Halogen Bonding in Supramolecular Chemistry

Halogen bond-modulated solid-state reordering and symmetry breaking of azahelicenes

Spontaneous symmetry breaking predominately occurs during the aggregation of discrete molecules in solution. Herein, we report a unique solid-state symmetry breaking process of dynamically chiral aza[4]helicenes that emerged in vacuum-driven transformation of halogen bond-woven crystals. Due to the weak feature of the halogen bonding, the halides in the cocrystals can be completely removed under vacuum at an elevated temperature. Interestingly, the aza[4]helicene molecules released from the halogen bond network solely adopt one chiral conformation upon reordering and symmetry breaking instantly occurs in a solid state. The Cotton effects gradually increase with the extension of vacuum-heating treatment, indicating a unidirectional transformation of the chiral conformations and an amplification of symmetry breaking during the solid-state reorganization. Moreover, the use of aza[6]helicene as a chiral inducer further enables a precise manipulation for the absolute configuration of the solid-state symmetry breaking, paving a distinctive route to chiral organic materials from achiral/racemic precursors.

Vacuum ultraviolet spectroscopy of pyrimidine derivatives: the effect of halogenation

As a prototypical molecule in the important class of halopyrimidines, 2-chloropyrimidine has been the subject of numerous spectroscopic studies. However, its absorption spectrum under vacuum ultraviolet (VUV) radiation has not yet been reported. Here, we close this gap by presenting high-resolution VUV photoabsorption cross-sections in the 3.7-10.8 eV range. Based on time-dependent density functional theory (TDDFT) calculations performed within the nuclear ensemble approach, we are able to characterize the main features of the measured spectrum. By comparing the present results for 2-chloropyrimidine with those of 2-bromopyrimidine and pyrimidine, we find that the effect of the halogen atom increases remarkably with the photon energy. The two lowest-lying absorption bands are overall similar for the three molecules, apart from some differences in the vibrational progressions in band I (3.7-4.6 eV) and minor energy shifts in band II (4.6-5.7 eV). Larger shifts appear in band III (5.7-6.7 eV), especially when comparing pyrimidine with the two halogenated species. The three molecules absorb more strongly in the region of band IV (6.7-8.2 eV), where the bands look qualitatively different because the mixing of excited configurations is strongly dependent on the species. At higher energies (8.2-10.8 eV) the three spectra no longer resemble each other. An important finding of this study is the very satisfactory comparison between experiment and theory, as the combination of TDDFT calculations with the nuclear ensemble approach yields cross-sections much closer to experiments than the simpler vertical approximation, in shape and magnitude, and across the whole spectral range surveyed here.

CBr4-Catalyzed Substituent-Dependent Michael Addition/Paal-Knorr Cyclization of Indole with α,β-Unsaturated Ketones

We report CBr4 catalyzed Michael addition of indole to α,β-unsaturated ketones for the synthesis of β-indolylketones through halogen bonding catalysis. This reaction is compatible with a diverse range of chalcones, including drug-derived chalcones containing sensitive functional groups such as amides, yielding the addition products in good yields. Additionally, 3-indolyl furanoid motifs have been synthesized through the Michael addition followed by Paal-Knorr cyclization by utilizing various unsymmetrical 1,4-enediones in a one-pot process with good yields.

Crystal structure of 1-amino-3-(4-chloro-phen-yl)-2-cyano-3H-benzo[4,5]thia-zolo[3,2-a]pyridine-4-carboxamide

In the structure of the title compound, C19H13ClN4OS, the four atoms of the pyridinic ring that are not fused with the thia-zole, including the sp 3 C atom, lie significantly outside the benzo-thia-zole plane. A short intra-molecular S⋯O contact of 2.5992 (4) Å is observed. The amide NH2 group is planar, whereas the amine NH2 group is pyramidalized. The three-dimensional packing involves two inter-connected layer structures. The first, parallel to the bc plane, involves three classical hydrogen bonds N-Hamine⋯O (one of two), N-Hamine⋯Cl and one N-Hamide ⋯Ncyano; the second, parallel to the ab plane, involves two hydrogen bonds, N-Hamide⋯O and the second N-Hamine⋯O, together with the short and linear contact Ncyano⋯Cl-C, which may be regarded as a halogen bond.

