Anticancer activity, DFT study, ADMET prediction, and molecular docking of novel α-sulfamidophosphonates

A series of novel α-sulfamidophosphonate derivatives (3a-3 g) were synthesized and evaluated for anticancer activity against different human cancer cell lines (PRI, K562, and JURKAT). The antitumor activity of all compounds using the MTT test remains moderate compared to the standard drug chlorambucil. Compounds 3c and 3 g were found to be more active anticancer agent against PRI and K562 cells with IC50 value 0.056-0.097 and 0.182-0.133 mM, respectively. Molecular docking study related to binding affinity and binding mode analysis showed that synthesized compounds had potential to inhibit glutamate carboxypeptidase II (GCPII). Furthermore, computational analysis was performed through Density Functional Theory (DFT) utilizing the B3LYP 6-31 G (d, p) basis set and the theoretical results were correlated with experimental data. The ADME/toxicity analyses carried out by Swiss ADME and OSIRIS software show that all synthesized molecules exhibited good pharmacokinetics, bioavailability, and had no toxicity profile.

Improved Analytical Performance of an Amphiphilic Probe upon Protein Encapsulation: Spectroscopic Investigation along with Computational Rationalization

An easily synthesizable pyrene-based amphiphilic probe (Pybpa) has been developed, which exhibited no responses with metal ions in the pure aqueous medium despite possessing a metal ion-chelating bispicolyl unit. We believe that spontaneous aggregation of Pybpa in aqueous medium makes the ion binding unit not accessible to the metal ions. However, the sensitivity and selectivity of Pybpa toward Zn²⁺ ions drastically improve in the presence of serum albumin protein, HSA. The differences in the microenvironment inside the protein cavity, in terms of local polarity, and conformational rigidity might be attributing factors for that. The mechanistic investigations also suggest that there might be the involvement of polar amino acid residues that take part in coordination with Zn²⁺ ions. Pybpa shows no detectable spectroscopic changes with Zn²⁺ ions in aqueous medium in the absence of HSA. However, it can effectively recognize Zn²⁺ ions in the protein-bound form. Moreover, the photophysical behavior of Pybpa and its zinc complex have been investigated with DFT and docking studies. Noteworthy, such an unusual sensing aspect of Zn²⁺ exclusively in the protein-bound state and particularly in aqueous medium is truly rare and innovative.

New Luminescent Pyridine-based Disc type Molecules: Synthesis, Photophysical, Electrochemical, and DFT studies

The design and synthesis of new conjugated luminescent molecules have attracted the attention of researchers because of their various applications, especially in the field of optoelectronic devices. Most of the applications were mainly based on the intramolecular charge transfer (ICT). For this purpose, we designed and synthesized a series of new donor-acceptor based disc type molecules i.e. 2,4,6-tris(4-(alkyloxy)phenyl)pyridines carrying variable alkoxy chains [i.e. n = 2, 4, 6, 8, 10, 12, 14, 16]. Further, the structures of all the synthesized compounds were confirmed by using ATR-IR, ¹H-NMR, ¹³C-NMR, and ESI-MS analysis. Moreover, the photophysical property study indicated that all the molecules are blue light emitting materials, however the change of alkoxy chain length in phenyl arms does not affect their absorption, emission, and energy levels. Besides, the thermal study revealed that core is stable up to 350 °C. Also, the DFT study showed that the photo induced electron transfer caused by HOMO-LUMO excitation in the studied molecules. Therefore, all the molecules have potential applications in optoelectronic applications.

Thioether-based novel transition metal complexes: Synthesis, DNA interaction, in vitro biological assay, DFT calculations, and molecular docking studies

