Search Results (17)

During flotation, the hydration behavior of collector head groups plays an important role in determining collector hydrophilicity and interfacial adsorption behavior. However, although computation-assisted flotation studies have extensively investigated collector–mineral interactions, systematic comparisons of the intrinsic hydration characteristics of different collector head groups under unified computational conditions remain limited. In this work, density functional theory (DFT) calculations using the B3LYP functional with Grimme dispersion correction were conducted to investigate the hydration interactions between water molecules and representative head groups of five sulfide mineral collectors, including xanthate (X), dithiocarbamate (DTC), dithiophosphate (DTP), dithiophosphinate (3418A), and thiocarbamate (Z-200), and five oxide mineral collectors, including oleate (OA), oxidized paraffin soap (OPS–C₁₂), dodecyl sulfonate (DS), styrene phosphonic acid (SPA), and salicylhydroxamic acid (BHA). The results show that oxide mineral collectors exhibit significantly stronger hydration interactions than sulfide mineral collectors. Sulfide collectors mainly form weak S···H–O hydrogen bonds with relatively long H-bond distances (2.27–2.61 Å), whereas oxide collectors predominantly form stronger O···H–O hydrogen bonds with shorter distances (1.66–2.24 Å). The total hydration binding energies of sulfide collectors range from −150 to −290 kJ/mol, while those of oxide collectors range from −244 to −491 kJ/mol. Among the studied collectors, SPA exhibits the strongest hydration tendency due to its highly charged phosphonate group, whereas Z-200 shows the weakest hydration interaction. The results indicate that hydration behavior is strongly influenced by head group type, charge state, and hydrogen-bond characteristics. Full article

This work presents the results of a theoretical investigation of the electronic and optical properties of van der Waals Janus nanoheterostructures MoS₂/SeMoS and MoSe₂/SMoSe, carried out within the framework of density functional theory (DFT) using the generalized gradient approximation (GGA-PBE) together with the Grimme-D3 dispersion correction. The calculated band structures show that both heterostructures possess an indirect bandgap whose magnitude is highly sensitive to an external electric field. In the MoS₂–SeMoS system, increasing the applied field leads to a gradual narrowing of the bandgap and a transition to a metallic state at approximately 75 V, whereas in MoSe₂–SMoSe, the bandgap first increases (up to 20 V) and then decreases, indicating a nonlinear field-dependent behavior. Analysis of the dielectric function reveals an enhancement of the static dielectric permittivity and a red shift in the absorption spectra with increasing field strength, which can be attributed to charge redistribution and an increased contribution from ionic polarizability. These results demonstrate the possibility of effectively controlling the bandgap width, polarizability, and optical response of Janus nanoheterostructures using an external electric field. This opens up promising prospects for their application in tunable photodetectors, light modulators, valleytronic components, and next-generation optoelectronic systems. Full article

This study investigates the antioxidant properties of aucubin (AU), an iridoid compound, focusing on its ability to scavenge hydroxyl radicals (^•OH) through its hydroxyl functional groups. Gaussian software was employed to model and validate the underlying antioxidant reaction mechanisms. Three primary pathways were examined: hydrogen atom transfer (HAT), sequential electron transfer-proton transfer (SET-PT), and sequential proton loss–electron transfer (SPLET). All calculations were performed using the M06-2X functional within density functional theory (DFT) at the def2-TZVP level, incorporating Grimme’s D3 dispersion correction and the implicit solvation model based on solute electron density (SMD) for water. Various thermodynamic parameters were determined to analyze and compare the antioxidant reactions, including the O-H bond dissociation energy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), electron transfer enthalpy (ETE), and proton affinity (PA) of the hydroxy groups. The results indicated that the HAT mechanism is the dominant pathway in the scavenging of ^•OH radicals by AU. The key active sites were identified as the 6-OH group in the aglycone structure and the 6′-OH group in the sugar moiety. Moreover, the polar aqueous environment promoted O-H bond homolysis to enhance the antioxidant activity. Full article

