Crystal and molecular structure of chelate compounds of Co(II) and Ni(II) with (2-mercapto-5-ethyl-3-thenylidene)cyclohexylamine

Chelate compounds of Co(II) and Ni(II) with (2-mercapto-5-ethyl-3-thenylidene)-cyclohexylamine were subjected to x-ray diffraction analysis. It was established that the investigated chelates are isostructural and that the metal atoms are tetrahedrally coordinated. It is shown that an intermediate distribution of the multiple bonds is realized in the examined chelate compound, just as in the starting ligand, and that their structures cannot be described within the framework of canonical structures.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1484–1488, November, 1981.     

Molecular structure of the macrocyclic copper(II) chelate with 6,7,13,14-tetramethyl-3,10-dithio-1,2,4,5,8,9,11,12-octaazatetradecatetraene-1,5,7,11 according to quantum-chemical DFT calculations

The key parameters of the molecular structure of macrotetracyclic (NNNN)-coordinated chelate of Cu(II) with 6,7,13,14-tetramethyl-3,10-dithio-1,2,4,5,8,9,11,12-octaazatetradecatetraene-1,5,7,11 have been calculated by means of the DFT-based B3LYP6-31G(d) method in GAUSSIAN-09 software. The complex may be formed via self-assembly of Cu(II), thiocarbohydrazide, and diacetyl in the gelatin-immobilized matrix implants. The bond lengths, bond angles, and torsion angles are presented; it has been shown that the metal chelate and the chelating ligand are almost planar.     

Copper(II) perchlorate complexes with antipyrine: synthesis,structure, cytotoxicity and DFT calculations

The synthesis, structure and properties of copper(II) perchlorate complexes with antipyrine (AP), [Cu(AP)₄(H₂O)](ClO₄)₂ and [Cu(AP)₅](ClO₄)₂, are described and compared with those of alternative compounds containing different AP ligands.     

Synthesis,X-ray structure,and DFT studies of five- and eight-coordinated Cd(II) complexes with s-triazine N-pincer chelate

Abstract

The synthesis and spectral characterizations of [CdLCl₂] (1 C. J. Moulton, B.L. Shaw. J. Chem. Soc. Dalton Trans., 1020 (1976).[Crossref] , [Google Scholar]) and [CdL(NO₃)₂(H₂O)] (2 G. van Koten. Pure Appl. Chem., 61, 1681 (1989).[Crossref], [Web of Science ®] , [Google Scholar]) pincer complexes of the s-triazine core ligand (L), 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine), are presented. Complexes 1 and 2 have five- and eight-coordinated Cd(II) ions, respectively, where L acts as a neutral tridentate N-chelate. The coordination sphere is completed by two coordinated Cl^– anions in 1 and with one water molecule and two bidentate nitrate anions in 2. The neutral complex units of 1 and 2 are packed by the polar Cl…H and O…H hydrogen bonds, respectively. Using Hirshfeld analysis, the percentages of these contacts are 24.5% and ～36.8%, respectively. Both complexes showed some anion-π stacking interactions. Thermogravimetric analysis showed that 1 is thermally more stable than 2. The orbital-orbital interactions included in the Cd-Cl, Cd-O, and Cd-N coordinate bonds were analyzed using DFT calculations. The calculated NMR results correlated very well with the experimental data.     

Synthesis and DFT calculations of new ruthenium(II) nitrosyl complexes using cis-fac-dichlorotetrakis(dimethylsulfoxide)ruthenium(II) precursor and different oximes as sources of nitrosyl ligand

Abstract

Three NO⁺-ruthenium(II) complexes were prepared by using cis-[RuCl₂(DMSO)₄] as precursor, P, and the compounds benzohydroxamic acid (BHA), 1′, anti-diphenylglyoxime (H₂dpg), 2′, and dimethylglyoxime (H₂dmg), 3′, as sources of NO moiety. The three complexes [RuCl₂(DMSO)₃(NO)]⁺(BA)^?, 1, [RuCl₂(DMSO)₃(NO)]⁺(Hdpg)^?, 2, and [RuCl₂(DMSO)₃(NO)]⁺(Hdmg)^?, 3, were characterized by (FT-IR, NMR, UV-Vis) spectroscopy, thermogravimetry, and microanalysis. From FT-IR spectral data, two modes of coordination of DMSO to Ru atom through both S and O atoms were detected for 1 and 2. For 3, only S coordination was reported. Computational studies on the [RuCl₂(DMSO)₃(NO)]⁺ cationic parts, 1″, 2″ and 3″, of the investigated complexes 1, 2 and 3 were carried out by DFT. The molecular geometry and mode of attachment of Ru(II) with DMSO were performed with the B3LYP/LANL2DZ level of theory and basis set. Theoretical to the experimental agreement was achieved for analysis of IR data of the investigated complexes. Additional information about binding between the ruthenium atom and the DMSO ligand has been obtained by NBO analysis.     

