Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 Roberto Cerbino, Pietro Cicuta
Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.
Ab initio electronic transport and thermoelectric properties of solids from full and range-separated hybrid functionals J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 Giuseppe Sansone, Andrea Ferretti, Lorenzo Maschio
Within the semiclassical Boltzmann transport theory in the constant relaxation-time approximation, we perform an ab initio study of the transport properties of selected systems, including crystalline solids and nanostructures. A local (Gaussian) basis set is adopted and exploited to analytically evaluate band velocities as well as to access full and range-separated hybrid functionals (such as B3LYP, PBE0, or HSE06) at a moderate computational cost. As a consequence of the analytical derivative, our approach is computationally efficient and does not suffer from problems related to band crossings. We investigate and compare the performance of a variety of hybrid functionals in evaluating Boltzmann conductivity. Demonstrative examples include silicon and aluminum bulk crystals as well as two thermoelectric materials (CoSb3, Bi2Te3). We observe that hybrid functionals other than providing more realistic bandgaps—as expected—lead to larger bandwidths and hence allow for a better estimate of transport properties, also in metallic systems. As a nanostructure prototype, we also investigate conductivity in boron-nitride (BN) substituted graphene, in which nanoribbons (nanoroads) alternate with BN ones.
Verlet-like algorithms for Car-Parrinello molecular dynamics with unequal electronic occupations J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 Arcesio Castañeda Medina, Rochus Schmid
The ab initio molecular dynamics simulations of metallic, charged, and electrochemical systems require, in principle, the inclusion of unequally occupied electronic states. In this contribution, the general approach to work with fixed but arbitrary occupations within the Car-Parrinello molecular dynamics scheme is revisited, focusing on the procedure which is required to maintain the orthonormality constraints in the commonly used position-Verlet integrator. Expressions to constrain also the orbital velocities, as it is demanded by a velocity-Verlet integrator, are then derived. The generalized unequal-occupation SHAKE algorithm is compared with the standard procedure for damped dynamics (energy optimization) of systems including fully unoccupied electronic states. In turn, the proposed unequal-occupation RATTLE algorithm is validated by the corresponding microcanonical ensemble simulations. It is shown that only with the proper orthogonalization method, a correct ordering of states and energy conserving dynamics can be achieved.
Effect of dielectric discontinuity on a spherical polyelectrolyte brush J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 Vinicius B. Tergolina, Alexandre P. dos Santos
In this paper we perform molecular dynamics simulations of a spherical polyelectrolyte brush and counterions in a salt-free medium. The dielectric discontinuity on the grafted nanoparticle surface is taken into account by the method of image charges. Properties of the polyelectrolyte brush are obtained for different parameters, including valency of the counterions, radius of the nanoparticle, and the brush total charge. The monovalent counterions density profiles are obtained and compared with a simple mean-field theoretical approach. The theory allows us to obtain osmotic properties of the system.
Equivalence of the EMD- and NEMD-based decomposition of thermal conductivity into microscopic building blocks J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 Hiroki Matsubara, Gota Kikugawa, Mamoru Ishikiriyama, Seiji Yamashita, Taku Ohara
Thermal conductivity of a material can be comprehended as being composed of microscopic building blocks relevant to the energy transfer due to a specific microscopic process or structure. The building block is called the partial thermal conductivity (PTC). The concept of PTC is essential to evaluate the contributions of various molecular mechanisms to heat conduction and has been providing detailed knowledge of the contribution. The PTC can be evaluated by equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) in different manners: the EMD evaluation utilizes the autocorrelation of spontaneous heat fluxes in an equilibrium state whereas the NEMD one is based on stationary heat fluxes in a non-equilibrium state. However, it has not been fully discussed whether the two methods give the same PTC or not. In the present study, we formulate a Green-Kubo relation, which is necessary for EMD to calculate the PTCs equivalent to those by NEMD. Unlike the existing theories, our formulation is based on the local equilibrium hypothesis to describe a clear connection between EMD and NEMD simulations. The equivalence of the two derivations of PTCs is confirmed by the numerical results for liquid methane and butane. The present establishment of the EMD–NEMD correspondence makes the MD analysis of PTCs a robust way to clarify the microscopic origins of thermal conductivity.
Quantum Singwi-Tosi-Land-Sjölander approach for interacting inhomogeneous systems under electromagnetic fields: Comparison with exact results J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 Taichi Kosugi, Yu-ichiro Matsushita
For inhomogeneous interacting electronic systems under a time-dependent electromagnetic perturbation, we derive the linear equation for response functions in a quantum mechanical manner. It is a natural extension of the original semi-classical Singwi-Tosi-Land-Sjölander (STLS) approach for an electron gas. The factorization ansatz for the two-particle distribution is an indispensable ingredient in the STLS approaches for the determination of the response function and the pair correlation function. In this study, we choose an analytically solvable interacting two-electron system as the target for which we examine the validity of the approximation. It is demonstrated that the STLS response function reproduces well the exact one for low-energy excitations. The interaction energy contributed from the STLS response function is also discussed.
The kinetic energy operator for distance-dependent effective nuclear masses: Derivation for a triatomic molecule J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 Mykhaylo Khoma, Ralph Jaquet
The kinetic energy operator for triatomic molecules with coordinate or distance-dependent nuclear masses has been derived. By combination of the chain rule method and the analysis of infinitesimal variations of molecular coordinates, a simple and general technique for the construction of the kinetic energy operator has been proposed. The asymptotic properties of the Hamiltonian have been investigated with respect to the ratio of the electron and proton mass. We have demonstrated that an ad hoc introduction of distance (and direction) dependent nuclear masses in Cartesian coordinates preserves the total rotational invariance of the problem. With the help of Wigner rotation functions, an effective Hamiltonian for nuclear motion can be derived. In the derivation, we have focused on the effective trinuclear Hamiltonian. All necessary matrix elements are given in closed analytical form. Preliminary results for the influence of non-adiabaticity on vibrational band origins are presented for H3+.
Interfering resonance as an underlying mechanism in the adaptive feedback control of radiationless transitions: Retinal isomerization J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 Cyrille Lavigne, Paul Brumer
Control of molecular processes via adaptive feedback often yields highly structured laser pulses that have eluded physical explanation. By contrast, coherent control approaches propose physically transparent mechanisms but are not readily visible in experimental results. Here, an analysis of a condensed phase adaptive feedback control experiment on retinal isomerization shows that it manifests a quantum interference based coherent control mechanism: control via interfering resonances. The result promises deep insight into the physical basis for the adaptive feedback control of a broad class of bound state processes.
