From graham@sentex.net Thu Feb 23 00:52:08 1995 Received: from granite.sentex.net for graham@sentex.net by www.ccl.net (8.6.9/930601.1506) id XAA26037; Wed, 22 Feb 1995 23:57:17 -0500 Received: from kw-ttyd3.sentex.net (kw-ttyd3.sentex.net [204.50.3.21]) by granite.sentex.net (8.6.5/8.6.9) with SMTP id XAA15921; Wed, 22 Feb 1995 23:48:31 -0500 Message-Id: <199502230448.XAA15921@granite.sentex.net> X-Sender: graham@mail.sentex.net X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Feb 1995 23:32:59 -0500 To: marvin@biosym.com (Marvin Waldman), CHEMISTRY@ccl.net From: graham@sentex.net (Graham Hurst) Subject: Re: CCL:conformational isomers At 02:47 PM 2/22/95 -0800, Marvin Waldman wrote: >On Tue, 21 Feb 95 4:08:12 EST, Dongchul Lim wrote: > >> Is there a simple way of testing if two given conformational isomers >> are equivalent? [good stuff deleted] >The ideal/correct solution would be to >compare both the energy as well as all combinations of RMS comparisons >of topologically equivalent atoms until the RMS difference found >for a given comparison pair fell below some threshold. I am not >aware of a software package that has actually implemented such >an algorithm, and would be very interested to hear about one that >does. The Conformational Search module of the ChemPlus set of extensions for HyperChem uses energy and RMS compairisons of topologically equivalent atom pairings. I've been following this discussion with some interest. When I wrote the Conformational Search module of ChemPlus, I implemented the following tests to compare for equivalent conformations that might result from the search. The comparisons available are (in the order that the program can optionally execute them) are: 1. Changed chirality (R or S) of chiral centers with 4 bonded neighbours. (Chiral centers are determined by HyperChem.) 2. Energy (from HyperChem) within a user adjustable range. 3. Varied torsions within a user adjustable range. This test is turned off by default, since it doesn't handle topologically equivalent dihedral angles. 4. R.M.S. deviation for a least-squares overlay of atoms. As Marvin Waldman pointed out, one needs to compare with all topologically equivalent permutations of atom order and this option (discussed further below) is available in ChemPlus. A subset of atoms can also be specified for the comparision. I initially included an option for comparison of inertial moments (suggested earlier by Leif Norskov ) but I abandoned it because it seemed too sensitive a measure, with suitable tolerances varying widely with the number of atoms. If the option to use equivalent atoms in the RMS comparison is turned on, the program generates all equivalent atom order permutations. The algorithm I used for this is basically brute force, O(N!) at worst, but being able to compare element type and number of bonds for each topological "node" allows considerable trimming of the paths. Further trimming results from only considering a subset of atoms (eg. no hydrogens or only backbone atoms) so that permutations of ignored atoms are unnecessary (assuming equivalent sets are either all included or all excluded). >So, the bottom line answer to the question, is: No, I don't think >there is a SIMPLE way to do this. I agree! It took me about a month to puzzle out and implement an algorithm for generating equivalent atom orders! As Valery Golender pointed out, the conformational isomer problem is a specific instance of isomorphism of 3D objects. Cheers, Graham P.S. If you want more ChemPlus or HyperChem product info, please send email to info@hyper.com, not to me because I don't work there anymore. ------- Graham Hurst, PhD or Cambridge, Ontario, Canada From CHEM8@vax.york.ac.uk Thu Feb 23 08:53:37 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id IAA01260; Thu, 23 Feb 1995 08:37:41 -0500 Via: uk.ac.york.vax; Thu, 23 Feb 1995 13:33:32 +0000 Date: Thu, 23 Feb 95 13:34 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Jerry N. Silverman, where are you? Message-ID: <"leeman.yor.444:23.01.95.13.33.43"@york.ac.uk> Does anyone out there know of the whereabouts of Prof. Jerry N. Silverman of PVRR fame? I wish, urgently, to get back in contact with him. He was last heard of in Fort Worth, Texas and prior to that in Cambridge UK. A phone number would be most useful and/or a postal (e-mail) address. (Our beloved supervisor, Jan, has sanctioned this request). Hopefully, John Waite From CHEM8@vax.york.ac.uk Thu Feb 23 09:00:14 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id IAA01111; Thu, 23 Feb 1995 08:27:42 -0500 Via: uk.ac.york.vax; Thu, 23 Feb 1995 13:23:14 +0000 Date: Thu, 23 Feb 95 13:24 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Summary: 'ghost' writers available Message-ID: <"leeman.yor.210:23.01.95.13.23.26"@york.ac.uk> Hi Netters, Just over a week ago I asked CCL about getting in contact with a 'ghost' writer. Below are the replies of people interested in doing this. My thanks to all who replied and CCL, John From: sparkin@com.imag-alchemy (Steven H. Parkin) Professor Waite: Both my wife, an extremely proficient editor, and I, a sometime computational physical chemist, are interested in your proposal to be "ghost" writers. Your terms seem satisfactory, and we think we fill your fluency/access requirements. FYI, my wife is Linda Parkin. Our phone/fax is (619) 329-2774; our address is 67-642 Club House Road, Desert Hot Springs, CA 92241, USA; and our e-mail address is found in my signature. We look forward to working with you in the future. Steven H. Parkin Imaginative Alchemy sparkin@imag-alchemy.com From: sparkin@com.imag-alchemy (Steven H. Parkin) Professor Waite: In our haste to respond to your post regarding a 'ghost writer,' we failed to include a list of qualifications. My wife, Linda Parkin, has a BS in English, Drama, and Journalism from BYU. She has taught English writing in the 8-10 grades and Journalism in the 9-12 grades. She also worked in and managed the publications department of Hughes Semiconductors (Newport Beach, CA) for 7 years, editing the works of the engineers and scientists for publication and in the preparation of grant proposals. She currently operates an editing and desktop publishing service for several companies in So. California. I have an BS in Chemistry from Stanford, an MS in Chemistry from Univ. of So. California, and I am still trying to finish a Ph.D. in Theoretical Chemical Physics from Univ. of Calif., Irvine. I have over 30 years experience in various fields of chemistry, including 7 years as the owner/operator of an analytical biochemistry laboratory that was sold to Smith, Kline & French, and 5 years as a principal in a pharmaceutical manufacturing company in Los Angeles and Beirut (prior to the war!!). Over the last 4 years, I have been working on the development of an instrument, really a prototype, to test one of my theories of a new paradigm to non-destructively analyze metals in aircraft for corrosion and fatigue. This is why we coined the name - Imaginative Alchemy. Also, as I recall, I have been the author or co-author of 4 or 5 publications, abstracts and posters, dealing primarily in the use of HPLC and GC in the analysis of hormones and toxic substances. I hope this additional information is of value to you, and that Linda and I can assist you as 'ghost writers' in the future. Thank you for your consideration. Steven H. Parkin Imaginative Alchemy sparkin@imag-alchemy.com From: stan@pl.gda.univ.chem.sun1 (Stanislaw Oldziej) Dear Mr Waite, i'm finishing my PhD Thesis and i'm looking for new good scientific theme. It's an intresting offer for me. Best regards, Stan Stanislaw Oldziej Faculty of Chemistry University of Gdansk Sobieskiego 18, 80-952 Gdansk POLAND fax: (048-58)-41-03-57 e-mail: stan@sun1.chem.univ.gda.pl or stan@icm.edu.pl From: champagn@be.ac.fundp.scf.messiaen (Benoit Champagne) Hello Dr. Waite, My name is Benoit CHAMPAGNE and I am interested by your proposition. I got my PhD in the University of Namur under the supervision