Overlap Population Research Articles

First principles study of breaking energy and mechanical strength of Kevlar-29

The first principles study is performed for the mechanical strength of Kevlar-29, and is based on density functional theory. The bond strength is investigated relative to the displacement of central nitrogen atom along X, Y and Z directions, respectively. The structural property analysis explains the asymmetric nature. A higher bond breaking energy is observed during compression along Z direction and vice versa for elongation. It is an insulator of forbidden energy gap which increases while compression and reduces during elongation. Crystal orbital overlap population reveals the higher strength of anti-bonding orbitals. It is mechanically stronger along the Z-axis and weaker along the Y-axis.

Li and Na Adsorption on Graphene and Graphene Oxide Examined by Density Functional Theory, Quantum Theory of Atoms in Molecules, and Electron Localization Function.

Adsorption of Li and Na on pristine and defective graphene and graphene oxide (GO) is studied using density functional theory (DFT) structural and electronic calculations, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF) analyses. DFT calculations show that Li and Na adsorptions on pristine graphene are not stable at all metal coverages examined here. However, the presence of defects on graphene support stabilizes both Li and Na adsorptions. Increased Li and Na coverages cause metal nucleation and weaken adsorption. Defective graphene is associated with the presence of band gaps and, thus, Li and Na adsorptions can be used to tune these gaps. Electronic calculations show that Li– and Na–graphene interactions are Coulombic: as Li and Na coverages increase, the metal valences partially hybridize with the graphene bands and weaken metal–graphene support interactions. However, for Li adsorption on single vacancy graphene, QTAIM, ELF, and overlap populations calculations show that the Li-C bond has some covalent character. The Li and Na adsorptions on GO are significantly stronger than on graphene and strengthen upon increased coverages. This is due to Li and Na forming bonds with both carbon and oxygen GO atoms. QTAIM and ELF are used to analyze the metal–C and metal–metal bonds (when metal nucleation is present). The Li and Na clusters may contain both covalent and metallic intra metal–metal bonds: This effect is related to the adsorption support selection. ELF bifurcation diagrams show individual metal–C and metal–metal interactions, as Li and Na are adsorbed on graphene and GO, at the metal coverages examined here.

Thermopower Modulation Clarification of the Operating Mechanism in Wide Bandgap BaSnO3 -SrSnO3 Solid-Solution Based Thin Film Transistors.

The transparent oxide semiconductor (TOS) with large bandgap (Eg ≈ 4 eV) based thin-film transistors (TFTs) showing both high carrier mobility and UV-visible transparency has attracted increasing attention as a promising component for next generation optoelectronics. Among TOSs, BaSnO3 -SrSnO3 solid-solutions (Eg = 3.5-4.2 eV) are good candidates because the single crystal shows very high mobility. However, the TFT performance has not been optimized due to the lack of fundamental knowledge especially the effective thickness (teff ) and the carrier effective mass (m*). Here, it is demonstrated that the electric field thermopower (S) modulation method addresses this problem by combining with the standard volume carrier concentration (n3D ) dependence of S measurements. By comparing the electric field accumulated sheet carrier concentration (n2D ) and n3D at same S, it is clarified that the teff (n2D /n3D ) of the conducting channel becomes thicker with increasing Sr concentration, whereas the m* becomes lighter. The former would be due to the increase of Eg and latter would be due to the enhancement of overlap population of neighboring Sn 5s orbitals. The present analyses technique is useful to experimentally clarify the teff and m*, and essentially important to realize advanced TOS-based TFTs showing both high optical transparency and high mobility.

Sodium rubidium hydrogen citrate, NaRbHC6H5O7, and sodium caesium hydrogen citrate, NaCsHC6H5O7: crystal structures and DFT comparisons.

