We present a density functional theory (DFT) study on the reactivity of piperazine (PIP) and m-phenylenediamine (MPDA) with trimesoyl chloride (TMC) to examine the better selective rejection behavior of bivalent salt ions using corresponding thin film composite (TFC) membranes. The conceptual DFT analyses showed that the rejection of bivalent salt ions would be higher with piperazine based TFC membranes compared to m-phenylenediamine based TFC membranes. The global and local reactivity descriptors derived from conceptual DFT analysis suggest that the reaction between m-phenylenediamine (MPDA) and trimesoyl chloride (TMC) for the preparation of TFC membrane would be much facile compared to the case of piperazine (PIP) with trimesoyl chloride (TMC), which leads to the better selectivity of bivalent salt rejection in the later case. The unreacted acyl moieties in piperazine based TFC membranes are responsible for the development of charges on the surface, which causes the rejection of bivalent counter ions. The positional isomers of MPDA, o-phenylenediamine (OPDA) and p-phenylenediamine (PPDA) also shows the higher reactivity with TMC compared to piperazine (PIP) with trimesoyl chloride (TMC). This computational approach sheds light on the complex reactivity pattern of these polymeric membranes in an elegant manner, which otherwise requires more intensive computational analysis for such problems.