Crystal Orbital Overlap Population Research Articles

Surface hydration of zircon and its influence on the adsorption of typical flotation collectors: First-principle calculations

Zirconium and hafnium are critical metals mainly extracted from the zircon mineral. However, due to the unclear surface properties of zircon, most designed flotation collectors (Surfactants to selectively enhance the hydrophobicity of targeted materials) cannot recover zircon effectively. Herein, zircon surface hydration microstructures and their effects on the adsorption of typical flotation collectors (i.e., phosphates, hydroxamic acids, carboxylic acids) have been revealed by systematic first-principles calculations. The speciation diagram and the surface hydration microstructures of zircon have shown that surface Zr sites with small coordination numbers have stronger water affinity. Water molecules have affected the final stable adsorption configurations of the collector. The further obtained adsorption energy of collectors shows that water molecules have weakened the activity of zircon surfaces and reduced the interaction intensity between collectors and surfaces. These results indicate that collectors with stronger negative charges and a lower highest occupied molecular orbital (HOMO) energy can tightly bind with the zircon surface. The electron localization function, density of states, and crystal orbital overlap population have consistently shown that collectors have formed ionic bonds with surface Zr sites. These conclusions should be meaningful for further design of flotation collectors to realize selective zircon flotation.

DFT study of superlight ambient temperature reversible H2 storage media based on Li decorated on new planar BCN

A novel 2D pm-BCN monolayer with unique porous geometry, superlight mass, and superior stability is a promising candidate for hydrogen storage. However, pure 2D materials suffer from the weak Van de Waals interaction between the H2, and modification becomes necessary to improve their performance. Here, we design a new complex by decorating active Li ions on the 2D pm-BCN substrate. The decoration of Li can transfer a partial electron to the substrate pm-BCN, which enhances the original π bonding among pm-BCN and induce more active sites on it. Both Li and BCN can act as the adsorption sites. The H2 can realize reversible adsorption under an ambient condition with average adsorption energy of −0.20 eV/H2 and a gravimetric capacity of 6.34 wt%, which surpasses the targe value set by U.S. Department of Energy (DOE). Rigorous analysis of its electronic properties, including a partial density of states, charge density, and crystal orbital overlap population, illustrates that the polarization mechanism contributes to the enhancement of the hydrogen storage capacity of Li@pm-BCN.

Adjusting OH tolerance of Ni4 clusters supported on ultra-small carbon nanotube with lattice vacancies for hydrogen oxidation catalysts

The hydroxide (OH) binding on Ni4 clusters supported on the (5, 5) ultra-small carbon nanotubes (CNTs) with lattice vacancies is theoretically investigated by applying the density functional theory (DFT) method. All Ni4 clusters are strongly adsorbed on the (5, 5) ultra-small CNTs with lattice vacancies and formed very stable Ni4/Vn structures. The results show that the OH binding energy (OHBE) at a Ni site nearly increases linearly with increasing Ni d band center. On the other side, this OHBE also increases as the number of vacancies increases. These findings could be attributed to interactions with carbon dangling bonds, which alter the electronic structure of the CNT-supported Ni4 clusters. Furthermore, an unusual behavior is observed for a Ni4 cluster supported on the (5, 5) ultra-small without a vacancy, where its OHBE is noticeably stronger than the others. These assertions are also supported by the projected crystal orbital overlap population (pCOOP), the projected crystal overlap Hamiltonian population (pCOHP), and the Mulliken–Löwdin analyses, which confirm the presence of bonding, anti-bonding, and non-bonding of OH states on Ni4/Vn. As a result, we can conclude that OH strongly binds to all Ni4/Vn. Adjusting OHBE tolerance to the Ni4 clusters is regarded as evidence of the CNT support effect, resulting in an increase in the activity of the hydrogen oxidation reaction (HOR) catalyst in an alkaline environment. It is necessary to make the high performance of the Ni cluster catalysts.

