Annual Review of Physical Chemistry - Volume 51, 2000

The surface-sensitive optical technique of surface plasmon resonance (SPR) imaging is used to characterize ultrathin organic and biopolymer films at metal interfaces in a spatially resolved manner. Because of its high surface sensitivity and its ability to measure in real time the interaction of unlabeled biological molecules with arrays of surface-bound species, SPR imaging has the potential to become a powerful tool in biomolecular investigations. Recently, SPR imaging has been successfully implemented in the characterization of supported lipid bilayer films, the monitoring of antibody-antigen interactions at surfaces, and the study of DNA hybridization adsorption. The following is included in this review: (a) an introduction to the principles of surface plasmon resonance, (b) the details of SPR imaging instrumental design, (c) a short discussion concerning resolution, sensitivity, and quantitation in SPR imaging, (d) the details of DNA array fabrication on chemically modified gold surfaces, and (e) two examples that demonstrate the application of the SPR imaging technique to the study of protein-DNA interactions.

Thermionic emission is discussed as a long time (microseconds) decay mode of energy-rich large molecules, metallic and metcar clusters, and fullerenes. We review what is known and consider the many experiments, systems, and theoretical and computational studies that still need to be done. We conclude with a wish list for future work. Particular attention is given to the experimental signatures, such as the dependence on the mode of energy acquisition, and theoretical indications of a not-quite-statistical delayed ionization and to the competition of electron emission with other decay modes, such as fragmentation or radiative cooling. Coupling of the electronic and nuclear modes can be a bottleneck and quite long time-delayed ionization can be observed, as in the decay of high Rydberg states probed by ZEKE spectroscopy, before the onset of complete energy partitioning.

Although it has long been recognized that dynamics in supercooled liquids might be spatially heterogeneous, only in the past few years has clear evidence emerged to support this view. As a liquid is cooled far below its melting point, dynamics in some regions of the sample can be orders of magnitude faster than dynamics in other regions only a few nanometers away. In this review, the experimental work that characterizes this heterogeneity is described. In particular, the following questions are addressed: How large are the heterogeneities? How long do they last? How much do dynamics vary between the fastest and slowest regions? Why do these heterogeneities arise? The answers to these questions influence practical applications of glass-forming materials, including polymers, metallic glasses, and pharmaceuticals.

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Theoretical aspects of dynamical processes at metal surfaces are reviewed. Experimental challenges to theory are presented and progress toward meeting these challenges is appraised. Topics include adsorbate vibrational energy flow, inelastic molecule-surface scattering, adsorption, transient mobility, dissociation, desorption, photochemistry, and electron-induced chemistry at metal surfaces. Experimental examples cited illustrate the richness of dynamical phenomena to be understood and the necessity of developing multidimensional, beyond Born-Oppenheimer, formulations of adsorbate dynamics. Classical mechanical and quantum mechanical treatments of dynamics are contrasted. The importance of including phonon and electron-hole pair dissipation in theories of adsorbate dynamics is emphasized, and strategies for doing this in classical and quantum treatments are presented.

This article provides a review of recent studies of the properties of unsolvated (and partially solvated) peptides and proteins. The methods used to produce vapor-phase peptide and protein ions are described along with some of the techniques used to study them, such as H/D exchange, blackbody infrared radiative dissociation, and ion mobility measurements. Studies of unsolvated peptides and proteins provide information about their intrinsic intramolecular interactions. The topics covered include the role of zwitterions and salt bridges in the vapor phase, Coulomb interactions in multiply charged ions, the unfolding and refolding of vapor-phase proteins, and the stability of unsolvated helices and sheets. Finally, dehydration and rehydration studies of proteins in the vapor phase are described. These can provide exquisitely detailed information about hydration interactions, such as the enthalpy and entropy changes associated with adsorbing individual water molecules.

This review summarizes and assesses recent theoretical and experimental advances, with special emphasis on the effective interaction between charge-stabilized colloids, in the bulk or in confined geometries, and on the ambiguities of defining an effective charge of the colloidal particles. Some consideration is given to the often neglected discrete solvent effects.

