An important task in quantum computing is unitary circuit synthesis compatible with physical hardware constraints. This problem has a natural hybrid structure as local single-qubit gates are continuous variables on the Lie group $SU(2)$ while the entangling circuit structure is discrete and hardware-dependent. In this work, we use generative models to perform quantum circuit synthesis incorporating both the natural $SU(2)$ manifold geometry of quantum gates and hardware constraints that determine the overall circuit structure. Our model comprises two components: a circuit skeleton selector that chooses an entangling circuit and a diffusion model that generates quantum gates on the given circuit template by performing diffusion on the curved manifold $\mathrm{SU(2)} \simeq S^3$ itself. We demonstrate this approach with unitary compilation of physically motivated three-qubit Hamiltonian simulation targets such as the Transverse Field Ising Model and the Heisenberg-XXZ Model and show that Lie group diffusion outperforms comparable baselines. The synthesised circuits can also be customised subject to constraints, which we demonstrate by producing circuits with large and small gate rotation angles for the same target unitary evolution. We also investigate the fidelity-complexity frontier of the synthesised gates to demonstrate that the circuit selector learns to select circuits that balance fidelity with complexity rather than collapsing onto the most expansive entangling template. These results demonstrate that Lie group diffusion provides a natural generative framework for hardware-aware quantum circuit synthesis.

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