Showing papers in "Annual Review of Physical Chemistry in 2010"
TL;DR: This work focuses on the use of range-separated hybrids within a GKS approach as a practical remedy for dealing with the deleterious long-range self-repulsion plaguing many approximate implementations of DFT.
Abstract: We review density functional theory (DFT) within the Kohn-Sham (KS) and the generalized KS (GKS) frameworks from a theoretical perspective for both time-independent and time-dependent problems. We focus on the use of range-separated hybrids within a GKS approach as a practical remedy for dealing with the deleterious long-range self-repulsion plaguing many approximate implementations of DFT. This technique enables DFT to be widely relevant in new realms such as charge transfer, radical cation dimers, and Rydberg excitations. Emphasis is put on a new concept of system-specific range-parameter tuning, which introduces predictive power in applications considered until recently too difficult for DFT.
667 citations
TL;DR: A mechanism for specific ion effects is elucidated for aqueous systems containing charged and uncharged polymers, polypeptides, and proteins and a hydrogen-bonding mechanism is tested for the urea denaturation of proteins with some of these same systems.
Abstract: The study of the interactions of salts and osmolytes with macromolecules in aqueous solution originated with experiments concerning protein precipitation more than 100 years ago. Today, these solutes are known to display recurring behavior for myriad biological and chemical processes. Such behavior depends both on the nature and concentration of the species in solution. Despite the generality of these effects, our understanding of the molecular-level details of ion and osmolyte specificity is still quite limited. Here, we review recent studies of the interactions between anions and urea with model macromolecular systems. A mechanism for specific ion effects is elucidated for aqueous systems containing charged and uncharged polymers, polypeptides, and proteins. The results clearly show that the effects of the anions are local and involve direct interactions with macromolecules and their first hydration shell. Also, a hydrogen-bonding mechanism is tested for the urea denaturation of proteins with some of these same systems. In that case, direct hydrogen bonding can be largely discounted as the key mechanism for urea stabilization of uncollapsed and/or unfolded structures.
557 citations
TL;DR: The basic components of transition-path theory and path-finding algorithms are reviewed and connections with the classical transition-state theory are discussed.
Abstract: Transition-path theory is a theoretical framework for describing rare events in complex systems. It can also be used as a starting point for developing efficient numerical algorithms for analyzing such rare events. Here we review the basic components of transition-path theory and path-finding algorithms. We also discuss connections with the classical transition-state theory.
534 citations
TL;DR: A form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules is discussed, which offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales.
Abstract: Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (approximately 10-20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule-based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales.
509 citations
TL;DR: A theoretical perspective of the dynamics of glass-forming liquids and the glass transition is reviewed, a perspective developed during this past decade based on the structure of trajectory space, which is characterized in terms of dynamical heterogeneity, facilitation, and excitation lines.
Abstract: We review a theoretical perspective of the dynamics of glass-forming liquids and the glass transition, a perspective developed during this past decade based on the structure of trajectory space. This structure emerges from spatial correlations of dynamics that appear in disordered systems as they approach nonergodic or jammed states. It is characterized in terms of dynamical heterogeneity, facilitation, and excitation lines. These features are associated with a newly discovered class of nonequilibrium phase transitions. Equilibrium properties have little, if anything, to do with it. The broken symmetries of these transitions are obscure or absent in spatial structures, but they are vivid in space-time (i.e., trajectory space). In our view, the glass transition is an example of this class of transitions. The basic ideas and principles we review were originally developed through the analysis of idealized and abstract models. Nevertheless, the central ideas are easily illustrated with reference to molecular dynamics of more realistic atomistic models, and we use that illustrative approach here.
483 citations
TL;DR: Diabatic states have a long history in chemistry, beginning with early valence bond pictures of molecular bonding and extending through the construction of model potential energy surfaces to the modern proliferation of methods for computing these elusive states as mentioned in this paper.
Abstract: Diabatic states have a long history in chemistry, beginning with early valence bond pictures of molecular bonding and extending through the construction of model potential energy surfaces to the modern proliferation of methods for computing these elusive states. In this review, we summarize the basic principles that define the diabatic basis and demonstrate how they can be applied in the specific context of constrained density functional theory. Using illustrative examples from electron transfer and chemical reactions, we show how the diabatic picture can be used to extract qualitative insight and quantitative predictions about energy landscapes. The review closes with a brief summary of the challenges and prospects for the further application of diabatic states in chemistry.
307 citations
TL;DR: It is shown that such functional motifs exist and reviewed the experimental evidence that they control cellular responses as expected and adopted an engineer's approach to control systems.
