Opinions seem to vary on the best way to accomplish your objective. Here's one (about the middle of the page treats with equations by themselves), and here's another (the Geological Society of America, which shows the equation terms within paragraphs).

This image gives a better idea of what I'm trying to do. On paragraphs I use small caps, but when elements appear on their own lines I don't. I'm not sure this is the right way to do it since I couldn't find anything that specific (chemical notation) in Bringhurst's book.

Since you appear to be working in Portuguese, I'm not sure the Chicago Manual of Style is relevant, but...

(a) small caps are usualy reserved for acronyms, which chemical notations are NOT; and

(b) when used within paragraphs, chemical and mathematical notations are treated in the same way as words from a foreign language, which means they appear in normal uppercase, but italicized.

Method (b) seems to me to be a better approach, if for no other reason than a small caps O (oxygen) might easily be confused for a lowercase o or, if you use oldstyle numbers, a zero, whereas an italicized uppercase O would always be recognized as such.

Thank you! That's all I needed to know. For some time I've had the Chicago Manual of Style on my Amazon wishlist, I think it's time to buy it. It's really impressive (or depressive?) we don't have anything like it in portuguese; in Portugal maybe, but not in Brazil. Thanks again.