Previous Density Functional Theory Research Articles

Interaction between Olivine and Water Based on Density Functional Theory Calculations

The understanding of the interaction of water with mineral surfaces is fundamental for the description of solid–liquid interface reactions such as adsorption and desorption of solutes in natural and industrial systems. First-principles calculations can aid in the understanding of these interactions at the molecular level, allowing to formulate mechanistic laws of reaction. In this work, the adsorption of water (H2O) on forsteritic olivine (Mg2SiO4) is studied on the stoichiometric (100) surface using density functional theory (DFT) based electronic structure calculations to predict stability and reactivity of this surface under atmospheric and hydrothermal conditions. The structure and the energetics were analyzed for H2O interacting at different reactive surface sites comprising magnesium, silicon, and oxygen atoms showing that H2O can be adsorbed molecularly, dissociatively, or in some combination of the two. Ab initio thermodynamics was employed to extend the first-principles DFT calculations at 0 K in vacuum to atmospheric and hydrothermal conditions providing predictions of the changes in surface stability as a function of temperature and pressure. The type of interaction was analyzed through the surface energy, Bader charge analysis, and the projected density of state (PDOS) of the most stable hydroxylated surface over a wide range of temperatures. This analysis shows that the most stable configuration is the adsorption of two water molecules on two surface sites leading to the formation of a hydronium ion, H3O+, bridging two Mg1 atoms and elongating their bonds with the surrounding surface oxygen atoms and a H+ binding to a Si atom. Bader charge and density of states analyses indicate that upon interaction significant charge is lost from the surface atoms toward the water molecule groups, suggesting that the hydronium ion is chemisorbed at the Mg surface atoms resulting in reduced stability compared to the Si atom. Finally, the coverage effect up to two layers of water molecules (20 H2O/nm2) was investigated to validate our calculations. Below 6 H2O/nm2, our calculations agree with previous DFT studies available at low coverage predicting that water dissociates at the most reactive sites. At higher coverage, our energetics agree with the experimental data from calorimetric measurements and show that at the most stable hydrated surface water can both dissociate and be molecularly adsorbed, thereby creating a hydrogen-bonding network involving the first and the second water layer.

Molecular dynamics study of Zn(aβ) and Zn(aβ)2.

The aggregation of Aβ-peptide (Aβ) is widely considered to be the critical step in the pathology of Alzheimer's disease. Small, soluble Aβ oligomers have been shown to be more neurotoxic than large, insoluble aggregates and fibrils. Recent studies suggest that biometal ions, including Zn(II), may play an important role in the aggregation process. Experimentally determining the details of the binding process is complicated by the kinetic lability of zinc. To study the dynamic nature of the zinc-bound Aβ complexes and the potential mechanisms by which Zn(II) affects Aβ oligomerization we have performed atomistic molecular dynamics (MD) simulations of Zn(Aβ) and Zn(Aβ)2. The models were based on NMR data and predicted coordination environments from previous density functional theory calculations. When modeled as 4-coordinate covalently bound Zn(Aβ)n complexes (where n = 1 or 2), zinc imposes conformational changes in the surrounding Aβ residues. Moreover, zinc reduces the helix content and increases the random coil content of the full peptide. Although zinc binds at the N-terminus of Aβ, β-sheet formation is observed exclusively at the C-terminus in the Zn(Aβ) and most of the Zn(Aβ)2 complexes. Furthermore, initial binding to zinc promotes the formation of intra-chain salt-bridges, while subsequent dissociation promotes the formation of inter-chain salt-bridges. These results suggest that Zn-binding to Aβ accelerates the aggregation of Aβ by unfolding the helical structure in Aβ peptide and stabilizing the formation of vital salt-bridges within and between Aβ peptides.

First-principles phonon calculations on the lattice dynamics and thermodynamics of rare-earth intermetallics TbCu and TbZn

The structural, lattice dynamical, and thermodynamical properties of rare-earth intermetallics TbZn and TbCu with CsCl-type structure have been investigated by performing the first principles calculations, in which the density-functional theory (DFT) and density-functional perturbation theory (DFPT) have been employed within the plane-wave basis projector augmented wave (PAW) method. The quasiharmonic approximation (QHA) has been used to estimate the free energies. The phonon frequencies, thermal expansion coefficients, heat capacities, and the elastic moduli at finite temperature are presented. The calculated results for the benchmark metal Cu are in better agreement with the experimental data in comparison with the previous DFT results. Both the elastic moduli and the phonon-dispersion curves demonstrate that the anisotropy of TbZn is larger than that of TbCu. The thermal expansion coefficient of TbZn as a function of temperature is larger than that of TbCu.

