From chemistry-request@server.ccl.net  Wed May 17 01:29:57 2000
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From: Valentine Ananikov <val@cacr.ioc.ac.ru>
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Subject: MP2/UMP2  vs  B3LYP/UB3LYP
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  Dear CCL,

I am a little surprised with the following problem and
would be grateful for helpful comments.

On a substituted carbene compound MP2/UMP2 optimization of
singlet and triplet states respectively leads to energy gap
of about 9 kcl/mol and low lying singlet state. However,
in the case of B3LYP/UB3LYP optimized structures triplet
state is more stable by approximately the same value.
Geometry parameters are also different. Unfortunately,
experimental data for this compound is not available.

Is this a known thing ? any precedents ?

Does anybody have an idea on the possible explanation and what
accuracy one would expect from MP2 and B3LYP calculated s/t gaps?

Thank you!

best regards,  Valentin.

====================================================================
                                             ,         ,      ,   ,
Valentine P. Ananikov                        |\\\\ ////|     /////|
NMR Group                                    | \\\|/// |    ///// |
ND Zelinsky Institute of Organic Chemistry   |  |~~~|  |   |~~~|  |
Leninsky Prospect 47                         |  |===|  |   |===|  |
Moscow  117913                               |  |   |  |   |   |  |
Russia                                       |  | A |  |   | Z |  |
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e-mail: val@cacr.ioc.ac.ru                     \|===|/     |===|/
http://nmr.ioc.ac.ru/Staff/AnanikovVP/          '---'      '---'
  Fax +7 (095)1355328   Phone +7 (095)9383536
====================================================================

From chemistry-request@server.ccl.net  Wed May 17 01:56:42 2000
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Dear Monica,

I've recently come across a similar problem with VO (4 sigma ground
state). The problem was, that initial guess of occupied MO was totally
wrong (the distribution of electrons between different irreps). As I'm
using G98, the solution was quite easy: Guess=Alter (+ appropriate
labes of MO to exchange), and that was enough to get the proper electronic
state.


Tomek Borowski
Chemistry Department
Jagiellonian Univ. 
Krakow



On Tue, 16 May 2000, Monica Concha wrote:

> 
> Hi all,
> 
>     I have been trying to optimize the vanadium dimer with multiplicity
> of 3, using various dft methods. The problem is that depending on the
> initial bond length, the dimer optimizes to different bond lengths with
> different energies, and differ s**2 values.  The bond lengths only
> differ
> by about 0.01 Angstroms but the energies differ by 35 kcal.  The odd
> thing is that the lowest energy corresponds to an s**2 value of 2.55
> rather than the expected value of 2.0. Any suggestions?
> 
> --
> 
> Monica C. Concha
> Research Associate
> Dept. Of Chemistry
> University of New Orleans
> New Orleans LA 70148
> E-mail mconcha@uno.edu
> 
> 
> 
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To Admins
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> 
> 
> 
> 
> 
> 


From chemistry-request@server.ccl.net  Wed May 17 04:07:39 2000
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Date: Wed, 17 May 2000 10:05:28 +0200 (MET DST)
From: Emad Tajkhorshid <E.Tajkhorshid@DKFZ-Heidelberg.de>
To: ccl CCL <chemistry@ccl.net>
Subject: Summary of replies: resonance effect in O and S
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Hi

This is a summary of the answers I got from CCL:

*********************************************************************
Question:

> Hi
>
> I am looking for some references (experiment or calculations, text book,
> etc.) comparing the ability of O and S in sharing the lone pair with the
> pi-electronic system. As far as I remmeber, S was a weaker electron
> donating group (lower resonance effect), although its electronegativity is
> less. Any comment is welcome.
>
Emad

*********************************************************************
From: Leticia Gonzalez Herrero <leti@chemie.fu-berlin.de>
To: Emad Tajkhorshid <E.Tajkhorshid@DKFZ-Heidelberg.de>
Subject: Re: CCL:resonance effect in O and S

Dear Emad, 
mabye this helps?
Gonzlez, L., M, O. and Yez, M. (1997): High level ab initio calculations
on the intramolecular hydrogen bond in
thiomalonaldehyde. J. Phys. Chem. 101, 9710-9719. 

thiomalonaldehyde contains both O and S with pi system,so we made some
discussion about your question. 

