Showing papers in "Annual Review of Physical Chemistry in 2013"
TL;DR: The current state of the development of molecular structure design rules, based on first-principles theoretical considerations, is described along with initial examples of implementation.
Abstract: A survey is provided of recent progress in the understanding of singlet fission, a spin-allowed process in which a singlet excited molecule shares its energy with a ground-state neighbor to produce two triplet excited molecules. It has been observed to occur in single-crystal, polycrystalline, and amorphous solids, on timescales from 80 fs to 25 ps, producing triplet yields as high as 200%. Photovoltaic devices using the effect have shown external quantum efficiencies in excess of 100%. Almost all the efficient materials are alternant hydrocarbons of the acene series or their simple derivatives, and it is argued that a wider structural variety would be desirable. The current state of the development of molecular structure design rules, based on first-principles theoretical considerations, is described along with initial examples of implementation.
849 citations
TL;DR: This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems.
Abstract: This article reviews the ring-polymer molecular dynamics model for condensed-phase quantum dynamics. This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems. The review covers the theory, implementation, applications, and limitations of the approximation.
597 citations
TL;DR: The development of a model for TMAO is presented that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.
Abstract: Proteins are marginally stable, and the folding/unfolding equilibrium of proteins in aqueous solution can easily be altered by the addition of small organic molecules known as cosolvents. Cosolvents that shift the equilibrium toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the molecular mechanism of its action has been vigorously debated in the literature. Here we review recent experimental as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the molecular mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed molecular simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.
366 citations
TL;DR: The present status of experiments and applications of multiplex HD-VSFG spectroscopy are described, in particular with regard to the orientation and structure of interfacial water at charged, neutral, and biorelevant water interfaces.
Abstract: Vibrational sum-frequency generation (VSFG) spectroscopy is a powerful tool to study interfaces. Recently, multiplex heterodyne-detected VSFG (HD-VSFG) has been developed, which enables the direct measurement of complex second-order nonlinear susceptibility [χ(2)]. HD-VSFG has remarkable advantages over conventional VSFG. For example, the imaginary part of χ(2) [Imχ(2)] obtained with this interferometric technique is the direct counterpart to the infrared [Imχ(1)] and Raman [Imχ(3)] spectra in the bulk, and it is free from the spectral deformation inevitable in conventional VSFG [|χ(2)|2] spectra. The Imχ(2) signal is obtained with a sign that contains unambiguous information about the up/down orientation of interfacial molecules. Furthermore, HD-VSFG can be straightforwardly extended to time-resolved measurements when combined with photoexcitation. In this review, we describe the present status of experiments and applications of multiplex HD-VSFG spectroscopy, in particular with regard to the orientation...
236 citations
TL;DR: A review of a number of key developments in the long-timescale dynamics of macromolecular systems, providing an overview of several methods along with their relative regimes of applicability.
Abstract: The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade, various approaches have been developed to discover the collective motions associated with this dynamics. The corresponding collective variables are used in many applications, e.g., to understand the reaction mechanism, to quantify the system's free energy landscape, to enhance the sampling of the reaction path, and to determine the reaction rate. In this review we focus on a number of key developments in this field, providing an overview of several methods along with their relative regimes of applicability.
221 citations
TL;DR: Phase-sensitive sum-frequency spectroscopy allows the complete measurement of the complex spectra of surface nonlinear response coefficients and provides many new research opportunities for surface science.
Abstract: Phase-sensitive sum-frequency spectroscopy (SFS) allows the complete measurement of the complex spectra of surface nonlinear response coefficients. Similar to linear spectroscopy, the spectrum of the imaginary part of a surface response coefficient directly characterizes surface resonances without complication. This newly developed technique has greatly enhanced the capability of surface SFS and provides many new research opportunities for surface science. This article describes the experimental schemes and underlying theory for the technique and briefly reviews works that have clearly demonstrated its power.
217 citations
TL;DR: Recent developments in the design, fundamental understanding, and self-assembly of various peptide-polymer conjugates are discussed, as well as emerging biological and nonbiological applications that range from nanomedicine, to separation, and beyond.
Abstract: Peptide/protein-polymer conjugates make up a new class of soft matter comprising natural and synthetic building blocks. They have the potential to combine the advantages of proteins and synthetic polymers (i.e., the precise chemical structure and diverse functionalities of biomolecules and the stability and processability of synthetic polymers) to generate hybrid materials with properties yet to be realized with either component alone. Here we briefly discuss recent developments in the design, fundamental understanding, and self-assembly of various peptide-polymer conjugates, as well as emerging biological and nonbiological applications that range from nanomedicine, to separation, and beyond.