A qualitative quantum rate model for hydrogen transfer in soybean lipoxygenase J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 S. Jevtic, J. Anders
The hydrogen transfer reaction catalysed by soybean lipoxygenase (SLO) has been the focus of intense study following observations of a high kinetic isotope effect (KIE). Today high KIEs are generally thought to indicate departure from classical rate theory and are seen as a strong signature of tunnelling of the transferring particle, hydrogen or one of its isotopes, through the reaction energy barrier. In this paper, we build a qualitative quantum rate model with few free parameters that describes the dynamics of the transferring particle when it is exposed to energetic potentials exerted by the donor and the acceptor. The enzyme’s impact on the dynamics is modelled by an additional energetic term, an oscillatory contribution known as “gating.” By varying two key parameters, the gating frequency and the mean donor-acceptor separation, the model is able to reproduce well the KIE data for SLO wild-type and a variety of SLO mutants over the experimentally accessible temperature range. While SLO-specific constants have been considered here, it is possible to adapt these for other enzymes.
A robust variant of block Jacobi-Davidson for extracting a large number of eigenpairs: Application to grid-based real-space density functional theory J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 M. Lee, K. Leiter, C. Eisner, A. Breuer, X. Wang
In this work, we investigate a block Jacobi-Davidson (J-D) variant suitable for sparse symmetric eigenproblems where a substantial number of extremal eigenvalues are desired (e.g., ground-state real-space quantum chemistry). Most J-D algorithm variations tend to slow down as the number of desired eigenpairs increases due to frequent orthogonalization against a growing list of solved eigenvectors. In our specification of block J-D, all of the steps of the algorithm are performed in clusters, including the linear solves, which allows us to greatly reduce computational effort with blocked matrix-vector multiplies. In addition, we move orthogonalization against locked eigenvectors and working eigenvectors outside of the inner loop but retain the single Ritz vector projection corresponding to the index of the correction vector. Furthermore, we minimize the computational effort by constraining the working subspace to the current vectors being updated and the latest set of corresponding correction vectors. Finally, we incorporate accuracy thresholds based on the precision required by the Fermi-Dirac distribution. The net result is a significant reduction in the computational effort against most previous block J-D implementations, especially as the number of wanted eigenpairs grows. We compare our approach with another robust implementation of block J-D (JDQMR) and the state-of-the-art Chebyshev filter subspace (CheFSI) method for various real-space density functional theory systems. Versus CheFSI, for first-row elements, our method yields competitive timings for valence-only systems and 4-6× speedups for all-electron systems with up to 10× reduced matrix-vector multiplies. For all-electron calculations on larger elements (e.g., gold) where the wanted spectrum is quite narrow compared to the full spectrum, we observe 60× speedup with 200× fewer matrix-vector multiples vs. CheFSI.
Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Julija Zavadlav, Matej Praprotnik
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.
Theoretical spectroscopic parameters for isotopic variants of HCO+ and HOC+ J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Mirjana Mladenović
Theoretical spectroscopic parameters are derived for all isotopologues of HCO+ and HOC+ involving H, D, 16O, 17O, 18O, 12C, and 13C by means of a two-step procedure. Full-dimensional rovibrational calculations are first carried out to obtain numerically exact rovibrational energies for J = 0–15 in both parities. Effective spectroscopic constants for the vibrational ground state, ν1, ν2, and ν3 are determined by fitting the calculated rovibrational energies to appropriate spectroscopic Hamiltonians. Combining our vibration-rotation corrections with the available experimental ground-state rotational constants, we also derive the new estimate for the equilibrium structure of HCO+, re(CH) = 1.091 98 Å and re(CO) = 1.105 62 Å, and for the equilibrium structure of HOC+, re(HO) = 0.990 48 Å and re(CO) = 1.154 47 Å. Regarding the spectroscopic parameters, our estimates are in excellent agreement with available experimental results for the isotopic variants of both HCO+ and HOC+: the agreement for the rotational constants Bv is within 3 MHz, for the quartic centrifugal distortion constants Dv within 1 kHz, and for the effective ℓ-doubling constants qv within 2 MHz. We thus expect that our results can provide useful assistance in analyzing expected observations of the rare isotopologues of HCO+ and HOC+ that are not yet experimentally known.
Entropy based fingerprint for local crystalline order J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Pablo M. Piaggi, Michele Parrinello
We introduce a new fingerprint that allows distinguishing between liquid-like and solid-like atomic environments. This fingerprint is based on an approximate expression for the entropy projected on individual atoms. When combined with local enthalpy, this fingerprint acquires an even finer resolution and it is capable of discriminating between different crystal structures.
Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Yang Yang, Kurt R. Brorsen, Tanner Culpitt, Michael V. Pak, Sharon Hammes-Schiffer
Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation (epc) functionals that produce even qualitatively accurate proton densities. Herein an electron-proton correlation functional, epc17, is derived analogously to the Colle-Salvetti formalism for electron correlation and is implemented within the nuclear-electronic orbital (NEO) framework. The NEO-DFT/epc17 method produces accurate proton densities efficiently and is promising for diverse applications.
On the applicability of a wavefunction-free, energy-based procedure for generating first-order non-adiabatic couplings around conical intersections J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Benjamin Gonon, Aurelie Perveaux, Fabien Gatti, David Lauvergnat, Benjamin Lasorne
The primal definition of first-order non-adiabatic couplings among electronic states relies on the knowledge of how electronic wavefunctions vary with nuclear coordinates. However, the non-adiabatic coupling between two electronic states can be obtained in the vicinity of a conical intersection from energies only, as this vector spans the branching plane along which degeneracy is lifted to first order. The gradient difference and derivative coupling are responsible of the two-dimensional cusp of a conical intersection between both potential-energy surfaces and can be identified to the non-trivial eigenvectors of the second derivative of the square energy difference, as first pointed out in Köppel and Schubert [Mol. Phys. 104(5-7), 1069 (2006)]. Such quantities can always be computed in principle for the cost of two numerical Hessians in the worst-case scenario. Analytic-derivative techniques may help in terms of accuracy and efficiency but also raise potential traps due to singularities and ill-defined derivatives at degeneracies. We compare here two approaches, one fully numerical, the other semianalytic, where analytic gradients are available but Hessians are not, and investigate their respective conditions of applicability. Benzene and 3-hydroxychromone are used as illustrative application cases. It is shown that non-adiabatic couplings can thus be estimated with decent accuracy in regions of significant size around conical intersections. This procedure is robust and could be useful in the context of on-the-fly non-adiabatic dynamics or be used for producing model representations of intersecting potential energy surfaces with complete obviation of the electronic wavefunctions.
Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Stefanie Winkelmann, Christof Schütte
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.
