scholarly journals Nitroisatin dithiocarbazate: Synthesis, structural characterization, DFT, and docking studies

2021 ◽  
Vol 12 (3) ◽  
pp. 235-241
Author(s):  
Pedro Henrique do Nascimento Pereira ◽  
Jackelinne Camargo Lima ◽  
Victor Marcelo Deflon ◽  
Geoffroy Roger Pointer Malpass ◽  
Ronaldo Junio De Oliveira ◽  
...  
Keyword(s):  
Parent Compound ◽  
Thioredoxin Reductase ◽  
Polarizable Continuum Model ◽  
Docking Studies ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Electronic Distribution ◽  
Thioredoxin Reductase 1 ◽  
Ft Ir ◽  
Polarizable Continuum

The reaction between 5-nitroisatin with S-benzyl dithiocarbazate affords a new isatindithio carbazate so-called NO2Isadtc (Benzyl 2-(5-nitro-2-oxoindolin-3-ylidene)hydrazinecarbodi thioate) which was characterized by means of 1H NMR, FT-IR, UV-visible and single crystal X-ray diffraction - Crystal data for C16H12N4O3S2 (M =372.42 g/mol): triclinic space group P-1, (n°. 02), a = 6.640 Å, b = 8.256 Å, c = 15.908 Å, V = 849.6 Å3, Z = 2, T = 293 K, μ(MoKα) = 0.337 mm-1, Dcalc = 1.456 g/cm3, 27515 reflections measured (2.499° ≤ 2Θ ≤ 26.524°), 3518 unique (Rint = 0.0533, Rsigma =0.0222) which were used in all calculations. The final R1 was 0.0367 (I > 2σ(I)) and wR2 was 0.1045 (all data). Computational methods were applied to NO2Isadtc and its nonsubstituted parent compound Isadtc for structure optimization, electronic distribution, and infrared calculations using B3LYP functional with 6-31G(d,p) basis set in ethanol as a polarizable continuum model. Furthermore, docking studies using human thioredoxin reductase 1 (TrxR) as enzyme target also were performed using NO2Isadtc and the optimized structure of Isadtc. The results demonstrated that both NO2Isadtc and Isadtc may act as inhibitors of TrxR, having different interactions detected, highlighting the contact between the NO2 group and the S111 at the helix which is found for NO2Isadtc.

Structural, spectral and docking studies of a coordination polymer of zinc(II) formed by a pyridine-derived linker

2018 ◽  
Vol 73 (6) ◽  
pp. 369-375 ◽  
Author(s):  
Farzin Marandi ◽  
Keyvan Moeini ◽  
Fereshteh Alizadeh ◽  
Zahra Mardani ◽  
Ching Kheng Quah ◽  
...  
Keyword(s):  
Coordination Polymer ◽  
Docking Studies ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Docking Calculations ◽  
Ft Ir ◽  
Zinc Coordination ◽  
Linear Coordination

AbstractA mixed ligand zinc coordination polymer, {Zn(μ-DPE)(DBM)2}n (1) (HDBM: dibenzoylmethane and DPE: (E)-1,2-di(pyridin-4-yl)ethene), was prepared and identified by elemental analysis, FT-IR, 1H NMR spectroscopy and single-crystal X-ray diffraction. In the 1D linear coordination polymer of 1, the zinc atom has a ZnN2O4 environment with octahedral geometry. These complex units are linked by the bridging of the planar N2 donor DPE ligands. In the coordination network of complex 1, in addition to the hydrogen bonds, the network is more stabilized by π–π stacking interactions between pyridine and β-diketone moieties of the ligands. These interactions increase the ability of the compound to interact with biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) as investigated by docking calculations.

Reaction of 2-[(2-aminoethyl)amino]ethanol with pyridine-2-carbaldehyde and complexation of the products with CuII and CdII along with docking studies

2019 ◽  
Vol 75 (7) ◽  
pp. 951-959 ◽  
Author(s):  
Zahra Mardani ◽  
Mohammad Hakimi ◽  
Keyvan Moeini ◽  
Fabian Mohr
Keyword(s):  
Crystal Packing ◽  
Docking Studies ◽  
Molar Ratio ◽  
Distorted Octahedral Geometry ◽  
X Ray Diffraction ◽  
Donor Ligand ◽  
X Ray ◽  
H Nmr ◽  
Distorted Octahedral ◽  
Ft Ir

