Daily Papers

Large language models (LLMs) have shown remarkable potential in various domains, but they often lack the ability to access and reason over domain-specific knowledge and tools. In this paper, we introduced CACTUS (Chemistry Agent Connecting Tool-Usage to Science), an LLM-based agent that integrates cheminformatics tools to enable advanced reasoning and problem-solving in chemistry and molecular discovery. We evaluate the performance of CACTUS using a diverse set of open-source LLMs, including Gemma-7b, Falcon-7b, MPT-7b, Llama2-7b, and Mistral-7b, on a benchmark of thousands of chemistry questions. Our results demonstrate that CACTUS significantly outperforms baseline LLMs, with the Gemma-7b and Mistral-7b models achieving the highest accuracy regardless of the prompting strategy used. Moreover, we explore the impact of domain-specific prompting and hardware configurations on model performance, highlighting the importance of prompt engineering and the potential for deploying smaller models on consumer-grade hardware without significant loss in accuracy. By combining the cognitive capabilities of open-source LLMs with domain-specific tools, CACTUS can assist researchers in tasks such as molecular property prediction, similarity searching, and drug-likeness assessment. Furthermore, CACTUS represents a significant milestone in the field of cheminformatics, offering an adaptable tool for researchers engaged in chemistry and molecular discovery. By integrating the strengths of open-source LLMs with domain-specific tools, CACTUS has the potential to accelerate scientific advancement and unlock new frontiers in the exploration of novel, effective, and safe therapeutic candidates, catalysts, and materials. Moreover, CACTUS's ability to integrate with automated experimentation platforms and make data-driven decisions in real time opens up new possibilities for autonomous discovery.

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.

In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce SCHEMA ACTIVATED IN CONTEXT LEARNING (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. SCHEMA ACTIVATED IN CONTEXT LEARNING not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge. To support advancements in chemistry-focused natural language processing (NLP), we present ChemRxivQuest, a curated dataset of 970 high-quality question-answer (QA) pairs derived from 155 ChemRxiv preprints across 17 subfields of chemistry. Each QA pair is explicitly linked to its source text segment to ensure traceability and contextual accuracy. ChemRxivQuest was constructed using an automated pipeline that combines optical character recognition (OCR), GPT-4o-based QA generation, and a fuzzy matching technique for answer verification. The dataset emphasizes conceptual, mechanistic, applied, and experimental questions, enabling applications in retrieval-based QA systems, search engine development, and fine-tuning of domain-adapted large language models. We analyze the dataset's structure, coverage, and limitations, and outline future directions for expansion and expert validation. ChemRxivQuest provides a foundational resource for chemistry NLP research, education, and tool development.

Vision language models (VLMs) demonstrate remarkable capabilities on English multimodal tasks, but their performance on low-resource languages with genuinely multimodal educational content remains largely unexplored. In this work, we test how VLMs perform on Vietnamese educational assessments, investigating whether VLMs trained predominantly on English data can handle real-world cross-lingual multimodal reasoning. Our work presents the first comprehensive evaluation of VLM capabilities on multimodal Vietnamese exams through proposing ViExam, a benchmark containing 2,548 multimodal questions. We find that state-of-the-art VLMs achieve only 57.74% while open-source models achieve 27.70% mean accuracy across 7 academic domains, including Mathematics, Physics, Chemistry, Biology, Geography, Driving Test, and IQ Test. Most VLMs underperform average human test-takers (66.54%), with only the thinking VLM o3 (74.07%) exceeding human average performance, yet still falling substantially short of human best performance (99.60%). Cross-lingual prompting with English instructions while maintaining Vietnamese content fails to improve performance, decreasing accuracy by 1 percentage point for SOTA VLMs. Human-in-the-loop collaboration can partially improve VLM performance by 5 percentage points. Code and data are available at: https://vi-exam.github.io.

In this paper, we evaluate the ability of large language models (LLMs) to perform multiple choice symbol binding (MCSB) for multiple choice question answering (MCQA) tasks in zero-shot, one-shot, and few-shot settings. We focus on Vietnamese, with fewer challenging MCQA datasets than in English. The two existing datasets, ViMMRC 1.0 and ViMMRC 2.0, focus on literature. Recent research in Vietnamese natural language processing (NLP) has focused on the Vietnamese National High School Graduation Examination (VNHSGE) from 2019 to 2023 to evaluate ChatGPT. However, these studies have mainly focused on how ChatGPT solves the VNHSGE step by step. We aim to create a novel and high-quality dataset by providing structured guidelines for typing LaTeX formulas for mathematics, physics, chemistry, and biology. This dataset can be used to evaluate the MCSB ability of LLMs and smaller language models (LMs) because it is typed in a strict LaTeX style. We focus on predicting the character (A, B, C, or D) that is the most likely answer to a question, given the context of the question. Our evaluation of six well-known LLMs, namely BLOOMZ-7.1B-MT, LLaMA-2-7B, LLaMA-2-70B, GPT-3, GPT-3.5, and GPT-4.0, on the ViMMRC 1.0 and ViMMRC 2.0 benchmarks and our proposed dataset shows promising results on the MCSB ability of LLMs for Vietnamese. The dataset is available for research purposes only.

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic study of whether synchronized iterative retrieval and reasoning can surpass an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze behavior with diagnostics spanning retrieval coverage gaps, anchor-carry drop, query quality, composition fidelity, and control calibration. Across models, Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but remaining failure modes include incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, staged retrieval is often more influential than the mere presence of ideal evidence; we provide practical guidance for deploying and diagnosing RAG systems in specialized scientific settings and a foundation for more reliable, controllable iterative retrieval-reasoning frameworks.

We introduce FrontierScience, a benchmark evaluating expert-level scientific reasoning in frontier language models. Recent model progress has nearly saturated existing science benchmarks, which often rely on multiple-choice knowledge questions or already published information. FrontierScience addresses this gap through two complementary tracks: (1) Olympiad, consisting of international olympiad problems at the level of IPhO, IChO, and IBO, and (2) Research, consisting of PhD-level, open-ended problems representative of sub-tasks in scientific research. FrontierScience contains several hundred questions (including 160 in the open-sourced gold set) covering subfields across physics, chemistry, and biology, from quantum electrodynamics to synthetic organic chemistry. All Olympiad problems are originally produced by international Olympiad medalists and national team coaches to ensure standards of difficulty, originality, and factuality. All Research problems are research sub-tasks written and verified by PhD scientists (doctoral candidates, postdoctoral researchers, or professors). For Research, we introduce a granular rubric-based evaluation framework to assess model capabilities throughout the process of solving a research task, rather than judging only a standalone final answer.

Large language models (LLMs) increasingly rely on reinforcement learning (RL) to enhance their reasoning capabilities through feedback. A critical challenge is verifying the consistency of model-generated responses and reference answers, since these responses are often lengthy, diverse, and nuanced. Rule-based verifiers struggle with complexity, prompting the use of model-based verifiers. However, specialized verifiers lack flexibility, while general LLM judges can be inconsistent. Existing research primarily focuses on building better verifiers, yet a systematic evaluation of different types of verifiers' performance across domains remains lacking, severely constraining the reliable development of Reinforcement Learning with Verifiable Reward (RLVR). To address this, we propose VerifyBench--a cross-domain comprehensive benchmark for systematically evaluating verifiers. We construct 4,000 expert-level questions covering mathematics, physics, chemistry, and biology. Each question is equipped with reference answers and diverse responses. The reliability of the evaluation is ensured through a rigorous annotation process conducted by a multidisciplinary expert team. We design a four-dimensional experimental framework to comprehensively compare the performance boundaries of specialized verifiers and general LLMs under combined conditions of extracted answers vs. complete responses, and short vs. long outputs. Our evaluation uncovers fundamental trade-offs in verifiers: while specialized verifiers achieve leading accuracy, they exhibit deficiencies in recall; general models show stronger inclusivity but unstable precision. More importantly, we discover verifiers' high sensitivity to input structure and inherent limitations in cross-domain generalization, providing critical insights into the bottlenecks of current verifier technology.

