Off-center Sites Research Articles

Spontaneous directional flow of active magnetic particles

We predict the emergence of large-scale polar order and spontaneous directional flows in a class of self-propelled autonomous particles that interact via passive repulsion between off-center sites. The coupling of active motion with the passive torque acting about the particle centers results in hybrid active-passive interactions responsible for a macroscopic phase transition from an isotropic state to a polar-aligned state in systems of particles with front interaction sites. We employ a continuum kinetic theory to explain that the emergence of long-ranged orientational order, which occurs in unbounded domains at finite densities, can be externally activated independently of the self-propulsion mechanism and drives a macroscopic particle flow in a direction selected by symmetry breaking.

A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions.

A fixed multi-site interaction charge (FMIC) model was proposed for the accurate prediction of intermolecular electrostatic interactions based on the quantum mechanical linear response of a molecule to an external electric field. In such a model, some additional off-center interaction sites were added for capturing multipole interactions for a given molecule. By multivariate least-square fitting analysis of the calculated QM/MM interactions of a given molecule with the electrostatic environment and the electrostatic potentials of the environment at the pre-defined distributed interaction sites, the FMIC of the molecule was obtained. The model system of CO in myoglobin (Mb) was utilized to demonstrate the derivation of the FMIC. The accuracy of FMIC in predicting the electrostatic interactions between CO and the Mb environment was investigated using 10 000 different Mb-CO configurations generated from the 400 ps QM/MM MD simulation. In comparison to the QM/MM calculations at the B3LYP/aug-cc-pVTZ/ff99SB level, the mean unsigned error (MUE) of the results based on the FMIC model was merely 0.10 kcal mol-1, and the root mean square error (RMSE) was only 0.13 kcal mol-1, which are significantly lower than the results predicted by the ESP charge model (MUE = 1.45 kcal mol-1, and RMSE = 1.7 kcal mol-1, respectively). The transferability of FMIC was tested by applying the obtained FMIC in the wild type Mb-CO system to the mutants of V68F and H64L Mb-CO systems. The MUEs of the obtained results for 10 000 different configurations are both smaller than 0.2 kcal mol-1 for the V68F and H64L Mb-CO systems in comparison to the B3LYP/aug-cc-pVTZ/ff99SB calculations, and the RMSEs are also lower than 0.2 kcal mol-1 for both mutants. The applications of FMIC were extended to model the electrostatic interactions between a hydrogen fluoride molecule and 492 waters in a truncated octahedron box; our study showed that the FMIC could give satisfactory results with a MUE of 0.12 kcal mol-1 and a RMSE of 0.16 kcal mol-1 in comparison to the B3LYP/aug-cc-pVDZ/TIP3P calculations for 10 000 different configurations generated using the 10 ns classical MD simulation. Therefore, the FMIC method provides an accurate and efficient tool for predicting intermolecular electrostatic interactions, which can be utilized in the future development of molecular force fields.

Wertheim Model for Quantum Associating Hard Spheres

In this article we analyze the introduction of quantum effects in the modeling of a quantum fluid formed by hard spheres with an off-center square-well attractive site, a quantum associating hard-spheres (QAHS) system. Semiclassical Monte Carlo simulations for the QAHS fluid were performed in order to study the variation of the fraction of free monomers with the thermal de Broglie wavelength λB = h/(2πmkT)1/2, where T is the temperature, h and k are the Planck’s and Boltzmann’s constants, respectively, and m is the hard-spheres mass. We present a quantum extension of the Wertheim model by considering the effect of the quantum nature of the system using the Slater sum for quantum hard spheres. Excellent agreement is found between theory and simulation results for the case of a bulk fluid.

