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28 Nov 2011

Volume 135, Issue 20, Articles (20xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 204501 (2011); http://dx.doi.org/10.1063/1.3658855 (5 pages)

Orsika Miholics, Tamás Rica, Dezső Horváth, and Ágota Tóth
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Communication: Partial linearized density matrix dynamics for dissipative, non-adiabatic quantum evolution

Pengfei Huo and David F. Coker

J. Chem. Phys. 135, 201101 (2011); http://dx.doi.org/10.1063/1.3664763 (4 pages) | Cited 3 times

Online Publication Date: 23 November 2011

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An approach for treating dissipative, non-adiabatic quantum dynamics in general model systems at finite temperature based on linearizing the density matrix evolution in the forward-backward path difference for the environment degrees of freedom is presented. We demonstrate that the approach can capture both short time coherent quantum dynamics and long time thermal equilibration in an application to excitation energy transfer in a model photosynthetic light harvesting complex. Results are also presented for some nonadiabatic scattering models which indicate that, even though the method is based on a “mean trajectory” like scheme, it can accurately capture electronic population branching through multiple avoided crossing regions and that the approach offers a robust and reliable way to treat quantum dynamical phenomena in a wide range of condensed phase applications.
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82.50.-m Photochemistry
82.20.Fd Collision theories; trajectory models
82.20.Gk Electronically non-adiabatic reactions
82.20.Rp State to state energy transfer
33.80.Be Level crossing and optical pumping
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Communication: Length scale dependent oil-water energy fluctuations

Robin Underwood and Dor Ben-Amotz

J. Chem. Phys. 135, 201102 (2011); http://dx.doi.org/10.1063/1.3664604 (4 pages) | Cited 1 time

Online Publication Date: 23 November 2011

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Interfacial fluctuations in the cohesive (van der Waals) interaction energy of spherical oil-drops with water provide evidence of a length scale dependent transition from linear to non-linear response behavior. For sub-nanometer oil-drop sizes, energy fluctuations are found to be independent of the van der Waals coupling strength, while nanometer (and larger) size oil drops experience highly non-linear energy fluctuations. The latter behavior is linked to enhanced hydrophobic density fluctuations and the emergence of entropic contributions to oil-water cohesive interaction free energies.
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68.08.Bc Wetting
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Communication: Superatom molecular orbitals: New types of long-lived electronic states

Y. Pavlyukh and J. Berakdar

J. Chem. Phys. 135, 201103 (2011); http://dx.doi.org/10.1063/1.3665089 (3 pages)

Online Publication Date: 28 November 2011

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We present ab initio calculations of the quasiparticle decay times in a Buckminsterfullerene based on the many-body perturbation theory. A particularly lucid representation arises when the broadening of the quasiparticle states is plotted in the angular momentum (ℓ) and energy (ɛ) coordinates. In this representation the main spectroscopic features of the fullerene consist of two occupied nearly parabolic bands, and delocalized plane-wave-like unoccupied states with a few long-lived electronic states (the superatom molecular orbitals, SAMOs) embedded in the continuum of Fermi-liquid states. SAMOs have been recently uncovered experimentally by Feng et al. [Science 320, 359 (2008)10.1126/science.1155866] using scanning tunneling spectroscopy. The present calculations offer an explanation of their unusual stability and unveil their long-lived nature making them good candidates for applications in the molecular electronics. From the fundamental point of view these states illustrate a concept of the Fock-space localization [B. L. Altshuler, Y. Gefen, A. Kamenev, and L. S. Levitov, Phys. Rev. Lett. 78, 2803 (1997)10.1103/PhysRevLett.78.2803] with properties drastically different from the Fermi-liquid excitations.
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71.20.Tx Fullerenes and related materials; intercalation compounds
71.10.Ay Fermi-liquid theory and other phenomenological models
61.48.-c Structure of fullerenes and related hollow and planar molecular structures
71.15.-m Methods of electronic structure calculations
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Communication: Time-domain measurement of high-pressure N2 and O2 self-broadened linewidths using hybrid femtosecond/picosecond coherent anti-Stokes Raman scattering

