Computational Study of Structural, Molecular Orbitals, Optical and Thermodynamic Parameters of Thiophene Sulfonamide Derivatives

An integrative computational approach for the identification of dual inhibitors of isocitrate dehydrogenase 1 and 2 from phytocompounds of Phyllantus amarus

Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic IDH1_R132H and IDH2_R140Q mutations which lead to the production of an oncometabolite. Hence, their inhibition is widely considered a therapeutic strategy in the treatment of many cancers. While many inhibitors of the mutant enzymes have been developed, an inhibitor that is capable of co-inhibiting both enzymes are currently lacking while drug resistance has also limited the clinical usage of previously identified mono inhibitors. Consequently, this study employed molecular modeling approaches, such as molecular docking, molecular mechanics generalized Born Surface area (MM/GBSA), molecular dynamics (MD) simulation, and density functional theory (DFT) analysis to identify potential dual inhibitors of the previously mentioned mutant IDH1/2 from the phytocompounds of Phyllantus amarus. Of the 31 phytocompounds identified, 20 showed good binding affinities for both IDH1 _R132H and IDH2 _R140Q (ranging from -5.2 Kca/mol to -9.6 Kcal/mol) and had desirable pharmacokinetic properties. However, ellagic acid and pinoresinol possessed better pharmacokinetic properties, rendering suitable hits. Investigation of the behavior of the IDH1_R132H and IDH2_R140Q complexes with ellagic acid and pinoresinol via the RMSD, RMSF, and contact map analyses showed that all the complexes-maintained stability throughout the simulation time. Ultimately, ellagic acid and pinoresinol were identified as promising hits for the development of IDH1_R132H and IDH2_R140Q dual inhibitors. However, further experimental studies are needed to confirm their potential as therapies.Communicated by Ramaswamy H. Sarma.

Efficiency and Mechanism of Catalytic Siloxane Exchange in Vitrimer Polymers: Modeling and Density Functional Theory Investigations

Of late, siloxane-containing vitrimers have gained significant interest due to their fast dynamic characteristics over a reasonable temperature range (180-220 °C), making them well-suited for diverse applications. The exchange reaction pathway in the siloxane vitrimers is accountable for the covalent adaptive network, with the reaction's effectiveness being regulated by either organic or organometallic catalysts. However, directly studying the exchange reaction pathway in the bulk phase using experimental approaches is challenging because of the intricate and interconnected structure of these vitrimers. Here, we perform comprehensive density functional theory (DFT) and experimental investigations to discover the detailed catalytic efficacy of siloxane exchange and provide direction for the reaction process using a 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) catalyst. The calculated transition barrier energy and catalytic efficiency of hexamethyldisiloxane and dihydroxy-dimethylsilane exchange derived from the nudged elastic band with transition-state calculations strongly agree with the experimental findings. In addition, Fukui indices, along with partial charges, are employed to evaluate the nucleophilic and electrophilic behaviors of silanol and siloxane molecules. Our analysis revealed that by utilizing the Fukui indices of both the acid and the base, we can make an approximate estimation of the respective kinetics of the SN2 process in the siloxane exchange reaction mechanism. These findings establish a foundation for comprehending a crucial aspect of the exchange mechanism in siloxane vitrimer systems and could aid in the development of novel catalysts.

Styrene monomer as potential material for design of new optoelectronic and nonlinear optical polymers: density functional theory study

Using density functional theory, we have studied the intrinsic properties of styrene. First, we determine the optimized structures, structural parameters and thermodynamic properties to make our simulations more realistic to experimental results and check the stability. Second, we investigate optoelectronic, electronic and global descriptors, transport properties of holes and electrons, natural bond orbital analysis, absorption and fluorescence properties. Finally, we study nonlinear optical (NLO) properties: first- and second-order hyperpolarizability, second and third-order optical susceptibilities, hyper-Rayleigh scattering hyperpolarizability, electro-optical Pockel effect, direct current Kerr effects and quadratic refractive index. The bandgap energy E g = 5.146 eV and dielectric constantε r = 3.062 show that styrene is a good insulator with an average electric field value of 4.43 × 108 Vm-1. Thermodynamic findings show that our molecule is thermodynamically and chemically stable. Electron and hole reorganization energies of 0.393 and 0.295 eV, respectively, show that styrene is more favourable to hole transport than electron transport. Styrene is transparent with linear refractive index n = 1.750 and quadratic n 2 = 1.748 × 10-20 m2 W-1. At the NLO, styrene has a non-zero value ofβ H R S , which confirms the existence of first-order NLO activity. Globally the study shows that the styrene monomer is suitable for the architecture design of new polymer materials for NLO applications and optoelectronic by functionalization.

