Volume 136, Issue 13, 07 April 2012

We have observed large secondorder nonlinear optical and vibrational circular dichroism (VCD) responses in a chargetransfertype LHistidinium salt. Using Xray Diffraction, VCD spectroscopy, and timedependent density functional theory to characterize the compound, we employ a twolevel model to explain and quantify the strongly enhanced optical signals. We find that both linear and nonlinear optical responses are greatly enhanced by a single lowlying chargetransfer state.
 ARTICLES

 Theoretical Methods and Algorithms

Largescale firstprinciples molecular dynamics for electrochemical systems with O(N) methods
View Description Hide DescriptionA method for largescale firstprinciples molecular dynamics (MD) simulations on electrochemical systems has been developed by combining the effective screening medium (ESM) method with O(N) density functional theory(DFT). This implementation has been significantly simplified by the introduction of neutral atom potentials, which minimizes the modifications to existing DFT code. In order to demonstrate ability of this implementation, it has been applied to an electrochemical system consisting of a HSi(111) electrode, which is a candidate anode for highcapacity Liion secondary batteries, and a propylene carbonate (PC)solvent to simulate how PC molecules in the vicinity of the electrode surface respond to an imposed electric field. The largescale MD simulation clearly demonstrates that the combination of the ESM and O(N) DFT methods provides a useful tool for firstprinciples investigation of complicated electrochemical systems such as highcapacity batteries.

Resolution of identity approach for the KohnSham correlation energy within the exactexchange randomphase approximation
View Description Hide DescriptionTwo related methods to calculate the KohnSham correlationenergy within the framework of the adiabaticconnection fluctuationdissipation theorem are presented. The required couplingstrengthdependent densitydensity response functions are calculated within exactexchange timedependent densityfunctional theory, i.e., within timedependent densityfunctional response theory using the full frequencydependent exchange kernel in addition to the Coulomb kernel. The resulting resolutionofidentity exactexchange randomphase approximation (RIEXXRPA) methods in contrast to previous EXXRPA methods employ an auxiliary basis set (RI basis set) to improve the computational efficiency, in particular, to reduce the formal scaling of the computational effort with respect to the system size N from N ^{6} to N ^{5}. Moreover, the presented RIEXXRPA methods, in contrast to previous ones, do not treat products of occupied times unoccupied orbitals as if they were linearly independent. Finally, terms neglected in previous EXXRPA methods can be included, which leads to a method designated RIEXXRPA+, while the method without these extra terms is simply referred to as RIEXXRPA. Both EXXRPA methods are shown to yield total energies, reaction energies of small molecules, and binding energies of noncovalently bonded dimers of a quality that is similar and in some cases even better than that obtained with quantum chemistry methods such as MøllerPlesset perturbation theory of second order (MP2) or with the coupled cluster singles doubles method. In contrast to MP2 and to conventional densityfunctional methods, the presented RIEXXRPA methods are able to treat static correlation.

A resonance mechanism of efficient energy transfer mediated by FennaMatthewsOlson complex
View Description Hide DescriptionThe WignerWeisskopftype model developed by Alicki and Giraldi [J. Phys. B44, 154020 (2011)]10.1088/09534075/44/15/154020 is applied to the biological process of energy transfer from a large peripheral light harvesting antenna to the reaction center. This process is mediated by the FennaMatthewsOlson (FMO) photosynthetic complex with a remarkably high efficiency. The proposed model provides a simple resonance mechanism of this phenomenon employing exciton coherent motion and is described by analytical formulas. A coupling to the vibrational environment is a necessary component of this mechanism as well as a finetuning of the FMO complex Hamiltonian. The role of the relatively strong coupling to the energy sink in achieving the resonance condition and the absence of heating of the vibrational environment are emphasized.

A comparison of the value of viscosity for several water models using Poiseuille flow in a nanochannel
View Description Hide DescriptionThe viscositytemperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nanochannel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.

