The realization of spin-based logical gates crucially depends on magnetically-coupled spin qubits. Thus, understanding decoherence when spin qubits are in close proximity will become a roadblock to overcome. Herein, we provide a general first-principles model that straightforwardly evaluates the spin bath effect on the qubit phase memory time . The method is applied to a ground-spin magnetic molecule 1 displaying atomic clock transitions, which remarkably increase at unusually high spin concentrations. Besides reproducing experimental values calculated by recent models in simple spin-1/2 systems, our approach unveils the causes that limit the coherence reached at the clock transitions in more challenging systems such as 1, where these previous models fail.

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