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As far as I understand $\ce{SO4^2-}$ structure, sulfur makes two coordinate bonds with two oxygen atoms and two double bonds are formed with oxygen after sulfur expands it's valance shell to 6. At this point calculating formal charge of those two coordinate bonded oxygen gives total formal charge of −2 and the formal charge on $\ce S$ and the double bonded $\ce O$ is zero. Thus the minus 2 charge on $\ce{SO4^2-}$ can be shown but initially all the atoms were neutral. While making bonds electrons were shared only.

How did excess 2 negative charge pop up?

Please help, I am certainly making some mistakes

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The ion is not one S atom and 4 O atoms together. The ion on the whole is having two negative charges, Thus it is somewhat like 1Sulphur + 4 Oxygen+2 electrons. It is not as though there was one sulphur and four neutral oxygen atoms, and they became negatively charged during bond formation. The bond must have formed in some reaction, and in that reaction the charge would have been conserved.

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    $\begingroup$ Yes, consider sulfuric acid- H2SO4. It is a strong acid and when it completely disassociates, it loses 2 H+ atoms. This leaves a $\ce{SO4^{2-}}$ ion which must be -2 charged due to the conservation of charges. $\endgroup$ – Nanoputian Oct 14 '15 at 10:12
  • $\begingroup$ Yeah I made some mistakes myself. . S and 2 O are not connected with coordinate bonds but normal covalent bonds and extra electrons come from reactions. I was thinking wrong in the first place $\endgroup$ – Anindya Oct 16 '15 at 9:46
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Tho sulfur and oxygen are not neutral atoms. The oxidation state of sulfur is 6+, and of each oxygen is 2-. It slightly helps to think about it as being bonded ionically, even though the bond nature is rather covalent. Together it all ends up being 2-.

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There are partial charges on the S and the O in SO4[2-], the Sulfate ion. Sulfate ions are found in sulfuric acid = H2SO4, which ionizes into SO4[2-] + 2 H+

Oxygen is electro-negative. It has a partial negative charge. Think of water = H2O, which can break down into H+ and OH-. With oxygen pulling the electrons toward itself, the sulfur gets a partial positive charge.

Sulfur can have either a partial positive charge or a partial negative charge. Hydrogen Sulfide = H2S, which can break down to H+ and HS- [sort of like water].

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An S atom has 6 valence electrons and a O atom has 6 valence elections

SO4 => (6x1) + (6x4) = 30 valence electrons

We would need 32 valence electrons for 4 full outer shells(8x4) but only have 30. Thus the charge is 2- for the ion.

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