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Classical molecular dynamics simulations are carried out between 190 and 250 K on an ultrathin ice film doped by HCl deposition with a coverage varying from 0.3 to 1.0 monolayer. These conditions are similar to those defined in the experiments described in the companion paper. Within the assumption that the hydracid molecule remains in its molecular form, the order parameters and the diffusion coefficients for the H[sub 2]O molecules are determined in the HCl doped ice film, and compared to the experimental data. The residence times of HC1 at the ice surface are also calculated. Below 200 K, the HC1 molecules are found to remain localized at the ice surface, while above 200 K, the HC1 diffusion inside the film is easy and leads to a strong disorder of the ice structure. Although the formation of hydrates cannot be interpreted by the present calculations, the lowering of the ice melting temperature by 15 K measured in neutron experiments for an HC1 doped ice film is qualitatively explained by simulation results. [ABSTRACT FROM AUTHOR]

Some fluids are known to behave anomalously. The so-called structural anomaly which means that the fluid becomes less structures under isothermal compression is among the most frequently discussed ones. Several methods for quantifying the degree of structural order are described in the literature and are used for calculating the region of structural anomaly. It is generally thought that all of the structural order determinations yield qualitatively identical results. However, no explicit comparison was made. This paper presents such a comparison for the first time. The results of some definitions are shown to contradict the intuitive notion of a fluid. On the basis of this comparison, we show that the region of structural anomaly can be most reliably determined from the behavior of the excess entropy. [ABSTRACT FROM AUTHOR]

Smoothed dissipative particle dynamics (SDPD) is a novel coarse grained method for the numerical simulation of complex fluids. It has considerable advantages over more traditional particle-based methods. In this paper we analyze the self-diffusion coefficient D of a SDPD solvent by using the strategy proposed by Groot and Warren [J. Chem. Phys. 107, 4423 (1997)]. An analytical expression for D in terms of the model parameters is developed and verified by numerical simulations. [ABSTRACT FROM AUTHOR]

For an isolated resonance of an isolated chromophore in a condensed phase, the absorption line shape is often more sharply peaked than the distribution of transition frequencies as a result of motional narrowing. The latter arises from the time-dependent fluctuations of the transition frequencies. It is well known that one can incorporate these dynamical effects into line shape calculations within a semiclassical approach. For a system of coupled chromophores, both the transition frequencies and the interchromophore couplings fluctuate in time. In principle one can again solve this more complicated problem with a related semiclassical approach, but in practice, for large numbers of chromophores, the computational demands are prohibitive. This has led to the development of a number of approximate theoretical approaches to this problem. In this paper we develop another such approach, using a time-averaging approximation. The idea is that, for a single chromophore, a motionally narrowed line shape can be thought of as a distribution of time-averaged frequencies. This idea is developed and tested on both stochastic and more realistic models of isolated chromophores, and also on realistic models of coupled chromophores, and it is found that in all cases this approximation is quite satisfactory, without undue computational demands. This approach should find application for the vibrational spectroscopy of neat liquids, and also for proteins and other complicated multichromophore systems. [ABSTRACT FROM AUTHOR]

Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an adequate basis for the treatment of excited states, a chemically meaningful identification of the different excited-state processes is difficult within such a delocalized orbital basis. In this work, starting from an initial set of supermolecular canonical molecular orbitals, we provide a simple one-step top-down embedding procedure for generating a set of orbitals, which are localized in terms of the supermolecule but delocalized over each subsystem composing the supermolecule. Using an orbital partitioning scheme based on such sets of localized orbitals, we further present a procedure for the construction of local excitations and charge-transfer states within the linear response framework of time-dependent density functional theory (TDDFT). This procedure provides direct access to approximate diabatic excitation energies and, under the Tamm–Dancoff approximation, also their corresponding electronic couplings—quantities that are of primary importance in modeling energy transfer processes in complex biological systems. Our approach is compared with a recently developed diabatization procedure based on subsystem TDDFT using projection operators, which leads to a similar set of working equations. Although both of these methods differ in the general localization strategies adopted and the type of basis functions (Slaters vs Gaussians) employed, an overall decent agreement is obtained. [ABSTRACT FROM AUTHOR]

In this study, we perform accurate calculations via multireference configuration interaction and coupled cluster methodologies on the dimolybdenum molecule in conjunction with complete series of correlation and weighted core correlation consistent basis sets up to quintuple size. The bonding, the dissociation energies, and the spectroscopic parameters of the seven states that correlate with the ground state products are calculated. The ground state has a sextuple chemical bond, and each of the calculated excited states has one less bond than the previous state. The calculated values for the ground X 1 Σ g + state of Mo2 have been extrapolated to the complete basis set limits. Our final values, re = 1.9324 Å and De (D0) = 4.502 ± 0.007(4.471 ± 0.009) eV, are in excellent agreement with the experimental values of re = 1.929, 1.938(9) Å and D0 = 4.476(10) eV. Mo2 in the Σ g + 13 state is a weakly bound dimer, forming 5s⋯5pz bonds, with De = 0.120 eV at re = 3.53 Å. All calculated excited states (except Σ g + 13 ) have a highly multireference character (C0 = 0.25–0.55). The ordering of the molecular bonding orbitals changes as the spin is increased from quintet to septet state resulting in a change in energy separation Δ S,S−1 of the calculated states. The quite low bond dissociation energy of the ground state is due to the splitting of the molecular bonding orbitals in two groups differing in energy by ∼3 eV. Finally, the bond breaking of Mo2, as the multiplicity of spin is increased, is analyzed in parallel with the Mo–Mo bond breaking in a series of Mo2Clx complexes when x is increased. Physical insight into the nature of the sextuple bond and its low dissociation energy is provided. [ABSTRACT FROM AUTHOR]

