In this systematic work, the Semi organic S-(4,6-dimethyl-2-pyrimidinyl) O-(p-methoxybenzyl) thiocarbonate single crystal was grown by slow evaporation method with high-quality non linear optical response. The crystal was characterized optically, spectroscopically and theoretically. The XRD parameters were evaluated and related crystal lattice (orthorhombic) and space group (P212121) of molecule was validated. The least attractive dispersion forces of efficient Birefringence of crystal emphasized the second and third order optical harmonic frequency conversion. The optimized molecular setup in crystal array was viewed from the parametric calculations performed by B3LYP method. The charge orientation assignment in the molecular site driven by chemical potential was measured and the cause of polar scattering process was validated. The SHG and parametric oscillation coefficients were measured from which NLO activity performance (efficiency = I2ω = 15 X I2ω) was evaluated. The biaxial crystal characteristics were interpreted by dipole-dipole interactive dispersion process induced by molecular electrostatic potential field. The arrangement of electron path was identified and kinetics in the path by driving potential mechanism in the pyridine ring was studied. The modification of charge atmosphere in and around the molecules is monitored and the molecular kinematics was studied. The dipole moment and polarization activity of polar and non polar bonds in the material were confirmed by performing vibrational studies in various regions of IR and Raman spectra. The chemical energy restoring mechanism in various chemi-potential zones were determined and chemical reaction path in core and allied C of the molecule.