Annual Review of Physical Chemistry - Volume 66, 2015

After my acceptance of the kind invitation from Todd Martínez and Mark Johnson, Co-Editors of this journal, to write this article, I had to decide just how to actually do this, given the existence of a fairly personal and extended autobiographical account of recent vintage detailing my youth, education, and assorted experiences and activities at the University of Colorado, Boulder, and later also at Ecole Normale Supérieure in Paris (1). In the end, I settled on a differently styled recounting of the adventures with my students, postdocs, collaborators, and colleagues in trying to unravel, comprehend, describe, and occasionally even predict the manifestations and consequences of the myriad assortment of molecular dances that contribute to and govern the rates and mechanisms of chemical reactions in solution (and elsewhere). The result follows.

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

Bimolecular reactions of phenyl-type radicals with the C4 and C5 hydrocarbons vinylacetylene and (methyl-substituted) 1,3-butadiene have been found to synthesize polycyclic aromatic hydrocarbons (PAHs) with naphthalene and 1,4-dihydronaphthalene cores in exoergic and entrance barrierless reactions under single-collision conditions. The reaction mechanism involves the initial formation of a van der Waals complex and addition of a phenyl-type radical to the C1 position of a vinyl-type group through a submerged barrier. Investigations suggest that in the hydrocarbon reactant, the vinyl-type group must be in conjugation with a –C≡CH or –HC=CH2 group to form a resonantly stabilized free radical intermediate, which eventually isomerizes to a cyclic intermediate followed by hydrogen loss and aromatization (PAH formation). The vinylacetylene-mediated formation of PAHs might be expanded to more complex PAHs, such as anthracene and phenanthrene, in cold molecular clouds via barrierless reactions involving phenyl-type radicals, such as naphthyl, which cannot be accounted for by the classical hydrogen abstraction–acetylene addition mechanism.

Ultrafast energy transfer is used to transmit electronic excitation among the many molecules in photosynthetic antenna complexes. Recent experiments and theories have highlighted the role of coherent transfer in femtosecond studies of these proteins, suggesting the need for accurate dynamical models to capture the subtle characteristics of energy transfer mechanisms. Here we discuss how to think about coherence in light harvesting and electronic energy transfer. We review the various fundamental concepts of coherence, spanning from classical phenomena to the quantum superposition, and define coherence in electronic energy transfer. We describe the current status of experimental studies on light-harvesting complexes. Insights into the microscopic process are presented to highlight how and why this is a challenging problem to elucidate. We present an overview of the applicable dynamical theories to model energy transfer in the intermediate coupling regime.

Solvated electrons were first discovered in solutions of metals in liquid ammonia. The physical and chemical properties of these species have been studied extensively for many decades using an arsenal of electrochemical, spectroscopic, and theoretical techniques. Yet, in contrast to their hydrated counterpart, the ultrafast dynamics of ammoniated electrons remained completely unexplored until quite recently. Femtosecond pump-probe spectroscopy on metal-ammonia solutions and femtosecond multiphoton ionization spectroscopy on the neat ammonia solvent have provided new insights into the optical properties and the reactivities of this fascinating species. This article reviews the nature of the optical transition, which gives the metal-ammonia solutions their characteristic blue appearance, in terms of ultrafast relaxation processes involving bound and continuum excited states. The recombination processes following the injection of an electron via photoionization of the solvent are discussed in the context of the electronic structure of the liquid and the anionic defect associated with the solvated electron.

Mechanisms of bimolecular chemical reactions in solution are amenable to study on picosecond timescales, both by transient absorption spectroscopy and by computer simulation. The dynamics of exothermic reactions of CN radicals and of Cl and F atoms with organic solutes in commonly used solvents are contrasted with the corresponding dynamics in the gas phase. Many characteristics of the gas-phase reaction dynamics persist in solution, such as efficient energy release to specific vibrational modes of the products. However, additional complexities associated with the presence of the solvent are open to investigation. These features of liquid-phase reactions include the role of solvent-solute complexes, solvent caging, coupling of the product motions to the solvent bath, thermalization of internally excited reaction products, incipient hydrogen bond formation, and involvement of charge-separated states that arise from proton transfer.

This review describes some important physical characteristics of the pathways (i.e., dynamical processes) by which molecular, nanoscale, and micrometer-scale self-assembly occurs. We highlight the existence of features of self-assembly pathways that are common to a wide range of physical systems, even though those systems may differ with respect to their microscopic details. We summarize some existing theoretical descriptions of self-assembly pathways and highlight areas—notably, the description of self-assembly pathways that occur far from equilibrium—that are likely to become increasingly important.

The liquid interface is a narrow, highly anisotropic region, characterized by rapidly varying density, polarity, and molecular structure. I review several aspects of interfacial solvation and show how these affect reactivity at liquid/liquid interfaces. I specifically consider ion transfer, electron transfer, and SN2 reactions, showing that solvent effects on these reactions can be understood by examining the unique structure and dynamics of the liquid interface region.

