Volume 136, Issue 23, 21 June 2012

In situoptimization of a set of localized orbitals with respect to a systematically improvable basis set independent of the position of the atoms, such as psinc functions, would theoretically eliminate the correction due to Pulay forces from the total ionic forces. We demonstrate that for strict localization constraints, especially with small localization regions, there can be nonnegligible Pulay forces that must be calculated as a correction to the HellmannFeynman forces in the ground state. Geometry optimization calculations, which rely heavily upon accurate evaluation of the total ionic forces, show much better convergence when Pulay forces are included. The more conventional case, where the local orbitals remain fixed to pseudoatomic orbital multipleζ basis sets, also benefits from this implementation. We have validated the method on several test cases, including a DNA fragment with 1045 atoms.
 ARTICLES

 Theoretical Methods and Algorithms

Pulay forces from localized orbitals optimized in situ using a psinc basis set
View Description Hide DescriptionIn situoptimization of a set of localized orbitals with respect to a systematically improvable basis set independent of the position of the atoms, such as psinc functions, would theoretically eliminate the correction due to Pulay forces from the total ionic forces. We demonstrate that for strict localization constraints, especially with small localization regions, there can be nonnegligible Pulay forces that must be calculated as a correction to the HellmannFeynman forces in the ground state. Geometry optimization calculations, which rely heavily upon accurate evaluation of the total ionic forces, show much better convergence when Pulay forces are included. The more conventional case, where the local orbitals remain fixed to pseudoatomic orbital multipleζ basis sets, also benefits from this implementation. We have validated the method on several test cases, including a DNA fragment with 1045 atoms.

Umbrella integration with higherorder correction terms
View Description Hide DescriptionUmbrella integration is a method to analyze umbrella sampling simulations. It calculates freeenergy changes from distributions obtained from molecular dynamics. While it can be formulated on the full sampled distributions, they are generally approximated by normal distributions. This is equivalent to the truncation of a power series of the free energy with respect to the reaction coordinate after the quadratic term or by a truncation of a cumulant expansion. Here, expressions for additional terms in the power series are derived. They can be calculated from the central moments of the distributions. This extension allows to test the approximations in applications.

Steered transition path sampling
View Description Hide DescriptionWe introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying the dynamics based on that probability, and then reweighting to calculate averages. Because the progress constraint can be formulated in terms of occurrences of events within time intervals, the method is particularly well suited for controlling the sampling of currents of dynamic events. We demonstrate the method for calculating transition probabilities in barrier crossing problems and survival probabilities in strongly diffusive systems with absorbing states, which are difficult to treat by shooting. We discuss the relation of the algorithm to other methods.

Nearfield for electrodynamics at subwavelength scales: Generalizing to an arbitrary number of dielectrics
View Description Hide DescriptionWe extend the recently developed nearfield (NF) method to include an arbitrary number of dielectrics. NF assumes that the dipoles and fields respond instantaneously to the density, without retardation. The central task in NF is the solution of the Poisson equation for every time step, which is here done by a conjugate gradient method which handles any dielectric distribution. The optical response of any metaldielectric system can now be studied very efficiently in the near field region. The improved NF method is first applied to simple benchmark systems: a gold nanoparticle in vacuum and embedded in silica. The surface plasmons in these systems and their dependence on the dielectrics are reproduced in the new NF approach. As a further application, we study a silvernanoparticlebasedstructure for the optical detection of a “lipid” (i.e., dielectric) layer in water, where the layer is wrapping around part of the metallic nanostructure. We show the ∼0.10.15 eV shift in the spectrum due to the presence of the layer, for both spherical and nonspherical (sphere+rod) systems with various polarizations.

Fast timereversible algorithms for molecular dynamics of rigidbody systems
View Description Hide DescriptionIn this paper, we present timereversible simulation algorithms for rigid bodies in the quaternion representation. By advancing a timereversible algorithm [Y. Kajima, M. Hiyama, S. Ogata, and T. Tamura, J. Phys. Soc. Jpn.80, 114002 (2011)10.1143/JPSJ.80.114002] that requires iterations in calculating the angular velocity at each time step, we propose two kinds of iterationfree fast timereversible algorithms. They are easily implemented in codes. The codes are compared with that of existing algorithms through demonstrative simulation of a nanometersized water droplet to find their stability of the total energy and computation speeds.

