Pseudopotential Density Functional Theory Calculations Research Articles

Improving the precision of work-function calculations within plane-wave density functional theory

Abstract Work function is a fundamental property of metals and is related to many surface-related phenomena of metals. Theoretically, it can be calculated with a metal slab supercell in density functional theory (DFT) calculations. In this paper, we discuss how the commensurability of atomic structure with the underlying fast Fourier transform (FFT) grid affects the accuracy of work function obtained from plane-wave pseudopotential DFT calculations. We show that the macroscopic average potential, which is an important property in work function calculations under the ‘bulk reference’ method, is more numerically stable when it is calculated with commensurate FFT grids than with incommensurate FFT grids. Due to the stability of the macroscopic average potential, work function calculated with commensurate FFT grids shows better convergence with respect to basis set size, vacuum length and slab thickness of a slab supercell. After we control the FFT grid commensurability issue in our work function calculations, we obtain well-converged work functions for Al, Pd, Au and Pt of (100), (110) and (111) surface orientations. For all the metals considered, the ordering of our calculated work functions of the three surface orientations agrees with experiment. Our findings reveal the importance of the FFT grid commensurability issue, which is usually neglected in practice, in obtaining accurate metal work functions, and are also meaningful to other DFT calculations which can be affected by the FFT grid commensurability issue.

Validation of Pseudopotential Calculations for the Electronic Band Gap of Solids.

Nowadays pseudopotential (PP) density functional theory calculations constitute the standard approach to tackle solid-state electronic problems. These rely on distributed PP tables that were built from all-electron atomic calculations using few popular semilocal exchange-correlation functionals, while PPs based on more modern functionals, such as meta-generalized gradient approximation and hybrid functionals, or for many-body methods, such as GW, are often not available. Because of this, employing PPs created with inconsistent exchange-correlation functionals has become a common practice. Our aim is to quantify systematically the error in the determination of the electronic band gap when cross-functional PP calculations are performed. To this end, we compare band gaps obtained with norm-conserving PPs or the projector-augmented wave method with all-electron calculations for a large data set of 473 solids. We focus, in particular, on density functionals that were designed specifically for band gap calculations. On average, the absolute error is about 0.1 eV, yielding absolute relative errors in the 5–10% range. Considering that typical errors stemming from the choice of the functional are usually larger, we conclude that the effect of choosing an inconsistent PP is rather harmless for most applications. However, we find specific cases where absolute errors can be larger than 1 eV or others where relative errors can amount to a large fraction of the band gap.

ZnO nanorods decorated with nanocrystalline (nc) Au Particles:Electronic structure and magnetic behaviours

Electronic structures and magnetic behaviours of zinc oxide nanorods (ZnO-NRs) decorated with nanocrystalline “Au”-particles (nc-Au) have been studied using different spectroscopies, superconducting quantum interference device-type magnetometer and plane wave pseudopotential density functional theory calculations. The presence of intrinsic defects viz. zinc interstitials (Zni) and/or oxygen vacancies (VO) are established using different spectroscopies measurements. Ultraviolet photoelectron spectroscopy and valence band photoemission spectroscopy suggests that the valence band density of states of O 2p - Zn 4sp hybridized states of nc-Au/ZnO-NRs is higher than pure ZnO-NRs that could be correlated with its higher ferromagnetic behaviour. An enhanced room temperature ferromagnetism has been observed when nanocrystalline (nc) gold (Au) particles are decorated on the surface of ZnO-nanorods (ZnO-NRs). This enhanced magnetic moment in nc-Au/ZnO-NRs comes from the metallic electrons of nc-Au that induces large orbital magnetic moment at the nc-Au/ZnO-NR interface. Theoretical calculations shows the enhancement of the density of states at the valence band region of ZnO with a decoration of optimum content nc-Au particles along with the increase of oxygen vacancies in nc-Au/ZnO-NRs; that further confirms the enhancement of magnetization.

