Daily Papers

Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models for tasks such as reaction product prediction rarely abide by this most basic constraint. In this work, we recast the problem of reaction prediction as a problem of electron redistribution using the modern deep generative framework of flow matching. Our model, FlowER, overcomes limitations inherent in previous approaches by enforcing exact mass conservation, thereby resolving hallucinatory failure modes, recovering mechanistic reaction sequences for unseen substrate scaffolds, and generalizing effectively to out-of-domain reaction classes with extremely data-efficient fine-tuning. FlowER additionally enables estimation of thermodynamic or kinetic feasibility and manifests a degree of chemical intuition in reaction prediction tasks. This inherently interpretable framework represents a significant step in bridging the gap between predictive accuracy and mechanistic understanding in data-driven reaction outcome prediction.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Ammonia (NH3) is mainly produced through the traditional Haber-Bosch process under harsh conditions with huge energy consumption and massive carbon dioxide (CO2) emission. The nitrogen electroreduction reaction (NERR), as an energy-efficient and environment-friendly process of converting nitrogen (N2) to NH3 under ambient conditions, has been regarded as a promising alternative to the Haber-Bosch process and has received enormous interest in recent years. Although some exciting progress has been made, considerable scientific and technical challenges still exist in improving the NH3 yield rate and Faradic efficiency, understanding the mechanism of the reaction and promoting the wide commercialization of NERR. Single-atom catalysts (SACs) have emerged as promising catalysts because of its atomically dispersed activity sites and maximized atom efficiency, unsaturated coordination environment, and its unique electronic structure, which could significantly improve the rate of reaction and yield rate of NH3. In this review we briefly introduce the unique structural and electronic features of SACs, which contributes to comprehensively understand the reaction mechanism owing to their structural simplicity and diversity, and in turn expedite the rational design of fantastic catalysts at the atomic scale. Then, we summarize the most recent experimental and computational efforts on developing novel SACs with excellent NERR performance, including precious metal-, nonprecious metal- and nonmetal-based SACs. Finally, we present challenges and perspectives of SACs on NERR, as well as some potential means for advanced NERR catalyst.

The paper has two goals: It presents basic ideas, notions, and methods for reduction of reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds, and limiting steps. It describes briefly the current state of the art and some latest achievements in the broad area of model reduction in chemical and biochemical kinetics, including new results in methods of invariant manifolds, computation singular perturbation, bottleneck methods, asymptotology, tropical equilibration, and reaction mechanism skeletonisation.

The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions etc), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We proved two consequences of the detailed balance for these mechanisms: the structural condition and the algebraic condition that form together the extended form of detailed balance. The algebraic condition is the principle of detailed balance for the reversible part. The structural condition is: the convex hull of the stoichiometric vectors of the irreversible reactions has empty intersection with the linear span of the stoichiometric vectors of the reversible reaction. Physically, this means that the irreversible reactions cannot be included in oriented pathways. The systems with the extended form of detailed balance are also the limits of the reversible systems with detailed balance when some of the equilibrium concentrations (or activities) tend to zero. Surprisingly, the structure of the limit reaction mechanism crucially depends on the relative speeds of this tendency to zero.

While Vision-Language Models (VLMs) have demonstrated significant potential in chemical visual understanding, current models are predominantly optimized for direct visual question-answering tasks. This paradigm often results in "black-box" systems that fail to utilize the inherent capability of Large Language Models (LLMs) to infer underlying reaction mechanisms. In this work, we introduce ChemVLR, a chemical VLM designed to prioritize reasoning within the perception process. Unlike conventional chemical VLMs, ChemVLR analyzes visual inputs in a fine-grained manner by explicitly identifying granular chemical descriptors, such as functional groups, prior to generating answers. This approach ensures the production of explicit and interpretable reasoning paths for complex visual chemical problems. To facilitate this methodology, we implement a cross-modality reverse-engineering strategy, combined with a rigorous filtering pipeline, to curate a large-scale reasoning-and-captioning dataset comprising 760k high-quality samples across molecular and reaction tasks. Furthermore, we adopt a three-stage training framework that systemically builds model perception and reasoning capacity. Experiments demonstrate that ChemVLR achieves state-of-the-art (SOTA) performance, surpassing both leading proprietary models and domain-specific open-source baselines. We also provide comprehensive ablation studies to validate our training strategy and data generation designs. Code and model weights will be available at https://github.com/xxlllz/ChemVLR.

World models learn to predict future states of an environment, enabling planning and mental simulation. Current approaches default to Transformer-based predictors operating in learned latent spaces. This comes at a cost: O(N^2) computation and no explicit spatial inductive bias. This paper asks a foundational question: is self-attention necessary for predictive world modeling, or can alternative computational substrates achieve comparable or superior results? I introduce FluidWorld, a proof-of-concept world model whose predictive dynamics are governed by partial differential equations (PDEs) of reaction-diffusion type. Instead of using a separate neural network predictor, the PDE integration itself produces the future state prediction. In a strictly parameter-matched three-way ablation on unconditional UCF-101 video prediction (64x64, ~800K parameters, identical encoder, decoder, losses, and data), FluidWorld is compared against both a Transformer baseline (self-attention) and a ConvLSTM baseline (convolutional recurrence). While all three models converge to comparable single-step prediction loss, FluidWorld achieves 2x lower reconstruction error, produces representations with 10-15% higher spatial structure preservation and 18-25% more effective dimensionality, and critically maintains coherent multi-step rollouts where both baselines degrade rapidly. All experiments were conducted on a single consumer-grade PC (Intel Core i5, NVIDIA RTX 4070 Ti), without any large-scale compute. These results establish that PDE-based dynamics, which natively provide O(N) spatial complexity, adaptive computation, and global spatial coherence through diffusion, are a viable and parameter-efficient alternative to both attention and convolutional recurrence for world modeling.

The origin of a chemical reaction between two reactant atoms is associated to the activation energy, with the assumption that, high-energy collisions between these atoms, are the ones that overcome the activation energy. Here, we (i) show that a stronger attractive van der Waals (vdW) and electron-ion Coulomb interactions between two polarized atoms are responsible to initiate a chemical reaction, either before or after the collision. We derive this stronger vdW attraction formula exactly using the quasi one-dimensional Drude model within the ionization energy theory and the energy-level spacing renormalization group method. Along the way, we (ii) expose the precise physical mechanism responsible for the existence of a stronger vdW interaction for both long and short distances, and also show how to technically avoid the electron-electron Coulomb repulsion between polarized electrons from these two reactant atoms. Finally, we properly and correctly associate the existence of this stronger attraction to Ramachandran's 'normal limits' (distance shorter than what is allowed by the standard vdW bond) between chemically nonbonded atoms.

We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Green's functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an example, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e. the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.

Chemical transport models (CTMs), which simulate air pollution transport, transformation, and removal, are computationally expensive, largely because of the computational intensity of the chemical mechanisms: systems of coupled differential equations representing atmospheric chemistry. Here we investigate the potential for machine learning to reproduce the behavior of a chemical mechanism, yet with reduced computational expense. We create a 17-layer residual multi-target regression neural network to emulate the Carbon Bond Mechanism Z (CBM-Z) gas-phase chemical mechanism. We train the network to match CBM-Z predictions of changes in concentrations of 77 chemical species after one hour, given a range of chemical and meteorological input conditions, which it is able to do with root-mean-square error (RMSE) of less than 1.97 ppb (median RMSE = 0.02 ppb), while achieving a 250x computational speedup. An additional 17x speedup (total 4250x speedup) is achieved by running the neural network on a graphics-processing unit (GPU). The neural network is able to reproduce the emergent behavior of the chemical system over diurnal cycles using Euler integration, but additional work is needed to constrain the propagation of errors as simulation time progresses.