A novel Schiff base ligand 2-(((2-(benzylthio)phenyl)imino)methyl)-4-chlorophenol and its cobalt, nickel, copper, and zinc metal complexes were prepared. Using B3LYP/6-31++G(d,p) method with LanL2DZ as basis set, the molecular structure of metal complexes has been optimized, and their parameters have been explored. The distorted octahedral geometries have been observed in cobalt, nickel, and copper complexes. In contrast, zinc complex exhibited distorted tetrahedral geometry indicating the coordination of metal ions with ligands through ONS binding sites, which are confirmed by various spectroscopic techniques, magnetic measurements, molar conductivity, elemental analysis, and DFT studies. The intercalative binding mode between CT-DNA and synthesized metal complexes has been determined by absorption and fluorescence spectroscopy. The binding constant values of metal complexes found to be varied from 5.28 × 10³ M^-1 to 9.18 × 10⁴ M^-1. Furthermore, several methods have been used to scrutinize the bioactivities, such as in vitro anti-diabetic, anti-inflammatory, and antioxidant. From the obtained results, it can be concluded that zinc metal complex exhibited excellent anti-inflammatory and anti-diabetic activity compared to others. However, the copper complex has good antioxidant property. Besides deducing the prospective binding energies of inhibitors, molecular docking simulations have also been conducted utilizing the enzyme structures of B-DNA, 6-COX, α-amylase, and α-glucosidase.

Synthesis and Biological Evaluation of Octahydroquinazolinones as Phospholipase A2, and Protease Inhibitors: Experimental and Theoretical Exploration

Phospholipase A2 (PLA2) promotes inflammation via lipid mediators and releases arachidonic acid (AA), and these enzymes have been found to be elevated in a variety of diseases, including rheumatoid arthritis, sepsis, and atherosclerosis. The mobilization of AA by PLA2 and subsequent synthesis of prostaglandins are regarded as critical events in inflammation. Inflammatory processes may be treated with drugs that inhibit PLA2, thereby blocking the COX and LOX pathways in the AA cascade. To address this issue, we report herein an efficient method for the synthesis of a series of octahydroquinazolinone compounds (4a-h) in the presence of the catalyst Pd-HPW/SiO₂ and their phospholipase A2, as well as protease inhibitory activities. Among eight compounds, two of them exhibited overwhelming results against PLA2 and protease. By using FT-IR, Raman, NMR, and mass spectroscopy, two novel compounds were thoroughly studied. After carefully examining the SAR of the investigated compounds against these enzymes, it was found that compounds (4a, 4b) containing both electron-donating and electron-withdrawing groups on the phenyl ring exhibited higher activity than compounds with only one of these groups. DFT studies were employed to study the electronic nature and reactivity properties of the molecules by optimizing at the BLYP/cc-pVDZ. Natural bond orbitals helped to study the various electron delocalizations in the molecules, and the frontier molecular orbitals helped with the reactivity and stability parameters. The nature and extent of the expressed biological activity of the molecule were studied using molecular docking with human non-pancreatic secretory phospholipase A2 (hnps-PLA2) (PDB ID: 1DB4) and protease K (PDB ID: 2PWB). The drug-ability of the molecule has been tested using ADMET, and pharmacodynamics data have been extracted. Both the compounds qualify for ADME properties and follow Lipinski's rule of five.

Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 Mpro

Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than -8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Reactions of nicotine and the hydroxyl radical in the environment: Theoretical insights into the mechanism, kinetics and products

Nicotine (NCT) is a prevalent and highly poisonous tobacco alkaloid found in wastewater discharge. Advanced oxidative processes (AOP) are radical interactions between harmful pollutants and ambient free radicals that, theoretically, result in less toxic compounds. For a better understanding of the chemical transformations and long-term environmental effects of toxic discharges, the study of these processes is crucial. Here, quantum chemical calculations are used to investigate the AOP of the NCT in aqueous and lipidic environments. It was found that NCT interacted with HO^• in polar and nonpolar media, with an overall rate constant k_overall = 10⁶ - 10¹⁰ M^-1 s^-1. The computed kinetic data are reasonably accurate as seen by the comparison with the experimental rate constant in water (pH = 7.0), which results in a k_calculated/k_experimetal ratio of 1.4. The hydrogen transfer (C7, C9, C12)-single electron transfer pathways are the main mechanisms for the HO^• + NCT reaction in pentyl ethanoate solvent to form the cations as the primary products of the two-step reaction. However, in aqueous environments, the degradation of NCT by HO^• radicals increases with increasing pH levels. It is predicted that oxidation products are less toxic than nicotine itself, especially in an aqueous environment with a pH < 7.0.

