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The Journal of Chemical Physics : The Alzheimer ß-amyloid (Aß1–39) dimer in an implicit solvent

By: Priya Anand, Fateh S. Nandel, and Ulrich H. E. Hansmann

Description: Oligomers of Aβ peptides are suspected as the underlying cause of Alzheimer disease. Knowledge of their structural properties could therefore lead to a deeper understanding of the mechanism behind the outbreak of this disease. As a step in this direction we have studied Aβ dimers by all-atom molecular dynamics simulations. Equilibrated structures at 300 K were clustered into different families with similar structural features. The dominant cluster has parallel N-terminals and a well defined segment Leu17-Ala21 that are stabilized by salt bridges between Lys28 of one chain and either Glu22 or Asp23 of the other chain. The formation of these salt bridges may be the limiting step in oligomerization and fibrillogenesis....

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The Journal of Chemical Physics : Intrinsic thermal expansivity and hydrational properties of amyloid peptide Aß42 in liquid water

By: I. Brovchenko, R. R. Burri, A. Krukau, A. Oleinikova, and R. Winter

Description: Volumetric and conformational properties of the amyloid β(1–42) peptide (Aβ42) are studied in relation to the properties of hydration water in a wide temperature range by computer simulations. The apparent volume of Aβ42, which is the change in the total volume of the solution due to the presence of Aβ42, shows a quite different temperature dependence below and above T ≈ 320 K. The apparent thermal expansion coefficient αapp(Aβ42) is about 1.5×10−3 K−1 at T ≤ 320 K and about 0.6×10−3 K−1 at T>320 K. By evaluation of the thermal expansivity of hydration water, the intrinsic expansivity of the biomolecule in liquid water was determined for the first time. The intrinsic thermal expansion coefficient of Aβ42 is found to be negative: αint(Aβ42) ≈ −0.8×10−3 K−1. The negative thermal expansion coefficient of Aβ42 can be attributed to its rubberlike (entropic) elasticity and/or to a decreasing number of intrapeptide hydrogen bonds. Upon heating, Aβ42 transforms from an extended chain with a significant content of α-helices to a compact coil with noticeable content of β-structures. A hydrogen-bonded spanning network of hydration...

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The Journal of Chemical Physics : Simulated morphological landscape of polymer single crystals by phase field model

By: Dong Wang, Tongfei Shi, Jizhong Chen, Lijia An, and Yuxi Jia

Description: The novel phase field model with the “polymer characteristic” was established based on a nonconserved spatiotemporal Ginzburg–Landau equation (TDGL model A). Especially, we relate the diffusion equation with the crystal growth faces of polymer single crystals. Namely, the diffusion equations are discretized according to the diffusion coefficient of every lattice site in various crystal growth faces and the shape of lattice is selected based on the real proportion of the unit cell dimensions. Spatiotemporal growth of syndiotactic polypropylene single crystals during isothermal crystallization has been investigated theoretically based on this phase field model. Two dimensional numerical calculations are performed to elucidate the faceted single crystal growth including square, rectangular, lozenge-shaped, and hexagonal single crystals. Our simulated patterns are in good agreement with the experimental morphologies, and the physical origin of polymer single crystal growth is discussed....

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The Journal of Chemical Physics : Noise-induced effective oscillation in oil-water membrane oscillator

By: Yaping Li, Yi Xing, Weiliang Cao, and Qianshu Li

Description: Noise-induced oscillation (NIO) was investigated in a model of an oil-water membrane oscillator. First, we analyzed an unexcitable region and an excitable region of the system by proposing a critical threshold of NIO appearance and found a linearlike relation between the critical threshold and noise intensity. Then the phenomenon of noise-induced coherence resonance was investigated by calculating the signal-to-noise ratio. Furthermore, it was found that an optimal noise intensity range could most improve the appearance of effective oscillation (EO). The presence of EO regions made the stochastic model show EO at a more extended region than the deterministic description....

