arXiv subjects

Omar M. Yaghi

Publications and source records attributed to Omar M. Yaghi.

10 recordsLinked to original sources

arXiv2026

Local Structure and Dynamics of Three-Dimensional Covalent Organic Frameworks

Resolving and controlling the local dynamical properties of covalent organic frameworks (COFs) remains a central challenge, particularly when assembled from large, flexible building units. Here, we combine synchrotron X-ray pair distribution function (PDF) analyses with machine learning-accelerated molecular dynamics (MD) simulations to resolve the local structure and dynamics of two three-dimensional imine-linked COFs, COF-682 {[(DHP)(TAM)]$_{imine}$}, assembled from 6,13-dihydropentacene (DHP) and tetrakis(4-aminophenyl)methane (TAM), and COF-612 {[(HBC-LA$_{12}$)(HAPT)$_2$]$_{imine}$}, assembled from nanographene dodecabenzaldehyde hexakis{[3,5-bis($p$-formylphenyl)-4,6-dimethoxyphenyl]}hexabenzocoronene (HBC-LA$_{12}$) and 2,3,6,7,14,15-hexa(4-aminophenyl)triptycene (HAPT). Validated against the experimental PDFs through ensemble-averaged calculations, the simulations show that the exposed $π$-surface and V-shaped geometry of the DHP linker endow COF-682 with enhanced local flexibility through face-to-face and offset $π$-stacking interactions differing in both their average interplanar separation and their ring-plane tilt angle. In contrast, the extended nanographene linker rigidifies COF-612 by maintaining the planarity of its fused cores, while the linker pendant aryl rings equip both COFs with enhanced librational ability. The simulations further provide quantitative measures of the translational and reorientational mobility of the linkers, revealing how local COF dynamics may be tuned by balancing non-covalent interactions and different degrees of aromatic rigidity. The PDF-MD experimental-computational approach holds promise as a general method beyond conventional crystallography to gain insights into the local properties of COFs with the aim of directing their dynamic function.

cond-mat.mtrl-sci↗

arXiv2026

Data-driven Design of Metal-Organic Frameworks with Tunable Negative Thermal Expansion

Materials with negative thermal expansion (NTE) are essential for applications requiring precise control of thermal expansion. Owing to their exceptional chemical tunability, flexible architectures, and low-energy lattice vibrations, metal-organic frameworks (MOFs) represent a rich platform for exploring NTE. However, uncovering the structural motifs that govern NTE across the enormous MOF design space remains experimentally challenging, and large-scale first-principles phonon calculations are computationally prohibitive. Here, we comprehensively evaluate the factors influencing NTE in MOFs by utilizing a high-throughput workflow based on MACE-MP-MOF0, a machine learning interatomic potential fine-tuned for MOFs with near-ab initio accuracy, to construct PhononMOFdb, a database of phonons, inelastic neutron scattering spectra, bulk moduli, and heat capacities for over 12,000 MOFs. High-throughput screening of this database reveals that highly porous cubic topology frameworks with heavier, lower-valent metal nodes favor strong NTE, while linker functionalization provides a practical handle for tuning NTE magnitude and sign without compromising mechanical stability. Experimental validation via high-resolution temperature-dependent synchrotron powder X-ray diffraction on the Ce-UiO-66 MOF and its brominated variants confirms the design recipe and yields volumetric NTE coefficients surpassing current records. This work establishes a data-driven strategy for engineering NTE in MOFs, showing how machine learning-accelerated discovery and targeted experimental validation together unlock predictive materials design.

