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JCP Spotlight Collections

The Journal of Chemical Physics has created a new Perspectives section, featuring invited papers on topics currently generating a great deal of interest in the research community. JCP Spotlight Collections, which will be home to the collected perspectives, along with the seminal articles they reference, provide a comprehensive look at the history of the field and where it is headed.

https://player.vimeo.com/video/12601990

Marsha I. Lester discusses JCP's Spotlight Collections (published 15 June 2010).

Perspectives will be a regular feature of the journal and freely available to the community. We hope these collections will be a useful research tool, as well as a valuable resource for those interested in learning more about the broad range of topics in Chemical Physics.


Perspective: Fundamental aspects of time-dependent density functional theory

Neepa T. Maitra
Department of Physics and Astronomy, Hunter College and the Physics Program at the Graduate Center of the City University of New York, 695 Park Avenue, New York, New York 10065, USA

Perspective: Fundamental aspects of time-dependent density functional theory

In the thirty-two years since the birth of the foundational theorems, time-dependent density functional theory has had a tremendous impact on calculations of electronic spectra and dynamics in chemistry, biology, solid-state physics, and materials science. Alongside the wide-ranging applications, there has been much progress in understanding fundamental aspects of the functionals and the theory itself. This Perspective looks back to some of these developments, reports on some recent progress and current challenges for functionals, and speculates on future directions to improve the accuracy of approximations used in this relatively young theory.

J. Chem. Phys. 144, 220901 (2016)


Perspective: The first ten years of broadband chirped pulse Fourier transform microwave spectroscopy

G. Barratt Park1,2,a) and Robert W. Field3,b)
1 Institute for Physical Chemistry, University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
2 Max Planck Institute for Biophysical Chemistry, Göttingen, Am Faßberg 11, 37077 Göttingen, Germany
3 Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

The first ten years of broadband chirped pulse Fourier transform microwave spectroscopy

Since its invention in 2006, the broadband chirped pulse Fourier transform spectrometer has transformed the field of microwave spectroscopy. The technique enables the collection of a ≥10 GHz bandwidth spectrum in a single shot of the spectrometer, which allows broadband, high-resolution microwave spectra to be acquired several orders of magnitude faster than what was previously possible. We discuss the advantages and challenges associated with the technique and look back on the first ten years of chirped pulse Fourier transform spectroscopy. In addition to enabling faster-than-ever structure determination of increasingly complex species, the technique has given rise to an assortment of entirely new classes of experiments, ranging from chiral sensing by three-wave mixing to microwave detection of multichannel reaction kinetics. However, this is only the beginning. Future generations of microwave experiments will make increasingly creative use of frequency-agile pulse sequences for the coherent manipulation and interrogation of molecular dynamics.

J. Chem. Phys. 144, 200901 (2016)


Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Arieh Warshel1 and Ram Prasad Bora1
1 Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA

Defining and quantifying the role of dynamics in enzyme catalysis

Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme’s conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.

J. Chem. Phys. 144, 180901 (2016)


Perspective: Polarizable continuum models for quantum-mechanical descriptions

Filippo Lipparini1 and Benedetta Mennucci2
1 Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D55128 Mainz, Germany
2Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy

Polarizable continuum models for quantum-mechanical descriptions

Polarizable continuum solvation models are nowadays the most popular approach to describe solvent effects in the context of quantum mechanical calculations. Unexpectedly, despite their widespread use in all branches of quantum chemistry and beyond, important aspects of both their theoretical formulation and numerical implementation are still not completely understood. In particular, in this perspective we focus on the numerical issues of their implementation when applied to large systems and on the theoretical framework needed to treat time dependent problems and excited states or to deal with electronic correlation. Possible extensions beyond a purely electrostatic model and generalizations to environments beyond common solvents are also critically presented and discussed. Finally, some possible new theoretical approaches and numerical strategies are suggested to overcome the obstacles which still prevent a full exploitation of these models.

J. Chem. Phys. 144, 16090 (2016)


Perspective: How good is DFT for water?

Michael J. Gillan 1,2,3, Dario Alfè1,2,3,4 and Angelos Michaelides1,2,3
1 London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
2 Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
3 Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
4 Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom

How good is DFT for water?

Kohn-Sham density functional theory(DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology, and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures, and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments.

