Atoms Of Ligand Research Articles

Crystal structure of μ3-tetra-thio-anti-monato-tris[(cyclam)zinc(II)] tetra-thio-anti-monate aceto-nitrile disolvate dihydrate showing Zn disorder over the cyclam ring planes (cyclam = 1,4,8,11-tetra-aza-cyclo-tetra-deca-ne).

Reaction of Zn(ClO4)2·6H2O with cyclam (cyclam = 1,4,8,11-tetra-aza-cyclo-tetra-decane, C10H24N4) and Na3SbS4 in an aceto-nitrile/water mixture led to the formation of crystals of the title compound, [Zn3(SbS4)(C10H24N4)3](SbS4)·2CH3CN·2H2O or [(Zn-cyclam)3(SbS4)2](H2O)2(aceto-nitrile)2. The set-up of the crystal structure is similar to that of [(Zn-cyclam)3(SbS4)2].8H2O reported recently [Danker et al. (2021 ▸). Dalton Trans. 50, 18107-18117]. The crystal structure of the title compound consists of three crystallographically independent ZnII cations (each disordered around centers of inversion), three centrosymmetric cyclam ligands, one SbS4 3- anion, one water and one aceto-nitrile mol-ecule occupying general positions. The aceto-nitrile mol-ecule is equally disordered over two sets of sites. Each Zn2+ cation is bound to four nitro-gen atoms of a cyclam ligand and one sulfur atom of the SbS4 3- anion within a distorted square-pyramidal coordination. The cation disorder of the [Zn(cyclam)]2+ complexes is discussed in detail and is also observed in other compounds, where identical ligands are located above and below the [Zn(cyclam)]2+ plane. In the title compound, the building units are arranged in layers parallel to the bc plane forming pores in which the aceto-nitrile solvate mol-ecules are located. Inter-molecular C-H⋯S hydrogen bonding links these units to the SbS4 3- anions. Between the layers, additional water solvate mol-ecules are present that act as acceptor and donor groups for inter-molecular N-H⋯O and O-H⋯S hydrogen bonding.

Synthesis and structure of сopper(II) thiocyanate and nitrate complexes with 1-tert-butyl1H-1,2,4-triazolе

Complexes [Сu(NCS)2L3], [Сu(NO3)2L4] and [Cu(NCS)2L4]·L have been prepared by direct synthesis involving the interaction of metallic copper, ammonium salts NH4X (Х = NCS, NO3) and 1-tert-butyl-1H-1,2,4-triazole (L). Their composition and structure were determined by elemental analysis, single crystal X-ray analysis, and IR spectroscopy (range of 4000–500 cm–1). All the complexes showed mononuclear structure. In them triazole acts as a monodentate ligand, being coordinated by the N4 atom of the heterocycle. The NCS– and NO–3 anions display monodentate N- and O-coordination, accordingly. In [Сu(NCS)2L3], copper(II) cation has square-pyramidal environment of nitrogen atoms of two ligands L and two thiocyanate anions in the basal sites, and one nitrogen atom of ligand L in the apical position. In complexes [Сu(NO3)2L4] and [Cu(NCS)2L4]·L, copper(II) cations are octahedrally surrounded by nitrogen atoms of ligand L in the equatorial sites and by O or N atoms of corresponding anions in the axial positions.

Heterometallic iron(IV) μ-nitrido complexes supported by a tetradentate Schiff base ligand

