Chalcogen Bonds Research Articles

Chalcogen and Hydrogen Bond Team up in Driving Anion⋅⋅⋅Anion Self-Assembly.

H-selenite anions (HSeO3 - ) form in the solid unprecedented anionic supramolecular chains wherein single units are assembled via alternating short Se⋅⋅⋅O and H⋅⋅⋅O contacts. Crystallographic analyses and computational studies (the quantum theory of "atoms-in-molecules", QTAIM, and the noncovalent interaction plot, NCIPlot) consistently prove the attractive nature of these chalcogen bonds (ChBs) and hydrogen honds (HBs), the Janus-type character of HSeO3 - anions which act as both donors and acceptors of ChB and HB, and the possible stability of anion dimers in solution. The effectiveness of the ChBs herein described may lead to consider the HSeO3 - moiety as a new entry in the toolbox of crystal engineering based on ChB.

Cooperative Bifurcated Chalcogen Bonding and Hydrogen Bonding as Stereocontrolling Elements for Selective Strain-Release Septanosylation.

The exploitation of noncovalent interactions (NCIs) is emerging as a vital handle in tackling broad stereoselectivity challenges in synthesis. In particular, there has been significant recent interest in the harnessing of unconventional NCIs to surmount difficult selectivity challenges in glycosylations. Herein, we disclose the exploitation of an unconventional bifurcated chalcogen bonding and hydrogen bonding (HB) network, which paves the way for a robust catalytic strategy into biologically useful seven-membered ring sugars. Through 13C nuclear magnetic resonance (NMR) in situ monitoring, NMR titration experiments, and density functional theory (DFT) modeling, we propose a remarkable contemporaneous activation of multiple functional groups consisting of a bifurcated chalcogen bonding mechanism working hand-in-hand with HB activation. Significantly, the ester moiety installed on the glycosyl donor is critical in the establishment of the postulated ternary complex for stereocontrol. Through the 13C kinetic isotopic effect and kinetic studies, our data corroborated that a dissociative SNi-type mechanism forms the stereocontrolling basis for the excellent α-selectivity.

Interplay of Hydrogen, Pnicogen, and Chalcogen Bonding in X(H2O)n=1-5 (X = NO, NO+, and NO-) Complexes: Energetics Insights via a Molecular Tailoring Approach.

Nitric oxide (NO) and its redox congeners (NO+ and NO-), designated as X, play vital roles in various atmospheric and biological events. Understanding the interaction between X and water is inevitable to explain the different reactions that occur during these events. The present study is a unified attempt to explore the noncovalent interactions in microhydrated networks of X using the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level of theory. The interactions between X and water have been probed by the molecular electrostatic potential (MESP) by exploiting the features of the most positive (Vmax) and most negative potential (Vmin) sites. The individual energy and cooperativity contributions of various types of noncovalent interactions present in X(H2O)n=1-5 complexes are estimated with the help of a molecular tailoring-based approach (MTA-based). The MTA-based analysis reveals that among various possible interactions in NO(H2O)n complexes, the water···water hydrogen bonds (HBs) are the strongest. Neutral NO can form hydrogen and pnicogen bonds (PBs) with water depending on the orientation; however, such HBs and PBs are the weakest. On the other hand, in the NO+(H2O)n complexes, the NO+···water interactions that occur through PBs are the strongest; the next one is the chalcogen bonding (CB), and the water···water HBs are the weakest. In the case of the NO-(H2O)n complexes, the HB interactions via both N and O atoms of NO- and water molecules are the strongest ones. The strength of water···water HB interactions is also seen to increase with the increase in the number of water molecules in NO-(H2O)n. The present study exemplifies the applicability of MTA-based calculations for quantifying various types of individual noncovalent interactions and their interplay in microhydrated networks of NO and its related ions.

