Preprint scanner project / Issue 2026-07-01

Useful Chemistry

A weekly review of arXiv, ChemRxiv, and bioRxiv for ai-enabled methodological advances. Up to twenty papers reviewed every week; a quiet week may publish none.

10 selected / 247 reviewed Jun 24, 2026–Jun 30, 2026
Groups
Group roll call
96 followed groups Research-group roll call
  • Milad Abolhasani Abolhasani Lab North Carolina State University Site ↗
  • Surl-Hee (Shirley) Ahn Ahn Lab University of California, Davis Site ↗
  • Mohammed AlQuraishi AlQuraishi Laboratory Columbia University Site ↗
  • Sayan Banerjee Banerjee Group University of Tennessee, Knoxville Site ↗
  • Christopher J. Bartel Bartel Research Group University of Minnesota Twin Cities Site ↗
  • Jan-Niklas Boyn Boyn Research Group University of Minnesota Twin Cities Site ↗
  • Ting Cao Cao Group University of Washington Site ↗
  • Timothy Cernak Cernak Lab University of Michigan Site ↗
  • Ming Chen Ming Chen Group Purdue University Site ↗
  • Po-Yen Chen Chen Research Group University of Maryland, College Park Site ↗
  • Bingqing Cheng Cheng Group University of California, Berkeley Site ↗
  • Brian Cleary Algorithmic Lens on Experimental Biology Laboratory Boston University Site ↗
  • Connor W. Coley Coley Research Group Massachusetts Institute of Technology Site ↗
  • Yamil J. Colón Colón Group University of Notre Dame Site ↗
  • César de la Fuente Machine Biology Group University of Pennsylvania Site ↗
  • Julia Dshemuchadse Cape Crystal Cornell University Site ↗
  • Thomas P. Fay Fay Group University of California, Los Angeles Site ↗
  • Kara D. Fong Fong Lab California Institute of Technology Site ↗
  • Thomas E. Gartner III Gartner Group Lehigh University Site ↗
  • Rafael Gómez-Bombarelli Learning Matter Massachusetts Institute of Technology Site ↗
  • Jonathan Gootenberg Gootenberg Laboratory Harvard University Site ↗
  • Prashun Gorai 3D Materials Lab Rensselaer Polytechnic Institute Site ↗
  • Diptarka Hait Hait Group Columbia University Site ↗
  • Brian Hie Laboratory of Evolutionary Design Stanford University Site ↗
  • Guoxiang Hu Hu Group Georgia Institute of Technology Site ↗
  • Yong-Jie Hu Materials Computation and Informatics Group Drexel University Site ↗
  • Yifei Huang Huang Lab Pennsylvania State University Site ↗
  • Yunha Hwang Hwang Lab Massachusetts Institute of Technology Site ↗
  • Nicholas E. Jackson AI for Materials Group University of Illinois Urbana-Champaign Site ↗
  • William M. Jacobs Jacobs Group Princeton University Site ↗
  • Dipti Jasrasaria Jasrasaria Group University of Chicago Site ↗
  • Anupama Jha Jha Lab Yale University Site ↗
  • Kaiyi Jiang Jiang Lab Princeton University Site ↗
  • Adrian Jinich Jinich Lab University of California, San Diego Site ↗
  • Felipe Jornada Jornada Research Group Stanford University Site ↗
  • Kalli Kappel Kappel Lab University of California, Los Angeles Site ↗
  • Joshua Kretchmer Kretchmer Research Group Georgia Institute of Technology Site ↗
  • Aditi S. Krishnapriyan Krishnapriyan Research Group University of California, Berkeley Site ↗
  • Sebastian Kube Kube Lab University of Wisconsin–Madison Site ↗
  • Heather J. Kulik Kulik Research Group Massachusetts Institute of Technology Site ↗
  • Ambarish R. Kulkarni Kulkarni Research Group University of California, Davis Site ↗
  • Joseph S. Kwon Kwon Research Group The Ohio State University Site ↗
  • Joonho Lee Lee Group Harvard University Site ↗
  • Can Li Li Research Group Purdue University Site ↗
  • Wanlu Li Wanlu Li Research Group University of California, San Diego Site ↗
