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- Volume 73, 2022
Annual Review of Physical Chemistry - Volume 73, 2022
Volume 73, 2022
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Protein Structure Prediction with Mass Spectrometry Data
Vol. 73 (2022), pp. 1–19More LessKnowledge of protein structure is crucial to our understanding of biological function and is routinely used in drug discovery. High-resolution techniques to determine the three-dimensional atomic coordinates of proteins are available. However, such methods are frequently limited by experimental challenges such as sample quantity, target size, and efficiency. Structural mass spectrometry (MS) is a technique in which structural features of proteins are elucidated quickly and relatively easily. Computational techniques that convert sparse MS data into protein models that demonstrate agreement with the data are needed. This review features cutting-edge computational methods that predict protein structure from MS data such as chemical cross-linking, hydrogen–deuterium exchange, hydroxyl radical protein footprinting, limited proteolysis, ion mobility, and surface-induced dissociation. Additionally, we address future directions for protein structure prediction with sparse MS data.
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Ultrafast Imaging of Molecules with Electron Diffraction
Vol. 73 (2022), pp. 21–42More LessPhotoexcited molecules convert light into chemical and mechanical energy through changes in electronic and nuclear structure that take place on femtosecond timescales. Gas phase ultrafast electron diffraction (GUED) is an ideal tool to probe the nuclear geometry evolution of the molecules and complements spectroscopic methods that are mostly sensitive to the electronic state. GUED is a weak and passive probing tool that does not alter the molecular properties during the probing process and is sensitive to the spatial distribution of charge in the molecule, including both electrons and nuclei. Improvements in temporal resolution have enabled GUED to capture coherent nuclear motions in molecules in the excited and ground electronic states with femtosecond and subangstrom resolution. Here we present the basic theory of GUED and explain what information is encoded in the diffraction signal, review how GUED has been used to observe coherent structural dynamics in recent experiments, and discuss the advantages and limitations of the method.
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Molecular Polaritonics: Chemical Dynamics Under Strong Light–Matter Coupling
Vol. 73 (2022), pp. 43–71More LessChemical manifestations of strong light–matter coupling have recently been a subject of intense experimental and theoretical studies. Here we review the present status of this field. Section 1 is an introduction to molecular polaritonics and to collective response aspects of light–matter interactions. Section 2 provides an overview of the key experimental observations of these effects, while Section 3 describes our current theoretical understanding of the effect of strong light–matter coupling on chemical dynamics. A brief outline of applications to energy conversion processes is given in Section 4. Pending technical issues in the construction of theoretical approaches are briefly described in Section 5. Finally, the summary in Section 6 outlines the paths ahead in this exciting endeavor.
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Bimolecular Chemistry in the Ultracold Regime
Yu Liu, and Kang-Kuen NiVol. 73 (2022), pp. 73–96More LessAdvances in atomic, molecular, and optical physics techniques allowed the cooling of simple molecules down to the ultracold regime (1 mK) and opened opportunities to study chemical reactions with unprecedented levels of control. This review covers recent developments in studying bimolecular chemistry at ultralow temperatures. We begin with a brief overview of methods for producing, manipulating, and detecting ultracold molecules. We then survey experimental works that exploit the controllability of ultracold molecules to probe and modify their long-range interactions. Further combining the use of physical chemistry techniques such as mass spectrometry and ion imaging significantly improved the detection of ultracold reactions and enabled explorations of their dynamics in the short range. We discuss a series of studies on the reaction KRb + KRb → K2 + Rb2 initiated below 1 μK, including the direct observation of a long-lived complex, the demonstration of product rotational state control via conserved nuclear spins, and a test of the statistical model using the complete quantum state distribution of the products.
