631 results match your criteria Annual Review Of Physical Chemistry[Journal]


Atmospheric Spectroscopy and Photochemistry at Environmental Water Interfaces.

Annu Rev Phys Chem 2019 Apr 12. Epub 2019 Apr 12.

Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom; email:

Interferometric scattering microscopy (iSCAT) is an extremely sensitive imaging method based on the efficient detection of light scattered by nanoscopic objects. The ability to, at least in principle, maintain high imaging contrast independent of exposure time or scattering cross section of the object imaged allows for unique applications in single-particle tracking, label-free imaging of nanoscopic (dis)assembly, and quantitative single-molecule characterization.We illustrate these capabilities in areas as diverse as mechanistic studies of motor protein function, viral capsid assembly, and single-molecule mass measurement in solution. Read More

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https://www.annualreviews.org/doi/10.1146/annurev-physchem-0
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http://dx.doi.org/10.1146/annurev-physchem-050317-021247DOI Listing
April 2019
7 Reads

Multireference Theories of Electron Correlation Based on the Driven Similarity Renormalization Group.

Annu Rev Phys Chem 2019 Mar 20. Epub 2019 Mar 20.

Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA; emails: ,

The driven similarity renormalization group (DSRG) provides an alternative way to address the intruder state problem in quantum chemistry. In this review, we discuss recent developments of multireference methods based on the DSRG. We provide a pedagogical introduction to the DSRG and its various extensions and discuss its formal properties in great detail. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052416DOI Listing

Ultrafast Dynamic Microscopy of Carrier and Exciton Transport.

Annu Rev Phys Chem 2019 Mar 18. Epub 2019 Mar 18.

Department of Chemistry, Purdue University,West Lafayette, Indiana 47907, USA; email:

We highlight the recent progress in ultrafast dynamic microscopy that combines ultrafast optical spectroscopy with microscopy approaches, focusing on the application transient absorption microscopy (TAM) to directly image energy and charge transport in solar energy harvesting and conversion systems. We discuss the principles, instrumentation, and resolutions of TAM. The simultaneous spatial, temporal, and excited-state-specific resolutions of TAM unraveled exciton and charge transport mechanisms that were previously obscured in conventional ultrafast spectroscopy measurements for systems such as organic solar cells, hybrid perovskite thin films, and molecular aggregates. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052605DOI Listing

Microscopy and Cell Biology: New Methods and New Questions.

Annu Rev Phys Chem 2019 Mar 18. Epub 2019 Mar 18.

Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA; email:

Understanding the cellular basis of human health and disease requires spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052527DOI Listing

Kinetics of Drug Binding and Residence Time.

Annu Rev Phys Chem 2019 Feb 20. Epub 2019 Feb 20.

Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy; email:

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ k). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052340DOI Listing
February 2019

Single Photon Sources in Atomically Thin Materials.

Annu Rev Phys Chem 2019 Feb 8. Epub 2019 Feb 8.

Institute of Biomedical Materials and Devices, University of Technology Sydney, Ultimo, New South Wales 2007, Australia; email: ,

Layered materials are very attractive for studies of light-matter interactions at the nanoscale. In particular, isolated quantum systems such as color centers and quantum dots embedded in these materials are gaining interest due to their potential use in a variety of quantum technologies and nanophotonics. Here, we review the field of nonclassical light emission from van der Waals crystals and atomically thin two-dimensional materials. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052628DOI Listing
February 2019

Why Are DNA and Protein Electron Transfer So Different?

Authors:
David N Beratan

Annu Rev Phys Chem 2019 Jun 2. Epub 2019 Jun 2.

Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; email:

The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052353DOI Listing

Conical Intersections at the Nanoscale: Molecular Ideas for Materials.

Annu Rev Phys Chem 2019 Jan 11. Epub 2019 Jan 11.

Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.

The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052425DOI Listing
January 2019
1 Read

The Right Answer for the Right Reason: My Personal Goal for Quantum Chemistry.

Annu Rev Phys Chem 2019 Jan 2. Epub 2019 Jan 2.

