Chalcogen Bonds Research Articles

A Direct Route to closo‐SB n Cl n Thiaboranes from Simple Electron‐Precise Synthons: The Different Role of Chalcogen Bonding in SB5Cl5 and SB11Cl11 Crystals

Six‐vertex closo‐SB5Cl5 (1) and ten‐vertex closo‐1‐SB9Cl9 (2) thiaboranes have been prepared, besides the already known 12‐vertex closo‐SB11Cl11 (3), from the co‐pyrolysis reaction of B2Cl4 with S2Cl2 at 280 ºC in vacuo. The compounds are sublimable, off‐white solids. Their elemental composition has been determined by high‐resolution mass spectrometry. They were further characterized by one‐ and two‐dimensional 11B‐spectroscopy and X‐ray structure determination for 1 and 3. Ab initio/GIAO/NMR computations support octahedral, bicapped square‐antiprismatic, and icosahedral geometries for 1, 2 and 3, respectively, as expected based on their closo‐electron counts. 1 is the first isolated example of a neutral polyhedral closo‐thiaborane with a cluster size smaller than ten vertices. The solid‐state structure of 3 is one of the rare examples of a single‐crystal X‐ray structure determination of an icosahedral heteroborane reported. The corresponding crystal‐packing forces show the different role of chalcogen bonding in these octahedral and icosahedral crystals. In addition, there is a mass‐spectroscopy evidence for the recurrent formation of further thiaborane homologs of closo‐SBnCln with n = 4, 6, 10, and supra‐icosahedral 12.

Intermolecular interactions between metallylenes and carbonyl chalcogenides: Chalcogen bond and tetrel bond

The intermolecular interactions between the singlet metallylenes XH2 (X = Si, Ge, Sn, Pb) and carbonyl chalcogenides OCY (Y = S, Se, Te) have been studied by the high-level quantum chemical calculations. The chalcogen-bonded and tetrel-bonded complexes can be formed between XH2 and OCY due to their ambiphilic character. The structure and binding strength of the complexes have been explored on the basis of the MEP surfaces of the monomers, and geometrical parameters and interaction energies of the complexes. The nature of the complexes has been investigated by the NBO, AIM and SAPT analysis. The tetrel-bonded complexes exhibit a much stronger binding strength with larger interaction energies and shorter binding distances compared to the chalcogen-bonded complexes. The interaction energies of the complexes become larger with the increase of the Y atomic number, but become smaller with the increase of the X atomic number. NBO analysis reveals that the dominant orbital interactions in the chalcogen-bonded and tetrel-bonded complexes are LP(X) → σ*(C-Y) and LP(Y) → LP*(X), respectively. AIM analysis suggests that the chalcogen-bonded complexes are the purely noncovalent, but the tetrel-bonded complexes have partial covalent character. SAPT analysis indicates that the contribution of the energy component decreases in the order of Eele > Edisp > Eind for most chalcogen-bonded complexes, and this order is Eele > Eind > Edisp for most tetrel-bonded complexes.

Stereoselective Entry into α,α’‐C‐Oxepane Scaffolds through a Chalcogen Bonding Catalyzed Strain‐Release C‐Septanosylation Strategy

AbstractThe utility of unconventional noncovalent interactions (NCIs) such as chalcogen bonding has lately emerged as a robust platform to access synthetically difficult glycosides stereoselectively. Herein, we disclose the versatility of a phosphonochalcogenide (PCH) catalyst to facilitate access into the challenging, but biologically interesting 7‐membered ring α,α’‐C‐disubstituted oxepane core through an α‐selective strain‐release C‐glycosylation. Methodically, this strategy represents a switch from more common but entropically less desired macrocyclizations to a thermodynamically favored ring‐expansion approach. In light of the general lack of stereoselective methods to access C‐septanosides, a remarkable palette of silyl‐based nucleophiles can be reliably employed in our method. This include a broad variety of useful synthons, such as easily available silyl‐allyl, silyl‐enol ether, silyl‐ketene acetal, vinylogous silyl‐ketene acetal, silyl‐alkyne and silylazide reagents. Mechanistic investigations suggest that a mechanistic shift towards an intramolecular aglycone transposition involving a pentacoordinate silicon intermediate is likely responsible in steering the stereoselectivity.