Knowledge of the chemical bonding of HfO and HfB ground and low-lying electronic states provides essential insights into a range of catalysts and materials that contain Hf–O or Hf–B moieties. Here, we carry out high-level multi-reference configuration interaction theory and coupled cluster quantum chemical calculations on these systems. We compute full potential energy curves, excitation energies, ionization energies, electronic configurations, and spectroscopic parameters with large quadruple-ζ and quintuple-ζ quality correlation consistent basis sets. We also investigate equilibrium chemical bonding patterns and effects of correlating core electrons on property predictions. Differences in the ground state electron configuration of HfB(X4 Σ −) and HfO(X1 Σ +) lead to a significantly stronger bond in HfO than HfB, as judged by both dissociation energies and equilibrium bond distances. We extend our analysis to the chemical bonding patterns of the isovalent HfX (X = O, S, Se, Te, and Po) series and observe similar trends. We also note a linear trend between the decreasing value of the dissociation energy (De) from HfO to HfPo and the singlet–triplet energy gap (Δ ES–T) of the molecule. Finally, we compare these benchmark results to those obtained using density functional theory (DFT) with 23 exchange–correlation functionals spanning multiple rungs of "Jacob's ladder." When comparing DFT errors to coupled cluster reference values on dissociation energies, excitation energies, and ionization energies of HfB and HfO, we observe semi-local generalized gradient approximations to significantly outperform more complex and high-cost functionals. [ABSTRACT FROM AUTHOR]

We review the basic ideas underlying the electron free energy level diagrams that have been found useful in considering the thermodynamics of redox processes in molten silicates and related high temperature ionic liquid (IL) solvents, and then show how closely they link to behavior observable in ambient temperature ionic liquids. Much of the information available on redox levels in molten oxides has been gleaned from chemical analysis and spectroscopic species distribution studies, but it is simpler to obtain the data electrochemically. Here, we report some cyclic voltammetry measurements of the Fe(II)/Fe(III) redox equilibrium in aprotic ionic liquids whose anions provide oxide environments for the redox species that are of different electronic polarizability character from the high temperature solvents, and relate the observations to those of the earlier studies. Quasi-reversible behavior is found in each of the cases studied. As might be expected, the Fe(II)/Fe(III) equilibrium experiences a more basic environment in an acetate IL than it experiences in any of the common glassforming oxide media, while triflate anions contrast by providing a more acid environment than does the most acid of the molten oxide glassformers studied (an alkali phosphate). The difference can amount to well over 1 V, suggesting the possibility of a 'basicity cell' where the same redox couple locates in anode and cathode compartments of the cell, and only the anion environment is different. [ABSTRACT FROM AUTHOR]

The presence of space charge in the polymeric insulation of high-voltage cables is thought to be correlated with electric breakdown. However, a direct link between molecular properties, space charge formation and eventual breakdown has still to be established. It is clear that both physical (e.g., conformational disorder) and chemical defects (e.g., broken bonds and impurities) are present in insulating materials and that both may trap electrons. We have shown that by defining the defect energy in terms of the molecular electron affinity, a relationship is established between the electron trap and the molecular properties of the material. In a recent paper [M. Meunier and N. Quirke, J. Chem. Phys. 113, 369 (2000)] we proposed methods that have made it possible to provide estimates of the energy, number and residence times of electrons in conformational traps in polyethylene. Typical physical trap energies are of the order of 0.15 eV and all are less than 0.3 eV. In the present paper we focus on the role of chemical defects, where we expect much deeper traps but at very low concentrations. Following the methodology used in our previous paper we have used density-functional theory to calculate trap energies for a set of chemical impurities and additives commonly found in polyethylene used for high-voltage cable insulation. In an extension of our approach we have estimated the effect of neighboring molecules on the trap energies of such defects. The resulting trap energy-trap density distribution reveals some very deep (>1 eV) traps presumably implicated in the formation of long-lived space charge in polymeric insulators and consequently to changes in the dielectric properties of the material. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Analyzes the design of optimal laser pulses for the selective preparation of enantiomers. Role of the symmetry selection on the laser induced transitions; Quantum simulations of representative wave packets on torsional motions; Mechanisms of selective preparation of enantiomers.