Sum-frequency generation vibrational spectroscopy (SFG-VS) can provide detailed information and understanding of the molecular composition, interactions, and orientational and conformational structure of surfaces and interfaces through quantitative measurement and analysis. In this review, we present the current status of and discuss important recent developments in the measurement of intrinsic SFG spectral lineshapes and formulations for polarization measurements and orientational analysis of SFG-VS spectra. The focus of this review is to present a coherent description of SFG-VS and discuss the main concepts and issues that can help advance this technique as a quantitative analytical research tool for revealing the chemistry and physics of complex molecular surfaces and interfaces.

Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid and in some cases are surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assemble within their host cells and in vitro. We describe the thermodynamics and kinetics for the assembly of protein subunits into icosahedral capsid shells and how these are modified in cases in which the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques used to characterize capsid assembly, and we highlight aspects of virus assembly that are likely to receive significant attention in the near future.

The field of cold molecules has become an important source of new insight in fundamental chemistry and molecular physics. High-resolution spectroscopy benefits from translationally and internally cold molecules by increased interaction times and reduced spectral congestion. Completely new effects in scattering dynamics become accessible with cold and controlled molecules. Many of these experiments use molecular beams as a starting point for the generation of molecular samples. This review gives an overview of methods to produce beams of cold molecules, starting from supersonic expansions or effusive sources, and provides examples of applications in spectroscopy and molecular dynamics studies.

Recent experiments have demonstrated that the electron transmission yield through chiral molecules depends on the electron spin orientation. This phenomenon has been termed the chiral-induced spin selectivity (CISS) effect, and it provides a challenge to theory and promise for organic molecule–based spintronic devices. This article reviews recent developments in our understanding of CISS. Different theoretical models have been used to describe the effect; however, they all presume an unusually large spin-orbit coupling in chiral molecules for the effect to display the magnitudes seen in experiments. A simplified model for an electron's transport through a chiral potential suggests that these large couplings can be manifested. Techniques for measuring spin-selective electron transport through molecules are overviewed, and some examples of recent experiments are described. Finally, we present results obtained by studying several systems, and we describe the possible application of the CISS effect for memory devices.

This article is a rough, quirky overview of both the history and present state of the art of density functional theory. The field is so huge that no attempt to be comprehensive is made. We focus on the underlying exact theory, the origin of approximations, and the tension between empirical and nonempirical approaches. Many ideas are illustrated on the exchange energy and hole. Features unique to this article include how approximations can be systematically derived in a nonempirical fashion and a survey of warm dense matter.

We review recent progress in the modeling of organic solar cells and photovoltaic materials, as well as discuss the underlying theoretical methods with an emphasis on dynamical electronic processes occurring in organic semiconductors. The key feature of the latter is a strong electron-phonon interaction, making the evolution of electronic and structural degrees of freedom inseparable. We discuss commonly used approaches for first-principles modeling of this evolution, focusing on a multiscale framework based on the Holstein–Peierls Hamiltonian solved via polaron transformation. A challenge for both theoretical and experimental investigations of organic solar cells is the complex multiscale morphology of these devices. Nevertheless, predictive modeling of photovoltaic materials and devices is attainable and is rapidly developing, as reviewed here.

The past decade has seen a surge of exciting research and applications of carbon nanotubes (CNTs) stimulated by deeper understanding of their fundamental properties and increasing production capability. The intrinsic properties of various CNTs were found to strongly depend on their internal microstructures. This review summarizes the fundamental structure-property relations of seamless tube-like single- and multiwalled CNTs and conically stacked carbon nanofibers, as well as the organized architectures of these CNTs (including randomly stacked thin films, parallel aligned thin films, and vertically aligned arrays). It highlights the recent development of CNTs as key components in selected applications, including nanoelectronics, filtration membranes, transparent conductive electrodes, fuel cells, electrical energy storage devices, and solar cells. Particular emphasis is placed on the link between the basic physical chemical properties of CNTs and the organized CNT architectures with their functions and performance in each application.

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.

We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model.

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Now routine is the ability to investigate soluble and membrane protein complexes in the gas phase of a mass spectrometer while preserving folded structure and ligand-binding properties. Several recent transformative developments have occurred to arrive at this point. These include advances in mass spectrometry instrumentation, particularly with respect to resolution; the ability to study intact membrane protein complexes released from detergent micelles; and the use of protein unfolding in the gas phase to obtain stability parameters. Together, these discoveries are providing unprecedented information on the compositional heterogeneity of biomacromolecules, the unfolding trajectories of multidomain proteins, and the stability imparted by ligand binding to both soluble and membrane-embedded protein complexes. We review these recent breakthroughs, highlighting the challenges that had to be overcome and the physicochemical insight that can now be gained from studying proteins and their assemblies in the gas phase.