Regulating anionic redox activity of lithium-rich layered oxides via LiNbO3 integrated modification

Lithium-rich layered oxide cathodes suffer from severe interfacial degradation, capacity attenuation and voltage fading which mainly result from poor reversibility of anionic redox. In this study, a LiNbO3 integrated strategy including LiNbO3 coating, spinel heterostructure and Nb5+ doping has been proposed for stabilizing lattice oxygen and improving structural stability. Among them, the LiNbO3 coating layer can protect highly active peroxo-like oxygen from the electrolyte and spinel heterostructure with three-dimensional (3D) lithium transport channels facilitates the diffusion kinetics. More importantly, Nb5+ dopants inserting into subsurface lattice regulate localized electron configuration and strengthen the reversibility of anionic redox. Theoretical calculation results including density of states and crystal orbital overlap populations unravel the active O-O dimer still coordinates with crystal framework under fully delithiated state after Nb doping exhibiting enhanced anionic redox reversibility and structural stability. Corresponding analysis suggest that doping Nb5+ cations possessing no valence electron (4d0) and low electronegativity could transform Mn-O system into electrochemical inactive Nb-O system with large charge transfer and low d orbital repulsion (Mott-Hubbard regime). Moreover, this inactive Nb-O system cannot provide any reactive electron from Nb5+ cation and oxygen holes have to be isolated on O 2p orbitals, leading to the enhanced reversibility of anionic redox. This integrated modification strategy provides inspiring insights for understanding and regulating the reversibility of anionic redox, showing great potential in designing high-performance lithium-rich Mn-based cathodes.

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.

Peierls distortion of the cobalt chain in the low-temperature structure of CoIn2

Abstract CoIn2 (Z. Metallkd. 1970, 61, 342–343) forms by reaction of the elements at 1470 K followed by annealing at 770 K for five days. The room temperature structure is orthorhombic (CuMg2 type, Fddd, a = 529.95(10), b = 940.49(13), c = 1785.8(3) pm, wR2 = 0.0563, 444 F 2 values, 17 variables) and shows a phase transition at 195(1) K (DSC data). The low-temperature modification crystallizes in the translationengleiche monoclinic subgroup C2/c and exhibits a new structure type (a = 933.7(7), b = 526.91(10), c = 1000.8(2) pm, β = 117.81(5)°, wR2 = 0.0374, 843 F 2 values, 30 variables). The structural phase transition is a consequence of a Peierls type distortion. The equidistant cobalt chains in HT-CoIn2 (270.1 pm, 175.2° Co–Co–Co) show pairwise dislocation in LT-CoIn2 with shorter (252.4 pm) and longer (284.1 pm) Co–Co distances. Each cobalt atom has coordination number 10 in the form of slightly distorted square antiprisms of indium, capped by cobalt on the rectangular faces. Density-of-states calculations reveal metallic behavior for both modifications. Integrated crystal orbital overlap populations featuring the bonding characteristics indicate a slightly higher intensity area for LT-CoIn2 along with a shift to lower energy, manifesting the stabilization by pair formation through Peierls distortion.

