The Journal of Chemical Physics
Editors' Choice for 2011

Communication: Standard surface hopping predicts incorrect scaling for Marcus’ golden-rule rate: The decoherence problem cannot be ignored
Brian R. Landry and Joseph E. Subotnik

Surface hopping methods, which treat nuclei classically while maintaining the quantum character of electrons, are arguably the most widely used for modeling photo-induced nonadiabatic reactions, with possible applications in the fields of alternative energy and electronics. This paper evaluates the accuracy of Tully's surface hopping algorithm for the spin-boson model for the case of a small diabatic coupling parameter and finds that adding decoherence to the surface hopping algorithm is crucial for correct scaling.

J. Chem. Phys. 135, 191101 (2011 )

Communication: A packing of truncated tetrahedra that nearly fills all of space and its melting properties
Yang Jiao and Salvatore Torquato

This paper analytically constructs the densest known packing of an Archimedean truncated tetrahedron, a polyhedron with four hexagonal faces and four regular triangular faces. Because truncated tetrahedra have no central symmetry, they cannot be manipulated to completely fill a three-dimensional space. However, the calculated packing fraction, ϕ = 207/208 = 0.995192…, is so close to unity that the packing scheme, which is based on a new generalized scheme for polyhedra lacking central symmetry, may be optimal.

J. Chem. Phys. 135, 151101 (2011)

Communication: Rationale for a new class of double-hybrid approximations in density-functional theory
Julien Toulouse, Kamal Sharkas, Eric Brémond, and Carlo Adamo

LS1DH, a double-hybrid (DH) approximation that combines an exchange-correlation density functional with Hartree-Fock exchange weighted by λ and second-order Møller-Plesset (MP2) correlation weighted by λ³, has become increasingly popular for electronic-structure calculations. This paper confirms that LS1DH tends to be more accurate than the DS1DH model in which density scaling is applied to the Perdew-Burke-Ernzerhof correlation functional and will be more accurate than the DS1DH model when applied with a density-functional approximation that is inaccurate in the high-density limit.

J. Chem. Phys. 135, 101102 (2011)

Communication: Determination of the bond dissociation energy (D₀) of the water dimer, (H₂O)₂, by velocity map imaging
Blithe E. Rocher-Casterline, Lee C. Ch'ng, Andrew K. Mollner, and Hanna Reisler

The authors report the use of velocity map imaging to obtain the first direct determination of the dissociation energy of the water dimer—the smallest water cluster—in a supersonic molecular beam. An accurate experimental value of the dissociation energy (1105 ± 10 cm^-1)is important for evaluating the dimer’s absorption in the atmosphere.

J. Chem. Phys. 134, 211101 (2011)

Communication: Bubbles, crystals, and laser-induced nucleation
Brandon C. Knott, Jerry L. LaRue, Alec M. Wodtke, Michael F. Doherty, and Baron Peters

Intense nanosecond laser pulses have been shown to accelerate the nucleation of crystals from a variety of supersaturated solutions, through unknown mechanisms. The authors report that similar laser pulses can also induce bubble formation in carbonated water and, using an aqueous solution that is cosupersaturated with argon and glycine, show that escaping argon bubbles can induce crystal nucleation without a laser. These findings suggest a possible link between laser-induced nucleation of bubbles and crystals.

J. Chem. Phys. 134, 171102 (2011)

Communication: Highest occupied molecular orbital–lowest unoccupied molecular orbital gaps of doped silicon clusters from core level spectroscopy
J. Lau, Marlene Vogel, Andreas Langenberg, Konstantin Hirsch, Jochen Rittmann, Vicente Zamudio-Bayer, Thomas Moeller, and Bernd von Issendorff

The authors present an alternative method for determining size-selected and isolated nanoparticle band gaps based on a combination of core-level and valence band photoionization spectroscopy. A first application to vanadium-doped silicon clusters confirms a striking size-dependence of their highest occupied–lowest unoccupied molecular orbital gaps.

J. Chem. Phys. 134, 041102 (2011)

On the entropy of relaxing deterministic systems
Denis J. Evans, Stephen R. Williams, and Debra J. Searles

The roles of dissipation and entropy are explored in a new derivation for the constancy of the fine-grained Gibbs entropy for autonomous Hamiltonian systems. In the paper, the authors show that, away from equilibrium, dissipation is a powerful quantity that can always be defined and offer more precise arguments for why nonequilibrium entropy is not a useful concept.