of Professor J.M. Andre in 1992. Then I spent 7 months at the Quantum Theory Project of the University of Florida with Dr. Y. Ohrn as supervisor. Now, I am a Senior Research Assistant of the Belgium National Fund for Scientific Research. I am working on the development, characterization and use of techniques to compute the polarizabilities and hyperpolarizabilities of oligomers and polymers. Recent developments are the application of RPA to polymers to get the coupled Hartree-Fock asymptotic longitudinal polarizabilities per unit cell (static and dynamic); the use of the double harmonic approximation to evaluate the vibrational contribution to the polarizability of finite polyacetylene chains and the investigation of such correlation effects. If you want, I can give you a list of some reference papers. We have a phone, a fax,... Some comments would come in the future if considering computational chemistry and/or NLO properties. Sincerely yours, Benoit From antonio@linus.qui.ub.es Thu Feb 23 10:02:16 1995 Received: from morgana.ird.ub.es for antonio@linus.qui.ub.es by www.ccl.net (8.6.9/930601.1506) id JAA01677; Thu, 23 Feb 1995 09:01:53 -0500 Received: from linus.qui.ub.es by morgana.ird.ub.es with SMTP (16.7/16.2) id AA14432; Thu, 23 Feb 95 14:45:38 +0100 Received: by linus.qui.ub.es (931110.SGI/930416.SGI) for @merlin.ub.es:chemistry@ccl.net id AA04500; Thu, 23 Feb 95 14:59:16 -0800 From: "Antonio Buljan" Message-Id: <9502231459.ZM4498@linus.qui.ub.es> Date: Thu, 23 Feb 1995 14:59:15 -0800 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: DFT-plane waves codes Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear Netters! I would like to receive information about the opinions and experiences with the Density Functional codes using plane waves (commercial codes as castep from MSI, plane wave from Biosym or public domain codes like fhi93cp or others). I promise to summarize the answers. Thanks in advance Antonio Buljan Department of Physical-Chemistry e-mail: antonio@linus.qui.ub.es From matt@synthesis.chem.arizona.edu Thu Feb 23 10:05:52 1995 Received: from synthesis.chem.arizona.edu for matt@synthesis.chem.arizona.edu by www.ccl.net (8.6.9/930601.1506) id JAA02987; Thu, 23 Feb 1995 09:30:31 -0500 Received: by synthesis.chem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA10561; Thu, 23 Feb 1995 07:26:43 -0700 Date: Thu, 23 Feb 1995 07:26:43 -0700 (MST) From: Matt Stahl To: Marvin Waldman Cc: CHEMISTRY@ccl.net Subject: Re: CCL:conformational isomers In-Reply-To: <199502222247.OAA02375@iris131.biosym.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, The problem of duplicate conformer removal certainly is challenging, especially to anyone doing extensive conformational searches. The "easy" method of detection is to compare a unique identifier based on atomic coordinates. Shape descriptors such as the sum of interatomic distances, or the sum of all triangles in a molecule provide a single number to identify a conformation. In this sense, energy is also a "shape descriptor" because it is simply a function operated on a set of coordinates. As pointed out by Dr. Waldman, there is always the possibility of ambiguity when using this kind of descriptor. I have seen cases in larger bicyclo alkanes where very different conformations had the same mechanics energy to the 5th or 6th decimal place! There are several matters that must be addressed with regard to comparing conformations. Rms fitting may not be the best measure of similarity when comparing long acyclic chains because of the 'torque' effect. Torsional comparisons certainly have valid applications. In general, rms fits work well with the exception of the problems of automorphism and enantiomeric coordinates. Generating enantiomers is trivial. Simply multiply all of the x, y, or z coordinates by -1 to generate the mirror image. Automorphisms can be more of a problem. They can be discovered by connectivity matrix manipulations (see balasubramanian in j. chem. inf. comp. sci. may/june 