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.

Influence of Multiple Binding Sites on the Supramolecular Assembly of N-[(3-pyridinylamino) Thioxomethyl] Carbamates

In this study, we investigated how the presence of multiple intermolecular interaction sites influences the heteromeric supramolecular assembly of N-[(3-pyridinylamino) thioxomethyl] carbamates with fluoroiodobenzenes. Three targets—R-N-[(3-pyridinylamino) thioxomethyl] carbamate (R = methyl, ethyl, and isobutyl)—were selected and crystallized, resulting in three parent structures, five co-crystals, and one co-crystal solvate. Three hydrogen-bonded parent crystal structures were stabilized by N-H···N hydrogen bonding and assembled into layers that stacked on top of one another. Molecular electrostatic potential surfaces were employed to rank binding sites (Npyr > C=S > C=O) in order to predict the dominant interactions. The N-H⋯H hydrogen bond was replaced by I⋯Npyr in 3/6 cases, I⋯C=S in 4/6 cases, and I⋯O=C in 1 case. Interestingly, the I⋯C=S halogen bond coexisted twice with I⋯Npyr and I⋯O=C. Overall, the MEPs were fairly reliable for predicting co-crystallization outcomes; however, it is crucial to also consider factors such as molecular flexibility. Finally, halogen-bond donors are capable of competing for acceptor sites, even in the presence of strong hydrogen-bond donors.

Synthesis and cationic polymerization of halogen bonding vinyl ether monomers

Halogen bonding is rapidly becoming recognized as a viable and useful intermolecular interaction in supramolecular chemistry. While various monomers amenable to radical polymerization methods containing halogen bonding donors have been developed, this study aims to expand the type of monomers that incorporate this intermolecular interaction to facilitate use of cationic polymerization by developing three novel vinyl ether monomers containing halogen bonding donor moieties: 2,3,5,6-tetrafluoro-4-iodophenoxyethyl vinyl ether (C2I), 2,3,5,6-tetrafluoro-4-iodophenoxybutyl vinyl ether (C4I), and 2-(2,3,5,6-tetrafluoro-4-iodophenoxyethoxy)ethyl vinyl ether (O3I). Well controlled cationic polymerization is achievable through the use of a proton trap, 2,6-di-tert-butylpyridine. The use of SnCl₄ as a co-Lewis acid was found to accelerate the reaction. Between the three monomers, the difference in the chain length is shown to influence the reaction rate, with the longest chain demonstrating the fastest polymerization. Initial studies of the halogen bonding ability shows that halogen bonding exists for all three monomers but is most pronounced in C4I. The polymerized vinyl ethers also exhibit halogen bonding. Due to the ease of synthesis and polymerization, these are promising new monomers to increase functionality available for polymers synthesized using cationic polymerization.

Three novel vinyl ether monomers containing halogen bonding moieties were synthesized, polymerized via cationic polymerization and exhibited clear halogen bonding.

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.

Chalcogen Bonding in Co-Crystals: Activation through 1,4-Perfluorophenylene vs. 4,4'-Perfluorobiphenylene Cores

The ability of alkylseleno/alkyltelluroacetylenes such as bis(selenomethylethynyl)-perfluorobenzene (4F-Se) to act as a ditopic chalcogen bond (ChB) donor in co-crystals with ditopic Lewis bases such as 4,4′-bipyridine is extended here to the octafluorobiphenylene analog, 4,4′-bis(selenomethylethynyl)-perfluorobiphenyl (8F-Se), with the more electron-rich 4,4′-bipyridylethane (bpe), showing in the 1:1 (8F-Se)•(bpe) co-crystal a shorter and more linear C−Se•••N ChB interaction than in (4F-Se)•(bpe), with Se•••N distances down to 2.958(2) Å at 150 K, i.e., a reduction ratio of 0.85 vs. the van der Waals contact distance.

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.

