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+\chapter{\TeX/\LaTeX\ code for components of organic chemical structure
+ diagrams}\label{ch:txltx}
+\section{Conventions for drawing the diagrams}\label{sc:convntns}
+ The chemical structure of a molecule is defined by the spatial
+ arrangement of the atoms and the bonding between them.
+ Chemists use several standard methods for representing the
+ structures two-dimensionally by diagrams called structural
+ formulas; and this thesis will develop mechanisms for printing
+ such diagrams using the \TeX/\LaTeX\ system.
+
+ A very common structure representation, sometimes called a
+ dash structural formula, uses the element symbols for the
+ atoms and a dash for each covalent bond in the compound.
+ Thus the dash represents the pair of shared electrons that
+ constitutes the bond. Two dashes ($=$) represent a double
+ bond and three dashes ($\equiv $) a triple bond. ---
+ It is usually neither necessary nor practical to represent
+ each bond in a molecule explicitly by a dash.
+ Some molecules and some bonds are so common that a complete
+ dash formula would not be used except at a very introductory
+ level of presenting chemical information.
+ A condensed structural formula is one alternative. It does
+ not contain dashes but uses the convention that atoms
+ bonded to a carbon are written immediately after that
+ carbon and otherwise atoms are written from left to right
+ in the order in which they occur in the real structure.
+ The following two structural formulas are a dash formula
+ and a condensed formula, respectively, for the same
+ compound, ethanol.
+ \[ \parbox{4.5cm} {
+ \begin{picture}(400,900)(0,-110)
+ \put(0,0) {\cbranch{H}{S}{H}{S}{C}{S}{}{S}{H} }
+ \put(240,0) {\cbranch{H}{S}{}{Q}{C}{S}{O---H}{S}{H} }
+ \end{picture} }
+ \hspace{1.5cm}
+ {\rm CH_{3}CH_{2}OH} \]
+ Multiple bonds are usually not implied unless a very common
+ group, such as the cyano group, is shown. It can be found
+ as $-$C$\equiv $N or simply as $-$CN.
+
+ Another alternative to a complete dash formula is a diagram
+ where the symbols for carbon and for hydrogen on carbon are
+ not shown. Each corner and each open-ended bond in these
+ diagrams implies a carbon atom with as many hydrogen
+ atoms bonded to it as there are free valences. This
+ representation is the customary one for ring structures
+ (structures with a closed chain of atoms). Thus, the
+ following two diagrams both represent the compound
+ cyclopropane.
+ \[ \hetthree{Q}{H}{H}{H}{H}{S}{S}{C}
+ \hspace{3cm} \yi=330
+ \threering{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q} \]
+
+ \reinit
+ The three different kinds of structure representation can
+ be combined in one diagram, such that in part of the
+ diagram all bonds are represented by dashes and all
+ atoms by an element symbol, in another part a condensed
+ structural formula fragment is used, and in still
+ another part a cyclic fragment with implied carbon
+ and hydrogen atoms occurs.
+
+ The rest of this chapter describes how \LaTeX\ can be used
+ to position and typeset the bond lines and condensed
+ formula strings that are the components of structure
+ diagrams.
+
+ It should be mentioned that there are no binding rules
+ for many aspects of the two-dimensional representations
+ of a chemical structure. Structures and fragments of
+ structures can be oriented in different ways depending
+ on the availability of space, the emphasis given to
+ a certain part of a structure, or the spatial
+ relationship of the parts to each other.
+ Thus, a cyclopropane ring can be represented in various
+ orientations, $\bigtriangleup $, $\bigtriangledown $,
+ and others. Also, the angles between
+ the bond lines can be different in different representations
+ of one and the same compound. Since most molecules do not
+ have all their atoms lying in one plane it would not
+ even be possible to reproduce all bond angles in a
+ two-dimensional representation. The structures shown in
+ this thesis adopt the orientations and bond angles
+ found to prevail in Solomons' textbook (Solomons 84),
+ the organic chemistry text used for several years at
+ the University of Tennessee.
+
+ There are some methods to indicate the real,
+ three-dimensional structure (the stereochemistry)
+ of a molecule in the two-dimensional representation:
+ A dashed line and a wedge instead of a full bond
+ line mean that the real bond extends below or
+ above the plane, respectively.
