Computational Design of Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis.

In recent years, halogen bond-based organocatalysis has garnered significant attention as an alternative to hydrogen-based catalysis, capturing considerable interest within the scientific community. This transition has witnessed the evolution of catalytic scaffolds from monodentate to bidentate architectures, and from monovalent to hypervalent species. In this DFT-based study, we explored a bidentate hypervalent iodine(III)-based system that has already undergone experimental validation. Additionally, we explore various functionalisations (-CF$_3$, -CH$_3$, -tBu, -OH, -OMe, -NO$_2$, -CN) and scaffold modifications, such as sulfur oxidation, theoretically proposed for an indole-based Michael addition. The investigated systems favour bidentate O-type binding, underlining the importance of ligand coordination in catalytic activity. Electron-deficient scaffolds exhibited stronger binding and lower activation energies, indicating the pivotal role of electronic properties for $\sigma$-hole-based catalysis. Of these groups, Lewis-base-like moieties formed stabilising intramolecular interactions with hypervalent iodines when in the ortho-position. Furthermore, inductive electron withdrawal was deemed more effective than mesomeric withdrawal in enhancing catalytic efficacy for these systems. Lastly, increasing sulfur oxidation was theoretically proven to improve catalytic activity significantly.

Hypervalent Iodine (III)-Based Complexation for Chiroptical Supramolecular Glass, Deep Eutectic Solvent and Luminescent Switch.

Hypervalent iodine(III) have widely been utilized for organic synthetic reagents. They are also recognized as positive charge-assisted, exceptionally robust biaxial halogen bond donors, while their potential in supramolecular materials is barely explored. This work reports a cyclic diaryliodonium ion as biaxial halogen bonding donor that displays remarkable binding affinity toward phenanthroline or acridine acceptors with chiral pendants. Biaxial halogen bonding enables chiroptical evolution in solution, allowing for rational control over supramolecular chirality. Leveraging their strong binding affinity, the halogen bonding complexes manifested amorphous properties and deep eutectic behavior in the solid state. Capitalizing on these attributes, this work achieves the successful preparation of supramolecular glasses and deep eutectic solvents. Additionally, halogen bonding appended light irradiation-triggered luminescence through a hydrogen atom transfer process, showing applications in anti-counterfeit and display.

Functionalized Gold Nanoparticles and Halogen Bonding Interactions Involving Fentanyl and Fentanyl Derivatives.

Fentanyl (FTN) and synthetic analogs of FTN continue to ravage populations across the globe, including in the United States where opioids are increasingly being used and abused and are causing a staggering and growing number of overdose deaths each year. This growing pandemic is worsened by the ease with which FTN can be derivatized into numerous derivatives. Understanding the chemical properties/behaviors of the FTN class of compounds is critical for developing effective chemical detection schemes using nanoparticles (NPs) to optimize important chemical interactions. Halogen bonding (XB) is an intermolecular interaction between a polarized halogen atom on a molecule and e--rich sites on another molecule, the latter of which is present at two or more sites on most fentanyl-type structures. Density functional theory (DFT) is used to identify these XB acceptor sites on different FTN derivatives. The high toxicity of these compounds necessitated a "fragmentation" strategy where smaller, non-toxic molecules resembling parts of the opioids acted as mimics of XB acceptor sites present on intact FTN and its derivatives. DFT of the fragments' interactions informed solution measurements of XB using 19F NMR titrations as well as electrochemical measurements of XB at self-assembled monolayer (SAM)-modified electrodes featuring XB donor ligands. Gold NPs, known as monolayer-protected clusters (MPCs), were also functionalized with strong XB donor ligands and assembled into films, and their interactions with FTN "fragments" were studied using voltammetry. Ultimately, spectroscopy and TEM analysis were combined to study whole-molecule FTN interactions with the functionalized MPCs in solution. The results suggested that the strongest XB interaction site on FTN, while common to most of the drug's derivatives, is not strong enough to induce NP-aggregation detection but may be better exploited in sensing schemes involving films.

Crystal structure of 4,4'-(disulfanedi-yl)dipyridinium chloride triiodide.

4,4'-(Disulfanedi-yl)dipyridinium chloride triiodide, C10H10N2S2 2+·Cl-·I3 -, (1) was synthesized by reaction of 4,4'-di-pyridyl-disulfide with ICl in a 1:1 molar ratio in di-chloro-methane solution. The structural characterization of 1 by SC-XRD analysis was supported by elemental analysis, FT-IR, and FT-Raman spectroscopic measurements.

