Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation.

Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 106 nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data.

Expanding chalcogen bonds in thiophenes to interactions with halogens.

Compounds containing the thiophene moiety find several applications in physics and chemistry, such as electrical conduction, which depends on specific conformations to properly exhibiting the desired properties. In turn, chalcogen bonding has found to modulate the conformation of some N-thiophen-2-ylfomamides. Since halogens participate in a kin interaction (halogen bonding) and are abundant in agrochemicals, pharmaceuticals, and materials, we have quantum-chemically explored the interaction between organic halogen and thiophene as a conformational modulator in some model compounds. Although such interaction indeed appears, as demonstrated by atoms in molecules and natural bond orbital analysis, it is inefficient to control the conformational equilibrium. An energy decomposition analysis scheme demonstrated that halomethane and thiophene tend to move away from one another due to a core component (Pauli repulsion and exchange), which is mainly due to a deformation term. Therefore, chalcogen bonds with halogens appear weaker than with other chalcogens.

Fluxional halogen bonds in linear complexes of tetrafluorodiiodobenzene with dinitrobenzene.

The fluxional nature of halogen bonds (XBs) in small molecular clusters, supramolecules, and molecular crystals has received considerable attention in recent years. In this work, based on extensive density-functional theory calculations and detailed electrostatic potential (ESP), natural bonding orbital (NBO), non-covalent interactions-reduced density gradient (NCI-RDG), and quantum theory of atoms in molecules (QTAIM) analyses, we unveil the existence of fluxional halogen bonds (FXBs) in a series of linear (IC6F4I)m(OONC6H4NOO)n (m + n = 2-5) complexes of tetrafluorodiiodobenzene with dinitrobenzene which appear to be similar to the previously reported fluxional hydrogen bonds (FHBs) in small water clusters (H2O)n (n = 2-6). The obtained GS ⇌ TS ⇌ GS ' $$ \mathrm{GS}\rightleftharpoons \mathrm{TS}\rightleftharpoons {\mathrm{GS}}^{\hbox{'}} $$ fluxional mechanisms involve one FXB in the systems which fluctuates reversibly between two linear CI···O XBs in the ground states (GS and GS') via a bifurcated CI O2N van der Waals interaction in the transition state (TS). The cohesive energies (Ecoh) of these complexes with up to four XBs exhibit an almost perfect linear relationship with the numbers of XBs in the systems, with the average calculated halogen bond energy of Ecoh/XB = 3.48 kcal·mol-1 in the ground states which appears to be about 55% of the average calculated hydrogen bond energy (Ecoh/HB = 6.28 kcal·mol-1) in small water clusters.

Synthesis of Double Trivalent Perovskite Quantum Dots Cs3BiSbX9 (X = Cl, Br, I) for Efficient CO2 Photoreduction Performance.

Non-toxic Bi halides have great potential in the field of CO2 photoreduction, but strong charge localization limits their charge separation and transfer. In this study, a series of Cs3BiSbX9 (X = Cl, Br, I) perovskite quantum dots (PQDs) are synthesized by antisolvent recrystallization at room temperature, in which Cs3BiSbBr9 PQDs has high selectivity (94.51%) and yield (15.32 µmol g-1 h-1) of CO2 to CO. In situ DRIFTS and theoretical calculations suggest that the surface charge can be tailored by halogen modulation, allowing for the customization of intermediate species. The Bi─Br─Sb symmetric charge distribution induced by the halogen Br promotes the formation of b─HCOO and reduces the reaction energy barrier of the rate-limiting step, while the weak electronegativity of Cl and the high electronegativity of I leads to m─HCOO and ─COOH production, which are detrimental to CO generation. This work provides new insights into the design of halide alloy perovskites for CO2 photoreduction.

Halogen-bonding boosting the high performance X-ray imaging of organic scintillators.