The chemical functionalization of graphene nanomaterials allows for the enhancement of their properties for novel functional applications. However, a better understanding of the functionalization process by determining the amount and location of functional groups within individual graphene nanoplatelets remains challenging. In this work, we demonstrate the capability of tip-enhanced Raman spectroscopy (TERS) to investigate the degree and spatial variability of the appearance of disorder in graphitic nanomaterials on the nanoscale with three different levels of nitrogen functionalization. TERS results are in excellent agreement with those of confocal Raman spectroscopy and chemical analysis, determined using x-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry, of the functionalized materials. This work paves the way for a better understanding of the functionalization of graphene and graphitic nanomaterials at the nano-scale, micro-scale, and macro-scale and the relationship between the techniques and how they relate to the changes in material properties of industrial importance. [ABSTRACT FROM AUTHOR]

We present an extensive range of quantum calculations for the state-changing rotational dynamics involving two simple molecular anions that are expected to play some role in the evolutionary analysis of chemical networks in the interstellar environments, C2H− (X1Σ+) and C2N− (X3Σ−), but for which inelastic rates are only known for C2H−. The same systems are also of direct interest in modeling selective photo-detachment experiments in cold ion traps where the He atoms function as the chief buffer gas at the low trap temperatures. This study employs accurate, ab initio calculations of the interaction potential energy surfaces for these anions, treated as rigid rotors, and the He atom to obtain a wide range of state-changing quantum cross sections and rates at temperatures up to about 100 K. The results are analyzed and compared for the two systems to show differences and similarities between their rates of state-changing dynamics. [ABSTRACT FROM AUTHOR]

A central issue in the study of polymer physics is to understand the relation between the geometrical properties of macromolecules and various dynamics, most of which are encoded in the Laplacian spectra of a related graph describing the macrostructural structure. In this paper, we introduce a family of treelike polymer networks with a parameter, which has the same size as the Vicsek fractals modeling regular hyperbranched polymers. We study some relevant properties of the networks and show that they have an exponentially decaying degree distribution and exhibit the small-world behavior. We then study the Laplacian eigenvalues and their corresponding eigenvectors of the networks under consideration, with both quantities being determined through the recursive relations deduced from the network structure. Using the obtained recursive relations we can find all the eigenvalues and eigenvectors for the networks with any size. Finally, as some applications, we use the eigenvalues to study analytically or semi-analytically three dynamical processes occurring in the networks, including random walks, relaxation dynamics in the framework of generalized Gaussian structure, as well as the fluorescence depolarization under quasiresonant energy transfer. Moreover, we compare the results with those corresponding to Vicsek fractals, and show that the dynamics differ greatly for the two network families, which thus enables us to distinguish between them. [ABSTRACT FROM AUTHOR]

Structure of fluids is suitably characterized by distribution functions from which the most important is the pair correlation function. Theoretical approaches to get the pair distribution function are based mainly on the solution of the Ornstein–Zernike (OZ) integral equation. In this paper, the OZ equation for molecular fluids is modified to yield the average correlation function for systems of convex molecules. In our approach we employed the previously proposed method to separate the shape effect of molecular cores from that due to the variable surface–surface distances among three pairs of convex cores. The effect of nonspherical shape of hard cores in the convolution integral is expressed through the derivative with respect to three surface–surface distances of the expression for the hard convex body third virial coefficient. For simple fluids (with the pointwise cores) the derived expression reduces to the standard OZ equation. The modified OZ equation is solved numerically for the Percus–Yevick-type closure and the average correlation functions in the systems of hard spherocylinders with l/σ=0.4, 0,6 and 1 were determined. The obtained dependencies of the average correlation functions on the reduced distances calculated from the modified OZ equation agree well with the simulation data for the above systems at relatively high densities. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The jet-cooled FTIR spectrum of the ν[sub 6] fundamental band (C-O stretch) of vanadium hexacarbonyl, V(CO)[sub 6], is studied for the first time. The spectrum shows a very unusual structure consisting of three well-defined broad subbands, without the usual PQR structure. V(CO)[sub 6] being an open-shell system this is attributed to a dynamical F[sub 2g]xF[sub 1u] Jahn-Teller coupling which considerably complicates the analysis. A new theoretical model based on group theory and tensorial algebraic techniques is developed in this paper for the very first attempt to analyze such a rovibronic spectrum. The assumption of a negligible spin-orbit coupling is validated by the overall agreement between predicted and observed band profiles. The rovibronic Hamiltonian and dipole moment operators have been expanded in order to enable a simultaneous treatment of the four vibronic sublevels. We were able to satisfactorily reproduce the band profile and thus to give the first estimation of some rovibronic parameters for this molecule. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks of Alzheimer's disease. Numerous experiments and computational studies have shown that the aggregation of Aβ peptides in vitro is very complex and depends on many factors such as pH, agitation, temperature, and peptide concentration. The impact of a static electric field (EF) on amyloid peptide aggregation has been much less studied, although EFs may have some applications to treat Parkinson's disease symptoms. Here, we study the influence of an EF strength of 20 mV/nm, present in the human brains, on the conformation of the Aβ29-42 dimer. Our 7 μs non-equilibrium atomistic simulations in aqueous solution show that this field-strength promotes substantially the formation of β-hairpins, believed to be a very important intermediate state during aggregation. This work also suggests that structural biology experiments conducted under appropriate EF strengths may help reduce the conformational heterogeneity of Aβ1-40/Aβ1-42 dimers and provide significant insights into their structures that may be disease-causing. [ABSTRACT FROM AUTHOR]

We perform an extensive computational study of binary mixtures of water and short-chain alcohols resorting to two-scale potential models to account for the singularities of hydrogen bonded liquids. Water molecules are represented by a well studied core softened potential which is known to qualitatively account for a large number of water's characteristic anomalies. Along the same lines, alcohol molecules are idealized by dimers in which the hydroxyl groups interact with each other and withwater with a core softened potential as well. Interactions involving non-polar groups are all deemed purely repulsive. We find that the qualitative behavior of excess properties (excess volume, enthalpy, and constant pressure heat capacity) agrees with that found experimentally for alcohols such as t-butanol in water. Moreover, we observe that our simple solute under certain conditions acts as a "structuremaker," in the sense that the temperature of maximum density of the bulk water model increases as the solute is added, i.e., the anomalous behavior of the solvent is enhanced by the solute. [ABSTRACT FROM AUTHOR]

