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1.
J King Saud Univ Sci ; 35(6): 102758, 2023 Aug.
Article in English | MEDLINE | ID: covidwho-20235858

ABSTRACT

In this investigation a single crystal of (4-oxo-piperidinium ethylene acetal) trioxonitrate (4-OPEAN) was synthesized by modifying the mechanism of gradual evaporation at ambient temperature. The operational groupings are found in the complex material in the elaborate substance, according to the infrared spectrum. Single crystal X-ray diffraction suggests, (4-OPEAN) with the chemical formula (C7H12NO2)NO3 belongs to the orthorhombic space group Pnma and is centrosymmetric in three dimensions with the aforementioned network configurations, a = 11.7185(8) Å, b = 7.2729(6) Å, c = 11.0163(8) Å, Z = 4, V = 938.89(12) Å3, R = 0.0725 and wR = 0.1762. Many N-H…O and C-H…O hydrogen bridges, both bifurcated and non-bifurcated, link the 4-oxo-piperidinium ethylene acetal cations to the trigonal (NO3-) anions. Molecular geometry and optimal parameters of (4-OPEAN) have been determined via DFT computations at the theory-level B3LYP/6-311 ++ G(d, p), these have been contrasted with the X-ray data already available. Hirshfeld surface analysis has made it possible for the visualization and quantification of relationships between molecules in the crystal composition. Quantum theory atoms in molecules, electron location function, decreased density gradient, and localized orbital locator research have all been used to explore non-covalent interactions in crystal structure. In order to pinpoint both the nucleophilic and electrophilic locations that support hydrogen bond formation, the molecule electrostatic potential was determined. The greatest and lowest energies of occupied and unfilled molecular orbitals, together with additional derived atomic characteristics, show the material to be extremely stable and hard. According to a molecular docking study, 4-OPEAN may exhibit inhibiting effects on the 6Y84 and 7EJY virus proteins from corona (COVID-19).

2.
J Biomol Struct Dyn ; : 1-24, 2022 May 23.
Article in English | MEDLINE | ID: covidwho-20238252

ABSTRACT

This work deals with the synthesis and characterization of copper(II) complex [Cu(salen)(H2O)](1) of salen-type Schiff base ligand derived from the condensation of 5-bromo-2-hydroxy-3-methoxybenzaldehyde and ethylenediamine in EtOH. This complex was characterized by different spectroscopic and physicochemical methods. Single crystal X-ray crystallography study revealed that Cu(II) in complex (1) is five-coordinate and adopts a distorted square pyramidal geometry. A DFT calculation was employed to evaluate the optimized electronic structure, HOMO-LUMO, energy gap, and global parameters. A detailed structural and non-covalent interaction on the complex is investigated by single crystal structure analysis and computational approaches. The strength of the interaction and 3D topology of the crystal packing are visualized through an energy framework. Hirshfeld surface and 2D fingerprint plots have been explored in the crystal structure of the complex. The anticancer properties of copper(II) complex was studied against the selected cancerous cell lines of breast cancer, cervical cancer, colon cancer and hepatocellular carcinoma. Additionally, molecular docking and MD simulations was performed on the complex to predict the binding mode and interactions between the ligand and the main protease of the SARS-CoV-2 (PDB ID: 7CBT and 7D1M). The molecular docking calculations of the complex (1) with SARS-CoV-2 virus revealed the binding energy of -8.1 kcal/mol and -7.5 kcal/mol with an inhibition constant of 3.245 µM and 2.318 µM at inhibition binding site of receptor towards 7CBT and 7D1M main protease (Mpro), respectively. Besides this, molecular docking results (-7.6 kcal/mol, 3.196 µM) towards Escherichia coli PBP2 targets (PDB ID: 6G9S) was also studied. Communicated by Ramaswamy H. Sarma.

