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The study of a single-molecule reaction under nanoconfinement is beneficial for understanding the reactive intermediates and reaction pathways. However, the kinetics model of the single-molecule reaction under confinement remains elusive. Herein we engineered an aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics under nanoconfinement. By identifying the bond-forming and non-bond-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the frequency of individual reactants captured and the fraction of effective collision inside the nanopore confined space. This insight will guide the design of confined nanopore reactors for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry inside confined systems such as supramolecular cages, coordination cages, and micelles.
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http://dx.doi.org/10.1039/d1sc06837g | DOI Listing |
J Org Chem
September 2025
State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin 124221, P. R. China.
The Buchwald-Hartwig (B-H) reaction graph, a novel graph for deep learning models, is designed to simulate the interactions among multiple chemical components in the B-H reaction by representing each reactant as an individual node within a custom-designed reaction graph, thereby capturing both single-molecule and intermolecular relationship features. Trained on a high-throughput B-H reaction data set, B-H Reaction Graph Neural Network (BH-RGNN) achieves near-state-of-the-art performance with an score of 0.971 while maintaining low computational costs.
View Article and Find Full Text PDFJ Phys Chem B
September 2025
Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea.
Epidermal growth factor receptor (EGFR) dimerization plays a pivotal role in cellular signaling, influencing proliferation and disease progression, particularly in cancer. Despite extensive studies, the quantitative relationship between EGFR expression levels and dimerization efficiency remains incompletely understood. In this study, we investigated EGFR dimerization kinetics using ensemble-level biochemical assays and single-molecule tracking (SMT) in living cells.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
September 2025
Department of Physics and Chemistry, DGIST, Daegu, 42988, Republic of Korea.
Investigation of the fundamental microscopic processes occurring in organic reactions is essential for optimising both organocatalysts and synthetic strategies. In this study, single-molecule fluorescence microscopy was employed to study the Diels-Alder reaction catalysed by a first-generation MacMillan catalyst, providing direct insights into its kinetic dynamics. This reaction proceeds via a series of reversible processes under equilibrium conditions (S ⇄ IM ⇄ IM → P, IM and IM: N,O-acetal and iminium ion intermediates, respectively).
View Article and Find Full Text PDFJ Am Chem Soc
September 2025
Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, Jiangsu P. R. China.
Advances in molecular analysis and characterization techniques should revolutionize the methods for scientific exploration across physics, chemistry, and biology, fundamentally overturning our understanding of interactions and processes that govern molecular behavior at the microscopic level. Currently, the absence of a molecular analysis method that can both quantify molecules and achieve single-molecule spatial resolution hinders our study of complex molecular systems in sorption and catalysis. Here, we propose a quantitative analysis strategy for small molecules confined in ZSM-5, a zeolite material extensively used in catalysis and gas separation, based on low-dose transmission electron microscopy.
View Article and Find Full Text PDFACS Appl Mater Interfaces
September 2025
College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, P. R. China.
Exhaled breath analysis offers noninvasive, early lung cancer detection via volatile organic compound (VOC) biomarkers, surpassing blood-based methods. Surface-enhanced Raman spectroscopy (SERS) is ideal for this purpose, combining molecular fingerprint specificity with single-molecule sensitivity. However, conventional SERS substrates face a fundamental limitation: while porous materials such as metal-organic frameworks effectively adsorb VOCs through their subnanometer pores (0.
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