Article
Chemistry, Physical
Aljaz Godec, Dmitrii E. Makarov
Summary: In this paper, we discuss the practical challenges of using stochastic thermodynamics to determine the directionality of molecular machines from experimental single-molecule trajectories. Due to the limitations of spatiotemporal resolution in these experiments and the inability to detect both forward and backward transitions between the same states, distinguishing the forward and backward directions of ATP-consuming periodic molecular machines becomes a nontrivial task. By extending the commonly used Markov-state model to analyze single-molecule transition-path measurements, we show how irreversibility can be hidden in these measurements but can be revealed when non-Markov effects in low-dimensional single-molecule trajectories are considered.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Maximilian Topel, Ayesha Ejaz, Allison Squires, Andrew L. Ferguson
Summary: Single-molecule Fo''rster resonance energy transfer (smFRET) is used to track the real-time dynamics of molecules. The Takens' Delay Embedding Theorem guarantees that the atomistic dynamics of a system can be represented by a time-delayed embedding of scalar observables. A method called Single-molecule TAkens Reconstruction (STAR) is used to learn the transformation between atomic coordinates and delay-embedded distances accessible to smFRET. STAR has been applied to reconstruct molecular configurations with high accuracy. In this work, the role of signal-to-noise ratio, data volume, and time resolution in simulated smFRET data is investigated to assess the performance of STAR under experimental conditions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Multidisciplinary
Biao-Feng Zeng, Yu-Ling Zou, Gan Wang, Wenjing Hong, Zhong-Qun Tian, Yang Yang
Summary: Recent advances in single-molecule electronics have opened up new opportunities to investigate single-molecule chemistry. The focus has shifted towards quantitative analysis of the physical and chemical behavior of single molecules, including dynamic molecular configurations, redox states, single-molecule reactions, single-molecule sensing, and molecular adsorption behaviors.
Review
Nanoscience & Nanotechnology
Hongliang Chen, Chuancheng Jia, Xin Zhu, Chen Yang, Xuefeng Guo, J. Fraser Stoddart
Summary: Developing new materials is a long-standing goal in various fields, and understanding single-molecule reactions can deepen our understanding of chemical reactions and provide new frameworks in materials science. This review focuses on state-of-the-art chemical reactions in single-molecule junctions and highlights the advantages of real-time testbeds for studying reaction dynamics, intermediates, transition states, and solvent effects. The behavior of single-molecule reactions is compared with reactions in ensemble states, and the potential of leveraging single-molecule catalysis for large-scale materials production is explored.
NATURE REVIEWS MATERIALS
(2023)
Article
Chemistry, Physical
Ruizheng Hou, Zhisong Wang
Summary: This study introduces a method to deduce the effective potential from motor trajectories and finds that it can yield a motor's stall force. This finding reduces the difficulty of stall force measurement and provides a method for measuring an important quantity relevant to efficient energy conversion of molecular motors.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Multidisciplinary Sciences
Chih-Ping Mao, Shih-Chin Wang, Yu-Pin Su, Ssu-Hsueh Tseng, Liangmei He, Annie A. Wu, Richard B. S. Roden, Jie Xiao, Chien-Fu Hung
Summary: Characterizing individual biomarker protein molecules in patient blood samples using single-molecule imaging techniques holds promise for early disease diagnosis and effective treatment. However, current methods have detection limits that are orders of magnitude higher than needed, making them unsuitable for clinical use. The development of SMAC, with its ability to quantify and characterize protein molecules down to the subfemtomolar range, presents a new avenue for noninvasive disease profiling with single-molecule imaging.
Article
Chemistry, Multidisciplinary
Lei-Lei Nian, Tao Wang, Jing-Tao Lu
Summary: This study theoretically predicts that the emitted light from the plasmon mode in an STM single molecular junction can be squeezed with reduced quantum fluctuations under external laser drive. By selectively exciting energy levels, the squeezed plasmon can exhibit sub-or superPoissonian statistical properties. It is also demonstrated that the molecular excitonic mode can be squeezed simultaneously.
