Showing papers in "Annual Review of Physical Chemistry in 2007"

Localized Surface Plasmon Resonance Spectroscopy and Sensing

Abstract: Localized surface plasmon resonance (LSPR) spectroscopy of metallic nanoparticles is a powerful technique for chemical and biological sensing experiments. Moreover, the LSPR is responsible for the electromagnetic-field enhancement that leads to surface-enhanced Raman scattering (SERS) and other surface-enhanced spectroscopic processes. This review describes recent fundamental spectroscopic studies that reveal key relationships governing the LSPR spectral location and its sensitivity to the local environment, including nanoparticle shape and size. We also describe studies on the distance dependence of the enhanced electromagnetic field and the relationship between the plasmon resonance and the Raman excitation energy. Lastly, we introduce a new form of LSPR spectroscopy, involving the coupling between nanoparticle plasmon resonances and adsorbate molecular resonances. The results from these fundamental studies guide the design of new sensing experiments, illustrated through applications in which researchers use both LSPR wavelength-shift sensing and SERS to detect molecules of chemical and biological relevance.

Stochastic Simulation of Chemical Kinetics

Abstract: Stochastic chemical kinetics describes the time evolution of a wellstirred chemically reacting system in a way that takes into account the fact that molecules come in whole numbers and exhibit some degree of randomness in their dynamical behavior. Researchers are increasingly using this approach to chemical kinetics in the analysis of cellular systems in biology, where the small molecular populations of only a few reactant species can lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. After reviewing the supporting theory of stochastic chemical kinetics, I discuss some recent advances in methods for using that theory to make numerical simulations. These include improvements to the exact stochastic simulation algorithm (SSA) and the approximate explicit tau-leaping procedure, as well as the development of two approximate strategies for simulating systems that are dynamically stiff: implicit tau-leaping and the slow-scale SSA.

Highly fluorescent noble-metal quantum dots.

Abstract: Highly fluorescent, water-soluble, few-atom noble-metal quantum dots have been created that behave as multielectron artificial atoms with discrete, size-tunable electronic transitions throughout the visible and near infrared. These molecular metals exhibit highly polarizable transitions and scale in size according to the simple relation EFermi/N1/3, predicted by the free-electron model of metallic behavior. This simple scaling indicates that fluorescence arises from intraband transitions of free electrons, and these conduction-electron transitions are the low-number limit of the plasmon—the collective dipole oscillations occurring when a continuous density of states is reached. Providing the missing link between atomic and nanoparticle behavior in noble metals, these emissive, water-soluble Au nanoclusters open new opportunities for biological labels, energy-transfer pairs, and light-emitting sources in nanoscale optoelectronics.

Molecular architectonic on metal surfaces.

Abstract: The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.

Spectral and Dynamical Properties of Multiexcitons in Semiconductor Nanocrystals

Abstract: Because of the strong spatial confinement of electronic wave functions and reduced dielectric screening, the effects of carrier-carrier Coulomb interactions are greatly enhanced in semiconductor nanocrystals (NCs) compared with those in bulk materials. These interactions open a highly efficient decay channel via Auger recombination, which represents a dominant recombination pathway for multiexcitons in NCs. Furthermore, strong Coulomb coupling between charge carriers leads to extremely efficient direct photogeneration of multiexcitons by single photons via carrier (or exciton) multiplication. This review focuses on spectral and dynamical properties of multiexcitons in semiconductor NCs. The specific topics discussed here include the structure of NC electronic states, spectral signatures of multiexcitons in transient absorption and photoluminescence, exciton-exciton interaction energies, Auger recombination, and carrier multiplication. This chapter also briefly reviews the implications of multiexciton effects for practical technologies, such as NC lasing and photovoltaics.

Isomerization through conical intersections.

Abstract: The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.

Theory of structural glasses and supercooled liquids.