A Halogen-Bonded Fluorescent Molecular Photoswitch: Transition from 3D Cubic Lattice to 1D Helical Superstructure for Polarization Inversion of Circularly Polarized Luminescence.

The fabrication of materials that can switch between circularly polarized luminescence (CPL) signals is both essential and challenging. Here, two new halogen-bonded fluorescent molecular photoswitches, namely, HB-switch 1 and HB-switch 2, containing α-cyano-substituted diarylethene compounds with different end groups were developed. Upon exposure to specific UV or visible light wavelengths, they exhibited controllable and reversible Z/E photoisomerization. When these switches were integrated into blue-phase liquid crystals (BPLCs), the temperature range of BP significantly expanded. Notably, the BP system incorporating HB-switch 1 exclusively achieved reversible polarization inversion of CPL signals under specific UV/visible light irradiation and during cooling/heating. The photo/thermal dual-response behavior of the CPL signals can be attributed to the phase transition from a high-symmetry 3D BP I lattice to a low-symmetry 1D helical superstructure induced by the Z/E photoisomerization of HB-switch 1 and temperature changes. This study underscores the significance of employing halogen-bond assembly strategies to design materials with switchable CPL signals, opening new possibilities for CPL-active systems.

Computational and Spectroscopic Studies on the Formation of Halogen-Bonded Complexes Between Tertiary Amines and CBr4 and Application in the Light-Mediated Amino Acid Coupling.

In recent years, halogen-bonded complexes (XBCs), in solution, have played a pivotal role in inducing photochemical organic reactions. In this work, we explore the ability of various tertiary amines to act as XB acceptors in the presence of the XB donor CBr4 by computational and spectroscopic studies. DFT studies clearly showcase the formation of XBCs between the studied tertiary amines and CBr4. Simultaneously, computational and experimental UV-Vis studies display intense red shifts that are consistent with charge transfer observed from tertiary amines to CBr4. A detailed NMR study revealed a clear chemical shift of the carbon carrying the bromine atoms upon mixing the XB acceptor with the donor, suggesting that this spectroscopic technique is indeed an experimental tool to identify the generation of XBCs. An application of the ability of such XBCs to activate a carboxylic acid under UVA irradiation or sunlight is presented for amino acid coupling. Among the various tertiary amines studied, the pair DABCO-CBr4 was found to work well for the photochemical amide bond formation. Direct infusion-HRMS studies allowed us to propose a general mechanism for the photochemical amino acid coupling in the presence of a tertiary amine and CBr4, initiated by the photoactivation of an XBC.

Halogen, Chalcogen, Pnictogen, and Tetrel Bonding in Non-Covalent Organocatalysis: An Update.

The use of noncovalent interactions based on electrophilic halogen, chalcogen, pnictogen, or tetrel centers in organocatalysis has gained noticeable attention. Herein, we provide an overview on the most important developments in the last years with a clear focus on experimental studies and on catalysts which act via such non-transient interactions.

Utilizing "Latent" Carbon: Repositioning Hydrogen-Bonded Synthons and Assemblies via Halogen Bonding to π-Systems.

Molecules bearing carboxylic acid, amide, and hydroxyl groups are ubiquitous in crystal engineering, where robust hydrogen-bonded synthons centred on these functionalities enable reliable crystal structure design. We now show that halogen bonding to the carbon π-system of such molecules, traditionally ignored in crystal engineering, permits the recognition and directional assembly of the resulting hydrogen-bonded structural subunits, leaving the archetypal hydrogen-bonded ring, ladder, and chain homosynthons intact, but repositioned in space. When applied to heteromolecular synthons, this enables rearranging more complex hydrogen-bonded motifs and the evolution of binary cocrystals into ternary ones through "latent" carbon-based recognition sites, demonstrating a rational approach to build higher-order solid-state supramolecular assemblies.

Tailoring supramolecular solvents with phosphoryl groups for highly efficient extraction of chlorophenols in natural waters.