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eScience Infrastructures in Physical Chemistry
Vol. 73 (2022), pp. 97–116More LessAs the volume of data associated with scientific research has exploded over recent years, the use of digital infrastructures to support this research and the data underpinning it has increased significantly. Physical chemists have been making use of eScience infrastructures since their conception, but in the last five years their usage has increased even more. While these infrastructures have not greatly affected the chemistry itself, they have in some cases had a significant impact on how the research is undertaken. The combination of the human effort of collaboration to create open source software tools and semantic resources, the increased availability of hardware for the laboratories, and the range of data management tools available has made the life of a physical chemist significantly easier. This review considers the different aspects of eScience infrastructures and explores how they have improved the way in which we can conduct physical chemistry research.
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Double and Charge-Transfer Excitations in Time-Dependent Density Functional Theory
Vol. 73 (2022), pp. 117–140More LessTime-dependent density functional theory has emerged as a method of choice for calculations of spectra and response properties in physics, chemistry, and biology, with its system-size scaling enabling computations on systems much larger than otherwise possible. While increasingly complex and interesting systems have been successfully tackled with relatively simple functional approximations, there has also been increasing awareness that these functionals tend to fail for certain classes of approximations. Here I review the fundamental challenges the approximate functionals have in describing double excitations and charge-transfer excitations, which are two of the most common impediments for the theory to be applied in a black-box way. At the same time, I describe the progress made in recent decades in developing functional approximations that give useful predictions for these excitations.
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Quantitative Surface-Enhanced Spectroscopy
Vol. 73 (2022), pp. 141–162More LessSurface-enhanced Raman scattering (SERS), a powerful technique for trace molecular detection, depends on chemical and electromagnetic enhancements. While recent advances in instrumentation and substrate design have expanded the utility, reproducibility, and quantitative capabilities of SERS, some challenges persist. In this review, advances in quantitative SERS detection are discussed as they relate to intermolecular interactions, surface selection rules, and target molecule solubility and accessibility. After a brief introduction to Raman scattering and SERS, impacts of surface selection rules and enhancement mechanisms are discussed as they relate to the observation of activation and deactivation of normal Raman modes in SERS. Next, experimental conditions that can be used to tune molecular affinity to and density near SERS substrates are summarized and considered while tuning these parameters is conveyed. Finally, successful examples of quantitative SERS detection are discussed, and future opportunities are outlined.
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Neural Network Potentials: A Concise Overview of Methods
Emir Kocer, Tsz Wai Ko, and Jörg BehlerVol. 73 (2022), pp. 163–186More LessIn the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field.
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Capturing Atom-Specific Electronic Structural Dynamics of Transition-Metal Complexes with Ultrafast Soft X-Ray Spectroscopy
Vol. 73 (2022), pp. 187–208More LessThe atomic specificity of X-ray spectroscopies provides a distinct perspective on molecular electronic structure. For 3d metal coordination and organometallic complexes, the combination of metal- and ligand-specific X-ray spectroscopies directly interrogates metal–ligand covalency—the hybridization of metal and ligand electronic states. Resonant inelastic X-ray scattering (RIXS), the X-ray analog of resonance Raman scattering, provides access to all classes of valence excited states in transition-metal complexes, making it a particularly powerful means of characterizing the valence electronic structure of 3d metal complexes. Recent advances in X-ray free-electron laser sources have enabled RIXS to be extended to the ultrafast time domain. We review RIXS studies of two archetypical photochemical processes: charge-transfer excitation in ferricyanide and ligand photodissociation in iron pentacarbonyl. These studies demonstratefemtosecond-resolution RIXS can directly characterize the time-evolving electronic structure, including the evolution of the metal–ligand covalency.
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Vibrational Spectroscopy of the Water Dimer at Jet-Cooled and Atmospheric Temperatures
Vol. 73 (2022), pp. 209–231More LessThe vibrational spectroscopy of the water dimer provides an understanding of basic hydrogen bonding in water clusters, and with about one water dimer for every 1,000 water molecules, it plays a critical role in atmospheric science. Here, we review how the experimental and theoretical progress of the past decades has improved our understanding of water dimer vibrational spectroscopy under both cold and warm conditions. We focus on the intramolecular OH-stretching transitions of the donor unit, because these are the ones mostly affected by dimer formation and because their assignment has proven a challenge. We review cold experimental results from early matrix isolation to recent mass-selected jet expansion techniques and, in parallel, the improvements in the theoretical anharmonic models. We discuss and illustrate changes in the vibrational spectra of complexes upon increasing temperature, and the difficulties in recording and calculating these spectra. In the atmosphere, water dimer spectra at ambient temperature are crucial.