A nitrido-bridged heterometallic iron(IV) chloride complex supported by a tetradentate Schiff base ligand has been synthesized and its chloride substitution reactions have been studied. Treatment of the Fe(II) Schiff base complex [Fe(Br4saloph)(py)] (H2Br4saloph = N,N’-bis(3,5-dibromosalicylidene)-1,2-phenylenediamine; py = pyridine) with the Ru(VI) nitride [Ru(N)Cl2(LOEt)] (1, LOEt− = [(η5-C5H5)Co{P(O)(OEt)2}3]−) afforded the μ-nitrido complex [(LOEt)(py)ClRu(μ-N)Fe(Br4saloph)Cl] (2-Cl). The short Fe-N(nitrido) [1.668(4) Å] and Ru-N(nitrido) [1.709(4) Å] distances and the roughly linear Fe-N-Ru linkage [172.9(3)o] in diamagnetic 2-Cl are indicative of the Fe(IV)=N=Ru(IV) bonding picture. Salt metathesis of 2-Cl with [Ag(CF3CO2)] and [Ag(ReO4)] afforded [{(LOEt)(py)ClRu(μ-N)Fe(Br4saloph)(CF3CO2)}⋅Ag(CF3CO2)] (2-CF3CO2⋅Ag(CF3CO2)) and [(LOEt)(py)ClRu(μ-N)Fe(Br4saloph)(ReO4)] (2-ReO4), respectively. Chloride abstraction of 2-Cl with TlPF6, followed by recrystallization in air led to isolation of the μ-oxo complex [{2}2(μ3-O)Tl](PF6)2 (3), which is paramagnetic with a magnetic moment of 2.0 μB. Complex 3 features a [Ru-N-Fe-O(Tl)-Fe-N-Ru]2+ unit, the Tl atom of which is coordinated to the μ-oxo ligand and the oxygen atoms of the Schiff base ligands. The Ru-N(nitrido) (av. 1.709 Å), Fe-N(nitrido) (av. 1.659 Å) and Fe-O(oxo) (av. 1.991 Å) distances in 3 are consistent with M = N double bonds and Fe-O single bonds, respectively. Treatment of 2-Cl with [Tl(SC6F5)] afforded the Fe(III)/Ru(IV) nitrido complex [(LOEt)(py)ClRu(μ-N)Fe(Br4saloph)] (4) that has a longer Fe-N(nitrido) distance [1.753(4) Å] than the Fe(IV) congener 2-Cl does. The crystal structures of complexes 2-Cl, 2-CF3CO2⋅Ag(CF3CO2), 2-ReO4, 3, and 4 have been determined.

A centipede like thiocyanate-bridged muti-nuclear copper(I/II) complex derived from 2-(((2-(dimethylamino)ethyl)imino)methyl)-5-fluorophenol with urease inhibitory activity

A centipede like thiocyanate-bridged multi-nuclear copper(I/II) complex, [Cu2L(CH3OH)(NCS)3]n, derived from 2-(((2-(dimethylamino)ethyl)imino)methyl)-5-fluorophenol (HL), was prepared and characterized by elemental analysis, IR and UV–vis spectra, as well as single crystal X-ray diffraction. The Cu1 ion in the +2 oxidation state is coordinated by the tridentate Schiff base ligand in a square pyramidal geometry, with the other two sites occupied by one N atom of the thiocyanate ligand and one methanol O atom. The Cu2 ion in the +1 oxidation state is coordinated by one N and three S atoms from four thiocyanate ligands, forming a tetrahedral geometry. The CuI ions are linked by thiocyanate ligands to form a one-dimensional chain with [CuI 2(μ 1,3,3-NCS)2] as the repeat unit. The [CuIIL(CH3OH)] moieties are linked to the chain through thiocyanate ligands. The complex has remarkable inhibitory activity on Jack bean urease with an IC50 value of 1.3 μmol L–1.

Crystal structure of di-μ-chlorido-bis-{chlorido-[(-)-5,6-pinenebi-pyridine]-cobalt(II)} aqua-dichlorido[(-)-5,6-pinenebi-pyridine]cobalt(II).

