We present a formalism for accurate estimation of dipole moments using quantum mechanics for complex molecules having conformational degrees of freedom. Dipole moments of complex molecules are often needed for use in correlations for estimating viscosities and other thermophysical properties. However, experimentally measured dipole moments are not available for many molecules, especially those used in proprietary industrial processes and products. Many complex molecules have dipole moments that change significantly in response to the conformation of the molecules. We show that proper accounting of the conformation-dependent dipole moment may be required to achieve an acceptably accurate estimate of the experimental dipole moment and provide recommendations on efficient estimation techniques. We also demonstrate that for molecules with dipole moments above about 1.3 D reasonably accurate estimation of the dipole moment is required for reliable prediction of vapor phase viscosity, whereas estimation of thermal conductivity is less sensitive to the dipole moment.