Again, using glob seems simplest.

use strict;
use warnings;

use 5.010;

my %molecules = (
   a => 3,
   b => 2,
   c => 3,
   );

my $globStr =
   join
      q{},
      map { qq{{@{ [ join q{,}, 1 .. $molecules{ $_ } ] }}} }
      sort keys %molecules;

say for glob $globStr;
[download]

Produces.

111
112
113
121
122
123
211
212
213
221
222
223
311
312
313
321
322
323
[download]

I hope this is helpful.