The crystal structure of [Co2Cl4(C17H18N2)2][CoCl2(C17H18N2)(H2O)] or [Co(L)Cl(μ-Cl)]2[Co(L)(Cl)2(OH2)], where L is the enanti-opure bidentate ligand (-)-5,6-pinenebi-pyridine (C17H18N2), has been determined. Crystals suitable for X-ray structure analysis were obtained by slow evaporation of an ethano-lic solution containing equimolar amounts of L and CoCl2·6H2O. The CoII cations all have a coordination number of five, and in each case the coordination polyhedron is a trigonal bipyramid. The Co-N bonds lengths range from 2.037 (7) to 2.195 (7) Å, and Co-Cl bonds lengths range from 2.284 (2) to 2.509 (2) Å. The asymmetric unit contains two discrete complexes, one dinuclear and the other mononuclear. Between the two mol-ecules, two types of inter-molecular inter-actions have been evidenced: π-π stackings involving the bi-pyridine units, and O-H⋯Cl hydrogen bonds between the hydrogen atoms of the aqua ligand coordinating to the mononuclear complex and the non-bridging chlorido ligand coordinating to the dinuclear mol-ecule. These inter-actions lead to a two-dimensional supra-molecular arrangement parallel to the ab plane.

Bimetallic Organoplatinum(II)‐Ag(I) Cluster Cations with Ag−Pt Interactions Unsupported by Conventional Bridging Ligands

AbstractThe organoplatinum complex of a primary amine and AgClO4 aggregate in methanol to oligonuclear mixed‐metal species. A perchlorate salt 3 with the empirical formula C96H146Ag7Cl13N12O62Pt6 could be isolated and structurally characterized with the help of X‐ray diffraction at the DESY synchrotron. The product contains both a penta‐ and a tetra‐nuclear complex cation in which Ag(I) and Pt(II) alternate, held together without any conventional bridge. The cationic species feature short Ag⋅⋅⋅Pt distances between 2.7 and 2.9 Å and contacts longer than 2.4 Å between Ag and C atoms in aromatic rings. In addition to the interactions with Ag(I) cations, Pt(II) is in a square‐planar arrangement, coordinated by a chelating and a terminal amine and an aqua ligand. The central Ag(I) in the pentanuclear cation is located on a twofold crystallographic axis and not involved in any obvious coordinative bond; it exclusively shows short contacts to the neighboring Pt(II) ions and the Pt‐bonded, formally anionic carbon atoms of the cyclometallated organic ligand. Powder diffraction shows that 3 melts and re‐solidifies without decomposition.

Pharmacophore Based Design of Probable FGFR-1 Inhibitors from the 3D Crystal Structure of Infigratinib - A Drug Used in the Treatment of Cholangiocarcinomas

Background: Pemigatinib (INCB054828) and Infigratinib (BGJ398) are the few selective drugs that are approved by the FDA to treat cholangiocarcinoma, a rare form of bile duct cancer. Infigratinib is a pan FGFR inhibitor and has been found promising in Phase-3, first-line PROOF clinical trial. So, screening drug-like compounds having similar pharmacophoric features like infigratinib is the inspiration of the present work. Objective: The objective was to identify drug-like compounds with similar pharmacophoric features as in infigratinib. The compounds screened through the 3D query pharmacophore of infigratinib were also predicted for ADMET properties so that the compounds may have good bioavailability. Method: A pharmacophore was generated from the crystal structure of infigratinib with several pharmacophoric features such as hydrogen bond donor, hydrophobic, positive ionizable, and ring aromatic. MayBridge database containing 65,263 compounds was used for virtual screening (VS) using LibDock. The initial Hit compounds were subjected to ADMET predictions. Finally, two Hit compounds were selected and docked with the FGFR-1 receptor to predict the interaction of the ligand atoms with the amino acid residues of the receptor's active site. Result: The fit score for infigratinib, N-(4-fluorophenyl)-2-(5-((2-(4-methoxy-2,5-dimethylphenyl)-2- oxoethyl)thio)-4-methyl-4H-1,2,4-triazol-3-yl)acetamide (Hit-1) and 4-(4-((2-(5,6-dimethyl-1H-benzo[d] imidazol-2-yl)ethyl)carbamoyl)pyridin-2-yl)-1-methylpiperazin-1-ium (Hit-4) is 4.58901, 4.36649, and 3.71732, respectively. The LibDock score of infigratinib, Hit-1, and Hit-4 is 122.474, 123.289, and 123.353, respectively. The binding affinity score (-PLP1) of infigratinib, Hit-1, and Hit-4 is -143.19, - 102.72, and -91.71. Conclusion: The present study concluded that the two compounds designated as Hit-1 and Hit-4 have been identified as binders of FGFR-1, and Hit-4 occupies the whole pharmacophoric space of infigratinib, and both the compounds LibDock scores are better than the infigratinib. The two compounds Hit-1 and Hit-4 may be synthesized and studied for their enzyme inhibition assay on FGFR-1 and biologically evaluated on different cell lines for Cholangiocarcinoma.

