The structural and electronic properties of acid sites in zeolites are important in determining their catalytic behavior. Kohn-Sham density functional theory calculations are used to probe the local environment of the acid site in realistic zeolite clusters and to study its interaction with ammonia. The long-range electrostatic effects on the adsorption are incorporated self-consistently in the electronic structure calculations. We examine their effect on the acidity of the cluster and on both the structure and the energetics of adsorption. Systematic structural relaxations of the aluminum-substituted framework show that there are significant structural rearrangements from the entirely siliceous cluster, in the vicinity of the substitution site. In the case of ammonia adsorption, the energetics of adsorption are sensitive to the structural arrangement of the ammonia. Configurations where the adsorbed molecule interacts with three lattice bridging oxygen molecules are favored. The theoretical predictions are compared to recent solid state NMR and microcalorimetry experiments.