Exploring the Halogen-Bonded Cocrystallization Potential of a Metal-Organic Unit Derived from Copper(ii) Chloride and 4-Aminoacetophenone

In this work, we describe a novel halogen-bonded metal-organic cocrystal involving a square-planar Cu(ii) complex and 1,4-diiodotetrafluorobenzene (14tfib) by utilizing an amine ligand whose pendant acetyl group enables halogen bonding. The cocrystal was prepared by both mechanochemical synthesis (liquid-assisted grinding) and the conventional solution-based method. Crystal structure determination by single crystal X-ray diffraction revealed that the dominant supramolecular interactions are the I···O halogen bond between 14tfib and CuCl₂(aap)₂ building blocks, and the N–H···Cl hydrogen bonds between CuCl₂(aap)₂ molecules. The combination of halogen and hydrogen bonding leads to the formation of a 2D network. Overall, this work showcases an example of the possibility for extending the complexity of metal-organic crystal structures by using halogen bonding in a way that does not affect other hydrogen bonding synthons.

The effect of halogen bonding on protonated hexacyanoferrate networks in hexacyanoferrates of halogenopyridines

Hydrogen bonded network of protonated hexacyanoferrate anions is determined by geometry and halogen bonding proclivity of the halogenopyridinium cation.

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.

A Crystallographic Charge Density Study of the Partial Covalent Nature of Strong N⋅⋅⋅Br Halogen Bonds

The covalent nature of strong N-Br⋅⋅⋅N halogen bonds in a cocrystal (2) of N-bromosuccinimide (NBS) with 3,5-dimethylpyridine (lut) was determined from X-ray charge density studies and compared to a weak N-Br⋅⋅⋅O halogen bond in pure crystalline NBS (1) and a covalent bond in bis(3-methylpyridine)bromonium cation (in its perchlorate salt (3). In 2, the donor N-Br bond is elongated by 0.0954 Å, while the Br⋅⋅⋅acceptor distance of 2.3194(4) is 1.08 Å shorter than the sum of the van der Waals radii. A maximum electron density of 0.38 e Å^-3 along the Br⋅⋅⋅N halogen bond indicates a considerable covalent contribution to the total interaction. This value is intermediate to 0.067 e Å^-3 for the Br⋅⋅⋅O contact in 1, and approximately 0.7 e Å^-3 in both N-Br bonds of the bromonium cation in 3. A calculation of the natural bond order charges of the contact atoms, and the σ*(N1-Br) population of NBS as a function of distance between NBS and lut, have shown that charge transfer becomes significant at a Br⋅⋅⋅N distance below about 3 Å.

Halogen bonding, chalcogen bonding, pnictogen bonding, tetrel bonding: origins, current status and discussion

The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen. This article is based upon my Closing Remarks Lecture at the 203^rd Faraday Discussion meeting on Halogen Bonding in Supramolecular and Solid State Chemistry, held in Ottawa, Canada, on 10-12^th July, 2017. The Discussion included papers on fundamentals and applications of halogen bonding in the solid state and solution phase. Analogous interactions involving main group elements outside group 17 were also examined. In the closing lecture and in this article these contributions have been grouped into the four themes: (a) fundamentals, (b) beyond the halogen bond, (c) characterisation, and (d) applications. The lecture and paper also include a short reflection on past work that has a bearing on the Discussion.

Halogen-bonded cocrystallization with phosphorus, arsenic and antimony acceptors

The formation of non-covalent directional interactions, such as hydrogen or halogen bonds, is a central concept of materials design, which hinges on using small compact atoms of the 2nd period, notably nitrogen and oxygen, as acceptors. Heavier atoms are much less prominent in that context, and mostly limited to sulfur. Here, we report the experimental observation and theoretical study of halogen bonds to phosphorus, arsenic and antimony in the solid state. Combining 1,3,5-trifluoro-2,4,6-triiodobenzene with triphenylphosphine, -arsine, and -stibine provides cocrystals based on I···P, I···As and I···Sb halogen bonds. The demonstration that increasingly metallic pnictogens form halogen bonds sufficiently strong to enable cocrystal formation is an advance in supramolecular chemistry which opens up opportunities in materials science, as shown by colossal thermal expansion of the cocrystal involving I···Sb halogen bonds.

Halogen bonding can be exploited for the design of functional supramolecular materials, but heavier elements that are known to accept a halogen bond remain limited. Here, the authors demonstrate the formation of two-component cocrystals based on halogen bonds with phosphorus, arsenic and antimony.

