Density functional theory has been used in combination with the correlation consistent and polarization consistent basis sets to investigate the structures and energetics for a series of first-row closed shell and several second-row molecules of potential importance in atmospheric chemistry. The impact of basis set choice upon molecular description has been examined, and irregular convergence of molecular properties with respect to increasing basis set size for several functionals and molecules has been observed. The possible reasons and solutions for this unexpected behavior including the effect of contraction and uncontraction, of the basis set diffuse sp basis functions, basis set superposition error (BSSE) and core-valence sets also have been examined.