Annual Review of Physical Chemistry - Volume 47, 1996

The experimental and computational study of clusters has been an active field of research for over a decade. This review provides an overview of some of the methods that have been developed to study clusters and some of the results that have been obtained. Included are computational approaches to explore the potential energy surface for clusters, methods to extract thermodynamic properties from the potential surface information and approaches to insure simulation studies are performed in an ergodic fashion. The methods have proved to be useful in studying the structural transition from clusters to bulk phases, phase changes in small clusters and the importance of quantum effects. The review ends with a discussion of problems in cluster chemistry and physics that are of interest for future investigations.

Radical-radical reactions generally proceed on potential energy surfaces that have no maximum. Collisional deactivation leads to a stable molecular product; alternatively, radical or molecular products can be formed via dissociation channels additional to those regenerating the reactants. Models of the transition states must take into account the loose internal motion of the fragments, and a variational approach is necessary. The competition between dissociation and collisional stabilization may be modeled using a master equation (ME). The types of behavior encountered in radical-radical reactions and their analysis using the ME are illustrated by reference to the reactions CH3 + H, CH3 + CH3, and CH3 + OH.

Experimental and theoretical studies of polar solvation dynamics and spectral line broadening are described. Photon echo and fluorescence Stokes shift experiments are discussed, and the relationship between the information content of the two techniques clarified. The interaction of the chromophore with its solvent bath is described by a spectral density, and the connection of this spectral density with the liquid's instantaneous normal modes discussed. The ubiquity of the ultrafast phase of solvation dynamics is demonstrated, and a discussion of its physical origin given. The slower phases of solvation vary strongly from solvent to solvent. Molecular theories of liquid dynamics are able to rationalize such variations over at least a 2000-fold range of time scale. The review concludes with a brief discussion of the relevance of ultrafast solvation to chemical dynamics.

The NMR chemical shift serves as a paradigm for molecular electronic properties. We consider the factors that determine the general magnitudes of the shifts, the state of the art in theoretical calculations, the nature of the shielding tensor, and the multidimensional shielding surface that describes the variation of the shielding with nuclear positions. We also examine the nature of the intermolecular shielding surface as a general example of a supermolecule property surface. The observed chemical shift in the zero-pressure limit is determined not only by the value of the shielding at the equilibrium geometry, but the dynamic average over the multidimensional shielding surface during rotation and vibration of the molecule. In the gas, solution, or adsorbed phase it is an average of the intermolecular shielding surface over all the configurations of the molecule with its neighbors. The temperature dependence of the chemical shift in the isolated molecule, the changes upon isotopic substitution, the changes with environment, are well characterized experimentally so that quantum mechanical descriptions of electronic structure and theories related to dynamics averaging of any electronic property can be subjected to stringent test.

Crystallization is necessary to obtain the three-dimensional structure of proteins and nucleic acids; it often represents the bottleneck in structure determination. Our understanding of crystallization mechanisms is still incomplete. In this review, we emphasize fundamental aspects of the crystallization process.

Protein-protein contacts in crystals are complex, involving a delicate balance of specific and nonspecific interactions. Depending on solution conditions, these interactions can lead to nucleation of crystals or to amorphous aggregation; this stage of crystallization has been successfully studied by light scattering. Post nucleation crystal growth may proceed by mechanisms involving crystal defects or two-dimensional nucleation, as observed by atomic force and interference microscopy. Cessation of growth has been observed but remains incompletely understood. Impurities may play important roles during all stages of crystallization. Phase diagrams can guide optimization of conditions for nucleation and subsequent crystal growth; a theoretical understanding relating these to the intermolecular interactions is beginning to develop.

