Showing papers on "Tetrahedral molecular geometry published in 2021"

Spodium bonding in five coordinated Zn(II): a new player in crystal engineering?

Abstract: This manuscript evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(II) spodium atoms Four families of compounds have been found analysing the Cambridge structural database (CSD) where the interaction is very important to understand the crystal packing: (i) multi-dentate Schiff-base complexes, (ii) Zn-porphyrins, (iii) aza-crown ethers and (iv) polyoxometalates, the latter as SpB acceptors The square-pyramidal around the metal center facilitates the approximation of the electron rich atom (ElR) to the Zn(II), contrariwise to the four-coordinated tetrahedral geometry where the steric crowd of the Zn ligands usually impedes the formation of the SpB This highlight concentrates on the SpB interaction, which is different from the classical coordination bond in the sense that Y–Sp⋯A distances are longer (around the sum of van der Waals radii), the interaction weaker and it involves the σ* orbital of the Y–Sp bond (Y = any atom) A theoretical study on one representative family of compounds (Zn-porphyrins) has been also carried out indicating that the SpB energies range from −1 to −74 kcal mol−1 Finally, a statistical analysis of the CSD evidences that the interaction can be somewhat directional

Tridentate imidazole-based Schiff base metal complexes: molecular docking, structural and biological studies

Abstract: A novel Schiff base was synthesized by the condensation of imidazole-2-carboxaldehyde with l-histidine in an equimolar ratio. The prepared Schiff base was characterized by elemental analysis and spectral characterization techniques. It was then complexed with a series of 3-d metal(II) ions like manganese, iron, cobalt, nickel, copper and zinc. The coordination properties, nature of bonding and stability of the complexes were deduced from elemental analysis, IR, UV-vis, 1H NMR, mass, electronic spectra, magnetic, conductivity and thermogravimetric analysis. IR studies support the tridentate behaviour of Schiff base as well as its coordination to the central metal ion through an azomethine nitrogen, deprotonated carboxylic oxygen and imidazole ring nitrogen atoms of histidine. The electronic spectra and magnetic moment data demonstrate that the complexes have an octahedral geometry, except zinc complex, which has a tetrahedral geometry. In vitro antimicrobial activity of the synthesized compounds has been shown to exhibit excellent antibacterial and antifungal activities. The antibacterial property of the prepared Schiff base was further confirmed by conducting a docking study of target proteins involved in the antibacterial mechanism.Communicated by Ramaswamy H. Sarma.

Synthesis and photoluminescence of manganese(II) naphtylphosphonic diamide complexes.

Abstract: Manganese(II) halide complexes with N,N,N′,N′-tetramethyl-P-naphtalen-2-ylphosphonic diamide were synthesized from anhydrous MnX2 salts (X = Cl, Br, I) and characterized. Single-crystal X-ray diffraction revealed in all the cases slightly distorted tetrahedral geometry of the coordination sphere. The photoluminescence spectra showed the superimposition of a green emission, related to the 4T1(4G) → 6A1(6S) transition of Mn(II), with a band in the red range. Different possible attributions to the lowest-energy emission were taken into account. The emission spectra of the isolated products are dependent upon the nature of the halide and, in the case of X = Br, also upon the excitation wavelength.

Rare proximity enforced copper hydrogen interactions in copper(I)-chalcogenones

Abstract: Copper(I) chalcogenones with rare Cu⋯H–C(sp3) hydrogen bonding interactions have been reported. The copper(I) bis(benzimidazole-2-chalcogenone) complexes [Cu(L1)4]+BF4− (1) and [Cu(L2)4]+BF4− (2) (L1 = bis(1-isopropyl-benzimidazole-2-selone)-3-ethyl; L2 = bis(1-isopropyl-benzimidazole-2-thione)-3-ethyl) have been synthesized and characterized. Both complexes possess distorted tetrahedral geometry with a semi-trans arrangement of the benzimidazole-chalcogenone ligands around the Cu(I) center. The structures of 1 and 2 reveal homoleptic coordination with the Cu(I) center with the (sp3)C–H groups of the ethylene linker directed towards the Cu(I) center to maximize the rare proximity-enforced intramolecular Cu⋯H–C interactions. The Cu⋯H–C interactions are found to have a hydrogen bonding nature in the crystalline state, as these interactions are absent in the solution state.

Spectroscopic, X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides.