Stereoselective Entry into α,α'-C-Oxepane Scaffolds through a Chalcogen Bonding Catalyzed Strain-Release C-Septanosylation Strategy.

The utility of unconventional noncovalent interactions (NCIs) such as chalcogen bonding has lately emerged as a robust platform to access synthetically difficult glycosides stereoselectively. Herein, we disclose the versatility of a phosphonochalcogenide (PCH) catalyst to facilitate access into the challenging, but biologically interesting 7-membered ring α,α'-C-disubstituted oxepane core through an α-selective strain-release C-glycosylation. Methodically, this strategy represents a switch from more common but entropically less desired macrocyclizations to a thermodynamically favored ring-expansion approach. In light of the general lack of stereoselective methods to access C-septanosides, a remarkable palette of silyl-based nucleophiles can be reliably employed in our method. This include a broad variety of useful synthons, such as easily available silyl-allyl, silyl-enol ether, silyl-ketene acetal, vinylogous silyl-ketene acetal, silyl-alkyne and silylazide reagents. Mechanistic investigations suggest that a mechanistic shift towards an intramolecular aglycone transposition involving a pentacoordinate silicon intermediate is likely responsible in steering the stereoselectivity.

Chalcogen-Bond-Assisted Formation of the N→C Dative Bonds in the Complexes between Chalcogenadiazoles/Chalcogenatriazoles and Fullerene C60.

The existence of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative bonds in the complexes formed by fullerene C60 with 1,2,5-chalcogenadiazoles, 2,1,3-benzochalcogenadiazoles, and 1,2,4,5-chalcogenatriazoles, respectively. It was found that the N→C dative bonds are formed along with the formation of the N-Ch···C (Ch = S, Se, Te) chalcogen bonds. In the gas phase, from S-containing complexes through Se-containing complexes to Te-containing complexes, the intrinsic interaction energies become more and more negative, which indicates that the N-Ch···C chalcogen bonds can facilitate the formation of the N→C dative bonds. The intrinsic interaction energies are compensated by the large deformation energy of fullerene C60. The total interaction energies of Te-containing complexes are negative, while both total interaction energies of the S-containing complexes and Se-containing complexes are positive. This means that the N→C dative bonds in the Te-containing complexes are more easily observed in experiments in comparison with those in the S-containing complexes and Se-containing complexes. This study provides a new theoretical perspective on the experimental observation of the N→C dative bonds in complexes involving fullerenes. Further, the formation of stable N→C dative bonds in the complexes involving fullerenes can significantly change the properties of fullerenes, which will greatly simulate and expand the application range of fullerenes.

On-Surface Molecular Recognition Driven by Chalcogen Bonding

On-Surface Molecular Recognition Driven by Chalcogen Bonding

Platinum(II) phosphoryl-substituted thiourea complexes with bis-phosphine ligands and some triphenylarsine and triphenylstibine analogues

Reactions between the phosphorylthiourea ligands (EtO)2PONHC(S)NHPh (L1), (EtO)2PONHC(S)NHCH(CH3)3) (L2) and (EtO)2PONHC(S)NHCH2CH3 (L3) and cis-[PtCl2(PPh3)2] gave complexes in which the ligands bind to the platinum(II) centre as dianionic ligands. For ligands L1 and L3, the ligand binds through the thiourea sulfur and the N-alkyl nitrogen atoms, giving the distal isomer. In contrast, the ligand L2, on account of the bulky t-butyl substituent on the ligand, coordinates via the sulfur and N-phosphoryl nitrogen atoms, giving the proximal isomer. The identities of the isomers were confirmed by single crystal X-ray analysis and 31P{1H} NMR spectroscopy. The latter showing that the appearance or absence of 3J(PP) couplings between the ligand and ancillary ligands provides indicative isomeric information. Further reactions between the ligand L1 and a series of bis-phosphine, triphenylarsine and triphenylstibine platinum(II) starting complexes gave the corresponding products also as the distal linkage isomer. Computational analysis reveals a possible chalcogen bond non-covalent interaction that may be responsible for the preference for the distal isomer.