+
+\section{Bond line drawing and positioning}
+\subsection{Review of \TeX/\LaTeX\ facilities for line-drawing}
+\label{sc:review}
+ The easiest way to produce horizontal and vertical lines representing
+ chemical bonds is by the use of keyboard characters and simple control
+ sequences provided by \TeX. By typing one, two, or three hyphens,
+ a normal hyphen, a medium dash designed for number ranges, and a
+ punctuation dash are produced, - -- ---, respectively. When a hyphen
+ is typed in \TeX's math mode, it is interpreted as a minus sign and
+ the spacing around it will be different from text mode. ---
+ The equal sign can represent a double bond for chemistry typesetting.
+ It can be typed in text mode and in math mode, again resulting in
+ different spacing around the symbol. --- The control sequence
+ \verb+\equiv+ can be used as a triple bond ($\equiv $). It has to
+ be typed in math mode.
+
+ Vertical lines are available through the keyboard character or the
+ control sequences \verb+\vert+ and \verb+\mid+, all three to be
+ entered in math mode.
+ A double vertical bar is produced by \verb+\|+ or \verb+\Vert+,
+ again both in math mode.
+
+ The spacing around all these symbols can be controlled by adding
+ extra (positive or negative) space with the horizontal spacing
+ commands. The symbols, just as any other part of a line, can also
+ be raised or lowered respective to the normal baseline. The length
+ and height of the symbols however depend on the font currently
+ in use.
+
+ Where control of length and height of the bond lines is needed,
+ \TeX's or \LaTeX's command sequences for printing horizontal and
+ vertical ``rules'' can be used. The systems recognize several
+ length units, including the inch, centimeter, millimeter, and
+ printer point (Knuth 84, p. 57). One printer point (pt), an often
+ used unit in typesetting, measures about 0.35 mm. --- \LaTeX's
+ rule-printing command has the format
+ $$\hbox{\verb+\rule[raise-length]{width}{height}+}$$
+ Thus it can be used to produce horizontal and vertical rules.
+ Using the \verb+\rule+ command one can also print multiple
+ bond lines of user-controlled length, e.~g. $\dbond{16}{10} $,
+ $\tbond{16}{11} $, with the short control sequences \verb+\dbond+
+ and \verb+\tbond+ defined in this thesis. The vertical spacing
+ between the bonds depends on the current line spacing in the
+ document and may have to be adjusted. The control sequences
+ are set up for math mode.
+
+ When bond lines other than horizontal and vertical ones are to
+ be printed, and when a coordinate system is needed to control
+ placement of structure components relative to one another,
+ \LaTeX's picture environment (Lamport~86, pp.~101--111) is a
+ necessity.
+
+ A picture environment uses length units which are dimensionless
+ and have to be defined by the user before entering the
+ environment. This is done by the \verb+\setlength+ command.
+ In this study, \verb+\setlength{\unitlength}{0.1pt}+
+ is the definition used for most diagrams. Such a small
+ unitlength was chosen to have fine control over the appearance
+ of the diagram.
+
+ The picture environment starts with the statement
+ $$\hbox{\verb+\begin{picture}(width,height)+}$$
+ where picture width and height reserve space on the page
+ and are specified in terms of unitlengths. Optionally, one
+ can include the coordinates of the lower left corner of the
+ picture:
+ $$\hbox{\verb+\begin{picture}(width,height)(x+$_i$\verb+,y+$_i$\verb+)+}$$
+ The default value for these coordinates is (0,0).
+ Objects are placed into the picture with the \verb+\put+
+ command with their reference point at the coordinates (x,y):
+ \verb+\put(x,y){picture object}+.
+
+ The picture objects of most interest to this study are
+ straight lines. They are drawn by the \verb+\line+
+ command:
+ $$\hbox{\verb+\line(x+$_s$\verb+,y+$_s$\verb+){length}+}$$
+ where the coordinate pair specifies the slope of the line,
+ and the nonnegative value of length specifies the length
+ of the projection of the line on the x-axis for all
+ nonvertical lines, and the length of the line for vertical
+ lines. The reference point of a line is one of its ends.