J. Chem. Phys. 135, 194107 (2011)

Potential-functional embedding theory for molecules and materials
Chen Huang and Emily Carter

Accurate and detailed electronic properties and energies are necessary to understand and predict material properties on a variety of length scales, but accurate determinations are complicated in many-atom systems. Embedding schemes are used to describe the interaction between clusters of atoms that can be evaluated with greater accuracy and their (optionally) less accurately defined environment. The authors solve some problems in density embedding theory by minimizing the total energy with respect to the embedding potential, rather than the density. This potential functional embedding theory is tested for some systems relevant to applications in materials science.

J. Chem. Phys. 135, 194104 (2011)

Prospects for release-node quantum Monte Carlo
Norm M. Tubman, Jonathan L. DuBois, Randolph Q. Hood, and Berni J. Alder

The diffusion Monte Carlo (DMC) method can simulate quantum states without systematic bias in bosonic but not fermionic systems. To determine the fermionic ground state, an alternative method—release-node quantum Monte Carlo (RN-QMC)—can be used. The authors performed RN-QMC on first-row diatomic molecules and estimated the ground-state energies, in atomic units, of Li₂ (−14.9947(1)), Be₂ (−29.3367(7)), and B₂ (−49.410(2)).

J. Chem. Phys. 135, 184109 (2011)

Construction of a disorder variable from Steinhardt order parameters in binary mixtures at high densities in three dimensions
Takeshi Kawasaki and Akira Onuki

The particle configuration of a binary particle system is much more complicated than that of a one-component system. Using a molecular dynamics simulation that incorporates a disorder variable for each particle, the authors investigated the structural disorder in crystal, polycrystal, and glass in a Lennard-Jones binary mixture composed of N₁ + N₂ = 4096 particles at a low temperature in three dimensions.

J. Chem. Phys. 135, 174109 (2011)

Rapid calculation of partition functions and free energies of fluids
Hainam Do, Jonathan D. Hirst, and Richard J. Wheatley

Free energy provides the impetus for change in the natural world, whether in the formation of protein molecules or weather patterns or the destruction of cancer cells or the ozone layer, and knowing the free energy allows one to predict many physical and chemical phenomena. The authors present a Monte Carlo technique that simplifies the process of calculating the free energies of continuous systems. Using the method, which is demonstrated for water, the free energy can be calculated directly as a function of temperature.

J. Chem. Phys. 135, 174105 (2011)

Projected quasiparticle theory for molecular electronic structure
Gustavo E. Scuseria, Carlos A. Jiménez-Hoyos, Thomas M. Henderson, Kousik Samanta, and Jason K. Ellis

Symmetry-projected Hartree-Fock-Bogoliubov equations are derived and applied to the molecular electronic structure problem. All symmetries—particle number, spin, spatial, and complex conjugation—are deliberately broken and restored in a self-consistent variation-after-projection approach that yields a comprehensive black-box treatment of static correlations with effective one-electron computational cost.

J. Chem. Phys. 135, 124108 (2011)

NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface
Trond S. Ingebrigtsen, Søren Toxvaerd, Ole J. Heilmann, Thomas B. Schrøder, and Jeppe C. Dyre

An algorithm for computer simulation of geodesic motion on a constant-potential-energy hypersurface is described. The algorithm for NVU dynamics—dynamics that conserve the potential energy U for a system of N classical particles at constant volume V—in conjunction with compensation for center-of-mass drift is absolutely stable, with potential energy, step length, and center-of-mass position conserved for indefinitely long runs.

J. Chem. Phys. 135, 104101 (2011)

How accurate are the non-linear chemical Fokker-Planck and chemical Langevin equations?
Ramon Grima, Philipp Thomas, Arthur V. Straube

A system-size expansion is used to evaluate the accuracy of chemical Fokker-Planck estimates and chemical Langevin equations—commonly used approximations of the chemical master equation, the accepted mathematical description of chemical systems in well-mixed conditions. High accuracy is realized for chemical systems in small volumes, such as biochemical reactions inside cells.

J. Chem. Phys. 135, 084103 (2011)

Dynamic kinetic energy potential for orbital-free density functional theory
Daniel Neuhauser, Shlomo Pistinner, Arunima Coomar, Xu Zhang, and Gang Lu

A dynamic kinetic energy potential is developed for time-dependent orbital-free density functional theory applications. It makes the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas, enabling extension from the static case to dynamic processes. This approach may provide a means of embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory) in a large background described by time-dependent orbital-free density functional theory.