cond-mat.mtrl-sci↗

arXiv2026

A chemical language model for reticular materials design

Reticular chemistry has enabled the synthesis of tens of thousands of metal-organic frameworks (MOFs), yet the discovery of new materials still relies largely on intuition-driven linker design and iterative experimentation. As a result, researchers explore only a small fraction of the vast chemical space accessible to reticular materials, limiting the systematic discovery of frameworks with targeted properties. Here, we introduce Nexerra-R1, a building-block chemical language model that enables inverse design in reticular chemistry through the targeted generation of organic linkers. Rather than generating complete frameworks directly, Nexerra-R1 operates at the level of molecular building blocks, preserving the modular logic that underpins reticular synthesis. The model supports both unconstrained generation of low-connectivity linkers and scaffold-constrained design of symmetric multidentate motifs compatible with predefined nodes and topologies. We further combine linker generation with flow-guided distributional targeting to steer the generative process toward application-relevant objectives while maintaining chemical validity and assembly feasibility. The generated linkers are subsequently assembled into three-dimensional frameworks and are structurally optimized to produce candidate materials compatible with experimental synthesis. Using Nexerra-R1, we validate this strategy by rediscovering known MOFs and by proposing the experimental synthesis of a previously unreported framework, CU-525, generated entirely in silico. Together, these results establish a general inverse-design paradigm for reticular materials in which controllable chemical language modelling enables the direct translation from computational design to synthesizable frameworks.

cond-mat.mtrl-sci↗

arXiv2025

AI4X Roadmap: Artificial Intelligence for the advancement of scientific pursuit and its future directions

Artificial intelligence and machine learning are reshaping how we approach scientific discovery, not by replacing established methods but by extending what researchers can probe, predict, and design. In this roadmap we provide a forward-looking view of AI-enabled science across biology, chemistry, climate science, mathematics, materials science, physics, self-driving laboratories and unconventional computing. Several shared themes emerge: the need for diverse and trustworthy data, transferable electronic-structure and interatomic models, AI systems integrated into end-to-end scientific workflows that connect simulations to experiments and generative systems grounded in synthesisability rather than purely idealised phases. Across domains, we highlight how large foundation models, active learning and self-driving laboratories can close loops between prediction and validation while maintaining reproducibility and physical interpretability. Taken together, these perspectives outline where AI-enabled science stands today, identify bottlenecks in data, methods and infrastructure, and chart concrete directions for building AI systems that are not only more powerful but also more transparent and capable of accelerating discovery in complex real-world environments.

physics.soc-ph↗

arXiv2025

System of Agentic AI for the Discovery of Metal-Organic Frameworks

Generative models and machine learning promise accelerated material discovery in MOFs for CO2 capture and water harvesting but face significant challenges navigating vast chemical spaces while ensuring synthetizability. Here, we present MOFGen, a system of Agentic AI comprising interconnected agents: a large language model that proposes novel MOF compositions, a diffusion model that generates crystal structures, quantum mechanical agents that optimize and filter candidates, and synthetic-feasibility agents guided by expert rules and machine learning. Trained on all experimentally reported MOFs and computational databases, MOFGen generated hundreds of thousands of novel MOF structures and synthesizable organic linkers. Our methodology was validated through high-throughput experiments and the successful synthesis of five "AI-dreamt" MOFs, representing a major step toward automated synthesizable material discovery.

cond-mat.mtrl-sci↗

arXiv2024

Single and Multi-Hop Question-Answering Datasets for Reticular Chemistry with GPT-4-Turbo

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

cs.CL↗

arXiv2023

Image and Data Mining in Reticular Chemistry Using GPT-4V

The integration of artificial intelligence into scientific research has reached a new pinnacle with GPT-4V, a large language model featuring enhanced vision capabilities, accessible through ChatGPT or an API. This study demonstrates the remarkable ability of GPT-4V to navigate and obtain complex data for metal-organic frameworks, especially from graphical sources. Our approach involved an automated process of converting 346 scholarly articles into 6240 images, which represents a benchmark dataset in this task, followed by deploying GPT-4V to categorize and analyze these images using natural language prompts. This methodology enabled GPT-4V to accurately identify and interpret key plots integral to MOF characterization, such as nitrogen isotherms, PXRD patterns, and TGA curves, among others, with accuracy and recall above 93%. The model's proficiency in extracting critical information from these plots not only underscores its capability in data mining but also highlights its potential in aiding the creation of comprehensive digital databases for reticular chemistry. In addition, the extracted nitrogen isotherm data from the selected literature allowed for a comparison between theoretical and experimental porosity values for over 200 compounds, highlighting certain discrepancies and underscoring the importance of integrating computational and experimental data. This work highlights the potential of AI in accelerating scientific discovery and innovation, bridging the gap between computational tools and experimental research, and paving the way for more efficient, inclusive, and comprehensive scientific inquiry.