Multilayer coarsegraining polarization model for treating electrostatic interactions of solvated αconotoxin peptides
View Description Hide DescriptionA multilayer coarsegraining (CG) model is presented for treating the electrostatic interactions of solvated αconotoxin peptides. According to the sensitivity to the electrostatic environment, a hybrid set of electrostatic parameters, such as secondarystructure and residuebased dipoles, and atomcentered partial charges, are adopted. For the polarization “inert” secondarystructures and residues, the fragment dipole moments are distributed within narrow ranges with the magnitude close to zero. The coarsegraining fragment dipoles are parameterized from a large training set (10 000 configurations) to reproduce the electrostatic features of molecular fragments. In contrast, the electrostatically “sensitive” atoms exhibit large fluctuations of charges with the varied environments. The environmentdependent variable charges are updated in each energetic calculation. The electrostatic interaction of the whole chemical system is hence partitioned into several subterms coming from the fragment dipoledipole, (fragment) dipole(atom) charge, and atom chargecharge interactions. A large number of test calculations on the relative energies of cyclopeptide conformers have demonstrated that the multilayer CG electrostatic model presents better performance than the nonpolarized force fields, in comparison with the densityfunctional theory and the fully polarized force field model. The selection of CG fragment centers, mass or geometric center, has little influence on the fragmentbased dipoledipole interactions. The multilayer partition of electrostaticpolarization is expected to be applied to many biologically interesting and complicated phenomena.

Soft repulsive mixtures under gravity: Brazilnut effect, depletion bubbles, boundary layering, nonequilibrium shaking
View Description Hide DescriptionA binary mixture of particles interacting via longranged repulsive forces is studied in gravity by computer simulation and theory. The more repulsive Aparticles create a depletion zone of less repulsive Bparticles around them reminiscent to a bubble. Applying Archimedes’ principle effectively to this bubble, an Aparticle can be lifted in a fluid background of Bparticles. This “depletion bubble” mechanism explains and predicts a brazilnut effect where the heavier Aparticles float on top of the lighter Bparticles. It also implies an effective attraction of an Aparticle towards a hard container bottom wall which leads to boundary layering of Aparticles. Additionally, we have studied a periodic inversion of gravity causing perpetuous mutual penetration of the mixture in a slit geometry. In this nonequilibrium case of timedependent gravity, the boundary layering persists. Our results are based on computer simulations and density functional theory of a twodimensional binary mixture of colloidal repulsive dipoles. The predicted effects also occur for other longranged repulsive interactions and in three spatial dimensions. They are therefore verifiable in settling experiments on dipolar or charged colloidal mixtures as well as in charged granulates and dusty plasmas.

Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent
View Description Hide DescriptionQuantum mechanical/molecular mechanical (QM/MM) free energy calculation presents a significant challenge due to an excessive number of QM calculations. A useful approach for reducing the computational cost is that based on the mean field approximation to the QM subsystem. Here, we describe such a meanfield QM/MM theory for electronically polarizable systems by starting from the Hartree product ansatz for the total system and invoking a variational principle of free energy. The MM part is then recast to a classical polarizable model by introducing the charge response kernel. Numerical test shows that the potential of mean force (PMF) thus obtained agrees quantitatively with that obtained from a direct QM/MM calculation, indicating the utility of selfconsistent meanfield approximation. Next, we apply the obtained method to prototypical reactions in several qualitatively different solvents and make a systematic comparison of polarization effects. The results show that in aqueous solution the PMF does not depend very much on the water models employed, while in nonaqueous solutions the PMF is significantly affected by explicit polarization. For example, the free energy barrier for a phosphoryl dissociationreaction in acetone and cyclohexane is found to increase by more than 10 kcal/mol when switching the solvent model from an empirical to explicitly polarizable one. The reason for this is discussed based on the parametrization of empirical nonpolarizable models.