J. Chem. Phys. 134, 144101 (2011)

Entanglement of polar molecules in pendular states
Qi Wei, Sabre Kais, Bretislav Friedrich, and Dudley Herschbach

Arrays of ultracold polar molecules are considered among the most promising platforms for quantum computers. This paper evaluates entanglement, as measured by pairwise concurrence, for the prototype case of two ultracold diatomic polar molecules in pendular states and trapped in distinct optical lattice sites.

J. Chem. Phys. 134, 124107 (2011)

Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges
Daniel Healion, Haitao Wang, and Shaul Mukamel

In this paper, the researchers calculated the stimulated x-ray Raman spectroscopy (SXRS) signal of N-methylacetamide (NMA), a small organic molecule used as a convenient model system for the peptide bond forming the backbones of proteins, using a higher-level description of core excitations, the static-exchange approximation (STEX). Compared with the equivalent-core approximation, STEX predicts the correct spin symmetry of the excited states and provides an improved description for both the occupied and virtual orbitals.

J. Chem. Phys. 134, 124101 (2011)

Catalytic conversion reactions mediated by single-file diffusion in linear nanopores: Hydrodynamic versus stochastic behavior
David M. Ackerman, Jing Wang, Joseph H. Wendel, Da-Jiang Liu, Marek Pruski, and James W. Evans

The spatiotemporal behavior of species concentrations is analyzed in a diffusion-mediated conversion reaction that occurs at catalytic sites within linear pores of nanometer diameter. Both transient and steady-state behavior is characterized by kinetic Monte Carlo simulations.

J. Chem. Phys. 134, 114107 (2011)

An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion
Leif D. Jacobson and John M. Herbert

The researchers introduce a new quantum chemistry method for studying intermolecular interactions called explicit polarization (XPol)/symmetry-adapted perturbation theory (SAPT), or XPS, which represents a promising path toward accurate, systematically improvable, and parameter-free simulation of clusters and molecular liquids. This fragment-based electronic structure method incorporates electronic polarization (induction) in a self-consistent fashion but treats intermolecular exchange and dispersion interactions perturbatively.

J. Chem. Phys. 134, 094118 (2011)

Dynamical mean-field theory from a quantum chemical perspective
Dominika Zgid and Garnet Kin-Lic Chan

This paper presents an initial study of dynamical mean-field theory (DMFT) from a quantum chemical perspective. DMFT provides a powerful framework to extend quantum chemical correlation hierarchies to infinite problems through a self-consistent embedding view of the crystal. Studies are carried out for a cubic hydrogen model, which provides a simple but challenging test for correlation methods.

J. Chem. Phys. 134, 094115 (2011)

Local ab initio methods for calculating optical band gaps in periodic systems. I. Periodic density fitted local configuration interaction singles method for polymers
Marco Lorenz, Denis Usvyat, and Martin Schütz

This paper describes a density-fitted local configuration interaction singles method for calculating optical band gaps in one-dimensional periodic systems. The method can be used to calculate the excitonic band gaps of polymers with up to a few dozen atoms.

J. Chem. Phys. 134, 094101 (2011)

Double-hybrid density-functional theory made rigorous
Kamal Sharkas, Julien Toulouse, and Andreas Savin

The authors rigorously derive a class of double-hybrid approximations combining Hartree–Fock exchange and a second-order Møller–Plesset (MP2) correlation with a semilocal exchange-correlation density functional. The performance of these double-hybrid schemes is assessed by atomization energies and reaction barrier heights, and compared with other hybrid approximations, including range-separated hybrids.

J. Chem. Phys. 134, 064113 (2011)

Sum frequency generation-compressive sensing microscope
Xiaojun Cai, Bian Hu, Ting Sun, Kevin F. Kelly, and Steven Baldelli

The authors describe an efficient new sum frequency generation (SFG) imaging system using the compressive sensing sampling technique, which enables the use of a “single pixel detector” such as a photomultiplier tube or a photodiode instead of charge-coupled device cameras or complementary metal-oxide-semiconductor chips. SFG images of a gold pattern on silicon wafer were successfully acquired and reconstructed.