Joseph D. Miller, Sukesh Roy, James R. Gord, and Terrence R. Meyer

J. Chem. Phys. 135, 201104 (2011); http://dx.doi.org/10.1063/1.3665932 (4 pages)

Online Publication Date: 28 November 2011

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The direct measurement of self-broadened linewidths using the time decay of pure-rotational hybrid femtosecond/picosecond coherent anti-Stokes Raman scattering (fs/ps RCARS) signals is demonstrated in gas-phase N2 and O2 from 1–20 atm. Using fs pump and Stokes pulses and a spectrally narrowed ps probe pulse, collisional dephasing rates with time constants as short as 2.5 ps are captured with high accuracy for individual rotational transitions. S-branch linewidths of N2 and O2 from ∼0.06 to 2.2 cm−1 and the line separation of O2 triplet states are obtained from the measured dephasing rates and compared with high-resolution, frequency-domain measurements and S-branch approximations using the modified exponential gap model. The accuracy of the current measurements suggests that the fs/ps RCARS approach is well suited for tracking the collisional dynamics of gas-phase mixtures over a wide range of pressures.
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33.70.Jg Line and band widths, shapes, and shifts
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.15.Mt Rotation, vibration, and vibration-rotation constants
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back to top Theoretical Methods and Algorithms

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

Xiongwu Wu and Bernard R. Brooks

J. Chem. Phys. 135, 204101 (2011); http://dx.doi.org/10.1063/1.3662489 (15 pages)

Online Publication Date: 23 November 2011

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The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space.
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87.15.H- Dynamics of biomolecules
36.20.Hb Configuration (bonds, dimensions)
87.10.Tf Molecular dynamics simulation
87.14.E- Proteins
87.15.ap Molecular dynamics simulation

Collapse transition of a square-lattice polymer with next nearest-neighbor interaction

Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee

J. Chem. Phys. 135, 204102 (2011); http://dx.doi.org/10.1063/1.3663712 (4 pages)

Online Publication Date: 28 November 2011

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We study the collapse transition of a polymer on a square lattice with both nearest-neighbor and next nearest-neighbor interactions, by calculating the exact partition function zeros up to chain length 36. The transition behavior is much more pronounced than that of the model with nearest-neighbor interactions only. The crossover exponent and the transition temperature are estimated from the scaling behavior of the first zeros with increasing chain length. The results suggest that the model is of the same universality class as the usual θ point described by the model with only nearest-neighbor interaction.
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64.60.F- Equilibrium properties near critical points, critical exponents
82.35.Jk Copolymers, phase transitions, structure
82.35.Lr Physical properties of polymers
61.41.+e Polymers, elastomers, and plastics

Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory

Nicholas D. M. Hine, Jacek Dziedzic, Peter D. Haynes, and Chris-Kriton Skylaris

J. Chem. Phys. 135, 204103 (2011); http://dx.doi.org/10.1063/1.3662863 (17 pages) | Cited 1 time

Online Publication Date: 29 November 2011

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We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such cases the effects of PBCs on the calculations need to be avoided, so that the results obtained represent the open rather than the periodic boundary. The very large systems encountered in LS-DFT make the demands of the supercell approximation for isolated systems more difficult to manage, and we show cases where the open boundary (infinite cell) result cannot be obtained from extrapolation of calculations from periodic cells of increasing size. We discuss, implement, and test three very different approaches for overcoming or circumventing the effects of PBCs: truncation of the Coulomb interaction combined with padding of the simulation cell, approaches based on the minimum image convention, and the explicit use of open boundary conditions (OBCs). We have implemented these approaches in the ONETEP LS-DFT program and applied them to a range of systems, including a polar nanorod and a protein. We compare their accuracy, complexity, and rate of convergence with simulation cell size. We demonstrate that corrective approaches within PBCs can achieve the OBC result more efficiently and accurately than pure OBC approaches.
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31.15.E- Density-functional theory
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Variational solution of the three-dimensional Schrödinger equation using plane waves in adaptive coordinates

