Density Functional Study Research Articles

Identification of dimethyl 2,2’-((methylenebis(2-(2H-benzo[d][1,2,3]triazol-2-yl)-4-(2,4,4-trimethylpentan-2-yl)-6,1phenylene))bis(oxy))diacetate (TAJ4) as antagonist of NEK-Family: a future for potential drug discovery

The purpose of the current study was to analyze and validate the existing gap in knowledge, by conducting a differential expression analysis and validation of NEK6, NEK7, and NEK9 in breast, cervical, and glioblastoma cancer and targeting these proteins through development of novel site specific inhibitor with favorable pharmacokinetic and safety profile, using open-source databases. The analysis revealed that the targeted kinases were overexpressed in all three types of cancer. Their expression was significantly linked to overall survival rates, which suggests that they play a major role in the development and progression of these cancers. After, having the prognostic importance of These findings provided a rationale for synthesizing novel compound i.e., dimethyl 2,2’-((methylenebis(2-(2H-benzo[d][1,2,3]triazol-2-yl)-4-(2,4,4-trimethylpentan-2-yl)-6,1phenylene))bis(oxy))diacetate (TAJ4)), capable of effectively targeting these proteins using in-vitro cytotoxicity assays and comprehensive computational approaches. Then the inhibitory potential of TAJ4 was evaluated against cell lines of the respective cancers (HeLa cells, MCF-7 cells, and Vero cells). The growth inhibitory values (GI50) suggested that TAJ4 exhibited strong inhibitory potential towards MCF-7 cells (GI50 = 3.18 ± 0.11 µM) in comparison to the HeLa cell line (GI50 = 8.12 ± 0.43 µM), surpassing that of standard drugs. Furthermore, in-silico investigations, including density functional theory (DFT) calculations and molecular docking studies, revealed a substantial reactivity profile of TAJ4, with promising molecular interactions against NEK7, NEK9, TP53, NF-KAPPA-B, and caspase-3 proteins. Further investigation using in-vitro and in-vivo approaches is recommended to fully establish the therapeutic efficacy and safety profile of TAJ4.

Correction to: Density functional study of structural and optoelectronic properties of SnTe: rocksalt and orthorhombic phases

Correction to: Density functional study of structural and optoelectronic properties of SnTe: rocksalt and orthorhombic phases

Zr4+-doped sodium manganese oxide: enhanced electrochemical performance as a cathode in sodium ion batteries.

Sodium manganese oxides are regarded as a valuable class of cathode materials for sodium-ion batteries. By varying the stoichiometry of Na, Mn and O, it is possible to obtain layered, tunnel and spinel type structures, which can withstand the electrochemically-triggered sodiation-desodiation process. In this work, we report the electrochemical performance of Na4Mn2O5, a sodium-rich manganese oxide, which has been previously reported to suffer from structural instability due to the Jahn-Teller distortion of the Mn3+ ion. It was observed that the Na4Mn2-xZrxO5 (x = 0.1) cathode delivered a discharge capacity of ∼203 mA h g-1 post 250 cycles with a capacity retention rate of ∼82.8% on doping with Zr4+ ions. The improvement in cycling ability and rate capability is attributed to the enhanced structural stability and improved electronic conduction brought about by the substitution of Mn3+ by Zr4+ in Na4Mn2O5. Density functional theory-based studies were conducted, which adequately support the obtained results.

Computational studies molecular structure investigation and experimental characterization of Bis(2-aminothiazolium): quantum chemical analysis, electronic transitions, interaction mechanisms, and molecular dynamics

