# loop over the array values, not indexes, making $key
# refer to each one in turn
foreach my $key (@hydrogen_split) {

# chomp is probably not needed if your data is already
# in an array.  chomp removes the end-of-line character
# from a line of input

# use the %hydrogen_split hash to keep track of which
# keys were seen how many times
   $hydrogen_split{$key}++ 
}

# print in sorted order each key that was encountered more than once
foreach my $key ( sort grep { $hydrogen_split{$key} > 1 } keys %hydrogen_split ) {
    print "$key\n";
}