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Lipid Droplet Targeting Drives Substrate Access during Very Long Chain Fatty Acid Activation by Fat1
Carolin Willner, Jennifer Sapia, Bianca M. Esch, Pia Erdbrügger, Lisa Kauffmann, Alicia Damm, Sergej Limar, Sebastian Eising, Stefan Walter, Abdou Rachid Thiam, Carolin Körner, Stefano Vanni, Florian Fröhlich
bioRxiv 2026. DOI: 10.64898/2026.02.09.704383
A searchable metadata network graph for microbiome metabolomics
Vincent Charron-Lamoureux, Shipei Xing, Abubaker Patan, Corinn Walker, Ricardo-Almada Monter, Yasin El Abiead, Haoqi Nina Zhao, Lucas Patel, Yuhan Weng, Antonio Gonzalez, Gail Ackermann, Victoria Deleray, Vishant Gandhi, Ipsita Mohanty, Andres Mauricio Caraballo-Rodriguez, Kine Eide Kvitne, Simone Zuffa, Annabelle Norman, Anthony Martin, Loryn Chin, Rocio Paz-Gonzalez, Marta Sala-Climent, Nadia Suryawinata, Jasmine Zemlin, Harsha Gouda, Zhewen Hu, Grant Norton, Prajit Rajkumar, Anthony JA Molina, Jaclyn Bergstrom, Monae Pinner, Sadie Giddings, Allegra T. Aron, Liang Liang, Samira Dahesh, Santosh Lamichhane, Erin R. Reilly, Victor Nizet, Anna Skrip, April L. Lukowski, Selene F.H. Shore, Subhomitra Ghoshal, Melinda A. Engevik, Thomas D. Horvath, Simone Renwick, Julius Agongo, Maria L. Marco, Sarkis K.Mazmanian, Mingxun Wang, Heejung Yang, Daniel McDonald, Monica Guma, Evi Stegmann, Naybel Hernandez Perez, Paolo Stincone, Eric Kemen, Abzer Kelminal. Pakkir Shah, Lars Bode, Daniel Petras, Dionicio Siegel, Manuela Raffatellu, Andrew D. Patterson, Suzanne Devkota, Adrian Jinich, Rob Knight, Karsten Zengler, Pieter C. Dorrestein
bioRxiv 2026. DOI: 10.64898/2026.02.04.703849
From Evaluation to Design: Using Potential Energy Surface Smoothness Metrics to Guide Machine Learning Interatomic Potential Architectures
Ryan Liu, Eric Qu, Tobias Kreiman, Samuel M. Blau, Aditi S. Krishnapriyan
arXiv 2026. DOI: 10.48550/arXiv.2602.04861
Atomic-Level Insights into the Molecular Recognition of Anticancer Naphthoquinones by Human Serum Albumin: The Role of Apolar Side Chains in Binding Stability
Flavio Kock, Erick Cirilo, JesĂşs Valdiviezo, Tiago Venancio
Research Square 2026. DOI: 10.21203/rs.3.rs-8683311/v1
Comparative partitioning of model drugs across five pharmaceutical oils: Implications for passive loading in emulsions and oleosomes
Shengnan Zhao, Jieyu Zuo, Marlon C. Mallillin III, Nadia Bou-Chacra, Maryam Salami, Tyson S. Le, Neal M. Davies, Raimar Löbenberg
J. Drug Delivery Sci. Technol. 2026, 118, 108084. DOI: 10.1016/j.jddst.2026.108084
Cytogenotoxic Effects and Physicochemical and Molecular Profiles of Eugenol-Derived Triazoles With Phytotoxic Potential
Thayllon de Assis Alves, Thammyres de Assis Alves, Poliana Aparecida Rodrigues Gazolla, Ângela Maria Almeida Lima, Mariana Belizario de Oliveira, William dos Santos Belarmino, Camila Luiz Sena, Róbson Ricardo Teixeira, Elias Terra Werner, Othon Souto Campos, Adilson Vidal Costa, Milene Miranda Praça-Fontes
Chem. Biodiversity 2026, 23 (1), e03621. DOI: 10.1002/cbdv.202503621
Desymmetrization of Meso-Pyrrolidines via Oxoammonium-Catalyzed Enantioselective Hydride Transfer
Jonas Rein, Bartosz Górski, Ayça M Keskin, Minh Hoang Le, Song Lin
ChemRxiv 2026. DOI: 10.26434/chemrxiv.10001724/v1
Assessing Boltz-2 Performance for the Binding Classification of Docking Hits
Guillaume Bret, François Sindt, Didier Rognan
J. Chem. Inf. Model 2026, 66, 3, 1511–1521. DOI: 10.1021/acs.jcim.5c02630
Development of a Chemical Probe to Enable Characterization of the Casein Kinase 1Îł Subfamily