The crystal structure of sodium rubidium hydrogen citrate, NaRbHC6H5O7 or [NaRb(C6H6O7)] n , has been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. This compound is isostructural to NaKHC6H5O7. The Na atom is six-coordinate, with a bond-valence sum of 1.16. The Rb atom is eight-coordinate, with a bond-valence sum of 1.17. The distorted [NaO6] octa-hedra share edges to form chains along the a-axis direction. The irregular [RbO8] coordination polyhedra share edges with the [NaO6] octa-hedra on either side of the chain, and share corners with other Rb atoms, resulting in triple chains along the a-axis direction. The most prominent feature of the structure is the chain along [111] of very short, very strong hydrogen bonds; the O⋯O distances are 2.426 and 2.398 Å. The Mulliken overlap populations in these hydrogen bonds are 0.140 and 0.143 electrons, which correspond to hydrogen-bond energies of about 20.3 kcal mol-1. The crystal structure of sodium caesium hydrogen citrate, NaCsHC6H5O7 or [NaCs(C6H6O7)] n , has also been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. The Na atom is six-coordinate, with a bond-valence sum of 1.15. The Cs atom is eight-coordinate, with a bond-valence sum of 0.97. The distorted trigonal-prismatic [NaO6] coordination polyhedra share edges to form zigzag chains along the b-axis direction. The irregular [CsO8] coordination polyhedra share edges with the [NaO6] polyhedra to form layers parallel to the (101) plane, unlike the isolated chains in NaKHC6H5O7 and NaRbHC6H5O7. A prominent feature of the structure is the chain along [100] of very short, very strong O-H⋯O hydrogen bonds; the refined O⋯O distances are 2.398 and 2.159 Å, and the optimized distances are 2.398 and 2.347 Å. The Mulliken overlap populations in these hydrogen bonds are 0.143 and 0.133 electrons, which correspond to hydrogen-bond energies about 20.3 kcal mol-1.

Potentially Antibacterial Mixed-Ligand Oxidovanadium(IV) Salicylhydroxamate Complex [VO(acac)SHA]: Synthesis, Characterization and Quantum Mechanical Study

The oxidovanadium(IV) complex of composition [VO(acac)(SHA)] (where acac = [CH3COCHCOCH3−]); (SHA = [2-OHC6H4C(O)NHO−]) has been synthesized by the reaction of [VO(acac)2] with salicylhydroxamic acid (SH2A) in methanol + tetrahydrofuran and characterized by physicochemical and various spectral studies. The FTIR spectra indicated that salicylhydroxamate ion is bonded through carbonyl and hydroxamic oxygen (CONHO) atoms [O, O mode]. An optimized distorted square-pyramidal geometry around vanadium has been obtained by DFT/SIESTA using standard conjugate-gradient (CG) technique. From the HOMO–LUMO energy values, the molecular properties, viz. ionization potential (IP), electron affinity (EA), chemical potential (µ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω), have been calculated. The energy-resolved visualization of chemical bonding and molecular orbital contributions have been studied from the density of states, partial density of states and overall population density of states/crystal orbital overlap population and crystal orbital Hamiltonian population. The antibacterial activity of complex assayed against four bacterial strains, viz. E. coli, S. aureus, S. epidermidis and K. pneumoniae by MIC method, has shown it as promising growth-inhibiting agent.

Physical and chemical insights into molecular adsorption of copolymer’s monomers on Rutile surface

The adsorption of triblock copolymer’s moieties such as DME, 1,2-DME, and 1,2-DMP on a Rutile surface has been studied by DFT. The insights into their adsorption mechanism have been investigated by analyzing various physical and chemical properties such as the adsorption energies, the structural properties, difference of charge density, density of state, bond overlap population, and the atomic partial charge. Dispersion interaction plays a major role on the absorption energy in 1,2-DME, and the upward bridging oxygen configurations of DME and 1,2-DMP; whilst electrostatic and polarization energies are insignificant. A new Ob-Ti bond has been formed from the overlap of lone-pair electrons between orbital O 2p and Ti 3d in downward bridging oxygen configurations of DME and 1,2-DMP, which results in a significantly larger adsorption energies compared with other configurations. The molecular torsion is considered as a barrier that prevent Ob-down of 1,2-DME to create the bond with Ti.

