Generalized Gradient Approximation Density Functional Theory Research Articles

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal-Organic Frameworks.

A collection of more than 20,000 experimentally derived crystal structures for metal-organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

Diffusion of excessively adsorbed hydrogen atoms on hydrogen terminated Si(100)(2×1) surface

The diffusion properties of an excess H atom adsorbed on a fully H-terminated Si(100)(2 × 1)-H surface have been analyzed by means of density functional theory-generalized gradient approximation calculations. Our diffusion pathway models consist of sequences of hops between metastable Si surface atomic structures with an excess H atom. We analyzed the reaction path and corresponding barrier height in each hop using the climbing image nudged elastic band method. The activation energies for diffusion along intra-dimer, intra-row, and inter-row pathways are found to be 0.11, 0.54, and 0.74 eV, respectively, which are quite small compared to the common H diffusion running with a vacant site of hydrogen termination. The weak adsorption energy of the excess H atom is responsible for the small activation energy of diffusion. The present diffusion mechanism suggests that the physical substance of the “hot atom mechanism” proposed in the previous investigations on H exposure onto the Si surface is related to the metastable structures of excessively adsorbed hydrogen atoms.

Conformational analysis of tannic acid: Environment effects in electronic and reactivity properties.

Polyphenols are natural molecules of crucial importance in many applications, of which tannic acid (TA) is one of the most abundant and established. Most high-value applications require precise control of TA interactions with the system of interest. However, the molecular structure of TA is still not comprehended at the atomic level, of which all electronic and reactivity properties depend. Here, we combine an enhanced sampling global optimization method with density functional theory (DFT)-based calculations to explore the conformational space of TA assisted by unsupervised machine learning visualization and then investigate its lowest energy conformers. We study the external environment's effect on the TA structure and properties. We find that vacuum favors compact structures by stabilizing peripheral atoms' weak interactions, while in water, the molecule adopts more open conformations. The frontier molecular orbitals of the conformers with the lowest harmonic vibrational free energy have a HOMO-LUMO energy gap of 2.21 (3.27) eV, increasing to 2.82 (3.88) eV in water, at the DFT generalized gradient approximation (and hybrid) level of theory. Structural differences also change the distribution of potential reactive sites. We establish the fundamental importance of accurate structural consideration in determining TA and related polyphenol interactions in relevant technological applications.

Electron properties of 13-atom nanoparticle superlattices

A density functional theory (DFT) study of electronic properties and Seebeck coefficient S of d-metal (Au, Ag, Pt, Pd, Ta) 13-atom nanoparticle superlattices is presented. The geometry optimization, calculations of electronic structure and density of electron states (DOS) was performed in DFT generalized gradient approximation in Perdiew-Burke-Ernzerhoff form (GGA-PBE) with full relativistic pseudopotentials. From the band structure S values are calculated using semi-classical Boltzmann equation in τ approximation. A size-dependent appearance of features in DOS near Fermi level is shown. The influence of these features on S is discussed. Potential usage of such model materials with strong DOS features near Fermi level as a source of varied energy monochromatic photons in metal insulator semiconductor structures for resonant excitation of long-lived forbidden states, including nuclear ones is discussed.

Structural and Electronic Rearrangements in Fe2S2, Fe3S4, and Fe4S4 Atomic Clusters under the Attack of NO, CO, and O2.

We report results, based on density functional theory-generalized gradient approximation calculations, that shed light on how NO, CO, and O2 interact with Fe2S2, Fe3S4, and Fe4S4 clusters and how they modify their structural and electronic properties. The interest in these small iron sulfide clusters comes from the fact that they are at the protein cores and that elucidating fundamental aspects of their interaction with those light molecules which are known to modify their functionality may help in understanding complex behaviors in biological systems. CO and NO are found to bind molecularly, leading to moderate relaxations in the clusters, but nevertheless to changes in the spin-polarized electronic structure and related properties. In contrast, dissociative chemisorption of O2 is much more stable than molecular adsorption, giving rise to significant structural distortions, particularly in Fe4S4 that splits into two Fe2S2 subclusters. As a consequence, oxygen tends to strongly reduce the spin polarization in Fe and to weaken the Fe-Fe interaction inducing antiparallel couplings that, in the case of Fe4S4, clearly arise from indirect Fe-Fe exchange coupling mediated by O. The three molecules (particularly CO) enhance the stability of the iron-sulfur clusters. This increase is noticeably more pronounced for Fe2S2 than for the other iron-sulfur clusters of different compositions, a result that correlates with the fact that in recent experiments of CO reaction with FemSm (m = 1-4), the Fe2S2CO product results as a prominent one.

