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The distribution of the electron density around covalently bonded atoms is anisotropic, and this determines the presence, on atoms surface, of areas of higher and lower electron density where the electrostatic potential is frequently negative and positive, respectively. The ability of positive areas on atoms to form attractive interactions with electron rich sites became recently the subject of a flurry of papers. The halogen bond (HaB), the attractive interaction formed by halogens with nucleophiles, emerged as a quite common and dependable tool for controlling phenomena as diverse as the binding of small molecules to proteinaceous targets or the organization of molecular functional materials. The mindset developed in relation to the halogen bond prompted the interest in the tendency of elements of groups 13-16 of the periodic table to form analogous attractive interactions with nucleophiles. This Account addresses the chalcogen bond (ChB), the attractive interaction formed by group 16 elements with nucleophiles, by adopting a crystallographic point of view. Structures of organic derivatives are considered where chalcogen atoms form close contacts with nucleophiles in the geometry typical for chalcogen bonds. It is shown how sulfur, selenium, and tellurium can all form chalcogen bonds, the tendency to give rise to close contacts with nucleophiles increasing with the polarizability of the element. Also oxygen, when conveniently substituted, can form ChBs in crystalline solids. Chalcogen bonds can be strong enough to allow for the interaction to function as an effective and robust tool in crystal engineering. It is presented how chalcogen containing heteroaromatics, sulfides, disulfides, and selenium and tellurium analogues as well as some other molecular moieties can afford dependable chalcogen bond based supramolecular synthons. Particular attention is given to chalcogen containing azoles and their derivatives due to the relevance of these moieties in biosystems and molecular materials. It is shown how the interaction pattern around electrophilic chalcogen atoms frequently recalls the pattern around analogous halogen, pnictogen, and tetrel derivatives. For instance, directionalities of chalcogen bonds around sulfur and selenium in some thiazolium and selenazolium derivatives are similar to directionalities of halogen bonds around bromine and iodine in bromonium and iodonium compounds. This gives experimental evidence that similarities in the anisotropic distribution of the electron density in covalently bonded atoms translates in similarities in their recognition and self-assembly behavior. For instance, the analogies in interaction patterns of carbonitrile substituted elements of groups 17, 16, 15, and 14 will be presented. While the extensive experimental and theoretical data available in the literature prove that HaB and ChB form twin supramolecular synthons in the solid, more experimental information has to become available before such a statement can be safely extended to interactions wherein elements of groups 14 and 15 are the electrophiles. It will nevertheless be possible to develop some general heuristic principles for crystal engineering. Being based on the groups of the periodic table, these principles offer the advantage of being systematic.

Herein, four different coordination networks were isolated and structurally characterized by combining two aminocarboxylate ligands, 4,4′-[biphenyl-4,4′-diylbis(azanediyl)]dibenzoic acid and 5,5′-[biphenyl-4,4′-diylbis(azanediyl)]diisophthalic acid (H2L1 and H4L2, respectively), with different transition metals (Zn(II), Zr(IV) and Cd(II)) under solvothermal conditions. The reaction between H2L1 and Zn(NO3)2·6H2O led to two different coordination networks. In PUMflex1-Zn, which has the formula {[Zn4O(L1)3(DMF)2](DMF)5}n·(DMF)x, the ligand always displays a syn conformation (with respect to the central biphenylene scaffold), whereas in the polymorph PUMflex1.1-Zn, one of the three ligands composing the asymmetric unit adopts an anti conformation. Although the two supramolecular isomers have equivalent stoichiometry and dimensionality, they show different topologies and entanglement types: parallel polycatenation of the 63-hcb and 2-fold interpenetration of the 44-sql layers, respectively. In the case of PUMflex1-Zr, with the formula {[Zr6O4(OH)8(L1)4(H2O)2]n·(DMF)x, H2L1 exclusively adopts the syn conformation, forming 1D-chains of rugby-ball shaped aggregates (topological type 2,8C1) interconnected through H-bonds with water molecules. In contrast, H4L2 behaves as a dianionic ligand in PUMflex2-Cd, with the formula [Cd(κ2-COO)2(DMF)3(DMF)]n, forming 1D zig-zag chains connected through the N–H⋯OC(OH) H-bonds to provide planar layers of sql topology. In all cases, the ability of the amine functions to interact with the H-bond active guests is structurally highlighted by the recurrent N–H⋯ODMF interaction modelled in the X-ray structures.

