From jose@dqo.uncor.edu Wed Feb 12 10:22:41 1997 Received: from dqo.uncor.edu for jose@dqo.uncor.edu by www.ccl.net (8.8.3/950822.1) id JAA27523; Wed, 12 Feb 1997 09:51:41 -0500 (EST) Received: (from jose@localhost) by dqo.uncor.edu (8.6.9/8.6.9) id LAA00681; Wed, 12 Feb 1997 11:58:12 +1130 Date: Wed, 12 Feb 1997 11:58:11 +1130 From: "Lic. Jose Santiago Duca (h)" Subject: subscription to CCL To: chemistry@www.ccl.net cc: "Lic. Jose Santiago Duca (h)" Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL manager: I would like to subsribe to the CCL list. My name is Dr. Jose Santiago DUCA, Jr. and my main interest are related with computational chemistry on electron transfer processes and physical organic chemistry. I am working here at the National University of Cordoba, Argentina and I received my Ph.D degree in December 1995. Best regards, Jose Dr. Jose Santiago DUCA, Jr. e-mail: jose@dqo.uncor.edu From och6@us.wfl.com Wed Feb 12 11:22:43 1997 Received: from relay.us.wfl.com for och6@us.wfl.com by www.ccl.net (8.8.3/950822.1) id KAA28062; Wed, 12 Feb 1997 10:56:31 -0500 (EST) Received: from localhost by relay.us.wfl.com (relay-us); id KAA27417; Wed, 12 Feb 1997 10:55:15 -0500 Received: from unknown(143.193.195.2) by relay.us.wfl.com via smap (g3.0.1) id sma027390; Wed, 12 Feb 97 10:54:46 -0500 Received: from furan by us.wfl.com (nytimes); id LAA02873; Wed, 12 Feb 1997 11:08:41 -0500 Received: by furan (940816.SGI.8.6.9/920502.SGI.AUTO) for chemistry@www.ccl.net id KAA08746; Wed, 12 Feb 1997 10:35:51 -0500 Reply-To: och6@us.wfl.com (Jim Bentley) From: "Jim Bentley" Message-Id: <9702121035.ZM8744@furan.bwco.com> Date: Wed, 12 Feb 1997 10:35:49 -0500 In-Reply-To: "Dr. Dave Winkler" "CCL:Molecular multipole moments" (Feb 11, 2:02pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Molecular multipole moments Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dave, Try the PDMxx series of programs by Donald Williams. An older version (PDM88) is available from the QCPE: http://www.ccl.net/ccl/qcpe/QCPE/ent/e03/568.html I have seen web announcements of more recent versions. Regards, Jim ________________________________________________________________________ Jim Bentley, Ph.D. | Internet: och6@us.wfl.com Glaxo Wellcome Inc. | Phone: (919) 483-7390 Five Moore Drive | FAX: (919) 315-0034 Research Triangle Park, NC 27709 | ________________________________________________________________________ On Feb 11, 2:02pm, Dr. Dave Winkler wrote: > Subject: CCL:Molecular multipole moments > > Australian Science - Australia's Future > > Does anyone know of any software (Unix or Mac preferably), which allows > calculation of molecular multipole moments? I think the Oxford Molecular > software does but I'm interested in any other. > > Cheers, > > Dave > > Dr. David A. Winkler Voice: 61-3-9542-2477 > Principal Research Scientist Fax: 61-3-9543-8160 > CSIRO Division of Chemicals and Polymers http://www.csiro.au > Private Bag 10,Clayton South MDC, http://www.wark.csiro.au > Clayton 3169, Australia > -- From robert@pauli.utmb.edu Wed Feb 12 12:22:43 1997 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id LAA28320; Wed, 12 Feb 1997 11:30:35 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA27211; Wed, 12 Feb 97 10:43:35 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA26920; Wed, 12 Feb 1997 10:28:27 -0600 From: "Robert Fraczkiewicz" Message-Id: <9702121028.ZM26918@pauli.utmb.edu> Date: Wed, 12 Feb 1997 10:28:26 -0600 In-Reply-To: "CCL:solvent accessible surface" (Feb 11, 6:52pm) References: <01IFATB8UKP00003BT@CHEMNA.DICHI.UNINA.IT> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net, Subject: Re: CCL:solvent accessible surface Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Feb 11, 6:52pm, wrote> > I am looking for a program or routine to compute the EXACT solvent accessible > surface area of molecules. > > Any help is appreciated. > > Thanx > > Luigi Luigi, We will be giving away program AREA that does EXACT, analytical calculations of the solvent accessible surface area (and its gradient, if necessary) based on the Gauss-Bonnet theorem. Please, consult this URL for more details on the method: http://www.scsb.utmb.edu/comp_biol.html/poster1/ Cheers, Robert Fraczkiewicz University of Texas Medical Branch From badertscher@org.chem.ethz.ch Wed Feb 12 12:33:27 1997 Received: from org.chem.ethz.ch for badertscher@org.