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Probing the Nature of the Transition-Metal-Boron Bonds and Novel Aromaticity in Small Metal-Doped Boron Clusters Using Photoelectron Spectroscopy
Vol. 73 (2022), pp. 233–253More LessPhotoelectron spectroscopy combined with quantum chemistry has been a powerful approach to elucidate the structures and bonding of size-selected boron clusters (Bn−), revealing a prevalent planar world that laid the foundation for borophenes. Investigations of metal-doped boron clusters not only lead to novel structures but also provide important information about the metal-boron bonds that are critical to understanding the properties of boride materials. The current review focuses on recent advances in transition-metal-doped boron clusters, including the discoveries of metal-boron multiple bonds and metal-doped novel aromatic boron clusters. The study of the RhB− and RhB2O− clusters led to the discovery of the first quadruple bond between boron and a transition-metal atom, whereas a metal-boron triplebond was found in ReB2O− and IrB2O−. The ReB4− cluster was shown to be the first metallaborocycle with Möbius aromaticity, and the planar ReB6− cluster was found to exhibit aromaticity analogous to metallabenzenes.
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Stochastic Vector Techniques in Ground-State Electronic Structure
Vol. 73 (2022), pp. 255–272More LessWe review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce algorithmic complexity, facilitate efficient parallelization, simplify computational tasks, accelerate calculations, and diminish memory requirements. While their scope is vast, we limit our study to ground-state and finite temperature density functional theory (DFT) and second-order many-body perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere. We start by explaining how to use stochastic vectors in computations, characterizing the associated statistical errors. Next, we show how to estimate the electron density in DFT and discuss effective techniques to reduce statistical errors. Finally, we review the use of stochastic vectors for calculating correlation energies within the second-order Møller-Plesset perturbation theory and its finite temperature variational form. Example calculation results are presented and used to demonstrate the efficacy of the methods.
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Calculating Multidimensional Optical Spectra from Classical Trajectories
Vol. 73 (2022), pp. 273–297More LessMultidimensional optical spectra are measured from the response of a material system to a sequence of laser pulses and have the capacity to elucidate specific molecular interactions and dynamics whose influences are absent or obscured in a conventional linear absorption spectrum. Interpretation of complex spectra is supported by theoretical modeling of the spectroscopic observable, requiring implementation of quantum dynamics for coupled electrons and nuclei. Performing numerically correct quantum dynamics in this context may pose computational challenges, particularly in the condensed phase. Semiclassical methods based on calculating classical trajectories offer a practical alternative. Here I review the recent application of some semiclassical, trajectory-based methods to nonlinear molecular vibrational and electronic spectra.
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Path Integrals for Nonadiabatic Dynamics: Multistate Ring Polymer Molecular Dynamics
Vol. 73 (2022), pp. 299–322More LessThis review focuses on a recent class of path-integral-based methods for the simulation of nonadiabatic dynamics in the condensed phase using only classical molecular dynamics trajectories in an extended phase space. Specifically, a semiclassical mapping protocol is used to derive an exact, continuous, Cartesian variable path-integral representation for the canonical partition function of a system in which multiple electronic states are coupled to nuclear degrees of freedom. Building on this exact statistical foundation, multistate ring polymer molecular dynamics methods are developed for the approximate calculation of real-time thermal correlation functions. The remarkable promise of these multistate ring polymer methods, their successful applications, and their limitations are discussed in detail.
