Intermolecular Halogen Research Articles

Structure of inorganic compounds halogen bonds in derivatives of 2,5-diiod-1,4-dimethylbenzene

The synthesis of 1,4-di(bromomethyl)-2,5-diiodo-benzene (1), diacetate of 2,5-diiodo–1,4-di(hydroxymethyl)benzene (2) and diiodide of 1,1’-[(2,5-diiodo-1,4-phenylene)bis(methylene)]dipyridinium (3) is described and their crystallographic data are given. All three crystal structures are characterized by the stacked packing of planar molecules and the presence of halogen bonds I–Br, I–O, and I–I, respectively. The number of halogen bonds is maximum in compound 1: two I–Br bonds for each halogen atom. Compounds 2 and 3 contain one halogen bond per halogen atom, but they are significantly shorter than in compound 1. All crystals were investigated by IR spectroscopy and synchronized thermal analysis. Compound 1, which has no ionic or hydrogen bonds, melts at a higher temperature than ionic compound 3 (218 and 200°C, respectively) due to the presence of a large number of intermolecular halogen bonds. Compound 2 melts at a lower temperature (151°C), which is characteristic of esters.

Pyrazolyliodonium platinum(II) trichloride features the highest positive electrostatic potential on the iodine atom among uncharged halogen bond donors

This study presents a new uncharged platinum(II) complex with a pyrazolyliodonium ligand, which features an exceptionally large σ-hole on the iodine atom. Single-crystal X-ray diffraction analysis reveals the structure of the [LPtCl3]·2DMF complex, highlighting two types of intermolecular halogen bonds: a C−I⋯O bond with DMF and C−I⋯Cl bonds with the platinum complex. Quantum chemical calculations confirm the high positive electrostatic potential on the iodine σ-hole, demonstrating its significant halogen bond donor ability.

Dual Emission with Efficient Phosphorescence Promoted by Intermolecular Halogen Interactions in Luminescent Tetranuclear Zinc(II) Clusters.

The development of Zn-based phosphorescent materials, associated with a ligand-centered (LC) transition, is extremely limited. Herein, we demonstrated dual emissions including fluorescence and phosphorescence in luminescent tetranuclear Zn(II) clusters [Zn4LI4(μ3-OMe)2X2] (HLI = methyl-5-iode-3-methoxysalicylate; X = I, Br, Cl), incorporating iodine-substituted ligands. Single-crystal X-ray structural analyses and variable-temperature emission spectra studies revealed the presence of iodine substitutions, and intermolecular halogen interactions produced the internal/external heavy-atom effects and yielded strong green phosphorescence with a long emission lifetime (λmax = 510-522 nm, Φem = 0.28-0.47, τav = 0.78-0.95 ms, at 77 K). This work provided a new example that the introduction of halogen interactions is an advantageous approach for inducing phosphorescence in fluorescent metal complexes.

The dawn of hydrogen and halogen bonds and their crucial role in collisional processes probing long-range intermolecular interactions.

This perspective review focuses on the results of an internally consistent study developed in the Perugia laboratory, centered on the fundamental interaction components that, at large intermolecular distances, determine the formation of weak intermolecular hydrogen (HB) and halogen (XB) bonds. This investigation exploits old and novel molecular beam scattering experiments involving several gaseous prototypical systems. In particular, we focus on the kinetic energy dependence of the total (elastic + inelastic) integral cross-sections. Of particular interest is the measure of quantum interference patterns in the energy dependence of cross-sections of targeted systems and their shift compared to that of known reference systems. We interpreted these findings as interaction energy stabilization components, such as charge transfer, σ-hole, and polar flattening, that emerge at intermediate separation distance ranges and selectively manifest for specific geometries of collision complexes. Another significant observable we discuss is the absolute value of the cross-section and its dependence on permanent multipole moments of the collisional partners. Specifically, we show how the spontaneous orientation of rotationally cold and polar molecules, due to the electric field gradient associated with the interaction between permanent multipole moments, can significantly modify the magnitude of the total cross-section, even at high values of the impact parameter. We are confident that the present results can help extend the force field formulation to various interacting systems and carry out molecular dynamics simulations under conditions of application interest.