The reaction between 2-[2-(aminoethyl)amino]ethanol and pyridine-2-carbaldehyde in a 1:2 molar ratio affords a mixture containing 2-({2-[(pyridin-2-ylmethylidene)amino]ethyl}amino)ethanol (PMAE) and 2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine (POPME). Treatment of this mixture with copper(II) chloride or cadmium(II) chloride gave trichlorido[(2-hydroxyethyl)({2-[(pyridin-2-ylmethylidene)amino]ethyl})azanium]copper(II) monohydrate, [Cu(C10H16N3O)Cl3]·H2O or [Cu(HPMAE)Cl3]·H2O, 1, and dichlorido{2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine}cadmium(II), [CdCl2(C16H18N4O)] or [CdCl2(POPME)], 2, which were characterized by elemental analysis, FT–IR, Raman and 1H NMR spectroscopy and single-crystal X-ray diffraction. PMAE is potentially a tetradentate N3O-donor ligand but coordinates to copper here as an N2 donor. In the structure of 1, the geometry around the Cu atom is distorted square pyramidal. In 2, the Cd atom has a distorted octahedral geometry. In addition to the hydrogen bonds, there are π–π stacking interactions between the pyridine rings in the crystal packing of 1 and 2. The ability of PMAE, POPME and 1 to interact with ten selected biomolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies and compared with doxorubicin.

Coordination of a triazine ligand with CuII and AgI investigated by spectral, structural, theoretical and docking studies

2019 ◽  
Vol 75 (10) ◽  
pp. 1389-1397
Author(s):  
Farzin Marandi ◽  
Keyvan Moeini ◽  
Harald Krautscheid
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Docking Studies ◽  
Planar Geometry ◽  
X Ray Diffraction ◽  
Aromatic Rings ◽  
X Ray ◽  
Square Planar ◽  
Binuclear Structure ◽  
Ft Ir

Two complexes of 5-phenyl-3-(pyridin-2-yl)-1,2,4-triazine (PPTA), namely (ethanol-κO)bis(nitrato-κO)[5-phenyl-3-(pyridin-2-yl-κN)-1,2,4-triazine-κN 2]copper(II), [Cu(NO3)2(C14H10N4)(C2H6O)] or [Cu(NO3)2(PPTA)(EtOH)] (1), and bis[μ-5-phenyl-3-(pyridin-2-yl)-1,2,4-triazine]-κ3 N 1:N 2,N 3;κ3 N 2,N 3:N 1-bis[(nitrato-κO)silver(I)], [Ag2(NO3)2(C14H10N4)2] or [Ag2(NO3)2(μ-PPTA)2] (2), were prepared and characterized by elemental analysis, FT–IR spectroscopy and single-crystal X-ray diffraction. The X-ray structure analysis of 1 revealed a copper complex with square-pyramdial geometry containing two O-donor nitrate ligands along with an N,N′-donor PPTA ligand and one O-donor ethanol ligand. In the binuclear structure of 2, formed by the bridging of two PPTA ligands, each Ag atom has an AgN3O environment and square-planar geometry. In addition to the four dative interactions, each Ag atom interacts with two O atoms of two nitrate ligands on adjacent complexes to complete a pseudo-octahedral geometry. Density functional theory (DFT) calculations revealed that the geometry around the Cu and Ag atoms in 1 opt and 2 opt (opt is optimized) for an isolated molecule is the same as the experimental results. In 1, O—H...O hydrogen bonds form R 1 2(4) motifs. In the crystal network of the complexes, in addition to the hydrogen bonds, there are π–π stacking interactions between the aromatic rings (phenyl, pyridine and triazine) of the ligands on adjacent complexes. The ability of the ligand and complexes 1 and 2 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies. The results show that the studied compounds can interact with proteins better than doxorubicin (except for TrxR and Top II).

Theoretical Raman and Infrared Spectra for Amphetamine, Methamphetamine and 3,4-Methylenedioxymethamphetamine

2020 ◽  
Vol 12 (6) ◽  
pp. 703-710
Author(s):  
Leandro G. Silva ◽  
Abel F. G. Neto ◽  
José F. S. Costa ◽  
Tais S. S. Pereira ◽  
Mozaniel S. Oliveira ◽  
...  
Keyword(s):  
Infrared Spectra ◽  
Continuum Model ◽  
Illicit Drugs ◽  
Normal Modes ◽  
Polarizable Continuum Model ◽  
Program Package ◽  
Basis Set ◽  
Hybrid Functional ◽  
Polarizable Continuum

Molecules used in the synthesis of illicit drugs, such as amphetamine, methamphetamine and 3,4-methylenedioxymethamphetamine which were studied in order to provide parameters to do their identification. Thus, Raman and Infrared spectra were calculated taking into account the polarizable continuum model and considering different solvents (water, toluene, acetone, chloroform and ethanol) at 298.15 K and 1 atm. The assignment of the normal modes of vibrations of these molecules was made. All calculations were carried out by quantum methods based on DFT with B3LYP hybrid functional and 6-311++g(d. p) basis set available in the Gaussian G03 program package. These informations can be helpful as a forensic data.

