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Journal of Chemical Theory and Computation

Exploring Chemical Space with Chemistry-Inspired Dynamic Quantum Circuits in the NISQ Era

Lung-Yi Chen, Tai-Yue Li, Yi‐Pei Li, Nan-Yow Chen, Fengqi You

Published Jun 19, 2025• 5 citations
Publisher

Abstract

The generation of chemical molecular structures is crucial for advancements in drug design, materials science, and related fields. With the rise of artificial intelligence, numerous generative models have been developed to propose promising molecular structures to specific challenges. However, exploring the vast chemical space using classical generative models demands extensive chemical structure data, considerable computational resources, and a large number of model parameters, which hinders their efficiency. Quantum computing presents a promising alternative by exploiting quantum parallelism and entanglement, potentially reducing the computational overhead required for such tasks. In this study, we designed a quantum-based molecular generator (QMG) specifically tailored to generate small molecules containing carbon, nitrogen, and oxygen atoms. This model imposes strict constraints on the quantum circuit's output quantum states, significantly eliminating mathematically invalid connection graphs and enabling more efficient sampling of valid molecular structures. Remarkably, our quantum circuit, utilizing only 134 parameters, is capable of enumerating all molecular structures comprising up to nine heavy atoms, showcasing the parameter efficiency achievable through quantum superposition and entanglement. Our experimental results show that the output generated by this circuit exhibits a high degree of validity and uniqueness after Bayesian optimization, showing comparable performance to classical deep generative models. Furthermore, by fixing specific parameters in the quantum circuits, the quantum generator can constrain the chemical space and exclusively generate chemical molecules containing specified functional groups. This feature underscores its potential value for targeted applications in specific domains, especially in drug discovery. Overall, this compact design not only reduces parameter demands but also enables efficient exploration of a nontrivial portion of chemical space, demonstrating a key advantage of quantum-based generative models over larger classical counterparts.

