Magnetite was chemically treated with an active 3-(trimethoxysilyl)-1-propanethiol, to prepare TMSPT-FCMNPs with controlled morphology, stability, and low spin-orbit quantum properties. It was characterized using hyphenated FESEM- AFM, FTIR, XRD, AAS for successful adsorption of anionic Congo red (CR) dye, from real wastewater samples with high recoveries at different conditions. The low spin gives rise to enhanced pseudo 2nd order kinetics so that capacities reached 228.78 (mg g− 1 ) under Freundlich isothermal conditions with spontaneous and enthalpy directed thermodynamics. QSDFT, DFT and NLDFT, proved that the average Cassie approximation contact angle for CR/TMSPT-FCMNP is about 96.228o , which agrees with the requirements for spin orbit QM and low spin calculations. HSE06 calculations showed that FCMNPs have a cubic nominal inverse spinel structure with bulk Fe3+ Tet(S = − 5 /2) configuration, and equal distribution of Fe2+ Oct(S = 2) and Fe3+ Oct(S = 5 /2). Spin reordering could be obtained so that Fe3+ Oct− Tet has d5 (t 5 2g − eg 0) low spin configuration, while the Fe2+ Oct has d6 (t 6 2g − eg 0) low spin configuration and Fe2+ Tet has d6 (t 4 2g − eg 2) high spin configuration at the optimized molar ratio (0.5) with MExperimental net = +3.97μB per formula unit is obtained. NBO studies augmented the CR/ TMSPT-FCMNPs system stability as described by the energy gaps between HOMO and LUMO orbitals. The 4 binding affinity components ΔGelectrostatic , ΔGvan der Waals , ΔGpolar , and ΔGSASA were typically -47.308, -2.765, 28.546, -7.17 kJ/mol.