Halogen-Bonded Supramolecular Parallelograms: From Self-Complementary Iodoalkyne Halogen-Bonded Dimers to 1:1 and 2:2 Iodoalkyne Halogen-Bonded Cocrystals

The formation of supramolecular parallelograms utilizing iodoalkyne-pyridine halogen bonding is described. The crystal structures of four iodoalkynyl-substituted (phenylethynyl)pyridines demonstrate the feasibility of discrete self-complementary dimer formation. These compounds 3-(2-iodoethynyl-phenylethynyl) pyridine (1), 2-(3-iodoethynyl-phenylethynyl) pyridine (2), 3-(4,5-difluoro-2-iodoethynyl-phenylethynyl) pyridine (3), and 2-(5-iodoethynyl-2,4-dimethylphenylethynyl) pyridine (4) all form parallelogram-shaped dimers with two self-complementary short N-I halogen bonds. The potential formation of iodoalkynyl halogen-bonded supramolecular macrocycles is demonstrated by the formation of a discrete halogen-bonded parallelogram-shaped complex in the 1:1 cocrystal formed from the bis iodoalkyne, 1-iodoethynyl-2-(3-iodoethynyl-phenylethynyl)-4,5-dimethoxybenzene (6), and the dipyridyl, 5-phenyl-2-(pyridin-3-ylethynyl)pyridine (7). Furthermore, discrete supramolecular parallelograms form within the 2:2 cocrystal formed between 1,2-bis(iodoethynyl)-4,5-difluorobenzene and the dipyridyl 4-(3-pyridylethynyl) pyridine (8).

Rapid Access to Encapsulated Molecular Rotors via Coordination-Driven Macrocycle Formation

Macrocycle formation that relies upon trans metal coordination of appropriately placed pyridine ligands within an arylene ethynylene construct provides rapid and reliable access to molecular rotators encapsulated within macrocyclic stators. Showing no significant close contacts to the central rotators, X-ray crystallography of AgI -coordinated macrocycles provides plausibility for unobstructed rotation or wobbling of rotators within the central cavity. Solid-state 13 C NMR of PdII -coordinated macrocycles supports the notion of unobstructed movement of simple arenes in the crystal lattice. Solution 1 H NMR studies indicate complete and immediate macrocycle formation upon the introduction of PdII to the pyridyl-based ligand at room temperature. Moreover, the formed macrocycle is stable in solution; a lack of significant changes in the 1 H NMR spectrum upon cooling to -50 °C is consistent with the absence of dynamic behavior. The synthetic route to these macrocycles is expedient and modular, providing access to rather complex constructs in four simple steps involving Sonogashira coupling and deprotection reactions.

π-Complexation and C-H hydrogen bonding in the formation of colored cocrystals

The present study evaluates the potential combination of charge-transfer electron-donor-acceptor π-π complexation and C-H hydrogen bonding to form colored cocrystals. The crystal structures of the red 1:1 cocrystals formed from the isomeric pyridines 4- and 3-{2-[4-(dimethylamino)phenyl]ethynyl}pyridine with 1-[2-(3,5-dinitrophenyl)ethynyl]-2,3,5,6-tetrafluorobenzene, both C₁₄H₄F₄N₂O₄·C₁₅H₁₄N₂, are reported. Intermolecular interaction energy calculations confirm that π-stacking interactions dominate the intermolecular interactions within each crystal structure. The close contacts revealed by Hirshfeld surface calculations are predominantly C-H interactions with N, O, and F atoms.

