Quantum Simulation of Ligand-like Molecules through Sample-based Quantum Diagonalization in Density Matrix Embedding Framework

The accurate treatment of electron correlation in extended molecular systems remains computationally challenging using classical electronic structure methods. Hybrid quantum-classical algorithms offer a potential route to overcome these limitations; however, their practical deployment on existing quantum computers requires strategies that both reduce problem size and mitigate hardware noise. In this work, we investigate ground-state energy calculations of ligand-like molecules using Sample-based Quantum Diagonalization (SQD) within the Density Matrix Embedding Theory (DMET) framework, focusing on low-symmetry systems with diverse bonding motifs that exhibit subsystem-dependent variations in fragment-environment entanglement. These entanglement-based variations directly influence bath orbital construction, impurity sizes, and the structure of the embedded Hamiltonians, posing nontrivial challenges for both embedding and quantum sampling. By combining DMET fragmentation with SQD-based construction of reduced configuration spaces through quantum sampling and iterative configuration recovery, we perform quantum simulations on IBM's Eagle R3 superconducting quantum hardware (IBM Sherbrooke), thereby showing that the entanglement structure across embedding subsystems plays a central role in determining the efficiency and accuracy of the simulations. Despite these complexities, we show that the DMET-SQD framework yields ground-state energies in strong agreement with DMET-FCI benchmarks, achieving chemical accuracy (1~kcal/mol) across all systems studied. These results demonstrate that SQD-based quantum simulations can be robustly extended to low-symmetry, chemically realistic, industry-relevant molecules and highlight the importance of entanglement-aware embedding strategies for scalable quantum electronic structure calculations.