Organic scintillators with efficient X-ray excited luminescence are essential for medical diagnostics and security screening. However, achieving excellent organic scintillation materials is challenging due to low X-ray absorption coefficients and inferior radioluminescence (RL) intensity. Herein, supramolecular interactions are incorporated, particularly halogen bonding, into organic scintillators to enhance their radioluminescence properties. By introducing heavy atoms (X = Cl, Br, I) into 9,10-bis(4-pyridyl)anthracene (BPA), the formation of halogen bonding (BPA-X) enhances their X-ray absorption coefficient and restricts the molecular vibration and rotation, which boosts their RL intensity. The RL intensity of BPA-Cl and BPA-Br fluorochromes increased by over 2 and 6.3 times compared to BPA, respectively. Especially, BPA-Br exhibits an ultrafast decay time of 8.25 ns and low detection limits of 25.95 ± 2.49 nGy s-1. The flexible film constructed with BPA-Br exhibited excellent X-ray imaging capabilities. Furthermore, this approach is also applicable to organic phosphors. The formation of halogen bonding in bromophenyl-methylpyridinium iodide (PYI) led to a fourfold increase in RL intensity compared to bromophenyl-methyl-pyridinium (PY). It suggests that halogen bonding serves as a promising and effective molecular design strategy for the development of high-performance organic scintillator materials, presenting new opportunities for their applications in radiology and security screening.

Rational Design of the Alkali Metal Sn-Based Mixed Halides with Large Birefringence and Wide Transparent Range.

Birefringent materials are widely used in various advanced optical systems, owing to their vital role in creating and controlling polarized light. Currently, Sn2+-based compounds containing stereochemically active lone-pair (SCALP) cations are extensively investigated and considered as one class of promising birefringent materials. To solve the problem of relatively narrow bandgap of Sn2+-based compounds, alkali metals and multiple halogens are introduced to widen the bandgap during the research. Based on this strategy, four new Sn2+-based halides, A2Sn2F5Cl and ASnFCl2 (A = Rb and Cs), with large birefringence, short ultraviolet (UV) cutoff edge, and wide transparent range are successfully found. The birefringences of A2Sn2F5Cl (A = Rb and Cs) are 0.31 and 0.28 at 532 nm, respectively, which are among the largest in Sn-based halide family. Remarkably, A2Sn2F5Cl possess relatively shorter UV cutoff edge (<300 nm) and broad infrared (IR) transparent range (up to 16.6 µm), so they can become promising candidates as birefringent materials applied in both UV and IR regions. In addition, a comprehensive analysis on crystal structures and structure-property relationship of metal Sn2+-based halides is performed to fully understand this family. Therefore, this work provides insights into designing birefringent materials with balanced optical properties.

Bulk Photovoltaic Effect Induced by Non-Covalent Interactions in Bilayered Hybrid Perovskite for Efficient Passive X-Ray Detection.

Hydrogen bonding as a multifunctional tool has always influenced the structure of hybrid perovskites. Compared with the research on hydrogen bonding, the study of halogen-halogen interactions on the structure and properties of hybrid perovskites is still in its early stages. Herein, a polar bilayered hybrid perovskite (IEA)2FAPb2I7 (IEA+ is 2-iodoethyl-1-ammonium, FA is formamidinium) with iodine-substituted spacer is successfully constructed by changing the configuration of interlayer cations and regulating non-covalent interactions at the organic-inorganic interface, which shows a shorter interlayer spacing and higher density (ρ = 3.862 g cm-3). The generation of structure polarity in (IEA)2FAPb2I7 is caused by the synergistic effect of hydrogen bonding and halogen-halogen interactions. Especially, as the length of the carbon chain in organic cations decreases, the I---I interaction in the system gradually strengthens, which may be the main reason for the symmetry-breaking. Polarity-induced bulk photovoltaics (Voc = 1.0 V) and higher density endow the device based on (I-EA)2FAPb2I7 exhibit a high sensitivity of 175.6 µC Gy-1 cm-2 and an ultralow detection limit of 60.4 nGy s-1 at 0 V bias under X-ray irradiation. The results present a facile approach for designing polar multifunctional hybrid perovskites, also providing useful assistance for future research on halogen-halogen interactions.

Halogen-Site Regulation in Cs3Bi2X9 Quantum Dots for Efficient and Selective Oxidation of Benzyl Alcohol Driven by Solar Light.

