From orena@anvax1.cineca.it Wed Apr 24 03:48:38 1996 Received: from ICINECA.CINECA.IT for orena@anvax1.cineca.it by www.ccl.net (8.7.1/950822.1) id DAA11148; Wed, 24 Apr 1996 03:11:02 -0400 (EDT) From: Received: from anvax1 by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Wed, 24 Apr 96 08:50:20 SOL Date: Wed, 24 Apr 1996 08:51:01 +0200 Message-Id: <96042408510172@anvax1.cineca.it> To: chemistry@www.ccl.net Subject: Re: Molecular Mechanics X-VMS-To: SMTP%"chemistry@www.ccl.net" Dear Frederic, you can see: K. Gundertofte et al. J.Comp.Chem. ''A comparison of conformational energies calculated by several molecular mechanics methods'' In this article you can find something about the accuracy of CFF91 force field. I hope this help. Cheers, Roberta ************************************************************************** Dr. Roberta Galeazzi Universita' di Ancona Dipartimento di Scienze dei Materiali e della Terra via Brecce Bianche, I-60131 Ancona, Italy fax: 39-71-2204714 e-mail: orena@anvax1.unian.it From hans@hartree.quantchem.kuleuven.ac.be Wed Apr 24 04:48:38 1996 Received: from hartree.quantchem.kuleuven.ac.b for hans@hartree.quantchem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id EAA11462; Wed, 24 Apr 1996 04:30:37 -0400 (EDT) Received: by hartree.quantchem.kuleuven.ac.be id AA19008 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Wed, 24 Apr 1996 10:30:15 +0100 Date: Wed, 24 Apr 1996 10:30:14 +0100 (NFT) From: Vansweevelt Hans To: chemistry@www.ccl.net Subject: cone angles of phosphorus ligands Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear readers, does someone know (or has) a program to calculate the cone angles, solid angles and solid angle factors of phosphorus ligands as defined by P.B.Dias et al. in "Coord, Chem. Rev. 1994, 135/136, 737" ? Thanks a priori. Hans Vansweevelt hans@hartree.quantchem.kuleuven.ac.be From s196232@ccs.sogang.ac.kr Wed Apr 24 05:48:38 1996 Received: from ccs.sogang.ac.kr for s196232@ccs.sogang.ac.kr by www.ccl.net (8.7.1/950822.1) id FAA11778; Wed, 24 Apr 1996 05:33:42 -0400 (EDT) Received: from localhost by ccs.sogang.ac.kr (8.7.5/Sogang) id SAA21870; Wed, 24 Apr 1996 18:32:16 +0900 (KST) Date: Wed, 24 Apr 1996 18:32:15 +0900 (KST) From: Lee Tae Bum X-Sender: s196232@ccs To: chemistry@www.ccl.net Subject: CCL:Gaussian94 + large molecule Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I try to run the Gaussian94 on PC (RAM 64MB). I am interested in the interaction and geometry of molecules. (ex: (H2O)n + Urea, Urea + Hydrocarbon, Urea cluster, or urea inclusion compound) I would like to know how many atoms are computed in one time on the PC. In expectation of CCLer's answer, my email adress - s196232@ccs.sogang.ac.kr Truly yours, From craig@occam.gh.wits.ac.za Wed Apr 24 06:08:34 1996 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.7.1/950822.1) id FAA11769; Wed, 24 Apr 1996 05:29:00 -0400 (EDT) Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id LAA11980; Wed, 24 Apr 1996 11:26:00 +0200 Date: Wed, 24 Apr 1996 11:25:59 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Vansweevelt Hans cc: chemistry@www.ccl.net Subject: Re: CCL:cone angles of phosphorus ligands In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Vansweevelt, > does someone know (or has) a program to calculate the cone angles, solid > angles and solid angle factors of phosphorus ligands as defined by > P.B.Dias et al. in "Coord, Chem. Rev. 1994, 135/136, 737" ? We have a program to calculate cone and solid angles of any molecular ligands. Several papers have been published on these calculations, and most of the work has involved phosphorous ligands. Additional calculations include angular and radial profiles, conformer averaged calculations from trajectory files and orthogonal calculations (volume, and projected areas). The program can be found at: ftp://hobbes.gh.wits.ac.za/pub/steric/ with some information and a recent paper in html format at: http://www.gh.wits.ac.za/craig/steric/ Some of the references for this paper are included here: ----------------------------------------------------------------- 3. D. White, B.C. Taverner, P.G.L. Leach and N.J. Coville, J. Comp. Chem., 14, 1042 (1993)

4. D. White, B.C. Taverner, P.G.L. Leach and N.J. Coville, Adv. Organomet. Chem., 478, 205 (1994)

5. D. White, B.C. Taverner, N.J. Coville and P.W. Wade, J. Organomet. Chem., accepted (1995)