197 citations
TL;DR: The analysis methods of SAXS data from macromolecular solutions are described, ranging from the computation of overall structural parameters to advanced three-dimensional modeling.
Abstract: Small-angle X-ray scattering (SAXS) is a powerful method to study the structural properties of materials at the nanoscale. Recent progress in instrumentation and analysis methods has led to rapidly growing applications of this technique for the characterization of biological macromolecules in solution. Ab initio and rigid-body modeling methods allow one to build three-dimensional, low-resolution models from SAXS data. With the new approaches, oligomeric states of proteins and macromolecular complexes can be assessed, chemical equilibria and kinetic reactions can be studied, and even flexible objects such as intrinsically unfolded proteins can be quantitatively characterized. This review describes the analysis methods of SAXS data from macromolecular solutions, ranging from the computation of overall structural parameters to advanced three-dimensional modeling. The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles.
189 citations
TL;DR: The challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states are highlighted.
Abstract: We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.
176 citations
TL;DR: It is discussed possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.
Abstract: New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear time-resolved experiments in molecules. Valence-electron motions can be triggered impulsively by core excitations and monitored with high temporal and spatial resolution. We discuss possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.
165 citations
TL;DR: The practical considerations in designing single-molecule fluorescence imaging in cells are discussed, including the choice of fluorescent probes, labeling methods, instrumentation, and imaging techniques, and what can be learned from such characterizations.
Abstract: The transition of single-molecule fluorescence detection and imaging from in vitro to living cells has greatly enriched our knowledge on the behavior of single biomolecules in their native environments and their roles in cellular processes. Here we review recent advances of single-molecule biophysical approaches to live-cell studies based on fluorescence imaging. We start by discussing the practical considerations in designing single-molecule fluorescence imaging in cells, including the choice of fluorescent probes, labeling methods, instrumentation, and imaging techniques. We then describe representative examples in detail to illustrate the physicochemical parameters that can be obtained by imaging individually labeled biomolecules in cells and what can be learned from such characterizations.
TL;DR: An overview of important classes of ultrafast photochemical reactions, namely electron and proton transfer as well as isomerization, are presented, and several examples how nonequilibrium effects can affect their dynamics are illustrated.
Abstract: Ultrafast photochemical processes can occur in parallel with the relaxation of the optically populated excited state toward equilibrium. The latter involves both intra- and intermolecular modes, namely vibrational and solvent coordinates, and takes place on timescales ranging from a few tens of femtoseconds to up to hundreds of picoseconds, depending on the system. As a consequence, the reaction dynamics can substantially differ from those usually measured with slower photoinduced processes occurring from equilibrated excited states. For example, the decay of the excited-state population may become strongly nonexponential and depend on the excitation wavelength, contrary to the Kasha and Vavilov rules. In this article, we first give a brief account of our current understanding of vibrational and solvent relaxation processes. We then present an overview of important classes of ultrafast photochemical reactions, namely electron and proton transfer as well as isomerization, and illustrate with several examples how nonequilibrium effects can affect their dynamics.
TL;DR: Simulation studies of atmospherically relevant aqueous liquid-air interfaces are reviewed, with an emphasis on ions that play important roles in the chemistry of atmospheric aerosols.
Abstract: Chemistry occurring at or near the surface of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the structure and reactivity of aqueous interfaces in the atmosphere. Here we review simulation studies of atmospherically relevant aqueous liquid-air interfaces, with an emphasis on ions that play important roles in the chemistry of atmospheric aerosols. In addition to surveying results from simulation studies, we discuss challenges to the refinement and experimental validation of the methodology for simulating ion adsorption to the air-water interface and recent advances in elucidating the driving forces for adsorption. We also review the recent development of a dielectric continuum theory capable of reproducing simulation and experimental data on ion behavior at aqueous interfaces.
TL;DR: The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods.
Abstract: The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.
TL;DR: This review discusses recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices.
Abstract: Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.
TL;DR: This review on the extractive methods of ambient ionization focuses on chemical aspects, mechanistic considerations, and the accelerated chemical reactions occurring in charged liquid droplets generated in the spray process.