We investigate the applicability of the linearized semiclassical initial value representation (LSCIVR) method to excitation energy transfer (EET) problems in molecular aggregates by simulating the EET dynamics of a dimer model in a wide range of parameter regime and comparing the results to those obtained from a numerically exact method. It is found that the LSC-IVR approach yields accurate population relaxation rates and decoherence rates in a broad parameter regime. However, the classical approximation imposed by the LSC-IVR method does not satisfy the detailed balance condition, generally leading to incorrect equilibrium populations. Based on this observation, we propose a post-processing algorithm to solve the long time equilibrium problem and demonstrate that this long-time correction method successfully removed the deviations from exact results for the LSC-IVR method in all of the regimes studied in this work. Finally, we apply the LSC-IVR method to simulate EET dynamics in the photosynthetic Fenna-Matthews-Olson complex system, demonstrating that the LSC-IVR method with long-time correction provides excellent description of coherent EET dynamics in this typical photosynthetic pigment-protein complex. [ABSTRACT FROM AUTHOR]

Combining analytic calculations, computer simulations, and classical density functional theory we determine the interfacial tension of orientable two-dimensional hard rectangles near a curved hard wall. Both a circular cavity holding the particles and a hard circular obstacle surrounded by particles are considered. We focus on moderate bulk densities (corresponding to area fractions up to 50%) where the bulk phase is isotropic and vary the aspect ratio of the rectangles and the curvature of the wall. The Tolman length, which gives the leading curvature correction of the interfacial tension, is found to change sign at a finite density, which can be tuned via the aspect ratio of the rectangles. [ABSTRACT FROM AUTHOR]

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example and show that its transition paths are bifurcating. We then derive a criterion to predict the bifurcation of transition paths in a generalized coupled bistable system. We confirm the validity of the theory for the example system by numerical simulation. We also demonstrate in the example system that, if the steady states of individual gene circuits are not changed by the coupling, the bifurcation pattern is not dependent on the number of gene circuits. We further show that the transition rate exponentially decreases with the number of gene circuits when the transition path does not bifurcate, while a bifurcation facilitates the transition by lowering the quasi-potential energy barrier. [ABSTRACT FROM AUTHOR]

We study the surface tension of ionic solutions at air/water and oil/water interfaces by using fieldtheoretical methods and including a finite proximal surface-region with ionic-specific interactions. The free energy is expanded to first-order in a loop expansion beyond the mean-field result. We calculate the excess surface tension and obtain analytical predictions that reunite the Onsager-Samaras pioneering result (which does not agree with experimental data), with the ionic specificity of the Hofmeister series. We derive analytically the surface-tension dependence on the ionic strength, ionic size, and ion-surface interaction, and show consequently that the Onsager-Samaras result is consistent with the one-loop correction beyond the mean-field result. Our theory fits well a wide range of salt concentrations for different monovalent ions using one fit parameter per electrolyte and reproduces the reverse Hofmeister series for anions at the air/water and oil/water interfaces. [ABSTRACT FROM AUTHOR]

We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities. [ABSTRACT FROM AUTHOR]

We formulate a multiple-encounter model of the radical pair mechanism that is based on a random coupling of the radical pair to a minimal model environment. These occasional pulse-like couplings correspond to the radical encounters and give rise to both dephasing and recombination. While this is in agreement with the original model of Haberkorn and its extensions that assume additional dephasing, we show how a nonlinear master equation may be constructed to describe the conditional evolution of the radical pairs prior to the detection of their recombination. We propose a nonlinear master equation for the evolution of an ensemble of independently evolving radical pairs whose nonlinearity depends on the record of the fluorescence signal. We also reformulate Haberkorn's original argument on the physicality of reaction operators using the terminology of quantum optics/open quantum systems. Our model allows one to describe multiple encounters within the exponential model and connects this with the master equation approach. We include hitherto neglected effects of the encounters, such as a separate dephasing in the triplet subspace, and predict potential new effects, such as Grover reflections of radical spins, that may be observed if the strength and time of the encounters can be experimentally controlled. [ABSTRACT FROM AUTHOR]

Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions. [ABSTRACT FROM AUTHOR]

A laminar stationary flow of viscous fluid in a cylindrical tube enhances the rate of diffusion of Brownian particles along the tube axis. This so-called Aris-Taylor dispersion is due to the fact that cumulative times, spent by a diffusing particle in layers of the fluid moving with different velocities, are random variables which depend on the realization of the particle stochastic trajectory in the radial direction. Conceptually similar increase of the diffusivity occurs when the particle randomly jumps between two states with different drift velocities. Here we develop a theory that contains both phenomena as special limiting cases. It is assumed (i) that the particle in the flow can reversibly bind to the tube wall, where it moves with a given drift velocity and diffusivity, and (ii) that the radial and longitudinal diffusivities of the particle in the flow may be different. We derive analytical expressions for the effective drift velocity and diffusivity of the particle, which show how these quantities depend on the geometric and kinetic parameters of the model. [ABSTRACT FROM AUTHOR]