A structural and computational comparison of close contacts and related intermolecular energies of interaction in the structures of 1,3-diiodo-5-nitrobenzene, 1,3-dibromo-5-nitrobenzene, and 1,3-dichloro-5-nitrobenzene

1,3-Diiodo-5-nitrobenzene, C6H3I2NO2, and 1,3-dibromo-5-nitrobenzene, C6H3Br2NO2, crystallize in the centrosymmetric space group P21/m, and are isostructural with 1,3-dichloro-5-nitrobenzene, C6H3Cl2NO2, that has been redetermined at 100 K for consistency. While the three-dimensional packing in all three structures is similar, the size of the halogen atom affects the nonbonded close contacts observed between molecules. Thus, the structure of 1,3-diiodo-5-nitrobenzene features a close Type 1 I...I contact, the structure of 1,3-dibromo-5-nitrobenzene features a self-complementary nitro-O...Br close contact, while the structure of 1,3-dichloro-5-nitrobenzene also has a self-complementary nitro-O...Cl interaction, as well as a bifurcated C—H...O(nitro) close contact. Notably, the major energetically attractive intermolecular interaction between adjacent molecules in each of the three structures corresponds to a π-stacked interaction. The self-complementary halogen...O(nitro) and C—H...O(nitro) interactions correspond to significant cohesive attraction between molecules in each structure, while the Type 1 halogen–halogen contact is weakly cohesive.

Co-operative halogen bonds and nonconventional sp-C-H...O hydrogen bonds in 1:1 cocrystals formed between diethynylpyridines and N-halosuccinimides

The rapid evaporation of 1:1 solutions of diethynylpyridines and N-halosuccinimides, that react together to form haloalkynes, led to the isolation of unreacted 1:1 cocrystals of the two components. The 1:1 cocrystal formed between 2,6-diethynylpyridine and N-iodosuccinimide (C₄H₄INO₂·C₉H₅N) contains an N-iodosuccinimide-pyridine I...N halogen bond and two terminal alkyne-succinimide carbonyl C-H...O hydrogen bonds. The three-dimensional extended structure features interwoven double-stranded supramolecular polymers that are interconnected through halogen bonds. The cocrystal formed between 3,5-diethynylpyridine and N-iodosuccinimide (C₄H₄INO₂·C₉H₅N) also features an I...N halogen bond and two C-H...O hydrogen bonds. However, the components form essentially planar double-stranded one-dimensional zigzag supramolecular polymers. The cocrystal formed between 3,5-diethynylpyridine and N-bromosuccinimide (C₄H₄BrNO₂·C₉H₅N) is isomorphous to the cocrystal formed between 3,5-diethynylpyridine and N-iodosuccinimide, with a Br...N halogen bond instead of an I...N halogen bond.

5-{[4-(Dimethylamino)phenyl]ethynyl}pyrimidine–1,2,3,5-tetrafluoro-4,6-diiodobenzene (1/2)

The treatment of 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine with a threefold excess of 1,2,3,5-tetrafluoro-4,6-diiodobenzene in dichloromethane solution led to the formation of the unexpected 1:2 title co-crystal, C14H13N3·2CF4I2. In the extended structure, two unique C—I...N halogen bonds from one of the 1,2,3,5-tetrafluoro-4,6-diiodobenzene molecules to the pyrimidine N atoms of the 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine molecule generate [110] chains and layers of these chains are π-stacked along the a-axis direction. The second 1,2,3,5-tetrafluoro-4,6-diiodobenzene molecule resides in channels formed parallel to the a-axis direction between stacks of 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine molecules and interacts with them via C—I...π(alkyne) contacts.

Conformational control through co-operative nonconventional C-H...N hydrogen bonds

We report the design, synthesis, and crystal structure of a conjugated aryleneethynyl molecule, 2-(2-{4,5-dimethoxy-2-[2-(2,3,4-trifluorophenyl)ethynyl]phenyl}ethynyl)-6-[2-(pyridin-2-yl)ethynyl]pyridine, C₃₀H₁₇F₃N₂O₂, that adopts a planar rhombus conformation in the solid state. The molecule crystallizes in the space group P-1, with Z = 2, and features two intramolecular sp²-C-H...N hydrogen bonds that co-operatively hold the arylethynyl molecule in a rhombus conformation. The H atoms are activated towards hydrogen bonding since they are situated on a trifluorophenyl ring and the H...N distances are 2.470 (16) and 2.646 (16) Å, with C-H...N angles of 161.7 (2) and 164.7 (2)°, respectively. Molecular electrostatic potential calculations support the formation of C-H...N hydrogen bonds to the trifluorophenyl moiety. Hirshfeld surface analysis identifies a self-complementary C-H...O dimeric interaction between adjacent 1,2-dimethoxybenzene segments that is shown to be common in structures containing that moiety.