Structural, electronic and magnetic properties of small FemVn (m + n ≤ 6) clusters: First-principles calculation

In this paper, the structural, electronic and magnetic properties of small Fe[Formula: see text]V[Formula: see text] (m+n [Formula: see text] 6) clusters have been investigated systematically within the framework of the generalized gradient approximation density-functional theory. The results indicate that the low lying isomers of Fe[Formula: see text]V[Formula: see text] alloy clusters all present the classical closely packed geometries with different chemical order when m + n [Formula: see text] 4; the ground state structures prefer to form the Fe–V as much as possible in small proportion V doping. The binding energy of Fe[Formula: see text]V[Formula: see text] clusters always increases with the successive V substitution. The V atom mono-doped and bi-doped make the magnetism of Fe[Formula: see text] clusters decrease 7 [Formula: see text], respectively. With V atom doping increasing, the magnetism presents an overall decreased tendency. The magnetic order bewteen Fe and V atoms undergoes a transition from antiferromagnetic coupling in Fe-rich clusters to the coexistence of antiferromagnetic and ferromagnetic couplings in V-rich clusters, and the atom net charge usually transfer from V to Fe atom in Fe[Formula: see text]V[Formula: see text] alloy clusters.

Structural, Electronic and Tunable Magnetic Properties of Transition Metal Doped Rh8 Cluster from First Principles Calculation

The configurations, electronic and magnetic properties of the Rh7M (M = 3d, 4d transition metal) are systematically investigated within the framework of the generalized gradient approximation density-functional theory (DFT-GGA). The results indicated that the ground state structures of Rh7M (M = 3d) clusters prefer to a bicapped octahedron configuration, while the Rh7M (M = 4d) clusters present a different degree of geometry reconstruction relative to the perfect cubic structure of Rh8 cluster. In most cases, the doped clusters show relatively higher stability, indicating that impurity atoms could stabilize the pure Rh8 cluster; the Rh7M (M = 3d, 4d) have smaller frontier orbital energy gaps in comparison to the host. The magnetic moments of Rh7M (M = 3d, 4d) exhibit a tunable magnetism with range from 3μB to 13μB and the Fe atom doping enhances the magnetic moment of mixed cluster.

Structure, stability, and electronic and magnetic properties of small Rh n Mn (n = 1–12) clusters

The structure, stability, and magnetic properties of Rhn+1 and Rh n Mn clusters (n = 1–12) are systematically investigated within the framework of the generalized gradient approximation density-functional theory (DFT-GGA). The overall structural evolutionary trend shows that the ground state structures of the Rh n Mn are similar to that of the corresponding pure rhodium clusters except for n = 7, 9, 12, while the Rh7Mn, Rh9Mn and Rh12Mn clusters occur substantially geometry reconstruction. The binding energy of Rh n Mn is decreased with the substitution of one Mn atom, thus indicating that Mn doping can weaken the stability of the Rh clusters. The fragmentation energy and the second-order difference energy of the ground-state Rh n Mn clusters imply that the Rh3Mn, Rh5Mn, Rh8Mn and Rh11Mn clusters are more stable than their neighbors. Compared with corresponding pure Rh n clusters, the Mn atom doping increases the total magnetic moment of the Rh n Mn clusters in various degrees, and the physics origin of such a phenomenon is analyzed in detail based on the average bond length, magnetic coupling, and density of state.

A density functional theory based elementary reaction mechanism for early steps of Fischer-Tropsch synthesis over cobalt catalyst. 1. Reaction kinetics

Fischer-Tropsch synthesis (FTS), an efficient process for production of valuable fuel products from synthesized gas (syngas), has been the subject of many theoretical and experimental studies for decades. This work involves detailed molecular and microkinetic modeling of this catalytic process. By adopting an existing elementary reaction mechanism in the literature, density functional theory (DFT) calculations have been applied to model the kinetics and thermodynamics of FTS elementary steps on a flat Co(0001) catalyst surface. In this regard, using the DFT generalized gradient approximation (GGA) and canonical transition state theory, the rate constants and the activation energies of individual elementary reactions have been calculated. In addition, the necessity for modification of the existing proposed elementary steps and considerations of alternative mechanisms have been probed. Finally, it was determined that the favorable path for CO dissociation, as one of the key steps in the FTS, occurs through a hydrogen-assisted mechanism and the estimated rate parameters have been compared with those of other theoretical studies.