Department of Chemistry, University of Washington, Seattle, Washington 98195, USA; email:

A brief history of quantum theory is given to illustrate the barriers to progress caused by preconceived ideas. The biases in my own thinking which I had to overcome to approach the right answer for the right reason are discussed. This is followed by a personal autobiography illustrating how I have led a life of serendipity with no real sense of purpose. Read More

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http://dx.doi.org/10.1146/annurev-physchem-042018-052300DOI Listing
January 2019
1 Read

Exploring Energy Landscapes.

Authors:
David J Wales

Annu Rev Phys Chem 2018 04;69:401-425

Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; email:

Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021219DOI Listing

Vibrational and Nonadiabatic Coherence in 2D Electronic Spectroscopy, the Jahn-Teller Effect, and Energy Transfer.

Authors:
David M Jonas

Annu Rev Phys Chem 2018 04;69:327-352

Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA; email:

Femtosecond two-dimensional (2D) Fourier transform spectroscopy generates and probes several types of coherence that characterize the couplings between vibrational and electronic motions. These couplings have been studied in molecules with Jahn-Teller conical intersections, pseudo-Jahn-Teller funnels, dimers, molecular aggregates, photosynthetic light harvesting complexes, and photosynthetic reaction centers. All have closely related Hamiltonians and at least two types of vibrations, including one that is decoupled from the electronic dynamics and one that is nonadiabatically coupled. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050602DOI Listing

Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes.

Annu Rev Phys Chem 2018 04;69:253-271

Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA; email:

Measurement of the electrostatic interactions that give rise to biological functions has been a longstanding challenge in biophysics. Advances in spectroscopic techniques over the past two decades have allowed for the direct measurement of electric fields in a wide variety of biological molecules and systems via the vibrational Stark effect (VSE). The frequency of the nitrile stretching oscillation has received much attention as an electric field reporter because of its sensitivity to electric fields and its occurrence in a relatively transparent region of the infrared spectrum. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-045011DOI Listing
April 2018
1 Read

Elementary Chemical Reactions in Surface Photocatalysis.

Annu Rev Phys Chem 2018 04 28;69:451-472. Epub 2018 Feb 28.

State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, Liaoning, China; email: , , , , ,

Photocatalytic hydrogen evolution and organic degradation on oxide materials have been extensively investigated in the last two decades. Great efforts have been dedicated to the study of photocatalytic reaction mechanisms of a variety of molecules on TiO surfaces by using surface science methods under ultra-high vacuum (UHV) conditions, providing fundamental understanding of surface chemical reactions in photocatalysis. In this review, we summarize the recent progress in the study of photocatalysis of several important species (water, methanol, and aldehydes) on different TiO surfaces. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044933DOI Listing
April 2018
10 Reads

Characterization of Intermediate Oxidation States in CO Activation.

Annu Rev Phys Chem 2018 04 28;69:231-252. Epub 2018 Feb 28.

JILA and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA; email: ,

Redox chemistry during the activation of carbon dioxide involves changing the charge state in a CO molecular unit. However, such changes are usually not well described by integer formal charges, and one can think of COO functional units as being in intermediate oxidation states. In this article, we discuss the properties of CO and CO-based functional units in various charge states. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021122DOI Listing
April 2018
9 Reads

Addressing the Challenge of Molecular Change: An Interim Report.

Authors:
Raphael D Levine

Annu Rev Phys Chem 2018 04 28;69:1-21. Epub 2018 Feb 28.

The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; email:

Invited by the editorial committee of the Annual Review of Physical Chemistry to "contribute my autobiography," I present it here, as I understand the term. It is about my parents, my mentors, my coworkers, and my friends in learning and the scientific problems that we tried to address. Courtesy of the editorial assistance of Annual Reviews, some of the science is in the figure captions and sidebars. Read More

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http://dx.doi.org/10.1146/annurev-physchem-102717-010036DOI Listing

Sensing Chirality with Rotational Spectroscopy.

Annu Rev Phys Chem 2018 04 28;69:499-519. Epub 2018 Feb 28.

Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.