BACKGROUND: Chlorophenols are routinely determined in aquatic systems to check compliance with the restrictive international legislations set for protection of human and aquatic life. Their control requires affordable analytical methods, particularly in labs at low- and medium-income countries. Liquid chromatography-UV detection is a convenient technique for this purpose, but the availability of suitable sample processing remains pending. Organic solvents are inefficient for extracting the whole range of chlorophenols whereas solid-phase extractions are expensive and labour-intensive. So, an efficient, fast and cheap extraction of chlorophenols, amenable to any lab, would help to cope with their worldwide analytical control in natural waters. RESULTS: A supramolecular solvent (SUPRAS) was tailored for providing mixed interaction mechanisms aimed at the efficient extraction of chlorophenols prior to LC-UV. The SUPRAS was synthesized from the self-assembly of hexylphosphonic acid under acidic conditions and consisted of sponge-like nanostructures made up of amphiphile and water. The phosphoryl (PO) group was selected as the major driver of the extraction because of its ability to act as halogen and hydrogen bond acceptor for chlorophenols. Additional interactions were hydrogen bonds from O-H amphiphilic groups and the surrounding water, and dispersion and CH-π interactions in the hydrocarbon chains. The number of binding sites in the SUPRAS could be modulated by addition of salt. The SUPRAS formed in situ in the sample, the extraction took 5 min, the concentration factor was around 220, quantification limits (0.1-0.3 µg L-1) were below the EU standards, and the method worked for natural waters. SIGNIFICANCE: A fast, low-cost, and organic solvent-free sample processing only requiring conventional lab equipment (stirrers and centrifuges) provided SUPRAS extracts that could be directly analyzed by LC-UV. SUPRAS synthesis occurred spontaneously in the water sample under addition of hexylphosphonic acid and the whole process required low skills. The method meets the analytical and operational performances for the analytical control of chlorophenols in natural waters and it is within the reach of any lab.

Facile construction of a stable core-shell spherically magnetic polyimide covalent organic framework for efficient extraction of phenylurea herbicides.

Efficient enrichment is crucial for the highly sensitive monitoring of phenylurea herbicides (PUHs) in various environmental waters. In this work, a stable core-shell spherically magnetic polyimide covalent organic framework (COF) was synthesized via a simple template-mediated precipitation polymerization method under mild conditions using tri(4-aminophenyl)amine (TAPA) and 3,3',4,4'-biphenyltetracarboxylic dianhydride (BPDA) as the building units (denoted as Fe3O4@TAPA-BPDA). The Fe3O4@TAPA-BPDA exhibits remarkable adsorption performance for PUHs with an optimized adsorption time of only 10 min. The adsorption of PUHs by Fe3O4@TAPA-BPDA followed the pseudo-second-order kinetic model and the Langmuir model. Furthermore, hydrogen bonding, halogen bonding, hydrophobic interaction, electro donor-acceptor interaction and π-π interactions are identified as the dominant mechanisms contributing to excellent adsorption performance. It was demonstrated that halogen bonds play an important role in the adsorption of substances containing chlorine atoms. The Fe3O4@TAPA-BPDA is easy to operate and highly regenerable. A simple magnetic solid-phase extraction (MSPE) method based on the Fe3O4@TAPA-BPDA was then developed for the rapid extraction of five PUHs in real samples, coupled with high-performance liquid chromatography (HPLC) determination. The analytical method developed has a linear range of 0.5-50 ng/mL, and the limit of detection (LOD) ranges from 0.06 to 0.10 ng/mL. The method exhibits good accuracy with recoveries ranged from 74.5 % to 111.4 %. The analytical method was successfully applied to the highly sensitive detection of PUHs in environmental water samples, which highlighting the potential application of the Fe3O4@TAPA-BPDA in the sample pretreatment.

Hydrogen- and halogen-bonding-directed trimeric supramolecular motifs in dihalogenated 1,2,4-triazoles.

Hydrogen-bonding and halogen-bonding interactions are important noncovalent interactions that play a significant role in the crystal structure of organic molecules. An in-depth analysis is given of the crystal packing of two previously reported crystal structures of dihalogenated 1,2,4-triazole derivatives, namely 3,5-dichloro-1H-1,2,4-triazole and 3,5-dibromo-1H-1,2,4-triazole. This work provides insights into the complex interplay of hydrogen-bonding and halogen-bonding interactions resulting in the formation of multiple trimeric motifs in the crystal structure of 1,2,4-triazole derivatives. Analysis of the crystal packing of these isostructural crystal structures revealed that the molecular arrangement in these molecules is primarily stabilized by the formation of different trimeric motifs stabilized by N-H...N hydrogen bonds, N-H...X (X = Cl/Br) halogen bonds and C-X...X halogen-bonding interactions. Computational studies further revealed that all these trimers are energetically stable. A crystallographic database search further reveals that while the cyclic trimers reported in this study are present in other molecules, structures analyzed in this study are the sole instances where all are present simultaneously.

Diphenylene Iodonium as a Prominent Halogen Bond Donor: The Case of Human Monoamine Oxidase B.

