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  • Articles  (54,905)
  • American Institute of Physics (AIP)  (54,371)
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  • 1
    Publication Date: 2016-07-13
    Description: A glassy dilute glycerol-water solution undergoes a mutual polyamorphic transition relating to the transition between high- and low-density amorphous ices of solvent water. The polyamorphic transition behavior depends on the glycerol concentration, indicating that the glycerol affects the water polyamorphism. Here, we used the glassy dilute glycerol-water solution of the solute molar fraction of 0.07 and examined the effect of the polyamorphic change in solvent water on the molecular vibrations of glycerol via Raman spectroscopy. It is found that the molecular vibration of glycerol in high-density liquid like solvent water is different from that in the low-density liquid like solvent water and that the change in the molecular vibration of glycerol is synchronized with the polyamorphic transition of solvent water. The dynamical change of the solute molecule relates to the polyamorphic state of solvent water. This result suggests that the polyamorphic fluctuation of water structure emanated from the presumed liquid-liquid critical point plays an important role for the function of aqueous solution under an ambient condition such as the conformational stability of solute, the functional expression of solute, and so on.
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  • 2
    Publication Date: 2016-07-13
    Description: We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.
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  • 3
    Publication Date: 2016-07-13
    Description: Resonantly enhanced multiphoton ionization via the E F 1 Σ g + , v ′ = 6 double-well state has been used to probe the energy region below the third dissociation limit of H 2 where several high vibrational levels of the 4 1 Σ u + state are expected. Theoretical ab initio potential energy curves for this state predict a deep inner well and shallow outer well where vibrational levels above v = 8 are expected to exhibit the double-well character of the state. Since the 4 1 Σ u + state has f -state character, transitions to it from the ground state are nominally forbidden. However, the d character of the outer well of the E F 1 Σ g + state allows access to this state. We report observations of transitions to the v = 9–12 levels of the 4 1 Σ u + state and compare their energies to predicted energies calculated from an ab initio potential energy curve with adiabatic corrections. Assignments are based on measured energies and linewidths, rotational constants, and expected transition strengths. The amount of agreement between the predicted values and the observations is mixed, with the largest discrepancies arising for the v = 9 level, owing to strong nonadiabatic electronic mixing in this energy region.
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  • 4
    Publication Date: 2016-07-13
    Description: The photodissociation dynamics of the methyl perthiyl radical (CH 3 SS) have been investigated using fast-beam coincidence translational spectroscopy. Methyl perthiyl radicals were produced by photodetachment of the CH 3 SS − anion followed by photodissociation at 248 nm (5.0 eV) and 193 nm (6.4 eV). Photofragment mass distributions and translational energy distributions were measured at each dissociation wavelength. Experimental results show S atom loss as the dominant (96%) dissociation channel at 248 nm with a near parallel, anisotropic angular distribution and translational energy peaking near the maximal energy available to ground state CH 3 S and S fragments, indicating that the dissociation occurs along a repulsive excited state. At 193 nm, S atom loss remains the major fragmentation channel, although S 2 loss becomes more competitive and constitutes 32% of the fragmentation. The translational energy distributions for both channels are very broad at this wavelength, suggesting the formation of the S 2 and S atom products in several excited electronic states.
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  • 5
    Publication Date: 2016-07-14
    Description: The static and dynamic properties of water in small silicon-carbide and carbon nanotubes have been studied over the temperature range 100 K–298 K, using extensive molecular dynamics simulations. The computed properties include the radial distribution function, the cage correlation function, the space-time autocorrelation function, the velocity autocorrelation function, and the self-diffusivity. They all indicate that, under the conditions that we study, water does not freeze in small nanotubes; the Stokes-Einstein relation breaks down, and the self-diffusivity exhibits a transition around 230 K, very close to 228 K, the temperature at which a fragile-to-strong dynamic crossover is supposed to happen. The cage correlation function C ( t ) decays according to a stretched-exponential function, C ( t ) ∼ exp[ − ( t / τ ) β ], where τ is a relaxation time and β is a topological exponent.
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  • 6
    Publication Date: 2016-07-14
    Description: Feasibility of laser-cooling AlCl molecule is investigated using ab initio quantum chemistry. Potential energy curves, permanent dipole moments, and transition dipole moments for the X 1 Σ + , a 3 Π, and A 1 Π states are studied based on multi-reference configuration interaction plus Davidson corrections (MRCI+Q) method with ACVQZ basis set, spin-orbit coupling effects are considered at the MRCI+Q level. Highly diagonally distributed Franck–Condon factors ( f 00 = 0.9988 and f 11 = 0.9970) and branching ratios ( R 00 = 0.9965, R 01 = 2.85 × 10 −3 , R 02 = 6.35 × 10 −4 , and R 03 = 2.05 × 10 −6 ) for the A 1 Π 1 ( ν ′ = 0 ) → X 1 Σ 0 + + ( ν ″ = 0 ) transition are determined. A sufficiently radiative lifetime τ ( A 1 Π 1 ) = 4.99 ns is predicted for rapid laser cooling. The proposed cooling wavelength is deep in the ultraviolet region at λ 00 = 261.75 nm. Total emission rates for the a 3 Π 0 + → X 1 Σ 0 + + , a 3 Π 1 → X 1 Σ 0 + + , A 1 Π 1 → a 3 Π 0 + , and A 1 Π 1 → a 3 Π 1 transitions are particularly small (∼10 s −1 –650 s −1 ). The calculated vibrational branching loss ratio to the intermediate a 3 Π 0 + and a 3 Π 1 states can be negligible. The results imply the probability of laser cooling AlCl molecule with three-electronic-level.
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  • 7
    Publication Date: 2016-07-14
    Description: This paper presents an explanation based on torsionally mediated proton-spin–overall-rotation interaction for the observation of doublet hyperfine splittings in some Lamb-dip sub-millimeter-wave transitions between ground-state torsion-rotation states of E symmetry in methanol. These unexpected doublet splittings, some as large as 70 kHz, were observed for rotational quantum numbers in the range of J = 13 to 34, and K = − 2 to +3. Because they increase nearly linearly with J for a given branch, we confined our search for an explanation to hyperfine operators containing one nuclear-spin angular momentum factor I and one overall-rotation angular momentum factor J (i.e., to spin-rotation operators) and ignored both spin-spin and spin-torsion operators, since they contain no rotational angular momentum operator. Furthermore, since traditional spin-rotation operators did not seem capable of explaining the observed splittings, we constructed totally symmetric “torsionally mediated spin-rotation operators” by multiplying the E-species spin-rotation operator by an E-species torsional-coordinate factor of the form e ± ni α . The resulting operator is capable of connecting the two components of a degenerate torsion-rotation E state. This has the effect of turning the hyperfine splitting pattern upside down for some nuclear-spin states, which leads to bottom-to-top and top-to-bottom hyperfine selection rules for some transitions, and thus to an explanation for the unexpectedly large observed hyperfine splittings. The constructed operator cannot contribute to hyperfine splittings in the A-species manifold because its matrix elements within the set of torsion-rotation A 1 and A 2 states are all zero. The theory developed here fits the observed large doublet splittings to a root-mean-square residual of less than 1 kHz and predicts unresolvable splittings for a number of transitions in which no doublet splitting was detected.
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  • 8
    Publication Date: 2016-07-15
    Description: In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least n b local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified n b and number of seeds n s . This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of n b and n s , we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β -Ga.
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  • 9
    Publication Date: 2016-07-15
    Description: Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states.
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  • 10
    Publication Date: 2016-07-15
    Description: An automated property optimization method was developed based on the ab initio O( N ) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.
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  • 11
    Publication Date: 2016-07-15
    Description: We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems. A test set of supramolecular complexes containing up to 158 atoms and 1960 contracted basis functions has been employed to demonstrate the general applicability of the DEC-RI-MP2 method and to analyze the errors of the DEC approximation. Moreover, the test set contains molecules of complicated electronic structures and is thus deliberately chosen to stress test the DEC-RI-MP2 gradient implementation. Additionally, as a showcase example the full molecular gradient for insulin (787 atoms and 7604 contracted basis functions) has been evaluated.
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  • 12
    Publication Date: 2016-07-21
    Description: Hydrodynamic interactions with confining boundaries often lead to drastic changes in the diffusive behaviour of microparticles in suspensions. For axially symmetric particles, earlier numerical studies have suggested a simple form of the near-wall diffusion matrix which depends on the distance and orientation of the particle with respect to the wall, which is usually calculated numerically. In this work, we derive explicit analytical formulae for the dominant correction to the bulk diffusion tensor of an axially symmetric colloidal particle due to the presence of a nearby no-slip wall. The relative correction scales as powers of inverse wall-particle distance and its angular structure is represented by simple functions in sines and cosines of the particle’s inclination angle to the wall. We analyse the correction for translational and rotational motion, as well as the translation-rotation coupling. Our findings provide a simple approximation to the anisotropic diffusion tensor near a wall, which completes and corrects relations known from earlier numerical and theoretical findings.
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  • 13
    Publication Date: 2016-07-21
    Description: This manuscript presents the second, consistent density functional in the QTP (Quantum Theory Project) family, that is, the CAM-QTP(01). It is a new range-separated exchange-correlation functional in which the non-local exchange contribution is 100% at large separation. It follows the same basic principles of this family that the Kohn-Sham eigenvalues of the occupied orbitals approximately equal the vertical ionization energies, which is not fulfilled by most of the traditional density functional methods. This new CAM-QTP(01) functional significantly improves the accuracy of the vertical excitation energies especially for the Rydberg states in the test set. It also reproduces many other properties such as geometries, reaction barrier heights, and atomization energies.
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  • 14
    Publication Date: 2016-07-21
    Description: Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.