2,1,3-Benzoselenadiazole-containing zinc(II) halide complexes: Chalcogen bonding in the solid state and catalytic activity in the Schiff condensation

XRD study of crystals of zinc(II) halide complexes featuring 2,1,3-benzoselenadiazole (L) ligands [ZnL2X2] (X = Cl, Br, I) indicated availability of intramolecular chalcogen bonds between the Se atom and the halide ligands, which affect a rotation barrier around the Zn–N bonds and thus control a geometry of these species. In the solid state, the Se atom additionally forms intermolecular chalcogen bonds with the N atom of the 2,1,3-benzoselenadiazole ligands, which results in formation of infinite 1D chains. Theoretical calculations and experimental kinetic study indicated that although the Se atom serves as a Lewis acid, coordination of the organic ligand to the zinc(II) center does not provide enhanced catalytic activity of the latter in the model reaction of the Schiff condensation.

An Unusual Macrocyclic Hexamer of an Iso-Tellurazole N-Oxide Featuring CTe… O Chalcogen Bonds is Formed by κ6 -O Complexation to Fe(II) and Ni(II).

Studies of the supramolecular chemistry of iso-tellurazole N-oxides have been confined to non-polar media until now. To overcome that limitation, an iso-tellurazole N-oxide was derivatized with a primary alcohol group; the compound is soluble in polar solvents and stable in acidic to neutral aqueous media. Nickel (II) and iron (II) form macrocyclic complexes with six molecules of that iso-tellurazole N-oxide in a hitherto not-observed macrocyclic arrangement defined by CTe⋅⋅⋅O chalcogen bonds and κ6 -O bound to the metal ion. This behaviour is in sharp contrast with the κn -Te (n=1,2,4) complexes formed by soft metal ions.

Chalcogen bond stabilisation of platinum(II) sulfonyl-substituted thiourea complexes with ancillary phosphine ligands

A series of sulfonyl-substituted thiourea platinum(II) complexes bearing ancillary phosphine ligands were prepared by the reaction between cis-[PtCl2(PR3)2] (PR3 = triphenylphosphine, tris(2-cyanoethyl)phosphine and 1,3,5-triaza-7-phosphaadamantane) and either p-TolSO2NHC(S)NHPh or EtSO2NHC(S)NHPh, in a refluxing Et3N/methanol mixture. The mixed ligand complexes, bearing a single phosphine and pyridine, were also prepared by the reactions between cis-[PtCl2(COD)] (COD = cyclooctadiene), pyridine and p-TolSO2NHC(S)NHPh or EtSO2NHC(S)NHPh. For each complex, the thiourea ligand binds as a dianion through the S and NPh groups in the distal isomer with a remote NSO2R group. Only in the case of the reaction between the complex cis-[PtCl2(PPh3)2] and TolSO2NHC(S)NHCH(CH3)3) was the proximal isomer formed on account of the bulky t-butyl substituent on the thiourea. X-ray structures and computational analysis revealed another reason for this preferential distal isomer formation is most likely due to the presence of a stabilising chalcogen bond, which is otherwise unavailable in the proximal isomer.

Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te).

In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported in the literature. Herein, the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes formed between XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) were systematically studied by using quantum chemical computations. The model complexes are stabilized via one primary X∙∙∙Y chalcogen bond (ChB) and the secondary C-H∙∙∙O hydrogen bonds. The binding energies of the studied complexes are in the range of -21.6~-60.4 kJ/mol. The X∙∙∙Y distances are significantly smaller than the sum of the van der Waals radii of the corresponding two atoms. The X∙∙∙Y ChBs in all the studied complexes except for the SO2∙∙∙CH3OCH3 complex are strong in strength and display a partial covalent character revealed by conducting the quantum theory of atoms in molecules (QTAIM), a non-covalent interaction plot (NCIplot), and natural bond orbital (NBO) analyses. The symmetry-adapted perturbation theory (SAPT) analysis discloses that the X∙∙∙Y ChBs are primarily dominated by the electrostatic component.

Transition between the Noncovalency and Covalency of σ-Hole Bonds.

The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.

