A 3D copper (II) coordination polymer based on sulfanilic acid ligand (CP 1) for efficient biomolecular interaction with bovine serum albumin: spectroscopic, molecular modelling and DFT analysis

Several biochemical reactions occur during the interaction of metal complexes and proteins due to conformational modifications in the structure of the protein, which provide fundamental knowledge of the effect, mechanism, and transport of many drugs throughout the body. Here, we report the synthesis, identification, and impact of the 3-dimensional Copper(II)sulfanilic acid coordination polymer (CP 1) on interactions with bovine serum albumin (BSA). The CP 1 was synthesized via a simple hot stirring method, and the single crystal XRD confirms the effective bonding interactions between metal and organic ligand, forming a crystalline polymeric chain and the topological study shows the sql type of underlying net topology. Powder XRD, Fourier transform infrared spectroscopy, and thermogravimetric analysis were also performed. Moreover, DFT/B3LYP calculations provide chemical precision for the resulting complex. Further, the changes that occur in the secondary structure of protein when CP 1 binds with BSA as well as its binding capacity were investigated via circular dichroism analysis and spectroscopic methods such as UV-absorption spectroscopy and fluorescence spectroscopy, respectively. The CP 1/BSA complex melting point was also measured, and its temperature-dependent heat denaturation was studied along with molecular docking.Communicated by Ramaswamy H. Sarma.

Growth, studies of milled and irradiated crystalline samples of DBNT for macro-photonic and electro-mechano functionalities

Single crystals of organic type of NLO crystalline material of DBNT - 8, 9-Dimethoxybenzo[b]naphtho [2,3-d] thiophene are proceeded to be grown by slow evaporation procedure and milled to micro scale and irradiated of Co-60 source of 100 Gy, 500 Gy and 5000 Gy for better scope of classification of system of the monoclinic type of DBNT-pure, micro and irradiated ones. The hardness study specifies the reverse indentation size effect (RISE) with work hardening coefficient above two of all DBNT specimen leads to the micro-tribological workings for springs with proper elastic parameters; the transmittance of DBNT of 5 specimens are 321 nm, 323 nm, 341 nm, 351 nm, and 352 nm for macro, micro, 100 Gy, 500 Gy, 5000 Gy. The photonic utility of identity for 3.86 eV and is 3.8629 eV by the transmittance data. The Non Linear Optical - NLO component this of 1.9, 1.94, 1.95, 1.96, 1.99 times that of KDP from which phase matching provision is enabled the influx property for the DBNT specimens is in the order of microns the (110) and (111) indexing represent for display device configuration. The dielectric behaviour of DBNT shows that polarization properly enabled for all categories by electrical performance, the abnormal variation is due to the vacancies created in the molecule by irradiation.

Virtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma

HDAC protein is associated with hepatocellular carcinoma. Different medicinal plants were selected for this study to analyze the inhibitory efficacy against the target protein, HDAC. Using virtual screening, we filtered out the best compounds, and molecular docking (XP) was carried out for the top compounds which filtered out. The molecular docking results showed that the title compound (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate (MEMNC) has the highest docking score of about -7.7 kcal/mol against the targeted protein histone deacetylase (HDAC) compared with the other selected phytocompounds. From the molecular dynamics analysis, the RMSD and RMSF plots depicted the overall stability of the protein-ligand complex. Toxicity properties show the acceptable range of various kinds of toxicity that were predicted using the ProTox-II server. In addition, DFT quantum chemical and physicochemical properties of the MEMNC molecule were reported. Initially, the molecular structure of the MEMNC molecule was optimized and harmonic vibrational frequencies were calculated using DFT/B3LYP method with a cc-pVTZ basis set using Gaussian 09 program. The calculated vibrational wavenumber values were assigned based on Potential Energy Distribution calculations using the VEDA 4.0 program and correlated well with the previous literature values. The molecule has bioactivity as a result of intramolecular charge transfer interactions, as demonstrated by frontier molecular orbital analysis. Molecular electrostatic potential surface and Mulliken atomic charge distribution analyses validate the reactive sites of the molecule. Thus, the title compound can be used as a potential inhibitor of HDAC protein, which paves the way for designing novel drugs to treat Hepatocellular carcinoma.Communicated by Ramaswamy H. Sarma.

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Introduction: Non-Small Cell Lung Cancer is the most prevalent type of cancer in lung cancer. Chemotherapy, radiation therapy, and other conventional cancer treatments have a low success rate. Thus, creating new medications is essential to halt the spread of lung cancer. Methods: In this study bioactive nature of lochnericine against Non-Small Cell Lung Cancer (NSCLC) was analyzed using various computational approaches such as quantum chemical calculations, molecular docking, and molecular dynamic simulation. Furthermore, the MTT assay shows the anti-proliferation activity of lochnericine. Results and Discussion: Using Frontier Molecular Orbital (FMO), the calculated band gap energy value associated with bioactive compounds and the molecule's potential bioactivity is confirmed. The H38 hydrogen atom and O1 oxygen atom in the molecule are effectively electrophilic, and potential nucleophilic attack sites were confirmed through analysis of the Molecular electrostatic potential surface. Furthermore, the electrons within the molecule were delocalized, which confers bioactivity on the title molecule and was authorized through Mulliken atomic charge distribution analysis. A molecular docking study revealed that lochnericine inhibits non-small cell lung cancer-associated targeted protein. The lead molecule and targeted protein complex were stable during molecular dynamics simulation studies till the simulation period. Further, lochnericine demonstrated remarkable anti-proliferative and apoptotic features against A549 lung cancer cells. The current investigation powerfully suggests that lochnericine is a potential candidate for lung cancer.