RE 3Rh2Sn4 (RE = Y, Gd–Tm, Lu) – first stannides with Lu3Co2In4 type structure

Abstract The stannides RE 3Rh2Sn4 (RE = Y, Gd–Tm, Lu) were synthesized from the elements by arc-melting and subsequent annealing (1220 K for RE = Y, Gd–Tm and 1170 K for RE = Lu) in sealed silica ampoules for 11 days. X-ray powder diffraction studies confirm the hexagonal Lu3Co2In4 type structure, space group P 6 ‾ $P\overline{6}$ . The structure of Gd3Rh2Sn4 was refined from single crystal X-ray diffractometer data for a twinned crystal: a = 744.04(6), c = 409.23(4) pm, wR2 = 0.0288, 567 F 2 values and 21 variables. The RE 3Rh2Sn4 stannides derive from the well-known equiatomic stannides RERhSn (≍RE 3Rh3Sn3) by Rh/Sn ordering within the RE 6 trigonal prisms. The striking structural motif is the trigonal planar tin coordination of the Sn2 atoms with 288 pm Sn2–Sn1 distances. The Sn2 atoms carry substantially more negative charge than the Sn1 atoms. This is underlined by 119Sn isomer shifts of δ = 1.86(1) mm s−1 for Sn1 and δ = 2.26(1) mm s−1 for Sn2 detected in the Mössbauer spectrum of Lu3Rh2Sn4. From atoms in molecules (AIM) analysis of the charge density obtained with calculation based on density functional theory (DFT) for Y3Rh2Sn4, the charge transfer proceeds from yttrium towards more electronegative rhodium. Little departure from neutrality is observed for tin whose itinerant s-like states are little involved with the bonding. The site projected density of states (DOS) and the crystal orbital overlap population (COOP) plots further illustrate these observations and reveal major Y–Rh and Rh–Sn bonding, while Y–Sn bonding is weaker.

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.

Population analysis with Wannier orbitals.

We formulate Wannier orbital overlap population and Wannier orbital Hamilton population to describe the contribution of different orbitals to electron distribution and their interactions. These methods, which are analogous to the well-known crystal orbital overlap population and crystal orbital Hamilton population, provide insight into the distribution of electrons at various atom centers and their contributions to bonding. We apply this formalism in the context of a plane-wave density functional theory calculation. This method provides a means to connect the non-local plane-wave basis to a localized basis by projecting the wave functions from a plane-wave density functional theory calculation to a localized Wannier orbital basis. The main advantage of this formulation is that the spilling factor is strictly zero for insulators and can systematically be made small for metals. We use our proposed method to study and obtain bonding and electron localization insights in five different materials.

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning.

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C2H4) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousands of C2H4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number, outperform those trained using CO and NO spectra. A python package, pDOS_overlap, for implementing the electron density-based analysis on any combination of adsorbates and materials, is also made available.

Crystal Orbital Overlap Population and X-ray Absorption Spectroscopy.

We present an extension of an ab initio numerical tool calculating X-ray absorption spectroscopies and crystal orbital overlap populations at the same time. Density functional theory is used to calculate the electronic structure in both occupied (valence to core X-ray emission spectroscopy) and nonoccupied states (i.e., X-ray absorption near the edge structure and X-ray magnetic circular dichroism) and to evaluate the orbital overlap typifying the covalency between neighboring atoms. We show how the different features in the experimental spectra can be correlated to the chemical bonds around the absorbing atoms in several examples including acrylonitrile molecules, rutile TiO2, Li2RuO3 high-energy density cathode, ZnO, and anti-ferromagnetic V2O3.

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.

Electronic and elastic properties of brownmillerite

The elastic and electronic properties of brownmillerite (Ca2AlFeO5), the fourth component in mass of Portland cement, have been determined using Density Functional Theory. The Young’s modulus obtained in this work (E = 169 ± 2 GPa) is much closer to the experimental value than all the previously reported classical calculations. The electronic structure has been analyzed by calculating the band structure, the density of states and the crystal orbital overlap population curves. Results show that there are anti-bonding bonds between the iron and oxygen atoms which may create instability in the structure. The presence of those anti-bonding bonds might explain the limitation of force-field simulations when modeling the elastic properties of brownmillerite. Such a limitation may be extended to other structures derived from perovskites that present anti-bonding states.