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The Journal of Chemical Physics : Structure of gold atoms on stoichiometric and defective ceria surfaces

By: Changjun Zhang, Angelos Michaelides, David A. King, and Stephen J. Jenkins

Description: Within the framework of the GGA+U implementation of density functional theory, we investigate atomistic and electronic structures of Au adsorbed on the stoichiometric and the defective CeO2{111} surfaces, in the latter of which either O or Ce vacancies are presented. We show that on the stoichiometric surface, the most stable adsorption site of Au is not on the top of the outermost O atoms, as previously suggested, but on a bridgelike site in which the Au directly binds to two O atoms. We suggest that on both sites, the original empty Ce 4f states near the Fermi level facilitate the oxidation of the Au; the preference of the Au for being on the bridgelike site is due to the larger O 2p-d(Au) mixing, accompanied by more significant electron redistributions. On the reduced surface with O vacancies, the most stable adsorption site of Au is near the vacancy position. Unlike that on the stoichiometric surface, strong ionic bonding character exists between Au and Ce, as the former becomes Auδ− due to the occupation of the 6s(Au) orbitals. Upon substitution for one of the Ce atoms in the lattice, the Au possesses a much strong...

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The Journal of Chemical Physics : Kinetic hindrance during the surface oxidation of Cu(100)…c(10×2)-Ag

By: K. Lahtonen, M. Lampimäki, M. Hirsimäki, and M. Valden

Description: The influence of c(10×2)-Ag superstructure on the oxidation kinetics and oxygen adsorption-induced nanostructures on Cu(100) has been investigated as a function of O2 exposure at 373 K by employing scanning tunneling microscopy and x-ray photoelectron spectroscopy. The oxygen adsorption-induced segregation of Cu through the Ag overlayer is found to trigger agglomeration of Ag and subsequent formation of ordered oval-shaped nanosize metallic Ag islands separated by Cu(100)–(2√2×√2)R45°-O surface phase. As oxygen exposure is further increased, all Ag is eventually covered by oxidized Cu. The presence of Ag delays the completion of the fully reconstructed (2√2×√2)R45°-O surface and the nucleation and growth of Cu2O islands by limiting Cu diffusion toward the surface. Once Cu2O grows into the bulk deeper than buried Ag, the oxidation kinetics follow that of the unalloyed clean Cu(100) surface. Similar kinds of Cu–O nanostructures are found on both clean Cu(100) and Cu(100)–c(10×2)-Ag surfaces. Details of the morphology of the Ag structures and kinetic control of the surface oxidation mechanism on Cu(100)–c(10×2)-Ag are disc...

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The Journal of Chemical Physics : Monte Carlo simulations of amphiphilic nanoparticle self-assembly

By: Jonathan R. Davis and Athanassios Z. Panagiotopoulos

Description: Grand canonical Monte Carlo simulations on a cubic lattice are used to examine aggregation and phase separation of model amphiphiles with bulky head groups. The amphiphiles studied consist of a rigid, roughly spherical nanoparticle attached to one or more flexible chains. Overlapping distributions of energy and density are combined via histogram reweighting to obtain the free energy and osmotic pressure as a function of temperature and concentration. Finite size effects are used to distinguish between first order transitions to a disordered liquid or lamellar phase and continuous transitions to micelles. The transition type depends on the relative size of the solvophobic and neutral portions of the amphiphiles; none of the systems studied here exhibit both types of transition. The critical micellar concentration increases with temperature over the range of conditions examined. Solvophobic nanoparticles with neutral chains phase separate when the attached chain is short and form micelles for longer attached chains. For structures with neutral nanoparticles and solvophobic chains, amphiphile geometry plays a key role in d...

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The Journal of Chemical Physics : First-principles study of crystal structure, electronic structure, and secondharmonic generation in a polar double perovskite Bi2ZnTiO6

By: Sheng Ju and Guang-Yu Guo

Description: Within the density functional theory with the generalized gradient approximation, we present a systematic ab initio investigation of crystal structure, electronic structure, and linear and nonlinear optical responses in a polar double perovskite Bi2ZnTiO6. The effect of B-site ordering is explored by comparing three possible configurations: A-type with alternative Zn and Ti layers stacking along the c axis; C-type with Zn and Ti c axis chains; and G-type with every Zn(Ti) atoms is surrounded by its nearby six Ti(Zn) atoms. It is found that the system with G-type B-site ordering is energetically favorable, which is lower in the total energies of 0.055 and 0.133 eV/formula unit than C-type and A-type, respectively. Optical calculations indicate that all the three configurations show large second-harmonic generation (SHG) coefficients, and the largest static SHG observed in the C-type system reaches 123 (10−9 esu), the value of which is much larger than ever known polar oxides, e.g., 72 (10−9 esu) in LiNbO3. The predicted significant nonlinear optical properties are consistent with the calculated high tetragonality as well...

