Today's chemistry papers cluster around three interrelated methodological trends: the integration of physical constraints into learned representations, the development of uncertainty quantification and active-learning workflows for efficient data use, and the deployment of language models as reasoning engines for inverse design. On the representation side, papers spanning nuclear quantum effects, interatomic potentials, and electronic structure all embed domain knowledge, whether quadratic actions, equivariance symmetries, or Ewald reciprocal-space formulations, directly into neural architectures rather than expecting models to rediscover these structures from data alone. A second cohort addresses the practical bottleneck of expensive quantum-mechanical labeling by combining active learning (last-layer projection regression, query-by-committee, farthest-point sampling) with transfer learning from cheaper sources (classical force fields, experimental data, intermediate SCF trajectories), consistently achieving full-data accuracy with fractional label budgets. The third pattern treats language models not as end-to-end predictors but as constrained reasoners: systems like Ara and Reaction-Network Reasoning enforce chemical graph invariance or explicit reaction networks to guide hypothesis generation toward multi-criteria targets, while others couple LLMs with orbital energies and electron densities to enable mechanistic feedback rather than scalar scores. Across these threads runs a shared principle: leverage what is known about chemistry, conservation laws, symmetries, reaction mechanisms, solvent effects, to reduce what must be learned from data, and structure the learning problem to surface interpretability and physical meaning rather than compress them into latent spaces.
Cole Brennan
Showing of papers
Nuclear quantum effects are rigorously captured by imaginary-time path integrals, which map the quantum Boltzmann distribution onto a ring polymer of classical replicas. Yet the nuclear masses, the coupling to the environment, and the boundary conditions of the path remain hard-wired in the simulation or the trained model, even though this quantum context enters the path measure only through a quadratic action known in closed form. Here we show that a denoiser trained on classical Boltzmann statistics alone, composed at sampling time with an analytic Gaussian component carrying the entire quantum context, yields the quantum Boltzmann distribution of the nuclei. Such a composition exists and is exact whenever the training noise does not exceed the intrinsic quantum uncertainty of the target ensemble, and it is invariant across all quantum contexts admitted by this bound. We show exact transfer across temperature, isotopic mass, dissipation strength, and the boundary conditions of the path in theory and in numerical experiments, without retraining. The last yields the end-to-end displacement and momentum distributions of a tagged nucleus from open imaginary-time paths. The same invariance extends in principle to the permuted boundary conditions of bosonic exchange, with the identical denoiser. In this view, the noise of generative modeling and the quantum fluctuations of the nuclei are two faces of the same quadratic structure.
Determining molecular structures from spectroscopic data remains fundamentally challenging because the inverse problem is intrinsically underdetermined: individual spectra are sparse, low-dimensional, and encode only partial structural evidence relative to the vast space of possible molecules. We address this challenge by formulating automated structure elucidation as a scalable hypothesis-refinement paradigm that tightly integrates spectral evidence with large-scale molecular priors. To supply structure-resolving NMR signals for multimodal learning, we construct \textbf{QM9SPIN}, a DFT-derived dataset comprising diverse 1D and 2D spectra, including J-coupling, DEPT experiments, and explicit spin--spin interactions. On this foundation, we introduce \textbf{SpectroMol}, a spectrum-to-structure model that proposes chemically valid molecular hypotheses conditioned on multimodal spectral inputs. Complementarily, we develop \textbf{MS-Mol2Mol}, a high-resolution mass-constrained molecular generator that integrates molecular formula, exact mass, and degree of unsaturation within a conditional generative prior trained on 400 million molecules, ensuring global compositional consistency and chemically realistic refinement. The integrated system achieves 93.8\% top-1 accuracy on the simulated benchmark, adapts effectively from simulated to experimental spectra with limited experimental fine-tuning, and further improves experimental predictions through mass-guided refinement, establishing a scalable route toward automated, data-driven organic structure elucidation.
Machine-learning force fields (MLFFs) are reliable only near their training distribution, making efficient construction of diverse training sets a major bottleneck for both train-from-scratch and foundation fine-tuning workflows. Active learning can reduce this cost, but standard model-committee uncertainty is impractical for foundation MLFFs because each committee member requires a separate fine-tuning run. We present an active-learning workflow based on last-layer-projection regression (LLPR), a forward-pass-cheap per-configuration uncertainty estimator. Across molecular, condensed-phase, and electrolyte systems, LLPR identifies compact, high-value training sets that recover full-data accuracy using only a small fraction of electronic-structure labels. In foundation-model fine-tuning, LLPR-selected configurations reach the full-pool fine-tuning ceiling with substantially fewer labels than random selection. In iterative electrolyte fine-tuning, LLPR detects unphysical local coordination before DFT labelling, provides an absolute force-error threshold, and enables automatic termination of the learning loop. The resulting models reproduce reference density and ion-coordination structure, providing a scalable uncertainty-quantification strategy across MLFF training regimes.