Chiroptical spectroscopy techniques for the differentiation of enantiomers in the condensed phase are based on an established paradigm that relies on symmetry breaking using circularly polarized light. We review a novel approach for the study of chiral molecules in the gas phase using broadband rotational spectroscopy, namely microwave three-wave mixing, which is a coherent, nonlinear, and resonant process. This technique can be used to generate a coherent molecular rotational signal that can be detected in a manner similar to that in conventional Fourier transform microwave spectroscopy. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050629DOI Listing
April 2018
2 Reads

Enhancing Analytical Separations Using Super-Resolution Microscopy.

Annu Rev Phys Chem 2018 04 28;69:353-375. Epub 2018 Feb 28.

Department of Chemistry, Rice University, Houston, Texas 77251, USA; email:

Super-resolution microscopy is becoming an invaluable tool to investigate structure and dynamics driving protein interactions at interfaces. In this review, we highlight the applications of super-resolution microscopy for quantifying the physics and chemistry that occur between target proteins and stationary-phase supports during chromatographic separations. Our discussion concentrates on the newfound ability of super-resolved single-protein spectroscopy to inform theoretical parameters via quantification of adsorption-desorption dynamics, protein unfolding, and nanoconfined transport. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-045018DOI Listing

Computational Design of Clusters for Catalysis.

Annu Rev Phys Chem 2018 04 28;69:377-400. Epub 2018 Feb 28.

Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA; email:

When small clusters are studied in chemical physics or physical chemistry, one perhaps thinks of the fundamental aspects of cluster electronic structure, or precision spectroscopy in ultracold molecular beams. However, small clusters are also of interest in catalysis, where the cold ground state or an isolated cluster may not even be the right starting point. Instead, the big question is: What happens to cluster-based catalysts under real conditions of catalysis, such as high temperature and coverage with reagents? Myriads of metastable cluster states become accessible, the entire system is dynamic, and catalysis may be driven by rare sites present only under those conditions. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-014216DOI Listing
April 2018
1 Read

Membrane-Mediated Cooperativity of Proteins.

Authors:
Thomas R Weikl

Annu Rev Phys Chem 2018 04 28;69:521-539. Epub 2018 Feb 28.

Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany; email:

Besides direct protein-protein interactions, indirect interactions mediated by membranes play an important role for the assembly and cooperative function of proteins in membrane shaping and adhesion. The intricate shapes of biological membranes are generated by proteins that locally induce membrane curvature. Indirect curvature-mediated interactions between these proteins arise because the proteins jointly affect the bending energy of the membranes. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050637DOI Listing

Connections Between Theory and Experiment for Gold and Silver Nanoclusters.

Annu Rev Phys Chem 2018 04 28;69:205-229. Epub 2018 Feb 28.

Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA; email:

Ligand-stabilized gold and silver nanoparticles are of tremendous current interest in sensing, catalysis, and energy applications. Experimental and theoretical studies have closely interacted to elucidate properties such as the geometric and electronic structures of these fascinating systems. In this review, the interplay between theory and experiment is described; areas such as optical absorption and doping, where the theory-experiment connections are well established, are discussed in detail; and the current status of these connections in newer fields of study, such as luminescence, transient absorption, and the effects of solvent and the surrounding environment, are highlighted. Read More

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http://www.annualreviews.org/doi/10.1146/annurev-physchem-05
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http://dx.doi.org/10.1146/annurev-physchem-052516-050932DOI Listing
April 2018
10 Reads

Computational Photophysics in the Presence of an Environment.

Annu Rev Phys Chem 2018 04 28;69:473-497. Epub 2018 Feb 28.

Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Wien, Austria; email: ,

Most processes triggered by ultraviolet (UV) or visible (vis) light in nature take place in complex biological environments. The first step in these photophysical events is the excitation of the absorbing system or chromophore to an electronically excited state. Such an excitation can be monitored by the UV-vis absorption spectrum. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021013DOI Listing

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

Annu Rev Phys Chem 2018 04 28;69:273-298. Epub 2018 Feb 28.

Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; email:

Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021322DOI Listing
April 2018
6 Reads

Dynamics at Conical Intersections.