Large language models (LLMs) have shown increasing capability in problem-solving and decision-making, largely based on the step-by-step chain-of-thought reasoning processes. However, it has been increasingly challenging to evaluate the reasoning capability of LLMs. Concretely, existing outcome-based benchmarks begin to saturate and become less sufficient to monitor the progress. To this end, we present a process-based benchmark MR-BEN that demands a meta reasoning skill, where LMs are asked to locate and analyse potential errors in automatically generated reasoning steps. MR-BEN is a comprehensive benchmark comprising 5,975 questions collected from human experts, covering various subjects such as physics, chemistry, logic, coding, and more. Through our designed metrics for assessing meta-reasoning on this benchmark, we identify interesting limitations and weaknesses of current LLMs (open-source and closed-source models). For example, open-source models are seemingly comparable to GPT-4 on outcome-based benchmarks, but they lag far behind on our benchmark, revealing the underlying reasoning capability gap between them. Our dataset and codes are available on https://randolph-zeng.github.io/Mr-Ben.github.io/.

Automated Essay Scoring (AES) holds significant promise in the field of education, helping educators to mark larger volumes of essays and provide timely feedback. However, Arabic AES research has been limited by the lack of publicly available essay data. This study introduces AR-AES, an Arabic AES benchmark dataset comprising 2046 undergraduate essays, including gender information, scores, and transparent rubric-based evaluation guidelines, providing comprehensive insights into the scoring process. These essays come from four diverse courses, covering both traditional and online exams. Additionally, we pioneer the use of AraBERT for AES, exploring its performance on different question types. We find encouraging results, particularly for Environmental Chemistry and source-dependent essay questions. For the first time, we examine the scale of errors made by a BERT-based AES system, observing that 96.15 percent of the errors are within one point of the first human marker's prediction, on a scale of one to five, with 79.49 percent of predictions matching exactly. In contrast, additional human markers did not exceed 30 percent exact matches with the first marker, with 62.9 percent within one mark. These findings highlight the subjectivity inherent in essay grading, and underscore the potential for current AES technology to assist human markers to grade consistently across large classes.

Benchmarks shape scientific conclusions about model capabilities and steer model development. This creates a feedback loop: stronger benchmarks drive better models, and better models demand more discriminative benchmarks. Ensuring benchmark reliability is therefore essential for trustworthy evaluation and meaningful progress. In this work, we study benchmark reliability from a distributional perspective and introduce benchmark harmony, which measures how uniformly a model's performance is distributed across the subdomains of a benchmark. We posit that high harmony is a desirable benchmark property, indicating that the aggregate metric reflects uniform competence across subdomains. Across 19 multiple-choice benchmarks and five model families, we map each benchmark onto a mean-variance plane of harmony computed across models, where high mean and low variance signal more reliable evaluation. Our analysis shows that less harmonious benchmarks can give misleading results, since overall accuracy may be disproportionately influenced by specific subdomains. For instance, ARC-Easy is overwhelmed by questions on Biological Concepts, overshadowing other critical subdomains such as Geography, Physics, Chemistry, and Environmental Science. By recommending that harmony should be reported alongside accuracy, we reframe evaluation from simple performance averages to a more robust, distributionally reliable measurement of performance.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

Contemporary vision-language models (VLMs) perform well on existing multimodal reasoning benchmarks (78-85\% accuracy on MMMU, MathVista). Yet, these results fail to sufficiently distinguish true scientific reasoning articulation capabilities from pattern-matching. To address this gap, we introduce mmJEE-Eval, a multimodal bilingual (English and Hindi) benchmark comprising 1,460 questions from India's JEE Advanced examination (2019-2025) spanning pre-college Physics, Chemistry, and Mathematics domains. Our evaluation of 17 state-of-the-art models reveals that while frontier VLMs (GPT-5, Gemini 2.5 Pro/Flash) achieve 77-84\% accuracy on held-out 2025 questions, open-source models plateau at 37-45\% despite scaling to 400B parameters, a significant difference not observed on existing benchmarks. While closed frontiers from Google and OpenAI show high problem-solving accuracies (up to 100\% pass@3 scores), they fully collapse when the reasoning load is increased meta-cognitively (GPT-5 fixes just 5.2\% errors). Systematic ablations show mmJEE-Eval's difficulty stems from complexity and reasoning depth rather than memorization. Effectively, our benchmark segregates superior training and reasoning methodologies where alternatives fail. We publicly release our code and data: https://mmjee-eval.github.io

The African continent lacks enough qualified teachers which hampers the provision of adequate learning support. An AI could potentially augment the efforts of the limited number of teachers, leading to better learning outcomes. Towards that end, this work describes and evaluates the first key output for the NSMQ AI Grand Challenge, which proposes a robust, real-world benchmark for such an AI: "Build an AI to compete live in Ghana's National Science and Maths Quiz (NSMQ) competition and win - performing better than the best contestants in all rounds and stages of the competition". The NSMQ is an annual live science and mathematics competition for senior secondary school students in Ghana in which 3 teams of 2 students compete by answering questions across biology, chemistry, physics, and math in 5 rounds over 5 progressive stages until a winning team is crowned for that year. In this work, we built Brilla AI, an AI contestant that we deployed to unofficially compete remotely and live in the Riddles round of the 2023 NSMQ Grand Finale, the first of its kind in the 30-year history of the competition. Brilla AI is currently available as a web app that livestreams the Riddles round of the contest, and runs 4 machine learning systems: (1) speech to text (2) question extraction (3) question answering and (4) text to speech that work together in real-time to quickly and accurately provide an answer, and then say it with a Ghanaian accent. In its debut, our AI answered one of the 4 riddles ahead of the 3 human contesting teams, unofficially placing second (tied). Improvements and extensions of this AI could potentially be deployed to offer science tutoring to students and eventually enable millions across Africa to have one-on-one learning interactions, democratizing science education.

[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 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.

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.

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.

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.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website https://alchemy.tencent.com. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

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.

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.

Advanced observational facilities allow to trace back the chemical evolution of the Universe, on the one hand, from local objects of different ages and, secondly, by direct observations of redshifted objects. The chemical enrichment serves as one of the cornerstones of cosmological evolution. In order to understand this chemical evolution in morphologically different astrophysical objects models are constructed based on analytical descriptions or numerical methods. For the comparison of their chemical issues, as there are element abundances, gradients, and ratios, with observations not only the present-day values are used but also their temporal evolution from the first era of metal enrichment. Here we will provide some insight into basics of chemical evolution models, highlight advancements, and discuss a few applications.

In an ongoing effort to understand planet formation the link between the chemistry of the protoplanetary disk and the properties of resulting planets have long been a subject of interest. These connections have generally been made between mature planets and young protoplanetary disks through the carbon-to-oxygen (C/O) ratio. In a rare number of systems, young protoplanets have been found within their natal protoplanetary disks. These systems offer a unique opportunity to directly study the delivery of gas from the protoplanetary disk to the planet. In this work we post-process 3D numerical simulations of an embedded Jupiter-massed planet in its protoplanetary disk to explore the chemical evolution of gas as it flows from the disk to the planet. The relevant dust to this chemical evolution is assumed to be small, co-moving grains with a reduced dust-to-gas ratio indicative of the upper atmosphere of a protoplanetary disk. We find that as the gas enters deep into the planet's gravitational well, it warms significantly (up to sim 800 K), releasing all of the volatile content from the ice phase. This change in phase can influence our understanding of the delivery of volatile species to the atmospheres of giant planets. The primary carbon, oxygen, and sulfur carrying ices: CO_2, H_2O, and H_2S are released into the gas phase and along with the warm gas temperatures near the embedded planets lead to the production of unique species like CS, SO, and SO_2 compared to the protoplanetary disk. We compute the column densities of SO, SO_2, CS, and H_2CS in our model and find that their values are consistent with previous observational studies.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

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.

