Plane-wave Density Functional Theory Research Articles

BTEX adsorption on TiO2 anatase and rutile surfaces: DFT functionals.

Benzene, toluene, ethylbenzene, and xylenes are volatile hydrocarbons known as BTEX, which present concerns about environmental problems. Density functional theory (DFT) functionals were used for the BTEX gas phase adsorption on TiO2 (110) of rutile and (101) of anatase surfaces. Dispersion terms have shown the importance to treat weak interactions and were used to study these adsorptions using plane wave DFT calculations. All BTEX molecules have the same trend for the adsorption on rutile and anatase surfaces. The inclusion of dispersion terms has a significant contribution for the interaction energy. Density of states results suggest the hybridization between the d state of pentacoordinated titanium atoms (Ti5C) and carbon p states of benzene. The adsorption energy values indicate an effective interaction between the BTEX and surfaces, mainly due to the aromatic π interaction, which is present in all adsorbates. However, for p-xylene the methyl hydrogen directs the second major influence. Graphical abstract Charge difference showing the system with the smallest interaction and the one with the largest interaction.

A full additive QM/MM scheme for the computation of molecular crystals with extension to many-body expansions.

An additive quantum mechanics/molecular mechanics (QM/MM) model for the theoretical investigation of molecular crystals (AC-QM/MM) is presented. At the one-body level, a single molecule is chosen as the QM region. The MM region around it consists of a finite cluster of explicit MM atoms, represented by point charges and Lennard-Jones potentials, with additional background charges to mimic periodic electrostatics. Cluster charges are QM-derived and calculated self-consistently to ensure a polarizable embedding. We have also considered the extension to many-body QM corrections, calculating the interactions of a central molecule to neighboring units in the crystal. Full gradient expressions have been derived, also including symmetry information. The scheme allows for the calculation of molecular properties as well as unconstrained optimizations of the molecular geometry and cell parameters with respect to the lattice energy. Benchmarking the approach with the X23 reference set confirms the convergence pattern of the many-body extension although a comparison to plane-wave density functional theory reveals a systematic overestimation of cohesive energies by 6-16 kJ mol-1. While the scheme primarily aims to provide an inexpensive and flexible way to model a molecule in a crystal environment, it can also be used to reach highly accurate cohesive energies by the straightforward application of wave function correlated approaches. Calculations with local coupled cluster with singles, doubles, and perturbative triples, albeit limited to numerical gradients, show an impressive agreement with experimental estimates for small molecular crystals.

Modeling halogen bonding with planewave density functional theory: Accuracy and challenges.

Inspired by the recent interest of halogen bonding (XB) in the solid state, we detail a comprehensive benchmark study of planewave DFT geometry and interaction energy of lone-pair (LP) type and aromatic (AR) type halogen bonded complexes, using PAW and USPP pseudopotentials. For LP-type XB dimers, PBE-PAW generally agrees with PBE/aug-cc-pVQZ(-pp) geometries but significantly overbinds compared to CCSD(T)/aug-cc-pVQZ(-pp). Grimme's D3 dispersion corrections to PBE-PAW gives better agreement to the MP2/cc-pVTZ(-pp) results for AR-type dimers. For interaction energies, PBE-PAW may overbind or underbind for weaker XBs but clearly overbinds for stronger XBs. D3 dispersion corrections exacerbate the overbinding problem for LP-type complexes but significantly improves agreement for AR-type complexes compared to CCSD(T)/CBS. Finally, for periodic XB crystals, planewave PBE methods slightly underestimate the XB lengths by 0.03 to 0.05 Å. © 2019 Wiley Periodicals, Inc.

Covalent bonding versus total energy: On the attainability of certain predicted low-energy carbon allotropes

On the basis of first-principles calculations, we contrast the favorable total energies of certain carbon allotropes with their uncompetitive bonding strengths as compared with those of graphite or diamond. Clearly, our tentative approach draws from ideas of organic synthesis and retrosynthesis by focusing at those bonds that have to be formed and stabilized or cleaved for preparing a certain C-based material. In particular, the covalent C–C bonds of the carbon allotropes are studied by extracting their crystal orbital Hamilton population (COHP) energies from plane-wave density-functional theory because this quantum-mechanical measure of covalent bond strength allows for a simple, yet numerically precise allotropic ranking including graphite and diamond. While many of the lowest-energy allotropes feature plainly imperfect bonding, we found a single one (topology 32.4T203 in SACADA) with both strong bonding and favorable total energy at the same time. To help experimentalists in distinguishing this very allotrope from all the other predicted carbon allotropes, we propose IR spectroscopy and predict certain vibrational fingerprints such as to identify 32.4T203 in exploratory syntheses.

DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components.

Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems.

The Glycine Zwitterion is Stabilized by Four Water Molecules

We performed plane-wave density functional theory calculations to survey the potential energy surface of neutral glycine (GlyNE) and its zwitterion (GlyZW) solvated by up to four water molecules. Our previous conformation study of Gly suggested the inadequacy of the commonly used local basis function sets in dealing with a high-energy isomer, such as Gly. We find the potential energy surface of GlyNE and GlyZW to be smoother than previously thought and to be without many local minima. Two water molecules can create a local minimum around GlyZW. With three water molecules, the energy difference between GlyNE and GlyZW is reduced to a mere 27 meV with an energy barrier of 115 meV from GlyNE. GlyZW becomes energetically more stable by 122 meV when solvated by four water molecules. Water molecules become catalysts in the tautomerization and sometimes engage in a switching transfer of a proton over the water bridge. Our results are consistent with experimental findings that the effective hydration number of Gly is 3 ~ 4.

Eu3+ doped (Li, Na, K) LaMgWO6 red emission phosphors: An example to rational design with theoretical and experimental investigation

Various theoretical methods were comprehensively applied in (Li, Na, K) LaMgWO6: Eu3+ phosphors to achieve the rational design of phosphors. The detailed structural characteristics were analyzed by using geometric optimization and Rietveld analysis for the first time. The plane-wave density functional theory (DFT) was used for all electronic structure, electronic distribution, and phonon dispersion calculations. The evolution of the octahedral tilting in the (Li, Na, K) LaMgWO6 crystal structures was studied in detail. The relationship between crystal structure, environmental factors, Judd–Ofelt intensity parameters and fluorescence properties were analyzed. Combined with experimental results and theoretical calculations, the detailed luminescence process is deduced starting from the different ionic radius of Li+, Na+, and K+. Notably, the redshift of CTB can be ascribed to the value variation of environmental factors, which can represent the ionic radius, coordination number, covalency, and polyhedral tilting to qualify comparison and even quantify analysis.

ODE integration schemes for plane-wave real-time time-dependent density functional theory.

Integration schemes are implemented with a plane-wave basis in the context of real-time time-dependent density functional theory. Crank-Nicolson methods and three classes of explicit integration schemes are explored and assessed in terms of their accuracy and stability properties. Within the framework of plane-wave density functional theory, a graphene monolayer system is used to investigate the error, stability, and serial computational cost of these methods. The results indicate that Adams-Bashforth and Adams-Bashforth-Moulton methods of orders 4 and 5 outperform commonly used methods, including Crank-Nicolson and Runge-Kutta methods, in simulations where a relatively low error is desired. Parallel runtime scaling of the most competitive serial methods is presented, further demonstrating that the Adams-Bashforth and Adams-Bashforth-Moulton methods are efficient methods for propagating the time-dependent Kohn-Sham equations. Our integration schemes are implemented as an extension to the Quantum ESPRESSO code.

Exploring the chemical nature of super-heavy main-group elements by means of efficient plane-wave density-functional theory.

The design, implementation, and evaluation of a computationally efficient approach for exploring the chemical nature and bulk properties of the super-heavy main-group elements (SHEs) Cn-Og with nuclear charges of Z = 112-118 is described. The approach combines plane-wave density-functional theory (DFT) based on a newly devised set of projector-augmented wave potentials (PAWs) with the D3 dispersion correction, whose parameter-space is extended for this purpose. Regarding both, the fitting of the PAWs as well as the calculation of the D3 parameters, it is shown that the peculiar electronic structure of the SHEs with strong relativistic effects makes it necessary to adapt the well established computational protocols. Eventually, the methodology is tested employing various common functionals (PW91, PBE, PBE-D3, PBE0-D3, PBEsol and SCAN) by comparison to experimental and high-level results for the bulk of Cn and Og, as well as by calculating adsorption energies of Cn-Og on a gold surface and comparing these to the lighter congeners Hg-Rn as well as experimentally derived data. These tests establish that our approach provides a consistent and accurate description of the reactivity of the SHEs and is largely in excellent agreement with experimental and high-level references, and moreover underline the great relevance of dispersion interactions, as well the game-changing impact of spin-orbit coupling on SHE reactivity. Ultimately, the conducted calculations provide novel insights into the chemical behavior and nature of the SHEs, showcase the breakdown of periodic trends in the seventh period, and allow us to revisit and confirm an empirical relation between adsorption on gold and the cohesive energy.