Field induced gradient simulations: A high throughput method for computing chemical potentials in multicomponent systems
View Description Hide DescriptionWe present a simulation method for direct computation of chemical potentials in multicomponent systems. The method involves application of a field to generate spatial gradients in the species number densities at equilibrium, from which the chemical potential of each species is theoretically estimated. A single simulation yields results over a range of thermodynamic states, as in high throughput experiments, and the method remains computationally efficient even at high number densities since it does not involve particle insertion at high densities. We illustrate the method by Monte Carlo simulations of binary hard sphere mixtures of particles with different sizes in a gravitational field. The results of the gradient Monte Carlo method are found to be in good agreement with chemical potentials computed using the classical Widom particle insertion method for spatially uniform systems.

Quantum dynamics in continuum for proton transport—Generalized correlation
View Description Hide DescriptionAs a key process of many biological reactions such as biological energy transduction or human sensory systems, protontransport has attracted much research attention in biological, biophysical, and mathematical fields. A quantum dynamics in continuum framework has been proposed to study proton permeation through membrane proteins in our earlier work and the present work focuses on the generalized correlation of protons with their environment. Being complementary to electrostatic potentials, generalized correlations consist of protonproton, protonion, protonprotein, and protonwater interactions. In our approach, protons are treated as quantum particles while other components of generalized correlations are described classically and in different levels of approximations upon simulation feasibility and difficulty. Specifically, the membrane protein is modeled as a group of discrete atoms, while ion densities are approximated by Boltzmann distributions, and water molecules are represented as a dielectric continuum. These protonenvironment interactions are formulated as convolutions between number densities of species and their corresponding interaction kernels, in which parameters are obtained from experimental data. In the present formulation, generalized correlations are important components in the total Hamiltonian of protons, and thus is seamlessly embedded in the multiscale/multiphysics total variational model of the system. It takes care of nonelectrostatic interactions, including the finite size effect, the geometry confinement induced channel barriers, dehydration and hydrogen bond effects, etc. The variational principle or the EulerLagrange equation is utilized to minimize the total energy functional, which includes the total Hamiltonian of protons, and obtain a new version of generalized LaplaceBeltrami equation, generalized PoissonBoltzmann equation and generalized KohnSham equation. A set of numerical algorithms, such as the matched interface and boundary method, the Dirichlet to Neumann mapping, Gummel iteration, and Krylov space techniques, is employed to improve the accuracy, efficiency, and robustness of model simulations. Finally, comparisons between the present model predictions and experimental data of currentvoltage curves, as well as currentconcentration curves of the Gramicidin A channel, verify our new model.

Longitudinal static optical properties of hydrogen chains: Finite field extrapolations of matrix product state calculations
View Description Hide DescriptionWe have implemented the sweep algorithm for the variational optimization of SU(2) ⊗ U(1) (spin and particle number) invariant matrix product states (MPS) for general spin and particle number invariant fermionic Hamiltonians. This class includes nonrelativistic quantum chemical systems within the BornOppenheimer approximation. Highaccuracy ab initio finite field results of the longitudinal static polarizabilities and second hyperpolarizabilities of onedimensional hydrogen chains are presented. This allows to assess the performance of other quantum chemical methods. For small basis sets, MPS calculations in the saturation regime of the optical response properties can be performed. These results are extrapolated to the thermodynamic limit.

