The Chalcogen Bond in Crystalline Solids: A World Parallel to Halogen Bond

Non-covalent bridging of bithiophenes through chalcogen bonding grips

In this work, chalcogen functionalized dithiophenes, equipped on both extremities with chalcogen-bonding recognition heterocycles, have been prepared following two synthetic pathways.

Synthesis and study ofC-substituted methylthio derivatives of cobalt bis(dicarbollide)

The C-methylthio derivatives of cobalt bis(dicarbollide) were synthesized by reaction of anhydrous CoCl₂ with nido-carborane [7-MeS-7,8-C₂B₉H₁₁]⁻ and isolated as a mixture of rac-[1,1′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[1,2′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂]⁻ isomers. The structures of both isomers were studied using DFT quantum chemical calculations. The most preferable geometry of rotamers and the stabilization energy of C-methylthio derivatives of cobalt bis(dicarbolide) were calculated. The (BEDT-TTF)[1,1′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂] salt was prepared and its structure was determined by single crystal X-ray diffraction. The cisoid conformation of the rac-[1,1′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂]⁻ anion is stabilized by short intramolecular CH⋯S hydrogen and BH⋯S chalcogen bonds between the dicarbollide ligands, that is in good agreement with the data of quantum chemical calculations.

The C-methylthio derivatives of cobalt bis(dicarbollide) rac-[1,1′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[1,2′-(MeS)₂-3,3′-Co(1,2-C₂B₉H₁₀)₂]⁻ were synthesized and studied by DFT calculations and X-ray diffraction.

Halogen and Chalcogen Bond Energies Evaluated Using Electron Density Properties

Halogen (X-bond) and chalcogen bond (Ch-bond) energies for 36 complexes have been obtained at the RI-MP2/def2-TZVP level of theory, involving the heavier halogen and chalcogen atoms (Br, I, Se, Te). We have explored the existence of linear relationships between the interaction energies and the local kinetic energy densities at the bond critical points that characterize the σ-hole interactions (both electronic G(r) and potential V(r) energy densities). Interestingly, we have found strong relationships for halogen and chalcogen bonding energies, especially for the V(r) energy density, thus allowing to estimate the interaction energy without computing the separate monomers. This is also useful to estimate the interaction in monomeric systems (intramolecular X/Ch-bonds), as illustrated using several examples. Remarkably, we have also found a good relationship when in the same representation both halogen and chalcogen atoms are included, thus allowing to use the same empirical correlation for both interactions.

Chiral Chalcogen Bond Donors Based on the 4,4'-Bipyridine Scaffold

Organocatalysis through chalcogen bonding (ChB) is in its infancy, as its proof-of-principle was only reported in 2016. Herein, we report the design and synthesis of new chiral ChB donors, as well as the catalytic activity evaluation of the 5,5′-dibromo-2,2′-dichloro-3-((perfluorophenyl)selanyl)-4,4′-bipyridine as organocatalyst. The latter is based on the use of two electron-withdrawing groups, a pentafluorophenyl ring and a tetrahalo-4,4′-bipyridine skeleton, as substituents at the selenium center. Atropisomery of the tetrahalo-4,4′-bipyridine motif provides a chiral environment to these new ChB donors. Their synthesis was achieved through either selective lithium exchange and trapping or a site-selective copper-mediated reaction. Pure enantiomers of the 3-selanyl-4,4′-bipyridine were obtained by high performance liquid chromatography enantioseparation on specific chiral stationary phase, and their absolute configuration was assigned by comparison of the measured and calculated electronic circular dichroism spectra. The capability of the selenium compound to participate in σ-hole-based interactions in solution was studied by ¹⁹F NMR. Even if no asymmetric induction has been observed so far, the new selenium motif proved to be catalytically active in the reduction of 2-phenylquinoline by Hantzsch ester.

Synthesis and Structure of Methylsulfanyl Derivatives of Nickel Bis(Dicarbollide)

Symmetrically and unsymmetrically substituted methylsulfanyl derivatives of nickel(III) bis(dicarbollide) (Bu₄N)[8,8'-(MeS)₂-3,3'-Ni(1,2-C₂B₉H₁₀)₂], (Bu₄N)[4,4'-(MeS)₂-3,3'-Ni(1,2-C₂B₉H₁₀)₂], and (Bu₄N)[4,7'-(MeS)₂-3,3'-Ni(1,2-C₂B₉H₁₀)₂] were synthesized, starting from [Ni(acac)₂]₃ and the corresponding methylsulfanyl derivatives of nido-carborane (Bu₄N)[10-MeS-7,8-C₂B₉H₁₁] and (Bu₄N)[10-MeS-7,8-C₂B₉H₁₁]. Structures of the synthesized metallacarboranes were studied by single-crystal X-ray diffraction and quantum chemical calculations. The symmetrically substituted 8,8'-isomer adopts transoid conformation stabilized by two pairs of intramolecular C-H···S hydrogen bonds between the dicarbollide ligands. The unsymmetrically substituted 4,7'-isomer adopts gauche conformation, which is stabilized by two nonequivalent C-H···S hydrogen bonds and one short chalcogen B-H···S bond (2.53 Å, -1.4 kcal/mol). The gauche conformation was found to be also preferred for the 4,7'-isomer.