The novel tetrahydropyrimidine derivative as inhibitor of SARS CoV-2: synthesis, modeling and molecular docking analysis

N-(1,3-Benzothiazol-2-yl)-N-(1,4,5,6-tetrahydro-1H-pyrimidine-2-yl) amine was synthesized and characterized by elemental analysis, FT-IR, NMR and X-ray single crystal diffraction. The compound structure belongs to the triclinic system with the P-1 space group with unit cell parameters a = 11.9290(4), b = 13.2547(4) and c = 15.3904(5) Å. Hirhsfeld surface analysis is performed to revealintermolecular interactions with these interactions. The molecular structure, vibrational spectroscopic data and HOMOs and LUMOs analyses were calculated by using the DFT/B3LYP method with the 6-311 + G(d,p)) basis set. Some of pharmacokinetic parameters and drug-likeness properties of the compound were also performed. Besides these, the present work is a searching to test N-(1,3-benzothiazol-2-yl)-N-(1,4,5,6-tetrahydro-1H-pyrimidine-2-yl) amine as an inhibitor for the SARS-CoV-2. For this aim, the molecular docking analysis of the synthesized compound was applied along with Favipiravir. Besides the docking results, ADMET properties of the compound were also calculated.Communicated by Ramaswamy H. Sarma.

Exploration of plant-derived natural polyphenols toward COVID-19 main protease inhibitors: DFT, molecular docking approach, and molecular dynamics simulations

Recent outbreaks of coronavirus have brought serious challenges to public health around the world, and it is essential to find effective treatments. In this study, the 3C-like proteinase (3CLpro) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been considered as an important drug target because of its role in viral replication. We initially optimized 251 compounds at the PM7 level of theory for docking with 3CLpro, and then we selected the top 12 compounds for further optimization with the B3LYP-D3/6-311G** method and obtained the top four compounds by further molecular docking. Quantum chemistry calculations were performed to predict molecular properties, such as the electrostatic potential and some CDFT descriptors. We also performed molecular dynamics simulations and free energy calculations to determine the relative stability of the selected four potential compounds. We have identified key residues controlling the 3CLpro/ligand binding from per-residue based decomposition of the binding free energy. Convincingly, the comprehensive results support the conclusion that the compounds have the potential to become a candidate for anti-coronavirus treatment.

The combination of molecular dynamics simulations and quantitative calculations as a powerful tool for screening molecules.

Growth, crystal structure, Hirshfeld surface and vibrational properties of a new supramolecular hybrid material: (C4H7N2)2TeBr6

A novel tellurium (IV) hybrid compound with 2-methylimidazole was prepared. The crystal was grown by slow evaporation method from aqueous solutions at room temperature giving birth to a new compound with formula (C4H7N2)2TeBr6. The structure was determined by single-crystal X-ray diffraction. It crystallizes in the monoclinic system, space group C 2/c, with the following parameters: a = 18.577(2)Å, b = 9.1497(10)Å, c = 13.5355(17)Å, α = 90°, β = 123.835(5)°, γ = 90° and Z = 8. The structure was solved with a final R = 0.044 for 2783 independent reflections. The crystal arrangement consists of [TeBr6]2− anions surrounded by [C4H7N2]2+ cations. The stability of the structure was ensured by hydrogen bonding contacts (N–H…Br) lengths that are in the range of 3.490–3.682 Å. The infrared spectra (FTIR) were recorded in the 4000–550 cm−1, confirming the existence of vibrational modes that correspond to the organic and inorganic groups. The crystal packing was stabilized mainly by Br…H (73.6%) interactions. Hirshfeld surface calculations were conducted to further investigate intermolecular interactions, associated 2D fingerprint plots and enrichment ratio, revealing the quantitatively relative contribution of these interactions in the crystal packing.

SERS and DFT studies of 2-(trichloroacetyl)pyrrole chemisorbed on the surface of silver and gold coated thin films: In perspective of biosensor applications

