From lith!kestas@ucdavis.edu Tue Nov 16 07:27:10 1993 Received: from ucdavis.ucdavis.edu for lith!kestas@ucdavis.edu by www.ccl.net (8.6.1/930601.1506) id HAA05234; Tue, 16 Nov 1993 07:22:10 -0500 Received: from lith.UUCP by ucdavis.ucdavis.edu (4.1/UCD2.05) id AA29412; Tue, 16 Nov 93 04:18:55 PST Received: by lith.UUCP (smail2.5.3-coh) id AA00080; 15 Nov 93 21:44:05 PST (Mon) Subject: Summary: CD-ROM To: CHEMISTRY@ccl.net From: Kestutis Sliupas X-Mailer: ELM [version 2.3 PL11] Message-Id: <9311152144.AA00078@lith.UUCP> Date: 15 Nov 93 21:44:05 PST (Mon) Hi: I posted to the list regarding CDROM access. I received three replies, but since they were so similar I will paraphrase the answers. The consensus is to extract the needed data from ACD (a MACCS database) since it is readily available. This also does not violate the Aldrich CD-ROM copyright (which I hadn't read). Many thanks to: Jeff Blaney (chiremv!andromeda!jeffb) Scott Presnell (srp@zgi.com) Wayne Weber (kodak.com!weber) -- Regards, Kestas Kestutis Sliupas x (510) 231-1540 (work voice) ucdavis!lith!kestas x (510) 231-1285 (work FAX) USA CA From leboeuf@CHIMCN.UMontreal.CA Tue Nov 16 08:27:11 1993 Received: from condor.CC.UMontreal.CA for leboeuf@CHIMCN.UMontreal.CA by www.ccl.net (8.6.1/930601.1506) id IAA05712; Tue, 16 Nov 1993 08:06:57 -0500 Received: from chims1.CHIMCN.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA28114 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Tue, 16 Nov 1993 08:04:57 -0500 Received: by chims1.CHIMCN.UMontreal.CA (930416.SGI/5.17) id AA08421; Tue, 16 Nov 93 08:04:20 -0500 From: leboeuf@CHIMCN.UMontreal.CA (Leboeuf Martin) Message-Id: <9311161304.AA08421@chims1.CHIMCN.UMontreal.CA> Subject: CRC Handbook summary To: chemistry@ccl.net Date: Tue, 16 Nov 1993 08:04:20 -0500 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 629 Hi Netters, A few days ago, I asked wether there existed a CD-ROM version of the CRC Handbook, or something like that. Here is the summary: ---------------------------------------------------------------------- (Prof.) Leslie Glasser: Dear Martin: An abbreviated version of the CRC Handbook is available for use withinMathCAD. It works quite well, and one can transfer info from the handbo k to a MathCAD document - but not always as one might like. Leslie ---------------------------------------------------------------------- Thanks to All who responded, Martin Leboeuf From R1JJH@VM1.CC.UAKRON.EDU Tue Nov 16 11:28:00 1993 Received: from phem3 for R1JJH@VM1.CC.UAKRON.EDU by www.ccl.net (8.6.1/930601.1506) id LAA07490; Tue, 16 Nov 1993 11:12:56 -0500 Received: from VM1.CC.UAKRON.EDU (MAILER@AKRONVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H5DQHLI3FK8XFUJN@phem3.acs.ohio-state.edu>; Tue, 16 Nov 1993 11:12:48 EST Received: from AKRONVM (NJE origin R1JJH@AKRONVM) by VM1.CC.UAKRON.EDU (LMail V1.1d/1.7f) with BSMTP id 3792; Tue, 16 Nov 1993 11:11:24 -0500 Date: Tue, 16 Nov 1993 11:03:12 -0500 (EST) From: Jack Houser Subject: Dummies in Gaussian To: Supercomputer bulletin board Message-id: <01H5DQHLI3FM8XFUJN@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear Netters: I am trying to construct a Z-matrix for Gaussian 90 using two dummy atoms, but the program crashes with the message "Too many symbols in list", or something like that. I am using variable names, but they all are spelled correctly and none are missing. The only thing I can figure is that the id number of the second dummy never appears in the distance column, though it does in the angle and dihedral columns. Does every dummy have to be shown as having some other atom bonded to it (as opposed to its being bonded to another atom), or can you only have one dummy in the Z-matrix? Thanks. Jack Houser From noy@tci002.uibk.ac.at Tue Nov 16 12:27:24 1993 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.1/930601.1506) id LAA07802; Tue, 16 Nov 1993 11:47:21 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA18470 (5.65c/IDA-1.4.4 for ); Tue, 16 Nov 1993 17:47:12 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA24134; Tue, 16 Nov 1993 17:47:10 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9311161647.AA24134@tci002.uibk.ac.at> Subject: Molecular Dynamics program To: chemistry@ccl.net Date: Tue, 16 Nov 1993 17:47:09 +0100 (NFT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 976 Dear Netters, Does anybody know where I can get a molecular dynamics program, namely, KGNMCYL mentioned in MOTECC-89 of which implemented by Prof. Lie and Prof. Clementi ? Both FTP site and personal e-mail address are appreciated. Thanks a lot in advance. best wishes, Noy ---------------------------------------------------------------------------- NAME : Teerakiat Kerdcharoen (NOY) ADDRESS : Theoretische Chemie, Innrain 52 a, Universitaet Innsbruck A-6020, Innsbruck, Austria E-MAIL : noy@tci.uibk.ac.at,noy@tci2.uibk.ac.at, noy@tci5.uibk.ac.at : noy@tci6.uibk.ac.at, c72454@tci3.