Question Answering (QA) effectively evaluates language models' reasoning and knowledge depth. While QA datasets are plentiful in areas like general domain and biomedicine, academic chemistry is less explored. Chemical QA plays a crucial role in both education and research by effectively translating complex chemical information into readily understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a QAMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. We first address the issue of imbalanced label distribution by re-weighting the instance-wise loss based on the inverse frequency of each class, ensuring minority classes are not dominated by majority ones during optimization. Next, we utilize the unlabeled data to enrich the learning process, generating a variety of augmentations based on a SoftMix operation and ensuring their predictions align with the same target, i.e., pseudo-labels. To ensure the quality of the pseudo-labels, we propose a calibration procedure aimed at closely aligning the pseudo-label estimates of individual samples with a desired ground truth distribution. Experiments show that our QAMatch significantly outperforms the recent similar-scale baselines and Large Language Models (LLMs) not only on our ScholarChemQA dataset but also on four benchmark datasets. We hope our benchmark and model can facilitate and promote more research on chemical QA.

The blue bottle experiment was first introduced to the chemical education literature as a simple demonstration on kinetics. Its original formulation contains only glucose, NaOH and small amount of methylene blue. The solution turns blue when shaken and fades to colorless upon standing. This bluing/de-bluing cycle may be repeated and may be compared to blood colors in animal's respiratory cycle. Inspired by the blue bottle experiment, the colorful chemical bottle experiment kit was commercially developed in 2006. The kit is a versatile pedagogical tool, not only for physical chemistry but also for analytical, biological and organic chemistry. It also helps teaching concepts in scientific method and laboratory safety. This manuscript contains four parts, brief review on literature relating to the blue bottle experiment, description of the colorful chemical bottle experiment kit, pedagogical discussion of the experiments and preliminary evaluation from students.

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.

The Sun provides a standard reference against which we compare the chemical abundances found anywhere else in the Universe. Nevertheless, there is not a unique 'solar' composition, since the chemical abundances found in the solar interior, the photosphere, the upper atmosphere, or the solar wind, are not exactly the same. The composition of the solar photosphere, usually preferred as a reference, changes with time due to diffusion, convection, and probably accretion. In addition, we do not know the solar photospheric abundances, inferred from the analysis of the solar spectrum using model atmospheres, with high accuracy, and uncertainties for many elements exceed 25%. This paper gives an overview of the methods and pitfalls of spectroscopic analysis, and discusses the chemistry of the Sun in the context of the solar system.

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.

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.

Half of the JWST high-contrast imaging objects will only have photometric data {{as of Cycle 2}}. However, to better understand their atmospheric chemistry which informs formation origin, spectroscopic data are preferred. Using HIP 65426 b, we investigate to what extent planet properties and atmospheric chemical abundance can be retrieved with only JWST photometric data points (2.5-15.5 mum) in conjunction with ground-based archival low-resolution spectral data (1.0-2.3 mum). We find that the data is consistent with an atmosphere with solar metallicity and C/O ratios at 0.40 and 0.55. We rule out 10x solar metallicity and an atmosphere with C/O = 1.0. We also find strong evidence of silicate clouds but no sign of an enshrouding featureless {{dust}} extinction. This work offers guidance and cautionary tales on analyzing data in the absence of medium-to-high resolution spectral data.

Solar photospheric abundances and CI-chondrite compositions are reviewed and updated to obtain representative solar system abundances of the elements and their isotopes. The new photospheric abundances obtained here lead to higher solar metallicity. Full 3D NLTE photospheric analyses are only available for 11 elements. A quality index for analyses is introduced. For several elements, uncertainties remain large. Protosolar mass fractions are H (X = 0.7060), He (Y = 0.2753), and for metals Li to U (Z = 0.0187). The protosolar (C+N)/H agrees within 13% with the ratio for the solar core from the Borexino experiment. Elemental abundances in CI-chondrites were screened by analytical methods, sample sizes, and evaluated using concentration frequency distributions. Aqueously mobile elements (e.g., alkalis, alkaline earths, etc.) often deviate from normal distributions indicating mobilization and/or sequestration into carbonates, phosphates, and sulfates. Revised CI-chondrite abundances of non-volatile elements are similar to earlier estimates. The moderately volatile elements F and Sb are higher than before, as are C, Br and I, whereas the CI-abundances of Hg and N are now significantly lower. The solar system nuclide distribution curves of s-process elements agree within 4% with s-process predictions of Galactic chemical evolution models. P-process nuclide distributions are assessed. No obvious correlation of CI-chondritic to solar elemental abundance ratios with condensation temperatures is observed, nor is there one for ratios of CI-chondrites/solar wind abundances.

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

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

High-throughput data generation methods and machine learning (ML) algorithms have given rise to a new era of computational materials science by learning relationships among composition, structure, and properties and by exploiting such relations for design. However, to build these connections, materials data must be translated into a numerical form, called a representation, that can be processed by a machine learning model. Datasets in materials science vary in format (ranging from images to spectra), size, and fidelity. Predictive models vary in scope and property of interests. Here, we review context-dependent strategies for constructing representations that enable the use of materials as inputs or outputs of machine learning models. Furthermore, we discuss how modern ML techniques can learn representations from data and transfer chemical and physical information between tasks. Finally, we outline high-impact questions that have not been fully resolved and thus, require further investigation.

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.

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.

Accurate knowledge of the properties of hydrogen at high compression is crucial for astrophysics (e.g. planetary and stellar interiors, brown dwarfs, atmosphere of compact stars) and laboratory experiments, including inertial confinement fusion. There exists experimental data for the equation of state, conductivity, and Thomson scattering spectra. However, the analysis of the measurements at extreme pressures and temperatures typically involves additional model assumptions, which makes it difficult to assess the accuracy of the experimental data. rigorously. On the other hand, theory and modeling have produced extensive collections of data. They originate from a very large variety of models and simulations including path integral Monte Carlo (PIMC) simulations, density functional theory (DFT), chemical models, machine-learned models, and combinations thereof. At the same time, each of these methods has fundamental limitations (fermion sign problem in PIMC, approximate exchange-correlation functionals of DFT, inconsistent interaction energy contributions in chemical models, etc.), so for some parameter ranges accurate predictions are difficult. Recently, a number of breakthroughs in first principle PIMC and DFT simulations were achieved which are discussed in this review. Here we use these results to benchmark different simulation methods. We present an update of the hydrogen phase diagram at high pressures, the expected phase transitions, and thermodynamic properties including the equation of state and momentum distribution. Furthermore, we discuss available dynamic results for warm dense hydrogen, including the conductivity, dynamic structure factor, plasmon dispersion, imaginary-time structure, and density response functions. We conclude by outlining strategies to combine different simulations to achieve accurate theoretical predictions.

