Density Functional Theory Description Research Articles

Performance of range-separated long-range SOPPA short-range density functional theory method for vertical excitation energies.

In this paper, benchmark results are presented on the calculation of vertical electronic excitation energies using a long-range second-order polarization propagator approximation (SOPPA) description with a short-range density functional theory description based on the Perdew-Burke-Ernzerhof (PBE) functional. The excitation energies are investigated for 132 singlet states and 71 triplet states across 28 medium-sized organic molecules. The results show that overall SOPPA-srPBE always performs better than PBE and that SOPPA-srPBE performs better than SOPPA for singlet states, but slightly worse than SOPPA for triplet states when CC3 results are the reference values.

Origin of Stability and Activity Enhancements in Pt-based Oxygen Reduction Reaction Catalysts via Defect-Mediated Dopant Adsorption.

Platinum alloys are highly efficient electrocatalysts for the oxygen reduction reaction (ORR) in acidic conditions. However, these alloys are susceptible to metal loss through leaching and degradation, leading to reduced catalyst stability and activity. Recently, it has been shown that doping with oxophilic elements can significantly alleviate these problems, with a prominent example being Mo-doped Pt alloys. Here, to achieve atomic scale understanding of the exceptional activity and stability of these alloys, we present a detailed density functional theory description of the dopants' structures and impact on electrocatalyst properties. Beginning with the Mo/Pt system, we demonstrate that Mo can be stabilized in the form of low-dimensional oxyhydroxide moieties on Pt defects. The resulting structures enhance stability and activity via distinct physical processes, with the Mo moieties both directly inhibiting Pt dissolution at defects and indirectly enhancing ORR activity by generation of strain fields on surrounding Pt terraces. We then generalize these analyses to other metal dopant elements, and we demonstrate that similar low-dimensional oxyhydroxide structures control the electrocatalytic properties through an intricate interplay of the structures' acid stability, intrinsic activity for the ORR, and ability to induce ORR-promoting strain fields on Pt.

Origin of Stability and Activity Enhancements in Pt‐based Oxygen Reduction Reaction Catalysts via Defect‐Mediated Dopant Adsorption

AbstractPlatinum alloys are highly efficient electrocatalysts for the oxygen reduction reaction (ORR) in acidic conditions. However, these alloys are susceptible to metal loss through leaching and degradation, leading to reduced catalyst stability and activity. Recently, it has been shown that doping with oxophilic elements can significantly alleviate these problems, with a prominent example being Mo‐doped Pt alloys. Here, to achieve atomic scale understanding of the exceptional activity and stability of these alloys, we present a detailed density functional theory description of the dopants’ structures and impact on electrocatalyst properties. Beginning with the Mo/Pt system, we demonstrate that Mo can be stabilized in the form of low‐dimensional oxyhydroxide moieties on Pt defects. The resulting structures enhance stability and activity via distinct physical processes, with the Mo moieties both directly inhibiting Pt dissolution at defects and indirectly enhancing ORR activity by generation of strain fields on surrounding Pt terraces. We then generalize these analyses to other metal dopant elements, and we demonstrate that similar low‐dimensional oxyhydroxide structures control the electrocatalytic properties through an intricate interplay of the structures’ acid stability, intrinsic activity for the ORR, and ability to induce ORR‐promoting strain fields on Pt.

What can lattice DFT teach us about real-space DFT?

In this paper we establish a connection between density functional theory (DFT) for lattice models and common real-space DFT. We consider the lattice DFT description of a two-level model subject to generic interactions in Mermin's DFT formulation in the grand canonical ensemble at finite temperature. The case of only density-density and Hund's rule interaction studied in earlier work is shown to be equivalent to an exact-exchange description of DFT in the real-space picture. In addition, we also include the so-called pair-hopping interaction which can be treated analytically and, crucially, leads to non-integer occupations of the Kohn-Sham (KS) levels even in the limit of zero temperature. Treating the hydrogen molecule in a minimal basis is shown to be equivalent to our two-level lattice DFT model. By means of the fractional occupations of the KS orbitals (which, in this case, are identical to the many-body ones) we reproduce the results of full configuration interaction, even in the dissociation limit and without breaking the spin symmetry. Beyond the minimal basis, we embed our HOMO-LUMO model into a standard DFT calculation and, again, obtain results in overall good agreement with exact ones without the need of breaking the spin symmetry.

