Annual Review of Physical Chemistry - Volume 50, 1999

This paper reviews the way in which, in the Italy of the years immediately after World War II, interest in the dynamics of molecular processes was awakened. The narrative begins with the work of a small number of chemists and physicists who, in the initial stage, interacted closely. In the course of the years, their interests diverged and younger people joined the newly formed groups. Even now, after half a century, a common approach can still to be seen regarding how to attack problems and perform experiments. Experimental work is discussed, bringing out the common viewpoint of fields as diverse as mass spectrometry, isotope effects, chemical kinetics, molecular beams, molecule-molecule interactions, molecule-ion interactions, molecule-surface interactions, and plasma chemistry.

This paper reviews recent developments in the field of nonlinear chemical kinetics. Five topics are dealt with: (a) new approaches to complex reaction mechanisms, stoichiometric network analysis, classification of chemical oscillators and formulation of their mechanisms by deduction from experiments, and correlation metric construction of reaction pathways from measurements; (b) thermodynamic and stochastic theory of nonequilibrium processes, the eikonal approximation, the evaluation of stochastic potentials, experimental tests of the thermodynamic and stochastic theory of relative stability, and fluctuation-dissipation relations in nonequilibrium chemical systems; (c) chemical kinetics and cellular automata and lattice gas automata; (d) theoretical approaches and experimental studies of stochastic resonance in chemical kinetics; and (e) rate processes in disordered systems, stochastic Liouville equations, stretched exponential relaxation in disordered systems, and universality classes for rate processes in systems with static or dynamic disorder.

Atoms and small molecules react with transition metal clusters in ways that are analogous to the physisorption and chemisorption reactions observed on the corresponding extended metal surface. However, often underlying these similarities are size-dependent variations in the reaction mechanisms and rates, the interpretation of which requires a detailed understanding of the structures of both the bare metal cluster substrates and the cluster-molecule complexes. Although polyatomic transition metal clusters cannot be characterized by the traditional methods of molecular spectroscopy, the combination of other physical and chemical probes can provide qualitative and semiquantitative structural information. These techniques, when combined with equilibrium geometries calculated using ab initio or semiempirical methods, provide a detailed picture of the structural origin of metal cluster reactivity and its variation with size.

Experimental and computational studies of photophysical processes in silver halide imaging materials are presented. Recent investigations that have refined our understanding of carrier recombination paths, exciton behavior, quantum confinement effects, and the structure and function of small surface silver clusters are detailed. The theory and mechanism of electron and hole injection from photoexcited surface-adsorbed dye molecules are outlined. The carrier trapping properties and subsequent photophysics of transition-metal dopant complexes are presented. Particular emphasis is given to the role of relaxation processes in electron and hole trapping events.

Polyelectrolytes are electrolytes asymmetric both in charge and size. Their properties in solution are dominated by Coulombic forces, and without a detailed understanding of these interactions, no interpretation of experimental data is possible. This paper is a review of recent developments in the theory of highly asymmetric electrolytes of spherical shape resembling surfactant micelles. Three different models are discussed: (a) the cell model, which is focused on the small ion-macroion interaction; (b) the model that treats the solution as an effective one-component fluid of macroions; and (c) the isotropic model, where the solution is represented as a mixture of charged spheres. Traditionally, the electrostatic interactions are accounted for via the solution of the Poisson-Boltzmann equation. This theory, however, ignores the fluctuations around the most probable distribution and may yield poor results for systems with multivalent ions. This paper focuses on developments beyond the Poisson-Boltzmann theory; the results of computer simulations and integral equation theories represent the major part of the review.

This review focuses on time-dependent methods suitable for simulating the quantum dynamics of processes in large clusters and condensed-phase environments. A number of mean field, quantum-classical, and quantum statistical approximations that avoid the conventional exponential scaling with the number of degrees of freedom are reviewed. In addition, rigorous semiclassical and path integral approaches are described that are feasible in certain physical situations. Select chemical applications illustrating the capabilities of these methods are discussed.

