From 94970459@vax1.dcu.ie Mon May 8 10:04:30 1995 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.6.10/930601.1506) id KAA29395; Mon, 8 May 1995 10:01:47 -0400 Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01HQ9J50ZZ4W937RRT@vax1.dcu.ie>; Mon, 8 May 1995 14:59:53 GMT Date: Mon, 08 May 1995 14:59:52 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: Dr. Andy Holder's Comparison of semi-empirical methods To: chemistry@ccl.net Message-id: <01HQ9J5124AQ937RRT@vax1.dcu.ie> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Ccl'ers, With refefence to my recent promise to post Dr Andy Holder's comparisons of semi-empirical methods, I have received 28 (and still growing) requests for this information. Accordingly, I would prefer to post one message to everybody. Please find below Dr. Andy Holder's messages with additonal comments by Ernie Chamot. Regards, Paddy Paddy Kane Dublin City University Dublin Ireland $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ A question was recently posted as to the difference between MNDO and AM1. I'll be happy to give my take on this. 1. The basic difference between the two methods is the addition of Gaussian functions to some of the core repulsion functions (CRFs) for certain elements. These functions have a position, a width, and an intensity, all of which can be taken as parameters. They were initially intended to adjust the SHAPE of the CRF so that it would more closely correspond to "reality", whatever that is. In essence, they were used as patches for specific types of systems that could not be handled in general parameterization without disrupting other chemically important items. In my experience, the Gaussians were added one at a time and with great deliberation, and only after the other parameters were pretty much settled on. This is because they could potentially have such a large effect on the chemistry of the elements. An example of this are the Al-Cl systems for AM1. When I was finishing parameters for Al in AM1, these systems would simply not come out correctly. A carefully placed Gaussian solved the problem. Another example of a "problem" Gaussian function is the one found at about 3.0 angstroms in the phosphorous parameters for AM1. This Gaussian can cause extensive problems when there are TWO P atoms at about this distance in a compound. All in all, Gaussians MUST be used with extreme care and anytime one is added to repair a problem, it will almost certainly cause another. As with all things, it is a matter of trade-offs. The above discussion has led to my conclusion (tongue firmly in cheek) that Gaussians are "evil." I think I would amend that to be a "neccessary evil." 2. Another difference that must be mentioned is additional flex- ibility in the parameters for the lighter elements in the case of AM1. For instance, for most of the lighter elements (rows 1 and 2) only one zeta value (exponent of the slater orbitals) and one beta value (resonance) was used for both s and p orbitals in the valence shell within MNDO. This approximation was abandoned for the heavier elements in MNDO and completely for AM1. This assumption was made in the case of MNDO for computational efficiency. 3. The third difference is the added computational power available for parameterization searches when AM1 was parameterized. Much more extensive grid searches and trial parameter examination could be carried out more quickly as timne went by. Most of the AM1 parameter sets are substantially different than the MNDO ones indicating that definitely different parameter minima were located. All in all, the methods are basically the same in theory differing only in the details. The same can be said about PM3, in that it was a different parameterization method, not a different theory. For most cases, the performance of AM1 is considered to be generally superior to MNDO. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Asst. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | aholder@cctr.umkc.edu K | (816) 235-2293, FAX (816) 235-5502 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: aholder@CCTR.UMKC.EDU -- Original Sender From: Address: aholder@CCTR.UMKC.EDU CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Date: Thu, 31 Mar 1994 11:24:04 -0600 From: Ernie Chamot Subject: References Comparing Calculated IPs and EAs I have been trying to follow the relative accuracy of various methods (molecular mechanics, semiempirical, ab initio SCF, and density functional) in calculating properties for different classes of compounds, and am particular interested in comparisons with experimental data. Here are a couple compilations (which should be a good source of references) and a couple newer references that I found useful because each gave comparisons of ionization potentials or electron affinities for a series of compounds: "Density Functional Methods in Chemistry", Labanowski & Andzelm Ed., Springer- Verlag (1991). "Reviews in Computational Chemistry," Lipkowitz & Boyd, VCH, 1990. W. Thiel, Theo. Chem. Acta., 81, 391- (1992). J. J. P. Stewart, J. Comp. Chem., 12(3), 320-41, 1991. Ziegler & Gutsev, J. Comp. Chem., 13, 70-75 (1992). J. Baker, et. al., J. Comp. Chem., 7(3), 49-58 (1986). Also, the Ampac 4.0, 4.5, and 5.0 literature from Andy Holder summarizes results from testing he, Dewar, and others have done in developing SAM1. I would be very interested in a summary of other references you find useful, if you don't summarize your responses to the CCL. Thanks. EC From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01HB3KTFN1GW9N8CYS@VAX1.UMKC.EDU>; Tue, 12 Apr 1994 19:33:55 CST Date: Tue, 12 Apr 1994 19:33:55 -0600 (CST) Subject: AM1 vs. PM3 To: CHEMISTRY@ccl.net Message-id: <01HB3KTFNUEA9N8CYS@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Netters, A few weeks ago, Jeffrey Nauss asked about a comparison between the AM1 and PM3 semiempirical methods. Both of these semiempirical methods are included in most programs that support semiempirical calculations (AMPAC, MOPAC, etc.). Please note that the following discussion is MY OPINION and a compendium of MY EXPERIENCES. I hope you find it somewhat useful. The lead references to each method follows: AM1: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. PM3: Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209. AM1 stands for "Austin Model 1" and PM3 stands for "Parameterization Method 3". Both methods implement the same basic NDDO theory pioneered by Michael Dewar while at the University of Texas at Austin. The differ- erence is in how the parameters that the semiempirical methods utilize to replace portions of the full ab initio implementation of Hartree-Fock theory. Perhaps the most important difference between AM1 and PM3 is the involvement of the researcher in the parameterization process. PM3 was developed using a largely undirected mathematical optimization process with greatly reduced guidance from chemical knowledge or intuition, an addition that the Dewar methods consider essential. The human researcher knows for which molecules it is necessary to obtain the best fit. For instance, it is useless to obtain parameters for carbon and hydrogen that describe the properties of cubane correctly if the results for benzene are significantly different from experiment. An attentive and knowledgeable chemist can also guide the search into areas of the parameter hypersurface that make sense as far as the absolute magnitude of the parameters themselves are concerned. As with many chemical properties, the parameter values should vary periodically. While this should not unduly constrain the final values, parameters should follow well-defined general trends for proper interaction with other elements. In terms of the actual NDDO model, the actual parameters allowed to vary in the two methods are quite different. In AM1, a large number of values we used from spectroscopy for some of the one-center terms and the other parameters derived with these values fixed. (This is possible only for the lighter elements in the Main Group.) PM3 allowed ALL of these values to float, resulting in substantially more parameters. AM1 also had a quite different concept as to the application of the Guassian functions introduced with AM1 to adjust the core-electron/core- electron repulsion function. Workers in the Dewar group and subsequently in my group see Gaussian functions as PATCHES to the theory, not integral parts. All models fail at some point and the Gaussians were introduced to help with some of the systematic errors in MNDO. Traditionally, these patches were applied to adjust for difficult