Good luck. 
Leticia
=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=
  Dr. Leticia Gonzalez                      Tel: ()49 30 838 520 97
  Freie Universitaet Berlin                 Fax: ()49 30 838 547 92 
  Institut fuer Chemie                      Room: 35.17 
  Takustrasse 3                          leti@chemie.fu-berlin.de         
  D-14195 Berlin        http://userpage.chemie.fu-berlin.de/~leti
=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=
        If you find a solution and become attached to it,
        the solution may become your next problem.

*********************************************************************
From: Yirong Mo <chymo@hotmail.com>
To: E.Tajkhorshid@DKFZ-Heidelberg.de
Cc: ymo@chem.umn.edu
Subject: Re: CCL:resonance effect in O and S

Hi, Emad:

I did some calcualtions on 5-member rings and their corresponding
linear forms using recently developed block-localized wavefunction
(J.Chem.Phys.  109, 1687(1998) and JACS 121, 5737(1999)), however, the
manscript is still to be worked out.  In these calculations, I did
compare the resonance effect of O via S (also N via P etc).  For the
cyclic C4H4X, the vertical resonance energies for X=O and S are -35.8
and -31.0 kcal/mol, while for linear C4H6X, the resonance energies are
-14.8 and -9.2 kcal/mol with 6-31G(d).  Thus, We may conclude that S is
a slightly weaker electron donating group.  On the other hand,
Prof.Schleyer's NICS calculations give the data -13.6 and -13.9 ppm for
C4H4O and C4H4S, respectively, suggesting that O and S have similar
donating ability.

Hope this may help you a little.

Wishes, Yirong

Yirong Mo, PhD, Research Associate
Department of Chemistry
University of Minnesota

*********************************************************************
From: Piotr Paneth <paneth@ck-sg.p.lodz.pl>
To: Emad Tajkhorshid <E.Tajkhorshid@DKFZ-Heidelberg.de>
Subject: Re: CCL:resonance effect in O and S

Hi
look into papers of Perry Fry from mid 80'. I've been trying to calculate
=POS- using continuum solvent models and didn't see yet any level that
significantly differentiate charge distribution with the change of polarity
although Perry's and our own experimental results (isotope effects) suggest
that this should be so. Will be glad to see what responses you've got.
Cheers,
Piotr
***********************************************************************
Professor Piotr Paneth
Department of Chemsitry, Technical University
Zeromskiego 116, 90-924 Lodz, Poland
fax/phone: (+48 42) 6313199  fax: (+48 42) 6365008



Thanx to everybody for replying.

Regards

Emad
*********************************************************************
E. Tajkhorshid            http://genome.dkfz-heidelberg.de/users/emad
German Cancer Research Center; DKFZ      Email: E.Tajkhorshid@dkfz.de
Dept. Molecular Biophysics (H0200)              Tel: +49 6221 42 2340
P.O.Box 101949,  69009 Heidelberg, Germany      FAX: +49 6221 42 2333
*********************************************************************
*                 "Science is talking to each other"                *
*********************************************************************


From chemistry-request@server.ccl.net  Wed May 17 05:57:10 2000
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 Wed, 17 May 2000 11:58:38 +0200
From: Xiao-Ping Zhang <zhang@server.biokemi.su.se>
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Dear Autodock users,

I would appreciate very much if somebody allow me to share
his experience on fixing the "Non-integral charge" of molecule 
(especially the ligand).

Thank you for your help!

