The encapsulation of a small molecule inside a fullerene cage through advances in synthetic chemistry have created a new platform to study the dynamics of a freely rotating and translating quantum rotors entrapped inside a symmetric cage potential. These endohedral fullerene complexes are of great interest because the fullerene cages uniquely provide the entrapped molecules a high level of isolation, homogeneity, symmetry and stability. The endohedral fullerene complexes discussed in this thesis are the H2@C60, H2@C70 and H2O@C60. Both variants of small molecules studied in this thesis, H2 and H2O, exhibits spin isomerism, where the spins of both protons in the molecule are able to combine either symmetrically with total spin I=1 (ortho) or anti-symmetrically with total spin I=0 (para). The H2@C60 is the union between the simplest molecule and the most symmetrical molecule in the universe. This thesis discusses the temperature dependence of cold neutron scattering study in this complex to investigate the statistical distribution of the energy states. The H2@C70 is a less symmetric endohedral fullerene which has a prolate ellipsoidal symmetry cage. This thesis discusses the low temperature thermal neutron scattering and the temperature dependence of cold neutron scattering investigations in the complex to study the effect of the ellipsoidal cage on the quantum dynamics of the molecules. H2O@C60 is different to the dihydrogen variant of the small molecule endohedral fullerenes because H2O has a permanent electric dipole moment and is less symmetric than H2. The quantum dynamics of the H2O@C60 is investigated using low temperature thermal neutron scattering, temperature dependence cold neutron scattering and milli-Kelvin NMR. Unlike the dihydrogen endohedral fullerenes, the H2O@C60 also exhibits slow nuclear spin-isomer conversion at low temperatures. This low temperature ortho-H2O to para-H2O conversion process is investigated with both INS and NMR to study the conversion mechanism.