José M. Pérez-Jordá

J. Chem. Phys. 135, 204104 (2011); http://dx.doi.org/10.1063/1.3663278 (7 pages)

Online Publication Date: 29 November 2011

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A series of improvements for the solution of the three-dimensional Schrödinger equation over a method introduced by Gygi [F. Gygi, Europhys. Lett. 19, 617 (1992)10.1209/0295-5075/19/7/009; F. Gygi, Phys. Rev. B 48, 11692 (1993)10.1103/PhysRevB.48.11692] are presented. As in the original Gygi's method, the solution (orbital) is expressed by means of plane waves in adaptive coordinates u, where u is mapped from Cartesian coordinates, u = f(r). The improvements implemented are threefold. First, maps are introduced that allow the application of the method to atoms and molecules without the assistance of the supercell approximation. Second, the electron-nucleus singularities are exactly removed, so that pseudo-potentials are no longer required. Third, the sampling error during integral evaluation is made negligible, which results in a true variational, second-order energy error procedure. The method is tested on the hydrogen atom (ground and excited states) and the H2+ molecule, resulting in milli-Hartree accuracy with a moderate number of plane waves.
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31.15.xt Variational techniques
31.15.B- Approximate calculations

Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms

Martin Lísal, John K. Brennan, and Josep Bonet Avalos

J. Chem. Phys. 135, 204105 (2011); http://dx.doi.org/10.1063/1.3660209 (18 pages)

Online Publication Date: 29 November 2011

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Numerical integration schemes based upon the Shardlow-splitting algorithm (SSA) are presented for dissipative particle dynamics (DPD) approaches at various fixed conditions, including a constant-enthalpy (DPD-H) method that is developed by combining the equations-of-motion for a barostat with the equations-of-motion for the constant-energy (DPD-E) method. The DPD-H variant is developed for both a deterministic (Hoover) and stochastic (Langevin) barostat, where a barostat temperature is defined to satisfy the fluctuation-dissipation theorem for the Langevin barostat. For each variant, the Shardlow-splitting algorithm is formulated for both a velocity-Verlet scheme and an implicit scheme, where the velocity-Verlet scheme consistently performed better. The application of the Shardlow-splitting algorithm is particularly critical for the DPD-E and DPD-H variants, since it allows more temporally practical simulations to be carried out. The equivalence of the DPD variants is verified using both a standard DPD fluid model and a coarse-grain solid model. For both models, the DPD-E and DPD-H variants are further verified by instantaneously heating a slab of particles in the simulation cell, and subsequent monitoring of the evolution of the corresponding thermodynamic variables as the system approaches an equilibrated state while maintaining their respective constant-energy and constant-enthalpy conditions. The original SSA formulated for systems of equal-mass particles has been extended to systems of unequal-mass particles. The Fokker-Planck equation and derivations of the fluctuation-dissipation theorem for each DPD variant are also included for completeness.
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05.70.Ce Thermodynamic functions and equations of state
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.30.-f Function theory, analysis
02.60.Jh Numerical differentiation and integration
02.30.Cj Measure and integration

A method for analyzing the vibrational energy flow in biomolecules in solution

Miguel Angel Soler, Adolfo Bastida, Marwa H. Farag, José Zúñiga, and Alberto Requena

J. Chem. Phys. 135, 204106 (2011); http://dx.doi.org/10.1063/1.3663707 (8 pages)

Online Publication Date: 30 November 2011

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A method is proposed to analyze the intra- and intermolecular vibrational energy flow occurring in biomolecules in solution during relaxation processes. It is based on the assumption that the total energy exchanged between the vibrational modes is minimal and the global process is essentially statistical. This statistical minimum flow method is shown to provide very useful information about the amount and the rate at which energy is transferred between the individual vibrations of the molecule. To demonstrate the performance of the method, an application is made to the relaxation of the amide I mode of N-methylacetamide-d in aqueous D2O solution which yields a detailed quantitative description of the process.
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87.15.N- Properties of solutions of macromolecules
87.15.La Mechanical properties
87.14.-g Biomolecules: types
36.20.Ey Conformation (statistics and dynamics)
87.15.H- Dynamics of biomolecules