How reliable is DFT in predicting relative energies of polycyclic aromatic hydrocarbon isomers? comparison of functionals from different rungs of jacob's ladder.

Density functional theory (DFT) is the only quantum-chemical avenue for calculating thermochemical/kinetic properties of large polycyclic aromatic hydrocarbons (PAHs) such as graphene nanoflakes. Using CCSD(T)/CBS PAH isomerization energies, we find that all generalized gradient approximation (GGA) and meta GGA DFT functionals have severe difficulties in describing isomerization energies in PAHs. The poor performance of these functionals is demonstrated by the following root-mean-square deviations (RMSDs) obtained for a database of C14 H10 and C18 H12 isomerization energies. The RMSDs for the GGAs range between 6.0 (BP86-D3) and 23.0 (SOGGA11) and for the meta GGAs they range between 3.5 (MN12-L) and 11.9 (τ-HCTH) kJmol-1 . These functionals (including the dispersion-corrected methods) systematically and significantly underestimate the isomerization energies. A consequence of this behavior is that they all predict that chrysene (rather than triphenylene) is the most stable C18 H12 isomer. A general improvement in performance is observed along the rungs of Jacob's Ladder; however, only a handful of functionals from rung four give good performance for PAH isomerization energies. These include functionals with high percentages (40-50%) of exact Hartree-Fock exchange such as the hybrid GGA SOGGA11-X (RMSD = 1.7 kJmol-1 ) and the hybrid-meta GGA BMK (RMSD = 1.3 kJmol-1 ). Alternatively, the inclusion of lower percentages (20-30%) of exact exchange in conjunction with an empirical dispersion correction results in good performance. For example, the hybrid GGA PBE0-D3 attains an RMSD of 1.5 kJmol-1 , and the hybrid-meta GGAs PW6B95-D3 and B1B95-D3 result in RMSDs below 1 kJmol-1 . © 2016 Wiley Periodicals, Inc.

Simulation of the phase transition of graphite to the diamond-like LA3 phase

The phase transition of graphite to a diamond-like LA3 phase is simulated by the methods of the density functional theory (DFT). The calculations are performed in the local density approximation (LDA) and the generalized gradient approximation (GGA). It is found that the structural transformation must occur at a pressure of 60 or 74 GPa according to calculations based on the DFT–LDA and DFT–GGA, respectively. The height of the potential barrier separating the structural state corresponding to the LA3 phase from the state corresponding to graphite exceeds 0.13 eV/atom. This indicates the possibility of stable existence of the diamond-like LA3 phase under standard conditions.

First-principles DFT + U calculations on the energetics of Ga in Pu, Pu2O3 and PuO2

First-principles density functional theory–generalized gradient approximation methods are used to calculate the energetics of Ga in Ga-stabilized δ phase Pu, Pu2O3 and PuO2, in order to elucidate the relative stability of Ga in the Pu oxide layers. The Hubbard parameter U is used to describe the strongly correlated electron behavior of Pu 5f electrons. Three incorporation sites for Ga, i.e., interstitial site, Pu and O vacancies, are considered. The results indicate that the energetics of Ga significantly depend on the inherent properties of the host materials and the incorporation sites in them. Ga incorporation into interstitial sites and O vacancies of both Pu2O3 and PuO2 are energetically unfavorable. Ga incorporation into Pu vacancy of PuO2 is the most energetically favorable, followed by Ga incorporation into Pu vacancies of Pu2O3 and Pu. However, this does not mean that there would be the highest concentration of Ga in PuO2 among these three Ga-stabilized Pu substances because it is most difficult for Pu vacancy formation in PuO2. The distribution of Ga in the Pu oxide layers is proposed to be strongly dependent on the distribution and the concentration of Pu vacancy, as a result, Ga concentration likely decrease with the transitions of Pu→Pu2O3→PuO2.

