Annual Review of Physical Chemistry - Volume 59, 2008

This article contains a very personal account of my evolution as a physical chemist/chemical physicist, with commentary on some of the influences on that evolution and summary accounts of research accomplishments in four of the subject areas that have engaged my attention, ranging from isolated molecules to condensed matter.

It has become increasingly clear that heterogeneous and multiphase chemistry of tropospheric aerosols can change the chemical balance of the atmosphere. In this review, we focus on recent laboratory studies of the heterogeneous and multiphase chemistry and photochemistry of mineral dust aerosol, a large mass fraction of the tropospheric aerosol. Mineral dust aerosol contains a mixture of oxides, clays, and carbonates. Molecular-based studies of reactions of these dust components provide insights into the chemistry of Earth's atmosphere. We discuss several different types of heterogeneous and multiphase reactions, including (a) ozone decomposition, (b) nitrogen dioxide and nitrate photochemistry, and (c) the dissolution and redox chemistry of Fe-containing dust. We also review some of the important chemical concepts that have recently emerged.

Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.

Most RNA comprises one strand and therefore can fold back on itself to form complex structures. At the heart of these structures is the hairpin, which is composed of a stem having Watson-Crick base pairing and a loop wherein the backbone changes directionality. First, we review the structure of hairpins including diversity in the stem, loop, and closing base pair. The function of RNA hairpins in biology is discussed next, including roles for isolated hairpins, as well as hairpins in the context of complex tertiary structures. We describe the kinetics and thermodynamics of hairpin folding including models for hairpin folding, folding transition states, and the cooperativity of folding. Lastly, we discuss some ways in which hairpins can influence the folding and function of tertiary structures, both directly and indirectly. RNA hairpins provide a simple means of controlling gene expression that can be understood in the language of physical chemistry.

Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

Studies of ordered, yet nonperiodic, metallic alloys known as quasicrystals have generated exciting questions and fundamental insights about the relationship between surface atomic structure and surface properties. In this review, I give examples from oxidation, friction, heterogeneous catalysis, and solid film growth, in which the Al-rich quasicrystals exhibit unusual properties, relative to crystalline materials of similar composition.

Surfactants have their primary utility, both scientific and industrial, at the liquid-liquid interface. We review recent X-ray surface scattering experiments that probe the molecular ordering and phase behavior of surfactants at the water-oil interface. The presence of the oil modifies the interfacial ordering in a manner that cannot be understood simply from analogies with studies of Langmuir monolayers of surfactants at the water-vapor interface or from the traditional view that the solvent is fully mixed with the interfacial surfactants. These studies explored the role of chain flexibility and head group interactions on the ordering of long-chain alkanols and alkanoic acids. Small changes in the surfactant may produce large changes in the interfacial ordering. The interfacial monolayer can be spatially homogeneous or inhomogeneous. Investigators have observed interfacial phase transitions as a function of temperature between homogenous phases, as well as between homogeneous and inhomogeneous phases. Finally, varying the solvent chain length can alter the fundamental character of the phase transitions and lead to the formation of multilayer interfacial structures.

Metal films with patterns of subwavelength holes (grids or meshes) have interesting optical properties including the extraordinary transmission effect. These optically thick metal films transmit more radiation than that incident on the holes owing to the excitation of surface plasmons (SPs). Meshes present a new and simple way to excite SPs at perpendicular incidence (i.e., without the need to vary the angle of the incident beam). This represents a new opportunity to integrate SPs with experiments and devices—a new instrument in the toolbox of SP techniques that may broaden the range of SP applications. This review discusses the discovery, basic optical physics, the role of SPs, and applications of the extraordinary transmission of subwavelength hole arrays.

