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Annual Review of Physical Chemistry

Hong-Gang Liao, Haimei Zheng
Liquid cell transmission electron microscopy (TEM) has attracted significant interest in recent years. With nanofabricated liquid cells, it has been possible to image through liquids using TEM with subnanometer resolution, and many previously unseen materials dynamics have been revealed. Liquid cell TEM has been applied to many areas of research, ranging from chemistry to physics, materials science, and biology. So far, topics of study include nanoparticle growth and assembly, electrochemical deposition and lithiation for batteries, tracking and manipulation of nanoparticles, catalysis, and imaging of biological materials...
May 27, 2016: Annual Review of Physical Chemistry
Jong-In Hahm
Recent bioapplications of one-dimensional (1D) zinc oxide (ZnO) nanomaterials, despite the short development period, have shown promising signs as new sensors and assay platforms offering exquisite biomolecular sensitivity and selectivity. The incorporation of 1D ZnO nanomaterials has proven beneficial to various modes of biodetection owing to their inherent properties. The more widely explored electrochemical and electrical approaches tend to capitalize on the reduced physical dimensionality, yielding a high surface-to-volume ratio, as well as on the electrical properties of ZnO...
May 27, 2016: Annual Review of Physical Chemistry
Dor Ben-Amotz
Hydrophobic interactions are driven by the combined influence of the direct attraction between oily solutes and an additional water-mediated interaction whose magnitude (and sign) depends sensitively on both solute size and attraction. The resulting delicate balance can lead to a slightly repulsive water-mediated interaction that drives oily molecules apart rather than pushing them together and thus opposes their direct (van der Waals) attraction for each other. As a consequence, competing solute size-dependent crossovers weaken hydrophobic interactions sufficiently that they are only expected to significantly exceed random thermal energy fluctuations for processes that bury more than ∼1 nm(2) of water-exposed area...
May 27, 2016: Annual Review of Physical Chemistry
Sergio Dominguez-Medina, Sishan Chen, Jan Blankenburg, Pattanawit Swanglap, Christy F Landes, Stephan Link
Fluctuation correlation spectroscopy (FCS) is a well-established analytical technique traditionally used to monitor molecular diffusion in dilute solutions, the dynamics of chemical reactions, and molecular processes inside living cells. In this review, we present the recent use of FCS for measuring the size of colloidal nanoparticles in solution. We review the theoretical basis and experimental implementation of this technique and its advantages and limitations. In particular, we show examples of the use of FCS to measure the size of gold nanoparticles, monitor the rotational dynamics of gold nanorods, and investigate the formation of protein coronas on nanoparticles...
May 27, 2016: Annual Review of Physical Chemistry
Erik D Holmstrom, David J Nesbitt
Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids...
May 27, 2016: Annual Review of Physical Chemistry
Joseph E Subotnik, Amber Jain, Brian Landry, Andrew Petit, Wenjun Ouyang, Nicole Bellonzi
We present a current, up-to-date review of the surface hopping methodology for solving nonadiabatic problems, 25 years after Tully published the fewest switches surface hopping algorithm. After reviewing the original motivation for and failures of the algorithm, we give a detailed examination of modern advances, focusing on both theoretical and practical issues. We highlight how one can partially derive surface hopping from the Schrödinger equation in the adiabatic basis, how one can change basis within the surface hopping algorithm, and how one should understand and apply the notions of decoherence and wavepacket bifurcation...
May 27, 2016: Annual Review of Physical Chemistry
Charles Cherqui, Niket Thakkar, Guoliang Li, Jon P Camden, David J Masiello
Electron energy-loss spectroscopy (EELS) offers a window to view nanoscale properties and processes. When performed in a scanning transmission electron microscope, EELS can simultaneously render images of nanoscale objects with subnanometer spatial resolution and correlate them with spectroscopic information at a spectral resolution of ∼10-100 meV. Consequently, EELS is a near-perfect tool for understanding the optical and electronic properties of individual plasmonic metal nanoparticles and few-nanoparticle assemblies, which are significant in a wide range of fields...
May 27, 2016: Annual Review of Physical Chemistry
Matthew B Hillyer, Bruce C Gibb
This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins...