The coldest Y spectral type brown dwarfs are similar in mass and temperature to cool and warm (sim200 -- 400 K) giant exoplanets. We can therefore use their atmospheres as proxies for planetary atmospheres, testing our understanding of physics and chemistry for these complex, cool worlds. At these cold temperatures, their atmospheres are cold enough for water clouds to form, and chemical timescales increase, increasing the likelihood of disequilibrium chemistry compared to warmer classes of planets. JWST observations are revolutionizing the characterization of these worlds with high signal-to-noise, moderate resolution near- and mid-infrared spectra. The spectra have been used to measure the abundances of prominent species like water, methane, and ammonia; species that trace chemical reactions like carbon monoxide; and even isotopologues of carbon monoxide and ammonia. Here, we present atmospheric retrieval results using both published fixed-slit (GTO program 1230) and new averaged time series observations (GO program 2327) of the coldest known Y dwarf, WISE 0855-0714 (using NIRSpec G395M spectra), which has an effective temperature of sim 264 K. We present a detection of deuterium in an atmosphere outside of the solar system via a relative measurement of deuterated methane (CH_{3}D) and standard methane. From this, we infer the D/H ratio of a substellar object outside the solar system for the first time. We also present a well-constrained part-per-billion abundance of phosphine (PH_{3}). We discuss our interpretation of these results and the implications for brown dwarf and giant exoplanet formation and evolution.

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.

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.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Organosulfur species are potential major carriers of sulfur in the interstellar medium, as well as interesting ingredients in prebiotic chemistry. The most fundamental question regarding these species is under which conditions they reside in the gas versus solid phase. Here, we characterize the thermal desorption kinetics, binding energies, and entrapment of the organosulfur methyl mercaptan (CH_3SH, or MeSH) in different ice environments, comparing them with those of methanol (CH_3OH, or MeOH) ices. The derived multi-layer (pure MeSH-MeSH) and sub-monolayer (layered MeSH-H_2O) binding energies are surprisingly similar, corresponding to snow line locations where the disk midplane temperature is ~105 K. In both H_2O-dominated and more realistic H_2O:CO_2-dominated ices, 100% of the MeSH is entrapped, almost exclusively desorbing at the molecular volcano desorption peak, indicating that MeSH is retained at the water snow line if initially mixed with water ice during formation. Additionally, the presence of MeSH in an ice mixture enhances the entrapment of CO_2 and MeOH (up to 100%) until the onset of volcano desorption; without MeSH, both desorb at their respective pure desorption temperatures and also co-desorb with water. Compared to MeOH, MeSH binds less well to water, explaining why MeSH escapes during water ice crystallization rather than co-desorbing with water. These results show the larger relative size of MeSH compared to MeOH significantly impacts its ability to bind to water and its entrapment efficiency. Therefore, molecular size plays an important role in the adsorption and retention of S-bearing organics and, in turn, other volatiles in ices.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS~70 disk and report the first chemical inventory of the system. With a spatial resolution of 0.4''-0.5'' (sim50 au), 12 species are detected, including CO isotopologues and formaldehyde, small hydrocarbons, HCN and HCO+ isotopologues, and S-bearing molecules. SO and CH3OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub-)mm continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the non detections. Excitation temperature is obtained for H2CO. Deuteration and nitrogen fractionation profiles from the hydro-cyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon to oxygen ratio C/O>1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

HeH^+ was the first heteronuclear molecule to form in the metal-free Universe after the Big Bang. The molecule gained significant attention following its first circumstellar detection in the young and dense planetary nebula NGC 7027. We target some hydride ions associated with the noble gases (HeH^+, ArH^+, and NeH^+) to investigate their formation in harsh environments like the nova outburst region. We use a photoionization modeling (based on previously published best-fit physical parameters) of the moderately fast ONe type nova, QU Vulpeculae 1984, and the CO type novae, RS Ophiuchi and V1716 Scorpii. Our steady-state modeling reveals a convincing amount of HeH^+, especially in the dense clump of RS Ophiuchi and V1716 Scorpii. The calculated upper limit on the surface brightness of HeH^+ transitions suggests that the James Webb Space Telescope (JWST) could detect some of them, particularly in sources like RS Ophiuchi and V1716 Scorpii, which have similar physical and chemical conditions and evolution. It must be clearly noted that the sources studied are used as templates, and not as targets for observations. The detection of these lines could be useful for determining the physical conditions in similar types of systems and for validating our predictions based on new electron-impact ro-vibrational collisional data at temperatures of up to 20,000 K.

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 introduce GAIA, a benchmark for General AI Assistants that, if solved, would represent a milestone in AI research. GAIA proposes real-world questions that require a set of fundamental abilities such as reasoning, multi-modality handling, web browsing, and generally tool-use proficiency. GAIA questions are conceptually simple for humans yet challenging for most advanced AIs: we show that human respondents obtain 92\% vs. 15\% for GPT-4 equipped with plugins. This notable performance disparity contrasts with the recent trend of LLMs outperforming humans on tasks requiring professional skills in e.g. law or chemistry. GAIA's philosophy departs from the current trend in AI benchmarks suggesting to target tasks that are ever more difficult for humans. We posit that the advent of Artificial General Intelligence (AGI) hinges on a system's capability to exhibit similar robustness as the average human does on such questions. Using GAIA's methodology, we devise 466 questions and their answer. We release our questions while retaining answers to 300 of them to power a leader-board available at https://huggingface.co/gaia-benchmark.

A physically motivated equation that determines the number of electrons of a molecule is proposed based on chemical common sense. It shows that all molecules are entangled in the number of electrons and results in the fundamental assumption of molecular energy convexity that underpins molecular quantum mechanics. The proposed physical principle includes the molecular size consistency principle as a special case. Application of wavefunction theory to the principle shows that an individual molecule with a noninteger number of electrons is locally physical albeit locally unreal. The energy of a molecule is piecewise linear with respect to its continuous number of electrons. The continuity of the number of electrons allows the definition of an electronic chemical potential of a single molecule. A state function equivalent to the energy of a molecule can be defined using the chemical potential as a variable. The aforementioned physical principle can alternatively be expressed as a simple additivity with the new state function. The latter also shows that the quantum entanglement in the number of electrons can be viewed as all molecules sharing the same chemical potential.

The stars of the Milky Way carry the chemical history of our Galaxy in their atmospheres as they journey through its vast expanse. Like barcodes, we can extract the chemical fingerprints of stars from high-resolution spectroscopy. The fourth data release (DR4) of the Galactic Archaeology with HERMES (GALAH) Survey, based on a decade of observations, provides the chemical abundances of up to 32 elements for 917 588 stars that also have exquisite astrometric data from the Gaia satellite. For the first time, these elements include life-essential nitrogen to complement carbon, and oxygen as well as more measurements of rare-earth elements critical to modern-life electronics, offering unparalleled insights into the chemical composition of the Milky Way. For this release, we use neural networks to simultaneously fit stellar parameters and abundances across the whole wavelength range, leveraging synthetic grids computed with Spectroscopy Made Easy. These grids account for atomic line formation in non-local thermodynamic equilibrium for 14 elements. In a two-iteration process, we first fit stellar labels to all 1 085 520 spectra, then co-add repeated observations and refine these labels using astrometric data from Gaia and 2MASS photometry, improving the accuracy and precision of stellar parameters and abundances. Our validation thoroughly assesses the reliability of spectroscopic measurements and highlights key caveats. GALAH DR4 represents yet another milestone in Galactic archaeology, combining detailed chemical compositions from multiple nucleosynthetic channels with kinematic information and age estimates. The resulting dataset, covering nearly a million stars, opens new avenues for understanding not only the chemical and dynamical history of the Milky Way, but also the broader questions of the origin of elements and the evolution of planets, stars, and galaxies.

Scientific text is a promising source of data in materials science, with ongoing research into utilising textual data for materials discovery. In this study, we developed and tested a novel approach to extract material-property relationships from scientific publications using the Question Answering (QA) method. QA performance was evaluated for information extraction of perovskite bandgaps based on a human query. We observed considerable variation in results with five different large language models fine-tuned for the QA task. Best extraction accuracy was achieved with the QA MatBERT and F1-scores improved on the current state-of-the-art. This work demonstrates the QA workflow and paves the way towards further applications. The simplicity, versatility and accuracy of the QA approach all point to its considerable potential for text-driven discoveries in materials research.