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  • 15
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    American Institute of Physics (AIP)
    Publication Date: 2016-07-21
    Description: Details of crystallization processes of a polymer at the crystallization temperature T c from its melt kept initially at the melt temperature T m depend profoundly on the nature of the initial melt state and often are accompanied by memory effects. This phenomenon is in contrast to small molecular systems where the supercooling ( T m 0 − T c ), with T m 0 being the equilibrium melting temperature, and not ( T m − T c ), determines the nature of crystallization. In addressing this five-decade old puzzle of melt-memory in polymer crystallization, we present a theory to describe melt-memory effects, by invoking an intermediate inhomogeneous melt state in the pathway between the melt and crystalline states. Using newly introduced dissolution temperature T 1 0 for the inhomogeneous melt state and the transition temperature T t 0 for the transition between the inhomogeneous melt and crystalline states, analytical formulas are derived for the nucleation rate as a function of the melt temperature. The theory is general to address different kinds of melt-memory effects depending on whether T m is higher or lower than T m 0 . The derived results are in qualitative agreement with known experimental data, while making predictions for further experiments on melt-memory.
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  • 16
    Publication Date: 2016-07-21
    Description: Long-lived spin coherence and rotationally ordered radical pairs have previously been identified as key requirements for the radical pair mechanism of the avian magnetic compass sense. Both criteria are hard to meet in a biological environment, where thermal motion of the radicals creates dynamic disorder and drives efficient spin relaxation. This has long been cited as a major stumbling block of the radical pair hypothesis. Here we combine Redfield relaxation theory with analytical solutions to a rotational diffusion equation to assess the impact of restricted rotational motion of the radicals on the operation of the compass. The effects of such motions are first investigated generally in small, model systems and are then critically examined in the magnetically sensitive flavin-tryptophan radical pair that is formed photochemically in the proposed magnetoreceptor protein, cryptochrome. We conclude that relaxation is slowest when rotational motion of the radicals within the protein is fast and highly constrained; that in a regime of slow relaxation, the motional averaging of hyperfine interactions has the potential to improve the sensitivity of the compass; and that consideration of motional effects can significantly alter the design criteria for an optimal compass. In addition, we demonstrate that motion of the flavin radical is likely to be compatible with its role as a component of a functioning radical-pair compass, whereas the motion of the tryptophan radical is less ideal, unless it is particularly fast.
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  • 17
    Publication Date: 2016-07-21
    Description: Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
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  • 18
    Publication Date: 2016-07-22
    Description: In this work, a new rigid-nonpolarizable model of methanol is proposed. The model has three sites, located at the same positions as those used in the OPLS model previously proposed by Jorgensen [J. Phys. Chem. 90 , 1276 (1986)]. However, partial charges and the values of the Lennard-Jones parameters were modified by fitting to an adequately selected set of target properties including solid-fluid experimental data. The new model was denoted as OPLS/2016. The overall performance of this model was evaluated and compared to that obtained with other popular models of methanol using a similar test to that recently proposed for water models. In the test, a certain numerical score is given to each model. It was found that the OPLS/2016 obtained the highest score (7.4 of a maximum of 10) followed by L1 (6.6), L2 (6.4), OPLS (5.8), and H1 (3.5) models. The improvement of OPLS/2016 with respect to L1 and L2 is mainly due to an improvement in the description of fluid-solid equilibria (the melting point is only 14 K higher than the experimental value). In addition, it was found that no methanol model was able to reproduce the static dielectric constant and the isobaric heat capacity, whereas the better global performance was found for models that reproduce the vaporization enthalpy once the so-called polarization term is included. Similar conclusions were suggested previously in the analysis of water models and are confirmed here for methanol.
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  • 19
    Publication Date: 2016-07-22
    Description: We investigate the link between dynamic localization, characterized by the Debye–Waller factor, 〈 u 2 〉, and solute self-diffusivity, D , in a polymer system using atomistic molecular dynamics simulations and vapor sorption experiments. We find a linear relationship between ln D and 1/〈 u 2 〉 over more than four decades of D , encompassing most of the glass formation regime. The observed linearity is consistent with the Langevin dynamics in a periodically varying potential field and may offer a means to rapidly assess diffusion based on the characterization of dynamic localization.
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  • 20
    Publication Date: 2016-07-22
    Description: It is general wisdom that the pair potential of charged colloids in a liquid may be closely approximated by a Yukawa interaction, as predicted by the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. We experimentally determine the effective forces in a binary mixture of like-charged particles, of species 1 and 2, with blinking optical tweezers. The measured forces are consistent with a Yukawa pair potential but the (12) cross-interaction is not equal to the geometric mean of the (11) and (22) like-interactions, as expected from DLVO. The deviation is a function of the electrostatic screening length and the size ratio, with the cross-interaction measured being consistently weaker than DLVO predictions. The corresponding non-additivity parameter is negative and grows in magnitude with increased size asymmetry.
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  • 21
    Publication Date: 2016-07-26
    Description: The associative and dissociative adsorption of water molecules at low-coverage situations on rutile TiO 2 (110) surface with step defects was investigated by the density functional theory calculations. Structural optimization of the hydroxylated/hydrated configurations at step edges along the 1 1 ̄ 1 crystal directions and the dynamic process of water dissociation were discussed to get a better description of the water/TiO 2 interface. Our results indicate that steps on the TiO 2 (110) surface could be an active site for water dissociation. The results of geometry optimization suggest that the stability of hydroxylated configuration is largely dependent on the locations of the H species and the recombination of water molecules from hydroxyls is observed in the fully hydroxylated condition. However, these hydroxyls can be stabilized by the associatively absorbed water nearby by forming competitive intermolecular hydrogen bonds. The dynamics of water dissociation and hydrogen diffusion were studied by the first principles molecular dynamics simulation and our results suggest that the hydrogen released by water dissociation can be transferred among the adsorbates, such as the unsaturated oxygen atoms–H 2 O–hydroxyl (TiO–H 2 O–OH) complex at step edges, or gradually diffuses to the bulk water system in the form of hydronium (H 3 O + ) at higher water coverage.
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  • 22
    Publication Date: 2016-07-26
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  • 23
    Publication Date: 2016-07-26
    Description: A series of CH stretch modes in phenyl radical (C 6 H 5 ) has been investigated via high resolution infrared spectroscopy at sub-Doppler resolution (∼60 MHz) in a supersonic discharge slit jet expansion. Two fundamental vibrations of a 1 symmetry, ν 1 and ν 2 , are observed and rotationally analyzed for the first time, corresponding to in-phase and out-of-phase symmetric CH stretch excitation at the ortho/meta/para and ortho/para C atoms with respect to the radical center. The ν 1 and ν 2 band origins are determined to be 3073.968 50(8) cm −1 and 3062.264 80(7) cm −1 , respectively, which both agree within 5 cm −1 with theoretical anharmonic scaling predictions based on density functional B3LYP/6-311g++(3df,3dp) calculations. Integrated band strengths for each of the CH stretch bands are analyzed, with the relative intensities agreeing remarkably well with theoretical predictions. Frequency comparison with previous low resolution Ar-matrix spectroscopy [A. V. Friderichsen et al. , J. Am. Chem. Soc. 123 , 1977 (2001)] reveals a nearly uniform Δν ≈ + 10-12 cm −1 blue shift between gas phase and Ar matrix values for ν 1 and ν 2 . This differs substantially from the much smaller red shift (Δν ≈ − 1 cm −1 ) reported for the ν 19 mode, and suggests a simple physical model in terms of vibrational mode symmetry and crowding due to the matrix environment. Finally, the infrared phenyl spectra are well described by a simple asymmetric rigid rotor Hamiltonian and show no evidence for spectral congestion due to intramolecular vibrational coupling, which bodes well for high resolution studies of other ring radicals and polycyclic aromatic hydrocarbons. In summary, the combination of slit jet discharge methods with high resolution infrared lasers enables spectroscopic investigation of even highly reactive combustion and interstellar radical intermediates under gas phase, jet-cooled (T rot ≈ 11 K) conditions.
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  • 24
    Publication Date: 2016-07-26
    Description: The paper deals with a model-free approach to the analysis of quasielastic neutron scattering intensities from anomalously diffusing quantum particles. All quantities are inferred from the asymptotic form of their time-dependent mean square displacements which grow ∝ t α , with 0 ≤ α 〈 2. Confined diffusion ( α = 0) is here explicitly included. We discuss in particular the intermediate scattering function for long times and the Fourier spectrum of the velocity autocorrelation function for small frequencies. Quantum effects enter in both cases through the general symmetry properties of quantum time correlation functions. It is shown that the fractional diffusion constant can be expressed by a Green-Kubo type relation involving the real part of the velocity autocorrelation function. The theory is exact in the diffusive regime and at moderate momentum transfers.
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  • 25
    Publication Date: 2016-07-26
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  • 26
    Publication Date: 2016-07-26
    Description: Adiabatic approximations in time-dependent density functional theory (TDDFT) will in general yield unphysical time-dependent shifts in the resonance positions of a system driven far from its ground-state. This spurious time-dependence is explained in Fuks et al. [Phys. Rev. Lett. 114 , 183002 (2015)] in terms of the violation of an exact condition by the non-equilibrium exchange-correlation kernel of TDDFT. Here we give details on the derivation and discuss reformulations of the exact condition that apply in special cases. In its most general form, the condition states that when a system is left in an arbitrary state, the TDDFT resonance position for a given transition in the absence of time-dependent external fields and ionic motion is independent of the state. Special cases include the invariance of TDDFT resonances computed with respect to any reference interacting stationary state of a fixed potential, and with respect to any choice of appropriate stationary Kohn-Sham reference state. We then present several case studies, including one that utilizes the adiabatically exact approximation, that illustrate the conditions and the impact of their violation on the accuracy of the ensuing dynamics. In particular, charge-transfer across a long-range molecule is hampered, and we show how adjusting the frequency of a driving field to match the time-dependent shift in the charge-transfer resonance frequency results in a larger charge transfer over time.