+ Thus the statement
+ $$\hbox
+ {\verb+\put(x,y)+
+ \verb+{\line(x+$_s$\verb+,y+$_s$\verb+){len}}+}
+ $$
+ draws a line that begins at (x,y), has a slope of ${\rm y_s\mbox{/}x_s}$,
+ and extends for length len as explained above.
+
+ Only a limited number of slopes is available through the line
+ fonts in \LaTeX. The possible values for ${\rm x_s}$ and ${\rm y_s}$ are
+ integers between $-6$ and $+6$, inclusive. These values translate
+ into 25 different absolute angle values, which are listed
+ in Appendix~\ref{ap:slopes}.
+
+\subsection{Bonds in structural formulas written on one line}
+\label{sc:onelinebonds}
+ The application of some of the bond-drawing mechanisms for this
+ simplest type of structural diagrams is illustrated in
+ Figure~\ref{fg:oneline}.
+ \begin{figure}\centering
+ \begin{picture}(900,700)
+ \put(0,600) {a \ $CH\equiv C-CH=CH_{2}$}
+ \put(0,350) {b \ $CH$\raise.1ex\hbox{$\equiv$}$C-CH=CH_{2}$}
+ \put(0,100) {c \ $CH\tbond{14}{20} C\sbond{14}
+ CH\dbond{14}{19} CH_{2}$}
+ \end{picture}
+ \caption{One-line structural formulas}
+ \label{fg:oneline}
+ \end{figure}
+
+ For Figure~\ref{fg:oneline}a only keyboard characters and the \TeX\
+ command \verb+\equiv+ were used to produce the bonds.
+ Figure~\ref{fg:oneline}b
+ shows a slight improvement through raising the triple bond.
+ Figure~\ref{fg:oneline}c was printed using the \verb+\sbond+,
+ \verb+\dbond+, and \verb+\tbond+ command sequences from
+ this thesis, choosing a length of 14pt for the bonds.
+ It can be seen that each of the formulas in Figure~\ref{fg:oneline}
+ is a
+ creditable representation of the structure. Depending on the
+ design of the page, the reason for displaying the structure
+ at a particular place, and the emphasis put on features of the
+ structure in the text, one would choose shorter or longer
+ bonds and take more or less trouble to produce the structure.
+
+ The picture environment is not needed for one-line structural
+ formulas, unless one of these formulas has to be attached to
+ another structural fragment, as in Figure~\ref{fg:picline}
+ Then the
+ coordinate system of the picture environment makes it
+ possible to fit the two fragments together.
+ \begin{figure}
+ \hspace{5cm}
+ \parbox{70 pt} {
+ \begin{picture}(400,200)
+ \put(-155,0) {$CH_{3}-CH-CH_{2}-CH_{2}-CH_{2}-CH_{3}$}
+ \end{picture} }
+ \hspace{5cm} \yi=200 \pht=600
+ \sixring{Q}{Q}{Q}{Q}{Q}{}{D}{D}{D} \\
+ \caption{One-line structure in picture environment}
+ \label{fg:picline}
+ \end{figure}
+\subsection{Bonds in acyclic structures with vertical branches}
+ Structure diagrams with vertical, single- or double-bonded, branches,
+ going up or down, are frequently seen. Several experiments with \TeX\
+ and \LaTeX\ were made to see how this type of structure can be
+ handled. One method is to align the vertical bonds by using the
+ mechanisms for tabbing or for printing tables and matrices.
+ Here a structure such as the one shown in Figure~\ref{fg:vertbranch}
+ is treated
+ as a set of columns as indicated by the vertical dividing lines
+ drawn into the second version of this structure in
+ Figure~\ref{fg:vertbranch}.