Photodetachment is a general property of condensed-phase anions exposed to visible or ultraviolet light, but its mechanism has not been fully explored until recently. The combination of femtosecond pump-probe experiments in both bulk liquids and solvated clusters and quantum mechanical descriptions of the relevant excited states has provided new insight into the spectroscopy, energetics, and dynamics of the detachment process. We review detachment phenomena for the prototypical atomic systems, iodide in water and sodide in tetrahydrofuran, and these systems provide the relevant framework for molecular systems. The iodide system has been studied in gas-phase clusters as well as bulk solution. This article also contrasts mechanisms as a function of energy from purely charge-transfer-to-solvent detachment to regimes in which there is direct and indirect participation of the bulk conduction band.

Energy flows anisotropically through the residues and vibrational states of globular proteins. A variety of experimental and computational studies have identified energy transport channels traversing many residues, in some cases connecting functional regions, potentially important in allostery, and in other cases having no apparent function. This property and the diffusion of energy in proteins are mimicked by transport on a percolation cluster. I review work that addresses connections between globular proteins, percolation clusters, and the similarity of energy flow and thermal transport in these systems. I also review experimental and theoretical studies of the anisotropic flow of energy through the vibrational states of a protein, a property that also can be understood by comparison with simple model disordered systems.

Calculations of the electronic structure of solids began decades ago, but only recently have solid-state quantum techniques become sufficiently reliable that their application is nearly as routine as quantum chemistry is for molecules. We aim to introduce chemists to the pros and cons of first-principles methods that can provide atomic-scale insight into the properties and chemistry of bulk materials, interfaces, and nanostructures. The techniques we review include the ubiquitous density functional theory (DFT), which is often sufficient, especially for metals; extensions such as DFT + U and hybrid DFT, which incorporate exact exchange to rid DFT of its spurious self-interactions (critical for some semiconductors and strongly correlated materials); many-body Green's function (GW and Bethe-Salpeter) methods for excited states; quantum Monte Carlo, in principle an exact theory but for which forces (hence structure optimization and dynamics) are problematic; and embedding theories that locally refine the quantum treatment to improve accuracy.

We present a detailed discussion of the complimentary fields of the application of two-dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Transient 2D-IR (T2D-IR) spectroscopy of nonequilibrium ensembles is probably one of the most promising strengths of 2D-IR spectroscopy, as the possibilities of 2D-NMR spectroscopy are limited in this regime. T2D-IR spectroscopy uniquely combines ultrafast time resolution with microscopic structural resolution. In this article we summarize our recent efforts to investigate the ultrafast structural dynamics of small peptides, such as the unfolding of peptide secondary structure motifs. The work requires two ingredients: 2D-IR spectroscopy and the possibility of triggering a structural transition of a peptide on an ultrafast timescale using embedded or intrinsic photoswitches. Several photoswitches have been tested, and we discuss our progress in merging these two pathways of research.

This article summarizes theoretical studies of molecular state determination by wave-packet interferometry (WPI) and recounts some recent experimental applications of molecular WPI. Calculations predict that two-color nonlinear WPI data can be used to reconstruct a rovibronic target wave packet evolving under an incompletely characterized nuclear Hamiltonian. This can be accomplished by the isolation via phase cycling or wave-vector matching of an exhaustive collection of overlaps between the unknown target and the members of a family of reference wave packets whose form is known by construction. This review highlights recent experiments employing WPI to gain amplitude-level information about the photoexcited-state dynamics of small molecules in the gas phase and in rare-gas crystals. I briefly describe a new semiclassical theory for condensed-phase WPI and other coherence-spectroscopy measurements, such as time-resolved coherent anti-Stokes Raman scattering, and mention our initial studies of nonlinear WPI from electronic energy-transfer complexes.

The surfaces of aqueous solutions are traditionally viewed as devoid of inorganic ions. Molecular simulations and surface-selective spectroscopic techniques show, however, that large polarizable anions and hydronium cations can be found (and even enhanced) at the surface and are involved in chemistry at the air/water interface. Here, we review recent studies of ions at the air/water interface and compare from this perspective water with other polar solvents. For water, we focus in particular on the surface behavior of its ionic product (i.e., hydronium and hydroxide ions). We also investigate the feasibility of dielectric models for the description of the protein/water interface, in analogy to the air/water interface. Little correlation is found between these two interfaces in terms of ion segregation. Therefore, we suggest a local model of pairing of ions from the solution with charged and polar groups at the protein surface. We also describe corresponding results of experimental studies on aqueous model systems.