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.

We study the effects of H2O on CO2 adsorption in an amine-appended variant of the metal-organic framework Mg2(dobpdc), which is known to exhibit chaining behavior that presents in a step-shaped adsorption isotherm. We first show how the presence of different levels of local H2O affects this chaining behavior and the energetics of CO2 adsorption, based on a series of ab initio calculations, giving insight into the atomic-scale environment. In particular, we predict a novel adsorbed configuration, in which H2O and CO2 intertwine to make a braided chain down the MOF pore. We then show how an existing lattice model can be adapted to incorporate the effect of water, and predict the CO2 isotherms for the various water levels, observing a sharp shift the uptake at low partial pressures. In addition to the physical further work on this and related materials.

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.

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.

Deep spectrophotometry has proved to be a fundamental tool to improve our knowledge on the chemical content of planetary nebulae. With the arrival of very efficient spectrographs installed in the largest ground-based telescopes, outstanding spectra have been obtained. These data are essential to constrain state-of-the-art nucleosynthesis models in asymptotic giant branch stars and, in general, to understand the chemical evolution of our Galaxy. In this paper we review the last advances on the chemical composition of the ionized gas in planetary nebulae based on faint emission lines observed through very deep spectrophotometric data.

In this technical report, we propose ChemVLM, the first open-source multimodal large language model dedicated to the fields of chemistry, designed to address the incompatibility between chemical image understanding and text analysis. Built upon the VIT-MLP-LLM architecture, we leverage ChemLLM-20B as the foundational large model, endowing our model with robust capabilities in understanding and utilizing chemical text knowledge. Additionally, we employ InternVIT-6B as a powerful image encoder. We have curated high-quality data from the chemical domain, including molecules, reaction formulas, and chemistry examination data, and compiled these into a bilingual multimodal question-answering dataset. We test the performance of our model on multiple open-source benchmarks and three custom evaluation sets. Experimental results demonstrate that our model achieves excellent performance, securing state-of-the-art results in five out of six involved tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

We report the measurement of the electric dipole moment of aluminum monochloride (AlCl) using a cryogenic buffer-gas beam source. Our measurements provide values for the dipole moments of the two lowest vibrational states of the X^1Sigma^+ and the A^1Pi electronic states. We also show that spin-orbit coupling with an extended number of spin states is essential in the ab initio calculation to correctly describe both the dipole moment and the Te energy of AlCl. We further lay out the implications of these results for astrophysical models of stellar and planetary evolution that have used a substitute value for the dipole moment of AlCl until now.

We provide here a dataset for tasks related to natural language understanding and natural language inference. The dataset contains logical puzzles in natural language from three domains: comparing puzzles, knighs and knaves, and zebra puzzles. Each puzzle is associated with the entire set of atomic questions that can be generated based on the relations and individuals occurring in the text. For each question we provide the correct answer: entailment, contradiction or ambiguity. The answer's correctness is verified against theorem provers. Good puzzles have two properties: (i) each piece of information is necessary and (ii) no unnecessary information is provided. These properties make puzzles interesting candidates for machine comprehension tasks.

This report is a primarily survey on the chemical nature of some exotic species containing the positively charged muon and the muonic Helium, i.e., the negatively charged muon plus helium nucleus, as exotic isotopes of hydrogen, using the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis, employing ab initio non-Born-Oppenhiemer wavefunctions. Accordingly, the "atoms in molecules" analysis performed on various asymmetric exotic isotopomers of hydrogen molecule, recently detected experimentally [Science 331, 448 (2011)], demonstrates that both the exotic isotopes are capable of forming atoms in molecules and retaining the identity of hydrogen atom. Various derived properties of atomic basins containing muonic helium cast no doubt that apart from its short life time, it is a heavier isotope of hydrogen while the properties of basins containing the positively charged muon are more remote from those of the orthodox hydrogen basins, capable of appreciable donation of electrons as well as large charge polarization; however, with some tolerance, they may be categorized also as hydrogen basins though with a smaller electronegativity. All in all, present study also clearly demonstrates that the MC-QTAIM analysis is an efficient approach to decipher the chemical nature of species containing exotic constituents, hard to be elucidated by experimental and/or alternative theoretical schemes.

Understanding where elements were formed has been a key goal in astrophysics for nearly a century, with answers involving cosmology, stellar burning, and cosmic explosions. Since 1957, the origin of the heaviest elements (formed via the rapid neutron capture process; r-process) has remained a mystery, identified as a key question to answer this century by the US National Research Council. With the advent of gravitational wave astronomy and recent measurements by the James Webb Space Telescope we now know that neutron star mergers are a key site of heavy element nucleosynthesis. We must now understand the heavy element yield of these events as well as mapping when these mergers occurred back through cosmic time, currently thought to peak when the universe was half its current age. This requires an extremely sensitive ultraviolet, optical, and infrared telescope which can respond rapidly to external discoveries of neutron star mergers. We here describe how the Habitable Worlds Observatory can provide the first complete answer to one of the questions of the century.

The paper introduces SceMQA, a novel benchmark for scientific multimodal question answering at the college entrance level. It addresses a critical educational phase often overlooked in existing benchmarks, spanning high school to pre-college levels. SceMQA focuses on core science subjects including Mathematics, Physics, Chemistry, and Biology. It features a blend of multiple-choice and free-response formats, ensuring a comprehensive evaluation of AI models' abilities. Additionally, our benchmark provides specific knowledge points for each problem and detailed explanations for each answer. SceMQA also uniquely presents problems with identical contexts but varied questions to facilitate a more thorough and accurate assessment of reasoning capabilities. In the experiment, we evaluate both open-source and close-source state-of-the-art Multimodal Large Language Models (MLLMs), across various experimental settings. The results show that further research and development are needed in developing more capable MLLM, as highlighted by only 50% to 60% accuracy achieved by the strongest models. Our benchmark and analysis will be available at https://scemqa.github.io/

Researchers and scientists increasingly rely on specialized information retrieval (IR) or recommendation systems (RS) to support them in their daily research tasks. Paper recommender systems are one such tool scientists use to stay on top of the ever-increasing number of academic publications in their field. Improving research paper recommender systems is an active research field. However, less research has focused on how the interfaces of research paper recommender systems can be tailored to suit the needs of different research domains. For example, in the field of biomedicine and chemistry, researchers are not only interested in textual relevance but may also want to discover or compare the contained chemical entity information found in a paper's full text. Existing recommender systems for academic literature do not support the discovery of this non-textual, but semantically valuable, chemical entity data. We present the first implementation of a specialized chemistry paper recommender system capable of visualizing the contained chemical structures, chemical formulae, and synonyms for chemical compounds within the document's full text. We review existing tools and related research in this field before describing the implementation of our ChemVis system. With the help of chemists, we are expanding the functionality of ChemVis, and will perform an evaluation of recommendation performance and usability in future work.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Three epochs in development of chemical dynamics are presented. We try to understand the modern research programs in the light of classical works. Three eras (or waves) of chemical dynamics can be revealed in the flux of research and publications. These waves may be associated with leaders: the first is the van't Hoof wave, the second may be called the Semenov--Hinshelwood wave and the third is definitely the Aris wave. Of course, the whole building was impossible without efforts of hundreds of other researchers. Some of of them are mentioned in our brief review.

