Volume 141, Issue 1, 07 July 2014

Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogenbonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbatesubstrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanolmethanol and methanolsurface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.
 ARTICLES

 Theoretical Methods and Algorithms

An analytic mapping of oligomer potential energy surfaces to an effective Frenkel model
View Description Hide DescriptionWhile the use of Frenkeltype models for semiconducting polymer assemblies and related molecular aggregates is well established, the direct parametrization of such models based on electronic structure data is attempted less frequently. In this work, we develop a systematic mapping procedure which is adapted to Jtype and Htype homoaggregate systems. The procedure is based upon the analytic solution of an inverse eigenvalue problem for an effective Frenkel Hamiltonian with nearestneighbor couplings. Vibronic interactions are included for both sitelocal and sitecorrelated modes. For illustration, an application is presented to the excitedstate ab initio potential energy surfaces (PESs) of an oligothiophene octamer. The procedure performs a pointwise mapping of the PESs of oligomers of arbitrary chain length n, provided that the electronic ground state and any two of the n lowest adiabatic states of the excitonic manifold of interest are known. These three states are reproduced exactly by the procedure while the remaining n − 2 states of the excitonic manifold can be predicted. Explicit conditions are derived permitting to verify whether a given data set is compatible with the effective Frenkel model under study.

Lattice Boltzmann method for mixtures at variable Schmidt number
View Description Hide DescriptionWhen simulating multicomponent mixtures via the Lattice Boltzmann Method, it is desirable to control the mutual diffusivity between species while maintaining the viscosity of the solution fixed. This goal is herein achieved by a modification of the multicomponent BhatnagarGrossKrook evolution equations by introducing two different timescales for mass and momentum diffusion. Diffusivity is thus controlled by an effective drag force acting between species. Numerical simulations confirm the accuracy of the method for neutral binary and charged ternary mixtures in bulk conditions. The simulation of a charged mixture in a charged slit channel show that the conductivity and electroosmotic mobility exhibit a departure from the HelmholtzSmoluchowski prediction at high diffusivity.

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models
View Description Hide DescriptionEarlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnPtype models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of , which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

Analyzing the errors of DFT approximations for compressed water systems
View Description Hide DescriptionWe report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchangecorrelation functionals, and we characterize their errors before and after correction for 1 and 2body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm^{3} where the experimental pressure is 15 kilobars; second, thermal samples of compressed water clusters from the trimer to the 27mer. For the liquid, we report four firstprinciples molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1 and 2body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutrondiffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2body and beyond2body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond2body errors of DFT make a substantial contribution to the overall errors, so that correction for 1 and 2body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput.9, 1103 (2013)] gives a reasonably good way of correcting for beyond2body errors, after which the remaining errors are typically 0.5 mE h ≃ 15 meV/monomer for the liquid and the clusters.

Rates of exponential decay in systems of discrete energy levels by Stieltjes imaging
View Description Hide DescriptionAn isolated bound state coupled to a continuum shows an exponential decay of its survival probability. Rates of the exponential decay occurring due to the boundcontinuum coupling can be recovered from discretized continuum (L ^{2}) calculations using a computational technique known as StieltjesChebyshev moment theory or Stieltjes imaging. At the same time, some genuinely discrete level systems, e.g., BixonJortner model, also show an exponential (or approximately exponential) decay of the initially populated level before the onset of quantum revivals. Here, we demonstrate numerically that Stieltjes imaging can be used for calculation of the rates of the exponential decay in such discrete level systems. We apply the Stieltjes imaging technique to the approximately exponential decay of innervalence vacancies in transbutadiene in order to show that the breakdown of the molecular orbital picture of ionization in the inner valence region can be physically interpreted as an energyforbidden CosterKronig transition.

Yukawa particles in a confining potential
View Description Hide DescriptionWe study the density distribution of repulsive Yukawa particles confined by an external potential. In the weak coupling limit, we show that the meanfield theory is able to accurately account for the particle distribution. In the strong coupling limit, the correlations between the particles become important and the meanfield theory fails. For strongly correlated systems, we construct a density functional theory which provides an excellent description of the particle distribution, without any adjustable parameters.

How to calculate linear absorption spectra with lifetime broadening using fewest switches surface hopping trajectories: A simple generalization of groundstate Kubo theory
View Description Hide DescriptionIn this paper, we develop a surface hopping approach for calculating linear absorption spectra using ensembles of classical trajectories propagated on both the ground and excited potential energy surfaces. We demonstrate that our method allows the dipoledipole correlation function to be determined exactly for the model problem of two shifted, uncoupled harmonic potentials with the same harmonic frequency. For systems where nonadiabatic dynamics and electronic relaxation are present, preliminary results show that our method produces spectra in better agreement with the results of exact quantum dynamics calculations than spectra obtained using the standard groundstate Kubo formalism. As such, our proposed surface hopping approach should find immediate use for modeling condensed phase spectra, especially for expensive calculations using ab initio potential energy surfaces.