3.
Journal of Molecular Structure ; 1288:135782, 2023.
Article in English | ScienceDirect | ID: covidwho-2322730

ABSTRACT

The synthesis and characterization of 5-Amino-4-Phenylazo-3-Methyl-1-(2-hydroxyethyl) Pyrazole (AD2a) were investigated in our study. The novel synthesized pyrazole-based disperse diazo dye has been elucidated by using UV–Vis, FT-IR, elemental analysis, LC/MS-MS, NMR and X-ray analysis. The AD2a molecule containing pyrazole and phenyl rings, hydroxy‑ethyl and azo group moieties crystallized in the orthorhombic space group Pbca. The crystal structures of AD2a are consolidated by N(3)-H(3A)⋯O(1) and O(1)-H(1)⋯N(5) intermolecular hydrogen bonds. The geometry of AD2a has been optimized with the DFT calculation B3LYP/6–31G(d,p) level and it has been observed that the obtained results give very good results with the X-ray diffraction data. The theoretical vibrational analysis, frontier orbital energies, electronic absorption spectrum, electronic properties, global reactivity descriptors and other theoretical parameters were obtained by using the same DFT method. Additionally, Hirshfeld surface analysis (HSA) with 2D fingerprint plots (FP) was performed to estimate contacts and the energy framework diagrams of AD2a (Eele, Edis and Etot) were determined. The inhibitor-receptor relationship established by the molecular docking study confirmed the inhibition activity of the AD2a construct against COVID-19. It showed that the AD2a molecule, shown as a drug candidate, binds strongly to SARS-CoV-2 (Mpro) (-6.5 kcal/mol) receptors.

4.
Journal of Molecular Structure ; 1287:135710.0, 2023.
Article in English | ScienceDirect | ID: covidwho-2320984

ABSTRACT

N-(6-(((E)-4-methoxybenzylidene) amino) hexyl)-1-(4-methoxyphenyl) methanimine (1) and its hydrate (2) were synthesized by refluxing hexamethylene diamine and anisaldehyde in presence of catalytic amount of H-Beta zeolite in solvent methanol. Resulting imines were characterized by spectroscopic analysis augmented by Single crystal X-ray diffraction. Both compounds crystalize in monoclinic crystal systems with different point groups P 21 and C 2/c. Pair wise aromatic π-CH and CH- π interactions with distance 2.887 and 2.786 Ao and iminic CH- π interactions with the distance of 2.73 Ao are mainly responsible for extending the structure along 3 dimensions. However, hydrated structure exhibited an addition hydrogen bonding with H of water molecules with the distance of 2.030 Ao , also methoxy O is involved in hydrogen bonding interaction with CH with the distance of 2.641 Ao. Probable contact points and most important crystal packing contributions were determined by employing Hirshfeld surface analysis. H…H and C…H contacts are the most important contributors in the Hirshfeld Surface. Electronic and structural characteristics of both compounds has been calculated using B3LYP/6-311G (d,p) theory. In addition, FMO and MEPS analyses were also accomplished for optimized structures. Molecular Docking studies of compound 1 and 2 were carried out with protease enzyme of 2019-nCoV (PDB-ID 7BRO), monohydrate(2) was involved in more favourable interactions hence accounting for greater binding energy (-7.98 kcal/mol) and inhibition constant (12.96 mM) than compound 1 exhibiting inhibition constant of 39.25 mM and binding energy of -6.23 kcal/mol.

