Exploiting the Mechanical Bond Effect for Enhanced Molecular Recognition and Sensing

The ubiquity of charged species in biological and industrial processes has resulted in ever-increasing interest in their selective recognition, detection, and environmental remediation. Building on the established coordination chemistry principles of the chelate and macrocyclic effects, and host preorganization, supramolecular chemists seek to construct specific 3D binding cavities reminiscent of biotic systems to enhance host-guest binding affinity and selectivity. Mechanically interlocked molecules (MIMs) present a wholly unique platform for synthetic host design, wherein topologies afforded by the mechanical bond enable the decoration of 3D cavities for non-covalent interactions with a range of target guest geometries. Notably, MIM host systems exhibit mechanical bond effect augmented affinities and selectivities for a variety of charged guest species, compared to non-interlocked acyclic and macrocycle host analogs. Furthermore, the modular nature of MIM synthesis facilitates incorporation of optical and electrochemical reporter groups, enabling fabrication of highly sensitive and specific molecular sensors. This review discusses the development of recognition and sensing MIMs, from the first reports in the late 20th century through to the present day, delineating how their topologically preorganized and dynamic host cavities enhance charged guest recognition and sensing, demonstrating the mechanical bond effect as a potent tool in future chemosensing materials.

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

Enhancing Effects of the Cyano Group on the C-X∙∙∙N Hydrogen or Halogen Bond in Complexes of X-Cyanomethanes with Trimethyl Amine: CH3−n(CN)nX∙∙∙NMe3, (n = 0–3; X = H, Cl, Br, I)

In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH_3−n(CN)_nX∙∙∙NMe₃ (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach.

Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts

We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.

Halogen-bonded one-dimensional chains of functionalized ditopic bipyridines co-crystallized with mono-, di-, and triiodofluorobenzenes

A series of halogen-bonded (XB) 1D and zigzag supramolecular architectures involving a sterically hindered class of homologous para-xylenes bearing bipyridyl moieties at peripheries co-crystallized with mono-, di-, and triiodofluorobenzenes as XB donors are prepared.

Dissecting the packing forces in mixed perfluorocarbon/aromatic co-crystals

The nature and role of non-covalent interactions involving fluorous molecules and aromatic molecules are studied by a combined theoretical/crystallographic approach.

Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals

This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.

Halogen-Bonded Assemblies of Arylene Imides and Diimides: Insight from Electronic, Structural, and Computational Studies

Halogen-bonding interactions in electron-deficient π scaffolds have largely been underexplored. Herein, the halogen-bonding properties of arylene imide/diimide-based electron-deficient scaffolds were studied. The influence of scaffold size, from small (phthalimide) to moderately sized (pyromellitic diimide or naphthalenediimides) to large (perylenediimide), axial-group modification, and number of halo substituents on the halogen bonding and its self-assembly was probed in a set of nine compounds. The structural modification leads to tunable optical and redox properties. The first reduction potential E 1 / 2 1 ranges between -1.09 and -0.17 V (vs. SCE). Two of the compounds, that is, 6 and 9, have deep-lying LUMOs with values reaching -4.2 eV. Single crystals of all nine systems were obtained, which showed Br⋅⋅⋅O, Br⋅⋅⋅Br, or Br⋅⋅⋅π halogen-bonding interactions, and a few systems are capable of forming all three types. These interactions lead to halogen-bonded rings (up to 12-membered), which propagate to form stacked 1D, 2D, or corrugated sheets. A few outliers were also identified, for example, molecules that prefer C-H⋅⋅⋅O hydrogen bonding over halogen bonding, or noncentrosymmetric rather than centrosymmetric organization. Computational studies based on Atoms in Molecules and Natural Bond Orbital analysis provided further insight into the halogen-bonding interactions. This study can lead to a predictive design tool-box to further explore related systems on surfaces reinforced by these weak directional forces.

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

The synthesis of 4,5-diiodo-1,3-dimesityl-1,2,3-triazolium salts with different anions have been developed. These triazolium salts show diverse aggregation via halogen bonding between C-I bonds and anions. Triazolium with halide anions exists as a tetramer with saddle conformation. Triazolium tetrafluoroborate exists as a trimer with Chinese lantern shape conformation. Triazolium trifluoroacetate and acetate exist as dimers, respectively, while the former shows boat conformation and the latter forms rectangle conformation. Triazolium salts form a linear polymer with polyiodide.