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) : teera@chulkn.chula.ac.th ( Bangkok ) : oitkc@cuuc.chula.ac.th ( Bangkok ) RESEARCH : Computer Aided Molecular/Material Design ( CAMMD ) ----------------------------------------------------------------------------- From news@nntp-server.caltech.edu Tue Nov 16 13:27:13 1993 Received: from punisher.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.1/930601.1506) id NAA08565; Tue, 16 Nov 1993 13:24:24 -0500 Received: from gap.cco.caltech.edu (gap-gw.cco.caltech.edu) by punisher.caltech.edu (4.1/DEI:4.41) id AA15581; Tue, 16 Nov 93 10:24:21 PST Received: by gap.cco.caltech.edu (4.1/DEI:4.41) id AA05668; Tue, 16 Nov 93 10:23:20 PST To: mlist-chemistry@nntp-server.caltech.edu Path: nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: mlist.chemistry Subject: "Bead" or quasiparticle force fields for proteins Date: 16 Nov 93 10:24:13 Organization: Materials Simulations Center Lines: 18 Message-Id: Nntp-Posting-Host: bach.wag.caltech.edu I sent this message to bionet without much luck, so I thought I'd try here. I'm interested in "bead" or quasiparticle force fields to model protein dynamics, minimization, and so on. By such a model I mean one in which an entire amino acid is modelled using a single particle. Any pointers people can give me to good review articles on the subject would be greatly appreciated. Thanks in advance. Rick -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX From Patrick.Bultinck@rug.ac.be Tue Nov 16 13:31:39 1993 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.1/930601.1506) id NAA08516; Tue, 16 Nov 1993 13:16:18 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA27028 (5.65c/IDA-1.4.4 for ); Tue, 16 Nov 1993 19:15:56 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA08735; Tue, 16 Nov 93 19:13:42 +0100 Date: Tue, 16 Nov 1993 19:02:22 +0100 (MET) From: Patrick Bultinck Subject: Summary / MM parameters macrocycles??? To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 17023 Hi netters, About a week ago I wrote the message beneath. I would like to thank everybody who gave his opinion, advice or comment to the questions I asked. Also many thanks for the good-luck wishes... Please find a summary of the answers below. MY MESSAGE : Dear Netters, On Nov. 24th. I will have to pass a test to see if I get a scholar-ship for the next year of my doctoral research. I am now going to start performing ab initio calculations involving complexes formed between some alkaline-earth metal ions and some crown structures and macrocycles. In my project paper I referred to molecular mechanics as the most widely used (but non-quantumchemical) method to computationaly study these compounds. I have found some articles in which was stated that a major problem with MM is that the method is only as good as the used parameters. There appear to be some problems obtaining good values for these parameters. As the examination jury are probably going to ask me why this is such a problem I would like to know if someone can help me with a reference to some article that explaind the trouble or if someone knows a good textbook. Off course I would also be grateful if someone just gives his opinion why this constitutes a problem ! Summary : hopefully before the end of the week ***********************Patrick Bultinck********************************** ************Lab. for General and Inorganic Chemistry********************* **********************University of Ghent******************************** ****************************Belgium************************************** **************E-mail : Patrick.Bultinck@rug.ac.be************************ But come on Heisenberg you must be sure about something......... RECEIVED MESSAGES: From: "John M. Simmie, University College, Galway, Ireland" <0001877S@bodkin.ucg.ie> Subject: mm parameters To: patrick.bultinck@rug.ac.be Patrick: Molecule A consists of atom X bonded to Y, Z, etc Molecule B consists of atom X bonded to Y, Z, etc deduce the parameters X(Y)(Z).. from fitting the experimental data for A now attempt to predict data for B from parameters BUT A is not = B therefore no good reason why prediction should be exact (close maybe as you expand