Jacob L. Capener, Thomas W. Kramer, Frances M. Bashore, Emily Flory, Fengling Li, Blair L. Strang, Alison D. Axtman
J. Med. Chem. 2026. DOI: 10.1021/acs.jmedchem.5c02609
Accuracy and Efficiency Benchmarks of Pretrained Machine Learning Potentials for Molecular Simulations
Peter Eastman, Evan Pretti, Thomas E. Markland
arXiv 2026. DOI: 10.48550/arXiv.2601.16331
A Practical and Efficient Asymmetric Synthesis of the Tobacco Natural Alkaloids (S)-Anatabine and (S)-Anabasine via an Allylation/Metathesis-based Approach
Daisy C. Romero, Ruben Tapia, Enrique Botana, Alberto Martinez Cuezva, Mateo Alajarin, Corin Wagen, Arien Wagen, Jose M. Villalgordo
Synlett 2026. DOI: 10.1055/a-2795-3115
Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model
Justin Airas, Bin Zhang
arXiv 2026. DOI: 10.48550/arXiv.2601.05388
AceFF: A State-of-the-Art Machine Learning Potential for Small Molecules
Stephen E. Farr, Stefan Doerr, Antonio Mirarchi, Francesc Sabanes Zariquiey, Gianni De Fabritiis
arXiv 2026. DOI: 10.48550/arXiv.2601.00581
ChemRefine: An open-source automated and interoperable platform for machine learning and quantum chemistry simulations
Ignacio Migliaro, Markus G. S. Weiss, Alistair J. Sterling
ChemRxiv 2025. DOI: 10.26434/chemrxiv-2025-cvg1x
Orthogonal Cleavage of the HMPB Linker from Solid Support Using HFIP
Michael Desgagné, Dennis A. Kutateladze, Bradley L. Pentelute
Org. Lett. 2025, 27, 50, 13707–13710. DOI: 10.1021/acs.orglett.5c04086
Density Functional Theory Surrogate Enables Fast and Broad Computational Evaluation of Homogeneous Transition Metal Catalytic Energy Landscapes
Daniel H. Ess, Kevin P. Quirion, Wang-Yeuk Kong, Britton Stanley, Jyothish Joy
ChemRxiv 2025. DOI: 10.26434/chemrxiv-2025-z1s3s
Controlled Self-Immolative Release of β-Lapachone via an Optimized para-Hydroxybenzyl Linker for Targeted Pancreatic Cancer Therapy
Julie B. Becher, Nisita Dutta, Claudio D. Navo, Lavinia Dunsmore, Roman Misteli, Enrique Gil de Montes, Grant G. Simpson, Christine C. Alewine, Gonzalo Jiménez-Osés, Gonçalo J. L. Bernardes
JACS 2025. DOI: 10.1021/jacs.5c17598
Machine Learning-Guided Photocatalytic Cross-Coupling of Phenols and Heteroaryl Halides
Matthew C. Carson, Alice Wu, Kalyana B. Duggal, Madeline E. Rotella, Marisa C. Kozlowski
ChemRxiv 2025. DOI: 10.26434/chemrxiv-2025-5vcsz
Facile Synthesis of Non-Proteinogenic Sulfur-Containing Cyclic Dipeptides and Their Structure–Antioxidant Activity Relationship
Vijay M., Jugun Prakash Chinta
Chem. Asian J. 2025, 21, 1, e00968. DOI: 10.1002/asia.202500968
Universally Converging Representations of Matter Across Scientific Foundation Models
Sathya Edamadaka, Soojung Yang, Ju Li, Rafael GĂłmez-Bombarelli
arXiv 2025. DOI: 10.48550/arXiv.2512.03750
An inositol pyrophosphate interaction screen provides insight into the regulation of plant casein kinase II
Kristina Sturm, Oded Pri-Tal, Felix Rico-Resendiz, Yash Verma, Annika Richter, Houming Chen, Larissa Broger, Ludwig A. Hothorn, Dorothea Fiedler, Vikram Govind Panse, Michael Hothorn
bioRxiv 2025. DOI: 10.1101/2025.11.27.691040
Molecular Determinants of Per- and Polyfluoroalkyl Substances Binding to Estrogen Receptors
Sahith Mada, Samuel Jordan, Joshua Mathew, Coby Loveranes, James Moran, Harrish Ganesh, Sivanesan Dakshanamurthy
Toxics 2025, 13(11), 903. DOI: 10.3390/toxics13110903
Electrochemical oxidation enables aromatic C–H amination with dual mechanisms
Griffin Stewart, Eva Maria Alvarez, Chris Rapala, Jonathan H. Sklar, Julia A. Kalow, Christian A. Malapit
Nat. Synth. 2025. DOI: 10.1038/s44160-025-00890-9
Are neural scaling laws leading quantum chemistry astray?