Solar photodegradation of Rhodamine B dye by Cu2O/TiO2 heterostructure: experimental and computational studies of degradation and toxicity

CONTEXT AND RESULTS

In this study, the heterojunction Cu₂O/TiO₂ is used for the degradation of a cationic dye, Rhodamine B, under solar light irradiation over a wide pH range. The physical and optical properties of both semiconductors Cu₂O and TiO₂ are correlated with the photo-electrochemical characterization to establish the energy diagram of the heterojunction Cu₂O/TiO₂. X-ray diffraction, UV-visible, SEM, EDX, and BET analyses are conducted for both photocatalysts. The band gap (E_g) of 3.26 eV is obtained for TiO₂ with an indirect optical transition. In the case of Cu₂O, the transition is directly allowed at 2.05 eV. According to the BET analysis, the specific surface area of TiO₂ particles is higher (82.65 m² g^-1) than that of Cu₂O (29.81 m² g^-1). The flat band potentials, determined from the Mott-Schottky plots, are 0.3 and - 0.32 V_SCE for TiO₂ and Cu₂O, respectively. The photocatalytic activity is directly proportional to the mass ratio, and the best result is obtained for the mass ratio 1:1 of Cu₂O/TiO₂.

COMPUTATIONAL AND THEORETICAL TECHNIQUES

Furthermore, a theoretical study is conducted by using density functional theory to optimize the structure, reactivity sites of the RhB molecule, and physical parameters like the energy of the frontier molecular orbitals and electronegativity and to predict the proposed mechanism of RhB degradation as well as its intermediates. Also, molecular dynamics simulation is used to determine the adsorption behavior of RhB on TiO₂ (101) and Cu₂O (111) surfaces. The ecotoxicity evaluation showed that degradation products have significantly lower acute toxicity than RhB.

Systematic DFT studies of CO-Tolerance and CO oxidation on Cu-doped Ni surfaces

Nickel-based surfaces have received significant attention as an efficient substrate for electrooxidation. This work studied doped nickel surfaces with Cu atoms to enhance the CO-Tolerance. A comparative study was performed for CO adsorption upon different cleavage facets of pristine and Cu-doped nickel surfaces, whereas the adsorption energy, charge transfer, and density of state for CO were estimated using GGA-RPBE calculation method. Several adsorption probabilities were considered, and the change in adsorption energy and bond lengths were used to explain the CO adsorption mechanism. Otherwise, the density of state was employed to study the 3σ and 1π orbital to demonstrate the adsorption of CO onto the different facets. According to our analysis, the Cu-doped nickel surface showed higher CO tolerance than the pristine nickel surface. Whereas the calculated CO adsorption energies of Cu-doped surfaces have more positive values than the non-doped counterparts. The catalytic ability of pristine and Cu-doped Ni(111) was studied to evaluate the ability of surface poisoning resistance. Thus, oxidation of CO to CO₂ was studied using the Eley-Rideal mechanism upon the pristine and Cu-doped surfaces of Ni(100) where the rate-determining step for CO oxidation upon the reported surfaces was estimated as CO + O₂* → CO₂* + O* by an energy barrier of 1.05 and 0.9 eV for pristine, and Cu-doped Ni (100).

Theoretical investigation on hydrolysis mechanism of cis-platin analogous Pt(II)/Pd(II) complex by DFT calculation and molecular docking approach for their interaction with DNA & HSA

The properties to be an active drug candidate of the complex Pt(TEEDA)Cl₂, C1; Pd(TEEDA)Cl₂, C2 and their hydrolysed product [Pt(TEEDA)(OH₂)₂]²⁺, C1' and [Pd(TEEDA)(OH₂)₂]²⁺, C2' were predicted by Lipinski's rule of 5 and PASS (prediction of activity spectra for substances) web tool. Their structural profile, HOMO-LUMO energy and electronic potential surface ware analysed by DFT calculation. Their TD-DFT spectra were compared with experimental UV-Vis spectra. The hydrolysis mechanisms of C1 & C2 to the diaqua form C1' and C2' were extensively investigated by DFT method in different levels of theory and using CPCM/water model and compared with recognised Pt based anticancer drugs. All the stationary states, including the transition state for the reactions were identified by the DFT calculation. The IRC calculation confirmed that the transition states are well connected and corelate with reactants and products. Interaction of the complexes with DNA & HSA was also investigated by molecular docking study.