Properties of Silicon Carbide Polytypes under High Pressure Influence Calculated Using DFT

Theoretical molecular dynamic simulations based on plane-wave and pseudopotential density functional theory (DFT) calculations with CASTEP code were employed to explore the pressure influence on the properties of silicon carbide polytypes. The changes in lattice and electronic structures of 2H-, 4H-, and 6H-SiC polytypes at room temperature were investigated when pressures from 10 GPa to 200 GPa were applied. It’s found that the applied pressures didn’t cause a change in the hexagonal structure of the crystals, however the structural and electronic properties clearly affected by the compression. The dependences of volume reduction (V/Vo) and lattice parameters (a and c) on pressure were obtained successfully. The lattice parameters of the polytypes and c/a ratio showed a same trend under the compression with a clear similarity between 4H and 6H. The total energy-volume and enthalpy-pressure relations were estimated. The calculated energy gaps showed a reduction in the band gap width of 4H and 6H with the pressure increase while 2H band gap increased gradually with pressure. The tendency toward decreasing the density of state (DOS) at the conduction band edge was similar among the polytypes.

Structure and bonding nature of [PbCl]+ adsorption on the kaolinite(0 0 1) surface in aqueous system

Adsorption of [PbCl]+ on the basal hydroxylated (001) surface of kaolinite in aqueous system was investigated by the plane-wave pseudopotential density functional theory calculations. Structures of the adsorption complexes including the coordination geometry and effective coordination number on the two different types of surface sites were examined, with the PbO (or Cl) bonding mechanism explored. [PbCl]+ prefers to bind with the hydroxylated kaolinite(001) surface in monodentate way on the site of Ou in “upright” hydroxyl. Complexation of [PbCl]+ in bidentate way on OuOl (oxygen of “lying” hydroxyl) site of single Al center is also probable. All adsorption complexes feature coordination number of 3–5 within the hemidirected geometry. Charge transfer occurs with ligating atoms of oxygen denoting some electrons to Pb(II) and Cl. Upon the partial density of states (PDOS) projections and Mulliken bond populations, both bonding and antibonding state filling are involved in the PbO (or Cl) interaction. Pb 6p interacting with the antibonding combination of Pb 6s and O 2p states is the dominant orbital contribution of Pb(II) with surface oxygen, while the bonding Pb 6sCl 3p state filling is primarily responsible for the PbCl interaction.

Using First-Principles Calculations to Investigate the Effect of Oxidation on Graphene Spectroscopic Properties

Molecular vibrational spectroscopy is an important method to study the atomic structure of graphene oxide. To investigate the effect of oxidation on the structural and spectroscopic properties of graphene, pseudo-potential density functional theory calculations were applied. Several models were considered, covering the most relevant functional groups that have been postulated to decorate the surface of graphene layer on carbon materials. Different arrangements of these units produced a range of vibrational spectra. The results suggested the possibility of creating and tuning graphene’s spectroscopic properties by varying the oxidation levels and the relative position of epoxy and hydroxyl functional groups on the surface. Spectra characteristics for local structures from this work shed light on the structural and vibrational properties of graphene oxide, which could be very helpful for experimental groups to further understand the structure of graphene oxide and reduce graphene oxide.

Van der Waals effects at molecule-metal interfaces

We present the results of plane-wave pseudopotential periodic density functional theory (DFT) calculations on the geometries, energetics, and electronic structure of small molecules on Au(111). The chosen molecules---benzene, ammonia and cytosine---are representative of different adsorption regimes and interaction strengths. The chosen substrate is a prototype noble-metal surface that is widely employed as a support for organic materials. We assess the relevance of van der Waals effects in the adsorption process and the accuracy of different first-principle density functionals that have been recently developed to embody such effects. We find that there is no unique functional that is optimal for any system. In particular, our results reveal that functionals designed to reduce the short-term repulsion between the adsorbate and the substrate usually overestimate the adsorption strength and may even predict the wrong adsorption orientation. We show that an accurate description of the substrate does not ensure an accurate evaluation of the adsorption energetics, while the electronic structure is less sensitive to the specific choice. We propose the best choice for DFT calculations of DNA bases on Au(111) and similar systems in which both short-range and long-range interactions exist.