Benzoselenadiazole-Functionalized H-Bonded Arylamide Foldamers: Solvent-Responsive Properties and Helix Self-Assembly Directed by Chalcogen Bonding in Solid State.

In this study, a series of H-bonded arylamide foldamers bearing benzoselenadiazole ends with solvent-responsive properties have been synthesized. In dichloromethane or dimethyl sulfoxide solvents, the molecules exhibit meniscus or linear structures, respectively, which can be attributed to the unique intramolecular hydrogen bonding behavior evidenced by 1D 1H NMR and 2D NOESY spectra. UV-vis spectroscopy experiments show that the absorption wavelength of H-bonded arylamide foldamers are significantly red-shifted due to the presence of benzoselenadiazole group. In addition, the crystal structures reveal that effective intermolecular dual Se ⋅ ⋅ ⋅ N interactions between benzoselenadiazole groups induce further assembly of the monomers. Remarkably, supramolecular linear and double helices structures are constructed under the synergistic induction of intramolecular hydrogen bonding and intermolecular chalcogen bonding. Additionally, 2D DOSY diffusion spectra and theoretical modelling based on density functional theory (DFT) are performed to explore the persistence of intermolecular Se ⋅ ⋅ ⋅ N interactions beyond the crystalline state.

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations.

Among various non-covalent interactions, selenium-centered chalcogen bonds (SeChBs) have garnered considerable attention in recent years as a result of their important contributions to crystal engineering, organocatalysis, molecular recognition, materials science, and biological systems. Herein, we systematically investigated π-hole-type Se∙∙∙O/S ChBs in the binary complexes of SeO2 with a series of O-/S-containing Lewis bases by means of high-level ab initio computations. The results demonstrate that there exists an attractive interaction between the Se atom of SeO2 and the O/S atom of Lewis bases. The interaction energies computed at the MP2/aug-cc-pVTZ level range from -4.68 kcal/mol to -10.83 kcal/mol for the Se∙∙∙O chalcogen-bonded complexes and vary between -3.53 kcal/mol and -13.77 kcal/mol for the Se∙∙∙S chalcogen-bonded complexes. The Se∙∙∙O/S ChBs exhibit a relatively short binding distance in comparison to the sum of the van der Waals radii of two chalcogen atoms. The Se∙∙∙O/S ChBs in all of the studied complexes show significant strength and a closed-shell nature, with a partially covalent character in most cases. Furthermore, the strength of these Se∙∙∙O/S ChBs generally surpasses that of the C/O-H∙∙∙O hydrogen bonds within the same complex. It should be noted that additional C/O-H∙∙∙O interactions have a large effect on the geometric structures and strength of Se∙∙∙O/S ChBs. Two subunits are connected together mainly via the orbital interaction between the lone pair of O/S atoms in the Lewis bases and the BD*(OSe) anti-bonding orbital of SeO2, except for the SeO2∙∙∙HCSOH complex. The electrostatic component emerges as the largest attractive contributor for stabilizing the examined complexes, with significant contributions from induction and dispersion components as well.

Synthesis, characterization, and biological activity of cationic ruthenium-arene complexes with sulfur ligands.

Five cationic ruthenium-arene complexes with the generic formula [Ru(SAc)(S2C·NHC)(p-cymene)](PF6) (5a-e) were prepared in almost quantitative yields using a straightforward one-pot, two-step experimental procedure starting from [RuCl2(p-cymene)]2, an imidazol(in)ium-2-dithiocarboxylate (NHC·CS2) zwitterion, KSAc, and KPF6. These half-sandwich compounds were fully characterized by various analytical techniques and the molecular structures of two of them were solved by X-ray diffraction analysis, which revealed the existence of an intramolecular chalcogen bond between the oxygen atom of the thioacetate ligand and a proximal sulfur atom of the dithiocarboxylate unit. DFT calculations showed that the C=S…O charge transfer amounted to 2.4kcalmol-1. The dissolution of [Ru(SAc)(S2C·IMes)(p-cymene)](PF6) (5a) in moist DMSO-d6 at room temperature did not cause the dissociation of its sulfur ligands. Instead, p-cymene was slowly released to afford the 12-electron [Ru(SAc)(S2C·IMes)]+ cation that could be detected by mass spectrometry. Monitoring the solvolysis process by 1H NMR spectroscopy showed that more than 22days were needed to fully decompose the starting ruthenium-arene complex. Compounds 5a-e exhibited a high antiproliferative activity against human glioma Hs683 and human lung carcinoma A549 cancer cells. In particular, the IMes derivative (5a) was the most potent compound of the series, achieving toxicities similar to those displayed by marketed platinum drugs.