Understanding the manybody expansion for large systems. I. Precision considerations
View Description Hide DescriptionElectronic structure methods based on loworder “nbody” expansions are an increasingly popular means to defeat the highly nonlinear scaling of ab initio quantum chemistry calculations, taking advantage of the inherently distributable nature of the numerous subsystem calculations. Here, we examine how the finite precision of these subsystem calculations manifests in applications to large systems, in this case, a sequence of water clusters ranging in size up to . Using two different computer implementations of the nbody expansion, one fully integrated into a quantum chemistry program and the other written as a separate driver routine for the same program, we examine the reproducibility of total binding energies as a function of cluster size. The combinatorial nature of the nbody expansion amplifies subtle differences between the two implementations, especially for n ⩾ 4, leading to total energies that differ by as much as several kcal/mol between two implementations of what is ostensibly the same method. This behavior can be understood based on a propagationoferrors analysis applied to a closedform expression for the nbody expansion, which is derived here for the first time. Discrepancies between the two implementations arise primarily from the Coulomb selfenergy correction that is required when electrostatic embedding charges are implemented by means of an external driver program. For reliable results in large systems, our analysis suggests that script or driverbased implementations should read binary output files from an electronic structure program, in full double precision, or better yet be fully integrated in a way that avoids the need to compute the aforementioned selfenergy. Moreover, fourbody and higherorder expansions may be too sensitive to numerical thresholds to be of practical use in large systems.

Spin dynamics simulation of electron spin relaxation in Ni^{2 +}(aq)
View Description Hide DescriptionThe ability to quantitatively predict and analyze the rate of electron spin relaxation of openshell systems is important for electron paramagnetic resonance and paramagnetic nuclear magnetic resonance spectroscopies. We present a combined molecular dynamics (MD), quantum chemistry (QC), and spin dynamics simulation method for calculating such spin relaxation rates. The method is based on the sampling of a MD trajectory by QC calculations, to produce instantaneous parameters of the spin Hamiltonian used, in turn, to numerically solve the Liouvillevon Neumann equation for the time evolution of the spin density matrix. We demonstrate the approach by simulating the relaxation of electron spin in an aqueous solution of Ni ^{2 +} ion. The spinlattice (T 1) and spinspin (T 2) relaxation rates are extracted directly from the simulations of the time dependence of the longitudinal and transverse magnetization, respectively. Good agreement with the available, indirectly obtained experimental data is obtained by our method.

Firstorder nonadiabatic coupling matrix elements between excited states: A Lagrangian formulation at the CIS, RPA, TDHF, and TDDFT levels
View Description Hide DescriptionAnalytic expressions for the firstorder nonadiabatic coupling matrix elements between electronically excited states are first formulated exactly via both timeindependent equation of motion and timedependent response theory, and are then approximated at the configuration interaction singles, particlehole/particleparticle random phase approximation, and timedependent density functional theory/HartreeFock levels of theory. Note that, to get the Pulay terms arising from the derivatives of basis functions, the standard response theory designed for electronic perturbations has to be extended to nuclear derivatives. The results are further recast into a Lagrangian form that is similar to that for excitedstate energy gradients and allows to use atomic orbital based direct algorithms for large molecules.

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates
View Description Hide DescriptionPrincipal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a lowdimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the smallamplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and wellresolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.
 Advanced Experimental Techniques

Vibrational dynamics of zerofieldsplitting hamiltonian in gadoliniumbased MRI contrast agents from ab initio molecular dynamics
View Description Hide DescriptionThe electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zerofieldsplitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zerofieldsplitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zerofieldsplitting was significantly influenced by this substitution.
 Atoms, Molecules, and Clusters

