The metformin structure was analyzed using Hyperchem software to determine the structural properties for absorption process in chitosan cross linking with genipin for medical applications. The theoretical calculations were Gibbs free energy, electrostatic potential and FTIR spectroscopy. Optimized structures and their molecular electrostatic potentials were calculated using the AM1 and PM3 method, and the results were used to calculate the molecular interactions of metformin. The quantitative structure-property relationship model was also used to estimate the activity of the chemicals on the basis their molecular structures. Fourier transform infrared (FTIR) spectroscopy reveals information about the metformin properties. The molecular electrostatic potential (MESP) is a powerful tool that has provided insights into intermolecular association and molecular properties of small molecules, for example, actions of drug molecules and their analogs. The nucleophilic and electrophilic regions were calculated using the MESP. The Log P value (P is the partition coefficient of the molecule in the wateroctanol system), showed the hydrophobic character of drug.