Low-dimensional compounds containing bioactive ligands. Part XVIII: Design, synthesis and crystal structural investigations of ionic heteroleptic Pd(II) complexes based on halo and nitro 8-hydroxyquinoline derivatives

The construction of coordination compounds with desired properties and fascinating structures is a topic of a great interest. In this context, noncovalent interactions can play a dominant role in synthesis, catalysis and design of materials. Here, new heteroleptic palladium(II) coordination compounds bearing 8-hydroxyquinolinium (8-HQH) as cation and [PdCl2(XQ)]- as anion, where HXQ = 5-chloro-7-iodo-8-hydroxyquinoline (1), 5-chloro-8-hydroxyquinoline (2), 5-nitro-8-hydroxyquinoline (3) or 5,7-dibromo-8-hydroxyquinoline (4), have been synthesized via one-pot reaction. Single crystal structure analysis reveals that Pd(II) is coordinated via the N- and O- donor atoms of the XQ ligands besides two cis-chlorido ligands. Both the anions and cations are connected by ionic interaction as well as hydrogen bonds to form infinite chains. The formed chains are assembled into 3D structures by π-π interactions between the aromatic quinoline rings. In addition, complexes 1 and 4 contain two water molecules of crystallization that are involved in the hydrogen bond system. Furthermore, elemental analysis and FT-IR spectroscopy were employed to prove the compositions of the produced compounds. The 1H and 13C NMR spectra measured in DMSO‑d6 confirm the presence of quinoline moieties in all the complexes and give a remarkable distinction between the coordinated and non-coordinated quinoline moieties. Collectively, this study provides a concrete starting point for the design and construction of ionic complexes of Pd(II) with 8-HQ derivatives including covalent and different non-covalent interactions and thus tuning the conformation, properties, and finally the functions of the compounds.

New cobalt(III) complex with triethylenetetramine and 2,2′-bipyridine: synthesis, crystal structure, DNA interaction, hirshfeld surface, DFT analysis, and cytotoxicity

In this study, a new cobalt (III) complex, [Co(trien)(bpy)](ClO4)2Cl (bpy = 2,2-Bipyridine), was successfully synthesized and thoroughly characterized using elemental analyses, IR, UV-visible, Mass spectrum and single-crystal X-ray crystallography. The complex formed in a monoclinic system with space group P21/c, a = 14.6681(4) Å, b = 10.7617(3) Å, c = 15.1670(4) Å, α = 90°, β = 97.75°, and γ = 90°. The distorted octahedral geometry adopted by Co(III) ion coordinated through two N atoms from the 2,2-Bipyridine ligand and four N donor atoms of Triethylenetetramine ligand. UV-Vis absorption, fluorescence spectroscopic, and cyclic voltammetric techniques were used to investigate the binding of this cobalt (III) complex with calf thymus DNA (CT-DNA). Furthermore, the cleavage of pBR322 DNA with cobalt (III) complex was investigated using gel electrophoresis method. The exhibited potent cytotoxic effects against human cell line (HepG2). The primary coordination sphere of Co(III) complex is optimized, structural parameters are calculated and energy gaps of frontier orbital (HOMO-LUMO) have been calculated with B3LYP/6-31G(d,p)/LANL2DZ level of theory in the gaseous phase. The calculated geometric and spectral results closely matched the experimental data. Theoretically calculated molecular orbitals (HOMO-LUMO) and their energies indicate that charge transfer occurs within the complex. NBO and QTAIM analyses were also carried to evaluate occupied and unoccupied localized orbitals and nature of interactions between the ligand and metal ion.