Herein we have investigated the formation and interplay of several noncovalent interactions (NCIs) involved in the inhibition of human monoamine oxidase B (MAO B). Concretely, an inspection of the Protein Data Bank (PDB) revealed the formation of a halogen bond (HlgB) between a diphenylene iodonium (DPI) inhibitor and a water molecule present in the active site, in addition to a noncovalent network of interactions (e. g. lone pair-π, hydrogen bonding, OH-π, CH-π and π-stacking interactions) with surrounding protein residues. Several theoretical models were built to understand the strength and directionality features of the HlgB in addition to the interplay with other NCIs present in the active site of the enzyme. Besides, a computational study was carried out using DPI as HlgB donor and several electron rich molecules (CO, H2O, CH2O, HCN, pyridine, OCN-, SCN-, Cl- and Br-) as HlgB acceptors. The results were analyzed using several state-of-the-art computational tools. We expect that our results will be useful for those scientists working in the fields of rational drug design, chemical biology as well as supramolecular chemistry.

Halogen Bond-Assisted Supramolecular Dimerization of Pyridinium-Fused 1,2,4-Selenadiazoles via Four-Center Se2N2 Chalcogen Bonding.

The synthesis and structural characterization of α-haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles with various counterions is reported herein, demonstrating a strategy for directed supramolecular dimerization in the solid state. The compounds were obtained through a recently discovered 1,3-dipolar cycloaddition reaction between nitriles and bifunctional 2-pyridylselenyl reagents, and their structures were confirmed by the X-ray crystallography. α-Haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles exclusively formed supramolecular dimers via four-center Se···N chalcogen bonding, supported by additional halogen bonding involving α-haloalkyl substituents. The introduction of halogens at the α-position of the substituent R in the selenadiazole core proved effective in promoting supramolecular dimerization, which was unaffected by variation of counterions. Additionally, the impact of cocrystallization with a classical halogen bond donor C6F3I3 on the supramolecular assembly was investigated. Non-covalent interactions were studied using density functional theory calculations and topological analysis of the electron density distribution, which indicated that all ChB, XB and HB interactions are purely non-covalent and attractive in nature. This study underscores the potential of halogen and chalcogen bonding in directing the self-assembly of functional supramolecular materials employing 1,2,4-selenadiazoles derived from recently discovered cycloaddition between nitriles and bifunctional 2-pyridylselenyl reagents.

Fluoro and Trifluoromethyl Benzoyl Hypoiodite Complexes with Substituted Pyridines.

Based on the prior observation of the trifluoroacetate hypoiodite, CF3C(O)OI, demonstrating the largest σ-hole of a neutral halogen bond donor, a series of mono- and bis-carbonyl hypoiodites utilising trifluoromethyl or fluorine substituents at various positions of a parent benzoyl skeleton have been synthesised. The carbonyl hypoiodite complexes were prepared via cation exchange of the silver(I) cations with iodine(I) from the respective silver(I) carboxylates and dicarboxylates as the synthetic precursors. A range of pyridinic Lewis bases of varying nucleophilicities were used to stabilise the carbonyl hypoiodites to further probe their properties. The silver(I) intermediates with these Lewis bases were also isolated for silver(I) pentafluorobenzoate, providing additional insight into the cation exchange reaction. All complexes were characterised both in solution (1H, 1H-15N HMBC, 19F) and in the solid state (SCXRD), permitting insights into the formation of the elusive pyridine-iodine(I) cation.

Leveraging Halogen Interactions for a Supramolecular Nanotube.

We demonstrate the formation of supramolecular nanotubes from molecular triangles in a single crystal by balancing the hydrogen bonds and halogen interactions between individual macrocycles. Thereby, we template the supramolecular nanotube growth by intermolecular interactions encoded directly in the macrocycles instead of those provided by the crystallization solvent. Ultimately, we show that replacing bromines for iodines in the macrocycle is necessary to achieve this supramolecular organization by enhancing the strength of the halogen interactions and concomitant reduction of the detrimental hydrogen bonds. We investigated the nature and the interplay of the individual intermolecular interactions by analysis of the experimental single crystal data and quantum chemical calculations. This work enriches the available toolbox of supramolecular interactions and will aid and abet the development of rationally-designed materials with a long-range 1D tubular organization.

A Halogen Bonding [2]Rotaxane Shuttle for Chloride-Selective Optical Sensing.