5.
Polycyclic Aromatic Compounds ; 43(4):3024-3050, 2023.
Article in English | ProQuest Central | ID: covidwho-2312625

ABSTRACT

Two coordination complexes, a cobalt(II) complex tris(1,10-phenanthroline)-cobalt perchlorate hydrate, [Co(phen)3]·(ClO4)2·H2O(1), and a copper(II) complex tris(1,10-phenanthroline)-copper perchlorate 4-bromo-2-{[(naphthalene-1-yl)imino]methyl}phenol hydrate, [Cu(phen)3]·(ClO4)2·HL·[O] (2), [where, phen = 1,10-phenathroline as aromatic heterocyclic ligand, HL = 4-bromo-2-((Z)-(naphthalene-4-ylimino) methyl) phenol] have been synthesized and structurally characterized. Single crystal X-ray analysis of both complexes has revealed the presence of a distorted octahedral geometry around cobalt(II) and copper(II) ions. density functional theory (DFT)-based quantum chemical calculations were performed on the cationic complex [Co(phen)3]2+ and copper(II) complex [Cu(phen)3]2+ to get the structure property relationship. Hirshfeld surface and 2-D fingerprint plots have been explored in the crystal structure of both the metal complexes. To find potential SARS-CoV-2 drug candidates, both the complexes were subjected to molecular docking calculations with SARS-CoV-2 virus (PDB ID: 7BQY and 7C2Q). We have found stable docked structures where docked metal chelates could readily bound to the SARS-CoV-2 Mpro. The molecular docking calculations of the complex (1) into the 7C2Q-main protease of SARS-CoV-2 virus revealed the binding energy of −9.4 kcal/mol with a good inhibition constant of 1.834 µM, while complex (2) exhibited the binding energy of −9.0 kcal/mol, and the inhibition constant of 1.365 µM at the inhibition binding site of receptor protein. Overall, our in silico studies explored the potential role of cobalt(II) complex (1), and copper(II) complex (2) complex as the viable and alternative therapeutic solution for SARS-CoV-2.

6.
Journal of Molecular Structure ; 1286:135633, 2023.
Article in English | ScienceDirect | ID: covidwho-2308387

ABSTRACT

We present the synthesis and characterization of stereoselective thione. The synthetic procedure includes readily available starting materials and minimum side products. The reaction of meso‑stilbenediamine with carbon disulphide in the presence of strong base gave cis-4,5-diphenylimidazolidine-2-thione (DPIT) in an excellent yield. The thione compound was characterized via FT-IR and mass spectroscopy. In addition, the crystal structure of it was determined by single crystal X-rays diffraction analysis which inferred that the molecular configuration was stabilized by intramolecular π⋯π stacking interaction. The crystal packing was mainly stabilized by N-H⋯S bonding. Hirshfeld surface analysis was performed for the exploration of the intermolecular interactions. Void analysis was carried out to predict the mechanical stability. Interaction energy between the molecular pairs is calculated which showed that the dispersion energy played a dominant role in the stabilization of the crystal packing. Moreover, the quantum computational methods were used to study the molecular structure and electronic properties of entitled compound. The molecular geometries were optimized for possible thione and thiole tautomeric structures. A comparison of total energy of molecular tautomers indicates that thione tautomer possesses lower total energy which is about 20.18 Kcal/mol lower than thiole tautomer. The electronic properties of thione derivative were studied including 3-D wavefunction delocalization of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) orbitals and their orbital energy gap. The HOMO-LUMO energy gap for DPIT was found to be 4.874 eV. The delocalization of wavefunction indicates the probable presence of HOMO and HOMO-1 are mainly localized over C-S bond owing to the presence of lone pair of electrons in the sulfur atom. Additionally, the molecular docking study was also carried out for main protease (Mpro) of SARS-CoV-2. The binding energy calculation and investigation of intermolecular interactions highlighted the probable inhibition tendency of DPIT for SARS-CoV-2. The present experimental and computational studies indicate a significant potential of entitled molecule for electronic and biological perspectives.