Bis(2-aminothiazolium) succinate succinic acid (ATSA), was synthesized and evaluated using standard spectroscopic studies. Density Functional studies were employed for the theoretical investigation of the substance, aiding in the determination of the chemical molecule’s structure and form. The molecule’s structural stability and the flow of charges within and between molecules were explored using natural bond orbital calculations. The primary binding sites and subtle interactions of the molecule were identified through topological analyses analysis endorse the ultimate charge transfer (CT) within the molecule. In the calculation of a chemical’s potential as a therapeutic candidate, pharmacological research is undertaken. This assessment encompasses molecule’s drug-likeness, pharmaceutical profile, and environmentally friendly toxicity contemplations. A molecular docking technique was used toward ligand spanning different antimicrobial targets, and the associated characteristics were imparted. When likened with positive controls and other pathogens, studies on antimicrobial activity expose that the compounds linked to Enterococcus faecalis, Staphylococcus aureus, Rhizopus stolonifer, and Penicillium notatum exhibit notable antimicrobial efficacy.

Density functional study of neutral bimetallic copper–gold clusters and their hydrides

Bimetallic Cu m Au n clusters and their hydrides Cu m Au n H (m + n ≤ 6) have been studied systematically using DFT to investigate the adsorption capacity of the copper–gold clusters for hydrogen atoms and understand the evolution of structural, electronic, and energetic properties as a function of size and composition of the system. The stability and charge transfer from Cu to Au are maximised when the composition of Cu m Au n clusters is nearly balanced. In Cu m Au n clusters, Au atoms favour the surface/edges/vertices with negative charges and Cu atoms tend to be inside with positive charges, which is convenient for partial charge transfer from Cu to Au atoms and give rise to larger electrostatic interaction energy. The structure of Cu m Au n H hydride does not always come from that of the lowest energy bare Cu m Au n cluster plus an attached H atom. Among various possible adsorption sites, the top and bridge sites are energetically preferred for smaller Cu m Au n with m + n ≤ 4, while only the bridge site is preferred for bigger clusters (5 ≤ m + n ≤ 6). Electrons always transfer from bimetallic clusters to adsorbate H, however, there is no simple relationship between H chemisorption energy and the charge transfer. There exists an approximately linear correlation between the metal−H bond length and the metal−H stretching frequency.

Experimental and density functional theory calculation study on the NO2 adsorption and reduction by KOH activated biochar

Biochar prepared from waste biomass as an adsorption and reduction material can effectively decrease decrease nitrogen dioxide (NO2) emissions. This work aims to select suitable materials to prepare biochar and improve its ability to adsorb and reduce NO2. In this study, the process of adsorption and reduction of NO2 by biochar and the effect of KOH activation on these reactions are studied by using fixed-bed reactor and density functional theory calculation. Experimental results indicate a positive correlation between the adsorption and reduction capabilities of biochar for NO2 and its specific surface area and surface oxygen groups. The biochar sample prepared by pyrolysis at 800 ℃ with the addition of 3 wt% KOH solution exhibits the highest adsorption capacity, likely due to the catalytic role of potassium (K) in the adsorption-reduction reaction. It is worth noting that the theoretical calculation results confirm this point. The K atom primarily facilitates the breaking of the N-O bond in NO2 and the desorption of the NO molecule on biochar through van der Waals forces, thereby lowering the reaction energy barrier. Thermodynamic and kinetic analyses further confirm these findings. This study has a new understanding of the mechanism of NO2 adsorption and reduction of by KOH activated biochar, which provides experimental basis and theoretical guidance for the application of this technology.

Density functional study of structural and optoelectronic properties of SnTe: rocksalt and orthorhombic phases

Density functional study of structural and optoelectronic properties of SnTe: rocksalt and orthorhombic phases

Assessing [DMAP-DABCO]AcO as an effective dual basic ionic liquid for the synthesis of chromeno[2,3-d]pyrimidine derivatives and exploring their anti-cancer activity through computational analysis