Various aspects of molecular solvation are reviewed from the perspective provided by gas-phase aromatic solute-(solvent)n clusters. Particular emphasis is placed on hydrogen-bonded clusters, varying from 1:1 aromatic-H2O complexes up to clusters containing several water or methanol molecules. Recent advances in experimental methods for obtaining accurate structures, binding energies, and intermolecular and intramolecular vibrational spectra are highlighted. Many of these methods provide size and conformation selectivity and can be readily extended to both ground and electronically excited neutral states. The π hydrogen bond, hydrogen bonding to aromatic alcohols, water complexation to indole and its derivatives, and the hydrogen-bonded networks of benzene-(H2O)n and benzene-(CH3OH)n clusters are reviewed in special detail.

NMR relaxation experiments can provide information on overall and internal motions in proteins. This review consists of a concise report on the evolution of the theories for nuclear relaxation followed by an overview of mathematical models for internal motions in proteins. Next, the method of spectral density mapping with recent developments is reviewed. This is followed by a discussion of pulse sequences for relaxation experiments. Finally, we review recent studies correlating relaxation parameters, in particular spectral density functions, with structural features of proteins and with results of molecular dynamics simulations.

The history of superconductivity, including superconductivity in the high-Tc cuprates, is reviewed very briefly, and the differences between conventional superconductors and the high-Tc cuprates are summarized. The basic crystal structures of the major series of high-Tc cuprates are described and compared. The relation of structures to superconducting properties is reviewed with an emphasis on the orthorhombic-tetragonal transition in (La2−x Srx)CuO4; the corresponding transition, and also the transition to the low-temperature tetragonal phase in (La2−xBax)CuO4; and the effects of oxygen vacancies, oxygen-vacancy ordering, frozen-in disorder, and occupation of the off-chain O(5) sites in YBa2Cu3O7−δ. The effects of chemical substitutions of lanthanide elements on the La/Sr sites in (La2−xSrx)CuO4 and on the Y sites in YBa2Cu3O7−δ, and of 3d elements and sp elements on the Cu sites in both systems are reviewed. The difference between the effects of the lanthanide substitutions, particularly Pr, in the two systems are considered. Major properties of the Bi-, Tl-, and Hg-cuprates, are described briefly. A comparison of the high-Tc cuprates with noncuprate oxide superconductors is given.

This review involves chemical kinetics of atmospheric reactions, with emphasis on gas phase and heterogeneous processes related to the following topics: (a) in the troposphere, chemistry of CFC/Halon replacement compounds and chemistry of sulfur species and (b) in the stratosphere, chemistry of fluorine, bromine, and iodine species and of heterogeneous processes occurring on sulfuric acid aerosols. The results of laboratory measurements of rate parameters are summarized, and current views are presented on the physical chemistry foundation underlying the interpretation of these kinetics parameters.

NMR has emerged as an important tool for studies of protein folding because of the unique structural insights it can provide into many aspects of the folding process. Applications include measurements of kinetic folding events and structural characterization of folding intermediates, partly folded states, and unfolded states. Kinetic information on a time scale of milliseconds or longer can be obtained by real-time NMR experiments and by quench-flow hydrogen-exchange pulse labeling. Although NMR cannot provide direct information on the very rapid processes occurring during the earliest stages of protein folding, studies of isolated peptide fragments provide insights into likely protein folding initiation events. Multidimensional NMR techniques are providing new information on the structure and dynamics of protein folding intermediates and both partly folded and unfolded states.

A simple method for calculating the electronic energy of extended solids is discussed in this review. This method is based on the Hückel or tight-binding theory in which an explicit pairwise repulsion is added to the generally attractive forces of the partially filled valence electron bands. An expansion based on the power moments of the electronic density of states is discussed, and the structural energy difference theorem is reviewed. The repulsive energy is found to vary linearly with the second power moment of the electronic density of states. These results are then used to show why there is such a diversity of structure in the solid state. The elemental structures of the main group are rationalized by the above methods. It is the third and fourth power moments (which correspond in part to triangles and squares of bonded atoms) that account for much of the elemental structures of the main group elements of the periodic table. This serves as an introduction to further rationalizations of transition for noble metal alloy, binary and ternary telluride and selenide, and other intermetallic structures.Thus a cohesive picture of both covalent and metallic bonding is presented in this review, illustrating the importance of atomic orbitals and their overlap integrals.