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  • 27
    Publication Date: 2016-07-27
    Description: Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF − molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.
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  • 28
    Publication Date: 2016-07-27
    Description: We report on the computational design of an all-metal aromatic sandwich, [Sb 4 Au 4 Sb 4 ] 2− . The triple-layered, square-prismatic sandwich complex is the global minimum of the system from Coalescence Kick and Minima Hopping structural searches. Following a standard, qualitative chemical bonding analysis via canonical molecular orbitals, the sandwich complex can be formally described as [Sb 4 ] + [Au 4 ] 4− [Sb 4 ] + , showing ionic bonding characters with electron transfers in between the Sb 4 /Au 4 /Sb 4 layers. For an in-depth understanding of the system, one needs to go beyond the above picture. Significant Sb → Au donation and Sb ← Au back-donation occur, redistributing electrons from the Sb 4 /Au 4 /Sb 4 layers to the interlayer Sb–Au–Sb edges, which effectively lead to four Sb–Au–Sb three-center two-electron bonds. The complex is a system with 30 valence electrons, excluding the Sb 5s and Au 5d lone-pairs. The two [Sb 4 ] + ligands constitute an unusual three-fold (π and σ) aromatic system with all 22 electrons being delocalized. An energy gap of ∼1.6 eV is predicted for this all-metal sandwich. The complex is a rare example for rational design of cluster compounds and invites forth-coming synthetic efforts.
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  • 29
    Publication Date: 2016-07-27
    Description: We employ a field-theoretical variational approach to study the behavior of ionic solutions in the grand canonical ensemble. To describe properly the hardcore interactions between ions, we use a cutoff in Fourier space for the electrostatic contribution of the grand potential and the Carnahan-Starling equation of state with a modified chemical potential for the pressure one. We first calibrate our method by comparing its predictions at room temperature with Monte Carlo results for excess chemical potential and energy. We then validate our approach in the bulk phase by describing the classical “ionic liquid-vapor” phase transition induced by ionic correlations at low temperature, before applying it to electrolytes at room temperature confined to nanopores embedded in a low dielectric medium and coupled to an external reservoir of ions. The ionic concentration in the nanopore is then correctly described from very low bulk concentrations, where dielectric exclusion shifts the transition up to room temperature for sufficiently tight nanopores, to high concentrations where hardcore interactions dominate which, as expected, modify only slightly this ionic “capillary evaporation.”
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  • 30
    Publication Date: 2016-07-27
    Description: The Orsay-Trento bosonic density functional theory model is extended to include dissipation due to the viscous response of superfluid 4 He present at finite temperatures. The viscous functional is derived from the Navier-Stokes equation by using the Madelung transformation and includes the contribution of interfacial viscous response present at the gas-liquid boundaries. This contribution was obtained by calibrating the model against the experimentally determined electron mobilities from 1.2 K to 2.1 K along the saturated vapor pressure line, where the viscous response is dominated by thermal rotons. The temperature dependence of ion mobility was calculated for several different solvation cavity sizes and the data are rationalized in the context of roton scattering and Stokes limited mobility models. Results are compared to the experimentally observed “exotic ion” data, which provides estimates for the corresponding bubble sizes in the liquid. Possible sources of such ions are briefly discussed.
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  • 31
    Publication Date: 2016-07-28
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  • 32
    Publication Date: 2016-07-28
    Description: In this paper, we present a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD- NV ( p ) T ). This method is suitable for systems for which conventional constant NPT -setups are difficult to implement. In this implementation, each replica has an individual volume, with normal pressure maintained for each replica in the simulation. We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine ( Ala 2 ) in the bulk and in the presence of a graphene layer. Compared to conventional constant NPT -REMD and NVT -REMD simulations, we find that the structural properties of our new method are in good agreement with simulations in the NPT -ensemble at all temperatures. The structural properties of the systems considered are affected by high pressures at elevated temperatures in the constant NVT -ensemble, an effect that our method corrects for. Unprojected distributions reveal that essential motions of the peptide are affected by the presence of the barostat in the NPT implementation but that the dynamical eigenmodes of the NV(p)T method are in close quantitative agreement with the NVT-ensemble.
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  • 33
    Publication Date: 2016-07-28
    Description: In order to study the dependence of water solubility and hydration behavior of nanoparticles on their surface polarity, we designed polar nanoparticles with varying surface polarity by assigning atomic partial charge to the surface of C60. The water solubility of the nanoparticle is enhanced by several orders of magnitude after the introduction of surface polarity. Nevertheless, when the atomic partial charge grows beyond a certain value ( q M ), the solubility continuously decreases to the level of nonpolar nanoparticle. It should be noted that such q M is comparable with atomic partial charge of a variety of functional groups. The hydration behaviors of nanoparticles were then studied to investigate the non-monotonic dependence of solubility on the surface polarity. The interaction between the polar nanoparticle and the hydration water is stronger than the nonpolar counterpart, which should facilitate the dissolution of the nanoparticles. On the other hand, the surface polarity also reduces the interaction of hydration water with the other water molecules and enhances the interaction between the nanoparticles which may hinder their dispersion. Besides, the introduction of surface polarity disturbs and even rearranges the hydration structure of nonpolar nanoparticle. Interestingly, the polar nanoparticle with less ordered hydration structure tends to have higher water solubility.
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  • 34
    Publication Date: 2016-07-28
    Description: We study the translational single particle dynamics of hydration water of lysozyme upon cooling by means of molecular dynamics simulations. We find that water close to the protein exhibits two distinct relaxations. By characterizing their behavior upon cooling, we are able to assign the first relaxation to the structural α -relaxation also present in bulk water and in other glass-forming liquids. The second, slower, relaxation can be ascribed to a dynamic coupling of hydration water motions to the fluctuations of the protein structure. Both relaxation times exhibit crossovers in the behavior upon cooling. For the α -process, we find upon cooling a crossover from a fragile behavior to a strong behavior at a temperature which is about five degrees higher than that of bulk water. The long -relaxation time appears strictly connected to the protein motion as it shows upon cooling a temperature crossover from a strong behavior with a lower activation energy to a strong behavior with a higher activation energy. The crossover temperature coincides with the temperature of the protein dynamical transition. These findings can help experimentalists to disentangle the different information coming from total correlators and to better characterize hydration water relaxations in different biomolecules.
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  • 35
    Publication Date: 2016-07-28
    Description: We extend a previously introduced model of stochastic gene regulation of cancer to a nonlinear case having both gene and pseudogene messenger RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean genetic elements and possesses noise-induced multistability (multimodality). We obtain analytical expressions for probabilities for the case of constant but finite number of microRNA molecules which act as a noise source for the competing gene and pseudogene mRNAs. The probability distribution functions display both the global bistability regime as well as even-odd number oscillations for a certain range of model parameters. Statistical characteristics of the mRNA’s level fluctuations are evaluated. The obtained results of the extended model advance our understanding of the process of stochastic gene and pseudogene expressions that is crucial in regulation of cancer.
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  • 36
    Publication Date: 2016-07-28
    Description: We analyse van der Waals interactions between a pair of dielectrically anisotropic plane-layered media interacting across a dielectrically isotropic solvent medium. We develop a general formalism based on transfer matrices to investigate the van der Waals torque and force in the limit of weak birefringence and dielectric matching between the ordinary axes of the anisotropic layers and the solvent. We apply this formalism to study the following systems: (i) a pair of single anisotropic layers, (ii) a single anisotropic layer interacting with a multilayered slab consisting of alternating anisotropic and isotropic layers, and (iii) a pair of multilayered slabs each consisting of alternating anisotropic and isotropic layers, looking at the cases where the optic axes lie parallel and/or perpendicular to the plane of the layers. For the first case, the optic axes of the oppositely facing anisotropic layers of the two interacting slabs generally possess an angular mismatch, and within each multilayered slab the optic axes may either be the same or undergo constant angular increments across the anisotropic layers. In particular, we examine how the behaviors of the van der Waals torque and force can be “tuned” by adjusting the layer thicknesses, the relative angular increment within each slab, and the angular mismatch between the slabs.
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  • 37
    Publication Date: 2016-07-28
    Description: The static and dynamic first ( β ‖ ) and second ( γ ‖ ) hyperpolarizabilities of water, methanol, and dimethyl ether have been evaluated within the response function approach using a hierarchy of coupled cluster levels of approximation and doubly augmented correlation consistent atomic basis sets. For the three compounds, the electronic β ‖ and γ ‖ values calculated at the CCSD and CC3 levels are in good agreement with gas phase electric field-induced second harmonic generation (EFISHG) measurements. In addition, for dimethyl ether, the frequency dispersion of both properties follows closely recent experimental values [V. W. Couling and D. P. Shelton, J. Chem. Phys. 143 , 224307 (2015)] demonstrating the reliability of these methods and levels of approximation. This also suggests that the vibrational contributions to the EFISHG responses of these molecules are small.
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  • 38
    Publication Date: 2016-07-28
    Description: Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145 , 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.
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  • 39
    Publication Date: 2016-07-29
    Description: The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal C α -trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl . As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.
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  • 40
    Publication Date: 2016-07-29
    Description: Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relative to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.