Voltage effects on the stability of Pd ensembles in Pd-Au/Au(111) surface alloys.

The catalytic performance of multimetallic electrodes is often attributed to a beneficial combination of ligand, strain, and ensemble effects. Understanding the influence of the electrochemical environment on the stability of the alloy surface structure is thus a crucial component to the design of highly active and durable electrocatalysts. In this work, we study the effects of an applied voltage to electrocatalytic Pd-Au/Au(111) surface alloys in contact with a model continuum electrolyte. Using planewave density functional theory, two-dimensional cluster expansions are parameterized and used to simulate dilute Pd-Au surface alloys under electrochemical conditions via Metropolis Monte Carlo within an extended canonical ensemble. While Pd monomers are stable at all potentials considered, different extents of surface electrification are observed to promote the formation of Pd dimers and trimers, as well as clusters of Pd monomers. We find that the relative proportion of monomer, dimer, and trimer surface fractions is in good agreement with in situ scanning tunneling microscopy measurements. The further development and refinement of the approaches described herein may serve as a useful aid in the development of next-generation electrocatalysts.

Probing O-H Bonding through Proton Detected 1H-17O Double Resonance Solid-State NMR Spectroscopy.

The ubiquity of oxygen in organic, inorganic, and biological systems has stimulated the application and development of 17O solid-state NMR spectroscopy as a probe of molecular structure and dynamics. Unfortunately, 17O solid-state NMR experiments are often hindered by a combination of broad NMR signals and low sensitivity. Here, it is demonstrated that fast MAS and proton detection with the D-RINEPT pulse sequence can be generally applied to enhance the sensitivity and resolution of 17O solid-state NMR experiments. Complete 2D 17O → 1H D-RINEPT correlation NMR spectra were typically obtained in less than 10 h from less than 10 mg of material, with low to moderate 17O enrichment (less than 20%). Two-dimensional 1H-17O correlation solid-state NMR spectra allow overlapping oxygen sites to be resolved on the basis of proton chemical shifts or by varying the mixing time used for 1H-17O magnetization transfer. In addition, J-resolved or separated local field (SLF) blocks can be incorporated into the D-RINEPT pulse sequence to allow the direct measurement of one-bond 1H-17O scalar coupling constants (1 JOH) or 1H-17O dipolar couplings ( DOH), respectively, the latter of which can be used to infer 1H-17O bond lengths. 1 JOH and DOH calculated from plane-wave density functional theory (DFT) show very good agreement with experimental values. Therefore, the 2D 1H-17O correlation experiments, 1H-17O scalar and dipolar couplings, and plane-wave DFT calculations provide a method to precisely determine proton positions relative to oxygen atoms. This capability opens new opportunities to probe interactions between oxygen and hydrogen in a variety of chemical systems.

First-Principles Calculation of Third-Order Elastic Constants via Numerical Differentiation of the Second Piola-Kirchhoff Stress Tensor.

A general method is presented to calculate from first principles the full set of third-order elastic constants of a material of arbitrary symmetry. The method here illustrated relies on a plane-wave density functional theory scheme to calculate the Cauchy stress and the numerical differentiation of the second Piola-Kirchhoff stress tensor to evaluate the elastic constants. It is shown that finite difference formulas lead to a cancellation of the finite basis set errors, whereas simple solutions are proposed to eliminate numerical errors arising from the use of Fourier interpolation techniques. Applications to diamond, silicon, aluminum, magnesium, graphene, and a graphane conformer give results in excellent agreement with both experiments and previous calculations based on fitting energy density curves, demonstrating both the accuracy and generality of our new methodology to investigate nonlinear elastic behaviors of materials.