Abstract: The signal-response characteristics of a living cell are determined by complex networks of interacting genes, proteins, and metabolites. Understanding how cells respond to specific challenges, how these responses are contravened in diseased cells, and how to intervene pharmacologically in the decision-making processes of cells requires an accurate theory of the information-processing capabilities of macromolecular regulatory networks. Adopting an engineer's approach to control systems, we ask whether realistic cellular control networks can be decomposed into simple regulatory motifs that carry out specific functions in a cell. We show that such functional motifs exist and review the experimental evidence that they control cellular responses as expected.
294 citations
TL;DR: Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems.
Abstract: Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states.
236 citations
TL;DR: The critical timescales at play for ET reactions in fluctuating media are discussed, highlighting issues of the Condon approximation, average medium versus fluctuation-controlled electron tunneling, gated and solvent relaxation controlled electron transfer, and the influence of inelastic tunneling on electronic coupling pathway interferences.
Abstract: Central to theories of electron transfer (ET) is the idea that nuclear motion generates a transition state that enables electron flow to proceed, but nuclear motion also induces fluctuations in the donor-acceptor (DA) electronic coupling that is the rate-limiting parameter for nonadiabatic ET. The interplay between the DA energy gap and DA coupling fluctuations is particularly noteworthy in biological ET, where flexible protein and mobile water bridges take center stage. Here, we discuss the critical timescales at play for ET reactions in fluctuating media, highlighting issues of the Condon approximation, average medium versus fluctuation-controlled electron tunneling, gated and solvent relaxation controlled electron transfer, and the influence of inelastic tunneling on electronic coupling pathway interferences. Taken together, one may use this framework to establish principles to describe how macromolecular structure and structural fluctuations influence ET reactions. This framework deepens our understanding of ET chemistry in fluctuating media. Moreover, it provides a unifying perspective for biophysical charge-transfer processes and helps to frame new questions associated with energy harvesting and transduction in fluctuating media.
187 citations
TL;DR: In this paper, the nature of the coupling between nanocrystal atoms and its response to vibrations and deformations of the nanocrystals molecule bonds are discussed. And the authors discuss synthetic approaches, predicted and observed physical properties, and prospects and challenges toward this new class of materials.
Abstract: Quantum dots, which have found widespread use in fields such as biomedicine, photovoltaics, and electronics, are often called artificial atoms due to their size-dependent physical properties. Here this analogy is extended to consider artificial nanocrystal molecules, formed from well-defined groupings of plasmonically or electronically coupled single nanocrystals. Just as a hydrogen molecule has properties distinct from two uncoupled hydrogen atoms, a key feature of nanocrystal molecules is that they exhibit properties altered from those of the component nanoparticles due to coupling. The nature of the coupling between nanocrystal atoms and its response to vibrations and deformations of the nanocrystal molecule bonds are of particular interest. We discuss synthetic approaches, predicted and observed physical properties, and prospects and challenges toward this new class of materials.
164 citations
TL;DR: Surface polarity is a key concept for predicting the stability of oxide surfaces and is discussed using ZnO as an example, and the role of surface defects for surface reactivity, and their interplay with defects in the bulk, for the case of TiO(2).
Abstract: Most metals are oxidized under ambient conditions, and metal oxides show interesting and technologically promising properties. This has motivated much recent research on oxide surfaces. The combination of scanning tunneling microscopy with first-principles density functional theory–based computational techniques provides an atomic-scale view of the properties of metal-oxide materials. Surface polarity is a key concept for predicting the stability of oxide surfaces and is discussed using ZnO as an example. This review also highlights the role of surface defects for surface reactivity, and their interplay with defects in the bulk, for the case of TiO2. Ultrathin metal-oxide films, grown either through reactive evaporation on metal single crystals or through oxidation of metal alloys (such as Al2O3/NiAl), have gained popularity as supports for planar model catalysts. The surface oxides that form upon oxidation on Pt-group metals (e.g., Ru, Rh, Pd, and Pt) are considered as model systems for CO oxidation.
TL;DR: This work reviews recent developments in picosecond and femtosecond XAS applied to molecular systems in solution and examples on ultrafast photoinduced processes such as intramolecular electron transfer, low-to-high spin change, and bond formation are presented.
Abstract: The ability to visualize molecular structure in the course of a chemical reaction or a biological function has been a dream of scientists for decades. X-ray absorption spectroscopy (XAS) is ideal in this respect because it is chemically selective and can be implemented in any type of medium. Furthermore, using X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in laser pump/X-ray probe experiments allows the retrieval of not only the local geometric structure of the system under study, but also the underlying electronic structure changes that drive the structural dynamics. We review recent developments in picosecond and femtosecond XAS applied to molecular systems in solution. Examples on ultrafast photoinduced processes such as intramolecular electron transfer, low-to-high spin change, and bond formation are presented.