Incoherent population mixing contributions to phase-modulation two-dimensional coherent excitation spectra J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-19 Pascal Grégoire, Ajay Ram Srimath Kandada, Eleonora Vella, Chen Tao, Richard Leonelli, Carlos Silva
We present theoretical and experimental results showing the effects of incoherent population mixing on two-dimensional (2D) coherent excitation spectra that are measured via a time-integrated population and phase-sensitive detection. The technique uses four collinear ultrashort pulses and phase modulation to acquire two-dimensional spectra by isolating specific nonlinear contributions to the photoluminescence or photocurrent excitation signal. We demonstrate that an incoherent contribution to the measured line shape, arising from nonlinear population dynamics over the entire photoexcitation lifetime, generates a similar line shape to the expected 2D coherent spectra in condensed-phase systems. In those systems, photoexcitations are mobile such that inter-particle interactions are important on any time scale, including those long compared with the 2D coherent experiment. Measurements on a semicrystalline polymeric semiconductor film at low temperatures show that, in some conditions in which multi-exciton interactions are suppressed, the technique predominantly detects coherent signals and can be used, in our example, to extract homogeneous line widths. The same method used on a lead-halide perovskite photovoltaic cell shows that incoherent population mixing of mobile photocarriers can dominate the measured signal since carrier-carrier bimolecular scattering is active even at low excitation densities, which hides the coherent contribution to the spectral line shape. In this example, the intensity dependence of the signal matches the theoretical predictions over more than two orders of magnitude, confirming the incoherent nature of the signal. While these effects are typically not significant in dilute solution environments, we demonstrate the necessity to characterize, in condensed-phase materials systems, the extent of nonlinear population dynamics of photoexcitations (excitons, charge carriers, etc.) in the execution of this powerful population-detected coherent spectroscopy technique.
Direct infrared observation of hydrogen chloride anions in solid argon J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 Tzu-Ping Huang, Hui-Fen Chen, Meng-Chen Liu, Chih-Hao Chin, Marcus C. Durrant, Yin-Yu Lee, Yu-Jong Wu
To facilitate direct spectroscopic observation of hydrogen chloride anions (HCl−), electron bombardment of CH3Cl diluted in excess Ar during matrix deposition was used to generate this anion. Subsequent characterization were performed by IR spectroscopy and quantum chemical calculations. Moreover the band intensity of HCl− decays slowly when the matrix sample is maintained in the dark for a prolonged time. High-level ab inito calculation suggested that HCl− is only weakly bound. Atom-in-molecule charge analysis indicated that both atoms of HCl− are negatively charged and the Cl atom is hypervalent.
Anomalous doping of a molecular crystal monitored with confocal fluorescence microscopy: Terrylene in a p-terphenyl crystal J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-19 Magda Białkowska, Irena Deperasińska, Artur Makarewicz, Bolesław Kozankiewicz
Highly terrylene doped single crystals of p-terphenyl, obtained by co-sublimation of both components, showed bright spots in the confocal fluorescence images. Polarization of the fluorescence excitation spectra, blinking and bleaching, and saturation behavior allowed us to attribute them to single molecules of terrylene anomalously embedded between two neighbor layers of the host crystal, in the (a,b) plane. Such an orientation of terrylene molecules results in much more efficient absorption and collection of the fluorescence photons than in the case of previously investigated molecules embedded in the substitution sites. The above conclusion was supported by quantum chemistry calculations. We postulate that the kind of doping considered in this work should be possible in other molecular crystals where the host molecules are organized in a herringbone pattern.
Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 Biswaroop Mukherjee, Christine Peter, Kurt Kremer
Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.
CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 Ilaria Gimondi, Matteo Salvalaglio
In this work, we describe the thermodynamics and mechanism of CO2 polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics, and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO2 molecules, which unfolds via an anisotropic expansion of the CO2 supercell. Furthermore, at high pressures, we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability, and a suitable description of a complex, collective polymorphic transition mechanism.
Crystalline structures of particles interacting through the harmonic-repulsive pair potential J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 V. A. Levashov
The behavior of identical particles interacting through the harmonic-repulsive pair potential has been studied in 3D using molecular dynamics simulations at a number of different densities. We found that at many densities, as the temperature of the systems decreases, the particles crystallize into complex structures whose formation has not been anticipated in previous studies on the harmonic-repulsive pair potential. In particular, at certain densities, crystallization into the structure Ia3¯d (space group #230) with 16 particles in the unit cell occupying Wyckoff special positions (16b) was observed. This crystal structure has not been observed previously in experiments or in computer simulations of single component atomic or soft matter systems. At another density, we observed a liquid which is rather stable against crystallization. Yet, we observed crystallization of this liquid into the monoclinic C2/c (space group #15) structure with 32 particles in the unit cell occupying four different non-special Wyckoff (8f) sites. In this structure particles located at different Wyckoff sites have different energies. From the perspective of the local atomic environment, the organization of particles in this structure resembles the structure of some columnar quasicrystals. At a different value of the density, we did not observe crystallization at all despite rather long molecular dynamics runs. At two other densities, we observed the formation of the βSn distorted diamond structures instead of the expected diamond structure. Possibly, we also observed the formation of the R3¯c hexagonal lattice with 24 particles per unit cell occupying non-equivalent positions.
Three-body interactions and the elastic constants of hcp solid 4He J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 Ashleigh L. Barnes, Robert J. Hinde
The effect of three-body interactions on the elastic properties of hexagonal close packed solid 4He is investigated using variational path integral (VPI) Monte Carlo simulations. The solid’s nonzero elastic constants are calculated, at T = 0 K and for a range of molar volumes from 7.88 cm3/mol to 20.78 cm3/mol, from the bulk modulus and the three pure shear constants C0, C66, and C44. Three-body interactions are accounted for using our recently reported perturbative treatment based on the nonadditive three-body potential of Cencek et al. Previous studies have attempted to account for the effect of three-body interactions on the elastic properties of solid 4He; however, these calculations have treated zero point motions using either the Einstein or Debye approximations, which are insufficient in the molar volume range where solid 4He is characterized as a quantum solid. Our VPI calculations allow for a more accurate treatment of the zero point motions which include atomic correlation. From these calculations, we find that agreement with the experimental bulk modulus is significantly improved when three-body interactions are considered. In addition, three-body interactions result in non-negligible differences in the calculated pure shear constants and nonzero elastic constants, particularly at higher densities, where differences of up to 26.5% are observed when three-body interactions are included. We compare to the available experimental data and find that our results are generally in as good or better agreement with experiment as previous theoretical investigations.
Amorphous chalcogenides as random octahedrally bonded solids: I. Implications for the first sharp diffraction peak, photodarkening, and Boson peak J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Alexey Lukyanov, Vassiliy Lubchenko
We develop a computationally efficient algorithm for generating high-quality structures for amorphous materials exhibiting distorted octahedral coordination. The computationally costly step of equilibrating the simulated melt is relegated to a much more efficient procedure, viz., generation of a random close-packed structure, which is subsequently used to generate parent structures for octahedrally bonded amorphous solids. The sites of the so-obtained lattice are populated by atoms and vacancies according to the desired stoichiometry while allowing one to control the number of homo-nuclear and hetero-nuclear bonds and, hence, effects of the mixing entropy. The resulting parent structure is geometrically optimized using quantum-chemical force fields; by varying the extent of geometric optimization of the parent structure, one can partially control the degree of octahedrality in local coordination and the strength of secondary bonding. The present methodology is applied to the archetypal chalcogenide alloys AsxSe1−x. We find that local coordination in these alloys interpolates between octahedral and tetrahedral bonding but in a non-obvious way; it exhibits bonding motifs that are not characteristic of either extreme. We consistently recover the first sharp diffraction peak (FSDP) in our structures and argue that the corresponding mid-range order stems from the charge density wave formed by regions housing covalent and weak, secondary interactions. The number of secondary interactions is determined by a delicate interplay between octahedrality and tetrahedrality in the covalent bonding; many of these interactions are homonuclear. The present results are consistent with the experimentally observed dependence of the FSDP on arsenic content, pressure, and temperature and its correlation with photodarkening and the Boson peak. They also suggest that the position of the FSDP can be used to infer the effective particle size relevant for the configurational equilibration in covalently bonded glassy liquids, where the identification of the effective rigid molecular unit is ambiguous.