A Computational Study on Selected Alkaloids as SARS-CoV-2 Inhibitors: PASS Prediction, Molecular Docking, ADMET Analysis, DFT, and Molecular Dynamics Simulations

Despite treatments and vaccinations, it remains difficult to develop naturally occurring COVID-19 inhibitors. Here, our main objective is to find potential lead compounds from the retrieved alkaloids with antiviral and other biological properties that selectively target the main SARS-CoV-2 protease (Mpro), which is required for viral replication. In this work, 252 alkaloids were aligned using Lipinski's rule of five and their antiviral activity was then assessed. The prediction of activity spectrum of substances (PASS) data was used to confirm the antiviral activities of 112 alkaloids. Finally, 50 alkaloids were docked with Mpro. Furthermore, assessments of molecular electrostatic potential surface (MEPS), density functional theory (DFT), and absorption, distribution, metabolism, excretion, and toxicity (ADMET) were performed, and a few of them appeared to have potential as candidates for oral administration. Molecular dynamics simulations (MDS) with a time step of up to 100 ns were used to confirm that the three docked complexes were more stable. It was found that the most prevalent and active binding sites that limit Mpro'sactivity are PHE294, ARG298, and GLN110. All retrieved data were compared to conventional antivirals, fumarostelline, strychnidin-10-one (L-1), 2,3-dimethoxy-brucin (L-7), and alkaloid ND-305B (L-16) and were proposed as enhanced SARS-CoV-2 inhibitors. Finally, with additional clinical or necessary study, it may be able to use these indicated natural alkaloids or their analogs as potential therapeutic candidates.

Computational Study of Benzothiazole Derivatives for Conformational, Thermodynamic and Spectroscopic Features and Their Potential to Act as Antibacterials

Benzothiazole analogs are very interesting due to their potential activity against several infections. In this research, five benzothiazole derivatives were studied using density functional theory calculations. The optimized geometry, geometrical parameters and vibrational spectra were analyzed. The charge distribution diagrams, such as FMO (HOMO-LUMO), energies of HOMO-LUMO, polarizability, hyperpolarizability, MESP and density of states, were calculated. The computed energies of HOMO and LUMO showed that the transfer of charge occurred within the compound. The effect of the change of substituents on the ring on the value of the HOMO-LUMO energy gap was also observed. It was observed that, in this series, compound 4 with CF3 substituent had the lowest energy gap of HOMO-LUMO, and compound 5 with no substituent had highest HOMO-LUMO energy gap. From the energies of HOMO and LUMO, the reactivity descriptors, such as electron affinity (A), ionization potential (I), chemical softness (σ), chemical hardness (ƞ), electronic chemical potential (μ), electrophilicity index (ω), were calculated. In addition, the 13C and 1H NMR chemical shifts of the molecules were calculated using the gauge-independent atomic orbit (GIAO) method; the shifts were in good agreement with the experimental values. The anti-bacterial potential of compounds 1 to 5 was tested by molecular docking studies toward target proteins 2KAU and 7EL1 from Klebsiella aerogenes and Staphylococcus aureus. Compounds 3 and 1 showed high affinity toward 2KAU and 7EL1, respectively.

Facile Synthesis of 5-Aryl-N-(pyrazin-2-yl)thiophene-2-carboxamides via Suzuki Cross-Coupling Reactions, Their Electronic and Nonlinear Optical Properties through DFT Calculations

Synthesis of 5-aryl-N-(pyrazin-2-yl)thiophene-2-carboxamides (4a–4n) by a Suzuki cross-coupling reaction of 5-bromo-N-(pyrazin-2-yl)thiophene-2-carboxamide (3) with various aryl/heteroaryl boronic acids/pinacol esters was observed in this article. The intermediate compound 3 was prepared by condensation of pyrazin-2-amine (1) with 5-bromothiophene-2-carboxylic acid (2) mediated by TiCl₄. The target pyrazine analogs (4a–4n) were confirmed by NMR and mass spectrometry. In DFT calculation of target molecules, several reactivity parameters like FMOs (E_HOMO, E_LUMO), HOMO–LUMO energy gap, electron affinity (A), ionization energy (I), electrophilicity index (ω), chemical softness (σ) and chemical hardness (η) were considered and discussed. Effect of various substituents was observed on values of the HOMO–LUMO energy gap and hyperpolarizability. The p-electronic delocalization extended over pyrazine, benzene and thiophene was examined in studying the NLO behavior. The chemical shifts of ¹H NMR of all the synthesized compounds 4a–4n were calculated and compared with the experimental values.