Further insights in the ability of classical nonadditive potentials to model actinide ion–water interactions

Pursuing our efforts on the development of accurate classical models to simulate radionuclides in complex environments (Réal et al., J. Phys. Chem. A 2010, 114, 15913; Trumm et al. J. Chem. Phys. 2012, 136, 044509), this article places a large emphasis on the discussion of the influence of models/parameters uncertainties on the computed structural, dynamical, and temporal properties. Two actinide test cases, trivalent curium and tetravalent thorium, have been studied with three different potential energy functions, which allow us to account for the polarization and charge‐transfer effects occurring in hydrated actinide ion systems. The first type of models considers only an additive energy term for modeling ion/water charge‐transfer effects, whereas the other two treat cooperative charge‐transfer interactions with two different analytical expressions. Model parameters are assigned to reproduce high‐level ab initio data concerning only hydrated ion species in gas phase. For the two types of cooperative charge‐transfer models, we define two sets of parameters allowing or not to cancel out possible errors inherent to the force field used to model water/water interactions at the ion vicinity. We define thus five different models to characterize the solvation of each ion. For both ions, our cooperative charge‐transfer models lead to close results in terms of structure in solution: the coordination number is included within 8 and 9, and the mean ion/water oxygen distances are 2.45 and 2.49 Å, respectively, for Th(IV) and Cm(III). © 2012 Wiley Periodicals, Inc.     

Low-energy Sr2MSbO5.5 (M = Ca and Sr) structures show significant distortions near oxygen vacancies

Inspired by significant local distortions found near vacancies in a neutron pair distribution function analysis study (G. King et al., Inorg. Chem. 2012, 51, 13060) of Sr₂ MSbO_5.5 (M = Ca and Sr), this computational study finds minimum-energy structures with these and related distortions using density functional theory (DFT) with the Perdew-Burke-Ernzerhof (PBE) functional as implemented in the Vienna Ab Initio Simulations Package (VASP) (G. Kresse and J. Furthmüller, Phys. Rev. B, 1996, 54, 11169; G. Kresse and J. Hafner, Phys. Rev. B, 1993, 47, 558; G. Kresse and J. Furthmüller, Comput. Mater. Sci., 1996, 6, 15). All structures were optimized using the conjugate gradient method. The global minima found for both systems featured trigonal bipyramid SbO₅ structures and edge sharing with M-centered polyhedra. However, while calcium ions occupied full and partial octahedra, the larger strontium ions were more commonly found in full and partial pentagonal bipyramids. Molecular dynamics with velocity rescaling at 1200 K revealed movements of the oxygen vacancy via polyhedral rotations. This work highlights the need to consider both square pyramid to trigonal bipyramid rearrangements around small ions and rotational polyhedral movements in simulating oxygen vacancy conduction in oxygen-deficient double perovskites.     

Adsorption‐induced changes of intramolecular optical transitions: PTCDA/NaCl and PTCDA/KCl

Structural and optical properties of isolated perylene‐3,4,9,10‐tetracarboxylic acid dianhydride molecules adsorbed on (100) oriented NaCl and KCl surfaces were studied theoretically to analyze the recently observed red‐shift of the optical excitation spectrum after adsorption (Müller et al., Phys. Rev. B, 2011, 83, 241203; Paulheim et al. Phys. Chem. Chem. Phys., 2013, 15, 4906). The ground‐state structures were obtained by periodic dispersion‐corrected density functional theory (DFT) calculations. For the excited‐state calculations, nonperiodic time‐dependent DFT methods were applied for a cluster model embedded in point charges. The range‐separated hybrid functional CAM‐B3LYP was used. Correlation‐consistent basis sets were used and the calculated excitation energies were extrapolated to the complete basis set limit. The shift of the first optical excitation energy was analyzed in terms of electronic and geometric contributions. It was found that both the distortion of the molecule due to the interaction with the surface and the electrostatic potential of the surface play an important role. © 2015 Wiley Periodicals, Inc.     

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson‐Boltzmann equation

SMPBS (Size Modified Poisson‐Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson‐Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson‐Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile‐friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware‐accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc.     