Halogen bond-catalyzed Pictet-Spengler reaction

We report an efficient halogen bond-catalyzed Pictet-Spengler reaction using diaryliodonium salts as catalysts as a metal-free alternative to traditional acid catalysis. Through systematic optimization, exceptional catalytic activity was achieved with only 0.5 mol% of a simple dibenzoiodolium with a perfluorinated borate counterion. The protocol demonstrates a broad substrate scope, converting various N-protected tryptamines and diverse carbonyl compounds (aromatic, heteroaromatic, and aliphatic aldehydes) into the corresponding tetrahydro-β-carbolines (THβCs) in up to 98% yield. The reaction versatility was further demonstrated by a successful oxa-variant using tryptophol. Control experiments revealed the crucial role of halogen bonding in ensuring efficient reaction progress.

Emerging Role of Noncovalent Interactions and Disulfide Bond Formation in the Cellular Uptake of Small Molecules and Proteins

Intracellular delivery of proteins and small molecules is an important barrier in the development of strategies to deliver functional proteins and therapeutics into the cells to realize their full potential in biotechnology, biomedicine, cell-based therapies, and gene editing protein systems. Most of the intracellular protein delivery strategies involve the conjugation of cell penetrating peptides to enable the permeability of plasma membrane of mammalian cells to allow proteins to enter cytosol. The conjugations of small molecules such as (p-methylphenyl) glycine, pyrenebutyrate and cysteines are used for the same purpose. Molecular level interactions are governed mostly by ionic (cationic/anionic), covalent and noncovalent interactions with various molecular entities of glycocalyx matrix on plasma membrane lipid bilayer. Although the role of noncovalent interactions in cellular uptake is not fully understood, several recent advances have focused on the noncovalent interaction-based strategies of intracellular delivery of small molecules and proteins into mammalian cells. These are achieved by simple modification of protein surfaces with chemical moieties which can form noncovalent interactions other than hydrogen bonding. In this review, we describe the recent advances and the mechanistic aspects of intracellular delivery and role of noncovalent interactions in the cellular uptake of proteins and small molecules.

Twisted Cucurbit[14]uril-Based Supramolecular Self-Assembly Induces Fluorescence Emission of Dye Molecules for Multi-Channel Cell Imaging

In this study, a supramolecular fluorescent material was constructed by using double-cavity twisted cucurbit[14]uril (tQ[14]) and positively charged Astrazon Pink FG (APFG) based on the non-covalent host-guest interaction for the first time. The thermodynamic parameters of the APFG@tQ[14] in aqueous solution were determined by isothermal titration calorimetry (ITC), the results indicated that the spontaneous assembly of APFG@tQ[14] is mainly driven by enthalpy. The intramolecular charge transfer (ICT) effect induced the APFG@tQ[14] probe to emit a strong orange-red fluorescence. Due to its good optical properties and low toxicity, APFG@tQ[14] was successfully applied to multi-channel imaging of HK2 cells. This demonstrates the great potential of APFG@tQ[14] in labeling and tracking living cells.

Crystal structures of six complexes of phosphane chalcogenides R 1 R 2 R 3PE (R = tert-butyl or isopropyl, E = S or Se) with the metal halides MX 2 (M = Pd or Pt, X = Cl or Br), two halochalcogenyl-phospho-nium derivatives ( t Bu2 iPrPEBr)2[Pd2Br6] and one hydrolysis product