Annu Rev Phys Chem 2018 04 28;69:427-450. Epub 2018 Feb 28.

National Research Council of Canada, Ottawa, Ontario K1A 06A, Canada; email:

The nonadiabatic coupling of electronic and vibrational degrees of freedom is the defining feature of electronically excited states of polyatomic molecules. Once considered a theoretical curiosity, conical intersections (CIs) are now generally accepted as being the dominant source of coupled charge and vibrational energy flow in molecular excited states. Passage through CIs leads to the conversion of electronic to vibrational energy, which drives the ensuing photochemistry, isomerization being a canonical example. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050721DOI Listing
April 2018
2 Reads

Electronic Transport in Two-Dimensional Materials.

Annu Rev Phys Chem 2018 04 20;69:299-325. Epub 2018 Feb 20.

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA; email:

Two-dimensional (2D) materials have captured the attention of the scientific community due to the wide range of unique properties at nanometer-scale thicknesses. While significant exploratory research in 2D materials has been achieved, the understanding of 2D electronic transport and carrier dynamics remains in a nascent stage. Furthermore, because prior review articles have provided general overviews of 2D materials or specifically focused on charge transport in graphene, here we instead highlight charge transport mechanisms in post-graphene 2D materials, with particular emphasis on transition metal dichalcogenides and black phosphorus. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021353DOI Listing

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.

Annu Rev Phys Chem 2018 04 31;69:125-149. Epub 2018 Jan 31.

Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea.

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-020915DOI Listing
April 2018
2 Reads
16.840 Impact Factor

Permutationally Invariant Potential Energy Surfaces.

Annu Rev Phys Chem 2018 04 31;69:151-175. Epub 2018 Jan 31.

Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA; email:

Over the past decade, about 50 potential energy surfaces (PESs) for polyatomics with 4-11 atoms and for clusters have been calculated using the permutationally invariant polynomial method. This is a general, mainly linear least-squares method for precise mathematical fitting of tens of thousands of electronic energies for reactive and nonreactive systems. A brief tutorial of the methodology is given, including several recent improvements. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021139DOI Listing
April 2018
2 Reads

Excitons in Single-Walled Carbon Nanotubes and Their Dynamics.

Annu Rev Phys Chem 2018 04 24;69:81-99. Epub 2018 Jan 24.

Department of Chemistry, University of Rochester, Rochester, New York 14627, USA; email:

Understanding exciton dynamics in single-walled carbon nanotubes (SWCNTs) is essential to unlocking the many potential applications of these materials. This review summarizes recent progress in understanding exciton photophysics and, in particular, exciton dynamics in SWCNTs. We outline the basic physical and electronic properties of SWCNTs, as well as bright and dark transitions within the framework of a strongly bound one-dimensional excitonic model. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-014241DOI Listing
April 2018
1 Read

Slow Photoelectron Velocity-Map Imaging of Cryogenically Cooled Anions.

Annu Rev Phys Chem 2018 04 24;69:101-124. Epub 2018 Jan 24.

Department of Chemistry, University of California, Berkeley, California 94720, USA; email: ,

Slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled anions (cryo-SEVI) is a powerful technique for elucidating the vibrational and electronic structure of neutral radicals, clusters, and reaction transition states. SEVI is a high-resolution variant of anion photoelectron spectroscopy based on photoelectron imaging that yields spectra with energy resolution as high as 1-2 cm. The preparation of cryogenically cold anions largely eliminates hot bands and dramatically narrows the rotational envelopes of spectral features, enabling the acquisition of well-resolved photoelectron spectra for complex and spectroscopically challenging species. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-020808DOI Listing

Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry.

Annu Rev Phys Chem 2018 04 2;69:177-203. Epub 2018 Feb 2.

Coimbra Chemistry Center and Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal; email:

Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Read More

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http://dx.doi.org/10.1146/annurev-physchem-050317-021148DOI Listing

Biomimetic Structural Materials: Inspiration from Design and Assembly.

Annu Rev Phys Chem 2018 04 13;69:23-57. Epub 2017 Dec 13.