Machine learning interatomic potentials (MLPs) have revolutionized atomistic modeling, offering the potential to replace traditional methods like Density Functional Theory (DFT). However, inference time of MLPs is orders of magnitude slower than that of classical force fields, hindering real-world applications for biomolecular systems that require timescales of microseconds and beyond. Implicit solvent MLPs can address this issue, but are faced with data challenges associated with coarse-grained modeling. Consequently, previous approaches relied on empirical force field data, thereby inherently limiting the MLP's accuracy. Here, we introduce the Transferable Water Implicit Network (TWIN), an implicit water MLP parametrized entirely by an Equivariant Graph Neural Network and trained solely on ab initio and experimental labels. We demonstrate TWIN's transferability across drug-like molecules, peptides, and proteins, achieving excellent results on ab initio and experimental crystallographic and NMR benchmarks, consistently outperforming previous machine-learning-based implicit solvent or coarse-grained models. Furthermore, TWIN closely matches DFT-based explicit solvent MLPs while providing a two-order-of-magnitude faster timestep evaluation, paving the way for efficient ab initio-level modeling of biomolecular systems in aqueous environments.
Catalysts are essential for sustainable chemical manufacturing, yet discovering novel architectures remains a bottleneck dominated by trial-and-error experimentation and computationally intensive screening. In complex reactions such as electrochemical carbon dioxide reduction, product selectivity is governed by dynamic interfacial, electrolyte, and potential factors as well as kinetic pathway competition. Conventional descriptor-based machine learning and computational potentials struggle to resolve these mechanistic branch points, primarily relying on static ground-state descriptors or bulk structural correlations rather than end-to-end topological pathway analysis. Here, we show that frontier language models, when strictly constrained to reason over explicit reaction networks, can discover novel catalysts by identifying the physical levers that govern pathway competition. We developed a human-AI co-thinking framework that enforces network invariance to extract testable hypotheses from complex chemical graphs. Applied to CO2 electroreduction, the framework identified ketene desorption and hydroxide capture as the acetate-forming pathway, and predicted a distinct adsorbed CO and CH2 coupling route to ketene. By isolating actionable control levers, specifically local alkalinity, controlled iron incorporation, and restricted interfacial proton-donor accessibility, the framework guided the prospective synthesis of a copper-iron oxide catalyst demonstrating a threefold increase in acetate selectivity over matched Cu-rich baselines. This mechanism-guided reasoning architecture shifts the computational paradigm from retrospective statistical prediction to forward-looking hypothesis generation, providing a broadly applicable blueprint for mechanism-guided materials discovery.
Understanding the physics of many-body complex dynamical systems may be a non-trivial task. High-dimensional analysis approaches are often deemed necessary to prevent losing important information. Typically, these use order parameters or descriptors capturing information related to, e.g., relative positions, symmetries, etc., of the units in the studied system. However, in many cases, gaining information related to the relative positions of the constitutive units (or their velocities) alone may be insufficient, and to reach a more complete physical knowledge, one should ideally learn and correlate with each other both structure and dynamics. Here we demonstrate how to achieve such a goal efficiently by building and navigating high-dimensional Time-Derivatives (TiDe) spaces. A TiDe space can be generated for virtually any type of system/phenomenon from the time-series data collected along its observation over time. Each TiDe's dimension corresponds to a growing-order time-derivative of the extracted data, thus containing information related to different physical phenomena/events, which can be easily extracted via unsupervised approaches. We demonstrate how, by definition, TiDes can be directly analyzed without a need for prior dimensionality reduction, providing results that are intrinsically intuitive to interpret. We show the potential of the method by analyzing two prototypical example datasets extracted from molecular dynamics simulations or experimental tracking of different types of complex dynamical systems. Our results demonstrate how efficiently one can navigate and learn in information-rich TiDe spaces, which provide a robust general framework for data analysis and for studying complex dynamical systems from the data collected along their observation over time.
