Investigation of the effect of the N-oxidation process on the interaction of selected pyridine compounds with biomacromolecules: structural, spectral, theoretical and docking studies

2019 ◽  
Vol 75 (6) ◽  
pp. 750-757
Author(s):  
Mohammad Hakimi ◽  
Fereshteh Sadeghi ◽  
Nourollah Feizi ◽  
Keyvan Moeini ◽  
Monika Kučeráková ◽  
...  
Keyword(s):  
Density Functional ◽  
Distribution Patterns ◽  
Nbo Analysis ◽  
Docking Studies ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Neutral Compound ◽  
Docking Calculations ◽  
Ft Ir

Two new N-oxide compounds, namely glycinium 2-carboxy-1-(λ1-oxidaneyl)-1λ4-pyridine-6-carboxylate–glycine–water (1/1/1), C2H6NO2 +·C7H4NO5 −·C2H5NO2·H2O or [(2,6-HpydcO)(HGLY)(GLY)(H2O)], 1, and methyl 6-carboxy-1-(λ1-oxidaneyl)-1λ4-pyridine-2-carboxylate, C8H7NO5 or 2,6-HMepydcO, 2, were prepared and identified by elemental analysis, FT–IR, Raman spectroscopy and single-crystal X-ray diffraction. The X-ray analysis of 1 revealed an ionic compound containing a 2,6-HpydcO− anion, a glycinium cation, a neutral glycine molecule and a water molecule. Compound 2 is a neutral compound with two independent units in its crystal structure. In addition to the hydrogen bonds, the crystal network is stabilized by π–π stacking interactions of the types pyridine–carboxylate and carboxylate–carboxylate. The thermodynamic stability and charge-distribution patterns for isolated molecules of 2,6-H2pydcO and 2,6-HMepydcO, and their two similar derivatives, pyridine-2,6-dicarboxylic acid (2,6-H2pydc) and dimethyl 1-(λ1-oxidaneyl)-1λ4-pyridine-2,6-dicarboxylate (2,6-Me2pydcO), were studied by density functional theory (DFT) and natural bond orbital (NBO) analysis, respectively. The ability of these compounds and their analogues to interact with nine selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) was investigated using docking calculations.

scholarly journals A binuclear Cd(II) complex containing bridging pyrimidine-based ligands

2020 ◽  
Vol 75 (3) ◽  
pp. 287-293
Author(s):  
Samireh Hosseini ◽  
Zahra Mardani ◽  
Keyvan Moeini ◽  
Cameron Carpenter-Warren ◽  
Alexandra M.Z. Slawin ◽  
...  
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Distribution Patterns ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
H Nmr ◽  
Crystal Network ◽  
Ft Ir ◽  
Orbital Analysis

AbstractIn this work, a pyrimidine-based ligand, N′-(amino(pyrimidin-2-yl)methylene)pyrimidine-2-carbohydrazonamide hydrate (APPH · H2O), and its binuclear complex of cadmium, [Cd(μ-APPH)Br]2, 1, were prepared and identified by elemental analysis, FT-IR, 1H NMR spectroscopy as well as single-crystal X-ray diffraction. X-ray structure analysis of 1 revealed octahedrally coordinated cadmium centers with a CdN4Br2 environment containing two bridging APPH ligands; each APPH ligand acts as an N4-donor (N2-donor toward each cadmium atom) and forms two five-membered chelate rings that are approximately perpendicular to each other. In the network of 1, the N–H · · · Br hydrogen bonds form motifs such as ${\rm{R}}_{\rm{2}}^{\rm{2}}(12,{\rm{ }}14),{\rm{ R}}_{\rm{6}}^{\rm{6}}(24,{\rm{ }}26,{\rm{ }} \ldots ,{\rm{ }}46).$ The crystal network is further stabilized by π-π stacking interactions between pyrimidine rings. The optimized structures of the ligand and complex were investigated along with their charge distribution patterns by density functional theory and natural bond orbital analysis, respectively.