The L 2 MX 2 complexes 1-5 (1: L = t BuiPr2PSe, M = Pd, X = Cl; 2: L = t Bu2 iPrPSe, M = Pd, X = Cl; 3: L = t Bu2 iPrPSe, M = Pd, X = Br; 4: L = t Bu2 iPrPS, M = Pd, X = Br; 5: L = t Bu2 iPrPS, M = Pt, X = Cl) {systematic names: (tert-butyl-diiso-propyl-phosphine selenide-κSe)di-chlorido-palladium(II), [PdCl2(C10H23PSe)2] (1), (di-tert-butyl-iso-propyl-phosphine selenide-κSe)di-chloridopalladium(II), [PdCl2(C11H25PSe)2] (2), di-bromido-(di-tert-butyl-iso-propyl-phosphine selenide-κSe)palladium(II), [PdBr2(C11H25PSe)2] (3), di-bromido-(di-tert-butyl-iso-propyl-phosphine sulfide-κS)palladium(II), [PdBr2(C11H25PS)2] (4), di-chlorido-(di-tert-butyl-iso-propyl-phosphine sulfide-κS)palladium(II), [PdCl2(C11H25PS)2] (5)} all display a trans configuration with square-planar geometry at the metal atom. Compounds 2 and 3 are isotypic. The mol-ecules of 1 and 4 display crystallographic inversion symmetry; compound 5 involves two independent mol-ecules, each with inversion symmetry but with differing orientations of the tri-alkyl-phosphane groups. Chemically equivalent bond lengths all lie in narrow ranges, whereby the values for palladium and platinum compounds scarcely differ. Compound 6, ( t BuiPr2PS)2Pd2Cl4 {systematic name: di-μ-chlorido-bis-[(tert-butyldiiso-propyl-phosphine sulfide-κS)chlorido-palladium(II)], [PdCl2(C10H23PS)2]}, is dinuclear with a central Pd2Cl2 ring, and displays crystallographic inversion symmetry. The bonds to the bridging are longer than those to the terminal chlorine atoms; the Pd-S bond is shorter than the M-S bonds in 4 and 5, reflecting the weaker trans influence of (bridging) chlorine compared to sulfur. Compounds 7 and 8, 2( t Bu2 iPrPEBr)+ [Pd2Br6]2- with E = S for 7 and Se for 8 {systematic names: (bromo-sulfan-yl)di-tert-butyl-iso-propyl-phosphanium di-μ-bromido-bis-[di-bromido-palladium(II)], (C11H25BrPS)2[Pd2Br6] (7) and (bromo-selan-yl)di-tert-butyl-iso-propyl-phosphanium di-μ-bromido-bis-[di-bromido-palladium(II)], (C11H25BrPS2)2[Pd2Br6], (8)}, were obtained by oxidizing the appropriate PdII precursors with elemental bromine; they are not isotypic. The ions are connected by very short halogen bonds Br⋯Br. For both compounds, two E⋯Br contacts further link the cations and anions to form ribbons. Compound 9 {systematic name: bis-[dimeth-yl(sulfanyl-idene)phosphin-ito-κSe]bis-(hy-droxy-diiso-propyl-phosphine selenide-κSe)palladium(II), [Pd(C6H14OP)2(C6H15OP)2], {(iPr2PSeO)2H}2Pd, is a hydrolysis product with inversion symmetry and contains an intra-molecular P-O⋯H-O-P group with a disordered hydrogen atom. Compounds 1-6 and 9 show few, if any, short inter-molecular contacts, although some H⋯M contacts are observed. A problem with atom-type assignment for structure refinement is discussed.

Stereoisomerism-dependent gelation and crystal structures of glycosylated N-methylbromomaleimide-based supramolecular hydrogels

In this study, we developed glycosylated N-methylbromomaleimide-based supramolecular hydrogels exhibiting colour change along with gel-sol transition and found that the stereoisomerism of the saccharide residue affects their gelation ability. Single-crystal X-ray diffraction analysis revealed the molecular packing and hydrogen-bonding networks contributed by the saccharide residues. Interestingly, it was found that water molecules were incorporated into the hydrogen-bonding network in the crystals of the compounds that showed gelation ability.

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 ' 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.

Charge-transfer energy through the dipole moment

The charge-transfer energy contribution is one of the most controversial components of the total interaction energy. Commonly, the energy associate to a charge-transfer process depends on population analysis. Therefore, the results further depend on how the population analysis is defined, and certainly, the results may be arbitrary. Moreover, another important feature of the current methods is the basis sets dependency. The results of methodologies that depend on orbital-based population analyses tend to have a strong dependency on the size of the basis set utilized. This basis set dependency is eliminated by using spatial partitioning population analyses. However, these methodologies still rely on the arbitrary choice of how to divide the space. In this work, we study the use of the molecular dipole moment as a reference to describe the charge transfer-free system, i.e., a system in which the charge-transfer process is avoided. We use the recently developed constrained dipole moment density functional theory methodology to constrain the dipole moment of several systems according to reference values. These dipole moment references do not present charge transfer nor polarization contributions. In this manner, we have calculated the charge-transfer energy contributions and the total interaction energies of 13 non-covalent complexes. In addition, we determined two long range charge-transfer excitations considering the dipole moment as a reference. The calculated charge-transfer energy contributions and excitation energies are in a very good agreement with the fragment-based Hirshfeld methodology. Nevertheless, the constrained dipole moments results do not depend on population analysis. Moreover, the method is robust with respect to the strength of the charge transfer and the basis set size.