Sincerely yours,

Xiao-Ping

******************************
Xiao-Ping Zhang
Department of Biochemistry
Arrhenius Laboratories of Natural Sciences
Stockholm Universities
106 91 Stockholm
Sweden

Phone:	046-08-162472 /162582
Fax:	046-08-153679
e-mail:	zhang@biokemi.su.se



From chemistry-request@server.ccl.net  Wed May 17 07:01:21 2000
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To: chemistry@ccl.net
From: Amiram Goldblum <amiram@vms.huji.ac.il>
Subject: Drugs directed to GPCRs

Dear All,

In its March 17 issue on drug discovery (Vol. 287 No. 5460),
Science published a review on drug discovery that had a diagram
(Fig. 3, p. 1962) of biochemical classes of drug TARGETS of
current therapies. It demonstrates that out of 483 targets, 45%
are receptors, and 7% more are "unknown" targets.

- May we safely assume that more than 45% of those targets are GPCRs ?

In addition, I am looking for the following information (including refereces
if possible):


1. The percentage of drugs on the market that are directed to GPCRs
    (based on the NUMBER of drugs on the market)

2. The percentage of sales of drugs directed to GPCRs out of the
     total sales of drugs (it will be helpful to have both % and $$)

3. A few examples of drugs for GPCRs that were recently ( 5 yrs) introduced.


I thank you in advance and promise to summarize.


Sincerely,

Amiram Goldblum

______________________________________
Amiram Goldblum, Ph.D.
Prof. of Medicinal Chemistry
School of Pharmacy

Hebrew University of Jerusalem, Israel 91120

Tel: 972-2-6758701 FAX: 972-2-6410740
email: amiram@vms.huji.ac.il
______________________________________




From chemistry-request@server.ccl.net  Wed May 17 11:48:57 2000
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Hello All,

	Sorry for the delay in this summary. The original question was:
	
> 	Forgive me those who are already sick of this subject, but I have one 
> simple question. I would like to know if the choice of a Fortran compiler is 
> associated only with the OS or it depends also on the CPU? For example, if I 
> were to buy a Fortran compiler, is it enought to decide if it will be to Windows 
> or Linux or do I have to compare compilers for, say, P-III 800 or AMD Athlon 
> 800MHz, etc? The speed of the processor is also important? (The compiler that is 
> best for a 600 MHz CPU is still the best for a 800 MHz CPU of the same type?)
> 

	Thank you all.
	
1111111111111111111111111111111111111111111111111111111111111111111111111111111

Yes, you may need to consider the underlying architecture, especially if
raw number crunching performance is important.  The speed is less of an
issue, at least for choosing an efficient compiler.  There seems to be
better support for the Intel chipset at the moment, but since more
machines with AMD chipsets are emerging, I expect support to be more
balanced in the future. 

For Linux, there are freeware compilers which aren't bad at all, and
the best commercial Fortran compilers for Linux seem to be the ones from
the Portland Group, and from AbSoft.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
Rick_Venable@nih.gov          |    \  /  |=|    position of the FDA; for that,
rvenable@speakeasy.org              \/   |=|    see   http://www.fda.gov  )

22222222222222222222222222222222222222222222222222222222222222222222222222222

> simple question. I would like to know if the choice of
> a Fortran compiler is associated only with the OS or it
> depends also on the CPU? For example, if I

I expect you have been inundated with answers but... In general the
choice of compiler is dependant on both the OS and the CPU TYPE. I mean
that the compiler for a Mac CPU will differ from that for an intel one
or an alpha one. However... all the chips you have listed are
IBM-compatible- they are all the same in terms of running programs. In
general then- you will need a different compiler for different OS's but
if you stick to intel and AMD chips you will need on one compiler for
all of the chips.

> 800MHz, etc? The speed of the processor is also
> important? (The compiler that is> best for a 600 MHz
> CPU is still the best for a 800 MHz CPU of the same type?)

No, they should all be the same. The difference comes between say a PII
and a PIII. The same program will run on both but it is possible to
optimised the program to be more effient on each chip- however, the
differences are subtile and so the same compile will tend to have
switches to specify different 'Target Architectures'.

For your information- the compiler needed depends on the instuction set-
the 'commands' built into the chip. The intel and AMD chips all have one
instruction set ans so all run the same programs. The Mac chips use
another instruction set and the alpha yet another.