New phases of binary compounds: CsCl-type RuGe and RuSn

We have discovered new phases of binary compounds of Ru and group-14 elements, CsCl-type cubic (Pm-3m) RuGe and RuSn. These materials are synthesized by heat treatment under high pressure, at more than 9.0 GPa for RuGe and 5.0 GPa for RuSn. Both polycrystalline samples exhibit metallic resistivity of . Pseudo-potential density functional theory calculations clarify that Ru 4d orbitals hybridized with Ge/Sn p orbitals dominantly form a Fermi surface. Calculated dynamic properties of these phases show the stability of the CsCl-type phases and the good agreement with the experimental results.

Thiol-based molecular overlayers adsorbed on C60: Role of the end-group and charge state on the stability of the complexes

We present pseudo-potential density functional theory calculations dedicated to analyze the stability and electronic properties of thiol-based molecular overlayers adsorbed on C60. We consider short molecules having a S atom as a headgroup, alkyl chains containing one to three C atoms, and a CH3 species as a terminal group. The thiol molecules are bonded to the carbon surface (through the S atom) with adsorption energies that vary in the range of ~1-2 eV and with S-C bond lengths of ~1.8 Å. For neutral C60(SCH3)n complexes, low energy atomic configurations are obtained when the thiol groups are distributed on the surface forming small molecular domains (e.g., pairs, trimers, or tetramer configurations of neighboring thiol molecules). In contrast, less stable random distributions are defined by orientationally disordered overlayers with highly distorted underlying carbon networks. The inclusion of London dispersion interaction slightly affects the structure of the molecular coating but increases the adsorption energies by values as large as 0.3 eV. Interestingly, the relative stability of the previous adsorbed phases differ from the one obtained when considering single sulfur adsorption on C60, a result that reveals the crucial role played by the terminal CH3 groups on the structure of the molecular coating. The positive (negative) charging of the [C60(SCH3)n](±q) complexes, with q as large as 8e, changes the geometrical structure and the chemical nature of the ligand shell inducing lateral molecular displacements, S-S bonding between neighboring thiols, as well as the partial degradation of the molecular coating. Finally, we consider the stability of two-component mixed overlayers formed by the coadsorption of CH3-, OH-, and NH2-terminated alkanethiols of the same length. In agreement with the results found on Au surfaces, we obtain lowest energy atomic configurations when molecular domains of a single component are stabilized on C60, a result that could be of fundamental importance in biomedical applications.

Theoretical and experimental study of the vibrational spectra of sarkinite Mn2(AsO4)(OH) and adamite Zn2(AsO4)(OH)

The arsenate hydroxyl-bearing minerals sarkinite and adamite were studied with vibrational spectroscopic (IR and Raman) and quantum theoretical methods. The observed IR bands in the higher (1100–600cm−1) and especially lower (600–450cm−1) frequency region of AsO4 vibrations could clearly discriminate between the studied analogues. The differences between their crystal structures are much pronounced in both IR and Raman OH-stretching regions. Namely, a single strong band is found in the case of orthorhombic adamite compared to four weaker bands observed in corresponding IR and Raman spectral regions of monoclinic sarkinite. Essentially all bands in the experimental spectra, collected at both room and liquid nitrogen temperature, were tentatively assigned. To support the tentative assignment of bands in the vibrational spectra of the mentioned minerals, periodic pseudopotential plane wave density functional theory calculations were carried out. Geometry optimizations of the 3D periodic systems included both optimizations of the atomic positions within the unit cell and of the unit cell itself. In most cases, the assignments were either supported or implied by the obtained theoretical data. It is worth mentioning that this is the first experimental and theoretical study of the vibrational spectra of the very-rare sarkinite mineral.

