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On Latin Wikipedia, there are a number of chemical elements with two Latin names, e.g. boron being borium and boracium. (Another example being nitrogen: nitrogenium or azotum.)

What is the etymology of borium and boracium and in what context should I use which?

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    Are you asking specifically about these two, or all of them? It might be better to ask about one at a time. – Nathaniel is protesting Feb 23 '16 at 19:39
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    @Nathaniel Ok, let me ask about boron, then. I was thinking there might be a trend, i.e. one historical name and one Latinized name from the modern name. – Earthliŋ Feb 23 '16 at 19:39
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    Many elements (including boron) weren’t known before modern times, because they don’t appear in elementary form in nature. – chirlu Feb 24 '16 at 3:01
  • @chirlu Even more reason that they should have one name and not several. – Earthliŋ Feb 24 '16 at 11:02
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The Online Etymology Dictionary gives this description for the etymology of boron:

Originally called boracium by Humphrey Davy because it was drawn from boracic acid.

So that form was originally used by the discoverer of boron. I think it is fair to assume that borium is just a simple Latinization of boron.

Azote was the original name coined for the element nitrogen, so its use is similar to boracium for boron, though additionally it is used as the term for the element in some other languages (see Wikipedia). Nitrogenium is also presumably just a Latinization of the English name.

So, at least for these two, it seems to be a preference for an older name for the element (though not a classical Latin one) versus Latinization of the modern English name.

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