Experimental and theoretical studies of fluoro-, chloro-, and bromo-substituted derivatives of barbituric acid and indandione show that imide protons form short hydrogen bonds and bromine or, to a ...

Decamethonium diiodide is reported to perform the chemo- and regioselective encapsulation of para-dihalobenzenes through the competitive formation of halogen-bonded cocrystals starting from solutions that also contain ortho and meta isomers. Selective caging in the solid occurs even when an excess ortho or meta isomers, or even a mixture of them, is present in the solution. A prime matching between the size and shape of the dication and the formed dianions plays a key role in enabling the selective self-assembly, as proven by successful encapsulation of halogen-bond donors as weak as 1,4-dichlorobenzene and by the results of cocrystallization trials involving mismatching tectons. Encapsulated para-dihalobenzenes guest molecules can be removed quantitatively by heating the cocrystals under reduced pressure and be recovered as pure materials. The residual decamethonium diiodide can be recycled with no reduction in selectivity.

The SbF3·4,4′-dipyridyl N,N′-dioxide cocrystal is prepared and characterized via infrared spectroscopy and 121Sb and 123Sb nuclear quadrupole resonance. Single crystal X-ray analysis proves that a ...

The use of Pd(0) mediated C N coupling reaction for the synthesis of large polydentate ligands functionalized with NH groups is described. The protocol has been applied to the synthesis of polycarboxylic ligands and polypyridyl ligands, starting from common aryl halides containing a central phenyl or biphenyl core as electrophiles. Different aromatic amines or isonicotinamide have been used as nucleophiles. In all cases the ligands have been isolated in high yields and purity. The products have been characterized by means of FTIR, 1H NMR, 13C{1H} NMR, EI-MS or CI-MS and elemental analysis. The X-ray structure of N,N′-(biphenyl-4,4′-diyl)diisonicotinamide has also been solved.

In crystals of a benzoselenazole dye, a network of hydrogen bonds with the dye cations locks two iodide anions at a distance allowing for an iodine molecule to be pinned at either ends via two halogen bonds. I42− supramolecular anions are formed as discrete species that lie in the confined space defined by cation molecules.

The presence of fluorine atom(s) in a molecule makes the σ-hole potentials of surrounding atoms more positive and thus increases their tendencies to interact attractively with nucleophiles. This review shows that in the crystal structures of fluorinated derivatives of the Group 15 atoms, close contacts between Group 15 atoms and negative sites (e.g. lone pair possessing atoms and anions) are quite common. These close contacts are taken as indications of attractive interactions. The collection of single crystal X-ray structures analysed in this paper demonstrates that the ability of fluorinated atoms of Group 15 to work as electrophilic sites, namely to function as pnictogen bond donors, is fairly general. The directionalities and separations of these pninctogen bonds are convincing experimental evidences that linking a fluorine to a pnictogen atom increases its electrophilicity to the point that pnictogen bonding formation may become a determinant of the lattice structures in crystalline solids. Pnictogen bonding formation may become an heuristic principle for predicting some of the short contacts that are present in the crystal structures of compounds containing fluorinated atoms of Group 15, particularly when polyfluorinated. Pnictogen derivatives containing other moieties may also work as effective electrophilic sites and a convenient design of the used tectons may allow pnictogen bond to become a general and reliable tool in crystal engineering.

Although instrumental for optimizing their pharmacological activity, a molecular understanding of the preferential interactions given by volatile anesthetics is quite poor. This paper confirms the ability of halothane to work as a hydrogen-bond (HB) donor and gives the first experimental proof that halothane also works as a halogen-bond (HaB) donor in the solid state and in solution. A halothane/hexamethylphosphortriamide co-crystal is described and its single-crystal X-ray structure shows short HaBs between bromine, or chlorine, and the phosphoryl oxygen. New UV/Vis absorption bands appear upon addition of diazabicyclooctane and tetra(n-butyl)ammonium iodide to halothane solutions, indicating that nitrogen atoms and anions may mediate the HaB-driven binding processes involving halothane as well. The ability of halothane to work as a bidentate/tridentate tecton by acting as a HaB and HB donor gives an atomic rationale for the eudismic ratio shown by this agent.