the number of parameters but this self-defeating if taken too far) Regards, John ------------------------------------------------- Dr. John M. Simmie Chemistry Department Roinn na Ceimice University College Colaiste na hOllscoile Galway Gaillimh Ireland Eire Fax: (+353)-91-25700 Fsn:(+353)-91-750388 ------------------------------------------------- XRASIMMIE@BODKIN.UCG.IE From: Tilman Brodmeier To: Patrick.Bultinck@rug.ac.be Subject: RE >> MM parameters/macrocycles ??? Hi, Have a look at the paper of my collegue: M. Badertscher et al., J. Comput. Chem. Vol 11, No 7, 819-28 (1990) Hope this can help you, bye Tilman From: young@slater.cem.msu.edu (Dave Young) To: Patrick.Bultinck@rug.ac.be Subject: MM parameters Hi, I thought I would point out some things about molecular mechanics that will seem obvious once I explain them but are often overlooked. What molecular mechanics does is to use an analytic form, such as a Morse potential for each of the forces acting on the atoms in a molecule. The constants within these equations are obtained from experimental or (less often) ab initio data. There are several direct consequences of this method. First: The analytic form being used may not describe the actual shape of the potential. There are a number of analytic forms being used. A Morse or Leonard-Jones potential has a fair chance of describing dissociation, but they are not exactly correct for all molecules. Some force fields even use a harmonic potential that won't dissociate at all, but they get reasonable equlibrium geometries. For an extreme case, look up the dissociation curve for the Cu2 dimer It has extra maxima and minima in it that none of these analytic expressions can touch. Second: Even if you adequately describe the behavior of an atom in one environment, it may behave differently in another environment. Thus to do really well you have to make new force field parameters fitted to experiment for every simulation you run. If you are willing to just accept the parameters in a known force field you are taking a good average behavior, but have no guarantees on how well it will work on your system. For this reason, you must be very careful in how much you trust the results from all-purpose force fields such as MM2, MM3 or Dreiding. This is also why there are specific force fields such as the "protein only" force fields. Third: The behavior of the chemistry is modeled based on which atoms are bonding together. I don't know of any force field taking second nearest neighbor interactions really well into account. For this reason, the difference in chemistry between a benzene ring and a benzene ring with an electron withdrawing group attached are too subtle for any standard force field. You could try doing this sort of thing by having two complete sets of parameters for these two types of benzene rings, but it would be really hard to get exactly right. Now, the way that you usually use mechanics is as follows. First look at the stuff I said above and ask yourself if it has a chance of working for the system you are interested in. Second, look through the literature for mechanics studies of systems similar to your own and see which force fields they used, whether they came up with a few new parameters for that specific case, and to what extent it was qualitative or quantitative when compared to experiment. If you need to fit your own parameters, you will either have to be really careful and follow closely how people justify their choices or work with someone who does this sort of thing. Present your work in guarded speach such as "We realize that there are appoximations in the force field approach, but this force field has a history of correctly giving the qualitative results we are interested in with systems very similar to ours." The mechanics/dynamics force field approach to chemistry can be a really great way to model chemistry as long as you always ask yourself if the method and results are chemically sensible and don't trust them for more than they can give. Good Luck Dave Young young@slater.cem.msu.edu youngdc@msucem From: alex@tammy.harvard.edu (Alex Mackerell) To: Patrick.Bultinck@rug.ac.be Subject: parameters Patrick, Congratulations, you have achieved a level of enlightment concerning the inherent limitations in empirical force field calculations which a majority of individuals using empirical force field calculations never achieve. Basically, the simplicity of the mathematical model used in empirical force field calculations leads to the limitations that the approach is only as good as the