Electron-phonon coupling and superconductivity in the doped topological crystalline insulator (Pb0.5Sn0.5)1−xInxTe

We present a neutron scattering study of phonons in single crystals of (Pb$_{0.5}$Sn$_{0.5}$)$_{1-x}$In$_x$Te with $x=0$ (metallic, but nonsuperconducting) and $x=0.2$ (nonmetallic normal state, but superconducting). We map the phonon dispersions (more completely for $x=0$) and find general consistency with theoretical calculations, except for the transverse and longitudinal optical (TO and LO) modes at the Brillouin zone center. At low temperature, both modes are strongly damped but sit at a finite energy ($\sim4$ meV in both samples), shifting to higher energy at room temperature. These modes are soft due to a proximate structural instability driven by the sensitivity of Pb-Te and Sn-Te $p$-orbital hybridization to off-center displacements of the metal atoms. The impact of the soft optical modes on the low-energy acoustic modes is inferred from the low thermal conductivity, especially at low temperature. Given that the strongest electron-phonon coupling is predicted for the LO mode, which should be similar for both studied compositions, it is intriguing that only the In-doped crystal is superconducting. In addition, we observe elastic diffuse (Huang) scattering that is qualitatively explained by the difference in Pb-Te and Sn-Te bond lengths within the lattice of randomly distributed Pb and Sn sites. We also confirm the presence of anomalous diffuse low-energy atomic vibrations that we speculatively attribute to local fluctuations of individual Pb atoms between off-center sites.

Pressure-induced quenching of planar rattling in Cu10Zn2Sb4S13 studied by specific heat and x-ray diffraction measurements

We have studied the pressure effect on the rattling of tetrahedrite Cu$_{10}$Zn$_{2}$Sb$_{4}$S$_{13\,}$(CZSS) and type-I clathrate Ba$_{8}$Ga$_{16}$Sn$_{30\,}$(BGS) by specific heat and x-ray diffraction measurements. By applying pressure $P$, the rattling energy for CZSS initially decreases and steeply increases for $P$ $\textgreater$ $1$ GPa. By contrast, the energy for BGS increases monotonically with $P$ up to 6.5 GPa. An analysis of the pressure dependent specific heat and x-ray diffraction indicates that the out-of-plane rattling of the Cu atoms in the S$_{3}$ triangle of CZSS originates from the chemical pressure, unlike the rattling of the Ba ions among off-center sites in an oversized cage of BGS. The rattling in CZSS ceases upon further increasing $P$ above 2 GPa, suggesting that Cu atoms escape away from the S$_{3}$ triangle plane.

Carbon Monoxide Stripe Motion Driven by Correlated Lateral Hopping in a 1.4 × 1.4 Monolayer Phase on Cu(111).

We report an ultra-high-vacuum low-temperature (4.6 K) scanning tunneling microscopy study of the molecular structure and dynamics of a carbon monoxide (CO) monolayer adsorbed at 20 K on Cu(111). We observe the well-known 1.4 × 1.4 phase of CO/Cu(111) for the first time in real-space imaging. At 4.6 K, the hexagonal symmetry of the monolayer is locally broken by the formation of stripes made of single and double CO rows of different apparent heights. Using density functional theory calculations, we assign the high rows to CO molecules adsorbed mostly at off-center top sites and the low rows to bridge sites. Groups of three or four very high molecules appear randomly and are assigned to nearest-neighbor, titled top site molecules. We observe simultaneous hopping of a few CO molecules between adjacent top and bridge sites, which produces the apparent motion of the stripe pattern.

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics.

Modern molecular mechanics force fields are widely used for modeling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. However, for molecules outside the training set, the parameters are potentially inaccurate and it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines bond, angle, torsion, charge, and Lennard-Jones parameter derivation methodologies alongside a method for deriving the positions and charges of off-center virtual sites from the partitioned quantum mechanical electron density. As a proof of concept, we have rederived a complete set of parameters for 109 small organic molecules and assessed the accuracy by comparing computed liquid properties with experiments. QUBEKit gives competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol, and 1.17 kcal/mol for the liquid density, heat of vaporization, and free energy of hydration, respectively. This indicates that the derived parameters are suitable for molecular modeling applications, including computer-aided drug design.

