Crystal Engineering Using Polyiodide Halogen and Chalcogen Bonding to Isolate the Phenothiazinium Radical Cation and Its Rare Dimer, 10-(3-Phenothiazinylidene)phenothiazinium

Anion⋯anion self-assembly under the control of σ- and π-hole bonds

The electrostatic attraction between charges of opposite signs and the repulsion between charges of the same sign are ubiquitous and influential phenomena in recognition and self-assembly processes. However, it has been recently revealed that specific attractive forces between ions with the same sign are relatively common. These forces can be strong enough to overcome the Coulomb repulsion between ions with the same sign, leading to the formation of stable anion⋯anion and cation⋯cation adducts. Hydroden bonds (HBs) are probably the best-known interaction that can effectively direct these counterintuitive assembly processes. In this review we discuss how σ-hole and π-hole bonds can break the paradigm of electrostatic repulsion between like-charges and effectively drive the self-assembly of anions into discrete as well as one-, two-, or three-dimensional adducts. σ-Hole and π-hole bonds are the attractive forces between regions of excess electron density in molecular entities (e.g., lone pairs or π bond orbitals) and regions of depleted electron density that are localized at the outer surface of bonded atoms opposite to the σ covalent bonds formed by atoms (σ-holes) and above and below the planar portions of molecular entities (π-holes). σ- and π-holes can be present on many different elements of the p and d block of the periodic table and the self-assembly processes driven by their presence can thus involve a wide diversity of mono- and di-anions. The formed homomeric and heteromeric adducts are typically stable in the solid phase and in polar solvents but metastable or unstable in the gas phase. The pivotal role of σ- and π-hole bonds in controlling anion⋯anion self-assembly is described in key biopharmacological systems and in molecular materials endowed with useful functional properties.

Comparison of N···I and N···O Halogen Bonds in Organoiodine Cocrystals of Heterocyclic Aromatic Diazine Mono-N-oxides

A series of cocrystals of halogen bond donors 1,4-diiodotetrafluorobenzene (p-F4DIB) and tetraiodoethylene (TIE) with five aromatic heterocyclic diazine mono-N-oxides based on pyrazine, tetramethylpyrazine, quinoxaline, phenazine, and pyrimidine as halogen bonding acceptors were studied. Structural analysis of the mono-N-oxides allows comparison of the competitive occurrence of N···I vs O···I interactions and the relative strength and directionality of these two types of interactions. Of the aromatic heterocyclic diazine mono-N-oxide organoiodine cocrystals examined, six exhibited 1:1 stoichiometry, forming chains that utilized both N···I and O···I interactions. Two cocrystals presented 1:1 stoichiometry with exclusive O···I interactions. Two cocrystals displayed a 2:1 stoichiometry-one characterized solely by O···I interactions and the other solely by N···I interactions. We have also compared these interactions to those present in the corresponding diazines, some of which we report here and some which have been previously reported. In addition, a computational analysis using density functional theory (M062X/def2-SVPD) was performed on these two systems and has been compared to the experimental results. The calculated complex formation energies were, on average, 4.7 kJ/mol lower for the I···O halogen bonding interaction as compared to the corresponding N···I interaction. The average I···O interaction distances were calculated to be 0.15 Å shorter than the corresponding I···N interactions.

Halogen, chalcogen, and hydrogen bonding in organoiodine cocrystals of heterocyclic thiones: imidazolidine-2-thione, 2-mercaptobenzimidazole, 2-mercapto-5-methylbenzimidazole, 2-mercaptobenzoxazole, and 2-mercaptobenzothiazole

Through the combination of heterocyclic thiones with variation in the identity of the heterocyclic elements, namely, imidazolidine-2-thione, 2-mercaptobenzimidazole, 2-mercapto-5-methylbenzimidazole, 2-mercaptobenzoxazole, and 2-mercaptobenzothiazole with the common halogen-bond donors 1,2-, 1,3-, and 1,4-diiodotetrafluorobenzene, 1,3,5-trifluorotriiodobenzene, and tetraiodoethylene, a series of 18 new crystalline structures were characterized. In most cases, N-H...S hydrogen bonding was observed, with these interactions in imidazole-containing structures typically resulting in two-dimensional motifs (i.e. ribbons). Lacking the second N-H group, the thiazole and oxazole hydrogen bonding resulted in only dimeric pairs. C-I...S and C-I...I halogen bonding, as well as C=S...I chalcogen bonding, served to consolidate the packing by linking the hydrogen-bonding ribbons or dimeric pairs.

Isolation of unique heterocycles formed from pyridine-thiocarboxamides as diiodine, iodide, or polyiodide salts

The reaction of pyridine-thiocarboxamides with I2 provided a variety of novel heterocyclic products as iodide, triiodide, and/or pentaiodide salts. Bismuth triiodide was incorporated as a crystallization aid to access other structural types.

