scholarly journals Design, Synthesis, and Evaluation of X-ray Crystal Structure, Biological Activities, DFT Calculations, and Molecular Docking of Phenyl Imidazolidin-2-One Derivatives

Crystals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 713
Author(s):  
Xile Deng ◽  
Can Jin ◽  
Yong Xie ◽  
Junbo Gao ◽  
Xiaomao Zhou
Keyword(s):  
Molecular Docking ◽  
Dft Calculations ◽  
Insecticidal Activity ◽  
Plutella Xylostella ◽  
Density Functional ◽  
Biological Activities ◽  
Phytophthora Sojae ◽  
Ring Closure ◽  
Binding Modes ◽  
X Ray

Eight phenyl imidazolinone derivatives were synthesized from N2-(2,4-dimethylphenyl)-N1-methyformamidine (DPMF) via scaffold-hopping method using the ring-closure approach. The prepared compounds were verified using 1H and 13C NMR and HRMS spectroscopies. The structure of compound 3c was confirmed by single-crystal X-ray diffraction analysis. The mean plane of the phenyl and imidazolinone moieties was almost coplanar with an angle of 8.85(4)°. In the crystal, molecules were interlinked with intermolecular hydrogen bonds (N–H···O and C–H···O), generating a network structure. Additionally, compound 3f displayed the highest insecticidal activity (86.7%) against Plutella xylostella at 600 mg/L, which was significantly higher than the insecticidal activity (23.0%) of DPMF. Also, compound 3d displayed good fungicidal activities against Phytophthora capsici, Phytophthora sojae, and Phytophthora infestans. Density functional theory (DFT) calculations were performed to explain the insecticidal and fungicidal activities of phenyl imidazolidin-2-one derivatives, especially potent compounds 3f and 3d. Moreover, the binding modes of compounds 3a–h and DPMF against octopamine receptor of Plutella xylostella were studied by homology modeling and molecular docking. Therefore, a preliminary structure–activity relationship (SAR) was derived and discussed. These results encourage the exploration of novel insecticides and fungicides based on DPMF.

scholarly journals Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

2020 ◽  
Vol 21 (11) ◽  
pp. 3922 ◽  
Author(s):  
Mohamed Hagar ◽  
Hoda A. Ahmed ◽  
Ghadah Aljohani ◽  
Omaima A. Alhaddad
Keyword(s):  
Dipole Moment ◽  
Molecular Docking ◽  
Dft Calculations ◽  
Binding Affinity ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Hydrophobic Interactions ◽  
Chemical Reactivity ◽  
Main Protease

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.

scholarly journals Synthesis, Crystal Structure, Thermal Analysis, and DFT Calculations of Molecular Copper(II) Chloride Complexes with Bitopic Ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 222
Author(s):  
Lider ◽  
Sukhikh ◽  
Smolentsev ◽  
Semitut ◽  
Filatov ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Coordination Compounds ◽  
Density Functional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Chloride Complexes ◽  
Functional Theory ◽  
X Ray ◽  
Lattice Water ◽  
Ir Bands

Two binuclear coordination compounds of Cu(II) chloride with the bitopic ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane (Pz4) of the composition [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O and [Cu2(µ2Pz4)(DMSO)2Cl4]∙2DMSO were prepared and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray diffraction, and powder diffraction analysis. It was shown that in contrast to silver(I) and copper(II) nitrates, copper(II) chloride forms discrete complexes instead of coordination polymers. The supramolecular structure of the complex [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O with lattice water molecules is formed by OH···Cl and OH···O hydrogen bonds. Density functional theory (DFT) calculations of vibrational frequencies of the ligand and its copper(II) complex allowed for assigning IR bands to specific vibrations.