Photodissociation dynamics of superexcited O_{2}: Dissociation channels O(^{5}S) vs. O(^{3}S)
View Description Hide DescriptionThe photodissociation dynamics of O2, O2 + hυ → O(^{3}P) + O(2p ^{3}(^{4}S)3s, ^{3}S/^{5}S), has been studied by combining the XUV laser pump / UV laser probe and velocity map imaging methods in the photon energy range 14.64–15.20 eV. The fragment yield spectra of O(^{3}S) and O(^{5}S) and their velocity map images have been recorded using the stateselective (1+1) REMPI method to detect the fragments. The fragment yield spectra show resolved fine structure that arises from the predissociated Rydberg states I, I^{′} and I^{″} (^{3}ΠΩ = 0,1,2). The branching ratios between the two decay channels have been measured by onephoton ionization of the fragments O(^{3}S) and O(^{5}S) simultaneously. It is surprising to find that the dissociation cross sections for the production of O(^{5}S) are larger than, or comparable to, those of O(^{3}S) for the I and I^{′} states, while the cross sections for the production of O(^{5}S) are smaller than those of O(^{3}S) for the I^{″} state. All fragments O(^{5}S) arise from perpendicular transitions, which provides direct experimental evidence about the symmetry assignments of the states I, I^{′} and I^{″} excited in this energy region. Although most of the fragments O(^{3}S) arise from perpendicular transitions, some of them are from parallel transitions. Based on the calculated ab initio potential energy curves, we propose that the neutral dissociation into O(^{3}P) + O(^{3}S) occurs mainly via the interaction of the Rydberg states I, I^{′}, and I^{″} with the vibrational continuum of the diabatic 8^{3}Πu state ( ), while the neutral dissociation into O(^{3}P) + O(^{5}S) occurs mainly via the interaction of Rydberg states I, I^{′}, and I^{″} with the diabatic 7^{3}Πu ( ).

Theoretical investigations of the IO,^{q+} (q = 2, 3, 4) multicharged ions: Metastability, characterization and spectroscopy
View Description Hide DescriptionUsing ab initio methodology, we studied the IO^{q+} (q = 2, 3, 4) multicharged ions. Benchmark computations on the IO(X^{2}Π) neutral species allow validate the current procedure. For IO^{2+}, several potential wells were found on the ground and the electronic excited states potentials with potential barriers with respect to dissociation, where this dication can exist in the gas phase as longlived metastable molecules. We confirm hence the recent observation of the dication by mass spectrometry. Moreover, we predict the existence of the metastable IO^{3+} trication, where a shallow potential well along the IO internuclear distance is computed. This potential well supports more than 10 vibrational levels. The IO^{3+} excited states are repulsive in nature, as well as the computed potentials for the IO^{4+} tetracation. For the bound states, we give a set of spectroscopic parameters including excitation transition energies, equilibrium distances, harmonic and anharmonic vibrational terms, and rotational constants. At the MRCI + Q/augccpV5Z(PP) level, the adiabatic double and triple ionization energies of IO are computed to be ∼28.1 eV and ∼55.0 eV, respectively.

Revisiting the relaxation dynamics of isolated pyrrole
View Description Hide DescriptionHerein, the interpretation of the femtosecondscale temporal evolution of the pyrrole ion signal, after excitation in the 267–217 nm interval, recently published by our group [R. Montero, A. Peralta Conde, V. Ovejas, M. FernándezFernández, F. Castaño, J. R. Vázquez de Aldana, and A. Longarte, J. Chem. Phys.137, 064317 (2012)] is revisited. The observation of a shift in the pyrrole^{+} transient respect to zero delay reference, initially attributed to ultrafast dynamics on the πσ^{*} type state (3s a1 ← π 1a2), is demonstrated to be caused by the existence of pump + probe populated states, along the ionization process. The influence of these resonances in pumpprone ionization experiments, when multiphoton probes are used, and the significance of a proper zerotime reference, is discussed. The possibility of preparing the πσ^{*} state by direct excitation is investigated by collecting 1 + 1 photoelectron spectra, at excitation wavelengths ranging from 255 to 219 nm. No conclusive evidences of ionization through this state are found.

Influence of surface coverage on the chemical desorption process
View Description Hide DescriptionIn cold astrophysical environments, some molecules are observed in the gas phase whereas they should have been depleted, frozen on dust grains. In order to solve this problem, astrochemists have proposed that a fraction of molecules synthesized on the surface of dust grains could desorb just after their formation. Recently the chemical desorption process has been demonstrated experimentally, but the key parameters at play have not yet been fully understood. In this article, we propose a new procedure to analyze the ratio of dioxygen and ozone synthesized after O atoms adsorption on oxidized graphite. We demonstrate that the chemical desorption efficiency of the two reaction paths (O+O and O+O2) is different by one order of magnitude. We show the importance of the surface coverage: for the O+O reaction, the chemical desorption efficiency is close to 80% at zero coverage and tends to zero at one monolayer coverage. The coverage dependence of O+O chemical desorption is proved by varying the amount of preadsorbed N2 on the substrate from 0 to 1.5 ML. Finally, we discuss the relevance of the different physical parameters that could play a role in the chemical desorption process: binding energy, enthalpy of formation, and energy transfer from the new molecule to the surface or to other adsorbates.

