New Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
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.
New Special Topic: Supramolecular Self-Assembly at Surfaces
Supramolecular self-assembly at surfaces is one of the most exciting and active fields in Surface Science today. Applications can take advantage of two key properties: (i) versatile pattern formation over a broad length scale and (ii) tunability of electronic structure and transport properties, as well as frontier orbital alignment. It provides a new frontier for Chemical Physics as it uniquely combines the versatility of Organic Synthesis and the Physics of Interfaces. The Journal of Chemical Physics is pleased to publish this Special Topic Issue, showcasing recent advances and new directions.
New Perspective: Vibrational-induced steric effects in bimolecular reactions
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.
JCP in the News: Articles Recently Featured in the Press
Asymmetric Coulomb fluids at randomly charge dielectric interfaces: Anti-fragility, overcharging, and charge inversion
Ali Naji, Malihe Ghodrat, Haniyeh Komaie-Moghaddam and Rudolf Podgornik
J. Chem. Phys. 141, 174704 (2014)
Read the Press Release
Molecular interactions with ice: Molecular embedding, adsorption, detection, and release
K. D. Gibson, Grant G. Langlois, Wenxin Li, Daniel R. Killelea and S. J. Sibener
J. Chem. Phys. 141, 18C514 (2014)
Read the Press Release
JCP Congratulates Associate Editor David Sherrill on being elected fellow of the AAAS
The Journal of Chemical Physics congraulates Associate Editor David Sherrill on being elected Fellow of the American Association for the Advancement of Science (AAAS), 2014. Prof. Sherrill has been elected in recognition of his “notable advances in electronic structure theory and their application in seminal studies of non-covalent pi interactions”.
Congratulations to Majed Chergui, recipient of the JCP Sponsored Plyler Prize
The Journal of Chemical Physics is proud to congratulate Majed Chergui on receiving the 2015 Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics, which recognizes outstanding research and notable contributions to the field of molecular spectroscopy and dynamics. Prof. Chergui has been recognized “for developing new methods and redefining the boundaries of molecular spectroscopy through extending the temporal and spectral range, and for his pioneering work in ultrafast X-Ray spectroscopy for studies in solution and the solid state.” Prof. Chergui will receive the award at the 2015 APS March Meeting in March in San Antonio, Texas.
Abstract: 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. Read the Perspective.
Abstract: 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. Read the Perspective.
JCP in the News: Article Recently Featured in the Press
Towards bio-silicon interfaces: Formation of an ultra-thin self-hydrated artificial membrane composed of dipalmitoylphosphatidylcholine (DPPC) and chitosan deposited in high vacuum from the gas-phase
María J. Retamal, Marcelo A. Cisternas, Sebastian E. Gutierrez-Maldonado, Tomas Perez-Acle, Birger Seifert, Mark Busch, Patrick Huber and Ulrich G. Volkmann
J. Chem. Phys. 141, 104201 (2014)
Read the Press Release
Congratulations to JCP Associate Editor Patricia Thiel: 2014 winner of the AVS Medard W. Welch Award
The Journal of Chemical Physics is proud to congratulate Patricia Thiel, Associate Editor of JCP, on receiving the 2014 AVS Medard W. Welch Award, which recognizes outstanding research in the fields of materials, interfaces and processing. She has been recognized for her “seminal contributions to the understanding of quasicrystalline surfaces and thin-film nucleation and growth.” Prof. Thiel will receive the award at the 2014 AVS 61st International Symposium & Exhibition this November in Balitimore.
JCP Welcomes New Associate Editor Carlos Vega
Carlos Vega, from the Universidad Complutense, Madrid, has joined the JCP team as a new Associate Editor. Carlos is a Professor of Physical Chemistry and leads the statistical dynamics of molecular fluids research group at the University. His research involves exploration of the fluid-solid equilibrium using computer simulations. His recent work was focused on water, with special interest into the calculation of its phase diagram and the development of simple potential models to describe the complex thermodynamic behavior of this simple molecule.
