Imidoester

An imidoester is an ester of an imidic acid. A common carbon-centred pattern is $\mathrm{R}-\mathrm{C}(=\mathrm{NH})-\mathrm{O}{\mathrm{R}}^{\prime }$, with an imino nitrogen in place of the carbonyl oxygen of an ordinary ester. Imidoesters react with amines to form amidines, which makes them useful for modifying protein amino groups.^[ref]

A formal net substitution illustrates the group change:The product has a carbon bonded to two nitrogens rather than an alkoxy group. This equation is structural bookkeeping, not a claim about every protonation state, kinetic pathway or experimental yield.

A bifunctional reagent such as dimethyl suberimidate has two reactive ends and can connect two amino groups. Those groups can lie on different proteins or within one folded protein.^[ref] Thus a detected cross-link constrains which reactive sites could be connected under the assay conditions; it is not automatically proof of direct atom-to-atom contact or a unique unperturbed protein arrangement.