Quantum-chemical cluster models of enzyme active sites have emerged as a valuable and practical approach for understanding enzymatic reaction mechanisms. However, the requisite trimming of the active-site model can exert a significant influence on the resulting energetics, as can the details of how the model is constrained for geometry optimization and vibrational frequency calculations. Fixed-atom constraints are popular but their use is marred by the emergence of numerous imaginary vibrational frequencies. These can be eliminated via ad hoc deletion of Hessian matrix elements associated with the fixed (anchor) atoms, yet the rigidity that is introduced by this approach may afford barrier heights and reaction energies that differ significantly from those obtained when soft harmonic confining potentials replace the fixed-atom constraints. The latter approach eliminates imaginary frequencies while offering a convenient means to account for both ZPE and finite-temperature vibrational entropy.