Identifying the Azobenzene/Aniline Reaction Intermediate on TiO2-(110): A DFT Study

Density functional theory (DFT) calculations, both with and without dispersion corrections, have been performed to investigate the nature of the common surface reaction intermediate that has been shown to exist on TiO2(110) as a result of exposure to either azobenzene (C6H5N═NC6H5) or aniline (C6H5NH2). Our results confirm the results of a previous DFT study that dissociation of azobenzene into two adsorbed phenyl imide (C6H5N) fragments, as was originally proposed, is not energetically favorable. We also find that deprotonation of aniline to produce this surface species is even more strongly energetically disfavored. A range of alternative surface species has been considered, and while dissociation of azobenzene to form surface C6H4NH species is energetically favored, the same surface species cannot form from adsorbed aniline. On the contrary, adsorbed aniline is much the most stable surface species. Comparisons with experimental determinations of the local adsorption site, the Ti–N bond length, the molecular orientation, and the associated C 1s and N 1s photoelectron core level shifts are all consistent with the DFT results for adsorbed aniline and are inconsistent with other adsorbed species considered. Possible mechanisms for the hydrogenation of azobenzene required to produce this surface species are discussed.

ReaxFF Reactive Force Field Study of the Dissociation of Water on Titania Surfaces

We studied the adsorption and dissociation of water at 300 K on the following TiO2 surfaces: anatase (101), (100), (112), (001), and rutile (110) at various water coverages, using a recently developed ReaxFF reactive force field. The molecular and dissociative adsorption configurations predicted by ReaxFF for various water coverages agree with previous theoretical studies and experiment. ReaxFF predicts a complex distribution of water on these surfaces depending on an intricate balance between the spacing of the adsorption sites (under-coordinated Ti and O surface atoms), water–surface interactions, and water–water interactions. Using molecular dynamics simulations to quantify water dissociation over the TiO2 surfaces at various water coverages, we find that the extent of water dissociation predicted by the ReaxFF reactive force field is in general agreement with previous density-functional theory studies and experiments. We demonstrate a correlation between the extent of water dissociation on different T...

Molecular dynamics study of one dimensional nanoscale Si/SiO2 interfaces

Classical molecular dynamics (CMD) simulations were carried out to optimizesilicon oxide interfaces with (100), (111), and (110) silicon surfaces. A three body interatomic potential (modified version of Stillinger-Weber) was used to model the interactions between the species. The resulting overall stress energies and average bond lengths and angles from CDM calculations were compared to previous density functional theory(DFT) calculations. The comparison yields similar trends in the stress energy and shows a good agreement for the bond lengths and angles. Perspectives for large scale molecular dynamics simulations on these systems are discussed.

Evolution of the structure and electronic properties of neutral and anion [formula omitted] (n = 1–7, μ = 0, −1) clusters: A comprehensive analysis

The structural evolution, stabilities and electronic properties of neutral and anionic FeSnμ (n=1–7, μ=0, −1) clusters have been investigated with the aid of previous photoelectron spectroscopy (PES) and density functional theory. For each sized iron–sulfur cluster, the low-lying isomers are generated using Saunders “kick” global optimization method. The theoretical vertical and adiabatic electron detachment energies (VDEs and ADEs) were compared with the experimental values to corroborate the ground state structures. The results indicate that the combination of photoelectron spectroscopy experiments and density functional theory calculation is powerful for obtaining the accurate electronic structures. By calculating the binding energies, fragmentation energies and second difference energies, we found FeS, FeS4, FeS2- and FeS4- clusters have the relative stronger stability. Furthermore, the two equal maxima of HOMO–LUMO gaps (2.81eV) for the most stable configurations appear at FeS and FeS2-. Additionally, to probe into the electron transfer information and redistribution of electron density induced by bonding, the natural population analysis (NPA) and electron density difference are investigated and discussed.

Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

Stability and equation of state of post-aragonite BaCO3

At ambient conditions, witherite is the stable form of BaCO3 and has the aragonite structure with space group Pmcn. Above *10 GPa, BaCO3 adopts a post- aragonite structure with space group Pmmn. High-pressure and high-temperature synchrotron X-ray diffraction exper- iments were used to study the stability and equation of state of post-aragonite BaCO3, which remained stable to the highest experimental P-T conditions of 150 GPa and 2,000 K. We obtained a bulk modulus K0 = 88(2) GPa with K 0 = 4.8(3) and V0 = 128.1(5) A u 3 using a third-order Birch- Murnaghan fit to the 300 K experimental data. We also carried out density functional theory (DFT) calculations of enthalpy (H) of two structures of BaCO3 relative to the enthalpy of the post-aragonite phase. In agreement with previous studies and the current experiments, the calcula- tions show aragonite to post-aragonite phase transitions at *8 GPa. We also tested a potential high-pressure post-post- aragonite structure (space group C2221) featuring four-fold coordination of oxygen around carbon. In agreement with previous DFT studies, DH between the C2221 structure and post-aragonite (Pmmn) decreases with pressure, but the Pmmn structure remains energetically favorable to pressures greater than 200 GPa. We conclude that post-post-aragonite phase transformations of carbonates do not follow system- atic trends observed for post-aragonite transitions governed solely by the ionic radii of their metal cations.

Ab initio study of symmetrical tilt grain boundaries in bcc Fe: structural units, magnetic moments, interfacial bonding, local energy and local stress

We present first-principle calculations on symmetric tilt grain boundaries (GBs) in bcc Fe. Using density functional theory (DFT), we studied the structural, electronic and magnetic properties of Σ3(111) and Σ11(332) GBs formed by rotation around the [110] axis. The optimized structures, GB energies and GB excess free volumes are consistent with previous DFT and classical simulation studies. The GB configurations can be interpreted by the structural unit model as given by Nakashima and Takeuchi (2000 ISIJ 86 357). Both the GBs are composed of similar structural units of three- and five-membered rings with different densities at the interface according to the rotation angle. The interface atoms with larger atomic volumes reveal higher magnetic moments than the bulk value, while the interface atoms with shorter bond lengths have reduced magnetic moments in each GB. The charge density and local density of states reveal that the interface bonds with short bond lengths have more covalent nature, where minority-spin electrons play a dominant role as the typical nature of ferromagnetic Fe. In order to understand the structural stability of these GBs, we calculated the local energy and local stress for each atomic region using the scheme of Shiihara et al (2010 Phys. Rev. B 81 075441). In each GB, the interface atoms with larger atomic volumes and enhanced magnetic moments reveal larger local energy increase and tensile stress. The interface atoms constituting more covalent-like bonds with reduced magnetic moments have lower local energy increase, contributing to the stabilization, while compressive stress is generated at these atoms. The relative stability between the two GBs can be understood by the local energies at the structural units. The local energy and local stress analysis is a powerful tool to investigate the structural properties of GBs based on the behavior of valence electrons.

Thermodynamic stability of Co–Al–W L12γ′

Co-based superalloys in the Co–Al–W system exhibit coherent L12 Co3(Al,W) γ′ precipitates in an face-centered cubic Co γ matrix, analogous to Ni3Al in Ni-based systems. Unlike Ni3Al, however, experimental observations of Co3(Al,W) suggest that it is not a stable phase at 1173K. Here, we perform an extensive series of density functional theory (DFT) calculations of the γ′ Co3(Al,W) phase stability, including point defect energetics and finite-temperature contributions. We first confirm and extend previous DFT calculations of the metastability of L12 Co3(Al0.5W0.5) γ′ at 0K with respect to hexagonal close-packed Co, B2 CoAl and D019 Co3W using the special quasi-random structure (SQS) approach to describe the Al/W solid solution, employing several exchange/correlation functionals, structures with varying degrees of disorder, and newly developed larger SQSs. We expand the validity of this conclusion by considering the formation of antisite and vacancy point defects, predicting defect formation energies similar in magnitude to Ni3Al. However, in contrast to the Ni3Al system, we find that substituting Co on Al sites is thermodynamically favorable at 0K, consistent with experimental observation of Co excess and Al deficiency in γ′ with respect to the Co3(Al0.5W0.5) composition. Lastly, we consider vibrational, electronic and magnetic contributions to the free energy, finding that they promote the stability of γ′, making the phase thermodynamically competitive with the convex hull at elevated temperature. Surprisingly, this is due to the relatively small finite-temperature contributions of one of the γ′ decomposition products, B2 CoAl, effectively destabilizing the Co, CoAl and Co3W three-phase mixture, thus stabilizing the γ′ phase.