Tom Grey
t.grey@ic.ac.uk

33333333333333333333333333333333333333333333333333333333333333333333333333333333

A compiler is specific for a processor family, but (with very few
exceptions) not for just one processor. So you need to get a
compiler for "Intel x86 and compatibles", and of course your OS.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

44444444444444444444444444444444444444444444444444444444444444444444444444444444

(...) 	A resposta a tua pergunta eh que compiladores mais modernos
apresentarao um desempenho maior uma vez que aproveitarao melhor as
propriedades dos novos processadores.

	The answer to your question is that more modern compilers will 
have a better performance, once they'll take better advantage of the
properties of the new processors.

Demetrio Filho
dasf@ifi.unicamp.br

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

From chemistry-request@server.ccl.net  Wed May 16 19:10:21 2000
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Errors-To: <morales@combichemlab.com>
Reply-To: <morales@combichemlab.com>
From: "Dr. Guillermo A. Morales" <morales@combichemlab.com>
To: "CCL" <CHEMISTRY@ccl.net>
Subject: RE: CombiChem + Synthesizer
Date: Tue, 16 May 2000 19:10:21 -0400
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I'm sending again this email since it did not go through the first time.

Guillermo Morales.

-----Original Message-----
From: Dr. Guillermo A. Morales [mailto:morales@combichemlab.com]
Sent: Saturday, May 13, 2000 6:15 PM
To: Jianhui Wu; chemistry@ccl.net
Subject: RE: CombiChem + Synthesizer


To answer your questions in order:

1)You can look at Tripos' Sybyl and the modules CombiLibMaker and
DiverseSolutions among other modules.

2)You might consider Bohdan's MiniBlocks, Charybdis Technologies' reaction
blocks, SyntraChem's SyntraPrep, Robbins Scientific FlexChem reactor blocks,
and other that might suit your throughput, needs and budget. Note that many
reaction blocks come in (6 x 8) 48-well format. Other companies offer blocks
in different formats.

You can stop by at CombiChem Lab (www.combichemlab.com) to read
comprehensive and up-to-date reviews on many items related to combinatorial
chemistry such as reaction blocks, workstations, software, etc.

I hope this helps.

Guillermo Morales
-----
Guillermo A. Morales
Morales Consulting
E-mail: morales@combichemlab.com
Website: www.combichemlab.com
Member of the Combi-Web Consortium (www.combi-web.com)



> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On
> Behalf Of Jianhui Wu
> Sent: Thursday, May 11, 2000 4:14 PM
> To: chemistry@ccl.net
> Subject: CCL:CombiChem + Synthesizer
>
>
> Dear All,
>
> I am seeking for advice from people which apply computional chemistry in
> combinatorial chemistry and have experience in organic synthesizer.
>
> (1) What software do you use?
> We are looking for a software that can generate combinatorial library
> according to the binding site of recepter (vdw, electrostatic,
> solvation). A designed compound will be useful only when it can be made
> in the lab. The construction of each compound should therefore comply
> with known organic reaction rules. The library will perhaps be screened
> by docking study (virtual screen) to obtain top 100-200 candiates for
> organic synthesizer. Do you cluster the library and virtually screen
> each sublibrary? What property people usually use to cluster a library?
>
> (2) Which model of synthesizer do you use?
> We are looking for a small organic synthesizer that have 20-40 vessels,
> capable of doing Solid phase/solution phase reaction and temperature can
> be adjusted. In other words, it should be cheap and still can do the job
> although it is small. If you have experience on this kind of parallel
> organic synthesizer, please give me some advice (what model, from which
> company, is it really doing the job?).
>
> Thanks a lot,
>
> Jian Hui Wu
> Institute Armand-Frappier
> 531 Boul des prairies
> Laval, Quebec H7N 4Z3
>
> Phone: 1-450-687-5010 ext 4329
> Fax:     1-450-686-5501, 1-450-9780198
> email:  JianHui_Wu@IAF.Uquebec.ca
>
>
>
> -= This is automatically added to each message by mailing script =-
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>
>
>
>
>
>


From chemistry-request@server.ccl.net  Wed May 17 10:48:30 2000
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Dear list members,

This is slightly off-topic since it doesn't concern computational chemistry
software exclusively.  On the other hand, since it *does* potentially affect
buyers and users (at least in the U.S.) of *all* software, including
computational chemistry, I'd like to pose the question to this list.  (I
apologize to those CCL members who are outside the U.S.; however, I believe
software users are facing similar issues in other countries as well.)