Catena-Poly[[tetra-kis-(3,5-dimethyl-1H-pyrazole-κN 2)copper(II)]-μ2-sulfato-κ2 O:O']: crystal structure and Hirshfeld surface analysis of a CuII coordination polymer.

The title coordination polymer, [Cu(SO4)(C5H8N2)4] n , was synthesized using a one-pot reaction of copper powder, anhydrous copper(II) sulfate and 3,5-dimethyl-1H-pyrazole (Hdmpz) in aceto-nitrile under ambient conditions. The asymmetric unit can be described as a chain consisting of four [Cu(SO4)(Hdmpz)4] formula units that are connected to each other by a μ2-sulfato-bridged ligand. The octa-hedral coordination geometry (O2N4) of all copper atoms is realized by coordination of four pyrazole ligands and two sulfate ligands. Four pyridine-like N atoms of the pyrazole ligands occupy the equatorial positions, while two oxygen atoms of two sulfate ligands are in axial positions. As a result of the sulfate ligand rotation, there is a pairwise alternation of terminal O atoms (which are not involved in coordination to the copper atom) of the SO4 tetra-hedra. The Cu⋯Cu distances within one asymmetric unit are in the range 7.0842 (12)-7.1554 (12) Å. The crystal structure is built up from polymeric chains packed in a parallel manner along the b-axis direction. Hirshfeld surface analysis suggests that the most important contributions to the surface contacts are from H⋯H (74.7%), H⋯O/O⋯H (14.8%) and H⋯C/C⋯H (8.2%) inter-actions.

CSiGaAl2 -/0 and CGeGaAl2 -/0 having planar tetracoordinate carbon atoms in their global minimum energy structures.

Density functional theory (DFT) is used to explore the structure, stability, and bonding in CSiGaAl2 -/0 and CGeGaAl2 -/0 systems having planar tetracoordinate carbon (ptC). The neutral systems have 17 valence electrons and the mono-anionic systems have 18 valence electrons. The ab initio molecular dynamics simulations for 2000 fs time at two different temperatures (300 and 500 K) supported the kinetic stability of the systems. From the natural bond orbital (NBO) analysis it is shown that there is a strong electron donation from the ligand atoms to the ptC atom. We have used Li+ ion for the neutralization of the mono-anionic systems and more interestingly it does not disrupt the planar structure. The most preferable site for binding of Li+ ion is along the AlAl bond in both of the mono-anionic systems. All the systems in this work have both σ and π aromaticity which is predicted from the computations of nucleus independent chemical shift (NICS). Although the anionic species obey the 18 valence electronic rule, the neutral systems break the rule with 17 valence electrons. However, both sets of systems are stable in the planar form. The bonding analysis of the systems includes molecular orbital, adaptive natural density partitioning (AdNDP), quantum theory of atoms in molecules (QTAIM), electron localization function (ELF) basin, and aromaticity analyses. The energy decomposition analysis (EDA) determines the interaction of Li+ ion with CSiGaAl2 - and CGeGaAl2 - in Li@SiGaAl2 and Li@GeGaAl2 , respectively.