J. Chem. Phys. 144, 130901 (2016)


Perspective: 4D ultrafast electron microscopy—Evolutions and revolutions

Dmitry Shorokhov and Ahmed H. Zewail
Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena, California 91125, USA

4D ultrafast electron microscopy

In this Perspective, the evolutionary and revolutionary developments of ultrafast electron imaging are overviewed with focus on the “single-electron concept” for probing methodology. From the first electron microscope of Knoll and Ruska [Z. Phys. 78, 318 (1932)], constructed in the 1930s, to aberration-corrected instruments and on, to four-dimensional ultrafast electron microscopy (4D UEM), the developments over eight decades have transformed humans’ scope of visualization. The changes in the length and time scales involved are unimaginable, beginning with the micrometer and second domains, and now reaching the space and time dimensions of atoms in matter. With these advances, it has become possible to follow the elementary structural dynamics as it unfolds in real time and to provide the means for visualizing materials behavior and biological functions. The aim is to understand emergent phenomena in complex systems, and 4D UEM is now central for the visualization of elementary processes involved, as illustrated here with examples from past achievements and future outlook.

J. Chem. Phys. 144, 080901 (2016)


Perspective: Computer simulations of long time dynamics

Ron Elber
Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA

Computer simulations Collection.png

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.

J. Chem. Phys. 144, 060901 (2016)


Perspective: Mechanochemistry of biological and synthetic molecules

Dmitrii E. Makarov
Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA

Mechanochemistry Collection.png

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

J. Chem. Phys. 143, 030901 (2016)


Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

Yao Xu and Martina Havenith
Lehrstuhl für Physikalische Chemie II, Ruhr Universität, 44801 Bochum, Germany

Martina Havenith Collection

Interview coming soon.

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a “hydration funnel.” Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

J. Chem. Phys. 143, 170901 (2015)


Perspective: Electrospray photoelectron spectroscopy: From multiply-charged anions to ultracold anions

Lai-Sheng Wang
Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA

Kulik Collection

Interview coming soon.

Electrospray ionization (ESI) has become an essential tool in chemical physics and physical chemistry for the production of novel molecular ions from solution samples for a variety of spectroscopic experiments. ESI was used to produce free multiply-charged anions (MCAs) for photoelectron spectroscopy (PES) in the late 1990 s, allowing many interesting properties of this class of exotic species to be investigated. Free MCAs are characterized by strong intramolecular Coulomb repulsions, which create a repulsive Coulomb barrier (RCB) for electron emission. The RCB endows many fascinating properties to MCAs, giving rise to meta-stable anions with negative electron binding energies. Recent development in the PES of MCAs includes photoelectron imaging to examine the influence of the RCB on the electron emission dynamics, pump-probe experiments to examine electron tunneling through the RCB, and isomer-specific experiments by coupling PES with ion mobility for biological MCAs. The development of a cryogenically cooled Paul trap has led to much better resolved PE spectra for MCAs by creating vibrationally cold anions from the room temperature ESI source. Recent advances in coupling the cryogenic Paul trap with PE imaging have allowed high-resolution PE spectra to be obtained for singly charged anions produced by ESI. In particular, the observation of dipole-bound excited states has made it possible to conduct vibrational autodetachment spectroscopy and resonant PES, which yield much richer vibrational spectroscopic information for dipolar free radicals than traditional PES.

J. Chem. Phys.143, 040901 (2015)


Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

Yuan-Pern Lee
Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan

Kulik Collection

Interview coming soon.

The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH2OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O2, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH2OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH2I + O2, which is critical to laboratory studies of CH2OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO2, SO2, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH3CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

J. Chem. Phys.143, 020901 (2015)


Perspective: Sloppiness and emergent theories in physics, biology, and beyond

Mark K. Transtrum1, Benjamin B. Machta2, Kevin S. Brown3,4 Bryan C. Daniels5, Christopher R. Myers6,7 and James P. Sethna6
1 Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA
2 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
3 Departments of Biomedical Engineering, Physics, Chemical and Biomolecular Engineering, and Marine Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
4 Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06030-1912, USA
5 Center for Complexity and Collective Computation, Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
6 Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
7 Institute of Biotechnology, Cornell University, Ithaca, New York 14853, USA

Kulik Collection

Interview coming soon.

Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are “sloppy,” i.e., exhibit behavior controlled by a relatively small number of parameter combinations. We review an information theoretic framework for analyzing sloppy models. This formalism is based on the Fisher information matrix, which is interpreted as a Riemannian metric on a parameterized space of models. Distance in this space is a measure of how distinguishable two models are based on their predictions. Sloppy model manifolds are bounded with a hierarchy of widths and extrinsic curvatures. The manifold boundary approximation can extract the simple, hidden theory from complicated sloppy models. We attribute the success of simple effective models in physics as likewise emerging from complicated processes exhibiting a low effective dimensionality. We discuss the ramifications and consequences of sloppy models for biochemistry and science more generally. We suggest that the reason our complex world is understandable is due to the same fundamental reason: simple theories of macroscopic behavior are hidden inside complicated microscopic processes.

J. Chem. Phys.143, 010901 (2015)


Perspective: Treating electron over-delocalization with the DFT+U method

Heather J. Kulik
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

Kulik Collection

Interview coming soon.

Many people in the materials science and solid-state community are familiar with the acronym “DFT+U.” For those less familiar, this technique uses ideas from model Hamiltonians that permit the description of both metals and insulators to address problems of electron over-delocalization in practical implementations of density functional theory (DFT). Exchange-correlation functionals in DFT are often described as belonging to a hierarchical “Jacob’s ladder” of increasing accuracy in moving from local to non-local descriptions of exchange and correlation. DFT+U is not on this “ladder” but rather acts as an “elevator” because it systematically tunes relative energetics, typically on a localized subshell (e.g., d or f electrons), regardless of the underlying functional employed. However, this tuning is based on a metric of the local electron density of the subshells being addressed, thus necessitating physical or chemical or intuition about the system of interest. I will provide a brief overview of the history of how DFT+U came to be starting from the origin of the Hubbard and Anderson model Hamiltonians. This history lesson is necessary because it permits us to make the connections between the “Hubbard U” and fundamental outstanding challenges in electronic structure theory, and it helps to explain why this method is so widely applied to transition-metal oxides and organometallic complexes alike.

J. Chem. Phys. 142, 240901 (2015)


Perspective: Single polymer mechanics across the force regimes

Omar A. Saleh
Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA

I review theoretical and experimental results on the force-extension response of single polymers, with a focus on scaling pictures of low-force elastic regimes, and recent measurements of synthetic and biological chains that explore those regimes. The mechanical response of single polymers is an old theoretical problem whose exploration was instigated by the curious thermomechanical behavior of rubber. Up until the 1990s, the main utility of those calculations was to explain bulk material mechanics. However, in that decade, it became possible to directly test the calculations through high-precision single-chain stretching experiments (i.e., force spectroscopy). I present five major single-chain elasticity models, including scaling results based on blob-chain models, along with analytic results based on linear response theory, and those based on freely jointed chain or worm-like chain structure. Each model is discussed in terms of the regime of force for which it holds, along with the status of its rigorous assessment with experiment. Finally, I show how the experiments can provide new insight into polymer structure itself, with particular emphasis on polyelectrolytes.

J. Chem. Phys.142, 194902 (2015)


Perspective: Stimulated Raman adiabatic passage: The status after 25 years

Klaas Bergmann1, Nikolay V. Vitanov2 and Bruce W. Shore3
1 Fachbereich Physik und Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Kaiserslautern, Germany
2 Department of Physics, St. Kliment Ohridski University of Sofia, James Bourchier 5 Blvd., 1164 Sofia, Bulgaria
3 618 Escondido Circle, Livermore, California 94550, USA

The first presentation of the STIRAP (stimulated Raman adiabatic passage) technique with proper theoretical foundation and convincing experimental data appeared 25 years ago, in the May 1st, 1990 issue of The Journal of Chemical Physics. By now, the STIRAP concept has been successfully applied in many different fields of physics, chemistry, and beyond. In this article, we comment briefly on the initial motivation of the work, namely, the study of reaction dynamics of vibrationally excited small molecules, and how this initial idea led to the documented success. We proceed by providing a brief discussion of the physics of STIRAP and how the method was developed over the years, before discussing a few examples from the amazingly wide range of applications which STIRAP now enjoys, with the aim to stimulate further use of the concept. Finally, we mention some promising future directions.

