Terms Of Density Functional Theory Research Articles

Systematic Assessment of the Catalytic Reactivity of Frustrated Lewis Pairs in C-H Bond Activation.

Unreactive C-H bond activation is a new horizon for frustrated Lewis pair (FLP) chemistry. This study provides a systematic assessment of the catalytic reactivity of recently reported intra-molecular FLPs on the activation of typical inert C-H bonds, including 1-methylpyrrole, methane, benzyl, propylene, and benzene, in terms of density functional theory (DFT) calculations. The reactivity of FLPs is evaluated according to the calculated reaction thermodynamic and energy barriers of C-H bond activation processes in the framework of concerted C-H activation mechanisms. As for 1-methylpyrrole, 14 types of N-B-based and 15 types of P-B-based FLPs are proposed to be active. Although none of the evaluated FLPs are able to catalyze the C-H activation of methane, benzyl, or propylene, four types of N-B-based FLPs are suggested to be capable of catalyzing the activation of benzene. Moreover, the influence of the strength of Lewis acid (LA) and Lewis base (LB), and the differences between the influences of LA and LB on the catalytic reactivity of FLPs, are also discussed briefly. This systematic assessment of the catalytic activity of FLPs should provide valuable guidelines to aid the development of efficient FLP-based metal-free catalysts for C-H bond activation.

Intersystem Crossing Rates in Photoexcited Rose Bengal: Solvation versus Isolation.

We compare the intersystem crossing rate, kISC, of Rose Bengal (RB) in an aqueous pH 12 solution with the corresponding relaxation rates of four different RB-derived anion and dianion species isolated in the gas phase: the doubly deprotonated dianion ([RB-2H]2-), the singly deprotonated monoanion ([RB-H]-), and the corresponding singly negatively charged sodium and cesium adducts ([RB-2H + Na]- and [RB-2H + Cs]-, respectively). Each of them was probed following photoexcitation of their first singlet excited states (S1) at or near room temperature. The solution was studied by transient absorption spectroscopy, whereas the mass-selected anions were characterized by time-resolved photoelectron spectroscopy─all with ca. 50 femtosecond temporal resolution. [RB-H]- shows an S1 lifetime of ca. 80 ps; the solution ensemble, thought to consist primarily of solvated dianion chromophores, shows a similar lifetime of ca. 70 ps. By contrast, the isolated dianion, [RB-2H]2-, has a much longer lifetime. Superimposed on S1 decay attributable mainly to intersystem crossing, all four isolated anions also show some rapid oscillatory features of the transient photoelectron signal on a 4-5 ps timescale after excitation. Interestingly, an analogous phenomenon is also seen in the transient absorption measurements. We attribute it to a librational oscillation as the S1 state, initially populated in the S0 geometry, relaxes into its excited state equilibrium structure. Some implications of these observations for RB photophysics and interpretation of solution measurements are discussed─also in terms of density functional theory and time-dependent density functional theory calculations of ground and excited states.

Design and study of SrSnX2 (X=N, P, Sb, As, Bi) semiconductors using density functional theory

A series of novel, low-cost materials SrSnX2 (X=N, P, Sb, As, Bi) is explored through density functional theory in terms of structural, electronic, and optical properties to underline the usage of these compounds as photo-absorber materials. Within the modified Becke-Johnson exchange-correlation potential, SrSnN2 shows a direct band gap of 1.94 eV while other materials in the series show a natural intermediate band which supports the two-step optical transition and hence increases the absorption in the visible energy region. Calculated values of the effective mass of electrons, effective densities of conduction, and valence states are found comparable with typical photovoltaic materials (Si and CdTe). We have obtained a high open-circuit voltage of 1.75 V, fill-factor of 0.92 with maximum efficiency of about 23% under one sun condition with a thickness of 10 nm which suggests that SrSnBi2 stands as a potential candidate for photovoltaics. The calculated band-edges concerning normalizing hydrogen electrode appeal their use as efficient photo-electrocatalyst for water splitting. Overall, we suggest that the natural intermediate band gap-materials are promising candidate for low-cost and efficient photovoltaic and photo-electrocatalytic applications.

