Annual Review of Physical Chemistry - Volume 60, 2009

In keeping with the tradition of prefatory articles for the Annual Review of Physical Chemistry, this is an autobiographical essay describing my scientific career. I begin with my background and education at Dartmouth and Caltech and follow with my half-century of research and teaching at MIT. I emphasize subjects that I found especially interesting or important, including average Hamiltonians and the beginnings of high-resolution nuclear magnetic resonance (NMR) in solids, broadband spin decoupling in liquids, NMR at milli-Kelvin temperatures, and the exploration of basic physical principles by computer. Throughout I recall with affection my mentors, colleagues, and students.

A wide variety of molecular systems undergo fast structural changes under thermal equilibrium conditions. Such transformations are involved in a vast array of chemical problems. Experimentally measuring equilibrium dynamics is a challenging problem that is at the forefront of chemical research. This review describes ultrafast 2D IR vibrational echo chemical exchange experiments and applies them to several types of molecular systems. The formation and dissociation of organic solute-solvent complexes are directly observed. The dissociation times of 13 complexes, ranging from 4 ps to 140ps, are shown to obey a relationship that depends on the complex's formation enthalpy. The rate of rotational gauche-trans isomerization around a carbon-carbon single bond is determined for a substituted ethane at room temperature in a low viscosity solvent. The results are used to obtain an approximate isomerization rate for ethane. Finally, the time dependence of a well-defined single structural transformation of a protein is measured.

Photofragment spectroscopy is combined with imaging techniques and time-resolved measurements of photoions and photoelectrons to explore the predissociation dynamics of weakly bound molecules. Recent experimental advances include measurements of pair-correlated distributions, in which energy disposal in one cofragment is correlated with a state-selected level of the other fragment, and femtosecond pump-probe experiments, in some cases with coincidence detection. An application in which coincident measurements are carried out in the molecular frame is also described. To illustrate these state-selective and time-resolved techniques, we review two recent applications: (a) the photoinitiated dissociation of the covalently bound NO dimer on the ground and excited electronic states and the role of state couplings and (b) the state-selected vibrational predissociation of hydrogen-bonded acetylene dimers with HCl (acid) and ammonia (base) and the importance of angular momentum constraints. We highlight the crucial role of theoretical models in interpreting results.

This review discusses recent advances in the nonlinear optics of environmental interfaces. We discuss the quantitative aspects of the label-free approaches presented here and demonstrate that nonlinear optics has now assumed the role of a Swiss Army knife that can be used to dissect, with molecular detail, the fundamental and practical aspects of environmental interfaces and heterogeneous geochemical environments. In this work, nonlinear optical methods are applied to complex organic molecules, such as veterinary antibiotics, and to small inorganic anions and cations, such as nitrate and chromate, or cadmium, zinc, and manganese. The environmental implications of the thermodynamic, kinetic, spectroscopic, structural, and electrochemical data are discussed.

Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.

Multiply charged anions (MCAs) are common in condensed phases but are challenging to study in the gas phase. An experimental technique, coupling photoelectron spectroscopy (PES) with electrospray ionization (ESI), has been developed to investigate the properties of free MCAs in the gas phase. This article reviews the principles of this technique and some initial findings about the intrinsic properties of MCAs. Examples include the observation of the repulsive Coulomb barrier that exists universally in MCAs and its effects on the dynamic stability and PES of MCAs. The solvation and solvent stabilization of MCAs have been studied in the gas phase and are also discussed. A second-generation low-temperature ESI-PES apparatus has been developed, which allows ion temperatures to be controlled from 10 to 350 K. New results from this low-temperature ESI-PES instrument are also reviewed, including doubly charged fullerene anions, inorganic metal complexes, and temperature-induced conformation changes of complex anions.

The spectroscopy of aerosols is developing into an active and important field. It allows us to characterize aerosols in a nonintrusive way, in real time, and on site. Understanding the spectroscopic features of these highly complex systems requires the development of novel experimental as well as theoretical methods. This review focuses on infrared extinction spectra. The main goal is to summarize how information about intrinsic particle properties (such as size, shape, and architecture) can be gathered from observed spectroscopic patterns. We discuss the limitations of standard continuum approaches, which have been used for decades to analyze infrared spectra, and we demonstrate the importance of molecular models for the analysis of spectroscopic data.

