Annual Review of Physical Chemistry - Volume 63, 2012

We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca²⁺ pumps, G protein–coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

Colloidal dispersions have been studied for decades as a result of their utility in numerous applications and as models for molecular and atomic condensed phases. More recently, a number of groups have exploited in such studies submicrometer-sized hydrogel particles (microgels) that have environmentally tunable sizes. The experimental convenience of tuning the dispersion's colloidal volume fraction while maintaining a constant number density of particles provides a clear advantage over more tedious studies that employ traditional hard-sphere particles. However, as studies delved deeper into the fundamental physics of colloidal dispersions comprising microgel particles, it became abundantly clear that a microgel's utility as a tunable hard sphere was limited and that the impact of softness was more profound than previously appreciated. Herein we review the brief history of microgel-based colloidal dispersions and discuss their transition from tunable hard spheres to a class of soft matter that has revealed a landscape of physics and chemistry notable for its extraordinary richness and diversity.

Relativistic effects can strongly influence the chemical and physical properties of heavy elements and their compounds. This influence has been noted in inorganic chemistry textbooks for a couple of decades. This review provides both traditional and new examples of these effects, including the special properties of gold, lead-acid and mercury batteries, the shapes of gold and thallium clusters, heavy-atom shifts in NMR, topological insulators, and certain specific heats.

A general overview of the field of single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) as it stands today is provided. After years of debates on the basic aspects of SM-SERS, the technique is emerging as a well-established subfield of spectroscopy and SERS. SM-SERS is allowing the observation of subtle spectroscopic phenomena that were not hitherto accessible. Examples of the latter are natural isotopic substitutions in single molecules, observation of the true homogeneous broadening of Raman peaks, Raman excitation profiles of individual molecules, and SM electrochemistry. With background examples of the contributions produced by our group, properly interleaved with results by other practitioners in the field, we present some of the latest developments and promising new leads in this new field of spectroscopy.

Nuclear singlet states may have lifetimes that are much longer than the conventional relaxation time of nuclear spin magnetization. This review covers how these states may be generated, observed, and exploited in solution nuclear magnetic resonance (NMR). Potential applications include the study of slow molecular processes, the elucidation of molecular geometry, and the transport of hyperpolarized nuclear spin order.

The chemistry that occurs at surfaces has been an intense area of study for many years owing to its complexity and importance in describing a wide range of physical phenomena. The vapor/water interface is particularly interesting from an environmental chemistry perspective as this surface plays host to a wide range of chemistries that influence atmospheric and geochemical interactions. The application of vibrational sum frequency generation (VSFG), an inherently surface-specific, even-order nonlinear optical spectroscopy, enables the direct interrogation of various vapor/aqueous interfaces to elucidate the behavior and reaction of chemical species within the surface regime. In this review we discuss the application of VSFG to the study of a variety of atmospherically important systems at the vapor/aqueous interface. Chemical systems presented include inorganic ionic solutions prevalent in aqueous marine aerosols, small molecular solutes, and long-chain fatty acids relevant to fat-coated aerosols. The ability of VSFG to probe both the organization and reactions that may occur for these systems is highlighted. A future perspective toward the application of VSFG to the study of environmental interfaces is also provided.

A pedagogical proof is presented for the extensivity of energies of metallic and nonmetallic crystals that proceeds by elucidating the asymptotic distance dependence of the effective chemical interactions: kinetic, Coulomb, exchange, and correlation. On this basis, a guideline for the size-consistent design of electronic and vibrational methods is proposed. This guideline underscores the significance of the distinct use of the intermediate and standard normalization of wave functions for extensive and intensive quantities, includes the extensive and intensive diagram theorems as the unambiguous criteria for determining size consistency of a method for extensive and intensive quantities, and introduces the extensive-intensive consistency theorem, which stipulates the precise balance between the determinant spaces reached by extensive and intensive operators. Electronic and vibrational methods for crystals are reviewed that are inspired by these formal analyses or developed in accordance with the guideline.