parameters employed. This simplicity is required due to the large size of the systems being studied via empirical approaches (thousands of atoms). In order to properly parameterize systems extensive amounts of experimental and ab initio data must be taken into account to insure that the parameters are not biased. As computer resources increase and the amount of experimental data to use as the basis for the development of parameters increases the quality of the parameters coninues to improve. Thus, empirical force field parameters will always contain room for improvement and, more importantly, when performing and analyzing results from empirical force field calculations the potential for the parameters to bias those results must always be taken into account. It should be remembered that all theoretical approaches for the study of chemical systems employ models which attempt to reproduce reality. None of those models are reality. Even molecular orbital calculations, which use a much more detailed model as compared to empirical force field calculations, also have limitations concerning the accuracy of the obtained results. I have spent the last 6 years optimizing the CHARMM22 all-hydrogen empirical force field parameters for proteins, nucleic acids and lipids. The end is not in sight. Good luck with your examination. Alex MacKerell From: burkhart@goodyear.com (Craig W. Burkhart) To: Patrick Bultinck Subject: Re: MM parameters/macrocycles ??? Patrick: There are several reasons why you should always look at a molecular mechanics force field with a great deal of scepticism. Among them are: 1. Force fields are usually tailored, through the use of its own database of structures, for a particular application in a particular range of temperature. 2. The form of the potential energy function is at best a crude approximation of the underlying quantum mechanical effects (e.g., polarizability). So whether you are using a standard Lennard-Jones or Buckingham function, be certain that it too is a MODEL of reality. 3. In dealing with special energy functions, such as hyperconjugation or hydrogen bonding, the form of the functions (Fourier parameterization, angle-dependent LJ functions, for example) the data used to make the coefficients are difficult to test for "goodliness". There are many more reasons to be sceptical, of course, but in my opinion these are the primary culprits. Be especially cognizant of Item 1. In your studies you should ALWAYS use a parameter set that has been "tuned" to your problem. DO NOT use a parameter set based on proteins for work with the thermodynamics of hydrocarbons. If you cannot readily find a force field suitable for what you want to accomplish, you will have to derive one for yourself. In your case you are interested in alkaline-earth metal complexes. Note that ionic species are difficult to parameterize, since the form of the potential energy function is different for each family. For example, the potential energy form is different for alkaline earth ions and transition metal ions. In the case of ionic species, you should also be sensitive to the fact that you will have to use a RELIABLE means of computing the charges of the species if it has covalent character (as in the case of some organolithium molecules). Just using MNDO is NOT enough. As for a reference on the usage and form of various potential functions, I can think of no better reference than this classic work: J.O. Hirschfelder, C.F. Curtiss and R.B. Byrd, THE MOLECULAR THEORY OF GASES AND LIQUIDS, Wiley, 1964. My copy has a green binder--thus, I call it the "green bible". It should be the first stop of anyone interested in the statistical mechanics of molecular systems. In Chapter 8, you will find the answers to why the temperature range is important as well. I have been in the field for about 13 years, and this book has never been far from my side. Good luck on your examinations. If I can be of further service, contact me at your convenience. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.4431 Akron Technical Center Fax: 216.796.3947 Akron, OH 44309-3531 -------------------------------------------------------------------------- "For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled." - Feynman -------------------------------------------------------------------------- From: stevens@rainbow.uchicago.edu (Jonathan Stevens) Apparently-To: Patrick.Bultinck@rug.ac.be Patrick, Here is one of those opinions you asked for. The problem is probably one of transferability. MM is like semiempirical theory in that the parameters used is the calculations are obtained by "fitting" them so that calculations on molecules that are known experimentally are made to reproduce the experimental data. The parameters thus obtained are then "transferred" to systems similar (but of course not identical) to the system from which the parameters were obtained. Since the new system is similar but not identical to the old, the parameters may or may not be good for accurate calculations of that system. Discussions of this phenomenon can probably be found in any book about semiempirical theory (or in your case MM); this is where you would have to go for more details. I know of no such book about MM myself. Hope this helps. Jon Stevens "Your brush with greatness is over." -"Flyin'" Brian Pillman From: sling@silver.ucs.indiana.edu To: Patrick.Bultinck@rug.ac.be Subject: Re: MM parameters/macrocycles ??? In principle, everything in the natural world should be treated quantum mechanically (see, e.g. E.H. Wichmann, Quantum Physics, Berkeley Physics Courses, Vol. 4, McGraw Hill, 1971), this includes both microscopic and macroscopic objects, from atoms and molecules to pendulums and clocks. However, the correspondence principle telles us that the quantum treat- ment to macroscopic objects would give us exatly the same results as that of classical mechanics. (Do not be bothered by quantum chaos here, at least for the time being Molecules are small enough that they should be treated quantum mechanically, but the present technology still presents much difficulties in so doing, therefore the molecular mechanics which is basically applications of classical mechanics. To some extent, molecular mechanics might be able to account for some phenomena that are classical in nature - treating atoms like little balls or point masses and ignoring their wave nature, but it is generally speaking not a valid approach in principle for atoms are waves as well as particles, it is the interference of the waves that form and break the chemical bonds, for example. Consequently some experimental parameters might be set in to guide the computations, some adjustable paramenters might be used to "variationally" match the experiments, and so on. These are natural extensions of the incompetence of the principle matter behind: classical mechanics. I am not saying that there is anything wrong so doing, but definitely like anything else that has a label of time value in science and technology, molecular mechanics will not be the ultimate theory for molecules because of its starting point. From: susan jackels Subject: Re: MM parameters/macrocycles ??? To: Patrick Bultinck Dear Patrick, There's an article by Benjamin Hay in Chem. Revs. (1993) on use of MM with crown ethers and alkali metals. Hope you find it useful. Susan C. Jackels Department of Chemistry Wake Forest University Winston-Salem, NC 27109 Phone: (919)759-5514 FAX: (919)759-4656 Internet: sjackels@ac.wfunet.wfu.edu On sabbatical for 1993-1994 at: Department of Medicinal Chemistry 308 Harvard Street S.E. University of Minnesota Minneapolis, MN 55455 Phone: (612)626-4429 To: Patrick.Bultinck@rug.ac.be From: dwhite@assistant.beckman.uiuc.edu Subject: MM Parameters/Macrocycles >There appear to be some problems obtaining good values for these >parameters. As the examination jury are probably going to ask me why this >is such a problem I would like to know if someone can help me with a >reference to some article that explaind the trouble or if someone knows a >good textbook. >Off course I would also be grateful if someone just gives his opinion why >this constitutes a problem ! For a godd philosophical type introduction to MM, there is an ACS monograf available (ACS monograf # 177, by Ulirch Burkert and Norman L Allinger). I would say the essential problem with MM and transition metals is the wide variety of geometries and oxidation states available compared to the organic family. In part this problem has been addressed by Rappe with the introduction of the Universal Force Field and one of his papers has an excellent introduction to MM and transition metal chemistry (Rappe, A.K.; Colwell, K.S.; Casewit, C.J. Inorg. Chem. 1993, 32, 3438). As far as the specific issue of chelkates and macrocycles goes, Rob Hancock has done a lot of work on this particular system. His papers are referenced in Rappe's (one is not: Hancock, R.D. Prog. Inorg. Chem. 1989, 37, 187). I know Rob is on meail, but do not have his address, at the moment he is a visiting professor at Texas A&M. One of his PhD graduates, Peter Wade, may