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

Combined analysis of chemical bonding in a CuIIdimer using QTAIM, Voronoi tessellation and Hirshfeld surface approaches

2015 ◽  
Vol 71 (5) ◽  
pp. 543-554 ◽  
Author(s):  
Anna V. Vologzhanina ◽  
Svitlana V. Kats ◽  
Larisa V. Penkova ◽  
Vadim A. Pavlenko ◽  
Nikolay N. Efimov ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Voronoi Tessellation ◽  
Quantitative Description ◽  
Hirshfeld Surface ◽  
Epr Spectra ◽  
Antiferromagnetic Coupling ◽  
X Ray Diffraction ◽  
Spin Distribution ◽  
X Ray

Interaction of 1-(1H-pyrazol-5-yl)ethanone oxime (H2PzOx) with copper(II) chloride in the presence of pyridine afforded a binuclear discrete [Cu2(HPzOx)2Cl2py2] complex, which was characterized by Fourier transform–IR and electron paramagnetic resonance (EPR) spectra, magnetochemistry and high-resolution X-ray diffraction experiments. Multipole refinement of X-ray diffraction data and density-functional theory (DFT) calculations of an isolated molecule allowed charge and spin distributions to be obtained for this compound. Magnetochemistry data, EPR spectra and DFT calculations of an isolated molecule show antiferromagnetic coupling between copper(II) ions. The spin distribution suggests an exchange pathwayviathe bridging pyrazole ring in the equatorial plane of the CuN4Cl coordination polyhedron, thus providing support for the classical superexchange mechanism; the calculated value of the magnetic coupling constant −2Jis equal to 220 cm−1, which compares well with the experimental value of 203 ± 2 cm−1. Chemical connectivity was derived by Bader's `quantum theory of atoms in molecules' and compared with Voronoi tessellation and Hirshfeld surface representations of crystal space. All methodologies gave a similar qualitative and semi-quantitative description of intra- and intermolecular connectivity.

scholarly journals Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography

2017 ◽  
Vol 81 (5) ◽  
pp. 1191-1202 ◽  
Author(s):  
Fernando Colombo ◽  
Enrico Mugnaioli ◽  
Oriol Vallcorba ◽  
Alberto García ◽  
Alejandro R. Goñi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Dft Calculations ◽  
Density Functional ◽  
Weak Interactions ◽  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

AbstractThe crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

scholarly journals Computer-Based Approaches for Determining the Pharmacological Profile of 5-(3-Nitro-Arylidene)-Thiazolidine-2,4-Dione

2021 ◽  
Vol 11 (6) ◽  
pp. 13806-13828
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Density Functional ◽  
Biological Activities ◽  
Computational Approach ◽  
Basis Set ◽  
Pharmacological Profile ◽  
Dft Methods ◽  
Starting Point ◽  
In Silico Studies

The development of novel and safe compounds is a challenging task in the drug discovery trajectory. Accordingly, the individuation of promising core molecules with biological activities could pave the way to develop effective drugs to treat a given disease. The use of a computational approach can reduce the time for identifying promising core molecules characterizing their potential pharmacological profile and providing hints for the synthesis of novel derivatives with increased predicted pharmacological activity. Following this strategy, starting from a core molecule thiazolidine-2,4-dione, the derivative of 5-(3-nitro-arylidene)-thiazolidine-2,4-dione was synthesized to investigate the biological and pharmacological potential. An extensive computational investigation was performed employing ab initio calculations by using Density Functional Theory (DFT), and subsequent in silico studies were accomplished by molecular docking calculation. The structures 5-(3-nitro-arylidene)-thiazolidine-2,4-dione were fully optimized using multiparametric DFT methods were calculated at the B3LYP/6-31+G (d, p) level basis set. Besides gaining insights into the potential pharmacological profile of the selected derivative, molecular docking against some selected drug targets, ADME, and PASS prediction were performed. According to charges and molecular electrostatic potential (MESP) calculation, the N-H region could offer promising active site interactions for protein binding. Furthermore, Homo-Lumo and global reactivity values indicate a good profile for the selected compound, and UV-Vis provides further insights about its properties, potentially helpful for further experimental analysis. Notably, the in silico investigation indicated that EGFR and ORF2 enzymes could represent the selected drug-like compound's possible targets. Conclusively, the proposed computational approach demonstrated that it is possible to evaluate a proposed compound's bioactivity profile. We characterized 5-(3-nitro-arylidene)-thiazolidine-2,4-dione derivative, suggesting it as a good starting point for developing interesting hit compounds with a relevant pharmacological profile.

