Annual review of physical chemistry最新文献

The movement of charges through a chiral medium results in a spin-polarized charge current. This phenomenon, known as the chirality-induced spin selectivity (CISS) effect, enables control over spin populations without the need for magnetic components and operates at room temperature. CISS has been discovered in a range of chiral media and most prominently studied in chiral organic molecular species. Chiral hybrid organic-inorganic perovskite semiconductors combine the unique and functional aspects of inorganic semiconductors with chiral molecules. The inorganic component borrows the homochirality of the organic component to yield a unique family of highly tunable chiral semiconductors, where the enantiomeric purity is defined by the organic component. Semiconductors already form the backbone of modern-day technologies. Adding chirality and control over spin through CISS provides new avenues for creative technological development. This review is intended to be an introduction to these unique systems and the demonstrations of CISS and spin control.

Molecular machines transduce free energy between different forms throughout all living organisms. Unlike their macroscopic counterparts, molecular machines are characterized by stochastic fluctuations, overdamped dynamics, and soft components, and operate far from thermodynamic equilibrium. In addition, information is a relevant free energy resource for molecular machines, leading to new modes of operation for nanoscale engines. Toward the objective of engineering synthetic nanomachines, an important goal is to understand how molecular machines transduce free energy to perform their functions in biological systems. In this review, we discuss the nonequilibrium thermodynamics of free energy transduction within molecular machines, with a focus on quantifying energy and information flows between their components. We review results from theory, modeling, and inference from experiments that shed light on the internal thermodynamics of molecular machines, and ultimately explore what we can learn from considering these interactions.

With markedly different reaction conditions compared to the chemistry of the outside atmosphere, indoor air chemistry poses new challenges to the scientific community that require combined experimental and computational efforts. Here, we review molecular dynamics simulations that have contributed to the mechanistic understanding of the complex dynamics of organic compounds at indoor surfaces and their interplay with experiments and indoor air models. We highlight the rich interactions between volatile organic compounds and silica and titanium dioxide surfaces, serving as proxies for glasses and paints, as well as the dynamics of skin oil lipids and their oxidation products, which sensitively affect the quality of indoor air in crowded environments. As the studies we review here are pioneering in the rapidly emerging field of indoor chemistry, we provide suggestions for increasing the potentially important role that molecular simulations can continue to play.

The C₆₀ fullerene molecule has been the subject of intense study for four decades, starting with its identification in the mass spectra of carbon soot in 1985. In this review, we focus on the achievement of ultra-high-resolution spectroscopy of gas phase neutral C₆₀, heralded by the observation of quantum state-resolved infrared spectra in 2019. C₆₀ is now the largest and most symmetric molecule for which rovibrational quantum state resolution has been achieved, motivating the use of large molecules for studying complex quantum systems with symmetries and degrees of freedom not readily available in other composite systems. We discuss the theory, challenges, and experimental techniques of high-resolution C₆₀ spectroscopy and recent experimental results probing the structure, dynamics, and interactions of C₆₀ enabled by quantum state resolution.

Vibrational spectroscopy and fluorescence spectroscopy have historically been two established but separate fields of molecular spectroscopy. While vibrational spectroscopy provides exquisite chemical information, fluorescence spectroscopy often offers orders of magnitude higher detection sensitivity. However, they each lack the advantages of each other. In recent years, a series of novel nonlinear optical spectroscopy studies have been developed that merge both spectroscopies into a single double-resonance process. These techniques combine the chemical specificity of Raman or infrared (IR) spectroscopy with the superb detection sensitivity and spatial resolution of fluorescence microscopy. Many facets have been explored, including Raman transition versus IR transition, time domain versus frequency domain, and spectroscopy versus microscopy. Notably, single-molecule vibrational spectroscopy has been achieved at room temperature without the need for plasmonics. Even superresolution vibrational imaging beyond the diffraction limit was demonstrated. This review summarizes the growing field of vibrational-encoded fluorescence microscopy, including key technical developments, emerging applications, and future prospects.

Investigating protein dynamic structural changes is fundamental for understanding protein function, drug discovery, and disease mechanisms. Traditional studies of protein dynamics often rely on investigations of purified systems, which fail to capture the complexity of the cellular environment. The intracellular milieu imposes distinct physicochemical constraints that affect macromolecular interactions and dynamics in ways not easily replicated in isolated experimental setups. We discuss the use of fluorescence resonance energy transfer, fluorescence anisotropy, and minimal photon flux imaging technologies to address these challenges and directly investigate protein conformational dynamics in mammalian cells. Key findings from the application of these techniques demonstrate their potential to reveal intricate details of protein conformational plasticity. By overcoming the limitations of traditional in vitro methods, these approaches offer a more accurate and comprehensive understanding of protein function and behavior within the complex environment of mammalian cells.

Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and provide optimal enhanced sampling of protein conformational changes and states. Since the pioneering work in the late 1990s, identifying the correct and objectively provable RCs has been a central topic in molecular biophysics and chemical physics. This review summarizes the major advances in identifying RCs over the past 25 years, focusing on methods aimed at finding RCs that meet the rigorous committor criterion, widely accepted as the true RCs. Notably, the newly developed physics-based energy flow theory and generalized work functional method provide a general and rigorous approach for identifying true RCs, revealing their physical nature as the optimal channels of energy flow in biomolecules.

Electrocyclic reactions are characterized by the concerted formation and cleavage of multiple σ and π bonds in a molecular system and have been extensively studied since they were introduced by Robert Burns Woodward and Roald Hoffmann in 1965. Recent advances and the integration of time-resolved experiments and nonadiabatic quantum molecular dynamics simulations have transformed the traditional understanding of electrocyclic reactions beyond the Woodward-Hoffmann rules. In this review, we focus on recent studies of 1,3-cyclohexadiene and two of its derivatives, α-phellandrene and α-terpinene, to shed light on the underlying mechanisms of electrocyclic photochemical reactions. We highlight recent progress in ultrafast electron diffraction techniques and the simulation approach of ab initio multiple spawning. Together, these approaches can elucidate molecular structure dynamics from femtosecond to picosecond timescales as well as nuclear and electronic responses at conical intersections.

This review provides focused coverage of the photophysical properties of noncanonical and synthetic nucleobases reported over the past decade. It emphasizes key research findings and physical insights gathered for prebiotic and fluorescent nucleobase analogs, sulfur- and selenium-substituted nucleobases, aza-substituted nucleobases, epigenetic nucleobases and their oxidation products, and nucleobases utilized for expanding DNA/RNA to reveal central structure-photophysical property relationships. Further research and development in this emerging field, coupled with machine learning methods, will enable the effective harnessing of nucleobases' modifications for applications in biotechnology, biomedicine, therapeutics, and even the creation of live semisynthetic organisms.

Metal ions play a critical role in various chemical, biological, and environmental processes. This review reports on emerging chemical mechanisms in the catalysis of DNA and RNA. We provide an overview of the metal-dependent mechanisms of DNA cleavage in CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems that are transforming life sciences through genome editing technologies, and showcase intriguing metal-dependent mechanisms of RNA cleavages. We show that newly discovered CRISPR-Cas complexes operate as protein-assisted ribozymes, highlighting RNA's versatility and the enhancement of CRISPR-Cas functions through strategic metal ion use. We demonstrate the power of computer simulations in observing chemical processes as they unfold and in advancing structural biology through innovative approaches for refining cryo-electron microscopy maps. Understanding metal ion involvement in nucleic acid catalysis is crucial for advancing genome editing, aiding therapeutic interventions for genetic disorders, and improving the editing tools' specificity and efficiency.