J. Chem. Phys. 142, 170901 (2015)


Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

D. J. Wales
University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom

This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

J. Chem. Phys. 142, 130901 (2015)


Perspective: Vibrational-induced steric effects in bimolecular reactions

Kopin Liu
Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan

Liu

The concept of preferred collision geometry in a bimolecular reaction is at the heart of reaction dynamics. Exemplified by a series of crossed molecular beam studies on the reactions of a C–H stretch-excited CHD3(v 1 = 1) with F, Cl, and O(3P) atoms, two types of steric control of chemical reactivity will be highlighted. A passive control is governed in a reaction with strong anisotropic entry valley that can significantly steer the incoming trajectories. This disorientation effect is illustrated by the F and O(3P) + CHD3(v 1 = 1) reactions. In the former case, the long-range anisotropic interaction acts like an optical “negative” lens by deflecting the trajectories away from the favored transition-state geometry, and thus inhibiting the bond rupture of the stretch-excited CHD3. On the contrary, the interaction between O(3P) and CHD3(v 1 = 1) behaves as a “positive” lens by funneling the large impact-parameter collisions into the cone of acceptance, and thereby enhances the reactivity. As for reactions with relatively weak anisotropic interactions in the entry valley, an active control can be performed by exploiting the polarization property of the infrared excitation laser to polarize the reactants in space, as demonstrated in the reaction of Cl with a pre-aligned CHD3(v 1 = 1) reactant. A simpler case, the end-on versus side-on collisions, will be elucidated for demonstrating a means to disentangle the impact-parameter averaging. A few general remarks about some closely related issues, such as mode-, bond-selectivity, and Polanyi’s rules, are made.

J. Chem. Phys. 142, 080901 (2015)


Perspective: The Asakura Oosawa model: A colloid prototype for bulk and interfacial phase behavior

Kurt Binder1, Peter Virnau1, and Antonia Statt2
1Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128 Mainz, Germany
2Graduate School of Excellence Material Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany

In many colloidal suspensions, the micrometer-sized particles behave like hard spheres, but when non-adsorbing polymers are added to the solution a depletion attraction (of entropic origin) is created. Since 60 years the Asakura-Oosawa model, which simply describes the polymers as ideal soft spheres, is an archetypical description for the statistical thermodynamics of such systems, accounting for many features of real colloid-polymer mixtures very well. While the fugacity of the polymers (which controls their concentration in the solution) plays a role like inverse temperature, the size ratio of polymer versus colloid radii acts as a control parameter to modify the phase diagram: when this ratio is large enough, a vapor-liquid like phase separation occurs at low enough colloid packing fractions, up to a triple point where a liquid-solid two-phase coexistence region takes over. For smaller size ratios, the critical point of the phase separation and the triple point merge, resulting in a single two-phase coexistence region between fluid and crystalline phases (of “inverted swan neck”-topology, with possibly a hidden metastable phase separation). Furthermore, liquid-crystalline ordering may be found if colloidal particles of non-spherical shape (e.g., rod like) are considered. Also interactions of the particles with solid surfaces should be tunable (e.g., walls coated by polymer brushes), and interfacial phenomena are particularly interesting experimentally, since fluctuations can be studied in the microscope on all length scales, down to the particle level. Due to its simplicity this model has become a workhorse for both analytical theory and computer simulation. Recently, generalizations addressing dynamic phenomena (phase separation, crystal nucleation, etc.) have become the focus of studies.

J. Chem. Phys. 141, 140901 (2014)


Perspective: Markov models for long-timescale biomolecular dynamics

C.R. Schwantes1, R.T. McGibbon1, and V.S. Pande1,2
1Department of Chemistry, Stanford University, Stanford, CA
2Department of Computer Science, Biophysics Program, Stanford University, Stanford, CA

Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

J. Chem. Phys. 141, 090901 (2014)


Perspective: Fifty years of density-functional theory in chemical physics

Axel D. Becke
Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, CA

Since its formal inception in 1964–1965, Kohn-Sham density-functional theory (KS-DFT) has become the most popular electronic structure method in computational physics and chemistry. Its popularity stems from its beautifully simple conceptual framework and computational elegance. The rise of KS-DFT in chemical physics began in earnest in the mid 1980s, when crucial developments in its exchange-correlation term gave the theory predictive power competitive with well-developed wave-function methods. Today KS-DFT finds itself under increasing pressure to deliver higher and higher accuracy and to adapt to ever more challenging problems. If we are not mindful, however, these pressures may submerge the theory in the wave-function sea. KS-DFT might be lost. I am hopeful the Kohn-Sham philosophical, theoretical, and computational framework can be preserved. This Perspective outlines the history, basic concepts, and present status of KS-DFT in chemical physics, and offers suggestions for its future development.

