We show that medium-sized Gaussian basis sets lead to significant intramolecular basis set superposition errors at Hartree–Fock and density functional levels of theory, with artificial stabilization of compact over extended conformations for a 186 atom deca-peptide. Errors of ∼80 and ∼10 kJ/mol are observed, with polarized double zeta and polarized triple zeta quality basis sets, respectively. Two ...