Analysis Of Electron Localization Function Research Articles

Metal-induced Enhancement of Tetrel Bonding. The Case of C···X-IrIII (X = Cl, Br) Tetrel Bond Involving a Methyl Group.

In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X = Cl 1, Br 2; THT = tetrahydrothiophene; Xyl = 2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe···X-IrIII (X = Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe···X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe···X-IrIII (X = Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.

Zinc chloride-assisted activation of açaí biomass for herbicide removal: Insights from adsorption and molecular modeling

In addressing the environmental impact of açaí pulp production waste, this study explores the sustainable transformation of Euterpe oleracea fruit pits into activated carbon using a zinc chloride (ZnCl2) activation process. The primary aim is to repurpose this agricultural by-product for the efficient removal of atrazine (ATZ) and 2,4-dichlorophenoxyacetic acid (2,4-D) herbicides from contaminated water. The produced activated carbon demonstrated superior adsorptive properties, with a specific surface area (SBET) of 920.5 m2 g-1, substantial pore volume (Vp) of 0.467 cm3 g-1, and an average pore diameter (Dp) of 1.126nm, showcasing its potential as an effective adsorbent. Experimental adsorption tests revealed that this carbonized material could remove up to 95% of ATZ and 89% of 2,4-D under optimized conditions. Advanced techniques, including Density Functional Theory (DFT) simulations and COSMO-RS analysis, provided profound insights into the adsorption mechanisms, particularly emphasizing the crucial role of hydrogen bonding interactions. Identified as key mediators, hydrogen bonding-induced contact energy facilitated herbicide adsorption, corroborated by Electron Localization Function (ELF) analysis. These findings not only suggest a viable method for mitigating the environmental issue posed by açaí pulp waste but also contribute to the development of eco-friendly adsorbents for water purification. The research underscores the potential of using biomass waste for environmental remediation, aligning with global sustainability objectives.

DFT Calculations, Molecular Docking, and Pharmacological Properties Investigation for 5-Benzoxazolecarboxylic Acid as a Target Anti-Cancer Agent

In this study, the electronic properties of the 5-Benzoxazolecarboxylic acid molecule, a benzoxazole derivative, were calculated at the DFT/B3LYP/6-311++G(d,p) level of theory. Electronic properties and chemical reactivity of the optimized structure, such as Frontier molecular orbital (FMO), global and chemical reactivity descriptors, molecular electrostatic potential (MEP), and charge analyses (APT, Hirshfeld, and NBO), were investigated. Also, electronic properties are supported by electron localization function (ELF) and localized orbital locator (LOL) analyses. Toxicity effects such as mutagenic, tumorigenic, irritant, reproductive effect, and physicochemical properties such as druglikeness and drugscore were investigated. Molecular docking studies were conducted with the vascular endothelial growth factor receptor VEGFR-2 and the PARP-2 inhibitor, which is involved in many critical cellular processes, including DNA single-stranded fracture repair and cell death control, and its effectiveness in cancer treatment was investigated.

Mechanisms, regio- and stereoselectivities involved in NHC[sbnd]catalyzed dearomatizing annulation of ester with ylide: A computational study

The catalytic mechanism for dearomatizing annulation of ester with ylide by a chiral NHC catalyst is investigated by density functional theory (M06–2X) computations. After precatalyst activation giving active NHC, the transformation proceeds via five steps: (1) nucleophilic addition of the NHC to ester, (2) α−CH deprotonation to generate acylazolium intermediate, (3) coupling acylazolium intermediate with ylide to form a new C − C bond, (4) ring closure and (5) elimination of the NHC with formation of the annulation product tricyclic dihydroisoquinoline. The regio- and stereoselectivity controlling step is C − C bond formation. For regioselectivity, local reactivity index analysis indicates that the C1-addition is more favorable than either C3 or C4 addition. The stereoselectivity for the formation of SS-configurational product is ascribed to a number of noncovalent interactions (C–H·O, C–H·N and C–H·π). Electron localization function (ELF) analyses reveal the important role of the NHC in Ccarbonyl−Ocarbonyl bond breaking. These results enable both in-depth understanding of NHC catalysis and rational design of catalytic reactions.

