Fullqubit alchemist: quantum algorithm for alchemical free energy calculations
Po‐Wei Huang, Gregory Boyd, Gian-Luca Anselmetti, Matthias Degroote, Nikolaj Moll, Raffaele Santagati, Michael Streif, Benjamin Ries, Daniel Marti-Dafcik, Hamza Jnane, Sophia Simon, Nathan Wiebe, Thomas R. Bromley, Bálint Koczor
Abstract Accurately computing the free energies of biological processes is a cornerstone of computer-aided drug design, but it is a daunting task. The need to sample vast conformational spaces and account for entropic contributions makes the estimation of binding free energies very expensive. While classical methods, such as thermodynamic integration and alchemical free energy calculations, have significantly contributed to reducing computational costs, they still face limitations in terms of efficiency and scalability. We tackle this through a quantum algorithm for the estimation of free energy differences by adapting the existing Liouvillian approach and introducing several key algorithmic improvements. We directly implement the Liouvillian operator and provide an efficient description of electronic forces acting on both nuclear and electronic particles on the quantum ground state potential energy surface. This leads to super-polynomial runtime scaling improvements in the precision of our Liouvillian simulation approach and quadratic improvements in the scaling with the number of particles relative to prior quantum algorithms. Second, our algorithm calculates free energy differences via a fully quantum implementation of thermodynamic integration and alchemy, thereby foregoing expensive entropy estimation subroutines used in prior works. Our results open new avenues towards the application of quantum computers in drug discovery.
Abstract Accurately computing the free energies of biological processes is a cornerstone of computer-aided drug design, but it is a daunting task. The need to sample vast conformational spaces and account for entropic contributions makes the estimation of binding free energies very expensive. While classical methods, such as thermodynamic integration and alchemical free energy calculations, have significantly contributed to reducing computational costs, they still face limitations in terms of efficiency and scalability. We tackle this through a quantum algorithm for the estimation of free energy differences by adapting the existing Liouvillian approach and introducing several key algorithmic improvements. We directly implement the Liouvillian operator and provide an efficient description of electronic forces acting on both nuclear and electronic particles on the quantum ground state potential energy surface. This leads to super-polynomial runtime scaling improvements in the precision of our Liouvillian simulation approach and quadratic improvements in the scaling with the number of particles relative to prior quantum algorithms. Second, our algorithm calculates free energy differences via a fully quantum implementation of thermodynamic integration and alchemy, thereby foregoing expensive entropy estimation subroutines used in prior works. Our results open new avenues towards the application of quantum computers in drug discovery.
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena, from how cells send and receive signals to how pharmaceutical compounds can be used to treat diseases. Quantitative and predictive free energy calculations require computational models that accurately capture both the varied and intricate electronic interactions between molecules as well as the entropic contributions from the motions of these molecules and their aqueous environment. However, accurate quantum-mechanical energies and forces can be obtained only for small atomistic models and not for large biomacromolecules. Here, we demonstrate how to consistently link accurate quantum-mechanical data obtained for substructures to the overall potential energy of biomolecular complexes using machine learning in an integrated algorithm. We do so using a two-fold quantum embedding strategy where the innermost quantum cores are treated at a very high level of accuracy. We demonstrate the viability of this approach for the molecular recognition of a ruthenium-based anticancer drug by its protein target by applying traditional quantum chemical methods. As such methods scale unfavorably with system size, we analyze the requirements for quantum computers to provide highly accurate energies that affect the resulting free energies. Once the requirements are met, our computational pipeline, FreeQuantum, is able to make efficient use of the quantum-computed energies, thereby enabling quantum computing-enhanced modeling of biochemical processes. This approach combines the exponential speedups of quantum computers for simulating interacting electrons with modern classical simulation techniques that incorporate machine learning to model large molecules.
Estimating vibrational entropy is a significant challenge in thermodynamics and statistical mechanics due to its reliance on quantum mechanical properties. This paper introduces a quantum algorithm designed to estimate vibrational entropy via energy derivatives. Our approach block encodes the exact expression for the second derivative of the energy and uses quantum linear systems algorithms to deal with the reciprocal powers of the gaps that appear in the expression. We further show that if prior knowledge about the values of the second derivative is used then our algorithm can ε-approximate the entropy using a number of queries that scales with the condition number κ, the temperature T, error tolerance ε and an analogue of the partition function Z, as O(εTZκ2). We show that if sufficient prior knowledge is given about the second derivative then the query scales quadratically better than these results. This shows that, under reasonable assumptions of the temperature and a quantum computer can be used to compute the vibrational contributions to the entropy faster than analogous classical algorithms would be capable of. Our findings highlight the potential of quantum algorithms to enhance the prediction of thermodynamic properties, paving the way for advancements in fields such as material science, molecular biology, and chemical engineering.