Synthesis and Characterization of New Strontium Complexes with Multidentate Ligands

AbstractA series of new strontium complexes, [Sr(tmtad)(btsa)]2 (1), [Sr(ptmtad)(btsa)]2 (2), [Sr(etmtad)(btsa)]2 (3), [Sr(tmtad)(tmhd)]2 (4), [Sr(ptmtad)(tmhd)]2 (5), and [Sr(etmtad)(tmhd)]2 (6), were successfully synthesized by substitution reactions between btsa, aminoalkoxide ligands, and tmhdH (btsa=bis(trimethylsilyl) amide, tmtadH=2,5,9,12‐tetramethyl‐2,5,9,12‐tetraazatridecan‐7‐ol, ptmtadH=2,5,7,9,12‐pentamethyl‐2,5,9,12‐tetraazatridecan‐7‐ol, etmtadH=7‐ethyl‐2,5,9,12‐tetramethyl‐2,5,9,12‐tetraazatridecan‐7‐ol, tmhdH=2,2,6,6‐tetramethyl‐3,5‐heptanedione). Thermogravimetric analysis (TGA) of the new strontium compounds showed low residual masses (4‐11 %) where complex 4 displayed the highest volatility and thermal stability. Single crystal X‐ray study of complexes 1, 3, and 6 revealed that the respective complexes crystalize in a triclinic space group as a dimer with a hexa‐ or hepta‐coordination. Furthermore, dimethylamino nitrogen atoms of aminoalkoxide ligands are freely pendent without coordinating to the central strontium metal due to their steric hindrance on the coordination sphere. Compounds 1–6 were characterized by 1H‐ and 13C‐nuclear magnetic resonance (NMR) spectroscopy, Fourier‐transform infrared (FT‐IR) spectroscopy, elemental analysis (EA), and thermogravimetric analysis.

Mechanism of Antioxidant Activity of Betanin, Betanidin and Respective C15-Epimers via Shape Theory, Molecular Dynamics, Density Functional Theory and Infrared Spectroscopy.

Betanin and betanidin are compounds with extensive interest; they are effectively free radical scavengers. The present work aims to elucidate the differences between the mechanism of the antioxidant activity of betanin, betanidin, and their respective C15-epimers. Shape Theory establishes comparisons between the molecules’ geometries and determines parallelisms with the descriptors BDE, PA, ETE IP, PDE, and infrared spectra (IR) obtained from the molecule simulations. Furthermore, the molecules were optimized using the B3LYP/6-31+G(d,p) protocol. Finally, the molecular docking technique analyzes the antioxidant activity of the compounds in the complex with the therapeutic target xanthine oxidase (XO), based on a new proposal for the geometrical arrangement of the ligand atoms in the framework of Shape Theory. The results obtained indicate that the SPLET mechanism is the most favorable in all the molecules studied and that the first group that loses the hydrogen atom in the four molecules is the C17COOH, presenting less PA the isobetanidin. Furthermore, regarding the molecular docking, the interactions of these compounds with the target were favorable, standing out to a greater extent the interactions of isobetanidin with XO, which were analyzed after applying molecular dynamics.

Deep red emissive octacoordinated heteroleptic Sm(III) complexes: Preparation and spectroscopic investigation

New samarium β-diketonate complexes comprising nitrogen-heterocyclic auxiliary moiety were prepared and characterized spectroscopically. Detailed inspection of complexes has suggested the octacoordinated environment about samarium ion and isostructural behavior of complexes. The samarium ion is coordinated via carbonyl oxygen of diketone ligand and nitrogen atoms of neutral ligand. The photoluminescent (PL) features of the complexes were explored in powder as well as in dimethylsulphoxide solvent. By examining the emission spectra, the sensitizing nature of ligands was revealed. The newly synthesized complexes have shown red emission around 648 nm due to electric dipole transition comparable to 4G5/2→6H9/2. Optical and electronic band gap were found in the range of semiconductor material i.e. 3-4 eV. The photophysical investigations and colorimetric analysis have demonstrated that these complexes could be utilized in electroluminescent devices, lasers, displays and single magnet molecules.

