Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep learning (DL) alternatives ignore key intermediates and mechanistic steps and often suffer from hallucinations. We present DeepMech, an interpretable graph-based DL framework employing atom- and bond-level attention, guided by generalized templates of mechanistic operations (TMOps), to generate CRMs. Trained on our curated ReactMech dataset (~30K CRMs with 100K atom-mapped and mass-balanced elementary steps), DeepMech achieves 98.98+/-0.12% accuracy in predicting elementary steps and 95.94+/-0.21% in complete CRM tasks, besides maintaining high fidelity even in out-of-distribution scenarios as well as in predicting side and/or byproducts. Extension to multistep CRMs relevant to prebiotic chemistry, demonstrates the ability of DeepMech in effectively reconstructing 2 pathways from simple primordial substrates to complex biomolecules such as serine and aldopentose. Attention analysis identifies reactive atoms/bonds in line with chemical intuition, rendering our model interpretable and suitable for reaction design.

Transition states (TSs) are crucial for understanding reaction mechanisms, yet their exploration is limited by the complexity of experimental and computational approaches. Here we propose TS-DFM, a flow matching framework that predicts TSs from reactants and products. By operating in molecular distance geometry space, TS-DFM explicitly captures the dynamic changes of interatomic distances in chemical reactions. A network structure named TSDVNet is designed to learn the velocity field for generating TS geometries accurately. On the benchmark dataset Transition1X, TS-DFM outperforms the previous state-of-the-art method React-OT by 30\% in structural accuracy. These predicted TSs provide high-quality initial structures, accelerating the convergence of CI-NEB optimization. Additionally, TS-DFM can identify alternative reaction paths. In our experiments, even a more favorable TS with lower energy barrier is discovered. Further tests on RGD1 dataset confirm its strong generalization ability on unseen molecules and reaction types, highlighting its potential for facilitating reaction exploration.

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.

Accurately predicting chemical reaction outcomes and potential byproducts is a fundamental task of modern chemistry, enabling the efficient design of synthetic pathways and driving progress in chemical science. Reaction mechanism, which tracks electron movements during chemical reactions, is critical for understanding reaction kinetics and identifying unexpected products. We demonstrate the high predictive performance of Reactron over existing product-only models by a large-scale reaction outcome prediction benchmark, and the adaptability of the model to learn new reactivity upon providing a few examples. Furthermore, it explores combinatorial reaction spaces, uncovering novel reactivities beyond its training data. With robust performance in both in-and out-of-distribution predictions, Reactron embodies human-like reasoning in chemistry and opens new frontiers in reaction discovery and synthesis design. Main In organic chemistry, a reaction mechanism is a theoretical trajectory that describes how the electron moves within organic molecules in a chemical reaction.

We introduce WarpSci, a domain agnostic framework designed to overcome crucial system bottlenecks encountered in the application of reinforcement learning to intricate environments with vast datasets featuring high-dimensional observation or action spaces. Notably, our framework eliminates the need for data transfer between the CPU and GPU, enabling the concurrent execution of thousands of simulations on a single or multiple GPUs. This high data throughput architecture proves particularly advantageous for data-driven scientific research, where intricate environment models are commonly essential.

Mechanistic understanding of organic reactions can facilitate reaction development, impurity prediction, and in principle, reaction discovery. While several machine learning models have sought to address the task of predicting reaction products, their extension to predicting reaction mechanisms has been impeded by the lack of a corresponding mechanistic dataset. In this study, we construct such a dataset by imputing intermediates between experimentally reported reactants and products using expert reaction templates and train several machine learning models on the resulting dataset of 5,184,184 elementary steps. We explore the performance and capabilities of these models, focusing on their ability to predict reaction pathways and recapitulate the roles of catalysts and reagents. Additionally, we demonstrate the potential of mechanistic models in predicting impurities, often overlooked by conventional models. We conclude by evaluating the generalizability of mechanistic models to new reaction types, revealing challenges related to dataset diversity, consecutive predictions, and violations of atom conservation.

Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many potential applications and can be modelled using a continuous-time Markov chain (CTMC). Here we present ViDa, a new visualization approach for DNA reaction trajectories that uses a 2D embedding of the secondary structure state space underlying the CTMC model. To this end, we integrate a scattering transform of the secondary structure adjacency, a variational autoencoder, and a nonlinear dimensionality reduction method. We augment the training loss with domain-specific supervised terms that capture both thermodynamic and kinetic features. We assess ViDa on two well-studied DNA hybridization reactions. Our results demonstrate that the domain-specific features lead to significant quality improvements over the state-of-the-art in DNA state space visualization, successfully separating different folding pathways and thus providing useful insights into dominant reaction mechanisms.

Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway simulations of such reactions. Here we present ViDa, a new approach for visualizing DNA reaction folding trajectories over the energy landscape of secondary structures. We integrate a deep graph embedding model with common dimensionality reduction approaches, to map high-dimensional data onto 2D Euclidean space. We assess ViDa on two well-studied and contrasting DNA hybridization reactions. Our preliminary results suggest that ViDa's visualization successfully separates trajectories with different folding mechanisms, thereby providing useful insight to users, and is a big improvement over the current state-of-the-art in DNA kinetics visualization.

A significant share of political discourse occurs online on social media platforms. Policymakers and researchers try to understand the role of social media design in shaping the quality of political discourse around the globe. In the past decades, scholarship on political discourse theory has produced distinct characteristics of different types of prominent political rhetoric such as deliberative, civic, or demagogic discourse. This study investigates the relationship between social media reaction mechanisms (i.e., upvotes, downvotes) and political rhetoric in user discussions by engaging in an in-depth conceptual analysis of political discourse theory. First, we analyze 155 million user comments in 55 political subforums on Reddit between 2010 and 2018 to explore whether users' style of political discussion aligns with the essential components of deliberative, civic, and demagogic discourse. Second, we perform a quantitative study that combines confirmatory factor analysis with difference in differences models to explore whether different reaction mechanism schemes (e.g., upvotes only, upvotes and downvotes, no reaction mechanisms) correspond with political user discussion that is more or less characteristic of deliberative, civic, or demagogic discourse. We produce three main takeaways. First, despite being "ideal constructs of political rhetoric," we find that political discourse theories describe political discussions on Reddit to a large extent. Second, we find that discussions in subforums with only upvotes, or both up- and downvotes are associated with user discourse that is more deliberate and civic. Third, social media discussions are most demagogic in subreddits with no reaction mechanisms at all. These findings offer valuable contributions for ongoing policy discussions on the relationship between social media interface design and respectful political discussion among users.

Understanding the set of elementary steps and kinetics in each reaction is extremely valuable to make informed decisions about creating the next generation of catalytic materials. With physical and mechanistic complexity of industrial catalysts, it is critical to obtain kinetic information through experimental methods. As such, this work details a methodology based on the combination of transient rate/concentration dependencies and machine learning to measure the number of active sites, the individual rate constants, and gain insight into the mechanism under a complex set of elementary steps. This new methodology was applied to simulated transient responses to verify its ability to obtain correct estimates of the micro-kinetic coefficients. Furthermore, experimental CO oxidation data was analyzed to reveal the Langmuir-Hinshelwood mechanism driving the reaction. As oxygen accumulated on the catalyst, a transition in the mechanism was clearly defined in the machine learning analysis due to the large amount of kinetic information available from transient reaction techniques. This methodology is proposed as a new data driven approach to characterize how materials control complex reaction mechanisms relying exclusively on experimental data.