Multireference Fock space coupled cluster method in the effective and intermediate Hamiltonian formulation for the (2,0) sector
View Description Hide DescriptionThe effective and intermediate Hamiltonian (IH) multireference coupled cluster (CC) method with singles (S) and doubles (D) within the double electron attached (2,0) sector of the Fock space (FS) is formulated and implemented. The intermediate Hamiltonian realization of the (2,0) FS problem allows to replace the iterative scheme of the FSCC equations based on the effective Hamiltonian with the diagonalization of the properly constructed matrix. The proposed method, IHFSCCSD (2,0), is rigorously sizeextensive, easy to code, and numerically very efficient with the results comparable or slightly better than equationofmotion ones at the CCSDT (T—triples) level. The performance of the method is discussed on the basis of test calculations for potential energy curves of the systems for which double positive ions dissociate into closed shell fragments (e.g., Na_{2} dimer). The double electron attachment (DEA) scheme can be also useful in determination of the excitation spectra for difficult cases. The example is a carbon atom which has two electrons out of the closed shell structure. The newly implemented method is also analyzed by plotting potential energy curve for twisted ethylene case as a function of a dihedral angle between two methylene groups. Using DEA scheme one obtains a smooth, cusp free curve.

Firstprinciples calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory
View Description Hide DescriptionDespite being one of the most important thermodynamic variables, pH has yet to be incorporated into firstprinciples thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a firstprinciples approach to calculate their formation energies under protonchemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to firstprinciple calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acidbase chemistry. By performing firstprinciples molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H^{+}, OH^{−}, NH_{3}, NH_{4} ^{+}, HCOOH, and HCOO^{−} in water. The deduced autodissociation constant of water and the difference in the pKa values of NH_{3} and HCOOH show good agreement with known experimental values. Our firstprinciples approach can be further extended and applied to other bio and electrochemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

The J = 1 para levels of the v = 0 to 6 np singlet Rydberg series of molecular hydrogen revisited
View Description Hide DescriptionThe energies and the widths of the J = 1 para levels of the v = 0 to 6 Rydbergnp singlet series of molecular hydrogen with absolute intensities of the R(0) and P(2) absorption lines were measured by a high – resolution synchrotron radiation experiment and calculated through a full ab initio multichannel quantum defect theory approach. On the basis of the agreement between theory and experiment, 31 levels were either reassigned or assigned for the first time.

Timeslice velocitymap ion imaging studies of the photodissociation of NO in the vacuum ultraviolet region
View Description Hide DescriptionThe timeslice velocitymap ion imaging and the resonant fourwave mixing techniques are combined to study the photodissociation of NO in the vacuum ultraviolet (VUV) region around 13.5 eV above the ionization potential. The neutral atoms, i.e., N(^{2}D^{o}), O(^{3}P_{2}), O(^{3}P_{1}), O(^{3}P_{0}), and O(^{1}D_{2}), are probed by exciting an autoionization line of O(^{1}D_{2}) or N(^{2}D^{o}), or an intermediate Rydberg state of O(^{3}P_{0,1,2}). Old and new autoionization lines of O(^{1}D_{2}) and N(^{2}D^{o}) in this region have been measured and newer frequencies are given for them. The photodissociation channels producing N(^{2}D^{o}) + O(^{3}P), N(^{2}D^{o}) + O(^{1}D_{2}), N(^{2}D^{o}) + O(^{1}S_{0}), and N(^{2}P^{o}) + O(^{3}P) have all been identified. This is the first time that a single VUVphoton has been used to study the photodissociation of NO in this energy region. Our measurements of the angular distributions show that the recoil anisotropy parameters (β) for all the dissociation channels except for the N(^{2}D^{o}) + O(^{1}S_{0}) channel are minus at each of the wavelengths used in the present study. Thus direct excitation of NO by a single VUVphoton in this energy region leads to excitation of states with Σ or Δ symmetry (ΔΩ = ±1), explaining the observed perpendicular transition.

Ultrafast structural and isomerization dynamics in the Rydbergexited Quadricyclane: Norbornadiene system
View Description Hide DescriptionThe quadricyclane – norbornadiene system is an important model for the isomerizationdynamics between highly strained molecules. In a breakthrough observation for a polyatomic molecular system of that complexity, we follow the photoionization from Rydberg states in the timedomain to derive a measure for the timedependent structuraldynamics and the timeevolving structural dispersion even while the molecule is crossing electronic surfaces. The photoexcitation to the 3s and 3pRydberg states deposits significant amounts of energy into vibrational motions. We observe the formation and evolution of the vibrational wavepacket on the Rydbergsurface and the internal conversion from the 3pRydberg states to the 3s state. In that state, quadricyclane isomerizes to norbornadiene with a time constant of τ_{2} = 136(45) fs. The lifetime of the 3pRydberg state in quadricyclane is τ_{1} = 320(31) and the lifetime of the 3sRydberg state in norbornadiene is τ_{3} = 394(32).