Intermolecular Chalcogen Bonding between Galectin-3 and an Orally Bioavailable Antagonist

Intermolecular Chalcogen Bonding between Galectin-3 and an Orally Bioavailable Antagonist

Expanding chalcogen bonds in thiophenes to interactions with halogens.

Compounds containing the thiophene moiety find several applications in physics and chemistry, such as electrical conduction, which depends on specific conformations to properly exhibiting the desired properties. In turn, chalcogen bonding has found to modulate the conformation of some N-thiophen-2-ylfomamides. Since halogens participate in a kin interaction (halogen bonding) and are abundant in agrochemicals, pharmaceuticals, and materials, we have quantum-chemically explored the interaction between organic halogen and thiophene as a conformational modulator in some model compounds. Although such interaction indeed appears, as demonstrated by atoms in molecules and natural bond orbital analysis, it is inefficient to control the conformational equilibrium. An energy decomposition analysis scheme demonstrated that halomethane and thiophene tend to move away from one another due to a core component (Pauli repulsion and exchange), which is mainly due to a deformation term. Therefore, chalcogen bonds with halogens appear weaker than with other chalcogens.

Weak Interaction Activates Esters: Reconciling Catalytic Activity and Turnover Contradiction by Tailored Chalcogen Bonding.

The activation of esters by strong Lewis acids via the formation of covalent adducts is a classic strategy to give reactivity; however, this approach frequently incurs limited turnover due to the low efficiency in the dissociation of catalyst from a stable catalyst-product complex. While the use of some weak interaction catalysts that can easily dissociate from any bonding complexes in the reaction system would solve this catalyst turnover problem, the poor catalytic activity in the ester activation that can be provided by these noncovalent forces in turn sets up a formidable challenge. Herein, we describe the activation and catalytic transformation of esters by weak interactions, which provides a promising platform to reconcile the catalytic activity and turnover problems. Several tailored chalcogen-bonding catalysts were developed for the activation of esters, enabling achieving several inherently low reactive Diels-Alder reactions as well as the ring-opening polymerization of lactones through weak chalcogen bonding interactions. This supramolecular catalysis approach is particularly highlighted by its capability to promote some uncommon Diels-Alder reactions involving using dienes bearing electron-withdrawing groups coupled by α,β-unsaturated ester as dienophiles and substrate incorporating competitive Lewis basic sites, in which typical strong Lewis acids showed low catalytic efficiency, while representative hydrogen and halogen bonding catalysts were inactive.

Neighboring Effects of Sulfur Oxidation State on Dynamic Covalent Bonds and Assemblies.

The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.

Fingerprints of Chalcogen Bonding Revealed Through 77Se-NMR.

77Se-NMR is used to characterise several chalcogen bonded complexes of derivatives of the organoselenium drug ebselen, exploring a range of electron demand. NMR titration experiments support the intuitive understanding that chalcogen bond donors bearing more electron withdrawing substituents give rise stronger chalcogen bonds. The chemical shift of the selenium nucleus is also shown to move upfield as it participates in a chalcogen bond. Solid-state NMR is used to explore chalcogen bonding in co-crystals. Due to the lack of molecular reorientation on the NMR timescale in the solid state, the shape of the chemical shift tensor can be determined using this technique. A range of co-crystals are shown to have extremely large chemical shift anisotropy, which suggests a strongly anisotropic electron density distribution around the selenium atom. A single crystal NMR experiment was conducted using one of the co-crystals, affording the absolute orientation of the chemical shift tensor within the crystal. This showed that the selenium nucleus is strongly shielded in the direction of the chalcogen bond (due to the approach of the lone pair of the Lewis base), and strongly deshielded in the perpendicular direction. The orientation of the deshielded axis is consistent with the presence of a second σ-hole which is not participating in a chalcogen bond, showing the profound effect of electron density anisotropy on the chemical shift.