Adaptive multilevel finite element solution of the Poisson–Boltzmann equation II. Refinement at solvent‐accessible surfaces in biomolecular systems

We apply the adaptive multilevel finite element techniques (Holst, Baker, and Wang 21 ) to the nonlinear Poisson–Boltzmann equation (PBE) in the context of biomolecules. Fast and accurate numerical solution of the PBE in this setting is usually difficult to accomplish due to presence of discontinuous coefficients, delta functions, three spatial dimensions, unbounded domains, and rapid (exponential) nonlinearity. However, these adaptive techniques have shown substantial improvement in solution time over conventional uniform‐mesh finite difference methods. One important aspect of the adaptive multilevel finite element method is the robust a posteriori error estimators necessary to drive the adaptive refinement routines. This article discusses the choice of solvent accessibility for a posteriori error estimation of PBE solutions and the implementation of such routines in the “Adaptive Poisson–Boltzmann Solver” (APBS) software package based on the “Manifold Code” (MC) libraries. Results are shown for the application of this method to several biomolecular systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1343–1352, 2000     

Electrostatic component of binding energy: Interpreting predictions from poisson–boltzmann equation and modeling protocols

Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson–Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔG_elec) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔG_elec. We argue that the sensitivity of the absolute ΔΔG_elec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM‐27, AMBER‐94, and OPLS‐AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔG_elec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔG_elec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.     

New Insights into the Band‐Gap Narrowing of (N,P)‐Codoped TiO2 from Hybrid Density Functional Theory Calculations

The electronic properties of anatase‐TiO₂ codoped by N and P at different concentrations have been investigated via generalized Kohn–Sham theory with the Heyd–Scuseria–Ernzerhof (HSE06) hybrid functional for exchange‐correlation in the context of density functional theory. At high doping concentrations, we find that the high photocatalytic activity of (N, P)‐codoped anatase TiO₂ vis‐à‐vis the N‐monodoped case can be rationalized by a double‐hole‐mediated coupling mechanism [Yin et al., Phys. Rev. Lett. 2011, 106, 066801] via the formation of an effective N? P bond. On the other hand, Ti³⁺ and Ti⁴⁺ ions’ spin double‐exchange results in more substantial gap narrowing for larger separations between N and P atoms. At low doping concentrations, double‐hole‐coupling is dominant, regardless of the N? P distance.     

Efficient “On‐the‐Fly” calculation of Raman Spectra from Ab‐Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second‐generation Car‐Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed‐up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite‐temperature Raman spectra “on‐the‐fly” by means of ab‐initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.     

A first‐order system least‐squares finite element method for the Poisson‐Boltzmann equation

The Poisson‐Boltzmann equation is an important tool in modeling solvent in biomolecular systems. In this article, we focus on numerical approximations to the electrostatic potential expressed in the regularized linear Poisson‐Boltzmann equation. We expose the flux directly through a first‐order system form of the equation. Using this formulation, we propose a system that yields a tractable least‐squares finite element formulation and establish theory to support this approach. The least‐squares finite element approximation naturally provides an a posteriori error estimator and we present numerical evidence in support of the method. The computational results highlight optimality in the case of adaptive mesh refinement for a variety of molecular configurations. In particular, we show promising performance for the Born ion, Fasciculin 1, methanol, and a dipole, which highlights robustness of our approach. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Power‐Law Kinetic Models for Synthesis of Ammonia Borane

In the past few years, there have been increasing numbers of studies for the production and dehydrogenation of ammonia borane (NH₃BH₃, AB), which has become a significant hydrogen storage material. However, kinetic model studies based on the synthesis of AB in the literature have not been encountered, though there are many kinetic modeling studies on dehydrogenation of AB (Akbayrak et al., Appl Catal B 2016, 198, 162–170; Choi et al., Phys Chem Chem Phys 2014, 16(17), 7959–7968; Esteruelas et al., Inorg Chem 2016, 55(14), 7176–7181; Park et al., Int J Hydrogen Energy 2015, 40(46), 16316–16322; Rakap, Appl Catal B 2015, 163, 129–134; Tonbul et al., Int J Hydrogen Energy 2016, 41(26), 11154–11162; Zhang et al., Int J Hydrogen Energy 2016, 41(39), 17208–17215). The paper describes the development of a kinetic model for synthesis of ammonia borane by using borohydride (NaBH₄) and ammonium salt (NH₄)₂SO₄. The synthesis of AB experiments was carried out at different temperature ranges between 25 and 50°C, different inlet molar ratios (NaBH₄/(NH₄)₂SO₄ = 1–4), and different molarities with respect to NaBH₄ (0.11–0.67 M NaBH₄). After the parametric experiments were conducted, empirical power law was evaluated for the synthesis reaction. The power‐law model represented the trends of the kinetics of the synthesis reaction and was reproduced as .     