Designing of Thiazolidinones for COVID-19 and its Allied Diseases: An In silico Evaluation.

In silico studies in terms of density functional theory (DFT), molecular docking, and ADMET (absorption, distribution, metabolism, excretion and toxicity) were performed for 55 thiazolidinones compounds derived from different amines and aldehydes. DFT is a computational quantum mechanical modeling method used to predict the various properties of the compounds. Different parameters such as Electronegativity (x), Chemical Hardness (ŋ), Chemical Potential (μ), Ionization potential (IP), and Electron Affinity (EA), etc. were calculated by Koopmans theorem. The compounds were docked with Molecular Operating Environment (MOE) software using already reported PDB files of BChE, AChE, and α‐glucosidase. To analyze the Spike Glycoprotein of SARS‐Cov‐2 and heterocyclic compounds, molecular interactions study was carried out between Spike Glycoprotein of SARS‐Cov‐2 (6VXX) and 55 synthetic heterocyclic compounds. It was performed by the utilization of PyRx Virtual Screening Tool and AutoDock Vina based virtual environment was used in PyRx. Maximum binding affinity was observed with compound A7 which was −8.7 kcal/mol and then with A5 which was −8.5 respectively. In the case of the AChE enzyme, B5 has a maximum docking score of −12.9027 kcal/mol while C7 depicted the maximum score for the BChE enzyme with a value of −8.6971 kcal/mol. The docking studies revealed that C6 compound has maximum binding capacity toward glucosidase (−14.8735 kcal/mol). ADMET properties of under consideration compounds were determined by Swiss online‐based software which concluded that these molecules have a drug‐like properties and having no violation.

Resonant inelastic soft x-ray scattering on LaPt2Si2

X-ray absorption and resonant inelastic x-ray scattering spectra of LaPt2Si2 single crystal at the Si 2p and La 4d edges are presented. The data are interpreted in terms of density functional theory, showing that the Si spectra can be described in terms of Si s and d local partial density of states (LPDOS), and the La spectra are due to quasi-atomic local 4f excitations. Calculations show that Pt d-LPDOS dominates the occupied states, and a sharp localized La f state is found in the unoccupied states, in line with the observations.

A closed local-orbital unified description of DFT and many-body effects

Density functional theory (DFT) is usually formulated in terms of the electron density as a function of position n(r). Here we discuss an alternative formulation of DFT in terms of the orbital occupation numbers {n α } associated with a local-orbital orthonormal basis set {ϕ α }. First, we discuss how the building blocks of DFT, namely the Hohenberg–Kohn theorems, the Levy–Lieb approach and the Kohn–Sham method, can be adapted for a description in terms of {n α }. In particular, the total energy is now a function of {n α }, E[{n α }], and a Kohn–Sham-like Hamiltonian is derived introducing the effects of the electron–electron interactions via effective potentials, . In a second step we consider the Hartree and exchange energies and discuss how to describe them, in the spirit of a DFT approach, in terms of the orbital occupation numbers. In this contribution special attention is paid to the description of the (intra-atomic) correlation energy and corresponding correlation potentials {V corr,α }. For this purpose, a model system is analyzed in detail, whereby an atomic Hamiltonian interacts with the environment via a simplified model; the use of this model allows us to obtain the correlation energy and potentials (in terms of {n α }) for different cases corresponding to low, intermediate and high electron correlations.

New 1,2,3-Triazole Scaffold Schiff Bases as Potential Anti-COVID-19: Design, Synthesis, DFT-Molecular Docking, and Cytotoxicity Aspects.