J. Chem. Phys. 135, 194202 (2011) | Read the press release

Micro-imaging of transient guest profiles in nanochannels
F. Hibbe, V. R. R. Marthala, C. Chmelik, J. Weitkamp, and J. Kärger

Researchers conducted micro-imaging experiments on the diffusion of methanol through the nano-sized pores of a synthetic mineral called ferrierite. The pore space of ferrierite consists of two mutually intersecting sets of parallel channels formed by rings of 10 oxygens and silicons and 8 oxygens and silicons, respectively. Curiously, the researchers found that methanol diffused 1,000 times faster through the 10-ring than through the 8-ring channels.

J. Chem. Phys. 135, 184201 (2011) | Read the press release

Nuclear magnetic relaxation in water revisited
Stefan Hartwig, Jens Voigt, Hans-Jürgen Scheer, Hans-Helge Albrecht, Martin Burghoff, and Lutz Trahms

Superconducting quantum interference device (SQUID)-based ultra-low field nuclear magnetic resonance (NMR) offers promise in biomedical imaging and in identifying the signature of explosives in cases, among other uses. The presence of additional relaxation mechanisms in aqueous systems in the low field range enables the utilization of contrasts in magnetic resonance images that are missed by conventional high field MRI. To better understand these mechanisms, this study evaluates nuclear magnetic relaxation in water.

J. Chem. Phys. 135, 054201 (2011)

Mapping the spatial overlap of excitons in a photosynthetic complex via coherent nonlinear frequency
Jahan M. Dawlaty, Doran I. G. Bennett, Vanessa M. Huxter, and Graham R. Fleming

A new nonlinear spectroscopic method is used to analyze electronic coupling—specifically, exciton–exciton interactions—between pigments in the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex (PPC). This protein complex is a light-harvesting assembly found in green sulfur bacteria. The wavefunctions of such two-exciton states contain information about the spatial overlap of single excitons and can be helpful in identifying coupling strengths and the structural connectivity of pigments.

J. Chem. Phys. 135, 044201 (2011)

Laser-induced fluorescence studies of HfF⁺ produced by autoionization
Huanqian Loh, Jia Wang, Matt Grau, Tyler S. Yahn, Robert W. Field, Chris H. Greene, and Eric A. Cornell

Trapped HfF⁺ has been identified as a promising candidate for testing fundamental symmetries and extensions to the standard model through an electron electric dipole momemt (eEDM) search. Such a high-precision search requires a sufficient number of HfF⁺ ions of a single isotope to be prepared in a particular rovibronic, Zeeman sublevel. Preparation of these ions in particular states is an important but nontrivial task. Autoionization of Rydberg states of HfF, prepared using the optical-optical double resonance technique, holds promise for this task. The authors characterize a vibronic band of Rydberg HfF above the lowest ionization threshold and directly probe the resultant ions by laser-induced fluorescence. The Rydberg HfF molecules show a propensity to decay into only a few ion rotational states of a given parity. This approach has promise for creating 30% of the total ion yield in the required state.

J. Chem. Phys. 135, 154308 (2011)

Theoretical studies of the tunneling splitting of Malonaldehyde using the multiconfiguration time-dependent Hartree approach
Markus Schröder, Fabien Gatti, and Hans-Dieter Meyer

The authors perform calculations of the full-dimensional symmetric and antisymmetric vibrational ground states of malonaldehyde—a prototype molecule to study intra-molecular proton transfer processes that play an important role in many reactions of biological interest—to obtain the tunneling splitting of the proton transfer. The results of these numerical studies are compared with experimental values.

J. Chem. Phys. 134, 234307 (2011)

Designing organic spin filters in the coherent tunneling regime
Carmen Herrmann, Gemma C. Solomon, and Mark A. Ratner

The researchers study which features of an electronic structure make an organic radical based on substituted benzene a good spin filter—a system that preferentially transports electrons of a certain spin orientation, which is important for spintronic schemes and in chemical and biological instances of spin-selective electronic communication—for coherent electron transport. They find that delocalization of the singly occupied molecular orbital and the spin density onto the benzene ring connected to the electrodes is a good indicator of spin filtering functionality.

