The interaction of electronic spin and molecular vibrations mediated by spin-orbit coupling governs spin relaxation in molecular qubits. We derive an extended molecular spin Hamiltonian that includes both adiabatic and non-adiabatic spin-dependent interactions, and we implement the computation of its matrix elements using state-of-the-art density functional theory. The new molecular spin Hamiltonian contains a novel spin-vibrational orbit interaction with a non-adiabatic origin, together with the traditional molecular Zeeman and zero-field splitting interactions with an adiabatic origin. The spin-vibrational orbit interaction represents a non-Abelian Berry curvature on the ground-state electronic manifold and corresponds to an effective magnetic field in the electronic spin dynamics. We further develop a spin relaxation rate model that estimates the spin relaxation time via the two-phonon Raman process. An application of the extended molecular spin Hamiltonian together with the spin relaxation rate model to Cu(II) porphyrin, a prototypical S = 1/2 molecular qubit, demonstrates that the spin relaxation time at elevated temperatures is dominated by the non-adiabatic spin-vibrational orbit interaction. The computed spin relaxation rate and its magnetic field orientation dependence are in excellent agreement with experimental measurements.
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