Achieving tunable long persistent luminescence in metal organic halides based on pyridine solvent

The research of long persistent luminescence (LPL) materials has yield brilliant results in many fields. However, the efforts are still needed for the regulation of the LPL performance. In this work, a series of LPL metal organic halides with rich halogen-bond interactions, Py-CdX2 (X = Cl, Br, I) were synthesized through self-assembly by CdX2 and pyridine solvent. The steady-state emission redshifted and phosphorescence lifetime declined as the halogen atoms are aggravated. Three halides exhibit adjustable emission from blue to green and multiple phosphorescence from green to yellow at room temperature by changing the excitation wavelengths. Surprisingly, Py-CdX2 can emit the visible color-tunable LPL from green to yellow after removing different excitation sources at ambient conditions. Combing the results of theoretical calculation and experimental analysis, it is found that heavy atom effect and the rich intermolecular halogen bond help realize LPL and multiple triplet states originated from the pyridine ring and the halogens.

Halogen bonding-driven chiral amplification of a bimetallic gold-copper cluster through hierarchical assembly.

Understanding the fundamentals and applications of chirality relies substantially on the amplification of chirality through hierarchical assemblies involving various weak interactions. However, a notable challenge remains for metal clusters chiral assembly driven by halogen bonding, despite their promising applications in lighting, catalysis, and biomedicine. Here, we used halogen bonding-driven assembly to achieve a hierarchical degree of achiral emissive Au2Cu2 clusters. From single crystals to one-dimensional ribbons and then to helixes, the morphologies were primarily modulated by intermolecular halogen bonding that evoked by achiral or/and chiral iodofluorobenzene (IFBs) molecules. Concomitantly, the luminescence and circularly polarized luminescence (CPL) changed a lot, ultimately leading to a substantial increase in the luminescence dissymmetry g-factor (glum) of 0.036 in the supramolecular helix. This work opens an avenue for hierarchical assemblies using predesigned metal clusters as building blocks though directional halogen bonding. This achievement marks a noteworthy advancement in the field of nanosized inorganic functional blocks.

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective.

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Comparison of Intermolecular Halogen...Halogen Distances in Organic and Organometallic Crystals.

Statistical analysis of halogen...halogen intermolecular distances was performed for three sets of homomolecular crystals under normal conditions: C-Hal1...Hal2-C distances in crystals consisting of: (i) organic compounds (set Org); (ii) organometallic compounds (set Orgmet); and (iii) distances M1-Hal1...Hal2-M2 (set MHal) (in all cases Hal1 = Hal2, and in MHal M1 = M2, M is any metal). When analyzing C-Hal...Hal-C distances, a new method for estimating the values of van der Waals radii is proposed, based on the use of two subsets of distances: (i) the shortest distances from each substance less than a threshold; and (ii) all C-Hal...Hal-C distances less than the same threshold. As initial approximations for these thresholds for different Hal, the Ragg values previously introduced in investigations with the participation of the author were used (Ragg values make it possible to perform a statistical assessment of the presence of halogen aggregates in crystals). The following values are recommended in this work to be used as universal values for crystals of organic and organometallic compounds: RF = 1.57, RCl = 1.90, RBr = 1.99, and RI = 2.15 Å. They are in excellent agreement with the results of some other works but significantly (by 0.10-0.17 Å) greater than the commonly used values. For the Orgmet set, slightly lower values for RI (2.11-2.09 Å) were obtained, but number of the C-I...I-C distances available for analysis was significantly smaller than in the other subgroups, which may be the reason for the discrepancy with value for the Org set (2.15 Å). Statistical analysis of the M-Hal...Hal-M distances was performed for the first time. A Hal-aggregation coefficient for M-Hal bonds is proposed, which allows one to estimate the propensity of M-Hal groups with certain M and Hal to participate in Hal-aggregates formed by M-Hal...Hal-M contacts. In particular, it was found that, for the Hg-Hal groups (Hal = Cl, Br, I), there is a high probability that the crystals have Hg-Hal...Hal-Hg distances with length ≤ Ragg.