DOI
10.1021/acs.jctc.5c00305

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The generation of chemical molecular structures is crucial for advancements in drug design, materials science, and related fields. With the rise of artificial intelligence, numerous generative models have been developed to propose promising molecular structures to specific challenges. However, exploring the vast chemical space using classical generative models demands extensive chemical structure data, considerable computational resources, and a large number of model parameters, which hinders their efficiency. Quantum computing presents a promising alternative by exploiting quantum parallelism and entanglement, potentially reducing the computational overhead required for such tasks. In this study, we designed a quantum-based molecular generator (QMG) specifically tailored to generate small molecules containing carbon, nitrogen, and oxygen atoms. This model imposes strict constraints on the quantum circuit's output quantum states, significantly eliminating mathematically invalid connection graphs and enabling more efficient sampling of valid molecular structures. Remarkably, our quantum circuit, utilizing only 134 parameters, is capable of enumerating all molecular structures comprising up to nine heavy atoms, showcasing the parameter efficiency achievable through quantum superposition and entanglement. Our experimental results show that the output generated by this circuit exhibits a high degree of validity and uniqueness after Bayesian optimization, showing comparable performance to classical deep generative models. Furthermore, by fixing specific parameters in the quantum circuits, the quantum generator can constrain the chemical space and exclusively generate chemical molecules containing specified functional groups. This feature underscores its potential value for targeted applications in specific domains, especially in drug discovery. Overall, this compact design not only reduces parameter demands but also enables efficient exploration of a nontrivial portion of chemical space, demonstrating a key advantage of quantum-based generative models over larger classical counterparts.
Existing drug discovery pipelines take 5–10 years and cost billions of dollars. Computational approaches aim to sample from regions of the whole molecular and solid-state compounds called chemical space, which could be on the order of106010^{60}1060. Deep generative models can model the underlying probability distribution of both the physical structures and property of drugs and relate them nonlinearly. By exploiting patterns in massive datasets, these models can distill salient features that characterize the molecules. Generative adversarial networks (GANs) discover drug candidates by generating molecular structures that obey chemical and physical properties and show affinity toward binding with the receptor for a target disease. However, classical GANs cannot explore certain regions of the chemical space and suffer from training instabilities. The practical utility of such models is limited due to the vast size of the search space, characterized by millions of parameters. A full quantum GAN may require more than 90 qubits even to generate small molecules with up to nine heavy atoms. The proposed quantum GAN with a hybrid generator (QGAN-HG) model is composed of a hybrid quantum generator that supports various number of qubits and quantum circuit layers, and a classical discriminator. The QGAN-HG with less than 20% of the original parameters can learn molecular distributions as efficiently as its classical counterpart. Another extended version of the proposed QGAN-HG, which utilizes multiple quantum subcircuits, considerably accelerates our standard QGAN-HG training process and avoids the potential gradient vanishing issue of deep neural networks.
Abstract Computer-aided design of novel molecules and compounds is a challenging task that can be addressed with quantum computing (QC) owing to its notable advances in optimization and machine learning. Here, we use QC-assisted learning and optimization techniques implemented with near-term QC devices for molecular property prediction and generation tasks. The proposed probabilistic energy-based deep learning model trained in a generative manner facilitated by QC yields robust latent representations of molecules, while the proposed data-driven QC-based optimization framework performs guided navigation of the target chemical space by exploiting the structure–property relationships captured by the energy-based model. We demonstrate the viability of the proposed molecular design approach by generating several molecular candidates that satisfy specific property target requirements. The proposed QC-based methods exhibit an improved predictive performance while efficiently generating novel molecules that accurately fulfill target conditions and exemplify the potential of QC for automated molecular design, thus accentuating its utility.
Drug discovery for a given protein target is a complex, resource-intensive process, often requiring years of research and billions of dollars in investment. Computational techniques, particularly deep learning models, have accelerated molecular generation, but they remain constrained by classical computational limitations and reliance on known chemical patterns. To address these challenges, we propose a hybrid quantum conditional GAN with gradient penalty for drug design, integrating quantum computing to enhance exploration of the vast chemical space. The proposed approach leverages a hybrid classical and quantum generative model to create novel molecular structures while ensuring they adhere to chemical and pharmacological properties. By conditioning the generative model on protein target sequences, we improve molecular specificity, increasing the likelihood of discovering viable drug candidates. Our framework generates chemically valid, diverse, and target-specific molecules, offering a promising avenue for more efficient and precise data-driven drug discovery.
Machine learning has made significant contributions to the fields of chemistry and materials science, enabling the exploration of vast chemical space through large-scale quantum chemical calculations. These models provide fast and accurate predictions of atomistic chemical properties, but they have limitations when it comes to capturing the electronic degrees of freedom of a molecule. This restricts their application in reactive chemistry and chemical analysis. To address this limitation, we introduce a deep learning framework that predicts the quantum mechanical wavefunction of a molecule in a local basis of atomic orbitals. The wavefunction serves as a foundational representation from which all other ground-state properties can be derived. Our approach maintains complete access to the electronic structure through the wavefunction, while achieving computational efficiency comparable to force-field methods. Moreover, the framework captures quantum mechanics in a form that can be analytically differentiated, allowing for efficient optimization and exploration of chemical systems. We demonstrate the potential of our approach through several examples. By leveraging the predicted wavefunction, we showcase the ability to perform inverse design of molecular structures to target specific electronic property optimizations. This opens exciting avenues for tailoring molecular structures to achieve desired electronic characteristics. Additionally, our framework paves the way for enhanced synergy between machine learning and quantum chemistry, enabling more comprehensive investigations into complex chemical systems.
Current drug discovery processes can cost billions of dollars and usually take five to ten years. People have been researching and implementing various computational approaches to search for molecules and compounds from the chemical space, which can be on the order of 1060 molecules. One solution involves deep generative models, which are artificial intelligence models that learn from nonlinear data by modeling the probability distribution of chemical structures and creating similar data points from the trends it identifies. These generative models can extract salient features that characterize the molecules. However, they often suffer from increased time complexity. Aiming for faster runtime and greater robustness when analyzing high-dimensional data, we designed and implemented a Hybrid Quantum-Classical Generative Adversarial Network (QGAN) to synthesize molecules. There are two parts in the QGAN: a quantum generator that creates molecules based on the probability distributions of likely combinations and a classical discriminator that differentiates real molecules from the generated ones. We hypothesized that a quantum generator would be more impactful, offering a runtime speedup and increasing generated molecule possibilities, because we could use quantum mechanical phenomena superposition, entanglement, and interference to analyze more atom-bond combinations than a classical generator. The PyTorch-PennyLane implementation of the QGAN generated seven chemically stable molecules out of 300, a 2.3% success rate. Although the QGAN is a work in progress, it has demonstrated a path towards more efficient drug development, which would accelerate the development of medicines and reduce costs for the whole R&D process.
Deep generative chemistry models emerge as powerful tools to expedite drug discovery. However, the immense size and complexity of the structural space of all possible drug-like molecules pose significant obstacles, which could be overcome with hybrid architectures combining quantum computers with deep classical networks. As the first step toward this goal, we built a compact discrete variational autoencoder (DVAE) with a Restricted Boltzmann Machine (RBM) of reduced size in its latent layer. The size of the proposed model was small enough to fit on a state-of-the-art D-Wave quantum annealer and allowed training on a subset of the ChEMBL dataset of biologically active compounds. Finally, we generated 2331 novel chemical structures with medicinal chemistry and synthetic accessibility properties in the ranges typical for molecules from ChEMBL. The presented results demonstrate the feasibility of using already existing or soon-to-be-available quantum computing devices as testbeds for future drug discovery applications.