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Laser-Induced Coulomb Explosion Imaging of Aligned Molecules and Molecular Dimers
Vol. 73 (2022), pp. 323–347More LessWe discuss how Coulomb explosion imaging (CEI), triggered by intense femtosecond laser pulses and combined with laser-induced alignment and covariance analysis of the angular distributions of the recoiling fragment ions, provides new opportunities for imaging the structures of molecules and molecular complexes. First, focusing on gas phase molecules, we show how the periodic torsional motion of halogenated biphenyl molecules can be measured in real time by timed CEI, and how CEI of one-dimensionally aligned difluoroiodobenzene molecules can uniquely identify four structural isomers. Next, focusing on molecular complexes formed inside He nano-droplets, we show that the conformations of noncovalently bound dimers or trimers, aligned in one or three dimensions, can be determined by CEI. Results presented for homodimers of CS2, OCS, and bromobenzene pave the way for femtosecond time-resolved structure imaging of molecules undergoing bimolecular interactions and ultimately chemical reactions.
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Intramolecular Vibrations in Excitation Energy Transfer: Insights from Real-Time Path Integral Calculations
Sohang Kundu, and Nancy MakriVol. 73 (2022), pp. 349–375More LessExcitation energy transfer (EET) is fundamental to many processes in chemical and biological systems and carries significant implications for the design of materials suitable for efficient solar energy harvest and transport. This review discusses the role of intramolecular vibrations on the dynamics of EET in nonbonded molecular aggregates of bacteriochlorophyll, a perylene bisimide, and a model system, based on insights obtained from fully quantum mechanical real-time path integral results for a Frenkel exciton Hamiltonian that includes all vibrational modes of each molecular unit at finite temperature. Generic trends, as well as features specific to the vibrational characteristics of the molecules, are identified. Weak exciton-vibration (EV) interaction leads to compact, near-Gaussian densities on each electronic state, whose peak follows primarily a classical trajectory on a torus, while noncompact densities and nonlinear peak evolution are observed with strong EV coupling. Interaction with many intramolecular modes and increasing aggregate size smear, shift, and damp these dynamical features.
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Imaging Dynamic Processes in Multiple Dimensions and Length Scales
Vol. 73 (2022), pp. 377–402More LessOptical microscopy has become an invaluable tool for investigating complex samples. Over the years, many advances to optical microscopes have been made that have allowed us to uncover new insights into the samples studied. Dynamic changes in biological and chemical systems are of utmost importance to study. To probe these samples, multidimensional approaches have been developed to acquire a fuller understanding of the system of interest. These dimensions include the spatial information, such as the three-dimensional coordinates and orientation of the optical probes, and additional chemical and physical properties through combining microscopy with various spectroscopic techniques. In this review, we survey the field of multidimensional microscopy and provide an outlook on the field and challenges that may arise.
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Photophysics of Two-Dimensional Semiconducting Organic–Inorganic Metal-Halide Perovskites
Vol. 73 (2022), pp. 403–428More LessTwo-dimensional organic–inorganic hybrid perovskites (2DHPs) consist of alternating anionic metal-halide and cationic organic layers. They have widely tunable structural and optical properties. We review the role of the organic cation in defining the structural and optical properties of 2DHPs through the example of lead iodide 2DHPs. Even though excitons reside in the metal-halide layers, the organic and inorganic frameworks cannot be separated—they must be considered as a single unit to fully understand the photophysics of 2DHPs. We correlate cation-induced distortion and disorder in the inorganic lattice with the resulting optical properties. We also discuss the role of the cation in creating and altering the discrete excitonic structure that appears at cryogenic temperatures in some 2DHPs, including the cation-dependent presence of hot-exciton photoluminescence. We conclude our review with an outlook for 2DHPs, highlighting existing gaps in fundamental knowledge as well as potential future applications.
