fixup for reading in atomic number in cantherm

didn't realize the qchem mod was not properly reading in atomic numbers.
Caused cantherm to crash when trying to write cartesian coordinates of
species to the output file
Added another example reaction

my isopentoxy example is too big (it has 30+ MB of qchem output files),
so I am adding a smaller one. I will add other small ones in the future
that include pdep. Also, I reverted a change in the C2H4+H example back
to what is on the master RMG-Py brach.