J. Chem. Phys. 134, 224306 (2011)

All-boron analogues of aromatic hydrocarbons: B₁₇⁻ and B₁₈⁻
Alina P. Sergeeva, Boris Averkiev, Hua-Jin Zhai, Alexander Boldyrev, and Lai-Sheng Wang

Because of its electron deficiency, boron forms interesting crystal structures dominated by cage-like structural units. Using photoelectron spectroscopy and ab initio calculations, the researchers have investigated the structural and electronic properties and chemical bonding of the B₁₇⁻ and B₁₈⁻ clusters and find that B₁₇⁻ can be viewed as an all-boron analogue of naphthalene and that the quasi-planarity of the two structures of the B₁₈⁻ cluster is due to the reduced size of the outer rings. The current work extends the concept of all-boron analogues of hydrocarbons.

J. Chem. Phys. 134, 224304 (2011)

Control of nitromethane photoionization efficiency with shaped femtosecond pulses
Jonathan Roslund, Ofer Shir, Arthur Dogariu, Richard Miles, and Herschel Rabitz

Pulses of near-infrared, femtosecond radiation were optimally shaped to selectively increase the photoionization cross section of nitromethane gas—a model for energetic molecules that rapidly dissociate upon photoirradiation—by controlling dynamic, intermediate molecular resonances. Such effective control demonstrates the ability of optical dynamic discrimination techniques to detect target molecules masked by structurally or spectroscopically similar agents.

J. Chem. Phys. 134, 154301 (2011)

A quantum defect model for the s, p, d, and f Rydberg series of CaF
Jeffrey J. Kay, Stephen L. Coy, Bryan M. Wong, Christian Jungen, and Robert W. Field

Calcium fluoride (CaF) is an unusually simple molecule, combining the electronic simplicity of an alkali atom with the structural simplicity of a diatomic molecule. Nearly all of its electronic states are Rydberg states. This paper presents an improved quantum defect theory model for the “s,” “p,” “d,” and “f” Rydberg series for CaF that accounts for the rovibronic energy level structure and nearly all dynamical processes—a level of spectroscopic characterization similar to that of NO and H₂.

J. Chem. Phys. 134, 114313 (2011)

Rotationally correlated reactivity in the CH (v = 0, J, F_i) + O₂ →　OH (A) + CO reaction
H. Ohoyama, K. Yamakawa, R. Oda, Y. Nagamachi, and T. Kasai

The role of molecular rotation on reaction dynamics has rarely been studied experimentally. This paper uses an electrostatic hexapole field to evaluate the reaction of CH (v = 0, J, F_i) + O₂ at different O₂ beam conditions. Significant effects of O₂ rotation on the rotational-state-selected reactive cross sections were observed and support a theoretically predicted reaction mechanism wherein the first step is an intermediate formation with no energy barrier, in which the C-atom of a CH molecule attacks one O atom of an O₂ molecule at a sideways configuration.

J. Chem. Phys. 134, 114306 (2011)

Photodissociation dynamics of H₂O: Effect of unstable resonances on the ¹A₁ electronic state
Yuan Cheng, Kaijun Yuan, Lina Cheng, Qing Guo, Dongxu Dai, and Xueming Yang

Photodissociation of the water molecule is an important process in the upper atmosphere and interstellar chemistry. This paper investigates the photodissociation dynamics of H₂O via different unstable resonances using the high-resolution H-atom Rydberg tagging technique and provides a fully quantum-state-resolved dynamical picture of H₂O photodissociation via different unstable resonances on the ¹A₁ electronic state.

J. Chem. Phys. 134, 064301 (2011)

Manifestations of probe presence on probe dynamics in supercooled liquids
Stephan A. Mackowiak, Jade M. Noble, and Laura J. Kaufman

Supercooled liquids often display apparent hydrodynamic behavior in a number of different experiments. Using molecular dynamics simulations, the authors show that the presence of a solute probe can lead to enhanced solvent dynamics, while the motion of the probe is simultaneously slowed — an unexpected and counterintuitive observation.

J. Chem. Phys. 135, 214503 (2011)

Influence of temperature on thymine-to-solvent vibrational energy transfer
Brantley A. West, Jordan M. Womick, and Andrew M. Moran

Many biological processes are initiated by energy exchange between solute molecules—such as DNA—and the environment. Electronic excited states in DNA bases are deactivated by internal conversion (IC) followed by vibrational cooling, which inhibits the formation of biologically damaging lesions. In this paper, the authors find that thymine undergoes vibrational cooling at a rate that is insensitive to temperature variation from 100 K to 300 K in a mixture of methanol and water, and evaluate three possible explanations.