Dispersion-Corrected DFT-D4 Study of the Adsorption of Halobenzenes and 1,3,5-Trihalobenzenes on the Cu(111) Surface─Effect of Sigma Hole Properties.

Halogen bonds, characterized by directionality, tunability, hydrophobicity, and variable sizes, are ideal noncovalent interactions to design and control the formation of self-assembled nanostructures. The specific self-assembly cases formed by the halogen-bonding interaction have been well studied by scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. However, there is a lack of systematic theoretical adsorption studies on halogenated molecules. In this work, the adsorption of halobenzenes and 1,3,5-trihalobenzenes on the Cu(111) surface was examined by dispersion-corrected DFT methods. The adsorption geometries, noncovalent molecule-surface interactions, electronic densities, and electrostatic potential maps were examined for their most stable adsorption sites using the DFT-D4 method. Our calculations revealed that the iodo compounds favor a different adsorption geometry from aryl chlorides and bromides. Down the halogen group (Cl to I), the adsorption energy increases and the distance between the halogen atom and Cu surface decreases, which indicates stronger molecule-surface interactions. This is supported by the changes in the density of states upon adsorption. Noncovalent interaction analysis was also employed to further understand the nature and relative strength of the molecule-surface interactions. Electrostatic potential maps revealed that the positive character of the halogen sigma hole becomes stronger upon adsorption. Thus, surface adsorption of the halogenated molecule will enhance the formation of intermolecular halogen bonds. The present theoretical findings are expected to contribute toward a more comprehensive understanding of halogen bonding on the Cu(111) surface.

Constructing a novel “turn-on” fluorescent sensor based on phenazine macrocycle through halogen bond interaction for the naked-eye detection of phenylenediamine isomers

Developing a visual color change pathway to differentiate and identify three phenylenediamine isomers remains an extremely fascinating and critical task. Herein, we first reasonably introduced iodine molecule(I2) to regulate the stimuli-responsive properties of phenazine macrocycle(PNH), and thus a novel “turn-on” fluorescence sensing platform(PNH-I2) was constructed through intermolecular halogen bonding. This platform PNH-I2 enabled the naked-eye identification and ultra-sensitive detection of o-phenylenediamine(OPD), m-phenylenediamine(MPD) and p-phenylenediamine(PPD) at low concentration levels(2 μM). The lowest detection limits(LODs) for OPD and MPD reached 6.97 × 10−9 M and 2.90 × 10−9 M, respectively, which were much lower than those reported literatures. More importantly, the test box based on PNH-I2 could be used as intelligent fluorescence display material, which had good application value in the detection and identification of three phenylenediamine isomers. Moreover, the fluorescence sensor PNH-I2 could successfully perceive the presence of OPD and MPD in real water sample. Such a novel strategy is expected to open up new applications of phenazine derivatives in environmental science.

Effect of the Solvent on the Crystallographic and Magnetic Properties of Rhenium(IV) Complexes Based on 2,2′-Bipyrimidine Ligand

Two solvated rhenium(IV) complexes with formula [ReCl4(bpym)]·MeCN (1) and [ReCl4(bpym)]·CH3COOH·H2O (2) (bpym = 2,2′-bipyrimidine) have been prepared and characterized by means of Fourier transform infrared spectroscopy (FT–IR), scanning electron microscopy and energy dispersive X-ray analysis (SEM–EDX), single-crystal X-ray diffraction (XRD) and SQUID magnetometer. 1 and 2 crystallize in the monoclinic system with space groups P21/n and P21/c, respectively. In both compounds, the Re(IV) ion is six-coordinate and bound to four chloride ions and two nitrogen atoms of a 2,2′-bipyrimidine molecule forming a distorted octahedral geometry around the metal ion. In the crystal packing of 1 and 2, intermolecular halogen⋯halogen and π⋯halogen-type interactions are present. Hydrogen bonds take place only in the crystal structure of 2. Both compounds exhibit a similar crystal framework based on halogen bonds. Variable temperature dc magnetic susceptibility measurements performed on microcrystalline samples of 1 and 2 show a similar magnetic behavior for both compounds, with antiferromagnetic exchange between the Re(IV) ions connected mainly through intermolecular Re-Cl⋯Cl-Re interactions.