Active control of the lifetime of excited resonance states by means of laser pulses
View Description Hide DescriptionQuantum control of the lifetime of a system in an excited resonance state is investigated theoretically by creating coherent superpositions of overlapping resonances. This control scheme exploits the quantum interference occurring between the overlapping resonances, which can be controlled by varying the width of the laser pulse that creates the superposition state. The scheme is applied to a realistic model of the Br_{2}(B)Ne predissociation decay dynamics through a threedimensional wave packet method. It is shown that extensive control of the system lifetime is achievable, both enhancing and damping it remarkably. An experimental realization of the control scheme is suggested.

Explicitly correlated Gaussian calculations of the ^{2} P ^{ o } Rydberg spectrum of the lithium atom
View Description Hide DescriptionAccurate quantummechanical nonrelativistic variational calculations are performed for the nine lowest members of the ^{2} P ^{ o }Rydberg series (1s ^{2} np ^{1}, n = 2, …, 10) of the lithium atom. The effect of the finite nuclear mass is included in the calculations allowing for determining the isotopic shifts of the energy levels. The wave functions of the states are expanded in terms of allelectron explicitly correlated Gaussian functions. The exponential parameters of the Gaussians are variationally optimized with the aid of the analytical energy gradient determined with respect to those parameters. The calculated state energies are compared with the available experimental data.

Computational study of the rovibrational spectrum of (OCS)_{2}
View Description Hide DescriptionIn this paper, we report a new intermolecular potential energy surface and rovibrational transition frequencies and line strengths computed for the OCS dimer. The potential is made by fitting energies obtained from explicitly correlated coupledcluster calculations and fit using an interpolating moving least squares method. The rovibrational Schroedinger equation is solved with a symmetryadapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. On the potential energy surface we find, previously unknown, crossshaped isomers and also polar and nonpolar isomers. The associated wavefunctions and energy levels are presented. To identify polar and cross states we use both calculations of line strengths and vibrational parent analysis. Calculated rotational constants differ from their experimental counterparts by less than 0.001 cm^{−1}.

Absolute photoionization crosssection of the propargyl radical^{a)}
View Description Hide DescriptionUsing synchrotrongenerated vacuumultraviolet radiation and multiplexed timeresolved photoionizationmass spectrometry we have measured the absolute photoionization crosssection for the propargyl (C3H3) radical, , relative to the known absolute crosssection of the methyl (CH3) radical. We generated a stoichiometric 1:1 ratio of C3H3 : CH3 from 193 nm photolysis of two different C4H6 isomers (1butyne and 1,3butadiene). Photolysis of 1butyne yielded values of Mb and Mb, whereas photolysis of 1,3butadiene yielded values of Mb and Mb. These measurements place our relative photoionization crosssection spectrum for propargyl on an absolute scale between 8.6 and 10.5 eV. The crosssection derived from our results is approximately a factor of three larger than previous determinations.

C–C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined nearedge xray absorption fine structure, xray photoemission spectroscopy, and density functional theory approach
View Description Hide DescriptionWe present the results of an experimental and theoretical investigation of monosubstituted ethyl, vinyl, and ethynylferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotronradiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1sXPS) spectroscopies, and density functional theory(DFT) calculations. Such a combined study is aimed at elucidating the role played by the C–C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1sNEXAFSspectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFSspectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the σ/π hyperconjugation in EtFC and the πconjugation in VFC and EFC.