Abstract: We review the random first-order transition theory of the glass transition, emphasizing the experimental tests of the theory. Many distinct phenomena are quantitatively predicted or explained by the theory, both above and below the glass transition temperature Tg. These include the following: the viscosity catastrophe and heat-capacity jump at Tg, and their connection; the nonexponentiality of relaxations and their correlation with the fragility; dynamic heterogeneity in supercooled liquids owing to the mosaic structure; deviations from the Vogel-Fulcher law, connected with strings or fractal cooperative rearrangements; deviations from the Stokes-Einstein relation close to Tg; aging and its correlation with fragility; and the excess density of states at cryogenic temperatures owing to two-level tunneling systems and the Boson peak.

Molecular Motors: A Theorist's Perspective

Abstract: Individual molecular motors, or motor proteins, are enzymatic molecules that convert chemical energy, typically obtained from the hydrolysis of ATP (adenosine triphosphate), into mechanical work and motion. Processive motor proteins, such as kinesin, dynein, and certain myosins, step unidirectionally along linear tracks, specifically microtubules and actin filaments, and play a crucial role in cellular transport processes, organization, and function. In this review some theoretical aspects of motor-protein dynamics are presented in the light of current experimental methods that enable the measurement of the biochemical and biomechanical properties on a single-molecule basis. After a brief discussion of continuum ratchet concepts, we focus on discrete kinetic and stochastic models that yield predictions for the mean velocity, V(F, [ATP], ...), and other observables as a function of an imposed load force F, the ATP concentration, and other variables. The combination of appropriate theory with single-molecule observations should help uncover the mechanisms underlying motor-protein function.

Theoretical studies of photoinduced electron transfer in dye-sensitized TiO2.

Abstract: This review describes recent research into the properties of the chromophore-TiO2 interface that forms the basis for photoinduced charge separation in dye-sensitized semiconductor solar cells. It focuses particularly on an atomistic picture of the electron-injection dynamics. The interface offers an excellent case study, pertinent as well to a variety of other photovoltaic systems, photo- and electrochemistry, molecular electronics, analytical detection, photography, and quantum confinement devices. The differences between chemists' and physicists' models for describing molecules and bulk materials, respectively, create challenges for the characterization of interfaces that include both of these components. We give an overall picture of the interface by starting with a description of the properties of the chromophores and semiconductor separately, and then by discussing the coupled system, including the chromophore-semiconductor binding, electronic structure, and electron-injection dynamics. Explicit time-dependent modeling is particularly valuable for an understanding of the ultrafast electron injection because it shows a variety of individual injection events with well-defined dynamical features that cannot be made apparent by an average reaction-rate description.

Femtosecond stimulated Raman spectroscopy.

Abstract: Femtosecond stimulated Raman spectroscopy (FSRS) is a new ultrafast spectroscopic technique that provides vibrational structural information with high temporal (50-fs) and spectral (10-cm(1)) resolution. As a result of these unique capabilities, FSRS studies of chemical and biochemical reaction dynamics are expected to grow rapidly, giving previously unattainable insight into the structural dynamics of reactively evolving systems with atomic spatial and femtosecond temporal resolution. This review discusses the experimental and theoretical concepts behind FSRS, with an emphasis on the origins of its unique temporal and spectral capabilities. We illustrate these capabilities with vibrational studies of ultrafast electronic dynamics, as well as the direct structural observation of nonstationary vibrational wave-packet motion in small molecules and in complex biochemical reaction dynamics.

Aging of Organic Aerosol: Bridging the Gap Between Laboratory and Field Studies

Abstract: The oxidation of organics in aerosol particles affects the physical properties of aerosols through a process known as aging. Atmospheric particles compose a huge set of specific organic compounds, most of which have not been identified in field measurements. Laboratory experiments inevitably address model systems of reduced complexity to isolate critical chemical phenomena, but growing evidence suggests that composition effects may play a central role in the atmospheric aging of organic particles. In this review we seek to address the connections between recent laboratory studies and recent field campaigns addressing the aging of organic aerosols. We review laboratory studies on the uptake of oxidants, the evolution of particle-water interactions, and the evolution of particle density with aging. Finally, we review field data addressing condensed-phase lifetimes of organic tracers. These data suggest that although matrix effects identified in the laboratory have taken a step toward reconciling laboratory-field disagreements, further work is needed to understand the actual aging rates of organics in ambient particles.