Atomistic tight-binding theory for acceptor states (C, Be, Mg, Zn, Si and Cd) of GaAs nanocrystals

The atomistic tight-binding theory is introduced as a new way to numerically calculate the binding energies of acceptors (C, Be, Mg, Zn, Si and Cd) in GaAs nanocrystals. In the present paper, the electronic structures and optical properties of spherical GaAs nanocrystals with a single substitutional acceptor impurity at the center and off-center sites are studied. The optical band gaps of undoped GaAs nanocrystals are larger for smaller nanocrystals, due to quantum confinement effects. Numerical results show that the acceptor binding energies are highly dependent on the nanoparticle sizes, impurity types and positions. Larger acceptor binding energies in doped GaAs nanocrystals are also seen for smaller nanocrystals. In term of acceptor varieties, the high-to-low order of binding energies is found in Cd, Si, Zn, Mg, Be and C acceptors, respectively. In term of positions, the acceptor binding energies are reduced with the increasing distances from the center of nanocrystals. In addition, the optical property is mainly improved in the presence of the substitutional acceptor impurity. Finally, these computational results provide an inroad to new materials not accessible via other means with the aim to implement novel applications based on the substitutional acceptor impurity in the nanostructures.

Asymmetry induced intrinsic magnetodielectric effects in manganite – Barium titanate solid solutions

Multiferroics, in which off-center magnetic ions induced ferroelectricity, are believed to exhibit enhanced magnetoelectric (ME) or magnetodielectric (MD) effects because their ferroelectricity and ferromagnetism are driven by the same originations. In this paper, multiferroics with off-center Mn ions were obtained in hexagonal manganite-barium titanate solid solutions. As an external magnetic field (H) was applied, intermediate and high frequency MD effects were observed. The MD (MD(%) = (ε(H = 3.5 kOe) − ε(H = 0 Oe)) × 100/ε(H = 0 Oe)) values at 10 MHz frequency were 3.37%, 3.21% and 2.65% for the three samples, respectively. The further discussion indicated that the MD effects did not originate from some extrinsic source such as grain boundary magnetoresistance (MR) and contributions from the electrode, but mainly attributed to the intrinsic ME coupling such as magnetic-field-induced variations of asymmetric hopping. The first-principles calculations also confirmed that the asymmetry of coplanar octahedrons aggravated when Mn ions occupied the off-center site in the hexagonal phases, especially in 0.1La0.7Ca0.3MnO3 − 0.9BaTiO3 solid solutions.

Ion-Exchangeable Microporous Polyoxometalate Compounds with Off-Center Dopants Exhibiting Unconventional Luminescence.

The synthesis of luminescent polyoxometalates (POMs) typically relies on the assembly of POM ligands with rare earth or transition metals, placing significant constraints on the composition, structure, and hence the luminescence properties of the resultant systems. Herein, we show that the ion-exchange strategy can be used for the synthesis of novel POM-based luminescent materials. We demonstrate that introducing bismuth ions into an ion-exchangeable, microporous POM compound yields an unconventional system luminescing in the near-infrared region. Experimental characterization, coupled with quantum chemical calculations, confirms that bismuth ions site-specifically occupy an off-center site in the lattice, and have an asymmetric coordination geometry unattainable by other means, thus giving rise to peculiar emission. Our findings offer an effective strategy for the synthesis of POM-based luminescent materials, and the design concept may potentially be adapted to the creation of POM-based systems with other functionalities.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.

Off-centering of rare-earth ion in (Ba,R)(Ti,Mg)O3 (R = Gd, Dy)

To investigate the off-centering behavior of rare-earth ions that were partially substituted for A site ions in ABO3-type crystals, accurate crystal structure analyses of (Ba,R)(Ti,Mg)O3 (R = Gd, Dy) were performed by high-energy synchrotron radiation X-ray powder diffraction analysis and the maximum entropy method (MEM)/Rietveld method. The R ions were observed at the six equivalent off-center sites in the 〈100〉 directions from the corner of a unit cell in the cubic phase. In the tetragonal phase, the R ions occupied one off-center site along the [001] direction. The R off-centering can be attributed to the covalent nature of the bond between the R and O ions in (Ba,R)(Ti,Mg)O3 crystals.

