Volume 137, Issue 15, 21 October 2012
Index of content:

Most chemical reactions in water are very sensitive to pH. Many environmentally important chemical reactions are known to take place at the watersurface (i.e., air/water interface). However, the pH of the watersurface is still controversial. Spectroscopic experiments and theoretical calculations indicate that the watersurface is more acidic than the bulk, whereas electrophoretic experiments provide a contrary view. Here, we report that a novel nonlinear optical experiment with a surfaceactive pH indicator can quantitatively evaluate the pH of the watersurface. The result clearly shows that the pH of the watersurface is lower than that of the bulk by 1.7. This is the first study to apply a principle of bulk pH measurements to the watersurface, and therefore provides a reliable experimental estimate for the pH difference between the watersurface and bulk. It is considered that the higher acidity of the watersurface plays a key role in marine and atmospheric chemical reactions.
 COMMUNICATIONS


Communication: Quantitative estimate of the water surface pH using heterodynedetected electronic sum frequency generation
View Description Hide DescriptionMost chemical reactions in water are very sensitive to pH. Many environmentally important chemical reactions are known to take place at the watersurface (i.e., air/water interface). However, the pH of the watersurface is still controversial. Spectroscopic experiments and theoretical calculations indicate that the watersurface is more acidic than the bulk, whereas electrophoretic experiments provide a contrary view. Here, we report that a novel nonlinear optical experiment with a surfaceactive pH indicator can quantitatively evaluate the pH of the watersurface. The result clearly shows that the pH of the watersurface is lower than that of the bulk by 1.7. This is the first study to apply a principle of bulk pH measurements to the watersurface, and therefore provides a reliable experimental estimate for the pH difference between the watersurface and bulk. It is considered that the higher acidity of the watersurface plays a key role in marine and atmospheric chemical reactions.

Communication: Imaging the indirect dissociation dynamics of temporary negative ion: N_{2}O^{−} → N_{2} + O^{−}
View Description Hide DescriptionWe reported an imaging study of the dissociationdynamics of temporary negative ion N_{2}O^{−} formed in the lowenergy electron attachment, e ^{−} + N_{2}O → N_{2}O^{−} → N_{2} + O^{−}. With the help of ab initiomolecular dynamics calculations, the evolution of momentum distributions of the O^{−} fragment in terms of the electron attachment energy is identified as the result of a competition between two distinctly different indirect pathways, namely, climbing over and bypassing the energy ridge after the molecular structure bending. These two pathways prefer leaving the N_{2} fragment at the high vibrational and rotational states, respectively.

 ARTICLES

 Theoretical Methods and Algorithms

Aqueous interaction site integralequation theory that exactly takes into account intramolecular correlations
View Description Hide DescriptionWe report the development of a formally exact integral equation for the threedimensional hydration structure around molecular solutes of arbitrary complexity. A distinctive feature of our theory—termed aqueous interaction site (AXIS) integralequation theory—is that it fully takes into account the intramolecular structural correlations of solvent water, which has been missing in the previous integralequation theories such as the threedimensional reference interaction site model (3DRISM) theory. With a simplifying approximation in which the intermolecular bridge function is neglected, an illustrative application of the AXIS theory is made on the equilibrium oxygen and hydrogen distributions of solvent water surrounding a solute water molecule at ambient and supercritical conditions. We demonstrate through a comparison with molecular dynamics simulation results that the inclusion of the exact intramolecular correlations improves upon the 3DRISM theory in describing the water distribution around molecular solute, in particular near the surface region of the solute molecule, though there still remain quantitative differences from the simulation results. To further improve the quantitative accuracy of the theory, one needs to incorporate the intermolecular bridge function, and a possible formulation for the approximate bridge function is suggested based on the angular decomposition.