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.

Choice of hydrogen bonds or halogen bonds by 2-halogenated 5-morpholinomethylphenyl triazolo[1,5-a]pyridine

The crystal structures of halogenated 1,2,4-triazolo[1,5-a]pyridine derivatives disclose intriguing structural chemistry features dictated by the formation of either hydrogen bonds (HBs) or halogen bonds (XBs).

Co-crystal synthesis: fact, fancy, and great expectations

Some strategies for driving co-crystal synthesis using a variety of competing non-covalent interactions are presented.

Halogen-bonded cocrystals ofN-salicylidene Schiff bases and iodoperfluorinated benzenes: hydroxyl oxygen as a halogen bond acceptor

Novel halogen bondedo-hydroxy imine cocrystals with 1,3,5-triiodotrifluoro-benzene and 1,2-, 1,3- and 1,4-diiodotetrafluorobenzene have been synthesized.

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.

Testing the limits of halogen bonding in coordination chemistry

To test the limit of halogen bonds fine-tuning of electron density was performedviaintroduction of heteroatoms and metal cations.

A 3D metal–organic framework with dual-aerial-octahedral trinucleate building units: synthesis, structure and fluorescence sensing properties

JLNU-2 can be used to detect nitrobenzene with high selectivity, sensitivity, anti-interference ability and recyclability through tracing the fluorescence quenching behaviour.

Cocrystal assembled by 1,4-diiodotetrafluorobenzene and phenothiazine based on C-I...π/N/S halogen bond and other assisting interactions

The halogen-bonded cocrystal of 1,4-diiodotetrafluorobenzene (1,4-DITFB) with the butterfly-shape non-planar heterocyclic compound phenothiazine (PHT) was successfully assembled by the conventional solution-based method. X-ray single-crystal diffraction analysis reveals a 3:2 stoichiometric ratio for the cocrystal (1,4-DITFB/PHT), and the cocrystal structure is constructed via C-I...π, C-I...N and C-I...S halogen bonds as well as other assisting interactions (e.g. C-H...F/S hydrogen bond, C-H...H-C and C-F...F-C bonds). The small shift of the 1,4-DITFB vibrational band to lower frequencies in FT-IR and Raman spectroscopies provide evidence to confirm the existence of the halogen bond. In addition, the non-planarity of the PHT molecule in the cocrystal results in PHT emitting weak phosphorescence and relatively strong delayed fluorescence. Thus, a wide range of delayed fluorescence and weak phosphorescence could play a significant role in selecting a proper π-conjugated system to engineer functional cocrystal and luminescent materials by halogen bonds.

A new tecton with parallel halogen-bond donors: a path to supramolecular rectangles

A new tecton, 1,8-diiodoethynylanthracene, with two halogen-bond donor sites was synthesized and characterized. This tecton is capable of forming two parallel halogen bonds at once, which makes it a useful building block for the construction of a variety of supramolecular squares and rectangles.

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.

Halogen bonded cocrystals of active pharmaceutical ingredients: pyrazinamide, lidocaine and pentoxifylline in combination with haloperfluorinated compounds

Six novel halogen-bonded cocrystals of active pharmaceutical ingredients with 1,4-diiodo- and 1,4-dibromotetrafluorobenzene have been synthesized.

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.

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.

Halogen bonding ofN-bromosuccinimide by grinding

Two halogen bonded cocrystals ofN-bromosuccinimide and 4,4′-bipyridine, with stoichiometric ratios 1 : 1 and 2 : 1, have been synthesized and characterized. We present the first mechanochemical cocrystallization ofN-bromosuccinimide.

Influence of the halogen substituent on the formation of halogen and hydrogen bonding in co-crystals formed from acridine and benzoic acids

A series of nine co-crystals formed from acridine and benzoic acids have been synthesized and structurally characterized and the influence of the halogen substituent on the formation of halogen and hydrogen bonding in the co-crystals of the title compounds has been investigated.

Stabilizing volatile liquid chemicals using co-crystallization

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

Molecular electrostatic potential dependent selectivity of hydrogen bonding

A molecular electrostatic potential based approach for anticipating the outcome of hydrogen-bond interactions in a competitive scenario is described.