The feasibility for separation of positional isomers using capillary electr
ochromatography (CEC) was investigated. Two groups of neutral isomers, trif
luoroacetophenone and bromobenzonitrile, were separated by CEC. Effects of
selected parameters, such as mobile phase pH, ionic strength, temperature,
organic modifier, buffer type, diluent type, voltage, and column length, we
re studied using bromobenzonitrile isomers to elucidate the separation mech
anisms. In parallel, the separation of the isomers was also performed by hi
gh-performance liquid chromatography (HPLC) to serve as a comparison. It wa
s found that the retention time behavior as a function of acetonitrile conc
entration in CEC was similar to that observed in HPLC. The effect of mobile
phase pH has a greater impact with CEC than with HPLC due to the change in
electroosmotic flow. The effect of temperature with liquid chromatography
showed a linear Van't Hoff plot, while deviations from linearity were noted
with CEC. The optimized CEC method was validated in terms of linearity, li
mit of detection, and injection precision. The experimental results indicat
e that the separation of positional isomers by CEC is feasible and is an ap
propriate alternative technique to reverse phase HPLC.