+
+ \begin{figure}
+ \hspace{1cm}
+ \begin{minipage}{180pt}
+ \begin{tabbing}
+ $CH_{3}CH_{2}$\= $CH$\= $CHCH_{2}$\= $CHCH_{2}CH_{3}$\+ \kill
+ $Br$\> \> $CH_{3}$ \\
+ \hspace{2pt}$\vert $\> \> \hspace{2pt}$\vert $ \- \\
+ $CH_{3}CH_{2}$\> $CH$\> $CHCH_{2}$\> $CHCH_{2}CH_{3}$\+ \+ \\
+ \hspace{2pt} $\vert $ \\
+ $CH_{2}CH_{3}$
+ \end{tabbing}
+ \end{minipage}
+ \hspace{2.5cm}
+ \begin{minipage}{180pt}
+ \begin{tabbing}
+ $CH_{3}CH_{2}$\= $\vert CH$\= $\vert CHCH_{2}$\= $\vert CHCH_{2}CH_{3}$
+ \+ \kill
+ $\vert Br$\> $\vert $ \> $\vert CH_{3}$
+ \\
+ $\vert $\hspace{2pt}$\vert $\> $\vert $ \> $\vert $\hspace{2pt}
+ $\vert $ \- \\
+ $CH_{3}CH_{2}$\> $\vert CH$ \> $\vert CHCH_{2}$\> $\vert CHCH_{2}CH_{3}$
+ \+ \\
+ $\vert $\> $\vert $\hspace{2pt}$\vert $ \> $\vert $
+ \\
+ $\vert $\> $\vert CH_{2}CH_{3}$
+ \end{tabbing}
+ \end{minipage}
+ \caption{Vertical branches}\label{fg:vertbranch}
+ \end{figure}
+
+ The structure diagram in Figure~\ref{fg:vertbranch}
+ uses \verb+\vert+ for the vertical
+ bonds and \LaTeX's tabbing environment for the alignment. One can also
+ use ``rules'' as the vertical bonds in order to give the horizontal
+ and vertical bonds the same lengths. Furthermore, vertical bonds can
+ also be double bonds. The following examples illustrate these features.
+ $$
+ \tbranch{O}{D}{H_{2}N-}{C-NH_{2}}{}{}{1} \hspace{2cm}
+ \tbranch{}{}{CH_{3}-CH_{2}-}{C-CH_{3}}{D}{NH}{1} \hspace{2cm}
+ \tbranch{}{}{H-}{C=\ }{S}{Br}{1}\tbranch{}{}{}{C-H}{S}{Br}{1}
+ $$
+ Similar structures were also generated with \TeX's \verb+\halign+
+ mechanism which forms templates for the columns rather than setting
+ tab stops. For the purpose of printing the structure diagrams, no
+ clearcut advantage was seen in one or the other method of
+ alignment. In each case the vertical spacing depends on the line
+ spacing in the document.
+
+ The alternative method of producing these structures is the use
+ of the picture environment. It provides better control over
+ horizontal and vertical spacing and over bond lengths. Also,
+ as illustrated in Section~\ref{sc:onelinebonds},
+ using a picture environment makes
+ it possible to attach one structural fragment to another at
+ a specific place. Thus, although the picture environment is not
+ necessary for drawing structures with vertical branches, it
+ has several advantages, and writing \LaTeX\ code for this
+ implementation is not more difficult than writing the code
+ for the tabbing method of alignment.
+
+\subsection{Bonds in Structures Containing Slanted Bond Lines}
+ Structure diagrams with slanted bond lines are frequently used for
+ acyclic compounds and have to be used to depict almost all cyclic
+ structures. Two examples are shown here:
+ $$ \cdown{$CH_{3}$}{S}{$N^{+}$}{D}{$O$}{S}{$O^{-}$}
+ \hspace{3cm} \sixring{$COOH$}{$OCOCH_{3}$}{Q}{Q}{Q}{Q}{S}{S}{C} $$
+
+ In developing diagrams for such structures in this thesis the
+ conventions described in Section~\ref{sc:convntns} are followed.
+ Thus the symbol for carbon is not
+ printed for the carbons that are ring members, but it is usually
+ printed in acyclic structures, unless the acyclic structure fragment
+ is a long chain, or space for the diagram is limited.
+
+ The picture environment is always needed for slanted lines. It was
+ explained in Section~\ref{sc:review} that \LaTeX\ can draw lines
+ only with a finite number of slopes. This is not a severe limitation
+ for creating the structure diagrams, since the conventions for
+ structure representation allow variations in the angles.