TL;DR: This work reviews recent progress in methods for accelerating the convergence of simulations of nonequilibrium systems, specifically nonequ equilibrium umbrella sampling (NEUS) and forward flux sampling (FFS), and recast FFS in the framework of NEUS to facilitate comparison of the two methods.
Abstract: We review recent progress in methods for accelerating the convergence of simulations of nonequilibrium systems, specifically nonequilibrium umbrella sampling (NEUS) and forward flux sampling (FFS). These methods account for statistics of dynamical paths between interfaces to enforce sampling of low probability regions of phase space for computing steady-state averages, including transition rates, for systems driven arbitrarily far from equilibrium. Recent advances in NEUS allow for efficient sampling of complex systems by focusing sampling in the vicinity of a one-dimensional manifold (string) that connects regions of interest in phase space; this procedure can be extended to the case of two strings that describe the forward and backward transition ensembles separately, which is useful, as they do not, in general, coincide. We recast FFS in the framework of NEUS to facilitate comparison of the two methods. We conclude by discussing selected applications of interest.
TL;DR: This article reviews the experimental and theoretical aspects of vibrational hyper-Raman scattering from molecules enhanced by nanostructured metal surfaces and by two-photon electronic resonance.
Abstract: This article reviews the experimental and theoretical aspects of vibrational hyper-Raman scattering from molecules. Particular emphasis is placed on hyper-Raman scattering enhanced by nanostructured metal surfaces and by two-photon electronic resonance.
TL;DR: New physics and new applications of secondary ion mass spectrometry using cluster ion probes, particularly C(60), exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process.
Abstract: This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C60, exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining the molecular specificity of mass spectrometry. When the beams are microfocused to a spot on the sample, bioimaging experiments in two and three dimensions are feasible. We describe emerging theoretical models that allow the energy-deposition process to be understood on an atomic and molecular basis. Moreover, experiments on model systems are described that allow protocols for imaging on biological materials to be implemented. Finally, we present recent applications of imaging to biological tissue and single cells to illustrate the future directions of this methodology.
TL;DR: These examples demonstrate how optical tweezers have been used to improve the understanding of the mechanical properties of biological systems at subcellular and molecular levels.
Abstract: The mechanical properties of cells are crucial for cell sensing and reaction to mechanical environments. This review describes the basic principles of optical tweezers and their use as force sensors for studying the mechanical properties of biological systems. It covers experiments of four groups of biological systems arranged by increasing complexity: (a) packaging DNA into viral capsids by bacteriophage portal motors and the dynamical stiffness of DNA upon protein binding, (b) actin-coated giant vesicles and the myosin-II embedded actin polymer network, (c) suspension cells, and (d) adhesion cells. These examples demonstrate how optical tweezers have been used to improve the understanding of the mechanical properties of biological systems at subcellular and molecular levels.
TL;DR: This work describes work that brings together statistical mechanics and cell biology to shed light on how key molecular/cellular components of the adaptive immune system are selected to enable pathogen-specific responses.
Abstract: Higher organisms, such as humans, have an adaptive immune system that usually enables them to successfully combat diverse (and evolving) microbial pathogens. The adaptive immune system is not preprogrammed to respond to prescribed pathogens. Yet it mounts pathogen-specific responses against diverse microbes and establishes memory of past infections (the basis of vaccination). Although major advances have been made in understanding pertinent molecular and cellular phenomena, the mechanistic principles that govern many aspects of an immune response are not known. We illustrate how complementary approaches from the physical and life sciences can help confront this challenge. Specifically, we describe work that brings together statistical mechanics and cell biology to shed light on how key molecular/cellular components of the adaptive immune system are selected to enable pathogen-specific responses. We hope these examples encourage physical chemists to work at this crossroad of disciplines where fundamental discoveries with implications for human health might be made.
TL;DR: A succinct overview of the architectural constraints leading to metamaterial behavior together with examples of biological material assembly that are particularly promising to comply with these constraints are provided.
Abstract: Biological systems offer more than an inspiration for the spontaneous hierarchical organization of matter at length scales between 1 and 1000 nm. They also provide useful principles and molecular building blocks that have recently emerged with the proven ability to generate extended three-dimensional structures of hybrid biotic/abiotic components arranged with molecular precision. These principles and tools draw from the methods of molecular biology and modern biochemistry and are expected to provide unmatched flexibility in building supramolecular architectures, notably structures made of artificial atoms whose coupled responses to electromagnetic or elastic excitations have been predicted to yield astonishing properties unparalleled by any conventional materials. To illustrate the potential of merging bio-enabled organization with metamaterials synthesis, we provide here a succinct overview of the architectural constraints leading to metamaterial behavior together with examples of biological material assembly that are particularly promising to comply with these constraints.