molecular systems AFTER semiempirical parameters were stabilized. PM3 includes these Gaussian functions (two for each element) FROM THE BEGINNING. Our experience indicates that in such a situtaion, the chemistry os the element will very likely be very strongly effected by the presence of these functions and the importance of the "real", "chemical" parameters will be reduced and swallowed up bu the Gaussians. In short, Gaussians should only be used where absolutely needed, and then viewed with askance. The essence of the difference between the two philosophies is evident: the theoretical basis for the method is either accepted or denied. Significant approximations are made to gain the speed advantage that semiempirical methods enjoy over their ab initio quantum mechanical brethren. But both the ab initio and semiempirical models are based on the Hartree-Fock set of ideas. These ideas possess theoretical rigor as regards solution of the Schrodinger Equation. If one simply views the semiempirical parameters as adjustables within a curve-fit scheme rather than as components of a theoretical model, little faith or importance resides in the meaning of their final values. Simply put, the method of parameterization described above and used so successfully with AM1 and MNDO (and now SAM1) expresses confidence in the theory. With a firmer footing in chemical reality, AM1 parameters are more likely to yield useful results for situations not specifically included in the molecular basis set for parameterization (MBSP). Some Practical Considerations ----------------------------- The differences in errors between the two methods as published are minimal, but that does not relate the real story of how the methods perform differently. Some key points: - PM3 is clearly better for NO2 compounds as a larger number of these were included in the MBSP. - PM3 is usually a little better for geometries, as these were also heavily weighted. - The molecular orbital picture with PM3 is usually different from that expected or that predicted by other methods. This is a direct consequence of the lack of attention paid to the absolute values of Uss and Upp. It can be seen in the lack of performance in ionization potentials. - PM3 charges are usually unreliable, again a result of the rather strange values that some of the parameters take on, even when other experimental data such as heats of formation and geometries are acceptable. This makes PM3 essentially useless for the derivation of molecular m echanics force fields. Perhaps the best known example of this is the case of formamide. The partial charges for the atoms in the molecules are listed below. The lack of any appreciable charge on N has led to a reversal of the actual bond dipole between C and N in this molecule! Atom AM1 PM3 HF/6-31G* --------------------------------------------- O -0.3706 -0.3692 -0.5541 C 0.2575 0.2141 0.5079 N -0.4483 -0.0311 -0.8835 O // H-C \ NH2 - Several papers have been published describing the performance of AM1 vs. PM3: Dewar, M. J. S.; Healy, E. F.; Yuan, Y.-C.; Holder, A. J. J. Comput. Chem. 1990, 11, 541. Smith, D.A. J. Fluor. Chem. 1990, 50, 427 Smith, D.A.; Ulmer, C.W.; Gilbert, M.J. J. Comput. Chem. 1992, 13, 640. - Most reserachers in my experience have stopped using PM3 and have returned to AM1. An Example of Parameterization Values for Aluminum -------------------------------------------------- Parameter AM1 MNDO PM3 Uss, eV -24.353585 -23.807097 -24.845404 Upp, eV -18.363645 -17.519878 -22.264159 zetas, au 1.516593 1.70288 } 1.444161 zetap, au 1.306347 1.073269 betas, eV -3.866822 -0.594301 } -2.670284 betap, eV -2.317146 -0.956550 alpha 1.976586 1.868839 1.521073 Gaussians: Intensity #1, eV 0.090000 - -0.473090 Width #1 12.392443 - 1.915825 Position #1 2.050394 - 1.451728 Intensity #2, eV - - -0.154051 Width #2 - - 6.005086 Position #2 - - 2.51997 The point on the potential surface located by PM3 is significantly different than that located by AM1. This is immediately apparent from the large discrepancy between the Upp values. These are the important one- electron energy values and they have strong influence on the parameter hypersurface. Also, the difference between Uss and Upp for both MNDO and AM1 is about 6 eV. This has been reduced to 2.5 eV in PM3. The real difficulty, however, is in the Beta values. These parameters are the two-center/one- electron resonance terms and are responsible for bonding interactions between atoms. The PM3 values are almost zero, resulting in the conclusion that there is very little bonding between atoms involving aluminum! (Note that the AM1 values for betas and betap spread out around the single MNDO value for beta. This suggests that the MNDO values were reasonable and AM1 adds greater flexibility.) PM3 regains the bonding interactions lost in the low beta values with two strongly attractive Gaussians spanning the bonding region. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From PEROTT@if.ufrgs.br Mon May 8 11:49:36 1995 Received: from if1.if.ufrgs.br for PEROTT@if.ufrgs.br by www.ccl.net (8.6.10/930601.1506) id LAA01859; Mon, 8 May 1995 11:41:08 -0400 From: Received: from if1.if.ufrgs.br by if1.if.ufrgs.br (PMDF V4.3-10 #7035) id <01HQ9ECU98PY000BTN@if1.if.ufrgs.br>; Mon, 08 May 1995 12:41:50 -0300 Date: Mon, 08 May 1995 12:41:50 -0300 Subject: Software for crystalline solids - summary To: chemistry@ccl.net Message-id: <01HQ9ECU98Q0000BTN@if1.if.ufrgs.br> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, Here is the summary of responses to my question. Thanks a lot to all !! Claudio. Original question: >I am a solid state physicist and I am interested in the >calculation of physical properties of crystalline solids >(such as lattice parameters, bulk modulus ... ) by ab >initio or semiempirical methods. > Could someone give me an indication of any >software (public domain or commercial) that could >handle with periodic systems? > > I will summarize to the net. > Thanks in advance. > > Claudio Perottoni > Instituto de Fisica - UFRGS > e-mail: PEROTT@IF.UFRGS.BR ----- End of the message ----- ------------------------------------------------------------ From: IN%"og845@adrian.pnl.gov" 2-MAY-1995 22:26:25.47 CRYSTAL92 is a Hartree-Fock program for the study of crystalline systems; to get informations about it, send an e-mail to CRYSTA92@itocsivm.csi.it Edoardo Apra' - PNL - Battelle Blvd Richland, WA 99352, MS K1-96 Tel: +1-509-375-6760 FAX: +1-509-375-6631 ------------------------------------------------------------ From: IN%"P8946019@csdvax.csd.unsw.EDU.AU" Claudio Try CRYSTAL 92, an ab initio Hartree Fock LCAO program for periodic systems. Hugh ------------------------------------------------------------ From: IN%"ostertag@alf.biochem.mpg.de" "Georg Ostertag" Hello Claudio, I read your posting in the CCL. I know a group at the university of Ulm. They are developing a semiempirical method. As I know, they are now programming a facility to calculate cristals or polymers. This would be perhaps an address for you. I think, they are also interested in having contact with people using their method or program. The address is: Abteilung fuer angewandte Physik Arbeitsgruppe Prof. Dr. P. Haegele Albert-Einsein-Alle 11 89081 Ulm Germany The people who are working on the program are Rainer Mallon (Dipl. Physiker) and Manfred Doser (student) E-Mail: Manfred.Doser@physik.uni-ulm.de manfred@model2an.physik.uni-ulm.de Rainer.Mallon@physik.uni-ulm.de Regards, Georg Ostertag MPI f. Biochemistry Martinsried / Munich Germany ostertag@alf.biochem.mpg.de ------------------------------------------------------------ From: IN%"work@hal6000.qf.ub.es" 3-MAY-1995 06:49:12.10 Hi Claudio, If you are interested in Hartree-Fock periodic calculation you should use CRYSTAL program. Contact Dr. Dovesi at the university of Turin. Depending on the solids you are interested in you can try a cluster approach. Best regards, Francesc Prof. Francesc Illas, Facultat de Quimica, Departament de Quimica Fisica, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, SPAIN e-mail: work at hal6000.qf.ub.es phone : 34-3-402 1229 FAX : 34-3-411 1492 ================================================== From: IN%"jperl@stc.chem.rochester.edu" 3-MAY-1995 12:58:18.92 There are several papers which discuss methods for predicting packing geometries of molecules in solids. These are 1)Gavezzotti, A. JACS 113, 4622(1991) 2)JR Holden, Z. Du, HL Ammon, J. Comput. Chem. 14, 422(1993) 3)HR Karfunkel, B. Rohde, FJJ Leusen, RJ Gdanitz, GJ Rihs, J. Comput.Chem 14, 1125(1993) 4) J Perlstein, JACS 116,11420,1994 As far as availability