The reaction of thiourea and 1,3-dimethylthiourea towards organoiodines: oxidative bond formation and halogen bonding

By varying the halogen-bond-donor molecule, 11 new halogen-bonding cocrystals involving thiourea or 1,3-dimethylthiourea were obtained, namely, 1,3-dimethylthiourea-1,2-diiodo-3,4,5,6-tetrafluorobenzene (1/1), C₆F₄I₂·C₃H₈N₂S, 1, thiourea-1,3-diiodo-2,4,5,6-tetrafluorobenzene (1/1), C₆F₄I₂·CH₄N₂S, 2, 1,3-dimethylthiourea-1,3-diiodo-2,4,5,6-tetrafluorobenzene (1/1), C₆F₄I₂·C₃H₈N₂S, 3, 1,3-dimethylthiourea-1,3-diiodo-2,4,5,6-tetrafluorobenzene-methanol (1/1/1), C₆F₄I₂·C₃H₈N₂S·CH₄O, 4, 1,3-dimethylthiourea-1,3-diiodo-2,4,5,6-tetrafluorobenzene-ethanol (1/1/1), C₆F₄I₂·C₃H₈N₂S·C₂H₆O, 5, 1,3-dimethylthiourea-1,4-diiodo-2,3,5,6-tetrafluorobenzene (1/1), C₆F₄I₂·C₃H₈N₂S, 6, 1,3-dimethylthiourea-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C₆F₃I₃·C₃H₈N₂S, 7, 1,3-dimethylthiourea-1,1,2,2-tetraiodoethene (1/1), C₆H₁₆N₄S₂·C₂I₄, 8, [(dimethylamino)methylidene](1,2,2-triiodoethenyl)sulfonium iodide-1,1,2,2-tetraiodoethene-acetone (1/1/1), C₅H₈I₃N₂S⁺·I^-·C₃H₆O·C₂I₄, 9, 2-amino-4-methyl-1,3-thiazol-3-ium iodide-1,1,2,2-tetraiodoethene (2/3), 2C₄H₇N₂S⁺·2I^-·3C₂I₄, 10, and 4,4-dimethyl-4H-1,3,5-thiadiazine-3,5-diium diiodide-1,1,2,2-tetraiodoethene (2/3), 2C₅H₁₂N₄S²⁺·4I^-·3C₂I₄, 11. When utilizing the common halogen-bond-donor molecules 1,2-, 1,3-, and 1,4-diiodotetrafluorobenzene, as well as 1,3,5-trifluoro-2,4,6-triiodobenzene, bifurcated I...S...I interactions were observed, resulting in the formation of isolated rings, chains, and sheets. Tetraiodoethylene (TIE) provided I...S...I cocrystals as well, but further yielded a sulfonium-containing product through the reaction of the S atom with TIE. This particular sulfonium motif is the first of its kind to be structurally characterized, and is stabilized in the solid state through a three-dimensional I...I halogen-bonding network. Thiourea reacted with acetone in the presence of TIE to provide two novel heterocyclic products, again stabilized in the solid state through I...I halogen bonding.

Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study

In this study, we provide experimental (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the involvement of charge assisted chalcogen bonding (ChB) interactions in the recognition and folding mechanisms of S-adenosylmethionine (SAM) riboswitches. Concretely, an initial PDB search revealed several examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine (EEM) molecules and uracil (U) bases belonging to RNA take place. While these interactions are usually described as a merely Coulombic attraction between the positively charged S/Se group and RNA, theoretical calculations indicated that the σ holes of S and Se are involved. Moreover, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader’s “Atoms in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot) visual index, and Natural Bonding Orbital (NBO) analyses. As far as our knowledge extends, this is the first time that ChBs in SAM–RNA complexes have been systematically analyzed, and we believe the results might be useful for scientists working in the field of RNA engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Polymorphism, Halogen Bonding, and Chalcogen Bonding in the Diiodine Adducts of 1,3- and 1,4-Dithiane

Through variations in reaction solvent and stoichiometry, a series of S-diiodine adducts of 1,3- and 1,4-dithiane were isolated by direct reaction of the dithianes with molecular diiodine in solution. In the case of 1,3-dithiane, variations in reaction solvent yielded both the equatorial and the axial isomers of S-diiodo-1,3-dithiane, and their solution thermodynamics were further studied via DFT. Additionally, S,S’-bis(diiodo)-1,3-dithiane was also isolated. The 1:1 cocrystal, (1,4-dithiane)·(I₂) was further isolated, as well as a new polymorph of S,S’-bis(diiodo)-1,4-dithiane. Each structure showed significant S···I halogen and chalcogen bonding interactions. Further, the product of the diiodine-promoted oxidative addition of acetone to 1,4-dithiane, as well as two new cocrystals of 1,4-dithiane-1,4-dioxide involving hydronium, bromide, and tribromide ions, was isolated.