Intermolecular Halogen and Hydrogen Bonding-Controlled Self-Assembly of Network Structures

Intermolecular Halogen and Hydrogen Bonding-Controlled Self-Assembly of Network Structures

Modulating room temperature phosphorescence through intermolecular halogen bonding

Room temperature phosphorescence materials based on halogenated-morpholine are obtained, wherein the halogen bonding is directly involved in the acceleration of the intersystem crossing and enhancement of solid-state phosphorescence quantum yield.

Decoding the infrared spectra changes upon formation of molecular complexes: the case of halogen bonding in pyridine⋯perfluorohaloarene complexes.

A recently developed computational scheme is employed to interpret changes in the infrared spectra of halogen-bonded systems in terms of intermolecular interaction energy components (electrostatic, exchange, induction, dispersion) taking pyridine⋯perfluorohaloarene complexes as examples. For all complexes, we find a strong linear correlation between the different terms of the interaction-induced changes of the IR band associated with an intermolecular halogen bond stretching mode and the corresponding terms of the interaction energy, which implies that the interaction components play similar roles in both properties. This is not true for other vibrational modes localized in one of the monomers studied here, for which the corresponding interaction-induced changes in IR bands may present a completely different decomposition than the interaction energy.

Enhanced Adsorption of Bromoform onto Microplastic Polyethylene Terephthalate Exposed to Ozonation and Chlorination.

This paper selected microplastic polyethylene terephthalate (PET), commonly found in water/wastewater plant effluent, to investigate the changes of PET oxidized under ozonation (designated as ozonized PET), followed by sodium hypochlorite oxidation (designated as ozonized-chlorinated PET) and studied their influence on the adsorption of the disinfection by-product bromoform (TBM). Fragmentation and cracks appeared on the oxidized PET surface. As the oxidation degree increased, the contact angle decreased from 137° to 128.90° and 128.50°, suggesting hydrophilicity was enhanced. FTIR and XPS analyses suggested that carbonyl groups increased on the surface of ozonized PET and ozonized-chlorinated PET, while the formation of intermolecular halogen bonds was possible when PET experienced dual oxidation. These physiochemical changes enhanced the adsorption of TBM. The adsorption capacity of TBM followed the order of ozonized-chlorinated PET (2.64 × 10−6 μg/μg) > ozonized PET (2.58 × 10−6 μg/μg) > pristine PET (2.43 × 10−6 μg/μg). The impact of raw water characteristics on the adsorption of TBM onto PETs, such as the pH, and the coexistence of inorganic ions and macromolecules (humic acid, surfactant, and bovine serum albumin) were studied. A different predominant adsorption mechanism between TBM and pristine PET or oxidized PETs was proposed.

Model for self-assembly of Br–H and Br–Br bonded Br4Py molecules

A model, based on the pairwise intermolecular halogen–hydrogen (Br–H) and halogen–halogen (Br–Br) bonding, is proposed to describe the self-assembly of Br4Py molecules into two different planar structures (Phase I and Phase II). The pair bonding interactions are calculated by the density functional theory for the two-molecule and four-molecule clusters. It is shown that about 60% of bonding strength is due to the electrostatic Br(top)–Br(belt) interactions, while the remaining originates from Br–H interactions. The obtained values of pair interactions are further used for Monte Carlo calculations. The model for these calculations is proposed on a square lattice. The two main pair interactions are needed for the emergence of the Phase I ordering, while the Phase II ordering is obtained using a single interaction. The obtained results explain the emergence of both phases.