Timeaveraging approximation in the interaction picture: Anisotropy of vibrational pumpprobe experiments for coupled chromophores with application to liquid water
View Description Hide DescriptionA timeaveraging approximation method developed to efficiently calculate the shorttime dynamics of coupled vibrational chromophores using mixed quantum/classical theories is extended in order to be applicable to the study of vibrational dynamics at longer time scales. A quantum mechanical time propagator for long times is decomposed into the product of shorttime propagators, and a timeaveraging approximation is then applied to each of the latter. Using the extended timeaveraging approximation, we calculate the anisotropy decay of the data obtained from impulsive vibrational pumpprobe experiments on the OH stretching modes of water, which is in excellent agreement with numerically exact results.

Relativistic diffusion Monte Carlo method: Zerothorder regular approximationdiffusion Monte Carlo method in a spinfree formalism
View Description Hide DescriptionA diffusionMonte Carlo (DMC) method for the relativistic zerothorder regular approximation (ZORA) is proposed. In this scheme, a novel approximate Green's function is derived for the spinfree ZORA Hamiltonian. Several numerical tests on atoms and small molecules showed that by combining with the relativistic cuspcorrection scheme, the present approach can include both relativistic and electroncorrelation effects simultaneously. The correlationenergies recovered by the ZORADMC method are comparable with the nonrelativistic DMC results and superior to the coupled cluster singles and doubles with perturbative triples correction results when the correlationconsistent polarized valence triplezeta Douglas–Kroll basis set is used. For the heavier CuH molecule, the ZORADMC estimation of its dissociation energy agrees with the experimental value within the error bar.

Comparison of two generationrecombination terms in the PoissonNernstPlanck model
View Description Hide DescriptionTwo phenomenological forms proposed to take into account the generationrecombination phenomenon of ions are investigated. The first form models the phenomenon as a chemical reaction, containing two coefficients describing the dissociation of neutral particles in ions, and the recombination of ions to give neutral particles. The second form is based on the assumption that in thermodynamical equilibrium, a welldefined density of ions is stable. Any deviation from the equilibrium density gives rise to a source term proportional to the deviation, whose phenomenological coefficient plays the role of a life time. The analysis is performed by evaluating the electrical response of an electrolytic cell to an external stimulus for both forms. For simplicity we assume that the electrodes are blocking, that there is only a group of negative and positive ions, and that the negative ions are immobile. For the second form, two cases are considered: (i) the generationrecombination phenomenon is due to an intrinsic mechanism, and (ii) the production of ions is triggered by an external source of energy, as in a solar cell. We show that the predictions of the two models are different at the impedance as well as at the admittance level. In particular, the first model predicts the existence of two plateaux for the real part of the impedance, whereas the second one predicts just one. It follows that impedance spectroscopy measurements could give information on the model valid for the generationrecombination of ions.

On the ChanDas gauge for the calculation of molecular magnetizabilities
View Description Hide DescriptionIt is proven that the common origin gauge proposed by Chan and Das for the calculation of molecular magnetizabilities within the conventional approach using gaugeless basis sets, i.e., the center of electronic charge, does not minimize the van Vleck paramagnetic contribution to the diagonal tensor components, unless the ArrighiniMaestroMoccia sum rules for gauge invariance, and charge conservation are satisfied. Additional quantum mechanical constraints for extremum values of formally diamagnetic and paramagnetic contributions have also been obtained for magnetizabilities calculated via procedures allowing for a continuous translation of the origin of the current density.

Chemical potential evaluation in NVT latticegas simulations
View Description Hide DescriptionThe discrete nature of the partition function of a latticegas system can be exploited to build an efficient strategy for the evaluation of the chemical potential of a periodic latticegas with arbitrarily ranged interactions during a simulation in the canonical ensemble, with the need of no additional sampling as it were required instead by the Widom insertion/deletion approach. The present method is based on the main concepts of the small system grand ensemble [for details, see G. SotoCampos, D. S. Corti, and H. Reiss, J. Chem. Phys.108, 2563 (1998)10.1063/1.475640], whose key idea is to study the properties of a sublattice (called small system) and of its complementary (the reservoir sublattice) as they were two separated subsystems. The accuracy of the measured chemical potential can be further improved by artificially “restoring” the missing connections among the reservoir sublattice sites located at the boundaries with the small system. We first illustrate the theory and then we compare μVT with NVT simulation results on several test systems.

