Volume 135, Issue 20, 28 November 2011

Horizontally propagating chemical fronts are studied in a thin solution layer of the acidcatalyzed chloritetetrathionate 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.
 ARTICLES

 Theoretical Methods and Algorithms

Forcemomentumbased selfguided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble
View Description Hide DescriptionThe selfguided Langevin dynamics (SGLD) is a method to accelerateconformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerateconformational 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 forcemomentumbased selfguided 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 momentumbased 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 accelerateconformational 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.

Collapse transition of a squarelattice polymer with next nearestneighbor interaction
View Description Hide DescriptionWe study the collapse transition of a polymer on a square lattice with both nearestneighbor and next nearestneighbor 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 nearestneighbor 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 nearestneighbor interaction.

Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linearscaling density functional theory
View Description Hide DescriptionWe 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 linearscaling (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 LSDFT 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 LSDFT 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.

Variational solution of the threedimensional Schrödinger equation using plane waves in adaptive coordinates
View Description Hide DescriptionA series of improvements for the solution of the threedimensional Schrödinger equation over a method introduced by Gygi [F. Gygi, Europhys. Lett.19, 617 (1992)10.1209/02955075/19/7/009; F. Gygi, Phys. Rev. B48, 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 , where is mapped from Cartesian coordinates, . 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 electronnucleus singularities are exactly removed, so that pseudopotentials are no longer required. Third, the sampling error during integral evaluation is made negligible, which results in a true variational, secondorder energy error procedure. The method is tested on the hydrogen atom (ground and excited states) and the molecule, resulting in milliHartree accuracy with a moderate number of plane waves.

Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlowlike splitting algorithms
View Description Hide DescriptionNumerical integration schemes based upon the Shardlowsplitting algorithm (SSA) are presented for dissipative particle dynamics (DPD) approaches at various fixed conditions, including a constantenthalpy (DPDH) method that is developed by combining the equationsofmotion for a barostat with the equationsofmotion for the constantenergy (DPDE) method. The DPDH variant is developed for both a deterministic (Hoover) and stochastic (Langevin) barostat, where a barostat temperature is defined to satisfy the fluctuationdissipation theorem for the Langevin barostat. For each variant, the Shardlowsplitting algorithm is formulated for both a velocityVerlet scheme and an implicit scheme, where the velocityVerlet scheme consistently performed better. The application of the Shardlowsplitting algorithm is particularly critical for the DPDE and DPDH 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 coarsegrain solid model. For both models, the DPDE and DPDH 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 constantenergy and constantenthalpy conditions. The original SSA formulated for systems of equalmass particles has been extended to systems of unequalmass particles. The FokkerPlanck equation and derivations of the fluctuationdissipation theorem for each DPD variant are also included for completeness.

A method for analyzing the vibrational energy flow in biomolecules in solution
View Description Hide DescriptionA 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 Nmethylacetamided in aqueous D_{2}O solution which yields a detailed quantitative description of the process.

Longrange corrected hybrid functionals for πconjugated systems: Dependence of the rangeseparation parameter on conjugation length
View Description Hide DescriptionLongrange corrected (rangeseparated hybrid) functionals represent a relatively new class of functionals for generalized KohnSham 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 longrange corrected density functional theory approaches can be improved dramatically, if the rangeseparation parameter (ω) is optimized for each system separately. In this work, we have optimized ω for a series of πconjugated molecular systems of increasing length by forcing the resulting functionals to obey the ionization potentialtheorem, 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 rangeseparation, i.e., 1/ω, grows almost linearly with the number of repeat units, for saturated alkane chains, however, 1/ω quickly saturates after 56 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 rangeseparation parameter and the degree of conjugation in the system.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photoelectron spectroscopic study of ironpyrene cluster anions
View Description Hide DescriptionIronpyrene cluster anions, [Fe_{m}(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 Fe_{1}(pyrene)_{1} and Fe_{2}(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 clusterbased magnetic material. A comparison of the structures and corresponding photoelectron spectra for the ironbenzene, ironpyrene, and ironcoronene cluster systems revealed that pyrene behaves more similarly to coronene than to benzene.

Extracting elements of molecular structure from the allparticle wave function
View Description Hide DescriptionStructural information is extracted from the allparticle (nonBorn–Oppenheimer) wave function by calculating radial and angular densities derived from nparticle densities. As a result, one and twodimensional motifs of classical molecular structure can be recognized in quantum mechanics. Numerical examples are presented for three (H^{−}, Ps^{−}, ), four (Ps_{2}, H_{2}), and fiveparticle (H_{2}D^{+}) systems.

Laser induced and controlled chemical reaction of carbon monoxide and hydrogen
View Description Hide DescriptionBimolecular chemical reaction control of gaseous CO and H_{2} 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 nonresonant 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 CO_{2} ^{+}, C_{2}H_{2} ^{+}, CH^{+}, and CH_{3} ^{+} were observed in the time of flight mass spectrum of the product gas, analyzed after irradiation. The formation of CO_{2} is shown to be dependent on laser intensity, irradiation time, and on the presence of H_{2} 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.