+ The representation does not have to reflect the true
+ atomic coordinates. In fact many chemistry publications contain
+ structure diagrams with angles significantly deviating from the real
+ bond angles, even where those could have been used easily. Thus,
+ Solomons' text (Solomons~84)
+ shows the carboxylic acid group often in this form
+ \pht=600
+ \[ \cright{}{S}{C}{D}{O}{S}{OH} \]
+ \pht=900
+ with an angle of about $90\circ$ between the OH and doublebonded O,
+ whereas the true angle is close to $120\circ$. --- The angles used
+ in this thesis for the regular hexagon of the sixring deviate by
+ % \parbox{4mm}{+\vspace{-18pt}\\ $-$}~$1^0$ from $120^0$
+ $\pm 1^\circ$ from $120^\circ$
+ because of \LaTeX's limited
+ number of slopes. This difference is not big enough to be
+ detected as a flaw.
+
+ To write the \LaTeX\ statement for a slanted bond line, one chooses the
+ origin and the slope and then uses trigonometric functions to calculate
+ the \LaTeX\ ``length'' of the line for the desired real length. Once the
+ \LaTeX\ length is determined, the coordinates of the end point of the
+ line can be calculated in case the end point is needed as the origin
+ of a connecting line. --- The origin and length of slanted double
+ bonds were also calculated with standard methods from trigonometry.
+ As an example, Figure~\ref{fg:calcpos}
+ shows how coordinates of the origin were
+ calculated for the inside part of a ring double bond that is at a
+ distance d from the outside bond.
+
+ \setlength{\unitlength}{1pt}
+
+ \begin{figure}
+ \begin{picture}(300,250)(0,-100)
+ \thicklines
+ \put(0,0) {\line(5,3) {120}}
+ \put(120,72) {\line(5,-3) {120}}
+ \put(240,0) {\line(0,-1) {100}}
+ \put(215,-6) {\line(-5,3) {88}}
+ \thinlines
+ \put(120,72) {\circle*{4}}
+ \put(125,72) {($x$,$y$)}
+ \put(127,47) {\circle*{4}}
+ \put(132,47) {($x_d$,$y_d$)}
+ \put(120,72) {\line(0,-1) {16}}
+ \put(120,72) {\line(-3,-5){9}}
+ \put(111,56) {\line(1,0) {16}}
+ \put(127,56) {\line(0,-1) {9}}
+ \put(111,56) {\line(5,-3) {16}}
+ \put(111,62) {\scriptsize d}
+ \put(116,46) {\scriptsize d}
+ \put(112,17) {{\small $\theta =30^{0}$}}
+ \put(114,28) {\vector(0,1){27}}
+ \put(270,35) {$x_{d}=x-d\sin ${\small $\theta $}$+d\cos ${\small $\theta $}}
+ \put(270,5) {$y_{d}=y-d\sin ${\small $\theta $}$-d\cos ${\small $\theta $}}
+ \end{picture}
+ \caption{Calculating position and length of double bond.}
+\label{fg:calcpos}
+ \end{figure}
+
+ \reinit
+
+ The \LaTeX\ command \verb+\multiput+ is similar to \verb+\put+ and provides
+ a shortcut for the coding of structures where several bond lines of the
+ same slope and length occur at regular intervals. Multiput has the
+ format
+$$\hbox {\verb+multiput(x,y)(x+$\Delta$\verb+,+$\Delta$\verb+y){n}+
+ \verb+{object}+}$$
+ where n is the number of objects, {\em e.g.,\/}
+ lines. A structure diagram
+ for which several \verb+\multiput+ statements are appropriate is
+ the structure of vitamin~A shown in Figure~\ref{fg:multidiag}
+
+ \begin{figure}
+ \hspace{2cm}
+ \parbox{5cm} {
+ \begin{picture}(900,900)(-300,-300)
+ \put(342,200) {\line(0,-1) {200}}
+ \put(342,0) {\line(-5,-3) {171}}
+ \put(171,-103) {\line(-5,3) {171}}
+ \put(0,0) {\line(0,1) {200}}
+ \put(0,200) {\line(5,3) {171}}
+ \put(171,303) {\line(5,-3) {171}}
+ \put(322,180) {\line(0,-1) {160}}
+ \put(342,0) {\line(5,-3) {128}}
+ \put(171,303) {\line(5,3) {128}}
+ \put(171,303) {\line(-5,3) {128}}
+ \multiput(342,200)(342,0){5}{\line(5,3){171}}
+ \multiput(513,303)(342,0){4}{\line(5,-3){171}}
+ \multiput(527,270)(342,0){4}{\line(5,-3){135}}
+ \multiput(855,303)(684,0){2}{\line(0,1){160}}
+ \put(1881,275){=O}
+ \end{picture} }
+ \caption{Diagram using $\backslash $multiput}
+\label{fg:multidiag}
+ \end{figure}
+
+ The size of objects in a picture environment can be scaled in a simple
+ way by changing the unitlength. Figure~\ref{fg:scaling}
+ illustrates scaling and
+ two problems associated with it. Changing the unitlength changes the
+ length of the lines only, not the width of the lines or the size of
+ text characters. Thus ``it does not provide true magnification and
+ reduction'' (Lamport~86, p.~102). However, the size of the text
+ characters can be varied separately, as will be discussed in the
+ next section of this chapter.