Siwoo Lee, Adji Bousso Dieng
arXiv 2025. DOI: 10.48550/arXiv.2509.26397
Advanced GC-MS Chemosensing Combined with Atomistic Modeling: A Synergistic Approach for Environmental Water Analysis
Sanja J. Armaković, Stevan Armaković
Chemosensors 2025, 13(9), 353. DOI: 10.3390/chemosensors13090353
Simulation and Machine Learning Assessment of P-Glycoprotein Pharmacology in the Blood–Brain Barrier: Inhibition and Substrate Transport
Christian Jorgensen, Elizabeth Oliphant, Milly Barker, Eduardo LĂłpez MartĂnez, Saaihasamreen Thulasi, Holly Prior, Ben William Franey, Charley Gregory, Jerry Oluwasegun, Anjalee Ajay, Roger R. Draheim
Int. J. Mol. Sci. 2025, 26(18), 905029. DOI: 10.3390/ijms26189050
Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets
Diego Barquero Morera, Giovanni Mattiotti, Alexandar Kocev, Amshuman Rousselot, Louis Meuret, Lucas Rouaud, Hubert Santuz, Marc Baaden, Antoine Taly, Samuela Pasquali
J. Chem. Theory Comput. 2025, 21, 18, 9120–9135. DOI: 10.1021/acs.jctc.5c00688
ZnO-Based Photocatalysts: Synergistic Effects of Material Modifications and Machine Learning Optimization
Sanja J. Armaković, Stevan Armaković, Andrijana Bilić, Maria M. Savanović
Catalysts 2025, 15(8), 793. DOI: 10.3390/catal15080793
Selective endo-Cyclic α-Functionalization of Saturated N-Alkyl Piperidines
Rachel C. Phillips, John C. K. Chu, Alex A. Rafaniello, Matthew J. Gaunt
J. Org. Chem. 2025, 90, 34, 12226–12239. DOI: 10.1021/acs.joc.5c01742
Open Molecular Crystals 2025 (OMC25) Dataset and Models
Vahe Gharakhanyan, Luis Barroso-Luque, Yi Yang, Muhammed Shuaibi, Kyle Michel, Daniel S. Levine, Misko Dzamba, Xiang Fu, Meng Gao, Xingyu Liu, Haoran Ni, Keian Noori, Brandon M. Wood, Matt Uyttendaele, Arman Boromand, C. Lawrence Zitnick, Noa Marom, Zachary W. Ulissi, Anuroop Sriram
arXiv 2025. DOI: 10.48550/arXiv.2508.02651
Contrasting sonochemical with electrochemical and catalytic processes for degrading representative pharmaceuticals in synthetic urine – Treatment of binary mixtures, theoretical calculations, and life cycle assessment
Yudy L. MartĂnez-Mena, Javier Silva-Agredo, Marcela Paredes-Laverde, Ricardo A. Torres-Palma, EfraĂm A. Serna-Galvis
J. Environ. Chem. Eng. 2025, 13, 5, 118295. DOI: 10.1016/j.jece.2025.118295
Room-temperature defluorination of PTFE and PFAS via sodium dispersion
Taichi Araki, Hibiki Ota, Yusuke Murata, Yuji Sumii, Jin Hamaura, Hiroaki Adachi, Takumi Kagawa, Hisao Hori, Jorge Escorihuela, Norio Shibata
Nat. Commun. 2025, 16, 6526. DOI: 10.1038/s41467-025-61819-6
Total Synthesis of Aporphine Alkaloids via Photocatalytic Oxidative Phenol Coupling and Biological Evaluation at the Serotonin 5-HT2 and Adrenergic α1A Receptors