Here, we report the synthesis of a new dual basic ionic liquid viz. 1-[3-(dimethylamino)propyl]-1,4-diazabicyclo[2.2.2]octan-1-ium acetate [DMAP-DABCO]AcO, and its use as a catalyst for the synthesis of chromeno[2,3-d]pyrimidine derivatives through multi-component reaction approach involving salicylaldehyde derivatives, secondary amines and malononitrile. The ionic liquid and the chromeno[2,3-d]pyrimidine derivatives were characterized using FT-IR, 1H and 13C NMR, and Mass spectrometry techniques. The synthesized derivatives were evaluated for their in vitro anti-cancer activity against the MCF7 cell line. The compound 4a showed the highest anti-cancer activity with an IC50 value of 65.25 µg/mL compared with the standard drug 5-FU. The anti-cancer activity of synthesized derivatives was additionally validated through computational studies, including molecular docking, density functional study (DFT), and absorption, distribution, metabolism, excretion, and (toxicity) ADME(T) analysis.

A density-functional theory study of the interaction of rimantadine drug molecule with X-doped fullerene (X = B, Al, Ga, Si, Ge, BN, AlN, GaN, SiN, GeN)

Abstract This research investigated the interaction of rimantadine (RMT) drug molecule with fullerene C60 and heterofullerenes through density-functional theory calculations. Heterofullerene was used as a nanomaterial through the introduction of the following dopants into fullerene C60: B, Al, Ga, Si, Ge, BN, AlN, GaN, SiN, GeN, AlN2, AlN3, (AlN3)2, (AlN)3, (AlN2)3, and (AlN3)3. The adsorption energy and charge transfer were analyzed to investigate the interaction between RMT and heterofullerene. The addition of the N dopant to C59Al heterofullerene enhanced the adsorption energy, which enabled the transport of three molecules of the RMT drug.

Influence of biaxial and isotropic strain on the thermoelectric performance of PbSnTeSe high-entropy alloy: A density-functional theory study

Strain engineering is an effective method to improve materials thermoelectric (TE) performance. In this study, both biaxial and isotropic strains ranging from −3% to +3 % and from −3% to −1%, respectively, were applied to improve the TE properties of PbSnTeSe high entropy alloy (HEA). The effects of strain on the TE transport properties of PbSnTeSe HEA were investigated using first-principles calculations combined with Boltzmann transport theory. Under biaxial strain, n-type doped PbSnTeSe HEA shows an increase in the optimal power factor (PF) with both compressive and tensile strains. For p-type doping, compressive strain enhances the PF, whereas tensile strain reduces it. Within a strain range of −3% to +3 %, the optimal PF are 7.8–9.5 mW/mK2 for n-type and 0.85–1.3 mW/mK2 for p-type doped PbSnTeSe HEA. The maximum figure of merit (ZT) value of 1.63 for n-type doped PbSnTeSe HEA at 300 K under 3 % tensile strain is 61 % higher than the ZT value of 1.1 without strain. Under isotropic strain ranging from 0 % to −3%, the PF increases from 7.8 to 14 mW/mK2 for n-type and from 1.1 to 3.4 mW/mK2 for p-type doped PbSnTeSe HEA. Additionally, isotropic strain boosts the maximum ZT value for p-type doped PbSnTeSe HEA at 300 K from 0.3 to 0.85 under −3% strain. This study confirms that strain engineering is an effective strategy to enhance the thermoelectric properties of PbSnTeSe HEA.

Cubic-like A4B4 (A = Be, Mg, Ca; B = O) clusters for novel potential applications under density functional study

A density functional investigation of A4B4 (A = Be, Mg, Ca; B = O) metal-oxide clusters series is carried out in search for the stable and potential candidates. The minimum energy isomers for each of the A4B4 systems are identified, and frontier molecular orbitals (FMOs) have been generated and analyzed for the same. It is noteworthy that two nearly cubic-like stable motifs have been identified along with favorable electronic and optical properties that may be utilized for developing novel, useful nanomaterials. All the A4O4 systems revealed to be of cubic-like lowest energy structures, very interestingly, cubic Mg4O4 (λ = 418 Å) and cubic Ca4O4 (λ = 552 Å) are obtained as visible active clusters, which certainly confirms their promises in developing novel cluster-assembled nanomaterials with different dimensions with applications in optical and semiconductor arenas. Simulated infrared spectra of these identified novel cubic-like cluster-building units might help experimentalists with the possible synthesis and applications.

