From leslie@ri.ac.uk Sun Feb 2 07:20:27 1997 Received: from mail-d.bcc.ac.uk for leslie@ri.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA22128; Sun, 2 Feb 1997 07:00:47 -0500 (EST) Received: from ri.ac.uk (actually davy.ri.ac.uk) by mail-d.bcc.ac.uk with SMTP (PP); Sun, 2 Feb 1997 11:59:58 +0000 Received: from faraday.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA13726; Sun, 2 Feb 1997 12:02:17 GMT Received: from localhost by faraday.ri.ac.uk (950413.SGI.8.6.12) id MAA15006; Sun, 2 Feb 1997 12:02:15 GMT Date: Sun, 2 Feb 1997 12:02:15 +0000 (WET) From: "Prof. Leslie Glasser" X-Sender: leslie@faraday To: "Douglas A. Smith Ph.D." Cc: CHEMISTRY@www.ccl.net, glasser@aurum.chem.wits.ac.za Subject: Re: CCL:crystal packing calculations and programs In-Reply-To: <199702011452.JAA19298@home.CTCnet.Net> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: Douglas Smith asks re the problem of crystal packing. This is not trivial for, even when you have a force field available to describe the interactions, the problem of choosing a space group and locating the molecules therein remains. Thus, this is a present research activity. I have a short review 'Packing Molecules and Ions in Crystals' in 'Fundamental Principles of Molecular Modelling' ed W Gans, A Amann and JCA Boeyens (Plenum, 1996) - from an IUPAC-sponsored conference at the Kruger Park in 1995 (I can't supply reprints now as I have none as yet). Some recent refs therein, and updated: J Perlstein, J Amer Chem Soc.(JACS), 116 (1994), 455 and 11420 A Gavezotti, JACS, 113 (1991), 4622 - applications in D Braga, et al., J Chem Soc., Dalton, (1995) 1215 KD Gibson and HA Scheraga, J Phys Chem 99 (1995) 3752 and 3765 - Program LMIN from QCPE 664 HR Karfunkel and RJ Gdanitz, J Comp Chem., 13 (1992) 1171 CM Freeman and CRA Catlow J Chem Soc., Chem. Commun., (1992) 89 TS Bush, CRA Catlow and PD Battle, J Mater Chem., 5 (1995) 1269 JR Holden et al., J Comp. Chem., 14 (1993) 422 - also HL Ammon et al., Acta Cryst., B50 (1994), 216 Y le Page et al., J Appl. Cryst., 29 (1996) 503, and refs therein. I trust this will be of some help. Leslie (Prof) L. Glasser glasser@aurum.chem.wits.ac.za [Chemistry, Univ. Witwatersrand, Johannesburg, South Africa] Mailing address until July, 1997: Chemical Crystallography, Inorganic Chemistry Lab., 9 Parks Road, Oxford OX1 3QS, England Tel: Intl + 44 1865 270 832 FAX: Intl + 44 1865 272 699 Institutional address: Royal Institution of Great Britain Tel: Intl + 44 + 171-409-2992 21 Albemarle St., FAX: Intl + 44 + 171-629-3569 London W1X 4BS, UK E-mail: leslie@ri.ac.uk On Sat, 1 Feb 1997, Douglas A. Smith Ph.D. wrote: > A very interesting (to me) paper has just appeared in J. Phys. Chem. B, > 1997, 101, 798 by Sorescu, Rice and Thompson. In this paper, they dev3elop > an intermolecular potential for RDX > (hexahydro-1,3,5-trinitro-1,3,5-s-triazine) and perform crystal packing, MC, > and MD studies. > > The authors parameterize their potential based on the known neutron > diffraction structure of RDX. They also reference several other packages > for performing crystal packing calculations. > > What are the options when one does not have the crystal structure available? > Can one reasonably start from a high quality ab initio calculation on a > single molecule (gas phase) and use that structure to pack a crystal? If > one does, what is the likelihood of getting the crystal structure correct? > Or does one need to perform ab initio calculations in the periodic solid > (e.g., CRYSTAL 95 calculations) before performing crystal packing? > > What packages are out there, commercial and "public domain" (free, QCPE, > etc.) that can perform crystal packing calculations? I would like to > predict space group, density, lattice energy, etc. > > Perhaps, since there are pedagogical questions here rather than just a > request for pointers to software, we could keep this discussion public on > the CCL, not just a series of replies directly to me. > > Doug > -- > Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 > The DASGroup, Inc. | fax: (814) 255-3517 > 