J. Chem. Phys. 140, 18A301 (2014)


Perspective: Detecting and measuring exciton delocalization in photosynthetic light harvesting

Gregory D. Scholes and Cathal Smyth
Department of Chemistry, University of Toronto, Toronto, CA

Photosynthetic units perform energy transfer remarkably well under a diverse range of demanding conditions. However, the mechanism of energy transfer, from excitation to conversion, is still not fully understood. Of particular interest is the possible role that coherence plays in this process. In this perspective, we overview photosynthetic light harvesting and discuss consequences of excitons for energy transfer and how delocalization can be assessed. We focus on challenges such as decoherence and nuclear-coordinate dependent delocalization. These approaches complement conventional spectroscopy and delocalization measurement techniques. New broadband transient absorption data may help uncover the difference between electronic and vibrational coherences present in two-dimensional electronic spectroscopy data. We describe how multipartite entanglement from quantum information theory allows us to formulate measures that elucidate the delocalization length of excitation and the details of that delocalization even from highly averaged information such as the density matrix.

J. Chem. Phys. 140, 110901 (2014)


Perspective: Bimolecular chemical reaction dynamics in liquids

Andrew J. Orr-Ewing
School of Chemistry, University of Bristol, UK

Bimolecular reactions in the gas phase exhibit rich and varied dynamical behaviour, but whether a profound knowledge of the mechanisms of isolated reactive collisions can usefully inform our understanding of reactions in liquid solutions remains an open question. The fluctuating environment in a liquid may significantly alter the motions of the reacting particles and the flow of energy into the reaction products after a transition state has been crossed. Recent experimental and computational studies of exothermic reactions of CN radicals with organic molecules indicate that many features of the gas-phase dynamics are retained in solution. However, observed differences may also provide information on the ways in which a solvent modifies fundamental chemical mechanisms. This perspective examines progress in the use of time-resolved infra-red spectroscopy to study reaction dynamics in liquids, discusses how existing theories can guide the interpretation of experimental data, and suggests future challenges for this field of research.

J. Chem. Phys. 140, 090901 (2014)


Perspective: Crystal structure prediction at high pressures

Yanchao Wang and Yanming Ma
Institute for Research in Fundamental Sciences (IPM)
State Key Laboratory of Superhard Materials, Jilin University, Changchun, China

Crystal structure prediction at high pressures unbiased by any prior known structure information has recently become a topic of considerable interest. We here present a short overview of recently developed structure prediction methods and propose current challenges for crystal structure prediction. We focus on first-principles crystal structure prediction at high pressures, paying particular attention to novel high pressure structures uncovered by efficient structure prediction methods. Finally, a brief perspective on the outstanding issues that remain to be solved and some directions for future structure prediction researches at high pressure are presented and discussed.

J. Chem. Phys. 140, 040901 (2014)


Perspective: Tipping the scales: Search for drifting constants from molecular spectra

Paul Jansen1, Hendrick L. Bethlem1 and Wim Ubachs1
1Institute for Research in Fundamental Sciences (IPM)
Department of Physics and Astronomy, LaserLaB, VU University Amsterdam

Transitions in atoms and molecules provide an ideal test ground for constraining or detecting a possible variation of the fundamental constants of nature. In this perspective, we review molecular species that are of specific interest in the search for a drifting proton-to-electron mass ratio μ. In particular, we outline the procedures that are used to calculate the sensitivity coefficients for transitions in these molecules and discuss current searches. These methods have led to a rate of change in μ bounded to 6 × 10−14/yr from a laboratory experiment performed in the present epoch. On a cosmological time scale, the variation is limited to |Δμ/μ| < 10−5 for look-back times of 10–12× 109 years and to |Δμ/μ| < 10−7 for look-back times of 7× 109 years. The last result, obtained from high-redshift observation of methanol, translates into µ/µ=(1.4±1.4)×10-17/yr if a linear rate of change is assumed.