This review focuses on nanofabrication tools, based on soft lithography, which can generate a wide range of noble-metal structures with exceptional optical properties. These techniques offer a scalable and practical approach for producing arrays of complementary plasmonic structures (nanoholes and nanoparticles) and, in addition, expand the possible architectures of plasmonic materials because the metal building blocks can be organized over multiple length scales. We describe the preparation and characterization of five different systems: subwavelength nanohole arrays, finite arrays of nanoholes, microscale arrays of nanoholes, multiscale arrays of nanoparticles, and pyramidal particles. We also discuss how the surface plasmon resonances of these structures can be tuned across visible and near-infrared wavelengths by varying different parameters. Applications and future prospects of these nanostructured metals are addressed.

Under the irradiation of light, the free electrons in a plasmonic nanoparticle are driven by the alternating electric field to collectively oscillate at a resonant frequency in a phenomenon known as surface plasmon resonance. Both calculations and measurements have shown that the frequency and amplitude of the resonance are sensitive to particle shape, which determines how the free electrons are polarized and distributed on the surface. As a result, controlling the shape of a plasmonic nanoparticle represents the most powerful means of tailoring and fine-tuning its optical resonance properties. In a solution-phase synthesis, the shape displayed by a nanoparticle is determined by the crystalline structure of the initial seed produced and the interaction of different seed facets with capping agents. Using polyol synthesis as a typical example, we illustrate how oxidative etching and kinetic control can be employed to manipulate the shapes and optical responses of plasmonic nanoparticles made of either Ag or Pd. We conclude by highlighting a few fundamental studies and applications enabled by plasmonic nanoparticles having well-defined and controllable shapes.

The ultrahigh vacuum (UHV) scanning tunneling microscope (STM) enables patterning and characterization of the physical, chemical, and electronic properties of nanostructures on surfaces with atomic precision. On hydrogen-passivated Si(100) surfaces, selective nanopatterning with the STM probe allows the creation of atomic-scale templates of dangling bonds surrounded by a robust hydrogen resist. Feedback-controlled lithography, which can remove a single hydrogen atom from the Si(100):H surface, demonstrates high-resolution nanopatterning. The resulting patterns can be used as templates for a variety of materials to form hybrid silicon nanostructures while maintaining a pristine background resist. The versatility of this UHV-STM nanolithography approach has led to its use on a variety of other substrates, including alternative hydrogen-passivated semiconductor surfaces, molecular resists, and native oxide resists. This review discusses the mechanisms of STM-induced hydrogen desorption, the postpatterning deposition of molecules and materials, and the implications for nanoscale device fabrication.

Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.

We review recent theoretical and experimental advances in the elucidation of the dynamics of light harvesting in photosynthesis, focusing on recent theoretical developments in structure-based modeling of electronic excitations in photosynthetic complexes and critically examining theoretical models for excitation energy transfer. We then briefly describe two-dimensional electronic spectroscopy and its application to the study of photosynthetic complexes, in particular the Fenna-Matthews-Olson complex from green sulfur bacteria. This review emphasizes recent experimental observations of long-lasting quantum coherence in photosynthetic systems and the implications of quantum coherence in natural photosynthesis.

The formic acid dimer (HCOOH)2 (FAD), an eight-membered ring with double hydrogen bonds, has been a model complex for physical chemists. The acidic protons of the complex interchange between the oxygens of different units in a concerted tunneling motion. This proton tunneling can be described by a symmetric double-well potential. The double well results in a splitting of each rovibrational level. The magnitude of the splitting depends sensitively on the shape of the potential and the reduced mass along the tunneling path. Experimentally, one can determine the proton transfer tunneling splittings in the ground and vibrationally excited states separately. It is possible to work out the splitting of the energy levels, assign the correct symmetry, and obtain the sum and the difference of the tunneling splitting in the ground and vibrationally excited states independently using isotopically labeled molecules. Conversely, an accurate prediction of tunneling splitting even for this small prototype system still remains a challenge for theoretical chemistry because of the splitting's great sensitivity to the shape and barrier height of the potential surface. The FAD therefore has evolved into a prototype system to study theoretical methods for a description of proton transfer.

The field of quantum coherent control, initially formulated with the goal of modifying and manipulating molecular systems, has had a number of applications in atomic and molecular spectroscopy in recent years. This review demonstrates how carefully designed femtosecond pulses could be used to enhance resolution and improve detection in several areas of nonlinear spectroscopy. The two effects that are most intensively studied in this context are two-photon absorption and coherent anti-Stokes Raman scattering. This article discusses the principles of the control of such processes and several possible applications in microscopy and remote sensing.

