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1. Single-Molecule Chemical Reactions Unveiled in Molecular Junctions

   https://doi.org/10.3390/pr10122574  

   Bunker, Ian ; Ayinla, Ridwan Tobi ; Wang, Kun ( December 2022 , Processes)

   Understanding chemical processes at the single-molecule scale represents the ultimate limit of analytical chemistry. Single-molecule detection techniques allow one to reveal the detailed dynamics and kinetics of a chemical reaction with unprecedented accuracy. It has also enabled the discoveries of new reaction pathways or intermediates/transition states that are inaccessible in conventional ensemble experiments, which is critical to elucidating their intrinsic mechanisms. Thanks to the rapid development of single-molecule junction (SMJ) techniques, detecting chemical reactions via monitoring the electrical current through single molecules has received an increasing amount of attention and has witnessed tremendous advances in recent years. Research efforts in this direction have opened a new route for probing chemical and physical processes with single-molecule precision. This review presents detailed advancements in probing single-molecule chemical reactions using SMJ techniques. We specifically highlight recent progress in investigating electric-field-driven reactions, reaction dynamics and kinetics, host–guest interactions, and redox reactions of different molecular systems. Finally, we discuss the potential of single-molecule detection using SMJs across various future applications. 

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2. Characterizing the fundamental bending vibration of a linear polyatomic molecule for symmetry violation searches

   https://doi.org/10.1088/1367-2630/ace471  

   Jadbabaie, Arian ; Takahashi, Yuiki ; Pilgram, Nickolas H ; Conn, Chandler J ; Zeng, Yi ; Zhang, Chi ; Hutzler, Nicholas R ( July 2023 , New Journal of Physics)

   Polyatomic molecules have been identified as sensitive probes of charge-parity violating and parity violating physics beyond the Standard Model (BSM). For example, many linear triatomic molecules are both laser-coolable and have parity doublets in the ground electronic$\tilde{X}{}^2{\mathrm{\Sigma }}^{+}(010)$state arising from the bending vibration, both features that can greatly aid BSM searches. Understanding the$\tilde{X}{}^2{\mathrm{\Sigma }}^{+}(010)$state is a crucial prerequisite to precision measurements with linear polyatomic molecules. Here, we characterize the fundamental bending vibration of${}^{174}$YbOH using high-resolution optical spectroscopy on the nominally forbidden$\tilde{X}{}^2{\mathrm{\Sigma }}^{+}(010)$$\to \tilde{A}{}^2{\mathrm{\Pi }}_{1/2}(000)$transition at 588 nm. We assign 39 transitions originating from the lowest rotational levels of the$\tilde{X}{}^2{\mathrm{\Sigma }}^{+}(010)$state, and accurately model the state’s structure with an effective Hamiltonian using best-fit parameters. Additionally, we perform Stark and Zeeman spectroscopy on the$\tilde{X}{}^2{\mathrm{\Sigma }}^{+}(010)$state and fit the molecule-frame dipole moment to$D_{\mathrm{m}\mathrm{o}\mathrm{l}}=2.16(1)$Dand the effective electrong-factor to$g_S=2.07(2)$. Further, we use an empirical model to explain observed anomalous line intensities in terms of interference from spin–orbit and vibronic perturbations in the excited$\tilde{A}{}^2{\mathrm{\Pi }}_{1/2}(000)$state. Our work is an essential step toward searches for BSM physics in YbOH and other linear polyatomic molecules.

    

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3. Beyond electrical conductance: progress and prospects in single-molecule junctions

   https://doi.org/10.1039/D2TC01155G  

   Tang, Chaolong ; Ayinla, Ridwan Tobi ; Wang, Kun ( September 2022 , Journal of Materials Chemistry C)

   The idea of using individual molecules as conducting wires, regulators, and interconnects for charges in electronic circuitry has catalyzed the vibrant development of the field of single-molecule electronics. The ability to reliably and repeatedly construct single-molecule junctions (SMJs) has enabled the study of charge transport through a broad spectrum of individual molecules. Over the past decade, the capability of the SMJ platform has been greatly expanded thanks to the development of new experimental techniques and the integration of knowledge and methodologies from other disciplines. New opportunities beyond electrical conductance have emerged at the atomic and molecular scale. It has been demonstrated in many recent studies that the SMJ can now serve as a powerful and versatile tool to address critical physical and chemical questions that are otherwise inaccessible. This perspective focuses on the new capabilities and functionalities of the SMJ beyond conductance measurements and how they have enabled the investigation of crucial single-molecule processes and advanced our understanding beyond molecular electronics. 

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4. Data-driven many-body potentials from density functional theory for aqueous phase chemistry

   https://doi.org/10.1063/5.0129613  

   Palos, Etienne ; Dasgupta, Saswata ; Lambros, Eleftherios ; Paesani, Francesco ( March 2023 , Chemical Physics Reviews)

   Density functional theory (DFT) has been applied to modeling molecular interactions in water for over three decades. The ubiquity of water in chemical and biological processes demands a unified understanding of its physics, from the single molecule to the thermodynamic limit and everything in between. Recent advances in the development of data-driven and machine-learning potentials have accelerated simulation of water and aqueous systems with DFT accuracy. However, anomalous properties of water in the condensed phase, where a rigorous treatment of both local and non-local many-body (MB) interactions is in order, are often unsatisfactory or partially missing in DFT models of water. In this review, we discuss the modeling of water and aqueous systems based on DFT and provide a comprehensive description of a general theoretical/computational framework for the development of data-driven many-body potentials from DFT reference data. This framework, coined MB-DFT, readily enables efficient many-body molecular dynamics (MD) simulations of small molecules, in both gas and condensed phases, while preserving the accuracy of the underlying DFT model. Theoretical considerations are emphasized, including the role that the delocalization error plays in MB-DFT potentials of water and the possibility to elevate DFT and MB-DFT to near-chemical-accuracy through a density-corrected formalism. The development of the MB-DFT framework is described in detail, along with its application in MB-MD simulations and recent extension to the modeling of reactive processes in solution within a quantum mechanics/MB molecular mechanics (QM/MB-MM) scheme, using water as a prototypical solvent. Finally, we identify open challenges and discuss future directions for MB-DFT and QM/MB-MM simulations in condensed phases. 

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5. Fluorescent Platforms for RNA Chemical Biology Research

   https://doi.org/10.3390/genes13081348  

   Du, Jinxi ; Dartawan, Ricky ; Rice, William ; Gao, Forrest ; Zhou, Joseph H. ; Sheng, Jia ( August 2022 , Genes)

   Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating. 

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