J. Chem. Phys. 140, 010901 (2014)


Perspective: Structural dynamics in condensed matter mapped by femtosecond x-ray diffraction

T. Elsaesser1 and M. Woerner1
1Institute for Research in Fundamental Sciences (IPM)
Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie

Ultrashort soft and hard x-ray pulses are sensitive probes of structural dynamics on the picometer length and femtosecond time scales of electronic and atomic motions. Recent progress in generating such pulses has initiated new directions of condensed matter research, exploiting a variety of x-ray absorption, scattering, and diffraction methods to probe photoinduced structural dynamics. Atomic motion, changes of local structure and long-range order, as well as correlated electron motion and charge transfer have been resolved in space and time, providing a most direct access to the physical mechanisms and interactions driving reversible and irreversible changes of structure. This perspective combines an overview of recent advances in femtosecond x-ray diffraction with a discussion on ongoing and future developments.

J. Chem. Phys. 140, 020901 (2014)


Perspective: Coulomb fluids – Weak coupling, strong coupling, in between and beyond

Ali Naji1, Matej Kanduc2,3, Jan Forsman4 and Rudolf Podgornik3,5
1Institute for Research in Fundamental Sciences (IPM)
2Free University Berlin
3J. Stefan Institute
4Chemical Center
5University of Ljubljana

We present a personal view on the current state of statistical mechanics of Coulomb fluids with special emphasis on the interactions between macromolecular surfaces, concentrating on the weak and the strong coupling limits. Both are introduced for a (primitive) counterion-only system in the presence of macroscopic, uniformly charged boundaries, where they can be derived systematically. Later we show how this formalism can be generalized to the cases with additional characteristic length scales that introduce new coupling parameters into the problem. These cases most notably include asymmetric ionic mixtures with mono- and multivalent ions that couple differently to charged surfaces, ions with internal charge (multipolar) structure and finite static polarizability, where weak and strong coupling limits can be constructed by analogy with the counterion-only case and lead to important new insights into their properties that cannot be derived by any other means.

J. Chem. Phys. 139, 150901 (2013)


Perspective: Reaches of chemical physics in biology

Martin Gruebele1 and D. Thirumalai2
1University of Illinois
2University of Maryland

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

J. Chem. Phys. 139, 121701 (2013)


Perspective: Coarse-grained models for biomolecular systems

W.G. Noid
The Pennsylvania State University

By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

J. Chem. Phys. 139, 090901 (2013)


Perspective: Nanomotors without moving parts that propel themselves in solution

Raymond Kapral
University of Toronto

Self-propelled nanomotors use chemical energy to produce directed motion. Like many molecular motors they suffer strong perturbations from the environment in which they move as a result of thermal fluctuations and do not rely on inertia for their propulsion. Such tiny motors are the subject of considerable research because of their potential applications, and a variety of synthetic motors have been made and are being studied for this purpose. Chemically-powered self-propelled nanomotors without moving parts that rely on asymmetric chemical reactions to effect directed motion are the focus of this article. The mechanisms they use for propulsion, how size and fuel sources influence their motion, how they cope with strong molecular fluctuations and how they behave collectively are described. The practical applications of such nanomotors are largely unrealized and the subject of speculation. Since molecular motors are ubiquitous in biology and perform a myriad of complex tasks, the hope is that synthetic motors might be able to perform analogous tasks. They may have the potential to change our perspective on how chemical dynamics takes place in complex systems.

J. Chem. Phys. 138, 020901 (2013)


Perspective: Alchemical free energy calculations for drug discovery

David Mobley
University of California, Irvine

Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery.

J. Chem. Phys. 137, 230901 (2012)


Perspective: Nonadiabatic Dynamics Theory

John Tully
Yale University

Nonadiabatic dynamics – nuclear motion evolving on multiple potential energy surfaces – has captivated the interest of chemists for decades. Exciting advances in experimentation and theory have combined to greatly enhance our understanding of the rates and pathways of nonadiabatic chemical transformations. Nevertheless, there is a growing urgency for further development of theories that are practical and yet capable of reliable predictions, driven by fields such as solar energy, interstellar and atmospheric chemistry, photochemistry, vision, single molecule electronics, radiation damage, and many more. This spotlight examines the most significant theoretical and computational obstacles to achieving this goal, and suggests some possible strategies that may prove fruitful.

