Annual Review of Physical Chemistry

Knowledge 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...

A significant advantage of organic semiconductors over many of their inorganic counterparts is solution processability. However, solution processing commonly yields heterogeneous films with properties that are highly sensitive to the conditions and parameters of casting and processing. Measuring the key properties of these materials in situ, during film production, can provide new insight into the mechanism of these processing steps and how they lead to the emergence of the final organic film properties. The excited-state dynamics is often of import in photovoltaic, electronic, and light-emitting devices...

We review our recent quantum stochastic model for spectroscopic lineshapes in the presence of a coevolving and nonstationary background population of excitations. Starting from a field theory description for interacting bosonic excitons, we derive a reduced model whereby optical excitons are coupled to an incoherent background via scattering as mediated by their screened Coulomb coupling. The Heisenberg equations of motion for the optical excitons are then driven by an auxiliary stochastic population variable, which we take to be the solution of an Ornstein-Uhlenbeck process...

Photosynthetic light harvesting exhibits near-unity quantum efficiency. The high efficiency is achieved through a series of energy and charge transfer steps within a network of pigment-containing proteins. Remarkably, high efficiency is conserved across many organisms despite differences in the protein structures and organization that allow each organism to respond to its own biological niche and the stressors within. In this review, we highlight recent progress toward understanding how organisms maintain optimal light-harvesting ability by acclimating to their environment...

Light-driven phenomena in organic molecular aggregates underpin several mechanisms relevant to optoelectronic applications. Modeling these processes is essential for aiding the design of new materials and optimizing optoelectronic devices. In this review, we cover the use of different atomistic models, excited-state dynamics, and transport approaches for understanding light-activated phenomena in molecular aggregates, including radiative and nonradiative decay pathways. We consider both intra- and intermolecular mechanisms and focus on the role of conical intersections as facilitators of internal conversion...

Chemical physics plays a large role in determining the isotopic compositions of gases in Earth's atmosphere, which in turn provide fundamental insights into the sources, sinks, and transformations of atmospheric gases and particulates and their influence on climate. This review focuses on the kinetic and photolysis isotope effects relevant to understanding the isotope compositions of atmospheric ozone, carbon dioxide, methane, nitrous oxide, and other gases and their historical context. The discussion includes non-mass-dependent isotope compositions of oxygen-containing species and a brief overview of the recent growth of clumped isotope measurements at natural isotopic abundances, that is, of molecules containing more than one rare isotope...

Localized surface plasmon resonances (LSPRs) in metallic nanostructures result in subwavelength optical confinement that enhances light-matter interactions, for example, aiding the sensitivity of surface spectroscopies. The dissipation of surface plasmons as electronic and vibrational excitations sets the limit for field confinement but also provides opportunities for photochemistry, photocatalysis, and photothermal heating. Optimization for either goal requires a deeper understanding of this photothermalization process...

Surfaces mediate the formation of stable glasses (SGs) upon physical vapor deposition (PVD) for a wide range of glass formers. The thermodynamic and kinetic stability of SGs and their anisotropic packing structures are controlled through the deposition parameters (deposition temperature and rate) as well by the chemical structure and composition of the glass former. The resulting PVD glass properties can be related to the structure and dynamics of the glass surface, which can have oriented packing, enhanced surface diffusion, and a lower glass transition temperature, and can facilitate an enhanced aging rate of the interfacial region...

Super-resolution fluorescence microscopy techniques are powerful tools to investigate polymer systems. In this review, we address how these techniques have been applied to hydrogel nano- and microparticles, so-called nano- or microgels. We outline which research questions on microgels could be addressed and what new insights could be achieved. Studies of the morphology, shape, and deformation of microgels; their internal compartmentalization; the cross-linker distribution and polarity inside them; and their dynamics and diffusion are summarized...

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units-accelerated quantum chemistry in the cloud, artificial intelligence-driven natural molecule input methods, and extended reality visualization...

Optical 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...

Two-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 example 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...

Reactions at solid-water interfaces play a foundational role in water treatment systems, catalysis, and chemical separations, and in predicting chemical fate and transport in the environment. Over the last century, experimental measurements and computational models have made tremendous progress in capturing reactions at solid surfaces. The interfacial reactivity of a solid surface, however, can change dramatically and unexpectedly when it is confined to the nanoscale. Nanoconfinement can arise in different geometries such as pores/cages (3D confinement), channels (2D confinement), and slits (1D confinement)...

All solid materials are created via nucleation. In this evolutionary process, nuclei form in solution or at interfaces and expand by monomeric growth, oriented attachment, and 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 determine 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...

Predicting the whole process of a chemical reaction while solving kinetic equations presents an opportunity to realize an on-the-fly kinetic simulation that directly discovers chemical reactions with their product yields. Such a simulation avoids the combinatorial explosion of reaction patterns to be examined by narrowing the search space based on the kinetic analysis of the reaction path network, and would open a new paradigm beyond the conventional two-step approach, which requires a reaction path network prior to performing a kinetic simulation...

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers. Expected final online publication date for the Annual Review of Physical Chemistry , Volume 74 is April 2023...

We 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 perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere...

This review focuses on a recent class of path-integral-based methods that simulate 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...

Molecular 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...

We 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...