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  • 41
    Publication Date: 2016-07-29
    Description: The trans -urocanic acid, a UV chromophore in the epidermis of human skin, was found to exhibit a wavelength dependent isomerization property. The isomerization quantum yield to cis -urocanic is greatest when being excited to the S 1 state, whereas exciting the molecule to the S 2 state causes almost no isomerization. The comparative photochemical behavior of the trans -urocanic on the S 1 and S 2 states continues to be the subject of intense research effort. This study is concerned with the unique photo-behavior of this interesting molecule on the S 2 state. Combining the on-the-fly surface hopping dynamics simulations and static electronic structure calculations, three decay channels were observed following excitation to the S 2 state. An overwhelming majority of the molecules decay to the S 1 state through a planar or pucker characterized minimum energy conical intersection (MECI), and then decay to the ground state along a relaxation coordinate driven by a pucker deformation of the ring. A very small fraction of molecules decay to the S 1 state by a MECI characterized by a twisting motion around the CC double bond, which continues to drive the molecule to deactivate to the ground state. The latter channel is related with the photoisomerization process, whereas the former one will only generate the original trans -form products. The present work provides a novel S 2 state decay mechanism of this molecule, which offers useful information to explain the wavelength dependent isomerization behavior.
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  • 42
    Publication Date: 2016-08-02
    Description: Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH 5 + . We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH 4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.
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  • 43
    Publication Date: 2016-08-02
    Description: The ionization potential (IP) of the aromatic alpha hydroxy carboxylic acid, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), is shifted by complexation with hydrogen bonding ligands such as water and formic acid. Generalized Kohn-Sham energy decomposition analysis decomposes the intermolecular binding energies into a frozen energy term, polarization, correlation, and/or dispersion energy terms, as well as terms of geometric relaxation and zero point energy. We observe that in each dimer the attractive polarization always increases upon ionization, enhancing binding in the cation and shifting the IP toward the red. For 9HFCA—H 2 O, a substantial decrease of the repulsive frozen energy in cation further shifts the IP toward red. For 9HFCA—HCOOH, the increase of the frozen energy actually occurs in the cation and shifts the IP toward blue. Consistent with the experimental measurements, our analysis provides new, non-intuitive perspectives on multiple hydrogen bonds interactions in carboxylic acids and water complexes.
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  • 44
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    American Institute of Physics (AIP)
    Publication Date: 2016-08-02
    Description: Nucleation in food colloids has been studied in detail using ultrasound spectroscopy. Our data show that classical nucleation theory (CNT) remains a sound basis from which to understand nucleation in food colloids and analogous model systems using n-alkanes. Various interpretations and modifications of CNT are discussed with regard to their relevance to food colloids. Much of the evidence presented is based on the ultrasound velocity spectrometry measurements which has many advantages for the study of nucleating systems compared to light scattering and NMR due to its sensitivity at low solid contents and its ability to measure true solid contents in the nucleation and early crystal growth stages. Ultrasound attenuation spectroscopy also responds to critical fluctuations in the induction region. We show, however, that a periodic pressure fluctuation such as a quasi-continuous (as opposed to a pulse comprising only a few pressure cycles) ultrasound field can alter the nucleation process, even at very low acoustic intensity. Thus care must be taken when using ultrasound techniques that the measurements do not alter the studied processes. Quasi-continuous ultrasound fields may enhance or suppress nucleation and the criteria to determine such effects are derived. The conclusions of this paper are relevant to colloidal systems in foods, pharmaceuticals, agro-chemicals, cosmetics, and personal products.
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  • 45
    Publication Date: 2016-08-02
    Description: In this paper we introduce two size consistent forms of the non-orthogonal configuration interaction with second-order Møller-Plesset perturbation theory method, NOCI-MP2. We show that the original NOCI-MP2 formulation [S. R. Yost, T. Kowalczyk, and T. VanVoorh, J. Chem. Phys. 193 , 174104 (2013)], which is a perturb-then-diagonalize multi-reference method, is not size consistent. We also show that this causes significant errors in large systems like the linear acenes. By contrast, the size consistent versions of the method give satisfactory results for singlet and triplet excited states when compared to other multi-reference methods that include dynamic correlation. For NOCI-MP2 however, the number of required determinants to yield similar levels of accuracy is significantly smaller. These results show the promise of the NOCI-MP2 method, though work still needs to be done in creating a more consistent black-box approach to computing the determinants that comprise the many-electron NOCI basis.
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  • 46
    Publication Date: 2016-08-02
    Description: An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.
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  • 47
    Publication Date: 2016-08-02
    Description: Aging kinetics of a glass is currently modeled in terms of slowing of its α-relaxation dynamics, whose features are interpreted in terms of dynamic heterogeneity, i.e., formation and decay of spatially and temporally distinct nm-size regions. To test the merits of this view, we studied the calorimetric effects of aging an orientational glass of levoglucosan crystal in which such regions would not form in the same way as they form in liquids, and persist in structural glasses, because there is no liquid-like molecular diffusion in the crystal. By measuring the heat capacity, C p , we determined the change in the enthalpy, H , and the entropy, S , during two aging-protocols: (a) keeping the samples isothermally at temperature, T a , and measuring the changes after different aging times, t a , and (b) keeping the samples at different T a s and measuring the changes after the same t a . A model-free analysis of the data shows that as t a is increased (procedure (a)), H and S decrease according to a dispersive rate kinetics, and as T a is increased (procedure (b)), H and S first increase, reach a local maximum at a certain T a , and then decrease. Even though there is no translational diffusion to produce (liquid-like) free volume, and no translational-rotational decoupling, the aging features are indistinguishable from those of structural glasses. We also find that the Kohlrausch parameter, originally fitted to the glass-aging data, decreases with decrease in T a , which is incompatible with the current use of the aging data for estimating the α-relaxation time. We argue that the vibrational state of a glass is naturally incompatible with its configurational state, and both change on aging until they are compatible, in the equilibrium liquid. So, dipolar fluctuations seen as the α-relaxation would not be the same motions that cause aging. We suggest that aging kinetics is intrinsically dispersive with its own characteristic rate constant and it does not yield the α-relaxation rate. In this view, thermodynamic and other properties define the fictive temperature; the real or imaginary components of a dynamic property do not define it. While particles’ overall motions may still play a crucial role in (structural) glass physics, we conclude that translational diffusion alone is not a requirement for structure stabilization on aging of a kinetically frozen state.
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  • 48
    Publication Date: 2016-08-03
    Description: Long-term creep (i.e., deformation under sustained load) is a significant material response that needs to be accounted for in concrete structural design. However, the nature and origin of concrete creep remain poorly understood and controversial. Here, we propose that concrete creep at relative humidity ≥ 50%, but fixed moisture content (i.e., basic creep), arises from a dissolution-precipitation mechanism, active at nanoscale grain contacts, as has been extensively observed in a geological context, e.g., when rocks are exposed to sustained loads, in liquid-bearing environments. Based on micro-indentation and vertical scanning interferometry data and molecular dynamics simulations carried out on calcium–silicate–hydrate (C–S–H), the major binding phase in concrete, of different compositions, we show that creep rates are correlated with dissolution rates—an observation which suggests a dissolution-precipitation mechanism as being at the origin of concrete creep. C–S–H compositions featuring high resistance to dissolution, and, hence, creep are identified. Analyses of the atomic networks of such C–S–H compositions using topological constraint theory indicate that these compositions present limited relaxation modes on account of their optimally connected (i.e., constrained) atomic networks.
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  • 49
    Publication Date: 2016-08-03
    Description: Building on a recently introduced inverse strategy, isotropic and convex repulsive pair potentials were designed that favor assembly of particles into kagome and equilateral snub square lattices. The former interactions were obtained by a numerical solution of a variational problem that maximizes the range of density for which the ground state of the potential is the kagome lattice. Similar optimizations targeting the snub square lattice were also carried out, employing a constraint that required a minimum chemical potential advantage of the target over select competing structures. This constraint helped to discover isotropic interactions that meaningfully favored the snub square lattice as the ground state structure despite the asymmetric spatial distribution of particles in its coordination shells and the presence of tightly competing structures. Consistent with earlier published results [W. Piñeros et al. , J. Chem. Phys. 144 , 084502 (2016)], enforcement of greater chemical potential advantages for the target lattice in the interaction optimization led to assemblies with enhanced thermal stability.
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  • 50
    Publication Date: 2016-08-03
    Description: The formation of (NO) 3 on Cu(111) was recently reported based on scanning tunneling microscopy observations [A. Shiotari et al. , J. Chem. Phys. 141 , 134705 (2014)]. We herein report studies into this system using electron energy loss spectroscopy and verify the above findings through vibrational analysis. For the surface covered with mixed isotopes of N 16 O and N 18 O, we observed four peaks corresponding to N-O stretching vibrations, which were ascribed to the four isotopic combinations of the trimer. Dynamic coupling within the trimer was evaluated from model calculations of the coupled oscillators. Furthermore, we observed hindered rotation and translation modes in the dipole scattering regime, suggesting that the molecular axis is tilted from the surface normal. These results provide spectroscopic support for the formation of (NO) 3 on Cu(111).
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  • 51
    Publication Date: 2016-08-03
    Description: The thermodynamic response of liquid nitrogen has been studied extensively, in part, due to the long-standing interest in the high pressure and high temperature dissociation of shocked molecular nitrogen. Previous equation of state (EOS) developments regarding shocked liquid nitrogen have focused mainly on the use of intermolecular pair potentials in atomistic calculations. Here, we present EOS developments for liquid nitrogen, incorporating analytical models, for use in continuum calculations of the shock compression response. The analytical models, together with available Hugoniot data, were used to extrapolate a low pressure reference EOS for molecular nitrogen [R. Span et al. , J. Phys. Chem. Ref. Data 29 , 1361 (2000)] to high pressures and high temperatures. Using the EOS presented here, the calculated pressures and temperatures for single shock, double shock, and multiple shock compression of liquid nitrogen provide a good match to the measured results over a broad range of P - T space. These calculations provide the first comparison of EOS developments with recently measured P - T states under multiple shock compression. The present EOS developments are general and are expected to be useful for other liquids that have low pressure reference EOS information available.