Understanding the physics of many-body complex dynamical systems is typically non-trivial. High-dimensional analysis approaches are often deemed necessary to prevent losing important information. Typically, these use order parameters or descriptors capturing information related to, e.g., relative positions, symmetries, etc., of the units in the studied system. However, in many cases, gaining information related to the relative positions (or velocities) of the constitutive units alone may be insufficient, and to reach a more complete physical knowledge, one should ideally learn and correlate with each other both structure and dynamics. Here we demonstrate how to efficiently achieve such a goal by building and navigating high-dimensional Time-Derivatives (TiDe) space. A TiDe space can be easily generated for virtually any type of system/phenomenon under study from the time-series data collected along its observation over time. Each TiDe's dimension corresponds to a growing-order time-derivative of the extracted data, thus containing information related to different types of physical phenomena/events that can be easily extracted via unsupervised approaches. We demonstrate how, by definition, TiDes can be directly analyzed without a need for prior dimensionality reduction, providing results that are intrinsically intuitive to interpret. We show the potential of the method by analyzing two prototypical example datasets extracted from molecular dynamics simulations or experimental tracking of different complex dynamical systems. Our results demonstrate how efficiently one can navigate and learn in such information-rich TiDe spaces, which provide robust general frameworks for data analysis and for studying complex dynamical systems from the data collected along their observation over time.
Quantum mechanical (QM) cluster models provide an effective framework for mechanistic studies of enzymatic reactions but remain computationally demanding. Neural network potentials (NNPs) offer a promising route to reduce this cost, but enzymes present challenges beyond small molecules, including large system sizes, implicit-solvent environments, substantial polarization, and charge transfer. Here, we present an integrated software framework for efficient NNP training for mechanistic studies of enzymes, demonstrated on QM cluster models of S-adenosyl-L-methionine-dependent methyltransferases (MTases). Our Enerzyme code introduces modular electrostatics-aware NNP architectures and combines automated QM-cluster construction with reactive dataset generation. The Enerzymette subpackage automates reaction pathway exploration at both NNP and DFT levels. We show that iterative flexible scans and nudged elastic band calculations impose stricter requirements on NNPs than conventional dataset metrics. Nevertheless, NNPs trained on fewer than 1,000 system-specific datapoints reproduce reaction energetics and transition-state structures for MTase clusters containing up to 545 atoms with near-chemical accuracy. Direct supervision of atomic charges and consistent dielectric screening substantially improve simulation stability and accuracy, while multitask-learned atomic charges capture charge transfer and polarization trends and provide chemically meaningful descriptors of reactivity. Finally, transferability across chemically diverse catechol O-methyltransferase substrates indicates that NNPs learn generalizable reactivity patterns as training data expand across multiple enzymes. Together, these results establish a foundation for accelerating enzyme mechanistic studies and guide future NNP development for biomolecular reactivity.
Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species. This work introduces ElemeNet, a unified, general-purpose software package for molecular machine learning. The ElemeNet software package enables the training of advanced ML models for diverse properties and datasets with an enlarged range of elemental compositions. We define molecular representations compatible with elements 1-100, supporting diverse organometallic and biological systems in addition to organic chemistry already well-served by the Chemprop ML toolkit. As well as more common atom-, bond-, and molecule-level predictions, we introduce moiety predictions. We also natively define optional conditioning on charge and spin states. Advanced E(3)-equivariant and transformer architectures are supported, as well as classical 2D models, with all classes including built-in uncertainty quantification through deterministic and statistical measures. We benchmark our protocols for ML model training against representative datasets from organic, inorganic, coordination, and biological chemistry, achieving competitive and SOTA performance relative to literature baselines and favorable scaling to millions of molecules. The entire workflow is exposed through a concise command-line interface, lowering the barrier to entry for non-expert users. We anticipate ElemeNet will empower non-computational researchers to leverage modern deep learning methods across the chemical and physical sciences.
$\mathrm{Cl}(3,0)$ interatomic potentials, despite their algebraic elegance, predict force magnitudes accurately but force directions poorly. Across ten rMD17 molecules, every $L \leq 1$ baseline in our twelve-model study attains aggregate force-cosine similarity below $0.25$. The cause is structural. The geometric product of two vectors in $\mathbb{R}^3$ realises only the $L=0$ and $L=1$ components of its irreducible representation content, leaving the symmetric-traceless rank-2 component absent from the per-edge bilinear that drives each message-passing layer. We address this with CliffordSTF, which couples the Clifford multivector to closed-form symmetric-traceless tensor tracks at ranks two and three through bilinear cross-track contractions, using a single learned bilinear and no Clebsch--Gordan tables, Wigner-$D$ matrices, or e3nn calls. On rMD17, CliffordSTF raises aggregate force-cosine similarity from $0.055$ (base Clifford) to $0.551$, an order-of-magnitude relative directional gain, alongside improved magnitude accuracy (force MAE $15.8\%$ lower; energy MAE $10.9\%$ lower). It outperforms all CG-free or body-ordered baselines in our study (all $\leq 0.17$). On catalysis benchmarks, CliffordSTF achieves the best out-of-distribution S2EF energy MAE on OC22 in our experiments, and the best in-distribution energy MAE among $L \geq 2$ methods on OC22 IS2RE. An eleven-variant ablation shows the two tracks are complementary: neither alone matches the combined model.