A Cartesian classical secondquantized manyelectron Hamiltonian, for use with the semiclassical initial value representation
View Description Hide DescriptionA new classical model for the general secondquantized manyelectron Hamiltonian in Cartesian coordinates and momenta is presented; this makes semiclassical (SC) calculations using an initial value representation (IVR) more useful than the classical Hamiltonian in actionangle variables given earlier by Miller and White [J. Chem. Phys.84, 5059–5066 (1986)]10.1063/1.450655. If only 1electron terms are included in this Hamiltonian, the classical equations of motion for the Cartesian variables are linear, and the SCIVR gives exact results for the propagator (and thus for transition probabilities, the energy spectrum, etc.), as confirmed by analytic proof and numerical calculations. Though this new Hamiltonian is not exact when 2electron interactions are included, we observe good results for the SCIVR transition probabilities for times that are not too long. Test calculations, for example, show that the SCIVR is accurate for times long enough to obtain good result for the eigenvalue spectrum (i.e., the energy levels of the electronic system).

Specification, construction, and exact reduction of state transition system models of biochemical processes
View Description Hide DescriptionBiochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction events. Since they often involve a large number of interactions, it can be difficult to construct such a model for a system, and since the resulting statelevel model can involve a huge number of states, model analysis can be difficult or impossible. Here, we describe methods for the highlevel specification of a system using hypergraphs, for the automated generation of a statelevel model from a highlevel model, and for the exact reduction of a statelevel model using information from the highlevel model. Exact reduction is achieved through the automated application to the highlevel model of the symmetry reduction technique and reduction by decomposition by independent subsystems, allowing potentially significant reductions without the need to generate a full model. The application of the method to biochemical reaction systems is illustrated by models describing a hypothetical ionchannel at several levels of complexity. The method allows for the reduction of the otherwise intractable example models to a manageable size.

Effective diffusivity through arrays of obstacles under zeromean periodic driving forces
View Description Hide DescriptionWe perform a numerical investigation of the transport of Brownian particles driven by a zeromean periodic force across twodimensional arrays of obstacles with finite length. By applying axial and transversal driving forces relative to the diffusiontransport direction, the effective diffusivity is determined as function of the array geometry and the driving frequency, finding excess diffusion peaks at certain frequency ranges. The results indicate that a suitable selection of the axial and transversal frequencies yields enhanced diffusiontransport along the axial direction. Symmetric and asymmetric arrays are considered, showing that the asymmetry has a detrimental effect in the magnitude of the excess diffusion peaks. This suggests that enhanced diffusion is obtained because the oscillatory driving force exploits preferential transport channels, whose effective obstacle spacing is maximized under symmetric configurations.

Model GW study of the late transition metal monoxides
View Description Hide DescriptionThe model GW method [F. Gygi and A. Baldereschi, Phys. Rev. Lett.62, 2160 (1989)]10.1103/PhysRevLett.62.2160 is an efficient simplification to the standard GW approximation which uses modeldielectric function to describe the long range Coulomb interactions in semiconductors. In this work, the model GW method is used to calculate the quasiparticleband structures of MnO, FeO, CoO, and NiO. All four late transition metal monoxides are predicted to be insulators. The band gaps,magnetic moments, and quasiparticlespectra are in good agreement with the experiments, except for the satellite structures which are missing in the density of states because the model GW selfenergy is static. The high accuracy of model GW is due to the usage of the accurate dielectric constants in the construction of the modeldielectric functions which ensures the correct asymptotic behavior of the long range Coulomb interactions. Besides, we find that the transition metal 4s states are irrelevant to the formation of the band gaps, which supports the local approaches and the experimental interpretations of the band gaps by photoemission and electron energy loss spectroscopy, while contradicts the recent calculations by hybrid functionals, exact exchange, and one shot GW approximations.