Adaptive multilevel finite element solution of the Poisson–Boltzmann equation I. Algorithms and examples

This article is the first of two articles on the adaptive multilevel finite element treatment of the nonlinear Poisson–Boltzmann equation (PBE), a nonlinear eliptic equation arising in biomolecular modeling. Fast and accurate numerical solution of the PBE is usually difficult to accomplish, due to the presence of discontinuous coefficients, delta functions, three spatial dimensions, unbounded domain, and rapid (exponential) nonlinearity. In this first article, we explain how adaptive multilevel finite element methods can be used to obtain extremely accurate solutions to the PBE with very modest computational resources, and we present some illustrative examples using two well‐known test problems. The PBE is first discretized with piece‐wise linear finite elements over a very coarse simplex triangulation of the domain. The resulting nonlinear algebraic equations are solved with global inexact Newton methods, which we have described in an article appearing previously in this journal. A posteriori error estimates are then computed from this discrete solution, which then drives a simplex subdivision algorithm for performing adaptive mesh refinement. The discretize–solve–estimate–refine procedure is then repeated, until a nearly uniform solution quality is obtained. The sequence of unstructured meshes is used to apply multilevel methods in conjunction with global inexact Newton methods, so that the cost of solving the nonlinear algebraic equations at each step approaches optimal O(N) linear complexity. All of the numerical procedures are implemented in MANIFOLD CODE (MC), a computer program designed and built by the first author over several years at Caltech and UC San Diego. MC is designed to solve a very general class of nonlinear elliptic equations on complicated domains in two and three dimensions. We describe some of the key features of MC, and give a detailed analysis of its performance for two model PBE problems, with comparisons to the alternative methods. It is shown that the best available uniform mesh‐based finite difference or box‐method algorithms, including multilevel methods, require substantially more time to reach a target PBE solution accuracy than the adaptive multilevel methods in MC. In the second article, we develop an error estimator based on geometric solvent accessibility, and present a series of detailed numerical experiments for several complex biomolecules. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1319–1342, 2000     

Multireference configuration interaction calculations for complexes of positronium and B, C, N, and O atoms

Positronium (Ps) binding energies for complexes of Ps and atoms with open shell electrons, PsX (X=B, C, N, and O), are calculated using the multireference singly and doubly excited configuration interaction (MRSDCI) method. The effectiveness of this method for the complexes is verified. The MRSDCI calculations are carried out with a frozen-core approximation so as to incorporate only the most important valence correlation effects. Many-body correlation effects and contributions from higher angular momentum orbitals are estimated by extrapolation techniques. The resulting Ps binding energies agree well with the results of diffusion Monte Carlo simulations by Bressanini et al. (Phys Rev A 57:1678,1998) and by Jiang and Schrader (J Chem Phys 109:9430,1998). For PsO the Ps binding energy obtained by Jiang and Schrader is about 1.8 times larger than that of Bressanini et al.; the present calculated value is close to that of Jiang and Schrader.     

Rearrangement Pathways of the <Emphasis Type="BoldItalic">a</Emphasis><Subscript><Emphasis Type="BoldItalic">4</Emphasis></Subscript> Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

The structure of the a ₄ ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by ‘action’ infrared spectroscopy in the 1000–2000 cm^–1 (‘fingerprint’) range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a ₄ ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N- terminus and an amide group –CO–NH₂ at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008, 112, 1286). Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer’s work.     

TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems

We introduce Topo MS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared‐memory parallel approach, Topo MS provides scalable, numerically robust, and topologically consistent analysis. Topo MS can be used as a command‐line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of Topo MS and compares it with state‐of‐the‐art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero‐de‐la‐Roza et al., Comput. Phys. Commun. 2014, 185, 1007). Topo MS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine‐grid solution, robustness against lattice bias, and topological consistency. Topo MS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc.     