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The Journal of Chemical Physics : Molecular dynamics simulation of confined fluids in isosurface-isothermal-isobaric ensemble

By: Hossein Eslami, Farkhondeh Mozaffari, Jalil Moghadasi, and Florian Müller-Plathe

Description: A method for the simulation of fluids confined between surfaces is developed. The molecular dynamics, with coupling to an external bath, simulation method of Berendsen et al. [J. Chem. Phys. 81, 3684 (1984) ] is extended for this purpose. We keep the temperature and the parallel component of pressure fixed and change the box length in the perpendicular direction with respect to the confining surfaces to archive equilibrium. The simulation is easy to perform, especially in the case of solvation force computation. Employing this method, the simulation results on the confined Lennard-Jones and water are presented and are compared to previous grand canonical ensemble Monte Carlo and molecular dynamics simulation results. While consistent with other methods, our results show that spherical Lennard-Jones particles and water form layered structures parallel to the confining surfaces with enhanced layering with increasing pressure. Also we studied the oscillatory behaviors of solvation force and number density of confined particles as well as the stepwise variation of particle numbers as a function of separation between confini...

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The Journal of Chemical Physics : Bond dissociation and correlation effects in molecular electronic devices

By: Ali Goker, Francois Goyer, and Matthias Ernzerhof

Description: We present a simple model for a fundamental process in molecular electronics: The change in conductance upon bond breaking. In our model, a diatomic molecule is attached to spin-polarized contacts. Employing a Hubbard Hamiltonian, electron interaction is explicitly considered in the molecule and neglected in the contacts, enabling us to study the impact of electron interaction on the molecular conductance. In the limit where the electron repulsion is strong compared to the binding energy (as is the case upon dissociation), electron transmission is strongly suppressed compared to the noninteracting case. On the other hand, the spin-polarized contacts introduce a coupling between the molecular singlet and triplet states, as a consequence of which the energy gap between the lowest resonances is reduced....

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The Journal of Chemical Physics : Spontaneous charging and crystallization of water droplets in oil

By: Joost de Graaf, Jos Zwanikken, Markus Bier, Arjen Baarsma, Yasha Oloumi et al

Description: We study the spontaneous charging and the crystallization of spherical micron-sized water droplets dispersed in oil by numerically solving, within a Poisson–Boltzmann theory in the geometry of a spherical cell, for the density profiles of the cations and anions in the system. We take into account screening, ionic Born self-energy differences between oil and water, and partitioning of ions over the two media. We find that the surface charge density of the droplet as induced by the ion partitioning is significantly affected by the droplet curvature and by the finite density of the droplets. We also find that the salt concentration and the dielectric constant regime in which crystallization of the water droplets is predicted is enhanced substantially compared to results based on the planar oil-water interface, thereby improving quantitative agreement with recent experiments....

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The Journal of Chemical Physics : Effect of solvent polarization on the reorganization energy of electron transfer from molecular dynamics simulations

By: Egor Vladimirov, Anela Ivanova, and Notker Rösch

Description: The solvent contribution λs to the reorganization energy of electron transfer can be estimated from averages of the potential energy gaps between neutral-pair and ion-pair states over an ensemble of structures generated from molecular dynamics simulations. Invoking a Marcus-type two-sphere model for charge separation and recombination in an aqueous environment, we explored the effect of a polarizable force field and noted a strong reduction of λs (by ∼ 45%) compared to the corresponding value obtained with a standard nonpolarizable force field. Both types of force fields yield λs values that in agreement with the Marcus theory, vary strictly linearly with the inverse of the donor-acceptor distance; the corresponding slopes translate into appropriate effective optical dielectric constants, ε∞ ≈ 1.0±0.2 for a nonpolarizable and ε∞ ≈ 1.7±0.4 for a polarizable force field. The reduction in the solvent reorganization energy due to a polarizable force field translates into a scaling factor that is essentially independent of the donor-acceptor distance. The corresponding effective optical dielectric constant, ε∞ ≈ 1.80, is in ...