Improved spatial direct method with gradientbased diffusion to retain full diffusive fluctuations
View Description Hide DescriptionThe spatial direct method with gradientbased diffusion is an accelerated stochastic reactiondiffusion simulation algorithm that treats diffusive transfers between neighboring subvolumes based on concentration gradients. This recent method achieved a marked improvement in simulation speed and reduction in the number of timesteps required to complete a simulation run, compared with the exact algorithm, by sampling only the net diffusion events, instead of sampling all diffusion events. Although the spatial direct method with gradientbased diffusion gives accurate means of simulation ensembles, its gradientbased diffusion strategy results in reduced fluctuations in populations of diffusive species. In this paper, we present a new improved algorithm that is able to anticipate all possible microscopic fluctuations due to diffusive transfers in the system and incorporate this information to retain the same degree of fluctuations in populations of diffusing species as the exact algorithm. The new algorithm also provides a capability to set the desired level of fluctuation per diffusing species, which facilitates adjusting the balance between the degree of exactness in simulation results and the simulation speed. We present numerical results that illustrate the recovery of fluctuations together with the accuracy and efficiency of the new algorithm.

Calculation and analysis of the harmonic vibrational frequencies in molecules at extreme pressure: Methodology and diborane as a test case
View Description Hide DescriptionWe present a new quantum chemical method for the calculation of the equilibrium geometry and the harmonic vibrational frequencies of molecular systems in dense medium at high pressures (of the order of GPa). The new computational method, named PCMXP, is based on the polarizable continuum model (PCM), amply used for the study of the solvent effects at standard condition of pressure, and it is accompanied by a new method of analysis for the interpretation of the mechanisms underpinning the effects of pressure on the molecular geometries and the harmonic vibrational frequencies. The PCMXP has been applied at the density functional theory level to diborane as a molecular system under high pressure. The computed harmonic vibrational frequencies as a function of the pressure have shown a satisfactory agreement with the corresponding experimental results, and the parallel application of the method of analysis has reveled that the effects of the pressure on the equilibrium geometry can be interpreted in terms of direct effects on the electronic charge distribution of the molecular solutes, and that the effects on the harmonic vibrational frequencies can be described in terms of two physically distinct effects of the pressure (curvature and relaxation) on the potential energy for the motion of the nuclei.

Chemically transferable coarsegrained potentials from conditional reversible work calculations
View Description Hide DescriptionThe representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of nalkanes, the coarsegrained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a freeenergybased coarsegraining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRWCG potentials may be readily obtained from a single simulation of the liquid state using the free energyperturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules.

On the spin separation of algebraic twocomponent relativistic Hamiltonians
View Description Hide DescriptionThe separation of the spinfree and spindependent terms of a given relativistic Hamiltonian is usually facilitated by the Dirac identity. However, this is no longer possible for the recently developed exact twocomponent relativistic Hamiltonians derived from the matrix representation of the Dirac equation in a kinetically balanced basis. This stems from the fact that the decoupling matrix does not have an explicit form. To resolve this formal difficulty, we first define the spindependent term as the difference between a twocomponent Hamiltonian corresponding to the full Dirac equation and its onecomponent counterpart corresponding to the spinfree Dirac equation. The series expansion of the spindependent term is then developed in two different ways. One is in the spirit of the DouglasKrollHess (DKH) transformation and the other is based on the perturbative expansion of a twocomponent Hamiltonian of fixed structure, either the twostep BaryszSadlejSnijders (BSS) or the onestep exact twocomponent (X2C) form. The algorithms for constructing arbitrary order terms are proposed for both schemes and their convergence patterns are assessed numerically. Truncating the expansions to finite orders leads naturally to a sequence of novel spindependent Hamiltonians. In particular, the orderbyorder distinctions among the DKH, BSS, and X2C approaches can nicely be revealed. The wellknown Pauli, zerothorder regular approximation, and DKH1 spindependent Hamiltonians can also be recovered naturally by appropriately approximating the decoupling and renormalization matrices. On the practical side, the sfX2C+soDKH3 Hamiltonian, together with appropriately constructed generally contracted basis sets, is most promising for accounting for relativistic effects in two steps, first spinfree and then spindependent, with the latter applied either perturbatively or variationally.

