From lars@lmspc3.ibs.fr Fri Mar 28 04:32:18 1997 Received: from ibs.ibs.fr for lars@lmspc3.ibs.fr by www.ccl.net (8.8.3/950822.1) id DAA26833; Fri, 28 Mar 1997 03:53:09 -0500 (EST) Received: from lmspc3.ibs.fr (lars@lmspc3.ibs.fr [192.134.36.143]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id JAA18899 for ; Fri, 28 Mar 1997 09:54:06 +0100 Received: (from lars@localhost) by lmspc3.ibs.fr (8.8.5/8.8.5) id JAA21386 for chemistry@www.ccl.net; Fri, 28 Mar 1997 09:50:40 +0100 Date: Fri, 28 Mar 1997 09:50:40 +0100 From: Lars Hemmingsen Message-Id: <199703280850.JAA21386@lmspc3.ibs.fr> To: chemistry@www.ccl.net Subject: CCL:Summary:MM parameters for NO3-,CO3--,SO4--,PO4---,HPO4-- Hi all ! This is a summary of the replies to a question I posted earlier this week: > Does anyone have MM parameters or references where parameters may be found > (atomic charges, force constants, van der Waals) for NO3-, CO3--, SO4--, > PO4--- or HPO4-- ? > All answers will be greatly appreciated. > > I will summarise if there is an interest in such a summary (judging > from the replies I get). > > Thanks in advance, yours Lars Hemmingsen Thanks to all who replied: ************************************************************************* Alexandre Hocquet wrote: Estimado Lars, Here is what i found in "published force field parameters" in Rev.Comp.Chem.Vol6 (1995) : amber nitrate : Guilbaud, J.Phys.Chem., 97, 5685 (1993) dreiding carbonate : Fan, Macromolecules, 27, 2383 (1994) opls sulfate : Cannon, J.Comput. Chem., 14, 995, (1993) Unfortunately they are all from different force fields. Moreover, i dont actually know these references so i cant tell if it is exactly what you need. Please forward me the results of your query. Amicalement, Alexandre Hocquet Laboratorio de Cristalografia Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago CHILE fax : 56 2 696 73 59 ahocquet@tamarugo.cec.uchile.cl *************************************************************************** Kenny Lipkowitz wrote: Try looking at Appendix I (Published Force Field Parameters by Osawa and Lipkowitz) in Reviews in Computaional Chemistry, Vol. 6, 1995, VCH Publishers, Inc. maybe something exists there. Kenny lipkowitz@chem.iupui.edu *************************************************************************** Bruno Manunza wrote: There have been a couple of postings regarding this subject today, yours an one from Sanjoy Bandyopadhyay asking for MM parameter for SO4-- and CH2/CH3. You'll probably have to compute charges fitting the Electrostatic potential of your molecules according to a strategie like RESP (gopher://www.ccl.net:73/11/software/SOURCES/FORTRAN/resp) (see also the AMBER page at this regard (http://www.amber.ucsf.edu/amber/amber.html). You may keep in mind also that either GAUSSIAN.XX, GAMESS and MOPAC have options which allow to compute the partial atomic charges according to this philosophy. The force constants and van der Waals parameters for CH2, CH3, PO4, CO3 may be taken from the Cornell et al. AMBER force field (http://www.amber.ucsf.edu/amber/ff94.html)or from the MM3 force field (http://europa.chem.uga.edu/cgi-bin/mm3para) (strike 8-9 blanks in the form field to obtain a complete list). By the way we are trynk to keep update a list of force field links on ur site and you may have a lok to the molecular databases page on http://antas.agraria.uniss.it. Hope it helps Regards Bruno -- Dr Bruno Manunza DISAABA - Environmental Sciences Dept. V.le ITALIA 39 07100 SASSARI, ITALY phone 39 79 229215 fax 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it ************************************************************************ Merete Sjovoll wrote: for a force field for sufate, look at reference J.D.Gale, Phil. Mag. B 73 (1996) 3-19 I would be very interested if somebody can give you the reference to the forcefield of nitrate, so please report this to the CClist or to me personally! Best regards Merethe Sjovoll -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From maricel@stark.udg.es Fri Mar 28 08:32:21 1997 Received: from stark.udg.es for maricel@stark.udg.es by www.ccl.net (8.8.3/950822.1) id HAA27489; Fri, 28 Mar 1997 07:51:39 -0500 (EST) Received: by stark.udg.es (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA22636; Fri, 28 Mar 97 13:58:19 -0800 Date: Fri, 28 Mar 97 13:58:19 -0800 From: maricel@stark.udg.es (Maricel Torrent) Message-Id: <9703282158.AA22636@stark.udg.es> To: chemistry@www.ccl.net Subject: G94: DFT + BQs = FAILURE Dear CCLers, In Gaussian 94 system (Revision B.3), DFT calculations with BQ's having no basis set fail in link 502 (spurious integrated densities, consistency failure number 2 in CalDSu, etc.). Has anyone already come up against this problem/bug when performing BSSE calculations at DFT level? Do you know how to solve it? Your advice will be very helpful. Thanks in advance, Maricel -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Maricel Torrent _/ _/ _/ _/_/_/_/ Institut de Quimica Computacional _/ _/ _/ _/ Universitat de Girona _/ _/ _/ _/ _/ _/ _/_/ Pl. Hospital, 6 _/ _/ _/ _/ _/ _/ 17071 Girona, CATALONIA (Spain) _/_/_/ _/ _/ _/ _/_/_/_/ Voice +34.72.41.83.58 FAX +34.72.41.83.57 _/ _/_/_/ _/_/_/ WWW: http://stark.udg.es/~maricel/ _/ _/ _/ _/ e-mail: maricel@stark.udg.es _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- From buyong@ibmnla.chem.uga.edu Fri Mar 28 12:32:32 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id LAA28607; Fri, 28 Mar 1997 11:55:18 -0500 (EST) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id LAA16942; Fri, 28 Mar 1997 11:55:18 -0500 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA14392; Fri, 28 Mar 1997 11:55:15 -0500 Date: Fri, 28 Mar 1997 11:55:11 -0500 (EST) To: Alexandre Hocquet Cc: chemistry@www.ccl.net Subject: Re: CCL:A question about MM3 and IR calculations In-Reply-To: <333B03E7.4D9@cec.uchile.cl> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Alexandre: =09The reason MM3 gives warning about low vibrational frequencies is your second explantion, i.e., its contribution to the calculated entropy will be high and thus increase possible inaccuracy of the entropy. Presently, the calculation of vibrational entropy is based on the assumption that vibrational is harmonic. However, as we know, the anharmonic contributions increase with decreasing vibrational frequencies. Thus, the possible errors increase with decreasing vibrational frequencies. =09Generaly, low vibrational freqencies come from the normal modes corresponding the torsional (rotational) motions. For some molecules, for example CH3CCCH3, methyl groups rotate almost without barrier. Therefore, the corresponding freqencies are extremly low. For some ring compounds (five members ring, for example), the barrier between different ring conformations are usually low even though the torsional motions for ring atoms are constraind. The change between those ring conformations are made via a mechanism "pseudorotation", its barriers are as low as a rotational mode. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D On Thu, 27 Mar 1997, Alexandre Hocquet wrote: > Dear CCLers, > A strange message in the MM3 output makes me once more request > your kind help... > As i perform (apprenti sorcier) MM3 calculations using Alchemy 2000, i > have no access to a manual that explains this strange warning : >=20 > "Warning!!! : There are 1 low frequencies (<40/cm) " >=20 > Does MM3 warn because if a low frequency is found, then if not very > accurate it could correspond to a negative frequency (and thus not > to a true minimum) ? >=20 > Or does it warn because if a low frequency is found, its contribution > to the calculated entropy will be high and thus increase possible > inaccuracy of the entropy ? >=20 > The following message tends to support the second explanation=20 > but is ever more confusing to me : >=20 > "Check if any of the above low frequenciescorrespond to pseudorotation > If the low frequencies are not accurate the contributions to entropy > and heat capacity will not be accurate and the user may wish to correct > them. If pseudorotation occurs, the numbers may be very poor" >=20 > Why is it so strange to find such a low frequency ?=20 > What is pseudorotation anyway ? > The output of MM3 categorises frequencies into : > free internal rotation (between 0 and 10/cm) > restricted internal rotation (between 10 and 40/cm) > Anybody can tell me what is the meaning of these strange terms ? >=20 > Thanks in advance for your wise comments ... > --=20 > Alexandre Hocquet >=20 > Laboratorio de Cristalograf=EDa > Facultad de Ciencias F=EDsicas > Universidad de Chile > Blanco Encalada, 2008 > Santiago Centro > Chile > fono : 56 2 678 45 19 > fax : 56 2 696 73 59 > email : ahocquet@cec.uchile.cl >=20 > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: ahocquet@tamarugo.cec.uchile.cl > -- Original Sender From: Address: ahocquet@tamarugo.cec.uchile.cl > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator > 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=20 >=20 >=20