The adsorption and orientations of 2-(trichloroacetyl)pyrrole (TCAP) adsorbed on a fabricated silver-coated thin film (SCF), and gold-coated thin film (GCF) were investigated using surface-enhanced Raman scattering (SERS) studies and compared with the normal Raman scattering (nRs) spectrum of TCAP. The observed nRs and SERS spectra of TCAP were validated theoretically using DFT quantum chemical calculations. Initially, the molecular structure of TCAP, TCAP-Ag₃ , and TCAP-Au₄ molecular systems were optimized and analyzed. The fabricated SCF and GCF are characterized using FESEM analysis, which confirms that the silver and gold nanoparticles of the corresponding films are spherical in shape. The obtained significant red-shift in UV-visible spectra of TCAP added on SCF and GCF surfaces reveal that the TCAP strongly adsorbed on SCF and GCF surfaces. The frontier molecular orbitals analysis authenticates the charge-transfer interaction from Ag₃ and Au₄ metal clusters to the TCAP molecule, leading to the adsorption of TCAP molecule on Ag₃ and Au₄ metal clusters, which validates the UV-vis results. SERS spectral analysis confirms that the TCAP chemisorbed on SCF and GCF surfaces with tilted orientation and the corresponding results were validated theoretically. The calculated SERS enhancement factor values illustrate that the GCF surface exhibits a higher SERS signal enhancement than the SCF surface. Therefore, the present investigation will be useful for the development of active SERS substrates and pyrrole-related biosensors.

Linear-nonlinear optical and quantum chemical studies on Quinolinium 3,5-dinitrobenzoate: A novel third order non-linear optical material for optoelectronic applications

An organic non-linear optical (NLO) crystal of Quinolinium 3,5-dinitrobenzoate (DNBAQ) was synthesized and good quality single crystals of DNBAQ were grown by conventional slow evaporation solution growth technique. Single crystal XRD was utilized to confirm the formation of the charge transfer complex. The crystalline property and the presence of required functional groups was verified employing Powder XRD and FTIR spectral analysis. UV-Vis-NIR and Fluorescence study was performed to determine the optical transmittance and the emission property of the grown crystal. The thermal, mechanical and surface damage threshold stability of the complex was analysed using thermal studies, Vicker's micro hardness studies and Laser damage threshold measurement. The solid state parameter of electronic polarizability of DNBAQ compound was computed through dielectric studies. The non-linear optical characterizations like Kurtz Perry powder technique and Z-Scan technique ensures the non-linear optical activity of the compound. The frequency conversion efficiency of the grown crystal was estimated to be 70% that of the standard Potassium Dihydrogen Phosphate (KDP). Z-Scan analysis confirms the suitability of the grown crystal for optical limiting and switching applications. Quantum chemical studies were adopted on the optimized geometry of DNBAQ molecule using Density Functional Theory (DFT). Frontier Molecular Orbital (FMO) analysis and Molecular Electrostatic Potential (MEP) analysis were performed. The non-linear optical behaviour of the complex was established by evaluating dipole moment, polarizability and hyperpolarizability features. All the above results confirm the resourceful candidature of DNBAQ material for optoelectronic and photonic applications.

Azaphenantherene derivatives as inhibitor of SARS CoV-2 Mpro: Synthesis, physicochemical, quantum chemical and molecular docking analysis

The crystal structure of 2-(1H-indol-3-yl)-4-phenyl-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ia) and 2-(5-bromo-1H-indol-3-yl)-4-(4-methoxyphenyl)-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ib) were elucidated using single crystal X-ray diffraction. The cyclohexadiene ring adopts screw boat conformation in compound (Ia) and distorted screw boat in compound (Ib). The pyridine ring is effectively planar. The qualitative and quantitative analyses of hydrogen bonding interactions in the compounds were done using Hirshfeld surface analysis, QTAIM and NCI. DFT/B3LYP level of theory was used to optimize both the compounds. These compounds drug-like behaviors were studied using HOMO-LUMO analysis. The molecular docking analysis against M^pro was carried out for the synthesized compounds and some suggested drugs for COVID-19. The docking results were then analyzed.

Azafluorene derivatives as inhibitors of SARS CoV-2 RdRp: Synthesis, physicochemical, quantum chemical, modeling and molecular docking analysis

The crystal structures of 2-(1H-indol-3-yl)-4-phenyl-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ia) and 2-(1H-indol-3-yl)-4-(4-methoxyphenyl)-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ib) were determined using single crystal X-ray diffraction. Both the compounds belong to the triclinic system with the P-1 space group. The azafluorene ring system in both the compounds is effectively planar. The intermolecular interactions present in the compounds are discussed using Hirshfeld surface analysis, QTAIM and NCI. Compound Ib formed a strong interaction (−24.174 kJ/mol) with the solvent molecule. Both the compounds were geometry optimized using DFT/B3LYP level of theory. The compound’s drug-like behaviors were studied using HOMO-LUMO analysis. The homology modeling of SARS CoV-2 RdRp was done utilizing the PDB 6NUR_A as a template. The model showed above 99% similarity with its preceder SARS CoV. The molecular docking analysis of the synthesized compounds was carried out along with some suggested drugs for COVID-19 and some phytochemicals. The docking results were then analyzed. The binding free energy of the complexes were calculated using MM-PB(GB)SA and ADMET properties of Ia and Ib were also predicted. Some suggestions are given from this analysis.

Synthesis, crystal growth, physicochemical properties and quantum chemical investigations of a D–π–A type organic single crystal: 2-amino-5-nitropyridinium p-phenolsulfonate (2A5NPP) for nonlinear optical (NLO) applications

Efficient organic NLO 2A5NPP single crystals have been grown by slow cooling method.