Solvation structure and dynamics of Ag+ in aqueous ammonia solutions: A molecular simulation study J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Stefano Sansotta, Dirk Zahn
We present an ab initio-based force-field for silver ion interactions with water and ammonia. Compared to quantum calculations, our model allows for rather large-scale molecular dynamics simulations of silver solutions of aqueous ammonia. For a series of NH3:H2O ratios ranging from 1 to 20 mol. %, Ag+ ions were mainly found as octahedral [Ag(NH3)x(H2O)]6−x+ coordination complexes with preferential values of x ranging from 0 to 3. In the first coordination structure, water ↔ ammonia exchanges occur within a 1-3 ps time scale and, depending on the NH3 concentration, imply significant fluctuations of x covering the whole range from 0 to 6. Based on ns-scale molecular dynamics simulations, chemical potentials are derived for all Ag+ coordination species as functions of temperature and ammonia concentration. Moreover, we compare the diffusion constants of the [Ag(H2O)6]+ to [Ag(H2O)3(NH3)3]+ coordination complexes, based on the solutions of the corresponding ammonia content.
Point-to-set dynamic length scale in binary Lennard-Jones glass-formers J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Baicheng Mei, Zhenhua Wang, Yuyuan Lu, Hongfei Li, Lijia An
Our recent molecular dynamics simulation results of binary particle glass-former systems demonstrated that the non-monotonic temperature T-dependence of the point-to-set dynamic length scale ξcdyn in harmonic (HM) systems is not an intrinsic property of bulk liquids but originates from wall effects. We would expect our results to apply equally to other simple models, such as Lennard-Jones (LJ) systems. However, Hocky et al. presented a monotonic T-dependent ξcdyn in a LJ system. Therefore, the present work employs molecular dynamics simulations to investigate the T-dependent behavior of ξcdyn in the LJ system employed by Hocky et al. to clarify our expectation. Results employing a geometry size d that is somewhat smaller than that employed by Hocky et al. reveal that a non-monotonic behavior exists in the LJ system. By varying the value of d, we demonstrate that the formation of a peak in ξcdyn with respect to T in the LJ system is the natural result of wall effects. More importantly, a new non-monotonic behavior is observed, where the temperature at which the ratio of the characteristic time required for the overlap profile of the system to decay to a given value for a point near the wall to the corresponding characteristic time at a point in the center attains a maximum is in good agreement with the temperature Tmax−c at which ξcdyn attains a maximum value, indicating that the non-monotonic behavior of ξcdyn with respect to T is a natural property of liquids in a sandwiched geometry. Furthermore, we find that, contrary to HM systems, where the values of Tmax−c obtained for all values of d considered were greater than the mode-coupling temperature Tc, the value of Tmax−c obtained for LJ systems can be either greater than, equal to, or less than Tc because an HM system has a stronger finite-size effect than that in a LJ system, indirectly implying that the conclusion derived from random first-order transition theory that a dramatic change occurs near Tc bears no necessary relationship with the non-monotonic evolution of ξcdyn with respect to T.
Phase separation of triethylamine and water in native and organically modified silica nanopores J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 J. Rachel Prado, Sergey Vyazovkin
A mixture of triethylamine and water is a lower critical solution temperature system that demixes (separates into individual phases) on heating. Differential scanning calorimetry has been applied to study the process of demixing in native and organically modified silica nanopores whose size varied from 4 to 30 nm. It has been found that in both types of nanopores, the temperature and enthalpy of demixing decrease significantly with decreasing the pore size. Isoconversional kinetic analysis has been utilized to determine the activation energy and pre-exponential factor of the process. It has been demonstrated that the depression of the transition temperature upon nanoconfinement is associated with acceleration of the process due to lowering of the activation energy. Nanoconfinement has also been found to lower the pre-exponential factor of the process that has been linked to a decrease in the molecular mobility.
An ab initio study of the electronic structure of indium and gallium chalcogenide bilayers J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 T. Ayadi, L. Debbichi, M. Said, S. Lebègue
Using first principle calculations, we have studied the structural and electronic properties of two dimensional bilayers of indium and gallium chalcogenides. With density functional theory corrected for van der Waals interactions, the different modes of stacking were investigated in a systematic way, and several of them were found to compete in energy. Then, their band structures were obtained with the GW approximation and found to correspond to indirect bandgap semiconductors with a small dependency on the mode of stacking. Finally, by analysing the electron density, it appeared that GaSe–InS is a promising system for electron-hole separation.
Spin polarization and magnetic characteristics at C6H6/Co2MnSi(001) spinterface J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-20 Meifang Sun, Xiaocha Wang, Wenbo Mi
Organic materials with mechanical flexibility, low cost, chemical engineering, and long spin lifetime attract considerable attention for building spintronic devices. Here, a C6H6/Co2MnSi(001) spinterface is investigated by first-principles calculations and spin-polarized scanning tunneling microscopy simulations. Several high symmetry adsorption sites are discussed, together with two possible surface terminations of Co2MnSi(001). An inversion of the spin polarization is induced near EF even in the case of an external electric field, indicating that C6H6 can act as a spin filter to exploit the spin injection efficiency in organic spintronic devices. Unlike previous studies on molecule/ferromagnet interfaces, this inversion is closely related to the electronic structure of the atoms in the subsurface layer of Co2MnSi according to the orbital symmetry analysis. Furthermore, the magnetic moment and magnetic anisotropic energy (MAE) in the outermost Co2MnSi layer are studied. Particularly, in the most stable configuration, the sign of MAE is inversed due to hybridization between C p and Co dz2 orbitals, which suggests that a greater modification on MAE can be achieved by the use of a highly chemically reactive organic molecule. These findings improve the study on the engineering of magnetic properties at molecule/ferromagnetic interfaces through a single π-conjugated organic molecule.
