From chemistry-request@server.ccl.net Sun Feb 4 20:58:52 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f151wqw15066 for ; Sun, 4 Feb 2001 20:58:52 -0500 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id UAA11627 for ; Sun, 4 Feb 2001 20:58:48 -0500 (EST) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au [138.194.46.107]) by mercury.chem.csiro.au (8.9.3/8.9.3) with ESMTP id MAA22705 for ; Mon, 5 Feb 2001 12:58:44 +1100 (EST) X-Sender: win097@clex1.vic.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Feb 2001 12:58:42 +1100 To: chemistry@ccl.net From: "Dr. Dave Winkler" Subject: DFT calculations of NMR shifts in norbornadiene Dear Netters, I hope someone can provide a simple answer to a frustrating problem. I've run DFT TZVP/bp calculation on cubane using DGauss and got excellent agreement between IGLO/LORG values and experiment or 13C shifts. I'm trying to do the same with norbornadiene (same basis set) and get crazy values compared with experiment, particularly for the proton shifts. The sp2 and sp3 carbon 13C shifts seemed to be reversed compared with experiment. The geometries are optimized at DFT TZVP/bp too. Gaussian HF calculations get much closer to experiment. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@server.ccl.net Sun Feb 4 23:12:45 2001 Received: from hermes.csd.unb.ca (root@hermes.csd.unb.ca [131.202.3.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f154Cjw15434 for ; Sun, 4 Feb 2001 23:12:45 -0500 Received: from pop.unb.ca (root@pop.unb.ca [131.202.3.36]) by hermes.csd.unb.ca (8.9.3/8.9.3) with ESMTP id AAA13158 for ; Mon, 5 Feb 2001 00:12:45 -0400 (AST) Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id AAA13596 for ; Mon, 5 Feb 2001 00:12:45 -0400 (AST) X-WebMail-UserID: z17b3 Date: Mon, 5 Feb 2001 00:17:02 -0400 Sender: z17b3 From: z17b3 To: chemistry@ccl.net X-EXP32-SerialNo: 00003025 Subject: What is a structural representation in chemistry? Message-ID: <3A785FC8@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.07 Dear colleagues, The following paper that proposes some revolutionary ideas related to the nature of structural representation in chemistry might be (either directly or indirectly) of interest to you: http://www.cs.unb.ca/profs/goldfarb/cadd.ps (the abstract is appended below). Please note that although the applied focus of the paper is the area of computer aided drug design, ANY other area of theoretical or applied chemistry could have been chosen instead. Best regards, Lev Goldfarb Tel: 506-458-7271 Faculty of Computer Science Tel(secret.): 453-4566 University of New Brunswick Fax: 506-453-3566 P.O. Box 4400 E-mail: goldfarb@unb.ca Fredericton, N.B., E3B 5A3 Home tel: 506-455-4323 Canada http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm ****************************************************************************** * WHAT IS A STRUCTURAL REPRESENTATION IN CHEMISTRY: TOWARDS A UNIFIED FRAMEWORK FOR CADD? Lev Goldfarb, Oleg Golubitsky, Dmitry Korkin Faculty of Computer Science University of New Brunswick, P.O Box 4400 Fredericton, N.B., Canada ABSTRACT. A fundamentally new (and, we believe, the first) model for structural representation of molecules, with general emphasis on drug design applications, is outlined. This is the first formal model that was motivated by the structural description of classes. The model, in particular, guarantees the inheritance of the chemical structural class information from the parent class to all its subclasses. Inadequacies of the conventional models used in computer aided drug design (CADD) for molecular representation and classification as well as the advantages of the proposed--evolving transformation system (ETS)--model are discussed. Some advantages of the ETS model is its capability to represent naturally all important structural features of molecules, e.g. different atoms and their bonding types (including hydrogen bonding), basic 2D and 3D isometries, the molecular class structure. The model allows one not only to classify a compound, but also to construct a chemically valid compound > from the class of compounds that was previously learned. Hence, in particular, the model offers a much more precise "language" for chemical structural formulas. The central role of the class learning problem in CADD is suggested. Moreover, we propose the ETS model as a unified framework for the class learning problem and therefore as a unified formal framework for CADD. This would allow considerable streamlining of the CADD by assigning to the chemist the role of an interactive user of the system rather that a role of a human weak link within the CADD process. From chemistry-request@server.ccl.net Mon Feb 5 04:25:53 2001 Received: from cheviot2.ncl.ac.uk (root@cheviot2.ncl.ac.uk [128.240.233.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f159Pqw16494 for ; Mon, 5 Feb 2001 04:25:52 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot2.