We present extensions to our previous work on Fukui functions and linear-response functions [W. Yang, A. J. Cohen, F. D. Proft, and P. Geerlings, J. Chem. Phys. 136, 144110 (2012)]. Viewed as energy derivatives with respect to the number of electrons and the external potential, all second-order derivatives (the linear-response function, the Fukui function, and the chemical hardness) are extended to fractional systems, and all third-order derivatives (the second-order response function, the Fukui response function, the dual descriptor, and the hyperhardness) for integer systems are also obtained. These analytical derivatives are verified by finite difference numerical derivatives. In the context of the exact linearity condition and the constancy condition, these analytical derivatives enrich greatly the information of the exact conditions on the energy functional through establishing real-space dependency. The introduction of an external nonlocal potential defines the nonlocal Fukui function and the nonlocal linear-response function. The nonlocal linear-response function so defined also provides the precise meaning for the time-dependent linear-response density-functional theory calculations with generalized Kohn-Sham functionals. These extensions will be useful to conceptual density-functional theory and density functional development. [ABSTRACT FROM AUTHOR]

The kinetic approach adapted to describe charge transmission in molecular junctions, is used for the analysis of the photocurrent under conditions of moderate light intensity of the photochromic molecule. In the framework of the HOMO-LUMO model for the single electron molecular states, the analytic expressions describing the temporary behavior of the transient and steady state sequential (hopping) as well as direct (tunnel) current components have been derived. The conditions at which the current components achieve their maximal values are indicated. It is shown that if the rates of charge transmission in the unbiased molecular diode are much lower than the intramolecular singlet-singlet excitation/de-excitation rate, and the threefold degenerated triplet excited state of the molecule behaves like a trap blocking the charge transmission, a possibility of a large peak-like transient switch-on photocurrent arises. [ABSTRACT FROM AUTHOR]

Milestoning is a method used to calculate the kinetics of molecular processes occurring on timescales inaccessible to traditional molecular dynamics (MD) simulations. In the method, the phase space of the system is partitioned by milestones (hypersurfaces), trajectories are initialized on each milestone, and short MD simulations are performed to calculate transitions between neighboring milestones. Long trajectories of the system are then reconstructed with a semi-Markov process from the observed statistics of transition. The procedure is typically justified by the assumption that trajectories lose memory between crossing successive milestones. Here we present Milestoning with Coarse Memory (MCM), a generalization of Milestoning that relaxes the memory loss assumption of conventional Milestoning. In the method, milestones are defined and sample transitions are calculated in the standard Milestoning way. Then, after it is clear where trajectories sample milestones, the milestones are broken up into distinct neighborhoods (clusters), and each sample transition is associated with two clusters: the cluster containing the coordinates the trajectory was initialized in, and the cluster (on the terminal milestone) containing trajectory's final coordinates. Long trajectories of the system are then reconstructed with a semi-Markov process in an extended state space built from milestone and cluster indices. To test the method, we apply it to a process that is particularly ill suited for Milestoning: the dynamics of a polymer confined to a narrow cylinder. We show that Milestoning calculations of both the mean first passage time and the mean transit time of reversal-which occurs when the end-to-end vector reverses direction-are significantly improved when MCM is applied. Finally, we note the overhead of performing MCM on top of conventional Milestoning is negligible. [ABSTRACT FROM AUTHOR]

Coupled-cluster methods offer unprecedented accuracy for a wide range of chemically important properties, but the steep scaling of computational cost with system size makes widespread use challenging. Local approximations, building on the short-range nature of electron correlation effects in insulators, help a great deal, but are much more complicated than their canonical counterparts. In this work we discuss an automated implementation scheme for local coupled-cluster methods, based on an interpreter and an underlying representation of sparse tensors. We demonstrate the efficacy of the approach through implementation of a very wide range of singles-and-doubles-based coupled-cluster schemes. [ABSTRACT FROM AUTHOR]

Numerical simulation of the time evolution of a spatially homogeneous chemical system is always of great interest. Gillespie first developed the exact stochastic simulation algorithm (SSA), which is accurate but time-consuming. Recently, many approximate schemes of the SSA are proposed to speed up simulation. Presented here is the N-leap method, which guarantees the validity of the leap condition and at the same time keeps the efficiency. In many cases, N-leap has better performance than the widely-used τ-leap method. The details of the N-leap method are described and several examples are presented to show its validity. [ABSTRACT FROM AUTHOR]

Inelastic electron tunneling spectroscopy (IETS) performed with the scanning tunneling microscope (STM) has been deemed as the ultimate tool for identifying chemicals at the atomic scale. However, direct IETS-based chemical analysis remains difficult due to the selection rules that await a definite understanding. We present IETS simulations of single formate and benzoate species adsorbed in the same upright bridge geometry on a (111)-cleaved Cu surface. In agreement with measurements on a related substrate, the simulated IET-spectra of formate/Cu(111) clearly resolve one intense C-H stretching mode whatever the tip position in the vicinity of the molecular fragment. At variance, benzoate/Cu(111) has no detectable IET signal. The dissimilar IETS responses of chemically related molecules-formate and benzoate adsorbates-permit us to unveil another factor that complements the selection rules, namely the degree of the vacuum extension of the tunneling active states perturbed by the vibrations. As a consequence, the lack of a topmost dangling bond orbital is entirely detrimental for STM-based inelastic spectroscopy but not for STM elastic imaging. [ABSTRACT FROM AUTHOR]