Excitation and desorption of physisorbed H2 via the electron scattering resonance J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Stig Andersson, Krister Svensson
Our high-resolution electron energy-loss measurements concern physisorbed H2 and comprise differential cross sections for the excitation of the internal H2 modes and the H2-surface bonding mode and their combinations and extend over the electron impact energy range of the classical low-energy H2 Σu2 resonance. Comparison with corresponding data for the excitation of the internal modes of gas phase H2 reveals that strong elastic electron reflectivity from the Cu(100) substrate profoundly distorts the inelastic scattering pattern for physisorbed H2. We find that this influence can be corrected for and that the resulting peak cross sections agree with the H2 gas phase data, in accordance with theoretical predictions for the excitation of the internal H2 vibration. We have used corrected cross sections for the rotational mode spectra of physisorbed H2, HD, and D2 in a model concerning electron induced desorption via rotation-translation energy conversion. These spectra include transitions from the ground state as well as excited levels of the physisorption potential well. H2 and HD can desorb from all levels while D2, for energetic reason, can only desorb from the excited levels. This model gives a satisfactory account of the observed desorption cross sections and predicts characteristic velocity distributions of the desorbing molecules. The cross section data for H2 and HD reveals that direct bound-free transitions also contribute to the electron induced desorption.
Comparative Monte-Carlo simulations of charge carrier transport in amorphous molecular solids as given by three most common models of disorder: The dipolar glass, the Gaussian disorder, and their mix J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-15 A. P. Tyutnev, S. V. Novikov, V. S. Saenko, E. D. Pozhidaev
We have performed Monte-Carlo simulations of the charge carrier transport in a model molecularly doped polymer using three most popular hopping theories (the dipolar glass model, the Gaussian disorder model, and an intermediate between them) in a wide range of applied electric fields and temperatures. Time of flight transients have been computed and analyzed in logarithmic coordinates to study the Poole-Frenkel field dependence, the non-Arrhenius mobility temperature dependence, and the nondispersive versus dispersive current shapes. We also have made an attempt to estimate the total disorder energy directly from simulation data at the lowest electric field thus checking the consistency of the model fitting. Computational results have been compared with the analytical and experimental information available in the literature.
The effect of crowder charge in a model polymer–colloid system for macromolecular crowding: Polymer structure and dynamics J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-18 Swomitra Palit, Lilin He, William A. Hamilton, Arun Yethiraj, Anand Yethiraj
We have examined the effect of crowder particle charge on macromolecular structure, studied via small-angle neutron scattering, and translational dynamics, studied via pulsed-field gradient NMR, in addition to bulk viscosity measurements, in a polymer macromolecule (polyethylene glycol)—nanoparticle crowder (polysucrose, Ficoll70) model system, in the case where polymer size and crowder size are comparable. While there are modest effects of crowder charge on polymer dynamics at relatively low packing fractions, there is only a tiny effect at the high packing fractions that represent the limit of molecular crowding. We find, via different measures of macromolecular mobility, that the mobility of the flexible polymer in the crowding limit is 10–100 times larger than that of the compact, spherical crowder in spite of their similar size, implying that the flexible polymer chain is able to squeeze through crowder interstices.
Order-order transitions of diblock copolymer melts under cylindrical confinement J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Meijiao Liu, Weihua Li, Xinping Wang
The self-assembly behavior of AB diblock copolymers under cylindrical confinement is investigated using the self-consistent field theory. We focus on the impact of the confinement on the order-order transitions of three-dimensional morphologies by constructing two types of phase diagrams with continuously varying block compositions. One type is with respect to the block composition and the immiscibility parameter for various pore sizes, in which the order-order transitions are shown to be strongly impacted by the pore curvature and thus largely different from the bulk ones. Note that the morphologies are categorized by the intrinsical geometry of their domains, i.e., that helical morphologies are regarded as one type of cylindrical phase. Another type of phase diagram is with respect to the block composition and the pore diameter, which exhibits a number of interesting order-order transitions, especially the transition sequence from a straight line of spheres, to one straight cylinder and stacked disks as the pore diameter increases. A critical point is observed at which the stability region of the straight cylinder vanishes and thereby the spheres transform into the stacked disks continuously. The mechanism of these phase transitions is rationalized in the context of the bulk factors as well as an additional factor, i.e., the competition between the spontaneous curvature of the copolymer and the imposed curvature by the nanopore.
Controlling polymer capture and translocation by electrostatic polymer-pore interactions J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Sahin Buyukdagli, T. Ala-Nissila
Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modeling of polymer capture to the nanopore followed by translocation therefore necessitates the consideration of the electrostatic barrier resulting from like-charge polymer-pore interactions. To this end, in this work we couple mean-field level electrohydrodynamic equations with the Smoluchowski formalism to characterize the interplay between the electrostatic barrier, the electrophoretic drift, and the electro-osmotic liquid flow. In particular, we find that due to distinct ion density regimes where the salt screening of the drift and barrier effects occurs, there exists a characteristic salt concentration maximizing the probability of barrier-limited polymer capture into the pore. We also show that in the barrier-dominated regime, the polymer translocation time τ increases exponentially with the membrane charge and decays exponentially fast with the pore radius and the salt concentration. These results suggest that the alteration of these parameters in the barrier-driven regime can be an efficient way to control the duration of the translocation process and facilitate more accurate measurements of the ionic current signal in the pore.
Charge-transfer mobility and electrical conductivity of PANI as conjugated organic semiconductors J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Yahong Zhang, Yuping Duan, Lulu Song, Daoyuan Zheng, Mingxing Zhang, Guangjiu Zhao
The intramolecular charge transfer properties of a phenyl-end-capped aniline tetramer (ANIH) and a chloro-substituted derivative (ANICl) as organic semiconductors were theoretically studied through the first-principles calculation based on the Marcus–Hush theory. The reorganization energies, intermolecular electronic couplings, angular resolution anisotropic mobilities, and density of states of the two crystals were evaluated. The calculated results demonstrate that both ANIH and ANICl crystals show the higher electron transfer mobilities than the hole-transfer mobilities, which means that the two crystals should prefer to function as n-type organic semiconductors. Furthermore, the angle dependence mobilities of the two crystals show remarkable anisotropic character. The maximum mobility μmax of ANIH and ANICl crystals is 1.3893 and 0.0272 cm2 V−1 s−1, which appear at the orientation angles near 176°/356° and 119°/299° of a conducting channel on the a-b reference plane. It is synthetically evaluated that the ANIH crystal possesses relatively lower reorganization energy, higher electronic coupling, and electron transfer mobility, which means that the ANIH crystal may be the more ideal candidate as a high performance n-type organic semiconductor material. The systematic theoretical studies on organic crystals should be conducive to evaluating the charge-transport properties and designing higher performance organic semiconductor materials.
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained -bonded polyglucose chains J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Emilia A. Lubecka, Adam Liwo
Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O⋯O⋯O virtual-bond angles (θ) and for the dihedral angles for rotation about the O⋯O virtual bonds (γ) of 1 → 4-linked glucosyl polysaccharides, for all possible combinations of [α,β]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α,β]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ=140° for all pairs except β-d−[α,β]-l-glucose, where the global minimum is shifted to θ=150° and a secondary minimum appears at θ=90°. The torsional potentials favor small negative γ angles for the α-d-glucose and extended negative angles γ for the β-d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo’s cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all torsional potentials very well, thus reducing the number of parameters significantly.