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id f159Pq421798; Mon, 5 Feb 2001 09:25:52 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id JAA10588; Mon, 5 Feb 2001 09:25:51 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Mon, 5 Feb 2001 09:25:51 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: "Dr. Dave Winkler" cc: Computational Chemistry List Subject: Re: CCL:DFT calculations of NMR shifts in norbornadiene In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 2.0 (cheviot2.ncl.ac.uk) I have been looking at GIAO calculations of phosphorus shifts in phosphorus sulfides which have norbornane structures, and have had similar experiences. One gets something like the right differences between isotropic shieldings at quite a low RHF level, even 3-21g* for both geometry and GIAO. By doing a least squares fit of shieldings to experimental shifts, i.e. calculating an effective shielding for the standard and hence absorbing a lot of systematic error, one can get useful information to allow one to distinguish between isomers, invertomers or rotamers, which is generally what I want to do as a synthetic chemist. Increasing the level of the calculations frequently helps little. Relative energies become more realistic as expected, e.g. reflecting observed isomer ratios, but relative NMR shieldings do not improve much. Whereas MPW1MPW91 seems better for inorganic bicycles than does B3LYP, going from HF to DF sometimes makes the GIAO shielding differences worse. For phosphorus (and selenium) I am using the Ahlrichs basis sets with a single polarisation function, usually either MPW1MPW91/SVP or RHF/TZV. Adding more polarisation functions seems to make the shieldings worse also. Optimising the geometries at a higher level seems to make more difference than going to higher level on the GIAO calculations. Bruce Tattershall Personal telephone no.: 00 44 191 222 6634 Personal Email: Bruce.Tattershall@newcastle.ac.uk Postal address: Dr. B.W. Tattershall Department of Chemistry University of Newcastle Newcastle upon Tyne England From chemistry-request@server.ccl.net Mon Feb 5 04:47:28 2001 Received: from earth.ox.ac.uk (root@darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f159lRw16631 for ; Mon, 5 Feb 2001 04:47:27 -0500 Received: from pauling.earth.ox.ac.uk (pauling [163.1.22.22]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id JAA27155 for ; Mon, 5 Feb 2001 09:47:25 GMT Resent-From: Keith Refson Resent-Date: Mon, 5 Feb 2001 09:47:25 GMT Resent-Message-ID: <14974.30379.412294.324856@gargle.gargle.HOWL> Resent-To: Computational Chemistry List CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14974.30285.307856.752522@gargle.gargle.HOWL> In-Reply-To: <20010201102319.F214706@gamow.scripps.edu> References: <20010201102319.F214706@gamow.scripps.edu> X-Mailer: VM 6.88 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid From: Keith Refson Subject: CCL:GPL'd MD packages Date: Mon, 5 Feb 2001 09:45:49 +0000 You will find links several MD packages on http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html However only a few are GPLed. I would have expected that the GPL be adopted more widely in science than it has been, since it is pretty much an expression of the purest ideals of freely sharing knowledge. However it seems that the constant pressure for cash is stifling these ideals. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Mon Feb 5 05:08:05 2001 Received: from earth.ox.ac.uk (root@darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15A84w16715 for ; Mon, 5 Feb 2001 05:08:05 -0500 Received: from pauling.earth.ox.ac.uk (pauling [163.1.22.22]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id KAA29516 for ; Mon, 5 Feb 2001 10:08:02 GMT From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14974.31618.126595.286294@gargle.gargle.HOWL> Date: Mon, 5 Feb 2001 10:08:02 +0000 To: chemistry@ccl.net Subject: CCL:programming language In-Reply-To: References: X-Mailer: VM 6.88 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid Don Steiger writes: > This may be true about FORTRAN77 but it is definitely not true about > FORTRAN90/95. The handling of global data and the dynamic manipulation of > array size is at least as good in FORTRAN90/95 as it is in C/C++. Indeed, the new Fortran standard offers all that is necessary for high-quality scientific programming. However it is equally true that so does the new C standard, C99. (restricted pointers, true dynamic arrays including multidimensional, complex data types and arithmetic). I don't believe compilers for C99 are widely available yet, but it seems to me that both languages are highly suitable and widely used in scientific programs. > The only reason not to use FORTRAN90/95 in large numerical > simulations is that it will soon become extinct because nobody is > using it. This is a highly contentious opinion and the complete opposite of my experience. Almost all of the large scientific Fortran programs I am familiar with do not compile under an F77 (+extensions) compiler. Even old codes which are undergoing development are using the new Fortran features. In any