Monte Carlo simulation based on dynamic disorder model in organic semiconductors: From coherent to incoherent transport
View Description Hide DescriptionThe dynamic disorder model for charge carriertransport in organic semiconductors has been extensively studied in recent years. Although it is successful on determining the value of bandlike mobility in the organic crystalline materials, the incoherent hopping, the typical transport characteristic in amorphous molecular semiconductors, cannot be described. In this work, the decoherence process is taken into account via a phenomenological parameter, say, decoherence time, and the projective and Monte Carlo method are applied for this model to determine the waiting time and thus the diffusion coefficient. It is obtained that the type of transport is changed from coherent to incoherent with a sufficiently short decoherence time, which indicates the essential role of decoherence time in determining the type of transport in organics. We have also discussed the spatial extent of carriers for different decoherence time, and the transition from delocalization (carrier resides in about 10 molecules) to localization is observed. Based on the experimental results of spatial extent, we estimate that the decoherence time in pentacene has the order of 1 ps. Furthermore, the dependence of diffusion coefficient on decoherence time is also investigated, and corresponding experiments are discussed.

A parameterfree, solidangle based, nearestneighbor algorithm
View Description Hide DescriptionWe propose a parameterfree algorithm for the identification of nearest neighbors. The algorithm is very easy to use and has a number of advantages over existing algorithms to identify nearestneighbors. This solidangle based nearestneighbor algorithm (SANN) attributes to each possible neighbor a solid angle and determines the cutoff radius by the requirement that the sum of the solid angles is 4π. The algorithm can be used to analyze 3D images, both from experiments as well as theory, and as the algorithm has a low computational cost, it can also be used “on the fly” in simulations. In this paper, we describe the SANN algorithm, discuss its properties, and compare it to both a fixeddistance cutoff algorithm and to a Voronoi construction by analyzing its behavior in bulk phases of systems of carbon atoms, LennardJones particles and hard spheres as well as in LennardJones systems with liquidcrystal and liquidvapor interfaces.

A probability generating function method for stochastic reaction networks
View Description Hide DescriptionIn this paper we present a probability generating function (PGF) approach for analyzing stochastic reaction networks. The master equation of the network can be converted to a partial differential equation for PGF. Using power series expansion of PGF and Padé approximation, we develop numerical schemes for finding probability distributions as well as first and second moments. We show numerical accuracy of the method by simulating chemical reaction examples such as a bindingunbinding reaction, an enzymesubstrate model, GoldbeterKoshland ultrasensitive switch model, and G _{2}/M transition model.

Sizeextensive vibrational selfconsistent field methods with anharmonic geometry corrections
View Description Hide DescriptionIn the sizeextensive vibrational selfconsistent field (XVSCF) method introduced earlier [M. Keçeli and S. Hirata, J. Chem. Phys.135, 134108 (2011)]10.1063/1.3644895, only a small subset of evenorder force constants that can form connected diagrams were used to compute extensive total energies and intensive transition frequencies. The meanfield potentials of XVSCF formed with these force constants have been shown to be effectively harmonic, making basis functions, quadrature, or matrix diagonalization in the conventional VSCF method unnecessary. We introduce two sizeconsistent VSCF methods, XVSCF(n) and XVSCF[n], for vibrationally averaged geometries in addition to energies and frequencies including anharmonic effects caused by up to the nthorder force constants. The methods are based on our observations that a small number of oddorder force constants of certain types can form open, connected diagrams isomorphic to the diagram of the meanfield potential gradients and that these nonzero gradients shift the potential minima by intensive amounts, which are interpreted as anharmonic geometry corrections. XVSCF(n) evaluates these meanfield gradients and force constants at the equilibrium geometry and estimates this shift accurately, but approximately, neglecting the coupling between these two quantities. XVSCF[n] solves the coupled equations for geometry corrections and frequencies with an iterative algorithm, giving results that should be identical to those of VSCF when applied to an infinite system. We present the diagrammatic and algebraic definitions, algorithms, and initial implementations as well as numerical results of these two methods. The results show that XVSCF(n) and XVSCF[n] reproduce the vibrationally averaged geometries of VSCF for naphthalene and anthracene in their ground and excited vibrational states accurately at fractions of the computational cost.

Equationofmotion coupledcluster method for the study of shape resonance
View Description Hide DescriptionThe equationofmotion coupledcluster method (EOMCC) is applied for the first time to calculate the energy and width of a shape resonance in an electronmolecule scattering. The procedure is based on inclusion of complex absorbing potential with EOMCC theory. We have applied this method to investigate the shape resonance in e ^{−}N_{2}, e ^{−}CO, and e ^{−}C_{2}H_{2}.