Adsorption and Diffusion of Hydrogen on C60-Supported Ptn Clusters

We present extensive pseudopotential density functional theory calculations dedicated to analyze the adsorption properties and migration behavior of hydrogen on C60-supported Ptn (n = 1, 2, 5, 13) clusters. When adsorbing Pt species on C60, we find that the systems gain energy when the platinum atoms aggregate on the fullerene surface, forming clusters of different sizes and symmetries. Notable structural variations around the adsorption sites are obtained, consisting in expansions and contractions of the C–C, Pt–Pt, and Pt–C bond lengths as large as 7%. The adsorption energies vary in the range of 1.5–3.1 eV, and there is a notable Pt → C charge transfer (∼0.15e) that leads to the formation of robust Pt–C bonds. When the C60Ptn compounds are exposed to molecular hydrogen, the Pt-rich regions of the surface are the ones favorable for the dissociative chemisorption of H2. The density of states around the Fermi level is very sensitive to the presence and location of the hydrogen species in our C60Ptn structures, a result that could have strong effects on the transport properties of our fullerene compounds and can be used as a fingerprint to identify precise structural features in these kind of complexes. Using the nudged-elastic-band method, we obtain that atomic hydrogen diffuses very easily on the surface of both free-standing and C60-supported Ptn clusters. However, H-atom migration on the carbon surface is very unlikely, since barriers of the order of 1.5 eV need to be overcome. Hydrogen transfer events between platinum and carbon regions on our here-considered C60Ptn structures, so-called spillover processes, are highly dependent on the local atomic environment. When going from the single Pt atom to the small cluster regime, the spillover energy barriers vary between 0.7–1.6 eV, a result that is important to consider in order to more clearly understand recent experimental studies addressing hydrogen storage in carbon nanostructures via chemical adsorption.

Atomic charges of Cl− ions confined in a model Escherichia coli ClC−Cl−/H+ ion exchanger: a density functional theory study

We present extensive semi-empirical and pseudo-potential density functional theory calculations dedicated to analyse the stability, charge density distribution and migration behaviour of Cl− ions confined in model Escherichia coli (ec) ClC−Cl−/H+ ion-exchangers. Following recent high-resolution crystal structure determination in these kinds of systems, we use a finite-cluster model approach and construct various chemically simplified pore structures made of a glutamate residue −CH2−CH2−COO− (E148) and its closets 15, 19, 23 and 26 amino acids into which the Cl− ions will be confined. We reveal the sequence of molecular rearrangements induced on the E148 chain, which blocks the middle of the conduction pathway, leading to the pore opening. The −CH2−CH2−COO− fragment shows notable variations in its average charge density for small changes in the intra-cellular environment varying from −0.4e to −0.3e to −0.1e in the presence of zero, one and two confined Cl− ions, respectively, a result that reveals an interesting functionality of the E148 chain during Cl− conduction. We also obtain complex fluctuations in the ionic charge of the confined Cl− ions varying from ∼−0.7e to −0.2e, which deviate significantly from the value (−1e) usually used in classical simulations. By attaching a single H species to one of the oxygens of the glutamate group, we obtain that the −CH2−CH2−COOH fragment has now a small effective charge of ∼+0.25e. The energy barriers opposing the exit of the Cl− ions from our considered ion-exchangers vary from 0.65 eV to 4.7 eV, the smallest values being obtained for model structures exhibiting a high degree of flexibility and having protonated E148 fragments. Our results reinforce previous findings and provide additional physical insight, at the atomic level, on the gating process. Finally, we underline the importance of using electronically polarisable force fields to describe the transport of anionic species through this kind of molecular constrictions.

Band-engineered CaTiO3 nanowires for visible light photocatalysis

We have theoretically investigated the structural, electronic, and optical properties of the perovskite CaTiO3 nanowires for visible light photocatalytic applications using pseudopotential density-functional theory calculations. The electronic structure calculations show that the band gap is greatly modified in the CaTiO3 nanowires compared with that of the bulk. For the TiO2-terminated nanowires, the electronic states on the valence band maxima induced by combining oxygen and calcium atoms on the surface lead to a shift in the valence band toward the conduction band without interference from the edge of the conduction band, which reduces the band gap. On the contrary, the electronic states induced by combining oxygen and calcium atoms on the surface of the CaO-terminated nanowires lead to a shift in the conduction band toward the valence band. The calculated optical results indicate that the absorption edge of the nanowires shifts towards the red-light region. These theoretical results suggest that the perovskite CaTiO3 nanowires are promising candidates for visible light photocatalysis such as solar-assisted water splitting reactions.

