Annual Review of Physical Chemistry - Volume 54, 2003

Anisotropic etchants selectively reveal a specific crystallographic plane. Although prized industrially, these etchants are poorly understood because they target specific defect sites on a surface. New methods, which rely on a combination of scanning tunneling microscopy, kinetic Monte Carlo simulations, and infrared spectroscopy, have been developed to quantify these reactions. By correlating the measured reaction rates with the structure of the defects, information about reaction mechanisms can be obtained. These techniques have also been extended to allow for the quantification of impurity reactions such as the reaction of dissolved O2, and of nonetching additives, such as alcohols. A complementary macroscopic technique, which utilizes microfabricated arrays of miscut surfaces to measure orientation-dependent kinetics, is also described.

The current state of understanding of molecular resonance energy transfer (RET) and recent developments in the field are reviewed. The development of more general theoretical approaches has uncovered some new principles underlying RET processes. This review brings many of these important new concepts together into a generalization of Förster's original theory. The conclusions of studies investigating the various approximations in Förster theory are summarized. Areas of present and future activity are discussed. The review covers Förster theory for donor-acceptor pairs and electronic coupling for singlet-singlet, triplet-triplet, and superexchange-mediated energy transfer. This includes the transition density picture of Coulombic coupling as well as electronic coupling between molecular aggregates (excitons). Spectral overlaps and ensemble energy transfer rates in disordered aggregates, the role of dielectric properties of the medium, weak versus strong coupling, and new models for energy transfer in complex molecular assemblies are also described.

Femtosecond time-resolved photoelectron spectroscopy is emerging as a useful technique for investigating excited state dynamics in isolated polyatomic molecules. The sensitivity of photoelectron spectroscopy to both electronic configurations and vibrational dynamics makes it well suited to the study of ultrafast nonadiabatic processes. We review the conceptual interpretation of wavepacket dynamics experiments, emphasizing the role of the final state. We discuss the advantages of the molecular ionization continuum as the final state in polyatomic wavepacket experiments and show how the electronic structure of the continuum can be used to disentangle electronic from vibrational dynamics. We illustrate these methods with examples from diatomic wavepacket dynamics, internal conversion in polyenes and polyaromatic hydrocarbons, excited state intramolecular proton transfer, and azobenzene photoiosomerization dynamics.

Carbonaceous compounds comprise a substantial fraction of atmospheric particulate matter (PM). Particulate organic material can be emitted directly into the atmosphere or formed in the atmosphere when the oxidation products of certain volatile organic compounds condense. Such products have lower volatilities than their parent molecules as a result of the fact that adding oxygen and/or nitrogen to organic molecules reduces volatility. Formation of secondary organic PM is often described in terms of a fractional mass yield, which relates how much PM is produced when a certain amount of a parent gaseous organic is oxidized. The theory of secondary organic PM formation is outlined, including the role of water, which is ubiquitous in the atmosphere. Available experimental studies on secondary organic PM formation and molecular products are summarized.

The electronic structure of conjugated polymers is of current interest because of the wide range of potential applications for such materials in optoelectronic devices. It is increasingly clear that the electronic properties of conjugated polymers depend sensitively on the physical conformation of the polymer chains and the way the chains pack together in films. This article reviews the evidence that interchain electronic species do form in conjugated polymer films, and that their number and chemical nature depend on processing conditions; the chain conformation, degree of interchain contact, and rate of energy transfer can be controlled by factors such as choice of solvent, polymer concentration, thermal annealing, presence of electrically charged side groups, and encapsulation of the polymer chains in mesoporous silica. Taken together, the results reconcile many contradictions in the literature and provide a prescription for the optimization of conjugated polymer film morphology for device applications.

This review provides a historical context for our understanding of the hydration shell surrounding halide ions and illustrates how the cluster systems can be used, in combination with theory, to elucidate the behavior of water molecules in direct contact with the anion. We discuss how vibrational predissociation spectroscopy, carried out with weakly bound argon atoms, has been employed to deduce the morphology of the small water networks attached to anions in the primary steps of hydration. We emphasize the importance of charge-transfer in the binary interaction, and discuss how this process affects the structures of the larger networks. Finally, we survey how the negatively charged water clusters (H2O)n⁻ are providing a molecular-level perspective on how diffuse excess electrons interact with the water networks.

We discuss experiments on the dynamics of photodissociation that employ methods to select the energy, sometimes quantum states, of the reactant and to determine the quantum states and energy, sometimes also the orientation and alignment, of products. A summary of new advances of experimental methods is followed by applications to photodissociation of various types. Representative examples of simple bond fission, molecular elimination, and three-body dissociation with determined electronic states—sometimes the orientation of their angular momentum—of product atoms or distributions of electronic and internal states of product molecules illustrate the detailed information and insight that one can derive from such experiments. Photodissociation of van der Waals complexes, ions, species adsorbed on surfaces, and species in solution is excluded from this review.

The master equation provides a quantitative description of the interaction between collisional energy transfer and chemical reaction for dissociation, isomerization, and association processes. The approach is outlined for both irreversible and reversible dissociation, isomerization, and association reactions. There is increasing interest, especially in combustion, in association reactions that involve several linked potential wells, with the possibility of isomerization, collisional stabilization, and dissociation along several product channels. A major aim of the application of the master equation to such systems is the linking of the eigenvalues obtained by its solution to the rate coefficients for the phenomenological chemical reactions that describe the system and that are used in combustion models. The approach is illustrated by reference to the reactions C2H5 + O2, H + SO2, and the dissociation and isomerization of alkyl radicals.