event, the poster enquired about what is the best language to *teach*, not the best for scientific programming. In my opinion you should be teaching *programming* not a particular language. Your students will probably not be aware of the distinction initially, but hopefully will by the end of the course. In my opinion C is a poor choice for a teaching language. Though it is powerful, it's design philosophy makes it too easy to shoot yourself in the foot ("if it stopped you from doing stupid things, that would prevent you from doing clever things too"). Your students would waste too much time wrestling with C-specific pitfalls, which would detract from their education in programming. A good choice is "F" which is a subset of Fortran 95, ie Fortran with the crufty old parts of Fortran 77 such as equivalence removed, thus removing much of Fortran's vertical ammunition trajectory potential. It is a complete and powerful subset and a great introduction to full Fortran and there are free compilers available. Avoid Visual Basic -- it's the computing equivalent of flipping burgers in McDonalds - only the lowest level grunt jobs want VB. Another approach is to avoid 3G languages altogether. We teach our undergrads using Matlab, which enables them to get to grips with high-level concepts, use robust numerical libraries and graphical output without worrying about the bookkeeping aspects of 3G languages. It's a good way of packing a lot into a short course. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Mon Feb 5 06:54:13 2001 Received: from oulu.fi (root@ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15BsCw17916 for ; Mon, 5 Feb 2001 06:54:13 -0500 Received: from cc.oulu.fi (lensink@sun3.oulu.fi [130.231.240.13]) by oulu.fi (8.8.5/8.8.5) with ESMTP id NAA26821 for ; Mon, 5 Feb 2001 13:54:10 +0200 (EET) Received: (from lensink@localhost) by cc.oulu.fi (8.8.5/8.8.5) id NAA06122 for chemistry@ccl.net; Mon, 5 Feb 2001 13:54:10 +0200 (EET) Message-Id: <200102051154.NAA06122@cc.oulu.fi> Subject: Na parameters To: chemistry@ccl.net Date: Mon, 5 Feb 2001 13:54:10 +0200 (EET) From: Marc Lensink Reply-To: marc.lensink@oulu.fi X-Mailer: ELM [version 2.4ME+ PL66 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Is anybody aware of any Na+ parameters for use in molecular dynamics simulations? Nothing fancy, it's for a down-to-earth basic protein simulation. I'm looking for partial charges for the environment of the Na+ to include polarization of that immediate environment. Something along the lines of (but then for Na): Y. Shiratori, S. Nakagawa, "Parametrization of the calcium binding site in proteins and molecular dynamics simulation of phospholipase A2", JCC12 (1991) 717-730. Cheers, Marc -- Marc Lensink tel +358 8 553 1161 dept of Biochemistry, Biocenter, University of Oulu PO Box 3000, 90014 Oulu, Finland fax +358 8 553 1141 From chemistry-request@server.ccl.net Mon Feb 5 07:55:44 2001 Received: from mail.takas.lt (srvr3.telecom.lt [212.59.0.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15Cthw18113 for ; Mon, 5 Feb 2001 07:55:43 -0500 Received: from julius (dialup166.vln.takas.lt [212.59.14.174]) by mail.takas.lt (8.9.1/8.9.0) with SMTP id OAA2081844 for ; Mon, 5 Feb 2001 14:55:41 +0200 (GMT+0200) Message-ID: <000e01c08f7b$4d114260$ae0e3bd4@ktl.mii.lt.lorka.ktl.mii.lt> From: "Olegas Eicher-Lorka" To: Subject: Gaussian Raman Intensities in Solution Date: Mon, 5 Feb 2001 14:55:22 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C08F83.AA4043C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C08F83.AA4043C0 Content-Type: text/plain; charset="x-user-defined" Content-Transfer-Encoding: quoted-printable We're using G98W to model a system in the gas phase and in solution. But = because we're using a DFT (B3LYP) Raman intensities are calculated but = they can't be calculated when using solvation models. We've tried = firstly calculating the SCRF (Cosmo) and then using the = Field=3DCheckpoint command and then calcuating the Raman intensities but = we got very different peak positions when compared. Can anyone help, or = is there a better way? Also when using the Freqchk.exe facility, and not requesting the = Hyperchem *.scr file, the output is put to screen but we've found it = inaccessible, how do we access the data, or save it to a file? Thanks very much! Dr. Olegas Eicher-Lorka Institute of Chemistry Akademijos 7 e-mail: lorka@takas.lt tel.: +(370-)2-729372 ------=_NextPart_000_000B_01C08F83.AA4043C0 Content-Type: text/html; charset="x-user-defined" Content-Transfer-Encoding: quoted-printable
We're using G98W to model a system in the gas phase and in = solution. But=20 because we're using a DFT (B3LYP) Raman intensities are calculated but = they=20 can't be calculated when using solvation models. We've tried firstly = calculating=20 the SCRF (Cosmo) and then using the Field=3DCheckpoint command and then = calcuating=20 the Raman intensities but we got very different peak positions when = compared.=20 Can anyone help, or is there a better way?
 