1994). A much quicker approach is to effectively do an atom-by-atom max common substructure search using comparisons of atom types. Once the automorphisms are discovered they can be used in both torsional and rms comparisons. Pat Walters and i have written a program called Padre (Population Analysis and Duplicate REmoval) that will read multi-structure files, automatically generate the automorphisms (and enantiomers if desired), and do rms or torsional comparisons and identify duplicate conformers. It will also map rings onto each other and compare all possible overlays. Padre is FAR from completion, but the features currently implemented are solid. Please contact me directly if you are interested in this software. sincerely, matt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mr. Matthew Stahl | Department of Chemistry | I'd rather be right half of the University of Arizona | time than half right all the Tucson, AZ 85721 | time. matt@synthesis.chem.arizona.edu | -Malcom S. Forbes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From dimitris@3dp.com Thu Feb 23 10:06:46 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id JAA03805; Thu, 23 Feb 1995 09:47:49 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA11498; Thu, 23 Feb 95 10:45:08 -0500 Received: by europa.3dp.com (931110.SGI) id AA13205; Thu, 23 Feb 95 10:41:26 -0500 From: "Dimitris Agrafiotis" Message-Id: <9502231041.ZM13203@europa.3dp.com> Date: Thu, 23 Feb 1995 10:41:26 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Summary Part 2: metrics of molecular diversity Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 There were two more replies to my posting regarding metrics for molecular diversity that I did not include in my previous message. One is attached, and the other was unfortunately not saved. It was sent by James Wikel >from Lilly Research Labs. Maybe he's kind enough to repost his message to the net. Sorry for the inconvenience. Ciao, ------------------------------------------------------------------------------ Date: Mon, 9 Jan 95 08:04:57 +0100 From: byw@novo.dk (Robert Bywater) Message-Id: <9501090704.AA25135@ligand.novo.dk> To: dimitris Status: OR Dear Dr. Agrafiotis You might wish to include the method of shape descriptors in your search for methods of studying molecular diversity in multidimensional physicochemical space. I am presently writing ( one or two more ) articles on this subject ( see the references to find what has already been published. You might also wish to consult a book, shortly to be published: " Molecular Similarity and Reactivity: from Quantum Chemistry to Phenomenonolgical Approaches " R. Carbo, Ed. Kluwer Verlag 1994/5 where you will find articles on essentially all aspects of this subject. Call me back if you have any specific enquiries. Robert Bywater \item Leicester S.E., Finney J.L., and Bywater R.P., Description of molecular surface shape using Fourier descriptors. J. Mol. Graph. (~1988~) {\bf 6} 104-108. \item Leicester S.E., Finney J.L. and Bywater R.P., A quantitative representation of molecular surface shape i) Theory and development of the method. {\em J. Math. Chem.} (~accepted for publication 1994~) \item Leicester S.E., Finney J.L. and Bywater R.P., A quantitative representation of molecular surface shape ii) Protein classification using Fourier descriptors and classical scaling. {\em J. Math. Chem.} (~accepted for publication 1994~) \item Max N.L. and Getzoff E.D. Spherical harmonic molecular surfaces. {\em IEEE Computer Graphics and Applications} (~1988~) {\ 8} 42-50. \end{itemize} ****************************** * * * Robert Bywater * * * * Biostructure Department * * NOVO NORDISK A/S * * * * email byw@novo.dk * * fax :: +45 4442 1400 * ****************************** -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From dimitris@3dp.com Thu Feb 23 10:07:43 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id JAA02495; Thu, 23 Feb 1995 09:22:31 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA11295; Thu, 