Crystal structures of ammonium citrates

The crystal structures of (NH4)H2C6H5O7 and (NH4)3C6H5O7 have been determined using a combination of powder and single crystal techniques. The structure of (NH4)2HC6H5O7 has been determined previously by single crystal diffraction. All three structures were optimized using density functional techniques. The crystal structures are dominated by N-H⋅⋅⋅O hydrogen bonds, though O-H⋅⋅⋅O hydrogen bonds are also important. In (NH4)H2C6H5O7 very strong centrosymmetric charge-assisted O-H-O hydrogen bonds link one end of the citrate into chains along the b-axis. A more-normal O-H⋅⋅⋅O hydrogen bond links the other end of the citrate to the central ionized carboxyl group. In (NH4)2HC6H5O7, the very strong centrosymmetric O-H-O hydrogen bonds link the citrates into zig-zag chains along the b-axis. The citrates occupy layers parallel to the bc plane, and the ammonium ions link the layers through N-H⋅⋅⋅O hydrogen bonds. In (NH4)3C6H5O7, the hydroxyl group forms a hydrogen bond to a terminal carboxylate, and there is an extensive array of N-H⋅⋅⋅O hydrogen bonds. The energies of the density functional theory-optimized structures lead to a correlation between the energy of an N-H⋅⋅⋅O hydrogen bond and the Mulliken overlap population: E(N-H⋅⋅⋅O) (kcal/mole) = 23.1(overlap)½. Powder patterns of (NH4)H2C6H5O7 and (NH4)3C6H5O7 have been submitted to International Centre for Diffraction Data for inclusion in the powder diffraction file.

PtP2 : An example of exploring the hidden Cairo tessellation in the pyrite structure for discovering novel two-dimensional materials

The Cairo tessellation refers to a pattern of type 2 pentagons that can pave an infinite plane without creating a gap or overlap. We reveal the hidden, layered Cairo tessellations in the pyrite structure with a general chemical formula of $AB_2$ and space group $pa\bar3$. We use this hidden tessellation along with density functional theory calculations to examine the possibility of obtaining a two-dimensional (2D) material with the Cairo tessellation from the bulk, using PtP$_2$ as an example. Unlike previously reported single-layer materials such as PdSe$_2$ with a buckled, pentagonal structure-strictly speaking, not belonging to the Cairo tessellation, we find that single-layer PtP$_2$ is completely planar exhibiting dynamically stable phonon modes. We also observe a reduction in the bandgaps PtP$_2$ from bulk to single layer using the Heyd-Scuseria-Ernzerhof (HSE) hybrid density functional, and the bandgap type switches from indirect to direct. By contrast, using the standard Perdew-Burke-Ernzerhof functional leads to the conclusion of single-layer PtP$_2$ being metallic. We further study the bonding characteristics of this novel single-layer material by computing the Bader charge transfer, the electron localization function, and the crystal orbit overlap population, which show mixed P-P covalent bonding and Pt-P ionic bonding, with the former being stronger. Finally, we study the surface states of single-layer PtP$_2$ and consider the spin-orbit coupling. We observe no spin-helical Dirac cone states, therefore ruling out single-layer PtP$_2$ as a topological insulator. We expect the example demonstrated in this work will stimulate interest in computationally identifying novel 2D materials from a variety of bulk materials with the pyrite structure.

Stability of intrinsic and extrinsic co-decorated boron sheets with Li and Mg

The structural and mechanical properties and stability nature of Li and Mg co-decorated planar η-1/8 boron sheet have been investigated by density functional theory calculations. It is shown that the boron sheet is differently impressed by adding Li and Mg, and this doping process results in different geometric patterns originated from different binding nature of the adsorption cases. Interestingly, due to the planar (or in-plane) residual forces between the atoms, the stable intrinsic doping cases exist in addition to the external doping cases. The cohesive energies, binding and adsorption energies are calculated. The clustering energies of the possible dope cases are analyzed. The detailed bonding characteristics of the systems are presented by employing Mulliken atomic charges, bond overlap populations, and 2D/3D electron density maps. To investigate mechanical stability and to determine some mechanical properties such as layer modulus, Young's and shear moduli, and Poisson ratio, the elastic constants are calculated. Moreover, the multiple layer cases (2- and 3) of the boron sheet are studied with the van der Waals interactions, and then possible diffusion barriers for different paths are determined. The designed 2- or 3-boron layer systems could be promising cathode candidates for battery applications.