Arylethynyl Helices Supported by π-Stacking and Halogen Bonding

Co-crystallization of a pyridyl-containing arylethynyl (AE) moiety with 1,4-diiodotetrafluorobenzene leads to unique, figure-eight shaped helical motifs within the crystal lattice. A slight twist in the AE backbone allows each AE unit to simultaneously interact with haloarene units that are stacked on top of one another. Left-handed (M) and right-handed (P) helices are interspersed in a regular pattern throughout the crystal. The major driving forces for assembly are 1) halogen bonding between the pyridyl nitrogen atoms and the iodine substituents of the haloarene, with N⋅⋅⋅I distances between 2.81 and 2.84 Å, and 2) π-π stacking of the haloarenes, with distances of approximately 3.57 Å between centroids. Halogen bonding and π-π stacking not only work in concert, but also seem to mutually enhance one another. Calculations suggest that the presence of π-π stacking modestly intensifies the halogen bonding interaction by <0.2 kcal/mol; likewise, halogen bonding to the haloarene enhances the π-π stacking interaction by 0.59 kcal/mol.

Ditopic halogen bonding with bipyrimidines and activated pyrimidines

The potential of pyrimidines to serve as ditopic halogen-bond acceptors is explored. The halogen-bonded cocrystals formed from solutions of either 5,5'-bipyrimidine (C₈H₆N₄) or 1,2-bis(pyrimidin-5-yl)ethyne (C₁₀H₆N₄) and 2 molar equivalents of 1,3-diiodotetrafluorobenzene (C₆F₄I₂) have a 1:1 composition. Each pyrimidine moiety acts as a single halogen-bond acceptor and the bipyrimidines act as ditopic halogen-bond acceptors. In contrast, the activated pyrimidines 2- and 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine (C₁₄H₁₃N₃) are ditopic halogen-bond acceptors, and 1:1 halogen-bonded cocrystals are formed from 1:1 mixtures of each of the activated pyrimidines and either 1,2- or 1,3-diiodotetrafluorobenzene. A 1:1 cocrystal was also formed between 2-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine and 1,4-diiodotetrafluorobenzene, while a 2:1 cocrystal was formed between 5-{[4-(dimethylamino)phenyl]ethynyl}pyrimidine and 1,4-diiodotetrafluorobenzene.

Triple-Pnictogen Bonding as a Tool for Supramolecular Assembly

Supramolecular assembly utilizing simultaneous formation of three pnictogen bonds around a single antimony vertex was explored via X-ray crystallography, solution NMR, and computational chemistry. An arylethynyl (AE) ligand was designed to complement the three electrophilic regions around the Sb compound. Though solution studies reveal large binding constants for individual pyridyl units with the Sb donor, the rigidity and prearrangement of the AE acceptor proved necessary to achieve simultaneous binding of three acceptors to the Sb-centered pnictogen-bond donor. Calculations and X-ray structures suggest that negative cooperativity upon sequential binding of three acceptors to a Sb center limits the utility of triple-pnictogen bonding pyridyl acceptors. These limitations can be negated, however, when positive cooperativity is designed into a complementary acceptor ligand.

Cooperative halogen bonding and polarized π-stacking in the formation of coloured charge-transfer co-crystals

Matched electron rich halogen bond acceptors and donor have been synthesized and the halogen bonded charge transfer cocrystals characterized.