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

Abstract: Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic behavior of a protein molecule could be simulated only in the neighborhood of the experimental conformation (or protein unfolding could be simulated at high temperature), the advent of distributed computing, new techniques such as replica-exchange MD, new approaches (based on, e.g., the stochastic difference equation), and physics-based reduced models of proteins now make it possible to study proteinfolding pathways from completely unfolded structures. In this review, we present algorithms for MD and their extensions and applications to protein-folding studies, using all-atom models with explicit and implicit solvent as well as reduced models of polypeptide chains.

Measurement of single-molecule conductance.

Abstract: What is the conductance of a single molecule? This basic and seemingly simple question has been a difficult one to answer for both experimentalists and theorists. To determine the conductance of a molecule, one must wire the molecule reliably to at least two electrodes. The conductance of the molecule thus depends not only on the intrinsic properties of the molecule, but also on the electrode materials. Furthermore, the conductance is sensitive to the atomiclevel details of the molecule-electrode contact and the local environment of the molecule. Creating identical contact geometries has been a challenging experimental problem, and the lack of atomiclevel structural information of the contacts makes it hard to compare calculations with measurements. Despite the difficulties, researchers have made substantial advances in recent years. This review provides an overview of the experimental advances, discusses the advantages and drawbacks of different techniques, and explores remaining issues.

Gas-phase spectroscopy of biomolecular building blocks.

Abstract: Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.

Density-Functional Theory for Complex Fluids

Abstract: Density-functional theory (DFT) and its variations provide a fruitful approach to the computational modeling of the microscopic structures and phase behavior of soft-condensed matter. The methodology takes deep root in quantum mechanics but shares a mathematical similarity with a number of classical approaches in statistical mechanics. This review discusses different strategies commonly used to formulate the free-energy functional of complex fluids for either phenomena-oriented applications or as a generic description of the thermodynamic nonideality owing to various components of intermolecular forces. We emphasize the connections among different schemes of DFT approximations, their underlying assumptions, and inherent limitations. We also address extensions of equilibrium DFT to phenomenological theories for the dynamic properties of complex fluids and for the kinetics of phase transitions. In addition, we highlight the recent literature concerning applications of DFT to diverse static and time-dependent phenomena in complex fluids.

Phosphorylation energy hypothesis : Open chemical systems and 'their biological functions

Abstract: Biochemical systems and processes in living cells generally operate far from equilibrium. This review presents an overview of a statistical thermodynamic treatment for such systems, with examples from several key components in cellular signal transduction. Open-system nonequilibrium steady-state (NESS) models are introduced. The models account quantitatively for the energetics and thermodynamics in phosphorylation-dephosphorylation switches, GTPase timers, and specificity amplification through kinetic proofreading. The chemical energy derived from ATP and GTP hydrolysis establishes the NESS of a cell and makes the cell—a mesoscopic–biochemical reaction system that consists of a collection of thermally driven fluctuating macromolecules—a genetically programmed chemical machine.

Copper and the Prion Protein: Methods, Structures, Function, and Disease

Abstract: The transmissible spongiform encephalopathies (TSEs) arise from conversion of the membrane-bound prion protein from PrP(C) to PrP(Sc). Examples of the TSEs include mad cow disease, chronic wasting disease in deer and elk, scrapie in goats and sheep, and kuru and Creutzfeldt-Jakob disease in humans. Although the precise function of PrP(C) in healthy tissues is not known, recent research demonstrates that it binds Cu(II) in an unusual and highly conserved region of the protein termed the octarepeat domain. This review describes recent connections between copper and PrP(C), with an emphasis on the electron paramagnetic resonance elucidation of the specific copper-binding sites, insights into PrP(C) function, and emerging connections between copper and prion disease.

