Monoribbed‐Functionalized Macrobicyclic Iron( II ) Complexes Decorated with Terminal Reactive and Vector Groups: Synthetic Strategy, Chemical Transformations and Structural Characterization

Avdeeva V.V., Garaev T.M., Breslav N.V., Burtseva E.I., Grebennikova T.V., Zhdanov A.P., Zhizhin K.Y., Malinina E.A., Kuznetsov N.T.

In this work, a synthetic approach to prepare an example of new class of the derivatives of the closo-decaborate anion with amino acids detached from the boron cluster by pendant group has been proposed and implemented. Compound Na2[B10H9–O(CH2)4C(O)–His–OMe] was isolated and characterized. This compound has an inorganic hydrophobic core which is the 10-vertex boron cage and the –O(CH2)4C(O)–His–OMe organic substituent. It has been shown to possess strong antiviral activity in vitro against modern strains of A/H1N1 virus at 10 and 5 µg/mL. The compound has been found to be non-cytotoxic up to 160 µg/mL. At the same time, the compound has been found to be inactive against SARS-CoV-2, indicating specific activity against RNA virus replication. Molecular docking of the target derivative of the closo-decaborate anion with a model of the transmembrane region of the M2 protein has been performed and the mechanism of its antiviral action is discussed.

Liu Y., Yu H., Wang Y., Li C., Wang X., Ye C., Yao H., Pan M., Su C.

Photodynamic therapy (PDT) has been extensively studied as a noninvasive treatment option; however, the current PDT agents are often restricted with poor solubility, difficult accumulation in tumor sites, low singlet oxygen yield and low penetration depth.

Gong W., Xie Y., Pham T.D., Shetty S., Son F.A., Idrees K.B., Chen Z., Xie H., Liu Y., Snurr R.Q., Chen B., Alameddine B., Cui Y., Farha O.K.

The rational design and synthesis of robust metal-organic frameworks (MOFs) based on novel organic building blocks are fundamental aspects of reticular chemistry. Beyond simply fabricating new organic linkers, however, it is important to elucidate structure-property relationships at the molecular level to develop high-performing materials. In this work, we successfully targeted a highly porous and robust cage-type MOF (NU-200) with an nbo-derived fof topology through the deliberate assembly of a cyclohexane-functionalized iron(II)-clathrochelate-based meta-benzenedicarboxylate linker with a Cu2(CO2)4 secondary building unit (SBU). NU-200 exhibited an outstanding adsorption capacity of xenon and a high ideal adsorbed solution theory (IAST) predicted selectivity for a 20/80 v/v mixture of xenon (Xe)/krypton (Kr) at 298 K and 1.0 bar. Our extensive computational simulations with grand canonical Monte Carlo (GCMC) and density functional theory (DFT) on NU-200 indicated that the MOF's hierarchical bowl-shaped nanopockets surrounded by custom-designed cyclohexyl groups─instead of the conventionally believed open metal sites (OMSs)─played a crucial role in reinforcing Xe-binding affinity. The optimally sized pockets firmly trapped Xe through numerous supramolecular interactions including Xe···H, Xe···O, and Xe···π. Additionally, we validated the unique pocket confinement effect by experimentally and computationally employing the similarly sized probe, sulfur dioxide (SO2), which provided significant insights into the molecular underpinnings of the high uptake of SO2 (11.7 mmol g-1), especially at a low pressure of 0.1 bar (8.5 mmol g-1). This work therefore can facilitate the judicious design of organic building blocks, producing MOFs featuring tailor-made pockets to boost gas adsorption and separation performances.

Shetty S., Baig N., Hassan A., Al-Mousawi S., Das N., Alameddine B.

We report the synthesis of metalorganic copolymers made from the palladium catalyzed Sonogashira cross-coupling reaction between various iron(ii) clathrochelate building blocks with diethynyl-triptycene and fluorene derivatives. The target copolymers CCP1-5 were isolated in excellent yield and characterized by various instrumental analysis techniques. Interestingly, investigation of the copolymers' porosity properties discloses BET surface areas up to 337 m2 g-1 for the target compounds bearing fluorinated iron(ii) clathrochelate units CCP2,5. Moreover, the fluorinated copolymers display an outstanding uptake capacity of iodine with a maximum adsorption of 200 wt%. The target metalorganic copolymers CCP1-5 reveal very good adsorption of organic dyes, namely, methyl blue and methylene blue, from aqueous media.

Xue Y., Hang X., Ding J., Li B., Zhu R., Pang H., Xu Q.