Spectroscopic properties of photosystem II reaction center revisited J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-21 Andrius Gelzinis, Darius Abramavicius, Jennifer P. Ogilvie, Leonas Valkunas
Photosystem II (PSII) is the only biological system capable of splitting water to molecular oxygen. Its reaction center (RC) is responsible for the primary charge separation that drives the water oxidation reaction. In this work, we revisit the spectroscopic properties of the PSII RC using the complex time-dependent Redfield (ctR) theory for optical lineshapes [A. Gelzinis et al., J. Chem. Phys. 142, 154107 (2015)]. We obtain the PSII RC model parameters (site energies, disorder, and reorganization energies) from the fits of several spectra and then further validate the model by calculating additional independent spectra. We obtain good to excellent agreement between theory and calculations. We find that overall our model is similar to some of the previous asymmetric exciton models of the PSII RC. On the other hand, our model displays differences from previous work based on the modified Redfield theory. We extend the ctR theory to describe the Stark spectrum and use its fit to obtain the parameters of a single charge transfer state included in our model. Our results suggest that ChlD1+PheoD1− is most likely the primary charge transfer state, but that the Stark spectrum of the PSII RC is probably also influenced by other states.
Erratum: “Stochastic multi-reference perturbation theory with application to the linearized coupled cluster method” [J. Chem. Phys. 146, 044107 (2017)] J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-15 Guillaume Jeanmairet, Sandeep Sharma, Ali Alavi
Unlike the smooth wings of common insects or birds, micro-scale insects such as the fairyfly have a distinctive wing geometry, comprising a frame with several bristles. Motivated by this peculiar wing geometry, we experimentally investigated the flow structure of a translating comb-like wing for a wide range of gap size, angle of attack, and Reynolds number, Re = O(10) − O(103), and the correlation of these parameters with aerodynamic performance. The flow structures of a smooth plate without a gap and a comb-like plate are significantly different at high Reynolds number, while little difference was observed at the low Reynolds number of O(10). At low Reynolds number, shear layers that were generated at the edges of the tooth of the comb-like plate strongly diffuse and eventually block a gap. This gap blockage increases the effective surface area of the plate and alters the formation of leading-edge and trailing-edge vortices. As a result, the comb-like plate generates larger aerodynamic force per unit area than the smooth plate. In addition to a quasi-steady phase after the comb-like plate travels several chords, we also studied a starting phase of the shear layer development when the comb-like plate begins to translate from rest. While a plate with small gap size can generate aerodynamic force at the starting phase as effectively as at the quasi-steady phase, the aerodynamic force drops noticeably for a plate with a large gap because the diffusion of the developing shear layers is not enough to block the gap.
Communication: Charge transfer dominates over proton transfer in the reaction of nitric acid with gas-phase hydrated electrons J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Jozef Lengyel, Jakub Med, Petr Slavíček, Martin K. Beyer
The reaction of HNO3 with hydrated electrons (H2O)n− (n = 35–65) in the gas phase was studied using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and ab initio molecular dynamics simulations. Kinetic analysis of the experimental data shows that OH−(H2O)m is formed primarily via a reaction of the hydrated electron with HNO3 inside the cluster, while proton transfer is not observed and NO3−(H2O)m is just a secondary product. The reaction enthalpy was determined using nanocalorimetry, revealing a quite exothermic charge transfer with −241 ± 69 kJ mol−1. Ab initio molecular dynamics simulations indicate that proton transfer is an allowed reaction pathway, but the overall thermochemistry favors charge transfer.
Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-14 Romain Vermorel, Fouad Oulebsir, Guillaume Galliero
The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.
Electronic orbital response of regular extended and infinite periodic systems to magnetic fields. I. Theoretical foundations for static case J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-08 Michael Springborg, Mohammad Molayem, Bernard Kirtman
A theoretical treatment for the orbital response of an infinite, periodic system to a static, homogeneous, magnetic field is presented. It is assumed that the system of interest has an energy gap separating occupied and unoccupied orbitals and a zero Chern number. In contrast to earlier studies, we do not utilize a perturbation expansion, although we do assume the field is sufficiently weak that the occurrence of Landau levels can be ignored. The theory is developed by analyzing results for large, finite systems and also by comparing with the analogous treatment of an electrostatic field. The resulting many-electron Hamilton operator is forced to be hermitian, but hermiticity is not preserved, in general, for the subsequently derived single-particle operators that determine the electronic orbitals. However, we demonstrate that when focusing on the canonical solutions to the single-particle equations, hermiticity is preserved. The issue of gauge-origin dependence of approximate solutions is addressed. Our approach is compared with several previously proposed treatments, whereby limitations in some of the latter are identified.
The parameter uncertainty inflation fallacy J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-08 Pascal Pernot
Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors caused by model inadequacy can be handled either by correcting the model’s results or by adapting the model’s parameter uncertainty to generate prediction uncertainties representative, in a way to be defined, of model inadequacy errors. The main advantage of the latter approach (thereafter called PUI, for Parameter Uncertainty Inflation) is its transferability to the prediction of other quantities of interest based on the same parameters. A critical review of implementations of PUI in several areas of computational chemistry shows that it is biased, in the sense that it does not produce prediction uncertainty bands conforming to model inadequacy errors.
A new insight into diffusional escape from a biased cylindrical trap J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-11 Alexander M. Berezhkovskii, Leonardo Dagdug, Sergey M. Bezrukov
Recent experiments with single biological nanopores, as well as single-molecule fluorescence spectroscopy and pulling studies of protein and nucleic acid folding raised a number of questions that stimulated theoretical and computational investigations of barrier crossing dynamics. The present paper addresses a closely related problem focusing on trajectories of Brownian particles that escape from a cylindrical trap in the presence of a force F parallel to the cylinder axis. To gain new insights into the escape dynamics, we analyze the “fine structure” of these trajectories. Specifically, we divide trajectories into two segments: a looping segment, when a particle unsuccessfully tries to escape returning to the trap bottom again and again, and a direct-transit segment, when it finally escapes moving without touching the bottom. Analytical expressions are derived for the Laplace transforms of the probability densities of the durations of the two segments. These expressions are used to find the mean looping and direct-transit times as functions of the biasing force F. It turns out that the force-dependences of the two mean times are qualitatively different. The mean looping time monotonically increases as F decreases, approaching exponential F-dependence at large negative forces pushing the particle towards the trap bottom. In contrast to this intuitively appealing behavior, the mean direct-transit time shows rather counterintuitive behavior: it decreases as the force magnitude, |F|, increases independently of whether the force pushes the particles to the trap bottom or to the exit from the trap, having a maximum at F = 0.