7.
Molecular Crystals and Liquid Crystals ; 2023.
Article in English | Scopus | ID: covidwho-2302365

ABSTRACT

Detailed structural and noncovalent interactions in two thiazole derivatives (N-(4-Bromophenyl)-2-(methylthio)thiazole-5-carboxamide and Ethyl-5-((4-bromophenyl)carbamoyl)thiazole-4-carboxylate) are investigated by single crystal X-ray diffraction study and computational approaches. The structure investigation revealed that various interactions like C-H…O, N-H…O, and N-H…N hydrogen bonds and Br…Br interactions are involved in constructing ring motifs to stabilize the crystal packing. Hirshfeld surface analysis and fingerprint plots were carried out to study the differences and similarities in the relative contribution of noncovalent interactions in both the molecules. The FMOs and other global reactive parameters are analyzed for thiazole derivatives. The strength and nature of weak interactions present in the molecule were characterized by RDG-based NCI and QTAIM analyses. Natural bond orbital (NBO) analysis unravels the importance of non-covalent and hyperconjugative interactions for the stability of the molecules in their solid state. Further, molecular docking of N-(4-Bromophenyl)-2-(methylthio)thiazole-5-carboxamide and Ethyl-5-((4-bromophenyl)carbamoyl)thiazole-4-carboxylate with SARS-Covid-19 have been carried out. © 2023 Taylor & Francis Group, LLC.

8.
Journal of Molecular Structure ; 1283, 2023.
Article in English | Scopus | ID: covidwho-2266025

ABSTRACT

The novel benzamide derivative NNN pincer type, N,N'-(azanediylbis(2,1-phenylene))bis(3-chlorobenzamide) (H3L), was synthesized from bis(2-nitrophenyl)amine starting material. The pincer ligand was characterized by 1H NMR, 13C NMR, COSY, HMQC, and FT-IR techniques. The geometry of pincer ligand was also confirmed by a single-crystal X-ray diffraction analysis. Structural analysis demonstrate that H3L is monoclinic and space group P21/n with Z = 4. It was find out the molecular conformation of the structure is promoted by intramolecular (N[sbnd]H⋅⋅⋅O, N[sbnd]H⋅⋅⋅N, and C[sbnd]H⋅⋅⋅O) and intermolecular (N(2)-H(2)⋅⋅⋅O(2)i, symmetry code (i) = 1/2 + x, 3/2-y, 1/2 + z) hydrogen bonds. The theoretical study of H3L was performed in the gaseous phase by B3LYP/6-311G(d,p) method to determine the structural properties of the title molecule, as a consequence the obtained data showed that the considerable agreement between the experimental and theoretical results. The reactivity and stability of the molecule were evaluated by calculating the HOMO–LUMO energy gap which was found as 6.5163 eV. In addition, FMO, NBO, NLO, DOS, RDG, MEP surface, and Mulliken atomic charge analyses were carried out. Hirshfeld surface analysis and two-dimensional fingerprint plots were investigated and the obtained data exposed that the most significant contributions to the crystal packing are from C···H/H···C (33.2%), H···H (31.5%), and H···Cl/Cl··H (18.9%) contacts. Furthermore, the molecular docking studies were performed to reveal the binding affinity between the title compound and the main protease (6LU7) of COVID-19 coronavirus. © 2023 Elsevier B.V.

9.
Polyhedron ; 235, 2023.
Article in English | Scopus | ID: covidwho-2260141

ABSTRACT

In this work, synthesis as well as detailed structural and computational analyses of the novel isoniazid derivative, namely N'-isonicotinoylpicolinohydrazonamide (1), are reported. The obtained compound was examined by microanalysis, IR, 1H NMR spectroscopy and single crystal X-ray diffraction. The crystal packing was studied by the Hirshfeld surface analysis. Molecules in the crystal structure of 1 are linked through N–H⋯O and N–H⋯N hydrogen bonds, and π⋯π interactions, yielding a 1D supramolecular chain. According to the Hirshfeld surface analysis, crystal packing of 1 is primarily dictated by H⋯H, H⋯C, H⋯N and H⋯O contacts, of which the latter three contacts are highly favoured. The crystal packing is further characterized by highly favoured C⋯C contacts. Compound 1 was also studied using DFT in gas phase, which revealed its pronounced electrophilic features. The most electron-rich (nucleophilic) sites were revealed for the carbonyl oxygen atom, and 4-pyridyl and imine nitrogen atoms, while the most electron-deficient (electrophilic) sites were found for the NH and NH2 hydrogen atoms. Compound 1 was predicted to belong to a fourth class of toxicity and exhibits negative blood–brain barrier penetration and positive gastrointestinal absorption property. In silico molecular docking was applied to probe 1 as a potential inhibitor of a series of the SARS-CoV-2 proteins and it was found that 1 is potentially active against all the applied proteins with the best activity against Nonstructural protein 3 (Nsp3_range 207–379-MES). It was also established that the best docking scores for 1 were found for the cavities, where initial ligands were located, except for the Papain-like protease (PLpro). The best binding affinity of the latter protein with 1 was revealed for the other cavity with about 0.8 kcal/mol being more efficient. Molecular dynamics simulations were also applied to evaluate the stability of complexes PLproI–1, PLproII–1 and Nsp_range 207–379-MES–1. Complex PLproI–1 was found to be highly unstable, while complexes PLproII–1 and Nsp_range 207–379-MES–1 are stable. © 2023 Elsevier Ltd

