This document describes biochemical pathways for producing adipic acid, 6-aminohexanoic acid, 6-hydroxhexanoic acid, hexamethylenediamine, caprolactam, or 1,6-hexanediol by forming one or two terminal functional groups, comprised of carboxyl, amine or hydroxyl group, in a C6 aliphatic backbone substrate. These pathways, metabolic engineering and cultivation strategies described herein rely on the enzymes or homologs accepting methyl ester shielded dicarboxylic acid substrates.