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Vibration-Cavity Polariton Chemistry and Dynamics
Vol. 73 (2022), pp. 429–451More LessMolecular polaritons result from light-matter coupling between optical resonances and molecular electronic or vibrational transitions. When the coupling is strong enough, new hybridized states with mixed photon-material character are observed spectroscopically, with resonances shifted above and below the uncoupled frequency. These new modes have unique optical properties and can be exploited to promote or inhibit physical and chemical processes. One remarkable result is that vibrational strong coupling to cavities can alter reaction rates and product branching ratios with no optical excitation whatsoever. In this work we review the ability of vibration-cavity polaritons to modify chemical and physical processes including chemical reactivity, as well as steady-state and transient spectroscopy. We discuss the larger context of these works and highlight their most important contributions and implications. Our goal is to provide insight for systematically manipulating molecular polaritons in photonic and chemical applications.
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Classical and Nonclassical Nucleation and Growth Mechanisms for Nanoparticle Formation
Vol. 73 (2022), pp. 453–477More LessAll solid materials are created via nucleation. In this evolutionary process, nuclei form in solution or at interfaces, expand by monomeric growth and oriented attachment, and undergo phase transformation. Nucleation determines the location and size of nuclei, whereas growth controls the size, shape, and aggregation of newly formed nanoparticles. These physical properties of nanoparticles can affect their functionalities, reactivities, and porosities, as well as their fate and transport. Recent advances in nanoscale analytical technologies allow in situ real-time observations, enabling us to uncover the molecular nature of nuclei and the critical controlling factors for nucleation and growth. Although a single theory cannot yet fully explain such evolving processes, we have started to better understand how both classical andnonclassical theories can work together, and we have begun to recognize the importance of connecting these theories. This review discusses the recent convergence of knowledge about the nucleation and growth of nanoparticles.
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Previous Volumes
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Volume 74 (2023)
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Volume 73 (2022)
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Volume 72 (2021)
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Volume 71 (2020)
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Volume 70 (2019)
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Volume 69 (2018)
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Volume 68 (2017)
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Volume 67 (2016)
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Volume 66 (2015)
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Volume 65 (2014)
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Volume 64 (2013)
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Volume 63 (2012)
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Volume 62 (2011)
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Volume 61 (2010)
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Volume 60 (2009)
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Volume 59 (2008)
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Volume 58 (2007)
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Volume 57 (2006)
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Volume 56 (2005)
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Volume 55 (2004)
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Volume 54 (2003)
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Volume 53 (2002)
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Volume 52 (2001)
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Volume 51 (2000)
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Volume 50 (1999)
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Volume 49 (1998)
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Volume 48 (1997)
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Volume 47 (1996)
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Volume 46 (1995)
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Volume 45 (1994)
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Volume 44 (1993)
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Volume 43 (1992)
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Volume 42 (1991)
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Volume 41 (1990)
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Volume 40 (1989)
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Volume 39 (1988)
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Volume 38 (1987)
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Volume 37 (1986)
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Volume 36 (1985)
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Volume 35 (1984)
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Volume 34 (1983)
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Volume 33 (1982)
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Volume 32 (1981)
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Volume 31 (1980)
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Volume 30 (1979)
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Volume 29 (1978)
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Volume 28 (1977)
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Volume 27 (1976)
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Volume 26 (1975)
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Volume 25 (1974)
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Volume 24 (1973)
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Volume 23 (1972)
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Volume 22 (1971)
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Volume 21 (1970)
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Volume 20 (1969)
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Volume 19 (1968)
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Volume 18 (1967)
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Volume 17 (1966)
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Volume 16 (1965)
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Volume 15 (1964)
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Volume 14 (1963)
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Volume 13 (1962)
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Volume 12 (1961)
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Volume 11 (1960)
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Volume 10 (1959)
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Volume 9 (1958)
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Volume 8 (1957)
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Volume 7 (1956)
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Volume 6 (1955)
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Volume 5 (1954)
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Volume 4 (1953)
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Volume 3 (1952)
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Volume 2 (1951)
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Volume 1 (1950)
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Volume 0 (1932)