J. Chem. Phys. 137, 22A301 (2012)


Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory

Angelos Michaelides1 and Jirí Klimeš1
1University College London

Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.

J. Chem. Phys. 137, 120901 (2012)


Special Topic: Photochemistry at Surfaces

Horia Metiu, Associate Editor
University of California, Santa Barbara

This Special Topic Section on Photochemistry at Surfaces contains invited essays by several leading scientists in the field. These essays present personal perspectives on the field and provide an overview of promising areas for future research on photo-initiated processes at surfaces using advanced experimental techniques. The authors focus on fundamental aspects of the field, which also has significant future applications in photovoltaic solar cells and photocatalytic water splitting.

Go to Special Topic: Photochemistry at Surfaces


Perspective: Supercooled Liquids and Glasses

Mark Ediger1 and Peter Harrowell2
1University of Wisconsin
2University of Sydney

Supercooled liquids and glasses are important for current and developing technologies. Here, Mark Ediger and Peter Harrowell provide perspective on recent progress in this field. The interpretation of supercooled liquid and glass properties is discussed in terms of the potential energy landscape. Connections are explored between amorphous structure, high frequency motions, molecular motion, structural relaxation, stability against crystallization, and material properties. Recent developments are described that may lead to new materials or new applications of existing materials.
- Photo Credit: Erberto Zani

J. Chem. Phys. 137, 080901 (2012)


Perspective: Quantum or Classical Coherence?

William H. Miller
Department of Chemistry and K. S. Pitzer Center for Theoretical Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1460, USA

Some coherence effects in chemical dynamics are described correctly by classical mechanics, while others only appear in a quantum treatment—and when these are observed experimentally it is not always immediately obvious whether their origin is classical or quantum. Semiclassical theory provides a systematic way of adding quantum coherence to classical molecular dynamics and thus provides a useful way to distinguish between classical and quantum coherence. Several examples are discussed which illustrate both cases. Particularly interesting is the situation with electronically non-adiabatic processes, where sometimes whether the coherence effects are classical or quantum depends on what specific aspects of the process are observed.

J. Chem. Phys. 136, 210901 (2012)


Perspective: Relativistic Effects

Jochen Autschbach
Department of Chemistry, State University of New York at Buffalo, New York 14260-3000, USA

This perspective article discusses some broadly-known and some less broadly-known consequences of Einstein's special relativity in quantum chemistry, and provides a brief outline of the theoretical methods currently in use, along with a discussion of recent developments and selected applications. The treatment of the electron correlation problem in relativistic quantum chemistry methods, and expanding the reach of the available relativistic methods to calculate all kinds of energy derivative properties, in particular spectroscopic and magnetic properties, requires on-going efforts.

J. Chem. Phys. 136, 150902 (2012)


Perspective on Density Functional Theory

Kieron Burke
University of California, Irvine

Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: Too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.

J. Chem. Phys. 136, 150901(2012)


Hydrogen: A Fresh Look at High Pressure

Roald Hoffmann1, Vanessa Labet1, Paulina Gonzalez-Morelos1, Neil Ashcroft1
1University of California, Irvine

Nobel Laureate and Professor Emeritus of Chemistry at Cornell University Roald Hoffmann joins colleagues Vanessa Labet and Neil Ashcroft in talking about their work on hydrogen at very high pressures. While at atmospheric pressures the hydrogen molecule remains one of the few exactly solvable problems as a diatomic molecule, it is not a solved problem under extreme pressure where the molecule’s properties change and the system becomes, as Hoffmann says, “the subject of intense experimental research and an important problem” .


The Dawning of the Age of Graphene

George W. Flynn
1Columbia University

Since the first reports of experiments on stand-alone, single-layer graphene crystals, this remarkable 2-dimensional material has attracted great scientific interest.