J. Chem. Phys. 135, 114505 (2011)

Resolving the controversy on the glass transition temperature of water?
S. Capaccioli and K. L. Ngai

Ordinary water or ice can be transformed by rapid cooling or compression into a material with the transparency, brittleness, hardness, and luster of glass and a random, disorganized molecular structure. This paper presents a detailed study—including the dynamics of water and the glass transition temperature—to determine the exact temperature at which water acquires glass-like properties: 136 Kelvin (-137 degrees Celsius).

J. Chem. Phys. 135, 104504 (2011 ) | Press Release

Quantum-classical simulation of electron localization in negatively charged methanol clusters
Letif Mones, Peter J. Rossky, and László Turi

The authors have performed mixed quantum-classical molecular dynamics simulations to investigate the energetic, structural, dynamic, and spectroscopic properties of methanol cluster anions following electron attachment to neutral clusters and found that smaller clusters (n ≤ 85) stabilize the excess electrons in a weakly bound, highly diffuse, surface-bound state, whereas with larger-size clusters (205 ≤ n), excess electrons diffuse into the interior on a sub-nanosecond time scale.

J. Chem. Phys. 135, 084501 (2011)

Dynamics of self-propelled nanomotors in chemically active media
Snigdha Thakur and Raymond Kapral

Synthetic chemically powered nano-sized motors—similar in size and moving at speeds similar to those of the biological motors that perform a variety of tasks in cells—have been fabricated and may be useful for the active transport of materials. Most of these self-propelled nanomotors do not carry their own fuel but are powered by the medium in which they move. This paper discusses how the propulsion properties of these nanomotors may be affected by a medium that is chemically active.

J. Chem. Phys. 135, 024509 (2011 )

Vibrationally quantum-state-specific dynamics of the reactions of CN radicals with organic molecules in solution
Rebecca A. Rose, Stuart J. Greaves, Thomas A. A. Oliver, Ian P. Clark, Gregory M. Greetham, Anthony W. Parker, Michael Towrie, and Andrew J. Orr-Ewing

To reveal how reaction dynamics change as a result of solvent interactions, the authors use ultrafast laser pump-probe methods with broadband infrared spectroscopy in a detailed study of the dynamics of reactions between CN radicals and small organic molecules in solutions of chloroform and dichloromethane and their deuterated variants. The data show that the dynamics of CN radical reactions with organic molecules in the chlorinated solvents retain the features of these reactions under single-collision conditions in the gas phase.

J. Chem. Phys. 134, 244503 (2011)

A powerful computational crystallography method to study ice polymorphism
M. Cogoni, B. D'Aguanno, L. N. Kuleshova, and D. W. M. Hofmann

Classical molecular dynamics simulations are used to investigate the structural properties of ice crystals under several temperature and pressure conditions. The study demonstrates the ability of the interaction potential model to estimate the relative stability of the 16 known crystal structures and to simulate the temperature and pressure dependence of static properties of ice crystals, such as structure, proton order-disorder relations, and phase stability.

J. Chem. Phys. 134, 204506 (2011)

Quantum process tomography of excitonic dimers from two-dimensional electronic spectroscopy I: General theory and application to homodimers
Joel Yuen-Zhou and Alán Aspuru-Guzik

The authors develop a model system—a coupled dimer—that allows the time-evolving quantum state of a multichromophoric system to be inferred from a sequence of two-dimensional electronic spectra as a function of waiting time. The work provides a quantum information processing (QIP) approach to spectroscopic experiments of excitonic systems, thus bridging the gap between the quantum information processing approach to study energy transport and the experimental techniques used to probe such systems in the chemical physics community.

J. Chem. Phys. 134, 134505 (2011)

The large quadrupole of water molecules
Shuqiang Niu, Ming-Liang Tan, and Toshiko Ichiye

The unique properties of water as a pure liquid and as a solvent derive from its hydrogen-bonded structure and the attraction between partially positive hydrogen and electronegative oxygen atoms. This paper investigates how multipole moments and electrostatic potentials from multisite models and moment expansions compare with results from quantum mechanical QM and QM/molecular mechanical (QM/MM) calculations of water molecules. The physical origin of the large quadrupole moment of water and factors producing the octupole moments are investigated using a cluster consisting of one QM and four hydrogen-bonded neighboring classical water molecules.