Optical diagnostics are used to probe the plasma or neutral gas above the substrate, particles in the gas or on the surface, the film surface and reactor walls, the film itself, and the substrate during thin film processing. The development and application of optical probes are highlighted, in particular for analyzing plasma/gas phase intermediates and products and film composition, and performing metrology, thermometry, and endpoint detection and control. Probing etching (particularly plasma etching) and deposition (particularly epitaxy) are emphasized.

The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

Noble metal particles have long fascinated scientists because of their intense color, which led to their application in stained glass windows as early as the Middle Ages. The recent resurrection of colloidal and cluster chemistry has brought about the strive for new materials that allow a bottoms-up approach of building improved and new devices with nanoparticles or artificial atoms. In this review, we discuss some of the properties of individual and some assembled metallic nanoparticles with a focus on their interaction with cw and pulsed laser light of different energies. The potential application of the plasmon resonance as sensors is discussed.

The problem of the binding of an excess electron to polar molecules and their clusters has long fascinated researchers. Although excess electrons bound to such species tend to be very extended spatially and to have little spatial overlap with the valence electrons of the neutral molecules, inclusion of electron correlation effects is essential for quantitatively describing the electron binding. The major electron correlation contribution may be viewed as a dispersion interaction between the excess electron and the electrons of the molecule or cluster. Recent work using a one-electron Drude model to describe excess electrons interacting with polar molecules is reviewed.

Angle-resolved photoelectron spectroscopy has been performed for more than 70 years in various guises, but recently its potential to help solve in detail problems in the photoionization dynamics and intramolecular dynamics of gas-phase molecules has been recognized. One key development has been the design of experiments in appropriate geometries to extract information that pertains to the molecular frame, another has been the development of imaging spectrometers, and a third is the use of ultrafast lasers to cause photoionization. In this review, which is aimed at experimentalists, simple expressions for photoelectron angular distributions (PADs) in various experimental geometries are given and their applications explained.

The simplest two-dimensional (2D) spectra show how excitation with one (variable) frequency affects the spectrum at all other frequencies, thus revealing the molecular connections between transitions. Femtosecond 2D Fourier transform (2D FT) spectra are more flexible and share some of the remarkable properties of their conceptual parent, 2D FT nuclear magnetic resonance. When 2D FT spectra are experimentally separated into real absorptive and imaginary refractive parts, the time resolution and frequency resolution can both reach the uncertainty limit set for each resonance by the sample itself. Coherent four-level contributions to the signal provide new molecular phase information, such as relative signs of transition dipoles. The nonlinear response can be picked apart by selecting a single coherence pathway (e.g., specifying the relative signs of energy level difference frequencies during different time intervals as in the photon echo). Because molecules are frozen on the femtosecond timescale, femtosecond 2D FT experiments can separate a distribution of instantaneous molecular environments and intramolecular geometries as inhomogeneous broadening. This review provides an introduction to two-dimensional Fourier transform experiments exploiting second- and third-order vibrational and electronic nonlinearities.

The use of a combination of tunneling and optical spectroscopy to investigate the size and shape-dependent level structure and single-electron charging phenomena in semiconductor nanocrystals is reviewed. The artificial atom character of semiconductor nanocrystal quantum dots is manifested in both the discrete level structure and in the charging multiplicity of the single-electron tunneling data, revealing s and p atomic-like states. Such states can be directly imaged using scanning tunneling microscopy, providing the extent and symmetry of the envelope wavefunctions. A detailed description of the effect of the tunneling geometry on the single-electron tunneling spectra is presented. Correlation of the optical and tunneling data allows for the assignment of the level spectrum. The generality of this powerful combination is further demonstrated in the study of quantum rods that manifest the transition from zero-dimensional quantum dots to one-dimensional quantum wires.

This review discusses recent quantum scattering calculations on bimolecular chemical reactions in the gas phase. This theory provides detailed and accurate predictions on the dynamics and kinetics of reactions containing three atoms. In addition, the method can now be applied to reactions involving polyatomic molecules. Results obtained with both time-independent and time-dependent quantum dynamical methods are described. The review emphasises the recent development in time-dependent wave packet theories and the applications of reduced dimensionality approaches for treating polyatomic reactions. Calculations on over 40 different reactions are described.

Proteins directly control the nucleation and growth of biominerals, but the details of molecular recognition at the protein-biomineral interface remain poorly understood. The elucidation of recognition mechanisms at this interface may provide design principles for advanced materials development in medical and ceramic composites technologies. Here, we describe both the theory and practice of double-quantum solid-state NMR (ssNMR) structure-determination techniques, as they are used to determine the secondary structures of surface-adsorbed peptides and proteins. In particular, we have used ssNMR dipolar techniques to provide the first high-resolution structural and dynamic characterization of a hydrated biomineralization protein, salivary statherin, adsorbed to its biologically relevant hydroxyapatite (HAP) surface. Here, we also review NMR data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules using double-quantum ssNMR spectroscopy.