From MEZEI@msvax.mssm.edu Mon May 24 19:30:07 1993 Date: Tue, 25 May 1993 00:30:07 -0500 (EST) From: MEZEI@msvax.mssm.edu Subject: Amber params for uncharged AA's To: chemistry@ccl.net Message-Id: <01GYKMXMMB2E001V9O@msvax.mssm.edu> We are looking for AMBER parameters for neutral Lysine (unprotonated) and neutral Arginine (protonated) sidechains. Has anybody developed such paramaters? If yes, who? And what are they? Thanks, Mihaly Mezei Physiology and Biophysics Mount Sinai School of Medicine, CUNY (212) 241-2186 From chp1aa@surrey.ac.uk Tue May 25 05:48:14 1993 From: Mr Andrew D Allen Message-Id: <9305250901.AA17020@central.surrey.ac.uk> Subject: modelling solvated systems. To: chemistry@ccl.net Date: Tue, 25 May 93 10:01:15 BST Dear All, I am interested in the modelling of solvated systems, especially those of a biological nature. I have had several pointers already as to how I should go about getting realistic data. First is to use a molecular mechanics approach, by putting my molecule in a box and adding solvent to it, adding solvent to my molecule and doing some kind of MD run in a periodic box. This seems ok but how would MM methods handle such effects as hydrophobicity, cavity's and solvent accessible surface area. The second approach I have considered is to use a package called AMSOL this used a parameterised AM1 method and seems quite extensive, my question to the net is has anyone done any extensive work with AMSOL or any other solvation methods. If so I would be glad to hear from you, I will summerise the pro's and con's of the various methods for the net. ANDY From martin@link.sunet.se Tue May 25 14:57:01 1993 Date: Tue, 25 May 93 12:57:01 +0200 Message-Id: <9305251057.AA27576@decnet.sunet.se> From: martin@link.sunet.se (Martin Norin, Dept. Biochem., Royal Inst. Technol., Stockholm, tel. +46-8-7907512, e-mail; martin@physchem.kth.se) To: "chemistry@ccl.net"@kth.sunet.se Subject: AMBER parameters for neutral lysines and arginines. Dear Mihaly Mezei, We have used the original AMBER force field to model neural lysines and arginines. The only parameters that we had to add were the charges for the sidechain atoms. These charges were taken from the protein dictionary of the Sybyl program, distributed by Tripos. There charges were modelled from electrostatic potentials derived from ab initio QM calculations. If you want to assign the charges yourself an alternative to the ab initio calculations could be a semiempirical approach, eg the MOPAC-ESP method. If you want more details send me your e-mail adress. Greetings, Martin Norin Dept. Biochem. Royal Inst. Technol. Stockholm e-mail: martin@physchem.kth.se From chenina@rhrk.uni-kl.de Tue May 25 08:51:02 1993 Subject: Informations about LIPIDAT wanted To: chemistry@ccl.net Date: Tue, 25 May 93 14:17:37 MET DST From: Robert Chenina Message-Id: <9305251417.aa26115@sun.rhrk.uni-kl.de> Hello World! I'm looking for any kind of informations about the database LIPIDAT. How do I get it? Is it free? Is it distribute on disc? (It's for a friend without net access). Any help will be appreciated! -- **************************************************************************** * Robert Chenina, Dpt. of Physical Chemistry, University of Kaiserslautern * * Erwin-Schroedinger-Str, D-6750 Kaiserslautern, Germany * * Phone: + 49 631 205 2534, Fax: + 49 631 205 3200 * * Email: chenina@rhrk.uni-kl.de * **************************************************************************** From djh@ccl.net Tue May 25 06:30:04 1993 From: David Heisterberg Date: Tue, 25 May 1993 10:30:04 -0400 Message-Id: <199305251430.AA01164@xipe.ccl.net> To: chemistry@ccl.net Subject: Diels-Alder transition states I'm trying to lend a hand to a real pot-boiling organic chemist who's interested in modeling Diels-Alder transition states. He was hoping to use Mopac, but we've found that with both AM1 and MNDO the diene ends up a good 7A from the dieneophile (system is ethylene and a substituted Cp). Is this kind of behavior something I should have expected? If so, recommendations for, say, a review paper accessible to the non-theorist would be appreciated! Thanks. -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) From jan@si.fi.ameslab.gov Tue May 25 04:43:53 1993 From: jan@si.fi.ameslab.gov (Jan Jensen) Message-Id: <9305251443.AA30594@si.fi.ameslab.gov> Subject: Water-Water potentials To: chemistry@ccl.net Date: Tue, 25 May 93 9:43:53 CDT Dear Netters: Most of the water potentials discussed by Jorgensen et al. in J. Chem. Phys. 1983, 79, 926, e.g. TIP3P and TIP4P, overestimate the dimerization energy of the linear water dimer by roughly one kcal/mol. Has anyone published a potential of the same form (3-4 site coulomb terms and a single Lennard-Jones term), or similar, that better reproduces this quantity (probably at the expense of the bulk properties)? Regards, Jan H. Jensen Dept. of Chemistry Iowa State University jan@si.fi.ameslab.gov From Tom_Kavassalis.XRCC@xerox.com Tue May 25 00:28:09 1993 Date: Tue, 25 May 1993 07:28:09 PDT From: Tom_Kavassalis.XRCC@xerox.com Subject: ACS Workshop on Molecular Simulation of Stucture and Properties of Polymer Systems To: chemistry@ccl.net Message-Id: <"25-May-93 10:28:08".*.Tom_Kavassalis.XRCC@Xerox.com> Conference Announcement MOLECULAR SIMULATION OF STRUCTURE AND PROPERTIES IN POLYMER SYSTEMS An Interdisciplinary Workshop October 17-20, 1993 Asilomar Conference Center Pacific Grove, California sponsored by division of polymer chemistry, inc. American Chemical Society Invited Speakers: J. Blackwell, Case Western Reserve University J. H. R. Clarke, UMIST, Manchester D. Frenkel, FOM Institute for Atomic and Molecular Physics, Amsterdam W. A. Goddard, California Institute of Technology G. Grest, Exxon Research and Engineering A. J. Hopfinger, University of Illinois, Chicago M. Karplus, Harvard University W. Mattice, University of Akron F. MHuller-Plathe, ETH - Zurich M. Muthukumar, University of Massachusetts J. de Pablo, University of Wisconsin P. C. Painter, Pennsylvania State University J. - P. Ryckaert, UniversitAe Libre de Bruxelles I. C. Sanchez, University of Texas, Austin R. G. Snyder, University of California, Berkeley U. Suter, ETH- Zurich Conference Organizers: S. - L. Hsu, University of Massachusetts (413-545-0433, fax: 413-545-0082) T. A. Kavassalis, Xerox Research Centre of Canada (416-823-7091, fax:416-822-7022) Who Should Attend: This interdisciplinary workshop has been organized to facilitate the dissemination of new research in the development and use of molecular simulation methodologies in polymer science and will be of interest to graduate students, university researchers and industrial researchers. The workshop will offer invited lectures dealing with: 1. Prediction of Polymer Structure and Properties 2. Simulation of Phase Behavior 3. The Link Between Experimentation and Molecular Simulation 4. New Developments in Molecular Simulation Poster Presentations: A poster session is planned in order to give the conferees the opportunity to present their innovative efforts in molecular simulation. Anyone wishing to present a poster should send a title with authors and affiliations and a 200 word abstract to Prof. S. L. Hsu Polymer Science and Engineering Dept The University of Massachusetts Amherst, Massachusetts 01003 or Dr. T. Kavassalis Xerox Research Centre of Canada by August 31, 1993. 2660 Speakman Drive Mississauga, Ontario Canada L5K 2L1 email kavassalis.xrcc@xerox.com (detach and mail by Sept 17 1993)------------------------------------- Housing and Registration Form Name Organization Mailing Address City State Country Zip/postal code Tel.(business) FAX Email Registration with accommodation: Circle choice (add $50 after September 17, 1993) $635 each ,three or four registrants sharing one roomo0 $735 each, two registrants sharing one room (potentially off-site)o0 o0 (you may designate roommate(s) or they will be assigned) $835, one registrant per room (potentially off-site) $1135, one registrant with nonparticipating accompanying guest sharing one room, $465, registration without accommodations (includes reception, breaks) Cancellation, in writing, postmarked after Sept. 17,1993 subject to $50 cancellation fee. Please send the registration form and your check for the full amount, made payable to Division of Polymer Chemistry, Inc., ACS by September 17, 1993 to Diane M. Morrill, Business Manager, Division of Polymer Chemistry, 1103 Hahn Hall, Virginia Polytechnic Institute, Blacksburg, VA 24061-0344, Phone (703) 231-3029, Fax (703) 231-8517 For payment by credit card complete the following Credit