Mixed bag, grew up in Detroit with auto worker uncles, lifeblood. But these days, it’s become another layer of bureaucracy, which is both sad, and good that workers don’t have to go to such extremes for basic decent working conditions. Yeah, OSHA.
It comes to the same thing, however you pronounce it. Either way, it is about the combination of radicals.
What would un-ionized even mean? If it’s no longer ionized, we already have a word for that: deionized. Would un-ionized simply mean it has never been ionized? Why would that ever need to be said?
Not only did I see it as union-ized, it took me a few seconds to figure out how the other definition would fit. Generally speaking, I’d expect that to always be spelled with a hyphen, “un-ionized,” as prefixes that could confuse usually are. Humans are generally greedy pattern matchers–we go with the longest pattern that could work.
You just said it, although you used the form “had never been ionized”.
But the use of hyphens like that is obsolete. Before posting this poll, first to make sure it really was a real word, I googled “unionized” with “chemical” and found many uses of the word in the chemistry sense spelled with no hyphen.
Good man. 
I’m no chemist, but I took this in college. I think the word as given could apply in a given context, in a given reaction, with given reagents, where a given ionization takes place at some stage in the process, where unionized would refer to atoms or radicals before it gets to that stage.
According to any style guide, “unionized” refers to organized labor and “un-ionized” refers to atoms. It is used as a classic example of the rule that you need to add a hyphen when words can be confused.
Like when?
“At the atomic energy plant where I work, the unionized workers became ionized after they tried to unionize themselves?”
I have to admit, I read it as un-ionized. But then a split second later realized it should read as union-ized.
To my defense, I’ve been reading a lot of science related papers and non-fiction lately. But I voted for the first option, anyhow.
I imagine the word ‘un-ionized’ would mostly be used depending on context, such as the atom or molecule in question are circumstatially given to be ionized by default, and this description would be used otherwise.
That’ll work, thanks!
I still haven’t answered my own poll because honestly I don’t know which definition comes to my mind first. I can’t help thinking of them both at once, thanks to Asimov.
I’m a chemistry geek with a ChemE degree, but I still read it as union-ized. My parents were both very active in their respective labor unions when I was a kid. 