6. D. White, B.C. Taverner and N.J. Coville, to be published.

7. D. White, P.G.L. Leach and R. Lemmer, to be published. ------------------------------------------------------------------ The program has been used for these calculations for some four years now, but is still being expanded and enhanced. Cheers, Craig "Imagine if every Thursday your shoes exploded if you tied them the usual way. This happens to us all the time with computers, and nobody thinks of complaining." -- Jeff Raskin, interviewed in Doctor Dobb's Journal Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig From orena@anvax1.cineca.it Wed Apr 24 07:48:40 1996 Received: from ICINECA.CINECA.IT for orena@anvax1.cineca.it by www.ccl.net (8.7.1/950822.1) id HAA12274; Wed, 24 Apr 1996 07:39:54 -0400 (EDT) From: Received: from anvax1 by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Wed, 24 Apr 96 13:36:54 SOL Date: Wed, 24 Apr 1996 13:38:24 +0200 Message-Id: <96042413382407@anvax1.cineca.it> To: chemistry@www.ccl.net Subject: more information about Molecular Mechanics X-VMS-To: SMTP%"chemistry@www.ccl.net" Dear netters, I'll give you the complete bibliography: K. Gundertofte et al. J. Computat. Chem. 1996,pag.429-449,vol.17 I found it very intersting. I hope this can help you. best wishes Roberta ******************************************************** Dr. Roberta Galeazzi Universita' di Ancona Dipartimento di Scienze dei Materiali e della Terra e-mail: orena@anvax1.unian.it fax: +39-71-2204714 From Frederic.Bouyer@der.edfgdf.fr Wed Apr 24 08:48:45 1996 Received: from cf01 for Frederic.Bouyer@der.edfgdf.fr by www.ccl.net (8.7.1/950822.1) id IAA12623; Wed, 24 Apr 1996 08:37:14 -0400 (EDT) Received: from clserv02.edf.fr (clserv02.edf.fr [130.98.118.118]) by cf01 (8.6.12/8.6.12) with ESMTP id OAA13448 for ; Wed, 24 Apr 1996 14:39:04 +0200 Received: from ret45ab.der.edf.fr (ret45ab.der.edf.fr [192.93.107.28]) by clserv02.edf.fr (8.6.12/8.6.12) with ESMTP id OAA05110 for <@mailhost.der.edf.fr:chemistry@www.ccl.net>; Wed, 24 Apr 1996 14:36:51 +0200 Received: by ret45ab.der.edf.fr (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id OAA04767; Wed, 24 Apr 1996 14:36:29 +0200 From: "Frederic Bouyer" Message-Id: <9604241436.ZM4765@ret45ab.der.edf.fr> Date: Wed, 24 Apr 1996 14:36:28 -0600 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: Thermochemistry on solids Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, Does anybody have done thermochemical calculations on solids? I was wondering if only vibrational contribution is necessary to compute Cp, S, H at each temperature. Do I have to take into account all frequencies of the corresponding atoms of the entire unit cell? Is there some litterature, references about it? Thanking you in advance, (in the meantime, happy computing) Frederic Bouyer -- __________________________________________________________________________ Frederic Bouyer Groupe Chimie Corrosion - RNE-EMA EDF-DER Les Renardieres Tel: (33) 1-60-73-69-65 Route de Sens, Ecuelles, BP1 Fax: (33) 1-60-73-68-89 77250 MORET-SUR-LOING - FRANCE Email: Frederic.Bouyer@der.edfgdf.fr __________________________________________________________________________ From owner-chemistry@ccl.net Wed Apr 24 10:48:42 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA13394; Wed, 24 Apr 1996 10:30:50 -0400 (EDT) Received: from gap.cco.caltech.edu for news@gap.cco.caltech.edu by bedrock.ccl.net (8.7.1/950822.1) id KAA04839; Wed, 24 Apr 1996 10:30:49 -0400 (EDT) Received: (from news@localhost) by gap.cco.caltech.edu (8.7.5/8.7.3) id XAA09812; Tue, 23 Apr 1996 23:32:22 -0700 (PDT) To: mlist-chemistry@nntp-server.caltech.edu Path: caribou From: caribou@ugcs.caltech.edu (Jonathan McDunn) Newsgroups: mlist.chemistry Subject: Help with Moffatt Oxidation mechanism Date: 24 Apr 1996 06:32:21 GMT Organization: California Institute of Technology, Pasadena Lines: 16 Message-ID: <4lkhtl$9ii@gap.cco.caltech.edu> NNTP-Posting-Host: dogbert.ugcs.caltech.edu X-Newsreader: NN version 6.5.0 #2 (NOV) I hope this is an appropriate place to request assistance with my current dilemma. I have been trying to find a spelled out rendition of the Moffatt Oxidation mechanism. So far I have found several variations on this mechanism in the literature, but I have been unable to come across the original, unadulterated mechanism. If anyone could be of any assistance, I would be greatly appreciative. Specifically, I am oxidizing a polyethylene glycol to it corresponding bis aldehyde with acetic anhydride and DMSO and I want to know what side products result from this process. Thank you very much, Jonathan McDunn caribou@ugcs.caltech.edu From owner-chemistry@ccl.net Wed Apr 24 11:48:43 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id LAA16758; Wed, 24 Apr 1996 11:25:54 -0400 (EDT) Received: from che.udel.edu for kotelyan@che.udel.