First-principles energetics of rare gases incorporation into uranium dioxide

First-principles density functional theory–generalized gradient approximation methods have been used to calculate the energetics (incorporation energy, formation energy and binding energy) of rare gases (He, Ne, Ar, Kr and Xe) at the three incorporation sites (octahedral interstitial, uranium and oxygen vacancies) of uranium dioxide. The Hubbard parameter U and van der Waals corrections have been used to describe the strongly correlated electronic behavior of uranium 5f electrons and the weak interactions of rare gases, respectively. The results indicate that the energetics of rare gases depend significantly on the incorporation sites and on the atomic properties such as atomic radius. All rare gases considered here are energetically unfavorable at the three incorporation sites. However, rare gases exhibit significant binding ability to both U and O vacancies. The main trends of relative stability of rare gases generally reflect a size effect: the rare gases become more unstable with increasing atomic number. Electronic structures of these systems containing rare gases also exhibit general trends in their relative stability and charge-transfer character.

Nanocrystal growth of single-phase Si1−xGex alloys

We present the formation of single-phase Si1−xGex (x=0.2, 0.4, 0.6, and 0.8) alloy nanocrystals dispersed in a SiO2 matrix. The studied samples were prepared by co-sputtering with excess Si1−xGex in SiO2 of approximately 33at%. Upon heat treatment, crystallization of Si1−xGex alloys was examined by using X-ray diffraction and high-resolution transmission electron microscopy measurements. Single structure of face-centered cubic nanocrystals in a space group Fd-3m was concluded. The average nanocrystal size (from 2nm to 10nm) and the lattice constant a of the single-phase Si1−xGex nanocrystals were found to increase with the Ge composition parameter x. Density functional theory-generalized gradient approximation calculation showed the replacement of Ge into the Si sites and vice versa.

Theoretical prediction of the band offsets at the ZnO/anatase TiO2 and GaN/ZnO heterojunctions using the self-consistent ab initio DFT/GGA-1/2 method

The band offsets of the ZnO/anatase TiO2 and GaN/ZnO heterojunctions are calculated using the density functional theory/generalized gradient approximation (DFT/GGA)-1/2 method, which takes into account the self-energy corrections and can give an approximate description to the quasiparticle characteristics of the electronic structure of semiconductors. We present the results of the ionization potential (IP)-based and interfacial offset-based band alignments. In the interfacial offset-based band alignment, to get the natural band offset, we use the surface calculations to estimate the change of reference level due to the interfacial strain. Based on the interface models and GGA-1/2 calculations, we find that the valence band maximum and conduction band minimum of ZnO, respectively, lie 0.64 eV and 0.57 eV above those of anatase TiO2, while lie 0.84 eV and 1.09 eV below those of GaN, which agree well with the experimental data. However, a large discrepancy exists between the IP-based band offset and the calculated natural band offset, the mechanism of which is discussed. Our results clarify band alignment of the ZnO/anatase TiO2 heterojunction and show good agreement with the GW calculations for the GaN/ZnO heterojunction.

Compton profiles and electronic structure of monoclinic zinc and cadmium tungstates

Abstract We report the first ever Compton scattering study of ZnWO 4 and CdWO 4 using 20 Ci 137 Cs Compton spectrometer at momentum resolution of 0.34 a.u. To compare the experimental Compton profiles, we have also deduced the momentum densities using density functional theory (DFT) within linear combination of atomic orbitals (LCAO) methods. It is seen that the experimental Compton profiles of both the tungstates give a better agreement with LCAO–DFT calculations within generalized gradient approximation (GGA) employing Perdew–Becke–Ernzerhof (PBE) exchange and correlation energies than other approximations included in the present work. Further, energy bands, density of states (DOS) and band gaps have also been calculated using LCAO–DFT–GGA–PBE scheme and full potential linearized augmented plane wave method. Both the computational schemes show a semiconducting nature of both the tungstates, with a direct band gap at Y point of Brillouin zone. Further, a relative nature of bonding on equal-valence-electron-density scale shows more covalent character in ZnWO 4 than CdWO 4 which reconciles with the conclusions drawn using integrated DOS and Mulliken’s population data.

