Phosphate diester

A phosphate diester is a phosphoric ester with two organic groups linked through oxygen to the same phosphorus. Its neutral-acid representation is $\mathrm{RO}-\mathrm{P}(=\mathrm{O})(\mathrm{OH})-\mathrm{O}{\mathrm{R}}^{\prime }$; deprotonating the remaining O–H group gives $\mathrm{RO}-\mathrm{P}(=\mathrm{O})({\mathrm{O}}^{-})-\mathrm{O}{\mathrm{R}}^{\prime }$ without breaking either ester linkage.^[ref]

For an original connectivity example, let the two organic groups be methyl groups. The fragment $\mathrm{C}{\mathrm{H}}_3\mathrm{O}-\mathrm{P}(=\mathrm{O})(\mathrm{OH})-\mathrm{OC}{\mathrm{H}}_3$ contains one phosphorus center but two organic O–P connections. Two separate molecules of $\mathrm{C}{\mathrm{H}}_3\mathrm{O}-\mathrm{P}(=\mathrm{O})(\mathrm{OH}{)}_2$ instead contain two phosphorus centers, each monoesterified. Counting phosphorus atoms alone therefore cannot determine the ester class.

A diester can bridge two different organic units or join two positions within one unit. In a cyclic nucleotide, the two attachments close a ring; they need not belong to two separate molecules.^[ref] In DNA and RNA, successive sugar units are joined through phosphodiester bonds. Cleaving one ester linkage changes chain connectivity, which is why the same local chemistry can govern the integrity of a much longer nucleic acid.

The word “diester” specifies connectivity at the phosphoric group. It does not mean a P–O–P chain of two phosphate units, and it does not by itself specify a reaction rate or the conditions required for hydrolysis.