We report a complex study on the crystal structures, electronic properties, reactivity and dynamics of three polyoxometalate compounds (C6NH8)4[H2P2Mo5O23]·5H2O (1), (C2H8N)5[HP2Mo5O23]·(C3H9NO2)0.5·(H2O)1.5 (2) and (C2H8N)3[PMo12O40]·(H2O)0.34 (3). These compounds were synthesized using a solution method and characterized by single-crystal X-ray diffraction. Crystallography confirmed three distinct symmetries P1[combining macron], P21/c and R3[combining macron]c for 1, 2, and 3, respectively, and unit cell constants a = 12.5609(2) Å, b = 13.2470(2) Å, c = 14.0353(2) Å, α = 107.1568(14)°, β = 101.2854(13)°, γ = 92.1445(14)° for 1, a = 15.8583(6) Å, b = 17.3578(5) Å, c = 14.8499 (4) Å, β = 114.933(3)° for 2, and a = 16.3798(3) Å, c = 50.2781(5) Å for 3. Semi-empirical calculations applied on the compounds provided information about their reactivity and electronic structures. In this context, several discussions concerning the frontier molecular orbitals, molecular electrostatic potential, thermodynamic properties and local ionization potential were mentioned. We also conducted molecular dynamics analysis in order to elucidate the dynamics of cations and anions and their energy variation.