I am a layman with a series of questions regarding chemical engineering. I'd prefer to contact my alma mater and contact someone there - is there a protocol for doing that? Is this an unusual thing?
It is not unusual for professors to receive questions from people outside of academia, and many are happy to share their expertise with others.
In general I think an email would be the best way to communicate with them if you have specific questions in mind. Keep your email concise and professional, bearing in mind that they receive numerous emails every day and may not have time to parse lengthy paragraphs. If you find it difficult to make your email brief and are looking for more of a discussion, you could contact them and see if they are available for an office-hours style meeting.
I suggest doing some cursory research on the university’s website on which person would be best suited to answer your specific queries. You do not have to worry too much about finding the most perfect person in the department, but it will likely benefit you more if you take this preliminary step. Additionally, be sure to manage your expectations by keeping in mind that professors hold a busy schedule and may not be able to devote time away from their duties; you may want to have more than one person in mind.
It isn't really unusual, and most places will be willing to talk to you informally. You could call the department office and let them know of your interest and desire to speak to someone who might be able to help.
Note, however, that people are busy but also schedule regular office hours so you would probably, then make an appointment with the person suggested.
If it is just a few questions there shouldn't be any issue, but if it is more extensive, you might want to enter into a consulting relationship which would require payment.
Based on your question history (e.g. in physics) and your job (software), I don't see a good basis for you to have a conversation with a chemE academic, on new reactions. It is VERY likely that you waste his time. Or get, properly, brushed off, before having the chance.
It's not even like you are coming from a refinery and know some practical things but may be weak on some theory, so that you can supply part of the problem and the academic can supply other part. It's a lot more likely you are wasting the person's time with some idea to make energy like Meatloaf in Roadie (the Blondie movie).
If you're not going to ask questions on SE (I think you should, to educate yourself), than I advise to use your network (Linkedin, 2nd degree) to find someone in the chemical industry (they got a lot of that in Texas) to talk to. He may not perfectly educate you either, but it least it gets you started. But honestly, I think this will be much more a case of you getting up to speed, on even basic variables, from a naive starting point, than of your synthesis itself needing exploration.
For that matter, chemE academics can be very narrow (getting their position for a thesis in one small experiment) and not even very broad on how industrial chemistry works. Not all of them of course. And it is also likely that many of your questions or ideas are extremely simple (and misguided) and can be a addressed by anyone with basic understanding of thermo, kinetics, etc. But if your questions WERE worthwhile, it would be more important for you to find the right expert. And you strike me as lacking the knowledge even to recognize subfields, etc.
-source: piled higher and deeper and several years in chemical industry, plus both engineering and financial consulting at several plants. BD and R&D, new products, existing, inorganic and organic. And there are still VAST swathes of the G-damned thing I don't know...but I know enough to know I don't know and to start researching any new area. But you're a software guy with a chemical idea--really not that far from a crank. Nice guy, I can tell. But you need to know what you don't know.