DFT and Thermal Decomposition Studies on Gemcitabine

2019 ◽  
Vol 233 (10) ◽  
pp. 1503-1527
Author(s):  
Ereen Rezkallah ◽  
Abeer Ibrahim ◽  
AbdelRahman Dahy ◽  
Ahmed Abdel Hakiem ◽  
Refaat Mahfouz
Keyword(s):  
Chemical Potential ◽  
Geometry Optimization ◽  
Docking Studies ◽  
Potential Energy Distribution ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
Air Atmosphere ◽  
Decomposition Processes ◽  
Potential Map ◽  
Ft Ir

Abstract Geometry optimization of gemcitabine was carried out by DFT with B3LYP/6-311++G(d,p) level in the gas phase. Chemical activity (electronegativity, electrophilicity, hardness, chemical softness and chemical potential) was predicted with the help of HOMO-LUMO energy values. Experimental FT-IR was recorded and computed values are also analyzed using the same level of DFT. A complete vibrational spectrum was made to analyze the potential energy distribution (PED). Stability of the molecule arising from the hyper-conjugative interaction was analyzed by the natural bond orbital (NBO). The molecular electrostatic potential map was used to detect the possible electrophilic and nucleophilic sites in the molecule. Nonisothermal decomposition of gemcitabine was carried out in an air atmosphere. The two decomposition steps of the molecule were analyzed kinetically by linear and nonlinear methods for elucidation of the kinetic triplet (Ea, ln A and f(α)) of the decomposition processes. Powder X-ray diffraction indicated that gemcitabine crystallizes in the monoclinic system (SG P2/m). Molecular docking studies were also described.

scholarly journals A Combined Experimental (FT-IR) and Computational Studies of 9-Chloroanthracene

2019 ◽  
Vol 31 (6) ◽  
pp. 1332-1342 ◽  
Author(s):  
KATTAESWAR SRIKANTH ◽  
RAMAIAH KONAKANCHI ◽  
JYOTHI PRASHANTH
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Protein Targets ◽  
Charge Delocalization ◽  
Fukui Functions ◽  
Homo And Lumo ◽  
Ft Ir

The experimental FT-IR spectral analysis of 9-chloroanthracene has worked out by using density functional theory (DFT). The optimized molecular structure and minimum energy of 9-chloroanthracene has analyzed using DFT/B3LYP functional employing 6-311++G(d,p) basis set. The vibrational frequencies along with IR intensities were computed, scaling was used for a better fit between the experimental and computed frequencies, they agreed with rms error 8.48 cm-1 for 9-chloroanthracene. The NLO behaviour of the molecule is investigated from first-order hyperpolarizability. The HOMO and LUMO energies are evaluated to demonstrate the chemical stability, reactivity of molecule. The MESP over the molecules were plotted to evaluate electron density regions and thermodynamic parameters are calculated. Hyper conjugative interactions and charge delocalization of the molecule study from NBO analysis and Fukui functions are evaluated for 9-chloroanthracene. The molecular docking studies were performed against anticancer protein targets Tyrosinase and HER2.

scholarly journals Synthesis, spectral characterization (FT-IR and NMR) and DFT (Conformational analysis, molecular structure, HOMO-LUMO, UV-vis, NLO) computational studies on 2,2’-((1E,1’E)-phenazine-2,3 dilbis(azanylylidene))bis(methanyly- lidene))diphenol

2017 ◽  
Vol 6 (1) ◽  
pp. 8
Author(s):  
Prabhakaran A ◽  
Dhinesh kumar E ◽  
Rajaraman D ◽  
Arockia doss M
Keyword(s):  
Dft Method ◽  
Polarizable Continuum Model ◽  
Molecular Architecture ◽  
Td Dft ◽  
Ft Ir ◽  
Experimental Values ◽  
First Time ◽  
Polarizable Continuum ◽  
Chloroform Methanol ◽  
Homo Lumo

A new Schiff base was synthesized for the first time by the phenazine-2,3-diamine and 2-hydroxy benzaldedye in ethanol (1:1). The structure of Schiff bases was experimentally characterized by using UV-vis, IR, 1H NMR and 13C NMR spectroscopic methods. Further, the synthesized compound was subjected to DFT for better understanding of the molecular architecture and optoelectronic properties. The optimized geometric parameters supported the available experimental values. The Mulliken and MEP analyses are utilized to identify reactive sites of title molecule. The energetic behaviors of compound 3 in hexane, chloroform, methanol solvents and gas phase were examined using by time-dependent DFT (TD-DFT) method by applying the polarizable continuum model (PCM). The calculated ΔE energies exposed that charge transfer takes place within the molecule. In addition to the polarizability and hyperpolarizability have been calculated which exhibit that compounds possess non-linear optical nature.