card Account No. Expiration date Signature American Airlines is offering up to 40% off their coach fare and 5% off their super saver fare to conference participants. Reservations may be made by calling American at 1-800-433-1790 and asking for the meeting services desk. Refer to the Polymer Division star record 16o3UF. em From topper@haydn.chm.uri.edu Tue May 25 11:04:38 1993 Date: Tue, 25 May 93 15:04:38 -0400 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9305251904.AA13751@haydn.chm.uri.edu> To: chemistry@ccl.net, topper@haydn.chm.uri.edu Subject: point-charge multipoles Dear chemnetters, I've attached a summary of responses to my question about the calculation of electrostatic multipoles and multipole interactions for point-charge models (heavily edited). It seems that the actual calculation of the moments themselves is rather simple (thanks to Kurt Hillig for a nice discussion of this). My next question; what is the best way to go about calculating the lowest-order, non-vanishing n-pole/n-pole contribution to the total electrostatic energy? For example, between two rigid methanes the lowest-order contribution would be the octupole-octupole energy, and it would be a function of the relative orientation and distance between the two methanes. As Bob Goldstein recently reminded us, the higher-order terms will depend on the origin, so I don't really care about those. Such a calculation for the two methanes would in this example allow me to break down the total e-static interaction into E = E(8-8) + E(higher-order terms). I'll be grateful for any comments on this point. Thanks to all who contributed! Best, Robert ******************************** * Dr. Robert Q. Topper, PRA * "...I assure you that the most * Department of Chemistry * wonderful and the most interesting * University of Rhode Island * phenomena of nature are almost * Kingston, RI 02881 USA * all of them produced by chemical ******************************** powers." * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * - Jane Marcet, author of * (401) 792-5072 [FAX] * Conversations on Chemistry ******************************** $$$$$$$$$$$$$$$$$$$$$$ ORIGINAL AND SECOND POSTINGS: $$$$$$$$$$$$$$$$$$$$$$ >From topper Wed May 19 18:07:34 1993 Hello again, sorry to waste bandwidth but based on several early responses to my previous query I was not sufficiently clear in what I am looking for. > > Dear netters; > > I have the need to compute electrostatic moments (quadrupole, octupole, > etc., etc. ...) for molecules, given their equilibrium geometries and > point charges defined for each atom. > > Before I re-create the wheel, does anyone know of publicly available > (shareware/freeware) software which will do this? I am not doing ab initio work on molecules, extracting point charges, and then trying to calculate multipoles. Rather, I am interested in evaluating some of the point-charge models which are commonly used in liquid simulation work. So, for example, I'd like to be able to calculate the octupole-octupole contribution to the interaction energy of two rigid molecules as a function of their relative orientation and distance apart. Apparently there has been some excellent work done on calculating multipole moments from ab initio wave functions, but this work isn't helpful to me. I need multipole moments extracted from point charge models. ############################################################ >From ryszard@MSI.COM Wed May 19 16:17:56 1993 I have two programs which do what are you looking for (MTP and LOCAL). If you are still in need let me know. Ryszard Czerminski, MSI P.S. These programs are free (non-commercial). ############################################################ >From ryszard@MSI.COM Wed May 19 16:44:49 1993 Hi Robert, LOCAL reads output from MONSTERGAUSS or GAMESS and calculates local (on atoms and between all atom pairs) multipoles (up to quadrupoles). MTP takes output from LOCAL and prepares local multipoles for MINTER which I have used to calculate intermolecular interactions. MINTER calculates intermolecular interactions (between rigid monomers) using semiempirical Claverie's method. You can find more about methodology and programs in the publication list which I am appending at the end and in references which you can find in these papers (specialy