In Silico Design and Characterization of a New Molecular Electride: Li@Calix[3]Pyrrole.

Electrides, in which anionic electrons are localized independentof the atoms in the compound, have shown promise especially as catalysts and optoelectronic materials. Here, we present a new computationally designed molecular electride, Li@calix[3]pyrrole (Li@C3P). Electron density and electron localization function analyses unequivocally confirm the existence of localized electride electron density,independent of any specific atoms. Non-covalent interaction plots further validate the character of the isolated localized electron, suggesting that the system can be accurately represented by Li+@calix[3]pyrrole⋅e-, denoting its distinct charge separation. The remarkable non-linear optical properties of Li@C3P, including average polarizability= 412.4 au, first hyperpolarizability= 4.46 × 104 au, and second hyperpolarizability= 18.40 × 106 au, are unparalleled in the previously reported and similar Li@C4P molecular electride. Furthermore, energy decomposition analysisin combination with natural orbital for chemical valencetheory sheds light on the mechanism of electron density transfer from Li to the C3P cage, yielding the charge-separated Li@C3P complex.In addition to the electron transfer, a key factor to its electride nature is the electronic structure of the CnP cage, which has its lowest unoccupied molecular orbitallocated in the void adjacent to the N-H groups at the back of the bowl-shaped CnP cage.

Computational study and ion diffusion analyses of native defects and indium alloying in β-Ga2O3 structures

Wide band gap semiconductors like gallium oxide are promising materials for high-power optoelectronic device applications. We show here a combined density functional theory and molecular dynamics study of diffusion pathways for different defects in β-Ga2O3. Molecular dynamics simulations result in a smaller equilibrium volume compared to density functional theory, but the overall lattice remains relatively unchanged even with the inclusion of defects, outside of the local distortions that occur to accommodate the presence of a defect. Slight thermal expansion occurs with elevated temperature and a combination of electron localization function and Bader charge analysis reveals that the oxygen interstitial is the most mobile defect as temperature is increased. However, interstitial cations may diffuse at elevated temperature due to a relatively small amount of charge transfer between the defect and lattice. The mobile oxygen defects are shown to increase the mobility of oxygen ions from the lattice, which can be beneficial for electrochemical applications when controlled through annealing processes.

Dynamic Covalent Bonds in the Ebselen Class of Antioxidants Probed by X-ray Quantum Crystallography.

Dynamic bonds are essential structural ingredients of dynamic covalent chemistry that involve reversible cleavage and formation of bonds. Herein, we explore the electronic characteristics of Se-N bonds in the organo-selenium antioxidant ebselen and its derivatives for their propensity to function as dynamic covalent bonds by employing high-resolution X-ray quantum crystallography and complementary computational studies. An analysis of the experimentally reconstructed X-ray wavefunctions reveals the salient electronic features of the Se-N bonds with very low electron density localized at the bonding region and a positive Laplacian value at the bond critical point. Bond orders and percentage covalency and ionicity estimated from the X-ray wavefunctions, along with localized orbital locator (LOL) and electron localization function (ELF) analyses show that the Se-N bond is unique in its closed shell-like features, despite being a covalent bond. Time-dependent DFT calculations simulate the cleavage of Se-N bonds in ebselen in the excited state, further substantiating their nature as dynamic bonds.

Insight into structural stability, electronic, optical and thermoelectric properties of the inverse perovskite Na3SCl compound from first-principles study