Also when using the Freqchk.exe facility, and not requesting the = Hyperchem=20 *.scr file, the output is put to screen but we've found it inaccessible, = how do=20 we access the data, or save it to a file?
 
Thanks very much!
 
Dr. Olegas Eicher-Lorka
Institute of Chemistry
Akademijos=20 7
e-mail: lorka@takas.lt
tel.:=20 +(370-)2-729372
------=_NextPart_000_000B_01C08F83.AA4043C0-- From chemistry-request@server.ccl.net Mon Feb 5 10:15:02 2001 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15FF2w18659 for ; Mon, 5 Feb 2001 10:15:02 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id HAA22880; Mon, 5 Feb 2001 07:15:02 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id HAA29772; Mon, 5 Feb 2001 07:15:01 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3A7EC639.BE6BE3F8@usc.edu> Date: Mon, 05 Feb 2001 07:26:49 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: z17b3 CC: chemistry@ccl.net Subject: Re: CCL:What is a structural representation in chemistry? References: <3A785FC8@webmail1> Content-Type: multipart/alternative; boundary="------------AACA5564F9660E6F27953648" --------------AACA5564F9660E6F27953648 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Lev, although I really appreciate your enthusiasm making publicity of this work, in my opinion this is not the forum for this. If we start sending messages like this we will fill our mail box with abstracts that we can consult perfectly via on-line tables of contents. With my message I am doing even more publicity to your job, I know, but maybe this prevent somebody else doing the same. Jordi z17b3 wrote: > Dear colleagues, > > The following paper that proposes some revolutionary ideas related to the > nature of structural representation in chemistry might be (either > directly or indirectly) of interest to you: > > http://www.cs.unb.ca/profs/goldfarb/cadd.ps > > (the abstract is appended below). > > Please note that although the applied focus of the paper is the area of > computer aided drug design, ANY other area of theoretical or applied > chemistry could have been chosen instead. > > Best regards, > > Lev Goldfarb Tel: 506-458-7271 > Faculty of Computer Science Tel(secret.): 453-4566 > University of New Brunswick Fax: 506-453-3566 > P.O. Box 4400 E-mail: goldfarb@unb.ca > Fredericton, N.B., E3B 5A3 Home tel: 506-455-4323 > Canada > > http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm > > ****************************************************************************** > * > > WHAT IS A STRUCTURAL REPRESENTATION IN CHEMISTRY: > TOWARDS A UNIFIED FRAMEWORK FOR CADD? > > Lev Goldfarb, Oleg Golubitsky, Dmitry Korkin > > Faculty of Computer Science > University of New Brunswick, P.O Box 4400 > Fredericton, N.B., Canada > > ABSTRACT. A fundamentally new (and, we believe, the first) model for > structural representation of molecules, with general emphasis on drug > design applications, is outlined. This is the first formal model that was > motivated by the structural description of classes. The model, in > particular, guarantees the inheritance of the chemical structural class > information from the parent class to all its subclasses. Inadequacies of > the conventional models used in computer aided drug design (CADD) for > molecular representation and classification as well as the advantages of > the proposed--evolving transformation system (ETS)--model are discussed. > Some advantages of the ETS model is its capability to represent naturally > all important structural features of molecules, e.g. different atoms and > their bonding types (including hydrogen bonding), basic 2D and 3D > isometries, the molecular class structure. The model allows one not only > to classify a compound, but also to construct a chemically valid compound > > from the class of compounds that was previously learned. Hence, in > particular, the model offers a much more precise "language" for chemical > structural formulas. The central role of the class learning problem in > CADD is suggested. Moreover, we propose the ETS model as a unified > framework for the class learning problem and therefore as a unified formal > framework for CADD. This would allow considerable streamlining of the CADD > by assigning to the chemist the role of an interactive user of the system > rather that a role of a human weak link within the CADD process. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 --------------AACA5564F9660E6F27953648 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Lev,