We report results of dissipative particle dynamics simulations and develop a semi-analytical theory of an anisotropic flow in a parallel-plate channel with two superhydrophobic striped walls. Our approach is valid for any local slip at the gas sectors and an arbitrary distance between the plates, ranging from a thick to a thin channel. It allows us to optimize area fractions, slip lengths, channel thickness, and texture orientation to maximize a transverse flow. Our results may be useful for extracting effective slip tensors from global measurements, such as the permeability of a channel, in experiments or simulations, and may also find applications in passive microfluidic mixing. [ABSTRACT FROM AUTHOR]

The contribution of scalar coupling relaxation of the second kind on the relaxation behaviour of nuclear spin singlet states has been derived. The analytical equation found for the relaxation rate constant of singlet state has been compared to the equation for the relaxation of longitudinal magnetization in order to find the conditions for which the singlet state remains long-lived even in the presence of this scalar relaxation mechanism. These results are relevant when the singlet state is formed in molecules with more than two interacting spins. [ABSTRACT FROM AUTHOR]

We present here the details of a phase retrieval technique that provides access to multidimensional modalities that are not currently available using existing interferometric techniques. The development of multidimensional optical spectroscopy has facilitated significant insights into electronic processes in physics, chemistry, and biology. The versatility and number of available techniques are, however, significantly limited by the requirement that the detection be interferometric. Many of these techniques are closely related to the vast range of multidimensional NMR spectroscopies, which revolutionized analytical chemistry more than 30 years ago. We focus here on the specific case of two-color multidimensional spectroscopy (analogous to heteronuclear NMR) and discuss the details of an iterative algorithm that recovers the relative phase relationships required to perform the Fourier transformation and find the unique solution for the 2D spectrum. A detailed guide is provided that describes the practical implementation of such algorithms. The effectiveness and accuracy of the phase retrieval process are assessed for simulated one- and two-color experiments. It is also compared with one-color experimental data for which the target phase information has been obtained independently by interferometry. In all the cases, the present algorithm yields results that compare well with the solutions obtained by other means. There are, however, some limitations and potential pitfalls that are identified and discussed. We conclude with a discussion of the potential applications and further advances that may be possible by adopting iterative phase retrieval algorithms of the type discussed here. [ABSTRACT FROM AUTHOR]

Large-scale quantum Monte Carlo (QMC) calculations of ground and excited singlet states of both conformers of azobenzene are presented. Remarkable accuracy is achieved by combining medium accuracy quantum chemistry methods with QMC. The results not only reproduce measured values with chemical accuracy but the accuracy is sufficient to identify part of experimental results which appear to be biased. Novel analysis of nodal surface structure yields new insights and control over their convergence, providing boost to the chemical accuracy electronic structure methods of large molecular systems. [ABSTRACT FROM AUTHOR]

In many dynamical systems, there is a large separation of time scales between typical events and 'rare' events which can be the cases of interest. Rare-event rates are quite difficult to compute numerically, but they are of considerable practical importance in many fields, for example, transition times in chemical physics and extinction times in epidemiology can be very long, but are quite important. We present a very fast numerical technique that can be used to find long transition times (very small rates) in low-dimensional systems, even if they lack detailed balance. We illustrate the method for a bistable nonequilibrium system introduced by Maier and Stein and a two-dimensional (in parameter space) epidemiology model. [ABSTRACT FROM AUTHOR]

We explore the potential of double core hole electron spectroscopy for chemical analysis in terms of x-ray two-photon photoelectron spectroscopy. The creation of deep single and double core vacancies induces significant reorganization of valence electrons. The corresponding relaxation energies and the interatomic relaxation energies are evaluated by complete active space self-consistent field (CASSCF) calculations. We propose a method on how to experimentally extract these quantities by the measurement of single ionization potentials (IPs) and double core hole ionization potentials (DIPs). The influence of the chemical environment on these DIPs is also discussed for states with two holes at the same atomic site and states with two holes at two different atomic sites. Electron density difference between the ground and double core hole states clearly shows the relaxations accompanying the double core hole ionization. The effect is also compared to the sensitivity of single core hole IPs arising in single core hole electron spectroscopy. We have demonstrated the method for a representative set of small molecules LiF, BeO, BF, CO, N2, C2H2, C2H4, C2H6, CO2, and N2O. The scalar relativistic effect on IPs and on DIPs are briefly addressed. [ABSTRACT FROM AUTHOR]

Markov state models (MSMs) are a powerful tool for modeling both the thermodynamics and kinetics of molecular systems. In addition, they provide a rigorous means to combine information from multiple sources into a single model and to direct future simulations/experiments to minimize uncertainties in the model. However, constructing MSMs is challenging because doing so requires decomposing the extremely high dimensional and rugged free energy landscape of a molecular system into long-lived states, also called metastable states. Thus, their application has generally required significant chemical intuition and hand-tuning. To address this limitation we have developed a toolkit for automating the construction of MSMs called MSMBUILDER (available at https://simtk.org/home/msmbuilder). In this work we demonstrate the application of MSMBUILDER to the villin headpiece (HP-35 NleNle), one of the smallest and fastest folding proteins. We show that the resulting MSM captures both the thermodynamics and kinetics of the original molecular dynamics of the system. As a first step toward experimental validation of our methodology we show that our model provides accurate structure prediction and that the longest timescale events correspond to folding. [ABSTRACT FROM AUTHOR]