Abstract: The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH2 single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their 1H-NMR spectra Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions

Electrocatalytic syngas generation with a redox non-innocent cobalt 2-phosphinobenzenethiolate complex.

Abstract: A cobalt complex supported by the 2-(diisopropylphosphaneyl)benzenethiol ligand was synthesized and its electronic structure and reactivity were explored. X-ray diffraction studies indicate a square planar geometry around the cobalt center with a trans arrangement of the phosphine ligands. Density functional theory calculations and electronic spectroscopy measurements suggest a mixed metal–ligand orbital character, in analogy to previously studied dithiolene and diselenolene systems. Electrochemical studies in the presence of 1 atm of CO2 and Bronsted acid additives indicate that the cobalt complex generates syngas, a mixture of H2 and CO, with faradaic efficiencies up to >99%. The ratios of H2 : CO generated vary based on the additive. A H2 : CO ratio of ∼3 : 1 is generated when H2O is used as the Bronsted acid additive. Chemical reduction of the complex indicates a distortion towards a tetrahedral geometry, which is rationalized with DFT predictions as attributable to the populations of orbitals with σ*(Co–S) character. A mechanistic scheme is proposed whereby competitive binding between a proton and CO2 dictates selectivity. This study provides insight into the development of a catalytic system incorporating non-innocent ligands with pendant base moieties for electrochemical syngas production.

Synthesis, structures, and catalytic efficiency in ring opening polymerization of rac-lactide with tridentate vs. bidentate cobalt(II), zinc(II), and cadmium(II) complexes containing N-substituted N,N-bis((3,5-dimethyl-1H-pyrazol-1-yl)methyl)amine ligands

Abstract: A series of Co(II), Zn(II), and Cd(II) complexes supported by 1-(3,5-dimethyl-1H-pyrazol-1-yl)-N-((3,5-dimethyl-1H-pyrazol-1-yl)methyl)-N-(furan-2-ylmethyl)methanamine (LA) and N,N-bis((3,5-dimethyl-1H-pyrazol-1-yl)methyl)-4-isopropylaniline (LB) were synthesized. The direct chelation of CoCl2·6H2O, ZnCl2, and CdBr2·4H2O by the ligands produced [LnMX2] (Ln = LA or LB; M = Zn or Co, with X = Cl; M = Cd, with X = Br) complexes in high yields. Structural studies revealed that [LBCoCl2] and [LBZnCl2] adopted distorted tetrahedral geometries, as LB coordinated the metal centers in a bidentate fashion, while LA coordinated the metal centers in a tridentate fashion through the nitrogen atoms of the pyrazole and amine moieties, so that [LACoCl2] and [LAZnCl2] exhibited trigonal bipyramidal geometries and [LACdBr2] a square pyramidal geometry. [LBCdBr2] has two Cd-containing structures per unit cell, whereby one Cd center adopted a distorted tetrahedral geometry and the other exhibited square bipyramidal geometry. The in situ-generated alkyl derivatives of the synthesized complexes were assessed in the ring-opening polymerization of rac-lactide. Heterotactic polylactides (PLAs) were furnished with all complexes. The [LBZnCl2]/MeLi system produced PLA with a superior heterotactic bias (Pr up to 0.94) at −25 °C. PLAs with wide-ranging polydispersity indices (1.16–2.23) and low molecular weights were produced in all cases, irrespective of the specific M(II) center and ancillary ligand utilized.

2D and 3D silver-based coordination polymers with thiomorpholine-4-carbonitrile and piperazine-1,4-dicarbonitrile: structure, intermolecular interactions, photocatalysis, and thermal behavior

Abstract: Four silver-based coordination polymers, {[Ag(L1)2]NO3}∞ (1), {[Ag(L1)2]ClO4}∞ (2), {[Ag(L2)2]NO3·H2O}∞ (3) and {[Ag(L2)2]ClO4}∞ (4), were synthesized using the thiomorpholine-4-carbonitrile (L1) and piperazine-1,4-dicarbonitrile (L2) ligands. Compounds 1 and 2 are two-dimensional, while 3 and 4 are three-dimensional. L1 and L2 are 1,4-bis-monodentate ligands in all compounds, while Ag(I) ions are four-coordinated in a slightly distorted tetrahedral geometry. Topological analysis in standard representations suggests that underlying nets in 1 and 2 have an sql topology, while 3 and 4 exhibit a dia topology. Thermal analysis shows that 3 loses crystalline water at room temperature, while other compounds show good thermal stability. All compounds show good photocatalytic activity for photocatalytic degradation of the mordant blue 9 dye, with reaction rates in the range 0.029 to 0.061 min−1. The best result was obtained for compound 4, which can be correlated to its largest lattice volume.

