Halogen Bonding: An Interim Discussion

Halogen bonding is a noncovalent interaction that is receiving rapidly increasing attention because of its significance in biological systems and its importance in the design of new materials in a variety of areas, for example, electronics, nonlinear optical activity, and pharmaceuticals. The interactions can be understood in terms of electrostatics/polarization and dispersion; they involve a region of positive electrostatic potential on a covalently bonded halogen and a negative site, such as the lone pair of a Lewis base. The positive potential, labeled a σ hole, is on the extension of the covalent bond to the halogen, which accounts for the characteristic near‐linearity of halogen bonding. In many instances, the lateral sides of the halogen have negative electrostatic potentials, allowing it to also interact favorably with positive sites. In this discussion, after looking at some of the experimental observations of halogen bonding, we address the origins of σ holes, the factors that govern the magnitudes of their electrostatic potentials, and the properties of the resulting complexes with negative sites. The relationship of halogen and hydrogen bonding is examined. We also point out that σ‐hole interactions are not limited to halogens, but can also involve covalently bonded atoms of Groups IV–VI. Examples of applications in biological/medicinal chemistry and in crystal engineering are mentioned, taking note that halogen bonding can be “tuned” to fit various requirements, that is, strength of interaction, steric factors, and so forth.     

Avoiding problems with hydrogen misplacement in reporting crystal structures

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one‐, two‐ or three‐dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space‐group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H‐atom electron densities associated with apparent D—H...A trios, while some H‐atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high‐quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen‐bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Formation of lithium,sodium and potassium complexes with 1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol (taci)

Single crystals of (1,3‐diamino‐5‐azaniumyl‐1,3,5‐trideoxy‐cis‐inositol‐κ³O²,O⁴,O⁶)(1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol‐κ³O²,O⁴,O⁶)lithium(I) diiodide dihydrate, [Li(C₆H₁₆N₃O₃)(C₆H₁₅N₃O₃)]I₂·2H₂O or [Li(Htaci)(taci)]I₂·2H₂O (taci is 1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol), (I), bis(1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol‐κ³O²,O⁴,O⁶)sodium(I) iodide, [Na(C₆H₁₅N₃O₃)₂]I or [Na(taci)₂]I, (II), and bis(1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol‐κ³O²,O⁴,O⁶)potassium(I) iodide, [K(C₆H₁₅N₃O₃)₂]I or [K(taci)₂]I, (III), were grown by diffusion of MeOH into aqueous solutions of the complexes. The structures of the Na and K complexes are isotypic. In all three complexes, the taci ligands adopt a chair conformation with axial hydroxy groups, and the metal cations exhibit exclusive O‐atom coordination. The six O atoms of the resulting MO₆ unit define a centrosymmetric trigonal antiprism with approximate D_3d symmetry. The interligand O...O distances increase significantly in the order Li < Na < K. The structure of (I) exhibits a complex three‐dimensional network of R—NH₂—H...NH₂—R, R—O—H...NH₂—R and R—O—H...O(H)—H...NH₂—R hydrogen bonds. The structures of the Na and K complexes consist of a stack of layers, in which each taci ligand is bonded to three neighbours via pairwise O—H...NH₂ interactions between vicinal HO—CH—CH—NH₂ groups.     

Generation and Identification of the Linear OCBNO and OBNCO Molecules with 24 Valence Electrons

Two structural isomers containing five second-row element atoms with 24 valence electrons were generated and identified by matrix-isolation IR spectroscopy and quantum chemical calculations. The OCBNO complex, which is produced by the reaction of boron atoms with mixtures of carbon monoxide and nitric oxide in solid neon, rearranges to the more stable OBNCO isomer on UV excitation. Bonding analysis indicates that the OCBNO complex is best described by the bonding interactions between a triplet-state boron cation with an electron configuration of (2s)⁰(2p_σ)⁰(2p_π)² and the CO/NO⁻ ligands in the triplet state forming two degenerate electron-sharing π bonds and two ligand-to-boron dative σ bonds.     

Lattice structures and electronic properties of MO/MoSe2 interface from first-principles calculations

Using first-principles plane-wave calculations within density functional theory, we theoretically studied the atomic structure, bonding energy and electronic properties of the perfect Mo (110)/MoSe₂ (100) interface with a lattice mismatch less than 4.2%. Compared with the perfect structure, the interface is somewhat relaxed, and its atomic positions and bond lengths change slightly. The calculated interface bonding energy is about −1.2 J/m², indicating that this interface is very stable. The MoSe₂ layer on the interface has some interface states near the Fermi level, the interface states are mainly caused by Mo 4d orbitals, while the Se atom almost have no contribution. On the interface, Mo-5s and Se-4p orbitals hybridize at about −6.5 to −5.0 eV, and Mo-4d and Se-4p orbitals hybridize at about −5.0 to −1.0 eV. These hybridizations greatly improve the bonding ability of Mo and Se atom in the interface. By Bader charge analysis, we find electron redistribution near the interface which promotes the bonding of the Mo and MoSe₂ layer.     

Synthesis,chiroptical properties of a helical polyacetylene derivative carrying urea moieties

A novel phenylacetylene derivative containing urea groups was synthesized and polymerized with a Rh catalyst to give the corresponding polymer, poly（1） with moderate number-average molecular weights. The poly（1） was soluble in toluene, CHCI3, CH2C12, THF, DMF, and DMSO, but insoluble in hexane, diethyl ether and MeOH. The specific rotation and circular dichroism （CD） spectroscopic studies revealed that poly（1） took predominantly one-handed helical structures. The presence of intramolecular hydrogen bonding was confirmed by liquid-state IR spectroscopy. The helicity of poly（1） could be tuned by temperature and anion. The helical conformation of the polymer was stable against Br but susceptible to F.     

On the strength of hydrogen bonding within water clusters on the coordination limit

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18 , 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice I_h). The strongest HBs within H₂O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H₂O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H₂O clusters.