Origin of the first-order ferroelectric phase transition in K0.957Li0.043TaO3 solid solution

The results of low-temperature linear and nonlinear susceptibilities and polarization measurements of the KLT-4.3%Li crystalline sample are presented. The following model of the mechanism of the ferroelectricity in the K0.957Li0.043TaO3 (KLT-4.3%Li) solid solution is proposed. Static quasi-frozen clusters of Li+ dipoles affect the ordering process of the remainder of the system: a dynamical correlation of the off-center motions of Ta ions along one of the equivalent off-center sites in the 〈111〉 cubic direction in the octahedral environment of O ions occurs and leads to the formation of a reversible spontaneous polarization.

Explicit-water theory for the salt-specific effects and Hofmeister series in protein solutions.

Effects of addition of salts on stability of aqueous protein solutions are studied theoretically and the results are compared with experimental data. In our approach, all the interacting species, proteins, ions, and water molecules, are accounted for explicitly. Water molecules are modeled as hard spheres with four off-center attractive square-well sites. These sites serve to bind either another water or to solvate the ions or protein charges. The ions are represented as charged hard spheres, and decorated by attractive sites to allow solvation. Spherical proteins simultaneously possess positive and negative groups, represented by charged hard spheres, attached to the surface of the protein. The attractive square-well sites, mimicking the protein-protein van der Waals interaction, are located on the surface of the protein. To obtain numerical results, we utilized the energy route of Wertheim's associative mean spherical approximation. From measurable properties, we choose to calculate the second virial coefficient B2, which is closely related to the tendency of proteins to aggregate and eventually crystalize. Calculations are in agreement with experimental trends: (i) For low concentration of added salt, the alkali halide salts follow the inverse Hofmeister series. (ii) At higher concentration of added salt, the trend is reversed. (iii) When cations are varied, the salts follow the direct Hofmeister series. (iv) In contrast to the colloidal theories, our approach correctly predicts the non-monotonic behavior of B2 upon addition of salts. (v) With respect to anions, the theory predicts for the B2 values to follow different sequences below and above the iso-ionic point, as also confirmed experimentally. (vi) A semi-quantitative agreement between measured and calculated values for the second virial coefficient, as functions of pH of solution and added salt type and concentration, is obtained.

“Glass-like” thermal conductivity gradually induced in thermoelectric Sr8Ga16Ge30 clathrate by off-centered guest atoms

The origin of the “glass-like” plateau in thermal conductivity of inorganic type I clathrates has been debated for more than a decade. Here, it is demonstrated that the low temperature thermal conductivity of Sr8Ga16Ge30 can be controlled by the synthesis method: A flux-grown sample has a “glass-like” plateau in thermal conductivity at low temperature, while a zone-melted sample instead has a crystalline peak. A combination of flux-growth and zone-melting produces an intermediate thermal conductivity. In a comprehensive study of three single crystal samples, it is shown by neutron diffraction that the transition from crystalline peak to “glass-like” plateau is related to an increase in Sr guest atom off-centering distance from 0.24 Å to 0.43 Å. By modifying ab initio calculated force constants for the guest atom to an isotropic model, we reproduce both measured heat capacity and inelastic neutron scattering data. The transition from peak to plateau in the thermal conductivity can be modeled by a combined increase of Rayleigh and disorder scattering. Measurement of heat capacity refutes simple models for tunneling of Sr between off-center sites. Furthermore, the electronic properties of the same samples are characterized by Hall carrier density, Seebeck coefficient, and resistivity. The present comprehensive analysis excludes tunneling and charge carrier scattering as dominant contributors to the “glass-like” plateau. The increased guest atom off-centering distance controlled by synthesis provides a possible microscopic mechanism for reducing the low temperature thermal conductivity of clathrates.

