Rb + Adsorption at the Quartz(101)–Aqueous Interface: Comparison of Resonant Anomalous X-ray Reflectivity with ab Initio Calculations
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electrical double layer structure↗
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Calculation and interpretation of classical turning surfaces in solids
Abstract Classical turning surfaces of Kohn–Sham potentials separate classically allowed regions (CARs) from classically forbidden regions (CFRs). They are useful for understanding many chemical properties of molecules but need not exist in solids, where the density never decays to zero. At equilibrium geometries, we find that CFRs are absent in perfect metals, rare in covalent semiconductors at equilibrium, but common in ionic and molecular crystals. In all materials, CFRs appear or grow as the internuclear distances are uniformly expanded. They can also appear at a monovacancy in a metal. Calculations with several approximate density functionals and codes confirm these behaviors. A classical picture of conduction suggests that CARs should be connected in metals, and disconnected in wide-gap insulators, and is confirmed in the limits of extreme compression and expansion. Surprisingly, many semiconductors have no CFR at equilibrium, a key finding for density functional construction. Nonetheless, a strong correlation with insulating behavior can still be inferred. Moreover, equilibrium bond lengths for all cases can be estimated from the bond type and the sum of the classical turning radii of the free atoms or ions.
Chemistry↗
Finite-size correction for slab supercell calculations of materials with spontaneous polarization
Abstract The repeated slab approach has become a de facto standard to accurately describe surface properties of materials by density functional theory calculations with periodic boundary conditions. For materials exhibiting spontaneous polarization, we show that the conventional scheme of passivation with pseudo hydrogen is unable to realize a charge-neutral surface. The presence of a net surface charge induces via Gauss’s law a macroscopic electric field through the slab and results in poor size convergence with respect to the thickness of the slab. We propose a modified passivation method that accounts for the effect of spontaneous polarization, describes the correct bulk limits and boosts convergence with respect to slab thickness. The robustness, reliability, and superior convergence of energetics and electronic structure achieved by the proposed method are demonstrated using the example of polar ZnO surfaces.
Chemistry↗
Radiative properties of quantum emitters in boron nitride from excited state calculations and Bayesian analysis
Abstract Point defects in hexagonal boron nitride (hBN) have attracted growing attention as bright single-photon emitters. However, understanding of their atomic structure and radiative properties remains incomplete. Here we study the excited states and radiative lifetimes of over 20 native defects and carbon or oxygen impurities in hBN using ab initio density functional theory and GW plus Bethe-Salpeter equation calculations, generating a large data set of their emission energy, polarization and lifetime. We find a wide variability across quantum emitters, with exciton energies ranging from 0.3 to 4 eV and radiative lifetimes from ns to ms for different defect structures. Through a Bayesian statistical analysis, we identify various high-likelihood charge-neutral defect emitters, among which the native V N N B defect is predicted to possess emission energy and radiative lifetime in agreement with experiments. Our work advances the microscopic understanding of hBN single-photon emitters and introduces a computational framework to characterize and identify quantum emitters in 2D materials.
Chemistry↗
Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations
We investigated the structure-dependent vibrational properties of different Mg(BH 4 ) 2 polymorphs (α, β, γ, and δ phases) with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH 4 - anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20–80 meV) are associated with the BH4 - librational modes. The features in the intermediate energy region (80–120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features in the high-energy region (120–200 meV) correspond to the BH 4 - symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. We can explain these differences using the spatial distribution of BH 4 - anions within various structures. An example of the possible identification of products after the hydrogenation of MgB 2 , using NVS measurements, is presented. Our results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Preservation of kinetics parameters generated by Monte Carlo calculations in two-step deterministic calculations
The generation of accurate kinetic parameters such as mean generation time Λ and effective delayed neutron fraction β eff via Monte Carlo codes is established. Employing these in downstream deterministic codes warrants another step to ensure no additional error is introduced by the low-order transport operator when computing forward and adjoint fluxes for bilinear weighting of these parameters. Another complexity stems from applying superhomogenization (SPH) equivalence in non-fundamental mode approximations, where reference and low-order calculations rely on a 3D full core model. In these cases, SPH factors can optionally be computed for only part of the geometry while preserving reaction rates and K-effective, but the impact of such approximations on kinetics parameters has not been thoroughly studied. This paper aims at studying the preservation of bilinearly-weighted quantities in the Serpent–Griffin calculation procedure. Diffusion and transport evaluations of IPEN/MB-01, Godiva, and Flattop were carried out with the Griffin reactor physics code, testing available modeling options using Serpent-generated multigroup cross sections and equivalence data. Verifying Griffin against Serpent indicates sensitivities to multigroup energy grid selection and regional application of SPH equivalence, introducing significant errors; these were demonstrated to be reduced through the use of a transport method together with a finer energy grid.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Effect of orientation anisotropy on calculating effective electrical conductivities
This paper develops an analytical effective medium theory (EMT) equation for calculating the effective conductivity of a mixture based on Maxwell's and Maxwell-Garnett’s theories, extended to higher volume fractions using Bruggeman's unsymmetrical treatment (BUT), with a long term goal of extending the treatment to mixtures more representative of real materials in order to calculate their effective electrical conductivity. The development accounts for spheroid shaped inclusions of varying degrees of anisotropic orientation. The orientation is described by the introduction of a distribution function. Two methodologies valid for the inclusion dilute limit were used to evaluate the effective conductivity: one based on Maxwell's far field approach, and the other based on the Maxwell-Garnett in the matrix approach. It was found that while the dilute limit equations for the effective conductivity were different, the final EMT equations derived by applying BUT collapsed to the same formula which was generalized for anisotropic orientation based on the distribution function presented.