Photodegradation of dye using Polythiophene/ZnO nanocomposite: A computational approach

Incorporating nanostructured photocatalysts in polymers is a strategic way to obtain novel water purification systems. Here, we present density functional theory (DFT) study of Polythiophene/Zinc oxide (PTh/ZnO) nanocomposite with high photocatalytic performance and stability which exhibits superior degradation of alizarine dye under the visible light condition with interaction energy of -149.55 kcal/mol between conducting polymer (PTh) and metal oxide, with PTh sponsoring more number of electrons to the conduction band of ZnO. The electrical and optical properties of optimized geometries of PTh/ZnO nanocomposite were studied by frontier molecular orbital analysis, natural bond orbital (NBO) charge simulation, natural electronic configuration, and UV-vis absorption spectra. The modulation of the energy band gap (∽ 2.60 eV) and exciton binding energy (∽ 0.36 eV) causes visible light absorption and hence enhances the photodegradation activity of PTh/ZnO. NBO analysis evidences the electron accepting behavior of ZnO in the composites as it withdraws electron cloud density of about 0.14e from the polymer unit.

Charge Transfer Chromophores Derived from 3d-Row Transition Metal Complexes

A series of new charge transfer (CT) chromophores of "α-diimine-M^II-catecholate" type (where M is 3d-row transition metals-Cu, Ni, Co) were derived from 4,4'-di-tert-butyl-2,2'-bipyridyl and 3,6-di-tert-butyl-o-benzoquinone (3,6-DTBQ) in accordance with three modified synthetic approaches, which provide high yields of products. A square-planar molecular structure is inherent for monomeric [Cu^II(3,6-Cat)(bipy^tBu)]∙THF (1) and Ni^II(3,6-Cat)(bipy^tBu) (2) chromophores, while dimeric complex [Co^II(3,6-Cat)(bipy^tBu)]₂∙toluene (3) units two substantially distorted heteroleptic D-M^II-A (where D, M, A are donor, metal and acceptor, respectively) parts through a donation of oxygen atoms from catecholate dianions. Chromophores 1-3 undergo an effective photoinduced intramolecular charge transfer (λ = 500-715 nm, extinction coefficient up to 10⁴ M^-1·cm^-1) with a concomitant generation of a less polar excited species, the energy of which is a finely sensitive towards solvent polarity, ensuring a pronounced negative solvatochromic effect. Special attention was paid to energetic characteristics for CT and interacting HOMO/LUMO orbitals that were explored by a synergy of UV-vis-NIR spectroscopy, cyclic voltammetry, and DFT study. The current work sheds light on the dependence of CT peculiarities on the nature of metal centers from various groups of the periodic law. Moreover, the "α-diimine-M^II-catecholate" CT chromophores on the base of "late" transition elements with differences in d-level's electronic structure were compared for the first time.

Influence of magnetite incorporation into chitosan on the adsorption of the methotrexate and in vitro cytotoxicity

Emerging pollutants are a group of substances involved in environmental contamination resulting mostly from incomplete drug metabolism, associated with inadequate disposal and ineffective effluent treatment techniques. Methotrexate (MTX), for instance, is excreted at high concentrations in unchanged form through the urine. Although the MTX is still effective in cancer and autoimmune disease treatment, this drug shows the ability of bioaccumulation and toxicity to the organism. Thus, the present work aimed to evaluate the adsorption of the MTX drug onto magnetic nanocomposites containing different amounts of incorporated magnetite (1:1, 1:5, and 1:10 wt%), combining the theoretical-experimental study as well as the in vitro cytotoxicity. Moreover, equilibrium studies (Langmuir, Freundlich, Temkin, Dubinin-Radushkevich, Hill, Redlich-Peterson, and Sips), kinetic (PFO, PSO, and IPD), and thermodynamic (ΔG°, ΔH°, and ΔS°) were used to describe the experimental data, and ab initio simulations were employed in the theoretical study. Magnetic nanocomposites were synthesized by the co-precipitation method using only FeCl₂ as the iron precursor. Adsorbents were characterized by FTIR, XRD, Raman, SEM-EDS, BET, and VSM analysis. Meanwhile, cytotoxic effects on L929 and A375 cell lines were evaluated through MTT, NR, and LDH assays. The adsorption of the MTX was carried out in a typical batch system, exploring the different experimental conditions. The theoretical study suggests the occurrence of chemisorption between CS·Fe₃O₄-MTX. The maximum adsorption capacity of MTX was 285.92 mg g^-1, using 0.125 g L^-1 of CS·Fe₃O₄ 1:1, with an initial concentration of the MTX (50 mg L^-1), pH 4.0 at 293 ± 1.00 K. The best adjustment of equilibrium and kinetic data were the Sips (low values for statistical errors) and PSO (q_e = 96.73 mg g^-1) models, respectively. Thermodynamic study shows that the adsorption occurred spontaneously (ΔG° < 0), with exothermic (ΔH° =  - 4698.89 kJ mol^-1) and random at the solid-solution interface (ΔS° = 1,476,022.00 kJ mol^-1 k^-1) behavior. Finally, the in vitro study shows that magnetic nanomaterials exhibit higher cytotoxicity in melanoma cells. Therefore, the magnetic nanocomposite reveals to be not only an excellent tool for water remediation studies but also a promising platform for drug delivery.