New Perspective: Fifty years of density functional theory in chemical physics
Axel D. Becke
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. Read the Perspective
This Special Topic of The Journal of Chemical Physics on Advances in Density Functional Theory contains a Preface, Retrospective article, Perspective article, and a collection of original research articles that showcase recent theoretical advances in the field. It has been fifty years since the publication of the Hohenberg-Kohn paper, which, along with the Kohn-Sham paper one year later, laid the foundation for the field. The preface by Yang introduces the special topic and gives interesting insight regarding DFT’s impact over the years. In the editorial article of Kohn and Sherrill, Kohn shares a retrospective of his personal interaction with leading quantum chemists. The perspective article of Becke gives a review of the past developments as well as a forward projection of the field. This Special Topic captures the current state of understanding of DFT and the most exciting recent methodology developments. We hope that this will be a valuable resource to the community that may help to set the stage for future research in this important and thriving field.
JCP in the News: Articles Recently Featured in the Press
Nuclear spin conversion of water inside fullerene cages detected by low-temperature nuclear magnetic resonance
Salvatore Mamone, Maria Concistrè, Elisa Carignani, Benno Meier et.al.
J. Chem. Phys. 140, 194306 (2014)
Read the Press Release
Call for Nominations for the 2015 Plyler Prize
The Earl K. Plyler Prize for Molecular Spectroscopy and Dynamics is given every year by the American Physical Society to recognize and encourage notable contributions to the field. The Journal of Chemical Physics proudly sponsors the Plyler Prize and would like to call on the Chemical Physics community to nominate qualified scientist for this award. The deadline for submission of nominations is July 1, 2014. For more information on the nomination and selection process see the APS website.
New Perspective: Bimolecular chemical reaction dynamics in liquids
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. Read the Perspective.
New Perspective: Tipping the scales: Search for drifting constants from molecular spectra
In this Perspective, the authors review molecular species that are of specific interest in the search for a drifting proton-to-electron mass ratio μ. In particular, they 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. Read the Perspective.
New Perspective: Structural dynamics in condensed matter mapped by femtosecond x-ray diffraction
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. Read the Perspective
Congratulations to Marsha I. Lester, recipient of the 2014 Garvan-Olin Medal
The Journal of Chemical Physics is proud to congratulate Marsha I. Lester, Editor of JCP, on receiving the 2014 Francis P. Garvan-John M. Olin Medal which recognizes distinguished service to chemistry by women chemists. Prof. Lester will be honored at an awards ceremony at the Spring ACS National Meeting in Dallas.
Congratulations to Lai-Sheng Wang, recipient of the 2014 Plyler Prize
The Journal of Chemical Physics is pleased to congratulate Lai-Sheng Wang on being awarded the Earle K Plyler Prize for Molecular Spectroscopy & Dynamics "for advancing the chemistry and physics of metal clusters using photoelectron spectroscopy, and for innovative development of cluster sources and photoelectron techniques." Prof. Wang will receive the award at the 2014 APS March Meeting in Denver.
DCP Focus Symposia at 2014 March Meeting
The Division of Chemical Physics is organizing five focus sessions at the 2014 March Meeting of the American Physical Society in Denver. Abstracts for contributed talks may be submitted on the APS website until November 15, 2013. The five sessions are:
- Quantum Control of Molecular, Nano, and Plasmonic Materials
- Surface Chemistry and Catalysis
- Solvation, Dynamics, and Reactivity in Complex Environments
- Recent Advances in Density Functional Theory
- Charge and Energy Transfer for Renewable Energy
For a list of invited speakers see the APS-DCP website.
JCP in the News: Articles Recently Featured in the Press
Catalytic micromotor generating self-propelled regular motion through random fluctuation
Daigo Yamamoto, Atsushi Mukai, Naoaki Okita, Kenichi Yoshikawa and Akihisa Shioi
J. Chem. Phys. 139, 034705 (2013)
Read the Press Release
Understanding the relationship between molecular order and charge transport properties in conjugated polymer based organic blend photovoltaic devices
Sebastian Wood, Jong Soo Kim, David T. James, Wing C. Tsoi, Craig E. Murphy and Ji-Seon Kim
J. Chem. Phys. 139, 064901 (2013)
Read the Press Release
New Perspective: Coulomb fluids - Weak coupling, strong coupling, in between and beyond
This Perspective presents 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 it is shown how this formalism can be generalized to the cases with additional characteristic length scales that introduce new coupling parameters into the problem. Read the Perspective.