Theoretical studies of the structural, electronic, and 19F NMR properties of linear and branched perfluorobutanesulfonate

2013 ◽  
Vol 91 (12) ◽  
pp. 1272-1280
Author(s):  
Xue Qin Ran ◽  
John D. Goddard
Keyword(s):  
Chemical Shifts ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Basis Set ◽  
Structural And Electronic Properties ◽  
J Coupling ◽  
Fermi Contact ◽  
J Coupling Constants ◽  
Polarizable Continuum ◽  
Nmr Properties

The structural and electronic properties of linear and branched perfluorobutanesulfonate (PFBS) in its anionic, acidic, and potassium or sodium salt forms were studied in a polarizable continuum model (PCM) of methanol solvent with the B3LYP functional and the 6-31G(d,p) basis set. The 19F chemical shifts and 19F−19F J-coupling constants were determined in a PCM of methanol solvent with GIAO B3LYP/6-31++G(d,p). The differences in energy, enthalpy, and free energy of the four PFBS isomers were compared. The data indicate that the linear PFBS species is less stable than the branched isomers and the isomer with the tert-butyl-like structure is the most stable. The J-coupling contributions via both a non-Fermi contact mechanism and a long chain of bonds (through-bond) indicate that 19F−19F J-coupling constants are long range in these branched PFBS isomers. The calculated and experimental 19F chemical shifts for the linear PFBS species are in good agreement. In addition, the results obtained establish the similarities between the geometries and electronic and NMR properties of linear PFBS and linear perfluorooctanesulfonate (PFOS).

scholarly journals Thermodynamic prediction of proton and hydrogen atom abstraction in dehydroascorbic acid and its bicyclic form

2021 ◽  
Vol 14 (1) ◽  
pp. 32-37
Author(s):  
Dagmar Štellerová ◽  
Vladimír Lukeš
Keyword(s):  
Vitamin C ◽  
Density Functional ◽  
Radical Scavenging ◽  
Dehydroascorbic Acid ◽  
Polarizable Continuum Model ◽  
Basis Set ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Radical Scavenging Ability ◽  
Polarizable Continuum

Abstract Conformation analysis of dehydroascorbic acid and its bicyclic form was performed using the density functional theory. For the energetically preferred conformations, ionization potentials (IP) and bond dissociation enthalpies (BDE) were calculated using the B3LYP functional and 6-311++G** basis set. The effects of aqueous solution were estimated using the solvation model based on density (SMD) and the polarizable continuum model (IEF-PCM). The obtained results were compared with available experimental data for reference L-ascorbic acid (vitamin C). Our calculations indicate that the investigated bicyclic metabolic product of vitamin C can also exhibit limited radical scavenging ability due to the thermodynamically preferred dissociation of tertiary —CH bonds.

scholarly journals Experimental and theoretical studies of 4-[(4-methyl-5-phenyl- 4H1,2,4-triazol-3-yl)sulfanyl]benzene-1,2-dicarbonitrile

2016 ◽  
Vol 35 (2) ◽  
pp. 169
Author(s):  
Ufuk Çoruh ◽  
Reşat Ustabaş ◽  
Hakkı Türker Akçay ◽  
Emra Menteşe ◽  
Ezequiel M. Vazquez Lopez
Keyword(s):  
Molecular Structure ◽  
Density Functional ◽  
Basis Set ◽  
Geometrical Parameters ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Ft Ir ◽  
Experimental And Theoretical Studies ◽  
Homo Lumo

In this study, 4-[(4-methyl-5-phenyl-4<em>H</em>-1,2,4-triazol-3-yl)sulfanyl]benzene-1,2-dicarbonitrile was synthesized and its molecular structure was characterized by means of FT-IR and X-ray diffraction methods. The crystal is monoclinic and belongs to the P21/n space group. There are three weak intermolecular C-H…N type hydrogen bonds in the molecular structure. The geometrical parameters, vibration frequencies, HOMO–LUMO energies, and molecular electrostatic potential (MEP) map of the compound (3) in ground state were calculated by using density functional theory (DFT/B3LYP) with the 6-311G(d) basis set. Calculated geometrical parameters were compared with X-ray diffraction geometric parameters. On the other hand, theoretical and experimental FT-IR results were also compared.

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