You definitely can! It’s early days so I don’t think there are any full demos of exactly this yet, but I do know some other people have used similar programs for this type of work. Personally I plan on doing something like this, but it’ll probably evolve over the next two years. I’ll demo it then 
Coming fresh into emacs also means there’s a learning curve for doing everything, so you just have to decide how much effort you want to put in 
But you can do it!
Several people have been putting together their own personal ‘brain-dumps’ that are perusable online, which is a stone’s throw away from simply a chemistry collection.
https://notes.andymatuschak.org/ is probably one of the slickest I’ve seen (don’t know if he’s using emacs and org or not). I don’t know all of the details that go into this type of streamlined writing-to-web-publishing, so I’ll let others comment and add some links if they do.
Starting out, org-mode is the hero that everything else is based off of. org-roam is mostly adding a layer on top for caching links between notes (and neat graphs). I personally think this is one of the greatest things in the world, but that’s why I’m here 
There are a ton of other tools that you might find useful, so it’s hard to just list a bunch of things, but here is an awesome list for emacs that might help – although I see they have yet to add org-roam to the list! 
Some of the links on that page I’ll also have highlighted below:
Starting out in emacs you can either begin from a blank slate and build your own configuration, or download a starter kit that has a lot of goodness baked in already. Both have difficulties, both can be confusing, and both have pros and cons. The easiest way to get started immediately testing org-roam out is probably using Doom emacs. Once you have it initially installed you can just add +roam to the org module in the init.el file and update! If that sounds like gibberish, I assure you it’s easier when you’re actually doing it. However if you are completely new to everything emacs it might help to go over some basic tutorials before jumping directly to a starter kit. Moving around the editor and actually writing/saving takes some initial practice. Doom itself is configured for vim style modal editing (evil-mode), but I think you can turn that off also if you want. Spacemacs is also popular, but it doesn’t have first-class support for getting started with org-roam right now (you can do it, it’s just not as easy).
These are some great introductory videos to starting from scratch with plain vanilla emacs and some packages
These are some great quick introductory videos about using Doom emacs
These are some great quick videos about just using org-mode
Basically youtube org-mode and you can find all sorts of things.
https://sachachua.com/blog/ is pretty much an infinite resource for finding things related to emacs
John Kitchin wrote org-ref and another emacs starter kit, scimax. His research is in chemical engineering, so you might get some ideas about writing chemistry stuff in org mode from his work.
Here’s a crazy neuromuscular resource a guy has been putting together forever, just as another example of creating a generic content base. Not exactly pretty but it works for him!