The mechanism of the SHJ reaction begins with the formation of the key cyclic cation 1. Nucleophilic attack at the anomeric position by the most nucleophilic nitrogen (N) then occurs, yielding the desired β-nucleoside 2. A second reaction of this nucleoside with 1 generates bis(riboside) 3. Depending on the nature of the Lewis acid used, coordination of the nucleophile to the Lewis acid may be significant. Reaction of this "blocked" nucleophile with 1 results in undesired constitutional isomer 4, which may undergo further reaction to 3. Generally Lewis acid coordination is not a problem when a Lewis acid such as trimethylsilyl triflate is used; it is much more important when a stronger Lewis acid like tin(IV) chloride is employed.
2-Deoxysugars are unable to form the cyclic cation intermediate 1 because of their missing benzoyl group; instead, under Lewis acidic conditions they form a resonance-stabilized oxocarbenium ion. The diastereoselectivity of nucleophilic attack on this intermediate is much lower than the stereoselectivity of attack on cyclic cation 1. Because of this low stereoselectivity, deoxyribonucleosides are usually synthesized using methods other than the SHJ reaction.