Article
Computer Science, Interdisciplinary Applications
Robin Strickstrock, Marco Huelsmann, Dirk Reith, Karl N. Kirschner
Summary: This study demonstrates that a diverse set of training observables can lead to a meaningful force field, even with a limited number of thermodynamic state points. By optimizing the force field parameters, additional information can be extracted from MD simulations. The study presents a new optimization strategy to expand the capabilities of existing force fields and evaluates its impact on reproducible observables.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Engineering, Environmental
Jin Li, Xia Long, Juexian Cao, Yong Hu
Summary: In this study, the authors achieved the in-situ label-free single-molecule detection of a thermal-reversible Diels-Alder reaction using scanning tunneling microscopy break junction technique. They found that external electric fields can selectively accelerate the forward reaction and stabilize the transition state dipole. The integration of reversible reactions into nanocircuits offers new opportunities for designing functional molecular-scale devices.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Nanoscience & Nanotechnology
Chen Yang, Weilin Hu, Xuefeng Guo
Summary: Chirality plays a crucial role in various processes and there is a need for accurate distinction among different chiralities. The article proposes a universal strategy for chirality detection and control by aligning the molecular frame with external stimuli.
NANO-MICRO LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Jun Koseki, Haruka Hirose, Masamitsu Konno, Teppei Shimamura
Summary: In this study, a strategy to predict the complex structure of DNA-binding proteins with arbitrary DNA and analyze the differences in their interactions was proposed. It was found that the binding affinity between the BCL-2-associated X sequence and the p53 tetramer is increased by the anticancer drug trifluoro-thymidine (FTD) incorporation, while in p53-binding sequences extracted from FTD-resistant cells, the binding affinity of DNA containing FTD was greatly reduced. This suggests that thymidine randomly substituted for FTD in resistant cells may acquire resistance by inhibiting binding to DNA-binding proteins. This versatile procedure, which considers energetics, will increase the importance of computational science in the life sciences.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Medicinal
Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao
Summary: Conventional molecular dynamics simulation suffers from low efficiency in sampling protein conformations and dynamics. This paper proposes a new adaptive sampling method, LAST, which utilizes deep learning variational autoencoders to accelerate the exploration of protein conformational space. The method is validated through sampling four structures of two protein systems, demonstrating its effectiveness in achieving large conformational changes in a shorter simulation time.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Yaorong Chen, Longfeng Huang, Hang Chen, Zhixin Chen, Hewei Zhang, Zongyuan Xiao, Wenjing Hong
Summary: Single-molecule devices, fabricated by bridging a single molecule through electrodes, offer a promising approach for studying the intrinsic chemical or physical properties of individual molecules. In addition to single-molecule wires, a variety of responsive single-molecule junctions or devices with unique properties have been designed by introducing external fields, providing opportunities for exploring conductive materials at the molecular level. This review summarizes recent studies on the behavior of single-molecule devices based on photon, thermal, electric, or magnetic responses and discusses the future development of responsive single-molecule devices.
CHINESE JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kai Qu, Ping Duan, Jin-Yun Wang, Bochao Zhang, Qian-Chong Zhang, Wenjing Hong, Zhong-Ning Chen
Summary: This study successfully identified the internal rotation of three crank-shaped molecules using scanning tunneling microscope break junction technique and theoretical simulation. Theoretical computational study demonstrated that the orbital energy changes with the conformational flipping, affecting the single-molecule conductance.
Article
Chemistry, Analytical
Fabrizio Mo, Chiara Elfi Spano, Yuri Ardesi, Massimo Ruo Roch, Gianluca Piccinini, Mariagrazia Graziano
Summary: Food contamination by aflatoxins is a global issue due to its high toxicity and difficulties in limiting its spread. However, current detection techniques using biosensing are unable to monitor aflatoxins throughout the agri-food chain. This study investigates a pyrrole-based Molecular Field Effect Transistor (MolFET) as a single-molecule sensor for the detection of aflatoxins. The use of a suitable gate voltage enhances sensor performance by increasing current modulation. This research encourages further investigation into miniaturized FET electrical detection for widespread measurement of aflatoxins.