Implicit solvent machine learning potentials (MLPs) offer a powerful route to bridging the gap between accuracy and efficiency in molecular simulations. However, existing models have largely focused on aqueous environments, overlooking the diverse and important roles of non-aqueous solvents in areas such as organic synthesis and battery technology. Here, we present ConSolv, a solvent-conditional MLP architecture that explicitly incorporates solvent effects on solute interactions through an attention-based solvent-embedding block. By combining experimental solvation free energy data with ab initio data, we train a single implicit solvent MLP that is transferable across 66 common organic solvents. ConSolv outperforms classical explicit solvent methods and selected ab initio implicit solvent approaches across multiple solvation free energy benchmarks, and demonstrates generalization to unseen solvents. Beyond solvation free energies, the model shows close agreement with experimental nuclear magnetic resonance (NMR) data for $γ$-fluorohydrin molecules in chloroform. ConSolv's architecture is readily extensible to broader chemical spaces and alternative training strategies, while its attention-based design supports explainable artificial intelligence (AI) analysis that can help elucidate complex, solvent-dependent molecular interactions.
Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve. Yet element-wise agreement with the converged Hamiltonian, an implicit fixed point of the self-consistent field iteration, does not determine the occupied subspace that governs orbital energies and densities. Here we present HamEvo, a neural operator that learns the single-step self-consistent update and returns the converged Hamiltonian as its fixed point. HamEvo is pre-trained on intermediate self-consistent trajectories and calibrated at equilibrium with density-matrix supervision. Across benchmarks from MD17 to drug-like QMugs, HamEvo lowers Hamiltonian errors by 35-49% over direct-regression and deep-equilibrium baselines, and predicts QMugs HOMO and LUMO energies with mean absolute errors of 0.036 and 0.053 eV, near the 1 kcal/mol chemical-accuracy scale. Few-shot fine-tuning with only 20 reference conformations extends HamEvo to molecules of up to 122 atoms, well beyond the size range covered by pre-training. With thermal molecular-dynamics sampling, HamEvo captures temperature-dependent HOMO-LUMO gap renormalization beyond the harmonic approximation. Inference is up to 242 times faster than conventional DFT.
Can a general-purpose large language model design molecules with the precision of a seasoned chemist? Current LLM-based frameworks answer this question with scalar feedback loops-generate, score, reject-that amount to informed trial-and-error. Here we show that replacing a single number with the full physicochemical rationale from first-principles calculations transforms the LLM from a stochastic sampler into a causal reasoner. Our system couples retrieval-augmented generation with a self-reflection module that feeds orbital energies, atomic charges, and electron densities-rather than compressed scores-back into the design loop. On HOMO-LUMO gap targets from 1.0 to 5.0 eV, this structure-property-relationship (SPR) reflection achieves a deviation as low as 0.0003 eV and a 100% success rate on moderate tasks, decisively outperforming scalar-feedback and non-reflective baselines. The framework generalizes seamlessly to dipole-moment design and proves robust across five distinct LLM backbones. These results establish a new paradigm: when the model understands not only that a molecule fails, but why, iterative molecular design becomes genuinely mechanistic.
Implicit solvent models are widely used to decrease the number of solvent degrees of freedom and enable the calculation of solvation energetics without water molecules. However, its accuracy often falls short compared to explicit models. Recent advancements in neural potentials have shown promise in drug discovery, but transferability remains a persistent challenge. Here, we introduce the Protein Hydration Neural Network (PHNN), an implicit solvent model that extends analytical continuum solvation by learning transferable corrections to model parameters instead of applying post hoc adjustments to final energies. The model is explicitly designed to maximize data efficiency by leveraging physical priors embedded in the data. We demonstrate that PHNN improves accuracy relative to traditional analytical methods and maintains predictive accuracy on out-of-domain protein systems.
Multiconfiguration pair-density functional theory (MC-PDFT) offers an efficient and accurate framework for computing electronic energies in strongly correlated molecular systems, with the quality of the on-top functional being a key determinant of its predictive accuracy. Here we introduce FunctionalAgent, an agentic system for fully automated functional development. FunctionalAgent orchestrates a team of specialized sub-agents to decompose the development process into dataset construction, active-space generation, MCSCF calculation and descriptor generation, loss-function construction, and functional fitting, optimization, and evaluation, thereby linking all stages into a closed-loop automated workflow. Using FunctionalAgent, we developed MC26, a hybrid meta-GGA on-top functional that achieves improved overall accuracy on the training set compared with other methods evaluated on the same benchmark dataset. We further introduce COF26, a new functional form that, owing to the optimized training process, achieves the best performance on both the training and test sets.