Conjugated polymers: A systematic investigation of their electronic and geometric properties using density functional theory and semi-empirical methods

Ten conjugated polymers (polypyrrole, polyfuran, polythiophene, polyborole, polycyclopentadiene, polysilole, polyphosphole, polycyclopentadienethione, polycyclopentadieneone, poly(p-phenylene)) have been investigated using density functional theory (DFT) and semi-empirical method. BP86-30% HF hybrid functional with CEP-31G* basis set combined with the quadratic regression provides bandgaps of polymers that are consistent with their optical experiment bandgaps. The higher contribution of quinoid character in polymer results in lower bandgap, and this observation is supported by shorter carbon – carbon bondlength of inter-rings of polymer with prefered quinoid character. The averaged crystal orbital overlap population (COOP) between carbon – carbon of inter-rings shows that polymer with higher orbital overlap population leads to lower bandgap. The resonance energies of polymers calculated using natural bond orbital method (NBO) show two opposite observations: very low bandgap polymer (≤0.19 eV) has highest resonance energy; however, with polymer having bandgap larger than 1 eV, higher resonance energy results in higher bandgap. This observation is due to the fact that resonance energy may be associated with electron delocalization over entire polymer backbone or within the rings. Band structures of polymers typically present direct bandgap at gamma point, and lower bandgap polymers do not essentially show higher carrier mobility.

Computational predictions of electronic properties of graphene with defects, adsorbed transition metal-oxides and water using density functional theory

The interfacial interactions between transition metal oxides (vanadium oxide VO2, vanadium pentoxide V2O5, cobalt oxide CoO and Co3O4, manganese oxide MnO2) and water adsorbates on graphene supports as solvated interfaces and influence of defects in graphene are studied using periodic density functional theory (DFT) calculations in view of their significance for applied electrochemistry. DFT complemented and synergized our experimental work. The optimized metal oxide adatom-graphene geometries identified the preferred adatom sites, whereas metal oxide-graphene strengths are correlated with the adatom distance from the graphene plane, the Metal-C overlap populations, and the adsorption energies. The presence of finite electronic density of states (DOS) near Fermi level and charge transfers between the adatom top layer and graphene supports reflect primarily covalent bonding nature. The presence of small orbital overlap integral of bonds between the s and p (and d) orbitals of the nearest carbon (graphene), carbon oxide (graphene oxide) and metal oxide atoms reveal localized orbital re-hybridization resulting in changes in DOS yielding high electrochemical activity. Moreover, for increased adatom coverage the extent of charge transfer reverses resulting in limited electroactivity. In fact, DFT calculations are corroborated with experimental findings, where graphene-based supports decorated with optimal mass loaded nanostructured Co3O4 and MnO2 (as well as V2O5) were capable of delivering maximum specific energy storage capacity (Cs) > 550 F·g−1 (Gupta et al. J. Mater. Res. 32, 301 (2017)) in contrast to higher or lower loading. The presence of defects in graphene materials results in new electronic states to endow unique functionalities that is not otherwise possible in the bulk and with adsorbed water molecules besides optimum C/O ratio in graphene oxide nanosheets that show redshift thus a decreasing bandgap and finite charge transfer from graphene to water molecules. The case examples studied in this work represent a first glimpse of what may become routine and integral step in materials design and discovery for alternative energy and sustainable environmental technologies.

