Mesoporous silica provides interesting opportunities for catalyst heterogenization by tethering organic functional groups on the silica surface. Acid-functionalized mesoporous silica catalysts were prepared by introducing functional groups such as arene-sulfonic acid, butyl-carboxylic acid, ethyl-phosphonic acid and propyl-sulfonic acid for applications such as trans-esterification reaction of free-fatty acid in bio-oils. Pyridine was used as a probe molecule to characterize the acid-strength of these functional groups using molecular simulation studies. Restricted Hartree-Fock (RHF) and Moller-Plesset second order perturbation (MP2) techniques were employed to simulate pyridine desorption from the functional groups of the mesoporous silica. The values of activation energy of desorption, elongation of the O-H bond, O-H bond dissociation energy obtained from these studies were used as metrics to compare acid strengths. The pyridine desorption energy values obtained from MP2 simulations were 80.34, 66.95, 77.19, 82.18 and 54.08 kJ/mol for arene-sulfonic, butyl-carboxylic, ethyl-phosphonic, propyl-sulfonic acid and silanol grops, respectively. Accordingly, butyl-carboxylic acid was the weakest and propyl-sulfonic acid, the strongest acidic group for the functionalized mesoporous silica. MP2 simulations were also performed to observe the elongation of the acidic O-H bonds upon adsorption of collidine (2,4,6-trimethylpyridine). The O-H bond elongation was correlated to the pKa values of the acidic functional groups thus using the O-H bond elongation as a measure of the acid strength.