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.

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 Structural, Non-Covalent Interaction, and Natural Bond Orbital Studies on Bromido-Tricarbonyl Rhenium(I) Complexes Bearing Alkyl-Substituted 1,4-Diazabutadiene (DAB) Ligands

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 267 ◽  
Author(s):  
Reza Kia ◽  
Azadeh Kalaghchi
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Carbonyl Groups ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Covalent Interaction ◽  
Distorted Octahedral ◽  
Elemental Analyses ◽  
Ft Ir ◽  
Solid State Structures

The synthesis, characterization, structural and computational studies of Re(I) tricarbonyl bromo complexes bearing alkyl-substituted 1,4-diazabutadiene ligands, [Re(CO)3(1,4-DAB)Br], where 1,4-DAB = N,N-bis(2,4-dimethylbenzene)-1,4-diazabutadiene, 2,4-Me2DAB (1); N,N-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene, 2,4-Me2DABMe (2); N,N-bis(2,4,6-trimethylbenzene)-1,4-diazabutadiene, 2,4,6-Me3DAB (3); and N,N-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene, 2,6-ipr2DAB (4) are reported. The complexes were characterized by different spectroscopic methods such as FT-IR, 1H-NMR, 13C-NMR, and elemental analyses and their solid-state structures were confirmed by X-ray diffraction. In each complex, the Re(I) centre shows a distorted octahedral shape with a facial geometry of carbonyl groups. The gas phase geometry of the complexes was identified by density functional theory. Interesting intermolecular n…π* interactions of complexes 1 and 3 were investigated by non-covalent interaction index (NCI), and natural bond orbital (NBO) analyses. The intramolecular n…σ*, σ…π*, π…σ* interactions were also studied in complexes 3 and 4.

Functionalisation of Imidazolin-2-imine to Corresponding Phosphinamine, Chalcogenide (O, S, Se, Te), and Borane Compounds

2015 ◽  
Vol 68 (1) ◽  
pp. 127 ◽  
Author(s):  
Kishor Naktode ◽  
Sayak Das Gupta ◽  
Abhinanda Kundu ◽  
Salil K. Jana ◽  
Hari Pada Nayek ◽  
...  
Keyword(s):  
Good Yield ◽  
Density Functional ◽  
Elemental Sulfur ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Tert Butyl ◽  
Imine Ligands ◽  
Orbital Analysis

1,3-Di-tert-butyl-imidazolin-2-ylidine-1,1-diphenylphosphinamine (2) was prepared from 1,3-di-tert-butyl-imidazolin-2-imine (1) and chlorodiphenylphosphine. Compound 2 was treated further with elemental sulfur, selenium, and tellurium to afford the corresponding chalcogenide derivatives, 1,3-di-tert-butyl-imidazolin-2-ylidine-P,P-diphenyl-phosphinothioicamide (4), 1,3-di-tert-butyl-imidazolin-2-ylidine-P,P-diphenyl-phosphinoselenoicamide (5), and 1,3-di-tert-butyl-imidazolin-2-ylidine-P,P-diphenyl-phosphinotelluroicamide (6) in good yield. 1,3-Di-tert-butyl-imidazolin-2-ylidine-P,P-diphenylphosphinicamide (3) was obtained by dissolving compound 2 in hydrochloric acid solution in THF. The corresponding borane adduct, 1,3-di-tert-butyl-imidazolin-2-ylidine-P,P-diphenyl-phosphinaminoborane (7) was isolated by the reaction of compound 2 and sodium borohydride in good yield. The molecular structures of compounds 2 and 4–7 were established by X-ray diffraction analyses. To analyse the electronic structure of chalcogenides of imidazolin-2-imine ligands, the protonation energies of the oxygen, sulfur, and selenide derivative of ligand 2 were calculated by means of density functional theory. Finally, the charge distribution in compounds 3, 4, and 5 were determined using natural bond orbital analysis.

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.