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id LAA28312; Wed, 12 Feb 1997 11:30:06 -0500 (EST) Received: from [129.132.67.36] (chn-c63d.ethz.ch [129.132.67.36]) by org.chem.ethz.ch (940816.SGI.8.6.9/8.6.10) with SMTP id RAA12955 for ; Wed, 12 Feb 1997 17:32:10 +0100 X-Sender: badertscher@aida.ethz.ch Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 12 Feb 1997 17:30:55 +0100 To: chemistry@www.ccl.net From: badertscher@org.chem.ethz.ch (Martin Badertscher) Subject: perception algorithms for aromaticity etc. Dimitris K. Agrafiotis wrote: > We are trying to find some good algorithms for perceiving aromaticity, > tautomerism and stereochemistry (RS, cis/trans) from a connection > table, and algorithms for canonicalizing molecular graphs. 1. Canonicalizing molecular graphs A molecular graph, or "constitution", can be coded as a connection table in more than one way. To prove that two connection tables code the same constitution is called the isomorphism problem. To solve the problem is notoriously expensive. One possible solution is to assign a canonical name (or canonical connection table) to the constitutions. If two such names are the same, the constitutions are too. This involves the perception of topological symmetry. Many algorithms have been proposed, e.g., the famous Morgan algorithm: H. L. Morgan, J. Chem. Doc., Vol. 5 (1965) p. 107 Most of them, including the Morgan algorithm, suffer from the fact that they are not rigorous. Shelley has published an "almost rigorous" algorithm: C. A. Shelley et al., J. Chem. Inf. Comput. Sci., Vol. 17, No. 2 (1977) p. 110 Ray Carhart, the wizzard, has found a counterexample (by summoning lower gods?): R. E. Carhart, J. Chem. Inf. Comput. Sci., Vol. 18, No. 2 (1978) p. 108 As a reaction Shelley placed a brute force algorithm on top of his former one. The resulting construct is rigorous: C. A. Shelley et al., J. Chem. Inf. Comput. Sci., Vol. 19, No. 4 (1979) p. 247 Due to Carhart's punishment the authors were too careful in writing their text. So the scientific community missed the fact that the problem was solved for almost 10 years. Chemists normally don't read mathematical journals where such problems are addressed in much more cryptic ways. I can dig out the FORTRAN77 code of the complete algorithm to canonicalize a connection table. It could certainly be translated easily into a more appropriate language. The copyright is with Morton E. Munk, Prof. of Chemistry at Arizona State University. He is surely willing to share the code with you. Contact me if you are interested. ====== 2. Perceiving stereochemistry This is a much more complicated problem as it (sensibly) involves the stability of molecules, not only mathematics. To my knowledge there is only a single algorithm published and coded that generates all stable stereoisomers out of a canonical connection table. It has its origin in Munk's lab too: M. Razinger et al., J. Chem. Inf. Comput. Sci., Vol. 33, No. 6 (1993) p. 812 ====== 3. Perceiving aromaticity Before the question of perceiving aromaticity can be addressed, it must be clear what the results are used for. You have to clearly define what aromaticity is. This can be done in a purely mathematical way. Benzene, furane, and thiophene might be considered aromatic in this way, butadiene could be non-aromatic, cyclobutadiene and cyclooctatetraene anti-aromatic. If you consider chemical behaviour such as reactivity, benzene and thiophene could be considered aromatic. Furane, butadiene, and cyclooctatetraene are non-aromatic. Cyclobutadiene is anti-aromatic and therefore rather unstable. Martin Badertscher, head of radiochemistry, dpt. of organic chemistry, federal institute of technology, Zurich, Switzerland E-Mail: badertscher@org.chem.ethz.ch