The generalized Langevin equation is widely used to model the influence of a heat bath upon a reactive system. This equation will here be studied from a geometric point of view. A dynamical phase space that represents all possible states of the system will be constructed, the generalized Langevin equation will be formally rewritten as a pair of coupled ordinary differential equations, and the fundamental geometric structures in phase space will be described. It will be shown that the phase space itself and its geometric structure depend critically on the preparation of the system: A system that is assumed to have been in existence forever has a larger phase space with a simpler structure than a system that is prepared at a finite time. These differences persist even in the long-time limit, where one might expect the details of preparation to become irrelevant. [ABSTRACT FROM AUTHOR]

The ground state of mixed (para-H2)N(ortho-D2)3 clusters of sizes ranging from N=8 to 37 is examined by means of the path integral ground state method. The chemical potential is calculated and reveals that magic numbers are consistent with those found in pure para-H2 and ortho-D2 clusters. The structural features of the mixed clusters are examined by analyzing density profiles, one-dimensional Pekeris distribution functions of the (ortho-D2)3 subsystem, and by direct visualization of density isosurfaces of the systems. The heavier (ortho-D2)3 complex resides in the center of the cluster for the various sizes under consideration. It is found that certain cluster sizes favor either equilateral, or near-linear isosceles (ortho-D2)3 configurations, while others show a coexistence between those two triangular geometries. [ABSTRACT FROM AUTHOR]

The instabilities of Hartree–Fock (HF) solutions at or near the equilibrium geometry of symmetric molecular species imply the existence of broken-symmetry solutions having a lower energy than the corresponding symmetry-adapted ones. Moreover, the distortion of the nuclear framework along the normal modes that are implied by such broken-symmetry solutions results in an anomalous or even singular behavior in the corresponding cuts of the potential energy surface (PES). Using such HF solutions as a reference, these anomalies propagate to a post-HF level and make it impossible to determine reliable harmonic or fundamental vibrational frequencies for such modes by relying on either numerical or analytical differentiation of the PES, requiring instead a numerical integration of the Schrödinger equation for the nuclear motion. This, in turn, requires a detailed knowledge on the PES in a wide range of geometries, necessitating a computation of the potential energy function in a large number of points. We present an alternative approach to this problem, referred to as the integral averaging method (IAM), which facilitates this task by significantly reducing the number of geometries for which one has to compute the potential energy while yielding results of practically the same accuracy as the solution of the Schrödinger equation. The IAM is applied to several ABA-type triatomics and to the allyl radical, whose asymmetric stretching mode potential suffers from an anomalous behavior due to the spin-preserving instabilities in restricted open-shell HF solutions. [ABSTRACT FROM AUTHOR]

We have used the ring polymer molecular dynamics method to study the diffusion of muonium, hydrogen, and deuterium atoms in liquid water and hexagonal ice over a wide temperature range (8–361 K). Quantum effects are found to dramatically reduce the diffusion of muonium in water relative to that predicted by classical simulation. This leads to a simple explanation for the lack of any significant isotope effect in the observed diffusion coefficients of these species in the room temperature liquid. Our results indicate that the mechanism of the diffusion in liquid water is similar to the intercavity hopping mechanism observed in ice, supplemented by the diffusion of the cavities in the liquid. Within the same model, we have also been able to simulate the observed crossover in the c-axis diffusion coefficients of hydrogen and deuterium in hexagonal ice. Finally, we have been able to obtain good agreement with experimental data on the diffusion of muonium in hexagonal ice at 8 K, where the process is entirely quantum mechanical. [ABSTRACT FROM AUTHOR]

Recently, we demonstrated via large-scale molecular dynamics simulations a “coexistence period” in polymer melt ordering before crystallization, where nucleation and growth mechanisms coexist with a phase-separation mechanism [Gee et al., Nat. Mater. 5, 39 (2006)]. Here, we present an extension of this work, where we analyze the directional displacements as a measure of the mobility of monomers as they order during crystallization over more than 100 ns of simulation time. It is found that the polymer melt, after quenching, rapidly separates into many ordered hexagonal domains separated by amorphous regions, where surprisingly, the magnitude of the monomer’s displacement in the ordered state, parallel to the domain axial direction, is similar to its magnitude in the melt. The monomer displacements in the domain’s lateral direction are found to decrease during the time of the simulation. The ordered hexagonal domains do not align into uniform lamellar structures during the timescales of our simulations. [ABSTRACT FROM AUTHOR]

Several theoretical models have been formulated to explain the growth of porous structures in anodized alumina. Using some basic assumptions, these models predict the size and shape of the pores in the anodic porous alumina as functions of pH and voltage. Additionally, they address issues of stability in the pore growth. In this work, we have carried out a systematic experimental investigation to study the stability phase diagram as a function of pH and applied voltage. We also obtain the dependence of pore dimensions on the pH, voltage, and acid type. Based on our results, and insight gained from recent chemical analysis of the porous alumina anodization process, we conclude that the models must include an appropriate weighting factor to account for the oxidation and dissolution mechanism during the pore formation. [ABSTRACT FROM AUTHOR]