Altering chemical reactivity and material structure in confined optical environments is on the rise, and yet, a conclusive understanding of the microscopic mechanisms remains elusive. This originates mostly from the fact that accurately predicting vibrational and reactive dynamics for soluted ensembles of realistic molecules is no small endeavor, and adding (collective) strong light-matter interaction does not simplify matters. Here, we establish a framework based on a combination of machine learning (ML) models, trained using density-functional theory calculations, and molecular dynamics to accelerate such simulations. We then apply this approach to evaluate strong coupling, changes in reaction rate constant, and their influence on enthalpy and entropy for the deprotection reaction of 1-phenyl-2-trimethylsilylacetylene, which has been studied previously both experimentally and using ab initio simulations. While we find qualitative agreement with critical experimental observations, especially with regard to the changes in kinetics, we also find differences in comparison with previous theoretical predictions. The features for which the ML-accelerated and ab initio simulations agree show the experimentally estimated kinetic behavior. Conflicting features indicate that a contribution of dynamic electronic polarization to the reaction process is more relevant then currently believed. Our work demonstrates the practical use of ML for polaritonic chemistry, discusses limitations of common approximations and paves the way for a more holistic description of polaritonic chemistry.

Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that can dramatically affect the reaction rate. The extreme case is that of a reaction coupled to a phase transformation, whose kinetics must depend on the order parameter -- and its gradients, at phase boundaries. This Account presents a general theory of chemical kinetics based on nonequilibrium thermodynamics. The reaction rate is a nonlinear function of the thermodynamic driving force (free energy of reaction) expressed in terms of variational chemical potentials. The Cahn-Hilliard and Allen-Cahn equations are unified and extended via a master equation for non-equilibrium chemical thermodynamics. For electrochemistry, both Marcus and Butler-Volmer kinetics are generalized for concentrated solutions and ionic solids. The theory is applied to intercalation dynamics in the phase separating Li-ion battery material Li_xFePO_4.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffe and the hard and soft acids and bases concept of Pearson. The sound theoretical basis allows for a systematic definition of such concepts. However, while they are often used to describe and compare chemical processes in terms of reactivity, their predictive power remains unclear. In this work, we elaborate on the predictive potential of chemical reactivity concepts, which can be crucial for autonomous reaction exploration protocols to guide them by first-principles heuristics that expoit these concepts.

While attaining external field control of bimolecular chemical reactions has long been a coveted goal of physics and chemistry, the role of hyperfine interactions and dc magnetic fields in achieving such control has remained elusive. We develop an extended coupled-channel statistical theory of barrierless atom-diatom chemical reactions, and apply it to elucidate the effects of magnetic fields and hyperfine interactions on the ultracold chemical reaction Li(^2S_{1/2}) + CaH(^2Σ^+) to LiH(^1Σ^+) + Ca(^1S_{0}) on a newly developed set of ab initio potential energy surfaces. We observe large field effects on the reaction cross sections, opening up the possibility of controlling ultracold barrierless chemical reactions by tuning selected hyperfine states of the reactants with an external magnetic field.

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models, and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential triangle G=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in phosphorylation-dephosphorylation cycle respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by "dissociation constants", which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule which can not be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein which can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science. With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation. Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20-35% gains over domain-specific baselines and outperforms general-purpose LLMs by 10-15% in Top-1 accuracy, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ the Langevin equation for the reaction coordinate. The Langevin equation contains current-induced forces and is used to define nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once the nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.

Macroscopic entropy production σ^{(tot)} in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation and a house-keeping heat: σ^{(tot)}=σ^{(fd)}+σ^{(hk)}; σ^{(fd)}=-rd A/rd t, where A is a generalized free energy function. This yields a novel nonequilibrium free energy balance equation rd A/rd t=-σ^{(tot)}+σ^{(hk)}, which is on a par with celebrated entropy balance equation rd S/rd t=σ^{(tot)}+η^{(ex)} where η^{(ex)} is the rate of entropy exchange with the environment.For kinetic systems with complex balance, σ^{(fd)} and σ^{(hk)} are the macroscopic limits of stochastic free energy dissipation and house-keeping heat, which are both nonnegative, in the Delbrück-Gillespie description of the stochastic chemical kinetics.Therefore, we show that a full kinetic and thermodynamic theory of chemical reaction systems that transcends mesoscopic and macroscopic levels emerges.

All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation, joint solution to such a construction under certain, often ad hoc chosen conditions and with ad hoc numerical coefficients leads to chemical oscillations. Kinetic perception of chemical oscillations reigns without exclusions. However, as it was recently shown by the author for the laser and for the electrochemical systems, chemical oscillations follow also from solutions to the basic expressions of discrete thermodynamics of chemical equilibria. Graphically those solutions are various fork bifurcation diagrams, and, in certain types of chemical systems, oscillations are well pronounced in the bistable bifurcation areas. In this work we describe a general thermodynamic approach to chemical oscillations as opposite to kinetic models, and depict some of their new features like spontaneity and fractality. The paper doubts exclusivity of the kinetic approach to chemical oscillations, and its aim is to discuss and exemplify thermodynamically predicted chemical oscillations in closed chemical systems.

We present subarcsecond-resolution ALMA mosaics of the Orion Bar PDR in [CI] 609 um, C2H (4-3), and C18O (3-2) emission lines, complemented by JWST images of H2 and aromatic infrared band (AIB) emission. The rim of the Bar shows very corrugated structures made of small-scale H2 dissociation fronts (DFs). The [CI] 609 um emission peaks very close (~0.002 pc) to the main H2-emitting DFs, suggesting the presence of gas density gradients. These DFs are also bright and remarkably similar in C2H emission, which traces 'hydrocarbon radical peaks' characterized by very high C2H abundances, reaching up to several x10^-7. The high abundance of C2H and of related hydrocarbon radicals, such as CH3, CH2, and CH, can be attributed to gas-phase reactions driven by elevated temperatures, the presence of C+ and C, and the reactivity of FUV-pumped H2. The hydrocarbon radical peaks roughly coincide with maxima of the 3.4/3.3 um AIB intensity ratio, a proxy for the aliphatic-to-aromatic content of PAHs. This implies that the conditions triggering the formation of simple hydrocarbons also favor the formation (and survival) of PAHs with aliphatic side groups, potentially via the contribution of bottom-up processes in which abundant hydrocarbon radicals react in situ with PAHs. Ahead of the DFs, in the atomic PDR zone (where [H]>>[H2]), the AIB emission is brightest, but small PAHs and carbonaceous grains undergo photo-processing due to the stronger FUV field. Our detection of trace amounts of C2H in this zone may result from the photoerosion of these species. This study provides a spatially resolved view of the chemical stratification of key carbon carriers in a PDR. Overall, both bottom-up and top-down processes appear to link simple hydrocarbon molecules with PAHs in molecular clouds; however, the exact chemical pathways and their relative contributions remain to be quantified.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobin, while ruffling has been correlated with electron transfer processes, such as in the case of Cytochrome c (Cyt c). The latter has indeed evolved to become an important electron transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe K-edge X-ray absorption near-edge structure (XANES) studies and femtosecond Fe Kalpha and Kbeta X-ray emission spectroscopy (XES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the Iron ion, causing the ferric heme to undergo doming, which we identify for the first time. We also argue that this pattern is common to all ferric haems, raising the question of the biological relevance of doming in such proteins.

Transformer-based deep neural networks have revolutionized the field of molecular-related prediction tasks by treating molecules as symbolic sequences. These models have been successfully applied in various organic chemical applications by pretraining them with extensive compound libraries and subsequently fine-tuning them with smaller in-house datasets for specific tasks. However, many conventional methods primarily focus on single molecules, with limited exploration of pretraining for reactions involving multiple molecules. In this paper, we propose ReactionT5, a novel model that leverages pretraining on the Open Reaction Database (ORD), a publicly available large-scale resource. We further fine-tune this model for yield prediction and product prediction tasks, demonstrating its impressive performance even with limited fine-tuning data compared to traditional models. The pre-trained ReactionT5 model is publicly accessible on the Hugging Face platform.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

A theoretical approach to describing transport of an entire ensemble of clusters with different sizes as a single species in gas has been developed. The major assumption is an existence of local partial chemical equilibrium between the clusters. It is shown that thermal diffusion emerges in the collective description as a significant factor even if it is negligible when transport of the original molecular species is considered. Analytical expressions for the effective diffusion and thermal diffusion coefficients at temperature, pressure, and chemical composition gradients have been derived. The theory has been applied to a technology of H2S conversion in a centrifugal plasma-chemical reactor and has made it possible to account for sulfur clusters in numerical process modeling.