Transferable pair potentials for CdS and ZnS crystals
View Description Hide DescriptionA set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe[E. Rabani, J. Chem. Phys.116, 258 (2002)]10.1063/1.1424321, can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II–VI semiconductor materials.

Numeric kinetic energy operators for molecules in polyspherical coordinates
View Description Hide DescriptionGeneralized curvilinear coordinates, as, e.g., polyspherical coordinates, are in general better adapted to the resolution of the nuclear Schrödinger equation than rectilinear ones like the normal mode coordinates. However, analytical expressions of the kinetic energy operators (KEOs) for molecular systems in polyspherical coordinates may be prohibitively complicated for large systems. In this paper we propose a method to generate a KEO numerically and bring it to a form practicable for dynamical calculations. To examine the new method we calculated vibrational spectra and eigenenergies for nitrous acid (HONO) and compare it with results obtained with an exact analytical KEO derived previously [F. Richter, P. Rosmus, F. Gatti, and H.D. Meyer, J. Chem. Phys.120, 6072 (2004)]10.1063/1.1651051. In a second example we calculated π → π* photoabsorption spectrum and eigenenergies of ethene (C_{2}H_{4}) and compared it with previous work [M. R. Brill, F. Gatti, D. Lauvergnat, and H.D. Meyer, Chem. Phys.338, 186 (2007)]10.1016/j.chemphys.2007.04.002. In this ethene study the dimensionality was reduced from 12 to 6 by freezing six internal coordinates. Results for both molecules show that the proposed method for obtaining an approximate KEO is reliable for dynamical calculations. The error in eigenenergies was found to be below 1 cm^{−1} for most states calculated.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Computational determination of the Ã state absorption spectrum of NH_{3} and of ND_{3} using a new quasidiabatic representation of the and Ã states and full sixdimensional quantum dynamics
View Description Hide DescriptionA recently developed method to represent adiabatic electronic states coupled by conical intersections has been used to construct a full sixdimensional quasidiabatic representation of the 1^{1}A and 2^{1}A states of NH_{3}. This representation is expected to be appropriate to simulate the photodissociation of ammonia when it is excited to the 2^{1}A electronic state. In this work, the electronic structure aspects of this quasidiabatic representation are analyzed. This representation is then used as the basis for a simulation of the ← absorptionspectrum, dominated by a progression in the v _{2} mode, using a full sixdimensional quantum mechanical treatment of the nuclear motion. Results are reported for both NH_{3} and ND_{3}. This simulation provides the most accurate computational determination of this absorptionspectrum reported to date. These results serve to validate the quasidiabatic representation and set the stage for subsequent studies of vibrationally mediated photodissociation of NH_{3}.

Nonadiabatic transitions from I_{2}( and ) states induced by collisions with M = I_{2}() and H_{2}O
View Description Hide DescriptionThe stepwise twostep twocolor and threestep threecolor laser excitation schemes are used for selective population of rovibronic levels of the firsttier ionpair and states of molecular iodine and studies of nonadiabatic transitions to the D and E states induced by collisions with M = I_{2}(X) and H_{2}O. Collection and analysis of the luminescence after excitation of the v _{ E } = 8, 13 and v _{ D } = 13, 18 vibronic levels of the E and D states in the pure iodine vapor and the gasphase mixtures with H_{2}O provide rate constants for the nonadiabatic transitions to the D and E state induced by collisions with these molecules. Vibrational distributions for the I_{2}() collisioninduced nonadiabatic transitions (CINATs) are obtained. Rather strong ≈ 3400 Å luminescence band is observed in the I_{2} + H_{2}O mixtures, whereas its intensity is ∼100 times less in pure iodine vapor. Radiative lifetimes and quenching rate constants of the I_{2}(E,v _{ E } = 8, 13 and D,v _{ D } = 13, 18) vibronic state are also determined. Rate constants of the I_{2}(), v _{ E } = 8–54, CINATs are measured again and compared with those obtained earlier. New data confirm resonance characters of the CINATs found in our laboratory about 10 years ago. Possible reasons of differences between rate constant values obtained in this and earlier works are discussed. It is shown, in particular, that differences in rate constants of nonresonant CINATs are due to admixture of water vapor in iodine.