One-pot synthesis, structural study, in silico and in vitro anticancer evaluation of spiropyrrolidine oxindoles obtained by the 3-CR of isatin, benzyl amine and a thiazolo[3,2-a]indole derivative

Stereoselective green synthesis of spiropyrrolidine oxindoles, in excellent yields, by the three-component reaction of isatins, benzyl amines and a thiazolo[3,2-a]indole derivative is reported here. In silico molecular docking studies of selected compounds in order to evaluate the MDM2 inhibition potential suggested that compound 4s was the best fit and further in vitro evaluation proved that 4s exhibited cell viability less than 80% with an effective dose of 25 µg/mL. Analysis of the single crystals of four derivatives showed that the S∙∙∙O chalcogen bond was a common feature which might be the reason for conformational locking and influence in the molecule's binding affinities to the biological target. QTAIM analysis revealed that two different modes of S∙∙∙O chalcogen bonds were present and Localized-Orbital Locator (LOL) plots suggested that the lone pairs on oxygen are oriented towards the sulphur atom supporting the S∙∙∙O interaction as a chalcogen bond of n→σ* type.

An Experimental and Theoretical Insight into I2 /Br2 Oxidation of Bis(pyridin-2-yl)Diselane and Ditellane.

The reactivity between bis(pyridin-2-yl)diselane o Py2 Se2 and ditellane o Py2 Te2 (L1 and L2, respectively; o Py=pyridyn-2-yl) and I2 /Br2 is discussed. Single-crystal structure analysis revealed that the reaction of L1 with I2 yielded [(HL1+ )(I- )⋅5/2I2 ]∞ (1) in which monoprotonated cations HL1+ template a self-assembled infinite pseudo-cubic polyiodide 3D-network, while the reaction with Br2 yielded the dibromide Ho PySeII Br2 (2). The oxidation of L2 with I2 and Br2 yielded the compounds Ho PyTeII I2 (3) and Ho PyTeIV Br4 (6), respectively, whose structures were elucidated by X-ray diffraction analysis. FT-Raman spectroscopy measurements are consistent with a 3c-4e description of all the X-Ch-X three-body systems (Ch=Se, Te; X=Br, I) in compounds 2, 3, Ho PyTeII Br2 (5), and 6. The structural and spectroscopic observations are supported by extensive theoretical calculations carried out at the DFT level that were employed to study the electronic structure of the investigated compounds, the thermodynamic aspects of their formation, and the role of noncovalent σ-hole halogen and chalcogen bonds in the X⋅⋅⋅X, X⋅⋅⋅Ch and Ch⋅⋅⋅Ch interactions evidenced structurally.

Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families

The Orange Carotenoid Protein (OCP) is a unique photoreceptor crucial for cyanobacterial photoprotection. Best studied Synechocystis sp. PCC 6803 OCP belongs to the large OCP1 family. Downregulated by the Fluorescence Recovery Protein (FRP) in low-light, high-light-activated OCP1 binds to the phycobilisomes and performs non-photochemical quenching. Recently discovered families OCP2 and OCP3 remain structurally and functionally underexplored, and no systematic comparative studies have ever been conducted. Here we present two first crystal structures of OCP2 from morphoecophysiologically different cyanobacteria and provide their comprehensive structural, spectroscopic and functional comparison with OCP1, the recently described OCP3 and all-OCP ancestor. Structures enable correlation of spectroscopic signatures with the effective number of hydrogen and discovered here chalcogen bonds anchoring the ketocarotenoid in OCP, as well as with the rotation of the echinenone's β-ionone ring in the CTD. Structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions. These data are expected to foster OCP research and applications in optogenetics, targeted carotenoid delivery and cyanobacterial biomass engineering.

Chalcogen Bond Catalysis with Telluronium Cations for Bromination Reaction: Importance of Electrostatic and Polarization Effects.

Recently, chalcogen bond catalysts with telluronium cations have garnered considerable attention in organic reactions. In this work, chalcogen bond catalysis on the bromination reaction of anisole with N-bromosuccinimide (NBS) with the telluronium cationic catalysts has been explored with density functional theory (DFT). The catalytic reaction is divided into two stages: the bromine transfer step and the proton transfer step. Based on the computational results, one can find the rate-determining step is the bromine transfer step. Moreover, the present study elucidates that a stronger chalcogen bond between catalysts and NBS will give better catalytic performance. Additionally, this work also clarified the importance of the electrostatic and polarization effects in the chalcogen bond between the oxygen atom of NBS and the Te atom of the catalyst in this bromination reaction. The electrostatic and polarization effects are significantly influenced by the electron-withdrawing ability of the substitution groups on the catalysts. Moreover, the structure-property relationship between the strength of chalcogen bond, electrostatic effect, polarization effect and catalytic performance are established for the design of more efficient chalcogen bond catalysts.