In the present work, we give a thorough analysis of the cubic inverse-perovskite Na3SCl's structural, electrical, optical, and thermoelectric properties using the FP-LAPW approach within the context of DFT. PBE-GGA has espoused for exchange-correlation the potential for the evaluation of structural characteristics. A well-known accurate potential for the computation of electronic structures known as TB-mBJ has also been added along with PBE-GGA for the computations of band structures and their density of states. The probe of cohesive energy, formation energy, and elastic aspects demonstrates that the material under study is chemically, and thermodynamically stable. The obtained lattice parameters and other structural data of the investigated Na3SCl are in well agreement with the reported results of similar compounds. A direct band gap of 3.493 eV identified from the band structure for Na3SCl demonstrates the semiconducting character of the examined antiperovskite. Charge density contours analysis reveals that Na3SCl possesses an ionic nature, which is confirmed by electron localization function (ELF) analysis. We additionally assessed optical constants for the Na3SCl, such as the dielectric function, optical reflectivity, refractive index, and electron energy loss, with radiation up to 12 eV. Furthermore, variations in temperature-dependent thermoelectric features in terms of Seebeck coefficient, thermal conductivity, electrical conductivity, power factor, and figure of merit have been determined for the first time using the BoltzTraP code. The perovskite under study has a p-type semiconducting nature, as indicated by the estimated positive Seebeck value, and holes rather than electrons are the predominant charge carriers for conduction. The obtained substantial figure of merit along with the low thermal-to-electrical conductivity ratio for the examined inverse perovskite imply it is suitable for thermoelectric applications in devices. Our examined Na3SCl inverse perovskite offers a fruitful framework for enhancing comprehensive TE efficacy for TE usage and green energy generation.

Superalkali nature of the Si9M5 (M = Li, Na, and K) Zintl clusters: a theoretical study on electronic structure and dynamic nonlinear optical properties.

Zintl clusters have attracted widespread attention because of their intriguing bonding and unusual physical properties. We explore the Si9 and Si9M5 (where M = Li, Na, and K) Zintl clusters using the density functional theory combined with other methods. The exothermic nature of the Si9M5 cluster formation is disclosed, and the interactions of alkali metals with pristine Si9 are shown to be noncovalent. The reduced density gradient analysis is performed, in which increased van der Waals interactions are observed with the enlargement of the size of alkali metals. The influence of the implicit solvent model is considered, where the hyperpolarizability (βo) in the solvent is found to be about 83 times larger than that in the gas phase for Si9K5. The frequency-dependent nonlinear optical (NLO) response for the dc-Kerr effect is observed up to 1.3 × 1011 au, indicating an excellent change in refractive index by an externally applied electric field. In addition, natural bonding orbitals obtained from the second-order perturbation analysis show the charge transfer with the donor-acceptor orbitals. Electron localization function and localized orbital locator analyses are also performed to better understand the bonding electrons in designed clusters. The studied Zintl clusters demonstrate the superalkali character in addition to their remarkable optical and nonlinear optical properties.

First-principles study of NO adsorption on defective hexagonal boron nitride monolayer

This study explored the potential of hexagonal boron nitride (h-BN) as a support for selective catalytic reduction (SCR) which means converting NOx to N2 and H2O with the aid of a catalyst. Specifically, we investigated the adsorption behavior of a NO molecule on a defective h-BN monolayer using density functional theory. Our results indicated that the initial configuration of N and O atoms over vacancy defects plays a key role in determining whether the NO molecule is adsorbed on the h-BN monolayer via covalent or ionic bonding. In the case of mono-vacancy, the ON configuration of the NO gas resulted in lower total energy (Etotal) compared with the NO configuration. Furthermore, electron localization function and Bader charge analysis, as well as projected density of states, revealed that the ON configuration over B or N vacancy resulted in chemisorption by hybridizing p-orbitals. Furthermore, the di-vacancy system led to an even lower Etotal compared with the mono-vacancy case. In particular, both N and O atoms were adsorbed chemically to the edge of vacancy defects, irrespective of the NO configurations above the di-vacancy. Our calculations revealed that the presence of vacancy defects contributed to improving the adsorption of the NO molecule to the h-BN monolayer.

Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives

The utilization of the density functional theory (DFT) methodology has developed as a highly efficient method for investigating molecular structure and vibrational spectra, and it is increasingly being employed in various applications relating to biological systems. This study focuses on conducting investigations, both experimental and computed, to analyze the molecular structure, electronic properties and features of (E)-4-(((9H-purin-6-yl)imino)methyl)-2-methoxyphenol (ANVA). The expression ANVA should be rewritten as follows: the compound is a derivative of adenine (primary amine), specifically a vanillin (aldehyde). The present study reports the synthesis, characterization, DFT, docking and antimicrobial activity of ANVA. The optimization of the molecular structure was conducted, and the determination of its structural features was performed using DFT with the B3LYP/cc-pVDZ method. The vibrational assignments were determined in detail by analyzing the potential energy distribution. A strong correlation was observed between the spectra that were observed and the spectra that were calculated. The calculation of intramolecular charge transfer was performed using natural bond orbital analysis. In addition, several computational methods were employed, including highest occupied molecular orbital–least unoccupied molecular orbital analysis, molecular electrostatic potential calculations, non-linear optical, reduced density gradient, localization orbital locator and electron localization function analysis. This paper examines the present use of adenine derivatives in combatting bacterial and fungal infections, as well as the inclusion of spectral and quantum chemical calculations in the discussion. Communicated by Ramaswamy H. Sarma

Enhancement of nonlinear optical properties of nanocarbon cluster C60 by aluminum doping

AbstractThe search for good nonlinear optical (NLO) materials is of utmost importance in laser technology and optical information science, making it a popular research topic in materials science. It is reported that the introduction of alkali metal Li can enhance the NLO properties of nanocarbon materials. Here, metal Al, which exhibits similar electron transfer characteristics to Li, was used for the first time to enhance the NLO properties of nanocarbon cluster C60, which possesses a large delocalized π structure and the highest yield in the fullerene family. Density functional theory calculations in combination with Boltzmann distribution showed that the most thermodynamically stable Al@Ih(1812)‐C60 exhibited good second‐order NLO properties, which originated from the noncentrosymmetry geometry and one extra delocalized electron on Ih(1812)‐C60 from the 3p shell of inner Al. Density of state analysis indicated that the molecular orbitals of Al@Ih(1812)‐C60 were primarily formed by Ih(1812)‐C60 with minimal Al participation, and the presence of Al always resulted in an antibonding orbital effect. Bond critical point and electron localization function analyses indicated almost no covalent interaction between Al and Ih(1812)‐C60. Exohedral functionalization was employed to further stabilize Al@Ih(1812)‐C60 with radical character, and the infrared spectrum was also analyzed in detail. This study has promising implications for expanding the potential applications of fullerenes in optical devices.

Structural, spectroscopic, and chemical bonding analysis of luminescent bis(diphenylphosphino)methane derived binuclear heteroleptic silver(I) complex of norharmane with argentophilic interaction

Silver(I) coordination compounds have a fascinating geometrical diversity, the ability to have different coordination numbers (typically from 2 to 4), and the ability to form argentophilic (Ag∙∙∙Ag) interactions. In this work, a binuclear Ag(I) heteroleptic complex with norharmane ‘β-carboline’ and bis(diphenylphosphino)methane (PP) ligands has been synthesized and characterized by various spectroscopic and single-crystal X-ray diffraction analyses. The bonding of Ag(I) coordination and Ag···Ag interaction is explored in depth. The theoretical approaches employed were perturbation theory within the context of the natural bond orbital (NBO) framework, quantum theory of atoms in the molecule (QTAIM), and electron localization function (ELF) analysis.

Interaction behavior study of HCl on (ZnS)n (n = 1–12) clusters and HCl effect on Hg0 adsorption

AbstractThe interaction behavior of HCl and (ZnS)n (n = 1–12) clusters and HCl effect on Hg0 adsorbed by (ZnS)n have been studied theoretically. The combined genetic algorithm and density functional theory (GA‐DFT) method has been used to obtain the structures of (ZnS)nHCl and (ZnS)nHgHCl (n = 1–12) clusters. The structural properties of (ZnS)nHCl and (ZnS)nHgHCl have been analyzed. The adsorption energies and interaction energies have been calculated. Bond length and bond order analysis has revealed that SH and ZnCl bonds form after HCl adsorbed on (ZnS)n clusters, while Hg0 can only weakly bind with (ZnS)nHCl clusters. According to thermodynamic adsorption analysis, the formation of (ZnS)nHCl clusters from (ZnS)n and HCl are spontaneous because of their negative Gibbs free energy changes. The formation of (ZnS)nHgHCl from (ZnS)nHCl and Hg are nonspontaneous for n = 1–4 and 9, and the Gibbs free energy changes have small negative values for other sizes. Electron localization function and noncovalent interaction (NCI) analysis of (ZnS)10HgHCl manifest that Hg and its nearest Zn form zinc amalgam. Projected density of state study has been performed to obtain the interaction nature of HCl and (ZnS)n clusters and Hg0 adsorption on (ZnS)nHCl clusters. Based on our study, HCl is chemical adsorbed by (ZnS)n clusters except (ZnS)4 cluster. After (ZnS)n adsorbs HCl, Hg0 can physically adsorb on (ZnS)nHCl clusters. The strength of Hg0 on (ZnS)nHCl is comparable to that of Hg0 on (ZnS)n, indicating that HCl can hardly affect the adsorption of Hg0 on ZnS clusters.

