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I don't understand why things like hydrogen phosphate are polyatomic ions but things like potassium nitrate are compounds. Can someone explain to me what the difference is, besides that ions are charged?

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    $\begingroup$ There is no other difference. $\endgroup$ – Ivan Neretin Aug 1 '17 at 21:19
  • $\begingroup$ We can think of polyatomic ions as a subset of chemical compounds. If a compound meets the criteria for a polyatomic ion (see Wikipedia), then you could refer to it as either. $\endgroup$ – airhuff Aug 1 '17 at 21:20
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The ions, by themselves, are charged and thus cannot be complete compounds which are electrically neutral.

We sometimes do have names for polyatomic ions as If they are compounds, like cyanidin (which is a cation containing a pyrylium ion function). But we understand that a "generic" counterion is needed to complete the compound. For example, "cyanidin" (a polyatomic cation) can't be completely isolated by itself, but it could be incorporated into cyanidin chloride (a compound), which in principle could be isolated.

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While you wrote hydrogen phosphate, I believe IUPAC prefers the term to be written without a space as hydrogenphosphate. This is because hydrogenphosphate is not a compound of positively charged hydrogen ions and negatively charged phosphate ions but actually a molecular entity whose sum formula is $\ce{HPO4^2-}$. A rough representation of the structure could be:

$$\ce{(\overset{-}{O}-)3\overset{+}{P}-O-H}$$

This is just a single ion that consists of more than one atom; it is therefore a polyatomic ion. In a crystal structure of e.g. sodium hydrogenphosphate (if you really, really went the extra lengths to determine the position of the hydrogen atoms), you would find sodium ions regularly arranged and $\ce{HPO4^2-}$ entities regularly arranged.

Potassium nitrate on the other hand, is an ionic compound. It consists of two types of ions: positively charged potassium ions and negatively charged polyatomic nitrate ions ($\ce{NO3-}$). Again, if you were to measure the crystal structure (no extra length needed here because all atoms involved have core electrons) you would see distinct potassium ions regularly arranged and $\ce{NO3-}$ entities regularly arranged.

Compounds are those entities that you could, in principle, put in jar and place in a shelf. Potassium nitrate is found in practically all chemistry labs that deal with inorganic chemistry at least partially. Hydrogenphosphate without a counterion cannot be synthesised and thus cannot be sold.

Note that just because the name ends in ide does not automatically mean we are dealing with ions at all. For example hydrogen sulphide is, in fact, a molecule (and IUPAC here definitely suggests a space between hydrogen and sulphide). Again, hydrogen sulphide can be put into gas bottles and technically also put in a shelf (if you lift). And in a simplified Lewis formality, it can be represented as follows:

$$\ce{H-S-H}$$

So, to sum this up:

  • Compounds are entities that can typically be isolated as they are written without the need of anything else. They can be made up of ions, molecules, molecular ions, zwitterions, metal atoms, etc.

  • Ions are charged species. Together with counterions of opposite charge, they can form compounds.

  • Polyatomic ions are charged species that consist of more than one atom. They too need counterions to form compounds.

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    $\begingroup$ @Linear Actually that was intended that way, but I’m fine with your change. $\endgroup$ – Jan Oct 2 '17 at 7:10
  • $\begingroup$ Ah, I see. I thought it was as if you were constantly thinking to yourself "don't use the word molecule, don't use the word molecule", and then used the word molecule. :} I guess now I have to say don't mislead the OP in using molecule for an electrically charged particle!! (+1) $\endgroup$ – Linear Christmas Oct 2 '17 at 8:26

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