Annual Review of Physical Chemistry - Volume 52, 2001

This review illustrates the experimental study of chemical reaction dynamics using methods that select the quantum states and energy of the reactants and determine the quantum states and energy of the products. The focus is reaction dynamics in systems in which at least one of the reactants or products is a polyatomic molecule. The approach taken is to select four prototype reaction systems as case studies to demonstrate the detail of information and insight that can come from such experiments. Thus, the review is selective and neither claims nor attempts to be comprehensive. Reference to and discussion of theoretical reaction dynamics are included where computational results directly connect with the experiments.

Sensitive and precise measurements of rate coefficients, branching fractions, and energy disposal from gas-phase radical reactions provide information about the mechanism of elementary reactions as well as furnish modelers of complicated chemical systems with rate data. This chapter describes the use of time-resolved infrared laser absorption as a tool for investigating gas-phase radical reactions, emphasizing the exploitation of the particular advantages of the technique. The reaction of Cl atoms with HD illustrates the complementarity of thermal kinetic measurements with molecular beam data. Measurements of second-order reactions, such as the self-reactions of SiH3 and C3H3 radicals, and determinations of product branching fractions in reactions such as CN + O2 rely on the wide applicability of infrared absorption and on the straightforward relationship of absorption to absolute concentration. Finally, investigations of product vibrational distributions, as in the CN + H2 reaction, provide additional insight into the details of reaction mechanisms.

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

We review a model for the free-solution electrophoretic mobility of oligomeric double-stranded (ds) DNA. We have found that the free-solution mobility of ds DNA increases as the molecular weight of the fragment increases, up to a few hundred base pairs. This insight is combined with recent advances in the nature of counterion condensation theory of very short DNA fragments to describe quantitatively the electrophoretic mobility of oligomeric single-stranded DNA in polyacrylamide gels. The model predicts, in agreement with recent experiments, that significant anomalous migration exists with short DNA sequences, the onset of which is dependent on the size of polyacrylamide gel pores. For terminal phosphate-labeled DNA fragments, the free-solution mobility is no longer proportional to the ratio of the total effective charge and the friction coefficient. These changes in properties affect the characteristics of migration of end-labeled DNA fragments in polyacrylamide gels.

Recent applications of various in situ techniques have dramatically improved our understanding of the self-organization process of adsorbed molecular monolayers on solid surfaces. The process involves several steps, starting with bulk solution transport and surface adsorption and continuing with the two-dimensional organization on the substrate of interest. This later process can involve passage through one or more intermediate surface phases and can often be described using two-dimensional nucleation and growth models. A rich picture has emerged that combines elements of surfactant adsorption at interfaces and epitaxial growth with the additional complication of long-chain molecules with many degrees of freedom.

Crossed-molecular-beam and laser techniques have enabled experimentalists to measure the state-resolved differential cross sections of elementary chemical reactions. This article reviews recent progress in this area. Particular emphasis is placed on some intriguing physical phenomena associated with a few benchmark reactions and how these measurements help in answering fundamental questions about reaction dynamics. We examine specifically the geometric phase effects in the reaction H + D2, the dynamical resonance phenomenon in F + HD, the unusually large spin-orbit reactivity in Cl(²P) + H2, the insertion reaction O(¹D) + H2, and the mode-specific reactivity in Cl + CH4(ν). The give-and-take between experiment and theory in unraveling the physical picture of the dynamics is illustrated throughout this review.

The application of coincidence techniques to the study of the reaction dynamics of isolated molecules is reviewed. Coincidence spectroscopy is a powerful approach for carrying out a number of measurements. At its most basic level, coincidence techniques can identify the source of a specific signal, as in the well-known photoelectron-photoion coincidence approach used for several years. By carrying out coincidence experiments in an increasingly differential manner, correlated energy and angular distributions of reaction products may be recorded. Completely energy- and angle-resolved measurements of photoelectrons and ionic or neutral products can reveal molecular-frame photoelectron and photofragment angular distributions and aid in the characterization of dissociative states of molecules and ions. Recent work in this area is reviewed, including examples from studies of dissociative photodetachment, dissociative photoionization, time-resolved studies of dissociative photoionization, and three-body dissociation processes.

Photoexcitation of a semiconductor with photons above the semiconductor band gap creates electrons and holes that are out of equilibrium. The rates at which the photogenerated charge carriers return to equilibrium via thermalization through carrier scattering, cooling by phonon emission, and radiative and nonradiative recombination are important issues. The relaxation processes can be greatly affected by quantization effects that arise when the carriers are confined to regions of space that are small compared with their deBroglie wavelength or the Bohr radius of bulk excitons. The effects of size quantization in semiconductor quantum wells (carrier confinement in one dimension) and quantum dots (carrier confinement in three dimensions) on the respective carrier relaxation processes are reviewed, with emphasis on electron cooling dynamics. The implications of these effects for applications involving radiant energy conversion are also discussed.

We outline recent developments in biological single-molecule fluorescence detection with particular emphasis on observations by ratiometric fluorescence resonance energy transfer (FRET) of biomolecules freely diffusing in solution. Single-molecule-diffusion methodologies were developed to minimize perturbations introduced by interactions between molecules and surfaces. Confocal microscopy is used in combination with sensitive detectors to observe bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract ratiometric observables such as FRET efficiency and polarization anisotropy. We describe the development of single-molecule FRET methodology and its application to the observation of the Förster distance dependence and the study of protein folding and polymer physics problems. Finally, we discuss future advances in data acquisition and analysis techniques that can provide a more complete picture of the accessible molecular information.