Illuminating the Performance of Electron Withdrawing Groups in Halogen Bonding

Throughout the halogen bonding literature, electron withdrawing groups are relied upon heavily for tuning the interaction strength between the halogen bond donor and acceptor; however, the interplay of electronic effects associated with various substituents is less of a focus. This work utilizes computational techniques to study the degree of σ- and π-electron donating/accepting character of electron withdrawing groups in a prescribed set of halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond donors. We examine how these factors affect the σ-hole magnitude of the donors as well as the binding strength of the corresponding complexes with an ammonia acceptor. Statistical analyses aid the interpretation of how these substituents influence the properties of the halogen bond donors and complexes, and show that the electron withdrawing groups that are both σ- and π-electron accepting form the strongest halogen bond complexes.

Data and Molecular Fingerprint-Driven Machine Learning Approaches to Halogen Bonding

The ability to predict the strength of halogen bonds and properties of halogen bond (XB) donors has significant utility for medicinal chemistry and materials science. XBs are typically calculated through expensive ab initio methods. Thus, the development of tools and techniques for fast, accurate, and efficient property predictions has become increasingly more important. Herein, we employ three machine learning models to classify the XB donors and complexes by their principal halogen atom as well as predict the values of the maximum point on the electrostatic potential surface (VS,max) and interaction strength of the XB complexes through a molecular fingerprint and data-based analysis. The fingerprint analysis produces a root-mean-square error of ca. 7.5 and ca. 5.5 kcal mol-1 while predicting the VS,max for the halobenzene and haloethynylbenzene systems, respectively. However, the prediction of the binding energy between the XB donors and ammonia acceptor is shown to be within 1 kcal mol-1 of the density functional theory (DFT)-calculated energy. More accurate predictions can be made from the precalculated DFT data when compared to the fingerprint analysis.

Crystal structures of six miscellaneous products arising from the oxidation of precursors R 1 R 2 R 3PEAuX (R = tert-butyl or isopropyl; E = S or Se; X = Cl, Br or I)

Compound 1, (disulfane-1,2-di-yl)bis-(tert-butyl-diiso-propyl-phospho-nium) bis-[tetra-chlorido-aurate(III)], ( t Bu i Pr2P)2S2·[AuCl4]2, contains the first structurally characterized dication of the form {(R 3P)2 E}2 2+. The ions are linked by S⋯Cl contacts and C-Hmethine⋯Cl hydrogen bonds to form ribbons of residues parallel to the a axis. Compound 2 is bis-(di-tert-butyl-iso-propyl-phosphine sulfide-κS)gold(I) triiodide/di-iodido-aurate(I)(0.905/0.095), [Au(C11H25PS)2][AuI2]0.095(I3)0.905, or [( t Bu2 i PrPS)2Au]I3 with 9.5% of the triiodide replaced by di-iodido-aurate(I). Chains of alternating anions and cations parallel to [110] are formed by two S⋯I contacts. Compound 3 is bis-(tert-butyl-diiso-propyl-phosphine sulfide-κS)gold(I) triiodide/di-iodido-aurate(I)(0.875/0.125), [Au(C10H23PS)2][AuI2]0.125(I3)0.875 or [( t Bu i Pr2PS)2Au]I3 with 12.5% of the triiodide replaced by di-iodo-aurate(I). Chains parallel to [101] are formed by two S⋯I contacts. Compound 4, bis-(di-tert-butyl-iso-propyl-phosphine sulfide-κS)gold(I) hepta-iodide, [Au(C11H25PS)2]I7 or [( t Bu2 i PrPS)2Au]I3·2I2, is formally the bis-diiodine adduct of 3, uncontaminated by di-iodido-aurate(I). The cations and anions display crystallographic twofold symmetry. The unbranched I7 - groups, I-I⋯I-I-I⋯I-I, are bent at the third and fifth atoms. The anions are linked by two S⋯I contacts to form a layer structure parallel to the bc plane. In all three structures 2-4, there are also weak C-Hmethine⋯I contacts. Compound 5, di-bromido-(di-tert-butyl-dithio-phosphato-κ2 S,S')gold(III), [AuBr2(C8H18PS2)] or [AuBr2( t Bu2PS2)], contains a four-membered chelate ring. It crystallizes with imposed mirror symmetry. An S⋯Br contact links the mol-ecules to form corrugated layers parallel to the bc plane. In compound 6, di-tert-but-yl{[di-tert-but-yl(hy-droxy)phosphan-yl]diselan-yl}phosphine oxide tetra-bromido-aurate(III), (C16H37O2P2Se2)[AuBr4] or [( t Bu2OPSe)2H][AuBr4], the cation has a central diselenide unit, and also displays an intra-cationic hydrogen bond O-H⋯O. Two Se⋯Br contacts link the residues to form zigzag chains parallel to [201]. The problem of determining whether an E⋯X contact (E = chalcogen, X = halogen) represents a halogen bond or a chalcogen bond is discussed.