Materials Science and Engineering Program, University of California, Riverside, California 92521, USA; email:

Nature assembles weak organic and inorganic constituents into sophisticated hierarchical structures, forming structural composites that demonstrate impressive combinations of strength and toughness. Two such composites are the nacre structure forming the inner layer of many mollusk shells, whose brick-and-mortar architecture has been the gold standard for biomimetic composites, and the cuticle forming the arthropod exoskeleton, whose helicoidal fiber-reinforced architecture has only recently attracted interest for structural biomimetics. In this review, we detail recent biomimetic efforts for the fabrication of strong and tough composite materials possessing the brick-and-mortar and helicoidal architectures. Read More

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http://www.annualreviews.org/doi/10.1146/annurev-physchem-04
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http://dx.doi.org/10.1146/annurev-physchem-040215-112621DOI Listing
April 2018
9 Reads

An Active Approach to Colloidal Self-Assembly.

Annu Rev Phys Chem 2018 04 6;69:59-79. Epub 2017 Nov 6.

Department of Chemistry, Columbia University, New York, NY 10027, USA; email:

In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. Read More

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http://www.annualreviews.org/doi/10.1146/annurev-physchem-05
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http://dx.doi.org/10.1146/annurev-physchem-050317-021237DOI Listing
April 2018
4 Reads

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

Annu Rev Phys Chem 2017 05;68:135-154

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; email: , , ,

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050827DOI Listing
May 2017
5 Reads

Ion-Molecule Reaction Dynamics.

Annu Rev Phys Chem 2017 05;68:333-353

Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, 6020 Innsbruck, Austria; email:

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. Read More

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http://www.annualreviews.org/doi/10.1146/annurev-physchem-05
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http://dx.doi.org/10.1146/annurev-physchem-052516-044918DOI Listing
May 2017
12 Reads

Molecules at Solid Surfaces: A Personal Reminiscence.

Authors:
Gerhard Ertl

Annu Rev Phys Chem 2017 05;68:1-17

Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin 14195, Germany; email:

I was fortunate to start my career in physical chemistry at a time when the development of the ultrahigh vacuum technique and of novel physical methods enabled the study of processes on well-defined surfaces at an atomic scale. These investigations included the mechanisms of heterogeneously catalyzed reactions, such as CO oxidation and ammonia synthesis, and phenomena of spatio-temporal self-organization, as described by the concepts of nonlinear dynamics. Read More

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http://www.annualreviews.org/doi/10.1146/annurev-physchem-05
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http://dx.doi.org/10.1146/annurev-physchem-052516-044758DOI Listing
May 2017
7 Reads

The Importance of Being Inconsistent.

Annu Rev Phys Chem 2017 05 6;68:555-581. Epub 2017 Feb 6.

Department of Chemistry, University of California, Irvine, California 92697; email:

We review the role of self-consistency in density functional theory (DFT). We apply a recent analysis to both Kohn-Sham and orbital-free DFT, as well as to partition DFT, which generalizes all aspects of standard DFT. In each case, the analysis distinguishes between errors in approximate functionals versus errors in the self-consistent density. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044957DOI Listing
May 2017
21 Reads

Criegee Intermediates: What Direct Production and Detection Can Teach Us About Reactions of Carbonyl Oxides.

Authors:
Craig A Taatjes

Annu Rev Phys Chem 2017 05;68:183-207

Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551-0969; email:

The carbonyl oxide intermediates in the ozonolysis of alkenes, often known as Criegee intermediates, are potentially important reactants in Earth's atmosphere. For decades, careful analysis of ozonolysis systems was employed to derive an understanding of the formation and reactions of these species. Recently it has proved possible to synthesize at least some of these intermediates separately from ozonolysis, and hence to measure their reaction kinetics directly. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050739DOI Listing
May 2017
6 Reads

Calculating Natural Optical Activity of Molecules from First Principles.