although I really appreciate your enthusiasm making publicity of this work, in my opinion this is not the forum for this. If we start sending messages like this we will fill our mail box with abstracts that we can consult perfectly via on-line tables of contents.
With my message I am doing even more publicity to your job, I know, but maybe this prevent somebody else doing the same.

Jordi

z17b3 wrote:

Dear colleagues,

The following paper that proposes some revolutionary ideas related to the
nature of structural representation in chemistry might be (either
directly or indirectly) of interest to you:

http://www.cs.unb.ca/profs/goldfarb/cadd.ps

(the abstract is appended below).

Please note that although the applied focus of the paper is the area of
computer aided drug design, ANY other area of theoretical or applied
chemistry could have been chosen instead.

Best regards,

Lev Goldfarb                   Tel: 506-458-7271
Faculty of Computer Science    Tel(secret.): 453-4566
University of New Brunswick    Fax: 506-453-3566
P.O. Box 4400                  E-mail: goldfarb@unb.ca
Fredericton, N.B., E3B 5A3     Home tel: 506-455-4323
Canada

http://www.cs.unb.ca/profs/goldfarb/goldfarb.htm

******************************************************************************
*

WHAT IS A STRUCTURAL REPRESENTATION IN CHEMISTRY:
TOWARDS A UNIFIED FRAMEWORK FOR CADD?

Lev Goldfarb, Oleg Golubitsky, Dmitry Korkin

Faculty of Computer Science
University of New Brunswick, P.O Box 4400
Fredericton, N.B., Canada

ABSTRACT. A fundamentally new (and, we believe, the first) model for
structural representation of molecules, with general emphasis on drug
design applications, is outlined. This is the first formal model that was
motivated by the structural description of classes. The model, in
particular, guarantees the inheritance of the chemical structural class
information from the parent class to all its subclasses. Inadequacies of
the conventional models used in computer aided drug design (CADD) for
molecular representation and classification as well as the advantages of
the proposed--evolving transformation system (ETS)--model are discussed.
Some advantages of the ETS model is its capability to represent naturally
all important structural features of molecules, e.g. different atoms and
their bonding types (including hydrogen bonding), basic 2D and 3D
isometries, the molecular class structure. The model allows one not only
to classify a compound, but also to construct a chemically valid compound
> from the class of compounds that was previously learned. Hence, in
particular, the model offers a much more precise "language" for chemical
structural formulas. The central role of the class learning problem in
CADD is suggested. Moreover, we propose the ETS model as a unified
framework for the class learning problem and therefore as a unified formal
framework for CADD. This would allow considerable streamlining of the CADD
by assigning to the chemist the role of an interactive user of the system
rather that a role of a human weak link within the CADD process.