TL;DR: Empirical tight-binding theory was employed to investigate the symmetry breaking and modulation of the electronic and optical properties of a SWNT in the field of an ionized DNA, and circular dichroism is predicted for DNA-SWNT hybrids, even when the nanotube itself is achiral.
Abstract: Helical wrapping of single-strand DNA around single-wall nanotubes (SWNTs) results in the symmetry breaking and modification of the nanotube band structure. Empirical tight-binding theory was employed to investigate this symmetry breaking and modulation of the electronic and optical properties of a SWNT in the field of an ionized DNA. The model allows the computation of the polarization component of the hybrid's energy of cohesion, with a typical value of 0.5 eV per DNA base. A screening parameter that quantifies the response of the SWNT electrons to the DNA perturbation was obtained. SWNT symmetry breaking shows up in the optical absorption for light polarized across the SWNT axis. In addition, circular dichroism is predicted for DNA-SWNT hybrids, even when the nanotube itself is achiral. These optical effects may be used for experimental determination of the DNA wrapping.
TL;DR: This review discusses the numerical algorithms used in conventional density-functional-theory calculations, which enable the simulations of systems up to one or two thousand atoms, and introduces methods designed specifically for nanostructure calculations.
Abstract: Experimentally relevant nanocrystals often contain a few thousands to hundreds of thousands of atoms. Yet, to understand their electronic structures, surface and impurity effects, atomic relaxations, interior electric fields, carrier dynamics, and transports, it is often necessary to carry out atomistic simulations. Owing to the advance of recent algorithm developments and improved supercomputer powers, it is now possible to calculate such nanocrystals based on ab initio methods. In this review, we discuss the numerical algorithms (the plane-wave pseudopotential method and the real-space finite-difference method) used in conventional density-functional-theory calculations, which enable the simulations of systems up to one or two thousand atoms. We also introduce methods designed specifically for nanostructure calculations. These methods [the charge-patching method (CPM) and the linear scaling three-dimensional fragment method (LS3DF)] can be used to calculate systems with hundreds of thousands of atoms. Whereas CPM is an approximation with ab initio quality, the LS3DF method is an O(N) method with essentially the same results as the direct methods. The computational aspects of the algorithms, especially for their parallelization scalability, are also emphasized in the review.
TL;DR: The dynamics of Saccharomyces cerevisiae yeast mitochondria are characterized with FICS and provide detailed information about the influence of specific cytoskeletal elements on the movement of this organelle.
Abstract: Novel high signal-to-noise spectroscopic experiments that probe the dynamics of microscopic objects have the potential to reveal complex intracellular biochemical mechanisms, or the slow relaxations of soft matter systems. This article reviews the implementation of Fourier imaging correlation spectroscopy (FICS), a phase-selective approach to fluorescence fluctuation spectroscopy that employs a unique route to elevate signal levels while acquiring detailed information about molecular coordinate trajectories. The review demonstrates the broad applicability of FICS by discussing two recent studies. The dynamics of Saccharomyces cerevisiae yeast mitochondria are characterized with FICS and provide detailed information about the influence of specific cytoskeletal elements on the movement of this organelle. In another set of experiments, polarization-modulated FICS captures conformational dynamics and molecular translational dynamics of the fluorescent protein DsRed, and analyses by four-point correlation and joint distribution functions of the corresponding data reveal statistically meaningful pathways of DsRed switching between different optical conformations.
TL;DR: This article tells of a lifelong fascination with light, a messenger bearing information from realms ranging from the galactic to the submicroscopic, and how personal interactions have shaped and informed this life journey.
Abstract: This article tells of a lifelong fascination with light, a messenger bearing information from realms ranging from the galactic to the submicroscopic. Personal interactions have shaped and informed this life journey. Accounts of some of the most important of these are related. Infrared and electronic spectra have been obtained, often for the first time, for many small free radicals and molecular ions-short-lived reaction intermediates in most chemical processes. The infrared spectrum of a molecule tells how its atoms vibrate with respect to one another and is as characteristic of the molecule as a fingerprint is of a person. Analysis of this spectrum provides sometimes surprising information about the structure and chemical bonding of the molecule in its lowest-energy electronic state. The electronic spectrum provides information on the molecule in more highly excited electronic states, in which its structure or reaction pattern may change or it may decompose.