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The Journal of Chemical Physics : A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions: D2O in hydration shells of Cl- ions

By: Bhabani S. Mallik, A. Semparithi, and Amalendu Chandra

Description: A theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions is presented from first principles without employing any empirical potential models. The present calculations are based on ab initio molecular dynamics for trajectory generation and wavelet analysis of the simulated trajectories for time dependent frequency calculations. Results are obtained for two different deuterated aqueous solutions: the first one is a relatively dilute solution of a single Cl− ion and the second one is a concentrated solution of NaCl ( ∼ 3M) dissolved in liquid D2O. It is found that the frequencies of OD bonds in the anion hydration shell, i.e., those which are hydrogen bonded to the chloride ion, have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the anion-water hydrogen bond distance. On the dynamical side, when the vibrational spectral diffusion is calculated exclusively for the hydration shell water molecules in the first solution, the dynamics reveals three time scales: a shor...

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The Journal of Chemical Physics : Equilibrium fluctuations of the Lennard-Jones cluster surface

By: D. I. Zhukhovitskii

Description: Spectra of the cluster surface equilibrium fluctuations are treated by decomposition into the bulk and net capillary ones. The bulk fluctuations without capillary ones are simulated by the surface of a cluster truncated by a sphere. The bulk fluctuation spectrum is shown to be generated primarily by the discontinuity in the spatial distribution of cluster internal particles. The net capillary fluctuation slice spectrum is obtained in molecular dynamics simulation by subtraction of the bulk fluctuation spectrum from the total one. This net spectrum is in the best agreement with a theoretical estimation if we assume the intrinsic surface tension to be independent of the wave number. The wave number cutoff is brought in balance with the intrinsic surface tension and excess surface area induced by the capillary fluctuations. It is shown that the ratio of the ordinary surface tension to the intrinsic one can be considered as a universal constant independent of the temperature and cluster size....

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The Journal of Chemical Physics : Monte Carlo simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB): Pressure and temperature effects for the solid phase and vapor-liquid phase equilibria

By: Neeraj Rai, Divesh Bhatt, J. Ilja Siepmann, and Laurence E. Fried

Description: The transferable potentials for phase equilibria (TraPPE) force field was extended to nitro and amino substituents for aromatic rings via parametrization to the vapor-liquid coexistence curves of nitrobenzene and aniline, respectively. These groups were then transferred to model 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Without any further parametrization to solid state data, the TraPPE force field is able to predict TATB’s unit cell lengths and angles at 295 K with mean unsigned percentage errors of 0.3% and 1.8% and the specific density within 0.5%. These predictions are comparable in accuracy to the GRBF model [ Gee et al., J. Chem. Phys. 120, 7059 (2004) ] that was parametrized directly to TATB’s solid state properties. Both force fields are able to reproduce the pressure dependence of TATB’s unit cell volume, but they underestimate its thermal expansion. Due to its energetic nature and unusually large cohesive energy, TATB is not chemically stable at temperature in its liquid range. Gibbs ensemble simulations allow one to determine TATB’s vapor-liquid coexistence curve at elevated temperatures and the predicted ...

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The Journal of Chemical Physics : Fluids of hard natural and Gaussian ellipsoids: A comparative study by integral equation theories

By: Aurélien Perera

Description: The hard Gaussian overlap (HGO) model for ellipsoids is compared to the hard ellipsoid of revolution (HER) model, in the isotropic fluid phase and within the framework of the Percus–Yevick (PY) and hypernetted chain (HNC) integral equation theories. The former model is often used in place of the latter in many approximate theories. Since the HGO model slightly overestimates the contact distance when the two ellipsoids are perpendicular to each other, it leads to small differences in the Mayer function of the two models, but nearly none in the integrals of these functions and particularly for the second virial coefficients. However, it leads to notable differences in the pair correlation functions, as obtained by the Percus–Yevick and the hypernetted chain theories, especially at high densities. The prediction of the stability of the isotropic phase with respect to orientational order, at high densities, is notably influenced by these small differences. Both theories predict that, for same aspect ratios, the HGO model overestimates the ordering, when compared to the HER model. This explains why the PY approximation predi...