Time-resolved photoelectron spectroscopy (TRPES) has become a powerful new tool in studying the dynamics of molecules and clusters. It has been applied to processes ranging from energy flow in electronically excited states of molecules to electron solvation dynamics in clusters. This review covers experimental and theoretical aspects of TRPES, focusing on studies of neutral and negatively charged species.

Pulsed electron paramagnetic resonance (EPR) methods such as ESEEM, PELDOR, relaxation time measurements, transient EPR, high-field/high-frequency EPR, and pulsed ENDOR, have been used successfully to investigate the local structure and dynamics of paramagnetic centers in biological samples. These methods allow different contributions to the EPR spectra to be distinguished and can help unravel complicated EPR spectra consisting of overlapping resonance lines, as are often found in disordered protein samples. The basic principles, specific potentials, technical requirements, and limitations of these advanced EPR techniques will be reviewed together with recent applications to metal centers, organic radicals, and spin labels in proteins.

IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T^1.3, that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electric field-coupling mechanism is tested by observing differences in the temperature dependence of the pure dephasing of Mb-CO mutations.

Significant advances toward understanding the structure of aqueous surfaces on a molecular level have been made in recent years. This review focuses on the recent contributions of surface vibrational sum frequency spectroscopy (VSFS) to this field of study. An overview of recent VSFS studies of the molecular structure and orientation of molecules at the vapor-water interface and the interface between water and an immiscible organic liquid is presented, with particular emphasis on studies that compare the molecular properties and adsorbate behavior at these two different but related interfaces. This discussion is preceded by a general introduction to VSFS studies at aqueous surfaces and a description of the fundamental principles underlying the technique.

Electrochemical processes leading to light emission are reviewed, with emphasis on aspects of this subject relevant to the understanding and optimization of electrogenerated luminescence (EL) in organic thin-film materials. The basic energetic requirements of light emission from electrochemically initiated solution redox reactions [electrogenerated chemiluminescence (ECL)] are reviewed first. This review is followed by a discussion of light-emitting electrochemical processes that have been observed in hybrids of ionically conducting polymers and electronically conducting polymers. Finally, the features of EL in insulating polymers and molecular thin films are reviewed, along with recent electrochemical and ECL studies of the small-molecule components of certain organic light-emitting diodes. These studies provide a conceptual framework for understanding and optimizing these materials and the EL process.

This review discusses the reactivities and thermodynamics of small-size-specific transition metal clusters and focuses on thermodynamic information, which has not been comprehensively discussed before. Because of this focus, guided-ion-beam mass spectrometry was used to acquire much of the data. The details of this technique and the associated data analysis methods are provided. Results on the stabilities of bare transition metal clusters are provided for neutral, cationic, and anionic species. Implications for the electronic and geometrical structures are discussed, as well as the extrapolation of these values to bulk phase behavior. Detailed results for reactions of transition metal clusters with D2 and the oxygen donors O2 and CO2 are reviewed. Available bond energies between size-specific clusters and one D atom and one and two O atoms are compiled, and their implications are evaluated and favorably compared with bulk phase analogs. Several additional thermodynamic studies of various cluster systems are also discussed.

Novel applications of solid state nuclear magnetic resonance (NMR) to the study of small molecules, synthetic polymers, biological systems, and inorganic materials continue at an accelerated rate. Instrumental to this uninterrupted expansion has been an improved understanding of the chemical physics underlying NMR. Such deeper understanding has led to novel forms of controlling the various components that make up the spin interactions, which have in turn redefined the analytical capabilities of solid state NMR measurements. This review presents a perspective on the basic phenomena and manipulations that have made this progress possible and describes the new opportunities and challenges that are being opened in the realms of spin-1/2 and quadrupole nuclei spectroscopies.

Beginning with simplified lattice and continuum “minimalist” models and progressing to detailed atomic models, simulation studies have augmented and directed development of the modern landscape perspective of protein folding. In this review we discuss aspects of detailed atomic simulation methods applied to studies of protein folding free energy surfaces, using biased-sampling free energy methods and temperature-induced protein unfolding. We review studies from each on systems of particular experimental interest and assess the strengths and weaknesses of each approach in the context of “exact” results for both free energies and kinetics of a minimalist model for a beta-barrel protein. We illustrate in detail how each approach is implemented and discuss analysis methods that have been developed as components of these studies. We describe key insights into the relationship between protein topology and the folding mechanism emerging from folding free energy surface calculations. We further describe the determination of detailed “pathways” and models of folding transition states that have resulted from unfolding studies. Our assessment of the two methods suggests that both can provide, often complementary, details of folding mechanism and thermodynamics, but this success relies on (a) adequate sampling of diverse conformational regions for the biased-sampling free energy approach and (b) many trajectories at multiple temperatures for unfolding studies. Furthermore, we find that temperature-induced unfolding provides representatives of folding trajectories only when the topology and sequence (energy) provide a relatively funneled landscape and “off-pathway” intermediates do not exist.

Driven by prospective applications, there is much interest in developing materials that can perform specific functions in response to external conditions. One way to design such materials is to create systems which, in response to external inputs, can self-assemble to form structures that are functionally useful. This review focuses on the principles that can be employed to design macromolecules that when presented with an appropriate two-dimensional surface, will self-assemble to form nanostructures that may be functionally useful. We discuss three specific examples: (a) biomimetic recognition between polymers and patterned surfaces. (b) control and manipulation of nanomechanical motion generated by biopolymer adsorption and binding, and (c) creation of patterned nanostructuctures by exposing molten diblock copolymers to patterned surfaces. The discussion serves to illustrate how polymer sequence can be manipulated to affect self-assembly characteristics near adsorbing surfaces. The focus of this review is on theoretical and computational work aimed toward elucidating the principles underlying the phenomena pertinent to the three topics noted above. However, synergistic experiments are also described in the appropriate context.