First-Principles Insight into a B4C3 Monolayer as a Promising Biosensor for Exhaled Breath Analysis

Nanomaterial-based room temperature gas sensors are used as a screening tool for diagnosing various diseases through breath analysis. The stable planar structure of boron carbide (B₄C₃) is utilized as a base material for adsorption of human breath exhaled VOCs, namely formaldehyde, methanol, acetone, toluene along, with interfering gases of carbon dioxide and water. The adsorption energy, charge density, density of states, energy band gap variation, recovery time, sensitivity, and work function of adsorbed molecules on pristine B₄C₃ are analyzed by density functional theory. The computed adsorption energies of VOC are in the range of - 0.176 to - 0.238 eV, and a larger interaction distance validate the physisorption behavior of these VOCs biomarkers on pristine boron carbide monolayer. Minute changes are determined from the electronic band structure of all adsorbed systems conserving the semiconducting nature of the B₄C₃ monolayer. The band gap variation upon adsorption of VOCs and interfering gases is examined between 0.05 and 0.52%. The 13.63 × 10^-9 s recovery time of methanol is slower among VOCs, and 0.556 × 10^-9 s of carbon dioxide (CO₂) is faster for desorption. The results reveal that boron carbide can be utilized as a biosensor at room temperature for the analysis of exhaled VOCs from human breath.

The hydroperoxyl radical scavenging activity of natural hydroxybenzoic acids in oil and aqueous environments: Insights into the mechanism and kinetics

Foods that contain hydroxybenzoic acid derivatives (HBA) include red fruits, black radish, onion, and potato peel. HBA are widely known for their anti-inflammatory, anti-cancer, and especially antioxidant capabilities; however, a comprehensive study of the mechanism and kinetics of the antiradical action of these compounds has not been performed. Here, we report a study on the mechanisms and kinetics of hydroperoxyl radical scavenging activity of HBA by density functional theory (DFT) calculations. According to the results, HBA exert low HOO^• antiradical activity in the nonpolar environment with overall rate constants in the range of k_overall = 5.90 × 10^-6 - 4.10 × 10³ M^-1 s^-1. However, most HBA exhibit significant HOO^• antiradical activity (k_overall = 10⁵ - 10⁸ M^-1 s^-1) by the single electron transfer (SET) reaction of the phenoxide anions in water at physiological pH. The overall rate constant increases with increasing pH values in the majority of the substances studied. At pH ≤ 4, gentisic acid had the best HOO^• antiradical activity (log(k_overall) = 3.7-4.8), however at pH > 4, the largest HOO^• radical scavenging activity (log(k_overall) = 4.8-9.8) was almost exclusively found for gallic and syringic acids. Salicylic and 5-sulphosalicylic acids have the lowest antiradical activity across most of the pH range. The activities of the majority of the acids in this study are faster than the reference compound Trolox. Thus, in the aqueous physiological environment, these HBA are good natural antioxidants.