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.

scholarly journals A novel ligand transfer reaction: Transferring an N3-donor amine ligand from Ni(II) to Cu(II)—structural, spectral, theoretical, and docking studies

2019 ◽  
Vol 43 (9-10) ◽  
pp. 330-339
Author(s):  
Zahra Mardani ◽  
Sima Dorjani ◽  
Keyvan Moeini ◽  
Majid Darroudi ◽  
Cameron Carpenter-Warren ◽  
...  
Keyword(s):  
Density Functional ◽  
Copper Chloride ◽  
Structural Data ◽  
Distribution Patterns ◽  
Nickel Atom ◽  
Docking Studies ◽  
X Ray ◽  
Pyramidal Geometry ◽  
Vis Spectroscopy ◽  
Docking Calculations

Two complexes of N1-(2-aminoethyl)propane-1,3-diamine (AEPD), [Ni(AEPD)2](NO3)2 (1) and [Cu2( μ-Cl)2(AEPD)2](NO3)2·2H2O (2), are prepared and identified by elemental analysis, Fourier transform infrared spectroscopy and UV–Vis spectroscopy, and single-crystal X-ray diffraction (for 2). Spectral and structural data reveal that the AEPD ligand transfers from nickel to copper in the reaction between 1 and copper chloride. All coordination modes of the AEPD-based ligands are studied by analysis of the Cambridge Structural Database. The nickel atom in 1 has octahedral geometry (NiN6) while X-ray structure analysis revealed that the copper atom in the binuclear structure of 2 has an elongated square-pyramidal geometry with a CuN3OCl2 environment. In the crystal network of 2, water molecules and cationic complex units along with the nitrate ions form different hydrogen bond motifs. The thermodynamic stability of the compounds and their charge distribution patterns is studied by density functional theory and natural bond orbital analysis. The ability of AEPD and its complexes to interact with 10 selected biomacromolecules is investigated by docking calculations.

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).

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.

scholarly journals Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 304 ◽  
Author(s):  
Jeannette Carolina Belmont-Sánchez ◽  
Noelia Ruiz-González ◽  
Antonio Frontera ◽  
Antonio Matilla-Hernández ◽  
Alfonso Castiñeiras ◽  
...  
Keyword(s):  
Density Functional ◽  
Amino Group ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Recognition Pattern ◽  
Ft Ir ◽  
Structural Database ◽  
Cation Recognition ◽  
Ft Ir Spectroscopy

The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap[Cd(HEDTA)(H2O)]·H2O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory (DFT) and quantum theory of “atoms-in-molecules” (QTAIM) methods. The crystal was mainly dominated by H-bonds, favored by the observed tautomer of the 2,6-diaminopurinium(1+) cation. Each chelate anion was H-bonded to three neighboring cations; two of them were also connected by a symmetry-related anti-parallel π,π-staking interaction. Our results are in clear contrast with that previously reported for H2(N1,N9)ade [Cu(HEDTA)(H2O)]·2H2O (EGOWIG in Cambridge Structural Database (CSD), Hade = adenine), in which H-bonds and π,π-stacking played relevant roles in the anion–cation interaction and the recognition between two pairs of ions, respectively. Factors contributing in such remarkable differences are discussed on the basis of the additional presence of the exocyclic 2-amino group in 2,6-diaminopurinium(1+) ion.

Structure-forming units of amino acid maleates. Case study ofL-valinium hydrogen maleate

2016 ◽  
Vol 72 (1) ◽  
pp. 160-163 ◽  
Author(s):  
Denis Rychkov ◽  
Sergey Arkhipov ◽  
Elena Boldyreva
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Bulk Powder ◽  
Ft Ir ◽  
The Stability ◽  
Almost All

A new salt of L-valinium hydrogen maleate was used as an example to study structure-forming units in amino acid maleates. This compound was crystallized, its structure solved from single-crystal X-ray diffraction data, and the phase purity of the bulk powder sample confirmed by X-ray powder diffraction and FT–IR spectra. The stability of the new salt was analyzed using density functional theory andPIXELcalculations with focus on theC22(12) structure-forming crystallographic motif. This motif was of particular interest as it is common for almost all maleates. The exceptionally high ability of maleic acid to form salts with various amino acids was rationalized.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

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