J. Chem. Phys. 134, 134501 (2011)

Ultrafast electrocyclic ring-opening of 7-dehydrocholesterol in solution: The influence of solvent on excited state dynamics
Kuo-Chun Tang, Aaron Rury, Michael B. Orozco, Joshua Egendorf, Kenneth G. Spears, and Roseanne J. Sension

Photochemical isomerization reactions of simple polyene chromophores, such as 7-dehydrocholesterol (provitamin D3, DHC), play a key role in the function of many important biological systems, and optical control of these chromophores could allow for synthetic constructs that operate as light-activated switches. The authors use femtosecond transient absorption experiments to study the excited electronic state properties of DHC and how its dynamics are influenced by the solvent environment.

J. Chem. Phys. 134, 104503 (2011)

Hot hole-induced dissociation of NO dimers on a copper surface
Natalia García Rey and Heike Arnolds

The first detailed reflection-absorption infrared spectroscopy study of the photochemistry of nitric oxide (NO) on the copper (110) face in the ultraviolet–visible range shows that the NO dimer, which is asymmetrically bound to the surface, is the only photoactive species of NO. The photoreaction mechanism is most likely the removal of an electron from the N–N bond (a.k.a., hot hole attachment).

J. Chem. Phys. 135, 224708 (2011)

Alignment dependent chemisorption of vibrationally excited CH₄(ν₃) on Ni(100), Ni(110), and Ni(111)
Bruce L. Yoder, Régis Bisson, P. Morten Hundt, and Rainer D. Beck

This stereodynamics study of the dissociative chemisorption of vibrationally excited methane on three different planes of a nickel single crystal surface—a model system for the reactive collisions of gas phase molecules with solid surfaces, which are fundamental to fuel production, industrial chemical reactions, and other processes—finds that methane dissociation depends on many parameters of the molecule/surface encounter.

J. Chem. Phys. 135, 224703 (2011)

Structure and dynamics of water confined in silica nanopores
Anatoli A. Milischuk and Branka M. Ladanyi

Porous silica glass is used widely to analyze the nanoconfinement of fluid, which is relevant to studies of the permeability of ion channels, transport through porous rocks and nanofluidic devices, and more. The paper evaluates the effects of confinement size and geometry on the mobility of water molecules at full hydration in approximately cylindrical silica nanopores ranging from 20 Å to 40 Å and shows that water forms two distinct molecular layers at the interface and exhibits uniform density in the core region.

J. Chem. Phys. 135, 174709 (2011)

The dissociative chemisorption of methane on Ni(100): Reaction path description of mode-selective chemistry
Bret Jackson and Sven Nave

Commercial sources of molecular hydrogen come mainly from the reaction of methane and water over a nickel (Ni) catalyst, with the dissociative chemisorption of methane on Ni serving as the rate-limiting step. The authors evaluate the dissociative sticking and vibrationally inelastic scattering of methane from a Ni(100) surface with a model that includes all 15 molecular degrees of freedom within the harmonic approximation and show that the ν₁ vibration is most efficient at promoting the reaction.

J. Chem. Phys. 135, 114701 (2011)

Hybrid density functional theory band structure engineering in hematite
Zachary D. Pozun and Graeme Henkelman

Hematite is a highly attractive material for solar cell applications because of its relatively low cost, ease of synthesis, and band gap, but its computational study is challenging. The authors show that hybrid density functionals can accurately predict the material, electronic, and optical properties of pure hematite, α-Fe₂O₃, and that a hybrid functional with 12% exact exchange accurately reproduces the experimental band gap and other material properties.

J. Chem. Phys. 134, 224706 (2011)

Structural and electronic properties of ZrX₂ and HfX₂ (X=S, and Se) from first principles calculations
Hong Jiang

The members of the ZrS₂ family of simple transition metal dichalcogenides (TMDC) materials are semiconductors with band gaps falling in the infrared to visible light range, making them promising candidates for third-generation solar cells. Using a first principles approach, the paper characterizes the structural and electronic properties of these materials. Their calculated band gaps show the materials have much promise for use in photovoltaic solar cells, although two, ZrS₂ and HfS₂ , cannot be used for water splitting.

J. Chem. Phys. 134, 204705 (2011)

Indications of field-directing and self-templating effects on the formation of organic lines on silicon
Janik Zikovsky, Stanislav A. Dogel, Mark H. Salomons, Jason L. Pitters, Gino A. DiLabio, and Robert A. Wolkow

The authors explore the possibility of using lithographically prepared, biased metal contacts on a silicon surface to generate an electric field that directs the orientation of nanostructures produced during the growth process. The formation of some nanostructures in a direction that was nearly perpendicular to the dimer rows was achieved, suggesting that it may be possible to produce this type of molecular pattern writer.