Schiff bases encompassing a 1,2,3-triazole motif were synthesized using an efficient multi-step synthesis. The formations of targeted Schiff base ligands were confirmed by different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and CHN analysis). The spectral data analysis revealed that the newly designed hydrazones exist as a mixture of trans-E and cis-E diastereomers. Densityfunctional theory calculations (DFT) for the Schiff bases showed that the trans-trans form has the lowest energy structure with maximum stability compared to the other possible geometrical isomers that could be present due to the orientation of the amidic NH–C=O group. The energy differences between the trans-trans on one side and syn-syn and syn-trans isomers on the other side were 9.26 and 5.56 kcal/mol, respectively. A quantitative structure-activity relationship investigation was also performed in terms of density functional theory. The binding affinities of the newly synthesized bases are, maybe, attributed to the presence of hydrogen bonds together with many hydrophobic interactions between the ligands and the active amino acid residue of the receptor. The superposition of the inhibitor N3 and an example ligand into the binding pocket of 7BQY is also presented. Further interesting comparative docking analyses were performed. Quantitative structure-activity relationship calculations are presented, illustrating possible inhibitory activity. Further computer-aided cytotoxicity analysis by Drug2Way and PASS online software was carried out for Schiff base ligands against various cancer cell lines. Overall, the results of this study suggest that these Schiff base derivatives may be considered for further investigation as possible therapeutic agents for COVID-19.

Glass formation mechanism in aqueous formic acid solutions

The glass-formation mechanism in the HCOOH–H2O system, which occurred at component molar ratios from 1:2 to 3:2, was studied by calorimetry and quantum chemistry. The results were analyzed and interpreted in light of the laws that guide the formation of stable H-bonded hetero associates in binary systems. The thermo analytical curves for 1:2, 1:1, and 3:2 glasses each showed three thermal events due to glass transition at about –130°С, crystallization, and melting of crystals. The structures and energy parameters were calculated in terms of density functional theory for polymeric chain moieties comprised of one or two types of the HCOOH⋅(H2O)2, (HCOOH)2⋅(H2O)2, and (HCOOH)3⋅(H2O)2 hetero associates. Glass formation was shown to occur precisely when [HCOOH]:[H2O] = 1:2–3:2 due to the ability of those hetero associates to be linked into strongly bonded, unlimitedly long polymeric chains. The energy parameters of 1:2, 1:1, and 3:2 samples derived from the calorimetric experiment were compared to those gained from the calculations of moieties that model polymeric structures in these samples, so all experimentally observed thermal events were interpreted at the molecular level. The glass-formation mechanism in the HCOOH–H2O system where the key role is played by hetero associates and not by individual molecules was elucidated.

Density Functional Theory Investigation of the NiO@Graphene Composite as a Urea Oxidation Catalyst in the Alkaline Electrolyte.

Developing efficient and low-cost urea oxidation reaction (UOR) catalysts is a promising but still challenging task for environment and energy conversion technologies such as wastewater remediation and urea electrolysis. In this work, NiO nanoparticles that incorporated graphene as the NiO@Graphene composite were constructed to study the UOR process in terms of density functional theory. The single-atom model, which differed from the previous heterojunction model, was employed for the adsorption/desorption of urea and CO2 in the alkaline media. As demonstrated from the calculated results, NiO@Graphene prefers to adsorb the hydroxyl group than urea in the initial stage due to the stronger adsorption energy of the hydroxyl group. After NiOOH@Graphene was formed in the alkaline electrolyte, it presents excellent desorption energy of CO2 in the rate-determining step. Electronic density difference and the d band center diagram further confirmed that the Ni(III) species is the most favorable site for urea oxidation while facilitating charge transfer between urea and NiO@Graphene. Moreover, graphene provides a large surface for the incorporation of NiO nanoparticles, enhancing the electron transfer between NiOOH and graphene and promoting the mass transport in the alkaline electrolyte. Notably, this work provides theoretical guidance for the electrochemical urea oxidation work.

Active learning for robust, high-complexity reactive atomistic simulations

Machine learned reactive force fields based on polynomial expansions have been shown to be highly effective for describing simulations involving reactive materials. Nevertheless, the highly flexible nature of these models can give rise to a large number of candidate parameters for complicated systems. In these cases, reliable parameterization requires a well-formed training set, which can be difficult to achieve through standard iterative fitting methods. Here, we present an active learning approach based on cluster analysis and inspired by Shannon information theory to enable semi-automated generation of informative training sets and robust machine learned force fields. The use of this tool is demonstrated for development of a model based on linear combinations of Chebyshev polynomials explicitly describing up to four-body interactions, for a chemically and structurally diverse system of C/O under extreme conditions. We show that this flexible training database management approach enables development of models exhibiting excellent agreement with Kohn-Sham density functional theory in terms of structure, dynamics, and speciation.