Abstract: Ambient ionization techniques allow complex chemical samples to be analyzed in their native state with minimal sample preparation. This brings the obvious advantages of simplicity, speed, and versatility to mass spectrometry: Desorption electrospray ionization (DESI), for example, is used in chemical imaging for tumor margin diagnosis. This review on the extractive methods of ambient ionization focuses on chemical aspects, mechanistic considerations, and the accelerated chemical reactions occurring in charged liquid droplets generated in the spray process. DESI uses high-velocity solvent droplets to extract analytes from surfaces. Nano-DESI employs liquid microjunctions for analyte dissolution, whereas paper-spray ionization uses DC potentials applied to wet porous material such as paper or biological tissue to field emit charged analyte-containing solvent droplets. These methods also operate in a reactive mode in which added reagents allow derivatization during ionization. The accelerated reaction rates seen in charged microdroplets are useful in small-scale rapid chemical synthesis.
TL;DR: The molecular contrast of SFG and CRS microscopy is discussed and several of the advanced imaging capabilities that have impacted biological and biomedical research are highlighted.
Abstract: Optical imaging with spectroscopic vibrational contrast is a label-free solution for visualizing, identifying, and quantifying a wide range of biomolecular compounds in biological materials. Both linear and nonlinear vibrational microscopy techniques derive their imaging contrast from infrared active or Raman allowed molecular transitions, which provide a rich palette for interrogating chemical and structural details of the sample. Yet nonlinear optical methods, which include both second-order sum-frequency generation (SFG) and third-order coherent Raman scattering (CRS) techniques, offer several improved imaging capabilities over their linear precursors. Nonlinear vibrational microscopy features unprecedented vibrational imaging speeds, provides strategies for higher spatial resolution, and gives access to additional molecular parameters. These advances have turned vibrational microscopy into a premier tool for chemically dissecting live cells and tissues. This review discusses the molecular contrast of SFG and CRS microscopy and highlights several of the advanced imaging capabilities that have impacted biological and biomedical research.
TL;DR: The solvation of small ions at the air-water interface is discussed, whose surface propensities challenge a basic understanding of how aqueous fluctuations accommodate solutes in heterogeneous environments.
Abstract: Liquid water consistently expands our appreciation of the rich statistical mechanics that can emerge from simple molecular constituents. Here I review several interrelated areas of recent work on aqueous systems that aim to explore and explain this richness by revealing molecular arrangements, their thermodynamic origins, and the timescales on which they change. Vibrational spectroscopy of OH stretching features prominently in these discussions, with an emphasis on efforts to establish connections between spectroscopic signals and statistics of intermolecular structure. For bulk solutions, the results of these efforts largely verify and enrich existing physical pictures of hydrogen-bond network connectivity, dynamics, and response. For water at interfaces, such pictures are still emerging. As an important example I discuss the solvation of small ions at the air-water interface, whose surface propensities challenge a basic understanding of how aqueous fluctuations accommodate solutes in heterogeneous environments.
TL;DR: This review details how three key experimental observables have been employed to provide detail on dynamic heterogeneity in supercooled liquids, including the potential for, but also the challenges in, discriminating spatial and temporal heterogeneity and detailing the length scales and timescales of heterogeneity in these systems.
Abstract: Bulk approaches to studying heterogeneous systems obscure important details, as they report average behavior rather than the distribution of behaviors in such environments. Small-molecule and polymeric supercooled liquids, which display heterogeneity in their dynamics without an underlying structural heterogeneity that sets those dynamics, are important constituents of this category of condensed matter systems. A variety of approaches have been devised to unravel ensemble averaging in supercooled liquids. This review focuses on the ultimate subensemble approach, single-molecule measurements, as they have been applied to the study of supercooled liquids. We detail how three key experimental observables (single-molecule probe rotation, translation, and fluorescence lifetime) have been employed to provide detail on dynamic heterogeneity in supercooled liquids. Special attention is given to the potential for, but also the challenges in, discriminating spatial and temporal heterogeneity and detailing the length scales and timescales of heterogeneity in these systems.
TL;DR: The ultrafast spectroscopic investigation of novel retinal proteins challenges existing notions concerning the course of primary events in these natural photoreceptors, providing a first glimpse at a cooperative multichromophore function, which is probably characteristic of many other proteins as well.