36 MATERIALS SCIENCE↗
Ab-initio calculations of electronic, transport, and structural properties of boron phosphide
We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus, 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Ring-polymer molecular dynamics: Rate coefficient calculations for energetically symmetric (near thermoneutral) insertion reactions (X + H{sub 2}) → HX + H(X = C({sup 1}D), S({sup 1}D))
Following our previous study of prototypical insertion reactions of energetically asymmetric type with the RPMD (Ring-Polymer Molecular Dynamics) method [Y. Li, Y. Suleimanov, and H. Guo, J. Phys. Chem. Lett. 5, 700 (2014)], we extend it to two other prototypical insertion reactions with much less exothermicity (near thermoneutral), namely, X + H{sub 2} → HX + H where X = C({sup 1}D), S({sup 1}D), in order to assess the accuracy of this method for calculating thermal rate coefficients for this class of reactions. For both chemical reactions, RPMD displays remarkable accuracy and agreement with the previous quantum dynamic results that make it encouraging for the future application of the RPMD to other barrier-less, complex-forming reactions involving polyatomic reactants with any exothermicity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multi-layer Lanczos iteration approach to calculations of vibrational energies and dipole transition intensities for polyatomic molecules
We report a rigorous full dimensional quantum dynamics algorithm, the multi-layer Lanczos method, for computing vibrational energies and dipole transition intensities of polyatomic molecules without any dynamics approximation. The multi-layer Lanczos method is developed by using a few advanced techniques including the guided spectral transform Lanczos method, multi-layer Lanczos iteration approach, recursive residue generation method, and dipole-wavefunction contraction. The quantum molecular Hamiltonian at the total angular momentum J = 0 is represented in a set of orthogonal polyspherical coordinates so that the large amplitude motions of vibrations are naturally described. In particular, the algorithm is general and problem-independent. An application is illustrated by calculating the infrared vibrational dipole transition spectrum of CH{sub 4} based on the ab initio T8 potential energy surface of Schwenke and Partridge [Spectrochimica Acta, Part A 57, 887 (2001)] and the low-order truncated ab initio dipole moment surfaces of Yurchenko et al. [J. Mol. Spectrosc. 291, 69 (2013)]. A comparison with experiments is made. The algorithm is also applicable for Raman polarizability active spectra.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reactive scattering calculations for {sup 87}Rb+{sup 87}RbHe→Rb{sub 2}({sup 3}Σ{sub u}{sup +},v)+He from ultralow to intermediate energies
We investigate atom-diatom reactive collisions, as a preliminary step, in order to assess the possibility of forming Rb{sub 2} molecules in their lowest triplet electronic state by cold collisions of rubidium atoms on the surface of helium nanodroplets. A simple model related to the well-known Rosen treatment of linear triatomic molecules [N. Rosen, J. Chem. Phys. 1, 319 (1933)] in relative coordinates is used, allowing to estimate reactive probabilities for different values of the total angular momentum. The best available full dimensional potential energy surface [Guillon et al., J. Chem. Phys. 136, 174307 (2012)] is employed through the calculations. Noticeable values of the probabilities in the ultracold regime, which numerically fulfill the Wigner threshold law, support the feasibility of the process. The rubidium dimer is mainly produced at high vibrational states, and the reactivity is more efficient for a bosonic helium partner than when the fermion species is considered.
74 ATOMIC AND MOLECULAR PHYSICS↗
Computationally efficient dielectric calculations of molecular crystals
The microscopic dielectric response is a key quantity for electronic materials such as organic semiconductors. Calculations of this response for molecular crystals are currently either expensive or rely on extreme simplifications such as multipole expansions which lack microscopic detail. We present an alternate approach using a microscopic analogue of the Clausius-Mossotti equation, which constructs the dielectric response of a crystal from an eigenvalue decomposition of the dielectric response of individual molecules. This method can potentially be used to examine the effects of defects, disorder, and surfaces on the dielectric properties of molecular solids.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations
The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH{sub 4}-H{sub 2}O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Spin-orbit couplings within the equation-of-motion coupled-cluster framework: Theory, implementation, and benchmark calculations
We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Improved analytical flux surface representation and calculation models for poloidal asymmetries
An orthogonalized flux-surface aligned curvilinear coordinate system has been developed from an up-down asymmetric variation of the “Miller” flux-surface equilibrium model. It is found that the new orthogonalized “asymmetric Miller” model representation of equilibrium flux surfaces provides a more accurate match than various other representations of DIII-D [J. L. Luxon, Nucl. Fusion 42, 614–633 (2002)] discharges to flux surfaces calculated using the DIII-D Equilibrium Fitting tokamak equilibrium reconstruction code. The continuity and momentum balance equations were used to develop a system of equations relating asymmetries in plasma velocities, densities, and electrostatic potential in this curvilinear system, and detailed calculations of poloidal asymmetries were performed for a DIII-D discharge.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints
Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions. Availability and implementation Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA Supplementary information Supplementary data are available at Bioinformatics online.
Chan, Siu H. J. (ORCID:000000027707656X)↗