scholarly journals Crystal structure, spectral characterization, molecular modeling studies and structural effects of the proton transfer process for (E)-5-methoxy-2-[(3,4-dimethylphenylimino) methyl]phenol

2017 ◽  
Vol 36 (2) ◽  
pp. 265
Author(s):  
Basak Kosar Kirca ◽  
Gonca Ozdemir Tarı ◽  
Cıgdem Albayrak Kastas ◽  
Mustafa Odabasoglu ◽  
Orhan Buyukgungor
Keyword(s):  
Proton Transfer ◽  
Dft Calculations ◽  
Density Functional ◽  
Tautomeric Form ◽  
Bond Distance ◽  
Molecular Geometry ◽  
Spectroscopic Properties ◽  
Intramolecular Proton Transfer ◽  
X Ray ◽  
Pes Scan

The main purpose of this study is to characterize a new organic material, (E)-5-methoxy-2-[(3,4-dimethylphenylimino)methyl]phenol, which was synthesized and grown as a single crystal. The molecular structure and spectroscopic properties of the ortho-hydroxy Schiff base compound were determined by X-ray diffraction analysis, Fourier-transform infrared (FT-IR), ultraviolet-visible (UV-Vis) and nuclear magnetic resonance (NMR) spectroscopy techniques, experimentally and computationally with density functional theory (DFT) calculations. X-ray and UV-Vis studies show that the compound exists in an OH tautomeric form in the solid and solvent media. The gas phase geometry optimizations of two possible forms of the title compound, resulting from the prototropic tautomerism, were obtained using DFT calculations at the B3LYP/6-311G+(d,p) level of theory. A relaxed potential energy surface (PES) scan was performed based on the optimized geometry of the OH tautomeric form by varying the redundant internal coordinate, the O-H bond distance. According to the PES scan process, the molecular geometry is strongly affected by the intramolecular proton transfer. The calculated first hyperpolarizability indicates that the compound could be a good material for non-linear optical applications. 

scholarly journals Substituent Effects in 3,3’ Bipyrazole Derivatives. X-ray Crystal Structures, Molecular Properties and DFT Analysis

2021 ◽  
Vol 68 (3) ◽  
pp. 718-727
Author(s):  
Ibrahim Bouabdallah ◽  
Tarik Harit ◽  
Mahmoud Rahal ◽  
Fouad Malek ◽  
Monique Tillard ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Solid State ◽  
Dft Calculations ◽  
Single Crystal ◽  
Crystal Structures ◽  
Density Functional ◽  
Substituent Effects ◽  
Functional Theory ◽  
X Ray

The single crystal X-ray structure of new 1,1’-bis(2-nitrophenyl)-5,5’-diisopropyl-3,3’-bipyrazole, 1, is triclinic P I–, a = 7.7113(8), b = 12.3926(14), c = 12.9886(12) Å, α = 92.008(8), β = 102.251(8), γ = 99.655(9)°. The structural arrangement is compared to that of 5,5’-diisopropyl-3,3’-bipyrazole, 5, whose single crystal structure is found tetragonal I41/a, a = b = 11.684(1), c = 19.158(1) Å. The comparison is also extended to the structures previously determined for 1,1’-bis(2-nitrophenyl)-5,5’-propyl-3,3’-bipyrazole, 2, 1,1’-bis(4-nitrophenyl)-5,5’-diisopropyl-3,3’-bipyrazole, 3, and 1,1’-bis(benzyl)-5,5’-diisopropyl-3,3’-bipyrazole, 4. Density Functional Theory (DFT) calculations are used to investigate the molecular geometries and to determine the global reactivity parameters. The geometry of isolated molecules and the molecular arrangements in the solid state are analyzed according to the nature of the groups connected to the bipyrazole core.

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