Quantum computation strengthens the physics layer of our design engine—it does not replace classical computation or experimentation. Dark genome–derived molecules often occupy non-natural, high-complexity sequence space, where classical approximations of folding, electronic interactions, and reaction energetics begin to break down. We use quantum computation selectively to improve energy landscape modeling, electronic structure estimation, and catalytic mechanism analysis for a small but critical subset of candidates. This enables more accurate prioritization before experimental validation, reducing false positives and unnecessary wet-lab cycles.