+ \begin{figure}
+ \pht=750\centering
+ \setlength{\unitlength}{.07pt}
+ \sixring{$OH$}{Q}{Q}{Q}{Q}{$Br$}{S}{D}{S}
+ \hspace{1.5cm}
+ \setlength{\unitlength}{0.08pt}
+ \sixring{$OH$}{Q}{Q}{Q}{Q}{$Br$}{S}{D}{S}
+ \hspace{1.5cm} \yi=150
+ \setlength{\unitlength}{0.15pt}
+ \sixring{$OH$}{Q}{Q}{Q}{Q}{$Br$}{S}{D}{S}
+ \caption{Scaling (unitlength=0.07pt, 0.08pt, 0.15pt)}
+ \label{fg:scaling}
+ \end{figure}
+
+ The smallest diagram in Figure~\ref{fg:scaling}
+ illustrates a limitation that
+ is unfortunate for the printing of structure diagrams. The shortest
+ slanted line that can be printed by \LaTeX's line fonts is
+ one with an x-axis projection of about~3.6mm.
+ If a shorter slanted line is requested, \LaTeX\ just prints
+ nothing. A chemist would occasionally want to draw shorter lines,
+ especially for the purpose of generating dashed lines indicating
+ stereochemical features.
+
+\section{Atomic symbols and condensed structural fragments}
+\label{sc:fragments}
+ Special considerations for the printing of condensed structural
+ fragments are required since many of them contain subscripts.
+ \TeX\ considers the printing of subscripts a part of mathematics
+ typesetting which has to be done in the special math mode.
+ As it is known, typesetting of mathematics
+ documents is one of the strong points of \TeX; the fonts of type
+ for the math mode are designed to agree with all conventions
+ of high quality mathematics publishing. Each typestyle in math
+ mode consists of a family of three fonts (Knuth~84, p.~153),
+ a textfont for normal symbols, a scriptfont for first-level
+ sub- and superscripts, and a scriptscriptfont for higher-level
+ sub- and superscripts. When structural fragments such as
+ ${\rm C_{2}H_{5}}$ are typeset, the textfont is used
+ for the C and the~H.
+
+ As \TeX\ enters math mode it selects \verb+\textfont1+ as the textfont
+ unless otherwise instructed.
+ \verb+\textfont1+ is defined by the \TeX\
+ macros as math italic, a typestyle that prints letters (not
+ numbers) similar to the italic style, but with certain
+ features adapted for mathematics typesetting. The italic
+ style letters, lower and upper case, are the ones commonly
+ seen in typeset mathematical formulas. Chemical formulas
+ on the other hand are not usually printed with slanted
+ letters. In this thesis, two methods were employed
+ to produce chemistry-style letters in \TeX's math mode which
+ has to be used because of the presence of subscripts.
+
+ For a document that contains many chemical formulas it is
+ convenient to redefine
+ \verb+\textfont1+ at the beginning of the
+ \TeX\ input file. The statement \verb+\textfont1=\tenrm+
+ was used at the beginning of the input file that produced this
+ document and causes \TeX\
+ to select the roman font as the textfont in math mode.
+ The roman typestyle is the one normally used by \TeX\
+ outside of math mode and it is the style in which this
+ thesis is printed. The ten point size, which is slightly
+ smaller than the eleven point size of the text in this document,
+ was chosen because it appears to look better for the
+ chemical formulas which consist largely of capital letters.