Fast convergence to equilibrium for longchain polymer melts using a MD/continuum hybrid method
View Description Hide DescriptionEffective and fast convergence toward an equilibrium state for longchain polymer melts is realized by a hybrid method coupling molecular dynamics and the elastic continuum. The required simulation time to achieve the equilibrium state is reduced compared with conventional equilibration methods. The polymers move on a wide range phase space due to largescale fluctuation generated by the elastic continuum. A variety of chain structures is generated in the polymer melt which results in the fast convergence to the equilibrium state.
 Advanced Experimental Techniques

Eddy current effects in plain and hollow cylinders spinning inside homogeneous magnetic fields: Application to magnetic resonance
View Description Hide DescriptionWe present a thorough analysis of eddycurrents that develop in a rectangular cross section toroid rotating in a uniform magnetic field. The slow rotation regime is assumed. Compact expressions for the current density, the total dissipated power, and the braking torque are given. Examination of the topology of current lines reveals that depending upon the relative dimensions of the side and length of the toroid two different regimes exist. The conditions of existence of the two regimes are analytically established. In view of nuclear magnetic resonance(NMR) applications, we derive the angular variation of the magnetic field created by eddycurrents and lay down the formalism necessary for calculating the effect of this field on the NMR spectra of the conductor itself or of a sample corotating with the conductor, a situation encountered when dealing with rotating detectors. Examples of calculations for cases of practical interest are presented. The theory is confronted with available data, and we give guidelines for the design of optimized rotating microcoils.

Crossed molecular beams study of inelastic nonadiabatic processes in gas phase collisions between sodium ions and ZnBr_{2} molecules in the 0.10–3.50 keV energy range
View Description Hide DescriptionInelastic electronically nonadiabatic reactions between Na^{+} ions and neutral ZnBr_{2} molecules, both in their electronic ground state, have been studied using crossed beams techniques and measuring the decaying emission radiation of the excited species produced. The fluorescent emission corresponding to Na(3 ^{2} P) produced by a charge transferreaction was observed, as well as that corresponding to the decay of Zn(4s 5s ^{3} S), generated by dissociation of the neutral target molecule, to Zn(4s 4p ^{3} P). The phosphorescent decaying emission of Zn^{*}(4s 4p ^{3} P) to the zincground state was also observed. For each emission process, the cross section energy dependences have been measured in the 0.10–3.50 keV energy range in the laboratory system. The ground electronic state of the (NaZnBr_{2})^{+} collision system has been characterized by ab initio chemical structure calculations at the second order MöllerPlesset perturbation level of theory using pseudopotentials. By performing restricted open shell HartreeFock calculations for C_{2v} geometries, four singlet and four triplet potential energy surfaces of the system have been calculated and used to interpret qualitatively the observed reactions. A simple twostate dynamical model is presented that allows an estimation of the maximum values for measured cross sections at high collision energies to be made.
 Atoms, Molecules, and Clusters

Firstprinciples calculations of rovibrational energies, dipole transition intensities and partition function for ethylene using MULTIMODE
View Description Hide DescriptionLargescale, rovibrational variational calculations are performed for ethylene, using the potential energy surface published by Avila and Carrington [J. Chem. Phys.135, 064101 (2011)10.1063/1.3617249]. Energies for J = 0 are in very good agreement with their benchmark results. Corresponding energies for J = 1 and J = 2 are also given. Calculations with a slightly reduced basis permit energies to J = 40, allowing a reliable determination of the partition function at 296 K. Using a new ab initiodipole momentsurface, reported here, the infrared spectra of five dipoleallowed fundamentals are calculated. Both the partition function and infrared spectra are shown to be in excellent agreement with those in the experimental HITRAN database, with the exception of one band, which we believe is partially misassigned in HITRAN.