Matthew C. Carson, Jorge de Lima Neto, Kalyana B. Duggal, Paulo H. Menezes, Marisa C. Kozlowski
J. Med. Chem. 2025, 68, 14, 14628–14644. DOI: 10.1021/acs.jmedchem.5c00771
Representing local protein environments with atomistic foundation models
Meital Bojan, Sanketh Vedula, Advaith Maddipatla, Nadav Bojan Sellam, Federico Napoli, Paul Schanda, Alex M. Bronstein
arXiv 2025. DOI: 10.48550/arXiv.2505.23354
Be sure to check out Meital and Sanketh's blog post about this paper too!
The contribution of cyclic imide stereoisomers on cereblon-dependent activity
Yuka Amako, Saki Ichikawa, Hannah C. Lloyd, Connor Payne, Zhi Lin, Andrew S. Boghossian, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Qian Zhu, Bogdan Budnik, Ralph Mazitschek, Christina M. Woo
Chemical Science 2025, 16, 11519-11529. DOI: 10.1039/d5sc01371b
Similar Binding Mode of a 5-Sulfonylthiouracil Derivative Antagonist at Chemerin Receptors CMKLR1 and GPR1
Tina Schermeng, Alexander FĂĽrll, Fabian Liessmann, Lukas von Bredow, Jan Stichel, C. David Weaver, Maik Tretbar, Jens Meiler, Annette G. Beck-Sickinger
J. Med. Chem. 2025, 68 (11), 11149–11173. DOI: 10.1021/acs.jmedchem.5c00135
Insights into the transformations, antimicrobial activity, and degradation efficiency of a representative carbapenem antibiotic by high-frequency ultrasound hybridized with the (photo)Fenton process
EfraĂm A. Serna-Galvis, Kevin P. Celis-Llamoca, Ingrit E. Collantes-DĂaz, Ricardo A. Torres-Palma, Jessica I. Nieto-Juárez
Ultrason. Sonochem. 2025, 119, 107379. DOI: 10.1016/j.ultsonch.2025.107379
Green and Tandem Synthesis of Heterocyclic α,α'-Dibromocycloamides and Their Target Predictions and ADMET Analysis
Dinesh S Shinde, Aarzoo F Qazi, Harshal R Patil, Ritvika Shukla, Rajendra D Patil, Pawan Gupta
ChemistrySelect 2025. DOI: 10.1002/slct.202501499
Strategic atom replacement enables regiocontrol in pyrazole alkylation
Alexander Fanourakis, Yahia Ali, Liao Chen, Patrick Q. Kelly, Abigail J. Bracken, Christopher B. Kelly, Mark D. Levin
Nature 2025. DOI: 10.1038/s41586-025-08951-x
Carbonic anhydrase II simulated with a universal neural network potential
Timothy T. Duignan
arXiv 2025. DOI: 10.48550/arXiv.2503.13789
Foundation Models for Atomistic Simulation of Chemistry and Materials
Eric C.-Y. Yuan, Yunsheng Liu, Junmin Chen, Peichen Zhong, Sanjeev Raja, Tobias Kreiman, Santiago Vargas, Wenbin Xu, Martin Head-Gordon, Chao Yang, Samuel M. Blau, Bingqing Cheng, Aditi Krishnapriyan, Teresa Head-Gordon
arXiv 2025. DOI: 10.48550/arXiv.2503.10538
Roadmapping Report: Focused Research Organizations in Atomistic Simulation
Sam Holton
OSF Preprints 2024. DOI: 10.31219/osf.io/aq92k