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  • 52
    Publication Date: 2016-08-03
    Description: Energy relaxation from an excited phenyl group chemisorbed to the surface of a crystalline thin film of α-1,3,5-trinitro-1,3,5-triazacyclohexane (α-RDX) at 298 K and 1 atm is simulated using molecular dynamics. Two schemes are used to excite the phenyl group. In the first scheme, the excitation energy is added instantaneously as kinetic energy by rescaling momenta of the 11 atoms in the phenyl group. In the second scheme, the phenyl group is equilibrated at a higher temperature in the presence of static RDX geometries representative of the 298 K thin film. An analytical model based on ballistic phonon transport that requires only the harmonic part of the total Hamiltonian and includes no adjustable parameters is shown to predict, essentially quantitatively, the short-time dynamics of the kinetic energy relaxation (∼200 fs). The dynamics of the phenyl group for times longer than about 6 ps follows exponential decay and agrees qualitatively with the dynamics described by a master equation. Long-time heat propagation within the bulk of the crystal film is consistent with the heat equation.
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  • 53
    Publication Date: 2016-08-03
    Description: Electron ionization of neat tungsten hexacarbonyl (W(CO) 6 ) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO) 6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO) n + (0 ≤ n ≤ 6) and W 2 (CO) n + (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO) n + (0 ≤ n ≤ 3) and W 2 C(CO) n + (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.
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  • 54
    Publication Date: 2016-08-03
    Description: We propose a procedure to analyze the relation between the exact factorization of the electron-nuclear wave function and the Born-Oppenheimer approximation. We define the adiabatic limit as the limit of infinite nuclear mass. To this end, we introduce a unit system that singles out the dependence on the electron-nuclear mass ratio of each term appearing in the equations of the exact factorization. We observe how non-adiabatic effects induced by the coupling to the nuclear motion affect electronic properties and we analyze the leading term, connecting it to the classical nuclear momentum. Its dependence on the mass ratio is tested numerically on a model of proton-coupled electron transfer in different non-adiabatic regimes.
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  • 55
    Publication Date: 2016-08-03
    Description: Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a “+U” correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc–Cu) and ligand strength (CO, NH 3 , and H 2 O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.
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  • 56
    Publication Date: 2016-08-03
    Description: A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n -pentane from constant- NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.
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  • 57
    Publication Date: 2016-08-03
    Description: We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.
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  • 58
    Publication Date: 2016-08-03
    Description: This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green’s function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.
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  • 59
    Publication Date: 2016-08-04
    Description: New, wide-range reference equations for the thermal conductivity of ethene and propene as a function of temperature and density are presented. The equations are based in part upon a body of experimental data that have been critically assessed for internal consistency and for agreement with theory whenever possible. For ethene, we estimate the uncertainty (at the 95% confidence level) for the thermal conductivity from 110 to 520 K at pressures up to 200 MPa to be 5% for the compressed liquid and supercritical phases. For the low-pressure gas phase (to 0.1 MPa) over the temperature range 270–680 K, the estimated uncertainty is 4%. The correlation is valid from 110 to 680 K and up to 200 MPa, but it behaves in a physically reasonable manner down to the triple point and may be used at pressures up to 300 MPa, although the uncertainty will be larger in regions where experimental data were unavailable. In the case of propene, data are much more limited. We estimate the uncertainty for the thermal conductivity of propene from 180 to 625 K at pressures up to 50 MPa to be 5% for the gas, liquid, and supercritical phases. The correlation is valid from 180 to 625 K and up to 50 MPa, but it behaves in a physically reasonable manner down to the triple point and may be used at pressures up to 100 MPa, although the uncertainty will be larger in regions where experimental data were unavailable. For both fluids, uncertainties in the critical region are much larger, since the thermal conductivity approaches infinity at the critical point and is very sensitive to small changes in density.
    Print ISSN: 0047-2689
    Electronic ISSN: 1529-7845
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  • 60
    Publication Date: 2016-08-05
    Description: Suitable metal nanostructures may induce surface-enhanced Raman scattering (SERS) enhancement factors (EFs) large-enough to reach single-molecule sensitivity. However, the gap hot-spot EF probability density function (PDF) has the character of a long-tail distribution, which dramatically mines the reproducibility of SERS experiments. Herein, we carry out electrodynamic calculations based on a 3 D finite element method of two plasmonic nanostructures, combined with Monte Carlo simulations of the EF statistics under different external conditions. We compare the PDF produced by a homodimer of nanoparticles with that provided by a self-similar trimer. We show that the PDF is sensitive to the spatial distribution of near-field enhancement specifically supported by the nanostructure geometry. Breaking the symmetry of the plasmonic system is responsible for inducing particular modulations of the PDF tail resembling a multiple Poisson distribution. We also study the influence that molecular diffusion towards the hottest hot-spot, or selective hot-spot targeting, might have on the EF PDF. Our results quantitatively assess the possibility of designing the response of a SERS substrate so as to contain the intrinsic EF PDF variance and significantly improving, in principle, the reproducibility of SERS experiments.
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  • 61
    Publication Date: 2016-08-05
    Description: In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl( v = 0 → 1) and HCl( v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl( v = 2 → 3) channel could not be observed—presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl( v = 0 → 1) excitation probabilities [Q. Ran et al. , Phys. Rev. Lett. 98 , 237601 (2007)]—50 times smaller than those reported here—were influenced by erroneous assignment of spectroscopic lines used in the data analysis.
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  • 62
    Publication Date: 2016-08-05
    Description: We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.
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  • 63
    Publication Date: 2016-08-05
    Description: The strong-localization limit of three-dimensional Wigner molecules, in which repulsively interacting particles are confined by a weak spherically symmetric potential, is investigated. An explicit prescription for computation of rovibrational wavefunctions and energies that are asymptotically exact at this limit is presented. The prescription is valid for systems with arbitrary angularly-independent interparticle and confining potentials, including those involving Coulombic and screened (i.e., Yukawa/Debye) interactions. The necessary derivations are greatly simplified by explicit constructions of the Eckart frame and the parity-adapted primitive wavefunctions. The performance of the new formalism is illustrated with the three- and four-electron harmonium atoms at their strong-correlation limits. In particular, the involvement of vibrational modes with the E symmetry is readily pinpointed as the origin of the “anomalous” weak-confinement behavior of the 1 S + state of the four-electron species that is absent in its 1 D + companion of the strong-confinement regime.
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  • 64
    Publication Date: 2016-08-05
    Description: The Full Configuration Interaction Quantum Monte Carlo (FCIQMC) method has proved able to provide near-exact solutions to the electronic Schrödinger equation within a finite orbital basis set, without relying on an expansion about a reference state. However, a drawback to the approach is that being based on an expansion of Slater determinants, the FCIQMC method suffers from a basis set incompleteness error that decays very slowly with the size of the employed single particle basis. The FCIQMC results obtained in a small basis set can be improved significantly with explicitly correlated techniques. Here, we present a study that assesses and compares two contrasting “universal” explicitly correlated approaches that fit into the FCIQMC framework: the [2] R 12 method of Kong and Valeev [J. Chem. Phys. 135 , 214105 (2011)] and the explicitly correlated canonical transcorrelation approach of Yanai and Shiozaki [J. Chem. Phys. 136 , 084107 (2012)]. The former is an a posteriori internally contracted perturbative approach, while the latter transforms the Hamiltonian prior to the FCIQMC simulation. These comparisons are made across the 55 molecules of the G1 standard set. We found that both methods consistently reduce the basis set incompleteness, for accurate atomization energies in small basis sets, reducing the error from 28 mE h to 3-4 mE h . While many of the conclusions hold in general for any combination of multireference approaches with these methodologies, we also consider FCIQMC-specific advantages of each approach.
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  • 65
    Publication Date: 2016-08-06
    Description: The crystal-vapor surface free energy γ is an important physical parameter governing physical processes, such as wetting and adhesion. We explore exact and approximate routes to calculate γ based on cleaving an intact crystal into non-interacting sub-systems with crystal-vapor interfaces. We do this by turning off the interactions, Δ V , between the sub-systems. Using the soft-core scheme for turning off Δ V , we find that the free energy varies smoothly with the coupling parameter λ , and a single thermodynamic integration yields the exact γ . We generate another exact method, and a cumulant expansion for γ by expressing the surface free energy in terms of an average of e − β Δ V in the intact crystal. The second cumulant, or Gaussian approximation for γ is surprisingly accurate in most situations, even though we find that the underlying probability distribution for Δ V is clearly not Gaussian. We account for this fact by developing a non-Gaussian theory for γ and find that the difference between the non-Gaussian and Gaussian expressions for γ consist of terms that are negligible in many situations. Exact and approximate methods are applied to the (111) surface of a Lennard-Jones crystal and are also tested for more complex molecular solids, the surface of octane and nonadecane. Alkane surfaces were chosen for study because their crystal-vapor surface free energy has been of particular interest for understanding surface freezing in these systems.
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  • 66
    Publication Date: 2016-08-06
    Description: A systematic route to go beyond the exact exchange plus random phase approximation (RPA) is to include a physical exchange-correlation kernel in the adiabatic-connection fluctuation-dissipation theorem. In the previous study [D. Lu, J. Chem. Phys. 140 , 18A520 (2014)], we found that non-local kernels with a screening length depending on the local Wigner-Seitz radius, r s ( r ), suffer an error associated with a spurious long-range repulsion in van der Waals bounded systems, which deteriorates the binding energy curve as compared to RPA. We analyze the source of the error and propose to replace r s ( r ) by a global, average r s in the kernel. Exemplary studies with the Corradini, del Sole, Onida, and Palummo kernel show that while this change does not affect the already outstanding performance in crystalline solids, using an average r s significantly reduces the spurious long-range tail in the exchange-correlation kernel in van der Waals bounded systems. When this method is combined with further corrections using local dielectric response theory, the binding energy of the Kr dimer is improved three times as compared to RPA.