Long-range corrected hybrid functionals for π-conjugated systems: Dependence of the range-separation parameter on conjugation length

Thomas Körzdörfer, John S. Sears, Christopher Sutton, and Jean-Luc Brédas

J. Chem. Phys. 135, 204107 (2011); http://dx.doi.org/10.1063/1.3663856 (6 pages)

Online Publication Date: 30 November 2011

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Long-range corrected (range-separated hybrid) functionals represent a relatively new class of functionals for generalized Kohn-Sham theory that have proven to be very successful, for instance, when it comes to predicting ionization potentials and energy gaps for a wide range of molecules and solids. The results obtained from long-range corrected density functional theory approaches can be improved dramatically, if the range-separation parameter (ω) is optimized for each system separately. In this work, we have optimized ω for a series of π-conjugated molecular systems of increasing length by forcing the resulting functionals to obey the ionization potential-theorem, i.e., that their highest occupied eigenvalue be equal to the ΔSCF ionization potential. The optimized ω values are observed to vary substantially from their default values for the functionals. For highly conjugated chains such as oligoacenes and polyenes, we find that the characteristic length scale of the range-separation, i.e., 1/ω, grows almost linearly with the number of repeat units, for saturated alkane chains, however, 1/ω quickly saturates after 5-6 repeat units. For oligothiophenes, we find that 1/ω grows linearly for the shorter oligomers but then saturates at around 10 repeat units. Our results point to a close relation between the optimal range-separation parameter and the degree of conjugation in the system.
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31.15.E- Density-functional theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.xr Self-consistent-field methods
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photoelectron spectroscopic study of iron-pyrene cluster anions

Xiang Li, Kit H. Bowen, Jr., Puru Jena, and Anil K. Kandalam

J. Chem. Phys. 135, 204301 (2011); http://dx.doi.org/10.1063/1.3661984 (9 pages)

Online Publication Date: 22 November 2011

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Iron-pyrene cluster anions, [Fem(pyrene)n]− (m = 1–2, n = 1–2) were studied in the gas phase by photoelectron spectroscopy, resulting in the determination of their electron affinity and vertical detachment energy values. Density functional theory calculations were also conducted, providing the structures and spin multiplicities of the neutral clusters and their anions as well as their respective electron affinity and vertical detachment energy values. The calculated magnetic moments of neutral Fe1(pyrene)1 and Fe2(pyrene)1 clusters suggest that a single pyrene molecule could be a suitable template on which to deposit small iron clusters, and that these in turn might form the basis of an iron cluster-based magnetic material. A comparison of the structures and corresponding photoelectron spectra for the iron-benzene, iron-pyrene, and iron-coronene cluster systems revealed that pyrene behaves more similarly to coronene than to benzene.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.E- Density-functional theory
33.60.+q Photoelectron spectra
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Extracting elements of molecular structure from the all-particle wave function

Edit Mátyus, Jürg Hutter, Ulrich Müller-Herold, and Markus Reiher

J. Chem. Phys. 135, 204302 (2011); http://dx.doi.org/10.1063/1.3662487 (12 pages)

Online Publication Date: 23 November 2011

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Structural information is extracted from the all-particle (non-Born–Oppenheimer) wave function by calculating radial and angular densities derived from n-particle densities. As a result, one- and two-dimensional motifs of classical molecular structure can be recognized in quantum mechanics. Numerical examples are presented for three- (H−, Ps−, H2+), four- (Ps2, H2), and five-particle (H2D+) systems.
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31.15.xt Variational techniques
03.65.Ge Solutions of wave equations: bound states
33.15.Bh General molecular conformation and symmetry; stereochemistry
36.10.Dr Positronium