The measured neutron flux from the Moons south polar region shows evidence of locally enhanced hydrogen concentrations, likely in the form of water ice, within most permanently shadowed regions (PSR), poleward of 77 deg S latitude. Results are consistent with the original findings of Watson et al, 1961, which found that the PSRs cryogenic surfaces create exclusive conditions for the sequestration of water ice, due to their extremely low sublimation rates. Widespread PSR hydrogenation is demonstrated in several studies by showing that the contrasting PSR area distribution is being instrumentally blurred. The PSRs expected hydrogen observations are correlated by their area fraction of the fixed 30 km diameter footprint area of the Collimated Sensor for Epithermal Neutrons (CSETN), which is part of the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO). The correlation indicates that the PSRs are similarly hydrogenated, with an expected concentration = 0.27 wt%, relative to that of the anhydrous reference terrain (lower bounds). Hydrogen concentrations are demonstrated to be correlated to maximum temperature distributions within the basins of Haworth, Shoemaker and Faustini PSRs. Cabeus-1 PSR shows an anomalously enhanced hydrogen concentration indicating a second process contributes to its hydrogen budget. Results are consistent with ongoing processes that introduce volatiles to the surface including outgassing, solar wind production with regolith silicates, and mixing from small scale meteor impacts and diurnal temperature variation. We validate the bandpass filter used to subtract CSETNs detection of uncollimated neutrons with profiles of several PSRs neutron suppression before and after processing. Keywords: Moon, Epithermal Neutron, Hydrogen, Water, Ice, Volatiles, LRO, LEND, Diviner, LOLA

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a basis-function-independent self-consistent field scheme. Versatile interfaces, making use of open standards like python, mediate the integration of molsturm with existing third-party packages. In this way both rapid extension of the present set of methods for electronic structure calculations as well as adding new basis function types can be readily achieved. This makes molsturm well-suitable for testing novel approaches for discretising the electronic wave function and allows comparing them to existing methods using the same software stack. This is illustrated by two examples, an implementation of coupled-cluster doubles as well as a gradient-free geometry optimisation, where in both cases, an arbitrary basis functions could be used. molsturm is open-source and can be obtained from https://molsturm.org.

Interior models of gas giants in the Solar System traditionally assume a fully convective molecular hydrogen envelope. However, recent observations from the Juno mission suggest a possible depletion of alkali metals in Jupiter's molecular hydrogen envelope, indicating that a stable radiative layer could exist at the kilobar level. Recent studies propose that deep stable layers help reconcile various Jupiter observations, including its atmospheric water and CO abundances and the depth of its zonal winds. However, opacity tables used to infer stable layers are often outdated and incomplete, leaving the precise molecular hydrogen envelope composition required for a deep radiative zone uncertain. In this paper, we determine atmospheric compositions that can lead to the formation of a radiative zone at the kilobar level in Jupiter and Saturn today. We computed radiative opacity tables covering pressures up to 10^5 bar, including the most abundant molecules present in the gas giants of the Solar System, as well as contributions from free electrons, metal hydrides, oxides, and atomic species, using the most up-to-date line lists published in the literature. These tables were used to calculate Rosseland-mean opacities for the molecular hydrogen envelopes of Jupiter and Saturn, which were then compared to the critical mean opacity required to maintain convection. We find that the presence of a radiative zone is controlled by the existence of K, Na, and NaH in the atmosphere of Jupiter and Saturn. For Jupiter, the elemental abundance of K and Na must be less than sim 10^{-3} times solar to form a radiative zone. In contrast, for Saturn, the required abundance for K and Na is below sim 10^{-4} times solar.

Exploratory synthesis efforts for iron-based superconductors (FeSC) have been driven by hopes of improving superconducting critical temperatures (TCs), providing high-quality samples for in-depth studies of intrinsic properties, and exploring potential superconductivity in similar families of materials. This manuscript summarizes the synthesis routes that are used for producing FeSC and their undoped parents, in single crystal and polycrystalline forms. A few of the materials challenges are summarized.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

The Shannon entropy in the atomic, molecular and chemical physics context is presented by using as test cases the hydrogenic-like atoms H_c, {He_c}^+ and {Li_c}^{2+} confined by an impenetrable spherical box. Novel expressions for entropic uncertainty relation and Shannon entropies S_r and S_p are proposed to ensure their physical dimensionless characteristic. The electronic ground state energy and the quantities S_r, S_p and S_t are calculated for the hydrogenic-like atoms to different confinement radii by using a variational method. The global behavior of these quantities and different conjectures are analyzed. The results are compared, when available, with those previously published.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

The overwhelming majority of molecules remains unexplored. This is mostly due to the sheer number of them, which prohibits any enumeration of chemical space, the set of all such molecules. In practice, only subsets of chemical space are considered, but those subsets exhibit substantial bias, prohibiting data-driven characterization of chemical space itself. In this work, we provide a method produce unbiased representative random samples of chemical space without enumeration of constituent molecules and to estimate the number of molecules in any custom chemical space. The approach is applicable to molecules which can be represented as graph and runs efficiently even for molecules of 30 atoms. We use it to estimate the representativeness of current databases with respect to their underlying chemical space and to establish a necessary criterion for a lower bound of database sizes to be representative of an underlying chemical space.

Science and Engineering fairs offer K-12 students opportunities to engage with authentic STEM practices. Particularly, students are given the chance to experience authentic and open inquiry processes, by defining which themes, questions and approaches will guide their scientific endeavors. In this study, we analyzed data from over 5,000 projects presented at a nationwide science fair in Brazil over the past 20 years using topic modeling to identify the main topics that have driven students' inquiry and design. Our analysis identified a broad range of topics being explored, with significant variations over time, region, and school setting. We argue those results and proposed methodology can not only support further research in the context of science fairs, but also inform instruction and design of contexts-specific resources to support students in open inquiry experiences in different settings.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Using {\em ab initio} density functional theory calculations, we characterize changes in the electronic structure of MoS_{2} monolayers introduced by missing or additional adsorbed sulfur atoms. We furthermore identify the chemical and electronic function of substances that have been reported to reduce the adverse effect of sulfur vacancies in quenching photoluminescence and reducing electronic conductance. We find that thiol-group containing molecules adsorbed at vacancy sites may re-insert missing sulfur atoms. In presence of additional adsorbed sulfur atoms, thiols may form disulfides on the MoS_{2} surface to mitigate the adverse effect of defects.

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

Photoionized nebulae comprise basically HII regions and planetary nebulae, and their abundances give important clues on the nucleosynthesis and chemical evolution of their host galaxies. There is presently a large amount of data on these objects, especially for the elements He and N, which are strongly affected by the evolution of intermediate mass stars, as well as O, Ne, S, and Ar, which are essentially synthesized in stars with larger masses. The abundances of these elements in several systems in the Local Group are discussed on the basis of distance-independent correlations.

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.

Naturally occurring information-seeking questions often contain questionable assumptions -- assumptions that are false or unverifiable. Questions containing questionable assumptions are challenging because they require a distinct answer strategy that deviates from typical answers for information-seeking questions. For instance, the question "When did Marie Curie discover Uranium?" cannot be answered as a typical "when" question without addressing the false assumption "Marie Curie discovered Uranium". In this work, we propose (QA)^2 (Question Answering with Questionable Assumptions), an open-domain evaluation dataset consisting of naturally occurring search engine queries that may or may not contain questionable assumptions. To be successful on (QA)^2, systems must be able to detect questionable assumptions and also be able to produce adequate responses for both typical information-seeking questions and ones with questionable assumptions. Through human rater acceptability on end-to-end QA with (QA)^2, we find that current models do struggle with handling questionable assumptions, leaving substantial headroom for progress.

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great attention in drug discovery, such as molecule generation, molecular property prediction, retrosynthesis prediction, and reaction prediction. While most existing surveys only focus on one of the applications, limiting the view of researchers in the community. In this paper, we present a comprehensive review on the aforementioned four aspects, and discuss the relationships among different applications. The latest literature and classical benchmarks are presented for better understanding the development of variety of approaches. We commence by summarizing the molecule representation format in these works, followed by an introduction of recent proposed approaches for each of the four tasks. Furthermore, we review a variety of commonly used datasets and evaluation metrics and compare the performance of deep learning-based models. Finally, we conclude by identifying remaining challenges and discussing the future trend for deep learning methods in drug discovery.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem.

