Generating a computing specification to be executed by a quantum processor includes: accepting a problem specification that corresponds to a second-quantized representation of a fermionic Hamiltonian, and transforming the fermionic Hamiltonian into a first qubit Hamiltonian including a first set of qubits that encode a fermionic state specified by occupancy of spin orbitals. An occupancy of any spin orbital is encoded in a number of qubits that is logarithmic in the number of spin orbitals, and a parity for a transition between any two spin orbitals is encoded in a number of qubits that is logarithmic in the number of spin orbitals. An eigenspectrum of a second qubit Hamiltonian, including the first set of qubits and a second set of qubit, includes a low-energy subspace and a high-energy subspace, and an eigenspectrum of the first qubit Hamiltonian is approximated by a set of low-energy eigenvalues of the low-energy subspace.