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Abstract Molecular simulations generally require fermionic encoding in which fermion statistics are encoded into the qubit representation of the wave function. Recent calculations suggest that fermionic encoding of the wave function can be bypassed, leading to more efficient quantum computations. Here we show that the two-electron reduced density matrix (2-RDM) can be expressed as a unique functional of the unencoded N -qubit-particle wave function without approximation, and hence, the energy can be expressed as a functional of the 2-RDM without fermionic encoding of the wave function. In contrast to current hardware-efficient methods, the derived functional has a unique, one-to-one (and onto) mapping between the qubit-particle wave functions and 2-RDMs, which avoids the over-parametrization that can lead to optimization difficulties such as barren plateaus. An application to computing the ground-state energy and 2-RDM of H 4 is presented.