Information extraction and textual comprehension from materials literature are vital for developing an exhaustive knowledge base that enables accelerated materials discovery. Language models have demonstrated their capability to answer domain-specific questions and retrieve information from knowledge bases. However, there are no benchmark datasets in the materials domain that can evaluate the understanding of the key concepts by these language models. In this work, we curate a dataset of 650 challenging questions from the materials domain that require the knowledge and skills of a materials student who has cleared their undergraduate degree. We classify these questions based on their structure and the materials science domain-based subcategories. Further, we evaluate the performance of GPT-3.5 and GPT-4 models on solving these questions via zero-shot and chain of thought prompting. It is observed that GPT-4 gives the best performance (~62% accuracy) as compared to GPT-3.5. Interestingly, in contrast to the general observation, no significant improvement in accuracy is observed with the chain of thought prompting. To evaluate the limitations, we performed an error analysis, which revealed conceptual errors (~64%) as the major contributor compared to computational errors (~36%) towards the reduced performance of LLMs. We hope that the dataset and analysis performed in this work will promote further research in developing better materials science domain-specific LLMs and strategies for information extraction.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

This paper introduces MedMCQA, a new large-scale, Multiple-Choice Question Answering (MCQA) dataset designed to address real-world medical entrance exam questions. More than 194k high-quality AIIMS \& NEET PG entrance exam MCQs covering 2.4k healthcare topics and 21 medical subjects are collected with an average token length of 12.77 and high topical diversity. Each sample contains a question, correct answer(s), and other options which requires a deeper language understanding as it tests the 10+ reasoning abilities of a model across a wide range of medical subjects \& topics. A detailed explanation of the solution, along with the above information, is provided in this study.

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

The present study aims to explore the capabilities of Language Models (LMs) in tackling high-stakes multiple-choice tests, represented here by the Exame Nacional do Ensino M\'edio (ENEM), a multidisciplinary entrance examination widely adopted by Brazilian universities. This exam poses challenging tasks for LMs, since its questions may span into multiple fields of knowledge, requiring understanding of information from diverse domains. For instance, a question may require comprehension of both statistics and biology to be solved. This work analyzed responses generated by GPT-3.5 and GPT-4 models for questions presented in the 2009-2017 exams, as well as for questions of the 2022 exam, which were made public after the training of the models was completed. Furthermore, different prompt strategies were tested, including the use of Chain-of-Thought (CoT) prompts to generate explanations for answers. On the 2022 edition, the best-performing model, GPT-4 with CoT, achieved an accuracy of 87%, largely surpassing GPT-3.5 by 11 points. The code and data used on experiments are available at https://github.com/piresramon/gpt-4-enem.

Molecular hydrogen (H_2) is by far the most abundant molecule in the Universe. However, due to the low emissivity of H_2, carbon monoxide (CO) is widely used instead to trace molecular gas in galaxies. The relative abundances of these molecules is expected to depend on both physical (e.g., density) and chemical (e.g., metal enrichment) properties of the gas, making direct measurements in diverse environments crucial. We present a systematic search for CO in absorption toward 34 stars behind H_2 gas in the Magellanic Clouds using the Hubble Space Telescope. We report the first two definitive detections of CO absorption in the Large Magellanic Cloud (LMC) and one in the Small Magellanic Cloud (SMC), along with stringent upper limits for the remaining sightlines. Non-detections of CO are consistent with models of low thermal pressures and/or low metallicities while detections at the lower metallicities of the Magellanic Clouds require higher thermal pressures, P_{rm th}=10^5-10^6,K,cm^{-3} than detections the Milky Way at similar N({rm H_2}). Notably, the high density derived from the rotational excitation of CO towards SK,143 in the SMC suggests full molecularization of CO in the absorbing cloud, with CO/H_2 = 8.3^{+2.0}_{-1.6}times10^{-5} consistent with the standard ratio (3.2times10^{-4}) measured in dense molecular gas in the Milky Way, scaled to the SMC's 0.2,Z_{odot} metallicity.

Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.

Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would enable high-throughout, high-accuracy molecular screening campaigns to explore vast regions of chemical space and facilitate ab initio simulations at sizes and time scales that were previously inaccessible. However, a fundamental challenge to creating ML models that perform well across molecular chemistry is the lack of comprehensive data for training. Despite substantial efforts in data generation, no large-scale molecular dataset exists that combines broad chemical diversity with a high level of accuracy. To address this gap, Meta FAIR introduces Open Molecules 2025 (OMol25), a large-scale dataset composed of more than 100 million density functional theory (DFT) calculations at the omegaB97M-V/def2-TZVPD level of theory, representing billions of CPU core-hours of compute. OMol25 uniquely blends elemental, chemical, and structural diversity including: 83 elements, a wide-range of intra- and intermolecular interactions, explicit solvation, variable charge/spin, conformers, and reactive structures. There are ~83M unique molecular systems in OMol25 covering small molecules, biomolecules, metal complexes, and electrolytes, including structures obtained from existing datasets. OMol25 also greatly expands on the size of systems typically included in DFT datasets, with systems of up to 350 atoms. In addition to the public release of the data, we provide baseline models and a comprehensive set of model evaluations to encourage community engagement in developing the next-generation ML models for molecular chemistry.

We present a novel method for obtaining high-quality, domain-targeted multiple choice questions from crowd workers. Generating these questions can be difficult without trading away originality, relevance or diversity in the answer options. Our method addresses these problems by leveraging a large corpus of domain-specific text and a small set of existing questions. It produces model suggestions for document selection and answer distractor choice which aid the human question generation process. With this method we have assembled SciQ, a dataset of 13.7K multiple choice science exam questions (Dataset available at http://allenai.org/data.html). We demonstrate that the method produces in-domain questions by providing an analysis of this new dataset and by showing that humans cannot distinguish the crowdsourced questions from original questions. When using SciQ as additional training data to existing questions, we observe accuracy improvements on real science exams.

We present two new interatomic potentials for platinum (Pt) in angular-dependent potential (ADP) and modified Tersoff (MT) formats. Both potentials have been trained on a reference database of first-principles calculations without using experimental data. The properties of Pt predicted by the ADP and MT potentials agree better with DFT calculations and experimental data than the potentials available in the literature. Future applications of the MT model to mixed-bonding metal-covalent systems are discussed.

Large language models (LLMs) are increasingly considered as tutoring aids in science education. Yet their readiness for unsupervised use in undergraduate instruction remains uncertain, as reliable teaching requires more than fluent recall: it demands consistent, principle-grounded reasoning. Thermodynamics, with its compact laws and subtle distinctions between state and path functions, reversibility, and entropy, provides an ideal testbed for evaluating such capabilities. Here we present UTQA, a 50-item undergraduate thermodynamics question answering benchmark, covering ideal-gas processes, reversibility, and diagram interpretation. No leading 2025-era model exceeded our 95\% competence threshold: the best LLMs achieved 82\% accuracy, with text-only items performing better than image reasoning tasks, which often fell to chance levels. Prompt phrasing and syntactic complexity showed modest to little correlation with performance. The gap concentrates in finite-rate/irreversible scenarios and in binding visual features to thermodynamic meaning, indicating that current LLMs are not yet suitable for unsupervised tutoring in this domain.

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.

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 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.