The experimental charge density distribution of two new iodoperfluoroalkylimidazole derivatives has been determined with the aspherical atom model against single-crystal X-ray diffracted intensities and analyzed by means of the Bader Quantum Theory of Atoms In Molecules. The compounds self-assemble in the solid state forming infinite chains through strong I···N halogen bonds. The topological and energetic features of these interactions have been determined and compared with those of a previously reported I···N interaction formed by an iodoperfluoroarene derivative, allowing elucidation of the role of hybridization of the carbon atom bonded to the halogen atom in the nature of the halogen bonding interaction. The weaker interactions present in the crystal structures have been investigated as well, with particular attention to F···F interactions. They have also been analyzed through the Interacting Quantum Atoms approach in order to elucidate their role in stabilizing the crystal structure.

The diselenide moiety is labeled as a novel and robust chalcogen bond (ChB) donor group. The molecular electrostatic potential of two prototype diselenide derivatives shows the presence of two σ-holes along both the covalent bonds in which each selenium atom is involved. The propensity of selenium atoms of diselenides to work as electrophilic sites is confirmed by computational studies on the bis(o-anilinium)diselenide cation, and single crystal X-ray analysis of salts of this cation reveals the presence of close selenium···anion contacts. Comparison with halogen bonds in crystal structures of ionic λ3-iodane derivatives supports the rationalization of these close contacts as charge-assisted ChBs. Discrete adducts or two-dimensional networks are formed, suggesting the profitable use of the diselenide moiety in ChB based crystal engineering.

The σ-hole and π-hole interactions allow for a systematic understanding of some features of the attractive interactions involving elements of groups 13–18 of the periodic table and of some other groups. Areas of depleted electron density, where the electrostatic potential can be positive, exist on these atoms and these areas can form attractive interactions with electron rich sites (nucleophiles). When the electrophilic atom belongs to groups 14, 15, 16, or 17, the resulting interactions are named tetrel, pnictogen, chalcogen, and halogen bond, respectively. Here we discuss the tetrel bonds (TtBs) formed in crystalline solids on interaction of sp3 hybridized carbon atoms with lone pair possessing atoms and anions. A mapping of the specific short contacts formed in the solid by C(sp3) atoms is realized by discussing selected structures from the Cambridge Structural Database. This mapping led to the identification of some functional groups particularly tailored to form TtBs which can affect or control the packing in crystalline solids. Specifically, it is shown that methyl and methylene groups bound to ammonium, pyridinium, and sulfonium residues can give rise to particularly short and directional TtBs. Topologically, the formed adducts can exist as discrete species or one, two, or three dimensional networks. Fluorine atoms and perfluorinated residues as well as nitro and cyano substituents can also lead to the formation of TtBs which can control molecular conformation and packing in the solid.

Modeling indicates the presence of a region of low electronic density (a "σ-hole") on group 14 elements, and this offers an explanation for the ability of these elements to act as electrophilic sites and to form attractive interactions with nucleophiles. While many papers have described theoretical investigations of interactions involving carbon and silicon, such investigations of the heavier group 14 elements are relatively scarce. The purpose of this review is to rectify, to some extent, the current lack of experimental data on interactions formed by germanium and tin with nucleophiles. A survey of crystal structures in the Cambridge Structural Database is reported. This survey reveals that close contacts between Ge or Sn and lone-pair-possessing atoms are quite common, they can be either intra- or intermolecular contacts, and they are usually oriented along the extension of the covalent bond formed by the tetrel with the most electron-withdrawing substituent. Several examples are discussed in which germanium and tin atoms bear four carbon residues or in which halogen, oxygen, sulfur, or nitrogen substituents replace one, two, or three of those carbon residues. These close contacts are assumed to be the result of attractive interactions between the involved atoms and afford experimental evidence of the ability of germanium and tin to act as electrophilic sites, namely tetrel bond (TB) donors. This ability can govern the conformations and the packing of organic derivatives in the solid state. TBs can therefore be considered a promising and robust tool for crystal engineering. Graphical abstract Intra- and intermolecular tetrel bonds involving organogermanium and -tin derivatives in crystalline solids.