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and difficult to scale. Here, we introduce a hybrid quantum-classical framework that combines Mining Minima sampling with quantum mechanically refined ligand partial charges, QM/MM interaction evaluation, and variational quantum eigensolver (VQE)-based electronic energy correction. This design enables explicit treatment of polarization, charge redistribution, and electronic correlation effects that are often underestimated in purely classical scoring schemes, while retaining computational efficiency. Across 23 protein targets and 543 ligands, the method achieves a mean absolute error of about 1.10 kcal/mol with strong rank-order fidelity (Pearson R = 0.75, Spearman rho = 0.76, Kendall tau = 0.57), consistent with the performance of contemporary FEP protocols. Notably, the workflow requires only about 25 minutes per ligand on standard compute resources, resulting in an approximate 20-fold reduction in computational cost relative to alchemical free energy approaches. This level of accuracy and efficiency makes the method well-suited for high-throughput lead optimization and iterative design cycles in pharmaceutical discovery. The framework also provides a natural foundation for future integration with machine learning models to enable predictive, large-scale, and adaptive screening strategies.
Accurate prediction of binding affinities and efficient lead optimization remain central challenges in computational drug discovery, particularly for complex biological targets characterized by rugged energy landscapes, conformational heterogeneity, and high-dimensional interaction spaces. Classical computational methods—such as molecular docking, force-field–based simulations, and deep learning models—have made substantial progress, yet they often struggle to capture quantum-mechanical effects and long-range correlations critical to molecular recognition. This study explores a quantum-enhanced framework that integrates Variational Quantum Algorithms (VQAs), quantum-inspired Hamiltonian modeling, and hybrid quantum–classical optimization workflows to improve the fidelity and scalability of drug discovery pipelines. By encoding molecular interactions into parameterized quantum circuits, the framework leverages quantum superposition and entanglement to explore complex chemical space more efficiently, enabling refined estimation of binding energies and accelerated identification of high-quality leads. Preliminary simulations indicate that VQA-based estimators outperform classical baselines for challenging protein–ligand systems, reducing prediction error while maintaining computational tractability. These findings highlight the emerging potential of quantum technologies to enable more accurate, data-efficient, and mechanistically grounded drug discovery for next-generation therapeutics.
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular properties can be expressed an energy derivative, including molecular forces, which are essential for applications such as molecular dynamics simulations. Here, we introduce new quantum algorithms for computing molecular energy derivatives with significantly lower complexity than prior methods. Under cost models appropriate for noisy-intermediate scale quantum devices, we demonstrate how low-rank factorization and other tomography schemes can be optimized for energy derivative calculations. We numerically demonstrate that our techniques reduce the number of circuit repetitions required by many orders of magnitude for even modest systems, and that the cost of estimating an entire force vector may in some systems be lower than the cost of estimating the energy. In the context of fault-tolerant algorithms, we develop new methods of estimating energy derivatives with Heisenberg limited scaling, incorporating state-of-the-art techniques for block encoding fermionic operators. In contrast to our near-term results, we find that the cost of estimating forces with any of our Heisenberg-limited methods is bounded by the cost of estimating energies, due to inner loops requiring either energy estimation or reflections around the ground state. This implies that applications such as geometry optimization, coupling parameter estimation, and spectral prediction may be practical on fault-tolerant quantum devices, but tractable molecular dynamics simulations of large-scale systems requires further algorithmic advances.
Accurate prediction of binding energies between drug candidates and target molecules is essential in computational drug discovery, as stronger (more negative) binding energies suggest higher efficacy. This energy corresponds to the ground state of the molecular system and can be computed using methods such as Full Configuration Interaction (FCI), Hartree-Fock (HF), Variational Quantum Eigensolver (VQE), and Quantum Phase Estimation (QPE). While FCI offers benchmark accuracy, its computational cost renders it impractical for larger systems. HF scales efficiently but at the expense of precision. QPE, though theoretically robust, is currently constrained by hardware limitations. VQE emerges as a practical alternative for Noisy Intermediate-Scale Quantum (NISQ) devices, balancing accuracy and feasibility. Nevertheless, quantum noise significantly affects VQE performance. To address this, we incorporate Zero Noise Extrapolation (ZNE) to mitigate errors and improve energy estimates. This study compares these approaches and demonstrates the efficacy of the VQEZNE framework in generating reliable binding energy calculations for drug design applications.