Coherent-optical-control schemes exploit the coherence of laser pulses to change the phases of interfering dynamical pathways and manipulate dynamical processes. These active control methods are closely related to dynamical decoupling techniques, popularized in the field of quantum information. Inspired by nuclear magnetic resonance spectroscopy, dynamical decoupling methods apply sequences of unitary operations to modify the interference phenomena responsible for the system dynamics thus also belonging to the general class of coherent-control techniques. This article reviews related developments in the fields of coherent optical control and dynamical decoupling, emphasizing the control of tunneling and decoherence in general model systems. Considering recent experimental breakthroughs in the demonstration of active control of a variety of systems, we anticipate that the reviewed coherent-control scenarios and dynamical-decoupling methods should raise significant experimental interest.

In traditional physicochemical modeling, one derives evolution equations at the (macroscopic, coarse) scale of interest; these are used to perform a variety of tasks (simulation, bifurcation analysis, optimization) using an arsenal of analytical and numerical techniques. For many complex systems, however, although one observes evolution at a macroscopic scale of interest, accurate models are only given at a more detailed (fine-scale, microscopic) level of description (e.g., lattice Boltzmann, kinetic Monte Carlo, molecular dynamics). Here, we review a framework for computer-aided multiscale analysis, which enables macroscopic computational tasks (over extended spatiotemporal scales) using only appropriately initialized microscopic simulation on short time and length scales. The methodology bypasses the derivation of macroscopic evolution equations when these equations conceptually exist but are not available in closed form—hence the term equation-free. We selectively discuss basic algorithms and underlying principles and illustrate the approach through representative applications. We also discuss potential difficulties and outline areas for future research.

The past decade has witnessed the emergence of new measurement approaches and applications for chiral thin films and materials enabled by the observations of the high sensitivity of second-order nonlinear optical measurements to chirality. In thin films, the chiral response to second harmonic generation and sum frequency generation (SFG) from a single molecular monolayer is often comparable with the achiral response. The chiral specificity also allows for symmetry-allowed SFG in isotropic chiral media, confirming predictions made ∼50 years ago. With these experimental demonstrations in hand, an important challenge is the construction of intuitive predictive models that allow the measured chiral response to be meaningfully related back to molecular and macromolecular structure. This review defines and considers three distinct mechanisms for chiral effects in uniaxially oriented assemblies: orientational chirality, intrinsic chirality, and isotropic chirality. The role of each is discussed in experimental and computational studies of bacteriorhodopsin films, binaphthol, and collagen. Collectively, these three model systems support a remarkably simple framework for quantitatively recovering the measured chiral-specific activity.

The relative simplicity of viruses makes it possible to apply generic physical approaches to the understanding of their structure and function. We focus here on viruses that have double-stranded (ds)DNA genomes that are enclosed in a protein container called the capsid. Their structures are now known in precise detail from cryo-electron microscopy. dsDNA is a stiff, highly charged polymer, and typical viral DNAs have contour lengths 1000 times longer than the radius of the capsid into which they are introduced in the assembly process, which is driven by a biological motor. As a result, the confined DNA is highly stressed. The energy stored in the dsDNA, which is compressed to crystalline densities, drives the ejection of the genome into the host at the start of an infection. Experiments have examined the packaging and ejection of the genomes, which have also been the subject of analytic theories and simulations.

Recent advances in ultrafast laser technology have spurred investigations of microheterogeneous solutions. In particular, researchers have explored details of reverse micelles (RMs), which present isolated droplets of polar solvent sequestered from a continuous nonpolar phase by a surfactant layer. This review explores recent studies utilizing a variety of ultrafast laser techniques to uncover details about structure and dynamics in various RMs. Using ultrafast vibrational spectroscopy, researchers have probed hydrogen-bond dynamics and vibrational energy relaxation in RMs. These studies have developed our understanding of reverse micellar structure, identifying varying water environments in the RMs. In a plethora of experiments employing probe molecules, researchers have explored the confined environment presented by RMs and their impact on a range of chemical reactions. These studies have shown that confinement, rather than the specific interactions with surfactants, is an important factor determining the impact of the reverse micellar environment on the chemistry.