A series of water-soluble molecules based on 8-isopropyl-2-methyl-5-nitroquinoline and 1,10-phenanthroline core were designed by introducing a π-conjugated bridge, vinyl unit –CH=CH–. We present the selective conversion of methyl groups located on the C2 and C9 positions in the constitution of selected quinoline or 1,10-phenanthroline derivatives, respectively, into vinyl (or styryl) products by applying Perkin condensation. The two groups of ligands differ in the presence of one or two arms. The structure of the molecule ((1E,1′E)-(1,10-phenanthroline-2,9-diyl)bis(ethene-2,1-diyl))bis(benzene-4,1,3-triyl) tetraacetate was determined by single-crystal X-ray diffraction measurements. The X-ray, NMR, and DFT computational studies indicate the influence of rotation (rotamers) on the physical properties of studied styryl molecules. The results show that the styryl molecules with the vinyl unit –CH=CH– exhibit significant static and dynamic hyperpolarizabilities. Quantum chemical calculations using density functional theory and B3LYP/6-311++G(d,p) with Grimme’s dispersion correction approach predict the existence and relative stability of different spatial cis(Z)- and trans(E)-conformers of styryl derivatives of quinoline and 1,10-phenanthroline, which exhibit different electronic distribution and conjugation within the molecular skeleton, dipole moments, and steric interactions, leading to variations in their photophysical behavior and various applications. Our studies indicate that the rotation and isomerization of aryl groups can significantly influence the electronic and optical properties of π-conjugated systems, such as vinyl units (–CH=CH–). The rotation of aryl groups around the single bond that connects them to the vinyl unit can lead to changes in the effective π-conjugation between the aryl group and the rest of the π-conjugated system. The rotation and isomerization of aryl groups in π-conjugated systems significantly impact their electronic and optical properties. These changes can modify the efficiency of π-conjugation, affecting charge transfer processes, absorption properties, light emission, and electrical conductivity. In designing optoelectronic materials, such as organic dyes, organic semiconductors, or electrochromic materials, controlling the rotation and isomerization of aryl groups can be crucial for optimizing their functionality. Full article

We studied the noncovalent interactions of gadolinium bisphthalocyanine (GdPc₂) with cluster models for graphene and hexagonal boron nitride (hBN) of variable size by using the PBE functional of the generalized gradient approximation in conjunction with Grimme’s dispersion correction and a DND double numerical basis set (that is, PBE-D2/DND). We found that in terms of the bonding strength, changes in the Gd-N bond lengths, the charge and spin of the Gd central ion, and the spin of the GdPc₂ molecule, the behaviors of the graphene- and hBN-based model systems are rather similar. As expected, when increasing the size of the graphene and hBN cluster models, the strength of the interaction with GdPc₂ increases, in which the bonding with the hBN models is usually stronger by a few kcal/mol. One of the main questions addressed in the present work was whether a change in the antiferromagnetic spin alignment to a ferromagnetic one, which is typical for GdPc₂, is (at least theoretically) possible, as it has been observed previously for a number of graphene models when a smaller basis set DN was employed. We found that the use of a larger DND basis set dramatically reduces the occurrence of ferromagnetic adsorption complexes but does not exclude this possibility completely. Full article

This study employs density functional theory (DFT) calculations at the B3LYP/6-311+g(d,p) level to investigate the interaction of XH₃ gases (X = N, P, As) with the Mn-phthalocyanine molecule (MnPc). Grimme’s D3 dispersion correction is applied to consider long-range interactions. The adsorption behavior is explored under the influence of an external static electric field (EF) ranging from −0.514 to 0.514 V/Å. Chemical adsorption of XH₃ molecules onto the MnPc molecule is confirmed. The adsorption results in a significant decrease in the energy gap (E_g) of MnPc, indicating the potential alteration of its optical properties. Quantum theory of atoms in molecules (QTAIM) analysis reveals partially covalent bonds between XH₃ and MnPc, and the charge density differenc (Δρ) calculations suggest a charge donation-back donation mechanism. The UV-vis spectrum of MnPc experiences a blue shift upon XH₃ adsorption, highlighting MnPc’s potential as a naked-eye sensor for XH₃ molecules. Thermodynamic calculations indicate exothermic interactions, with NH₃/MnPc being the most stable complex. The stability of NH₃/MnPc decreases with increasing temperature. The direction and magnitude of the applied electric field (EF) play a crucial role in determining the adsorption energy (E_ads) for XH₃/MnPc complexes. The E_g values decrease with an increasing negative EF, which suggests that the electrical conductivity (σ) and the electrical sensitivity (ΔE_g) of the XH₃/MnPc complexes are influenced by the magnitude and direction of the applied EF. Overall, this study provides valuable insights into the suggested promising prospects for the utilization of MnPc in sensing applications of XH₃ gases. Full article