Crystallographic Evidence for Bi(I) as the Heaviest Halogen Bond Acceptor

Complexation of the green bismuthinidene (RBi) with two equivalents of a highly fluorinated aryl iodide at low temperature allows the crystallographic identification of an unstable red species that can be regarded as an intermediate in an overall Bi(I) → Bi(III) oxidation process. Both C-I bonds are orientated toward the filled 6p orbital of bismuth (Bi-I distances 3.44-3.52 Å), leading to an elongation of the C-I bonds by 0.05 and 0.07 Å. Density functional theory (DFT) calculations confirm that the Bi(I) center is indeed acting as an electron donor, establishing two strong and directional halogen bonds. The color change from green to red upon halogen bond formation is a consequence of the energetic stabilization of a Bi(I) lone pair by interactions with the sigma-holes of the halogen bond donors. Overall, this study presents the first structural proof of bismuth, and more generally of heavy organopnictogen(I) compounds, acting as halogen bond acceptors.

A Highly Selective Fluorescent Probe for Monitoring the Thyroid Hormone Transporter Activity in Mammalian Cells

Monocarboxylate transporter 8 (MCT8) is a trans-membrane transporter, which mediates the cellular delivery of thyroid hormones, L-thyroxine (T4) and 3,5,3'-triiodo-L-thyronine (T3). In humans, the MCT8 protein is encoded by the SLC16A2 gene and mutations in the transporter cause a genetic neurological disorder known as Allan-Herndon-Dudley Syndrome (AHDS). MCT8 deficiency leads to impaired transport of thyroid hormones in the brain. Radiolabelled T4 and T3 or LC/MS-MS methods have been used to monitor the thyroid hormone uptake through MCT8. Herein, we developed a fluorescent based assay to monitor the thyroid hormone uptake through MCT8. A dansyl-based fluorescent probe having L-thyroxine moiety is found to be highly selective towards MCT8 in living cells. The high selectivity of the probe towards MCT8 can be attributed to the halogen bond-mediated recognition by the transporter protein. The presence of a free carboxylic acid group is essential for the specificity of the probe towards MCT8. Additionally, the selectivity of the probe for MCT8 is abolished upon esterification of the carboxylic group. Similarly, MCT8 does not recognize the probe when it contains a free amine group.

Phosphine selenides: versatile NMR probes for analyzing hydrogen OH⋯Se and halogen I⋯Se bonds

Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for studying the structure and dynamics of various non-covalent interactions. However, often spectral parameters that are applicable for estimation of parameters of one type of non-covalent interaction will be inapplicable for another. Therefore, researchers are compelled to use spectral parameters that are specifically tailored to the type of non-covalent interaction being studied. This complexity makes it difficult to compare different types of non-covalent interactions with each other and, consequently, to establish a strict unified classification for them. This pioneering study proposes to use phosphine selenides as universal probes for investigating hydrogen and halogen bonding in solution. The study was carried out using the example of triethylphosphine selenide Et3PSe complexes with hydrogen bonds of Se⋯HO type and R3PSe (where R: Me, Et, n-Bu, t-Bu and Ph) with halogen bonds of Se⋯X type (where X: I and Br) in solution. The presence of non-covalent interactions was confirmed experimentally by means of 1H, 31P and 77Se NMR, as well as by quantum chemical calculation methods (optimization: PW6B95-D3/def2-QZVP; NMR: B97-2/pcsSeg-2).