• Utilizations of coordination cages themselves as catalysts are summarized. • Coordination cages encapsulating catalytic cofactors for catalysis are overviewed. • Challenges and prospects of coordination cages for catalysis are discussed. Coordination cages with well-defined cavities have attracted sustained attention for their applications in many fields, including host-guest chemistry, molecular recognition, and catalysis, due to their structural aesthetics and unique properties. This review covers the achievements in the catalytic application of these materials in specific chemical transformations. The developments in the utilizations of the coordination cages themselves as catalysts and their abilities to encapsulate catalytic cofactors for catalysis are summarized. In addition, the current challenges and great application potential of coordination cages in catalysis are discussed.

Selin R.O., Klemt I., Chernii V.Y., Losytskyy M.Y., Chernii S., Mular A., Gumienna-Kontecka E., Kovalska V.B., Voloshin Y.Z., Vologzhanina A.V., Dorovatovskii P.V., Mokhir A.

A fluorescein-tagged iron(ii) cage complex was obtained in a moderate total yield using a two-step synthetic procedure starting from its propargylamine-containing clathrochelate precursor. An 11-fold decrease in fluorescence quantum yield is observed in passing from the given fluorescein-based dye to its clathrochelate derivative. An excitation energy transfer from the terminal fluorescent group of the macrobicyclic molecule to its quasiaromatic highly π-conjugated clathrochelate framework can explain this effect. The kinetics of the hydrolysis of the acetyl groups of acetylated fluorescein azide and its clathrochelate derivative in the presence of one equivalent of BSA evidenced no strong supramolecular host-guest interactions between BSA and the tested compounds. Study of a chemical stability of the deacetylated iron(ii) clathrochelate suggested the formation of a supramolecular 1 : 1 BSA-clathrochelate assembly. Moreover, an addition of BSA or HSA to its solution caused the appearance of strong clathrochelate-based ICD outputs. The fluorescence emission anisotropy studies also evidenced the supramolecular binding of the fluorescein-tagged iron(ii) clathrochelate to the BSA macromolecule, leading to a high increase in this type of anisotropy. Subcellular uptake of the fluorescein-tagged molecules was visualized using fluorescence microscopy and showed its distribution to be mainly in the cytosol without entering the nucleus or accumulating in any other organelle. An X-rayed crystal of the above propargylamide macrobicyclic precursor with a reactive terminal C[triple bond, length as m-dash]C bond contains the clathrochelate molecules of two types, A and B. The encapsulated iron(ii) ion in these molecules is situated in the center of its FeN6-coordination polyhedron, the geometry of which is intermediate between a trigonal prism (TP) and a trigonal antiprism (TAP). The Fe-N distances vary from 1.8754(6) to 1.9286(4) Å and the heights h of their distorted TP-TAP polyhedra are very similar (2.30 and 2.31 Å); their values of φ are equal to 25.3 and 26.6°. In this crystal, the molecules of types A and B participate in different types of hydrogen bonding, giving H-bonded clathrochelate tetramers through their carboxylic and amide groups, respectively; these tetramers are connected to H-bonded chains.

Fu H., Zhou S., Fan X., Zhang L., Zhang J.

A hexameric [Ti 6 Co 12 ] ring has been assembled through Ti-capped cobalt(II) clathrochelates. In this work, titanium-capped cobalt clathrochelates have been applied as secondary building units (SBUs) for the construction of supramolecular rings. Two heterometallic wheel-like [Ti 6 Co 12 ] complexes based on cobalt clathrochelates, [C 6 H 15 N 4 ] 2 [TiCo 2 ( μ 2 -Oipr)(Oipr) 2 (Dmg) 3 ] 6 ( 2 , Dmg = dimethylglyoxime) and H 6 [TiCo 2 ( μ 2 -Oipr)(Oipr) 2 (Dmg) 3 ] 6 ( 3 ), have been successfully synthesized and characterized. The supramolecular stacking modes of these wheels are largely dependent on the applied synthetic conditions, which further impact their gas adsorption properties.

Sudan S., Li R., Jansze S.M., Platzek A., Rudolf R., Clever G.H., Fadaei-Tirani F., Scopelliti R., Severin K.

The design of structurally defined heteroleptic coordination cages is a challenging task, and only few examples are known to date. Here we describe a selection approach that allowed the identification of a novel hexanuclear Pd cage containing two types of dipyridyl ligands. A virtual combinatorial library of [PdnL2n](BF4)2n complexes was prepared by mixing six different dipyridyl ligands with substoichiometric amounts of [Pd(CH3CN)4](BF4)2. Analysis of the equilibrated reaction mixture revealed the preferential formation of a heteroleptic [Pd6L6L'6](BF4)12 assembly. The complex was prepared on a preparative scale by a targeted synthesis, and its structure was elucidated by single-crystal X-ray diffraction. It features an unprecedented trigonal-antiprismatic cage structure with two triangular Pd3L3 macrocycles bridged by six L' ligands. A related but significantly larger [Pd6L6L'6](BF4)12 cage was obtained by using metalloligands instead of organic dipyridyl ligands.