Extending Fluorescence of meso-Aryldipyrrin Indium(III) Complexes to Near-Infrared Regions via Electron Withdrawing or π-Expansive Aryl Substituents.

Abstract: The absorption and fluorescence spectra of 14 In(III) dipyrrin-based complexes are studied using time-dependent density functional theory (TDDFT). Calculations confirm that both heteroatom substitution of oxygen (N2O2-type) by nitrogen (N4-type) in dipyrrin ligand and functionalization at the meso-position by aromatic rings with strong electron-withdrawing (EW) substituents or extended π-conjugation are efficient tools in extending the fluorescence spectra of In(III) complexes to the near-infrared (NIR) region of 750-960 nm and in red-shifting the lowest absorption band to 560-630 nm. For all complexes, the emissive singlet state has π-π* character with a small addition of intraligand charge transfer (ILCT) contributing from the meso-aryl substituents to the dipyrrin ligand. Stronger EW nitro group on the meso-phenyl or meso-aryl group with extended π-conjugation induces red-shifted electronic absorption and fluorescence. More tetrahedral geometry of the complexes with N4-type ligands leads to less intensive but more red-shifted fluorescence to NIR, compared to the corresponding complexes with N2O2-type ligands that have a more planar geometry.

Synthesis of Terminal Bis(hydrosulfido) and Disulfido Complexes of Ni(II) from a Geometrically Frustrated Tetrahedral Ni(II) Chloride Complex

Abstract: Recent studies have highlighted how reactive sulfur species (RSS) can be regulated and transported by metal-sulfur coordination compounds. We report herein the reactivity of PhB(tBuIm)3NiCl (1) with RSS, including the hydrosulfide anion ([Bu4N][SH]) and a reduced tetrasulfide ([K18-C-6]2[S4]). The strongly donating tris(carbene) ligand in 1 is geometrically constrained to a tetrahedral geometry, and the energetically preferable square planar geometry is not achievable with the [PhB(tBuIm)3]- ligand. Upon reaction of 1 with [Bu4N][SH] and [K18-C-6]2[S4], the square planar complexes PhB(tBuIm)2(tBuImH)Ni(SH)2 (2) and PhB(tBuIm)2(tBuImH)Ni(η2-S2) (3) are formed, respectively, via the protonation of one carbene ligand donor atom. Mechanistic investigation suggest that protonation occurs either from decomposition of 1 during the reaction progress, reactions with advantageous [Bu4N]+/[K18-C-6]+ countercations or from the generation of transient unidentified RSS that facilitate proton transfer reactions.

Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

Abstract: Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

π-Extended Boron Difluoride [NՈNBF2] Complex, Crystal Structure, Liquid NMR, Spectral, XRD/HSA Interactions: A DFT and TD-DFT Study

Abstract: The novel tetrahedral 10-(4-carboxyphenyl)-2,8-diethyl-5,5-difluoro-1,3,7,9-tetramethyl-5H-di-pyrrolo[1,2-c:2’,1’-f][1,3,2]diazaborinin-4-ium-5-uide [NՈNBF2] BODIPY complex was prepared in a very good yield and via one-pot synthesis. The desired [NՈNBF2] has been used as a model complex for XRD/HSA interactions and DFT/B3LYP/6-311G(d,p) computations. The tetrahedral geometry around the boron center was demonstrated by DFT optimization and XRD-crystallography. The 1H, 11B, and 19F-NMR spectra were used also to support the high symmetrical BODIPY via π-extended phenomena. Moreover, the values of the DFT-calculated structural bond lengths/angles and DFT-IR were matched to the corresponding experimental XRD and IR parameters, respectively. The crystal lattice interactions were correlated to Hirshfeld surface analysis (HSA) calculations. Calculations of the Mulliken Atomic Charge (MAC), Natural Population Analysis (NPA), Global reactivity descriptors (GRD), and Molecular Electrostatic Potential (MEP) quantum parameters were performed to support the XRD/HSA interactions result. Analysis of the predicted Density of States (DOS), molecular orbital, and time-dependent density functional theory (TD-DFT) calculations have been combined to explain the experimental UV-vis spectra and electron transfer behavior in [NՈNBF2] complex using MeOH and other four solvents.