Recent studies on fast (<10 ns) and ultrafast (<10 ps) photothermal and photoacoustic phenomena occurring at solid-liquid interfaces are discussed, including related topics, with emphasis placed on interfaces between aqueous solutions and metals under electrochemical potential control. Details of transient reflecting grating measurements for metal-liquid interfaces are considered as they relate to mesoscopic interface structures and nano-environments. Dependencies of fast photothermal phenomena on the electrochemical potential and types of anions in the solutions are shown. Ultrafast photothermal phenomena observed by transient reflectivity measurements are considered in connection with interface femtochemistry and hot electron reactions. Technical progress in measuring fast and ultrafast photothermal phenomena is reviewed for solid-liquid interfaces, including colloidal solutions.

Recent applications of density functional theory to biologically relevant metal centers are reviewed. The emphasis is on reaction mechanisms, structures, and modeling. The accuracy of different functionals is discussed for standard benchmark tests of first- and second-row molecules and for transition metal systems. Modeling aspects of the protein metal complexes are discussed regarding both the size of the model being treated quantum mechanically and the treatment of the protein surrounding it. To illustrate the effects, structures computed without the effects of the protein are compared with experimental structures from enzymes, and results from simple dielectric models of the protein for electron transfer processes are described. The choice of spin state is discussed for multimetal complexes. Examples of mechanisms studied recently by density functional theory are described, such as O2 and methane activation in methane monooxygenase and O2 formation in photosystem II.

Recent progress in combining the techniques of time-resolved molecular spectroscopy with shock compression science is reviewed. Shock wave spectroscopy probes the response of molecules to high-speed, large-amplitude mechanical transients and is an important way of studying physical chemical phenomena that involve large-amplitude displacements. A brief discussion of the continuum model for shock compression and a molecular model for the shock front is presented. Methods for generating and detecting shock effects are reviewed. Several applications of shock spectroscopy are reviewed, including high explosives, the nanoshock technique that uses ultrafast lasers, and shock compression of biological molecules.

The elastic, thermodynamic, and transport properties of crystals and fluids at high temperature and pressure play a central role in the earth and planetary sciences as well as in a variety of technologies. These properties also constitute a principal experimental constraint on the description of intermolecular interactions at short distances. Aspects of “impulsive stimulated scattering,” when adapted to measurements in the diamond-anvil high-pressure cell, provide an approach to the determination of a subset of equilibrium and dynamic properties at high density.

Except for ortho- and para-H2, little is known about nuclear spin isomers (or spin modifications) of molecules. The main reason is the lack of practical enrichment techniques. Recently, a few enrichment methods were developed, which opened up new possibilities in the field. These methods are briefly reviewed. Substantial progress in the field has been made by the introduction of light-induced drift as a gas-phase separation tool. This is illustrated by extensive data on CH3F, which reveal that the gas-phase ortho-para conversion is governed by intramolecular mixing of the nuclear spin states. The role of direct ortho-para transitions is small. Various aspects of the conversion were investigated in detail: pressure and collision partner dependence, isotope effect, and temperature dependence. The most decisive information on the spin conversion mechanism is derived from the observation of level-crossing resonances in an electric field and the quantum Zeno effect induced by collisions.

This article reviews recent progress in our understanding of gas-phase neutral reaction dynamics as made possible by improvements in the crossed molecular beam scattering technique for measuring reactive differential cross sections. A selection of crossed-beam studies on systems that play a fundamental role in our basic understanding of reaction phenomena are discussed to illustrate the capabilities of the experimental method. The examples include benchmark atom-diatom abstraction and insertion reactions, and four-atom radical reactions for which state-to-state, state-resolved, or state-averaged differential cross sections have recently been measured. The results are discussed in the light of the latest related theoretical developments regarding the treatment of potential energy surfaces and the dynamics of the systems. Recent results on crossed-beam studies of chemically relevant reactions of carbon, nitrogen, and oxygen atoms are also reviewed, and the latest developments in the technique are noted.