10.
Journal of Molecular Structure ; 1282, 2023.
Article in English | Scopus | ID: covidwho-2258419

ABSTRACT

Oxadiazines are heterocyclic compounds containing two nitrogen and one oxygen atom in a six-membered ring. The synthesis and crystal structure of 4-(4-methoxyphenyl)-6-methyl-3-phenyl-4H-1,2,4-oxadiazin-5(6H)-one (MPMP-OXA) was reported. The organic crystal structure of the synthesized compound was fully characterized by various spectroscopic techniques (Fourier Transform Infrared Spectroscopy, NMR and LC/MS-TOF) and single-crystal X-ray diffraction studies. The MPMP-OXA crystal structure crystallizes in the triclinic system and space group P-1 with a = 5.9395(15) Å, b = 11.471(3) Å, c = 11.901(3) Å, α = 70.075(4)°, β = 83.454(4)°, γ = 78.016(4)°, V = 744.9(3) Å3, Z = 2 cell parameters. This work is aimed to study the weak interactions in the crystal packing of a new synthesized oxadiazine derivate. The contributions of the most important intermolecular interactions in the crystal structure were investigated by 3D-Hirshfeld surface (HS) and 2D-fingerprint analysis. The C[sbnd]H···O interactions as the most important contributors to the crystal packing between the oxygen of the oxadiazine ring and the hydrogen atom of phenyl ring appear as bright red spots visible on the HS surface. The hydrogen-bonded interaction of MPMP-OXA has been investigated using noncovalent interactions approach. The molecular docking studies for the synthesized compound were performed to gain insight into the inhibition nature of this molecule against DNA Gyrase B Candida and 3-chymotrypsin-like protease (SARS-CoV main protease) proteins and resulted in good activities for new anti-agents. Lastly, Bioavailability, druggability as well as absorption, distribution, metabolism, excretion, and toxicity parameters (ADMET), and gastrointestinal absorption (BOILED-Egg method) properties of newly synthesized compound using smile codes were performed in detail. © 2023 Elsevier B.V.

11.
Acta Crystallogr E Crystallogr Commun ; 79(Pt 3): 192-200, 2023 Feb 01.
Article in English | MEDLINE | ID: covidwho-2285038

ABSTRACT

The title compound, C30H33N4O2F, can be obtained via a two-step synthetic scheme involving 1-benzyl-6-fluoro-4-oxo-7-(piperidin-1-yl)-1,4-di-hydro-quino-line-3-carbo-nitrile as a starting compound that undergoes substitution with hydroxyl-amine and subsequent cyclization with 4-methyl-cyclo-hexane-1-carb-oxy-lic acid. It crystallizes from 2-propanol in the triclinic space group P with a mol-ecule of the title compound and one of 2-propanol in the asymmetric unit. After the mol-ecular structure was clarified using NMR and LC/MS, the mol-ecular and crystalline arrangements were defined with SC-XRD. A Hirshfeld surface analysis was performed for a better understanding of the inter-molecular inter-actions. One strong (O-H⋯O) and three weak [C-H⋯F (intra-molecular) and two C-H⋯O] hydrogen bonds were found. The contributions of short contacts to the Hirshfeld surface were estimated using two-dimensional fingerprint plots showing that O⋯H/H⋯O, C⋯H/H⋯C and C⋯C contacts are the most significant for the title compound and O⋯H for the 2-propanol. The crystal structure appears to have isotropically packed tetra-mers containing two mol-ecules of the title compound and two mol-ecules of 2-propanol as the building unit according to analysis of the distribution of pairwise inter-action energies. A mol-ecular docking study was carried out to evaluate the inter-actions of the title compound with the active centers of macromolecules corresponding to viral targets, namely, anti-hepatitis B activity [HBV, capsid Y132A mutant (VCID 8772) PDB ID: 5E0I] and anti-COVID-19 main protease activity (PDB ID: 6LU7). The data obtained revealed a noticeable affinity towards them that exceeded that of the reference ligands.

