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Annual Review of Physical Chemistry - Early Publication
Reviews in Advance appear online ahead of the full published volume. View expected publication dates for upcoming volumes.
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Generating Superrotors and Dynamics of Molecules in Extremely High Rotational States
First published online: 14 February 2025More LessThe optical centrifuge was demonstrated in 2000 as a tool for preparing ensembles of molecules in extreme rotational states. Highly rotationally excited molecules, so-called superrotors, are observed as products of photodissociation and molecular collisions, in high-temperature environments in the atmospheres of Earth and exoplanets, and in the interstellar medium. Traditional optical excitation is limited to small changes in rotation, limiting experiments to relatively low rotational states. In this review, I discuss the use of a tunable optical centrifuge to prepare molecules in selected ranges of excited rotational states and investigations of their collisional relaxation using state-resolved polarization-sensitive transient IR probing. I examine the decay dynamics of population, alignment, and translational energy release, focusing on experimental results, and compare them with simulations that overestimate observed relaxation rates. A clear picture of near-resonant and nonresonant energy transfer pathways emerges and establishes the means to distinguish superrotor and bath collision products.
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Structure–Photophysical Property Relationships in Noncanonical and Synthetic Nucleobases
First published online: 14 February 2025More LessThis review provides a 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.
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Flow of Energy and Information in Molecular Machines
First published online: 14 February 2025More LessMolecular 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.
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Emerging Mechanisms of Metal-Catalyzed RNA and DNA Modifications
First published online: 14 February 2025More LessMetal 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.
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Memory and Friction: From the Nanoscale to the Macroscale
First published online: 14 February 2025More LessFriction is a phenomenon that manifests across all spatial and temporal scales, from the molecular to the macroscopic scale. It describes the dissipation of energy from the motion of particles or abstract reaction coordinates and arises in the transition from a detailed molecular-level description to a simplified, coarse-grained model. It has long been understood that time-dependent (non-Markovian) friction effects are critical for describing the dynamics of many systems, but that they are notoriously difficult to evaluate for complex physical, chemical, and biological systems. In recent years, the development of advanced numerical friction extraction techniques and methods to simulate the generalized Langevin equation has enabled exploration of the role of time-dependent friction across all scales. We discuss recent applications of these friction extraction techniques and the growing understanding of the role of friction in complex equilibrium and nonequilibrium dynamic many-body systems.
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Chirality-Induced Spin Selectivity in Hybrid Organic-Inorganic Perovskite Semiconductors
First published online: 14 February 2025More LessThe 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.
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Femtosecond Extreme Ultraviolet Absorption Spectroscopy of Transition Metal Complexes
First published online: 14 February 2025More LessIn this review, we survey the use of extreme ultraviolet absorption spectroscopy to measure electronic and vibrational dynamics in transition metal complexes. Photons in this 30–100 eV energy range probe 3p
$\mbox{\MVRightarrow}$ 3d transitions for 3d metals and 4f, 5p$\mbox{\MVRightarrow}$ 5d transitions in 5d metals, and the resulting spectra are sensitive to the spin state, oxidation state, and ligand field of the metal. Furthermore, the energy of the core level depends on the metal, providing elemental specificity. Use of tabletop high-harmonic sources allows these spectra to be measured with femtosecond to attosecond time resolution in a standard laser laboratory, revealing short-lived states in chromophores and photocatalysts that were unresolved using other techniques.
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Physical Considerations in Memory and Information Storage
First published online: 14 February 2025More LessInformation is an important resource. Storing and retrieving information faithfully are huge challenges and many methods have been developed to understand the principles behind robust information processing. In this review, we focus on information storage and retrieval from the perspective of energetics, dynamics, and statistical mechanics. We first review the Hopfield model of associative memory, the classic energy-based model of memory. We then discuss generalizations and physical realizations of the Hopfield model. Finally, we highlight connections to energy-based neural networks used in deep learning. We hope this review inspires new directions along the lines of information storage and retrieval in physical systems.
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Reaction Coordinates Are Optimal Channels of Energy Flow
First published online: 04 February 2025More LessReaction 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. Importantly, 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.
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Quantum State–Resolved Structure and Dynamics of C60 Fullerenes
Lee R. Liu, and Jun YeFirst published online: 04 February 2025More LessThe 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.
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Ultrafast Spectroscopy and Dynamics of Photoredox Catalysis
First published online: 03 February 2025More LessPhotoredox catalysis has emerged as a powerful platform for chemical synthesis, utilizing chromophore excited states as selective energy stores to surmount chemical activation barriers toward making desirable products. Developments in this field have pushed synthetic chemists to design and discover new photocatalysts with novel and impactful photoreactivity but also with uncharacterized excited states and only an approximate mechanistic understanding. This review highlights specific instances in which ultrafast spectroscopies dissected the photophysical and photochemical dynamics of new classes of photoredox catalysts and their photochemical reactions. After briefly introducing the photophysical processes and ultrafast spectroscopic methods central to this topic, the review describes selected recent examples that evoke distinct classes of photoredox catalysts with demonstrated synthetic utility and ultrafast spectroscopic characterization. This review cements the significant role of ultrafast spectroscopy in modern photocatalyzed organic transformations and institutionalizes the developing intersection of synthetic organic chemistry and physical chemistry.