This review provides a discussion of recent techniques for simulation of phase equilibria of complex fluids. Monte Carlo methods are emphasized over molecular dynamics methods. We describe recent developments, such as the use of expanded-ensemble, tempering, or histogram reweighting techniques. Our discussion of such developments is aimed at a general audience and is intended to provide an overview of the main advantages and limitations of each particular technique. References are provided to allow interested readers to identify and trace back most recent applications of a particular simulation technique. We conclude with general guidelines regarding selection of suitable simulation methods for particular problems and systems of interest.

This review is about understanding and controlling organic molecular adsorption on silicon. The goal is to provide a microscopic picture of structure and bonding in covalently attached molecule-silicon surface systems. The bias here is that an unprecedented, detailed understanding of adsorbate-surface structures is required in order to gain the control necessary to incorporate organic function into existing technologies or, eventually, to make new molecule-scale devices. A discussion of recent studies of adsorbate structure is presented. This includes simple alkenes, polyenes, benzene, and carene adsorbed on Si(100). Also included is a discussion of wet chemical procedures for forming alkyl and alkoxy covalently functionalized silicon. These discussions are presented together with comments on the related issues of adsorption dynamics and nano-scale manipulation in an effort to point the way toward principles and procedures that will allow the hybrid properties of organic molecules and surfaces to be harnessed.

In this overview we discuss the vibrational spectrum of phosphaethyne, HCP, in its electronic ground state, as revealed by complementary experimental and theoretical examinations. The main focus is the evolution of specific spectral patterns from the bottom of the potential well up to excitation energies of approximately 25,000 cm⁻¹, where large-amplitude, isomerization-type motion from H–CP to CP–H is prominent. Distinct structural and dynamical changes, caused by an abrupt transformation from essentially HC bonding to mainly PH bonding, set in around 13,000 cm⁻¹. They reflect saddle-node bifurcations in the classical phase space—a phenomenon well known in the nonlinear dynamics literature—and result in characteristic patterns in the spectrum and the quantum-number dependence of the vibrational fine-structure constants. Two polar opposites are employed to elucidate the spectral patterns: the exact solution of the Schrödinger equation, using an accurate potential energy surface and an effective or resonance Hamiltonian (expressed in a harmonic oscillator basis set and block diagonalized into polyads), which is defined by parameters adjusted to fit either the measured or the calculated vibrational energies. The combination of both approaches—together with classical mechanics and semiclassical analyses—provides a detailed spectroscopic picture of the breaking of one bond and the formation of a new one.

During protein folding, many of the events leading to secondary and tertiary structure occur in milliseconds or faster. Modern nuclear magnetic resonance and laser detection techniques, coupled with fast initiation of the folding reaction, are probing these events in great detail. Theory, ranging from analytical models to molecular dynamics calculations, is beginning to match up with experiment. As a result, timescales, from such elementary steps as the addition of a residue to a helix to strange kinetics of collapsing protein backbones, can now be measured and interpreted.

The basic principles and recent advances in electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry are reviewed. A brief history of electrospray ionization is provided, along with a complete technical description of the technique, electrospray ionization variations, and advantages. Next, the fundamental principles of Fourier transform ion cyclotron resonance mass spectrometry are covered, including ion cyclotron motion, ion cyclotron resonance excitation, and image current detection. Instrumentation and methods used to couple these techniques are then described. Topics include ion source configuration, ion transport through a strong magnetic field gradient, and ion trapping methods. The article concludes with selected applications that highlight the strengths of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

This paper describes the reproducing kernel Hilbert space (RKHS) method for constructing accurate, smooth, and efficient global potential energy surface (PES) representations for polyatomic systems using high-level ab initio data. The RKHS method provides a rigorous and effective framework for smooth multivariate interpolation of arbitrarily scattered data points and also for incorporating various physical requirements onto the PESs. Smoothness, permutation symmetry, and the asymptotic properties of polyatomic systems can be incorporated into the construction of reproducing kernels to render globally accurate PESs. Tensor products of one-dimensional generalized-spline-reproducing kernels are amenable to a fast algorithm, which makes a single evaluation of RKHS PESs essentially independent of the number of interpolated ab initio data points. This efficient implementation enables the study of the detailed dynamics of polyatomic systems based on high-quality RKHS PESs.