Experimental Evidence for Non‐Fermi‐Contact J Coupling Across Chalcogen Bonds in Ionic Salt Cocrystal Polymorphs

AbstractA pair of novel polymorphic ionic cocrystals of 3,4‐dicyanotelluradiazole and tetraphenylphosphonium bromide are synthesized and are characterized by single‐crystal XRD. Strong and directional non‐covalent chalcogen bonds (ChB) between Te and Br are analyzed via solid‐state NMR to reveal large and anisotropic J(125Te,79/81Br) coupling tensors, providing unequivocal evidence for non‐Fermi contact contributions across ChBs. Along with large 79/81Br quadrupolar couplings for the Br− anions, these data provide new tools to characterize chalcogen bonds and to differentiate between ChB polymorphs.

Experimental Evidence for Non-Fermi-Contact J Coupling Across Chalcogen Bonds in Ionic Salt Cocrystal Polymorphs.

A pair of novel polymorphic ionic cocrystals of 3,4-dicyanotelluradiazole and tetraphenylphosphonium bromide are synthesized and are characterized by single-crystal XRD. Strong and directional non-covalent chalcogen bonds (ChB) between Te and Br are analyzed via solid-state NMR to reveal large and anisotropic J(125Te,79/81Br) coupling tensors, providing unequivocal evidence for non-Fermi contact contributions across ChBs. Along with large 79/81Br quadrupolar couplings for the Br- anions, these data provide new tools to characterize chalcogen bonds and to differentiate between ChB polymorphs.

Harnessing Multistep Chalcogen Bonding Activation in the α-Stereoselective Synthesis of Iminoglycosides.

The use of noncovalent interactions (NCIs) has received significant attention as a pivotal synthetic handle. Recently, the exploitation of unconventional NCIs has gained considerable traction in challenging reaction manifolds such as glycosylation due to their capacity to facilitate entry into difficult-to-access sugars and glycomimetics. While investigations involving oxacyclic pyrano- or furanoside scaffolds are relatively common, methods that allow the selective synthesis of biologically important iminosugars are comparatively rare. Here, we report the capacity of a phosphonochalcogenide (PCH) to catalyze the stereoselective α-iminoglycosylation of iminoglycals with a wide array of glycosyl acceptors with remarkable protecting group tolerance. Mechanistic studies have illuminated the counterintuitive role of the catalyst in serially activating both the glycosyl donor and acceptor in the up/downstream stages of the reaction through chalcogen bonding (ChB). The dynamic interaction of chalcogens with substrates opens up new mechanistic opportunities based on iterative ChB catalyst engagement and disengagement in multiple elementary steps.

Controlled Cationic Polymerization with Organotellurium Catalysts Utilizing Redox-Mediated Chalcogen Bonding Interaction

Controlled Cationic Polymerization with Organotellurium Catalysts Utilizing Redox-Mediated Chalcogen Bonding Interaction

Strengthening of Noncovalent Bonds Caused by Internal Deformations.

It is usually assumed that the maximal noncovalent bond strength is achieved by full geometry optimization of the geometry of the dyad. Density functional theory calculations show this not to be the case. A number of systems are considered that include osme, tetrel, pnictogen, and chalcogen bonds, involving both σ- and π-holes, as well as hypervalency. By suitable adjustment of the bond angles within the Lewis acid, the base can be drawn closer than in the optimized structure, with an accompanying substantial strengthening of the noncovalent bond, by more than 10 kcal/mol in some cases. The energetic cost of this deformation from the optimized geometry can be surprisingly small in comparison to the gain in the interaction energy. Taking the opposite approach of first pushing the two subunits closer to one another and then permitting internal geometries to adjust to the shortened distance produces only minimal bond strengthening.