Abstract: The ultrafast spectroscopic investigation of novel retinal proteins challenges existing notions concerning the course of primary events in these natural photoreceptors. We review two illustrations here. The first demonstrates that changes in the initial retinal configuration can alter the duration of photochemistry by nearly an order of magnitude in Anabaena sensory rhodopsin, making it as rapid as the ballistic photoisomerization in visual pigments. This prompted a reinvestigation of the much studied bacteriorhodopsin, leading to a similar trend as well, contrary to earlier reports. The second involves the study of xanthorhodopsin, an archaeal proton pump that includes an attached light-harvesting carotenoid. Pump-probe experiments demonstrate the efficient transfer of energy from carotenoid to retinal, providing a first glimpse at a cooperative multichromophore function, which is probably characteristic of many other proteins as well. Finally, we discuss measures required to advance our knowledge from kinetics to mode-specific dynamics concerning this expanding family of biological photoreceptors.
TL;DR: An overview of how DNP methods in solids and solutions can significantly increase the understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments is provided.
Abstract: Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.
TL;DR: A critical state-of-the art overview of what is known and what remains to be understood and investigated about hydrated interfacial ions and electrons near hydrophobic interfaces of water, such as the air or vacuum interface of water or water protein/membrane interfaces is given.
Abstract: Charged particles such as hydrated ions and transient hydrated electrons, the simplest anionic reducing agents in water, and the special hydronium and hydroxide ions at water interfaces play an important role in many fields of science, such as atmospheric chemistry, radiation chemistry, and biology, as well as biochemistry. This article focuses on these species near hydrophobic interfaces of water, such as the air or vacuum interface of water or water protein/membrane interfaces. Ions at interfaces as well as solvated electrons have been reviewed frequently during the past decade. Although all species have been known for some time with seemingly familiar features, recently the picture in all cases became increasingly diffuse rather than clearer. The current account gives a critical state-of-the art overview of what is known and what remains to be understood and investigated about hydrated interfacial ions and electrons.
TL;DR: The population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence are discussed, which play important roles in ultrafast dynamics and relaxations in water.
Abstract: Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.
TL;DR: This contribution is very much a personal history of a journey through the wonderful world of anion chemistry, and a tale of how advances in laser technologies, theoretical methods, and computational capabilities continuously enabled advances in understanding.
Abstract: This contribution is very much a personal history of a journey through the wonderful world of anion chemistry, and a tale of how advances in laser technologies, theoretical methods, and computational capabilities continuously enabled advances in our understanding. It is a story of the excitement and joy that come from the opportunity to add to the fabric of science, and to do so by working as a group of excited explorers with common goals. The participants in this journey include me, my students and postdoctoral associates, my collaborators, and our many generous colleagues. It all happened, in the words of the Beatles, “with a little help from my friends.” Actually, it was so much more than a little help!
TL;DR: This review focuses on the impacts of metal-organic interfacial bonding interactions on the charge-transport dynamics involved in molecular junctions as well as organically capped nanoparticles.
Abstract: This review focuses on the impacts of metal-organic interfacial bonding interactions on the charge-transport dynamics involved in molecular junctions as well as organically capped nanoparticles. Whereas mercapto derivatives have been used extensively as the ligands of choice to functionalize metal and nanoparticle surfaces with the formation of metal-thiolate interfacial bonds, recent studies show that metal-carbon covalent linkages may be fabricated by the deliberate design and selection of functional moieties. With enhanced electronic interactions between metals and organic ligands, the interfacial contact resistance diminishes drastically, leading to the emergence of unprecedented optical and electronic properties of the junctions and nanoparticles. These mechanistic insights are of fundamental significance in the development of molecule- and nanoparticle-based electronic devices, in particular, in light of the diverse metal-nonmetal bonding interactions that have been extensively observed in organometallic chemistry.
TL;DR: Although my group and others have been studying this seemingly simple reaction for well over 30 years, it continues to provoke questions about the properties of matter.
Abstract: I seem to have started off on the wrong foot in life, but I am extremely fortunate that I soon found my footing in the company of physical chemists. I consider myself to be very lucky to be doing something that constantly brings me in contact with bright minds, stimulating conversations, and exciting experiments. My work has allowed me to learn astounding facts about the molecules and atoms that make up our surroundings and ourselves. For this article, I focus on one aspect of my research, understanding the fundamental principles of the simple reaction between a hydrogen atom and a hydrogen molecule. Although my group and others have been studying this seemingly simple reaction for well over 30 years, it continues to provoke questions about the properties of matter.