Refractive Index Functions of TiO2 Nanoparticles

Wavelength-dependent refractive index functions (RIFs) of (TiO2)n nanoparticles (n = 2, 8, 18, 28, or 38) have been calculated by using the data from our previous density functional theory and time-dependent density functional theory photoabsorption calculations. The results show significant blueshifts and increased anisotropy in the RIFs of the nanoparticles, when compared to experimental bulk values. On the basis of the results, we conclude that, in the case of these ultrasmall particles, the RIFs may depend notably on the shape and structure of the cluster and on the other hand the fundamental absorption characteristics do not depend much on the rather limited cluster size range. The results also support the proposition that, in light-scattering measurements, one should not use the bulk RIF to model nanosize particles, at least in the case of TiO2 particles. Our results shed some light into this computationally and experimentally very challenging area of nanoparticle properties.

First principles calculations of oxygen vacancy formation in barium-strontium-cobalt-ferrite

Perovskite-type barium-strontium-cobalt-ferrite (BSCF) is a potentially significant material in the development of electrodes for solid oxide fuel cells and electrolysis cells, primarily because of its large oxygen vacancy concentration and mobility. Using density functional theory (DFT) with the DFT + U approach, we perform first principles calculations of oxygen vacancy formation in bulk BSCF with the composition Ba0.5Sr0.5Co0.75Fe0.25O3−δ, in which a range of oxygen deficiencies (0.125 ≤ δ ≤ 0.875) is investigated. Contrary to previous DFT studies for δ = 0.125, DFT + U predicts that the non-stoichiometric structure is more stable than its stoichiometric counterpart with δ = 0, and that this originates from a significantly different atomic and electronic structure following the introduction of the Hubbard U term in the calculations. As more vacancies are created there is no tendency for ordering and the total vacancy formation energy becomes positive and increases as the oxygen deficiency increases. Using ab initio thermodynamics, the heat of formation of BSCF as a function of oxygen partial pressure and temperature is determined and the results are in broad agreement with available stoichiometry measurements.

Probing the structural, electronic and magnetic properties of multicenter Fe2S2 0/−, Fe3S4 0/− and Fe4S4 0/− clusters

The structural, electronic and magnetic properties of neutral and anion Fe2S2, Fe3S4 and Fe4S4 have been investigated with the aid of previous photoelectron spectroscopy and density functional theory calculations. Theoretical electron detachment energies (both vertical and adiabatic) of anion clusters for the lowest energy structure were computed and compared with the experimental results to verify the ground states. The optimized structures show that the ground state structures of Fe2S2(0/-), Fe3S4(0/-) and Fe4S4(0/-) favor high spin state and are similar to their structures in proteins. The electron delocalization pattern for all the clusters and the nature of bonding between Fe and S atoms were studied by analyzing molecular orbitals. Natural population analysis demonstrates that Fe atoms act as an electron donor in all clusters, and the electron density difference map clearly shows the direction of the electron flow over the whole complex. Furthermore, the investigated magnetism shows that the Fe atoms carried most of the magnetic moments, which is due mainly to the 3d state, while only very small magnetic moments are found on S atoms.

Rubidium superoxide: Ap-electron Mott insulator

Rubidium superoxide, RbO${}_{2}$, is a rare example of a solid with partially filled electronic $p$ states, which allows us to study the interplay of spin and orbital order and other effects of strong electronic correlations in a material that is quite different from the conventional $d$ or $f$ electron systems. Here we show, using a combination of density functional theory (DFT) and dynamical mean-field theory, that at room temperature RbO${}_{2}$ is indeed a paramagnetic Mott insulator. We construct the metal-insulator phase diagram as a function of temperature and Hubbard interaction parameters $U$ and $J$. Due to the strong particle-hole asymmetry of the RbO${}_{2}$ band structure, we find strong differences compared to a simple semielliptical density of states, which is often used to study the multiband Hubbard model. In agreement with our previous DFT study, we also find indications for complex spin and orbital order at low temperatures.