Electronic structure based design of thin film metallic glasses with superior fracture toughness

High fracture toughness is crucial for the application of metallic glasses as structural materials to avoid catastrophic failure of the material in a brittle manner. One fingerprint for fracture toughness in metallic glasses is the fraction of hybridized bonds, which is affected by alloying Pd57.4Al23.5Y7.8M11.3 with M = Fe, Ni, Co, Cu, Os, Ir, Pt, and Au. It is shown that experimental fracture toughness data is correlated to the fraction of hybridized bonds which scale with the localized bonds at the Fermi level. Thus, the localized bonds at the Fermi level are utilized quantitatively as a measure for fracture toughness. Based on ab initio calculations, the minimum fraction of hybridized bonds was identified for Pd57.4Al23.5Y7.8Ni11.3. According to the ansatz that the crystal orbital overlap population at the Fermi level scales with fracture toughness, for Pd57.4Al23.5Y7.8Ni11.3 a value of around 95 ± 20 MPa·m0.5 is predicted quantitatively for the first time. Consistent with this prediction, in micro-mechanical beam bending experiments Pd57.4Al23.5Y7.8Ni11.3 thin films show pronounced plasticity and absence of crack growth.

Molecular docking, spectroscopic studies on 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one and QSAR study of a group of dopamine agonists by density functional method.

Density functional theory is one of the most popular accepted computational quantum mechanical techniques used in the analysis of molecular structure and vibrational spectra. Experimental and theoretical investigations of the molecular structure, electronic and vibrational characteristics of 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one are presented in this work. The title compound was characterized using FT-IR, FT-Raman and UV-Vis spectroscopic techniques. The results were compared with the theoretical calculations obtained using DFT/B3LYP with 6-311++G(d,p) as basis sets and was found to be in good agreement. The complete optimization of the molecular geometry of the title compound was carried out. Further, the vibrational assignments and calculation of potential energy distribution (PED) were reported. NLO has emerged as a key factor in recent researches. Materials showing nonlinear optical properties form the basis of nonlinear optics and development of such materials plays an important role in the present scenario. The current work provides sufficient justification for the title compound to be selected as a good non-linear optical (NLO) candidate. The electronic properties were reported using TD-DFT approach. The HOMO (EHOMO = -5.96 eV), LUMO (ELUMO = -0.80 eV) energies, energy gap and electrophilicity (2.22) was calculated in order to understand the stability, reactivity and bioactivity of the compound under investigation. To comprehend the bonding interactions we have performed the total (TDOS), partial (PDOS) and overlap population or COOP (Crystal Orbital Overlap Population) density of states. The drug likeness values were analyzed to evaluate the potential of the title compound to be an active pharmaceutical component. As a positive proof the paper further explains the molecular docking studies of the said compound. In addition, the stereochemistry of the protein structure was checked using Ramachandran plot. The title compound is a directly acting dopamine D2 agonist. In order to establish relationship between molecular descriptors of compound and its biological activity, QSAR studies have been done within the framework of DFT for 10 dopamine agonist including the title compound. Hence, the research exploration provides requisite information pertaining to the geometry, stability, reactivity and bioactivity of the compound through spectroscopic and quantum chemical methods.

A Discovery of an Unexpected Metal Dissolution of Thin-Coated Cathode Particles: Its Theoretical and Experimental Explanations

The degree of metal dissolution of cathode materials is a critical parameter in determining Li-ion battery performance. Ultra-thin coated LiMn2O4 (LMO) cathode particles via Atomic Layer Deposition (ALD) exhibit superior battery performance over bare LMO particles. However, we have observed that ultra-thin CeO2 coating intensifies Mn dissolution of LMO during cycling of lithium-ion battery, whereas ultra-thin Al2O3 coating tends to inhibit Mn dissolution. A detailed study of Density Functional Theory (DFT) has been carried out to illustrate the experimental observations. First, the manganese vacancy formation energy is calculated, along with the bonding strengths of Mn-O of uncoated, Al2O3 coated, and CeO2 coated particles via Crystal Orbital Overlap Population (COOP) calculations. Further, the projected density of state calculation of Mn is used to confirm the electronic occupancy of Mn atom for each case. Surprisingly, the atomic analysis is consistent with the experimental observations. This is the first report that coatings can accelerate metal dissolution, which can show new insights into ALD coatings and their impact on metal dissolution in cathode materials.

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.

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.

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.