A theory based on dynamic complexation is used to describe analyte migration behavior in capillary electrophoresis (CE). This theory is based on a one-phase system, instead of the commonly accepted two-phase system. The migration behavior of an analyte is described by three parameters (the electrophoretic mobility of the free analyte, the electrophoretic mobility of the analyte–additive complex, and the equilibrium constant (formation constant) that determines the fractions of the free analyte and the complex at a certain additive concentration). Varying the additive concentration shifts the equilibrium and changes the viscosity of the background electrolyte. Viscosity correction is crucial in interpreting the observed migration behavior of analytes. While electroosmotic flow in a capillary often varies from one capillary to another, the viscosity of a buffer is characteristic of the buffer composition and is constant for each buffer. The electrophoretic mobility of a certain species and the equilibrium constant are intrinsic properties and are less sensitive to changes in the environment. Understanding these relationships is indispensable in CE method development and method validation. A universal resolution equation is proposed, with a separation factor that has taken both the electrophoretic mobilities and equilibria into consideration. This resolution equation gives clear guidance for the optimization of CE separations. A group of nucleosides and their phosphates are used as analytes, and β-cyclodextrin is used as the additive in the model system studied in this paper. Both the observed analyte migration behavior and the resolution of analytes agree well with this theory. Keywords: dynamic complexation capillary electrophoresis, nucleoside and nucleotide separation, capacity factor, resolution equation, viscosity correction.