well have some valuable insights for you, Peter can be contacted at pwade@nuustak.csir.co.za. I hope this helps. Good luck for the oral. Dave From schurko@CC.UManitoba.CA Tue Nov 16 14:27:11 1993 Received: from canopus.CC.UManitoba.CA for schurko@CC.UManitoba.CA by www.ccl.net (8.6.1/930601.1506) id NAA08767; Tue, 16 Nov 1993 13:44:49 -0500 Received: from pollux.cc.umanitoba.ca by canopus.CC.UManitoba.CA (4.1/25-eef) id AA01837; Tue, 16 Nov 93 12:44:41 CST Received: by pollux.cc.umanitoba.ca (4.1/25-eef) id AA29632; Tue, 16 Nov 93 12:44:42 CST Date: Tue, 16 Nov 1993 12:39:38 -0600 (CST) From: Robert Schurko Subject: Re: Dummies in Gaussian To: Jack Houser Cc: Supercomputer bulletin board In-Reply-To: <01H5DQHLI3FM8XFUJN@phem3.acs.ohio-state.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 16 Nov 1993, Jack Houser wrote: > Dear Netters: > > I am trying to construct a Z-matrix for Gaussian 90 using two dummy atoms, > but the program crashes with the message "Too many symbols in list", or > something like that. I am using variable names, but they all are spelled > correctly and none are missing. The only thing I can figure is that the > id number of the second dummy never appears in the distance column, though it > does in the angle and dihedral columns. Does every dummy have to be shown as > having some other atom bonded to it (as opposed to its being bonded to another > atom), or can you only have one dummy in the Z-matrix? Thanks. > > Jack Houser > You have to specify an arbitrary distance for connecting the two dummy atoms (I always use 1.0). Here is an example: This is a 3,5-difluoroaniline with two dummy atoms used to help define various angles and bond distances needed to complete an inversion on the NH2 centre: %mem=4500000 %chk=90_tmp # test rhf/6-31g* opt optcyc=40 iop(2/16=1) Aniline nh2 invert To: chemistry@ccl.net Subject: XPS of Perfluoropolyether (PFPE) oil Dear Netters, I need help with a thesis related question. An XPS sprectrum was obtained on PFPE oil (Bray 815Z) as a film on aluminum foil. Three peaks appeared at low binding energies: 10.69 ev, 16.59 ev and 20.56 ev. The spectroscopist refers to these peaks as "valence level density of States". The higher energy O, F and C peaks appeared normal. My simple AM1 model PFPE gives a HOMO energy of -13.4 ev which, according to Koopmans' theorem is about equivalent to the ionization potential. I would like to use the XPS data as evidence that my model is a good representation of reality but the 2.7 ev difference begs for an answer. My answer is that the work function of a specimen is often 2 to 4 ev lower than its (gas phase) ionization potential due to image forces. Conclusion: the XPS data supports the model. Comments are more than welcomed. Pat Hogue From news@nntp-server.caltech.edu Tue Nov 16 19:27:17 1993 Received: from punisher.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.1/930601.1506) id SAA10368; Tue, 16 Nov 1993 18:34:08 -0500 Received: from gap.cco.caltech.edu (gap-gw.cco.caltech.edu) by punisher.caltech.edu (4.1/DEI:4.41) id AA13004; Tue, 16 Nov 93 15:33:55 PST Received: by gap.cco.caltech.edu (4.1/DEI:4.41) id AA15596; Tue, 16 Nov 93 15:32:54 PST To: mlist-chemistry@nntp-server.caltech.edu Path: nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: mlist.chemistry Subject: Preliminary Summary -- Protein "Bead" Models Date: 16 Nov 93 15:33:52 Organization: Materials Simulations Center Lines: 77 Distribution: mlist Message-Id: Nntp-Posting-Host: bach.wag.caltech.edu Since there was so much interest in the protein "bead" models I decided to post a preliminary list of the references I've received, even though they are still pouring in. I'll post an updated list in a couple of days. Everyone was very helpful. Thanks for your generousity. ---------------- Crippen Bipol 29:1479 JMolBiol 227:876 Sippl JCompAidMolDes 7:473 JMolBiol 213:859 224:725 Schneller Weaver Biopol 33:1519 Gerber Biopol 32:1003 Covell Proteins 14:409 Wilson Doniach Proteins 6:193 Skolnick JMolBiol 212:787 215:183 221:499 PNAS 86:1229 AnRevPhysChem 40:207 Maggiora Meth Bioc Anal 35:1 Levitt CurrOpStrBio 1:224 Grest et al CompPhysComm 55:269 Godzik et al JCompAidMolDes 7:397 Miyazawa Jernigan Macromolecules 18:354 Bryant & Lawrence Proteins 16:92 Sun Protein Science 2:762 Head-Gordon Brooks Biopol 31:77 Book: Computer Simulation of Polymers, Roe, ed. Prentiss Hall, 1991 Thanks to Drs. Eofsson, Gordon, Garavelli, Black, Case, Godzik, Burkhart, Vasquez, Davis, Stouten, for the helpful replies. -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX