Overlap Population Analysis Research Articles

CO adsorption mechanisms on transition metal surfaces and factors influencing the adsorption

CO adsorption on transition metal (TM) surfaces has been extensively studied. Compared to the "vertical adsorption" (CO⊥M) in which the C–O bond is normal to the surface with the C bonded to the surface, few studies are devoted to the "parallel mode" (CO||M) where the C–O bond is (near) parallel to the surface with both C and O atoms interacting with the surface. Here we report density functional calculations of CO adsorption on the stable surfaces of 27 TMs. The results show that CO adsorbs only in CO⊥M mode on IB, IIB, VIIB and VIII TMs while both CO⊥M and CO||M modes exist on IIIB to VIB TMs, with CO||M being more stable. Overlap population analysis reveals that the interactions between metal d AOs and O 2p AOs dominate the CO||M mode where the CO π bond is greatly weakened, resulting in significantly activated CO. The adsorption mode and adsorption energy can be tuned by ensemble effect, lattice strain and crystal structure, while the ligand effect is weak and is not able to change the adsorption mode of CO. The present work demonstrates that ensemble effect, lattice strain and crystal structure can be utilized to modify surface chemistry and promote catalytic performance effectively.

First-principles study of the effect of S-atom doping on the optoelectronic properties of stanene.

Based on the first principles, the influence of S-atom doping on the electronic and optical properties of stanene is comprehensively examined in this work. The results show that pure stanene is a quasi-metal with zero bandgap. After doping with an S atom, opening the bandgap of pure stanene becomes possible and the state of the stanene is converted from quasi-metal to semiconductor. Analysis of the density of states reveals that the density of states of all doped systems is primarily made of the p-orbital of the Sn. The overlap population analysis showed that charge transfer occurs between S and Sn atoms under different doping concentrations. The charge transfer increases with increasing doping concentration. The charge transfer reaches a maximum at a doping concentration of 9.38%. The increase in doping concentration causes blue-shifting of the absorption and reflection peaks of the doped system as compared to those of pure stanene. It is expected that these studies can provide theoretical guidance for the practical application of stanene in optoelectronic devices. All simulations are undertaken with the Cambridge Sequential Total Energy Package (CASTEP) (Wei et al. Physica B: Condensed Matter 545:99, 2018; Bafekry et al. Phys Chem Chem Phys, 2021; Zala et al. Appl Surf Sci, 2022; Bafekry et al. Nanotechnology, 2021; Bafekry et al. Phys Chem Chem Phys, 2021; Bafekry et al. J Phys: Condens Matter, 2021), which is based on density functional theory (DFT). For the exchange correlation, the generalized gradient approximation (GGA) is implemented with the Perdew-Burke-Ernzerhof (PBE) functional Perdew et al. Phys Rev B Condens Matter 48:4978, 1993. Using the Monkhorst-Pack technique, a specific K-point sample of the Brillouin zone was carried out Monkhorst and Pack Phys Rev B 13:5188, 1976. After the convergence tests, the K-point grid was set to 3 × 3 × 1. The plane-wave truncation energy was set to 400eV. The residual stress for all atoms was 0.03eV/Å. The energy convergence criterion was 1.0 × 10-5eV. To prevent recurring interactions between the layers, a vacuum layer with a thickness of 20Å was established in the Z-direction.

Structural and bonding properties of small hydrocarbons inside Ca(squarate)-metal organic framework: ab-initio study

Ab−initio Molecular Dynamic (MD) and static Density Functional Theory (DFT) are used to study the structural and bonding properties of small hydrocarbon adsorbates inside Ca(squarate)−Metal Organic Framework (MOF). Car−Parrinello Molecular Dynamics (CPMD) simulations of a single−adsorbate−MOF structure are used to obtain the adsorbate most preferred site of adsorption. This site is used for further structural and bonding analyses using static DFT. Unlike many other MOFs; we found that the Ca(squarate)−MOF physisorbs and weakly binds small adsorbate molecules such as C2H2, C2H4, C2H6, and C3H8 with no observed charge transfer and minimal hybridization with the MOF orbitals. No covalent bonding is seen near the preferred site of adsorption. The calculated binding energies decreases as the H content in the adsorbate molecule increases and found to be −18.71 kJ/mol, −18.14 kJ/mol, −15.75 kJ/mol, and—4.47 kJ/mol for C2H2, C2H4, C2H6, and C3H8 molecules respectively. Density of State (DOS) and a Crystal Orbital Overlap Population (COOP) analyses show that the interactions between C and H atoms in the molecule and C and O atoms in the MOF have antibonding characteristics near the Fermi level. These antibonding states tend to destabilize the overall electronic structure of the combined adsorbate/MOF system and hence decrease the binding energies of these adsorbates inside the MOF.

Cs2AgBiBr6 as a mixed anion perovskites for photovoltaic applications: A first-principle study

Ab initio calculations were performed for cubic Fm-3 m (225) and tetragonal (I4/m) phases for Cs2AgBiBr6(CaB2). We used the Vienna Ab Initio Simulation Package (VASP) to calculate the ground state properties using two different exchange-correlation functionals, namely the Generalized gradient approximation method (GGA) and the screened hybrid functional as proposed byHeyd,Scuseria, andErnzerhof (HSE06) method. Tetragonal Cs2AgBiBr6 phase was stabilized in the tetragonal phase. The bandgap (Eg) was calculated using HSE06 for the polymorphs optimized at the PBE level and it is found that they belong to the indirect bandgap. The calculated bandgap for cubic and tetragonal phases in HSE06 for Cs2AgBiBr6 were 1.97 eV, and 2.4 eV, respectively. The character of chemical bonding in CaB2 is discussed based on electronic structures, charge density, charge transfer, and bond overlap population analyses.

Substitution effect on electronic and optical properties of Tetraphenyldipyranylidene; A theoretical study

Density functional theory was used to study the structural, electronic, and optical properties of Tetraphenyldipyranylidene (DPPh) solid structure and its derivatives including electron-acceptor atoms and electron-donor groups. The nature of chemical bonding was investigated by crystal orbital overlap population analysis. The simulation results show that DPPh having electron-acceptor atoms (F, Cl, and Br) represent more favorable electronic and optical properties than that of electron-donor groups (CH3, C(CH3)3, OCH3, and OCH2CH3). Also, Br and Cl atoms improve both hole and electron transport of DPPh, which can be considered as a new series of promising ambipolar semiconductors. Finally, DPPh-Br and DPPh-Cl semiconductors are suggested as the preferred candidates for use in electronic devices in comparison with others derivatives.

Prediction of Transition-State Scaling Relationships and Universal Transition-State Vibrational and Entropic Correlations for Dehydrogenations

Linear scaling relationships (LSRs) and Brønsted–Evans–Polanyi (BEP) or transition-state scaling (TSS) relations aid with the prediction of electronic energies. However, temperature effects and pre-exponentials are often taken as constants across metal surfaces or a homologous series. Vibrational scaling relationships (VSRs) offer a way to determine such parameters. Transition-state VSRs (TSVSRs) between local minima and transition states of AHX (A = C, N, O) surface diffusions correlate with BEP relations and broaden to thermochemical property scaling. Using density functional theory, we extend TSVSRs to AHX dehydrogenation reactions on transition-metal surfaces, relating vibrational modes of local minima to transition states. We first predict the slopes of the TSS relations by incorporating bond angles using the Slater–Koster structure factors and hybridization through crystal orbital overlap population analysis and energy overlap integrals between adsorbates and metal surfaces. Additionally, we uncover universal thermochemical property scaling, enabling the estimation of entropies and temperature corrections to enthalpies across a homologous series. We demonstrate both significant vibrational corrections in reactions with low intrinsic electronic barriers and considerable variation in the pre-exponential of a simple dehydrogenation reaction across metals and AHX adsorbates.

Linking the polyatomic arrangements of interstitial H2O and cations to bonding within Prussian blue analogues ab initio using gradient-boosted machine learning

Prussian blue analogues (PBAs) are model host compounds for the intercalation of monovalent cations for electrochemical energy storage and separations. However, the interactions among interstitial species and their effects on atomic arrangements therein are understood mainly at a phenomenological level. Analyzing correlations between electronic interactions and polyatomic arrangements in hydrated Prussian blue analogues is complicated by the nonlocal hydrogen-bonding interactions between zeolitic water and framework lattices. Here, we train machine-learning (ML) models to learn DFT-calculated energy landscapes of nickel hexacyanoferrate PBA lattices with various lattice hydration degrees, oxidation states, and types of intercalated alkali cations based on various three-particle feature parameters. This ML approach is enabled by using gradient-boosted regression trees with features that are rotationally invariant geometric parameters. ML model accuracy is shown to be a cation-specific indicator of correlations between energy and polyatomic arrangements. Overlap population analysis among correlated atoms further confirms that such correlations are caused by the competition for dative bonding between Lewis-acid intercalated cations and Lewis bases (cyanide and oxygen in ${\mathrm{H}}_{2}\mathrm{O}$). Examination of lowest-energy structures reveals that cation hydrophilicity and bare ionic radius determine dative-bonding strength, resulting in cation-${\mathrm{H}}_{2}\mathrm{O}$ ordering in interstitial space. The projected energy landscapes of hydrated PBA lattices is also explored in subspaces spanned by certain many-particle feature parameters inspired by ML analysis. The downhill traces in such landscapes indicate that lattice distortion is accompanied by two kinds of collective movements: (1) rearrangements in the hydration shells around small and hydrophilic cations and (2) collective attack of ${\mathrm{H}}_{2}\mathrm{O}$ molecules on nickel-cyanide bonds promoted by large, hydrophobic cations.

Mechanism of Gold Cyanidation in Bioleaching of Precious Metals from Waste Printed Circuit Boards

Biocyanidation is an environment-friendly technology for recovering precious metals from waste printed circuit boards (WPCBs). Although the leaching mechanism has been studied a lot, Au-release behavior still remains unknown. In this paper, density functional theory (DFT) was employed to investigate the electronic structure of the complex existing in the Au cyanidation process. Extended charge decomposition analysis (ECDA) showed that the adsorption of CN– to Au and the adsorption of O to the formed [AuCN]⁻ caused net electron transfer of 0.356 and 0.574 au, respectively. Dissociation of O from [AuCNO]⁻ had a Gibbs free energy change of −154.229 kcal/mol. Electron localization function (ELF) and localized orbital locator (LOL) confirmed that CN– covalent bonding led to a transformation of the orbit localization region of the adsorbed Au atom. It might cause electrostatic repulsion from the nondirectly contacted Au atom. This speculation was demonstrated by the Mulliken overlap population analysis, which showed that CN– bonding caused antibonding interaction. The repulsive interaction would be an important factor triggering the release of the adsorbed Au atom. This work presented a new interpretation of Au cyanidation, providing important insights into Au-release behavior. It might help construct the leaching kinetics of multimetal resources to facilitate the recovery of precious metals from waste printed circuit boards.

Lithium‐Ion Batteries: Discovery of an Unexpected Metal Dissolution of Thin‐Coated Cathode Particles and Its Theoretical Explanation (Adv. Theory Simul. 5/2020)

It is believed that a thin coating layer deposited via atomic-layer deposition onto lithium-ion battery active material particles can prevent the metal dissolution degradation. However, in article number 2000002, Jonghyun Park and co-workers observe that while an Al2O3 coating can prevent dissolution a CeO2 coating intensifies it. They employ first-principles calculations by calculating the manganese vacancy formation energy, crystal orbital overlap population (COOP) analysis, Mn–O bond length, and projected density of state (PDOS) analysis.

Stability of carbon-vacancy complexes in α-Fe

We investigated the stability and structure of C n V and N n V complexes in α-Fe using first-principles calculations. In the case of C n V complexes, C2 V is most stable due to the energy gain by forming the C-C bonding. However, N2 V is less stable than N1 V. This is due to the repulsive interaction between N atoms in N n V complex. The overlap population analysis reveals that the C 2s - C 2s antibinding interaction is reduced by the C 2s - C 2p bonding interaction. The interaction between the N 2s and N 2p orbitals is not strong enough to cancel the N 2s - N 2s antibonding interaction because the energy difference between the N 2s and N 2p orbitals is larger than that between the C 2s and C 2p orbitals.

Structural, electronic and transport properties of a single 1,4-benzenediamine molecule attached to metal contacts of Au, Ag and Cu

We investigated molecular junctions formed by a single 1,4-benzenediamine molecule bridging between Au, Ag or Cu electrodes. We show that the molecule interacts stronger with Cu than both Ag and Au, which is in good agreement with the atomic overlap population analysis. The DFT-computed transmission characteristics of junctions described are dominated by tunnelling effects through the highest-occupied molecular orbital (HOMO). Our results also reveal that junctions formed with Au electrodes are more conductive than those formed with Ag and Cu electrodes, consistent with the lower work functions for Ag and Cu. By analyzing the calculated I × V curves for the Au,Ag,Cu/BDAH4/Cu,Ag,Au junctions we verify an ohmic behavior. In addition, a weak rectifying performance is verified, for all junctions. Our results thus reinforce the fact that the nature of the metal-molecule interaction and the choice of the electrode materials are important factors for modulating the transport properties of single-molecule junctions.

Hydrogen physisorption on palygorskite dehydrated channels: A van der Waals density functional study

The interaction between H2 molecules within the structure of microporous clays is an interesting topic, with applications including gas storage, nuclear waste containment, and geochemistry. Microporous clays exhibit an intricate atomic structure with different polar species able to interact with H2. However, despite its numerous implications, the binding mechanism of H2 has not been discussed in detail. In this work, a first-principles study of the structure, energetics, and chemical bonding of the H2 in palygorskite clay is addressed. Total energy calculations including van der Waals interactions shown that, depending on water content, the structural channels of palygorskite clays offer different possibilities for the adsorption of H2. The calculated binding energies range between 6 and 24 kJ/mol. The larger H2 binding affinity corresponds to the case where the Mg2+ nearest to the inner surface of the palygorskite channel is exposed due to a partial loss of coordination water. The analysis of net atomic charges predicts a slight charge transfer from H2 to Mg2+. Electronic structure and overlap population analysis reveal orbital interactions between the 3s and 3p states of Mg2+ with the σ orbitals of the H2 molecule, explaining the charge transfer and large binding energy in this system (24 kJ/mol). In contrast, Al3+ does not induce charge transfer from H2, while dispersion forces and electrostatic interactions dominate the binding mechanism. The results of the present study suggest that the controlled dehydration of coordinated water in Mg-rich palygorskite is a potential route to the creation of microporous materials with enhanced gas adsorption.

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.

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.

First-principles investigations of the electronic and magnetic structures and the bonding properties of uranium nitride fluoride (UNF)

AbstractBased on geometry optimization and magnetic structure investigations within density functional theory, a unique uranium nitride fluoride, isoelectronic with UO2, is shown to present peculiar differentiated physical properties. These specificities versus the oxide are related to the mixed anionic substructure and the layered-like tetragonal structure characterized by covalent-like [U2N2]2+motifs interlayered by ionic-like [F2]2−ones and illustrated herein with electron localization function projections. Particularly, the ionocovalent chemical picture shows, based on overlap population analyses, stronger U–N bonding versus U–F andd(U–N)<d(U–F) distances. Further generalized gradient approximation+U calculations provide the ground state magnetic structure as insulating antiferromagnet with ±2 μBmagnetization per magnetic sub-cell and ~2 eV band gap.

Ab initio study of ionic nature of 0.75AgI:0.25AgCl

Ab initio calculations based on density functional theory are performed for zinc-blende structured new host 0.75AgI:0.25AgCl. Eight configurations are simulated for different positions of Cl atoms, and they are divided into three sets of configurations. Similar calculations are also performed for zinc blende β-AgI. Bond lengths are changed and p-d hybridization is observed in all configurations. Ionic nature of atomic bonds is analyzed by the ionicity factor. The charge density analysis also exhibits the ionic and least covalent nature of bonds of AgI and AgCl atoms. The structural parameters are calculated to observe the bulk modulus. Crystal orbital overlap population analysis explains the inter-atomic bond strength which explains the bond breaking energy and activation energy of all configurations.