Insights on the CN B ^{2}Σ^{+} + Ar potential from ultraviolet fluorescence excitation and infrared depletion studies of the CN–Ar complex
View Description Hide DescriptionUVlaserinduced fluorescence and IRUV fluorescence depletion studies have been used to characterize the intermolecular levels of the CN–Ar complex in the excited state correlating with CN B ^{2}Σ^{+} + Ar. Additional CN–Ar features are identified to lower wavenumber than reported previously. Fluorescence depletion spectra are recorded to confirm that these CN–Ar features and other higher energy features in the B–Xspectrum originate from a common ground state level. The UV depletion is induced by IR excitation of CN–Ar from the ground state zeropoint level to a hindered internal rotor state (n ^{ K } = 1^{1}) in the CN overtone region. The lowest energy feature in the B–Xspectrum at 25 714.1 cm^{−1} is assigned as a transition to the zeropoint level of the B state and also yields its binding energy,D _{0} = 186(2) cm^{−1}, which is in excellent accord with theoretical predictions. The next feature approximately 40 cm^{−1} higher is attributed to overlapping transitions to intermolecular levels with bend () or stretch (v _{s} = 1) excitation. Yet higher features (previously reported) are also assigned, based on their transition type and wavenumber, which are consistent with the intermolecular energy level pattern computed theoretically. Finally, the intensity profile of the lowest energy features in the B–Xspectrum reflects the predicted change in the CN (B ^{2}Σ^{+}, X ^{2}Σ^{+}) + Ar potentials upon electronic excitation from a weakly anisotropic potential about the linear N≡C–Ar configuration in the ground state to a more strongly bound linear C≡N–Ar structure in the excited B electronic state.

Experimental characterization of the CN X ^{2}Σ^{+} + Ar and H_{2} potentials via infraredultraviolet double resonance spectroscopy
View Description Hide DescriptionThe hindered internal rotor states (n ^{ K } = 0^{0}, 1^{1}, and 1^{0}) of the CNAr complex with two quanta of CN stretch (v _{CN} = 2), along with its ground state (v _{CN} = 0), have been characterized by IRUV double resonance and UV spectroscopy. Analysis of rotationally structured bands enable n ^{ K } assignments and reveal perturbations due to Coriolis coupling between two closely spaced hindered rotor states, n ^{ K } = 1^{1} and 1^{0}. A deperturbation analysis is carried out to derive accurate rotational constants and their associated CN centerofmass to Ar bond lengths as well as the magnitude of the coupling. The energetic ordering and spacings of the CNAr hindered rotor states provide a direct experimental probe of the angular dependence of the CN X ^{2}Σ^{+} + Ar potential and permit radially averaged anisotropy parameters (V _{10} = 5.2 cm^{−1} and V _{20} = 3.2 cm^{−1}) to be determined. This analysis indicates a relatively flat potential about a linear N≡C–Ar configuration with a barrier to CN internal rotation of only ∼12 cm^{−1}. The angular potentials determined from experiment and ab initio theory are in good accord, although theory predicts a higher barrier to CN internal rotation. A similar approach yields the infrared spectrum of H_{2}CN in the CN overtone region, which exhibits a rotationally resolved Σ ← Σ parallel band that is consistent with theoretical predictions for orthoH_{2}CN.

Product branching ratios in photodissociation of phenyl radical: A theoretical ab initio/Rice–Ramsperger–Kassel–Marcus study
View Description Hide DescriptionAb initio CCSD(T)/CBS//B3LYP/6311G** calculations of the potential energy surface for possible dissociation channels of the phenyl radical are combined with microcanonical Rice–Ramsperger–Kassel–Marcus calculations of reaction rate constants in order to predict statistical product branching ratios in photodissociation of cC_{6}H_{5} at various wavelengths. The results indicate that at 248 nm the photodissociation process is dominated by the production of orthobenzyne via direct elimination of a hydrogen atom from the phenyl radical. At 193 nm, the statistical branching ratios are computed to be 63.4%, 21.1%, and 14.4% for the oC_{6}H_{4} + H, lC_{6}H_{4} ((Z)hexa3ene1,5diyne) + H, and nC_{4}H_{3} + C_{2}H_{2} products, respectively, in a contradiction with recent experimental measurements, which showed C_{4}H_{3} + C_{2}H_{2} as the major product. Although two lower energy pathways to the iC_{4}H_{3} + C_{2}H_{2} products are identified, they appeared to be kinetically unfavorable and the computed statistical branching ratio of iC_{4}H_{3} + C_{2}H_{2} does not exceed 1%. To explain the disagreement with experiment, we optimized conical intersections between the ground and the first excited electronic states of C_{6}H_{5} and, based on their structures and energies, suggested the following photodissociation mechanism at 193 nm: cC_{6}H_{5} 1 → absorption of a photon → electronically excited 1 → internal conversion to the lowest excited state → conversion to the ground electronic state via conical intersections at CI2 or CI3 → nonstatistical decay of the vibrationally excited radical favoring the formation of the nC_{4}H_{3} + C_{2}H_{2} products. This scenario can be attained if the intramolecular vibrational redistribution in the CI2 or CI3 structures in the ground electronic state is slower than their dissociation to nC_{4}H_{3} + C_{2}H_{2} driven by the dynamical preference.