Halogenide anions as halogen and hydrogen bond acceptors in iodopyridinium halogenides

Structures of iodopyridinium halogenides have demonstrated why iodide, the weakest halogen bond acceptor among the halogenides, preferentially forms halogen bonds.

Halogen Bonds of Halotetrafluoropyridines in Crystals and Co-crystals with Benzene and Pyridine

The structures of the three para-substituted halotetrafluoropyridines with chlorine, bromine, and iodine have been determined in the solid state (X-ray diffraction). The structures of these compounds and that of pentafluoropyridine were also determined in the gas phase (electron diffraction). Structures in the solid state of the bromine and iodine derivatives exhibit halogen bonding as a structure-determining motif. On the way to an investigation of halogen bond formation of halotetrafluoropyridines in the solid state with the stronger Lewis base pyridine, co-crystals of benzene adducts were investigated to gain an understanding of the influence of aryl-aryl interactions. These co-crystals showed halogen bonding only for the two heavier halotetrafluoropyridines. In the pyridine co-crystals halogen bonding was observed for all three para-halotetrafluoropyridines. The formation of homodimers and heterodimers with pyridine is also supported by quantum-chemical calculations of electron density topologies and natural bond orbitals.

Identification of an Overlooked Halogen-Bond Synthon and Its Application in Designing Fluorescent Materials

Research on new supramolecular synthons facilitates the progress of materials design. Herein, the ability of sp² carbonyl oxygen atoms to act as halogen-bond acceptors was established through cocrystallization. Four sets of carbonyl compounds, including aldehydes, ketones, esters, and amides, were selected as halogen-bond acceptors. In the absence of strong hydrogen bonds, 14 out of 16 combinations of halogen-bond donors and acceptors could form cocrystals, whereby the supramolecular synthon C=O⋅⋅⋅X acts as the main interaction. Further, the geometric parameters of the C=O⋅⋅⋅X interaction were statistically revealed on the basis of the crystallographic database. The bifurcated interaction mode that has been observed in other halogen-bond synthons rarely occurs in the case of C=O⋅⋅⋅X. The robustness of C=O⋅⋅⋅X makes its application in crystal engineering possible and opens up new opportunities in designing multicomponent fluorescent materials, as indicated by multicolor emission of cocrystals D through C=O⋅⋅⋅X interactions.

Structure–property relationships in aromatic thioethers featuring aggregation-induced emission: solid-state structures and theoretical analysis

The evolution of the fluorescence quantum yields was correlated with the increase of C–H⋯π and the decrease of π⋯π interactions in the solid state.

Halogen bonding of the aldehyde oxygen atom in cocrystals of aromatic aldehydes and 1,4-diiodotetrafluorobenzene

Novel halogen bonded cocrystals of aromatic aldehydes have been synthesized. We present the halogen bond acceptor potential of the aldehyde group oxygen atom in competition with the hydroxy, methoxy and pyridine groups.

Halogen bonding driven crystal engineering of iodophthalonitrile derivatives

Various halogen bonding driven crystal structures can be obtained by simple modifications of iodophthalonitrile derivatives.

Comparison of isomericmeta- andpara-diiodotetrafluorobenzene as halogen bond donors in crystal engineering

The ability ofmeta- andpara-diiodotetrafluorobenzene to act as halogen bond donors in crystal engineering has been compared by the synthesis and crystal structure analysis of a family of 20 novel halogen-bonded cocrystals with simple monotopic and ditopic nitrogen-based acceptors.

Simple design for metal-based halogen-bonded cocrystals utilizing the M–Cl⋯I motif

The halogen bonding proclivity of the chlorine atom coordinated to the Co(ii) metal centre has been explored by synthesis and crystal structure analysis of a family of 12 novel metal-based halogen-bonded cocrystals with iodine-based donors.

Cooperative intermolecular S–Cl⋯O and F⋯F associations in the crystal packing of α,ω-di(sulfonyl chloride) perfluoroalkanes, ClSO2(CF2)nSO2Cl, where n = 4, 6

Halogen bonding between neighboring sulfonyl chloride groups and short fluorine–fluorine contacts supports crystal formation in the title compounds.

