Computational chemistry is the leading application to demonstrate the advantage of quantum computing in the near term. However, large-scale simulation of chemical systems on quantum computers is currently hindered due to a mismatch between the computational resource needs of the program and those available in today’s technology. In this paper we argue that significant new optimizations can be discovered by co-designing the application, compiler, and hardware. We show that multiple optimization objectives can be coordinated through the key abstraction layer of Pauli strings, which are the basic building blocks of computational chemistry programs. In particular, we leverage Pauli strings to identify critical program components that can be used to compress program size with minimal loss of accuracy. We also leverage the structure of Pauli string simulation circuits to tailor a novel hardware architecture and compiler, leading to significant execution overhead reduction by up to 99%. While exploiting the high-level domain knowledge reveals significant optimization opportunities, our hardware/software framework is not tied to a particular program instance and can accommodate the full family of computational chemistry problems with such structure. We believe the co-design lessons of this study can be extended to other domains and hardware technologies to hasten the onset of quantum advantage.