Atomic symbols and condensed structural fragments

As TEX enters math mode it selects \textfont1 as the textfont unless otherwise instructed. \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 \textfont1 at the beginning of the TEX input file. The statement \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 \textfont1=\tenmi. One can also switch to a math font different from the default \textfont1. Using one of L^ATEX's font definitions, \small, a statement {\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 ${\rm C_2H_5}$ produces C₂H₅ 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 L^ATEX (Lamport 86, p. 200) or with TEX's declarations. (Some of TEX's declarations are not defined in L^ATEX (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:

by100HC≡CH + H₂OCH₃ - CHO

Finally, condensed structural formulas sometimes have to be right-justified to be attached to the main structural diagram. Figure  illustrates this for the positioning of the substituent in the 4-position of the pyrazole ring. L^ATEX makes this positioning convenient with the \makebox command, especially in the picture environment where the command has the format

Figure: Right-justification of substituent formula