We performed a uniform and detailed abundance analysis of 12 refractory elements (Na, Mg, Al, Si, Ca, Ti, Cr, Ni, Co, Sc, Mn, and V) for a sample of 257 G- and K-type evolved stars from the CORALIE planet search program. To date, only one of these stars is known to harbor a planetary companion. We aimed to characterize this large sample of evolved stars in terms of chemical abundances and kinematics, thus setting a solid base for further analysis of planetary properties around giant stars. This sample, being homogeneously analyzed, can be used as a comparison sample for other planet-related studies, as well as for different type of studies related to stellar and Galaxy astrophysics. The abundances of the chemical elements were determined using an LTE abundance analysis relative to the Sun, with the spectral synthesis code MOOG and a grid of Kurucz ATLAS9 atmospheres. To separate the Galactic stellar populations both a purely kinematical approach and a chemical method were applied. We confirm the overabundance of Na in giant stars compared to the field FGK dwarfs. This enhancement might have a stellar evolutionary character, but departures from LTE may also produce a similar enhancement. Our chemical separation of stellar populations also suggests a "gap" in metallicity between the thick-disk and high-alpha metal-rich stars, as previously observed in dwarfs sample from HARPS. The present sample, as most of the giant star samples, also suffers from the B - V colour cut-off, which excludes low-log g stars with high metallicities, and high-logg star with low-[Fe/H]. For future studies of planet occurrence dependence on stellar metallicity around these evolved stars we suggest to use a sub-sample of stars in a "cut-rectangle" in the logg - [Fe/H] diagram to overcome the aforementioned issue.

The advent of artificial intelligence (AI) has enabled a comprehensive exploration of materials for various applications. However, AI models often prioritize frequently encountered materials in the scientific literature, limiting the selection of suitable candidates based on inherent physical and chemical properties. To address this imbalance, we have generated a dataset of 1,494,017 natural language-material paragraphs based on combined OQMD, Materials Project, JARVIS, COD and AFLOW2 databases, which are dominated by ab initio calculations and tend to be much more evenly distributed on the periodic table. The generated text narratives were then polled and scored by both human experts and ChatGPT-4, based on three rubrics: technical accuracy, language and structure, and relevance and depth of content, showing similar scores but with human-scored depth of content being the most lagging. The merger of multi-modality data sources and large language model (LLM) holds immense potential for AI frameworks to help the exploration and discovery of solid-state materials for specific applications.

Recent observations by JWST have revealed supersolar ^{14}N abundances in galaxies at very high redshift. On the other hand, these galaxies show subsolar metallicity. The observed N/O ratios are difficult to reproduce in the framework of chemical evolution models for the Milky Way. Our aim is to reproduce these high N/O ratios with chemical evolution models assuming different histories of star formation triggering galactic winds coupled with detailed nucleosynthesis prescriptions for ^{14}N, ^{12}C, ^{16}O and ^{56}Fe. We compute several models for small galaxies (10^{9} - 10^{10} M_{odot}) with high star formation efficiency and strong galactic winds. These winds are assumed to be differential, carrying out mainly the products of the explosion of core-collapse supernovae. We find that only models with high star formation rates, normal initial mass function, and differential galactic winds can reproduce the observed chemical abundances. We also find that with the same assumptions about star formation and galactic winds, but with a very rapid formation resulting from fast gas infall, we can also reproduce the estimated ages of these objects. We find no necessity to invoke peculiar nucleosynthesis from Population III stars, very massive stars and supermassive stars.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Recent JWST observations with NIRCam and MIRI of the ultra-short-period super-Earth 55 Cancri e indicate a possible volatile atmosphere surrounding the planet. Previous analysis of the NIRCam spectra suggested potential absorption features from CO2 or CO and significant sub-weekly variability. The MIRI low-resolution spectrum does not contain substantial features but was found to be consistent with effective heat redistribution models. In this work, we computed a grid of over 25000 self-consistent 1D forward models incorporating H-N-O-C-S-P-Si-Ti equilibrium chemistry and assessed plausible atmospheric compositions based on the current JWST data. Despite exhaustive analysis, the composition and properties of the atmosphere remain elusive. While our results statistically favour a global, hydrogen-free, nitrogen-dominated atmosphere enriched in PO and CO2, various alternative compositions, including H2O-,CO-, PH3-, or Si-bearing remain viable explanations. Unconstrained heat redistribution efficiency and absolute NIRCam flux are among the largest sources of uncertainty in our analysis. We also find that the heat redistribution factor and surface pressure are highly degenerate with atmospheric composition, and that these parameters cannot be independently constrained using current JWST observations. Furthermore, we show that the observed variability may arise from dynamic interactions between the atmosphere and an underlying magma ocean, driving rapid shifts in atmospheric chemistry and thermal emission. Our results highlight the importance of using self-consistent forward models when analysing novel JWST spectra with limited signal-to-noise ratios -- such as those of 55 Cancri e -- as it allows for a more comprehensive evaluation of potential atmospheric scenarios while also being less sensitive to subtle spectral differences than retrievals...

We introduce a high-quality dataset that contains 3,397 samples comprising (i) multiple choice questions, (ii) answers (including distractors), and (iii) their source documents, from the educational domain. Each question is phrased in two forms, normal and close. Correct answers are linked to source documents with sentence-level annotations. Thus, our versatile dataset can be used for both question and distractor generation, as well as to explore new challenges such as question format conversion. Furthermore, 903 questions are accompanied by their cognitive complexity level as per Bloom's taxonomy. All questions have been generated by educational experts rather than crowd workers to ensure they are maintaining educational and learning standards. Our analysis and experiments suggest distinguishable differences between our dataset and commonly used ones for question generation for educational purposes. We believe this new dataset can serve as a valuable resource for research and evaluation in the educational domain. The dataset and baselines will be released to support further research in question generation.

Making analogies is fundamental to cognition. Proportional analogies, which consist of four terms, are often used to assess linguistic and cognitive abilities. For instance, completing analogies like "Oxygen is to Gas as <blank> is to <blank>" requires identifying the semantic relationship (e.g., "type of") between the first pair of terms ("Oxygen" and "Gas") and finding a second pair that shares the same relationship (e.g., "Aluminum" and "Metal"). In this work, we introduce a 15K Multiple-Choice Question Answering (MCQA) dataset for proportional analogy completion and evaluate the performance of contemporary Large Language Models (LLMs) in various knowledge-enhanced prompt settings. Specifically, we augment prompts with three types of knowledge: exemplar, structured, and targeted. Our results show that despite extensive training data, solving proportional analogies remains challenging for current LLMs, with the best model achieving an accuracy of 55%. Notably, we find that providing targeted knowledge can better assist models in completing proportional analogies compared to providing exemplars or collections of structured knowledge.

Artificial intelligence is gradually demonstrating its immense potential, and increasing attention is being given to how AI can be harnessed to advance scientific research. In this vision paper, we present our perspectives on how AI can better assist scientific inquiry and explore corresponding technical approach. We have proposed and open-sourced a large model of our KALE-LM model series, Llama3-KALE-LM-Chem-8B, which has achieved outstanding performance in tasks related to the field of chemistry. We hope that our work serves as a strong starting point, helping to realize more intelligent AI and promoting the advancement of human science and technology, as well as societal development.

Planetary nebulae are the products of the evolution of low and intermediate mass stars. The chemical property studies of these objects give important information about the elemental abundances as He, O, Ne, Ar, S and their modifications associated with the evolution of the progenitor stars. The determination of accurate abundances in planetary nebulae is important from the perspective of the stellar evolution as well as the formation and chemical evolution of galaxies. Recently, new HeI emissivities and ionization correction factors (ICFs) were published in the literature. In this work, these new parameters are used in a code for the determination of chemical abundances in photoionized nebulae. This code is used for the recompilation of the chemical abundances of planetary nebulae from the Galactic bulge observed previously by our group and also for the determination of new chemical abundances of a sample of planetary nebulae located near the Galactic centre. The new emissivities and ICFs slightly modified the elemental abundances of He, N, O, Ar and Ne. On the other hand, S abundances are higher than previous determinations. The new ICFs can contribute to solve partially the sulphur anomaly.

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.