Claverie and Buckingham). I have not used these programs during last three years so they must be somewhat rusty. They were used by rather limited group of people so documentation is definitely not to good. I can recover them from tape tomorrow and send to you (tape or ftp?). The only request is for proper reference if you ever would publish a paper based on the calculation with these programs. I can promise you only limited help with how-to used them so you would have struggle with them mostly alone. On the other hand if you have charges and geometries and just want to calculate moments it is very straighforword and it would be probably simpler for you write a small program. Anyhow, let me know. Sincerely, Ryszard 1. R. Czermi\o"n\'"ski "Intermolecular Interactions : Reliability of Results Obtained for Small Hydrogen Bonded Dimers by Claveries Method" Int. J. Quant. Chem. 31, 649 (1987) 2. R. Czermi\o"n\'"ski "Reparametrization of Claverie's Method for Intermolecular Energy Calculation" J. Mol. Struct. 170, 245 (1988) ############################################################ >From mxm@iris80.biosym.com Wed May 19 17:42:13 1993 Me too! Please post a summary of any responses you receive. The only references I have for this are 1. A. J. Stone and M. A. Alderton, Mol. Phys. 56, 1047 (1985) "Distributed Multipole Analysis Methods and Applications", and 2. Nigel G. J. Richards and Sarah L. Price, Intl. J. of Quantum Chemistry: Quantum Biology Symposium 16, 73-85 (1989) "The Representation of Molecular electrostatics Using Interactive Graphics". Richards and Price used the charge density matrix, defined in terms of the Gaussian orbitals, from an ab Initio program called CADPAC and then calculated the distributed multipoles with a program called ORIENT. Good luck, Max Muir ############################################################ >From Kurt.Hillig@um.cc.umich.edu Thu May 20 10:15:49 1993 A few comments on multipole calculations.... First, the problem you face is that only the lowest non-vanishing multi- pole can be uniquely defined - or perhaps I should say has a value which is independent of your coordinate system. Non-vanishing in this case means "not required to be zero by symmetry", not "non-zero due to a fortuitous cancellation". In other words, if a molecule has a non-zero dipole moment, then the quadrupole and higher moments you calculate will depend on where you place the origin of your coordinate system. As an ex-microwave spectroscopist I ran in to this when working on van der Waals dimers. Many molecules have had their q'pole moments determined by MW, but nobody ever discussed in the literature what they meant. Since MW spectroscopy is based on molecular rotation in the gas phase, the implied coordinate system is centered on the center of mass and aligned with the principal inertial axes. Gaussian 90, in contrast, works in a center of nuclear charge frame; I'm not sure how the axes are aligned in the absence of symmetry. Furthermore, at short range (from the vdW distance out to 5-10 A) a simple mulipole expansion does a very poor job of describing the electric field around a molecule. Most of the electrostatic calculations used by MW'ers for vdW dimers involve a distributed multipole model, assigning charges and point dipole and q'pole moments to every atom. So if you're interested in short-range interactions, you're better off using an all-atom charge-charge model; save the multipole expansions for long-range stuff. So, to answer your question.... Monopole: Q = Sum(i) [ q(i) ] Dipole (3-vector): mu(j) = Sum(i) [ q(i) x(i,j) ] Q'pole (3x3 tensor): Theta(j,k) = Sum(i) [ q(i) x(i,j) x(i,k) ] : : : Where i is the atom index - Sum(i) means "sum over all atoms" - and j and k are coordinate indices x, y, or z - x(i,j) means "the j coordinate of atom i". For example (here where e.g. y(i) means "the y coordinate of atom i"): mu(y) = Sum(i) [ q(i) y(i) ] Theta(zz) = Sum(i) [ q(i) z(i)**2 ] 8-pole(xxy) = Sum(i) [ q(i) x(i)**2 y(i) ] 16-pole(xzzz) = Sum(i) [ q(i) x(i) z(i)**3 ] Hope this helps! ###(NOTE: This is from a second message from KH - rqt)### Remember that the o'pole moment is a 3 x 3 x 3 tensor with 27 elements. It's common - though incorrect - for people to report e.g. a single number for the quadrupole moment of a