23 Feb 95 10:19:46 -0500 Received: by europa.3dp.com (931110.SGI) id AA13183; Thu, 23 Feb 95 10:16:05 -0500 From: "Dimitris Agrafiotis" Message-Id: <9502231016.ZM13181@europa.3dp.com> Date: Thu, 23 Feb 1995 10:16:04 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Summary: metrics of molecular diversity Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Here is my original posting and a summary of the responses I received regarding metrics of molecular diversity. Thanks to all who responded, and sorry for the rather long delay in posting the summary. Ciao, -------------------------------------------------------------------------------- From: "Dimitris Agrafiotis" Message-Id: <9501061004.ZM3762@europa.3dp.com> Date: Fri, 6 Jan 1995 10:04:10 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: CCL:metrics for molecular diversity Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Sender: chemistry-request@ccl.net Errors-To: jkl@ccl.net Precedence: bulk Status: OR I am looking for a review of all the metrics that have been used to measure molecular diversity in multidimensional physicochemical space. I am not so much interested in metrics of distance between two compounds such as Minkowski indices etc, but rather indices that measure the diversity exhibited by a particular set of chemical compounds. I would appreciate any pointers to books/reviews/papers on that subject and will summarize the results in a future note. Thanks for your help. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 -------------------------------------------------------------------------------- Date: Fri, 6 Jan 95 15:46:56 -0800 From: moises@biosym.com (Moises Hassan) Message-Id: <9501062346.AA23727@iris123.biosym.com> To: dimitris (Dimitris Agrafiotis) Subject: Re: metrics for molecular diversity Status: ORp There is a recent review of molecular indices (topological,geometrical, electronic, ...) in the context of QSAR/QSPR in: Katritzky, Alan and Gordeeva, Ekaterina, J. Chem. Inf. Comput. Sci. 1993, 33, 835-857 I"m also very interested in the area of assessment of molecular similarity/diversity. Perhaps we can establish contact and share information -- =================================================================== Moises Hassan,Ph.D. Life Sciences Business Unit Biosym Technologies, Inc. Phone: (619) 546-5314 9685 Scranton Road Fax: (619) 458-0136 San Diego, CA 92121-2777 e-mail: moises@biosym.com =================================================================== -------------------------------------------------------------------------------- Date: Mon, 09 Jan 1995 08:59:09 -0600 (CST) From: MARTIN%cmda@randb.abbott.com Subject: Re: CCL:metrics for molecular diversity To: dimitris Message-Id: <01HLMXRPOWO28YM5S5@RANDB.PPRD.Abbott.Com> X-Vms-To: RANDB::IN%"dimitris@3dp.com" X-Vms-Cc: MARTIN Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Status: ORp Let me know what you hear. My favorite, unpublished per se, is to calculate distances between Hbond donors, acceptors, positively charged groups, and negatively charged groups; detect the cliques in common; count how many unique cliques there are. Sorry, I forgot to add "hydrophobic" groups, because they give shape. We are part way to being able to do this automatically, but have been diverted by more "practical" things. I'll see if I can dig up a place where I have published any of this. Yvonne -------------------------------------------------------------------------------- Date: Mon, 9 Jan 1995 10:12:19 -0500 (EST) From: Norah Shemetulskis Subject: Re: CCL:metrics for molecular diversity To: Dimitris Agrafiotis In-Reply-To: <9501061004.ZM3762@europa.3dp.