Annu Rev Phys Chem 2017 05;68:399-420

Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260; email:

Computations of natural optical activity (OA) from first principles (ab initio) have become indispensable in chiroptical studies of molecular systems. Calculations are used to assign absolute configurations and to analyze chiroptical data, providing a basis for understanding their origin as well as for assigning and predicting experimental results. In this article, methodology for OA computations is outlined and accompanied by a review of selected, mainly recent (ca. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044827DOI Listing
May 2017
5 Reads

Extending Quantum Chemistry of Bound States to Electronic Resonances.

Annu Rev Phys Chem 2017 05;68:525-553

Department of Chemistry, University of Southern California, Los Angeles, California 90089.

Electronic resonances are metastable states with finite lifetime embedded in the ionization or detachment continuum. They are ubiquitous in chemistry, physics, and biology. Resonances play a central role in processes as diverse as DNA radiolysis, plasmonic catalysis, and attosecond spectroscopy. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050622DOI Listing
May 2017
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The Hydrated Electron.

Annu Rev Phys Chem 2017 05 27;68:447-472. Epub 2017 Mar 27.

Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210; email:

Existence of a hydrated electron as a byproduct of water radiolysis was established more than 50 years ago, yet this species continues to attract significant attention due to its role in radiation chemistry, including DNA damage, and because questions persist regarding its detailed structure. This work provides an overview of what is known in regards to the structure and spectroscopy of the hydrated electron, both in liquid water and in clusters [Formula: see text], the latter of which provide model systems for how water networks accommodate an excess electron. In clusters, the existence of both surface-bound and internally bound states of the excess electron has elicited much debate, whereas in bulk water there are questions regarding how best to understand the structure of the excess electron's spin density. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050816DOI Listing
May 2017
6 Reads

From 50 Years Ago, the Birth of Modern Liquid-State Science.

Authors:
David Chandler

Annu Rev Phys Chem 2017 05 27;68:19-38. Epub 2017 Mar 27.

Department of Chemistry, University of California, Berkeley, California 94720; email:

The story told in this autobiographical perspective begins 50 years ago, at the 1967 Gordon Research Conference on the Physics and Chemistry of Liquids. It traces developments in liquid-state science from that time, including contributions from the author, and especially in the study of liquid water. It emphasizes the importance of fluctuations and the challenges of far-from-equilibrium phenomena. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044941DOI Listing
May 2017
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Ultrafast X-Ray Crystallography and Liquidography.

Annu Rev Phys Chem 2017 05 27;68:473-497. Epub 2017 Mar 27.

Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; email: , ,

Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050851DOI Listing
May 2017
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Roaming: A Phase Space Perspective.

Annu Rev Phys Chem 2017 05 31;68:499-524. Epub 2017 Mar 31.

School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom; email: , ,

In this review we discuss the recently described roaming mechanism for chemical reactions from the point of view of nonlinear dynamical systems in phase space. The recognition of the roaming phenomenon shows the need for further developments in our fundamental understanding of basic reaction dynamics, as is made clear by considering some questions that cut across most studies of roaming: Is the dynamics statistical? Can transition state theory be applied to estimate roaming reaction rates? What role do saddle points on the potential energy surface play in explaining the behavior of roaming trajectories? How do we construct a dividing surface that is appropriate for describing the transformation from reactants to products for roaming trajectories? How should we define the roaming region? We show that the phase space perspective on reaction dynamics provides the setting in which these questions can be properly framed and answered. We illustrate these ideas by considering photodissociation of formaldehyde. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050613DOI Listing
May 2017
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Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry.

Authors:
David L Osborn

Annu Rev Phys Chem 2017 05 15;68:233-260. Epub 2017 Mar 15.

Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550; email:

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. Read More

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http://dx.doi.org/10.1146/annurev-physchem-040215-112151DOI Listing
May 2017
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Metal-Free Motifs for Solar Fuel Applications.

Annu Rev Phys Chem 2017 05 15;68:305-331. Epub 2017 Mar 15.

Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403; email: , , , ,

Metal-free motifs, such as graphitic carbon nitride, conjugated polymers, and doped nanostructures, are emerging as a new class of Earth-abundant materials for solar fuel devices. Although these metal-free structures show great potential, detailed mechanistic understanding of their performance remains limited. Here, we review important experimental and theoretical findings relevant to the role of metal-free motifs as either photoelectrodes or electrocatalysts. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-050924DOI Listing
May 2017
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Ice Surfaces.