Re-entrant phase behavior in confined two-patch colloidal particles.

We present a version of density functional approach for the system of patchy colloidal particles confined in slitlike pores with hard walls. Each particle possesses two off-center sites of the types A and B, and in addition to single A-A and B-B bonds, formation of the double A-B-A and B-A-B bonds is allowed. The proposed approach is based on the fundamental measure theory and the second order perturbation theory of Wertheim. For the model in question, a re-entrant phase behavior in a bulk system has been found [Kalyuzhnyi Y. V.; Cummings, P. T., J. Chem. Phys. 2013, 139, 104905] . Our calculations revealed that the re-entrant phase diagrams are also observed in confined systems. The upper critical temperature decreases with the pore width, while the lower critical temperature increases very slightly.

Electronic structure calculations of substitutional and interstitial hydrogen in Nb

We report the results of a theoretical study on the effects of substitutional and interstitial hydrogen atoms in niobium. We confirm that any contaminated hydrogen will occupy the interstitial site over the substitutional site in niobium. For interstitial hydrogens, the lattice deformation increases with the percentage content of hydrogen, though it is negligible at low concentrations. Substitutional hydrogens are found to prefer off-center sites in the host lattice.

Sm@C2v(3)-C80: site-hopping motion of endohedral Sm atom and metal-induced effect on redox profile

A new metallofullerene Sm@C(2v)(3)-C(80) was synthesized and characterized. X-Ray analysis showed that the endohedral Sm atom undergoes a hopping motion between several off-center sites, even at low temperature. In addition, a comparative electrochemical study between Sm@C(2v)(3)-C(80) and Yb@C(2v)(3)-C(80) revealed their different redox potentials, suggesting a metal-induced effect on their redox profiles.

Li7NMR Investigation of Li-Li Pair Ordering in the Paraelectric Phase of Weakly Substitutionally DisorderedK1−xLixTaO3

Breaking of the average cubic symmetry in Li-doped potassium tantalate was observed with quadrupole-perturbed 7Li NMR at temperatures (150-400K) far above the nominal glass transition temperature (≈50 K for Li concentration x=0.03). The observed spectrum consists of contributions from both isolated Li ions (i.e., with no nearest-neighbor Li) and from Li-Li pairs. The isolated Li ions move among six equivalent off-center sites in a potential having cubic symmetry. These have zero average electric field gradient and, hence, exhibit no quadrupole splitting. In addition, very low intensity, but well resolved, quadrupole satellites having a temperature-dependent splitting were observed. This splitting indicates that the various Li-Li pair configurations are not all equally probable. These are the first direct observations of biased Li ion ordering that persists in the paraelectric phase at temperatures high above the glass phase.

Polarized Cluster Dynamics at the Paraelectric to Ferroelectric Phase Transition in BaTiO3

The mechanism of the prototype ferroelectric phase transition in BaTiO(3) is a matter of intense debate and to a large extent still wrapped in mystery. Precursor phenomena in the form of polarized clusters in paraelectric BaTiO(3) are by now believed to represent a key step into the ferroelectric phenomenon. The determination of a slower dynamics of cluster polarization flipping along with a faster order-disorder Ti hopping mode among <111> off-center sites suggests coexistence, instead of mutual exclusion, of displacive and order-disorder types, initially proposed as distinct models. However, no clear picture of the transition state has been proposed so far, which is able to provide insight into the coexistence of the paraelectric and ferroelectric phenomena. Here, by means of a dedicated molecular dynamics approach, we provide a detailed atomistic picture of intermediate regions along the transition. Therein, different time and length scales coexist as they characterize different portions of the same material. From an imbalance of dynamically and more statically polarized clusters in this highly inhomogeneous intermediate, a symmetry breaking step naturally results. Further, we find that ferroelectric nanodomains may host antiferroelectric defects, which appear as an intrinsic feature of the growing BaTiO(3) ferroelectric material.