CuII-benzotriazole complex activity in the electrocatalysis of oxygen reduction reaction: A theoretical study

The present work reports the findings of a quantum chemical study conducted in terms of density functional theory in order to analyze the parameters, such as bond length and angles, binding energy and vibrational frequencies, of CuIIBTAH complex isolatedly and of CuIIBTAH-O2 complex, aiming at assessing the catalytic activity of the complex in oxygen reduction reaction (ORR). The QTAIM and GAPT charges exhibited copper as electron acceptor and oxygen as electron donor during adsorption. The results show that CuIIBTAH-O2 complex can be used as a reference system to illustrate the importance of a redox pair of CuII/CuI and BTAH in ORR.

Atomistic modeling of electrocatalysis: Are we there yet?

AbstractElectrified interfaces play a prime role in energy technologies, from batteries and capacitors to heterogeneous electrocatalysis. The atomistic understanding and modeling of these interfaces is challenging due to the structural complexity and the presence of the electrochemical potential. Including the potential explicitly in the quantum mechanical simulations is equivalent to simulating systems with a surface charge. For realistic relationships between the potential and the surface charge (i.e., the capacity), the solvent and counter charge need to be considered. The solvent and electrolyte description are limited by the computational power: either molecules or ions are included explicitly or implicit solvent and electrolyte descriptions are adopted. The first option is limited by the phase‐space sampling that is at least 10 times too small to reach convergence, while the second is missing a realistic structuring of the interface. Both approaches suffer from a lack of validation against directly comparable experimental data. Furthermore, the limitations of density functional theory in terms of accuracy are critical for these metal/liquid interfaces. Nevertheless, the atomistic insight in electrocatalytic interfaces allows insights with unprecedented details. The joint theoretical and experimental efforts to design non‐noble hydrogen evolution catalysts are discussed as an example for the success of theory to spur and accelerate experimental discoveries.This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Electronic Structure Theory > Density Functional Theory

Real-space formulation of the stress tensor for O(N) density functional theory: Application to high temperature calculations.

We present an accurate and efficient real-space formulation of the Hellmann-Feynman stress tensor for O(N) Kohn-Sham density functional theory (DFT). While applicable at any temperature, the formulation is most efficient at high temperature where the Fermi-Dirac distribution becomes smoother and the density matrix becomes correspondingly more localized. We first rewrite the orbital-dependent stress tensor for real-space DFT in terms of the density matrix, thereby making it amenable to O(N) methods. We then describe its evaluation within the O(N) infinite-cell Clenshaw-Curtis Spectral Quadrature (SQ) method, a technique that is applicable to metallic and insulating systems, is highly parallelizable, becomes increasingly efficient with increasing temperature, and provides results corresponding to the infinite crystal without the need of Brillouin zone integration. We demonstrate systematic convergence of the resulting formulation with respect to SQ parameters to exact diagonalization results and show convergence with respect to mesh size to the established plane wave results. We employ the new formulation to compute the viscosity of hydrogen at 106 K from Kohn-Sham quantum molecular dynamics, where we find agreement with previous more approximate orbital-free density functional methods.

Extrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents

Discovery of potential lead molecule is a challenging, and complex process which require lots of money, patience, and manpower. Human beings are using natural products, predominantly secondary metabolites, for this purpose since ancient time and they are still working on them as a potent source for drug discovery due to their wide structural diversity. Phenolic phytochemicals such as hydroxytyrosol and tyrosol are natural antioxidant and involved in many biological disease cure. Herein, we have carried out the quantum chemical calculations for conformational analysis, geometry optimization and computation of electronic as well as optical properties of hydroxytyrosol and its analogues (1a–1k) in terms of density functional theory by using Gaussian 09 program suite. The eventual charge transfer within the molecules has been confirmed by the analysis of frontier molecular orbitals. The molecular docking studies of 1a–1k with cyclooxygenase-2 showed the noticeable binding affinity as compared to other nonsteroidal anti-inflammatory drugs viz. aspirin, naproxen and celecoxib. Computation of pharmacokinetics and pharmacological properties confirmed the lead/drug like potential of these screened molecules. Furthermore, the molecular dynamics simulation of best three docked ligands (1f, 1h and 1k)-receptor complex and their binding free energy calculations reveals that these molecules bind in the catalytic cavity of cyclooxygenase-2 and found stable during the 100 ns of simulation. Communicated by Ramaswamy H. Sarma

Cu/graphene interdigitated electrodes with various copper thicknesses for UV-illumination-enhanced gas sensors at room temperature.