Dynamical stability of the lanthanum dihydride under high pressure: A density functional lattice dynamics approach

We report first-principles pseudopotential method and density functional linear response theory calculations of the structural, electronic, vibrational and thermodynamical properties of LaH2 in fluoride phase at zero and high pressures. The electronic band structure and first time calculated pressure dependent lattice dynamic properties show that the LaH2 is metallic in nature at zero pressure. The pressure dependent electronic band structure calculations show that the bands are closing and reopening with pressure. The phonon mode softens at 11 GPa indicating an instability in lattice structure and pressure induced transverse acoustic phonon mode driven displacive type structural phase transition. The LaH2 also shows weak superconductivity at zero pressure. The valence charge electron density at 46 GPa shows a cage type charge contour and a space where hydrogen can be absorbed and filled easily. There is a considerable charge accumulation in the bonding region of La and H atoms, which strengthens covalent character of LaH2, and henceforth this material can be one of the best materials for hydrogen storage application at high pressures.

New acentric materials constructed from aminopyridines and 4-nitrophenol

Co-crystallization of 4-nitrophenol (I) with five aminopyridines (4-aminopyridine 1, 3,4-diaminopyridine 2, 2,3-diaminopyridine 3, 3-aminopyridine 4, 2-amino-6-methylpyridine 5) and 2,4-diaminopyrimidine 6 resulted in six adducts with the ratio of components 2 : 1 in five and 1 : 1 in one final compounds. Single crystals were grown by slow evaporation technique using ethanol as a solvent. Five adducts with 1–5 crystallize in acentric P21 and Pna21 space groups, and one, 2(I)·6 – in centrosymmetric P21/c space group. Compounds 2(I)·1, 2(I)·2, 2(I)·3 are isomorphous, and demonstrate similar H-bonding patterns despite the differences in aminopyridine molecules. Compound 2(I)·5 is isomorphous to two previously reported compounds. Adducts 2(I)·1, 2(I)·2, 2(I)·3, 2(I)·5, 2(I)·6 represent organic salts composed of pyridinium/pyrimidinium cation, 4-nitrophenolate anion, and 4-nitrophenol neutral molecule. The H-bonded 4-nitrophenol–4-nitrophenolate anionic dimers were found in all compounds with 2 : 1 molar ratio. In adduct I·4 both molecules are in neutral form. The IR spectral data support crystallographic conclusions on salts formation. Plane wave pseudopotential density functional theory calculations were used to predict hyperpolarizability tensor components. Our calculations suggest 2(I)·3 as the best candidate for nonlinear optical materials (14 times more active than urea).

Band-engineered SrTiO3 nanowires for visible light photocatalysis

We have theoretically investigated the structural, electronic, and optical properties of perovskite SrTiO3 nanowires for use in visible light photocatalytic applications using pseudopotential density-functional theory calculations. The electronic structure calculations show that the band gap is modified in the SrTiO3 nanowires compared with that of the bulk. For TiO2-terminated nanowires, the mid-band states induced by the combination of oxygen and strontium atoms on the surface lead to a shift in the valence band toward the conduction band without interference from the edge of the conduction band, which reduces the band gap. On the contrary, the electronic states induced by the combination of oxygen and strontium atoms on the surface of SrO-terminated nanowires lead to a shift in the conduction band toward the valence band. The calculated optical results indicate that the absorption edge of the nanowires shift towards the red-light region. These theoretical results suggest that perovskite SrTiO3 nanowires are promising candidates for use in visible light photocatalytic processes such as solar-assisted water splitting reactions.