cs.AI↗

arXiv2023

A GPT-4 Reticular Chemist for Guiding MOF Discovery

We present a new framework integrating the AI model GPT-4 into the iterative process of reticular chemistry experimentation, leveraging a cooperative workflow of interaction between AI and a human researcher. This GPT-4 Reticular Chemist is an integrated system composed of three phases. Each of these utilizes GPT-4 in various capacities, wherein GPT-4 provides detailed instructions for chemical experimentation and the human provides feedback on the experimental outcomes, including both success and failures, for the in-context learning of AI in the next iteration. This iterative human-AI interaction enabled GPT-4 to learn from the outcomes, much like an experienced chemist, by a prompt-learning strategy. Importantly, the system is based on natural language for both development and operation, eliminating the need for coding skills, and thus, make it accessible to all chemists. Our collaboration with GPT-4 Reticular Chemist guided the discovery of an isoreticular series of MOFs, with each synthesis fine-tuned through iterative feedback and expert suggestions. This workflow presents a potential for broader applications in scientific research by harnessing the capability of large language models like GPT-4 to enhance the feasibility and efficiency of research activities.

cs.AI↗

arXiv2023

ChatGPT Chemistry Assistant for Text Mining and Prediction of MOF Synthesis

We use prompt engineering to guide ChatGPT in the automation of text mining of metal-organic frameworks (MOFs) synthesis conditions from diverse formats and styles of the scientific literature. This effectively mitigates ChatGPT's tendency to hallucinate information -- an issue that previously made the use of Large Language Models (LLMs) in scientific fields challenging. Our approach involves the development of a workflow implementing three different processes for text mining, programmed by ChatGPT itself. All of them enable parsing, searching, filtering, classification, summarization, and data unification with different tradeoffs between labor, speed, and accuracy. We deploy this system to extract 26,257 distinct synthesis parameters pertaining to approximately 800 MOFs sourced from peer-reviewed research articles. This process incorporates our ChemPrompt Engineering strategy to instruct ChatGPT in text mining, resulting in impressive precision, recall, and F1 scores of 90-99%. Furthermore, with the dataset built by text mining, we constructed a machine-learning model with over 86% accuracy in predicting MOF experimental crystallization outcomes and preliminarily identifying important factors in MOF crystallization. We also developed a reliable data-grounded MOF chatbot to answer questions on chemical reactions and synthesis procedures. Given that the process of using ChatGPT reliably mines and tabulates diverse MOF synthesis information in a unified format, while using only narrative language requiring no coding expertise, we anticipate that our ChatGPT Chemistry Assistant will be very useful across various other chemistry sub-disciplines.

cs.IR↗

arXiv2015

Thermal Maps of Gases in Heterogeneous Reactions

Over 85% of all chemical industry products are made using catalysts, with the overwhelming majority of these employing heterogeneous catalysts functioning at the gas-solid interface. Consequently, optimizing catalytic reactor design attracts much effort. Such optimization relies on heat transfer and fluid dynamics modeling coupled to surface reaction kinetics. The complexity of these systems demands many approximations, which can only be tested with experimental observations of quantities such as temperature, pressure, concentrations, flow rates, etc. One essential measurement is a map of the spatial variation in temperature throughout the catalyst bed. We present here the first non-invasive maps of gas temperatures in catalyst-filled reactors, including high spatial resolution maps in microreactors enabled by parahydrogen. The thermal maps reveal energy flux patterns whose length scale correlates with the catalyst packing. By exploiting the motional averaging under a weak applied magnetic-field gradient, the nuclear magnetic resonance (NMR) linewidths are inversely proportional to temperature. Measurements during the hydrogenation of propylene in reactors packed with metal nanoparticles and metal-organic framework catalysts yield temperature coefficients of ~0.1 Hz/K, and temperature error <4%. Temperature sensitivity increases with gradient strength, enabling tuning of precision.

physics.ins-det↗