Laser induced and controlled chemical reaction of carbon monoxide and hydrogen

Anton du Plessis, Christien A. Strydom, Hermann Uys, and Lourens R. Botha

J. Chem. Phys. 135, 204303 (2011); http://dx.doi.org/10.1063/1.3662129 (7 pages)

Online Publication Date: 23 November 2011

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Bimolecular chemical reaction control of gaseous CO and H2 at room temperature and atmospheric pressure, without any catalyst, using shaped femtosecond laser pulses is presented. High intensity laser radiation applied to a reaction cell facilitates non-resonant bond breakage and the formation of a range of ions, which can then react to form new products. Stable reaction products are measured after irradiation of a reaction cell, using time of flight mass spectroscopy. Bond formation of C–O, C–C, and C–H bonds is demonstrated as CO2+, C2H2+, CH+, and CH3+ were observed in the time of flight mass spectrum of the product gas, analyzed after irradiation. The formation of CO2 is shown to be dependent on laser intensity, irradiation time, and on the presence of H2 in the reaction cell. Using negatively chirped laser pulses more C–O bond formation takes place as compared to more C–C bond formation for unchirped pulses.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.80.Rt Time of flight mass spectrometry

Comparison and assessment of procedures for calculating the R(12) line strength of the ν1+ 2 ν2 + ν3 band of CO2

Gerd Wübbeler, Gerardo J. Padilla Víquez, Karl Jousten, Olav Werhahn, and Clemens Elster

J. Chem. Phys. 135, 204304 (2011); http://dx.doi.org/10.1063/1.3662134 (12 pages)

Online Publication Date: 28 November 2011

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Recently, results for the CO2 R(12) line strength parameter have been reported, which differ significantly and are inconsistent with respect to quoted uncertainties. We investigate to what extent this inconsistency might be caused by the chosen data analysis methods. To this end, we assess and compare a parametric fitting procedure and a non-parametric approach. We apply the methods to simulated and measured line spectra, and we specify the conditions required for the safe application of the two procedures. For our present data, the corresponding conditions are satisfied for both methods, and consistent results are obtained. However, the simulations reveal that the fitting procedure can show shortcomings when the uncertainty in the wavenumber is large.
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33.20.Vq Vibration-rotation analysis

Nanopolaritonics with a continuum of molecules: Simulations of molecular-induced selectivity in plasmonics transport through a continuous Y-shape

Daniel Neuhauser

J. Chem. Phys. 135, 204305 (2011); http://dx.doi.org/10.1063/1.3663279 (7 pages)

Online Publication Date: 29 November 2011

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Using the recent NF (near-field) formulation for electrodynamics on the nanoscale, we simulate transport in a Y-shape gold nanostructure in the presence of 2-level molecules. NF is shown to be easily integrated with the Liouville equation, producing a simple and efficient nanopolaritons (plasmons-excitons) solver, with a large time step. Two cases are considered: coating of the gold structure with molecular layers thinner than the structure, and filling space with aligned molecules. In both cases significant effects on the radiation transport are obtained even for low molecular densities. At low densities the effects are primarily an overall reduction of the plasmonics peak, but at higher densities there is a significant selectivity control by the molecules. A redshift is predicted, especially for the space-filling case. The combined nanopolariton shows qualitative hybridization, and the spectral peaks separate with increasing coupling, i.e., with increasing molecular densities. The results open the way to “control of light by light,” i.e., controlling plasmonic light transport by inducing a change in the direction of the guiding molecular dipoles through radiation or other means.
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42.79.-e Optical elements, devices, and systems
71.36.+c Polaritons (including photon-phonon and photon-magnon interactions)
73.20.Mf Collective excitations (including excitons, polarons, plasmons and other charge-density excitations)

