The optimal exponent α values (αopt) in s‐type Gaussian‐type functions (GTFs) for quantum protons and deuterons, which are used for multicomponent molecular orbital calculations including nuclear quantum nature of protons and deuterons, are analyzed for several charged or polarized systems and their deuterated species. Ishimoto and coworkers (Ishimoto, Int. J. Quantum Chem. 2006, 106, 1465) have already proposed the average exponent values for five neutral molecules (αave), and demonstrated that their αave enables us to evaluate the H/D isotope effect on energies and geometries of various neutral species. The differences between total energies of several charged or polarized systems with previous αave and our αopt correspond to only less than 0.004% of the total energy (0.47 kcal·mol−1) except for HeH+ and HeD+ molecules, while the difference between interaction energies of H2OH+…OH2 and H2OD+…OH2 systems with previous αave is 19% (0.22 kcal·mol−1) smaller than that with our αopt. Meanwhile, the difference between OH bond lengths in H2OH+…OH2 system with αave and αopt values is 0.027 Å. We also found that the interaction energies with αopt value at the geometry optimized with previous αave value (αsp) well reproduce those at the geometry optimized with αopt value. We have demonstrated that the nuclear basis functions based on s‐type GTFs with previous αave values enable us to evaluate the H/D isotope effect on energies and geometries of charged or polarized systems. © 2016 Wiley Periodicals, Inc.