Annual Review of Physical Chemistry - Volume 64, 2013

I seem to have started off on the wrong foot in life, but I am extremely fortunate that I soon found my footing in the company of physical chemists. I consider myself to be very lucky to be doing something that constantly brings me in contact with bright minds, stimulating conversations, and exciting experiments. My work has allowed me to learn astounding facts about the molecules and atoms that make up our surroundings and ourselves. For this article, I focus on one aspect of my research, understanding the fundamental principles of the simple reaction between a hydrogen atom and a hydrogen molecule. Although my group and others have been studying this seemingly simple reaction for well over 30 years, it continues to provoke questions about the properties of matter.

This contribution is very much a personal history of a journey through the wonderful world of anion chemistry, and a tale of how advances in laser technologies, theoretical methods, and computational capabilities continuously enabled advances in our understanding. It is a story of the excitement and joy that come from the opportunity to add to the fabric of science, and to do so by working as a group of excited explorers with common goals. The participants in this journey include me, my students and postdoctoral associates, my collaborators, and our many generous colleagues. It all happened, in the words of the Beatles, “with a little help from my friends.” Actually, it was so much more than a little help!

Small-angle X-ray scattering (SAXS) is a powerful method to study the structural properties of materials at the nanoscale. Recent progress in instrumentation and analysis methods has led to rapidly growing applications of this technique for the characterization of biological macromolecules in solution. Ab initio and rigid-body modeling methods allow one to build three-dimensional, low-resolution models from SAXS data. With the new approaches, oligomeric states of proteins and macromolecular complexes can be assessed, chemical equilibria and kinetic reactions can be studied, and even flexible objects such as intrinsically unfolded proteins can be quantitatively characterized. This review describes the analysis methods of SAXS data from macromolecular solutions, ranging from the computation of overall structural parameters to advanced three-dimensional modeling. The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles.

Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.

Optical imaging with spectroscopic vibrational contrast is a label-free solution for visualizing, identifying, and quantifying a wide range of biomolecular compounds in biological materials. Both linear and nonlinear vibrational microscopy techniques derive their imaging contrast from infrared active or Raman allowed molecular transitions, which provide a rich palette for interrogating chemical and structural details of the sample. Yet nonlinear optical methods, which include both second-order sum-frequency generation (SFG) and third-order coherent Raman scattering (CRS) techniques, offer several improved imaging capabilities over their linear precursors. Nonlinear vibrational microscopy features unprecedented vibrational imaging speeds, provides strategies for higher spatial resolution, and gives access to additional molecular parameters. These advances have turned vibrational microscopy into a premier tool for chemically dissecting live cells and tissues. This review discusses the molecular contrast of SFG and CRS microscopy and highlights several of the advanced imaging capabilities that have impacted biological and biomedical research.

New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear time-resolved experiments in molecules. Valence-electron motions can be triggered impulsively by core excitations and monitored with high temporal and spatial resolution. We discuss possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.

Phase-sensitive sum-frequency spectroscopy (SFS) allows the complete measurement of the complex spectra of surface nonlinear response coefficients. Similar to linear spectroscopy, the spectrum of the imaginary part of a surface response coefficient directly characterizes surface resonances without complication. This newly developed technique has greatly enhanced the capability of surface SFS and provides many new research opportunities for surface science. This article describes the experimental schemes and underlying theory for the technique and briefly reviews works that have clearly demonstrated its power.

We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

Bulk approaches to studying heterogeneous systems obscure important details, as they report average behavior rather than the distribution of behaviors in such environments. Small-molecule and polymeric supercooled liquids, which display heterogeneity in their dynamics without an underlying structural heterogeneity that sets those dynamics, are important constituents of this category of condensed matter systems. A variety of approaches have been devised to unravel ensemble averaging in supercooled liquids. This review focuses on the ultimate subensemble approach, single-molecule measurements, as they have been applied to the study of supercooled liquids. We detail how three key experimental observables (single-molecule probe rotation, translation, and fluorescence lifetime) have been employed to provide detail on dynamic heterogeneity in supercooled liquids. Special attention is given to the potential for, but also the challenges in, discriminating spatial and temporal heterogeneity and detailing the length scales and timescales of heterogeneity in these systems.

This review describes major features of current research in renewable fuels derived from plants and from fatty acids. Recent and ongoing fundamental studies of biofuel molecular structure, oxidation reactions, and biofuel chemical properties are reviewed, in addition to combustion applications of biofuels in the major types of engines in which biofuels are used. Biofuels and their combustion are compared with combustion features of conventional petroleum-based fuels. Two main classes of biofuels are described, those consisting of small, primarily alcohol, fuels (particularly ethanol, n-butanol, and iso-pentanol) that are used primarily to replace or supplement gasoline and those derived from fatty acids and used primarily to replace or supplement conventional diesel fuels. Research efforts on so-called second- and third-generation biofuels are discussed briefly.

This review focuses on the impacts of metal-organic interfacial bonding interactions on the charge-transport dynamics involved in molecular junctions as well as organically capped nanoparticles. Whereas mercapto derivatives have been used extensively as the ligands of choice to functionalize metal and nanoparticle surfaces with the formation of metal-thiolate interfacial bonds, recent studies show that metal-carbon covalent linkages may be fabricated by the deliberate design and selection of functional moieties. With enhanced electronic interactions between metals and organic ligands, the interfacial contact resistance diminishes drastically, leading to the emergence of unprecedented optical and electronic properties of the junctions and nanoparticles. These mechanistic insights are of fundamental significance in the development of molecule- and nanoparticle-based electronic devices, in particular, in light of the diverse metal-nonmetal bonding interactions that have been extensively observed in organometallic chemistry.