A Shock Tube Study of H2 + OH → H2O + H Using OH Laser Absorption

The rate constant for the reaction of hydroxyl radicals (OH) with molecular hydrogen (H₂) was measured behind reflected shock waves using UV laser absorption of OH radicals near 306.69 nm. Test gas mixtures of H₂ and tert‐butyl hydroperoxide (TBHP) diluted in argon were shock‐heated to temperatures ranging from 902 to 1518 K at pressures of 1.15–1.52 atm. OH radicals were produced by rapid thermal decomposition of TBHP at high temperatures. The rate constant for the title reaction was inferred by best fitting the measured OH time histories with the simulated profiles from the comprehensive reaction mechanism of Wang et al. (USC‐Mech v2.0) (2007). The measured values can be expressed in the Arrhenius equation as k₁(T) = 4.38 × 10¹³ exp(–3518/T) cm³ mol^?1 s^?1 over the temperature range studied. A detailed error analysis was performed to estimate the overall uncertainty of the title reaction, and the estimated (2 – σ) uncertainties were found to be ±17% at 972 and 1228 K. The present measurements are in excellent agreement with the previous experimental studies from Frank and Just (Ber Bunsen‐Ges Phys Chem 1985, 89, 181–187), Michael and Sutherland (J Phys Chem 1988, 92, 3853–3857), Davidson et al. (Symp (Int) Combust 1988, 22, 1877–1885), Oldenborg et al. (J Phys Chem 1992, 96, 8426–8430), and Krasnoperov and Michael (J Phys Chem A 2004, 108, 5643–5648).In addition, the measured rate constant is in close accord with the non‐Arrhenius expression from GRI‐Mech 3.0 ( http://www.me.berkeley.edu/gri_mech/ ) and the theoretical calculation using semiclassical transition state theory from Nguyen et al. (Chem Phys Lett 2010, 499, 9–15).     

Structures and correlation functions of multicomponent and polydisperse hard-sphere mixtures from a density functional theory

The structures of nonuniform binary hard-sphere mixtures and the correlation functions of uniform ternary hard-sphere mixtures were studied using a modified fundamental-measure theory based on the weight functions of Rosenfeld [Rosenfeld, Phys. Rev. Lett. 63, 980 (1989)] and Boublik-Mansoori-Carnahan-Starling-Leland equation of state [Boublik, J. Chem. Phys. 53, 471 (1970); Mansoori et al., J. Chem. Phys. 54, 1523 (1971)]. The theoretical predictions agreed very well with the molecular simulations for the overall density profiles, the local compositions, and the radial distribution functions of uniform as well as inhomogeneous hard-sphere mixtures. The density functional theory was further extended to represent the structure of a polydisperse hard-sphere fluid near a hard wall. Excellent agreement was also achieved between theory and Monte Carlo simulations. The density functional theory predicted oscillatory size segregations near a hard wall for a polydisperse hard-sphere fluid of a uniform size distribution.     

A simple model for the Slater exchange potential and its performance for solids

A simple local model for the Slater exchange potential is determined by least square fit procedure from Hartree–Fock (HF) atomic data. Since the Slater potential is the exact exchange potential yielding HF electron density from Levy‐Perdew‐Sahni density functional formalism (Levy et al., Phys. Rev. A 1984, 30, 2745), the derived local potential is significantly more negative than the conventional local density approximation. On the set of 22 ionic, covalent and van der Waals solids including strongly correlated transition metal oxides, it has been demonstrated, that this simple model potential is capable of reproducing the band gaps nearly as good as popular meta GGA potentials in close agreement with experimental values.     

Ion strength limit of computed excess functions based on the linearized Poisson–Boltzmann equation

The linearized Poisson–Boltzmann (L‐PB) equation is examined for its κ‐range of validity (κ, Debye reciprocal length). This is done for the Debye–Hückel (DH) theory, i.e., using a single ion size, and for the SiS treatment (D. Fraenkel, Mol. Phys. 2010 , 108, 1435), which extends the DH theory to the case of ion‐size dissimilarity (therefore dubbed DH–SiS). The linearization of the PB equation has been claimed responsible for the DH theory's failure to fit with experiment at > 0.1 m; but DH–SiS fits with data of the mean ionic activity coefficient, γ_± (molal), against m, even at m > 1 (κ > 0.33 Å^?1). The SiS expressions combine the overall extra‐electrostatic potential energy of the smaller ion, as central ion—Ψ_a>b(κ), with that of the larger ion, as central ion—Ψ_b>a(κ); a and b are, respectively, the counterion and co‐ion distances of closest approach. Ψ_a>b and Ψ_b>a are derived from the L‐PB equation, which appears to conflict with their being effective up to moderate electrolyte concentrations (≈1 m). However, the L‐PB equation can be valid up to κ ≥ 1.3 Å^?1 if one abandons the 1/κ criterion for its effectiveness and, instead, use, as criterion, the mean‐field electrostatic interaction potential of the central ion with its ion cloud, at a radial distance dividing the cloud charge into two equal parts. The DH theory's failure is, thus, not because of using the L‐PB equation; the lethal approximation is assigning a single size to the positive and negative ions. © 2015 Wiley Periodicals, Inc.