C-I...N and C-I...π halogen bonding in the structures of 1-benzyliodoimidazole derivatives

Halogen bonding is a well-established and intensively studied intermolecular interaction that has also been used in the preparation of functional materials. While polyfluoroiodo- and polyfluorobromobenzenes have been widely used as aromatic halogen-bond donors, there have been very few studies of iodoimidazoles with regard to halogen bonding. We describe here the X-ray structures of three iodoimidazole derivatives, namely 1-benzyl-2-iodo-1H-imidazole, C₁₀H₉IN₂, (1), 1-benzyl-4-iodo-1H-imidazole, C₁₀H₉IN₂, (2), and 1-benzyl-2-iodo-1H-benzimidazole, C₁₄H₁₁IN₂, (3), and the halogen bonds that dominate the intermolecular interactions in each of these three structures. The three-dimensional structure of (1) is dominated by a strong C-I...N halogen bond, with an N...I distance of 2.8765 (2) Å, that connects the molecules into one-dimensional zigzag ribbons of molecules. In contrast, the three-dimensional structures of (2) and (3) both feature C-I...π halogen-bonded dimers.

Reactive Carbon-Chain Molecules: Synthesis of 1-Diazo-2,4-pentadiyne and Spectroscopic Characterization of Triplet Pentadiynylidene (H−C⋮C−C̈−C⋮C−H)

1-Diazo-2,4-pentadiyne (6a), along with both monodeuterio isotopomers 6b and 6c, has been synthesized via a route that proceeds through diacetylene, 2,4-pentadiynal, and 2,4-pentadiynal tosylhydrazone. Photolysis of diazo compounds 6a-c (lambda > 444 nm; Ar or N2, 10 K) generates triplet carbenes HC5H (1) and HC5D (1-d), which have been characterized by IR, EPR, and UV/vis spectroscopy. Although many resonance structures contribute to the resonance hybrid for this highly unsaturated carbon-chain molecule, experiment and theory reveal that the structure is best depicted in terms of the dominant resonance contributor of penta-1,4-diyn-3-ylidene (diethynylcarbene, H-C[triple bond]C-:C-C[triple bond]C-H). Theory predicts an axially symmetric (D(infinity h)) structure and a triplet electronic ground state for 1 (CCSD(T)/ANO). Experimental IR frequencies and isotope shifts are in good agreement with computed values. The triplet EPR spectrum of 1 (absolute value(D/hc) = 0.6157 cm(-1), absolute value(E/hc) = 0.0006 cm(-1)) is consistent with an axially symmetric structure, and the Curie law behavior confirms that the triplet state is the ground state. The electronic absorption spectrum of 1 exhibits a weak transition near 400 nm with extensive vibronic coupling. Chemical trapping of triplet HC5H (1) in an O2-doped matrix affords the carbonyl oxide 16 derived exclusively from attack at the central carbon.

Enediyne Isomers of Tetraethynylethene

Three isomers of tetraethynylethene (1, C10H4) have been prepared by palladium-catalyzed Negishi coupling of a trimethylsilylbutadiynyl zinc reagent with a bromoalkene, followed by mild deprotection with potassium carbonate in methanol. The unsubstituted enynes, 3-ethynyloct-3-ene-1,5,7-triyne (2), trans-dec-5-ene-1,3,7,9-tetrayne (3), and cis-dec-5-ene-1,3,7,9-tetrayne (4), exhibit modest stability at -20 degrees C but decompose rapidly at room temperature. Electronic absorption spectra of 2, 3, and 4 reveal a characteristic vibronic progression at 260-320 nm. Spectral features at shorter wavelength discriminate among the isomers, and permit the assignment of 2 and 3 as apparent dimerization products of triplet carbene H-CC-C-CC-H in matrices at low temperature. Computed relative energies of these C10H4 isomers (MP2/6-31G) are 1 (14.0 kcal/mol), 2 (6.8 kcal/mol), 3 (0.0 kcal/mol), and 4 (1.0 kcal/mol).