Sluggish charge kinetics and low selectivity limit the solar-driven selective organic transformations under mild conditions. Herein, an efficient strategy of halogen-site regulation, based on the precise control of charge transfer and molecule activation by rational design of Cs3Bi2X9 quantum dots photocatalysts, is proposed to achieve both high selectivity and yield of benzyl-alcohol oxidation. In situ PL spectroscopy study reveals that the Bi─Br bonds formed in the form of Br-associated coordination can enhance the separation and transfer of photoexcited carriers during the practical reaction. As the active center, the exclusive Bi─Br covalence can benefit the benzyl-alcohol activation for producing carbon-centered radicals. As a result, the Cs3Bi2Br9 with this atomic coordination achieves a conversion ratio of 97.9% for benzyl alcohol and selectivity of 99.6% for aldehydes, which are 56.9- and 1.54-fold higher than that of Cs3Bi2Cl9. Combined with quasi-in situ EPR, in situ ATR-FTIR spectra, and DFT calculation, the conversion of C6H5-CH2OH to C6H5-CH2* at Br-related coordination is revealed to be a determining step, which can be accelerated via halogen-site regulation for enhancing selectivity and photocatalytic efficiency. The mechanistic insights of this research elucidate how halogen-site regulation in favor of charge transfer and molecule activation toward efficient and selective oxidation of benzyl alcohol.

Modulating 3d Charge State via Halogen Ions in Neighboring Molecules of Metal-Organic Frameworks for Improving Water Oxidation.

Modulating the coordination environment of the metal active center is an effective method to boost the catalytic performances of metal-organic frameworks (MOFs) for oxygen evolution reaction (OER). However, little attention has been paid to the halogen effects on the ligands engineering. Herein, a series of MOFs X─FeNi-MOFs (X = Br, Cl, and F) is constructed with different coordination microenvironments to optimize OER activity. Theoretical calculations reveal that with the increase in electronegativity of halogen ions in terephthalic acid molecular (TPA), the Bader charge of Ni atoms gets larger and the Ni-3d band center and O-2p bands move closer to the Fermi level. This indicates that an increase in ligand negativity of halogen ions in TPA can promote the adsorption ability of catalytic sites to oxygen-containing intermediates and reduce the activation barrier for OER. Experimental also demonstrates that F─FeNi-MOFs exhibit the highest catalytic activity with an ultralow overpotential of 218 mV at 10 mA cm-2, outperforming most otate-of-the-art Fe/Co/Ni-based MOFs catalysts, and the enhanced mass activity by seven times compared with that for the sample before ligands engineering. This work opens a new avenue for the realization of the modulation of NiFe─O bonding by halogen ion in TPA and improves the OER performance of MOFs.

Halide Anions Tuning of Lead-Free Perovskite-Type Ferroelectric Semiconductors with Inverse High-Temperature Symmetry Breaking.

There is a noticeable gap in the literature regarding research on halogen-substitution-regulated ferroelectric semiconductors featuring multiple phase transitions. Here, a new category of 1D perovskite ferroelectrics (DFP)2SbX5 (DFP+ = 3,3-difluoropyrrolidium, X- = I-, Br-, abbreviated as I-1 and Br-2) with twophase transitions (PTs) is reported. The first low-temperature PT is a mmmFmm2 ferroelectric PT, while the high-temperature PT is a counterintuitive inverse temperature symmetry-breaking PT. By the substitution of iodine with bromine, the Curie temperature (Tc) significantly increases from 348 K of I-1 to 374 K of Br-2. Their ferroelectricity and pyroelectricity are improved (Ps value from 1.3 to 4.0 µC cm-2, pe value from 0.2 to 0.48 µC cm-2 K-1 for I-1 and Br-2), while their optical bandgaps increased from 2.1 to 2.7 eV. A critical slowing down phenomenon is observed in the dielectric measurement of I-1 while Br-2 exhibits the ferroelastic domain. Structural and computational analyses elucidate that the order-disorder movement of cations and the distortion of the chain perovskite [SbX5]2- anions skeleton lead to PT. The semiconductor properties are determined by [SbX5]2- anions. The findings contribute to the development of ferroelectric semiconductors and materials with multiple PTs and provide materials for potential applications in the optoelectronic field.

Structure-based improvement of the binding affinity and recognition specificity of peptide competitors to target pediatric IL-5R/IL-5 interaction by gluing halogen bonds at their complex interface.