Colloidal suspensions of uniformly sized microspheres can serve as powerful model systems for investigating many-body processes in condensed-matter physics. The ensemble of microspheres in such suspensions undergoes disorder-order transitions from fluids to crystals in direct analogy with the structural transitions experienced by atoms in conventional materials. Unlike atoms, however, colloidal spheres can be imaged and tracked using optical microscopy and computerized image processing. This review addresses issues in the physics of phase transitions that have been attacked through digital video microscopy of colloidal dispersions over the past decade. Particular emphasis is placed on microscopic mechanisms of melting and freezing and on the effects of geometric confinement on these fundamental processes.

The unprecedented high intensities made accessible by the development of ultrashort pulse laser systems have uncovered a host of new phenomena and changed the way that we think about atomic and molecular dynamics. We review these developments in the context of some of the basic models that have evolved to explain them. The successes and limitations of simple semiclassical models of strong-field atomic phenomena are discussed. Photodissociation dynamics have shown a rich complexity in strong fields—bond softening, above-threshold dissociation, coulomb explosion—which we review. The promise of the new laser systems in the field of coherent control of molecular dynamics is also discussed.

In recent years we have witnessed tremendous progress in our understanding of unimolecular reactions on a fully state-resolved level. Here we describe recent state-resolved experimental studies of resonances in unimolecular reactions, focusing on the transition from isolated to overlapping resonances. Depending on the well depth and extent of intramolecular vibrational energy redistribution, the resonances can exhibit properties ranging from mode- and state-selective to statistical behavior. In the statistical limit the resonances are usually overlapped, and interference effects may become prominent. We use recent studies of HCO, HFCO, and CH3O to examine the transition from mode-selective to statistical behavior in the isolated regime. Experimental and theoretical studies of NO2, including photofragment yield spectra, fully resolved NO quantum state distributions, and decomposition rates are used to examine unimolecular decomposition in the regime of overlapping resonances.

It is technologically important to understand how halogens react with semiconductor surfaces because halogen compounds are commonly used to etch semiconductor wafers in the microelectronics industry. Halogens are also model adsorbates for studying chemisorption on covalently bonded materials, such as semiconductors, owing to the simple nature of the bonds that they form. The growing use of III-V materials in the manufacture of optoelectronic devices has prompted investigations of the reactions of molecular halogens (XeF2, Cl2, Br2, and I2) with III-V semiconductor surfaces (GaAs, GaSb, InP, InAs, and InSb). This review examines the more fundamental of these investigations, which involve model systems in ultra-high vacuum, focusing on the chemistry of the halogen surface reactions and the physical and electronic structure of the reacted surfaces.

The interaction of light within tissue has been used to recognize disease since the mid-1800s. The recent developments of small light sources, detectors, and fiber optic probes provide opportunities to quantitatively measure these interactions, which yield information for diagnosis at the biochemical, structural, or (patho)physiological level within intact tissues. However, because of the strong scattering properties of tissues, the reemitted optical signal is often influenced by changes in biochemistry (as detected by these spectroscopic approaches) and by physiological and pathophysiological changes in tissue scattering. One challenge of biomedical optics is to uncouple the signals influenced by biochemistry, which themselves provide specificity for identifying diseased states, from those influenced by tissue scattering, which are typically unspecific to a pathology. In this review, we describe optical interactions pursued for biomedical applications (fluorescence, fluorescence lifetime, phosphorescence, and Raman from cells, cultures, and tissues) and then provide a descriptive framework for light interaction based upon tissue absorption and scattering properties. Finally, we review important endogenous and exogenous biological chromophores and describe current work to employ these signals for detection and diagnosis of disease.