Chalcogen Bonding Catalysis: Tellurium, the Last Frontier?

: Chalcogen bonding (ChB) is the non-covalent interaction occurring between chalcogen atoms as Lewis acid sites and atoms or groups of atoms able to behave as Lewis bases through their lone pair or p electrons. Analogously to its sister halogen bonding, the high directionality of this interaction was implemented for the precise structural organization in the solid state and in solution. Regarding catalysis, ChB is now accepted as a new mode of activation as demonstrated by the increased number of examples in the last five years. In the family of ChB catalysts, those based on tellurium rapidly appeared to overcome their lighter sulfur and selenium counterparts. In this review, we highlight the Lewis acid properties of tellurium-based derivatives in solution and summarize the start-of-the-art of their applications in catalysis.

Dimeric cation-cation aggregates stabilized by 2Ch-2N chalcogen bonds: Crystallographic and theoretical evidences

2Ch-2N chalcogen bonds (ChBs) between a pair of homocations were characterized via crystal structure database analysis and quantum chemical computations. We first collected several crystal structures consisting of such interactions from the Cambridge Structural Database (CSD). Then, based on the CSD survey results, a series of model homodimers of organic chalcogenated cations were selected to theoretically study inter-cation 2Ch-2N ChBs for the first time. The dicationic complexes under investigation are unfavorable but metastable in gas phase. Immersion of these systems in solvents leads to a remarkable increase in dimer stability and produces stable ChB complexes. 2Ch-2N interactions in gas phase generally exhibit a positive electrostatic component, while the orbital and dispersion terms play a stabilizing role. When immersed in the solvent medium, the electrostatic interaction becomes more favorable, and the solvent energy contributes significantly to the stability of the complexes, resulting in attractive cation-cation ChBs.

Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding.

The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.

The Ambiguous Origin of Thermochromism in Molecular Crystals of Dichalcogenides: Chalcogen Bonds versus Dynamic Se─Se/Te─Te Bonds.

We report thermochromism in crystals of diphenyl diselenide (dpdSe) and diphenyl ditelluride (dpdTe), which is at variance with the commonly known mechanisms of thermochromism in molecular crystals. Variable temperature neutron diffraction studies indicated no conformational change, tautomerization or phase transition between 100 K and 295 K. High-pressure crystallography studies indicated no associated piezochromism in dpdSe and dpdTe crystals. The evolution of the crystal structures and their electronic band structure with pressure and temperature reveal the contributions of intramolecular and intermolecular factors towards the origin of thermochromism - especially the intermolecular Se⋅⋅⋅Se and Te⋅⋅⋅Te chalcogen bonds and torsional modes of vibrations around the dynamic Se─Se and Te─Te bonds. Further, a co-crystal of dpdSe with iodine (dpdSe-I2) and an alloy crystal of dpdSe and dpdTe implied a predominantly intramolecular origin of the observed thermochromism associated with vibronic coupling.

The Ambiguous Origin of Thermochromism in Molecular Crystals of Dichalcogenides: Chalcogen Bonds versus Dynamic Se−Se/Te−Te Bonds

AbstractWe report thermochromism in crystals of diphenyl diselenide (dpdSe) and diphenyl ditelluride (dpdTe), which is at variance with the commonly known mechanisms of thermochromism in molecular crystals. Variable temperature neutron diffraction studies indicated no conformational change, tautomerization or phase transition between 100 K and 295 K. High‐pressure crystallography studies indicated no associated piezochromism in dpdSe and dpdTe crystals. The evolution of the crystal structures and their electronic band structure with pressure and temperature reveal the contributions of intramolecular and intermolecular factors towards the origin of thermochromism—especially the intermolecular Se⋅⋅⋅Se and Te⋅⋅⋅Te chalcogen bonds and torsional modes of vibrations around the dynamic Se−Se and Te−Te bonds. Further, a co‐crystal of dpdSe with iodine (dpdSe‐I2) and an alloy crystal of dpdSe and dpdTe implied a predominantly intramolecular origin of the observed thermochromism associated with vibronic coupling.