Crystal structures of seven mixed-valence gold compounds of the form [(R 1 R 2 R 3PE)2AuI]+[AuIII X 4]- (R = tert-butyl or isopropyl, E = S or Se, and X = Cl or Br)

During our studies of the oxidation of gold(I) complexes of tri-alkyl-phosphane chalcogenides, general formula R 1 R 2 R 3PEAuX, (R = tert-butyl or isopropyl, E = S or Se, X = Cl or Br) with PhICl2 or elemental bromine, we have isolated a set of seven mixed-valence by-products, the bis-(tri-alkyl-phosphane chalcogenido)gold(I) tetra-halogenidoaurates(III) [(R 1 R 2 R 3PE)2Au]+[AuX 4]-. These corres-pond to the addition of one halogen atom per gold atom of the AuI precursor. Com-pound 1, bis-(triiso-propyl-phosphane sulfide)-gold(I) tetra-chlorido-aur-ate(III), [Au(C9H21PS)2][AuCl4] or [( i Pr3PS)2Au][AuCl4], crystallizes in space group P21/n with Z = 4; the gold(I) atoms of the two cations lie on twofold rotation axes, and the gold(III) atoms of the two anions lie on inversion centres. Compound 2, bis-(tert-butyl-diiso-propyl-phosphane sulfide)-gold(I) tetra-chlorido-aurate(III), [Au(C10H23PS)2][AuCl4] or [( t Bu i Pr2PS)2Au][AuCl4], crystallizes in space group P1 with Z = 4; the asymmetric unit contains two cations and two anions with no imposed symmetry. A least-squares fit of the two cations gave an r.m.s. deviation of 0.19 Å. Compound 3, bis-(tri-tert-butyl-phosphane sulfide)-gold(I) tetra-chlorido-aurate(III), [Au(C12H27PS)2][AuCl4] or [( t Bu3PS)2Au][AuCl4], crystallizes in space group P1 with Z = 1; both gold atoms lie on inversion centres. Compound 4a, bis-(tert-butyl-diiso-propyl-phosphane sulfide)-gold(I) tetra-bromi-doaurate(III), [Au(C10H23PS)2][AuBr4] or [( t Bu i Pr2PS)2Au][AuBr4], crystallizes in space group P21/c with Z = 4; the cation lies on a general position, whereas the gold(III) atoms of the two anions lie on inversion centres. Compound 4b, bis-(tert-butyl-diiso-propyl-phosphane selenide)gold(I) tetra-bromido-aurate(III), [Au(C10H23PSe)2][AuBr4] or [( t Bu i Pr2PSe)2Au][AuBr4], is isotypic with 4a. Compound 5a, bis-(tri-tert-butyl-phosphane sulfide)-gold(I) tetra-bromido-aurate(III), [Au(C12H27PS)2][AuBr4] or [( t Bu3PS)2Au][AuBr4], is isotypic with compound 4a. Compound 5a, bis-(tri-tert-butyl-phosphane sulfide)-gold(I) tetra-bromido-aurate(III), [Au(C12H27PS)2][AuBr4] or [( t Bu3PS)2Au][AuBr4], crystallizes in space group P1 with Z = 1; both gold atoms lie on inversion centres. Compound 5b, bis-(tri-tert-butyl-phosphane selenide)gold(I) tetra-bromido-aurate(III), [Au(C12H27PSe)2][AuBr4] or [( t Bu3PSe)2Au][AuBr4], is isotypic with 5a. All AuI atoms are linearly coordinated and all AuIII atoms exhibit a square-planar coordination environment. The ligands at the AuI atoms are anti-periplanar to each other across the S⋯S vectors. There are several short intra-molecular H⋯Au and H⋯E contacts. Average bond lengths (Å) are: P-S = 2.0322, P-Se = 2.1933, S-Au = 2.2915, and Se-Au = 2.4037. The complex three-dimensional packing of 1 involves two short C-Hmethine⋯Cl contacts (and some slightly longer contacts). For 2, four C-Hmethine⋯Cl inter-actions combine to produce zigzag chains of residues parallel to the c axis. Additionally, an S⋯Cl contact is observed that might qualify as a 'chalcogen bond'. The packing of 3 is three-dimensional, but can be broken down into two layer structures, each involving an S⋯Cl and an H⋯Cl contact. For the bromido derivatives 4a/b and 5a/b, loose associations of the anions form part of the packing patterns. For all four compounds, these combine with an E⋯Br contact to form layers parallel to the ab plane.