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Merging Vibrational Spectroscopy with Fluorescence Microscopy: Combining the Best of Two Worlds
Naixin Qian, Hanqing Xiong, Lu Wei, Lixue Shi, and Wei MinFirst published online: 03 February 2025More LessVibrational 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 super-resolution 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.
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Electric Fields at Solid-Liquid Interfaces: Insights from Molecular Dynamics Simulation
First published online: 03 February 2025More LessIn this review, we explore the electrostatic environment of the interface between a solid and dilute electrolyte solution, with an emphasis on the electric field profiles that these systems produce. We review the theoretical formalism that connects electrostatic potential profiles, electric field profiles, and charge density fields. This formalism has served as the basis for our understanding of interfacial electric fields and their influences on microscopic chemical and physical processes. Comparing various traditional models of interfacial electrostatics to the results of molecular dynamics (MD) simulation yields mutually inconsistent descriptions of the interfacial electric field profile. We present MD simulation results demonstrating that the average electric field profiles experienced by particles at the interface differ from the properties of traditional models and from the fields derived from the mean charge density of atomistic simulations. Furthermore, these experienced electric field profiles are species-dependent. Based on these results, we assert that a single unifying electrostatic potential profile—the gradient of which defines a single unifying electric field profile—cannot correctly predict the electrostatic forces that act on species at the interface.
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Molecular Dynamics Simulations of the Interactions of Organic Compounds at Indoor Relevant Surfaces
First published online: 03 February 2025More LessWith 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.
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The Science of Nanostructure Acoustic Vibrations
First published online: 22 January 2025More LessUltrafast excitation of nanoparticles can excite the acoustic vibrational modes of the structure that correlate with the expansion coordinates. These modes are frequently seen in transient absorption experiments on metal nanoparticle samples and occasionally for semiconductors. The aim of this review is to give an overview of the physical chemistry of nanostructure acoustic vibrations. The issues discussed include the excitation mechanism, how to calculate the mode frequencies using continuum mechanics, and the factors that control vibrational damping. Recent results that demonstrate that the high frequencies inherent to the acoustic modes of nanomaterials trigger a viscoelastic response in surrounding liquids are also discussed, as well as vibrational coupling between nanostructures and mode hybridization within the nanostructures. Mode hybridization provides a way of manipulating the lifetimes of the acoustic modes, which is potentially useful for applications such as mass sensing.
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Odyssey in the Wonderland of Chemical Dynamics
First published online: 22 January 2025More LessThis is a recollection of my scientific trajectory. When I look back, I consider myself to be very fortunate for being able to do something I love and on topics of my own will. I am not a competitive person and tend to shy away from the limelight. Nonetheless, I survived in my profession and eventually made some modest contributions, which are beyond what I would have expected. We often forget about the human aspect of scientific endeavor. After all, science is done by individuals; humans have emotions and make mistakes. The frustrations of failures, the joys of finding problems and solutions to them, and the passion for fulfilling curiosity are all parts of this endeavor. Throughout the years, many people—mentors, students, postdocs, collaborators, and colleagues—have accompanied me in this exciting and fruitful journey, for which I am deeply grateful and feel very lucky to have them.
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Atomistic Insights into Elemental Two-Dimensional Materials and Their Heterostructures
First published online: 22 January 2025More LessInspired by the success of graphene, two-dimensional (2D) materials have been at the forefront of advanced (opto-)nanoelectronics and energy-related fields owing to their exotic properties like sizable bandgaps, Dirac fermions, quantum spin Hall states, topological edge states, and ballistic charge carrier transport, which hold promise for various electronic device applications. Emerging main group elemental 2D materials, beyond graphene, are of particular interest due to their unique structural characteristics, ease of synthetic exploration, and superior property tunability. In this review, we present recent advances in atomic-scale studies of elemental 2D materials with an emphasis on synthetic strategies and structural properties. We also discuss the challenges and perspectives regarding the integration of elemental 2D materials into various heterostructures.
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Recent Advances in Ozone Photochemistry: A Lambda Doublet Propensity and Spin-Forbidden Channels
First published online: 21 January 2025More LessRecent studies on ozone photodissociation in the Hartley and Huggins bands have provided new insights into the dissociation dynamics and product state distributions. A Λ-doublet propensity in the photodissociation has been identified through experiment and theory as the origin of the oscillatory O2(a1Δg) rotational distributions and provides a promising diagnostic for determining the relative contributions of 3A′ and 3A″ states in Huggins band spin-forbidden processes. Recent experiments on spin-forbidden dissociation have provided detailed information about the vibrational and rotational distributions of the O2 products and the branching ratios between the O2 electronic states, serving as a motivation for high-level theory.
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