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The Journal of Chemical Physics : Rovibrational matrix elements of the quadrupole moment of N2 in a solid parahydrogen matrix

By: Adya P. Mishra and T. K. Balasubramanian

Description: The present work pertains to the study of the rotational dynamics of N2 molecules solvated in a matrix of solid para-H2. It is shown that the mixing of the rotational states due to the anisotropic part of the N2–H2 pair potential in the solid gives rise to an additional 5.4% contribution to the intensity of quadrupole-induced double transitions involving N2–H2 pair. Hence the recently reported quadrupole moment matrix element of N2 in a solid para-H2 crystal [ A. P. Mishra and T. K. Balasubramanian, J. Chem. Phys. 125, 124507 (2006) ], which was deduced from a comparison of the theoretical intensity (with rotational mixing of states neglected) with the measured value is larger by ∼ 2.7%. The ground electronic state rovibrational matrix elements 〈v′J′|Q2(r)|vJ〉 of N2 molecule in a solid parahydrogen matrix for v,v′ ≤ 1 and J,J′ ≤ 4 have also been computed by taking into account the changes in the intramolecular potential of N2 due to the intermolecular interaction in the matrix. The computed quadrupole moment matrix elements agree well with a few available values (for v = v′ = 0) deduced from the observed transitions....

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The Journal of Chemical Physics : Intermolecular vibrations of different isotopologs of the water dimer: Experiments and density functional theory calculations

By: J. Ceponkus, P. Uvdal, and B. Nelander

Description: Far infrared spectra of seven different isotopologs of the water dimer have been measured in neon matrices at 2.8 K. The experiments are interpreted with the aid of density functional theory calculations, in particular the calculated harmonic isotopic shifts were utilized. All six intermolecular vibrational modes of the water dimer and the fully deuterated water dimer are assigned based the isotopic shifts induced. 31 of a total of 42 intermolecular fundamental modes of the seven different H, D, and 18O containing water dimers have been experimentally observed and assigned accordingly. The overall agreement between the calculations and the experiments of all isotopologs results in a complete and consistent description of these modes....

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The Journal of Chemical Physics : The multiconfigurational-reference internally contracted configuration interaction/complete basis set study of the excited states of the trifluoride anion F3-

By: Jirí Czernek and Oldrich Živný

Description: The multiconfigurational-reference internally contracted configuration interaction (MRCI)/aug-cc-pVQZ-based computational protocol was employed to search for the minima of the potential energy surface of the low-lying singlet and triplet electronic states of the trifluoride anion F3− in the D∞h, C∞v, C2v, and Cs symmetry groups. The 2 bound state was located (re = 1.8777 Å and θ = 103.39°), which was predicted to lie less than 1 eV above the X g+ ground state (re = 1.7382 Å) by both the MRCI and equation-of-motion coupled-cluster singles, doubles and triples approaches [the MRCI adiabatic excitation energy extrapolated to the complete basis set (CBS) limit was 0.91 eV]. The latter value is proposed as a reliable estimate of the singlet-triplet energy gap in F3−. The vertical transitions from the X g+ state were analyzed in terms of the reorganization of electrons leading to the excited states and the corresponding MRCI/CBS excitation energies....

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The Journal of Chemical Physics : Photodissociation dynamics of methyl formate at 193.3 nm: Branching ratios, kinetic-energy distributions, and angular anisotropies of products

By: Shih-Huang Lee

Description: We investigated the photodissociation dynamics of methyl formate-d (CH3OC(O)D) at 193.3 nm in a molecular-beam apparatus using undulator radiation as an ionization source. We measured kinetic-energy distributions, spatial angular anisotropies, and branching ratios of all photofragments. Fractions of energy release into product translation were calculated from the kinetic-energy distributions. Four primary dissociation pathways to asymptotes CH3O( 2E)+DCO( 2A′), CH3O( 2E)+DCO( 2A″), CH3OCO( 2A′)+D(2S), and CH3OD( 1A′)+CO(X 1Σ+) were identified; their branching ratios were determined to be 0.73, 0.06, 0.13, and 0.08, respectively. The former two dissociation paths were discernible in the time-of-flight spectra of fragment CH3O with a signal at m/z = 29. Nominal products DCO ( 2A″) and CH3OCO ( 2A′) were unobservable as DCO in state dissociated to D(2S)+CO(X 1Σ+) and internally hot CH3OCO ( 2A′) decomposed to CH3( 2A2″)+CO2( 1A1g). Products DCO and CH3O have angular anisotropy parameter β ≈ −0.37 but other products have nearly isotropic angular distributions with |β|<0.1. Nonadiabatic transitions might play an important r...

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