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  • 67
    Publication Date: 2016-08-06
    Description: We have implemented internally contracted complete active space second order perturbation theory (CASPT2) with the density matrix renormalization group (DMRG) as active space solver [Y. Kurashige and T. Yanai, J. Chem. Phys. 135 , 094104 (2011)]. Internally contracted CASPT2 requires to contract the generalized Fock matrix with the 4-particle reduced density matrix (4-RDM) of the reference wavefunction. The required 4-RDM elements can be obtained from 3-particle reduced density matrices (3-RDM) of different wavefunctions, formed by symmetry-conserving single-particle excitations op top of the reference wavefunction. In our spin-adapted DMRG code chemps2 https://github.com/sebwouters/chemps2 , we decompose these excited wavefunctions as spin-adapted matrix product states and calculate their 3-RDM in order to obtain the required contraction of the generalized Fock matrix with the 4-RDM of the reference wavefunction. In this work, we study the longitudinal static second hyperpolarizability of all-trans polyenes C 2 n H 2 n +2 [ n = 4–12] in the cc-pVDZ basis set. DMRG-SCF and DMRG-CASPT2 yield substantially lower values and scaling with system size compared to RHF and MP2, respectively.
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  • 68
    Publication Date: 2016-08-06
    Description: Density functional theory calculations were carried out to investigate the evolvement of charge transport properties of a set of new discotic systems as a function of ring and heteroatom (B, Si, S, and Se) substitution on the basic structure of perylene. The replacement of six-membered rings by five-membered rings in the reference compound has shown a prominent effect on the electron reorganization energy that decreases ∼0.2 eV from perylene to the new carbon five-membered ring derivative. Heteroatom substitution with boron also revealed to lower the LUMO energy level and increase the electron affinity, therefore lowering the electron injection barrier compared to perylene. Since the rate of the charge transfer between two molecules in columnar discotic systems is strongly dependent on the orientation of the stacked cores, the total energy and transfer integral of a dimer as a disc is rotated with respect to the other along the stacking axis have been predicted. Aimed at obtaining a more realistic approach to the bulk structure, the molecular geometry of clusters made up of five discs was fully optimized, and charge transfer rate and mobilities were estimated for charge transport along a one dimensional pathway. Heteroatom substitution with selenium yields electron transfer integral values ∼0.3 eV with a relative disc orientation of 25°, which is the preferred angle according to the dimer energy profile. All the results indicate that the tetraselenium-substituted derivative, not synthetized so far, could be a promising candidate among those studied in this work for the fabrication of n-type semiconductors based on columnar discotic liquid crystals materials.
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  • 69
    Publication Date: 2016-08-06
    Description: Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
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  • 70
    Publication Date: 2016-08-06
    Description: This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm −1 peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol’d diffusion, which connects different regions of phase-space by a resonance network known as the Arnol’d web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep. Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol’d web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.
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  • 71
    Publication Date: 2016-08-06
    Description: An increasing number of chemists have focused on the two-electron/multicenter bond (2e/mc) that was first introduced to interpret the bonding mechanism of radical dimers. Herein, we report the polar two-electron/twelve center (2e/12c) bonding character in a series of phenalenyl-azaphenalenyl radical hetero-dimers. Interestingly, the bonding energy of weaker polar hetero-dimer (P-TAP) is dominated by the overlap of the two different singly occupied molecular orbital of radicals, while that of stronger polar hetero-dimer (P-HAP) is dominated by the electrostatic attraction. Results show that the difference between the electronegativity of the monomers plays a prominent role in the essential attribution of the polar 2e/12c bond. Correspondingly, a stronger stacking interaction in the hetero-dimer could be effectively achieved by increasing the difference of nitrogen atoms number between the monomers. It is worthy of note that an interesting interlayer charge transfer character is induced in the polar hetero-dimers, which is dependent on the difference between the electronegativity of the monomers. It is our expectation that the new knowledge about the bonding nature of radical hetero-dimers might provide important information for designing radical based functional materials with various applications.
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  • 72
    Publication Date: 2016-08-06
    Description: Nonexponential kinetics imply the existence of at least one slow variable other than the observable, that is, the system has a “hidden” coordinate. We develop a simple, but general, model that allows multidimensional correlation functions to be calculated for these systems. Homogeneous and heterogeneous mechanisms are both included, and slow exchange of the rates is allowed. This model shows that 2D and 3D correlation functions of the observable measure the distribution and kinetics of the hidden coordinate controlling the rate exchange. Both the mean exchange time and the shape of the exchange relaxation are measurable. However, complications arise because higher correlation functions are sums of multiple “pathways,” each of which measures different dynamics. Only one 3D pathway involves exchange dynamics. Care must be used to extract exchange dynamics without contamination from other processes.
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  • 73
    Publication Date: 2016-07-30
    Description: Density-functional theory is used to evaluate the mechanism of copper surface oxidation. Reaction pathways of O 2 dissociation on the surface and oxidation of the sub-surface are found on the Cu(100), Cu(110), and Cu(111) facets. At low oxygen coverage, all three surfaces dissociate O 2 spontaneously. As oxygen accumulates on the surfaces, O 2 dissociation becomes more difficult. A bottleneck to further oxidation occurs when the surfaces are saturated with oxygen. The barriers for O 2 dissociation on the O-saturated Cu(100)-c(2×2)-0.5 monolayer (ML) and Cu(100) missing-row structures are 0.97 eV and 0.75 eV, respectively; significantly lower than those have been reported previously. Oxidation of Cu(110)-c(6×2), the most stable (110) surface oxide, has a barrier of 0.72 eV. As the reconstructions grow from step edges, clean Cu(110) surfaces can dissociatively adsorb oxygen until the surface Cu atoms are saturated. After slight rearrangements, these surface areas form a “1 ML” oxide structure which has not been reported in the literature. The barrier for further oxidation of this “1 ML” phase is only 0.31 eV. Finally the oxidized Cu(111) surface has a relatively low reaction energy barrier for O 2 dissociation, even at high oxygen coverage, and allows for facile oxidation of the subsurface by fast O diffusion through the surface oxide. The kinetic mechanisms found provide a qualitative explanation of the observed oxidation of the low-index Cu surfaces.
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  • 74
    Publication Date: 2016-07-30
    Description: The electronic structures of several small Ce–Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt 2 both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt 2 complexes are therefore ionic, with electronic structures described qualitatively as [CeO +2 ]Pt −2 and [CeO + ]Pt 2 − , respectively. The associated anions are described qualitatively as [CeO + ]Pt −2 and [CeO + ]Pt 2 −2 , respectively. In both neutrals and anions, the most stable molecular structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt 2 moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO 2 , which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO 2 ]Pt − . The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO 2 ]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt–O–Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt − daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.
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  • 75
    Publication Date: 2016-07-30
    Description: Nonlinear spectroscopy signals detected by fluorescence from dilute samples of N non-interacting molecules are usually adequately described by simply multiplying the single molecule response by N . We show that signals that scale with higher powers of N are generated by the joint detection of several particles. This can be accomplished by phase sensitive detection such as phase cycling, photo-acoustic modulation, or by Hanbury-Brown Twiss photon coincidence. Such measurements can dissect the ensemble according to the number of excited particles.
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  • 76
    Publication Date: 2016-07-12
    Description: We report the formation of nanoparticles with significant diamond character after UV multi-photon laser excitation of gaseous naphthalene, buffered in static helium gas, at room temperature. The nanoparticles are identified in situ by their absorption and scattering spectra between 400 and 850 nm, which are modeled using Mie theory. Comparisons of the particles’ spectroscopic and optical properties with those of carbonaceous materials indicate a sp 3 / sp 2 hybridization ratio of 8:1 of the particles formed. The particle extinction in the closed static (unstirred) gas-phase system exhibits a complex and quasi-oscillatory time dependence for the duration of up to several hours with periods ranging from seconds to many minutes. The extinction dynamics of the system is based on a combination of transport features and particle interaction, predominantly agglomeration. The relatively long period of agglomeration allows for a unique analysis of the agglomeration process of diamond-like carbon nanoparticles in situ .
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  • 77
    Publication Date: 2016-07-14
    Description: Ionic liquids with cyano anions have long been used because of their unique combination of low-melting temperatures, reduced viscosities, and increased conductivities. Recently we have shown that cyano anions in ionic liquids are particularly interesting for their potential use as electron donors to excited state photo-acceptors [B. Wu et al. , J. Phys. Chem. B 119 , 14790–14799 (2015)]. Here we report on bulk structural and quantum mechanical results for a series of ionic liquids based on the 1-ethyl-3-methylimidazolium cation, paired with the following five cyano anions: SeCN − , SCN − , N ( CN ) 2 − , C ( CN ) 3 − , and B ( CN ) 4 − . By combining molecular dynamics simulations, high-energy X-ray scattering measurements, and periodic boundary condition DFT calculations, we are able to obtain a comprehensive description of the liquid landscape as well as the nature of the HOMO-LUMO states for these ionic liquids in the condensed phase. Features in the structure functions for these ionic liquids are somewhat different than the commonly observed adjacency, charge-charge, and polarity peaks, especially for the bulkiest B ( CN ) 4 − anion. While the other four cyano-anion ionic liquids present an anionic HOMO, the one for Im 2 , 1 + / B ( CN ) 4 − is cationic.
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  • 78
    Publication Date: 2016-07-19
    Description: In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in this paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al. , Phys. Rev. Lett. 113 , 225701 (2014)] and shows that they are generic in nature, independent of density.