The excitation function for Li + HF → LiF + H at collision energies below 80 meV

Rolf Bobbenkamp, Hansjürgen Loesch, Marcel Mudrich, and Frank Stienkemeier

J. Chem. Phys. 135, 204306 (2011); http://dx.doi.org/10.1063/1.3664303 (8 pages)

Online Publication Date: 30 November 2011

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We have measured the dependence of the relative integral cross section of the reaction Li + HF → LiF + H on the collision energy (excitation function) using crossed molecular beams. By varying the intersection angle of the beams from 37° to 90° we covered the energy range 25  meV ⩽ Etr ⩽ 131 meV. We observe a monotonous rise of the excitation function with decreasing energy over the entire energy range indicating that a possible translational energy threshold to the reaction is significantly smaller than 25 meV. The steep rise is quantitatively recovered by a Langevin-type excitation function based on a vanishing threshold and a mean interaction potential energy ∝R−2.5 where R is the distance between the reactants. To date all threshold energies deduced from ab initio potentials and zero-point vibrational energies are at variance with our results, however, our findings support recent quantum scattering calculations that predict significant product formation at collision energies far below these theoretical thresholds.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
31.15.E- Density-functional theory
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
34.50.Lf Chemical reactions

Photoelectron spectroscopy of HC4N−

Kristen M. Vogelhuber, Scott W. Wren, Christopher J. Shaffer, Robert J. McMahon, Anne B. McCoy, and W. Carl Lineberger

J. Chem. Phys. 135, 204307 (2011); http://dx.doi.org/10.1063/1.3663617 (9 pages)

Online Publication Date: 30 November 2011

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We report the 364-nm photoelectron spectrum of HC4N−. We observe electron photodetachment from the bent math2A″ state of HC4N− to both the near-linear math3A″ and the bent ã 1A′ states of neutral HC4N. We observe an extended, unresolved vibrational progression corresponding to math3A″ ← math2A″ photodetachment, and we measure the electron affinity (EA) of the math3A″ state of HC4N to be 2.05(8) eV. Photodetachment to the bent ã 1A′ state results in a single intense origin peak at a binding energy of 2.809(4) eV, from which we determine the singlet-triplet splitting (ΔEST) of HC4N: 0.76(8) eV. For comparison and to aid in the interpretation of the HC4N− spectrum, we also report the 364-nm photoelectron spectra of HCCN− and DCCN−. Improved signal-to-noise over the previous HCCN− and DCCN− photoelectron spectra allows for a more precise determination of the EAs and ΔESTs of HCCN and DCCN. The EAs of HCCN and DCCN are measured to be 2.001(15) eV and 1.998(15) eV, respectively; ΔEST(HCCN) is 0.510(15) eV and ΔEST(DCCN) is 0.508(15) eV. These results are discussed in the context of other organic carbene chains.
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33.60.+q Photoelectron spectra
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.20.Tp Vibrational analysis
33.80.Eh Autoionization, photoionization, and photodetachment

Electronic transitions of cobalt monoboride

Y. W. Ng, H. F. Pang, and A. S.-C. Cheung

J. Chem. Phys. 135, 204308 (2011); http://dx.doi.org/10.1063/1.3663619 (5 pages)

Online Publication Date: 30 November 2011

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Electronic transition spectrum of cobalt monoboride (CoB) in the visible region between 495 and 560 nm has been observed and analyzed using laser-induced fluorescence spectroscopy. CoB molecule was produced by the reaction of laser-ablated cobalt atom and diborane (B2H6) seeded in argon. Fifteen vibrational bands with resolved rotational structure have been recorded, which included transitions of both Co10B and Co11B isotopic species. Our analysis showed that the observed transition bands are ΔΩ = 0 transitions with Ω″ = 2 and Ω″ = 3 lower states. Four transition systems have been assigned, namely, the [18.1]3Π2–X3Δ2, the [18.3]3Φ3–X3Δ3, the [18.6]3– X3Δ3, and the [19.0]2–X3Δ2 systems. The bond length, ro, of the X 3Δ3 state of CoB is determined to be 1.705 Å. The observed rotational lines showed unresolved hyperfine structure arising from the nuclei, which conforms to the Hund's case (aβ) coupling scheme. This work represents the first experimental investigation of the CoB spectrum.
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33.20.Kf Visible spectra
33.50.Dq Fluorescence and phosphorescence spectra
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
33.15.Dj Interatomic distances and angles
36.20.Ng Vibrational and rotational structure, infrared and Raman spectra
33.15.Pw Fine and hyperfine structure
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Oscillatory and stationary convective patterns in a reaction driven gravity current