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. There have been considerable attempts to address this problem, but given the exponentially large combinatorial space of synthesizable molecules, existing methods have shown limited coverage of the space and poor molecular optimization performance. To tackle these problems, we introduce ReaSyn, a generative framework for synthesizable projection where the model explores the neighborhood of given molecules in the synthesizable space by generating pathways that result in synthesizable analogs. To fully utilize the chemical knowledge contained in the synthetic pathways, we propose a novel perspective that views synthetic pathways akin to reasoning paths in large language models (LLMs). Specifically, inspired by chain-of-thought (CoT) reasoning in LLMs, we introduce the chain-of-reaction (CoR) notation that explicitly states reactants, reaction types, and intermediate products for each step in a pathway. With the CoR notation, ReaSyn can get dense supervision in every reaction step to explicitly learn chemical reaction rules during supervised training and perform step-by-step reasoning. In addition, to further enhance the reasoning capability of ReaSyn, we propose reinforcement learning (RL)-based finetuning and goal-directed test-time compute scaling tailored for synthesizable projection. ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.

The interstellar medium (ISM) is all but empty. To date, more than 300 molecules have already been discovered. Because of the extremely low temperature, the gas-phase chemistry is dominated by barrierless exothermic reactions of radicals and ions. However, several abundant molecules and organic molecules cannot be produced efficiently by gas-phase reactions. To explain the existence of such molecules in the ISM, gas-surface interactions between small molecules and dust particles covered with amorphous solid water (ASW) mantles must be considered. In general, surface processes such as adsorption, diffusion, desorption, and chemical reactions can be linked to the binding energy of molecules to the surface. Hence, a lot of studies have been performed to identify the binding energies of interstellar molecules on ASW surfaces. Cosmic radiation and free electrons may induce a negative charge on the dust particles, and the binding energies may be affected by this charge. In this study, we calculate the binding energies of CO, CH4, and NH3, on neutral and charged ASW surfaces using DFT calculations. Our results indicate that CO can interact with the surface charge, increasing its binding energy. In contrast, the binding energy of CH4 remains unchanged in the presence of surface charge, and that of NH3 typically decreases.

Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and efficiency. In this work, we take a step toward foundation models for chemical reactor modeling by introducing a neural network framework that generalizes across diverse reactor types and rapidly adapts to new chemical processes. Our approach leverages meta-learning to pretrain the model on a broad set of reactor dynamics, enabling efficient adaptation to unseen reactions with minimal data. To further enhance generalizability, we incorporate physics-informed fine-tuning, ensuring physically consistent adaptation to new reactor conditions. Our framework is evaluated across three integer-order fundamental reactor types - continuous stirred tank reactors, batch reactors, and plug flow reactors - demonstrating superior few-shot adaptation compared to conventional data-driven, physics-informed, and transfer learning approaches. By combining meta-learning with physics-informed adaptation, this work lays the foundation for a generalizable modeling framework, advancing the development of foundation models for chemical engineering applications. Source code is available at https://github.com/killingbear999/chemical-reactor-foundation-model.

The paper sets forth comprehensive basics of Discrete Thermodynamics of Chemical Equilibria (DTD), developed by the author during the last decade and spread over series of publications. Based on the linear equations of irreversible thermodynamics, De Donder's definition of the thermodynamic force, and the Le Chatelier principle, DTD brings forward a notion of chemical equilibrium as a balance of internal and external thermodynamic forces, acting against a chemical system. The basic expression of DTD is a logistic map that ties together energetic characteristics of the chemical transformation in the system, its deviation from true thermodynamic equilibrium, and the sum of thermodynamic forces, causing that deviation. System deviation from thermodynamic equilibrium is the major variable of the theory. Solutions to the basic map define the chemical system domain of states comprising bifurcation diagrams with four areas, from true thermodynamic equilibrium to chaos, having specific distinctive meaning for chemical systems. The theory is derived from the currently recognized ideas of chemical thermodynamics and binds classical and contemporary thermodynamics of chemical equilibria into a unique concept. DTD opens new opportunities in understanding and analysis of equilibria in chemical systems. Some new results, included in the paper, have never been published before.

Computational high-throughput virtual screening is essential for identifying redox-active molecules for sustainable applications such as electrochemical carbon capture. A primary challenge in this approach is the high computational cost associated with accurate quantum chemistry calculations. Machine learning foundation potentials (FPs) trained on extensive density functional theory (DFT) calculations offer a computationally efficient alternative. Here, we benchmark the MACE-OMol-0 and UMA FPs against a hierarchy of DFT functionals for predicting experimental molecular redox potentials for both electron transfer (ET) and proton-coupled electron transfer (PCET) reactions. We find that these FPs achieve exceptional accuracy for PCET processes, rivaling their target DFT method. However, the performance is diminished for ET reactions, particularly for multi-electron transfers involving reactive ions that are underrepresented in the OMol25 training data, revealing a key out-of-distribution limitation. To overcome this, we propose an optimal hybrid workflow that uses the FPs for efficient geometry optimization and thermochemical analysis, followed by a crucial single-point DFT energy refinement and an implicit solvation correction. This pragmatic approach provides a robust and scalable strategy for accelerating high-throughput virtual screening in sustainable chemistry.

Spectrum of ^7Li and elastic scattering reaction ^4He(^3H, ^3H)^4He are studied using the unified description of the Gamow shell model in the coupled-channel formulation (GSMCC). The reaction channels are constructed using the cluster expansion with the two mass partitions [^4He + ^3H], [^6Li + n].

Tunnelling reactions of molecules embedded on cryogenic noble-gas matrices are being used in fundamental studies of how reactivity varies with the nature of the supposedly inert matrix as well as pointers to the chemistry occurring in the interstellar medium on ice-grains. To these ends we present chemical kinetic rate constants for the cis to trans isomerisation of seleno-, thio- and monomeric formic acids and that of their three dimeric species, based on multidimensional calculations in the gas-phase, from 10~K to 300~K as a guide to the matrix reactions.

Temporal causal representation learning methods assume that causal mechanisms switch instantaneously between discrete domains, yet real-world systems often exhibit continuous mechanism transitions. For example, a vehicle's dynamics evolve gradually through a turning maneuver, and human gait shifts smoothly from walking to running. We formalize this setting by modeling transitional mechanisms as convex combinations of finitely many atomic mechanisms, governed by time-varying mixing coefficients. Our theoretical contributions establish that both the latent causal variables and the continuous mixing trajectory are jointly identifiable. We further propose TRACE, a Mixture-of-Experts framework where each expert learns one atomic mechanism during training, enabling recovery of mechanism trajectories at test time. This formulation generalizes to intermediate mechanism states never observed during training. Experiments on synthetic and real-world data demonstrate that TRACE recovers mixing trajectories with up to 0.99 correlation, substantially outperforming discrete-switching baselines.

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from being proven. One challenge in engineering and understanding biochemical computation is the intrinsic noise due to chemical fluctuations. In this paper, we draw insights from machine learning theory, chemical reaction network theory, and statistical physics to show that the broad and biologically relevant class of detailed balanced chemical reaction networks is capable of representing and conditioning complex distributions. These results illustrate how a biochemical computer can use intrinsic chemical noise to perform complex computations. Furthermore, we use our explicit physical model to derive thermodynamic costs of inference.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

Rigorous performance evaluation is essential for developing robust algorithms for high-throughput computational chemistry. Traditional benchmarking, however, often struggles to account for system-specific variability, making it difficult to form actionable conclusions. We present a Bayesian hierarchical modeling framework that rigorously quantifies performance metrics and their uncertainty, enabling a nuanced comparison of algorithmic strategies. We apply this framework to analyze the Dimer method, comparing Conjugate Gradient (CG) and L-BFGS rotation optimizers, with and without the removal of external rotations, across a benchmark of 500 molecular systems. Our analysis confirms that CG offers higher overall robustness than L-BFGS in this context. While the theoretically-motivated removal of external rotations led to higher computational cost (>40% more energy and force calls) for most systems in this set, our models also reveal a subtle interplay, hinting that this feature may improve the reliability of the L-BFGS optimizer. Rather than identifying a single superior method, our findings support the design of adaptive "chain of methods" workflows. This work showcases how a robust statistical paradigm can move beyond simple performance rankings to inform the intelligent, context-dependent application of computational chemistry methods.

Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using differentiable simulations (DiffSim) for the discovery and enhanced sampling of chemical transformations without a need to resort to preselected CVs, using only a distance metric. Reaction path discovery and estimation of the biasing potential that enhances the sampling are merged into a single end-to-end problem that is solved by path-integral optimization. This is achieved by introducing multiple improvements over standard DiffSim such as partial backpropagation and graph mini-batching making DiffSim training stable and efficient. The potential of DiffSim is demonstrated in the successful discovery of transition paths for the Muller-Brown model potential as well as a benchmark chemical system - alanine dipeptide.

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added subsequently to that original work, to explore the consequences of the purely statistical point of view. We show how standard methods in the equilibrium theory could have been derived simply from a description of the available problem information. In addition, our presentation leads to novel insights into questions associated with symmetry and non-equilibrium statistical mechanics. Two surprising consequences to be explored in further work are that (in)distinguishability factors are automatically predicted from the problem formulation and that a quantity related to the thermodynamic entropy production is found by considering information loss in non-equilibrium processes. Using the problem of ion channel thermodynamics as an example, we illustrate the idea of building up complexity by successively adding information to create progressively more complex descriptions of a physical system. Our result is that such statistical mechanical descriptions can be used to create transparent, computable, experimentally-relevant models that may be informed by more detailed atomistic simulations. We also derive a theory for the kinetic behavior of this system, identifying the nonequilibrium `process' free energy functional. The Gibbs relation for this functional is a fluctuation-dissipation theorem applicable arbitrarily far from equilibrium, that captures the effect of non-local and time-dependent behavior from transient driving forces. Based on this work, it is clear that statistical mechanics is a general tool for constructing the relationships between constraints on system information.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We characterize its scaling behavior in the macroscopic limit, its performances, and the impact of potential internal delays. We obtain analytical expressions for all quantities of interest, namely, the generated reverse chemical current, the output power, the transduction efficiency, and the correlations between the numbers of molecules. Due to a bound on the nonequilibrium response of its chemical reaction network, we find that, contrary to the electronic case, there is no way for the Maxwell demon to generate a finite output in the macroscopic limit. Finally, we analyze the information thermodynamics of the Maxwell demon from a bipartite perspective. In the limit of a fast demon, the information flow is obtained, its pattern in the state space is discussed, and the behavior of the partial efficiencies related to the measurement and the feedback processes is examined.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Light-matter interactions that lead to nonthermal changes in size of the sample constitute a photostrictive effect in many compounds. The photostriction phenomenon was observed in four main groups of materials, ferroelectrics, polar, and non-polar semiconductors, as well as in organic-based materials that are reviewed here. The key mechanisms of photostriction and its dependence on several parameters and perturbations are assessed. The major literature of the photostriction is surveyed, and the review ends with a summary of the proposed technical applications.

High-throughput reaction condition (RC) screening is fundamental to chemical synthesis. However, current RC screening suffers from laborious and costly trial-and-error workflows. Traditional computer-aided synthesis planning (CASP) tools fail to find suitable RCs due to data sparsity and inadequate reaction representations. Nowadays, large language models (LLMs) are capable of tackling chemistry-related problems, such as molecule design, and chemical logic Q\&A tasks. However, LLMs have not yet achieved accurate predictions of chemical reaction conditions. Here, we present MM-RCR, a text-augmented multimodal LLM that learns a unified reaction representation from SMILES, reaction graphs, and textual corpus for chemical reaction recommendation (RCR). To train MM-RCR, we construct 1.2 million pair-wised Q\&A instruction datasets. Our experimental results demonstrate that MM-RCR achieves state-of-the-art performance on two open benchmark datasets and exhibits strong generalization capabilities on out-of-domain (OOD) and High-Throughput Experimentation (HTE) datasets. MM-RCR has the potential to accelerate high-throughput condition screening in chemical synthesis.

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes when it folds. Understanding protein kinetics is essential as a protein needs to fold correctly for it to perform its biological functions optimally, and a misfolded protein can sometimes be contorted into shapes that are not ideal for a cellular environment giving rise to many degenerative, neuro-degenerative disorders and amyloid diseases. Monitoring at-risk individuals and detecting protein discrepancies in a protein's folding kinetics at the early stages could majorly result in public health benefits, as preventive measures can be taken. This research proposes an efficient pipeline for predicting protein folding kinetics with high accuracy and low memory footprint. The deployed machine learning (ML) model outperformed the state-of-the-art ML models by 4.8% in terms of accuracy while consuming 327x lesser memory and being 7.3% faster.

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source post-processing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures, in both strong confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture, built with `nix`, employing a `YAML`-`Lua` scripting pipeline. The software has been designed to be user-friendly and easy to extend. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogenous ice nucleation on a silver-exposed beta-AgI surface, homogenous ice nucleation, flat monolayer square ice formation and freezing of an ice nanotube.

Fundamental experimental measurements of quantities such as ignition delay times, laminar flame speeds, and species profiles (among others) serve important roles in understanding fuel chemistry and validating chemical kinetic models. However, despite both the importance and abundance of such information in the literature, the community lacks a widely adopted standard format for this data. This impedes both sharing and wide use by the community. Here we introduce a new chemical kinetics experimental data format, ChemKED, and the related Python-based package for validating and working with ChemKED-formatted files called PyKED. We also review past and related efforts, and motivate the need for a new solution. ChemKED currently supports the representation of autoignition delay time measurements from shock tubes and rapid compression machines. ChemKED-formatted files contain all of the information needed to simulate experimental data points, including the uncertainty of the data. ChemKED is based on the YAML data serialization language, and is intended as a human- and machine-readable standard for easy creation and automated use. Development of ChemKED and PyKED occurs openly on GitHub under the BSD 3-clause license, and contributions from the community are welcome. Plans for future development include support for experimental data from laminar flame, jet stirred reactor, and speciation measurements.

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 46% on molecular tasks and 66% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery.

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains underexplored. Here, we introduce RxnBench, a multi-tiered benchmark designed to rigorously evaluate MLLMs on chemical reaction understanding from scientific PDFs. RxnBench comprises two tasks: Single-Figure QA (SF-QA), which tests fine-grained visual perception and mechanistic reasoning using 1,525 questions derived from 305 curated reaction schemes, and Full-Document QA (FD-QA), which challenges models to synthesize information from 108 articles, requiring cross-modal integration of text, schemes, and tables. Our evaluation of MLLMs reveals a critical capability gap: while models excel at extracting explicit text, they struggle with deep chemical logic and precise structural recognition. Notably, models with inference-time reasoning significantly outperform standard architectures, yet none achieve 50\% accuracy on FD-QA. These findings underscore the urgent need for domain-specific visual encoders and stronger reasoning engines to advance autonomous AI chemists.

Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for zero-shot inference of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observation process. Second, a neural network model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that one and the same (pretrained) model can infer, in a zero-shot fashion, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are finetuned to the target datasets.

Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes without pre-specifying catalytic residues. We introduce DISCO (DIffusion for Sequence-structure CO-design), a multimodal model that co-designs protein sequence and 3D structure around arbitrary biomolecules, as well as inference-time scaling methods that optimize objectives across both modalities. Conditioned solely on reactive intermediates, DISCO designs diverse heme enzymes with novel active-site geometries. These enzymes catalyze new-to-nature carbene-transfer reactions, including alkene cyclopropanation, spirocyclopropanation, B-H, and C(sp^3)-H insertions, with high activities exceeding those of engineered enzymes. Random mutagenesis of a selected design further confirmed that enzyme activity can be improved through directed evolution. By providing a scalable route to evolvable enzymes, DISCO broadens the potential scope of genetically encodable transformations. Code is available at https://github.com/DISCO-design/DISCO.

Field evaporation from ionic or covalently bonded materials often leads to the emission of molecular ions. The metastability of these molecular ions, particularly under the influence of the intense electrostatic field (1010 Vm-1), makes them prone to dissociation with or without an exchange of energy amongst them. These processes can affect the analytical performance of atom probe tomography (APT). For instance, neutral species formed through dissociation may not be detected at all or with a time of flight no longer related to their mass, causing their loss from the analysis. Here, we evaluated the changes in the measured composition of FeO, Fe2O3 and Fe3O4 across a wide range of analysis conditions. Possible dissociation reactions are predicted by density-functional theory (DFT) calculations considering the spin states of the molecules. The energetically favoured reactions are traced on to the multi-hit ion correlation histograms, to confirm their existence within experiments, using an automated Python-based routine. The detected reactions are carefully analysed to reflect upon the influence of these neutrals from dissociation reactions on the performance of APT for analysing iron oxides.

Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation problem, where the typical SMILES is adopted for molecule representations. However, the general-purpose SMILES neglects the characteristics of chemical reactions, where the molecular graph topology is largely unaltered from reactants to products, resulting in the suboptimal performance of SMILES if straightforwardly applied. In this article, we propose the root-aligned SMILES (R-SMILES), which specifies a tightly aligned one-to-one mapping between the product and the reactant SMILES for more efficient synthesis prediction. Due to the strict one-to-one mapping and reduced edit distance, the computational model is largely relieved from learning the complex syntax and dedicated to learning the chemical knowledge for reactions. We compare the proposed R-SMILES with various state-of-the-art baselines and show that it significantly outperforms them all, demonstrating the superiority of the proposed method.

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.

Large-scale chemical reaction datasets are crucial for AI research in chemistry. However, existing chemical reaction data often exist as images within papers, making them not machine-readable and unusable for training machine learning models. In response to this challenge, we propose the RxnCaption framework for the task of chemical Reaction Diagram Parsing (RxnDP). Our framework reformulates the traditional coordinate prediction driven parsing process into an image captioning problem, which Large Vision Language Models (LVLMs) handle naturally. We introduce a strategy termed BBox and Index as Visual Prompt (BIVP), which uses our state-of-the-art molecular detector, MolYOLO, to pre-draw molecular bounding boxes and indices directly onto the input image. This turns the downstream parsing into a natural-language description problem. Extensive experiments show that the BIVP strategy significantly improves structural extraction quality while simplifying model design. We further construct the RxnCaption-15k dataset, an order of magnitude larger than prior real-world literature benchmarks, with a balanced test subset across four layout archetypes. Experiments demonstrate that RxnCaption-VL achieves state-of-the-art performance on multiple metrics. We believe our method, dataset, and models will advance structured information extraction from chemical literature and catalyze broader AI applications in chemistry. We will release data, models, and code on GitHub.

[Abridged] This review paper discussed which chemical effects may be at play in a planet-forming disk midplane, which effects are relevant under different conditions, and which tools are available for modelling chemical kinetics in a disk midplane. The review goes on to discuss some important efforts in the planet formation modelling community to treat chemical evolution, and, vice versa, efforts in the chemical modelling community to implement more physical effects related to planet formation into the chemical modelling. The aim of this review is both to outline some concepts related to planet formation chemistry, but also to encourage, not just collaboration between the planet formation modelling community and the astrochemical community, but also assistance and guidance from one community to the other. Guidance, regarding which effects, out of many, might be more relevant than others under certain planet formation conditions, and regarding why certain included effects lead to certain important modelling outcomes. As the research fields of exoplanet atmospheres and protoplanetary disks near new frontiers in observational insights with upcoming facilities, developing appropriate modelling frameworks (including physical and chemical effects) is paramount to ultimately enable the linking of a chemically characterised exoplanet atmospheres to its formation history in its natal protoplanetary disk.

Large language models (LLMs) have recently demonstrated promising capabilities in chemistry tasks while still facing challenges due to outdated pretraining knowledge and the difficulty of incorporating specialized chemical expertise. To address these issues, we propose an LLM-based agent that synergistically integrates 137 external chemical tools created ranging from basic information retrieval to complex reaction predictions, and a dataset curation pipeline to generate the dataset ChemToolBench that facilitates both effective tool selection and precise parameter filling during fine-tuning and evaluation. We introduce a Hierarchical Evolutionary Monte Carlo Tree Search (HE-MCTS) framework, enabling independent optimization of tool planning and execution. By leveraging self-generated data, our approach supports step-level fine-tuning (FT) of the policy model and training task-adaptive PRM and ORM that surpass GPT-4o. Experimental evaluations demonstrate that our approach significantly improves performance in Chemistry QA and discovery tasks, offering a robust solution to integrate specialized tools with LLMs for advanced chemical applications. All datasets and code are available at https://github.com/AI4Chem/ChemistryAgent .

We study the problem of the transformation of a given reactant species into an immiscible product species, as they flow through a chemically active porous medium. We derive the equation governing the evolution of the volume fraction of the species -- in a one-dimensional macroscopic description --, identify the relevant dimensionless numbers, and provide simple models for capillary pressure and relative permeabilities, which are quantities of crucial importance when tackling multiphase flows in porous media. We set the domain of validity of our models and discuss the importance of viscous coupling terms in the extended Darcy's law. We investigate numerically the steady regime and demonstrate that the spatial transformation rate of the species along the reactor is non-monotonous, as testified by the existence of an inflection point in the volume fraction profiles. We obtain the scaling of the location of this inflection point with the dimensionless lengths of the problem. Eventually, we provide key elements for optimization of the reactor.

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.

We study the self-diffusiophoresis of a spherical chemically active particle near a planar, impermeable wall, with a focus on the influence of particle orientation on propulsion. We analyze a Janus particle with asymmetric surface chemical activity, consisting of a small inert region within a catalytically active cap. While numerical simulations have been used to study such particles, they encounter difficulties resolving the flow and transport in the extreme near-wall regime due to geometric confinement and steep solute concentration gradients. We address this limitation through an asymptotic analysis in the near-contact limit, where the gap between the particle and the wall is narrow. In particular, we consider the distinguished limit in which the inert region is asymptotically comparable in size to the lubrication region. We analyze an axisymmetric configuration in which the inert face is oriented parallel to the wall and extend the analysis to slightly tilted orientations. We find that the capsize determines whether a tilted particle rotates back toward the axisymmetric state or continues to reorient, thereby characterizing its rotational stability in the near-contact regime.

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

Aromaticity is a common chemical functionalities in bioactive molecules. In interstellar and circumstellar environments benzene and other small aromatics are considered the precursor for more complex prebiotic molecules and they have shown to potentially have rich ice-phase photochemistry. The availability of small organic molecules in prebiotic networks depends on their photostability in astrophysical environments preceding planet formation, particularly during the protoplanetary disk stage, as the disk composition is linked to the chemical make-up of planets and planetesimals. We study the ultraviolet (UV) photodestruction (120-160 nm) of five aromatic molecules in undiluted ices and, for selected cases, in astrophysically relevant ice matrices (H2O, CO, CO2). For each ice, we measure the destruction cross sections as a function of photon exposure. In undiluted ices, aromatic molecules exhibit substantially lower photodestruction cross sections (sigma < 10-19 cm2) than aliphatic hydrocarbons, including cyclohexane, (sigma = 2.8-4x10-18 cm2). Furthermore, neither substituent nature nor size affects the aromatic stability in pure ices, suggesting that the strong intermolecular interactions among aromatic molecules provide protection against VUV exposure, even with small to mid-sized ring substituents. In mixed ices, the photodestruction and reactivity of aromatic molecules (sigma = 2.5-6.1x10-18 cm2) increases by more than an order of magnitude, but are still lower than in the gas-phase. We attribute this to a weaker cage effect and matrix-specific interactions. We use the experimental photodestruction cross sections to estimate the lifetime of aromatic molecules in protoplanetary disks, denileating the disks regions in which aromatic photochemistry is expected to be the most active.

Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular dynamics and miss thermodynamically relevant modes. Inspired by enhanced sampling, we encourage exploration by introducing a sequential bias along bespoke, information-rich, low-dimensional projections of atomic coordinates known as collective variables (CVs). We introduce a repulsive potential centered on the CVs from recent samples, which pushes future samples towards novel CV regions and effectively increases the temperature in the projected space. Our resulting method improves efficiency, mode discovery, enables the estimation of free energy differences, and retains independent sampling from the approximate Boltzmann distribution via reweighting by the bias. On standard peptide conformational sampling benchmarks, the method recovers diverse conformational states and accurate free energy profiles. We are the first to demonstrate reactive sampling using a diffusion-based sampler, capturing bond breaking and formation with universal interatomic potentials at near-first-principles accuracy. The approach resolves reactive energy landscapes at a fraction of the wall-clock time of standard sampling methods, advancing diffusion-based sampling towards practical use in molecular sciences.

Many environmental remediation and energy applications (conversion and storage) for sustainability need design and development of green novel materials. Discovery processes of such novel materials are time taking and cumbersome due to large number of possible combinations and permutations of materials structures. Often theoretical studies based on Density Functional Theory (DFT) and other theories, coupled with Simulations are conducted to narrow down sample space of candidate materials, before conducting laboratory-based synthesis and analytical process. With the emergence of artificial intelligence (AI), AI techniques are being tried in this process too to ease out simulation time and cost. However tremendous values of previously published research from various parts of the world are still left as labor-intensive manual effort and discretion of individual researcher and prone to human omissions. AIMS-EREA is our novel framework to blend best of breed of Material Science theory with power of Generative AI to give best impact and smooth and quickest discovery of material for sustainability. This also helps to eliminate the possibility of production of hazardous residues and bye-products of the reactions. AIMS-EREA uses all available resources -- Predictive and Analytical AI on large collection of chemical databases along with automated intelligent assimilation of deep materials knowledge from previously published research works through Generative AI. We demonstrate use of our own novel framework with an example, how this framework can be successfully applied to achieve desired success in development of thermoelectric material for waste heat conversion.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Effectively leveraging data from multiple quantum-chemical methods is essential for building machine-learned force fields (MLFFs) that are applicable to a wide range of chemical systems. This study systematically investigates two multi-fidelity training strategies, pre-training/fine-tuning and multi-headed training, to elucidate the mechanisms underpinning their success. We identify key factors driving the efficacy of pre-training followed by fine-tuning, but find that internal representations learned during pre-training are inherently method-specific, requiring adaptation of the model backbone during fine-tuning. Multi-headed models offer an extensible alternative, enabling simultaneous training on multiple fidelities. We demonstrate that a multi-headed model learns method-agnostic representations that allow for accurate predictions across multiple label sources. While this approach introduces a slight accuracy compromise compared to sequential fine-tuning, it unlocks new cost-efficient data generation strategies and paves the way towards developing universal MLFFs.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

Simulating atomic-scale processes, such as protein dynamics and catalytic reactions, is crucial for advancements in biology, chemistry, and materials science. Machine learning force fields (MLFFs) have emerged as powerful tools that achieve near quantum mechanical accuracy, with promising generalization capabilities. However, their practical use is often limited by long inference times compared to classical force fields, especially when running extensive molecular dynamics (MD) simulations required for many biological applications. In this study, we introduce BoostMD, a surrogate model architecture designed to accelerate MD simulations. BoostMD leverages node features computed at previous time steps to predict energies and forces based on positional changes. This approach reduces the complexity of the learning task, allowing BoostMD to be both smaller and significantly faster than conventional MLFFs. During simulations, the computationally intensive reference MLFF is evaluated only every N steps, while the lightweight BoostMD model handles the intermediate steps at a fraction of the computational cost. Our experiments demonstrate that BoostMD achieves an eight-fold speedup compared to the reference model and generalizes to unseen dipeptides. Furthermore, we find that BoostMD accurately samples the ground-truth Boltzmann distribution when running molecular dynamics. By combining efficient feature reuse with a streamlined architecture, BoostMD offers a robust solution for conducting large-scale, long-timescale molecular simulations, making high-accuracy ML-driven modeling more accessible and practical.

Approximations based on moment-closure (MA) are commonly used to obtain estimates of the mean molecule numbers and of the variance of fluctuations in the number of molecules of chemical systems. The advantage of this approach is that it can be far less computationally expensive than exact stochastic simulations of the chemical master equation. Here we numerically study the conditions under which the MA equations yield results reflecting the true stochastic dynamics of the system. We show that for bistable and oscillatory chemical systems with deterministic initial conditions, the solution of the MA equations can be interpreted as a valid approximation to the true moments of the CME, only when the steady-state mean molecule numbers obtained from the chemical master equation fall within a certain finite range. The same validity criterion for monostable systems implies that the steady-state mean molecule numbers obtained from the chemical master equation must be above a certain threshold. For mean molecule numbers outside of this range of validity, the MA equations lead to either qualitatively wrong oscillatory dynamics or to unphysical predictions such as negative variances in the molecule numbers or multiple steady-state moments of the stationary distribution as the initial conditions are varied. Our results clarify the range of validity of the MA approach and show that pitfalls in the interpretation of the results can only be overcome through the systematic comparison of the solutions of the MA equations of a certain order with those of higher orders.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD by providing inexpensive predictions of the forces, but they remain constrained to minuscule time integration steps, which are required by the fast time scale of atomic motion. In this work, we propose FlashMD, a method to predict the evolution of positions and momenta over strides that are between one and two orders of magnitude longer than typical MD time steps. We incorporate considerations on the mathematical and physical properties of Hamiltonian dynamics in the architecture, generalize the approach to allow the simulation of any thermodynamic ensemble, and carefully assess the possible failure modes of such a long-stride MD approach. We validate FlashMD's accuracy in reproducing equilibrium and time-dependent properties, using both system-specific and general-purpose models, extending the ability of MD simulation to reach the long time scales needed to model microscopic processes of high scientific and technological relevance.

The independent atom ansatz of density functional theory yields an accurate analytical expression for dynamic correlation energy in the H_{2} molecule: E_{c} = 0.5(1 - 2)(ab|ba) for the atom-additive self-consistent density rho = |a|^{2} + |b|^{2}. Combined with exact atomic self-exchange, it recovers more than 99.5 % of nearly exact SCAN exchange-correlation energy at R > 0.5 A, differing by less than 0.12 eV. The total energy functional correctly dissociates the H-H bond and yields absolute errors of 0.002 A, 0.19 eV, and 13 cm^{-1} relative to experiment at the tight binding computational cost. The chemical bond formation is attributed to the asymptotic Heitler-London resonance of quasi-orthogonal atomic states (- (ab|ba)) with no contributions from kinetic energy or charge accumulation in the bond.

Modern optimization in experimental chemistry employs algorithmic search through black-box parameter spaces. Here we demonstrate that pre-trained knowledge in large language models (LLMs) fundamentally changes this paradigm. Using six fully enumerated categorical reaction datasets (768 - 5,684 experiments), we benchmark LLM-guided optimization (LLM-GO) against Bayesian optimization (BO) and random sampling. Frontier LLMs consistently match or exceed BO performance across five single-objective datasets, with advantages growing as parameter complexity increases and high-performing conditions become scarce (<5% of space). BO retains superiority only for explicit multi-objective trade-offs. To understand these contrasting behaviors, we introduce a topology-agnostic information theory framework quantifying sampling diversity throughout optimization campaigns. This analysis reveals that LLMs maintain systematically higher exploration entropy than BO across all datasets while achieving superior performance, with advantages most pronounced in solution-scarce parameter spaces where high-entropy exploration typically fails - suggesting that pre-trained domain knowledge enables more effective navigation of chemical parameter space rather than replacing structured exploration strategies. To enable transparent benchmarking and community validation, we release Iron Mind (https://gomes.andrew.cmu.edu/iron-mind), a no-code platform for side-by-side evaluation of human, algorithmic, and LLM optimization campaigns with public leaderboards and complete trajectories. Our findings establish that LLM-GO excels precisely where traditional methods struggle: complex categorical spaces requiring domain understanding rather than mathematical optimization.