There has been an intense discussion in trade publications for months, and
recently also in the general press, about a new law proposal governing software
sales and licensing, the Uniform Computer Information Transaction Act (UCITA).
This draft model law is intended to be passed by the individual state
legislatures.  I'll not go into the history, background and details of UCITA,
all of which can be read about on web sites such as http://www.4cite.org/.

The general criticism I've seen voiced against UCITA is that it dramatically
shifts the balance of existing contract law in favor of software vendor.  
Specific provisions that have been deemed particulary worrisome include the
right for software vendors to shut down mission critical software remotely
without court approval and without incurring liability; to permit software
vendors to avoid liability for damage caused by bugs known to the vendor, and
undisclosed to the licensee, when the software was bought; to allow software
vendors to prohibit public criticism of their product; to bind the purchaser to
licensing terms disclosed only after the purchaser pays for the software, and
allows the software vendor to change the terms unilaterally by e-mail; and
others.

Such licensing terms were often part of license agreements in the past, but they
turned out to be rarely enforceable in court.  Now, the critics say, UCITA would
sanction all this by law.

I am not a legal expert, and I don't know how much the computational chemistry
software field would be affected by it.  Since UCITA is about to become law in
Maryland, I'd like to ask the CCL members how they see UCITA affecting their
future software purchases, and how they plan to handle the situation: just
accept it; or try to renegotiate licensing contracts with software vendors;
contact their legislators; ignore the licensing terms; simply not buy
UCITA-governed software; only use open source and GPL'd programs; or...?

I'll summarize the answers for the list.

Marc

(As always, these are my personal views and not necessarily those of NIH)
------------------------------------------------------------------------
 Marc C. Nicklaus                        National Institutes of Health
 E-mail: mn1@helix.nih.gov               Bldg 37, Rm 5B29
 Phone:  (301) 402-3111                  37 Convent Dr, MSC 4255       
 Fax:    (301) 402-2275                  BETHESDA, MD 20892-4255    USA 
      http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
    Laboratory of Medicinal Chemistry, National Cancer Institute
------------------------------------------------------------------------



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Subject: Re: CCL:Call for papers - Arts and tech symposium
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CALL FOR PAPERS, MUSIC COMPOSITIONS,
PRESENTATIONS, ART WORKS, THEATER, DANCE,
SCIENTIFIC VISUALIZATIONS AND INTERACTIVE INSTALLATIONS

THE EIGHTH BIENNIAL SYMPOSIUM ON ARTS AND TECHNOLOGY
March 1-3, 2001

THEME: FEEDBACK: Perception and Interaction in the Electronic Arts

DEADLINE FOR SUBMISSIONS: NOVEMBER 15, 2000

The Connecticut College Center for Arts and Technology is pleased to
announce The Eighth Biennial Symposium on Arts and Technology, March
1-3, 2001.  The symposium will consist of paper sessions, panel
discussions, art exhibitions, music concerts, animations, mixed media
works, video, dance, experimental theater and scientific visualization.
In an effort to demystify the artistic process and create a forum for
dialogue, we are encouraging all presenters and artists to attend the
symposium and speak about their work.

The Center encourages research papers and presentations in the specific
area of "FEEDBACK: Perception and Interaction in the Electronic Arts"
and in the general areas of Interactivity, Virtual Reality, Cognition,
Information Technologies, Applications in Video and Film, Music
(composition, performance, theory, interactivity, etc.), Experimental
Theater, Compositional Process, Innovative Use of Technology in
Education, Computer Simulations of Physical Phenomena, Scientific
Visualization and Social and Ethical Issues in Arts and Technology.
All submissions should be accompanied by a one page abstract for a
presentation about the work and each application should be prepared to
attend the symposium and make a presentation (paper, poster session,
short talk) about their work.