Historically, the physical chemistry of isotope effects and precise measurements in samples from nature have provided information on processes that could not have been obtained otherwise. With the discovery of a mass-independent isotopic fractionation during the formation of ozone, a new physical chemical basis for isotope effects required development. Combined theoretical and experimental developments have broadened this understanding and extended the range of chemical systems where these unique effects occur. Simultaneously, the application of mass-independent isotopic measurements to an extensive range of both terrestrial and extraterrestrial systems has furthered the understanding of events such as solar system origin and evolution and planetary atmospheric chemistry, present and past.

The behavior of water confined on nanometer length scales is important in a diverse set of technical and scientific contexts, ranging from the performance of fuel cells and biological molecular machines to the design of self-assembling nanoscale materials. Here, we review recent insights into the structure and thermodynamics of confined water that have been elucidated primarily by computer simulation studies. We emphasize investigations in which interfacial chemistry and molecular topography are varied systematically and in which a wide range of thermodynamic conditions of temperature and pressure are explored. We consider homogeneous interfaces ranging from the simplest hard wall to chemically realistic, but structurally ideal, hydrophobic and hydrophilic surfaces, and the continuous scale of surface polarity is investigated. Features associated with interface heterogeneities arising from chemical patterning or from the natural characteristics of protein surfaces are discussed. Finally, we provide our thoughts on important directions for further studies.

By low-temperature scanning tunneling microscopy, we study CO molecule chemisorption on a quasi–one-dimensional Cu(110)-(2×1)-O surface. Atom-resolved images reveal how the interaction of CO with the surface Cu-O- chains gives rise to orthogonal attractive and repulsive intermolecular interactions. First-principles calculations show that CO molecules induce unprecedented lifting of the host Cu atoms by 1 Å from the Cu-O- chains, enabling the Cu-CO unit to tilt by 45° from the surface normal. Contrary to the behavior of CO on metal surfaces, this structural distortion enables unprecedented, orthogonal, short-range intermolecular dipole-dipole attraction and long-range, surface-mediated repulsion. These interactions lead to self-assembly into molecular nanograting structures consisting of arrays of single-molecule-wide CO rows. The origin of the novel behavior of CO molecules in the electronic and geometrical properties of the quasi–one-dimensional substrate suggests that similar molecule-molecule and molecule-substrate interactions could play an important role at catalytic sites on reactive surfaces.

Living cells are structured to create a range of microenvironments that support specific chemical reactions and processes. Understanding how cells function therefore requires detailed knowledge of both the subcellular architecture and the location of specific molecules within this framework. Here we review the development of two correlated cellular imaging techniques that fulfill this need. Cells are first imaged using cryogenic fluorescence microscopy to determine the location of molecules of interest that have been labeled with fluorescent tags. The same specimen is then imaged using soft X-ray tomography to generate a high-contrast, 3D reconstruction of the cells. Data from the two modalities are then combined to produce a composite, information-rich view of the cell. This correlated imaging approach can be applied across the spectrum of problems encountered in cell biology, from basic research to biotechnological and biomedical applications such as the optimization of biofuels and the development of new pharmaceuticals.

The force induced on anisotropic nanoparticles in a nonuniform electric field can be used to attract, orient, and position the nanoparticles with respect to microelectrodes on a surface. For polarizable nanomaterials, such as nanowires, carbon nanotubes, or graphene sheets suspended in solvent, this dielectrophoretic force results in movement to regions of highest electric field strength. This review discusses the origin of this force, its production by different microelectrode designs, and its use for nanomaterials assembly, with a focus on efforts toward heterogeneous integration with on-chip electronics for single-particle characterization and device structures.

Surface-science investigations have contributed significantly to heterogeneous catalysis in the past several decades. Fundamental studies of reactive systems on metal single crystals have aided researchers in understanding the effect of surface structure on catalyst reactivity and selectivity for a number of important reactions. Recently, model systems, consisting of metal clusters deposited on planar oxide surfaces, have facilitated the study of metal particle-size and support effects. These model systems not only are useful for carrying out kinetic investigations, but are also amenable to surface spectroscopic techniques, thus enabling investigations under realistic pressures and at working temperatures. By combining surface-science characterization methods with kinetic measurements under realistic working conditions, researchers are continuing to advance the molecular-level understanding of heterogeneous catalysis and are narrowing the pressure and material gap between model and real-world catalysts.