J. Chem. Phys. 134, 114707 (2011)

Effective potentials between nanoparticles in suspension
Gary S. Grest, Qifei Wang, Pieter in't Veld, and David J. Keffer

Molecular dynamics simulations are used to model the relationship between a solvent and nanoparticles with diameters ranging from 10 to 25 times larger than that of solvent molecules that interact with the solvent to varying degrees. The authors find that as the strength of the interactions between nanoparticles and the solvent increases, a solvent layer forms around the nanoparticles, increasing their effective radii.

J. Chem. Phys. 134, 144902 (2011)

Mesophase formation in two-component cylindrical bottlebrush polymers
Igor Erukhimovich, Panagiotis E. Theodorakis, Wolfgang Paul, and Kurt Binder

Using two complementary theoretical methods, the researchers study the conditions under which temperature quenches in solutions of binary bottlebrush polymers—polymers in which two types of side chains (A,B) are grafted to a rigid backbone—lead to microphase separation, producing cylindrical brushes.

J. Chem. Phys. 134, 054906 (2011)

Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins
Ramachandran Gnanasekaran, Johnson K. Agbo, and David Leitner

The water surrounding or confined within protein molecules may help regulate chemical signaling, as is the case in the homodimeric hemoglobin molecule of the clam Scapharca inaequivalvis, which has two globular molecules connected by a network of water molecules. The authors calculate communication maps of energy transport in the molecular complex showing that water molecules are more than twice as thermally conductive as the proteins, indicating that a cluster of water molecules embedded in a biomolecule can be a conduit for efficient energy transport.

J. Chem. Phys. 135, 065103 (2011)

Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore
Suresh Alapati, Dolfred Vijay Fernandes, and Yong Kweon Suh

Nano-pore sequencing—in which the properties of a biomolecule are evaluated as it is electrophoretically driven from one side of the nano-pore to the other—offers a promising new way to characterize molecules such as DNA, but the dynamics of the process are not well understood. This numerical study of biopolymer translocation from the cis to the trans side of a membrane through a synthetic nano-pore shows that translocation speed mainly depends upon the applied potential difference.

J. Chem. Phys. 135, 055103 (2011)

Simulations of the confinement of ubiquitin in self-assembled reverse micelles
Jianhui Tian and Angel E. García

Using molecular dynamics simulations, the authors studied the confinement of the protein ubiquitin in reverse micelles—self-assembling structures that can encapsulate biomolecules in water within their interiors, mimicking the effects of cellular crowding—and found that confinement can result in altered protein dynamics due to the interactions between the protein and the surfactant.

J. Chem. Phys. 134, 225101 (2011)

Anomalous diffusion of oligomerized transmembrane proteins
Ulrich Schmidt and Matthias Weiss

Using coarse-grained simulations of membranes, the authors show that the short periods of anomalous diffusion (a.k.a., subdiffusion) frequently observed on biomembranes and in complex fluids are caused by the dynamic and transient formation of flexible polymers—or oligomers—from transmembrane proteins during protein sorting and signaling events.

J. Chem. Phys. 134, 165101 (2011)

Power-law dependence of the thermal melting temperature of ubiquitin on the volume fraction of macromolecular crowders
Matthias M. Waegele and Feng Gai

The normally congested conditions within cells can be mimicked using macromolecular crowding agents such as the polysaccharide dextran, but those agents may have their own effect on cellular conditions. This paper quantitatively examines the influence of different volume fractions of several crowding agents on the melting temperature of the protein ubiquitin and compares it to that predicted (not always accurately, it turns out) in a theoretical crowding model.

J. Chem. Phys. 134, 095104 (2011)

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: A case study of polymer cyclization
Ryan R. Cheng and Dmitrii E. Makarov

The authors have used simple one-dimensional models—including the Smoluchowski model, which describes a particle undergoing Brownian motion—to model the closure of a loop in a long polymer chain (an elementary step in the protein folding process). Although the Smoluchowski model, the paper reports, can successfully simulate the rate of this closure, it “fails rather dramatically” to describe just how long the process takes.

J. Chem. Phys. 134, 085104 (2011)