Cholesterol-Based B-Ring 2H-Pyran: Synthesis and Reaction Mechanism by Using Density Functional Theoretical Study

Abstract: The steroidal B-ring 2H-pyran 2 is synthesized by reacting steroidal B-ring α,β- unsaturated ketone 1 and 2-cyano-N-methylacetamide by refluxing for 18 h in methanol in the presence of a catalyst, i.e., chitosan. The product is obtained with a yield of 67%. The structure of the final product 2 is confirmed by utilizing IR, Mass, 13C and 1H NMR spectra. The reaction mechanism of the steroidal pyran ring formation is explored in this paper. The reaction pathway is described by using FMO analysis and relative energies of starting material, intermediate, and transition states, calculated by using the theoretical method, i.e., DFT with B3LYP/6-31G(d). It is found that two intermediates are formed throughout the reaction, which undergo a respective transition state (TS1 and TS2). The energy barrier of each step of the reaction is also calculated. It is also concluded that the reaction is endothermic. The green synthetic method reported in this study would be very useful for the synthetic and medicinal chemists involved in the synthesis of biologically important pyran ring-containing heterocyclic compounds.

First-principles density functional study of iodine molecule adsorption on stable CuS surfaces

The present work investigated the adsorption of gaseous iodine molecules (I2) on stable CuS surface, which has demonstrated excellent performance as an adsorbent for I2 removal, with first-principles density functional theory (DFT). In this work, a pair of asymmetric surfaces (marked as slab1 and slab2) formed by breaking the weakest bond along (001) direction are chosen to present CuS surfaces. The findings indicate that the adsorption of I2 molecules on the pristine CuS(001) surface is relatively weak, while surface defects significantly enhance the binding strength of I2. In particular, S-vacancy CuS(001) surfaces exhibit considerably higher adsorption energy for I2 compared to Cu-vacancy surfaces. We found that the hollow and Cu-top sites are typically the dominant adsorption sites, and the initial orientation of I2 relative to the surface also influences the adsorption performance.

Regulating Peripheral Nitrogen Dopants in Single-Atom Catalysts to Enhance Propane Dehydrogenation.

For single-atom catalysts (SACs), the dopants situated near the metal site have demonstrated a significant impact on the catalytic properties. However, the effect of dopants situated further away from the metal centers and their working mechanisms remain to be elucidated. Herein, we conduct density functional theory-driven studies on regulating the peripheral nitrogen dopants in graphene-based SACs, with a particular focus on Ir1 SAC, for propane dehydrogenation (PDH). It is found that increasing the distance between the N dopant and the Ir1 site results in a different energy change for the reaction process compared to the dense doping model with only first and second-shell N species. The proposed stochastic doping models demonstrate statistically that increasing the N dopant in farther shells not only enhances the activity of Ir1 but also maintains a high selectivity for propene, which is verified by experimental tests. The modulation of the d-band center of Ir1 by stochastic N dopants effectively modifies the binding strength of reaction intermediates, thereby enabling the optimization of the potential energy surface of PDH. These results deepen the understanding of dopant states around metal sites and provide an important implication for the doping engineering in heterogeneous catalysis.

Structural and energetic properties of cluster models of anatase-supported single late transition metal atoms: a density functional theory benchmark study.

