Subject: computational chemistry

From: "Lestaw K. Bieniasz" <[email-masked]>
Date: Wed, 16 Apr 1997 09:48:27 +0200 (MSZ)

Tuebingen, 16.04.97

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

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|                        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: [email-masked]           |
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| permanent address:                                                |
| Institute of Physical Chemistry of the Polish Academy of Sciences,| 
| Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland.   | 
|                   E-mail:  [email-masked]                 |
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