molecule; this makes an implicit assumption that the molecule has cylindrical symmetry - or, at least, a 3-fold axis. For molecules of lower symmetry all of the components are needed - but often can't be determined experimentally. In the case of methane, where by symmetry the o'pole is the first non- vanishing moment, the o'pole tensor has only one independent element and the rest can be derived from it (probably are either equal to it or are zero, but I'd have to check...) by symmetry. Thus [one] can report a single number for this moment. In the more general (lower symmetry) case, more elements are needed. Dr. Kurt Hillig Dept. of Chemistry I always tell the khillig@umich.edu University of Michigan absolute truth Telephone (313)747-2867 Ann Arbor, MI 48109-1055 as I see it. hillig@chem.lsa.umich.edu ############################################################ >From ng436@traken.pnl.gov Sun May 23 13:13:39 1993 Your posting is several days old, but here are some ideas and references. I'm afraid I'm still not clear what exactly you're looking for, so I'll cover several bases. (1) Multipole moments of an arbitrary array of point charges (through octupole): see J.G.C.M. Van Duijneveldt-Van de Rijdt and F.B. Van Duijneveldt, J. Mol. Structure (THEOCHEM) 89, 185 (1982). (2) Electrostatic interaction energy between molecules: see P. Isnard, D. Robert, and L. Galatry, Mol. Phys. 31, 1789 (1976). For a pro- gram, you might send email to Eric Glendening (ng972@spiff.pnl.gov). He's recently programmed the content of Isnard et al. (3) Experimental values: see "Theory of Molecular Fluids" by Grey and Gubbins (Oxford, 1984). One of the appendices. (4) Interaction energy between two arrays of arbitrary point charges: the elementary physics approach is the most simple one -- sum up the potential energy contributions over all i(A), j(B), where i is on molecule A and j is on molecule B. David Woon (ng436@traken.pnl.gov) Molecular Science Research Center Pacific Northwest Labs Richland, Washington EOF From GKING@arserrc.gov Sat May 25 13:48:58 1993 Date: 25 May 1993 17:48:58 -0400 (EDT) From: GKING@arserrc.gov Subject: Water-Water potentials To: chemistry@ccl.net Message-Id: <01GYLMUOM3PE000KVH@arserrc.gov> I spent a few months tweaking the SPC parameters (Berendsen et al., in "Intermolecular Forces", edited by B. Pullman, (Reidel, Dordrecht, 1981), pp. 331-342) to come up with water parameters that yield a heat of vaporization of 11.2 kcal/mol (experimental is 10.5 kcal/mol) and a reasonable oxygen-oxygen radial distribution function. The ref- erence is G. King and A. Warshel, J. Chem. Phys. 91(6), 3647-61, 1989 (the parameters are on p. 3653). Give them a try! Gregory King gking@arserrc.gov From hogue@canada.den.mmc.com Tue May 25 10:44:30 1993 Date: Tue, 25 May 93 16:44:30 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9305252244.AA01081@canada.den.mmc.com> To: chemistry@ccl.net Subject: Decomposition on Bare Metal I have come accross a few papers describing what seems to be the disintegration of perfluoropolyether molecules on atomically clean iron and aluminum. At least this is what XPS seems to indicate via growth of carbide, fluoride and oxide peaks. This is surprising to me. Can anyone point ot some references or personal experience that explains this? Thanks Pat Hogue From lim@rani.chem.yale.edu Tue May 25 18:21:06 1993 From: Dongchul Lim Message-Id: <9305260221.AA03966@rani.chem.yale.edu> Subject: Re: Diels-Alder transition states To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 25 May 93 22:21:06 EDT David Heisterberg writes: > > I'm trying to lend a hand to a real pot-boiling organic chemist who's > interested in modeling Diels-Alder transition states. He was hoping > to use Mopac, but we've found that with both AM1 and MNDO the diene > ends up a good 7A from the dieneophile (system is ethylene and a > substituted Cp). Is this kind of behavior something I should have > expected? If so, recommendations for, say, a review paper accessible > to the non-theorist would be appreciated! Thanks. > -- Are you sure you did the transition state optimization? It sounds like the optimization led to separate reactants. You may want to look a review by Houk (Angew. Chem. Int. Ed. Engl. 1992, 31, 682-708) and a recent paper JACS 1993, 115, 2936. -DCL