12.
J Chem Crystallogr ; : 1-14, 2023 Mar 09.
Article in English | MEDLINE | ID: covidwho-2284817

ABSTRACT

The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P212121. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield 1H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm-1 on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G + + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike. Graphical Abstract: Herein we present the solid state structure, noncovalent interaction and spectroscopic analysis of a prospective bioactive compound 4-hydroxy-1-[(4-nitrophenyl)sulphonyl]pyrrolidine-2-carboxyllic acid. Supplementary Information: The online version contains supplementary material available at 10.1007/s10870-023-00978-0.

13.
J Biomol Struct Dyn ; : 1-21, 2021 Nov 29.
Article in English | MEDLINE | ID: covidwho-2242381

ABSTRACT

A nickel(II) Schiff base complex, [Ni(L)(DMF)](1), was synthesized by treating NiCl2.6H2O with an ONS-donor Schiff base ligand(H2L) derived from the condensation 3,5-Dichlorosalicylaldehyde and 4,4-Dimethyl-3-thiosemicarbazide in DMF. The geometry around the center metal ion in [Ni(L)(DMF)](1) was square planar as revealed by the data collection from diffraction studies. DFT calculations were performed on the complex to get a structure-property relationship. Hirshfeld surface analysis was also carried out in the crystal structure of nickel (II) Schiff base complex. Additionally, inspiring from recent developments to find a potential inhibitor for SARS-CoV-2 virus, we have also performed molecular docking study of [Ni(L)(DMF)](1) to see if our novel complex show affinity for main protease (Mpro) of SARS-CoV-2 Mpro (PDB ID: 6LZE). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant was found to be -6.6 kcal/mol and 2.358 µM, respectively, for the best docked confirmation of complex [Ni(L)(DMF)](1) with Mpro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of complex [Ni(L)(DMF)](1) is found to be better than that of recently docking results of anti-SARS-CoV-2 drugs like chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) when targeted to the active-site of SARS-CoV-2 Mpro. Besides this, molecular docking against G25K GTP-nucleotide binding protein (PDB ID: 1A4R) was also studied. We believe that current results can intrigue not only for the biomedical community but also for the materials chemists who are engaged to explore the application coordination complexes.Communicated by Ramaswamy H. Sarma.

14.
Polyhedron ; 232:116296, 2023.
Article in English | ScienceDirect | ID: covidwho-2182384

ABSTRACT

Two co-ordination compounds, one nickel(II) complex [Ni(L1)(Phen)2]ClO4 (1) and one copper(II) complex [Cu(L2)] (2), were synthesized using Schiff base ligands derived from the condensation reaction of 5-Bromo-salicylaldehyde with 3-picoyl amine (L1H)(L1H = (E)-4-Bromo-2-(((pyridin-3-ylmethylene)amino) methyl) phenol) and ethylenediamine (L2H2), respectively(L2H2 = 2,2′-((1E,1′E)-(ethane-1,2-diylbis(azaneylylidene))bis(methanelylidene))bis (4-bromophenol)). The newly synthesized complexes were fully characterized, including X-ray crystallography. The crystal structure of both the complexes was determined using Single Crystal structure analysis. The electrochemical properties of (1) were studied using cyclic voltammetry. DFT calculations were done for the newly synthesized co-ordination complexes to have a relevant and reasonably accurate calculation of their molecular and electronic behavior. The Hirshfeld surface (HS) analysis was also performed using the crystallographic data for investigating the nature and quantitative contribution of all possible non-covalent intermolecular interactions within the crystal lattice. To explore potential SARS-CoV-2 drug candidates, both the co-ordination compounds were subjected to molecular docking calculations with the SARS-CoV-2 virus (PDB ID: 7EFP). The molecular docking calculations of Ni(II) complex (1) into the 7EFP-main protease of SARS-CoV-2 virus revealed the binding energy of −11.5 kcal/mol, while Cu(II) complex (2) exhibited the binding energy of −8.5 kcal/mol at the inhibition binding site of the receptor protein.