May 27, 2016: Annual Review of Physical Chemistry
Haiming Zhu, Ye Yang, Kaifeng Wu, Tianquan Lian
Understanding photoinduced charge transfer from nanomaterials is essential to the many applications of these materials. This review summarizes recent progress in understanding charge transfer from quantum dots (QDs), an ideal model system for investigating fundamental charge transfer properties of low-dimensional quantum-confined nanomaterials. We first discuss charge transfer from QDs to weakly coupled acceptors within the framework of Marcus nonadiabatic electron transfer (ET) theory, focusing on the dependence of ET rates on reorganization energy, electronic coupling, and driving force...
May 27, 2016: Annual Review of Physical Chemistry
Dvira Segal, Bijay Kumar Agarwalla
We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale...
May 27, 2016: Annual Review of Physical Chemistry
Baron Peters
Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation...
May 27, 2016: Annual Review of Physical Chemistry
Maria A Tesa-Serrate, Eric J Smoll, Timothy K Minton, Kenneth G McKendrick
The gas-liquid interface remains one of the least explored, but nevertheless most practically important, environments in which molecular collisions take place. These molecular-level processes underlie many bulk phenomena of fundamental and applied interest, spanning evaporation, respiration, multiphase catalysis, and atmospheric chemistry. We review here the research that has, during the past decade or so, been unraveling the molecular-level mechanisms of inelastic and reactive collisions at the gas-liquid interface...
May 27, 2016: Annual Review of Physical Chemistry
Leeor Kronik, Jeffrey B Neaton
Molecular solids have attracted attention recently in the context of organic (opto)electronics. These materials exhibit unique charge carrier generation and transport phenomena that are distinct from those of conventional semiconductors. Understanding these phenomena is fundamental to optoelectronics and requires a detailed description of the excited-state properties of molecular solids. Recent advances in many-body perturbation theory (MBPT) and density functional theory (DFT) have made such description possible and have revealed many surprising electronic and optical properties of molecular crystals...
May 27, 2016: Annual Review of Physical Chemistry
Dhabih V Chulhai, Zhongwei Hu, Justin E Moore, Xing Chen, Lasse Jensen
The vibrational spectroscopy of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude so that the detection and identification of single molecules are possible. The enhancement of most linear and nonlinear vibrational spectroscopies has been demonstrated. In this review, we discuss theoretical approaches to understanding linear and nonlinear surface-enhanced vibrational spectroscopies. A unified description of enhancement mechanisms classified as either electromagnetic or chemical in nature is presented...
May 27, 2016: Annual Review of Physical Chemistry
Mi Kyung Lee, Pengfei Huo, David F Coker
This article reviews recent progress in the theoretical modeling of excitation energy transfer (EET) processes in natural light harvesting complexes. The iterative partial linearized density matrix path-integral propagation approach, which involves both forward and backward propagation of electronic degrees of freedom together with a linearized, short-time approximation for the nuclear degrees of freedom, provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes...
May 27, 2016: Annual Review of Physical Chemistry
Jesse G McDaniel, J R Schmidt
Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy...
May 27, 2016: Annual Review of Physical Chemistry
Ji Yu
Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment...
May 27, 2016: Annual Review of Physical Chemistry
David Danovich, Sason Shaik
As we approach the Lewis model centennial, it may be timely to discuss novel bonding motifs. Accordingly, this review discusses no-pair ferromagnetic (NPFM) bonds that hold together monovalent metallic atoms using exclusively parallel spins. Thus, without any traditional electron-pair bonds, the bonding energy per atom in these clusters can reach 20 kcal mol(-1). This review describes the origins of NPFM bonding using a valence bond (VB) analysis, which shows that this bonding motif arises from bound triplet electron pairs that are delocalized over all the close neighbors of a given atom in the cluster...
May 27, 2016: Annual Review of Physical Chemistry
Giacinto Scoles
When I was facing the daunting task of recounting my approximately 70 years of scientific career and some aspects of my personal life, I decided to write this autobiographical piece in a "different" way. After a section on the almost bare facts of my life (Section 1), I include several other parts, loosely connected in time, in each of which I make an almost self-contained point, decreasing in this way the need for consistency and coherence in the whole article. I discuss, for example, the importance of original ideas, the independence of junior colleagues, and my work with molecular beams and in nanomedicine...
May 27, 2016: Annual Review of Physical Chemistry
Mike Reppert, Andrei Tokmakoff
Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra...
May 27, 2016: Annual Review of Physical Chemistry
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