  • Rebecca K. Lindsey Lindsey Lab University of Michigan Site ↗
  • Ge Liu Ge Liu Group University of Illinois Urbana-Champaign Site ↗
  • Yuanyue Liu Yuanyue Liu Group The University of Texas at Austin Site ↗
  • Yang Lu Lu Lab University of Wisconsin–Madison Site ↗
  • Jiankun Lyu Evnin Family Laboratory of Computational Molecular Discovery The Rockefeller University Site ↗
  • Cong Ma Cong Ma Lab University of Michigan Site ↗
  • Arkajit Mandal Mandal Group Texas A&M University Site ↗
  • Andrew J. Medford Medford Research Group Georgia Institute of Technology Site ↗
  • Ilias Mitrai Systems and AI Lab The University of Texas at Austin Site ↗
  • Jeetain Mittal Mittal Group Texas A&M University Site ↗
  • Joel A. Paulson Paulson Lab University of Wisconsin–Madison Site ↗
  • Elisa Pieri Pieri Lab University of North Carolina at Chapel Hill Site ↗
  • Doran Raccah MesoScience Lab The University of Texas at Austin Site ↗
  • Phillip Rauscher Rauscher Group New York University Site ↗
  • Wesley Reinhart Reinhart Group Pennsylvania State University Site ↗
  • Gabriel J. Rocklin Rocklin Lab Northwestern University Site ↗
  • Andrew S. Rosen Rosen Research Group Princeton University Site ↗
  • Grant M. Rotskoff Rotskoff Group Stanford University Site ↗
  • Janani Sampath Sampath Research Group University of Florida Site ↗
  • Elvira Sayfutyarova Sayfutyarova Group Pennsylvania State University Site ↗
  • Martin Seifrid Seifrid Group North Carolina State University Site ↗
  • Thomas P. Senftle Senftle Group Rice University Site ↗
  • Karthik Shekhar Shekhar Lab University of California, Berkeley Site ↗
  • Zachary M. Sherman Z Lab University of Washington Site ↗
  • Krishna Shrinivas Shrinivas Lab Northwestern University Site ↗
  • Rohit Singh Singh Lab Duke University Site ↗
  • Micheline Soley Soley Group University of Wisconsin–Madison Site ↗
  • Kevin V. Solomon Solomon Laboratory University of Delaware Site ↗
  • Jeff Spence Spence Lab University of California, San Francisco Site ↗
  • Kayla G. Sprenger Rational Design of Interfaces Lab University of Colorado Boulder Site ↗
  • Chong Sun Sun Lab Rutgers University–New Brunswick Site ↗
  • Yidan Sun Sun Lab Washington University in St. Louis Site ↗
  • Daniel Tabor Tabor Research Group Texas A&M University Site ↗
  • Ming Tang Mesoscale Materials Science Group Rice University Site ↗
  • Roel Tempelaar Tempelaar Team Northwestern University Site ↗
  • Erik Thiede Thiede Lab Cornell University Site ↗
  • Pratyush Tiwary Artificial Chemical Intelligence@Maryland University of Maryland, College Park Site ↗
  • Brian Trippe Trippe Lab Stanford University Site ↗
  • Alexander Urban Urban Research Group Columbia University Site ↗
  • David Van Valen Van Valen Lab California Institute of Technology Site ↗
  • Vojtech Vlcek Vlcek Group University of California, Santa Barbara Site ↗
  • Allon Wagner Wagner Lab University of California, Berkeley Site ↗
  • Shunzhi Wang Wang Lab New York University Site ↗
  • Michael A. Webb Webb Research Group Princeton University Site ↗
  • Mingjian Wen Wen Research Group University of Houston Site ↗
  • Hong-Zhou Ye Ye Group University of Maryland, College Park Site ↗
  • Shuwen Yue Yue Research Group Cornell University Site ↗
  • Daiwei (David) Zhang Daiwei Zhang Lab University of North Carolina at Chapel Hill Site ↗
  • Hongbo Zhao Zhao Research Group University of California, San Diego Site ↗
  • Jian Zhou Zhou Lab University of Chicago Site ↗
  • Tianyu Zhu Zhu Group Yale University Site ↗