A theoretical study on structures, energetics, and spectra of Br^{–}.nCO_{2} clusters: Towards bridging the gap between microdomain and macrodomain
View Description Hide DescriptionStructures, energetics, and spectra of Br^{–}.nCO_{2} (n = 18) clusters are studied based on ab initio electronic structure theory. The geometry of each size of clusters is evaluated by employing secondorder MollerPlesset (MP2) perturbation theory. It is observed that the solvent CO_{2} molecules approach the bromide moiety from one side in an asymmetric fashion except for the Br^{–}.8CO_{2} cluster. Simple electrostatic model for chargequadrupole interactions is valid for the Br^{–}.nCO_{2} clusters. Reduced variational space based energy decomposition method shows that the electrostatic interaction is the major component and polarization and charge transferenergies are the other significant components of the total interaction energy. Both adiabatic and vertical electron detachment energies and solvation energies are calculated at MP2 level of theory. We have observed an excellent agreement between theory and experiment for the vertical detachment and solvation energies. Calculated quantities based on the analytical expression which connects the finite domain to macroscopic one are found to be very good in agreement with the available experimental results. The present study reveals a 2.6 eV increase in the detachment energy of bromide anion due to the solvation effect of CO_{2}, which is relatively small compared to that of the corresponding 4.7 eV increase in detachment energy in water.

Electron attachment to antipyretics: Possible implications of their metabolic pathways
View Description Hide DescriptionThe emptylevel structures and formation of negative ion states via resonance attachment of lowenergy (0–15 eV) electrons into vacant molecular orbitals in a series of nonsteroidal antiinflammatory drugs (NSAIDs), namely aspirin, paracetamol, phenacetin, and ibuprofen, were investigated in vacuo by electron transmission and dissociative electron attachment (DEA) spectroscopies, with the aim to model the behavior of these antipyretic agents under reductive conditions in vivo. The experimental findings are interpreted with the support of density functional theory calculations. The negative and neutral fragments formed by DEA in the gas phase display similarities with the main metabolites of these commonly used NSAIDs generated in vivo by the action of cytochrome P450 enzymes, as well as with several known active agents. It is concluded that xenobiotic molecules which possess pronounced electronaccepting properties could in principle follow metabolic pathways which parallel the gasphase dissociative decay channels observed in the DEA spectra at incident electron energies below 1 eV. Unwanted side effects as, e.g., hepatoxicity or carcinogenicity produced by the NSAIDs under study in human organism are discussed within the “free radical model” framework, reported earlier to describe the toxic action of the wellknown model toxicant carbon tetrachloride.

SubDoppler infrared spectroscopy of CH_{2}D radical in a slit supersonic jet: Isotopic symmetry breaking in the CH stretching manifold
View Description Hide DescriptionFirst highresolution infrared absorption spectra in the fundamental symmetric/asymmetric CH stretching region of isotopically substituted methyl radical, CH_{2}D, are reported and analyzed. These studies become feasible in the difference frequency spectrometer due to (i) high density radical generation via dissociative electron attachment to CH_{2}DI in a discharge, (ii) low rotational temperatures (23 K) from supersonic cooling in a slit expansion, (iii) long absorption path length (64 cm) along the slit axes, and (iv) near shot noise limited absorption sensitivity (). The spectra are fully rovibrationally resolved and fit to an asymmetric top rotational Hamiltonian to yield rotational/centrifugal constants and vibrational band origins. In addition, the slit expansion collisionally quenches the transverse velocity distribution along the laser probe direction, yielding subDoppler resolution of spinrotation structure and even partial resolution of nuclear hyperfine structure for each rovibrational line. Global leastsquares fits to the line shapes provide additional information on spinrotation and nuclear hyperfine constants, which complement and clarify previous FTIR studies [K. Kawaguchi, Can. J. Phys.79, 449 (2001)]10.1139/p00093 of CH_{2}D in the outofplane bending region. Finally, analysis of the spectral data from the full isotopomeric CH_{m}D_{3–m} series based on harmonically coupled Morse oscillators establishes a predictive framework for describing the manifold of planar stretching vibrations in this fundamental combustion radical.