2,4,6-trinitrotoluene (TNT) is the most used explosive as main charge in landmines. There have been found contamination of soil and groundwater with munitions residues of TNT due to buried landmines. We are investigating the molecular structure, vibration behavior and the binding energy of TNT with the siloxane surface site of clay minerals in order to determine the spectroscopic signature of TNT in soil. Two different molecular symmetry structures were found with density functional theory (DFT) B3LYP method with 6-31G, 6-31G*, 6-311G, 6-311G*, and 6-311+G** basis sets from the Gaussian 98 systems of programs. Different deformations of the phenyl ring and distortions of the nitro and methyl groups with the ring were observed. In both structures, C1 and Cs, the nitro groups in positions 2 and 6 are out of plane with the phenyl ring due to steric interaction with the methyl group while the nitro group in position 4 is planar to the phenyl ring. The difference between the two structures is the internal rotation of the methyl group and 2, 6-nitro groups. Comparison of the calculated energies of the two structures in several basis sets reveals that the lowest-energy geometry for the TNT structure corresponds to Cs symmetry with B3LYP/6-311+G**. FTIR spectra of TNT are presented and assigned assisted by B3LYP/6-311+G** result. The lowest-energy molecular structure of TNT was interacted with the basal siloxane surface of clay minerals to determine the binding energy (Eb) between them. The binding energy was obtained by optimizing the vertical distance, the rotational and inclination angles between TNT and siloxane surface using the B3LYP hybrid functional with different basis sets.