Effective detection of NO2 and NH3 gases at room temperature (RT) is critical for environmental monitoring and protection. Here, graphene-based gas sensors (Cu/Gr device) of single layer graphene decorated by 6, 8 and 10 nm thick Cu layers with graphene instead of conventional metal as interdigital electrodes are designed and fabricated. The RT performance for both NO2 and NH3 detection can be greatly enhanced by UV light illumination which is closely related to the thickness of Cu layers in which the device with 8 nm thickness (8 nm Cu/Gr device) exhibits the best performances. Analysis of XPS reveals that Cu is partly oxidized to Cu+ and Cu2+ for 6 nm with extra Cuδ+ (1 < δ < 2) for 8 and 10 nm. The contents and distributions of copper oxides and copper in Cu layers influence the catalytic effects and the heterojunction barrier and thus the performances. The RT responses of -30.9% and -8.1% for 5 and 0.3 ppm NO2, and of +29.1% and +5.9% for 105 and 10 ppm NH3 are achieved for the 8 nm Cu/Gr device, respectively. The limits of detection (LODs) for NO2 and NH3 are 12 ppb and 17 ppb, respectively. The sensing mechanisms are discussed in terms of density functional theory (DFT) calculations and energy band diagrams. The study demonstrates an effective solution of improving the device performance by modifying the device configuration and incorporating combined oxides naturally oxidized, which provides the novel design alternatives for high performance sensors.

Symmetry-Adapted High Dimensional Neural Network Representation of Electronic Friction Tensor of Adsorbates on Metals

Nonadiabatic effects in chemical reaction at metal surfaces, due to excitation of electron-hole pairs, stand at the frontier of the studies of gas-surface reaction dynamics. However, the first principles description of electronic excitation remains challenging. In an efficient molecular dynamics with electronic friction (MDEF) method, the nonadiabatic couplings are effectively included in a so-called electronic friction tensor (EFT), which can be computed from first-order time-dependent perturbation theory (TDPT) in terms of density functional theory (DFT) orbitals. This second-rank tensor depends on adsorbate position and features a complicated transformation with regard to the intrinsic symmetry operations of the system. In this work, we develop a new symmetry-adapted neural network representation of EFT, based on our recently proposed embedded atom neural network (EANN) framework. Inspired by the derivation of the nonadiabatic coupling matrix, we represent the tensorial friction by the first and second derivatives of multiple outputs of NNs with respect to atomic Cartesian coordinates. This rigorously preserves the positive semidefiniteness, directional property, and correct symmetry-equivariance of EFT. Unlike previous methods, our new approach can readily include both molecular and surface degrees of freedom, regardless of the type of surface. Tests on the H2+Ag(111) system show that this approach yields an accurate, efficient, and continuous representation of EFT, making it possible to perform large scale TDPT-based MDEF simulations to study both adiabatic and nonadiabatic energy dissipation in a unified framework.

Investigations of Physical Properties of XTiH3 and Implications for Solid State Hydrogen Storage

Abstract This study adopts density functional theory to predict and thoroughly investigate new types of perovskite compounds for solid state storage of hydrogen. CaTiH3 and MgTiH3 perovskite hydrides are chosen and investigated using density functional theory in terms of ground state properties, electronic, mechanical, and thermodynamic properties for solid state storage of hydrogen. Stability of compounds are verified by calculating formation energies. Several crucial parameters; elastic constants, bulk, Young, Shear modulus, and Cauchy pressures are computed and analysed in great detail. Mechanical stability evaluation indicated that both compounds are mechanically stable whereas MgTiH3 is ductile whilst CaTiH3 is a brittle material. In addition, mechanical anisotropy is analysed using 2D surfaces. Both compounds showed anisotropic behaviour in all directions except for linear compressibility. Electronic band structures and their corresponding density of states of compounds are obtained. The results indicate that both compounds have metallic nature. From the results presented here, it can be predicted that MgTiH3 is a better material for hydrogen storage with a gravimetric density of ∼4.01 wt %.