Kadu B.S.

For more than 30 years, palladium has been extensively employed in the Suzuki–Miyaura cross coupling reaction (SMCR) for the synthesis of C–C coupled products. However, Pd-based reactions are associated with higher cost of the synthetic protocols, tedious work-ups, product contamination and metal leaching. In view of this scenario, other metals such as Ni, Cu, Co, Fe, Rh and Ru have gathered the attention of researchers for their usage in SMCR with a wide range of electrophiles that could lead the synthesis of industrially important compounds with various functional groups. In this review, we have discussed the advancements (within the last 4 years) in catalysis related to SMCR that would be beneficial for researchers in designing synthetic protocols for the preparation of pharmacophores as well as drug molecules.

Lu Y., Liu D., Cui Z., Lin Y., Jin G.

Vologzhanina A.V., Ushakov I.E., Korlyukov A.A.

Imatinib, one of the most used therapeutic agents to treat leukemia, is an inhibitor that specifically blocks the activity of tyrosine kinases. The molecule of imatinib is flexible and contains several functional groups able to take part in H-bonding and hydrophobic interactions. Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. The role of various types of intermolecular interactions in stabilization of the particular molecular conformation was studied in terms of (i) the likelihood of H-bond formation, and (ii) their contribution to the Voronoi molecular surface. It is shown that experimentally observed hydrogen bonds are in accord with the likelihood of their formation. The number of H-bonds in ligand-receptor complexes surpasses that in imatinib salts due to the large number of donors and acceptors of H-bonding within the binding pocket of tyrosine kinases. Contribution of hydrophilic intermolecular interactions to the Voronoi molecular surface is similar for both conformations, while π...π stacking is more typical for the folded conformation of imatinib.

Korlyukov A.A., Vologzhanina A.V., Trzybinski D., Malinska M., Wozniak K.

A high-resolution single-crystal X-ray diffraction study of abiraterone acetate (1) has been carried out. The charge density distribution in the crystal of this anticancer drug is reconstructed from experimental data. The nature and the contributions of various intermolecular interactions to the total crystal energy are studied by means of the quantum theory `Atoms-in-Molecules', a non-covalent interactions method and energy framework plots. In general, dispersion C—H...H—C and C—H...π interactions play the main role in crystal packing of 1. The Voronoi tessellation analysis of 1 confirmed that contribution of hydrophobic and hydrophilic interactions to the molecular surface is close to their contribution to the total crystal energy. Similar analysis of abiraterone complexes with the cytochrome P450 family demonstrated that contribution of the C—H...H—C and C—H...π interactions to the molecular surface of the drug remains unchanged to fit the binding pocket, despite the presence of water and heme molecules, and hydrophilic groups within the pocket.

Kovalska V., Vakarov S., Chornenka N., Gumienna-Kontecka E., Voloshin Y.

CD testing of a supramolecular binding of three constitutional isomers (ortho-, meta-, and para-substituted) of an inherently CD-silent monomethinemonocarboxyphenylsulfide iron(II) clathrochelate to globular proteins (serum albumins BSA and HSA, lysozyme and β-lactoglobulin) was performed. This type of isomerism is found to strongly affect an induced CD-activity of these clathrochelates upon their binding to protein. To study an effect of the additional ribbed functionalization on protein’s sensing properties, the CD outputs of clathrochelate analogs with biorelevant morpholine group were studied. Such a functionalization is found to substantially affect the protein’s CD-sensing properties; this is explained by a formation of hydrogen bonds between this substituent and aminoacid residues of a protein binding site, thus affecting and altering an arrangement of the corresponding clathrochelate–protein assembly. Molecular docking calculations were performed for structural modeling of the BSA–clathrochelate assemblies and to estimate an energy of these supramolecular processes.

Planes O.M., Jansze S.M., Scopelliti R., Fadaei-Tirani F., Severin K.

Nanometer-sized polycarboxylate ligands are interesting building blocks for metallasupramolecular chemistry, but access to these compounds is often limited by complicated synthetic pathways. Here, we describe a simple two-step protocol, which allows preparing linear and bent dicarboxylate ligands with lengths of up to 3 nm from commercially available compounds. The ligands are prepared by iron-templated polycondensation reactions involving arylboronic acids and nioxime. The final products contain two iron clathrochelate complexes and two terminal carboxyphenylene groups. To demonstrate that the new ligands are suitable for the construction of more complex molecular nanostructures, we have prepared a Cu-based metal-organic polyhedron, which represents the largest M4L4 cage described so far.