How genuine is the quadruple bond in AeF– (Ae = Be-Ba)?

Multiple bonding has fascinated chemist since its inception. Recently, genuine quadruple bond in AeF- (Ae = Be-Ba) has been proposed (Chem. Sci. 14 (2023) 4872–4887). The genuineness of such a quadruple bond is scrutinized here with electron localization function (ELF). ELF analysis reveals the presence of a disynptic Ae-F basin which integrates to <2.0 electrons, much lower than expected for quadruple bond. The presence of excess kinetic energy in the bonding basins makes these bonds a unique type called “Charge-Shift”.

Chromone-isoxazole hybrids molecules: synthesis, spectroscopic, MEDT, ELF, antibacterial, ADME-Tox, molecular docking and MD simulation investigations

A mechanistic study was performed within the molecular electron density theory at the B3LYP/6-311G (d,p) computational level to explain the regioselectivity observed. An electron localization function analysis was also performed, and the results confirm the zwitterionic-type (zw-type) mechanism of the cycloaddition reactions between nitrile oxide and alkylated 4H-chromene-2-carboxylate derivatives and shed more light on the obtained regioselectivity experimentally. In silico studies on the pharmacokinetics, ADME and toxicity tests of the compounds were also performed, and it was projected that compounds 5a, 5b, 5c and 5d are pharmacokinetic and have favorable ADME profiles. Moreover, docking and molecular dynamics investigations were conducted to evaluate the interactions, orientation and conformation of the target compounds on the active sites of four distinct enzymes. The results of this investigation showed that two compounds, 5a and 5c, interacted effectively with the S. aureus active site while maintaining acceptable binding energy. Communicated by Ramaswamy H. Sarma

Physical binding energies using the electron localization function in 4-hydroxyphenylboronic acid co-crystals with aza donors

Binding energies are traditionally simulated using cluster models by computation of each synthon for each individual co-crystal former. However, our investigation of the binding strengths using the electron localization function (ELF) reveals that these can be determined directly from the crystal supercell computations. We propose a new modeling protocol for the computation of physical binding energies directly from bulk simulations using ELF analysis. In this work, we establish a correlation between ELF values and binding energies calculated for co-crystals of 4-hydroxyphenylboronic acid (4HPBA) with four different aza donors using density functional theory with varying descriptions of dispersion. Boronic acids are gaining significant interest in the field of crystal engineering, but theoretical studies on their use in materials are still very limited. Here, we present a systematic investigation of the non-covalent interactions in experimentally realized co-crystals. Prior diffraction studies on these complexes have shown the competitive nature between the boronic acid functional group and the para-substituted phenolic group forming heteromeric interactions with aza donors. We determine the stability of the co-crystals by simulating their lattice energies, and the different dispersion descriptions show similar trends in lattice energies and lattice parameters. Our study bolsters the experimental observation of the boronic acid group as a competitive co-crystal former in addition to the well-studied phenolic group. Further research on correlating ELF values for physical binding could potentially transform this approach to a viable alternative for the computation of binding energies.