Issue 2026-07-01

Highlights from this week

Preprint—not peer reviewed

Contrastive Regularization of Machine Learning Potentials

Contrastive Regularized MSE adds a distribution-aware term to ordinary energy-and-force fitting and uses persistent Langevin samples from the potential itself to expose configurations that should be raised in energy. On ethanol and aspirin, the authors report that the correction restores energy, distance, and free-energy distributions to near-quantitative agreement with density functional theory while preserving force accuracy. The result makes a useful point for molecular simulation: a potential meant to generate trajectories must be trained against the distribution it produces.

AI–chemistryAI–materials Atomistic modelingNeural potentials
Abstract brief CC0 Preprint

Preprint—not peer reviewed

Autoregressive Boltzmann Generators

Autoregressive Boltzmann Generators replace flow-based Boltzmann generators with an autoregressive framework that avoids flow topology constraints and permits sequential interventions. The authors report that their 132-million-parameter transferable model reduces zero-shot energy error by more than 60% on 8-residue systems. The framework offers a likelihood-bearing route to more scalable equilibrium sampling for molecular systems.

AI–biochemistryAI–chemistry Atomistic modelingGenerative design
Abstract brief CC0 Preprint

Preprint—not peer reviewed

Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

NMRAgent combines specialized spectral-analysis tools with chemical knowledge graphs to plan structure elucidation, test peak-to-atom consistency, and refine candidate structures. The authors report a 46.5% improvement in top-1 accuracy and a 0.502 improvement in Tanimoto similarity on a scaffold-split benchmark. The resulting workflow makes molecular-structure proposals more inspectable and correctable when the test scaffolds are novel.

AI–chemistry Molecular representationScientific agents
Abstract brief CC0 Preprint

Preprint—not peer reviewed

BoltzProt-1: Towards Efficient De Novo Binder Design with Good Developability

BoltzProt-1 combines a refined generative binder model with BoltzPPI, a protein-interaction predictor used to rank designed nanobodies. Across ten novel targets, the authors report that confirmed-binder hit rates rise from 3.3 percent to 8.0 percent, while 58 percent of confirmed designs pass every measured developability criterion. Ranking designs by interaction quality rather than structure-prediction confidence connects de novo generation to two practical experimental bottlenecks: finding real binders and keeping the successful ones developable.

AI–biochemistry Biomolecular designGenerative designProtein engineering
Abstract brief CC BY Preprint

Preprint—not peer reviewed

Shape-Constrained Bayesian Active Learning of Self-Limiting Saturation Curves

This active-learning platform uses Bayesian monotonic I-spline regression so each posterior saturation curve rises from zero and never decreases. The authors report that it reaches noise-floor accuracy within a 20-measurement budget in every regime, in as few as seven measurements. The same shape-constrained surrogate can make sparse-data experiment selection physically consistent across self-limiting chemical and materials responses.

AI–chemistryAI–materials Surrogate modeling
Abstract brief CC0 Preprint

Preprint—not peer reviewed

Surrogate-Gated Generation and Foundation-Model Embeddings for Bayesian Materials Design

The workflow inserts a Gaussian-process acquisition gate between crystal generation and a property oracle in an RL-steered materials-design loop. The authors report that the gate comes within about 9% of exhaustive oracle spending at roughly one-fifth of the calls, while a density-functional-theory check confirms bulk-modulus predictions within 2.5% on average. This lets generative materials searches spend expensive calculations where a surrogate expects them to be most useful.

AI–materials Generative designSurrogate modeling
Abstract brief CC0 Preprint

Preprint—not peer reviewed

Identifying and Addressing Systematic Data Leakage in Protein-Ligand Affinity Benchmarks

The authors introduce the Novelty-Tiered Affinity Benchmark, which partitions test data into ligand novelty tiers to control target-mirroring leakage. They report that a ChEMBL 36 meta-analysis identifies more than 6,000 such assay pairs and that ligand-only models fall to r = 0.14 in the most challenging tier. The benchmark gives affinity models a more direct test of whether they generalize beyond localized leakage and memorized training data.

AI–biochemistryAI–chemistry Biomolecular structureDatasets + benchmarks
Abstract brief CC BY Preprint

Preprint—not peer reviewed

Interpretable Inverse Design of Metal-Organic Frameworks with Large Language Model Agents

LLM4MOF assigns one language-model agent to propose chemically interpretable design hypotheses and another to translate those hypotheses into constrained metal-organic framework candidates for simulation and revision. The authors report that ten autonomous iterations concentrate searches on strong candidates across six tasks within 400 property evaluations and outperform random search and a genetic algorithm during de novo simulated design. Because each candidate remains tied to explicit choices about nodes, linkers, pores, and functional chemistry, the loop can expose why a design succeeds instead of returning only a score.

AI–chemistryAI–materials Generative designScientific agents
Abstract brief CC0 Preprint

Preprint—not peer reviewed

Unsupervised Thermodynamics of Molecular Diffusion Models: Action-Operator Semantics and Auditable Free-Energy Readout

The paper defines an action-operator framework for molecular diffusion models and uses a noisy operator bridge to read out free-energy differences from endpoint ensembles. The authors report that endpoint coordinates and binary labels alone are sufficient to partially recover the operator shape and a centered free-energy scale without force or action supervision. This provides a route for turning diffusion models from coordinate samplers into thermodynamic estimators with an explicit physical interpretation.

AI–biochemistryAI–chemistry Atomistic modelingGenerative design
Abstract brief CC0 Preprint

Preprint—not peer reviewed

ReactionAtlas: Ab origine exploration of chemical reaction networks with machine learning

ReactionAtlas builds reaction networks from a handful of seed molecules without hand-crafted rules, using a generative model to propose reactions and a DFT-trained machine-learned force field to filter valid transition states. The authors report roughly 47,000 reactions among roughly 12,000 compounds from eight pre-biotic seeds, with 85% of machine-learned transition states within 0.5 Å RMSD of PBE0 references. This combination makes deep network exploration more tractable when the relevant products and transition states are not known in advance.

AI–chemistry Generative designNeural potentialsReaction modeling
Abstract brief CC0 Preprint