Connectivity and Topology Invariance in Self-Assembled and Halogen-Bonded Anionic (6,3)-Networks

We report here that the halogen bond driven self-assembly of 1,3,5-trifluorotriiodobenzene with tetraethylammonium and -phosphonium bromides affords 1:1 co-crystals, wherein the mutual induced fit of the triiodobenzene derivative and the bromide anions (halogen bond donor and acceptors, respectively) elicits the potential of these two tectons to function as tritopic modules (6,3). Supramolecular anionic networks are present in the two co-crystals wherein the donor and the acceptor alternate at the vertexes of the hexagonal frames and cations are accommodated in the potential empty space encircled by the frames. The change of one component in a self-assembled multi-component co-crystal often results in a change in its supramolecular connectivity and topology. Our systems have the same supramolecular features of corresponding iodide analogues as the metric aspects seem to prevail over other aspects in controlling the self-assembly process.

Cyclic networks of halogen-bonding interactions in molecular self-assemblies: a theoretical N-X...N versus C-X...N investigation

The geometries and energetics of molecular self-assembly structures that contain a sequential network of cyclic halogen-bonding interactions are investigated theoretically. The strength of the halogen-bonding interactions is assessed by examining binding energies, electron charge transfer (NBO analysis) and electron density at halogen-bond critical points (AIM theory). Specifically, structural motifs having intramolecular N-X...N (X = Cl, Br, or I) interactions and the ability to drive molecular self-assembly via the same type of interactions are used to construct larger self-assemblies of up to three unit motifs. N-X...N halogen-bond cooperativity as a function of the self-assembly size, and the nature of the halogen atom is also examined. The cyclic network of the halogen-bonding interactions provides a suitable cavity rich in electron density (from the halogen atom lone pairs not involved in the halogen bonds) that can potentially bind an electron-deficient species such as a metal ion. This possibility is explored by examining the ability of the N-X...N network to bind Na⁺. Likewise, molecular self-assembly structures driven by the weaker C-X...N halogen-bonding interactions are investigated and the results compared with those of their N-X...N counterparts.

Halogen bonding stabilizes acis-azobenzene derivative in the solid state: a crystallographic study

Crystals oftrans- andcis-isomers of a fluorinated azobenzene derivative have been prepared and characterized by single-crystal X-ray diffraction. The presence of F atoms on the aromatic core of the azobenzene increases the lifetime of the metastablecis-isomer, allowing single crystals of thecis-azobenzene to be grown. Structural analysis on thecis-azobenzene, complemented with density functional theory calculations, highlights the active role of the halogen-bond contact (N...I synthon) in promoting the stabilization of thecis-isomer. The presence of a long aliphatic chain on the azobenzene unit induces a phase segregation that stabilizes the molecular arrangement for both thetrans- andcis-isomers. Due to the rarity ofcis-azobenzene crystal structures in the literature, our paper makes a step towards understanding the role of non-covalent interactions in driving the packing of metastable azobenzene isomers. This is expected to be important in the future rational design of solid-state, photoresponsive materials based on halogen bonding.

Supramolecular nanotubes based on halogen bonding interactions: cooperativity and interaction with small guests

In this manuscript the formation of a series of self-assembled supramolecular nanotubes (SNTs) governed by noncovalent halogen bonding interactions is studied.

The halogen bonding proclivity of the ortho-methoxy–hydroxy group in cocrystals of o-vanillin imines and diiodotetrafluoro-benzenes

Novel halogen bondedo-hydroxy imine cocrystals with 1,2-, 1,3- and 1,4-diiodotetrafluorobenzene have been synthesized. We present an insight into the halogen bond acceptor potential of theortho-methoxy–hydroxy group of theo-vanillin moiety.

A quantitative measure of halogen bond activation in cocrystallization

Calculated energy profiles for XB show the activating effect of ring substituents. The results match the outcome of experimental studies by Aakeröy et al. Cryst.Growth Des., 2015, 15, 3853.