This article reveals the enabling aspects of nanografting (an atomic force microscopy–based lithography technique) in surface physical chemistry. First, we characterize self-assembled monolayers and multilayers using nanografting to place unknown molecules into a matrix with known structure or vice versa. The availability of an internal standard in situ allows the unknown structures to be imaged and quantified. The same approaches are applied to reveal the orientation and packing of biomolecules (ligands, DNA, and proteins) upon immobilization on surfaces. Second, nanografting enables systematic investigations of size-dependent mechanics at the nanometer scale by producing a series of designed nanostructures and measuring their Young's modulus in situ. Third, one can investigate systematically the influence of ligand local structure on biorecognition and protein immobilization by precisely engineering ligand nanostructures. Finally, we also demonstrate the regulation of the surface reaction mechanism, kinetics, and products via nanografting.

In 1999, researchers extended X-ray crystallography to allow the imaging of noncrystalline specimens by measuring the X-ray diffraction pattern of a noncrystalline specimen and then directly phasing it using the oversampling method with iterative algorithms. Since then, the field has evolved moving in three important directions. The first is the 3D structural determination of noncrystalline materials, which includes the localization of the defects and strain field inside nanocrystals, and quantitative 3D imaging of disordered materials such as nanoparticles and biomaterials. The second is the 3D imaging of frozen-hydrated whole cells at a resolution of 10 nm or better. A main thrust is to localize specific multiprotein complexes inside cells. The third is the potential of imaging single large protein complexes using extremely intense and ultrashort X-ray pulses. In this article, we review the principles of this methodology, summarize recent developments in each of the three directions, and illustrate a few examples.

Patterning physical, chemical, and biological functions at solid surfaces combines technological development with scientific discoveries in many disparate fields. A variety of top-down and bottom-up approaches has proved successful for applications in the solid state, affording large-area patterning at ever-shrinking length scales. Here we review a collection of recent efforts that highlight the versatility of short-wavelength ultraviolet light and photogenerated reactive oxygen species as a simple and cost-effective means to pattern a variety of challenging materials and thin-film configurations. In particular, we discuss two different classes of materials that present different challenges for patterning: fluid phospholipid bilayers at the buried solid-water interface and the surfaces of bulk elastomers. Despite the use of an identical patterning source, the generation and stabilization of patterns in these two classes of materials follow different mechanisms and produce different functionalities.

The equation-of-motion coupled-cluster (EOM-CC) approach is a versatile electronic-structure tool that allows one to describe a variety of multiconfigurational wave functions within single-reference formalism. This review provides a guide to established EOM methods illustrated by examples that demonstrate the types of target states currently accessible by EOM. It focuses on applications of EOM-CC to electronically excited and open-shell species. The examples emphasize EOM's advantages for selected situations often perceived as multireference cases [e.g., interacting states of different nature, Jahn-Teller (JT) and pseudo-JT states, dense manifolds of ionized states, diradicals, and triradicals]. I also discuss limitations and caveats and offer practical solutions to some problematic situations. The review also touches on some formal aspects of the theory and important current developments.

We describe the recent emergence of attosecond science, assessing the present state of the art and discussing several recent examples where attosecond electron dynamics has been studied in atomic and molecular systems. After introducing the generation and characterization of attosecond laser pulses, we describe the use of isolated attosecond pulses in a pump-probe experiment revealing the subcycle time dependence of a multiphoton ionization process and an experiment using the interference from a train of attosecond pulses to extract amplitude and phase information for electronic wave functions. We furthermore discuss experiments where ultrashort laser pulses with a reproducible waveform control electron dynamics in the D2⁺ molecular ion on attosecond timescales. Attosecond science is coming of age and presently is reaching a level of maturity and sophistication that allows detailed investigations of the role of multielectron dynamics in physics and chemistry.