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Molecular Orbital Theory shows how the different atomic orbitals of different atoms combine to form new bonding and non-bonding molecular orbitals for the chemical species. The relative energy levels of these molecular orbitals both to each other and in comparison to the atomic orbitals determine which orbitals are filled first and this affects the bonding characteristics of the compound. This works well for very simply molecules like H2, Li2, and CO2 that have a small number of atoms and relatively simply atomic symmetry. But as the molecules become larger and more complex, the molecular orbital diagrams become very complicated very quickly. So really the answer to your question is that different molecules have different atoms with different atomic orbital characteristics and symmetries, thus leading to a very large number of potential molecular orbitals depending on how you arrange the atoms to make chemical compounds.
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