Ultrafast photochemical processes can occur in parallel with the relaxation of the optically populated excited state toward equilibrium. The latter involves both intra- and intermolecular modes, namely vibrational and solvent coordinates, and takes place on timescales ranging from a few tens of femtoseconds to up to hundreds of picoseconds, depending on the system. As a consequence, the reaction dynamics can substantially differ from those usually measured with slower photoinduced processes occurring from equil-ibrated excited states. For example, the decay of the excited-state population may become strongly nonexponential and depend on the excitation wavelength, contrary to the Kasha and Vavilov rules. In this article, we first give a brief account of our current understanding of vibrational and solvent relaxation processes. We then present an overview of important classes of ultrafast photochemical reactions, namely electron and proton transfer as well as isomerization, and illustrate with several examples how nonequilibrium effects can affect their dynamics.

Proteins are marginally stable, and the folding/unfolding equilibrium of proteins in aqueous solution can easily be altered by the addition of small organic molecules known as cosolvents. Cosolvents that shift the equilibrium toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the molecular mechanism of its action has been vigorously debated in the literature. Here we review recent experimental as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the molecular mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed molecular simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.

The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade, various approaches have been developed to discover the collective motions associated with this dynamics. The corresponding collective variables are used in many applications, e.g., to understand the reaction mechanism, to quantify the system's free energy landscape, to enhance the sampling of the reaction path, and to determine the reaction rate. In this review we focus on a number of key developments in this field, providing an overview of several methods along with their relative regimes of applicability.

Liquid water consistently expands our appreciation of the rich statistical mechanics that can emerge from simple molecular constituents. Here I review several interrelated areas of recent work on aqueous systems that aim to explore and explain this richness by revealing molecular arrangements, their thermodynamic origins, and the timescales on which they change. Vibrational spectroscopy of OH stretching features prominently in these discussions, with an emphasis on efforts to establish connections between spectroscopic signals and statistics of intermolecular structure. For bulk solutions, the results of these efforts largely verify and enrich existing physical pictures of hydrogen-bond network connectivity, dynamics, and response. For water at interfaces, such pictures are still emerging. As an important example I discuss the solvation of small ions at the air-water interface, whose surface propensities challenge a basic understanding of how aqueous fluctuations accommodate solutes in heterogeneous environments.

Chemistry occurring at or near the surface of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the structure and reactivity of aqueous interfaces in the atmosphere. Here we review simulation studies of atmospherically relevant aqueous liquid-air interfaces, with an emphasis on ions that play important roles in the chemistry of atmospheric aerosols. In addition to surveying results from simulation studies, we discuss challenges to the refinement and experimental validation of the methodology for simulating ion adsorption to the air-water interface and recent advances in elucidating the driving forces for adsorption. We also review the recent development of a dielectric continuum theory capable of reproducing simulation and experimental data on ion behavior at aqueous interfaces.

A survey is provided of recent progress in the understanding of singlet fission, a spin-allowed process in which a singlet excited molecule shares its energy with a ground-state neighbor to produce two triplet excited molecules. It has been observed to occur in single-crystal, polycrystalline, and amorphous solids, on timescales from 80 fs to 25 ps, producing triplet yields as high as 200%. Photovoltaic devices using the effect have shown external quantum efficiencies in excess of 100%. Almost all the efficient materials are alternant hydrocarbons of the acene series or their simple derivatives, and it is argued that a wider structural variety would be desirable. The current state of the development of molecular structure design rules, based on first-principles theoretical considerations, is described along with initial examples of implementation.

This article reviews the ring-polymer molecular dynamics model for condensed-phase quantum dynamics. This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems. The review covers the theory, implementation, applications, and limitations of the approximation.

The opening of hard X-ray free-electron laser facilities, such as the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory in the United States, has ushered in a new era in structural determination. With X-ray pulse durations down to 10 fs or shorter, and up to 10¹³ transversely coherent photons per pulse in a narrow spectral bandwidth, focused irradiances of 10¹⁸ to 10²¹ W cm⁻² or higher can be produced at X-ray energies ranging from 500 eV to 10 keV. New techniques for determining the structure of systems that cannot be crystallized and for studying the time-resolved behavior of irreversible reactions at femtosecond timescales are now available.

The ultrafast spectroscopic investigation of novel retinal proteins challenges existing notions concerning the course of primary events in these natural photoreceptors. We review two illustrations here. The first demonstrates that changes in the initial retinal configuration can alter the duration of photochemistry by nearly an order of magnitude in Anabaena sensory rhodopsin, making it as rapid as the ballistic photoisomerization in visual pigments. This prompted a reinvestigation of the much studied bacteriorhodopsin, leading to a similar trend as well, contrary to earlier reports. The second involves the study of xanthorhodopsin, an archaeal proton pump that includes an attached light-harvesting carotenoid. Pump-probe experiments demonstrate the efficient transfer of energy from carotenoid to retinal, providing a first glimpse at a cooperative multichromophore function, which is probably characteristic of many other proteins as well. Finally, we discuss measures required to advance our knowledge from kinetics to mode-specific dynamics concerning this expanding family of biological photoreceptors.