Single-atom catalytic systems constitute an intriguing research topic due to their inherently different chemical behavior as compared to classic heterogeneous catalysts. In this study, cluster systems representing single late transition metal atoms adsorbed on anatase were constructed starting from previously generated periodic models and subjected to a density functional theory (DFT) benchmark study. The ability of different density functional approximations representing all rungs of the Jacob's Ladder classification to accurately describe bond lengths and adsorption energies was assessed for these clusters with the aim of revealing the functional that allows to retain the structural characteristics of the initial periodic system, while also delivering reliable energetics. In this regard, our results indicate that optimisation of the clusters with the meta-GGA functionals TPSS or RevTPSS provides the lowest mean unsigned error and root-mean-square deviations with respect to the periodic models. Moreover, these functionals and, to a slightly lesser degree, PW91 were also found to provide adsorption energies that are statistically the least deviating from the CCSD(T) reference data. More complex hybrid functionals appear to be performing less well. Cluster geometries were determined at the Kohn-Sham DFT level using the LANL2DZ basis set for the transition metals and the Pople 6-31G(d) basis set for O and H. The density functional approximations considered were SVWN, PBE, BP86, BLYP, PW91, TPSS, RevTPSS, M06L, M11L, B3LYP, PBE0, M06, M06-2X, MN15, ωB97X-D, CAM-B3LYP, M11, and MN12-SX. Reference adsorption energies of the metals on the support cluster were obtained at the CCSD(T)/LANL2TZ (transition metals)/6-311 + + G(d,p)//RevTPSS/LANLD2DZ (transition metals)/6-31G*. Besides the above-mentioned functionals, energy calculations using the double-hybrid functionals, DSDPBEP86, PBE0-DH, and B2PLYP, were also performed. All adsorption energy calculations were carried out on the RevTPSS geometries.

Cooperative Anion-π and C-H-Cl Interactions in Multifunctional Naphthalene-Based Receptors for Chloride Recognition: Cage-Size Modulation Through Substitution Patterns.

This study introduces a novel approach for chloride recognition utilizing multifunctional naphthalene-based receptors. By strategically modifying the substitution patterns on tetrafluoropyridines, a series of new receptors with customized cavities and enhanced binding capabilities were developed. Density functional theory (DFT) calculations and experimental studies combining NMR spectroscopy and mass spectrometry confirmed the efficacy of these receptors in capturing chloride ions. The relative chloride affinity order determined experimentally is in agreement with DFT predictions. The synergistic effect of anion-π and C-H…Cl interactions, mediated by the TFP groups, played a crucial role in achieving high binding affinity. This work provides valuable insights for designing future anion receptors with improved performance.

A density functional study of type I to type II crossover in g-C3N4/CoN4 heterostructure in presence of external perturbation

Herein, we report the impact of external perturbation on the photocatalytic performance of g-C3N4/CoN4 heterojunction and concomitant transition from type-I to type-II. The state-of-the-art theoretical modeling presented here is the first study on dynamic role of strain and electric field on g-C3N4/CoN4 heterojunction and its potential application as a solar-driven water splitting reaction. Utilizing the density functional theory (DFT) calculation, V. N. et al. recently reported the photocatalytic activity of g-C3N4/MN4 (M = Mn, Fe and Co) heterojunction [J. Comput. Chem. 2024, 45, 2518-2529, https://doi.org/10.1002/jcc.2746412] and subsequently established g-C3N4/CoN4 as a type I heterojunction for photocatalytic water splitting reaction [Phys. Chem. Chem. Phys. 2024, 26, 21117–21133]. In the present study, we applied external perturbation in the form of mechanical strain, electric field and evaluated the electronic structure properties of the system along with the detailed examination of concomitant optical and magnetic properties of g-C3N4/CoN4 heterojunction. The switching of photocatalytic feature from type I to type II originates due to the crossover between valence band maxima (VBM) of g-C3N4 and CoN4 in presence of external perturbation. Notably, the resulting system acts as a type II photocatalyst for water splitting reaction while applying compressive (negative) strain of −2 to −6% and an electric field of −0.5 and +0.5 V/Å, respectively. Accumulation of photogenerated electrons and holes separately in g-C3N4 and CoN4 units confirms the perceptible separation of charge carriers and thereby reduces the recombination compared to un-perturbed system. A red-shifted absorption maximum (689 nm), superior charge transfer (0.9e), and clear separation of photogenerated electrons and holes are the origin of enhanced photocatalytic efficiency of g-C3N4/CoN4 heterojunction in the presence of external perturbation. We believe that our work will provide enough evidence to the experimentalists to achieve such a system in practice leading to human-friendly applications.