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  • 79
    Publication Date: 2016-07-19
    Description: The periodic rotary motion of spherical sub-millimeter-sized plastic objects is generated under a direct-current electric field in an oil phase containing a small amount of anionic or cationic surfactant. Twin-rotary motion is observed between a pair of counter-electrodes; i.e., two vortices are generated simultaneously, where the line between the centers of rotation lies perpendicular to the line between the tips of the electrodes. Interestingly, this twin rotational motion switches to the reverse direction when an anionic surfactant is replaced by a cationic surfactant. We discuss the mechanism of this self-rotary motion in terms of convective motion in the oil phase where nanometer-sized inverted micelles exist. The reversal of the direction of rotation between anionic and cationic surfactants is attributable to the difference in the charge sign of inverted micelles with surfactants. We show that the essential features in the experimental trends can be reproduced through a simple theoretical model, which supports the validity of the above mechanism.
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  • 80
    Publication Date: 2016-07-19
    Description: The use of back-transformed pair natural orbitals in the calculation of excited state energies, ionization potentials, and electron affinities is investigated within the framework of equation of motion coupled cluster theory and its similarity transformed variant. Possible approaches to a more optimal use of pair natural orbitals in these methods are indicated.
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  • 81
    Publication Date: 2016-07-19
    Description: The pair association between two polyelectrolytes (PEs) of the same size but opposite charge is systematically studied in terms of the potential of mean force (PMF) along their center-of-mass reaction coordinate via coarse-grained, implicit-solvent, explicit-salt computer simulations. The focus is set on the onset and the intermediate transient stages of complexation. At conditions above the counterion-condensation threshold, the PE association process exhibits a distinct sliding-rod-like behavior where the polymer chains approach each other by first stretching out at a critical distance close to their contour length, then “shaking hand” and sliding along each other in a parallel fashion, before eventually folding into a neutral complex. The essential part of the PMF for highly charged PEs can be very well described by a simple theory based on sliding charged “Debye–Hückel” rods with renormalized charges in addition to an explicit entropy contribution owing to the release of condensed counterions. Interestingly, at the onset of complex formation, the mean force between the PE chains is found to be discontinuous, reflecting a bimodal structural behavior that arises from the coexistence of interconnected-rod and isolated-coil states. These two microstates of the PE complex are balanced by subtle counterion release effects and separated by a free-energy barrier due to unfavorable stretching entropy.
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  • 82
    Publication Date: 2016-07-19
    Description: In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. Starting from the stochastic Liouville equation, we have developed a non-perturbative theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole couplings, and Larmor frequencies. Here, we implement the general dipolar EMOR theory for a macromolecule-bound three-spin system, where one, two, or all three spins exchange with the bulk solution phase. In contrast to the previously studied two-spin system with a single dipole coupling, there are now three dipole couplings, so relaxation is affected by distinct correlations as well as by self-correlations. Moreover, relaxation can now couple the magnetizations with three-spin modes and, in the presence of a static dipole coupling, with two-spin modes. As a result of this complexity, three secondary dispersion steps with different physical origins can appear in the longitudinal relaxation dispersion profile, in addition to the primary dispersion step at the Larmor frequency matching the exchange rate. Furthermore, and in contrast to the two-spin system, longitudinal relaxation can be significantly affected by chemical shifts and by the odd-valued (“imaginary”) part of the spectral density function. We anticipate that the detailed studies of two-spin and three-spin systems that have now been completed will provide the foundation for developing an approximate multi-spin dipolar EMOR theory sufficiently accurate and computationally efficient to allow quantitative molecular-level interpretation of frequency-dependent water-proton longitudinal relaxation data from biophysical model systems and soft biological tissue.
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  • 83
    Publication Date: 2016-07-19
    Description: The ground state vibrational energy and spatial features of 4 He– 4 He–Li + and its triatomic isotopic complexes are studied using the slow variable discretization (SVD) method in the hyperspherical coordinates for the zero total angular momentum. Our results show that the dominant structure of the system is an isosceles triangle with the shorter side associated with the two Li + –He distances using the sum-of-potential approximation. Corrections caused by the induced dipole-induced dipole interactions on the He atoms are also investigated. The effects are seen to be small and have a minor influence on the binding energy and the structure of present system. The results are also compared with the full ab initio calculations including all the three-body interactions and information of three-body corrections is obtained.
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  • 84
    Publication Date: 2016-07-19
    Description: We present a comparative study of the glass forming ability of binary systems with varying composition, where the systems have similar global crystalline structure (CsCl+fcc). Biased Monte Carlo simulations using umbrella sampling technique show that the free energy cost to create a CsCl nucleus increases as the composition of the smaller particles is decreased. We find that systems with comparatively lower free energy cost to form CsCl nucleus exhibit more pronounced pre-crystalline demixing near the liquid/crystal interface. The structural frustration between the CsCl and fcc crystal demands this demixing. We show that closer to the equimolar mixture, the entropic penalty for demixing is lower and a glass forming system may crystallize when seeded with a nucleus. This entropic penalty as a function of composition shows a non-monotonic behaviour with a maximum at a composition similar to the well known Kob-Anderson (KA) model. Although the KA model shows the maximum entropic penalty and thus maximum frustration against CsCl formation, it also shows a strong tendency towards crystallization into fcc lattice of the larger “A” particles which can be explained from the study of the energetics. Thus for systems closer to the equimolar mixture although it is the requirement of demixing which provides their stability against crystallization, for KA model it is not demixing but slow dynamics and the presence of the “B” particles make it a good glass former. The locally favoured structure around “B” particles is quite similar to the CsCl structure and the incompatibility of CsCl and fcc hinders the fcc structure growth in the KA model. Although the glass forming binary systems studied here are quite similar, differing only in composition, we find that their glass forming ability cannot be attributed to a single phenomenon.
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  • 85
    Publication Date: 2016-07-19
    Description: Basis set incompleteness error and finite size error can manifest concurrently in systems for which the two effects are phenomenologically well-separated in length scale. When this is true, we need not necessarily remove the two sources of error simultaneously. Instead, the errors can be found and remedied in different parts of the basis set. This would be of great benefit to a method such as coupled cluster theory since the combined cost of n occ 6 n virt 4 could be separated into n occ 6 and n virt 4 costs with smaller prefactors. In this Communication, we present analysis on a data set due to Baardsen and co-workers, containing 2D uniform electron gas coupled cluster doubles energies for r s = 0.5, 1.0, and 2.0 a.u. at a wide range of basis set sizes and particle numbers. In obtaining complete basis set limit thermodynamic limit results, we find that within a small and removable error the above assertion is correct for this simple system. We then use this method to obtain similar results for the 3D electron gas at r s = 1.0, 2.0, and 5.0 a.u. and make comparison to the Ceperley–Alder quantum Monte Carlo results. This approach allows for the combination of methods which separately address finite size effects and basis set incompleteness error.
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  • 86
    Publication Date: 2016-07-19
    Description: Accurate and efficient empirical potential energy models that describe the atomistic interactions between water molecules in the liquid phase are essential for computer simulations of many problems in physics, chemistry, and biology, especially when long length or time scales are important. However, while models with non-polarizable partial charges at four or five sites in a water molecule give remarkably good values for certain properties, deficiencies have been noted in other properties and increasing the number of sites decreases computational efficiency. An alternate approach is to utilize a multipole expansion of the electrostatic potential due to the molecular charge distribution, which is exact outside the charge distribution in the limits of infinite distances or infinite orders of multipoles while partial charges are a qualitative representation of electron density as point charges. Here, a single-site multipole model of water is presented, which is as fast computationally as three-site models but is also more accurate than four- and five-site models. The dipole, quadrupole, and octupole moments are from quantum mechanical–molecular mechanical calculations so that they account for the average polarization in the liquid phase, and represent both the in-plane and out-of-plane electrostatic potentials of a water molecule in the liquid phase. This model gives accurate thermodynamic, dynamic, and dielectric properties at 298 K and 1 atm, as well as good temperature and pressure dependence of these properties.
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  • 87
    Publication Date: 2016-07-21
    Description: Using molecular dynamics simulations with embedded atom model potential, we study structural evolution of Cu 64.5 Zr 35.5 alloy during the cooling in a wide range of cooling rates γ ∈ (1.5 ⋅ 10 9 , 10 13 ) K/s. Investigating short- and medium-range orders, we show that the structure of Cu 64.5 Zr 35.5 metallic glass essentially depends on cooling rate. In particular, a decrease of the cooling rate leads to an increase of abundances of both the icosahedral-like clusters and Frank-Kasper Z16 polyhedra. The amounts of these clusters in the glassy state drastically increase at the γ min = 1.5 ⋅ 10 9 K/s. Analysing the structure of the glass at γ min , we observe the formation of nano-sized crystalline grain of Cu 2 Zr intermetallic compound with the structure of Cu 2 Mg Laves phase. The structure of this compound is isomorphous with that for Cu 5 Zr intermetallic compound. Both crystal lattices consist of two types of clusters: Cu-centered 13-atom icosahedral-like cluster and Zr-centered 17-atom Frank-Kasper polyhedron Z16. That suggests the same structural motifs for the metallic glass and intermetallic compounds of Cu–Zr system and explains the drastic increase of the abundances of these clusters observed at γ min .