The classic density-functional theory (DFT) formalism introduced by Hohenberg, Kohn, and Sham in the mid-1960s is based on the idea that the complicated N-electron wave function can be replaced with the mathematically simpler 1-electron charge density in electronic structure calculations of the ground stationary state. As such, ordinary DFT cannot treat time-dependent (TD) problems nor describe excited electronic states. In 1984, Runge and Gross proved a theorem making TD-DFT formally exact. Information about electronic excited states may be obtained from this theory through the linear response (LR) theory formalism. Beginning in the mid-1990s, LR-TD-DFT became increasingly popular for calculating absorption and other spectra of medium- and large-sized molecules. Its ease of use and relatively good accuracy has now brought LR-TD-DFT to the forefront for this type of application. As the number and the diversity of applications of TD-DFT have grown, so too has our understanding of the strengths and weaknesses of the approximate functionals commonly used for TD-DFT. The objective of this article is to continue where a previous review of TD-DFT in Volume 55 of the Annual Review of Physical Chemistry left off and highlight some of the problems and solutions from the point of view of applied physical chemistry. Because doubly-excited states have a particularly important role to play in bond dissociation and formation in both thermal and photochemistry, particular emphasis is placed on the problem of going beyond or around the TD-DFT adiabatic approximation, which limits TD-DFT calculations to nominally singly-excited states.

This review describes how conical intersections affect measured molecular spectra and simple photofragmentation processes. We consider excitations that result in electron ejection, that is, photoionization or photodetachment, as well as photoinduced H-atom elimination. Section 1 presents a brief overview of the history of conical intersections and their rise from an arcane theoretical concept to a major paradigm in nonadiabatic chemistry. In Section 2, the generic properties of conical intersections are discussed, as well as their characterization with modern electronic-structure methods. Section 3 briefly discusses computational tools used to compute the nuclear motion involving conical intersections. Section 4 describes how the ideas of Sections 2 and 3 are combined to simulate molecular spectra impacted by conical intersections. Section 5 describes selected recent experimental and computational studies of photoelectron, photodetachment, and photofragment spectra. Rather than providing an encyclopedic bibliography of the previous and current literature, we illustrate significant problems currently being addressed and describe what can be accomplished with current computational techniques and how these results are achieved. Section 6 suggests future directions in this field.

Nano- and microparticles have optical, structural, and chemical properties that differ from both their building blocks and the bulk materials themselves. These different physical and chemical properties are induced by the high surface-to-volume ratio. As a logical consequence, to understand the properties of nano- and microparticles, it is of fundamental importance to characterize the particle surfaces and their interactions with the surrounding medium. Recent developments of nonlinear light scattering techniques have resulted in a deeper insight of the underlying light-matter interactions. They have shed new light on the molecular mechanism of surface kinetics in solution, properties of interfacial water in contact with hydrophilic and hydrophobic particles and droplets, molecular orientation distribution of molecules at particle surfaces in solution, interfacial structure of surfactants at droplet interfaces, acid-base chemistry on particles in solution, and vesicle structure and transport properties.

Tip-enhanced Raman spectroscopy (TERS) is a very powerful variant of surface-enhanced Raman spectroscopy (SERS). In a sense, TERS overcomes most of the drawbacks of SERS but keeps its advantages, such as its high sensitivity. TERS offers the additional advantages of high spatial resolution, much beyond the Abbe limit, and the possibility to correlate TER and other scanning probe microscope images, i.e., to correlate topographic and chemical data. TERS finds application in a number of fields, such as surface science, material science, and biology. Single-molecule TERS has been observed even for TERS enhancements of “only” 10⁶–10⁷. In this review, TERS enhancements are discussed in some detail, including a condensed overview of measured contrasts and estimated total enhancements. Finally, recent developments for TERS under ultrahigh vacuum conditions are presented, including TERS on a C60 island with a diameter of a few tens of nanometers, deposited on a smooth Au(111) surface.

The behavior of halide salts at the vapor/water interface has been the focus of a tremendous amount of work in the past ten years. A molecular view of the interface has been introduced with the observation that large anions have some affinity for the interface, but a quantitative description of the driving forces that determine ion adsorption or repulsion at the interface is still missing. This review discusses recent developments that are based on classical and quantum-chemical molecular simulations as well as developments that are based on simple potential models.

Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.