Human interleukin-5 (IL-5) cytokine mediates the development of eosinophils and is involved in a variety of immune inflammatory responses that play a major role in the pathogenesis of childhood asthma, leukemia, and other pediatric allergic diseases. The immunomodulatory cytokine functions by binding to its cognate cell surface receptor IL-5R in a sheet-by-sheet manner, which can be conformationally mimicked and competitively disrupted by a double-stranded cyclic AF18748 peptide. In this study, we systematically examined the co-crystallized complex structure of human IL-5R with AF18748 peptide and rationally designed a halogen bond to glue at the protein-peptide complex interface by substituting the indole moiety of AF18748 Trp13 residue with a halogen atom (X = F, Cl, Br, or I). High-level theoretical calculations imparted presence of the halogen bond between the oxygen atom (O) of IL-5R Glu58 backbone and the halogen atom (X) of AF18748 Trp13 side chain. Experimental assays confirmed that the halogen bond can promote peptide binding moderately or considerably. More importantly, the halogen bond not only enhances peptide affinity to IL-5R, but also improves peptide selectivity for its cognate IL-5R over other noncognate IL-R proteins. As might be expected, the affinity and selectivity conferred by halogen bond increase consistently in the order: H < F < Cl < Br < I. Structural modeling revealed that the halogen bond plus its vicinal π-cation-π stacking co-define a ringed noncovalent system at the complex interface, which involves a synergistic effect to effectively improve the peptide binding potency and recognition specificity.

The Impact of ortho-substituents on Bonding in Silver(I) and Halogen(I) Complexes of 2-Mono- and 2,6-Disubstituted Pyridines: An In-Depth Experimental and Theoretical Study.

The coordination nature of 2-mono- and 2,6-disubstituted pyridines with electron-withdrawing halogen and electron-donating methyl groups for [N-X-N]+ (X=I, Br) complexations have been studied using 15 N NMR, X-ray crystallography, and Density Functional Theory (DFT) calculations. The 15 N NMR chemical shifts reveal iodine(I) and bromine(I) prefer to form complexes with 2-substituted pyridines and only 2,6-dimethylpyridine. The crystalline halogen(I) complexes of 2-substituted pyridines were characterized by using X-ray diffraction analysis, but 2,6-dihalopyridines were unable to form stable crystalline halogen(I) complexes due to the lower nucleophilicity of the pyridinic nitrogen. In contrast, the halogen(I) complexes of 2,6-dimethylpyridine, which has a more basic nitrogen, are characterized by X-crystallography, which complements the 15 N NMR studies. DFT calculations reveal that the bond energies for iodine(I) complexes vary between -291 and -351 kJ mol-1 and for bromine between -370 and -427 kJ mol-1 . The bond energies of halogen(I) complexes of 2-halopyridines with more nucleophilic nitrogen are 66-76 kJ mol-1 larger than those of analogous 2,6-dihalopyridines with less nucleophilic nitrogen. The experimental and DFT results show that the electronic influence of ortho-halogen substituents on pyridinic nitrogen leads to a completely different preference for the coordination bonding of halogen(I) ions, providing new insights into bonding in halogen(I) chemistry.

Halogen Bonding in N-Alkyl-bromo-/iodo-pyridinium Salts and its Application in Chromatography.

The alkylation of 3-/4-bromo- and -iodopyridine with methyl triflate smoothly affords the corresponding N-methylpyridinium triflate salts. An anion exchange with NaI or [PPh4]Y (Y = Cl, Br, I) yields the corresponding halide salts. Most of them could be structurally characterized and their strong halogen bonds were investigated. While the halogen atom of 4-halogenopyridinium is susceptible to nucleophilic substitution, 3-halogenopyridinium ions are far more stable against nucleophilic attacks. Due to the comparable interaction strength of halogen bonds and hydrogen bonds, the latter of which is widely used in chromatography, the potential of 3-halogenopyridinium moieties for an application in chromatography is obvious and was successfully employed in affinity chromatography of different proteins.

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.

Halogen Bonding Tripodal Metallo-Receptors for Phosphate Recognition and Sensing in Aqueous-Containing Organic Media.

The anion recognition and electrochemical anion-sensing properties of halogen-bonding (XB) tripodal zinc(II) receptors strategically designed and constructed for tetrahedral anion guest binding are described. The XB tris(iodotriazole)-containing hosts exhibit high affinities and selectivities for inorganic phosphate over other more basic, mono-charged oxoanions such as acetate and the halides in a competitive CD3 CN/D2 O (9 : 1 v/v) aqueous solvent mixture. 1 H NMR anion binding and electrochemical voltammetric anion sensing studies with redox-active ferrocene functionalised metallo-tripodal receptor analogues, reveal each of the XB tripods as superior anion complexants when compared to their tris(prototriazole)-containing, hydrogen bonding (HB) counterparts, not only exemplifying the halogen bond as a strong alternative interaction to the traditional hydrogen bond for molecular recognition but also providing rare evidence of the ability of XB receptors to preferentially bind the "harder" phosphate oxoanion over the "softer" and less hydrated halides in aqueous containing media.