We prove stability for a class of heterogeneous catalysis models in the L_p-setting. We consider a setting in a finite three-dimensional pore of cylinder-like geometry, with the lateral walls acting as a catalytic surface. Under a reasonable condition on the involved parameters, we show that given equilibria are normally stable, i.e. solutions are attracted at an exponential rate. The potential incidence of instability is discussed as well.

Graph neural networks (GNNs) are one of the most popular research topics for deep learning. GNN methods typically have been designed on top of the graph signal processing theory. In particular, diffusion equations have been widely used for designing the core processing layer of GNNs, and therefore they are inevitably vulnerable to the notorious oversmoothing problem. Recently, a couple of papers paid attention to reaction equations in conjunctions with diffusion equations. However, they all consider limited forms of reaction equations. To this end, we present a reaction-diffusion equation-based GNN method that considers all popular types of reaction equations in addition to one special reaction equation designed by us. To our knowledge, our paper is one of the most comprehensive studies on reaction-diffusion equation-based GNNs. In our experiments with 9 datasets and 28 baselines, our method, called GREAD, outperforms them in a majority of cases. Further synthetic data experiments show that it mitigates the oversmoothing problem and works well for various homophily rates.

Applying the method of moments to the chemical master equation (CME) appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using moment-based semidefinite programs (SDPs). In particular, they showed that moment-based SDPs can be used to calculate rigorous bounds on various descriptions of the stochastic chemical kinetic system's stationary distribution(s) -- for example, mean molecular counts, variances in these counts, and so on. In this paper, we show that these ideas can be extended to the corresponding dynamic problem, calculating time-varying bounds on the same descriptions.

We describe and analyse Levenberg-Marquardt methods for solving systems of nonlinear equations. More specifically, we propose an adaptive formula for the Levenberg-Marquardt parameter and analyse the local convergence of the method under Hölder metric subregularity of the function defining the equation and Hölder continuity of its gradient mapping. Further, we analyse the local convergence of the method under the additional assumption that the Łojasiewicz gradient inequality holds. We finally report encouraging numerical results confirming the theoretical findings for the problem of computing moiety conserved steady states in biochemical reaction networks. This problem can be cast as finding a solution of a system of nonlinear equations, where the associated mapping satisfies the Łojasiewicz gradient inequality assumption.

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We introduce Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), an active learning framework where large language models autonomously design, execute, and interpret atomistic simulations. In MASTER, a multimodal system translates natural language into density functional theory workflows, while higher-level reasoning agents guide discovery through a hierarchy of strategies, including a single agent baseline and three multi-agent approaches: peer review, triage-ranking, and triage-forms. Across two chemical applications, CO adsorption on Cu-surface transition metal (M) adatoms and on M-N-C catalysts, reasoning-driven exploration reduces required atomistic simulations by up to 90% relative to trial-and-error selection. Reasoning trajectories reveal chemically grounded decisions that cannot be explained by stochastic sampling or semantic bias. Altogether, multi-agent collaboration accelerates materials discovery and marks a new paradigm for autonomous scientific exploration.

We show how to extract from a sufficiently long time series of stationary fluctuations of chemical reactions an estimate of the entropy production. This method, which is based on recent work on fluctuation theorems, is direct, non-invasive, does not require any knowledge about the underlying dynamics, and is applicable even when only partial information is available. We apply it to simple stochastic models of chemical reactions involving a finite number of states, and for this case, we study how the estimate of dissipation is affected by the degree of coarse-graining present in the input data.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

Despite deep learning's success in chemistry, its impact is hindered by a lack of interpretability and an inability to resolve activity cliffs, where minor structural nuances trigger drastic property shifts. Current representation learning, bound by the similarity principle, often fails to capture these structural-activity discontinuities. To address this, we introduce MolEvolve, an evolutionary framework that reformulates molecular discovery as an autonomous, look-ahead planning problem. Unlike traditional methods that depend on human-engineered features or rigid prior knowledge, MolEvolve leverages a Large Language Model (LLM) to actively explore and evolve a library of executable chemical symbolic operations. By utilizing the LLM to cold start and an Monte Carlo Tree Search (MCTS) engine for test-time planning with external tools (e.g. RDKit), the system self-discovers optimal trajectories autonomously. This process evolves transparent reasoning chains that translate complex structural transformations into actionable, human-readable chemical insights. Experimental results demonstrate that MolEvolve's autonomous search not only evolves transparent, human-readable chemical insights, but also outperforms baselines in both property prediction and molecule optimization tasks.

Hiding an object in a chemical gradient requires to suppress the distortions it would naturally cause on it. To do so, we propose a strategy based on coating the object with a chemical reaction-diffusion network which can act as an active cloaking device. By controlling the concentration of some species in its immediate surrounding, the chemical reactions redirect the gradient as if the object was not there. We also show that a substantial fraction of the energy required to cloak can be extracted from the chemical gradient itself.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds (1fs=10^{-15}s). MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD. Furthermore, new MD simulations need to be performed for each molecular system studied. We present Timewarp, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of 10^{5} - 10^{6}:fs. Crucially, Timewarp is transferable between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD. Our method constitutes an important step towards general, transferable algorithms for accelerating MD.

Traditional AI methods often rely on task-specific model designs and training, which constrain both the scalability of model size and generalization across different tasks. Here, we introduce ChemFM, a large foundation model specifically developed for chemicals. By conducting a series of scaling experiments, we identify UniChem as the informative molecular database for pre-training the foundation model. ChemFM comprises 3 billion parameters and is pre-trained on 178 million molecules using self-supervised causal language modeling to extract generalizable molecular representations. This model can be adapted to diverse downstream chemical applications using either full-parameter or parameter-efficient fine-tuning methods. ChemFM consistently outperforms state-of-the-art task-specific AI models across all tested tasks. Notably, it achieves up to 67.48% performance improvement across 34 property prediction benchmarks, up to 33.80% reduction in mean average deviation between conditioned and actual properties of generated molecules in conditional molecular generation tasks, and up to 3.7% top-1 accuracy improvement across 4 reaction prediction datasets. Moreover, ChemFM demonstrates its superior performance in predicting antibiotic activity and cytotoxicity, highlighting its potential to advance the discovery of novel antibiotics. Furthermore, we demonstrate that, as a foundation model, ChemFM exhibits strong data efficiency, requiring significantly fewer labeled training samples to achieve state-of-the-art performance. We anticipate that ChemFM will significantly advance chemistry research by providing a foundation model capable of effectively generalizing across a broad range of tasks with minimal additional training.

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer and polarization effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding charge transfer (CT) and polarization (POL). Furthermore, we present an open-source parameterization tool, called FFAFFURR that enables the (system specific) parameterization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a Zinc finger protein.