Monte Carlo Simulation for the Double Layer Structure of an Ionic Liquid Using a Dimer Model: A Comparison with the Density Functional Theory

Theoretical difficulties in describing the structure and thermodynamics of an ionic liquid double layer are often associated with the nonspherical shapes of ionic particles and extremely strong electrostatic interactions. The recent density functional theory predictions for the electrochemical properties of the double layer formed by a model ionic liquid wherein each cation is represented by two touching hard spheres, one positively charged and the other neutral, and each anion by a negatively charged hard spherical particle, remain untested in this strong coupling regime. We report results from a Monte Carlo simulation of this system. Because for an ionic liquid the Bjerrum length is exceedingly large, it is difficult to perform simulations under conditions of strong electrostatic coupling used in the previous density functional theory study. Results are obtained for a somewhat smaller (but still large) Bjerrum length so that reliable simulation data can be generated for a useful test of the corresponding theoretical predictions. On the whole, the density profiles predicted by the theory are quite good in comparison with the simulation data. The strong oscillations of ionic density profiles and the local electrostatic potential predicted by this theory are confirmed by simulation, although for a small electrode charge and strong electrostatic coupling, the theory predicts the contact ionic densities to be noticeably different from the Monte Carlo results. The theoretical results for the more important electrostatic potential profile at contact are given with good accuracy.

Revisited Block Copolymer/Nanoparticle Composites: Extension of Interfacial Statistical Associating Fluid Theory

The mean-field intermolecular interaction contribution in interfacial statistical associating fluid theory (iSAFT) is extended to include correlation functions, which could be evaluated from molecular simulation and the density functional theory (DFT) itself. Order–disorder transitions (ODTs) between lamellar and disordered phases for pure block copolymers and copolymer nanoparticle composites are reported, and the extended theory has been shown to give good agreement with molecular simulations and considerable improvement over the previous mean-field dispersion description. The interaction parameters at ODT are also correlated with the length of copolymers. Concentration profiles of different species are then calculated and compared quantitatively with simulation. The scaled microstructures predicted by the theory agree with simulation for all the nanoparticle size and surface chemistry investigated. Improvements over previous DFT reports have also been observed for large selective nanoparticles. iSAFT has been shown to be capable of modeling BCP from different segregation regimes using a single framework and predicting characteristic exponent for chain length dependence of lamellar spacing, in good agreement with other theories in all segregation regimes.

A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the explorationmore » of other gas-phase formation routes to complex organic molecules.« less

Theoretical calculation of the zero‐temperature isotherm and phase stability of silver up to 2 Gbar using the linear combinations of gaussian type orbitals method

AbstractA systematic procedure has been developed for generating the static lattice zero temperature isotherm of a monatomic crystalline solid to arbitrarily high compressions using the linear combinations of Gaussian type orbitals‐fitting function electronic structure method. This procedure has been used to calculate the static‐lattice equation of state and phase stability of silver (Ag) up to 2 Gbar. The resulting isotherm is compared with previous density functional theory (DFT) calculations and experimental data at low pressures and with results from Thomas–Fermi–Dirac calculations at high pressures. The stabilities of three crystal structures (face centered cubic, fcc; body centered cubic, bcc; and hexagonal close packed, hcp) were determined from energy differences calculated up to 2 Gbar. The effects of relativity and DFT model selection were tested by repeating each calculation with and without relativistic corrections using two DFT models; the local density (LDA) and generalized gradient (GGA) approximations. The phase sequence for Ag is predicted to be fcc → hcp → fcc → hcp → bcc, although the second appearance of the hcp phase is questionable due to convergence issues. © 2012 Wiley Periodicals, Inc.

Diffusion quantum Monte Carlo study of the equation of state and point defects in aluminum

The many-body diffusion quantum Monte Carlo (DMC) method with twist-averaged boundary conditions is used to calculate the ground-state equation of state and the energetics of point defects in fcc aluminum using supercells up to 1331 atoms. The DMC equilibrium lattice constant differs from experiment by 0.008 A, or 0.2%, while the cohesive energy using DMC with backflow wave functions with improved nodal surfaces differs by 27 meV. DMC-calculated defect formation and migration energies agree with available experimental data, except for the nearest-neighbor divacancy, which is found to be energetically unstable, in agreement with previous density functional theory (DFT) calculations. DMC and DFT calculations of vacancy defects are in reasonably close agreement. Self-interstitial formation energies have larger differences between DMC and DFT, of up to 0.33eV, at the tetrahedral site. We also computed formation energies of helium interstitial defects where energies differed by up to 0.34eV, also at the tetrahedral site. The close agreement with available experiments demonstrates that DMC can be used as a predictive method to obtain benchmark energetics of defects in metals.