Application of computer simulation for research of spatial structure, growth, and electronic properties of zero-dimensional structures on example of silicon-niobium anionic clusters

The results of geometric structure optimization and calculated electron spectra of anion clusters NbSin− (n = 6 − 18) are presented. The calculations were carried out in the terms of density functional theory. Real geometric structures of NbSin− clusters were established by the comparison of calculated and known experimental data. On the basis of the optimized geometries, energetic properties are calculated for the most stable isomers of clusters, including the average binding energy, fragmentation energy, and the second-order difference of energy. The mechanism of cluster formation is considered.

Exploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent

Drug discovery for a vigorous and feasible lead candidate is a challenging scientific mission as it requires expertise, experience, and huge investment. Natural products and their derivatives having structural diversity are renowned source of therapeutic agents since many years. Tyrosol (a natural phenylethanoid) has been extracted from olive oil, and its structure was confirmed by elemental analysis, FT-IR, FT-NMR, and single crystal X-ray crystallography. The conformational analysis for tyrosol geometry was performed by Gaussian 09 in terms of density functional theory. Validation of bond lengths and bond angles obtained experimentally as well as theoretically were performed with the help of curve fitting analysis, and values of correlation coefficient (R) obtained as 0.988 and 0.984, respectively. The charge transfer within the tyrosol molecule was confirmed by analysis of HOMO→LUMO molecular orbitals. In molecular docking with COX-2 (PDB ID: 5F1A), tyrosol was found to possess satisfactory binding affinity as compared to other NSAIDs (Aspirin, Ibuprofen, and Naproxen) and a COX-2 selective drug (Celecoxib). ADMET prediction, drug-likeness and bioactivity score altogether confirm the lead/drug like potential of tyrosol. Further investigation of simulation quality plot, RMSD and RMSF plots, ligands behavior plot as well as post simulation analysis manifest the consistency of 5F1A-tyrosol complex throughout the 20 ns molecular simulation process that signifies its compactness and stability within the receptor pocket.AbbreviationsADMETAbsorption, Distribution, Metabolism, Excretion and ToxicityÅAngstromCOX-2Cyclooxygenase-2DFTDensity Functional TheoryDMFDimethylformamideFMOFrontier Molecular OrbitalFT-IRFourier-transform Infrared SpectroscopyFT-NMRNuclear Magnetic Resonance SpectroscopyHOMOHighest Occupied Molecular OrbitalLUMOLowest Unoccupied Molecular OrbitalMDMolecular DynamicsNSNanosecondNSAIDsNon-steroidal anti-inflammatory drugsOPEOsiris Property ExplorerRMSDRoot-Mean-Square DeviationRMSFRoot Sean Square FluctuationCommunicated by Ramaswamy H. Sarma

Geometric structure and electronic properties of wurtzite GaN/HfO2 interface: A first-principles study

III-V interface with high-k oxide, especially HfO2, is crucial to the development of high mobility microelectronic devices. In this work, we systematically investigated the wurtzite GaN/cubic HfO2 interface based on the first-principles calculations with density functional theory in terms of the geometric structure and electronic properties. In order to mimic the high-k growth conditions, the interfacial oxygen contents in the slab interface models varied to study the interface stability and the relevant electronic structures. It is found that the oxygen rich interface, i.e., oxygen content of 83.3% (O5), shows the most stability in a large range of the oxygen chemical potential from 0 eV to −4.34 eV. Through the calculations of local density of states and Bader charge analysis, we noticed that increasing the interfacial oxygen content leads to the increase of the valence band offset (VBO) and the decrease of the conduction band offset (CBO), respectively. More importantly, interface O5 displays a promising VBO (0.86 eV) and CBO (1.34 eV), which meets the industrial requirements to confine the carrier in the III-V channel materials. Furthermore, no interfacial gap states are observed in interface O5, indicating that O5 is free of Fermi level pinning. This theoretical exploration suggests that varying oxygen content at the interface could result in the optimal interface for the applications of high mobility electronic devices.