Hybrid Density Functional Study on the p-Type Conductivity Mechanism in Intrinsic Point Defects and Group V Element-Doped 2D β-TeO2.

The newly discovered two-dimensional (2D) β-TeO2 possesses extraordinarily high p-type carrier mobility and demonstrates immense potential in the electronics field. However, current research on its p-type conductivity mechanisms and the modifications of element doping remains relatively insufficient. In this study, the intrinsic point defects and extrinsic element doping in monolayer β-TeO2 are comprehensively analyzed to probe the potential sources of the intrinsic p-type conductivity and the extrinsic p-type doping possibility in 2D β-TeO2 through hybrid density functional calculations. Our results reveal that the vacancy defects with low formation energies have deep transition levels and thus cannot be used as sources of unintentional p-type conductivity in 2D β-TeO2. The investigations and discussions via Group V element doping modifications in 2D β-TeO2 indicate that bismuth (Bi) doping can easily and significantly enhance the p-type conductivity of 2D β-TeO2 under the presence of O-rich, which can be achieved experimentally. Furthermore, Bi doping can significantly increase carrier mobility without seriously affecting the electronic structure. The finding shows that the Bi element is an ideal dopant candidate for a p-type modification in 2D β-TeO2. Our calculations pave an alternative strategy to achieve the realization of superior p-type conductivity in 2D β-TeO2.

Boosting Suzuki coupling reaction via pore expanding and palladium–zinc alloying

A palladium–zinc alloy nanoparticles decorated nitrogen-doped porous carbon catalyst (PdZn30–NC) was synthesized and utilized for Suzuki coupling reaction. The alloying palladium (Pd) with zinc (Zn) and pore expanding are realized simultaneously. Density functional theory (DFT) calculations and experimental studies reveal that the alloying Pd with Zn can lower the energy barrier in Suzuki coupling reaction. Nitrogen adsorption–desorption measurements uncover that pore expansion caused by the zinc nitrate hexahydrate assisted calcination gives rise to the multiplication of mesopore with a pore diameter of 6 nm, which facilitates mass transfer during the reaction. As a result, the alloying Pd with Zn and pore expanding together endow PdZn30–NC with excellent catalytic activity. PdZn30–NC demonstrates exceptional catalytic activity and stability in Suzuki coupling reaction. A high biphenyl yield of 97.7 % within 40 min and stable reusability of 93.3 % yield after five reuse cycles can be achieved. This work not only offers a viable method for Suzuki coupling reaction, but also provides insights for designing new catalysts toward Suzuki coupling reaction.

Adsorption and Catalytic Reduction of Nitrogen Oxides (NO, N2O) on Disulfide Cluster Complexes of Cobalt and Iron-A Density Functional Study.

The reactivity of nitrogen oxide, NO, as a ligand in complexes with [Fe2-S2] and [Co2-S2] non-planar rhombic cores is examined by density functional theory (DFT). The cobalt-containing nitrosyl complexes are less stable than the iron complexes because the Co-S bonds in the [Co2-S2] core are weakened upon NO coordination. Various positions of NO were examined, including its binding to sulfur centers. The release of NO molecules can be monitored photochemically. The ability of NO to form a (NO)2 dimer provides a favorable route of electrochemical reduction, as protonation significantly stabilizes the dimeric species over the monomers. The quasilinear dimer ONNO, with trans-orientation of oxygen atoms, gains higher stability under protonation and reduction via proton-electron transfer. The first two reduction steps lead to an N2O intermediate, whose reduction is more energy demanding: in the two latter reaction steps the highest energy barrier for Co2S2(CO)6 is 109 kJ mol-1, and for Fe2S2(CO)6, it is 133 kJ mol-1. Again, the presence of favorable light absorption bands allows for a photochemical route to overcome these energy barriers. All elementary steps are exothermic, and the final products are molecular nitrogen and water.