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA07324; Wed, 24 Apr 1996 11:25:49 -0400 (EDT) Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA20412; Wed, 24 Apr 1996 11:25:39 -0400 Date: Wed, 24 Apr 1996 11:24:21 +22305133 (EDT) From: Michael Kotelyanskii Subject: Summary on Ions force-field parameters To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Here is a summary of the replies I've got for my query about the force-field for ions compatible with the BIOSYM's cvff force-field. Thank you very much for those who replied. My original posting was: Dear CCL'ers, I am trying to do simulations of the hydrated polymers in water and also with the presence of salts (Li+,Na+..... ions). For several reasons I am doing it with Biosym and CVFF forcefield, It was embarassing to find out that CVFF (at least the version we have here) has Lennard-Jones parameters only for Na+ and Ca. Biosym people suggest me to switch to CFF91, or some more recent version of it but unfortunately it is not good for our purposes. So, my question 1) Is anybody aware of such parameters ? 2) Any references to the experimental (or other simulaton) data which can be used to parametrize the force-field. And some not very expansive ways to parametrize it. I would like to avoid Large-scale ab-initio calculations. Thank you in advance, Of course I'll summarize the responses if there is an interes Mike Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 -------------------> Hi, We have used time-dependent density functional calculations to determine the 1/R^6 term. We have used the Zn+2 value quite successfully in the CVFF anc CFF91 force fields. To get the repulive term, we took radii >from Emsley book on the elements. A more prudent way would be to parameterize the repulsize term using some known ion-molecule distances. Given: -A/R^6 + B/R^12 -> gives epsilon and Rvdw. Thus knowing A (say our work) and Rvdw, then either B or epsilon can easily be calculated. I do not know if these cation values for A will be useful for your purposes, but you can find them in: Long range non-bonded attractive constants for some charged atoms, L.J. Bartolotti, L.G. Pedersen and P. Charifson, J. Comp. Chem. "12", 1125 (1991). Another approach for finding cation parameters has been given by J. Aqvist, J. Phys. Chem. "94", 8021 (1990) He gives values of both A and B for many of the cations of interest to you. Best wishes, Lee Bartolotti -------------------------------------------------------------------------------- Lee Bartolotti North Carolina Supercomputing Center Computational Scientist 3021 Cornwallis Rd. Research Institute Research Triangle Park, NC 27709 bartolot@ncsc.org (919) 248-1185 (919) 248-1101 FAX -------------------------------------------------------------------------------- Michael, As you are going to do simulations on ionic systems, I would like to attract your attention to a paper we wrote on truncation problems in MD simulations of ionic solutions P. Auffinger, D.L. Beveridge, A simple test for evaluating the truncation effects in simulqtions of systems involving charged groups. chem. phys. lett., 1995, 234, 413-415 as truncation problems appear to be more important than force field issues and should be solved first. Pascal PS: let me know if you are interested by reprints of our work -- ___________________ Pascal Auffinger IBMC 15 Rue Rene Descartes 67084 Strasbourg Cedex France Tel : (33) 88.41.70.49 Fax : (33) 88.60.22.18 ___________________ Hi - You should check out Aqvist's parameters, which seem to perform quite well for cluster calcs... J. Phys. Chem., 1990, v.94, p8021. - Erin (eduffy@franklin.csb.yale.edu) ---------------------> I don't know if this will be helpful, but: In C. C. Pye et al, 'An ab initio investigation of