JCP Spotlight Collections–

Perspective: Stochastic Algorithms for Chemical Kinetics
Daniel T. Gillespie
Dan T Gillespie Consulting, Castaic, CA

Andreas Hellander
Linda R. Petzold
University of California Santa Barbara, CA

Abstract   We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms.  We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years.  For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description.  We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis.  Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed.  In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes.

J. Chem. Phys. 138, 170901 (2013)

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Perspective: The Glass Transition
Giulio Biroli
CEA Saclay, Gif-sur-Yvette, France

Juan Garrahan
University of Nottingham, UK

Abstract   We provide here a brief perspective on the glass transition field. It is an assessment, written from the point of view of theory, of where the field is and where it seems to be heading. We first give an overview of the main phenomenological characteristics, or “stylised facts,” of the glass transition problem, i.e. the central observations that a theory of the physics of glass formation should aim to explain in a unified manner. We describe recent developments, with a particular focus on real space properties, including dynamical heterogeneity and facilitation, the search for underlying spatial or structural correlations, and the relation between the thermal glass transition and athermal jamming. We then discuss briefly how competing theories of the glass transition have adapted and evolved to account for such real space issues. We consider in detail two conceptual and methodological approaches put forward recently, that aim to access the fundamental critical phenomenon underlying the glass transition, be it thermodynamic or dynamic in origin, by means of biasing of ensembles, of configurations in the thermodynamic case, or of trajectories in the dynamic case. We end with a short outlook.

J. Chem. Phys. 138, 12A301 (2013)

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Perspective: Nanomotors without moving parts that propel themselves in solution
Raymond Kapral
University of Toronto

Abstract   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)

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Perspective: Alchemical free energy calculations for drug discovery
David Mobley
University of California, Irvine

Abstract   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)

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Perspective: Nonadiabatic Dynamics Theory
John Tully
Yale University

Abstract   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)

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Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory
Angelos Michaelides and Jiří Klimeš
University College London

Abstract   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)

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Special Topic: Photochemistry at Surfaces
Horia Metiu, Associate Editor
University of California, Santa Barbara

Abstract   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.

Click here to see the Special Topic

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Perspective: Supercooled Liquids and Glasses
Mark Ediger
University of Wisconsin

Peter Harrowell
University of Sydney

Abstract  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)

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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

Abstract  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)

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

Abstract  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)

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Perspective on Density Functional Theory
Kieron Burke
University of California, Irvine

Abstract  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)

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Hydrogen: A Fresh Look at High Pressure
Roald Hoffmann, Vanessa Labet, Paulina Gonzalez-Morelos, Neil Ashcroft
Cornell University

Abstract  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” .

J. Chem. Phys. 136, 074501 (2012)
J. Chem. Phys. 136, 074502 (2012)
J. Chem. Phys. 136, 074503 (2012)
J. Chem. Phys. 136, 074504 (2012)

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Abstract  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 π 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)

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Water Cluster Mediated Atmospheric Chemistry
Veronica Vaida
University of Colorado

Listen now to the interview Right-click to download MP3 file.

Abstract  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)

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

Abstract  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)

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Frontiers in Electronic Structure Theory
C. David Sherrill
Georgia Institute of Technology

Abstract  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)

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Cold and Ultracold Molecules: Spotlight on Orbiting Resonances
David W. Chandler
Sandia National Laboratories

Abstract  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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