Halogen Bonding Hot Spots as a Constraint in Virtual Screening: A Case Study of 5-HT7R

The recently developed and used molecular modeling approach to search for privileged amino acids for halogen bonding (XB hot spots) through XSAR sets has been applied to 5-HT7R. Herein, among all identified 5-HT7R XB hot spots, the S5x42 was employed in a virtual screening protocol as a constraint. Through a designed virtual screening protocol, 63 XSAR sets (156 compounds) were selected from more than 8 million commercially available compounds and examined using in vitro assay toward 5-HT7R. A 68% accuracy was found in predicting halogenated derivatives with higher affinity for 5-HT7R than their unsubstituted analogs. Moreover, it was observed that a halogen bond formed between S5x42 and a chlorine atom at the 3-position of the arylpiperazine fragment caused the most remarkable, 35.4-fold increase in binding affinity for 5-HT7R when compared to the nonhalogenated analog. Interestingly, molecular dynamics simulations showed the formation of a bifurcated halogen bond with S5x42.

Redox-Responsive Halogen Bonding as a Highly Selective Interaction for Electrochemical Separations

Leveraging specific noncovalent interactions can broaden the mechanims for selective electrochemical separations beyond solely electrostatic interactions. Here, we explore redox-responsive halogen bonding (XB) for selective electrosorption in nonaqueous media, by taking advantage of directional interactions of XB alongisde a cooperative and synergistic ferrocene redox-center. We designed and evaluated a new redox-active XB donor polymer, poly(5-iodo-4-ferrocenyl-1-(4-vinylbenzyl)-1H-1,2,3-triazole) (P(FcTS-I)), for the electrochemically switchable binding and release of target organic and inorganic ions at a heterogeneous interface. Under applied potential, the oxidized ferrocene amplifies the halogen binding site, leading to significantly enhanced uptake and selectivity towards key inorganic and organic species, including chloride, bisulfate, and benzenesulfonate, compared to the open-circuit potential or the hydrogen bonding donor analog. Density functional theory calculations, as well as spectroscopic analysis, offer mechanistic insight into the degree of amplification of σ-holes at a molecular level, with selectivity modulated by charge transfer and dispersion interactions. Our work highlights the potential of XB in selective electrosorption by uniquely leveraging noncovalent interactions for redox-mediated electrochemical separations.

In Situ X-Ray Techniques Unraveling Charge Distribution Induced by Halogen Bonds in Solvates of an Iodo-Substituted Squaraine Dye

The importance of halogen bonds (XBs) in the regulation of material properties through a variation in the electrostatic potential of the halogen atom is not attracted much attention. Herein, this study utilizes in situ single crystal X-ray diffraction and synchrotron-based X-ray techniques to investigate the cooling-triggered irreversible single-crystal-to-single-crystal transformation of the DMF solvated iodo-substituted squaraine dye (SQD-I). Transformation is observed to be mediated by solvent-involved XB formation and strengthening of electrostatic interaction between adjacent SQD-I molecules. By immersing a DMF solvate in acetonitrile a solvent exchange without loss of long-range ordering is observed. This is attributed to conservation of the molecular charge distribution of SQD-I molecules during the process. The different solvates can be used in combination for temperature-dependent image encryption. This work emphasizes the changes caused by XB formation to the electrostatic potentials of halogen containing molecules and their influence on material properties and presents the potential utility of XBs in the design of soft-porous crystals and luminescent materials.

Silver(I) complexes with voriconazole as promising anti-Candida agents

Recognizing that metal ions play an important role in modifying the pharmacological properties of known organic-based drugs, the present manuscript addresses the complexation of the antifungal agent voriconazole (vcz) with the biologically relevant silver(I) ion as a strategy for the development of new antimycotics. The synthesized silver(I) complexes with vcz were characterized by mass spectrometry, IR, UV-Vis and NMR spectroscopy and single-crystal X-ray diffraction analysis. The crystallographic results showed that complexes {[Ag(vcz)(H2O)]CH3SO3}n (1), {[Ag(vcz)2]BF4}n (2) and {[Ag(vcz)2]PF6}n (3) have polymeric structures in the solid state, in which silver(I) ions have a distorted tetrahedral geometry. On the other hand, DFT calculations revealed that the investigated silver(I) complexes 1-3 in DMSO exist as linear [Ag(vcz-N2)(vcz-N19)]+ (1a), [Ag(vcz-N2)(vcz-N4)]+ (2a) and [Ag(vcz-N4)2]+ (3a) species, respectively. The evaluated complexes showed an enhanced anti-Candida activity compared to the parent drug with minimal inhibitory concentration (MIC) values in the range of 0.02-1.05 μM. In comparison with vcz, the corresponding silver(I) complexes showed better activity in prevention hyphae and biofilm formation of C. albicans, indicating that they could be considered as promising agents against Candida that significantly inhibit its virulence. Also, these complexes are much better inhibitors of ergosterol synthesis in the cell membrane of C. albicans at the concentration of 0.5 × MIC. This is also confirmed by a molecular docking, which revealed that complexes 1a - 3a showed better inhibitory activity than vcz against the sterol 14α-demethylase enzyme cytochrome P450 (CYP51B), which plays a crucial role in the formation of ergosterol.

