2,3-Butanedione reacted with propylenediamine to form an initial intermediate: acetylated methyl-N-(3-aminopropyl) imine, which was a geometrical mixture of syn - and anti- isomers. The intermediate isomerized to anti- or syn-form via pyrimidine ring flip on heating. A steric factor of the isomers affected the formation of the final products. The mechanism based on NMR spectroscopy and molecular orbital calculation is proposed.