Spectral, structural and theoretical study of the effects of thiocyanato and dicyanamido ligands on the geometry of PbIIcomplexes containing a triazinic ligand

2019 ◽  
Vol 75 (8) ◽  
pp. 1023-1030
Author(s):  
Farzin Marandi ◽  
Keyvan Moeini ◽  
Zahra Mardani ◽  
Harald Krautscheid
Keyword(s):  
Density Functional ◽  
Aromatic Rings ◽  
Functional Theory ◽  
One Dimensional ◽  
X Ray ◽  
H Nmr ◽  
1D Coordination Polymer ◽  
Binuclear Structure ◽  
Ft Ir ◽  
Structural Database

Two lead(II) complexes of 5,6-bis(furan-2-yl)-3-(pyridin-2-yl)-1,2,4-triazine (DFPT), namely one-dimensional (1D)catena-poly[[bis[5,6-bis(furan-2-yl)-3-(pyridin-2-yl-κN)-1,2,4-triazine-κN2]lead(II)]-di-μ-thiocyanato-κ2N:S;κ2S:N], [Pb(NCS)2(C16H10N4O2)2]n,1, and binuclear di-μ-dicyanamido-κ2N1:N5;κ2N5:N1-bis{[5,6-bis(furan-2-yl)-3-(pyridin-2-yl-κN)-1,2,4-triazine-κN2](nitrato-κ2O,O′)lead(II)}, [Pb2(C2N3)2(NO3)2(C16H10N4O2)4],2, as well as DFPT itself, were prepared and identified by elemental analysis, FT–IR,1H NMR spectroscopy and single-crystal X-ray structural analyses. In the double-chain 1D coordination polymer of1and the binuclear structure of2, the Pb atom has ahemidirected-PbN6S2and a rareholodirected-PbN6O2environment, respectively, with a distorted cubic geometry. All the coordination modes of dicyanamide ligands within lead complexes were studied using the Cambridge Structural Database (CSD) to compare them with the structures of1and2. In addition to hydrogen bonds, the crystal networks are stabilized by π–π stacking interactions between the triazine, furyl and pyridine aromatic rings. The most stable theoretical structures of the title compounds predicted by density functional theory (DFT) calculations were compared with the solid-state results.

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.

On tungstates of divalent cations (III) – Pb5O2[WO6]

2020 ◽  
Vol 235 (8-9) ◽  
pp. 311-317
Author(s):  
Stephan G. Jantz ◽  
Florian Pielnhofer ◽  
Henning A. Höppe
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Quantum Chemical ◽  
Density Functional ◽  
Divalent Cations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
First Results ◽  
Electrostatic Calculations

Abstract${\text{Pb}}_{5}{\text{O}}_{2}\left[{\text{WO}}_{6}\right]$ was discovered as a frequently observed side phase during our investigation on lead tungstates. Its crystal structure was solved by single-crystal X-ray diffraction ($P{2}_{1}/n$, $a=7.4379\left(2\right)$ Å, $b=12.1115\left(4\right)$ Å, $c=10.6171\left(3\right)$ Å, $\beta =90.6847\left(8\right)$°, $Z=4$, ${R}_{\text{int}}=0.038$, ${R}_{1}=0.020$, $\omega {R}_{2}=0.029$, 4188 data, 128 param.) and is isotypic with ${\text{Pb}}_{5}{\text{O}}_{2}\left[{\text{Te}}_{6}\right]$. ${\text{Pb}}_{5}{\text{O}}_{2}\left[{\text{WO}}_{6}\right]$ comprises a layered structure built up by non-condensed [WO6]${}^{6-}$ octahedra and ${\left[{\text{O}}_{4}{\text{Pb}}_{10}\right]}^{12+}$ oligomers. The compound was characterised by spectroscopic measurements (Infrared (IR), Raman and Ultraviolet–visible (UV/Vis) spectra) as well as quantum chemical and electrostatic calculations (density functional theory (DFT), MAPLE) yielding a band gap of 2.9 eV fitting well with the optical one of 2.8 eV. An estimation of the refractive index based on the Gladstone-Dale relationship yielded $n\approx 2.31$. Furthermore first results of the thermal analysis are presented.

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