Density Functional Theory Investigation on Boron-Subphthalocyanine

In this article a Density Functional Theory (DFT) description of derivatives of boron-subphthalocyanines (SubPc) is investigated. Investigated structures are peripherally functionalized derivatives

A Full Quantum Mechanical Approach Assessing the Chemical and Electromagnetic Effect in TERS.

Tip-enhanced Raman spectroscopy (TERS) is a valuable method for surface analysis with nanometer to angstrom-scale resolution; however, the accurate simulation of particular TERS signals remains a computational challenge. We approach this challenge by combining the two main contributors to plasmon-enhanced Raman spectroscopy and to the high resolution in TERS, in particular, the electromagnetic and the chemical effect, into one quantum mechanical simulation. The electromagnetic effect describes the sample's interaction with the strong, highly localized, and inhomogeneous electric fields associated with the plasmonic tip and is typically the thematic focus for most mechanistic studies. On the other hand, the chemical effect covers the different responses to the extremely close-range and highly position-sensitive chemical interaction between the apex tip atom(s) and the sample, and, as we could show in previous works, plays an often underestimated role. Starting from a (time-dependent) density functional theory description of the chemical model system, comprised of a tin(II) phthalocyanine sample molecule and a single silver atom as the tip, we introduce the electromagnetic effect through a series of static point charges that recreate the electric field in the vicinity of the plasmonic Ag nanoparticle. By scanning the tip over the molecule along a 3D grid, we can investigate the system's Raman response on each position for nonresonant and resonant illumination. Simulating both effects on their own already hints at the achievable signal enhancement and resolution, but the combination of both creates even stronger evidence that TERS is capable of resolving submolecular features.

Impacts of polarizable continuum models on the SCF convergence and DFT delocalization error of large molecules.

Advances in algorithm developments have enabled density functional theory (DFT) description of large molecules, including whole proteins, but the self-consistent field (SCF) convergence issues often hamper practical applications. The conductor-like polarizable continuum model (CPCM), although initially introduced as an implicit solvent model, was reported to improve SCF convergence in some large molecules. However, the underlying mechanisms and applicable use cases were unclear. We investigated the impacts of CPCM on the SCF convergence of 25 peptides and found that the CPCM only effectively reduced the SCF iterations for molecules with charge separations (e.g., the zwitterionic form of peptides) but had little effect on non-charge-separated molecules. We observed that CPCM increased the HOMO-LUMO gap of both the zwitterionic and non-charge-separated molecules, but only the charge-separated molecules suffered from the vanishing HOMO-LUMO gap problem in the gas phase, which is the origin of the convergence issue. We revealed CPCM's gap-opening mechanism as the selective stabilization/destabilization of molecular orbitals (MOs) based on their local electrostatic environment. Compared to level-shifting, a traditional SCF improvement technique, CPCM has superior performance because the stabilization/destabilization of MOs is consistent through SCF iterations. Finally, we examined CPCM's impacts on DFT density delocalization error (DDE) when used as an SCF accelerator. CPCM can mitigate the DDE and reproduce the density-derived properties (e.g., dipole moments) matching high-level methods when a very low dielectric constant is used but tends to over-localize the electron density at higher dielectric constants.

Density functional thermodynamic description of spin, phonon and displacement degrees of freedom in antiferromagnetic-to-paramagnetic phase transition in YNiO3