The first example of a [2]rotaxane shuttle capable of selective optical sensing of chloride anions over other halides is reported. The rotaxane was synthesised via a chloride ion template-directed cyclisation of an isophthalamide macrocycle around a multi-station axle containing peripheral naphthalene diimide (NDI) stations and a halogen bonding (XB) bis(iodotriazole) based station. Proton NMR studies indicate the macrocycle resides preferentially at the NDI stations in the free rotaxane, where it is stabilised by aromatic donor-acceptor charge transfer interactions between the axle NDI and macrocycle hydroquinone moieties. Addition of chloride ions in an aqueous-acetone solvent mixture induces macrocycle translocation to the XB anion binding station to facilitate the formation of convergent XB⋅⋅⋅Cl- and hydrogen bonding HB⋅⋅⋅Cl- interactions, which is accompanied by a reduction of the charge-transfer absorption band. Importantly, little to no optical response was induced by addition of bromide or iodide to the rotaxane, indicative of the size discriminative steric inaccessibility of the interlocked cavity to the larger halides, demonstrating the potential of using the mechanical bond effect as a potent strategy and tool in chloride-selective chemo-sensing applications in aqueous containing solvent environments.

Perfect Polar Alignment of Parallel Beloamphiphile Layers: Improved Structural Design Bias Realized in Ferroelectric Crystals of the Novel "Methoxyphenyl Series of Acetophenone Azines".

An improved design is described for ferroelectric crystals and implemented with the "methoxyphenyl series" of acetophenone azines, (MeO-Ph, Y)-azines with Y=F (1), Cl (2), Br (3), or I (4). The crystal structures of these azines exhibit polar stacking of parallel beloamphiphile monolayers (PBAMs). Azines 1, 3, and 4 form true racemates whereas chloroazine 2 crystallizes as a kryptoracemate. Azines 1-4 are helical because of the N-N bond conformation. In true racemates the molecules of opposite helicity (M and P) are enantiomers A(M) and A*(P) while in kryptoracemates they are diastereomers A(M) and B*(P). The stacking mode of PBAMs is influenced by halogen bonding, with 2-4 showcasing a kink due to directional interlayer halogen bonding, whereas fluoroazine 1 demonstrates ideal polar stacking by avoiding it. Notably, (MeO-Ph, Y)-azines display a stronger bias for dipole parallel alignment, attributed to the linearity of the biphenyl moiety as compared to the phenoxy series of (PhO, Y)-azines with their non-linear Ph-O-Ph moiety. The crystals of 1-4 all feature planar biphenyls and this synthon facilitates their crystallization through potent triple T-contacts and enhances their nonlinear optical (NLO) performance by increasing conjugation length and affecting favorable chromophore conformations in the solids.

Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes.

Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.

Photochemical Synthesis of Lactones, Cyclopropanes and ATRA Products: Revealing the Role of Sodium Ascorbate.

Light-mediated processes have received significant attention, since they have re-surfaced unconventional reactivity platforms, complementary to conventional polar chemistry. γ-Lactones and cyclopropanes are prevalent moieties, found in numerous natural products and pharmaceuticals. Among various methods for their synthesis, light-mediated protocols are coming to the spotlight, although these are contingent upon the use of photoorgano- or metal-based catalysts. Herein, we introduce a novel photochemical activation of iodo-reagents via the use of cheap sodium ascorbate or ascorbic acid to enable their homolytic scission and addition onto double bonds. The developed protocol was applied successfully to the formal [3+2] cycloaddition for the synthesis of γ-lactones, traditional atom transfer radical addition (ATRA) reactions and the one-pot two-step conversion of alkenes to cyclopropanes. In all cases, the desired products were obtained in good to high yields, while the reaction mechanism was thoroughly investigated. Depending on the nature of the iodo-reagent, a halogen or a hydrogen-bonded complex is formed, which initiates the process.

A Halogen-Bond-Driven Artificial Chloride-Selective Channel Constructed from 5-Iodoisophthalamide-based Molecules.

Despite considerable emphasis on advancing artificial ion channels, progress is constrained by the limited availability of small molecules with the necessary attributes of self-assembly and ion selectivity. In this study, a library of small molecules based on 5-haloisophthalamide and a non-halogenated isophthalamide were examined for their ion transport properties across the lipid bilayer membranes, and the finding demonstrates that the di-hexyl-substituted 5-iodoisophthalamide derivative exhibits the highest level of activity. Furthermore, it was established that the highest active compound facilitates the selective chloride transport that occurs via an antiport-mediated mechanism. The crystal structure of the compound unveils a distinctive self-assembly of molecules, forming a zig-zag channel pore that is well-suited for the permeation of anions. Planar bilayer conductance measurements proved the formation of chloride selective channels. A molecular dynamics simulation study, relying on the self-assembled component derived from the crystal structure, affirmed the paramount significance of intermolecular hydrogen bonding in the formation of supramolecular barrel-rosette structures that span the bilayer. Furthermore, it was demonstrated that the transport of chloride across the lipid bilayer membrane is facilitated by the synergistic effects of halogen bonding and hydrogen bonding within the channel.