We present \textsc{dm-PhiSNet}, a physically constrained \textsc{PhiSNet}-based equivariant model that predicts one-electron reduced density matrices (1-RDMs) directly from molecular geometries in an atomic-orbital (AO) basis for accelerated self-consistent field (SCF) workflows. Training follows a two-stage schedule with progressively introduced physically motivated objectives, and the resulting predictions are refined by a lightweight analytic block. This block enforces electron-number conservation, drives the 1-RDM toward generalized idempotency in the AO metric, and regularizes the occupation spectrum of the Löwdin-orthogonalized density. Across six closed-shell systems -- H$_2$O, CH$_4$, NH$_3$, HF, ethanol, and NO$_3^-$ -- the refined 1-RDMs provide SCF initial guesses that substantially reduce iteration steps by 49--81\% relative to standard initializations. Beyond SCF acceleration, the learned 1-RDMs yield accurate one-shot total energies and Hellmann--Feynman atomic forces without force supervision, indicating that the model captures chemically meaningful electronic structure. These results demonstrate that combining equivariant learning with analytic constraint enforcement provides a simple, general route to solver-ready density-matrix initializations and accelerated SCF workflows.
Machine-learning interatomic potentials (MLIPs) have enabled molecular dynamics at near ab initio accuracy, yet remain limited to energies and forces by construction, leaving electronic observables such as dipole moments and polarizabilities inaccessible. We introduce DenSNet, a density-first approach to machine-learned electronic structure that learns the Hohenberg--Kohn map from nuclear configurations to the ground-state electron density. Our approach employs an SE(3)-equivariant neural network to predict density coefficients of a flexible atom-centered Gaussian basis, combined with a $Δ$-learning strategy that uses superposed atomic densities as a prior to accelerate training. A second equivariant network then maps the predicted density to the total energy, providing a unified framework for molecular dynamics and electronic structure. We validate DenSNet on ethanol, ethanethiol, and resorcinol, where infrared spectra from machine-learned trajectories show excellent agreement with experimental gas-phase measurements. To test scalability, we train on polythiophene oligomers with 1--6 monomers and extrapolate to chains of up to 12 monomers, generating stable long-time trajectories whose infrared spectra agree with reference density functional theory calculations. Here, we show that reinstating the electron density as the central learned quantity opens a practical route to transferable prediction of spectroscopic and electronic observables in large-scale molecular simulations.
Light-activated drugs are a promising way to treat localized diseases for which existing treatments have severe side effects. However, their development is complicated by the set of photophysical and biological properties that must be simultaneously optimized. Here we used computational techniques to find a set of promising candidates for the photoactive inhibition of the poly(ADP-ribose) polymerase 1 (PARP1) cancer target. Using our recently developed methods based on atomistic simulation and machine learning (ML), we screened a set of 5 million hypothetical photoactive ligands. Our workflow used protein-ligand docking to identify candidates with differential PARP1 binding under light and dark conditions; ML force fields and quantum chemistry calculations to predict p$K_\mathrm{a}$, absorption spectra, and thermal half-lives; graph-based surrogate models to screen additional compounds; excited-state nonadiabatic dynamics with ML force fields to estimate quantum yields; and free energy perturbation (FEP) to refine binding predictions. From these predictions, we prioritized a small set of synthetically feasible candidates expected to have red-shifted absorption spectra, thermal half-lives on the order of seconds to minutes, and isomer-dependent PARP1 binding under visible-light control. We synthesized 10 candidates and experimentally characterized their photobehavior and PARP1 inhibition constants. Among the validated compounds, \textbf{1} showed a 15-fold increase in inhibition of PARP1 upon green-light irradiation at 519 nm (208.8 $\pm$ 28.3 $μ$M vs 14.4 $\pm$ 1.9 $μ$M). These results validate the computation-guided screening strategy for identifying red-shifted PARP1 photoinhibitors, while also underscoring current limitations such as rapid thermal relaxation in aqueous media.