NMR diffusion experiments employing pulsed field gradients are well established as sensitive probes of the displacement of individual nuclear spins in a sample. Conventionally such measurements are used as a measure of translational diffusion, but here we demonstrate that under certain conditions rotational motion will contribute very significantly to the experimental data. This situation occurs when at least one spatial dimension of the species under study exceeds the root mean square displacement associated with translational diffusion, and leads to anomalously large apparent diffusion coefficients when conventional analytical procedures are employed. We show that in such a situation the effective diffusion coefficient is a function of the duration of the diffusion delay used, and that this dependence provides a means of characterizing the dimensions of the species under investigation. [ABSTRACT FROM AUTHOR]

We present a rigorous calculation of the contribution of water dimers to the absorption coefficient [formula] in the millimeter and far infrared domains, over a wide range (276–310 K) of temperatures. This calculation relies on the explicit consideration of all possible transitions within the entire rovibrational bound state manifold of the dimer. The water dimer is described by the flexible 12-dimensional potential energy surface previously fitted to far IR transitions [C. Leforestier et al., J. Chem. Phys. 117, 8710 (2002)], and which was recently further validated by the good agreement obtained for the calculated equilibrium constant Kp(T) with experimental data [Y. Scribano et al., J. Phys. Chem. A. 110, 5411 (2006)]. Transition dipole matrix elements were computed between all rovibrational states up to an excitation energy of 750 cm-1, and J=K=5 rotational quantum numbers. It was shown by explicit calculations that these matrix elements could be extrapolated to much higher J values (J=30). Transitions to vibrational states located higher in energy were obtained from interpolation of computed matrix elements between a set of initial states spanning the 0–750 cm-1 range and all vibrational states up to the dissociation limit (∼1200 cm-1). We compare our calculations with available experimental measurements of the water continuum absorption in the considered range. It appears that water dimers account for an important fraction of the observed continuum absorption in the millimeter region (0–10 cm-1). As frequency increases, their relative contribution decreases, becoming small (∼3%) at the highest frequency considered ν=944 cm-1. [ABSTRACT FROM AUTHOR]

Multicomponent homogeneous nucleation is considered in the case of dominant and trace species (with respect to embryo composition). The free energy of embryo formation for multicomponent homogeneous nucleation has been derived for systems with several dominant species, e.g., water+sulfuric acid and a number of trace substances. This treatment is based on a differential version of the capillarity approximation. It is considered that an embryo is formed due to the condensation of several different gaseous compounds containing water, sulfuric acid, nitric acid, organic compounds, etc. Henry’s law is employed to describe the chemical potential of trace species in embryos. The case of the surface free energy influenced by amounts of trace species transferred into an embryo is considered. It was found that the free energy of embryo formation for multicomponent nucleation depends upon the ratios of the partial pressures of the trace species to the Henry’s law constants of the species. The nucleation rate for a multicomponent system is found to be a product of the dominant species nucleation rate (e.g., binary or ternary nucleation rate) and the correction factor that is influenced by the trace species. It was shown that the multicomponent nucleation correction factor is likely to be in the range from 3 to 10[sup 10]. As an example of the approach developed, the formation of secondary atmospheric aerosols was considered as multicomponent homogeneous nucleation of water vapor, sulfuric acid, nitric acid, formic acid, and other hydrophilic compounds. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In the first ever attempt to study the adsorption of organic molecules on high-index Si surfaces, we investigated the adsorption of benzene on Si(5 5 12)-(2×1) by using variable-low-temperature scanning tunneling microscopy and density-functional theory (DFT) calculations. Several distinct adsorption structures of the benzene molecule were found. In one structure, the benzene molecule binds to two adatoms between the dimers of D3 and D2 units in a tilted butterfly configuration. This structure is produced by the formation of di-σ bonds with the substrate and of two C==C double bonds in the benzene molecule. In another structure, the molecule adsorbs on honeycomb chains with a low adsorption energy because of strain effects. Our DFT calculations predict that the adsorption energies of benzene are 1.03–1.20 eV on the adatoms and 0.22 eV on the honeycomb chains. [ABSTRACT FROM AUTHOR]

Gaussian split Ewald (GSE) is a versatile Ewald mesh method that is fast and accurate when used with both real-space and k-space Poisson solvers. While real-space methods are known to be asymptotically superior to k-space methods in terms of both computational cost and parallelization efficiency, k-space methods such as smooth particle-mesh Ewald (SPME) have thus far remained dominant because they have been more efficient than existing real-space methods for simulations of typical systems in the size range of current practical interest. Real-space GSE, however, is approximately a factor of 2 faster than previously described real-space Ewald methods for the level of force accuracy typically required in biomolecular simulations, and is competitive with leading k-space methods even for systems of moderate size. Alternatively, GSE may be combined with a k-space Poisson solver, providing a conveniently tunable k-space method that performs comparably to SPME. The GSE method follows naturally from a uniform framework that we introduce to concisely describe the differences between existing Ewald mesh methods. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A quantum theory of thermal reaction rates is presented which may be viewed as an extension of the recently developed “quantum instanton” (QI) model [W. H. Miller, Y. Zhao, M. Ceotto, and S. Yang, J. Chem. Phys. 119, 1329 (2003)]. It is based on using higher derivatives of the flux-flux autocorrelation function C(t) (as given by Miller, Schwartz, and Tromp) at t=0 to construct a short time approximation for C(t). Tests of this theory on 1d and collinear reactions, both symmetric and asymmetric, show it to be more accurate than the original QI model, giving rate constants to ∼5% for a wide range of temperature. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]