Chalcogenopheno[3,2-b]pyrrole-Containing Donor-Acceptor-Donor Organic Semiconducting Small Molecules for Organic Field-Effect Transistors.

A group of chalcogenopheno[3,2-b]pyrroles, including thieno[3,2-b]pyrrole (TP), furo[3,2-b]pyrrole (FP), and selenopheno[3,2-b]pyrrole (SeP), and thieno[3,2-b]thiophene (TT) electron-donating units were coupled with a thiophene-flanked diketopyrrolo[3,4-c]pyrrole (ThDPP) acceptor to generate four donor-acceptor-donor (D-A-D) semiconducting small molecules (ThDPP-TT, ThDPP-FP, ThDPP-TP, and ThDPP-SeP). This study systematically investigated the differences between chalcogenopheno[3,2-b]pyrroles and TT. From the characterizations, chalcogenopheno[3,2-b]pyrrole-containing molecules showed lower band gaps and binding-energy cold crystallization behavior. The enthalpies of cold crystallization were correlated with the weight of the chalcogen in ThDPP-FP, ThDPP-TP, and ThDPP-SeP, which were evaluated as intermolecular chalcogen-bond interactions between chalcogen and pyrrole nitrogen in chalcogenopheno[3,2-b]pyrroles. A stronger chalcogen bond interaction resulted in stronger self-aggregation in thin films with thermal treatment, which resulted in a polycrystalline structure in chalcogenopheno[3,2-b]pyrrole-containing molecules. For the application in an organic field-effect transistor, all four molecules showed good performance with the highest hole mobilities as 6.33 × 10-3 cm2 V-1 s-1 for ThDPP-TT, 2.08 × 10-2 cm2 V-1 s-1 for ThDPP-FP, 1.87 × 10-2 cm2 V-1 s-1 for ThDPP-TP, and 6.32 × 10-3 cm2 V-1 s-1 for ThDPP-SeP, and the change of mobility is well correlated to the root-mean-square roughness of the thin films. Overall, all the chalcogenopheno[3,2-b]pyrrole-containing molecules showed lower band gaps, polymorphism, and better charge transport properties compared to TT-containing molecules, which motivates replacing TT with chalcogenopheno[3,2-b]pyrroles in conjugated polymers, non-fullerene small molecular acceptors, and narrow-band-gap donors.

The Unique Ambiphilicity of Tellurium in the [MesitylTe(I)(I2)(I3)]− Anion

AbstractA first example of an aryltellurium(II) compound with three different bonding modes to iodine featuring covalent and non‐covalent bonds such as two orthogonal, ambiphilic σ‐hole interactions is introduced: [MesTe(I)(I2)(I3)]−. It is a member of a series of mesityltellurenyl anions, which are formed during reactions of (MesTe)2 with ZnI2, phenanthroline (phen) and iodine. [Zn(phen)3][MesTe(I)2] (1), [Zn(phen)3][{MesTe(I)‐(I)…Te(I)Mes}{MesTeI2}] (2) and [Zn(phen)3][MesTe(I)(I2)(I3)][MesTeI2] (3) are isolated depending on the amount of iodine used. The products contain tellurium atoms bonded to a variety of iodine species (I−, μ2‐I−, I2 and I3−) and are, thus, perfectly suitable to explore the amphiphilic behavior of tellurium(II) and its relevance for the formation of non‐covalent bonds, where tellurium acts as both donor and acceptor simultaneously. The character of chalcogen and halogen bonds are evaluated by the combination of crystallographic data and computational methods.

Chalcogen Bonding in the Decoration of the Secondary Coordination Sphere of Copper(II) Complexes: Activation of Nitriles, the Auxiliary Ligand Substituent Effect

Chalcogen Bonding in the Decoration of the Secondary Coordination Sphere of Copper(II) Complexes: Activation of Nitriles, the Auxiliary Ligand Substituent Effect