A DFT investigation on molecular structures of semicarbazone complexes with Co(II), Ni(II) and Zn(II) and reaction energies of their complexation

The structure optimizations of 2-formylpyridine (H2FoPyS), 3-formylpyridine (H3FoPyS), and 4-formylpyridine (H4FoPyS) semicarbazone complexes with Co(II), Ni(II), and Zn(II) were carried out using DFT calculations at the B3LYP/LANL2DZ level of theory. The B3LYP/LANL2DZ-optimized geometry parameters for the H2FoPyS and H3FoPyS complexes show good agreement with their corresponding X-ray crystallographic data. Due to the X-ray crystallographic structures of the [Zn(H3FoPyS)₂]²⁺ complex and the H4FoPyS complexes with Co(II), Ni(II), and Zn(II) and have not yet been observed, their B3LYP/LANL2DZ-optimized structures are therefore theoretically proposed. The reaction energies and thermodynamic properties of complexation for these complexes computed at the same level of theory are reported.     

Quantum-chemical simulation of the mechanisms of stereoisomerism of tetracoordinated Ni(II) complexes

Mechanism of stereoisomerism at the rotation of chelate rings of the bis-chelate tetracoordinated Ni(II) complexes is studied by the method of density functional theory [B3LYP/6-311++G(d,p)]. The reaction is shown to proceed with the change in multiplicity. Calculated energy barriers are consistent with the experimental data. The results obtained demonstrate the feasibility of the chosen approach for the theoretical simulation of intramolecular rearrangements of the transition metal complexes proceeding with the change in the system spin state.     

Oxamato-bridged trinuclear Ni(II)Cu(II)Ni(II) complexes with irregular spin state structures and a binuclear Ni(II)Cu(II) complex with an unusual supramolecular structure: crystal structure and magnetic properties

Four oxamato-bridged heterotrinuclear Ni(II)Cu(II)Ni(II) complexes of formula ([Ni(bispictn)](2)Cu(pba))(ClO(4))(2).2.5H(2)O (1), ([Ni(bispictn)](2)Cu(pbaOH))(ClO(4))(2).H(2)O (2), ([Ni(cth)](2)Cu(pba))(ClO(4))(2) (3), and ([Ni(cth)](2)Cu(opba))(ClO(4))(2).H(2)O (4) and a binuclear Ni(II)Cu(II) complex of formula [Cu(opba)Ni(cth)].CH(3)OH (5) have been synthesized and characterized by means of elemental analysis, IR, ESR, and electronic spectra, where pba = 1,3-propylenebis(oxamato), pbaOH = 2-hydroxyl-1,3-propylenebis(oxamato), opba = o-phenylenebis(oxamato), bispictn = N,N'-bis(2-pyridylmethyl)-1,3-propanediamine, and cth = rac-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane. The crystal structures of 1, 3, and 5 have been determined. The structures of complexes 1 and 3 consist of trinuclear cations and perchlorate anions, and that of 5 consists of neutral binuclear molecules which are connected by hydrogen bonds and pi-pi interactions to produce a unique supramolecular "double" sheet. In the three complexes, the copper atom in a square-planar or axially elongated octahedral environment and the nickel atom in a distorted octahedral environment are bridged by the oxamato groups, with Cu.Ni separations between 5.29 and 5.33 A. The magnetic properties of all five complexes have been investigated. The chi(M)T versus T plots for 1-4 exhibit the minimum characteristic of antiferromagnetically coupled NiCuNi species with an irregular spin state structure and a spin-quartet ground state. The chi(M)T versus T plot for 5 is typical of an antiferromagnetically coupled NiCu pair with a spin-doublet ground state. The Ni(II)-Cu(II) isotropic interaction parameters for the five complexes were evaluated and are between 102 and 108 cm(-)(1) (H = -JS(Cu).S(Ni)).     