Theoretical investigations of nitrogen doping on Co3O4 for water dissociation catalytically activity

We report the results of theoretical investigations of nitrogen doping on Co3O4 (100) bulk by means of the plane-wave periodic density functional theory (DFT) calculations combined with the Hubbard-U approach and statistical thermodynamics.Using accurate DFT+U calculations, we have shown that bulk Co ions denote charges in value 0.017 – 0.57e. For further water adsorption process studies was selected structures with most changes in charges in Co ions: (3) structure for n = 25%, (2) structure forn = 12.5% and structure for (1) structure.

Electrochemical deposition and plane-wave periodic DFT study on Dy2O3 nanoparticles and pseudocapacitance performance of Dy2O3/conductive polymer nanocomposite film

Abstract In view of the current trend to apply green chemistry to product development and to reduce the use of toxic materials, this work is based on the optimization of a green cathodic electrodeposition method and followed heat treatment to prepare nanostructured Dy2O3, in an aqueous solution of dysprosium (III) nitrate hydrate. Prepared Dy2O3 nanoparticles have been characterized by different analysis such as FT-IR spectroscopy, thermogravimetric-differential scanning calorimetry (TG-DSC), field-emission scanning electron microscopy (FE-SEM) and X-Ray diffraction (XRD). Not only from the XRD spectrum but also using the Nelson–Riley functions, various mechanical parameters referring to Dy2O3 nanoparticles, e.g. particle size, texture coefficient, strain, and lattice constant, were determined. To understand more details about the bulk structure and electronic properties of Dy2O3, periodic plane-wave density functional theory calculations have been conducted by Quantum Espresso code. Dy2O3 exhibits an indirect band gap of 2.0 eV was computed using first-principle density functional theory (DFT) calculations. For improving electrochemical properties of the poly ortho aminophenol (POAP), we fabricated POAP/Dy2O3 films by electro-polymerization of POAP in the presence of electrosynthesized Dy2O3 with porous structure, to serve as the active electrode for electrochemical supercapacitor. In terms of electrochemical methods, galvanostatic charge–discharge experiments, cyclic voltammetry (CV) and electrochemical impedance spectroscopy are carried out in order to investigate the performance of the system. The enhanced supercapacitor behavior observed for the prepared composite film can be attributed to synergistic effect existing between Dy2O3 nanoparticles and the conductive polymer.

Sr2FeIrO4: Square-Planar Ir(II) in an Extended Oxide.

Topochemical reduction of the double-perovskite oxide Sr2FeIrO6 under dilute hydrogen leads to the formation of Sr2FeIrO4. This phase consists of ordered infinite sheets of apex-linked Fe2+O4 and Ir2+O4 squares stacked with Sr2+ cations and is the first report of Ir2+ in an extended oxide phase. Plane-wave density functional theory calculations indicate high-spin Fe2+ (d6, S = 2) and low-spin Ir2+ (d7, S = 1/2) configurations for the metals and confirm that both ions have a doubly occupied d z2 orbital, a configuration that is emerging as a consistent feature of all layered oxide phases of this type. The stability and double occupation of d z2 in the Ir2+ ions invites a somewhat unexpected analogy to the extensively studied Ir4+ ion as both ions share a common near-degenerate (d xy/ xz/ yz)5 valence configuration. On cooling below 115 K, Sr2FeIrO4 enters a magnetically ordered state in which the Ir and Fe sublattices adopt type II antiferromagnetically coupled networks which interpenetrate each other, leading to frustration in the nearest-neighbor Fe-O-Ir couplings, half of which are ferromagnetic and half antiferromagnetic. The spin frustration drives a symmetry-lowering structural distortion in which the four equivalent Ir-O and Fe-O distances of the tetragonal I4/ mmm lattice split into two mutually trans pairs in a lattice with monoclinic I112/ m symmetry. This strong magneto-lattice coupling arises from the novel local electronic configurations of the Fe2+ and Ir2+ cations and their cation-ordered arrangement in a distorted perovskite lattice.