-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
Jordi Villa i Freixa                  
jorgevil@usc.edu   http://laetro.usc.edu/wgroup/people/jorgevil
Department of Chemistry, University of Southern California
Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
  --------------AACA5564F9660E6F27953648-- From chemistry-request@server.ccl.net Mon Feb 5 10:45:39 2001 Received: from gate.syntem-sa.fr (gate.syntem-sa.fr [146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15Fjdw19110 for ; Mon, 5 Feb 2001 10:45:39 -0500 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA50775 for <@firewall.syntem-sa.fr:chemistry@ccl.net>; Mon, 5 Feb 2001 16:42:36 +0100 (MET) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma050569; Mon, 5 Feb 01 16:41:46 +0100 Received: from syntem-sa.fr (eva.syntem-sa.fr [10.0.0.34]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA48495 for ; Mon, 5 Feb 2001 16:39:19 +0100 (MET) Sender: elie@syntem-sa.fr Message-ID: <3A7ECA73.AC17EDC5@syntem-sa.fr> Date: Mon, 05 Feb 2001 16:44:51 +0100 From: Elie Giraud Organization: syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: fr, en MIME-Version: 1.0 CC: Computational Chemistry List Subject: Schekel's Foxholes References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I want to graph the De Jong GA test function called Schekel's Foxholes. I'm looking for a freeware to do the job or a ready for use image (preferably a colour picture). Thanks in Advance Best Regards, E. ================================================================ Elie Giraud Synt:em Research Scientist Parc Scientifique G.Besse Pharmaco Informatics 30000 Nimes email: egiraud@syntem.com France Tel: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 ================================================================ Discover New Drugs, Discover Synt:em http://www.syntem.com ================================================================ From chemistry-request@server.ccl.net Mon Feb 5 17:09:08 2001 Received: from carrot.chem.duke.edu (carrot.chem.duke.edu [152.3.169.229]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15M98w21857 for ; Mon, 5 Feb 2001 17:09:08 -0500 Received: by carrot.chem.duke.edu id RAA0000000604; Mon, 5 Feb 2001 17:07:04 -0500 (EST) Date: Mon, 5 Feb 2001 17:07:04 -0500 (EST) From: Qin Wu Message-Id: <200102052207.RAA0000000604@carrot.chem.duke.edu> To: chemistry@ccl.net Subject: Error messages from Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: gcruvgl3CqOMUHkeIhTwCw== Dear all, Does anybody know a place that has the explanations for the error messages in running Gaussian? Personally I met a message as follows: "Erroneous read. Read -1 instead of 200. fd = 3" It's hard for me to tell what's wrong. Some explanations will be very useful, I think. Thanks in advance. Qin From chemistry-request@server.ccl.net Mon Feb 5 18:32:30 2001 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15NWTw22117 for ; Mon, 5 Feb 2001 18:32:30 -0500 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id RAA26719 for ; Mon, 5 Feb 2001 17:32:30 -0600 (CST) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id RAA17300 for ; Mon, 5 Feb 2001 17:32:30 -0600 (CST) Date: Mon, 5 Feb 2001 17:32:29 -0600 (CST) From: TREVOR D POWER To: chemistry@ccl.net Subject: Re: CCL:Error messages from Gaussian In-Reply-To: <200102052207.RAA0000000604@carrot.chem.duke.