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Chromophore–radical (C–R) dyads are a promising class of molecules with potential applications in magnetometry, nuclear magnetic resonance and quantum sensing. Given the vast chemical space that is possible in these systems, computational studies are vital to aid in the rational design of C–R molecules with desired electronic and spin properties. Multireference perturbation theory (MRPT) calculations have been shown to be useful for rationalizing spin correlations in C–R dyads. In this work we apply quasi-degenerate perturbation theory, specifically QD-NEVPT2, for the prediction of vertical transition energies (VTEs) as well as spin-correlation parameters in three-spin-center pentacene–radical dyads containing up to 153 atoms. We find that QD-NEVPT2 performs well in the prediction of JTR, the magnetic coupling parameter between the excited-state triplet and the radical, but underestimates VTEs; this underestimation is attributed to variational averaging over different spin states and active space limitations, and we show that addressing these shortcomings reduces error. The calculated magnitudes and signs of JTR are rationalized through molecular symmetry, coupling distance, and π-structure considerations. The predicted signs of JTR are consistent with and explained via mechanisms of kinetic and potential spin-exchange, allowing for future functional design of magnetic organic molecules. The role of active space choice on VTE accuracy and predicted magnetic coupling is additionally explored.