Bis-1,2,4-triazol derivatives: Synthesis, characterization, DFT, antileishmanial activity and molecular docking studyo

In this study, triazol derivatives, 4,4'-(((1E, 1E')-1,2-phenylenebis (methanylyidene)) bis (azanylidene)) bis (5-methyl-2,4-dihydro-3H-1,2,4-triazol-3-one (2), 4,4'-(((1E, 1E')-1,3-phenylenebis (methanylyidene)) bis (azanylidene)) bis (5-methyl-2,4-dihydro-3H-1,2,4-triazol-3-one (3) and 4,4'-(((1E, 1E')-1,4-phenylene bis (methanyl yidene)) bis (azanylidene)) bis (5-methyl-2,4-dihydro-3H-1,2,4-triazol-3-one (4) were synthesized from the reaction of 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazol-3-one and phthalaldehyde/isophthalaldehyde/terephthalaldehyde, respectively. Compounds 2-4 were characterized by Fourier transform infrared (FTIR), proton and carbon-13 nuclear magnetic resonance (¹H- and ¹³C- NMR) spectroscopic methods. Theoretical study for compounds 2-4 were carried out by DFT/B3LYP/6-311++G(d,p). Structural and spectroscopic parameters were determined theoreticaly and compared with experimental ones. Also, the molecular electrostatic potential (MEP) maps of compounds were obtained. Leishmanicidal activity of compounds 2-4 against to Leishmania infantum was determined by microdilution broth method containing alamar blue. As a result of the study, compounds 2-4 were found to be effective against the specie of Leishmania. Molecular docking analysis against Trypanothione Reductase (TRe) with compound 2 was carried out to see the necessary interactions responsible for antileishmanial activity. The docking calculations of compound 2 supported the antileishmanial activity exhibiting high inhibition constant.Communicated by Ramaswamy H. Sarma.

Fashionable Co-operative Sensing of Bivalent Zn2+ and Cd2+ in Attendance of OAc- by Use of Simple Sensor: Exploration of Molecular Logic Gate and Docking Studies

The Schiff-base probe H₂VL [6,6'-((1E,1'E)-hydrazine-1,2 diylidenebis(methanylylidene))bis(2-methoxyphenol)] is synthesized and structurally characterized by single crystal X-ray diffraction (SCXRD). H₂VL is able to detect selectively acetate ion (OAc-) colorimetrically over other anions with 1:1 co-ordination. The detection limit is found to be 4.93 µM. On the other hand, fluorescence intensity of the receptor is drastically enhanced with Zn²⁺ and Cd²⁺ in the presence of acetate as counter anion. N, N-Dimethyl formamide (DMF) or Dimethylsulphoxide (DMSO) and acetate (OAc-) was the best solvent and counter anion for Zn²⁺/Cd²⁺ -sensing compared with other solvents and anions, respectively. Detection limit for Zn²⁺ and Cd²⁺ are calculated to be 1.94 µM and 1.99 µM, respectively. The strong selective emissive behavior could be attributed to the CHEF (chelation-enhanced fluorescence) process. According to the changes in output emission intensity in DMSO in response to the set of ions (Zn²⁺, Cd²⁺ and OAc¯) as input variables, the function of 3-input multifunctional molecular logic circuits has been demonstrated. The molecular docking studies of H₂VL with DNA and BSA are also performed to confirm its possible bioactivity.

Theoretical Studies of a Silica Functionalized Acrylamide for Calcium Scale Inhibition

The calcium carbonate (CaCO₃) scale is one of the most common oilfield scales and oil and gas production bane. CaCO₃ scale can lead to a sudden halt in production or, worst-case scenario, accidents; therefore, CaCO₃ scale formation prevention is essential for the oil and gas industry. Scale inhibitors are chemicals that can mitigate this problem. We used two popular theoretical techniques in this study: Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). The objective was to investigate the inhibitory abilities of mixed oligomers, specifically acrylamide functionalized silica (AM-Silica). DFT studies indicate that Ca²⁺ does not bind readily to acryl acid and acrylamide; however, it has a good binding affinity with PAM and Silica functionalized PAM. The highest binding affinity occurs in the silica region and not the -CONH functional groups. AIMD calculations corroborate the DFT studies, as observed from the MD trajectory that Ca²⁺ binds to PAM-Silica by forming bonds with silicon; however, Ca²⁺ initially forms a bond with silicon in the presence of water molecules. This bonding does not last long, and it subsequently bonds with the oxygen atoms present in the water molecule. PAM-Silica is a suitable calcium scale inhibitor because of its high binding affinity with Ca²⁺. Theoretical studies (DFT and AIMD) have provided atomic insights on how AM-Silica could be used as an efficient scale inhibitor.

Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2

A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.

DFT insights into the degradation mechanism of carbendazim by hydroxyl radicals in aqueous solution

Advanced oxidation of carbendazim by OH radicals is a central step in its wastewater remediation. However, the understanding of the degradation mechanism of carbendazim has always been a challenge. In this paper, the degradation mechanism of carbendazim by •OH in aqueous solution has been explored using density functional theory (DFT) calculations. On account of the structural and electronic characteristics analysis, the nucleophilic aromatic substitution, dehydrogenation oxidation, and decarboxylation degradation pathways were mainly investigated. These degradation reactions may produce hydroxyl substitution products, oxidized aldehyde and carboxyl products, and decarboxylated carbamic acid products. Computational studies demonstrated that these possible degradation reactions are facile to take place kinetically and have large thermodynamic driving forces, indicating the feasibility of the relevant degradation pathways. Additionally, the ecological risk of carbendazim and its possible degradation products was evaluated, showing that the acute toxicity of degradation products decreases in varying degrees compared with that of carbendazim. The comprehensive mechanistic studies open an avenue for the understanding on the degradation of organic pollutants such as benzimidazole pollutants on molecular level.

DFT Study of Molecular Structure, Electronic and Vibrational Spectra of Tetrapyrazinoporphyrazine, Its Perchlorinated Derivative and Their Al, Ga and In Complexes

Electronic and geometric structures of metal-free, Al, Ga and In complexes with tetrapyrazinoporphyrazine (TPyzPA) and octachlorotetrapyrazinoporphyrazine (TPyzPACl₈) were investigated by density functional theory (DFT) calculations and compared in order to study the effect of chlorination on the structure and properties of these macrocycles. The nature of the bonds between metal atoms and nitrogen atoms was described using the NBO-analysis. Simulation and interpretation of electronic spectra were performed with the use of time-dependent density functional theory (TDDFT). A description of calculated IR spectra was carried out based on the analysis of the distribution of the potential energy of normal vibrational coordinates.

Antioxidant activity of erlotinib and gefitinib: theoretical and experimental insights

Erlotinib and gefitinib are quinazoline derivatives with antineoplastic properties. Usually, intake of antineoplastic agents results in much a greater degree of oxidative stress, i.e. the production of free radicals, than induced by cancer itself. Hence, anticancerous drugs must also exhibit antioxidant activity but this has not been studied thus far. In this study, the antioxidant activity of erlotinib and gefitinib was examined by experimental and computational studies. It was found that erlotinib and gefitinib exhibit good 2,2-dipheny l-1-picrylhydrazyl (DPPH) radical and hydroxyl radical scavenging (HRS) activities. In DPPH assay, the IC₅₀ for erlotinib and gefitinib were 0.584 and 0.696 mM, respectively, while IC₅₀ for HRS assay were 0.843 and 1.03 mM for erlotinib and gefitinib, respectively. Structural characteristics such as frontier molecular orbitals (FMOs), molecular electrostatic potential maps (MESPs), and global descriptive parameters were calculated at DFT/B3LYP/6-311++G (d,p) on the optimized geometries of erlotinib and gefitinib. UV-visible spectroscopy revealed the possible electronic transitions between the FMOs and their associated excitation energies of both drugs and found that erlotinib has π to π* transitions while gefitinib has π to π* and σ to π* transitions. To elucidate the antioxidant activity of erlotinib and gefitinib, three mechanisms namely hydrogen atom transfer (HAT), single electron transfer proton transfer (SETPT), and sequential proton-loss electron-transfer (SPLET) were employed and articulated the results in arithmetic parameters like bond dissociation energy (BDE), proton affinity (PA), ionization potential (IP), electron transfer enthalpy (ETE), and proton dissociation enthalpy (PDE). Further, molecular docking studies have been carried out to have a better understanding of binding sites and modes of interaction with a well-known antioxidant target protein monoamine oxidase-B (MAO-B) employing docking scores and types of interactions. All the calculated parameters point out that though gefitinib and erlotinib were interchangeable, erlotinib requires a lesser amount of energy for proton transfer and electron transfer, moreover it scavenges radicals easily.