15.
Journal of Molecular Structure ; : 134996, 2023.
Article in English | ScienceDirect | ID: covidwho-2181709

ABSTRACT

The 1-(4-chloro-benzoyl)-3-(2-trifluoromethyl-phenyl)thiourea compound was synthesized by a two-step reaction and a single crystal of it was obtained by recrystallization method. Its structure was elucidated by elemental analyzes, FT-IR, 1H NMR, and 13C NMR techniques, and its molecular and crystal structure was also determined by single-crystal X-ray diffraction analysis. The Hirshfeld surface analyzes of the crystal structure indicate that the most important contributions for crystal packing are from H···H (23.8%), H···S/S···H (14.5%), H···F/F···H (14.3%), C···H/H···C (14.2%), and Cl···F/F···Cl (9.0%). In addition, energy-framework calculations are used to analyze and visualize the three-dimensional topology of the crystal packing. The electrostatic energy framework is dominant over the dispersion energy framework. The density functional theory method with the basis set of B3LYP/6-311G(d,p) has been employed to obtain the optimized structural geometry, Mulliken charges, molecular electrostatic potential, frontier molecular orbitals, the total density of states, reduced density gradient analysis and natural bond orbitals. The experimental crystal structure parameters and optimized structure parameters are very similar. The HOMO-LUMO energy gap of the compound is 3.5307 eV. Different global chemical reactivity descriptor parameters were also calculated. Nonlinear optical properties such as anisotropy of polarizability, mean polarizability, static dipole moment, and first-order hyperpolarizability values were theoretically determined. The Fukui functions as electron density-based local reactivity descriptors were also calculated to explain the chemical selectivity or the reactivity site in the molecule. Molecular docking studies were also carried out to determine the inhibitory action of the title compound against the main protease (6LU7) of a new coronavirus (COVID-19).

16.
Polyhedron ; 233: 116304, 2023 Mar 15.
Article in English | MEDLINE | ID: covidwho-2182385

ABSTRACT

A new Zn(II) coordination polymer based on o-phthalato (Phth) and 2-aminopyridine (2-Ampy) viz. {[Zn(2-Ampy)2(Phth)]∙(H2O)]}n (1) has been synthesized at room temperature and characterized by elemental analyses, electronic spectroscopy, FT-IR spectroscopy, thermal analysis (TGA/DSC), powder X-ray diffraction (PXRD) and single crystal X-ray diffraction. The basic trimeric units of 1 form a polymeric chain by N-H⋯O and π⋯π interactions. These polymeric chains interconnect through various non-covalent interactions in two perpendicular directions to ultimately give rise to a 3D architecture of 1. The interesting non-covalent interactions in 1, contributing to its stability in the solid state are studied by Hirshfeld surface analysis and other different theoretical tools. Molecular docking study of 1 is performed against six different proteins of SARS-CoV-2. The drug potential of the synthesized compound is evaluated by ADMET calculations.