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  • 88
    Publication Date: 2016-07-21
    Description: Two-dimensional resonance Raman (2DRR) spectroscopy has recently been developed as a tool for studies of structural heterogeneity and photochemical dynamics in condensed phases. In this paper, 2DRR spectroscopy is used to investigate line broadening mechanisms of both oxygen- and water-ligated myoglobins. General signatures of anharmonicity and inhomogeneous line broadening are first established with model calculations to facilitate signal interpretation. It is shown that the present quasi-degenerate version of 2DRR spectroscopy is insensitive to anharmonicity, because signal generation is allowed for harmonic modes. Rather, the key information to be gained from 2DRR spectroscopy pertains to the line broadening mechanisms, which are fairly obvious by inspection of the data. 2DRR signals acquired for both heme protein systems reveal significant heterogeneity in the vibrational modes local to the heme’s propionic acid side chains. These side chains are known to interact with solvent, because they protrude from the hydrophobic pocket that encloses the heme. Molecular dynamics simulations suggest that the heterogeneity detected in our 2DRR experiments reflects fluctuations in the geometries of the side chains. Knowledge of such thermal motions will be useful for understanding protein function (e.g., ligand binding) because the side chains are an effective “gateway” for the exchange of thermal energy between the heme and solvent.
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  • 89
    Publication Date: 2016-07-21
    Description: We study effective mobility in 2 dimensional (2D) and 3 dimensional (3D) systems, where hopping transitions of carriers are described by the Marcus equation under a Gaussian density of states in the dilute limit. Using an effective medium approximation (EMA), we determined the coefficient C d for the effective mobility expressed by μ eff ∝ exp − λ / 4 k B T − C d σ 2 / k B T 2 / λ ( k B T ) 3 / 2 , where λ is the reorganization energy, σ is the standard deviation of the Gaussian density of states, and k B T takes its usual meaning. We found C d = 1/2 for both 2D and 3D. While various estimates of the coefficient C d for 3D systems are available in the literature, we provide for the first time the expected C d value for a 2D system. By means of kinetic Monte-Carlo simulations, we show that the effective mobility is well described by the equation shown above under certain conditions on λ . We also give examples of analysis of experimental data for 2D and 3D systems based on our theoretical results.
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  • 90
    Publication Date: 2016-07-21
    Description: The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as R I, R II , and R III , respectively, with qualitatively disparate dynamic behaviors: R I which can be described by “softness makes strong glasses,” R II where fragility is independent of softness and can only be tuned by density, and R III with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.
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  • 91
    Publication Date: 2016-07-21
    Description: A model of low-temperature polar liquids is constructed that accounts for the configurational heat capacity, entropy, and the effect of a strong electric field on the glass transition. The model is based on the Padé-truncated perturbation expansions of the liquid state theory. Depending on parameters, it accommodates an ideal glass transition of vanishing configurational entropy and its avoidance, with a square-root divergent enumeration function at the point of its termination. A composite density-temperature parameter ρ γ / T , often used to represent combined pressure and temperature data, follows from the model. The theory is in good agreement with the experimental data for excess (over the crystal state) thermodynamics of molecular glass formers. We suggest that the Kauzmann entropy crisis might be a signature of vanishing configurational entropy of a subset of degrees of freedom, multipolar rotations in our model. This scenario has observable consequences: (i) a dynamical crossover of the relaxation time and (ii) the fragility index defined by the ratio of the excess heat capacity and excess entropy at the glass transition. The Kauzmann temperature of vanishing configurational entropy and the corresponding glass transition temperature shift upward when the electric field is applied. The temperature shift scales quadratically with the field strength.
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  • 92
    Publication Date: 2016-07-21
    Description: Extensive computer simulations are performed for a few model glass-forming liquids in both two and three dimensions to study their dynamics when a randomly chosen fraction of particles are frozen in their equilibrium positions. For all the studied systems, we find that the temperature-dependence of the α relaxation time extracted from an overlap function related to the self-part of the density autocorrelation function can be explained within the framework of the Random First Order Transition (RFOT) theory of the glass transition. We propose a scaling description to rationalize the simulation results and show that our data for the α relaxation time for all temperatures and pin concentrations are consistent with this description. We find that the fragility parameter obtained from fits of the temperature dependence of the α relaxation time to the Vogel-Fulcher-Tammann form decreases by almost an order of magnitude as the pin concentration is increased from zero. Our scaling description relates the fragility parameter to the static length scale of RFOT and thus provides a physical understanding of fragility within the framework of the RFOT theory. Implications of these findings for the values of the exponents appearing in the RFOT theory are discussed.
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  • 93
    Publication Date: 2016-07-22
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  • 94
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    American Institute of Physics (AIP)
    Publication Date: 2016-07-22
    Description: Fewest-switches surface hopping (FSSH) is combined with transition path sampling (TPS) to produce a new method called nonadiabatic path sampling (NAPS). The NAPS method is validated on a model electron transfer system coupled to a Langevin bath. Numerically exact rate constants are computed using the reactive flux (RF) method over a broad range of solvent frictions that span from the energy diffusion (low friction) regime to the spatial diffusion (high friction) regime. The NAPS method is shown to quantitatively reproduce the RF benchmark rate constants over the full range of solvent friction. Integrating FSSH within the TPS framework expands the applicability of both approaches and creates a new method that will be helpful in determining detailed mechanisms for nonadiabatic reactions in the condensed-phase.
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  • 95
    Publication Date: 2016-07-22
    Description: The total and ionization cross sections for electron scattering by benzene, halobenzenes, toluene, aniline, and phenol are reported over a wide energy domain. The multi-scattering centre spherical complex optical potential method has been employed to find the total elastic and inelastic cross sections. The total ionization cross section is estimated from total inelastic cross section using the complex scattering potential-ionization contribution method. In the present article, the first theoretical calculations for electron impact total and ionization cross section have been performed for most of the targets having numerous practical applications. A reasonable agreement is obtained compared to existing experimental observations for all the targets reported here, especially for the total cross section.
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  • 96
    Publication Date: 2016-07-22
    Description: Inelastic scattering computations are presented for collisions of vibrationally and rotationally excited CO with H 2 in full dimension. The computations utilize a newly developed six-dimensional potential energy surface (PES) and the previously reported four-dimensional V12 PES [P. Jankowski et al. , J. Chem. Phys. 138 , 084307 (2013)] and incorporate full angular-momentum coupling. At low collision energies, pure rotational excitation cross sections of CO by para -, ortho -, and normal -H 2 are calculated and convolved to compare with recent measurements. Good agreement with the measured data is shown except for j 1 = 0 → 1 excitation of CO for very low-energy para -H 2 collisions. Rovibrational quenching results are presented for initially excited CO( v 1 j 1 ) levels with v 1 = 1, j 1 = 1–5 and v 1 = 2, j 1 = 0 for collisions with para -H 2 ( v 2 = 0, j 2 = 0) and ortho -H 2 ( v 2 = 0, j 2 = 1) over the kinetic energy range 0.1–1000 cm −1 . The total quenching cross sections are found to have similar magnitudes, but increase (decrease) with j 1 for collision energies above ∼300 cm −1 (below ∼10 cm −1 ). Only minor differences are found between para - and ortho -H 2 colliders for rovibrational and pure rotational transitions, except at very low collision energies. Likewise, pure rotational deexcitation of CO yields similar cross sections for the v 1 = 0 and v 1 = 1 vibrational levels, while rovibrational quenching from v 1 = 2, j 1 = 0 is a factor of ∼5 larger than that from v 1 = 1, j 1 = 0. Details on the PES, computed at the CCSD(T)/aug-cc-pV5Z level, and fitted with an invariant polynomial method, are also presented.
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  • 97
    Publication Date: 2016-07-22
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  • 98
    Publication Date: 2016-07-22
    Description: A compendium of phase change enthalpies published in 2010 is updated to include the period 1880–2015. Phase change enthalpies including fusion, vaporization, and sublimation enthalpies are included for organic, organometallic, and a few inorganic compounds. Part 1 of this compendium includes organic compounds from C 1 to C 10 . Part 2 of this compendium, to be published separately, will include organic and organometallic compounds from C 11 to C 192 . Sufficient data are presently available to permit thermodynamic cycles to be constructed as an independent means of evaluating the reliability of the data. Temperature adjustments of phase change enthalpies from the temperature of measurement to the standard reference temperature, T = 298.15 K, and a protocol for doing so are briefly discussed.
    Print ISSN: 0047-2689
    Electronic ISSN: 1529-7845
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  • 99
    Publication Date: 2016-07-23
    Description: Very recently, boron nitride atomic chains were successively prepared and observed in experiments [O. Cretu et al. , ACS Nano 8 , 11950 (2015)]. Herein, using a first-principles technique, we study the magnetism and spin-dependent electronic transport properties of three types of BN atomic chains whose magnetic moment is 1 μ B for B n N n−1 , 2 μ B for B n N n , and 3 μ B for B n N n+1 type atomic chains, respectively. The spin-dependent electronic transport results demonstrate that the short B n N n+1 chain presents an obvious spin-filtering effect with high spin polarization ratio (〉90%) under low bias voltages. Yet, this spin-filtering effect does not occur for long B n N n+1 chains under high bias voltages and other types of BN atomic chains (B n N n−1 and B n N n ). The proposed short B n N n+1 chain is predicted to be an effective low-bias spin filters. Moreover, the length-conductance relationships of these BN atomic chains were also studied.
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  • 100
    Publication Date: 2016-07-23
    Description: The atomic structure and electronic transport properties of a single hydrogen molecule connected to both symmetric and asymmetric Cu electrodes are investigated by using the non-equilibrium Green’s function formalism combined with the density functional theory. Our calculations show that in symmetric Cu–H 2 –Cu junctions, the low-bias conductance drops rapidly upon stretching, while asymmetric ones present a low-bias conductance spanning the 0.2–0.3 G 0 interval for a wide range of electrode separations. This is in good agreement with experiments on Cu atomic contacts in a hydrogen environment. Furthermore, the distribution of the calculated vibrational energies of the two hydrogen atoms in the asymmetric Cu–H 2 –Cu junction is also consistent with experiments. These findings provide clear evidence for the formation of asymmetric Cu–H 2 –Cu molecular junctions in breaking Cu atomic contacts in the presence of hydrogen and are also helpful for the design of molecular devices with Cu electrodes.
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