Mechanistic understanding and rational design of complex chemical systems depend on fast and accurate predictions of electronic structures beyond individual building blocks. However, if the system exceeds hundreds of atoms, first-principles quantum mechanical (QM) modeling becomes impractical. In this study, we developed FB-GNN-MBE by integrating a fragment-based graph neural network (FB-GNN) into the many-body expansion (MBE) theory and demonstrated its capacity to reproduce first-principles potential energy surfaces (PES) for hierarchically structured systems with manageable accuracy, complexity, and interpretability. Specifically, we divided the entire system into basic building blocks (fragments), evaluated their one-fragment energies using a QM model, and addressed many-fragment interactions using the structure-property relationships trained by FB-GNNs. Our investigation shows that FB-GNN-MBE achieves chemical accuracy in predicting two-body (2B) and three-body (3B) energies across water, phenol, and mixture benchmarks, as well as the one-dimensional dissociation curves of water and phenol dimers. To transfer the success of FB-GNN-MBE across various systems with minimal computational costs and data demands, we developed and validated a teacher-student learning protocol. A heavy-weight FB-GNN trained on a mixed-density water cluster ensemble (teacher) distills its learned knowledge and passes it to a light-weight GNN (student), which is later fine-tuned on a uniform-density (H2O)21 cluster ensemble. This transfer learning strategy resulted in efficient and accurate prediction of 2B and 3B energies for variously sized water clusters without retraining. Our transferable FB-GNN-MBE framework outperformed conventional non-FB-GNN-based models and showed high practicality for large-scale molecular simulations.
Predicting the perceived intensity of odorants remains a fundamental challenge in sensory science due to the complex, non-linear behavior of their response, as well as the difficulty in correlating molecular structure with human perception. While traditional deep learning models, such as Graph Convolutional Networks (GCNs), excel at capturing molecular topology, they often fail to account for the biological and perceptual context of olfaction. This study introduces VIANA, a novel "tri-pillar" framework that integrates structural graph theory, character value embeddings, and phenomenological behavior. This methodology systematically evaluates knowledge transfer across three distinct domains: molecular structure via GCNs, semantic odor character values via Principal Odor Map (POM) embeddings, and biological dose-response logic via Hill's law. We demonstrate that knowledge transfer is not inherently positive; rather, a balance must be maintained in the volume of information provided to the model. While raw semantic data led to "information overload" in domain-informed models, applying Principal Component Analysis (PCA) to distill the 95% most impactful semantic variance yielded a superior "signal distillation" effect. Results indicate that the synthesis of these three knowledge transfer pillars significantly outperforms baseline structural models, with VIANA achieving a peak R^2 of 0.996 and a test Mean Squared Error (MSE) of 0.19. In this context, VIANA successfully captures the physical ceiling of saturation, the sensitivity of detection thresholds, and the nuance of odor character value expression, providing a domain grounded simulation of the human olfactory experience. This research provides a robust framework for digital olfaction, effectively bridging the gap between molecular informatics and sensory perception.
Machine-learned interatomic potentials (MLIPs), particularly graph neural network (GNN)-based models, offer a promising route to achieving near-density functional theory (DFT) accuracy at significantly reduced computational cost. However, their practical deployment is often limited by the large volumes of expensive quantum mechanical training data required. In this work, we introduce a transfer learning framework, Transfer-PaiNN (T-PaiNN), that substantially improves the data efficiency of GNN-MLIPs by leveraging inexpensive classical force field data. The approach consists of pretraining a PaiNN MLIP architecture on large-scale datasets generated from classical molecular simulations, followed by fine-tuning (dubbed autotuning) using a comparatively small DFT dataset. We demonstrate the effectiveness of autotuning T-PaiNN on both gas-phase molecular systems (QM9 dataset) and condensed-phase liquid water. Across all cases, T-PaiNN significantly outperforms models trained solely on DFT data, achieving order-of-magnitude reductions in mean absolute error while accelerating training convergence. For example, using the QM9 data set, error reductions of up to 25 times are observed in low-data regimes, while liquid water simulations show improved predictions of energies, forces, and experimentally relevant properties such as density and diffusion. These gains arise from the model's ability to learn general features of the potential energy surface from extensive classical sampling, which are subsequently refined to quantum accuracy. Overall, this work establishes transfer learning from classical force fields as a practical and computationally efficient strategy for developing high-accuracy, data-efficient GNN interatomic potentials, enabling broader application of MLIPs to complex chemical systems.
