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Annual Review of Physical Chemistry

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https://www.readbyqxmd.com/read/28463655/qm-mm-geometry-optimization-on-extensive-free-energy-surfaces-for-examination-of-enzymatic-reactions-and-design-of-novel-functional-properties-of-proteins
#1
Shigehiko Hayashi, Yoshihiro Uchida, Taisuke Hasegawa, Masahiro Higashi, Takahiro Kosugi, Motoshi Kamiya
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463654/ion-molecule-reaction-dynamics
#2
Jennifer Meyer, Roland Wester
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463653/molecules-at-solid-surfaces-a-personal-reminiscence
#3
Gerhard Ertl
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.
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463652/the-importance-of-being-inconsistent
#4
Adam Wasserman, Jonathan Nafziger, Kaili Jiang, Min-Cheol Kim, Eunji Sim, Kieron Burke
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. This yields insights into the origins of many errors in DFT calculations, especially those often attributed to self-interaction or delocalization error. In many classes of problems, errors can be substantially reduced by using better densities...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463651/criegee-intermediates-what-direct-production-and-detection-can-teach-us-about-reactions-of-carbonyl-oxides
#5
Craig A Taatjes
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. Direct measurements have allowed new or more detailed understanding of each type of gas-phase reaction that carbonyl oxides undergo, often acting as a complement to highly detailed ozonolysis experiments...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463650/calculating-natural-optical-activity-of-molecules-from-first-principles
#6
Monika Srebro-Hooper, Jochen Autschbach
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. 2010-2016) achievements in optical rotation, electronic and vibrational circular dichroism, and Raman OA calculations...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28463649/extending-quantum-chemistry-of-bound-states-to-electronic-resonances
#7
Thomas-C Jagau, Ksenia B Bravaya, Anna I Krylov
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. This review describes novel equation-of-motion coupled-cluster (EOM-CC) methods designed to treat resonances and bound states on an equal footing. Built on complex-variable techniques such as complex scaling and complex absorbing potentials that allow resonances to be associated with a single eigenstate of the molecular Hamiltonian rather than several continuum eigenstates, these methods extend electronic-structure tools developed for bound states to electronic resonances...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28375692/the-hydrated-electron
#8
John M Herbert, Marc P Coons
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28375691/from-50-years-ago-the-birth-of-modern-liquid-state-science
#9
David Chandler
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.
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28375690/ultrafast-x-ray-crystallography-and-liquidography
#10
Hosung Ki, Key Young Oang, Jeongho Kim, Hyotcherl Ihee
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28375689/roaming-a-phase-space-perspective
#11
Frédéric A L Mauguière, Peter Collins, Zeb C Kramer, Barry K Carpenter, Gregory S Ezra, Stavros C Farantos, Stephen Wiggins
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301761/reaction-mechanisms-on-multiwell-potential-energy-surfaces-in-combustion-and-atmospheric-chemistry
#12
David L Osborn
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. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301760/metal-free-motifs-for-solar-fuel-applications
#13
Stefan Ilic, Marija R Zoric, Usha Pandey Kadel, Yunjing Huang, Ksenija D Glusac
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. First, the light-harvesting characteristics of metal-free photoelectrodes (band energetics, exciton binding energies, charge carrier mobilities and lifetimes) are discussed and contrasted with those in traditional inorganic semiconductors (such as Si)...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301759/ice-surfaces
#14
Mary Jane Shultz
Ice is a fundamental solid with important environmental, biological, geological, and extraterrestrial impact. The stable form of ice at atmospheric pressure is hexagonal ice, Ih. Despite its prevalence, Ih remains an enigmatic solid, in part due to challenges in preparing samples for fundamental studies. Surfaces of ice present even greater challenges. Recently developed methods for preparation of large single-crystal samples make it possible to reproducibly prepare any chosen face to address numerous fundamental questions...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301758/phospholipid-bilayers-stability-and-encapsulation-of-nanoparticles
#15
Elnaz Alipour, Duncan Halverson, Samantha McWhirter, Gilbert C Walker
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. The physical chemistry of bilayer formation and nanoparticle encapsulation is complex, touching on fundamental properties of hydrophobicity...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301757/random-phase-approximation-methods
#16
Guo P Chen, Vamsee K Voora, Matthew M Agee, Sree Ganesh Balasubramani, Filipp Furche
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. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301756/hot-charge-carrier-transmission-from-plasmonic-nanostructures
#17
Phillip Christopher, Martin Moskovits
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)...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28301755/computational-analysis-of-vibrational-sum-frequency-generation-spectroscopy
#18
Tatsuya Ishiyama, Akihiro Morita
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...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226223/progress-toward-a-molecular-mechanism-of-water-oxidation-in-photosystem-ii
#19
David J Vinyard, Gary W Brudvig
The active site of photosynthetic water oxidation is the oxygen-evolving complex (OEC) in the photosystem II (PSII) reaction center. The OEC is a Mn4CaO5 cluster embedded in the PSII protein matrix, and it cycles through redox intermediates known as Si states (i = 0-4). Significant progress has been made in understanding the inorganic and physical chemistry of states S0-S3 through experiment and theory. The chemical steps from S3 to S0 are more poorly understood, however, because the identity of the substrate water molecules and the mechanism of O-O bond formation are not well established...
May 5, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#20
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
May 5, 2017: Annual Review of Physical Chemistry
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