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: ORSp Hi Dimitris, I'd be interested in hearing about any work in this area. In case you might find the most recently published work out of Chiron useful see: Simon, R.J.; Martin, E. J.; Miller, S.M.; Zuckermann, R.N.; Moos, W.H. Using Peptoid Libraries[Oligo N-Substituted Glycines] for Drug Discovery. Tech Protein Chem. 1994, V, 533-539. and Zuckermann, R.N.;Martin E.J., Spellmeyer, D.C.;Stauber, G.B.;Shoemaker, K.R.;Kerr, J.M.;Figliozzi, G.M.;Goff, D.A.;Siana, M.A.; Simon, R.J.;Banville, S.C.;Brown, E.G.;Wang,L.;Richter,L.S.;Moos, W.H. Discovery of Nanomolar Ligands for 7-Transmembrane G-Protein- Coupled Receptors from a Diverse N-(Substituted)glycine Peptoid Library. J. Med.Chem. 1994,37(17),2678-2685. I'm not sure whether this reference will be much use to you, but just in case here it is (its on D-Optimal design): Baroni,M.'Clementi, S.;Cruciani, G.;Kettanch-Wold,N.;Wold,S. D-Optimal Designs in QSAR. Quant. Struct.-Act. Relat. 12, 225-231(1993). Happy New Year, Norah Norah E. Shemetulskis Biomolecular Structure and Drug Design Parke-Davis Pharmaceutical Research Division Warner Lambert Company (313)998-3360 shemetn@aa.wl.com -------------------------------------------------------------------------------- Date: Mon, 9 Jan 95 10:07:05 -0800 From: uunet.uu.net!chiremv!andromeda!martine (Eric Martin) Message-Id: <9501091807.AA20290@andromeda> To: uunet.uu.net!uunet!3dp.com!dimitris Subject: CCL:metrics for molecular diversity Status: ORSp Hello Dimitris, I am very interested in your summary of responses. Although it is not explicitly over a "multidimensional physicochemical space", I have used a simple method to compare "substructural diversity" of sets of compounds based on the Daylight database fingerprints. The Daylight fingerprint routines search through a molecular structure to find all of its substructures of up to 7 bonds. A hashing algorithm randomly assigns each substructure to one bit in a 2048 bit string. The number of bits set by the union of all fingerprints from a set of compounds is, thus, a measure of substructural diversity of that collection. Since several substructures may be assigned at random to the same bit, the number of fragments (f) required to set a given number of number of bits (b) is approximately f=2048(ln(2048/(2048-b))). Since my interest is in screening for orally available drugs, I have also divided this value by the average molecular weight of the set as a measure of "diversity density", i.e. how many substructures are available packed into small molecules. I do not have a reference, but the work is in review at J. Med. Chem. Good luck, -Eric Eric Martin martine@chiron.com 4560 Horton St., Emeryville, CA 94608 (510)601-3306, FAX (510)601-3360 -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From edel@batata.fh.huji.ac.il Thu Feb 23 11:54:00 1995 Received: from batata.fh.huji.ac.il for edel@batata.fh.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id LAA07042; Thu, 23 Feb 1995 11:40:01 -0500 Received: by batata.fh.huji.ac.il (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA23754; Thu, 23 Feb 95 18:38:58 +0200 Date: Thu, 23 Feb 95 18:38:58 +0200 From: edel@batata.fh.huji.ac.il (Arieh Edelstein) Message-Id: <9502231638.AA23754@batata.fh.huji.ac.il> To: chemistry@ccl.net Subject: New Book from Ellis Horwood Ellis Horwood Series in Physical Chemistry, 1995 Series Editor: Professor T.J.Kemp, University of Warwick Quantum Chemical and Statistical Theory of Solutions A Computational Approach B.Ya Simkin and I.I.Sheikhet Containing detailed reviews of developments in the investigation of various physical and chemical processes in liquids, this bookUs main emphasis lies in the theory of solutions used. The first part is theoretically based, and discusses methods of quantum chemistry and statistical physics as applied to simulation of liquid phase properties. Various methods are considered, including the semi-empirical and non-empirical methods of quantum chemistry, dielectric models, Monte Carlo and molecular dynamics methods. The influence of the calculational scheme on the results of calculations on solutions is discussed. The second part covers the applications of methods in the study of the properties of infinitely diluted electrolyte and non-electrolyte solutions, the mechanisms