Based on the reported research, hydroxyl radicals can be rapidly transformed into carbonate radicals in the carbonate–bicarbonate buffering system in vivo. Many of the processes considered to be initiated by hydroxyl radicals may be caused by carbonate radicals, which indicates that lipid peroxidation initiated by hydroxyl radicals can also be caused by carbonate radicals. To date, theoretical research on reactions of hydrogen abstraction from and radical addition to polyunsaturated fatty acids (PUFAs) of carbonate radicals has not been carried out systematically. This paper employs (3Z,6Z)-nona-3,6-diene (NDE) as a model for polyunsaturated fatty acids (PUFAs). Density functional theory (DFT) with the CAM-B3LYP method at the 6-311+g(d,p) level was used to calculate the differences in reactivity of carbonate radicals abstracting hydrogen from different positions of NDE and their addition to the double bonds of NDE under lipid solvent conditions with a dielectric constant of 4.0 (CPCM model). Grimme’s empirical dispersion correction was taken into account through the D3 scheme. The energy barrier, reaction rate constants, internal energy, enthalpy and Gibbs free energy changes in these reactions were calculated With zero-point vibrational energy (ZPVE) corrections. The results indicated that carbonate radicals initiate lipid peroxidation primarily through hydrogen abstraction from diallyl carbon atoms. The reaction of hydrogen abstraction from diallyl carbon atoms exhibits the highest reaction rate, with a reaction rate constant approximately 43-fold greater than the second-ranked hydrogen abstraction from allyl carbon atoms. This process has the lowest energy barrier, internal energy, enthalpy, and Gibbs free energy changes, indicating that it is also the most spontaneous process. Full article

We have undertaken a DFT study of the nitride cluster fullerenes (NCFs) Ln₃N@C₈₀ for the complete series of fourteen lanthanides plus lanthanum by using the PBE functional with the Grimme’s dispersion correction (PBE-D2). We tested the DN and DND basis sets, which are equivalent to 6-31G and 6-31G(d) Pople-type basis sets, respectively. Due to the known convergence problems when treating lanthanide-containing systems, only with the DN basis set was it possible to complete the calculations (geometry optimization and analysis of selected electronic parameters) for all the fifteen NCFs. We found that the bending of the Ln₃N cluster increases as the ionic radius increases, in general agreement with the available X-ray diffraction data. The Ln₃N cluster becomes more planar as the Ln–N bond length is contracted, and the C₈₀ cavity slightly deforms. The HOMO-LUMO energies and distribution, as well as the charge and spin of the encapsulated metal ions, are analyzed. Full article

Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme’s semi-classical models (DFT-D), to different Kohn–Sham exchange–correlation functionals sometimes leads to variable and inconsistent results, which recommend a careful prior evaluation. In a recent study, we proposed a simple optimization protocol for enhancing the accuracy of these DFT-D methods by following an alternative and system-specific approach. Here, adopting the same computational strategy, we show how the accurate MC intermolecular interactions of a large set of water clusters of variable sizes (i.e., 300 (H₂O)_n structures, n = 9, 15, 27) can be reproduced remarkably well by dispersion-corrected DFT models (i.e., B3LYP-D4, PBE-D4, revPBE(0)-D4) upon re-optimization, reaching a mean absolute error per monomer of ~0.1 kcal/mol. Hence, the obtained results support the use of this procedure for fine-tuning tailored DFT-D models for the accurate description of targeted molecular systems. Full article

Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using $\omega$B97X functional with Grimme D3 dispersion corrections as well as a Becke–Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability. Full article

Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections. Full article

Trimeric acylphloroglucinols (T-ACPLs) are a subclass of the large class of acylphloroglucinols—derivatives of 1,3,5-trihydroxybenzene containing an R–C=O group. T-ACPL molecules contain three acylphloroglucinol moieties linked by methylene bridges. Many of them are present in natural sources and exhibit biological activities, often better than the corresponding activities of monomeric acylphloroglucinols. All the stable conformers of T-ACPLs contain seven intramolecular hydrogen bonds, which constitute the dominant stabilising factors. A total of 38 different T-ACPLs, including both naturally occurring and model molecules, have been calculated at the HF and DFT/B3LYP levels. The DFT/B3LYP calculations were carried out both without and with Grimme’s dispersion correction, to highlight the dispersion (and, therefore, also electron correlation) effects for these molecules. The roles of dispersion are evaluated considering the effects of Grimme’s correction on the estimation of the conformers’ energies, the description of the characteristics of the individual hydrogen bonds, the conformers’ geometries and other molecular properties. Overall, the results offer a comprehensive overview of the conformational preferences of T-ACPL molecules, their intramolecular hydrogen bond patterns, and the correlation effects on their properties. Full article

: The Aza-Wittig reaction plays an important role in organic transformations and has seen considerable development in the construction of cyclic and acyclic compounds in neutral solvents in the absence of catalysts with a high yield of products. Today, the use of iminophosphoranes (phosphazenes) has become a powerful tool in organic synthesis strategies directed toward the construction of nitrogenous heterocycles. These can react with carbonyl compounds, an excellent method for the construction of C=N double bonds via intermolecular and intramolecular Aza-Wittig reactions. In this study, we are interested in the theoretical study of the reaction path of the Aza˗Wittig reaction between trimethyl-iminophosphoranes (CH₃)₃P=NR, R = CH₃ or Ph) for the two-substituent methyl and phenyl with acetaldehyde, including continuum solvation. Our calculations were carried out by means of ab initio calculations using DFT (Density Function Theory) with a dispersion correction term using the Grimme method in the program Gaussian09, using the functional B3LYP-GD3BJ with a 6-31G** base. The results obtained allowed us to highlight the mechanisms of the Aza-Wittig reaction in particular after the addition of the term of dispersion correction or van der Waals correction, which provides a new description of this reaction and its chemical path. Full article

Air quality monitors using low-cost optical PM_2.5 sensors can track the dispersion of wildfire smoke; but quantitative hazard assessment requires a smoke-specific adjustment factor (AF). This study determined AFs for three professional-grade devices and four monitors with low-cost sensors based on measurements inside a well-ventilated lab impacted by the 2018 Camp Fire in California (USA). Using the Thermo TEOM-FDMS as reference, AFs of professional monitors were 0.85 for Grimm mini wide-range aerosol spectrometer, 0.25 for TSI DustTrak, and 0.53 for Thermo pDR1500; AFs for low-cost monitors were 0.59 for AirVisual Pro, 0.48 for PurpleAir Indoor, 0.46 for Air Quality Egg, and 0.60 for eLichens Indoor Air Quality Pro Station. We also compared public data from 53 PurpleAir PA-II monitors to 12 nearby regulatory monitoring stations impacted by Camp Fire smoke and devices near stations impacted by the Carr and Mendocino Complex Fires in California and the Pole Creek Fire in Utah. Camp Fire AFs varied by day and location, with median (interquartile) of 0.48 (0.44–0.53). Adjusted PA-II 4-h average data were generally within ±20% of PM_2.5 reported by the monitoring stations. Adjustment improved the accuracy of Air Quality Index (AQI) hazard level reporting, e.g., from 14% to 84% correct in Sacramento during the Camp Fire. Full article

In the present work, a number of R–X⋯NH₃ (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH₃ complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH₃ molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]_n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems. Full article