Wang Y., Wu K., Pan M., Li K., Mo J., Duan X., He H., Shen J., Su C.

Cell membrane imaging by predesigned molecular and supramolecular photoluminescence probes is of great importance in understanding the nano-biointeractions for potential applications in cellular tracking, drug delivery, cancer diagnosis, and treatment. Herein, we report an effective strategy for cell membrane imaging in both living cell and tissue levels on the basis of a multifunctional nanocage (MOC-16) integrating one-/two-photon active phosphorescence, high charges, balanced hydrophobicity/lipophilicity, and proton sensitivity attributes. The intrinsic optical characters, including strong one-/two-photon excitation and pH-dependent red emission, make MOC-16 powerful optical probes for membrane imaging in living cell and tissue levels under both visible and near-infrared irradiations. Meanwhile, the highly positive charges of +28 endow MOC-16 with adequate water solubility and deprotonation ability while still maintaining its hydrophobicity, thus enabling balanced hydrophobic-lipophilic interactions at the nano-biointerface to facilitate a pH-dependent membrane absorption within the biological pH range of 5.3-7.4. However, the low-charged RuL3 metalloligand or polyethylene glycol (PEG)-modified MOC-16PEG with less hydrophobicity cannot offer enough nano-biointeractions for cell membrane tracking. These findings advance the fundamental understanding of nano-biointerface interactions of MOCs with cell membranes and provide further guidance in their biological applications.

Balatskiy D.V., Chuprin A.S., Dudkin S.V., Desdín García L.F., Corcho-Valdés A.L., Antuch M., Buznik V.M., Bratskaya S., Voloshin Y.Z.

Combined experimental 57Fe Mössbauer and theoretical DFT study of iron(ii) (pseudo)clathrochelates was performed. Molecular design of (pseudo)encapsulating ligands allows us to control their spin state and redox characteristics.

Chuprin A.S., Pavlov A.A., Vologzhanina A.V., Dorovatovskii P., Makarenkov A.V., Ol'shevskaya V.A., Dudkin S.V., Voloshin Y.Z.

A multistep general synthetic strategy towards the polytopic carboranyl-containing (semi)clathrochelate metal complexes, based on the template synthesis, transmetallation, amide condensation and 1,3-dipolar cycloaddition reactions, is developed. Their mono(semi)clathrochelate precursors with...

Limarev I.P., Zelinskii G.E., Mosov D.O., Vologzhanina A.V., Dorovatovskii P.V., Lazarenko V.A., Lebed E.G., Voloshin Y.Z.

Multistep synthetic pathway towards a series of the anisoleboron-capped ribbed-functionalized iron(II) cage complexes was developed. Their hexachloroclathrochelate precursor was obtained by the template condensation of three dichloroglyoximate chelating ligand synthons with two molecules of 4-methoxyphenylboronic acid as a Lewis-acidic cross-linking agent on the iron(II) ion as a matrix. It easily underwent a stepwise nucleophilic substitution with S2- and O2-dinucleophilic aliphatic (ethanedithiolate) or aromatic (pyrocatecholate) agents, forming the stable X2 (X = S or O)-six-membered ribbed substituent(s) at a quasiaromatic cage framework. Performing these reactions under the different reaction conditions (i.e., at various hexachloroclathrochelate-to-nucleophile molar ratios, a wide range of temperatures and a series of the solvents) allowed to control a predominant formation of its mono-, di- or triribbed-substituted macrobicyclic derivatives. Thus obtained iron(II) di- and tetrachloroclathrochelates can undergo their post-synthetic transformations with active nucleophilic agents. The latter complexes underwent a further nucleophilic substitution with the anionic derivative of n-butanthiol, thus giving the hexasulfide macrobicyclic compound with two functionalizing n-alkyl substituents in one of its three chelate α-dioximate fragments and two apical biorelevant anisole substituents. The obtained iron(II) clathrochelates, possessing a low-spin electronic d6 configuration, were characterized using elemental analysis, MALDI-TOF mass spectrometry, UV–Vis, 1H and 13C{1H} NMR spectroscopies, and by the single-crystal X-ray diffraction experiments for the hexachloroclathrochelate precursor, its dichlorotetrasulfide macrobicyclic derivative and the monoribbed-functionalized hexasulfide cage complex. In all their molecules, the encapsulated iron(II) ion is situated in the centre of its FeN6-coordination polyhedron, the geometry of which is intermediate between a trigonal prism and a trigonal antiprism with the distortion angles φ from 21.4 to 23.4°. Halogen bonding between the polyhalogenoclathrochelate molecules in their crystals is observed.