Properties of reactive oxygen species by quantum Monte Carlo
View Description Hide DescriptionThe electronic properties of the oxygen molecule, in its singlet and triplet states, and of many small oxygencontaining radicals and anions have important roles in different fields of chemistry, biology, and atmospheric science. Nevertheless, the electronic structure of such species is a challenge for ab initio computational approaches because of the difficulties to correctly describe the statical and dynamical correlation effects in presence of one or more unpaired electrons. Only the highestlevel quantum chemical approaches can yield reliable characterizations of their molecular properties, such as binding energies, equilibrium structures, molecular vibrations, charge distribution, and polarizabilities. In this work we use the variational Monte Carlo (VMC) and the lattice regularized Monte Carlo (LRDMC) methods to investigate the equilibrium geometries and molecular properties of oxygen and oxygen reactive species. Quantum Monte Carlo methods are used in combination with the Jastrow Antisymmetrized Geminal Power (JAGP) wave function ansatz, which has been recently shown to effectively describe the statical and dynamical correlation of different molecular systems. In particular, we have studied the oxygen molecule, the superoxide anion, the nitric oxide radical and anion, the hydroxyl and hydroperoxyl radicals and their corresponding anions, and the hydrotrioxyl radical. Overall, the methodology was able to correctly describe the geometrical and electronic properties of these systems, through compact but fullyoptimised basis sets and with a computational cost which scales as N ^{3} − N ^{4}, where N is the number of electrons. This work is therefore opening the way to the accurate study of the energetics and of the reactivity of large and complex oxygen species by first principles.

A timedependent densityfunctional theory and complete active space selfconsistent field method study of vibronic absorption and emission spectra of coumarin
View Description Hide DescriptionTimedependent densityfunctional theory (TDDFT) and complete active space multiconfiguration selfconsistent field (CASSCF) calculations have been used to determine equilibrium structures and vibrational frequencies of the ground state and several singlet lowlying excited states of coumarin. Vertical and adiabatic transition energies of S1, S2, and S3 have been estimated by TDB3LYP and CASSCF/PT2. Calculations predict that the dipoleallowed S1 and S3 states have a character of ^{1}(ππ*), while the dipoleforbidden ^{1}(nπ*) state is responsible for S2. The vibronic absorption and emission spectra of coumarin have been simulated by TDB3LYP and CASSCF calculations within the FranckCondon approximation, respectively. The simulated vibronic spectra show good agreement with the experimental observations available, which allow us to reasonably interpret vibronic features in the S0→S1 and S0→S3 absorption and the S0←S1 emission spectra. Based on the calculated results, activity, intensity, and density of the vibronic transitions and their contribution to the experimental spectrum profile have been discussed.

Helium in chirped laser fields as a timeasymmetric atomic switch
View Description Hide DescriptionTuning the laser parameters exceptional points in the spectrum of the dressed laser helium atom are obtained. The weak linearly polarized laser couples the ground state and the doubly excited Pstates of helium. We show here that for specific chirped laser pulses that encircle an exceptional point one can get the timeasymmetric phenomenon, where for a negative chirped laser pulse the ground state is transformed into the doubly excited autoionization state, while for a positive chirped laser pulse the resonance state is not populated and the neutral helium atoms remains in the ground state as the laser pulse is turned off. Moreover, we show that the results are very sensitive to the closed contour we choose. This timeasymmetric state exchange phenomenon can be considered as a timeasymmetric atomic switch. The optimal timeasymmetric switch is obtained when the closed loop that encircles the exceptional point is large, while for the smallest loops, the timeasymmetric phenomenon does not take place. A systematic way for studying the effect of the chosen closed contour that encircles the exceptional point on the timeasymmetric phenomenon is proposed.

Electron drift velocities in He and water mixtures: Measurements and an assessment of the water vapour crosssection sets
View Description Hide DescriptionThe drift velocity of electrons in mixtures of gaseous water and helium is measured over the range of reduced electric fields 0.1–300 Td using a pulsedTownsend technique. Admixtures of 1% and 2% water to helium are found to produce negative differential conductivity (NDC), despite NDC being absent from the pure gases. The measured drift velocities are used as a further discriminative assessment on the accuracy and completeness of a recently proposed set of electronwater vapour crosssections [K. F. Ness, R. E. Robson, M. J. Brunger, and R. D. White, J. Chem. Phys.136, 024318 (2012)]. A refinement of the momentum transfer crosssection for electronwater vapour scattering is presented, which ensures selfconsistency with the measured drift velocities in mixtures with helium to within approximately 5% over the range of reduced fields considered.