Adsorption of CO on pure and mixed clusters of tin and germanium up to five atoms: A theoretical study

The adsorptions of the CO molecule on the neutral mixed clusters of Sn and Ge up to five atoms are investigated theoretically. Electronic structures of the cluster-CO complexes are obtained by global optimization of the energy surface using Monte Carlo simulation coupled with simulated annealing followed by pseudopotential plane wave density functional theory calculations. An aug-cc-pVTZ basis set for C and O and aug-cc-pVTZ-pp for Sn and Ge atoms are employed. The CO adsorption energies and Gibbs free energy are calculated to establish the kinetic and thermodynamic stability of the cluster-CO complexes. The variations of adsorption energy, HOMO–LUMO gap, and NBO charge on CO fragment with the size of the clusters are reported. The CO adsorptions on Sn–Ge mixed clusters are confirmed by studying correlations among different parameters such as the increase in C–O bond length, the red shift in C–O stretching frequency, CO binding energy, changes in Gibbs free energy, and NBO charge on CO.

Surface effect on electronic and optical properties of Bi2Ti2O7 nanowires for visible light photocatalysis

We theoretically performed the structural, electronic, and optical properties of the pyrochlore Bi2Ti2O7 nanowires for photocatalytic applications using pseudopotential density-functional theory calculations. The groundwork of electronic structure calculations showed a possible band gap modification of the Bi2Ti2O7 nanowires compared to that of the bulk. The midband states induced by the oxygen atoms and bismuth atoms on the surface of nanowires leads to a shift in the valence band toward the conduction band, which enables reduction of the band gap. The calculated optical results indicated that the absorption edges shift of nanowires towards the red-light region. These theoretical results suggested that the pyrochlore Bi2Ti2O7 nanowires can be expected to be a promising candidate for photocatalytic applications such as solar-assisted water splitting reactions.

Adsorption of Nitric Oxide on Small Rhn± Clusters: Role of the Local Atomic Environment on the Dissociation of the N–O Bond

We present extensive pseudopotential density functional theory calculations dedicated to analyze the stability and dissociation behavior of NO molecules adsorbed on small nonmagnetic Rh(n)± clusters. Following the experimental work of Anderson et al. (J. Phys. Chem. A 2006, 110, 10992), we consider rhodium structures of different sizes (n = 3, 4, 6, and 13) and charge states onto which we attach NO species in both molecular and dissociative configurations. The relative stability between different Rh(n)± isomers depends on the ionization state of the clusters as well as on the presence of NO adsorbates on the surface. Various adsorbed configurations for the NO molecules are found when switching from cationic to neutral to anionic rhodium clusters. In particular adsorbed phases in which the NO molecule is attached with its N-O bond parallel to the plane of square or triangular facets are characterized by elongated nitrogen-oxygen interatomic distances, a fact that plays a fundamental role in the dissociation behavior of the adsorbate. We use the nudged elastic band method to analyze possible reaction pathways and transition states that could be present in our (Rh(n) + NO)± systems. We found (as in surface studies) that the dissociation of the N-O bond is more easily obtained on square facets than on triangular atomic environments, a fact that indirectly reveals the structure of Rh(n)± clusters present in the gas phase experiments. The energy barriers that need to be overcome to achieve the breaking of the N-O bond depend on the charge state of the systems, a result that could be used to tune the catalytic activity of these types of materials.

Stability, Electronic Properties, and Structural Isomerism in Small Copper Clusters

ABSTRACTWe present extensive pseudopotential density functional theory calculations dedicated to analyze the stability, electronic properties, and structural isomerism in Cu6 clusters. We consider structures of different symmetries and charge states. Our total energy calculations reveal a strong competition between two- and three-dimensional atomic arrays, the later being mostly energetically preferred for the anionic structures. The bond lengths and electronic spectra strongly depend on the local atomic environment, a result that is expected to strongly influence the catalytic activity of our clusters. Using the nudged elastic band method we analyze the interconversion processes between different Cu6 isomers. Complex atomic relaxations are obtained when we study the transition between different cluster structures; however relatively small energy barriers of approximately 0.3 eV accompany the atomic displacements. Interestingly, we obtain that by considering positively charged Cu6+ systems we reduce further the energy barriers opposing the interconversion process. The previous results could imply that, under a range of experimental conditions, it should be possible to observe different Cu6cluster structures in varying proportions.