+ When different typesizes are used in this way, all the
+ atomic symbols and formulas in any one structure, even
+ those without subscripts, have to be printed in math mode
+ so that they all have the same size. It could be a
+ problem with this method of selecting the roman font for
+ math mode that the lowercase Greek letters (and some other
+ symbols used in mathematics) are not available in this
+ font. To print these one can temporarily redefine
+ textfont1 to math italic with the statement
+ \verb+\textfont1=\tenmi+. One can also switch to
+ a math font different from the default \verb/\textfont1/.
+ Using one of \LaTeX's font definitions, \verb+\small+,
+ a statement \{\verb+\small$\theta$+\} will
+ print the Greek letter.
+
+ Another method for avoiding the math italic style for letters
+ in chemical formulas is to select the roman style in each
+ individual instance where a formula has to be printed in
+ math mode. A statement such as \verb+${\rm C_2H_5}$+
+ produces ${\rm C_{2}H_{5}}$ at the size of type currently used
+ in the document. When the typestyle is thus selected within
+ math mode, enclosed by dollar signs, \TeX\ changes the style
+ of the letters of the alphabet only; the lowercase Greek
+ letters and math symbols remain available.
+
+ The size of the letters in chemical formulas can be changed
+ with the ten size declarations provided by \LaTeX\ (Lamport~86,
+ p.~200) or with \TeX's declarations. (Some of \TeX's declarations
+ are not defined in \LaTeX\ (Lamport~86, p.~205)). The size
+ declaration has to be written outside of math mode.
+ One place in chemistry typesetting where a
+ smaller typesize is desirable is the writing on reaction
+ arrows. The size in the following example is scriptsize:
+ $$
+ \advance \yi by 100
+ HC\equiv CH + H_{2}O
+ \parbox{92pt} {\cto{Hg^{++}}{18\%\ H_{2}SO_{4},\ 90^\circ}{14}}
+ CH_{3}-CHO $$
+
+ Finally, condensed structural formulas sometimes have to be
+ right-justified to be attached to the main structural diagram.
+ Figure~\ref{fg:rightjus}
+ illustrates this for the positioning of the
+ substituent in the 4-position of the pyrazole ring. \LaTeX\
+ makes this positioning convenient with the \verb+\makebox+
+ command, especially in the picture environment where the command
+ has the format
+ $$\hbox{\verb+\makebox(width,height)[alignment]{content}+}$$
+ (Lamport~86, p.~104). The one-line piece of text that constitutes
+ the content of the (imaginary) box can be aligned with the
+ top, bottom, left side, or right side of the box.
+ \begin{figure}\centering
+ \parbox{\xbox pt} {
+ \begin{picture}(\pw,\pht)(-\xi,-\yi)
+ \put(200,-84) {\line(5,3) {110}} % bond 1,2
+ \put(342,200) {\line(0,-1) {140}} % bond 3,2
+ \put(342,200) {\line(-1,0) {342}} % bond 3,4
+ \put(0,200) {\line(0,-1) {200}} % bond 4,5
+ \put(0,0) {\line(5,-3) {140}} % bond 5,1
+ \put(135,-130) {$N$} % N-1 in ring
+ \put(310,-30) {$N$} % N-2 in ring
+ \put(171,-137) {\line(0,-1) {83}} % subst. on
+ \put(150,-283) {$C_{6}H_{5}$} % on N-1
+ \put(370,-17) {\line(5,-3) {100}} % subst. on
+ \put(475,-100) {$C_{6}H_{5}$} % N-2
+ \put(335,211) {\line(5,3) {128}} % outside
+ \put(349,189) {\line(5,3) {128}} % double O
+ \put(475,250) {$O$} % on C-3
+ \put(0,200) {\line(-5,3) {128}} % single subst.
+ \put(-430,234) {\makebox(300,87)[r]{$CH_{3}COCH_{2}CH_{2}$}}
+ \put(-7,11) {\line(-5,-3){128}} % outside
+ \put(7,-11) {\line(-5,-3){128}} % double O
+ \put(-200,-130){$O$} % on C-5
+ \end{picture} } % end pyrazole macro
+ \caption{Right-justification of substituent formula}
+ \label{fg:rightjus}
+ \end{figure}
+
+