A faithful description of chemical processes requires exploring extended regions of the molecular potential energy surface (PES), which remains challenging for strongly correlated systems. Transferable deep-learning variational Monte Carlo (VMC) offers a promising route by efficiently solving the electronic Schrödinger equation jointly across molecular geometries at consistently high accuracy, yet its stochastic nature renders direct exploration of molecular configuration space nontrivial. Here, we present a framework for highly accurate ab initio exploration of PESs that combines transferable deep-learning VMC with a cost-effective estimation of energies, forces, and Hessians. By continuously sampling nuclear configurations during VMC optimization of electronic wave functions, we obtain transferable descriptions that achieve zero-shot chemical accuracy within chemically relevant distributions of molecular geometries. Throughout the subsequent characterization of molecular configuration space, the PES is evaluated only sparsely, with local approximations constructed by estimating VMC energies and forces at sampled geometries and aggregating the resulting noisy data using Gaussian process regression. Our method enables accurate and efficient exploration of complex PES landscapes, including structure relaxation, transition-state searches, and minimum-energy pathways, for both ground and excited states. This opens the door to studying bond breaking, formation, and large structural rearrangements in systems with pronounced multi-reference character.
We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.
Long-range electrostatic and polarization interactions play a central role in molecular and condensed-phase systems, yet remain fundamentally incompatible with locality-based machine-learning interatomic potentials. Although modern SO(3)-equivariant neural potentials achieve high accuracy for short-range chemistry, they cannot represent the anisotropic, slowly decaying multipolar correlations governing realistic materials, while existing long-range extensions either break SO(3) equivariance or fail to maintain energy-force consistency. Here we introduce EquiEwald, a unified neural interatomic potential that embeds an Ewald-inspired reciprocal-space formulation within an irreducible SO(3)-equivariant framework. By performing equivariant message passing in reciprocal space through learned equivariant k-space filters and an equivariant inverse transform, EquiEwald captures anisotropic, tensorial long-range correlations without sacrificing physical consistency. Across periodic and aperiodic benchmarks, EquiEwald captures long-range electrostatic behavior consistent with ab initio reference data and consistently improves energy and force accuracy, data efficiency, and long-range extrapolation. These results establish EquiEwald as a physically principled paradigm for long-range-capable machine-learning interatomic potentials.
Accurate atomistic simulations of gas-surface scattering require potential energy surfaces that remain reliable over broad configurational and energetic ranges while retaining the efficiency needed for extensive trajectory sampling. Here, we develop a data-driven workflow for constructing a machine-learning interatomic potential (MLIP) tailored to gas-surface scattering dynamics, using nitric oxide (NO) scattering from highly oriented pyrolytic graphite (HOPG) as a benchmark system. Starting from an initial ab initio molecular dynamics (AIMD) dataset, local atomic environments are described by SOAP descriptors and analyzed in a reduced feature space obtained through principal component analysis. Farthest point sampling is then used to build a compact training set, and the resulting Deep Potential model is refined through a query-by-committee active-learning strategy using additional configurations extracted from molecular dynamics simulations over extended ranges of incident energies and surface temperatures. The final MLIP reproduces reference energies and forces with high fidelity and enables large-scale molecular dynamics simulations of NO scattering from graphite at a computational cost far below that of AIMD. The simulations provide detailed insight into adsorption energetics, trapping versus direct scattering probabilities, translational energy loss, angular distributions, and rotational excitation. Overall, the results reproduce the main experimental trends and demonstrate that descriptor-guided sampling combined with active learning offers an efficient and transferable strategy for constructing MLIPs for gas-surface interactions.
Machine learning interatomic potentials (MLIPs) have become widely used tools in atomistic simulations. For much of the history of this field, the most commonly employed architectures were based on short-ranged atomic energy contributions, and the assumption of locality still persists in many modern foundation models. While this approach has enabled efficient and accurate modelling for many use cases, it poses intrinsic limitations for systems where long-range electrostatics, charge transfer, or induced polarization play a central role. A growing body of work has proposed extensions that incorporate electrostatic effects, ranging from locally predicted atomic charges to self-consistent models. While these models have demonstrated success for specific examples, their underlying assumptions, and fundamental limitations are not yet well understood. In this work, we present a framework for treating electrostatics in MLIPs by viewing existing models as coarse-grained approximations to density functional theory (DFT). This perspective makes explicit the approximations involved, clarifies the physical meaning of the learned quantities, and reveals connections and equivalences between several previously proposed models. Using this formalism, we identify key design choices that define a broader design space of self-consistent electrostatic MLIPs. We implement salient points in this space using the MACE architecture and a shared representation of the charge density, enabling controlled comparisons between different approaches. Finally, we evaluate these models on two instructive test cases: metal-water interfaces, which probe the contrasting electrostatic response of conducting and insulating systems, and charged vacancies in silicon dioxide. Our results highlight the limitations of existing approaches and demonstrate how more expressive self-consistent models are needed to resolve failures.