Exciton Photophysics of Carbon Nanotubes

Abstract: The goal of this chapter is to review the importance of excitons to single-wall carbon nanotube (SWNT) optics. We have developed the presentation for both researchers in the SWNT field who want to learn more about the unusual aspects of SWNT exciton photophysics and researchers more knowledgeable about the physics of excitons, but not about SWNT physics. Excitons in SWNTs are special because graphite has two energy bands at the Fermi energy related to time-reversal symmetry and because SWNTs are actually one dimensional. This review discusses both theoretical and experimental points of view, thus aiming to provide a summary of the most important work in the field, as well as to identify open questions.

Intermolecular interactions in biomolecular systems examined by mass spectrometry.

Abstract: With the development of electrospray and matrix-assisted laser desorption ionization, mass spectrometry (MS) evolved into a powerful tool in the field of biochemistry. Whereas MS is primarily analytical in nature, an increasing number of MS research groups employ the method to address fundamental biochemical questions. Probing the interaction of noncovalently bound molecules in the mass spectrometer is one of the most interesting MS-based experiments possible today, with the potential of making a significant contribution to the basic understanding of the structure and function of biochemical complexes. Here we review a number of current research efforts employing primarily MS techniques to investigate intermolecular interactions in biochemical systems. Examples chosen include the interaction of biomolecules with solvent molecules; interactions between nucleic-acid molecules, in particular, interactions in duplex and quadruplex structures; and interactions between proteins involved in neurodegenerative diseases. Finally we conclude by presenting a few examples of very large biomolecular assemblies in the mega-Dalton range analyzed by MS.

State-to-State Dynamics of Elementary Bimolecular Reactions

Abstract: The study of state-to-state dynamics of elementary bimolecular reactions has provided remarkable insights into chemical reactivity at the most fundamental level. This review covers exciting developments in this important field in the past decade. I focus on recent studies of quantum-state-resolved molecular-beam reactive-scattering studies of elementary chemical reactions, from triatomic to polyatomic systems. Researchers have made great advances in the fundamental understanding of many elementary chemical reactions through state-to-state dynamics studies. The strong interaction between theory and experiment has significantly enhanced our understanding of the dynamics of these reactions. I hope this review provides a glimpse of this exciting research field to both experts and beginners.

Bending Mechanics and Molecular Organization in Biological Membranes

Abstract: The underlying structure of cell membranes consists of a highly heterogeneous fluid lipid bilayer. Within this milieu, complexes of proteins transiently assemble and dissolve in the performance of the functions of life. The length scales of these coordinated spatial rearrangements can approach the size of the cell, itself, enabling direct visualization in some cases with tantalizing clarity. There has been much interest in the physical driving forces responsible for the assembly of organized structures in cell membranes. Cholesterol-mediated miscibility phase separation within the lipid bilayer has attracted enormous attention over the past decade. This, however, is not the only ordering principle at play. In the following sections, I review recent experimental observations of bending-mediated force transduction and molecular organization in lipid membranes. These results have emerged largely from new experimental methodologies, which are discussed in parallel.

Single-molecule probing of adsorption and diffusion on silica surfaces.

Abstract: Single-molecule spectroscopy has emerged as a valuable tool in probing kinetics and dynamic equilibria in adsorption because advances in instrumentation and technology have enabled researchers to obtain high signal-to-noise ratios for common dyes at room temperature. Single-molecule spectroscopy was applied to the study of an important problem in chromatography: peak broadening and asymmetry in the chromatograms of pharmaceuticals, peptides, and proteins. Using DiI, a cationic dye that exhibits the same problematic chromatographic behavior, investigators showed that the adsorption sites that cause chromatographic problems are located at defects on the silica crystal surface.

