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I know that this might look a very dumb question but I have been spent my days to think about it and couldn't understand and finally decided to ask.

Consider Sharing of electrons to form covalent or coordinate bonds , elements can complete their octet by the method of sharing and unlike ionic bonds, they don't have to lose their electrons i.e. they only share and do do not lose electrons . The shared electron ( or a pair) is counted on both atoms then. For example, in Cl2 molecule, even though each chlorine atom had 7 electrons before, but after sharing, they both have 8 electrons and thus complete their octet. This is only possible if we count the shared electron in both the atoms while checking their octets.

NH3 + H(+) = NH4(+)

Consider an ammonium ( denoted as NH4+ ) , after bond formation, within the molecule, let's count for doublet of hydrogens. We find that each hydrogen had a complete doublet. Let's count for nitrogen, again, we see that nitrogen had 8 atoms and hence an octet ( the shared electron pair is also counted while counting for octet, as we do in chlorine molecule) . Now, my question is that if each hydrogen and nitrogen are having their valence shells filled, then from where an extra positive charge comes and people call it a cation .Positive charge comes when there is a deficiency of electrons , but in ammonium ; no atom is positively charged and hence the molecule.It would have been a cation if the nitrogen was positively charged, but clearly nitrogen has not lost it electrons, it had only shared . So why is there a positive charge on the ammonium?

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All your confusions will vanish if you recall that atoms also contain protons-positively charged entities. You are focusing on the valence shells only. The charge on a molecular species reflects this net balance.

Start from an electrically neutral ammonia molecule, which simply means that the number of electrons and protons are balanced in that molecule. Count the total number of electrons and protons in ammonia molecule. You add a hydrogen ion to it via chemical reaction. The hydrogen ion nothing but an hydrogen atom stripped on an electron. What is left? A single proton.

Once you added a proton to the neutral ammonia molecule, you disturbed that original charge balance. There is a shortage of a single electron in the new molecule so formed and this denoted by the plus sign on the ammonium ion.

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    $\begingroup$ @Shiva Enough is to remember some bonds are "2=1+1" and some "2=2+0". $\endgroup$
    – Poutnik
    May 30, 2022 at 6:22

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