DFT Calculation of Rhodium-Doped Silver Bromide Crystals: Defect Structures, Photoelectric Property and EPR

Abstract AgBr crystals containing impurity Rh2+ with and without a next nearest neighbor silver vacancy (VAg) in the [001] axis are theoretically studied. The defect structures, bandgap, Mulliken charge, density of states, ultraviolet-visible (UV-Vis) and electron paramagnetic resonance spectra are analysed for two distinct (i.e. tetragonally elongated and compressed) centres by using density functional theory calculations. The results demonstrate that the structural, photoelectric and spectroscopic properties of AgBr are significantly changed after Rh substitution. The covalency of Rh-Br bonds in the two centres is stronger than that of pure AgBr according to the larger magnitudes of the overlap population. Compared to pure AgBr, Rh doping also results in significantly enhanced red shifts of absorption bands in the UV-Vis region and some new d-d transitions in the visible and near-infrared regions. Meanwhile, the bandgap of Rh-doped AgBr is about 10 % narrower than that of pure AgBr. As a result, the visible light activity may be enhanced in AgBr:Rh systems. Rh dopants can induce the magnetic moments of about 1.73 μB for both centres. Therefore, transition-metal Rh dopants may effectively modulate the electronic, optical and magnetic properties of AgBr.

Strong interaction between 5f-electron atoms (Th-Cm) and point-defect graphene

The adsorption of actinides (An) atoms (AnThCm) on graphene surface with mono-vacancy (MV) and di-vacancy (DV) defects were studied with ZORA-DFT calculations. The interaction strengths of An and C in defective graphene are highly enhanced relative to pristine graphene. The magnetic moments of An-graphene with MV and DV defects are reduced by 2μb relative to the isolated An atoms due to the strong coupling between An and the neighboring carbon atoms. The AnC bondings show predominantly covalent nature, as observed by the electron density topological parameters. Bond overlap population (BOP) analysis indicates that the 6d orbitals of An atoms participate in the bonding to a higher degree than the 5f orbitals.

Investigation of electronic structure of {Nb2S4}4+ clusters by XES, XPS and DFT calculations

For the following compounds [Nb2S4(acac)4] (acac = acetylacetonate), К4[Nb2S4(ox)4] (ox = oxalate) and Nb2S4Br4 containing dinuclear cluster core {(Nb4+)2(μ-S22−)2}4+ (simply {Nb2S4}4+) the electronic structure has been experimentally and theoretically investigated through X-ray emission (XES), X-ray photoelectron (XPS) spectroscopies and Density functional theory (DFT). The bonding and antibonding highest occupied molecular orbitals (HOMOs) observed in the X-ray emission spectra have been characterized by the analysis of overlap populations and the partial atomic composition considering the nature of the electron density distribution. Furthermore, the effective atomic charges have been determined.

Defect Structures, Electronic Properties, UV–Vis, and EPR Parameters for Rh2+ Centers in LiD: A DFT Study

The defect structures and electronic properties of orthorhombic elongated (OE) and tetragonal compressed (TC) Rh2+ centers in LiD are theoretically studied using Density Functional Theory (DFT) with the periodic CP2K program. The calculations demonstrate obvious differences in defect structure between the two centers. OE center with one next nearest neighbor (nnn) cation vacancy (VLi) in [100] axis shows the Jahn‐Teller elongation of about 0.076 Å along [001] axis, whereas TC center with one nnn VLi in [001] axis exhibits a compression of about 0.049 Å along this direction. The ligand between the central Rh2+ and the VLi is found to move away from the VLi by about 0.038 or 0.035 Å for O­­E or TC center. The larger magnitude of the overlap population (≈ −0.5907 or −0.5494 e) of the RhD bonds in OE or TC center than that (≈0.2373 e) of the host LiD bonds in pure LiD indicates much stronger covalency of the former. The simulated UV–Vis and electron paramagnetic resonance (EPR) spectra with the embedded cluster model in ORCA code are consistent with the experimental data. The present results are discussed and compared with those of the previous perturbation calculations.

The alkaline earth-palladium-germanides Sr3Pd4Ge4 and BaPdGe

Abstract The germanides Sr3Pd4Ge4 and BaPdGe were obtained from high-temperature reactions in sealed niobium ampoules and their structures have been determined from single-crystal X-ray diffraction data: a=444.2(1), b=438.1(1), c=2472.2(7) pm, space group Immm, U3Ni4Si4 type, wR2=0.0471, 576 unique reflections, 25 parameters for Sr3Pd4Ge4 and a=677.09(8), space group P213, LaIrSi type, wR2=0.0322, 409 unique reflections, nine parameters for BaPdGe. Both germanides have pronounced three-dimensional [Pd4Ge4] δ− and [PdGe] δ− polyanionic networks with Pd–Ge bonding interactions. This is confirmed by the density functional theory (DFT)-based electronic structure investigations, the trends of charge transfer and crystal orbital overlap population (COOP) analyses.