of association, chemical reactions including electron and proton transfer, and the medium influence on spectral characteristics. Emphasis is given to the powerful and informative applications of statistical physics. In combining quantum chemical and statistical approaches in one volume, this book allows readers to find their bearings in a large number of theoretical methods, and assists in applying their findings to solve various problems in solution chemistry. Readership. Physical and organic chemists; biochemists and biophysicists engaged in investigation of properties of liquids and reaction mechanisms in solutions. From fant@bioc.rice.edu Thu Feb 23 12:52:46 1995 Received: from moe.rice.edu for fant@bioc.rice.edu by www.ccl.net (8.6.9/930601.1506) id MAA08611; Thu, 23 Feb 1995 12:27:27 -0500 Received: from babs.rice.edu by moe.rice.edu (AA18541); Thu, 23 Feb 95 11:27:26 CST Received: by babs.rice.edu (931110.SGI/) (for chemistry@ccl.net) id AA14994; Thu, 23 Feb 95 11:29:36 -0600 From: "Andrew Fant" Message-Id: <9502231129.ZM14992@babs.rice.edu> Date: Thu, 23 Feb 1995 11:29:36 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: where is Multi? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Greetings: I keeps seeing Multi, a molecular modeling program for SGI written at NIEHS, referenced both here and on site lists, but I can't seem to find it anymore. THe ftp site on the nameserver at niehs.nih.gov is gone now, and ftp.niehs.nih.gov only has some strange PC software that I don't need. Has anyone seen multi lately, and could you tell me where to find it now? Thanks In Advance, Andy From dec@proteus.co.uk Thu Feb 23 13:06:11 1995 Received: from eros.britain.eu.net for dec@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id MAA08252; Thu, 23 Feb 1995 12:11:59 -0500 Message-Id: <199502231711.MAA08252@www.ccl.net> Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Thu, 23 Feb 1995 17:11:25 +0000 From: David Clark Date: Thu, 23 Feb 95 16:12:41 GMT To: CHEMISTRY@ccl.net Subject: CCL: CPU ratios I am trying to compare CPU times from a DEC MicroVax 3500 with an R3000 SGI Indigo. Does anyone have any idea of an approximate ratio that would enable me to make a fair comparison? Many thanks David David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | From ALAMBERT@Marsh.VINU.edu Thu Feb 23 15:52:24 1995 Received: from VUNET.VINU.EDU for ALAMBERT@Marsh.VINU.edu by www.ccl.net (8.6.9/930601.1506) id PAA12997; Thu, 23 Feb 1995 15:26:35 -0500 Received: from marsh.vinu.edu by VUNET.VINU.EDU (IBM VM SMTP V2R2) with TCP; Thu, 23 Feb 95 15:27:01 EST Received: from MARSH/SMTPQueue by marsh.vinu.edu (Mercury 1.11); Thu, 23 Feb 95 15:23:24 GMT-5 Received: from Mailqueue by MARSH (Mercury 1.11); Thu, 23 Feb 95 15:23:19 GMT-5 To: chemistry@ccl.net From: "Allyn Lambert" Organization: Vincennes University, Shake LRC Date: Thu, 23 Feb 1995 15:23:14 EST (GMT-5) Subject: i have a problem Return-receipt-to: "Allyn Lambert" Priority: normal X-mailer: WinPMail v1.0 (R2) Message-ID: <3714A57200@marsh.vinu.edu> i have a problem and i need a quick answer how do i get off the chem list i sort of through away the hard copy of my letter telling me how to do all of the stuff I'm very sorry for taking up bandwidth. ------------------------------------------------------ = Allyn Lambert "Bert" = "I woke up in between/ = = Vincennes University = a memeory and a dream" = = alambert@marsh.vinu.edu = -Tom Petty '94 = ------------------------------------------------------ ====================================================== ========== //////// ================ ========= //// // //// ================ ======== // // // ================ ======= // // // ================ ====== // // // ================ ===== ///////////////// ================ ==== // ================ === //////// ================ ============================================ From kappler@SECS.UCSC.EDU Thu Feb 23 17:52:18 1995 Received: from MOLENG.UCSC.EDU for kappler@SECS.UCSC.EDU by www.ccl.net (8.6.9/930601.1506) id QAA14512; Thu, 23 Feb 1995 16:59:11 -0500 Received: by SECS.UCSC.EDU (MX V3.1C) id 14351; Thu, 23 Feb 1995 13:58:27 PST Date: Thu, 23 Feb 1995 13:58:25 PST From: Mick Kappler To: chemistry@ccl.net CC: kappler@SECS.UCSC.EDU Message-ID: <0098C6AD.FE72265B.14351@SECS.UCSC.EDU> Subject: conformational isomers - annotated synopsis On Tue, 21 Feb 95 4:08:12 EST, Dongchul Lim wrote: > Is there a simple way of testing if two given conformational isomers > are equiva lent? This question can be interpreted in two ways, as Joel Polowin indicated. On Wed, 22 Feb 95 10:29:54 -0500, Joel Polowin wrote: > I don't think the situation is quite so simple -- possibly depending on > what is meant by conformers being "the same". If one is interested in structural equivalency independent of conformation, the SEMA algorithm (JACS, 96, 4834, 1974) is a solution. If one is interested in structural equivalency dependent of conformation, the solution is more complex, as Marvin Waldman pointed out. On Wed, 22 Feb 1995 14:47:42 -0800, Marvin Waldman wrote: > This is, in fact, quite a difficult and subtle question. The SEMA > algorithm which Mick Sappler proposed can be used to detect if > two CONFIGURATIONAL isomers are equivalent (ie. they have the > same or different stereochemistry). However, it will not detect > if the same configurational isomers are equivalent or not in > a CONFORMATIONAL sense. SEMA cannot detect the difference between > the gauche and trans forms of n-butane. These are CONFORMATIONAL > isomers. This is correct. The ultimate solution to the structural equivalency dependent of conformation problem will depend on analytical features of the two structures only. On Thu, 23 Feb 1995 01:47:29 EST, CBAS25 ::P_BLADON ::CBAS25 wrote: > There are several points to consider. > > (1) If the problem involves small molecules like butane where the number > of stable conformers is known... We can not assume we have anything but the two conformations that we wish to compare. Given a hypothetical structure, who knows the set of stable conformers? > (2) If the structures are more complex... then the number of conformers > could be large. But suppose that you have a set of such structures... Again, let's not assume we know. > (3) To do the matching you could use atom to atom matching... This could take a long time, considering the size of the set of structures to compare. Is time an issue? I imagine it is if you have a large set of structures to compare. On Wed, 22 Feb 1995 23:36:21 -0800, Victor M. Rosas Garcia wrote: > ...The best implementation I have seen to solve this problem is in the > program GMMX, a global minimum search utility by Serena Software. If this works for you, this is great. Unfortunately, this technique is only as good as the software and comparison of conformation A by software X to conformation B by software Y is impossible. Hence, comparisons between research groups may be a problem. This is not to mention the multiple minima problem, as E. Lewars pointed out. On Wed, 22 Feb 1995 17:10:28 -0500, E. Lewars wrote: > ...enantiomers have precisely the same energies... On Wed, 22 Feb 1995 23:32:59 -0500, Graham Hurst wrote: > The Conformational Search module of the ChemPlus set of extensions > for HyperChem uses energy and RMS compairisons of topologically > equivalent atom pairings. RMS comparisons look promising at first. Unfortunately, before the comparison can be made, the conformations need to be superimposed, which is independent of the conformation itself. Although the superimposition can be solved analytically, it is sometimes solved iteratively, and can be a source of contention. Can we solve this problem indepedent of transformation? I would love to hear more from experts in this field. This is an interesting problem and this discussion has increased our interest in publishing our latest work relating to conformational comparisons. Mick Kappler Molecular Engineering Laboratory W. T. Wipke Group Univ. of California, Santa Cruz