A good example of this is ATP, or adenosine triphospate. I know that the periodic table has been esperantized, but chemistry has a lot of specialty terms that probably won't be voted on by the Akademio for a long time.
If something doesn't exist then use a loanword. In scientific literature, names for things change in time even in other languages, and generally slowly migrate to a single international nomenclature. The scientific community in your field is too small to have many different words for the same things. The key is understanding. I'd say that if an Esperanto word does not completely fit or is confusing, it may also be best to use a loanword if that will necessarily be understood better. You aren't going to break the language by using a loan word in a very specialized and esoteric context. Other languages face the same issues, and I'd have the same advice there. In scientific literature, the main thing is to be understood, language purity is totally unimportant. That's true even in English. On the other hand always think of your audience. And if a reasonable Esperanto word exists and does not cause confusion, there is no need to come up with a new one. Be consistent with the body of literature targeting the same audience.