Correlation between Am(III)/Eu(III) selectivity and covalency in metal–chalcogen bonds using density functional calculations

We applied density functional theory calculations to Am(III) and Eu(III) complexes with chalcogen-donor ligands of the formula N(EPMe2) 2 − (E = O, S, Se, Te). We calculated the equilibrium structures and relative stabilities of the complexes in the complexation reaction. The results indicated that the tendency of the relative stability is O ≪ S ~ Se ~ Te, which is consistent with the trend of soft acid classification. Molecular orbital overlap population analysis suggested that this tendency can be correlated with the bonding type in the covalent interaction between the f-orbitals of the metal atom and the chalcogen-donor atoms.

Conducting Behavior of Crystalline α-PbO2 as Revealed by DFT Calculations

PbO2 is one material that has recently emerged as potential transparent conducting oxide for applications in the modern opto-electronic industry. In this work the electronic structure of the α-PbO2 polymorph has been investigated, aiming to contribute to the understanding of its high levels of conductivity. DFT calculations using B3LYP hybrid density functional and considering long range interactions among the atoms have been performed. A direct band gap of 0.90 eV has been found, compatible with high conductivity values. Although the stoichiometric material is somewhat transparent, the band structure indicates that appropriated modifications in the material Fermi level can be performed in order to decrease the absorption of light. Charge distribution plus overlap population analysis show that the material is predominantly ionic. The charge distribution throughout the material is strongly dependent on the crystal direction. Results suggest that α-PbO2 can be potentially more interesting for opto-electronic purposes than the β polymorph.

X-ray emission study of the electronic structure of binuclear niobium complexes with (S2)2–disulfide bridging ligands

The electronic structure of binuclear niobium complexes [Nb2S4(acac)4] and K4[Nb2S4(ox)4] is studied by X-ray emission fluorescent spectroscopy and quantum chemistry techniques. Data on the partial atomic composition of highest occupied molecular orbitals of the complexes are obtained. The energy positions of bonding and antibonding frontier molecular orbitals observed in the X-ray emission spectra of binuclear [Nb2((S2)2–)2]4+ clusters are determined by the analysis of overlap populations.

Identifying specific prefrontal neurons that contribute to autism-associated abnormalities in physiology and social behavior.

Functional imaging and gene expression studies both implicate the medial prefrontal cortex (mPFC), particularly deep layer projection neurons, as a potential locus for autism pathology. Here, we explored how specific deep-layer prefrontal neurons contribute to abnormal physiology and behavior in mouse models of autism. First, we find that across three etiologically distinct models – in utero valproic acid (VPA) exposure, CNTNAP2 knockout, and FMR1 knockout – layer 5 subcortically-projecting (SC) neurons consistently exhibit reduced input resistance and action potential firing. To explore how altered SC neuron physiology might impact behavior, we took advantage of the fact that in deep layers of the mPFC, dopamine D2 receptors (D2Rs) are mainly expressed by SC neurons, and used D2-Cre mice to label D2R+ neurons for calcium imaging or optogenetics. We found that social exploration preferentially recruits mPFC D2R+ cells, but that this recruitment is attenuated in VPA-exposed mice. Stimulating mPFC D2R+ neurons disrupts normal social interaction. Conversely inhibiting these cells enhances social behavior in VPA-exposed mice. Importantly, this effect was not reproduced by nonspecifically inhibiting mPFC neurons in VPA-exposed mice, or by inhibiting D2R+ neurons in wildtype mice. These findings suggest that multiple forms of autism may alter the physiology of specific deep-layer prefrontal neurons which project to subcortical targets. Furthermore, a highly overlapping population – prefrontal D2R+ neurons – plays an important role in both normal and abnormal social behavior, such that targeting these cells can elicit potentially therapeutic effects.