First-principles analysis of acetonitrile reaction pathways to primary, secondary, and tertiary amines on Pd(111)

Nitrile hydrogenation using heterogeneous catalysis is an important commercial process for the production of primary, secondary, and tertiary amines. In recent years, modern experimental methods have investigated the detailed mechanism underlying the surface reactions of nitrile hydrogenation. These experimental studies provide new insights, but also raise additional questions. To help resolve these inconsistencies, modern theoretical techniques have been applied by way of periodic plane-wave Density Functional Theory (DFT) calculations to study acetonitrile adsorption and hydrogenation to primary (monoethylamine), secondary (diethylamine), and tertiary amines (triethylamine) over flat Pd surfaces. The presented theoretical analysis applies fundamental physical chemistry and reaction engineering principles to better understand surface reaction mechanisms in the kinetically-controlled regime at low surface coverages. Reaction pathways for acetonitrile hydrogenation and the most probable routes for secondary and tertiary amine formations are discussed. The presented first-principles analysis is in line with experimental observations of gas-phase acetonitrile hydrogenation on flat Pd surfaces. Key mechanistic findings are discussed in the context of larger alkane nitrile hydrogenation processes, which are ordinarily performed in the liquid phase.

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations.

We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here.

Hydrogen dynamics in solid formic acid: insights from simulations with quantum colored-noise thermostats

With an increase of computational capabilities, ab initio molecular dynamics becomes the natural choice for exploring the nuclear dynamics of solids. As based on classical mechanics, the validity of this approach is, in-principle, limited to the high-T regime, whilst low-temperature simulations require inclusion of quantum effects. The methods commonly used to account for nuclear quantum effects are based on the path-integral formalism, which become, however, particularly time consuming when high accuracy methods are used for calculating forces. Recently, new efficient alternative approaches to account for quantum nature of nuclei have been proposed, using so-called quantum thermostats. In this work, we examine the simulations performed with the quantum colored-noise thermostat introduced by Ceriotti [Phys. Rev. Lett., 103:030603, 2009]. We present the tests of portable implementation of the quantum thermostat in the ABIN program, which has been extended to periodic systems through the interface to CASTEP, a leading spectroscopy-oriented plane-wave density functional theory code. The range of applicability of quantum-thermostatted molecular dynamics simulations for the interpretation of neutron scattering data was examined and compared to classical molecular dynamics and lattice-dynamics simulations, using solid formic acid case as a test bed. We find that the approach is particularly useful for the modeling of low-temperature inelastic neutron scattering spectra as well as provides some theoretical estimate for the low-limit of the mean kinetic energy. While finding the quantum-thermostat to seriously affect the dynamic properties of the title system, we illustrate to which extent the unperturbed response can be successfully recovered.

A new six-dimensional potential energy surface for NO/Au(111)

ABSTRACTIn this contribution, we reinvestigate the interaction of nitric oxide with a gold(111) surface using plane-wave density functional theory, with particular emphasis on the role of intermode coupling. A new global representation of the potential energy surface is obtained from the ab initio data by non-linear adjustment, yielding a set of physically motivated parameters. The novel functional form improves on its parent [Marquardt et al. J. Chem. Phys. 132, 074108 (2010)] by addressing the variation of the charge transfer character of the electronic structure data, and by treating surface corrugation via translationally invariant weighting functions of lower-dimensional, high-symmetry sites. Contrary to previous studies, the adsorption minimum does not favour the hollow sites and is found at a strongly tilted orientation (circa 60) on top of a gold atom of the topmost layer. High-dimensional anharmonic vibrational analysis performed using a Lanczos-based contracted iterative procedure reveals that the low-lying excited vibrational states retain a strongly tilted orientation and remain predominantly localised at the atop site. These findings are expected to have important implications for the interpretation of recent NO scattering experiments.

Corresponding Orbitals Derived from Periodic Bloch States for Electron Transfer Calculations of Transition Metal Oxides.

An approach for modeling electron transfer in solids and at surfaces of iron-(oxyhydr)oxides and other redox active solids has been developed for electronic structure methods (i.e., plane-wave density functional theory) capable of performing calculations with periodic cells and large system sizes efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, V AB, and the electron transfer transmission factor, κel. This method is an extension of the valence bond theory electron transfer method for molecules and clusters implemented by Dupuis and others and used extensively by Rosso and co-workers in which scaled corresponding orbitals derived from the Bloch states are used to calculate the off-diagonal matrix elements H AB and S AB. A key development of the present work is the formulation of algorithms to improve the accuracy of the integration of the exact exchange integral in periodic boundary conditions. This method is demonstrated on model systems for electron small polaron transfer in iron-(oxyhydr)oxides, including bare Fe2+-Fe3+ ions, and in [Fe3+(OH2)2 (OH-)2)] nn+ chains representing the common edge-sharing Fe octahedral motif in these materials.