This work demonstrates a direct density functional description of the finite-temperature thermodynamic properties of solids exhibiting phase transitions through positional and spin symmetry breaking degrees of freedom. A classic example addressed here is the rare-earth (R) nickelates RNiO3 where the ground state is characterized by crystallographic and magnetic (e.g., antiferromagnetic) long-range order (LRO), whereas the higher temperature paramagnetic phase manifests a range of local spin and positional symmetry breaking motifs with short-range order (SRO). Unlike time-dependent simulations of spin and positional degrees of freedom, in the present work, phases are described via a superposition of static configurations constructed by populating a periodic base lattice supercell allowing for the formation of energy lowing distribution of positional and spin local motifs. The thermal populations of the configurations in such a superposition phase are obtained from the energy-minimized Density Functional Theory (DFT)-calculated partition functions at different temperatures. This approach offers flexible inclusion of different physical contributions to the free energy, such as elastic, electronic and phonon free energies, all obtained from the same underlying DFT total energy calculations of periodic structures. The thermodynamic and magnetic properties of both LRO and SRO crystallographic and spin phases, including antiferromagnetic (AFM) to paramagnetic (PM) Néel phase transition in YNiO3 are studied. Including spin and phonon contributions, we find a DFT-calculated Néel temperature to be 144 K in satisfactory agreement with the experimental value of 145 K; whereas omitting the phonon contribution, one obtains a Néel temperature of 81 K. We present phonon contributions to the DFT-calculated temperature-dependent SRO, heat capacities, and the polymorphous distribution of nonzero local magnetic moments in the PM phase. This approach thus extends to finite temperatures the symmetry-broken DFT description of both the AFM and PM phases, demonstrating that a thermodynamic superposition approach based on symmetry broken configurations evaluated by a mean-field like DFT is sufficient to obtain a consistent description of the thermal physics of the AFM, PM phases and their interconversion in 3d oxides illustrated by YNiO3.

Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory.

An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40-110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.

Density Functional Theory Description of Paramagnetic Hexagonal Close-Packed Iron.

The hexagonal close-packed (hcp) phase of iron is unstable under ambient conditions. The limited amount of existing experimental data for this system has been obtained by extrapolating the parameters of hcp Fe–Mn alloys to pure Fe. On the theory side, most density functional theory (DFT) studies on hcp Fe have considered non-magnetic or ferromagnetic states, both having limited relevance in view of the current understanding of the system. Here, we investigate the equilibrium properties of paramagnetic hcp Fe using DFT modelling in combination with alloy theory. We show that the theoretical equilibrium and the equation of state of hcp Fe become consistent with the experimental values when the magnetic disorder is properly accounted for. Longitudinal spin fluctuation effects further improve the theoretical description. The present study provides useful data on hcp Fe at ambient and hydrostatic pressure conditions, contributing largely to the development of accurate thermodynamic modelling of Fe-based alloys.

Dislocation-Limited Thermal Conductivity in LiF: Revisiting Perturbative Models

We revisit models to describe phonon–dislocation interactions and resulting dislocation-limited thermal conductivity (k), particularly as applied to describe the temperature-dependent k behavior of LiF with significant dislocation densities. Coupling semiempirical models of phonon scattering from dislocation strain fields provided by Klemens and Carruthers with density functional theory description of the phonons and input parameters, we find that both models significantly overpredict the measured k of LiF, as found previously. However, more direct application of the quantum perturbation theory description, from which the models were derived, gives significantly stronger phonon–dislocation scattering and strongly underpredicts the measured k data. We revisit the derivation of phonon–dislocation–strain field scattering and provide numerical details regarding its implementation. This work demonstrates that quantum perturbative calculations, now accessible to modern computational architectures, may provide a reasonable description of dislocation-limited k in materials as governed by phonon–strain field interactions provided that questions regarding the relevant strain field range can be resolved.

Global Performance of Covariant Density Functional Theory in Description of Charge Radii and Related Indicators

A short review of existing efforts to understand charge radii and related indicators on a global scale within the covariant density functional theory (CDFT) is presented. Using major classes of covariant energy density functionals (CEDFs), the global accuracy of the description of experimental absolute and differential charge radii within the CDFT framework has been established. This assessment is supplemented by an evaluation of theoretical statistical and systematic uncertainties in the description of charge radii. New results on the accuracy of the description of differential charge radii in deformed actinides and light superheavy nuclei are presented and the role of octupole deformation in their reproduction is evaluated. Novel mechanisms leading to odd-even staggering in charge radii are discussed. Finally, we analyze the role of self-consistency effects in an accurate description of differential charge radii.

Excited state dynamics in monolayer black phosphorus revisited: Accounting for many-body effects.

The dynamics of electron-hole recombination in pristine and defect-containing monolayer black phosphorus (ML-BP) has been studied computationally by several groups relying on the one-particle description of electronic excited states. Our recent developments enabled a more sophisticated and accurate treatment of excited states dynamics in systems with pronounced excitonic effects, including 2D materials such as ML-BP. In this work, I present a comprehensive characterization of optoelectronic properties and nonadiabatic dynamics of the ground state recovery in pristine and divacancy-containing ML-BP, relying on the linear-response time-dependent density functional theory description of excited states combined with several trajectory surface hopping methodologies and decoherence correction schemes. This work presents a revision and new implementation of the decoherence-induced surface hopping methodology. Several popular algorithms for nonadiabatic dynamics algorithms are assessed. The kinetics of nonradiative relaxation of lower-lying excited states in ML-BP systems is revised considering the new methodological developments. A general mechanism that explains the sensitivity of the nonradiative dynamics to the presence of divacancy defect in ML-BP is proposed. According to this mechanism, the excited states' relaxation may be inhibited by the presence of energetically close higher-energy states if electronic decoherence is present in the system.

Density Functional Theory and Machine Learning Description and Prediction of Oxygen Atom Chemisorption on Platinum Surfaces and Nanoparticles.

Elucidating chemical interactions between catalyst surfaces and adsorbates is crucial for understanding surface chemical reactivity. Herein, interactions between O atoms and Pt surfaces and nanoparticles are described as a linear combination of the properties of pristine surfaces and isolated nanoparticles. The energetics of O chemisorption onto Pt surfaces were described using only two descriptors related to surface geometrical features. The relatively high coefficient of determination and low mean absolute error between the density functional theory-calculated and predicted O binding energies indicate good accuracy of the model. For Pt nanoparticles, O binding is described by the geometrical features and electronic properties of isolated nanoparticles. Using a linear combination of five descriptors and accounting for nanoparticle size effects and adsorption site types, the O binding energy was estimated with a higher accuracy than with conventional single-descriptor models. Finally, these five descriptors were used in a general model that decomposes O binding energetics on Pt surfaces and nanoparticles. Good correlation was achieved between the calculated and predicted O binding energies, and model validation confirmed its accuracy. This is the first model that considers the nanoparticle size effect and all possible adsorption sites on Pt nanoparticles and surfaces.

A discrete interaction model/quantum mechanical method for simulating surface-enhanced Raman spectroscopy in solution.

Since surface-enhanced Raman scattering (SERS) is of considerable interest for sensing applications in aqueous solution, the role that solvent plays in the spectroscopy must be understood. However, these efforts are hindered due to a lack of simulation approaches for modeling solvent effects in SERS. In this work, we present an atomistic electrodynamics-quantum mechanical method to simulate SERS in aqueous solution based on the discrete interaction model/quantum mechanical method. This method combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule and a polarizable embedding method for the solvent. The explicit treatment of solvent molecules and nanoparticles results in a large number of polarizable dipoles that need to be considered. To reduce the computational cost, a simple cut-off based approach has been implemented to limit the number of dipoles that need to be treated without sacrificing accuracy. As a test of this method, we have studied how solvent affects the SERS of pyridine in the junction between two nanoparticles in aqueous solution. We find that the solvent leads to an enhanced SERS due to an increased local field at the position of the pyridine. We further demonstrate the importance of both image field and local field effects in determining the enhancements and the spectral signatures. Our results show the importance of describing the local environment due to the solvent molecules when modeling SERS.

Impact of Topological Edge Defects on Spin Transport Properties of Zigzag Graphene Nanoribbons

Herein, the spin‐dependent transport properties of a zigzag graphene nanoribbon (zGNR) with edges decorated with a fluoranthene group are studied. Atomically perfect zigzag edge, including phenyl‐edge functionalization, was synthesized by Ruffieux et al. in a bottom‐up chemical technique. By performing nearest‐neighbor tight‐binding model in combination with Landauer formalism and Green's function approach, as well as considering Coulomb electronic interaction computed both with density functional calculations and mean‐field approximation of the Hubbard model, the magnetic and spin‐resolved transmissions are studied. Both the model Hamiltonian and density functional theory (DFT) descriptions yield very similar results. Importantly, by generating a special supercell, three different antiferromagnetic alignments for phenyl‐edge zGNR have been calculated, which was not developed in previous studies. The results show that by adding pentagon rings on both sides of the zGNR, the conductance loses its step‐like behavior. Our structure of interest is a semiconductor with a transport gap of 0.56 eV. This kind of defective structure will enable the spin‐feature characteristic, such as spin filtering, and add the spin degree of freedom to graphene‐based logic devices.