Spin-lattice couplings in two-dimensional CrI3 from first-principles computations

Since thermal fluctuations become more important as dimensions shrink, it is expected that low-dimensional magnets are more sensitive to lattice distortions and phonons than bulk systems are. Here we present a fully relativistic first-principles study on the spin-lattice coupling, i.e. how the magnetic interactions depend on local lattice distortions, of the prototypical two-dimensional ferromagnet CrI$_3$. We extract an effective measure of the spin-lattice coupling in CrI$_3$ which is up to ten times larger than what is found for bcc Fe. The magnetic exchange interactions, including Heisenberg and relativistic Dzyaloshinskii-Moriya interactions, are sensitive both to the in-plane motion of Cr atoms and out-of-plane motion of ligand atoms. We find that significant magnetic pair interactions change sign from ferromagnetic (FM) to anti-ferromagnetic (AFM) for atomic displacements larger than 0.16 {\AA}. We explain the observed strong spin-lattice coupling by analyzing the orbital decomposition of isotropic exchange interactions, involving different crystal-field-split Cr$-3d$ orbitals. The competition between the AFM t$_{2g}$ - t$_{2g}$ and FM t$_{2g}$ - e$_{g}$ contributions depends on the bond angle formed by Cr and I atoms as well as Cr-Cr distance. In particular, if a Cr atom is displaced, the FM-AFM sign change when the I-Cr-I bond angle approaches 90$^\circ$. The obtained spin-lattice coupling constants, along with the microscopic orbital analysis can act as a guiding principle for further studies of the thermodynamic properties and combined magnon-phonon excitations in two-dimensional magnets.

Density functional theory screening of thiophene adsorbents and study of adsorption mechanism

Sulfides, widely found in fossil fuels, not only corrode equipment but also pollute the atmosphere. Adsorption desulphurization can not only remove sulfide effectively, but also reduce energy consumption, it is very necessary to develop desulphurization adsorbent. Metal-organic framework materials (MOFs) have great potential in adsorption desulfurization due to the unique structural properties. However, selecting high-performance adsorbents in the growing sea of MOFs by experiment still needs theoretical guidance. Therefore, the screening method based on density functional theory was adopted to develop the thiophene adsorbents and explore the overall picture of thiophene adsorption. Through applying a three-step screening strategy which involves, we evaluated adsorption performance of 12,020 computationally-ready experimental MOFs candidates. Three adsorbents were found the best activity with adsorption energy <-1.21 eV. According to the classification and electronic structure analysis, it is found that different combinations of ligand atoms and open metal site can induce different strength of d-band center movement during the adsorption process. The high-performance adsorbents are those d-band center of metal sites remain unchanged in the adsorption of thiophene. These results emphasize the importance of the structure-performance relationship of potential MOFs in adsorption desulfurization.

Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term.

Scoring functions are important components in molecular docking for structure-based drug discovery. Traditional scoring functions, generally empirical- or force field-based, are robust and have proven to be useful for identifying hits and lead optimizations. Although multiple highly accurate deep learning- or machine learning-based scoring functions have been developed, their direct applications for docking and screening are limited. We describe a novel strategy to develop a reliable protein–ligand scoring function by augmenting the traditional scoring function Vina score using a correction term (OnionNet-SFCT). The correction term is developed based on an AdaBoost random forest model, utilizing multiple layers of contacts formed between protein residues and ligand atoms. In addition to the Vina score, the model considerably enhances the AutoDock Vina prediction abilities for docking and screening tasks based on different benchmarks (such as cross-docking dataset, CASF-2016, DUD-E and DUD-AD). Furthermore, our model could be combined with multiple docking applications to increase pose selection accuracies and screening abilities, indicating its wide usage for structure-based drug discoveries. Furthermore, in a reverse practice, the combined scoring strategy successfully identified multiple known receptors of a plant hormone. To summarize, the results show that the combination of data-driven model (OnionNet-SFCT) and empirical scoring function (Vina score) is a good scoring strategy that could be useful for structure-based drug discoveries and potentially target fishing in future.