Papers and Presentations:
A detailed two-page abstract or complete paper including complete
technical requirements should be submitted by email or mail.  Upon
acceptance, finished papers must be submitted electronically following
the specific format of the symposium or in camera-ready form by January
15, 2001: Word, 10-12 font size, 8.5 x 11 sheet.  Papers may be grouped
in panel format. Complete technical requirements must be included.
Papers will be published by the Center.

Music Compositions:
Works for instruments and tape, or tape alone, or interactive
compositions are being solicited. Available instruments are: flute
(doubling on piccolo), oboe, clarinet (doubling on bass clarinet),
bassoon, trumpet, horn, trombone, percussion (two players), guitar,
string bass, piano, voice and strings (2,1,1,1).

Works should not exceed 15 minutes in length and should be submitted
with accompanying score, where appropriate.  Tapes for selection
purposes should be on cassette, CD's or DAT.  Tapes for performance
should be CD, ADAT or DAT.  Video works should be 3/4 inch Umatic or 1/2
inch VHS.  Musicians, dancers and actors may be available for live
performance pieces. All submissions should be accompanied by a one page
abstract for a presentation at the symposium about the work.  Complete
technical requirements must be included.

Artworks:
Works of computer-generated or computer-aided art, or
computer-controlled interactive art are encouraged.  Animations, video
or other works of computer art on tape will be shown in concert settings
and less formal settings throughout the Symposium.  All submissions
should be accompanied by a one page abstract for a presentation at the
symposium about the work. Slides, CD-ROM,  or video (VHS) and complete
descriptions of works must be included.   Art works accepted for
exhibition must be received by January 15 for inclusion in the
pre-symposium gallery showing, February 5 ? March 5. Complete technical
requirements must be included.

Dance and Theater Studies:
Computer-generated or -aided dance and theater is being solicited for
live demonstrations or for videotaped presentations.  Specially produced
dance or theater videos are of particular interest as opposed to concert
tapes or other archival uses of video.  Also of interest are proposals
for workshops, demonstrations of software for dance or theater
notation,  choreographic analysis,  interactive studies and/or
multi-media studies of performance in dance &  theater.  All submissions
should be accompanied by a one page abstract for a presentation at the
symposium about the work.  Videotapes or complete descriptions of
demonstration or workshop proposals should be submitted by the general
deadline of November 15, 2000.  Tapes for selection purposes should be
VHS.  Complete technical requirements must be included.

Panels:
Proposals for panels are encouraged.  Proposals should include
prospective panelists and should be directed to the theme or new issues
in collaborative work, as well as ethical issues in arts and technology.

Scientific Visualizations:
Submissions are solicited for computer animations and virtual realities
used to visualize complex scientific processes.  Special emphasis will
be given to works emphasizing  artistic content or educational modules.
Submissions should be on CD-ROM or Zip disk format. All submissions
should be accompanied by a one page abstract for a presentation at the
symposium about the work.  Complete technical requirements must be
included.

GENERAL INFORMATION ON SUBMISSIONS

SUBMISSION DEADLINE: NOVEMBER 15, 2000

All music, art, VR, visualization, multi-media installations, workshops,
dance and  theater submissions should be accompanied by a one page
abstract for a presentation about the work.

Technical information: Complete technical requirements must be included
for all submissions.  Please specify platform (MAC, PC-Windows, SGI).

Notification: Accepted proposals will be notified by December 22, 2000.

Return: Submissions, art works, slides, tapes, scores, videos will only
be returned if a self-addressed stamped envelope or packaging is
provided.

Send submissions to:
Center for Arts and Technology
Box 5365
Connecticut College
270 Mohegan Avenue
New London, CT USA 06320-4196
phone: [860] 439-2001
email:  cat@conncoll.edu