Authors:
Mary Jane Shultz

Annu Rev Phys Chem 2017 05 15;68:285-304. Epub 2017 Mar 15.

Laboratory for Water and Surface Studies, Department of Chemistry, Tufts University, Medford, Massachusetts 02155; email:

Ice is a fundamental solid with important environmental, biological, geological, and extraterrestrial impact. The stable form of ice at atmospheric pressure is hexagonal ice, I. Despite its prevalence, I remains an enigmatic solid, in part due to challenges in preparing samples for fundamental studies. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044813DOI Listing
May 2017
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Phospholipid Bilayers: Stability and Encapsulation of Nanoparticles.

Annu Rev Phys Chem 2017 05 15;68:261-283. Epub 2017 Mar 15.

Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada; email: , , ,

Nanoparticles are widely studied for their potential medical uses in diagnostics and therapeutics. The interface between a nanoparticle and its target has been a focus of research, both to guide the nanoparticle and to prevent it from deactivating. Given nature's frequent use of phospholipid vesicles as carriers, much attention has been paid to phospholipids as a vehicle for drug delivery. Read More

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http://dx.doi.org/10.1146/annurev-physchem-040215-112634DOI Listing
May 2017
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Random-Phase Approximation Methods.

Annu Rev Phys Chem 2017 05 16;68:421-445. Epub 2017 Mar 16.

Department of Chemistry, University of California, Irvine, California 92697-2025; email: ,

Random-phase approximation (RPA) methods are rapidly emerging as cost-effective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Read More

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http://dx.doi.org/10.1146/annurev-physchem-040215-112308DOI Listing
May 2017
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Hot Charge Carrier Transmission from Plasmonic Nanostructures.

Annu Rev Phys Chem 2017 05 16;68:379-398. Epub 2017 Mar 16.

Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106; email:

Surface plasmons have recently been harnessed to carry out processes such as photovoltaic current generation, redox photochemistry, photocatalysis, and photodetection, all of which are enabled by separating energetic (hot) electrons and holes-processes that, previously, were the domain of semiconductor junctions. Currently, the power conversion efficiencies of systems using plasmon excitation are low. However, the very large electron/hole per photon quantum efficiencies observed for plasmonic devices fan the hope of future improvements through a deeper understanding of the processes involved and through better device engineering, especially of critical interfaces such as those between metallic and semiconducting nanophases (or adsorbed molecules). Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044948DOI Listing
May 2017
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Computational Analysis of Vibrational Sum Frequency Generation Spectroscopy.

Annu Rev Phys Chem 2017 05 16;68:355-377. Epub 2017 Mar 16.

Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan; email:

Vibrational sum frequency generation (VSFG) spectroscopy is a widely used probe of interfaces and, having ideal surface sensitivity and selectivity, is particularly powerful when applied to wet and soft interfaces. Although VSFG spectroscopy can sensitively detect molecular details of interfaces, interpretation of observed spectra has, until recently, been challenging and often ambiguous. The situation has been greatly improved by remarkable advances in computational VSFG analysis on the basis of molecular modeling and molecular dynamics simulation. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044806DOI Listing

Progress Toward a Molecular Mechanism of Water Oxidation in Photosystem II.

Annu Rev Phys Chem 2017 05 2;68:101-116. Epub 2017 Feb 2.

Department of Chemistry, Yale University, New Haven, Connecticut 06520; email:

The active site of photosynthetic water oxidation is the oxygen-evolving complex (OEC) in the photosystem II (PSII) reaction center. The OEC is a MnCaO cluster embedded in the PSII protein matrix, and it cycles through redox intermediates known as S states (i = 0-4). Significant progress has been made in understanding the inorganic and physical chemistry of states S-S through experiment and theory. Read More

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http://dx.doi.org/10.1146/annurev-physchem-052516-044820DOI Listing
May 2017
8 Reads