Sulfenate anions (RSO-M+) represent emerging sulfur nucleophiles that can introduce an alkyl/aryl sulfinyl unit into a substrate as a single substitution event. The S-functionalization reaction can be directed though interactions of the sulfenate oxygen and its counterion. Using computational methods, we demonstrate the factors that direct the stereoselective S-alkylation of a protected cysteinesulfenate. In another study, our methods predict that a nearby boronic ester can direct and accelerate an S-benzylation reaction by preforming a Lewis complex between the sulfenate oxygen and the boron atom. An unexpected off-shoot of this study suggests an H-bonding interaction during the alkylation of a sulfenate may facilitate the substitution reaction.