Graphene is a single sheet of carbon atoms that constitutes the basic building block of macroscopic graphite crystals. Held together by a backbone of sp2 hybrids, graphene's 2p orbitals form p state bands that delocalize over an entire 2-dimensional macroscopic carbon sheet leading to a number of unusual characteristics that include large electrical and thermal conductivities. Recent discoveries have provided simple methods (e.g. mechanical cleavage of graphite) for preparing laboratory scale samples that can be used to investigate the fundamental physical and chemical characteristics of graphene. In addition a number of techniques have emerged that show promise for producing large-scale samples with the ultimate goal of developing devices that take advantage of graphene's unusual properties. As large samples become available, the possibility grows for applications of this material in solar cell technology (as flexible, transparent electrodes), in composite material development, and in electronic devices.

J. Chem. Phys. 135, 050901 (2011)


Water Cluster Mediated Atmospheric Chemistry

Veronica Vaida
University of Colorado

The importance of water in atmospheric and environmental chemistry initiated recent studies with results documenting catalysis, suppression and anti-catalysis of thermal and photochemical reactions due to hydrogen bonding of reagents with water. Water, even one water molecule in binary complexes, has been shown by quantum chemistry to stabilize the transition state and lower its energy. However, new results underscore the need to evaluate the relative competing rates between reaction and dissipation to elucidate the role of water in chemistry. Water clusters have been used successfully as models for reactions in gas-phase, in aqueous condensed phases and at aqueous surfaces. Fundamental issues in experimental and theoretical chemical physics remain but that work in this field accelerated recently, driven by the importance of this chemistry in planetary atmospheres including but not limited to Earth.

J. Chem. Phys. 135, 020901 (2011)


Ionic Liquids

Edward W. Castner, Jr.1 and James F. Wishart2
1Rutgers, The State University of New Jersey
2Brookhaven National Laboratory

Ionic liquids are an emerging class of materials with a diverse and extraordinary set of properties. Understanding the origins of these properties and how they can be controlled by design to serve valuable practical applications presents a wide array of challenges and opportunities to the chemical physics and physical chemistry community. We highlight here some of the signi_cant progress already made and future research directions in this exciting area.

J. Chem. Phys. 132, 120901 (2010)


Frontiers in Electronic Structure Theory

C. David Sherrill
Georgia Institute of Technology

Current and emerging research areas in electronic structure theory promise to greatly extend the scope and quality of quantum chemical computations. Two particularly challenging problems are the accurate description of electronic near-degeneracies (as occur in bond-breaking reactions, firstrow transition elements, etc.) and the description of long-range dispersion interactions in density functional theory. Additionally, even with the emergence of reduced-scaling electronic structure methods and basis set extrapolation techniques, quantum chemical computations remain very time consuming for large molecules or large basis sets. A variety of techniques, including density fitting and explicit correlation methods, are making rapid progress toward solving these challenges.

J. Chem. Phys. 132, 110902 (2010)


Ionic Liquids

Edward W. Castner, Jr.1 and James F. Wishart2
1Rutgers, The State University of New Jersey
2Brookhaven National Laboratory

Ionic liquids are an emerging class of materials with a diverse and extraordinary set of properties. Understanding the origins of these properties and how they can be controlled by design to serve valuable practical applications presents a wide array of challenges and opportunities to the chemical physics and physical chemistry community. We highlight here some of the signi_cant progress already made and future research directions in this exciting area.

J. Chem. Phys. 132, 120901 (2010)


Cold and Ultracold Molecules: Spotlight on Orbiting Resonances

David W. Chandler
Sandia National Laboratories

There is great interest in the production of cold molecules, at temperatures below 1 K, and ultracold molecules, at temperatures below 1 mK. Such molecules have potential applications in areas ranging from precision measurement to quantum information storage and processing, and quantum gases of ultracold polar molecules are expected to exhibit novel quantum phases. In addition, cold molecules open up a new domain for collision physics, dominated by long-range forces and scattering resonances. There have been major recent advances both in cooling molecules from room temperature and in forming molecules in ultracold atomic gases. As these techniques mature and cold and ultracold samples are more accessible collision studies at previously unavailable energies will be possible. This spotlight article will highlight some of the background and motivation for studying collisions at low energies and will direct readers to recent articles on the recent experimental advancements.

J. Chem. Phys. 132, 110901 (2010)

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