An experimental and computational study of pyrimidine based bis-uracil derivatives as efficient candidates for optical, nonlinear optical, and drug discovery applications

Influence of acceptors on the optical nonlinearity of 5H-4-oxa-1,6,9-trithia-cyclopenta[b]-as-indacene-based chromophores with a push-pull assembly: a DFT approach

Herein, a series of compounds (TPD1-TPD6) having a D-π-A architecture was quantum chemically designed via the structural modulation of TPR. Quantum chemical calculations were employed to gain a comprehensive insight into the structural and optoelectronic properties of the designed molecules at the M06/6-311G(d,p) level. Interestingly, all the designed chromophores displayed narrow energy gaps (2.123-1.788 eV) and wider absorption spectra (λmax = 833.619-719.709 nm) with a bathochromic shift in comparison to the reference compound (λmax = 749.602 nm and Egap = 3.177 eV). Further, Egap values were utilized to evaluate global reactivity parameters (GRPs), which indicate that all the chromophores expressed higher softness (σ = 0.134-0.559 eV-1) and lower hardness (η = 4.155-4.543 eV) values than the reference chromophore. Efficient charge transfer from donors towards acceptors was noted through FMOs, which was also supported by DOS and TDM analyses. Overall, the TPD3 derivative exhibited a remarkable reduction in the HOMO-LUMO band gap (1.788 eV) with a red shift as λmax = 833.619 nm. Furthermore, it exhibited prominent linear and non-linear characteristics such as μtotal = 24.1731 D, 〈α〉 = 2.89 × 10-22 esu, and βtotal = 7.24 × 10-27 esu, among all derivatives. The above findings revealed that significant non-linear optical materials could be achieved through structural tailoring with studied efficient acceptors.

Delivery of Apoplastic Extracellular Vesicles Encapsulating Green-Synthesized Silver Nanoparticles to Treat Citrus Canker

The citrus canker pathogen Xanthomonas axonopodis has caused severe damage to citrus crops worldwide, resulting in significant economic losses for the citrus industry. To address this, a green synthesis method was used to develop silver nanoparticles with the leaf extract of Phyllanthus niruri (GS-AgNP-LEPN). This method replaces the need for toxic reagents, as the LEPN acts as a reducing and capping agent. To further enhance their effectiveness, the GS-AgNP-LEPN were encapsulated in extracellular vesicles (EVs), nanovesicles with a diameter of approximately 30-1000 nm naturally released from different sources, including plant and mammalian cells, and found in the apoplastic fluid (APF) of leaves. When compared to a regular antibiotic (ampicillin), the delivery of APF-EV-GS-AgNP-LEPN and GS-AgNP-LEPN to X. axonopodis pv. was shown to have more significant antimicrobial activity. Our analysis showed the presence of phyllanthin and nirurinetin in the LEPN and found evidence that both could be responsible for antimicrobial activity against X. axonopodis pv. Ferredoxin-NADP⁺ reductase (FAD-FNR) and the effector protein XopAI play a crucial role in the survival and virulence of X. axonopodis pv. Our molecular docking studies showed that nirurinetin could bind to FAD-FNR and XopAI with high binding energies (-10.32 kcal/mol and -6.13 kcal/mol, respectively) as compared to phyllanthin (-6.42 kcal/mol and -2.93 kcal/mol, respectively), which was also supported by the western blot experiment. We conclude that (a) the hybrid of APF-EV and GS-NP could be an effective treatment for citrus canker, and (b) it works via the nirurinetin-dependent inhibition of FAD-FNR and XopAI in X. axonopodis pv.

Synthesis, Characterization, Crystal Structures, and Supramolecular Assembly of Copper Complexes Derived from Nitroterephthalic Acid along with Hirshfeld Surface Analysis and Quantum Chemical Studies

Two new Cu(II) carboxylate complexes, Cu-NTA and Cu-DNTA, were prepared by treating 2-nitroterephthalic acid with CuSO₄·5H₂O at room temperature. The synthesized complexes were characterized by elemental (CHN), FT-IR, and thermogravimetric analysis. The crystal structures of both complexes were explored by single crystal X-ray diffraction analysis, which inferred that the coordination geometry is slightly distorted octahedral and square pyramidal in Cu-NTA and Cu-DNTA, respectively. The non-covalent interactions that are the main feature of the supramolecular assembly were investigated by Hirshfeld surface analysis for both complexes. The propensity of each pair of chemical moieties involved in crystal-packing interactions was determined by the enrichment ratio. Quantum chemical computations were performed to optimize the molecular geometry of complex Cu-NTA and compared it with the experimental single crystal structure, which was found to be in sensible agreement with the experimental structure of the complex. The DFT method was used to see the potential of the selected Cu-NTA complex for linear and nonlinear optical properties. The static NLO polarizability <γ> of complex Cu-NTA was calculated to be 86.28 × 10^-36 esu at M06 functional and 6-31G*/LANL2DZ basis set, which was rationally large to look for NLO applications of complex Cu-NTA. Additionally, the molecular electrostatic potential and frontier molecular orbitals were also computed with the same methodology to see electronic characteristics and ground-state electronic charge distributions.