Molecular Motion at Soft and Hard Interfaces: From Phospholipid Bilayers to Polymers and Lubricants

Abstract: Spatially resolved and time-resolved understanding of complex fluid situations compose a new frontier in physical chemistry. Here we draw attention to the significance of spatially resolving systems whose ensemble average differs fundamentally from the spatially resolved individual elements. We take examples from the field of fluid phospholipid bilayers, to which macromolecules adsorb; the field of polymer physics, when flexible chains adsorb to the solidliquid interface; and from the field of lubrication, when two solids are squeezed close together with confined fluid retained between them.

Nanoscale fracture mechanics.

Abstract: Theoretical calculations on undefected nanoscale materials predict impressive mechanical properties. In this review we summarize the status of experimental efforts to directly measure the fracture strengths of inorganic and carbon nanotubes and discuss possible explanations for the deviations between the predicted and observed values. We also summarize the role of theory in understanding the molecular-level origin of these deviations. In particular, we consider the role of defects such as vacancies, Stone-Wales defects, adatoms and ad-dimers, chemical functionalization, and oxidative pitting.

Structure and dynamics of conjugated polymers in liquid crystalline solvents.

Abstract: A combination of single-molecule spectroscopy and analysis with simulations is used to provide detailed information about the structural and dynamic properties of a fluorescent polymer MEH-PPV (poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene]) immersed in a nematic and smectic solvent. In nematic solvents, single-polymer molecules are oriented strongly along the solvent director, much more so than the solvent molecules, confirming Onsager's old prediction. The diffusion anisotropy parallel and perpendicular to the solvent director, however, is less than two, which is similar to that of a spherical colloid in a nematic solvent. In smectic solvents, there is a second orientation of the dissolved polymer perpendicular to the solvent director, which we hypothesize is caused by the polymer occupying the interlayer volume. The research discussed here emphasizes the importance of organization in complex fluids and suggests that the interplay of order on different length scales could be exploited to fabricate novel nanostructured materials.

Modeling self-assembly and phase behavior in complex mixtures.

Abstract: Using a variety of computational techniques, I investigate how the self-assembly of complex mixtures can be guided by surfaces or external stimuli to form spatially regular or temporally periodic patterns. Focusing on mixtures in confined geometries, I examine how thermodynamic and hydrodynamic effects can be exploited to create regular arrays of nanowires or monodisperse, particle-filled droplets. I also show that an applied light source and chemical reaction can be harnessed to create hierarchically ordered patterns in ternary, phase-separating mixtures. Finally, I consider the combined effects of confining walls and a chemical reaction to demonstrate that a swollen polymer gel can be driven to form dynamically periodic structures. In addition to illustrating the effectiveness of external factors in directing the self-organization of multicomponent mixtures, the selected examples illustrate how coarse-grained models can be used to capture both the equilibrium phase behavior and the dynamics of these complex systems.

A Spectroscopist's View of Energy States, Energy Transfers, and Chemical Reactions

Abstract: This chapter describes a research career beginning at Berkeley in 1960, shortly after Sputnik and the invention of the laser. Following thesis work on vibrational spectroscopy and the chemical reactivity of small molecules, we studied vibrational energy transfers in my own lab. Collision-induced transfers among vibrations of a single molecule, from one molecule to another, and from vibration to rotation and translation were elucidated. My research group also studied the competition between vibrational relaxation and chemical reaction for potentially reactive collisions with one molecule vibrationally excited. Lasers were used to enrich isotopes by the excitation of a predissociative transition of a selected isotopomer. We also tested the hypotheses of transition-state theory for unimolecular reactions of ketene, formaldehyde, and formyl fluoride by (a) resolving individual molecular eigenstates above a dissociation threshold, (b) locating vibrational levels at the transition state, (c) observing quantum resonances in the barrier region for motion along a reaction coordinate, and (d) studying energy release to fragments.