Investigating the mechanism behind the synergistic ultraviolet photooxidation degradation of gaseous benzene through modified ACF

The effects of relative humidity were studied on the direct conversion efficiency, mineralization rate and components of waste gas from benzene photooxidation degradation. The adsorption energies, adsorption types, and molecular interaction forces of activated carbon fiber (ACF) modified with nitrogen and oxygen-containing functional groups were calculated using quantum chemical density functional theory (DFT) calculations and wave function analysis. Five polar intermediate products including acetone, acetol, hexanal, benzaldehyde, and acetophenone generated from benzene photooxidation degradation were selected as the computational object. The independent gradient model method based on Hirshfeld partition was used to study the weak interactions among the five equilibrium molecular adsorption configurations. The results demonstrated that the direct conversion efficiency of benzene increased first and then decreased with increasing relative humidity. The maximum direct conversion efficiency was 82% observed at a relative humidity of 50%. The mineralization rate decreased significantly at higher relative humidity, and the lowest value was 2%. The overall adsorption effect of nitrogen-containing functional groups on the modified ACF surface is higher than that of oxygen-containing functional groups. The functional groups with the best adsorption effect are ACF modified by pyridone, amino and carboxyl groups. Combined with electron localization function (ELF) analysis and Mayer bond-level calculation, it was found that all the modified ACF surfaces do not form chemical bonds for the equilibrium molecular adsorption configurations of the five organic compounds, which belong to physical adsorption. The adsorption of five intermediate products by modified ACF mainly depended on hydrogen bonds or van der Waals forces. The existence of hydrogen bonds greatly improved the adsorption capacity of modified ACF to organic molecules.

Efficient Approach for the Synthesis of Aryl Vinyl Ketones and Its Synthetic Application to Mimosifoliol with DFT and Autodocking Studies.

An efficient and elegant method was developed for the preparation of substituted phenyl vinyl ketones using low-cost and commercially available ethyl chloroformate and diisopropylethylamine as reagents. This methodology was also applied to the synthesis of natural products such as mimosifoliol and quinolines. Frontier molecular orbital (FMO) studies on mimosifoliol were carried out to understand its chemical reactivity. Electron localization function (ELF) and localized orbital locator (LOL) analysis gave information about localized and delocalized electrons. Reduced density gradient (RDG) analysis gave information on steric, van der Waals, and hydrogen-bonding interactions. Molecular electrostatic potential (MEP) and Fukui functions gave information about nucleophilic and electrophilic attack. Nonlinear optical (NLO) analysis represented the mimosifoliol good NLO material. Molecular docking showed that the mimosifoliol compound had effectively inhibited the aspulvinone dimethylallyltransferase enzyme.

A DFT investigation of the catalytic oxidation of benzyl alcohol using graphene oxide.

Metal-free heterogeneous materials have attracted great interest due to their potential to facilitate various organic transformations in line with circular economy and green chemistry principles. Among various 2D materials, graphene oxide (GO) is considered an attractive material for numerous applications in physics, chemistry, biology, material sciences, and catalysis. Furthermore, graphene-based catalysts exhibit good catalytic activity toward the selective oxidation of benzyl alcohol to benzaldehyde or benzoic acid under eco-friendly conditions. In this regard, a theoretical investigation was carried out to study both catalytic oxidation reaction pathways (i.e., benzyl alcohols to aldehyde and to benzoic acid) using GO as an eco-friendly and metal-free catalyst. In this study, we report a theoretical investigation at the B3LYP/6-31G level to better understand the oxidation of benzyl alcohol using GO as a metal-free catalyst. The possible bond formation was investigated using the global and local reactivity indexes derived from Fukui functions. Furthermore, we performed a non-covalent interaction (NCI) analysis to unveil the stability and the interaction nature between both reagents and GO surface. The effect of the solvent on the oxidation efficiency was also performed and the results indicate that the solvent significantly affects the decrease of reactivity by increasing the activation barriers through oxidation reactions of benzyl alcohol. Additionally, the electron localization function (ELF) analysis was performed for all intermediates showing the ionic nature of the studied epoxide structure of GO and rules out any type of covalent interaction during the oxidation reaction of benzyl alcohol. All these obtained results are in good agreement with experimental observations and reveal that the epoxide functions on the graphene surface promote an excellent catalyst turnover.