Explicitly time-dependent implementations of optical frequency modulation spectroscopy have been recently applied to a wide range of problems in chemical physics. We provide a brief description of the methodology, with an emphasis on its intrinsic advantages for interrogating transient species. Several examples highlight the application of the technique to high-resolution absorption spectra of free radicals, rate measurements for gas-phase reactions, and Doppler spectroscopy of the gas-phase products of photoinitiated reactions.

Dynamic processes in crystalline solids are reflected in the atomic displacement amplitudes determined, together with the atomic coordinates, by crystal structure analysis. The interpretation of such amplitudes poses two severe problems: (a) The relative phases of the atomic displacements are lost; and (b) the amplitudes may reflect disorder in the structure and systematic error in the diffraction experiment in addition to motion, but the three contributions cannot be separated on the basis of measurements at a single temperature. Several approximate ways to solve these problems, e.g. rigid-body and segmented-rigid-body analysis, are reviewed together with their limitations. A more recent approach that represents a significant advance with respect to both difficulties is also described: Crystal structures are determined over a range of temperatures; the mean square amplitude quantities are interpreted by taking explicit account of their temperature dependence, i.e. by exploiting the difference in behavior of a microscopic oscillator in the low-temperature, quantum regime and in the high-temperature, classical regime. A distinction between low-frequency and high-frequency motion, disorder, and systematic error becomes possible with this model; this is illustrated with the help of case studies.

Rotational tunneling of small molecular groups has been the subject of considerable theoretical and experimental activity for several decades. Much of this activity has been driven by the promise of exploiting the extreme sensitivity of quantum tunneling to interatomic potentials, but until recently, there was no straightforward means by which quantitative information about these potentials could be extracted. This review explains how a quantitative method, suitable for general application, was developed. It then goes on to show how this has been used to understand tunneling systems for which no previous satisfactory explanation had been found. The application of the methodology, and its results, to other disciplines is discussed.

The standard description of the vibrational and rotational motion of polyatomic molecules, as expressed by the distortable rotor/harmonic oscillator approximation, provides an adequate description of the molecular quantum states only in regions of low total state density. When the total state density is large, exceeding 100 states/cm⁻¹, the vibrational dynamics are “dissipative” and the fundamental process of intramolecular vibrational energy redistribution is operative. The presence of intramolecular vibrational energy redistribution leads to molecular quantum states of a qualitatively different nature. With respect to a normal-mode vibrational basis, these quantum states are “highly mixed” in their vibrational character and represent nuclear motion that is a combination of all the normal-mode motions. This review describes frequency domain spectroscopy techniques designed to probe the vibrational, rotational, and structural composition of these eigenstates. Recent work that investigates spectroscopy between highly mixed states is also reviewed.

Proteins and RNA undergo intricate motions as they carry out functions in biological systems. These motions frequently entail large-scale conformational changes that induce changes in the surface structure, or shape, of a molecule. This review describes the experimental characterization of large-scale shape changes in proteins and macromolecular complexes and the effects of such changes on macromolecular behavior. We describe several important results that have been obtained by using small-angle scattering, which is emerging as a powerful technique for determining macromolecular shapes and elucidating the quaternary structure of macromolecular assemblies.

Infrared (IR) spectroscopy is widely used to identify molecular adsorbates that form on metals in the course of surface chemical reactions. Because IR spectroscopy is one of the few surface-sensitive probes that provide molecule-specific information without perturbing the chemisorbed state, there is great interest in extracting as much structural information from the spectra as possible. The various ways IR spectroscopy is used to determine the structure of molecular adsorbates, from strictly qualitative interpretations based on symmetry selection rules to the use of ab initio electronic structure calculations to predict the IR spectrum of a chemisorbed molecule, are reviewed.