17.
J Mol Struct ; 1278: 134857, 2023 Apr 15.
Article in English | MEDLINE | ID: covidwho-2165720

ABSTRACT

In this study, polynuclear Cu(II) complex (1), Mn(II) and Mn(III) complex (2) have been prepared with a Schiff base ligand derived from 2-Hydroxy-3-methoxybenzaldehyde with 2-amino-2-methyl-1-propanol. The compounds were characterized by elemental analysis, FT-IR, and UV-Vis spectroscopy. The molecular and crystal structures of (1-2) were determined by the single-crystal x-ray diffraction technique. It turned out that Cu(II) complex (1) forms an S4 -symmetrical tetrameric cage structure, with square-planar coordinated Cu and bridging O atoms at the vertexes of the approximate cube. In the crystal structure of 1, there are large channels along the c-axis, between the tetramers; the solvent- DMSO molecules, occupies these channels. In turn, the complex (2) creates a centrosymmetric trimeric structure, with three octahedrally coordinated Mn ions bridged by O atoms from ligand molecules and acetate ions. The electrochemical behavior studies of the complexes in DMSO displayed the electronic effects of the groups on the redox potential. The redox behavior of Schiff base (1) and (2) complexes included quasi -reversible and irreversible voltammograms, respectively. Intermolecular interactions in the solid states were studied by Hirshfeld surface analysis. These studies provide a comprehensive description of these inter-contact exchanges using an attractive graphical representation using Hirshfeld surfaces and fingerprint plots, along with enrichment ratios. Furthermore, assessment of the inhibitory effect against coronavirus (main protease SARS-CoV-2) was performed by a molecular docking study for both complexes (1 and 2). Both complexes showed a good affinity for CoV-2 for PDB protein ID: 6M03 and 6Y2F.

18.
ChemistrySelect ; 7(45):1-15, 2022.
Article in English | Academic Search Complete | ID: covidwho-2157919

ABSTRACT

Crystalline organic compound,2‐(methacryloyloxy)ethyl‐6‐amino‐5‐cyano‐2‐methyl‐4‐(thiophen‐2‐yl)‐4H‐pyran‐3‐carboxylate (ACMP) was synthesized by one‐pot three components reaction. The title compound is characterized by spectral techniques and single‐crystal XRD. 2D and 3D Hirshfeld surface analysies were studied to understand the intermolecular contacts. The study revealed that H...H, O−H...N, and N−H...O are the most significant contributor towards crystal packing with a percentage contribution of 45.1, 13.2 and 16.8 %, respectively. Further, to get more insight into the electronic properties of the molecular structure of ACMP compound, chemical stability and reactivity have been well explored by the frontier molecular orbital (FMO) approach. Despite, the molecular docking study was employed to predict the binding affinity between the ACMP and COVID‐19 Mpro and spike protease. The analysis showed that the several interactions including H‐bond, pi‐alkyl and pi‐pi interactions with the active sites of amino acid residues of 6LU7 and 2AJF. [ FROM AUTHOR]

19.
Heliyon ; 8(10): e10831, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2105010

ABSTRACT

Isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate (IDPC) was synthesized and characterized via spectroscopic (FT-IR and NMR) techniques. Hirshfeld surface and topological analyses were conducted to study structural and molecular properties. The energy gap (Eg), frontier orbital energies (EHOMO, ELUMO) and reactivity parameters (like chemical hardness and global hardness) were calculated using density functional theory with B3LYP/6-311++G (d,p) level of theory. Molecular docking of IDPC at the active sites of SARS-COVID receptors was investigated. IDPC molecule crystallized in the centrosymmetric triclinic ( P 1 ¯ ) space group. The topological and Hirshfeld surface analysis revealed that covalent, non-covalent and intermolecular H-bonding interactions, and electron delocalization exist in the molecular framework. Higher binding score (-6.966 kcal/mol) of IDPC at the active site of SARS-COVID main protease compared to other proteases suggests that IDPC has the potential of blocking polyprotein maturation. H-bonding and π-cationic and interactions of the phenyl ring and carbonyl oxygen of the ligand indicate the effective inhibiting potential of the compound against the virus.

20.
Arab J Chem ; 15(11): 104230, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2031134

ABSTRACT

Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural-functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 Mpro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.

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