A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes

Planarizable push-pull probes have been introduced to demonstrate physical forces in biology. However, the donors and acceptors needed to polarize mechanically planarized probes are incompatible with their twisted resting state. The objective of this study was to overcome this "flipper dilemma" with chalcogen-bonding cascade switches that turn on donors and acceptors only in response to mechanical planarization of the probe. This concept is explored by molecular dynamics simulations as well as chemical double-mutant cycle analysis. Cascade switched flipper probes turn out to excel with chemical stability, red shifts adding up to high significance, and focused mechanosensitivity. Most important, however, is the introduction of a new, general and fundamental concept that operates with non-trivial supramolecular chemistry, solves an important practical problem and opens a wide chemical space.

Bifurcated Triel Bonds—Hydrides and Halides of 1,2-Bis(Dichloroboryl)Benzene and 1,8-Bis(Dichloroboryl)Naphthalene

MP2/aug-cc-pVTZ calculations were performed on hydrides, fluorides, and chlorides of 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene. The theoretical analysis of BHB−, BFB−, and BClB− arrangements occurring in these complexes and classified as bifurcated triel bonds was partly based on decomposition of the energy of interaction. The latter was carried out for structures optimized using the DFT method. The complexes analyzed were characterized by a partly covalent character of the links to the hydride and halide anions; these anions strongly influenced the geometry of the complexes. The boron centers’ links for the neutral 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene molecules were characterized by approximately trigonal and planar configurations, while for anionic complexes, tetrahedral configurations were observed. The crystal structures of compounds related to species calculated here were found in the Cambridge Structural Database (CSD).

Chalcogen bonding of two ligands to hypervalent YF4 (Y = S, Se, Te, Po)

The ability of two NH₃ ligands to engage in simultaneous chalcogen bonds to a hypervalent YF₄ molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another in a pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y = S, while Te, and Po tend toward the trans structure; they are nearly equally stable for Se. In either case, the binding energy rises rapidly with the size of the Y atom, exceeding 30 kcal mol^-1 for PoF₄.

Does Oxygen Feature Chalcogen Bonding?

Using the second-order Møller-Plesset perturbation theory (MP2), together with Dunning's all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R-M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.

Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra

Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A-F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm-1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55-422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm.

An Overview of Strengths and Directionalities of Noncovalent Interactions: σ-Holes and π-Holes

Quantum mechanics, through the Hellmann–Feynman theorem and the Schrödinger equation, show that noncovalent interactions are classically Coulombic in nature, which includes polarization as well as electrostatics. In the great majority of these interactions, the positive electrostatic potentials result from regions of low electronic density. These regions are of two types, designated as σ-holes and π-holes. They differ in directionality; in general, σ-holes are along the extensions of covalent bonds to atoms (or occasionally between such extensions), while π-holes are perpendicular to planar portions of molecules. The magnitudes and locations of the most positive electrostatic potentials associated with σ-holes and π-holes are often approximate guides to the strengths and directions of interactions with negative sites but should be used cautiously for this purpose since polarization is not being taken into account. Since these maximum positive potentials may not be in the immediate proximities of atoms, interatomic close contacts are not always reliable indicators of noncovalent interactions. This is demonstrated for some heterocyclic rings and cyclic polyketones. We briefly mention some problems associated with using Periodic Table Groups to label interactions resulting from σ-holes and π-holes; for example, the labels do not distinguish between these two possibilities with differing directionalities.

Selenium & tellurium chemistry at the beginning of the 3rd millennium: a celebration of ICCST

Vito Lippolis and Claudio Santi introduce theNew Journal of Chemistrythemed collection on selenium & tellurium chemistry at the beginning of the 3rd millennium: a celebration of ICCST.

2Ch–2N square and hexagon interactions: a combined crystallographic data analysis and computational study

2Ch–2N square and hexagon interactions were extensively investigated by the combination of crystallographic data analysis and computational approaches.

Recent progress in selenium-catalyzed organic reactions

Selenium-based catalysts, including organo- and inorganoselenium ones, in organic synthesis in the recent decade are reviewed.

Synthetic and structural investigations of bis(N-alkyl-benzoselenadiazolium) cations

A variety of supramolecular structures is formed by selenadiazolium cations linked by hydrocarbon bridges.

1st International Conference on Noncovalent Interactions

Welcome to this themed collection of RSC articles entitled: 1st International Conference on Noncovalent Interactions.

Rotational characterization of S⋯F chalcogen bonds in the complex of 2,2,4,4-tetrafluoro-1,3-dithietane and difluoromethane

The nature of S⋯F chalcogen bonds and C–H⋯F and C–F⋯F–C contacts was characterized by rotational spectroscopy for the first time.