Zn Metal–Organic Framework with High Stability and Sorption Selectivity for CO2

By the employment of 5-amino-1H-tetrazole and pyromellitic acid ligands to assemble with Zn2+ ions, a three-dimensional3,4-connect fry network {[Zn2(HATZ)(ATZ)2(PMA)0.5]·(H2O)5}n (GUPT-1, HATZ = 5-amino-1H-tetrazole, H4PMA = pyromellitic acid) was isolated in the hydrothermal reaction, which features high stability and exhibits high adsorption selectivity of CO2/N2 (118) under ambient conditions and 1 bar. Moreover, grand canonical Monte Carlo (GCMC) simulation and the dispersion-corrected density functional theory (DFT-D) calculations reveal two types of binding sites: first, the electrostatic interactions between CO2 molecules and −NH2 groups exposed inside the channels and, second, the C···O interactions between the C atoms in the CO2 molecules and O atoms in the pyromellitic acid ligands. Furthermore, the static binding energy of CO2 molecules on GUPT-1 calculated by the DFT-D-simulated results was 38.49 kJ·mol–1, which corresponded to the experimental adsorption enthalpy (Qst) calculated to be 37.01 kJ·mol–1.

Synthesis, Optoelectronic and Photoluminescent Characterizations of Green Luminous Heteroleptic Ternary Terbium Complexes

This article presents four ternary terbium complexes based on fluorinated 2-thenoyltrifluoroacetone (TTFA) and N donor bidentate neutral ligands. The prepared complexes were examined by elemental study, electrochemical analysis, spectroscopically and thermo-gravimetrically. Spectral analysis shows the bonding of Tb3+ ion with oxygen and nitrogen atom of diketone and neutral ligand respectively. Upon excitation in UV region, synthesized terbium complexes show luminescence in green region of electromagnetic spectrum. Photoluminescence emission spectra of complexes do not show any ligand based peak suggesting the effective transferal of energy from ligand to metal ion. Green emanation by terbium complexes is owing to intense peak ~547nm (5D4 → 7F5). The outcome of emission data and CIE coordinates correlate with each other and affirms the utility of green luminous complexes as potential emissive material for optoelectronic gadgets applied in lighting system.

Synthesis, characterization and exploration of supramolecular interactions of a Cu(II) based 1D zig-zag coordination polymer: X-ray structure determination and DFT study

A novel Cu(II) based one-dimensional (1D) zig-zag coordination polymer (CP) formulated as [Cu(muco)(4,4′-Me2bpy)(H2O)]·2H2O (1; H2muco = trans, trans-1,3-butadiene-1,4-dicarboxylic acid or trans, trans-muconic acid and 4,4′-Me2bpy = 4,4′-dimethyl-2,2′-bipyridine) was synthesized in a self-assembly reaction using slow evaporation technique. Single crystal X-ray analysis reveals that the compound 1 crystallizes in the triclinic system, space group Pī witha = 9.7436(12) Å,b = 11.1836(14) Å,c = 11.5063(14) Å; α = 61.520(1)°, β = 85.019(1)°, γ = 66.864(1)° and V = 1005.6(2) Å3. Its structure is composed of Cu(II) centres with a distorted square pyramidal configuration interconnected by muco ligand in an array to generate zig-zag chain. A three- dimensional (3D) supramolecular network is formed among 1D chains of 1 via hydrogen bonding and π··π interactions. Interestingly, the connectivity of lattice water molecules shows a water dimer cluster, which further undergoes hydrogen bonding along with coordinated water molecules and oxygen atoms of muco ligands to generate an octameric cluster with chair-like hexameric unit. The excellent coordinating characteristics of muco and bipyridine ligands owing to non-covalent interactions to stabilize compound1have been investigated by means of Hirshfeld analysis. The density functional theory (DFT) study is performed to calculate the HOMO-LUMO gap which enlightens the possible future application of 1 as a semiconducting device. The theoretical findings are also validated experimentally by band gap calculation utilising Tauc’s plot exploring the UV data.