Novel ferrocene imide derivatives: synthesis, conformational analysis and X-ray structure

The synthesis and structural characterization of the ferrocene imide derivatives Fc−CO−NH−CO−Me (4), Fc−CO−NH−CO−Fc (7) and Fc−CO−NH−CO−Fn−CO−NH−CO−Fc (8) have been reported. The mononuclear, dinuclear and trinuclear ferrocene imides were prepared by the reaction of ferrocenecarboxamide (3), with acetyl chloride, ferrocenecarbonyl chloride (2) and ferrocene-1,1’-(dicarbonyl chloride) (6), respectively. IR spectroscopic analysis revealed the absence of intramolecular hydrogen bonds in solutions of imides 4, 7 and 8. The crystal packing of N-acetylferrocenecarboxamide (4) is characterized by N−H⋯O hydrogen bonds forming centrosymmetric dimers, while the molecules of its homologue N-methylferrocenecarboxamide (5) are self-assembled by intermolecular N−H⋯O bonds into infinite chains. A detailed conformational analysis (DFT study) suggests the cis-trans configuration of ferrocene imide derivative 7 in solution. The effect of different substituents attached to bridged imide nitrogen on conformational properties of bis-ferrocenyl imides was further investigated and results compared to the existing experimental data.

Theoretical Investigation by DFT and Molecular Docking of Synthesized Oxidovanadium(IV)-Based Imidazole Drug Complexes as Promising Anticancer Agents

Vanadium compounds have been set in various fields as anticancer, anti-diabetic, anti-parasitic, anti-viral, and anti-bacterial agents. This study reports the synthesis and structural characterization of oxidovanadium(IV)-based imidazole drug complexes by the elemental analyzer, molar conductance, magnetic moment, spectroscopic techniques, as well as thermal analysis. The obtained geometries were studied theoretically using density functional theory (DFT) under the B3LYP level. The DNA-binding nature of the ligands and their synthesized complexes has been studied by the electronic absorption titrations method. The biological studies were carried with in-vivo assays and the molecular docking method. The EPR spectra asserted the geometry around the vanadium center to be a square pyramid for metal complexes. The geometries have been confirmed using DFT under the B3LYP level. Moreover, the quantum parameters proposed promising bioactivity of the oxidovanadium(IV) complexes. The results of the DNA-binding revealed that the investigated complexes bind to DNA via non-covalent mode, and the intrinsic binding constant (K_b) value for the [VO(SO₄)(MNZ)₂] H₂O complex was promising, which was 2.0 × 10⁶ M⁻¹. Additionally, the cytotoxic activity of the synthesized complexes exhibited good inhibition toward both hepatocellular carcinoma (HepG-2) and human breast cancer (HCF-7) cell lines. The results of molecular docking displayed good correlations with experimental cytotoxicity findings. Therefore, these findings suggest that our synthesized complexes can be introduced as effective anticancer agents.

Green Phosphorene as a Promising Biosensor for Detection of Furan and p-Xylene as Biomarkers of Disease: A DFT Study

In this work, Green Phosphorene (GP) monolayers are studied as an electronic sensing element for detecting prostate cancer biomarkers from human urine. The adsorption of furan, C₈H₁₀ (p-xylene), and H₂O on pristine GP and S- and Si-doped GP are investigated using the density functional theory (DFT) calculation. Furan and C₈H₁₀ molecules have been considered as important biomarkers of prostate cancer patients. First-principles DFT calculations are applied, and the results divulged that pristine GP could be a promising candidate for furan and C₈H₁₀ detection. It is manifested that furan and C₈H₁₀ are physisorbed on the S-, and Si-doped GP with small adsorption energy and negligible charge transfer. However, the calculations disclose that furan and C₈H₁₀ are chemically adsorbed on the pristine GP with adsorption energy of −0.73, and −1.46 eV, respectively. Moreover, we observe that a large charge is transferred from furan to the pristine GP with amount of −0.106 e. Additionally, pristine GP shows short recovery time of 1.81 s at room temperature under the visible light, which make it a reusable sensor device. Overall, our findings propose that the pristine GP sensor is a remarkable candidate for sensing of furan and other biomarkers of prostate cancer in the urine of patients.