In silico study of remdesivir with and without ionic liquids having different cations using DFT calculations and molecular docking

The new coronavirus is trying best to kill the humanity with its highly infectious nature and its first infection was reported in 2019; later this infection was named as COVID-19. Health-care systems are still the using repurposing drugs to cure the patients from this infection. Remdesivir is found to have good potential to cure the patients from this infection and is being extensively used during the 1^st and 2^nd wave of COVID-19. Therefore, in the present work, authors have studied the interaction of remdesivir with different ionic liquids with change in cations using density functional theory calculation in gaseous and water. Based on the DFT calculations, it was found that remdesivir interacts effectively with different ionic liquids based on the energy; further, the change in free energy for Remdesivir-[Bet-ester][Lev] (1) was found to be ?3223.5758 and ?3223.6533 hartree per particle in gaseous and water respectively and most stable; further, 2 and 3 have the comparable free energies. Further, the potential of remdesivir with and without ionic liquids against the main protease of SARS-CoV-2 was investigated using molecular docking. Results revealed that Remdesivir-[Chol][Lev] (2) and Remdesivir-[Chol-ether][Lev] (3) have shown promising results with binding energy of ?129.64 ?kcal/mol and ?125.44 ?kcal/mol respectively while Remdesivir [Bet-ester][Lev] (1) have a binding energy of -123.86 kcal/mol. It is important to mention that changing the cations in ionic liquid play an important role in the docking. It is also observed that the ionic liquid having sodium as cation, then the binding energy against Mpro of CoV is poor and even less than the remdesivir alone.     

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

Background  

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq₃, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq₃ in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies.     

Quantum-chemical calculation of molecular structures of Al2Mn3 and Al2Zn3 clusters by using DFT method

Structural Chemistry - By using DFT method in the OPBE/TZVP level, key parameters of molecular structures of five-atomic heteronuclear clusters having Al2M3 composition where M = Mn or...     

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K₃) having C _s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.     

Synthesis,spectroscopic characterization,X-ray structure and DFT calculations of copper(II) complex with 2-(2-pyridyl)benzimidazole

The reaction of copper(II) nitrate trihydrate and 2-(2-pyridyl)benzimidazole (pybzim) leads to [Cu(pybzim)₂(NO₃)](NO₃). The compound has been studied by IR, UV–Vis spectroscopy and X-ray crystallography. The electronic structure of the [Cu(pybzim)₂(NO₃)]⁺ cation has been calculated with the density functional theory (DFT) method. The spin-allowed doublet–doublet electronic transitions of [Cu(pybzim)₂(NO₃)]⁺ have been calculated with the time-dependent DFT method, and the UV–Vis spectrum of the title compound has been discussed on this basis.     

Preparation and crystal structure of a copper(II) homobinuclear chelate

Summary The structure of the homobinuclear complex Cu₂(aapen)H₂O, where aapen is the tetraanionic ligand derived from the condensation of 1,2-diaminocthane witho-acetoacetylphenol, has been determined from diffractometer data and refined to R = 6.1%. The crystals are monoclinic,P2₁/c, witha = 12.991(5),b = 8.530(4),c = 18.546(6) Å, and = 104.10(4)°; Z = 4. The ligand employed has two different coordination sets of atoms, N₂O₂ and O₂O₂, two oxygen atoms being common to both donor sets. In the complex, one copper atom is retained in the plane of the inner N₂O₂ chamber whilst the other, which is incorporated in the outer O₂O₂ chamber, is five-coordinate, being axially bonded to a water molecule.     

Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.     

The molecular structure of [Sn(P2C2But2)] using gas-phase electron diffraction and DFT calculations

The molecular structure of 2,4-di-tert-butyl-eta4-1,3-diphosphacyclobutadiene tin has been determined in the gas phase by electron diffraction using both the DYNAMITE and SARACEN methods. The suitability of many different theoretical methods for the calculation of structures of half-sandwich main-group metal complexes has been investigated, and, by comparison of the results with the experimental structures, suggestions have been made as to the most suitable methods for this class of compound.