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Qin, That message implies that you have run out of disk space (probably where you keep your scratch files). David power tdp0006@unt.edu On Mon, 5 Feb 2001, Qin Wu wrote: > Dear all, > Does anybody know a place that has the explanations for the error messages in running > Gaussian? Personally I met a message as follows: > "Erroneous read. Read -1 instead of 200. > fd = 3" > It's hard for me to tell what's wrong. Some explanations will be very useful, I think. > Thanks in advance. > Qin > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Feb 5 12:12:51 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15HCpw20225 for ; Mon, 5 Feb 2001 12:12:51 -0500 Received: from cornell.edu (phobos.mbg.cornell.edu [132.236.170.77]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA01898; Mon, 5 Feb 2001 12:12:49 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3A7EE01C.F8D6470A@cornell.edu> Date: Mon, 05 Feb 2001 12:17:16 -0500 From: Richard Gillilan Reply-To: reg8@cornell.edu X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-3 i686) X-Accept-Language: en MIME-Version: 1.0 To: Keith Refson CC: chemistry@ccl.net Subject: Re: CCL:programming language References: <14974.31618.126595.286294@gargle.gargle.HOWL> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Keith Refson wrote: > Another approach is to avoid 3G languages altogether. We teach our > undergrads using Matlab, which enables them to get to grips with > high-level concepts, use robust numerical libraries and graphical > output without worrying about the bookkeeping aspects of 3G > languages. It's a good way of packing a lot into a short course. > Matlab is great, and at least as easy as FORTRAN. I believe it is the main language taught to Engineers here at Cornell. Also used heavily in financial engineering and extensively for teaching and research in nerobiology (electronics interfacing course). Now that I think about it, I would probably recommend Matlab over Java, Python or Perl for a student starting out. If nothing else, students will continue to find it useful for general plotting and data analysis, though it is capable of the most advanced numerical computations. There is a free Matlab clone called Octave. The commercial Matlab is a bit expensive if you don't have some kind of Campus-wide deal. A limited educational Matlab version exists for cheap, but the array limits are severe. Richard Gillilan Cornell From chemistry-request@server.ccl.net Mon Feb 5 14:30:46 2001 Received: from sina.iums.ac.ir ([194.225.184.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f15JUew21069 for ; Mon, 5 Feb 2001 14:30:43 -0500 Received: from armin ([213.29.48.117]) by sina.iums.ac.ir (8.9.2/8.9.2) with SMTP id XAA06558 for ; Mon, 5 Feb 2001 23:00:06 +0330 (IST) Message-Id: <4.1.20010205225720.0092cc30@sina.iums.ac.ir> X-Sender: armin@sina.iums.ac.ir X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Mon, 05 Feb 2001 22:59:23 +0330 To: chemistry@ccl.net From: "Armin M. Sobhani" Subject: Re: CCL:Modelling of DNA-Protein interaction Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f15JUkw21070 At 03:35 È.Ù 31/01/2001 +0100, you wrote: >Dear cclers, > >I am looking for some good reviews about DNA-Protein interaction, both >on modelling and calculations. >Despite some experiences on protein studies, I have no idea on DNA >problems... so pratical suggestion on this topics are gratefully >accepted, too. > >This is a "first look" search, just for getting an idea of the state of >the art, so every good information could be useful. > >Thanks a lot. > >Ale Dear Alessandro, Just in case you want to know type of interactions, there is a good book that might be interesting: David M. J. Lilley (Ed.), (1995) DNA-Protein: Structural Interactions, IRL Press. Good luck, Armin p-------------------------------------------------------------------q | __ _________ ____ Armin M. Sobhani, Pharm.D | | / \ / _ _ \ / ____\ Ph.D Student of Pharmacology | | / \\ \\ \\ \/\ \___/_ mailto:armin@iums.ac.ir | | / /\ \\ \\ \\ \ \_____ \ URL: http://armin.iums.ac.ir/ | | ( ___ \\ \\ \\ \/____/\ \Tel: +98 21 8052265 | |( \__\_/\__\\__\\__\\__\/\_____/Fax: +98 21 8052264 | | \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6183, Tehran, IRAN | !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~! | Once you understand the universe at the atomic level everything | | else is easy. -Richard P. Feynman | b-------------------------------------------------------------------d