How can I specifiy a substance in AERMOD?
The POLLUTID key is used to specify some regular options.
Some examples:

PM2.5 can only evaluate averages greater than 24 hours (if you try to generate hourly averages it throws an error).
NO2 forces the use of options to simulate the conversion of NOx to NO2.
SO2 triggers the use of a 4-hour half-life for SO2 decay in urban zones.

All pollutants (gases and particles) are treated similarly, regardless of their weight or molecular density.