Extended screened exchange functional derived from transcorrelated density functional theory J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Naoto Umezawa
We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, H T C , is introduced by a similarity transformation of a many-body Hamiltonian, H , with respect to a complex function F: H T C = 1 F H F . It is proved that an expectation value of H T C for a normalized single Slater determinant, Dn, corresponds to the total energy: E [ n ] = ⟨ Ψ n | H | Ψ n ⟩ / ⟨ Ψ n | Ψ n ⟩ = ⟨ D n | H T C | D n ⟩ under the two assumptions: (1) The electron density n r associated with a trial wave function Ψ n = DnF is v -representable and (2) Ψ n and Dn give rise to the same electron density n r . This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H− ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.
Photobleaching of randomly rotating fluorescently decorated particles J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Swadhin Taneja, Andrew D. Rutenberg
Randomly rotating particles that have been isotropically labeled with rigidly linked fluorophores will undergo non-isotropic (patchy) photobleaching under illumination due to the dipole coupling of fluorophores with light. For a rotational diffusion rate D of the particle and a photobleaching time scale τ of the fluorophores, the dynamics of this process are characterized by the dimensionless combination D τ . We find significant interparticle fluctuations at intermediate D τ . These fluctuations vanish at both large and small D τ or at small or large elapsed times t. Associated with these fluctuations between particles, we also observe transient non-monotonicities of the brightness of individual particles. These non-monotonicities can be as much as 20% of the original brightness. We show that these novel photobleach-fluctuations dominate over variability of single-fluorophore orientation when there are at least 103 fluorophores on individual particles.
Many-body expansion of the Fock matrix in the fragment molecular orbital method J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13 Dmitri G. Fedorov, Kazuo Kitaura
A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.
Modeling the mechanism of CLN025 beta-hairpin formation J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13 Keri A. McKiernan, Brooke E. Husic, Vijay S. Pande
Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.
A thermally driven differential mutation approach for the structural optimization of large atomic systems J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-14 Katja Biswas
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.
Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-14 Daniel S. Kosov
Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ 1 and τ 2 means that the density matrix of the molecule is not fully renewed after time τ 1 and the probability of observing waiting time τ 2 for the second electron transfer depends on the previous electron waiting time τ 1 . The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.
Re-examination of the Cs2 ground singlet X 1 Σ g + and triplet a 3 Σ u + states J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Vladimir B. Sovkov, Feng Xie, A. Marjatta Lyyra, Ergin H. Ahmed, Jie Ma, Suotang Jia
This paper clarifies the disagreement in the depth of the potential energy curve of the cesium dimer singlet ground state which has lasted for nearly a decade. We point out that the origin of this disagreement must be a technical misprint in the values of the three binding energies reported by Danzl et al. [Science 321, 1062 (2008)], while the X 1 Σ g + state potential reported by Coxon and Hajigeorgiou [J. Chem. Phys. 132, 094105 (2010)], based on experimental data by Amiot and Dulieu [J. Chem. Phys. 117, 5155 (2002)], is quite correct. We have recalculated the potential energy function of the triplet ground state a 3 Σ u + by using the available experimental data spanning both the attractive and the repulsive branches so that the potential energy function complies asymptotically with the singlet ground state X 1 Σ g + potential energy function by Coxon and Hajigeorgiou. This is important for the simulation of the near dissociation properties such as Feshbach resonances, which are typically observed in modern experiments with ultracold atoms and molecules.
Near-infrared spectroscopy and anharmonic theory of the H2O+Ar1,2 cation complexes J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 J. Philipp Wagner, David C. McDonaldII, Michael A. Duncan
Weakly bound complexes of the water radical cation with argon (H2O+Arn, n = 1,2) were generated by an electrical discharge/supersonic expansion and probed with mid- and near-infrared photodissociation spectroscopy in the 2050–4550 and 4850–7350 cm−1 regions. To elucidate these spectra, these complexes were studied computationally at the CCSD(T) level including anharmonicity with the VPT2 method. The comparison between experiment and predicted spectra demonstrates that the VPT2 method is adequate to capture most of the vibrational band positions and their intensities. In addition to the fundamentals, overtones of the symmetric and the asymmetric water stretches and their combination were detected. Additional bands were assigned to combinations of the overtone of the bound O–H stretch with multiple excitation levels of the intermolecular Ar–H stretch. H2O+Ar2 could not be dissociated in the higher frequency region (4850–7350 cm−1).
Ce in the +4 oxidation state: Anion photoelectron spectroscopy and photodissociation of small CexOyHz− molecules J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13 Josey E. Topolski, Jared O. Kafader, Caroline Chick Jarrold
The anion photoelectron (PE) spectra of a range of small mono-cerium molecular species, along with the Ce2O4− and Ce3O6− stoichiometric clusters, are presented and analyzed with the support of density functional theory calculations. A common attribute of all of the neutral species is that the Ce centers in both the molecules and clusters are in the +4 oxidation state. In bulk ceria (CeO2), an unoccupied, narrow 4f band lies between the conventional valence (predominantly O 2p) and conduction (Ce 5d) bands. Within the CeO2−, CeO3H2−, and Ce(OH)4− series, the PE spectra and computational results suggest that the Ce 6s-based molecular orbital is the singly occupied HOMO in CeO2− but becomes destabilized as the Ce 4f-local orbital becomes stabilized with increasing coordination. CeO3−, a hyperoxide, undergoes photodissociation with 3.49 eV photon energy to form the stoichiometric neutral CeO2 and O−. In the CeO2−, Ce2O4− ,and Ce3O6− stoichiometric cluster series, the 6s destabilization with 4f stabilization is associated with increasing cluster size, suggesting that a bulk-like band structure may be realized with fairly small cluster sizes. The destabilization of the 6s-based molecular orbitals can be rationalized by their diffuse size relative to Ce—O bond lengths in a crystal structure, suggesting that 6s bands in the bulk may be relegated to the surface.
Single, double, and triple Auger decays from 1s shake-up states of the oxygen molecule J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-14 T. Kaneyasu, T. Odagiri, M. Nakagawa, R. Mashiko, H. Tanaka, J. Adachi, Y. Hikosaka
The single, double, and triple Auger decays from the 1s shake-up states of O2 have been studied using a multi-electron coincidence method. Efficient populations of two-hole final states are observed in single Auger decays of the π-π* shake-up states, which is understood as a characteristic property of the Auger transitions from shake-up states of an open-shell molecule. The O23+ populations formed by double Auger decays show similar profiles for both the O1s−1 and shake-up states, which is due to the contributions from cascade double Auger processes. While the cascade contributions to the double Auger decays increase with the initial shake-up energy, the probability of direct double Auger processes remains unchanged between the O1s−1 and shake-up states, which implies a weak influence of the excited electron on the double Auger emission that originates from the electron correlation effect.