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com > Johnstown, PA 15905 | WWW: http://www.dasgroup.com > > Contract R&D specialists in modeling, simulation, synthesis and risk > assessment for chemistry, materials science, and biotechnology. > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: dsmith@CTCnet.Net > -- Original Sender From: Address: dsmith@CTCnet.Net > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > 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 > > From kotelyan@plmsc.psu.edu Sun Feb 2 16:20:31 1997 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id PAA23635; Sun, 2 Feb 1997 15:51:00 -0500 (EST) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id PAA05764; Sun, 2 Feb 1997 15:50:44 -0500 (EST) Date: Sun, 2 Feb 1997 15:50:44 -0500 (EST) From: Mike Kotelyanskii To: "Douglas A. Smith Ph.D." cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:crystal packing calculations and programs In-Reply-To: <199702011452.JAA19298@home.CTCnet.Net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Well, this is a good and interesting question, and my personal opinion is that in general the answer is no. the molecular conformation in vacuum can be very different from it's in the crysdtal, unfortunately I cannot come up with an examples right now, but it's well known that conformational ststistics (gaich/trans ratio for instance) is different from what is obtained for a RIS - like calcs on a single monomer or dimer. Second, crystal structure obtained from calculations is probably more sensitive to the geometry (LJ sigma's bond length, equilibrium angles, etc.,) than tgo the energy parameters (bond and angle bending constants, LJ epsilon, charges, etc.) I think to judge about these parameters one would look at energy, vibration spectra etc... In principle, I think it all depends on the problem, as the tolerance to the possible errors in potentials is defined by it. That's my personal opinion, Mike ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsilvania State University University Park, PA 16802, USA -------------------------------------------------------------------------------- On Sat, 1 Feb 1997, Douglas A. Smith Ph.D. wrote: > A very interesting (to me) paper has just appeared in J. Phys. Chem. B, > 1997, 101, 798 by Sorescu, Rice and Thompson. In this paper, they dev3elop > an intermolecular potential for RDX > (hexahydro-1,3,5-trinitro-1,3,5-s-triazine) and perform crystal packing, MC, > and MD studies. > > The authors parameterize their potential based on the known neutron > diffraction structure of RDX. They also reference several other packages > for performing crystal packing calculations. > > What are the options when one does not have the crystal structure available? > Can one reasonably start from a high quality ab initio calculation on a > single molecule (gas phase) and use that structure to pack a crystal? If > one does, what is the likelihood of getting the crystal structure correct? > Or does one need to perform ab initio calculations in the periodic solid > (e.g., CRYSTAL 95 calculations) before performing crystal packing? > > What packages are out there, commercial and "public domain" (free, QCPE, > etc.) that can perform crystal packing calculations? I would like to > predict space group, density, lattice energy, etc. > > Perhaps, since there are pedagogical questions here rather than just a > request for pointers to software, we could keep this discussion public on > the CCL, not just a series of replies directly to me. > > Doug > -- > Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 > The DASGroup, Inc. | fax: (814) 255-3517 > 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com > Johnstown, PA 15905 | WWW: http://www.dasgroup.com > > Contract R&D specialists in modeling, simulation, synthesis and risk > assessment for chemistry, materials science, and biotechnology. > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: dsmith@CTCnet.Net > -- Original Sender From: Address: dsmith@CTCnet.Net > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > 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 > >