Should chemical compounds and elements be capitalized?
The names of chemical compounds and elements should be capitalized if they appear at the beginning of a sentence or in a title - that is, they are treated just like any other common noun.
For example, a title:

Why I Don't Like Zinc

or a sentence:

Boron is my favorite element.

Within a sentence:

We used boron and zinc in the experiment.
Vinegar contains acetic acid.

The symbols for chemical elements are always capitalized, no matter what:

We combined $\ce{As}$ and $\ce{W}$ to make a new alloy.