2013 Nobel Prize in Chemistry
The Journal of Chemical Physics congratulates the 2013 Nobel Laureates in Chemistry, Martin Karplus, Michael Levitt, and Arieh Warshel "for the development of multiscale models for complex chemical systems."
New Perspective: Reaches of chemical physics in biology by Martin Gruebele and D. Thirumalai
In this introduction to the special topic section on chemical physics of biological systems, the authors 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. Read the Perspective.
New Perspective: Coarse-grained models for biomolecular system by W.G. Noid
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. Read the Perspective.
Happy 80th Anniversary to The Journal of Chemical Physics!
The Journal of Chemical Physics is proud to be celebrating its 80th year as the leading and most cited journal in chemical physics. Celebrate the work that has been published in the journal since 1933 and view the 80th Anniversary Collection.
The Journal of Chemical Physics is pleased to announce a special topic section on the Chemical Physics of Biological Systems. This special topic will showcase the far reaches of the experimental, theoretical, and computational tools in physical chemistry and chemical physics that tackle problems of fundamental importance in biology. It features a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and systems-level approaches that captures the excitement in all of these rapidly growing areas. Martin Gruebele and Dave Thirumalai served as Guest Editors and worked with JCP Editor John Straub to produce this section. Read this issue online.
The Journal of Chemical Physics Retains the Top Spot as the Most Highly Cited Journal in the Atomic, Molecular, and Chemical Physics Category
Journal metrics just released by Thomson Reuters*, once again show JCP to be the most highly cited journal tracked in the Atomic, Molecular, and Chemical Physics Category, with 188,038 total citations in 2012.
IMPACT FACTOR: 3.164
*2012 Journal Citation Reports (Thomson Reuters, 2013)
Special Topic: Glass Transition
The Journal of Chemical Physics is pleased to announce a special topic section on the Glass Transition. This section provides a timely discussion of modern developments in our understanding of the behavior of supercooled liquids and amorphous materials, which have implications in diverse fields ranging from biology to materials science. In spite of decades of intense theoretical and experimental study, the fundamental causes of vitrification are still debated. David Reichman served as Guest Editor and worked with James Skinner and other JCP Associate Editors to produce this section.
JCP welcomes three new Associate Editors in 2013
Peter Hamm from the University of Zurich, Angelos Michaelides from University College London, and Patricia A. Thiel from Iowa State University.
CrossMark implemented on AIP journals
AIP Publishing is dedicated to scientific accuracy and integrity and as a result has implemented CrossMark on its publications. As of December 2012, a CrossMark logo will appear on an HTML page or PDF file indicating that the publisher is maintaining the published document through any updates, corrections, enhancements, retractions, and other such changes. Clicking the CrossMark logo reveals status information about the document and tells readers whether they are accessing the most recent and reliable version or not. A link to any updated version will be included. You can learn more about CrossMark from the CrossRef website.
Special Topic: Nonadiabatic Dynamics
The Journal of Chemical Physics is pleased to announce a special topic section on Nonadiabatic Dynamics. This section provides a timely discussion of modern developments, applications, and challenges in dynamics beyond the Born-Oppenheimer approximation. Xiaosong Li and Oleg Prezdho served as Guest Editors and worked with JCP Associate Editors Ernest Davidson and Todd Martinez to produce this section. This Special Topic leads off with a Perspective: Nonadiabatic Dynamics Theory by John C. Tully.
Special Topic: Photochemistry at Surfaces
The Journal of Chemical Physics is pleased to announce a special topic section on Photochemistry at Surfaces. Essays in this section 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. JCP Associate Editor Horia Metiu served as Editor of this section.
Congratulations to JCP award winning authors
Congratulations to the ACS 2013 Award winners including JCP prominent and recent authors.
Congratulations to the AAAS 2012 Fellows, including prominent and recent JCP authors.
JCP congratulates Associate Editor James Skinner, Pablo G. Debenedetti, and Monica Olvera de la Cruz on their election to the National Academy of Sciences.
Congratulations to the APS 2013 Award winners including JCP prominent and recent authors.