Orsika Miholics, Tamás Rica, Dezső Horváth, and Ágota Tóth

J. Chem. Phys. 135, 204501 (2011); http://dx.doi.org/10.1063/1.3658855 (5 pages)

Online Publication Date: 22 November 2011

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Horizontally propagating chemical fronts are studied in a thin solution layer of the acid-catalyzed chlorite-tetrathionate reaction. Unusual cellular patterns develop when significant amount of autocatalyst is bound to polyelectrolyte with low mobility: both oscillatory and stationary patterns evolve as a result of the interaction between the reaction front and the superposed gravity current. The concentration of the polyelectrolyte regulating the velocity of front propagation serves as a bifurcation parameter for switching between the two basic patterns.
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82.30.Vy Homogeneous catalysis in solution, polymers and zeolites
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.35.Rs Polyelectrolytes
47.20.Ky Nonlinearity, bifurcation, and symmetry breaking
47.55.P- Buoyancy-driven flows; convection

Two-dimensional infrared spectral signature and hydration of the oxalate dianion

Daniel G. Kuroda and Robin M. Hochstrasser

J. Chem. Phys. 135, 204502 (2011); http://dx.doi.org/10.1063/1.3658461 (12 pages)

Online Publication Date: 23 November 2011

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Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Two-dimensional infrared vibrational echo spectra and the vibrational dynamics obtained from them along with measurements of the anisotropy decay provide a picture in which the localization of the oxalate vibrational excitation onto the carboxylate groups occurs in ∼450 fs. Molecular dynamics simulations are used to characterize the vibrational dynamics in terms of dihedral angle motion between the two carboxylate planes and solvation dynamics. The localization of the oxalate vibrational excitation onto the carboxylates is induced by the fluctuations in the carboxylate vibrational frequencies which are shown by theory and experiment to have a similar correlation time as the anisotropy decay.
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33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
82.30.Nr Association, addition, insertion, cluster formation
31.15.xv Molecular dynamics and other numerical methods
33.15.Mt Rotation, vibration, and vibration-rotation constants

Semiclassical study of quantum coherence and isotope effects in ultrafast electron transfer reactions coupled to a proton and a phonon bath

Charulatha Venkataraman

J. Chem. Phys. 135, 204503 (2011); http://dx.doi.org/10.1063/1.3662095 (9 pages)

Online Publication Date: 23 November 2011

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The linearized semiclassical initial value representation is employed to describe ultrafast electron transfer processes coupled to a phonon bath and weakly coupled to a proton mode. The goal of our theoretical investigation is to understand the influence of the proton on the electronic dynamics in various bath relaxation regimes. More specifically, we study the impact of the proton on coherences and analyze if the coupling to the proton is revealed in the form of an isotope effect. This will be important in distinguishing reactions in which the proton does not undergo significant rearrangement from those in which the electron transfer is accompanied by proton transfer. Unlike other methodologies widely employed to describe nonadiabatic electron transfer, this approach treats the electronic and nuclear degrees of freedom consistently. However, due to the linearized approximation, quantum interference effects are not captured accurately. Our study shows that at small phonon bath reorganization energies, coherent oscillations and isotope effect are observed in both slow and fast bath regimes. The coherences are more substantially damped by deuterium in comparison to the proton. Further, in contrast to the dynamics of the spin-boson model, the coherences are not long-lived. At large bath reorganization energies, the decay is incoherent in the slow and fast bath regimes. In this case, the extent of the isotope effect depends on the relative relaxation timescales of the proton mode and the phonon bath. The isotope effect is magnified for baths that relax on picosecond timescales in contrast to baths that relax in femtoseconds.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
31.30.Gs Hyperfine interactions and isotope effects
82.20.Ln Semiclassical theory of reactions and/or energy transfer
82.20.Tr Kinetic isotope effects including muonium

Hydrogenation of fragment cations produced by femtosecond laser ablation of boron nitride