First principle calculations of nitric oxide on metallic Pt (1 1 1) and Pt (1 0 0), and bimetallic Au/Pt (1 1 1) and Au/Pt (1 0 0) surfaces

The chemisorption of NO on pure Pt (111) and Pt (100), bimetallic Au/Pt (111) and Au/Pt (100) surfaces has been investigated using the pseudo-potential plane-wave method within the generalized-gradient approximation density functional theory (GGA+DFT). The results show that different surfaces have various effects on the adsorption of NO. NO tends to be adsorbed on site coordinated with more Pt atoms, and the substitution number of the top-layer Pt by Au atoms affect the d-band center and adsorption energy. The local density of states of various surfaces are calculated. With the increasing atomic number of surface Au, the d-band center moves away from the Fermi level, and the adsorption energies decrease. The further electronic states analysis reveals that the interaction between NO and metal surfaces is mainly via the hybridization of NO 5σ/2π* orbitals and metal d-bands. And when the top-layer concentrations of Au are equal, Au/Pt (100) exhibits better catalytic toward NO adsorption than Au/Pt (111). It indicates that different compositions and facets can produce varied catalytic effects.

First principle calculations of hydrogen sulfide adsorption and dissociation on pure Pd (111) and Au (111), and alloy Pd/Au (111) and Au/Pd (111) surfaces

The hydrogen sulfide adsorption and dissociation on pure Pd (111) and Au (111), alloy Pd / Au (111) and Au / Pd (111) surfaces have been investigated using the pseudo-potential plane wave method within the generalized-gradient approximation density functional theory (GGA+DFT). The results show that H 2 S tends to be adsorbed on top site, HS prefers to locate on bridge site, and the S and H locate on fcc site on various surfaces. Compared the adsorption of sulfur-containing species and hydrogen on pure and alloy metal surfaces, a similar trend of adsorption energies on the metal surfaces ( Pd / Au (111) > Pd (111) > Au (111) > Au / Pd (111)) is found. In addition, the dissociation process on the Pd (111) and Pd / Au (111) surfaces is predicted to be exothermic. However, on Au (111) and Au / Pd (111), the dissociation process is endothermic. The work reveals that H 2 S dissociation is more likely to happen on Pd / Au (111) surface. Finally, the adsorption energies of adsorbate on metal surfaces have strong correlation with the d-band center. The d-band center moves away from the Fermi level, and the adsorption energy decreases. According to the LDOS analysis, the inner Au atoms of Pd / Au (111) can enhance the top-layer d-band intensity, whereas the inner Pd atoms of Au / Pd (111) cause the opposite effect. The further electronic state analysis reveals the interaction between H 2 S and metal surfaces.

Pressure-induced structure and properties of crystalline β-FOX-7 by LDA and GGA calculations

The structural, electronic, and absorption properties of crystalline β-FOX-7 were studied by density functional theory–generalized gradient approximation (GGA) and local density approximation (LDA) calculations. The results indicate that there are irregular changes occurred at 9, 17, 32, and 37 GPa for the GGA results and at 2, 7, 22, and 32 GPa for the LDA ones, in agreement with previous reports that the LDA generally underestimated, while the GGA overestimated the structure and properties of the crystals. The compression ratios of the lattice constants suggest that the structure of β-FOX-7 is much stiffer in a- and c-directions than in b-direction. The total decrease ratio of C–NO2 band lengths is larger than that of other bond lengths, indicating that the C–NO2 bond cleavage may trigger the initiation decomposition of β-FOX-7. An analysis of density of states suggests that the interactions between electrons are strengthened under the influence of pressure. The absorption spectra indicate that the bands in the fundamental absorption region have relatively high optical activity at high pressure.

Ab initio investigation of a new boron nitride allotrope

A new allotropic superhard and superdense structure of sp3-bonded boron nitride (hP3-BN) is proposed. Geometric, electronic, elastic, and optical properties of the structure are investigated by density functional theory-generalized gradient approximation (DFT-GGA) calculations. It is shown that the structure is an insulator with a band gap of 5.06 eV; its density is 5.03% higher than that of cubic boron nitride (c-BN) and its bulk modulus is 2.25% higher than that of c-BN. The calculated hP3-BN refractive index in the range 200–800 nm is significantly higher than the indexes of diamond and all known carbon allotropes, except for the analogous carbon h-P3 structure, and it has a large optical dispersion. In the range above 800 nm the refractive index changes from 2.60 to 2.35.