Lithium Ion hydration', we (JPC 100, 601 (1996) ) calculated (HF/6-31+G*) the first and second solvation spheres of Li+ and found that the STO-3G and 3-21G basis sets fail miserably (as well as others, see the Glendening/Feller references within that paper). These calculations were prompted by the first observation of a Li-O stretching mode in aqueous Lithium solution (Raman) and of its assignment to a tetracoordinate complex. Many people still believe that Li+ is hexa coordinated, but this is false (for details, see W. Rudolph et al., JPC, 99, 3793 (1995) ). The 3-21G basis set predicts that a pentacoordinate species is a stable minimum. Sometimes people create force fields or paramaters which try to duplicate the behavior of this basis set. This is fine for a lot of organic chemistry, but would be poor for thius system since the 3-21G result is false. Just a warning. -Cory Pye ************* ***************** ! Cory C. Pye *** ** ** ** ! Graduate Student and Unpaid Sys Admin ** * **** ! Theoretical and Computational Chemistry ** * * ! cory@bohr.chem.mun.ca ** * * ! http://www.ucs.mun.ca/~cory/index.html *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) --------------------- A listing of published parameters can be found in Reviews of Computational Chemistry, volume 6, Appendix 1, VCH Publishers, 1995. If the specific force field you are interested in isn't listed, ions from other EFFs can be found that may be useful. ---------------------> Dear Mike et al. The forcefields by Tony Rapp=E9 have the requisite atom types, might I suggest either Cerius-2 or a check into the work of Rapp=E9 Landis or Skiff. Also the Dreidiing force field has some of this data as well. MJD ------------------------------------------------- Michael J. Doyle MOLECULAR SIMULATIONS TEXAS FIELD OFFICE PHONE 713-364-8555 =46AX 713-364-0210 CAR 281-386-5211 E-mail (1) mdoyle@msi.com (2) xtal4@AOL.COM ------------------------------------------------- We had some problem of that kind too with Discover and were unable to solve them. We noticed that Discover had parameters for cation-cation interaction as well as for anion-anion interaction but did an average of the two for the anion-cation inetraction (!) so we try to not use it anymore. Anyway, I will be interested by the answers you will get. Regards Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** te: Mon, 4 Mar 1996 14:54:28 +0000 (WET) From: Grant Morrison To: Michael Kotelyanskii Subject: Re: Li+ params Hi Michael, a friend of mine forwarded your posting to me ( with regard to simulating polymers with Li+ and Na+ ). Firstly there is a biosym forcefield called cvff_aug that has Li+ params in it. It was derived for use with zeolites so I am not sure how useful this will be or even if you have that particukar forcefield. Secondly I am presently studying polymer systems with Li+ present and have used some of theses params (others I have derived for my specific systems using ab-initio potenetial energy surface fitting, but I'm not sure these would be appropiate to your systems since I'm not sure what systems you are loooking at. There is someone else working here who is looking at polymers with Na+ ions present and I believe he has also derived some parameters of his own If any of this is of interest then let me know Grant ----------------> From: stoutepf@carbon.dmpc.com (Pieter Stouten) Subject: Re: CCL:Force-field for Ions Status: RO X-Status: At 10:09 96/03/02, Michael Kotelyanskii wrote: >1) Is anybody aware of such parameters ? >2) Any references to the experimental (or other simulaton) data which can > be used to parametrize the force-field. > I assume this response is still relevant as I did not see a summary of responses. Both Lee Bartolotti and Aquist have derived Van der Waals parameters for several ions, that in principle can be used with any force field. Bartolotti's work well in FEP calculations. I do not know much about Aquist's. If I remember correctly, the Biosym parameters are similar to Aquist's. If you are interested I can get references to the Bartolotti and Aquist papers. Cheers, Pieter. -- Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 9090 || Internet: stoutepf@carbon.dmpc.com || Indiana Jones Thanks again for the replies Mike Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716