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For instance, copper can form $\ce{[Cu(H2O)6]^2+}$ so it accepts 6 electron pairs from $\ce{H2O}$ molecules to form dative covalent bonds. However it has one electron in the 4s subshell and 10 in the 3d subshell. To which shell does it accept these electrons? Is it to the 4d subshell? And how are these accepted electrons arranged?

Meep
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Copper is in +2 oxidation state so it has configuration $\ce{[Ar] 3d^9}$. Since 4s, 4p and 4d orbitals are vacant, Cu will show $\ce{sp^3d^2}$ hybridisation and will accept these elctron pairs in its 6 $\ce{sp^3d^2}$ hybridised orbitals. Read more about VBT here http://chemed.chem.purdue.edu/genchem/topicreview/bp/ch12/valence.php

Ayush Pateria
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