I presume that you are using the book/report class ?
If so put this in the preamble
\renewcommand{\theequation}{\arabic{equation}}
Incidentally \eqref{rxn1} from Amsmath automatically gives you the () and is a neater way to cross-reference
If you are using the article class then the automatic numbering is as you requested so no changes are needed at all
I prefer to use AmsMath’s align environment for multiple reactions and to use \mathrm{}
which sets reaction in a proper upright font, and aligns both your examples on the = in this case
You must have \usepackage{amsmath} in your preamble of course
\begin{align}
\mathrm{C_9H_7 + O_2} & = \mathrm{C_6H_{5O} + C_3H_{2O}} \label{C9H7O21}\\
\mathrm{C_9H_7 + O_2} & = \mathrm{C_7H_7 + CO + CO} \label{C9H7O22}
\end{align}
You can flushleft in addition but I don't think that this looks well to chemists ..
For single examples just use the \begin{equation} environment viz
\begin{equation}
\mathrm{C_9H_7 + O_2 = C_6H_{5O} + C_3H_2O} \label{C9H7O21}
\end{equation}
Finally, if you want to have separate counters for ordinary equations and chemical reactions then you have to
define a new environment (\chemeq ?) and a new counter … but that’s another story
Emeritus Professor John Simmie::Combustion Chemistry Centre::National University of Ireland, Galway
work:+353-91-492451, home:+353-91-592462::mobile:+353-87-805-9948
john.simmie+*+nuigalway.ie