A potential model for sodium chloride solutions based on the TIP4P/2005 water model J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13 A. L. Benavides, M. A. Portillo, V. C. Chamorro, J. R. Espinosa, J. L. F. Abascal, C. Vega
Despite considerable efforts over more than two decades, our knowledge of the interactions in electrolyte solutions is not yet satisfactory. Not even one of the most simple and important aqueous solutions, NaCl(aq), escapes this assertion. A requisite for the development of a force field for any water solution is the availability of a good model for water. Despite the fact that TIP4P/2005 seems to fulfill the requirement, little work has been devoted to build a force field based on TIP4P/2005. In this work, we try to fill this gap for NaCl(aq). After unsuccessful attempts to produce accurate predictions for a wide range of properties using unity ionic charges, we decided to follow recent suggestions indicating that the charges should be scaled in the ionic solution. In this way, we have been able to develop a satisfactory non-polarizable force field for NaCl(aq). We evaluate a number of thermodynamic properties of the solution (equation of state, maximum in density, enthalpies of solution, activity coefficients, radial distribution functions, solubility, surface tension, diffusion coefficients, and viscosity). Overall the results for the solution are very good. An important achievement of our model is that it also accounts for the dynamical properties of the solution, a test for which the force fields so far proposed failed. The same is true for the solubility and for the maximum in density where the model describes the experimental results almost quantitatively. The price to pay is that the model is not so good at describing NaCl in the solid phase, although the results for several properties (density and melting temperature) are still acceptable. We conclude that the scaling of the charges improves the overall description of NaCl aqueous solutions when the polarization is not included.
Variation of ionic conductivity in a plastic-crystalline mixture J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13 D. Reuter, C. Geiß, P. Lunkenheimer, A. Loidl
Ionically conducting plastic crystals (PCs) are possible candidates for solid-state electrolytes in energy-storage devices. Interestingly, the admixture of larger molecules to the most prominent molecular PC electrolyte, succinonitrile, was shown to drastically enhance its ionic conductivity. Therefore, binary mixtures seem to be a promising way to tune the conductivity of such solid-state electrolytes. However, to elucidate the general mechanisms of ionic charge transport in plastic crystals and the influence of mixing, a much broader database is needed. In the present work, we investigate mixtures of two well-known plastic-crystalline systems, cyclohexanol and cyclooctanol, to which 1 mol. % of Li ions were added. Applying differential scanning calorimetry and dielectric spectroscopy, we present a thorough investigation of the phase behavior and the ionic and dipolar dynamics of this system. All mixtures reveal plastic-crystalline phases with corresponding orientational glass-transitions. Moreover, their conductivity seems to be dominated by the “revolving-door” mechanism, implying a close coupling between the ionic translational and the molecular reorientational dynamics of the surrounding plastic-crystalline matrix. In contrast to succinonitrile-based mixtures, there is no strong variation of this coupling with the mixing ratio.
Liquid bridging of cylindrical colloids in near-critical solvents J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-08 M. Labbé-Laurent, A. D. Law, S. Dietrich
Within mean field theory, we investigate the bridging transition between a pair of parallel cylindrical colloids immersed in a binary liquid mixture as a solvent that is close to its critical consolute point Tc. We determine the universal scaling functions of the effective potential and of the force between the colloids. For a solvent that is at the critical concentration and close to Tc, we find that the critical Casimir force is the dominant interaction at close separations. This agrees very well with the corresponding Derjaguin approximation for the effective interaction between the two cylinders, while capillary forces originating from the extension of the liquid bridge turn out to be more important at large separations. In addition, we are able to infer from the wetting characteristics of the individual colloids the first-order transition of the liquid bridge connecting two colloidal particles to the ruptured state. While specific to cylindrical colloids, the results presented here also provide an outline for identifying critical Casimir forces acting on bridged colloidal particles as such and for analyzing the bridging transition between them.
Charge compensation at the interface between the polar NaCl(111) surface and a NaCl aqueous solution J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-08 Thomas Sayer, Chao Zhang, Michiel Sprik
Periodic supercell models of electric double layers formed at the interface between a charged surface and an electrolyte are subject to serious finite size errors and require certain adjustments in the treatment of the long-range electrostatic interactions. In a previous publication Zhang and Sprik [Phys. Rev. B 94, 245309 (2016)], we have shown how this can be achieved using finite field methods. The test system was the familiar simple point charge model of a NaCl aqueous solution confined between two oppositely charged walls. Here this method is extended to the interface between the (111) polar surface of a NaCl crystal and a high concentration NaCl aqueous solution. The crystal is kept completely rigid and the compensating charge screening the polarization can only be provided by the electrolyte. We verify that the excess electrolyte ionic charge at the interface conforms to the Tasker 1/2 rule for compensating charge in the theory of polar rock salt (111) surfaces. The interface can be viewed as an electric double layer with a net charge. We define a generalized Helmholtz capacitance CH which can be computed by varying the applied electric field. We find C H = 8.23 μ F c m − 2 , which should be compared to the 4.23 μ F c m − 2 for the (100) non-polar surface of the same NaCl crystal. This is rationalized by the observation that compensating ions shed their first solvation shell adsorbing as contact ions pairs on the polar surface.
Co-adsorption of water and oxygen on GaN: Effects of charge transfer and formation of electron depletion layer J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-11 Qi Wang, Ajinkya Puntambekar, Vidhya Chakrapani
Species from ambient atmosphere such as water and oxygen are known to affect electronic and optical properties of GaN, but the underlying mechanism is not clearly known. In this work, we show through careful measurement of electrical resistivity and photoluminescence intensity under various adsorbates that the presence of oxygen or water vapor alone is not sufficient to induce electron transfer to these species. Rather, the presence of both water and oxygen is necessary to induce electron transfer from GaN that leads to the formation of an electron depletion region on the surface. Exposure to acidic gases decreases n-type conductivity due to increased electron transfer from GaN, while basic gases increase n-type conductivity and PL intensity due to reduced charge transfer from GaN. These changes in the electrical and optical properties, as explained using a new electrochemical framework based on the phenomenon of surface transfer doping, suggest that gases interact with the semiconductor surface through electrochemical reactions occurring in an adsorbed water layer present on the surface.
Magnetic two-dimensional organic topological insulator: Au–1,3,5-triethynylbenzene framework J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Yu Chen, Qiang Sun
Based on first-principles calculations, we demonstrate that the recently-synthesized 2D organometallic framework consisting of Au atoms and 1,3,5-triethynylbenzene (Au-TEB) is a magnetic 2D organic topological insulator (OTI). The charge transfer and covalent bonding character lead to ferromagnetism and half-metallicity in the framework, and the weak spin-orbit coupling (SOC) of C pz orbitals mediated by Au d orbitals opens modest bandgaps in the vicinity of the Fermi level. Moreover, using tight-binding model simulations, we further characterize the nonzero Chern number and edge states of Au-TEB to confirm its topological nontriviality that remains intact when the framework is supported on an insulating substrate, and applying an external strain can increase the magnitude of SOC gaps, leading to an enhanced topological nontriviality. Our results suggest that the Au-TEB organometallic framework is promising for the potential applications in quantum spintronics with the merits of low cost and easy synthesis.
An ab initio study of hydroxylated graphane J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12 Francesco Buonocore, Andrea Capasso, Nicola Lisi
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with –H and –OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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