Recurrent neural networks (RNNs) provide a powerful approach in neuroscience to infer latent dynamics in neural populations and to generate hypotheses about the neural computations underlying behavior. However, past work has focused on relatively simple, input-driven, and largely deterministic behaviors - little is known about the mechanisms that would allow RNNs to generate the richer, spontaneous, and potentially stochastic behaviors observed in natural settings. Modeling with Hidden Markov Models (HMMs) has revealed a segmentation of natural behaviors into discrete latent states with stochastic transitions between them, a type of dynamics that may appear at odds with the continuous state spaces implemented by RNNs. Here we first show that RNNs can replicate HMM emission statistics and then reverse-engineer the trained networks to uncover the mechanisms they implement. In the absence of inputs, the activity of trained RNNs collapses towards a single fixed point. When driven by stochastic input, trajectories instead exhibit noise-sustained dynamics along closed orbits. Rotation along these orbits modulates the emission probabilities and is governed by transitions between regions of slow, noise-driven dynamics connected by fast, deterministic transitions. The trained RNNs develop highly structured connectivity, with a small set of "kick neurons" initiating transitions between these regions. This mechanism emerges during training as the network shifts into a regime of stochastic resonance, enabling it to perform probabilistic computations. Analyses across multiple HMM architectures - fully connected, cyclic, and linear-chain - reveal that this solution generalizes through the modular reuse of the same dynamical motif, suggesting a compositional principle by which RNNs can emulate complex discrete latent dynamics.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Transformers demonstrate impressive performance on a range of reasoning benchmarks. To evaluate the degree to which these abilities are a result of actual reasoning, existing work has focused on developing sophisticated benchmarks for behavioral studies. However, these studies do not provide insights into the internal mechanisms driving the observed capabilities. To improve our understanding of the internal mechanisms of transformers, we present a comprehensive mechanistic analysis of a transformer trained on a synthetic reasoning task. We identify a set of interpretable mechanisms the model uses to solve the task, and validate our findings using correlational and causal evidence. Our results suggest that it implements a depth-bounded recurrent mechanisms that operates in parallel and stores intermediate results in selected token positions. We anticipate that the motifs we identified in our synthetic setting can provide valuable insights into the broader operating principles of transformers and thus provide a basis for understanding more complex models.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Facing with grave climate change and enormous energy demand, catalyzer gets more and more important due to its significant effect on reducing fossil fuels consumption. Hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) by water splitting are feasible ways to produce clean sustainable energy. Here we systematically explored atomic structures and related STM images of Se defects in PtSe2. The equilibrium fractions of vacancies under variable conditions were detailly predicted. Besides, we found the vacancies are highly kinetic stable, without recovering or aggregation. The Se vacancies in PtSe2 can dramatically enhance the HER performance, comparing with, even better than Pt(111). Beyond, we firstly revealed that PtSe2 monolayer with Se vacancies is also a good OER catalyst. The excellent bipolar catalysis of Se vacancies were further confirmed by experimental measurements. We produced defective PtSe2 by direct selenization of Pt foil at 773 K using a CVD process. Then we observed the HER and OER performance of defective PtSe2 is much highly efficient than Pt foils by a series of measurements. Our work with compelling theoretical and experimental studies indicates PtSe2 with Se defects is an ideal bipolar candidate for HER and OER.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

Polymer membranes are typically assumed to be inert and nonresponsive to the flux and density of the permeating particles in transport processes. Here, we study theoretically the consequences of membrane responsiveness and feedback on the steady-state force--flux relations and membrane permeability using a nonlinear-feedback solution-diffusion model of transport through a slab-like membrane. Therein, the solute concentration inside the membrane depends on the bulk concentration, c_0, the driving force, f, and the polymer volume fraction, phi. In our model, solute accumulation in the membrane causes a sigmoidal volume phase transition of the polymer, changing its permeability, which, in return, affects the membrane's solute uptake. This feedback leads to nonlinear force--flux relations, j(f), which we quantify in terms of the system's differential permeability, P_sys^{Delta}mathrm{dj}/{df}. We find that the membrane feedback can increase or decrease the solute flux by orders of magnitude, triggered by a small change in the driving force, and largely tunable by attractive versus repulsive solute--membrane interactions. Moreover, controlling the input, c_0 and f, can lead to steady-state bistability of phi and hysteresis in the force--flux relations. This work advocates that the fine-tuning of the membrane's chemo-responsiveness will enhance the nonlinear transport control features, providing great potential for future (self-)regulating membrane devices.

Drug-protein binding and dissociation dynamics are fundamental to understanding molecular interactions in biological systems. While many tools for drug-protein interaction studies have emerged, especially artificial intelligence (AI)-based generative models, predictive tools on binding/dissociation kinetics and dynamics are still limited. We propose a novel research paradigm that combines molecular dynamics (MD) simulations, enhanced sampling, and AI generative models to address this issue. We propose an enhanced sampling strategy to efficiently implement the drug-protein dissociation process in MD simulations and estimate the free energy surface (FES). We constructed a program pipeline of MD simulations based on this sampling strategy, thus generating a dataset including 26,612 drug-protein dissociation trajectories containing about 13 million frames. We named this dissociation dynamics dataset DD-13M and used it to train a deep equivariant generative model UnbindingFlow, which can generate collision-free dissociation trajectories. The DD-13M database and UnbindingFlow model represent a significant advancement in computational structural biology, and we anticipate its broad applicability in machine learning studies of drug-protein interactions. Our ongoing efforts focus on expanding this methodology to encompass a broader spectrum of drug-protein complexes and exploring novel applications in pathway prediction.

Scalable and cost-effective solutions to renewable energy storage are essential to addressing the world's rising energy needs while reducing climate change. As we increase our reliance on renewable energy sources such as wind and solar, which produce intermittent power, storage is needed to transfer power from times of peak generation to peak demand. This may require the storage of power for hours, days, or months. One solution that offers the potential of scaling to nation-sized grids is the conversion of renewable energy to other fuels, such as hydrogen or methane. To be widely adopted, this process requires cost-effective solutions to running electrochemical reactions. An open challenge is finding low-cost electrocatalysts to drive these reactions at high rates. Through the use of quantum mechanical simulations (density functional theory), new catalyst structures can be tested and evaluated. Unfortunately, the high computational cost of these simulations limits the number of structures that may be tested. The use of machine learning may provide a method to efficiently approximate these calculations, leading to new approaches in finding effective electrocatalysts. In this paper, we provide an introduction to the challenges in finding suitable electrocatalysts, how machine learning may be applied to the problem, and the use of the Open Catalyst Project OC20 dataset for model training.

Generating molecules that satisfy precise numeric constraints over multiple physicochemical properties is critical and challenging. Although large language models (LLMs) are expressive, they struggle with precise multi-objective control and numeric reasoning without external structure and feedback. We introduce M olGen, a fragment-level, retrieval-augmented, two-stage framework for molecule generation under multi-property constraints. Stage I : Prototype generation: a multi-agent reasoner performs retrieval-anchored, fragment-level edits to produce a candidate near the feasible region. Stage II : RL-based fine-grained optimization: a fragment-level optimizer trained with Group Relative Policy Optimization (GRPO) applies one- or multi-hop refinements to explicitly minimize the property errors toward our target while regulating edit complexity and deviation from the prototype. A large, automatically curated dataset with reasoning chains of fragment edits and measured property deltas underpins both stages, enabling deterministic, reproducible supervision and controllable multi-hop reasoning. Unlike prior work, our framework better reasons about molecules by leveraging fragments and supports controllable refinement toward numeric targets. Experiments on generation under two sets of property constraints (QED, LogP, Molecular Weight and HOMO, LUMO) show consistent gains in validity and precise satisfaction of multi-property targets, outperforming strong LLMs and graph-based algorithms.

The two-body problem of variational electrodynamics possesses differential-delay equations of motion with state-dependent delays of neutral type and solutions that can have velocity discontinuities on countable sets. From a periodic orbit possessing some mild properties at breaking points, we define a synchronization function in R x R3, which is further used to construct two bounded oscillatory functions vanishing at breaking points and whose first derivatives are continuous and defined everywhere but at breaking points. The oscillatory functions are associated with a PDE identity in H2(R3), and we postulate ordering conditions for the PDE identity to define a Fredholm-Schroedinger operator with an O(1/r2) spin-orbit forcing term belonging to L2(R3). As an application, we introduce the Chemical Principle criterion to select orbits with asymptotically vanishing far-fields and estimate the Bohr radius parameter of the Fredholm-Schroedinger PDE using the boundary-layer of orbits chosen according to the Chemical Principle criterion. Last, working backward, we derive a Chemical Principle-like condition from the ordering conditions.