my anion bearing most of the negative charge. Have I missed something in the keyword specification ? does anybody have experienced this MOPAC feature with some success ? (some refs would be welcome ). --------------------------------------------------- I managed to fix my problem when I realized that I was starting the geometry optmization with a too short distance between the sparkle and the anion. This caused the sparkle to nearly overlap the molecule in the end. Starting with a distance longer than the supposed radius of the sparkle allowed convergence to a geometry where the sparkle stays at a reasonable distance from the anion. Thanks to all who replied to me. Remi Le Goas Computer Aided Molecular Design Rhone-Poulenc Agrochimie LYON - France e-mail: remi.le-goas -8 at 8- rp.fr *************************************************** from jstewart:~at~:fujitsuI.fujitsu.com : Please check that your copy of MOPAC has the following bug-fixes: 17 June 1993 ++++ In MOLDAT, after CALL CALPAR add DO 91 I=1,107 91 IF(AM(I).LT.1.D-4)AM(I)=1.D0 Reason: Sparkles were not being handled correctly 8 January 1994 ++++ In block.f, after DATA VS(104) /10.0D0/ insert DATA ALPAM1(104) / 1.5D0/ Reason: The AM1 sparkle `+' was not correctly specified. James J. P. Stewart ****************************************************************** Dear Dr. Le Goas, Sparkles are not really quantum mechanical objects, but are simply acting as "polarizers". They have no electrons and is the geometry is optimized with one being used, it will simply move toward the negative charge as you noted. If you want to try computing the geometry of an organic anion as if it were in solution, I would use one of the semi- empirical continuum models. In modern versions of MOPAC I think that this is COSMO. In our AMPAC proogram, it is AMSOL. I will be happy to send you info on that program if you would like. This is not perfect, but should be better that a "bare" anion. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry ** Internet Addr: aholder ^%at%^ vax1.umkc.edu Univ. of Missouri - Kansas City ** Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 ** FAX Number: (816) 235-5502 Kansas City, Missouri 64110 ** =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= *********************************************************************** Dear Dr Goas, It seems that the program worked correctly. Most probably you have asked the program to optimize the distance between the sparkle and the anion (or the atom concerned). Try to fix the distance (to see the effect of the potential created by the sparkle (or sparkles). But, as it is written in the Mopac Manual, you have to be very careful when using them. You could alternatively use COSMO within MOPAC if you do not wish to handle isolated anion species. I had problems getting rezonable results using sparkles when I tried to mimic iron atom within ferrocenophanes (J.Phys. Org. Chem. 1989,2,602-610) and then decided to develop my own molecular mechanics force field for this species (J.Phys.Org. Chem. 1992,5,382-394). You could also ask for help to MOPAC Forum that was opened for a while at no cost. Then you should get help from Dr Stewart directly. Wishes, Jerzy Rudzinski Dr Jerzy M Rudzinski Fujitsu Kyushu System Fukuoka, Japan jerzy[ AT ]fqs.fujitsu.co.jp ********************************************************************* Remi, Here is a sparkles job that i've run. It is not an acid counter ion but coordinates to the carbonyl of acrylic acid. The results of the four isomers of acrylic acid coordinated with the potassium sparkle mimic the corresponding results of ab initio calculations coordinated with Li+. This case should give you an idea of the use of the sparkle and can help you to determine if there are problems with your code. rick rjl /at\lilly.com internet address AM1 GNORM=0.001 SCFCRT=1.D-16 T=9999M HESS=1 EF CHARGE=1 acrylic acid cis,syn conformation coordinated with K+ FINAL HEAT OF FORMATION = -62.04709 KCAL C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.0565 C 1.329716 1 0.000000 0 0.000000 0 1 0 0 -0.2014 H 1.087972 1 123.151621 1 0.000000 0 1 2 0 0.0986 H 1.086237 1 122.310316 1 180.000000 0 1 2 3 0.0746 C 1.482676 1 121.909848 1 0.000000 0 2 1 3 0.2569 H 1.097405 1 120.693802 1 180.000000 0 2 1 3 0.1048 O 1.228531 1 125.734878 1 0.000000 0 5 2 1 -0.3987 O 1.396593 1 117.806960 1 180.000000 0 5 2 1 -0.0089 H 0.989783 1 120.953680 1 180.000000 0 8 5 2 0.0557 K 2.989783 1 120.953680 1 180.000000 0 7 5 8 0.0557 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 ********************************************************************* Dear Dr. Remi, Please take a look at our paper entitled: "Sparkle Model for the Quantum Chemical Calculation of Lanthanide Complexes" Chem. Phys. Lett. 227 (1994) 349-353. There you will find a description of how to optimize the sparkle parameters. It may be of help to you. I guess that you may have to reparametrize them to suit your needs. Sincerely, ************************************************************************ * * * Alfredo Mayall Simas e-mail: AMS #at# npd1.ufpe.br * * Departamento de Quimica Fundamental Fax: (081) 271-8442 * * Universidade Federal de Pernambuco Office: (081) 271-8440 x 37 * * 50.739-000 Recife, PE CCEN: (081) 271-8400 * * Brasil * * * ************************************************************************