path: root/info/digests/texline/no12/chemist.tex

{\overfullrule0pt\def\cite#1{[#1]}
%  Warning:  This is an input file for AMSTeX, rather than for LaTeX.
%            This is just so that I can use the commands for arrows
%            mentioned on pages 140-141 of "The Joy of TeX".
%            It may not be "good AmSTeX", since it's the first time
%            I've used AmSTeX seriously!
\title{Could  \LaTeXbf\ do more for chemists?}
From time to time I have seen queries in {\TeXhax} and
elsewhere from people   who wish to use \LaTeX\ for           documents
that involve chemical formulae, etc.  Since there are now plans for
\LaTeX\ 3.0 \cite{1},
I thought this might be a good time to consider
what facilities one could reasonably ask the people implementing the new
\LaTeX\     to provide for chemists.
 
I'm not a chemist myself, but have been involved in helping chemists
use \LaTeX\ 2.09 \cite{2} for producing theses, etc.
 
\section{Typesetting and artwork}
 It may help  to consider the division of labour within a traditional
publishing house.  A `copy-editor' \cite{3, p236} might divide the work on
chemical formulae up between `the printer' and `the draughtsman'. Thus,
some formulae can be typeset, but others are treated as `artwork' and are
drawn.
 
Although there have been valiant attempts \cite{4-5} to define \TeX\ macros
for drawing chemical structure diagrams, I think      it is inevitable that,
whatever \TeX\ macros are defined, there will be chemists who come along with
requirements that are beyond the abilities of the macro packages.  Therefore,
it seems sensible to retain the traditional division between typesetting and
artwork:  to typeset those formulae that can be typeset easily and to get the
other formulae drawn in some way.
 
In \TeX\   terms, artwork can be treated as `graphics' to be
`pasted' into a typeset document via |\special|.
For example, {\sans Chemdraw}
\cite{6} can produce `encapsulated {\PS}',
so a \LaTeX-ed document with {\sans Chemdraw} diagrams can be printed on
a {\PS} printer.
 
\section{Desirable facilities for chemists} 
\LaTeX\ is never going to be a system for producing `artwork',
so it seems to me that it would be unwise to attempt to provide
comprehensive facilities for `chemical artwork' in \LaTeX. However, it does
seem worth providing a limited number of facilities to make it
easier to produce the chemical formulae that should be
treated as `typesetting'.
 
\subsection{Environments} 
Chemists' problems start when they use \LaTeX's `mathematics'
environments for `chemistry'. Chemistry is not mathematics, and
the conventions for typesetting chemistry are different from those for
typesetting mathematics.  In terms of the \LaTeX\ philosophy \cite{2, p6},
`mathematics' and `chemistry' represent `logically distinct structural
elements'.
 
It would seem natural to:
\bi define environments for chemists that are
      analogous to the environments that are available for mathematicians
\bi within these `chemistry' environments,  aim to keep to
      whatever typesetting conventions are usual in chemistry.

\noindent
How about defining {\tt chem}, {\tt displaychem} and {\tt chem\-equation}
 environments,
by analogy with {\tt math}, {\tt displaymath} and {\tt equation}?
 
If such environments were defined, the style-file writer would then
have control over `mathematics' and `chemistry' separately.
In particular:
\bi The default would be {|\rm|} for chemistry (although
      a designer could change the default in a {\tt .sty} file).
      Individual
      authors would no longer have to        search through
      ``double bend'' sections of the \TB\ themselves
      \cite{7, pp163 \& 179}.
\bi A designer could implement a house-style  in which
      mathematical and chemical equations are numbered in separate
      sequences \cite{3, p224} or a house-style in which there is only one
      sequence of numbers \cite{8, p32}.
\bi It might be possible to arrange that subscripts will normally be
      at the same level \cite{7, p179} inside the environments
      for chemistry.

 
\subsection{Commands}
At first sight, the \LaTeX\ manual \cite{2, ch.\ 3} gives the impression that
\LaTeX\ 2.09 provides the `building blocks'        to give all the arrows,
harpoons and annotation that a chemist could want.  However, it is often
difficult to get these building blocks arranged in the ways required.
For example:

\bi How does one obtain CH${_3}$(C=O)OCl \cite{3, p235} in `math mode'?
      We can't
      use `='
      to mean ``double bond'', since \TeX\ puts space
      around it.
\bi To represent a reversible reaction with rate constants above\slash below
      a pair of harpoons, I ended up with
\begintt
\renewcommand{\arraystretch}{0.5}  
A     \begin\{array}{c}  
      \scriptstyle k_1\\[1mm]  
      \rightleftharpoons\\
      \scriptstyle k\_2
      \end{array}        B  
\endtt
      before it looked right.  Surely individual \LaTeX\ users shouldn't have
      to re-do the `tuning' needed to get these things         right?
\bi As in the above example, arrows and harpoons are often labelled  to show
reaction conditions. It is not clear how to get           
arrows\slash harpoons that expand to the width of the labels.

\noindent Many of these difficulties are  another consequence of trying to
use, for chemistry, the structural elements that were designed for
mathematics.
 