Design, synthesis and characterization of novel Ni(II) and Cu(II) complexes as antivirus drug candidates against SARS-CoV-2 and HIV virus

This paper describes the structure-based design, synthesis and anti-virus effect of two new coordination complexes, a Ni(II) complex [Ni(L)2] (1) and a Cu(II) complex [Cu(L)2] (2) of (E)-N-phenyl-2-(thiophen-2-ylmethylene) hydrazine-1-carbothioamide(HL). The synthesized ligand was coordinated to metal ions through the bidentate-N, S donor atoms. The newly synthesized complexes were characterized by various spectroscopic and physiochemical methods, powdered XRD analysis and also X-ray crystallography study. Ni(II) complex [Ni(L)2](1) crystallize in orthorhombic crystal system with the space group Pbca with four molecules in the unit cell (a = 9.857(3) Å, b = 7.749(2) Å, c = 32.292(10) Å, α = 90°, β = 90°, γ = 90°, Z= 4) and reveals a distorted square planar geometry. A Hirshfeld surface and 2D fingerprint plot has been explored in the crystal structure of Ni(II) complex [Ni(L)2] (1). Energy framework computational analysia has also been explored. DFT based calculations have been performed on the Schiff base and its metal complexes to study the structure-property relationship. Furthermore, the molecular docking studies of the ligand and its metal complexes with SARS-CoV-2 virus (PDB ID: 7BZ5) and HIV-1 virus (PDB ID: 6MQA) are also investigated. The molecular docking calculations of the Ni(II) complex [Ni(L)2] (1) and a Cu(II) complex [Cu(L)2] (2) with SARS-CoV-2 virus revealed that the binding affinities at inhibition binding site of receptor protein are 9.7 kcal/mol and -9.3 kcal/mol, respectively. The molecular docking results showed that the binding affinities of Ni(II) complex (1) and Cu(II) complex (2) against SARS-CoV-2 virus were found comparatively higher than the HIV-1 virus (-8.5 kcal/mol and -8.2 kcal/mol, respectively). As potential drug candidates, Swiss-ADME predictions analyses are also studied and the results are compared with Chloroquine (CQ) and Hydroxychloroquine (HCQ) as anti-SARS-CoV-2 drugs.

A Visible-Light-Promoted C-H Arylation and Heteroarylation of Uracil Derivatives with Diazoniums in Aqueous Conditions

The photoredox synthesis of C-5 (hetero)arylated uracil and uridine substrates with the corresponding diazonium salts is described. The coupling proceeds efficiently without protection of the hydroxyls at the ribose or pre-functionalization of the C5 position at the nucleobase. No transition-metal catalyst is used in this transformation, thereby avoiding metal contamination in the final products. The use of water as the medium also eliminates the impurities caused by the use of organic solvents. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5-aryl and 5-heteroaryl uracil derivatives Basic Protocol 2: Synthesis of 5-aryl uridine and deoxyuridine uridine derivatives.

Chemically Modified Quinoidal Oligothiophenes for Enhanced Linear and Third-Order Nonlinear Optical Properties

In the present investigation, quantum chemical calculations have been performed in a systematic way to explore the optoelectronic, charge transfer, and nonlinear optical (NLO) properties of different bis(dicyanomethylene) end-functionalized quinoidal oligothiophenes. The effect of different conformations (linking modes of thiophene rings) on conformational, optoelectronic, and NLO properties are studied from the best-performed dimer to octamer. The optical and NLO properties of all the selected systems (1-7) are calculated by means of density functional theory (DFT) methods. Among all the designed compounds, the largest linear isotropic (αiso) polarizability value of 603.1 × 10-24 esu is shown by compound 7 which is ∼12, ∼16, ∼9, ∼11, ∼10, and ∼4 times larger as compared to compounds 1-6, respectively. A relative investigation is performed considering the expansion in third-order NLO polarizability as a function of size and conformational modes. Among all the investigated systems, system 7 shows the highest value of static second hyperpolarizability ⟨γ⟩ with an amplitude of 7607 × 10-36 esu at the M06/6-311G** level of theory, which is ∼521, ∼505, ∼38, ∼884, ∼185, and ∼15 times more than that of compounds 1-6, respectively. The extensively larger ⟨γ⟩ amplitude of compound 7 with higher oscillator strength and lower transition energy indicates that NLO properties are remarkably dependent upon linking modes of thiophene rings and its chain length. Furthermore, to trace the origin of higher nonlinearities, TD-DFT calculations are also performed at the same TD-M06/6-311G** level of theory. Additionally, a comprehensive understanding of the effect of structure/property relationship on the NLO polarizabilities of these investigated quinoidal oligothiophenes is obtained through the inspection of Frontier molecular orbitals, the density of states (TDOS and PDOS), and molecular electrostatic potential diagrams including the transition density matrix. Hence, the current examination will not just feature the NLO capability of entitled compounds yet additionally incite the interest of experimentalists to adequately modify the structure of these oligothiophenes for efficient optical and NLO applications.