Improving the Description of Interlayer Bonding in TiS2 by Density Functional Theory

We investigate energetic and electronic properties of TiS2 , an archetypal van der Waals (vdW) material, from first principles, in the framework of the Density Functional Theory (DFT). In this system a recent experimental study showed a puzzling discrepancy between the distribution of the electron density in the interlayer region obtained by X-ray diffraction data and that computed by DFT, even adopting DFT functionals that should properly include vdW effects. Such a discrepancy could indicate a partial failure of state-of-the-art DFT approaches in describing the weak interlayer interactions of TiS2 and, possibly, of similar systems too. In order to shed light on this issue, we have carried out simulations based on different DFT functionals, basically confirming the mentioned discrepancy with the experimental findings. Subsequently, we have tried to reproduce the experimental interlayer electronic density deformation both by changing the parameters characterizing the rVV10 DFT functional (in such a way to artificially modify the strength of the vdW interactions at short or long range), and also by adopting a modified pseudopotential for Sulfur atoms, involving d orbitals. The latter approach turns out to be particularly promising. In fact, using this novel, more flexible pseudopotential, we obtain not only an electronic density deformation closer to the experimental profile, but also a better estimate of the interlayer binding energy. Interestingly, this improvement in the theoretical DFT description is not limited to TiS2 but also applies to other similar layered systems involving S atoms, such as TaS2 , HfS2 , and MoS2 .

Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water.

Experiment directed simulation (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of EDS to ab initio molecular dynamics (AIMD) simulation based on electronic density functional theory (DFT), the AIMD simulations of water were biased to reproduce its experimentally derived solvation structure. In particular, by solely biasing the O-O pair correlation function, other structural and dynamical properties that were not biased were improved. In this work, the hypothesis is tested that directly biasing the O-H pair correlation (and hence the H-O···H hydrogen bonding) will provide an even better improvement of DFT-based water properties in AIMD simulations. The logic behind this hypothesis is that for most electronic DFT descriptions of water the hydrogen bonding is known to be deficient due to anomalous charge transfer and over polarization in the DFT. Using recent advances to the EDS learning algorithm, we thus train a minimal bias on AIMD water that reproduces the O-H radial distribution function derived from the highly accurate MB-pol model of water. It is then confirmed that biasing the O-H pair correlation alone can lead to improved AIMD water properties, with structural and dynamical properties even closer to experiment than the previous EDS-AIMD model.

SAPT codes for calculations of intermolecular interaction energies.

Symmetry-adapted perturbation theory (SAPT) is a method for calculations of intermolecular (noncovalent) interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.

Shallow impurity band in ZrNiSn

ZrNiSn and related half Heusler compounds are candidate materials for efficient thermoelectric energy conversion with a reported thermoelectric figure-of-merit of n-type ZrNiSn exceeding unity. Progress on p-type materials has been more limited, which has been attributed to the presence of an impurity band, possibly related to Ni interstitials in a nominally vacant 4d position. The specific energetic position of this band, however, has not been resolved. Here, we report the results of a concerted theory-experiment investigation for a nominally undoped ZrNiSn, based on the electrical resistivity, the Hall coefficient, the Seebeck coefficient, and the Nernst coefficient, measured in a temperature range from 80 to 420 K. The results are analyzed with a semianalytical model combining a density functional theory (DFT) description for ideal ZrNiSn, with a simple analytical correction for the impurity band. The model provides a good quantitative agreement with experiment, describing all salient features in the full temperature span for the Hall, conductivity, and Seebeck measurements, while also reproducing key trends in the Nernst results. This comparison pinpoints the impurity band edge to 40 meV below the conduction band edge, which agrees well with a separate DFT study of a supercell containing Ni interstitials. Moreover, we corroborate our result with a separate study of the ZrNiSn0.9Pb0.1 sample showing similar agreement with an impurity band edge shifted to 32 meV below the conduction band.