The Hessian matrix (second derivatives) encodes far richer local curvature of the potential energy surface than energies and forces alone. However, training machine-learning interatomic potentials (MLIPs) with full Hessians is often impractical because explicitly forming and storing Hessian matrices scales quadratically in cost and memory. We introduce Projected Hessian Learning (PHL), a scalable second-order training framework that injects curvature information using only Hessian-vector products (HVPs). Rather than constructing the Hessian, PHL projects curvature along stochastic probe directions and uses an unbiased stochastic trace-based loss with favorable system-size scaling, enabling curvature-informed training without quadratic memory growth. We benchmark PHL on a chemically diverse dataset of reactants, products, transition states, intrinsic reaction coordinates, and normal-mode sampled geometries computed at omegaB97XD/6-31G(d). We compare energy-force training (E-F), two HVP-based schemes (E-F-HVP with one-hot or randomized probes), and full energy-force-Hessian training (E-F-H). With randomized probes per minibatch, both HVP schemes match full-Hessian training in energy, force, and Hessian accuracy while delivering >24x epoch speedups for the small molecular systems studied. In a fixed-probe regime with one HVP per molecule, randomized projections consistently outperform one-column probing, especially for far-from-equilibrium geometries. Overall, PHL replaces explicit Hessian supervision with force-complexity curvature training, retaining most second-order accuracy gains while scaling to larger, more complex molecular systems.
Physics-guided sampling with diffusion model priors has shown promise for solving partial differential equation (PDE) governed problems, but applications to chemically meaningful reaction-transport systems remain limited. We apply diffusion-based guided sampling to gas-phase chemical reactions by training on solutions of the advection-reaction-diffusion (ARD) equation across varying parameters. The method generates physically consistent concentration fields and accurately predicts outlet concentrations, including at unseen parameter values, demonstrating the potential of diffusion models for inference in reactive transport.
Covalent organic frameworks (COFs) are promising photocatalysts for solar hydrogen production, yet the most electronically favorable linkages, imines, hydrolyze rapidly in water, creating a stability--activity trade-off that limits practical deployment. Navigating the combinatorial design space of nodes, linkers, linkages, and functional groups to identify candidates that are simultaneously active and durable remains a formidable challenge. Here we introduce Ara, a large-language-model (LLM) agent that leverages pretrained chemical knowledge, donor--acceptor theory, conjugation effects, and linkage stability hierarchies, to guide the search for photocatalytic COFs satisfying joint band-gap, band-edge, and hydrolytic-stability criteria. Evaluated against random search and Bayesian optimization (BO) over a space consisting of candidates with various nodes, linkers, linkages, and r-groups, screened with a GFN1-xTB fragment pipeline, Ara achieves a 52.7\% hit rate (11.5$\times$ random, p = 0.006), finds its first hit at iteration 12 versus 25 for random search, and significantly outperforms BO (p = 0.006). Inspection of the agent's reasoning traces reveals interpretable chemical logic: early convergence on vinylene and beta-ketoenamine linkages for stability, node selection informed by electron-withdrawing character, and systematic R-group optimization to center the band gap at 2.0 eV. Exhaustive evaluation of the full search space uncovers a complementary exploitation--exploration trade-off between the agent and BO, suggesting that hybrid strategies may combine the strengths of both approaches. These results demonstrate that LLM chemical priors can substantially accelerate multi-criteria materials discovery.
Accurate prediction of the physicochemical properties of molecular mixtures using graph neural networks remains a significant challenge, as it requires simultaneous embedding of intramolecular interactions while accounting for mixture composition (i.e., concentrations and ratios). Existing approaches are ill-equipped to emulate realistic mixture environments, where densely coupled interactions propagate across hierarchical levels - from atoms and functional groups to entire molecules - and where cross-level information exchange is continuously modulated by composition. To bridge the gap between isolated molecules and realistic chemical environments, we present ChemFlow, a novel hierarchical framework that integrates atomic, functional group, and molecular-level features, facilitating information flow across these levels to predict the behavior of complex chemical mixtures. ChemFlow employs an atomic-level feature fusion module, Chem-embed, to generate context-aware atomic representations influenced by the mixture state and atomic characteristics. Next, bidirectional group-to-molecule and molecule-to-group attention mechanisms enable ChemFlow to capture functional group interactions both within and across molecules in the mixture. By dynamically adjusting representations based on concentration and composition, ChemFlow excels at predicting concentration-dependent properties and significantly outperforms state-of-the-art models in both concentration-sensitive and concentration-independent systems. Extensive experiments demonstrate ChemFlow's superior accuracy and efficiency in modeling complex chemical mixtures.