Comparison and assessment of procedures for calculating the R(12) line strength of the ν_{1}+ 2 ν_{2} + ν_{3} band of CO_{2}
View Description Hide DescriptionRecently, results for the CO_{2} 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 nonparametric 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.

Nanopolaritonics with a continuum of molecules: Simulations of molecularinduced selectivity in plasmonics transport through a continuous Yshape
View Description Hide DescriptionUsing the recent NF (nearfield) formulation for electrodynamics on the nanoscale, we simulate transport in a Yshape gold nanostructure in the presence of 2level molecules. NF is shown to be easily integrated with the Liouville equation, producing a simple and efficient nanopolaritons (plasmonsexcitons) 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 spacefilling 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.

The excitation function for Li + HF → LiF + H at collision energies below 80 meV
View Description Hide DescriptionWe 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 ⩽ E _{tr} ⩽ 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 Langevintype 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 zeropoint 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.

Photoelectron spectroscopy of HC4N^{−}
View Description Hide DescriptionWe report the 364nm photoelectron spectrum of HC4N^{−}. We observe electron photodetachment from the bent ^{2}A^{″} state of HC4N^{−} to both the nearlinear ^{3}A^{″} and the bent ã ^{1}A^{′} states of neutral HC4N. We observe an extended, unresolved vibrational progression corresponding to ^{3}A^{″} ← ^{2}A^{″} photodetachment, and we measure the electron affinity (EA) of the ^{3}A^{″} state of HC4N to be 2.05(8) eV. Photodetachment to the bent ã ^{1}A^{′} state results in a single intense origin peak at a binding energy of 2.809(4) eV, from which we determine the singlettriplet splitting (ΔEST) of HC4N: 0.76(8) eV. For comparison and to aid in the interpretation of the HC4N^{−} spectrum, we also report the 364nm photoelectron spectra of HCCN^{−} and DCCN^{−}. Improved signaltonoise 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.

Electronic transitions of cobalt monoboride
View Description Hide DescriptionElectronic transition spectrum of cobalt monoboride (CoB) in the visible region between 495 and 560 nm has been observed and analyzed using laserinduced fluorescencespectroscopy. CoB molecule was produced by the reaction of laserablated cobalt atom and diborane (B_{2}H_{6}) seeded in argon. Fifteen vibrational bands with resolved rotational structure have been recorded, which included transitions of both Co^{10}B and Co^{11}B 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]^{3}Π_{2}–X^{3}Δ_{2}, the [18.3]^{3}Φ_{3}–X^{3}Δ_{3}, the [18.6]3– X^{3}Δ_{3}, and the [19.0]2–X^{3}Δ_{2} systems. The bond length, r_{o}, of the X^{ 3}Δ_{3} 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 (a_{ β }) coupling scheme. This work represents the first experimental investigation of the CoB spectrum.
 Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Oscillatory and stationary convective patterns in a reaction driven gravity current
View Description Hide DescriptionHorizontally propagating chemical fronts are studied in a thin solution layer of the acidcatalyzed chloritetetrathionate 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.

Twodimensional infrared spectral signature and hydration of the oxalate dianion
View Description Hide DescriptionUltrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Twodimensional 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.

Semiclassical study of quantum coherence and isotope effects in ultrafast electron transfer reactions coupled to a proton and a phonon bath
View Description Hide DescriptionThe 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 spinboson model, the coherences are not longlived. 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.

Hydrogenation of fragment cations produced by femtosecond laser ablation of boron nitride
View Description Hide DescriptionCations (positive ions) produced by laser ablation of boron nitride (BN) have been mass analyzed and the sizedependent hydrogenation reactivity is revealed for the first time. The main product cations determined by femtosecond laserablation (fsLA) were a series of B(BN)_{n} ^{+}, with much lesser production of B_{2}(BN)_{k} ^{+} and N(BN)_{m}O^{+} series cations. Leastsquares fitting of the relative yields of hydrogenated cations indicates that the yield of B(BN)_{n}H^{+} almost diminishes for n ≥ 5 and that of B(BN)_{n}H_{2} ^{+} increases as n increases. Based on the different ndependence and electronic structures of B(BN)_{n} and B(BN)_{n} ^{+}, B(BN)_{n} is likely to be the precursor of B(BN)_{n}H^{+}, and B(BN)_{n} ^{+} that of B(BN)_{n}H_{2} ^{+}. 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.

Confined linear molecules inside an aperiodic supramolecular crystal: The sequence of superspace phases in nhexadecane/urea
View Description Hide DescriptionHighresolution studies of the hostguest inclusioncompoundnhexadecane/urea are reported at atmospheric pressure, using both cold neutrons and xray diffraction. This intergrowth crystal presents a misfit parameter, defined by the ratio c _{h}/c _{g} (c _{host}/c _{guest}), 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 P6_{1}22(00γ) down to T_{c1} = 149.5 ± 0.5 K; phase II, which persists down to T_{c2} = 127.8 ± 0.5 K is orthorhombic P2_{1}2_{1}2_{1}(00γ), and phase III is orthorhombic P2_{1}2_{1}2_{1}(00γ)(00δ).