From:	"Lestaw K. Bieniasz" <lestaw.k.bieniasz $#at#$ uni-tuebingen.
Date:	Mon, 14 Apr 1997 18:05:22 +0200 (MSZ)
Subject:	computational chemistry

					Tuebingen, 14.04.97

Dear Computational Chemists,

    I am new to this list, so please excuse me if questions similar to
those asked below have already been discussed. I need very much your help
and advice.

    Let me first introduce myself. For about 18 years my research has
been associated with the computer modelling of the transient experiments
in electrochemical kinetics. Briefly speaking this usually consists in
solving sets of reaction-diffusion partial differential equations with
various complications. I think my work has evolved from something one
might classify as applications of various computational methods to very
concrete electrochemical problems, to a more general approach, in which I
am trying to:

(a) Design universal computational strategies aplicable to a large class
of electrochemical kinetic problems.

(b) Pay more attention to the analysis of the computational methods
themselves, having in mind particular requirements of the electrochemical
kinetics.

(c) Better understand various rational procedures and reasoning processes
that are used in electrochemical kinetics, with the aim to enable automating
these processes as much as possible, and represent them in the form
of computer algorithms.

(d) Elaborate a comprehensive problem-solving environment for
electrochemical kinetic simulations, which apart from considering many
example problems, involves also elements of algorithms/software design
and pure programming.

    I have to say I have never thought of how to formally classify
the above area of investigations, and I was quite satisfied with the fact
that the reearch was interesting, seemingly modern and potentially very
promising for the future, if one takes into account the enormous recent
progress in computing technology. I also did not have much difficulties with
publishing the results of my work, which additionally reinforced my good
feeling that I have chosen the right direction. Unfortunately I am
beginning to encounter criticism from the side of several chemists in my
environment, who say that what I am doing is not electrochemistry,
because there is so much numerical mathematics and computational science
in my works. It seems that most electrochemists think that one needs to
solve very specific electrochemical problems (like finding out what
the mechanism of some reaction is, for example) in order to make progress in
electrochemistry. They don't notice that one might also make a progress
by making it possible that many tedious operations that the
electrochemists had so far to do by hand, can now be done easily and
rapidly by means of specially designed computer programs. They don't seem
to notice that certain traditional research paradigms do not longer make
much sense (for example, publishing long derivations for some kinetic
models in the situation when a properly designed program might even
create a whole paper automatically). These problems have drawn my
attention to the issue of how to classify and better justify my work,
and here go my questions:

(1) My first idea was to say that I am doing computational chemistry.
By analogy with computational physics which practically includes
everything that has to do with physics and computers simultaneously, I
would expect that my area of investigations might be called computational
electrochemistry. Logically, if computational chemistry is now a part
of chemistry, then I might keep saying that my area of interest belongs
to electrochemistry. How much I was mistaken, though! Most of the
computational chemists seem to put an equality sign between
quantum mechanical calculations and computational chemistry, as if there
existed no other possible uses of computers in chemistry. For example,
the Journal of Computational Chemistry publishes almost exclusively
quantum mechanical stuff. This fact was even reflected in one of the
first definitions of computational chemistry cited in the preface to
"Reviews of Computational Chemistry", vol. 1: "Use of molecular orbital
theorems to determine structure and properties of molecules".
Fortunately, the editors of this series officially accept a more elastic
definition, and in vol. 2 they write: "The quantitative modelling of
of chemical phenomena by computer-implemented techniques is how we view
the scope of the field, so it includes practically all aspects of
chemical research that are expedited or rendered practical by computers".
However, in the entire set of reviews (7 volumes) I have managed to trace
down only one article mentioning briefly some chemical kinetic simulation
program. The entire huge area of kinetic modelling seems therefore not to
exist in the consciousness of the computational chemists, as a part of
their area. I would be glad to know what you, the CCL subscribers, think
about this.

(2) After thinking for a while about point (1) I have started to have some
doubts, though. It might be that I do not precisely understand the
meaning of the word "computational", but for me it seems to mean something
close to "numerical calculations", whereas computers can do much more.
For example, they can do logical operations, largely used in AI methods,
e.g. in expert systems. Also, neural networks are becoming
increasingly popular in solving chemical problems, not necessarily
computational, but perhaps "intellectual", such as pattern recognition,
signal processing, machine learning for chemical purposes.
I feel a more general term like "computer-aided chemistry" would be more
adequate to describe the current developments at the junction
computers+chemistry. What do you think?

(3) To further extend point (2), I'd like to quote Allen Newell, an AI
expert [cf. D.G.Bobrow and P.J.Hayes, Artif. Intelligence 25(1985)3.]:
"We should, by the way, be prepared for some radical, and perhaps
surprising, transformations of the disciplinary structure of science
(technology included) as information processing pervades it. In
particular, as we become more aware of the detailed information processes
that go on in doing science, the sciences will find themselves
increasingly taking a metaposition, in which doing science (observing,
experimenting, theorizing, testing, archiving,...) will involve
understanding these processes, and building systems that do the
object-level science."
Isn't this what is happening now? Unfortunately, Allen Newell was not a
chemist, so that I can't use this argument to convince chemists. Does
anybody of you know about similar opinions being expressed by chemists?
If possible, by prominent chemists? I'd be happy to know (references or
addresses, please!) Or perhaps I am wrong, and even you, the declared
computational chemists, do not share the above opinion, and you rather
prefer to put clear dividing lines between all chemical and
computational aspects of the computational chemistry, seeing only
applications of computational science to chemistry, instead of a new
emerging area that combines both aspects? Do you use to say, "before
lunch we shall solve some chemical problem, and afternoon we shall work a
litle on numerical methods" ?

(4) By the way, do you know any papers, materials, internet resources, etc.
devoted to the predictions of how the use of computers in chemistry (and
in other natural sciences) may look like in the nearest decades? I'd like
to find such predictions.

(5) I wonder how those of you, who may possibly develop chemical expert
systems, classify your research. Do you think that a research on what can
be regarded as sound reasoning in chemistry is a subject belonging to
chemistry? Or to computational science? What do the referees of your
research proposals, and sponsors think about it?

I hope I am not taking too much of your (computational) time.

				Yours sincerely

							L.Bieniasz

*-------------------------------------------------------------------*
|                        Dr. Leslaw Bieniasz                        |
| temporary address: (3rd April 1997 - 31st August 1997)            |
|       Institut fuer Organische Chemie, Universitaet Tuebingen     |
|          Auf der Morgenstelle 18, 72076 Tuebingen, Germany.       |
|              E-mail: lestaw.k.bieniasz' at \`uni-tuebingen.de           |
*-------------------------------------------------------------------*
| permanent address:                                                |
| Institute of Physical Chemistry of the Polish Academy of Sciences,|
| Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland.   |
|                   E-mail:  nbbienia -8 at 8- cyf-kr.edu.pl                 |
*-------------------------------------------------------------------*








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