This is a lot of information to absorb in just one hour. You are progressing from the simplest Unix commands to a web server. Chemistry students are bright, but I don't think anyone starting from complete ignorance of Unix, and perhaps programming, is going to be able to understand all of this in real time.

I taught a Perl for Bioinformatics class a few years ago that also was an intro to the Linux CLI. We had 10 hour long lectures anlong with 10 two hour labs. At the end of the course, most students could write simple programs, but mabye 10% managed to clue into Perl's real power. Especially at the very beginning, programming is hard.

So I'd recommend at the very least a handout of your talk (not in raw POD) so that they can play with your examples on their own. And for the first time regexer, I'd recommend perlrequick rather than perlretut. It is written more simply and is less overwhelming.