Superfluorinated Ionic Liquid Crystals Based on Supramolecular, Halogen-Bonded Anions

Unconventional ionic liquid crystals in which the liquid crystallinity is enabled by halogen-bonded supramolecular anions [Cn F2 n+1 -I⋅⋅⋅I⋅⋅⋅I-Cn F2 n+1 ](-) are reported. The material system is unique in many ways, demonstrating for the first time 1) ionic, halogen-bonded liquid crystals, and 2) imidazolium-based ionic liquid crystals in which the occurrence of liquid crystallinity is not driven by the alkyl chains of the cation.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Intriguing I2 Reduction in the Iodide for Chloride Ligand Substitution at a Ru(II) Complex: Role of Mixed Trihalides in the Redox Mechanism

The compound [Ru(CN(t)Bu)4(Cl)2], 1, reacts with I2, yielding the halogen-bonded (XB) 1D species {[Ru(CN(t)Bu)4(I)2]·I2}n, (2·I2)n, whose building block contains I(-) ligands in place of Cl(-) ligands, even though no suitable redox agent is present in solution. Some isolated solid-state intermediates, such as {[Ru(CN(t)Bu)4(Cl)2]·2I2}n, (1·2I2)n, and {[Ru(CN(t)Bu)4(Cl)(I)]·3I2}n, (3·3I2)n, indicate the stepwise substitution of the two trans-halide ligands in 1, showing that end-on-coordinated trihalides play a key role in the process. In particular, the formation of ClI2(-) triggers electron transfer, possibly followed by an inverted coordination of the triatomic species through the external iodine atom. This allows I-Cl separation, as corroborated by Raman spectra. The process through XB intermediates corresponds to reduction of one iodine atom combined with the oxidation of one coordinated chloride ligand to give the corresponding zerovalent atom of I-Cl. This redox process, explored by density functional theory calculations (B97D/6-31+G(d,p)/SDD (for I and Ru atoms)), is apparently counterintuitive with respect to the known behavior of the corresponding free halogen systems, which favor iodide oxidation by Cl2. On the other hand, similar energy barriers are found for the metal-assisted process and require a supply of energy to be passed. In this respect, the control of the temperature is fundamental in combination with the favorable crystallizations of the various solid-state products. As an important conclusion, trihalogens, as XB adducts, are not static in nature but are able to undergo dynamic inner electron transfers consistently with implicit redox chemistry.

Coordination networks incorporating halogen-bond donor sites and azobenzene groups

A coordination network decorated with halogen-bond donor sites for specific guest binding.

Synergistic effects of halogen bond and π–π interactions in thiophene-based building blocks

The use of a thiophene-based building block (Pyr-T) to achieve a supramolecular assembly driven by halogen bonding (XB) is described. X-ray crystallography, NMR, Raman spectroscopy, and computational chemistry afford evidence of strong XB and π–π stacking.

Stabilizing volatile liquid chemicals using co-crystallization

A convenient, effective, and scalable protocol for stabilizing volatile liquid chemicals is reported.

Cooperative effects and optimal halogen bonding motifs for self-assembling systems

Halogen bonding, due to its directionality and tunable strength, is being increasingly utilized in self-assembling materials and crystal engineering. Using density functional theory (DFT) and molecular mechanics (OPLS/CM1Ax) calculations, multiply halogen bonded complexes of brominated imidazole and pyridine are investigated along with their potential in construction of self-assembling architectures. Dimers with 1–10 halogen bonds are considered and reveal maximal binding energies of 3–36 kcal/mol. Cooperative (nonadditive) effects are found in complexes that extend both along and perpendicular to the halogen bonding axes, with interaction energies depending on polarization, secondary interactions, and ring spacers. Four structural motifs were identified to yield optimal halogen bonding. For the largest systems, the excellent agreement found between the DFT and OPLS/CM1Ax results supports the utility of the latter approach for analysis and design of self-assembling supramolecular structures.

Azobenzene-based difunctional halogen-bond donor: towards the engineering of photoresponsive co-crystals

Halogen bonding is emerging as a powerful non-covalent interaction in the context of supramolecular photoresponsive materials design, particularly due to its high directionality. In order to obtain further insight into the solid-state features of halogen-bonded photoactive molecules, three halogen-bonded co-crystals containing an azobenzene-based difunctional halogen-bond donor molecule, (E)-bis(4-iodo-2,3,5,6-tetrafluorophenyl)diazene, C12F8I2N2, have been synthesized and structurally characterized by single-crystal X-ray diffraction. The crystal structure of the non-iodinated homologue (E)-bis(2,3,5,6-tetrafluorophenyl)diazene, C12H2F8N2, is also reported. It is demonstrated that the studied halogen-bond donor molecule is a reliable tecton for assembling halogen-bonded co-crystals with potential photoresponsive behaviour. The azo group is not involved in any specific intermolecular interactions in any of the co-crystals studied, which is an interesting feature in the context of enhanced photoisomerization behaviour and photoactive properties of the material systems.