of code, Gavezzotti has code available for his method, and Karfunkel's is commercially available in the CERIUS2 package. The code by Perlstein is available on request from the author for space groups P1,P21 and P212121. The first 3 papers can handle rigid molecules. The last paper can handle molecules with up to 12 exocyclic torsion bonds. ****************************************************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627 Email: perlstein@chem.chem.rochester.edu ------------------------------------------------------------ From: IN%"rcfort@maine.maine.edu" 3-MAY-1995 13:51:53.97 Take a look at CRYSTAL88, program #577, from QCPE. Professor Ray Fort, Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine E-mail: rcfort@maine.maine.edu Orono ME 04469 rfortjr@fort.umeche.maine.edu Computational organic chemistry, especially on wood- and paper-related problems ------------------------------------------------------------ From: IN%"v_uk@biosym.com" 3-MAY-1995 15:25:17.43 Dear Sir I am a researcher of BIOSYM technologies. We have a good ab-initio software for PBC system. 1) dsolid DFT soft based on the numerical basis set for PBC systems 2) Plane wave Plane_Wave is a first-principles (ab initio) quantum mechanics soft package that performs accurate calculations on solid-state systems. Plane_Wave calculates variational self-consistent solutions to the density functional theory (DFT) equations for insulating and semiconducting systems that are subject to 3D periodic boundary conditions. The method uses a plane-wave expansion for the wavefunctions and a pseudopotential representation of the ions. 3) ESOCS ESOCS is a first-principle (ab-initio) quantum mechanics packages that performs accurate theoretical calculations on a wide range of 3D solid-state systems including metals, semiconductors and surfaces. ESOCS stands for Electronic Structure of Close-packed Solids. It is based on spin density functional methods and the Atomic Sphere Approximation (ASA). The distinguishing feature of the code is a spherical wave expansion of the wave functions, which are centered at each atomic state of the solids.Because of this construction, the projection of quantities like densities of state onto atomic sites is particularly easily computed. Since ESOCS does not use the frozen core approximation, changes in the core spectra due to core relaxation can be calculated. Masahiko Katagiri v_uk@biosym.com Biosym Technologies, Inc. 9685 Scranton Road San Diego, CA 92121 ------------------------------------------------------------ From: IN%"ricart@quimica.urv.es" 4-MAY-1995 10:27:11.86 Dear Claudio: It is obvious that you need the program CRYSTAL, that permits the calculation of wave-function and properties of crystalline systems, using a Hartree-Fock-LCAO aproximation. You should contact with the Theoretical Chemistry Group of TORINO, for example by E-mail to CRYSTA92@ITOCSIVM.CSI.IT Good luck. Josep Manel Ricart Pla Departament de Quimica UNIVERSITAT ROVIRA I VIRGILI Placa Imperial Tarraco, 1 43005 - TARRAGONA (SPAIN) TEL: +34-(9)77-559568 FAX: +34-(9)77-559563 e-mail:ricart@quimica.urv.es ------------------------------------------------------------ From:IN%"ehlers@iodine.chem.vu.nl" "Andreas Ehlers" Dear Mr Perottoni, there is a good program called ADF_BAND that can calculate periodic structures using the density funtional theory. I have forwarded your mail to one of the authors, so he can tell you more details. I hope this helps, Andreas Ehlers ============================================== - Andreas Ehlers - Afdeling Theoretische Chemie,Faculteit Scheikunde -Vrije Universiteit Amsterdam -De Boelelaan 1083, 1081 HV Amsterdam ehlers@iodine.chem.vu.nl ============================================== From: "Prof. Carla Roetti" Dear Dr Perottoni, I read your mail to CCL about calculation of physical properties of crystalline solids. We developed in collaboration with VR SAunders CRYSTAL, an ab initio Hartree-Fock program for periodic systems (1-2-3 dimensions). The release 92 is now distributed, at the distribution cost of 450.000 Italian Lire (+-270$), by our university. We could send you further information if you supply your fax number and traditional address. Best regards, Carla Roetti ------------------------------------------------------------ From: IN%"julie@biosym.com" 4-MAY-1995 16:44:15.98 Dear Claudio One of my clients sent me your email. Which University are you at? We have a whole range of solid state chemistry and quantum tools that can help you with periodic systems. So please send your name and fax number and let's start communicating. Julie Bryant Julie Bryant BIOSYM Technologies, Inc. Phone: 619/597-9707 9685 Scranton Road Fax: 619/597-9777 San Diego, CA 92121 E-Mail:julie@biosym.com From stoutepf@chemsci1.dmpc.com Mon May 8 18:19:37 1995 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.dmpc.com by www.ccl.net (8.6.10/930601.1506) id SAA10963; Mon, 8 May 1995 18:06:00 -0400 Received: by gatekeeper.es.dupont.com; id AA09190; Mon, 8 May 95 18:05:53 -0400 Received: from [204.29.16.43] (llm200143.dmpc.com) by chemsci1.dmpc.com (4.1/SMI-4.1) id AA02754; Mon, 8 May 95 18:04:06 EDT X-Sender: stoutepf@chemsci1.dmpc.com (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora 1.5.1 for Macintosh Date: Mon, 8 May 1995 18:04:25 -0500 To: dibug@comp.bioz.unibas.ch, chemistry@ccl.net, water@gibbs.oit.unc.edu From: stoutepf@chemsci1.dmpc.com (Pieter Stouten) Subject: Solvation RefLib (28 Mar 95; replaces 15 Mar 95) An updated version of my library with solvation references is available as a Macintosh file in stuffed (.sit) and binhexed stuffed (.hqx) Endnote formats, and as an ASCII file in Refer format (.txt). Their URLS are: ftp://ftp.halcyon.com/local/stouten/solvation_refs.sit http://www.halcyon.com/stouten/solvation_refs.sit ftp://ftp.halcyon.com/local/stouten/solvation_refs.hqx http://www.halcyon.com/stouten/solvation_refs.hqx ftp://ftp.halcyon.com/local/stouten/solvation_refs.txt http://www.halcyon.com/stouten/solvation_refs.txt Originally, I used the library to keep all references of my 1993 solvation paper, and it contains references to papers that have little or nothing to do with solvation. Konrad Koehler recently provided me with 11 new references, and the present version of the library contains 123 references in total. If you notice any omissions just send me the references and I will incorporate them. If you have no internet access (i.e., cannot ftp or browse the web), let me know and I'll mail you a copy. Make sure you specify the format (.hqx or .txt). Enjoy! -- Pieter Stouten, Senior Research Scientist Computer Aided Drug Design Group The DuPont Merck Pharmaceutical Company P.O. Box 80353, Wilmington, DE 19880-0353 Phone: +1 (302) 695 3515 Fax: +1 (302) 695 2813 Internet: stoutepf@chemsci1.dmpc.com CompuServe: 73172,2004 WWW: http://www.halcyon.com/stouten/stouten.html From bkarlak@ren.onyx-pharm.com Mon May 8 19:19:38 1995 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.10/930601.1506) id TAA11610; Mon, 8 May 1995 19:04:54 -0400 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (8.6.10/1.37) id QAA22278; Mon, 8 May 1995 16:04:53 -0700 Received: by ren.onyx-pharm.com (940816.SGI.8.6.9/921111.SGI.AUTO) for chemistry@ccl.net id XAA02792; Mon, 8 May 1995 23:04:51 GMT From: "Brian Karlak" Message-Id: <9505081604.ZM2790@ren.onyx-pharm.com> Date: Mon, 8 May 1995 16:04:49 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Available drug databases Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Does anyone know a way to access that structures of drugs that are either commercially available or in preclinical trials? Are there any publically available databases that contain this information? Thanks. I will summarize available responses for those who wish a copy. Brian Karlak Onyx Pharmaceuticals -- This .sig is meaningless. From markm@portal.vpharm.com Mon May 8 23:19:41 1995 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.10/930601.1506) id XAA13869; Mon, 8 May 1995 23:04:44 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA14194; Mon, 8 May 1995 22:56:01 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9505090256.AA14194@portal.vpharm.com> Subject: Ki prediction methods To: chemistry@ccl.net Date: Mon, 8 May 1995 22:56:01 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 263 I've been reviewing the field of Ki prediction, and thought I would ask whether anyone in the group knows of any interesting work that hasn't yet been published (e.g. pre-prints, meeting abstracts). Thanks in advance for any help. / Mark (markm@vpharm.com)