The vibrational relaxation of noble gas–halogen van der Waals clusters has been fertile territory for the development of experimental and theoretical tools for state-to-state dynamics studies. Proceeding through the various combinations of noble gas atoms and halogen molecules, one goes from “simple” direct vibrational predissociation, through sequential relaxation pathways, to the statistical intramolecular vibrational relaxation limit. In some cases the vibrational processes dominate, in others electronically nonadiabatic processes, including chemical reactions, interfere. Thus the noble gas–halogen species provide test cases for most of the dynamical processes available to more “normal” molecules. This review discusses the current state-of-the-art for such studies and points to important problems that remain to be solved.

We review molecular dynamics simulations of nucleic acids, including those completed from 1995 to 2000, with a focus on the applications and results rather than the methods. After the introduction, which discusses recent advances in the simulation of nucleic acids in solution, we describe force fields for nucleic acids and then provide a detailed summary of the published literature. We emphasize simulations of small nucleic acids (∼6 to 24 mer) in explicit solvent with counterions, using reliable force fields and modern simulation protocols that properly represent the long-range electrostatic interactions. We also provide some limited discussion of simulation in the absence of explicit solvent. Absent from this discussion are results from simulations of protein-nucleic acid complexes and modified DNA analogs. Highlights from the molecular dynamics simulation are the spontaneous observation of A B transitions in duplex DNA in response to the environment, specific ion binding and hydration, and reliable representation of protein-nucleic acid interactions. We close by examining major issues and the future promise for these methods.

Ice particles found within polar stratospheric clouds (PSCs) and upper tropospheric cirrus clouds can dramatically impact the chemistry and climate of the Earth's atmosphere. The formation of PSCs and the subsequent chemical reactions that occur on their surfaces are key components of the massive ozone hole observed each spring over Antarctica. Cirrus clouds also provide surfaces for heterogeneous reactions and significantly modify the Earth's climate by changing the visible and infrared radiation fluxes. Although the role of ice particles in climate and chemistry is well recognized, the exact mechanisms of cloud formation are still unknown, and thus it is difficult to predict how anthropogenic activities will change cloud abundances in the future. This article focuses on the nucleation, chemistry, and microphysical properties of ice particles composing PSCs and cirrus clouds. A general overview of the current state of research is presented along with some unresolved issues facing scientists in the future.

Quantum Monte Carlo methods have recently made it possible to calculate the electronic structure of relatively large molecular systems with very high accuracy. These large systems range from positron complexes [NH2,Ps] with ∼10 electrons to C20 isomers with 120 electrons, to silicon crystal structures of 250 atoms and 1000 valence electrons. The techniques for such calculations and a sampling of applications are reviewed.

The growth and evolution of strained epitaxial Ge on a Si(001) surface provides a rich system for exploring the behavior of strongly interacting nanocrystals. In the temperature regime above 500°C, there are two different (metastable) shapes of defect-free nanocrystals, termed pyramids and domes, that dominate the system depending on the temperature of the substrate during growth and the amount of Ge deposited. In contrast to the usual case considered in nucleation theory, the relaxation of the strain energy at the surface of the nanocrystals makes those surfaces stabilizing, i.e. the surface contribution to the free energy of the Ge nanocrystals is negative. Given that the edges of the nanocrystals are destabilizing (positive free energy), the interaction of the surfaces and edges of the nanocrystals in an ensemble renders an internal free energy for the system that has a local minimum with respect to the size (volume) of the nanocrystal. At finite temperatures, this free energy yields a size distribution with a characteristic centroid, width, and skewness for each nanocrystal shape. The smaller pyramids transform into domes when they grow to the point where they can surmount a kinetic energy barrier between the two structures. However, the Ge nanocrystals also effectively repel one another strongly via the strain fields that are produced in the Si substrate. This repulsive interaction makes the ensemble of Ge nanocrystals a highly nonideal thermodynamic system and, in turn, makes the free energies of the nanocrystals a function of their number density, or equivalently a function of the amount of Ge deposited. The interplay of the stabilizing effect of the nanocrystal surfaces and the destabilizing influence of their repulsive interactions yields a complex behavior for the nanocrystal-size distributions that can nonetheless be modeled using simple thermodynamic expressions.