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.

Halogen and Chalcogen Activation by Nucleophilic Catalysis.

The high utility of halogenated organic compounds has prompted the development of numerous transformations that install the carbon-halogen motif. Halogen functionalities, deemed as "functional and functionalizable" molecules due to their capacity to modulate diverse internal properties, constitute a pivotal strategy in drug discovery and development. Traditional routes to these building blocks have commonly involved multiple steps, harsh reaction conditions, and the use of stoichiometric and/or toxic reagents. With the emergence of solid halogen carriers such as N-halosuccinimides, and halohydantoins as popular sources of halonium ions, the past decade has witnessed enormous growth in the development of new catalytic strategies for halofunctionalization. This review aims to provide a nuanced perspective on nucleophilic activators and their roles in halogen activation. It will highlight critical discoveries in effecting racemic and asymmetric variants of these reactions, driven by the development of new catalysts, activation modes, and improved understanding of chemical reactivity and reaction kinetics.

Hypervalent Iodine(III) Mediated Halogen Bonded Supramolecular Chiral System with Cholesteryl Naphthalimides.

Halogen bonding acknowledged as a noteworthy weak interaction, has gained growing recognition in the field of supramolecular chemistry. In this study, we selected structurally rigid diaryliodonium ions (I(III)) with two biaxial σ-holes as halogen-bond donors, to bind with three chiral acceptor molecules bearing cholesteryl and naphthalimides with distinct geometries. The abundant carbonyl oxygen atoms in side-arm substituents function as multiple acceptors for halogen bonding. The self-aggregation of chiral acceptor molecules demonstrates adaptiveness to solvent media, evidenced by the inversion of the Cotton effect and the morphological evolution from spherical to rod-like nanoarchitectures in different solvent systems. The distinct geometries of the acceptor molecules conferred various binding modes with I(III). The introduction of I(III) as a halogen-bond donor regulates the aggregation of the donors, achieving amplification of chiroptical signals and inheriting solvent responsiveness from the self-aggregated assembly. This study successfully utilized rational structural design and multimodal control strategies to achieve regulation of supramolecular chirality.

Ultrafast Halogen Dance Reactions of Bromoarenes Enabled by Catalytic Potassium Hexamethyldisilazide.

Lochmann-Schlosser base, a stoichiometric combination of nBuLi and KOtBu, is commonly used as a superbase for deprotonating a wide range of organic compounds. In the present study, we report that catalytic potassium hexamethyldisilazide (KHMDS) exhibits higher catalytic activity than KOtBu for successive bromine-metal exchanges. Accordingly, 1-10 mol% of KHMDS dramatically enhances halogen dance reactions to introduce various electrophiles to bromopyridine, bromoimidazole, bromothiophene, bromofuran, and bromobenzene derivatives with the bromo group translocated from the original position. A dual catalytic cycle is proposed to explain the ultrafast bromine transfer.

"Buttressing Effect" in the Halogen-Lithium Exchange in ortho-Bromo-N,N-dimethylanilines and Related Naphthalenes.

Non-covalent interactions such as coordination of an organolithium reagent by a directing group and steric repulsion of substituents strongly affect the halogen-lithium exchange process. Here we present the manifestation of the "buttressing effect" - an indirect interaction between two substituents issued by the presence of a third group - and its influence on the ease and selectivity of the bromine-lithium exchange and the reactivity of formed aryllithiums. The increase of the size of the "buttressing" substituent strongly affects the conformation of a NMe2 group, forcing it to hinder ortho-bromine and thus slowing down the exchange. In naphthalene substrates bearing two bromines, this suppresses regioselectivity of the reaction. The "buttressing effect" forces formed aryllithiums to deaggregate, thus boosting their reactivity. This facilitates the decomposition via protolisys by ethereal solvents even at low temperatures and in some cases initiates fast Wurtz-Fittig coupling.