So what commands might usefully be made available inside some future
`chemistry' environments?

It seems desirable \cite{3, p237} to have documented facilities for
single and double bonds.  Triple bonds might also be needed \cite{9}.
A documented facility for representing single
bonds by raised dots would also be useful \cite{10, p59}.
Might commands such as |\bond|,    |\doublebond| and
|\triplebond|
be appropriate?

It seems desirable to have specific commands for typesetting
arrows\slash harpoons with labels above\slash below (to indicate conditions or
rate constants).  An indication of the combinations
of arrows\slash harpoons that have  been typeset traditionally  is given
in \cite{11,~p371}. Thus, as well as providing simple arrows for one-way
reactions, it might be worth aiming to provide commands for: equilibrium
reactions (beginning at left and right); reversible reactions (beginning at
left and right); reactions beginning at left\slash right and completed to
left\slash right. Might it be worth defining some commands such as

\centerline{\vbox{\tt\halign{\char'134#\quad&\char'134#\cr
oneway\cr
equilibriumR &equilibriumL\cr
reversibleR &reversibleL\cr
rightright &rightleft\cr
leftright &leftleft\cr
}}}
\noindent that each accept two parameters:  one to give a label
above the symbol, the other to give a label below the symbol?
For example,
\begintt
\begin{chem}
2H_2 + O_2 
\oneway{catalyst}{300 K; 4 bar} 2 H_2O 
\end{chem} 
\endtt
might be a natural way to specify
%  This is the line that contains the command that made me use AMSTeX.
%  I couldn't find anything else ready-made in plain TeX or LaTeX.
\newdimen\bigaw
\def\oneway>#1>#2>{%
\setbox0\hbox{$\scriptstyle#1$}
\setbox1\hbox{$\scriptstyle#2$}
\bigaw\wd0\ifdim\wd1>\bigaw\bigaw\wd1\fi
\mathrel{\mathop{\hbox
to\bigaw{\rightarrowfill}}\limits^{#1}_{#2}}}
$${\rm2H}_2 + {\rm O}_2
     \oneway >{\rm catalyst} > {\rm 300 K; 4 bar} >
            {\rm 2H}_2{\rm O}
$$
 
\section{Work involved}
I'd guess that my suggestions about environments could be implemented
by slight modications of the code that implements the corresponding
environments for mathematics.
 
Some new work would be required for commands such as |\oneway|,
\dots\ , |\leftleft|.  The only similar facility that I've found
in an existing macro package is that for arrows in \AmSTeX\ \cite{12, p140},
but (from a chemist's point-of-view) this doesn't provide sufficient
choice of symbols.
 
It might be worth seeking advice about objectives
from people who typeset chemistry professionally.
%  Perhaps the UK's Royal Society of Chemistry would be prepared to advise
%  about details.  I've been in e-mail correspondence with their Publications
%  Manager about authors submitting mansuscripts electronically to them,
%  although they seem to be going the wordprocessor + chemdraw + SGML route.
 
\section{Documentation} 
If the facilities that I've outlined above were provided, I would
be inclined to give them less prominence in the documentation than
the analogous facilities for mathematicians.   This would help
give the impression that, whereas mathematicians can expect \LaTeX\
to do everything they want, chemists can only expect \LaTeX\ to do a certain
proportion of what they want.
For example, in the successor to \cite{2}, the description of facilities for
chemists might be relegated to an appendix, which            could start with a
paragraph explaining that the facilities are intended to support
`typesetting' but not `artwork'.
 
\section{Bibliography}{\parindent0pt\frenchspacing\raggedright
\everypar{\hangafter1\hangindent20pt}
\par
[1] Frank Mittelbach and Rainer Sch\"opf, 1989,
With \LaTeX\ into the Nineties
TUGboat 10,
681--690.



[2]
Leslie Lamport, 1986, 
\LaTeX: A Document Preparation System,
Addison-Wesley.



[3]
Judith Butcher, 1981,
Copy-editing
Cambridge University Press,



[4]
Roswitha T. Haas and Kevin C. O'Kane, 1987,
Typesetting chemical structure formulae with the text formatter
      \TeX\slash \LaTeX,
Computers and Chemistry 11, 
251-271.

[5]
Michael Ramek, 1990,
Chemical structure formulae and $x/y$ diagrams with \TeX\  {\it in:}
      \TeX: applications, uses, methods,       Malcolm Clark (editor),
Ellis Horwood.

[6]
{\sans Chemdraw} (A program for the Macintosh),
Cambridge Scientific Computing,
Cambridge, Massachusetts.

%
[7]
Donald E. Knuth, 1986,
The \TeX book,
Addison-Wesley.

[8]
Janet S. Dodd, 1986,
The ACS Style Guide
American Chemical Society

[9]
Handbook for Chemical Society Authors,  1961,
The Chemical Society

[10]
Hart's Rules, 1983,
Oxford University Press
1983


[11]
Chicago Manual of Style, 1982,
Chicago University Press
%  \publaddr Chicago

[12]
Michael Spivak,  1986,
The Joy of \TeX,
American Mathematical Society

}}
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\author{David Rhead}