Synthesis and Crystal Structures of Halogen-Substituted 2-Aryl-N-phenylbenzimidazoles

Four 2-arylbenzimidazoles (aryl = 4-Br-phenyl (1), 3-Br-phenyl (2), 4-I-phenyl (3), 3-I-phenyl (4)) were synthesized and characterized by 1H, 13C{1H} NMR, UV–Vis spectroscopy and single-crystal X-ray diffraction. Both pairs of benzimidazoles bearing the halogen atom at the same position form isostructural crystals, in which para-substituted compounds 1 and 3 are assembled by weak C–H···π and π···π interactions while their meta-isomers 2 and 4 are linked via intermolecular halogen···nitrogen and C–H···π contacts.

Spontaneous Resolution of Helical Building Blocks through the Formation of Homochiral Helices in Two Dimensions.

Spontaneous resolution leading to conglomerate crystals remains a significant challenge. Here we propose the formation of orthogonal homochiral supramolecular helices in at least two dimensions to allow spontaneous resolution. We suggest the design rationale that the chiral species is made into helical building blocks to allow the helix formation. As a proof-of-concept, acetylalanine was made into a helical short azapeptide, its N-amidothiourea derivative containing a β-turn structure, to which a halogen atom was further introduced at the phenylthiourea aromatic ring. The resultant folded species undergoes both intermolecular hydrogen and halogen bonding across the turn structure to form orthogonal intermolecular hydrogen-bonded and halogen-bonded supramolecular helices in two dimensions, and undergoes chiral resolution upon crystallization. Meanwhile, counterparts containing either an F-substituent with weak halogen bonding or no halogen atom crystallize as racemic compounds.

Spontaneous Resolution of Helical Building Blocks through the Formation of Homochiral Helices in Two Dimensions

AbstractSpontaneous resolution leading to conglomerate crystals remains a significant challenge. Here we propose the formation of orthogonal homochiral supramolecular helices in at least two dimensions to allow spontaneous resolution. We suggest the design rationale that the chiral species is made into helical building blocks to allow the helix formation. As a proof‐of‐concept, acetylalanine was made into a helical short azapeptide, its N‐amidothiourea derivative containing a β‐turn structure, to which a halogen atom was further introduced at the phenylthiourea aromatic ring. The resultant folded species undergoes both intermolecular hydrogen and halogen bonding across the turn structure to form orthogonal intermolecular hydrogen‐bonded and halogen‐bonded supramolecular helices in two dimensions, and undergoes chiral resolution upon crystallization. Meanwhile, counterparts containing either an F‐substituent with weak halogen bonding or no halogen atom crystallize as racemic compounds.

Substrate-Selective Intermolecular Interaction and the Molecular Self-Assemblies: 1,3,5-Tris(4-bromophenyl)benzene Molecules on the Ag(111) and Si(111) (√3 × √3)-Ag Surfaces.

We report the formation processes of the self-assembled layer of 1,3,5-tris(4-bromophenyl)benzene (TBB) molecules on the Ag(111) and Si(111) (√3 × √3)-Ag surfaces by STM measurements and density functional theory (DFT) calculations. The self-assembled layers on the surfaces show characteristic structures controlled by the interplay between the intermolecular interaction and the molecule-substrate interaction. Through the cooperative interplay between the molecule-substrate interaction and the intermolecular halogen bond (XB), the periodic arrangement of TBB molecules appears on the Ag(111) surface. On the other hand, the two types of TBB arrangement appear on the Si(111) (√3 × √3)-Ag surface (phases 1 and 2). Phase 1 is the periodic arrangement of the TBB molecules and is derived from the cooperative interplay between the molecule-substrate interaction and the intermolecular van der Waals (vdW) interaction and the hydrogen bond (HB), and phase 2 is a random arrangement and is derived from the competitive interplay between the molecule-substrate interaction and the intermolecular XB and HB. Our present study specifies the role of the substrate in the molecular self-assembly of the substrate. Although the structure of the molecular self-assembly is controlled by the choice of the substrate, the cooperative interplay between the molecule-substrate interaction and the intermolecular interaction is necessary to realize the ideal periodic arrangement.