Tohru Kobayashi and Yukari Matsuo

J. Chem. Phys. 135, 204504 (2011); http://dx.doi.org/10.1063/1.3662138 (5 pages)

Online Publication Date: 23 November 2011

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Cations (positive ions) produced by laser ablation of boron nitride (BN) have been mass analyzed and the size-dependent hydrogenation reactivity is revealed for the first time. The main product cations determined by femtosecond laser ablation (fsLA) were a series of B(BN)n+, with much lesser production of B2(BN)k+ and N(BN)mO+ series cations. Least-squares fitting of the relative yields of hydrogenated cations indicates that the yield of B(BN)nH+ almost diminishes for n ≥ 5 and that of B(BN)nH2+ increases as n increases. Based on the different n-dependence and electronic structures of B(BN)n and B(BN)n+, B(BN)n is likely to be the precursor of B(BN)nH+, and B(BN)n+ that of B(BN)nH2+. In contrast to fsLA, the production of H+ by nanosecond laser ablation is not observed and the production of various cationic species makes it difficult to identify either the fragment species or their hydrogenated products. This observation highlights the significant efficiency of fsLA in producing H+ (and presumably H) from the surface adsorbates.
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81.05.Ea III-V semiconductors
81.65.-b Surface treatments
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
79.20.Eb Laser ablation
68.43.Mn Adsorption kinetics
71.20.Nr Semiconductor compounds

Confined linear molecules inside an aperiodic supramolecular crystal: The sequence of superspace phases in n-hexadecane/urea

M. Huard, B. Toudic, P. Rabiller, C. Ecolivet, L. Guérin, P. Bourges, T. Breczewski, and Mark D. Hollingsworth

J. Chem. Phys. 135, 204505 (2011); http://dx.doi.org/10.1063/1.3663711 (8 pages) | Cited 1 time

Online Publication Date: 29 November 2011

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High-resolution studies of the host-guest inclusion compound n-hexadecane/urea are reported at atmospheric pressure, using both cold neutrons and x-ray diffraction. This intergrowth crystal presents a misfit parameter, defined by the ratio ch/cg (chost/cguest), which is temperature independent and irrational (γ = 0.486 ± 0.002) from 300 to 30 K. Three different structural phases are reported for this aperiodic crystal over this temperature range. The crystallographic superspaces are of rank 4 in phases I and II, whereas phase III is associated with an increase in rank to 5, with a supplementary misfit parameter (δ = 0.058 ± 0.002) that is constant throughout this phase. The superspace group of phase I is hexagonal P6122(00γ) down to Tc1 = 149.5 ± 0.5 K; phase II, which persists down to Tc2 = 127.8 ± 0.5 K is orthorhombic P212121(00γ), and phase III is orthorhombic P212121(00γ)(00δ).
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61.66.Hq Organic compounds
81.10.Dn Growth from solutions
61.72.Qq Microscopic defects (voids, inclusions, etc.)

Charge ordering and intermediate range order in ammonium ionic liquids

Leonardo J. A. Siqueira and Mauro C. C. Ribeiro

J. Chem. Phys. 135, 204506 (2011); http://dx.doi.org/10.1063/1.3662062 (7 pages)

Online Publication Date: 29 November 2011

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Molecular dynamics simulations were performed for ionic liquids based on the bis(trifluoromethylsulfonyl)imide anion, [NTf2], and ammonium cations with increasing length of the alkyl chain and ether functionalized chain. The signature of charge ordering is a sharp peak in the charge–charge structure factor, Sqq(k), whose intensity is barely affected for longer carbon chain in tetraalkylammonium systems, but decreases in ether functionalized ionic liquids. The first sharp diffraction peak (FSDP) and the corresponding intermediate range order (IRO) are observed in the total S(k) of ionic liquids containing ammonium cations with relatively long chains. The intensity of the FSDP is lower in the total S(k) of the ether derivative in comparison with the tetraalkylammonium counterpart of the same chain length. It is shown that the nature of the IRO is structural heterogeneity of polar and non-polar domains, even though domains defined by chain interactions in the ether derivatives become more polar. Charge correlation in the ether derivative is modified because cations can be coordinated by oxygen atoms of the ether functionalized chain of neighboring cations.
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61.20.Ja Computer simulation of liquid structure
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