Deciphering the influence of PdII and PdIV oxidation states on non-standard chemical bonds within bis(jN-heterocyclic carbene) complexes: insights from DFT

Bis-N-heterocyclic carbene ligands (bis(NHC)) have introduced a new approach to designing homogeneous and heterogeneous catalysts, demonstrating the versatility of ligand concepts in catalysis. This study presents a computational analysis of palladium (+ii and +iv) complexes containing either a normally (bis(nNHC)) or an abnormally (bis(aNHC)) bound CH2-bridged bis-N-heterocyclic carbene ligand; in addition, ancillary ligands are permuted from chlorides (X = Cl) to bromides (X = Br). Density functional theory at the B3PW91/6-31G(d)/Lanl2DZ level in the gas phase was used to investigate the electronic structure and bonding properties of bis(NHC)PdIIX2 and bis(NHC)PdIVX4 for bis(NHC) palladium(ii) dihalide and palladium(iv) tetrachloride complexes, respectively. Results indicate that all of the palladium complex structures prefer a flexible boat-type conformation with an average C 2v symmetry, according to bond property (Ccarbene-Pd and Pd-Cl[Br]) analysis. The strength of these bonds depends on coordinating halide ions (Cl- and Br-), the type of ligand (bis(nNHC) and bis(aNHC)), and the palladium oxidation state (+ii and +iv). Analysis of thermodynamic parameters (ΔH 0, ΔG 0, and ΔE bind) shows an increase in values from an abnormal to normal chelating mode in tetrahalides, whereas the opposite is observed for dihalide complexes. The lower π-backbonding ability of the metal, which is influenced by the quantity and size of halide ions involved, could be one possible explanation for this deficiency.

Influence of halogen-halogen interactions in the self-assembly of pillar[5]arene-based supramolecular polymers

Halogen-halogen interactions play a pivotal role in the formation and stability of supramolecular assemblies. Herein, we investigate the assembly dynamics and dissociation pathways of linear supramolecular polymers based on pillar[5]arene-mediated by guest halogen-halogen interactions (C-X × X-C) in both the solution and solid states. The structure of the solid-state supramolecular assembly was determined by single-crystal X-ray diffraction analysis. The binding affinities of four different 1,4-dihalobutane guests with pillar[5]arene were investigated by 1H NMR spectroscopic titration and isothermal titration calorimetry (ITC). The formation of the halogen-bonded linear supramolecular polymer in solution was demonstrated using diffusion-ordered spectroscopy (DOSY) and ITC. Our findings highlight the dependence of the dissociation process on halogen nature within the encapsulated guest, revealing that the process is entropically driven (TΔS = 27.12 kJ mol-1) and enthalpically disfavored (ΔH = 9.99 kJ mol-1). Moreover, the disassembly of supramolecular polymers promoted by N-containing compounds was investigated using 1H NMR spectroscopy and ITC, revealing that the process is driven both enthalpically (ΔH = -2.64 kJ mol-1) and entropically (TΔS = 15.70 kJ mol-1). Notably, the data suggest the formation of N⋯I bonding interactions at both ends of the inclusion guest, elucidating the intricate interplay of halogen interactions and host-guest chemistry in supramolecular polymer systems.

Perhalogenated Anilines as Bifunctional Donors of Hydrogen and Halogen Bonds in Cocrystals with Ditopic Nitrogen-Containing Acceptors

In this study, we examine the experimental and theoretical capabilities of two perhalogenated anilines, 2,3,5,6-tetrafluoro-4-bromoaniline (btfa) and 2,3,5,6-tetrafluoro-4-iodoaniline (itfa) as hydrogen and halogen bond donors. A series of 11 cocrystals derived from the two anilines and selected ditopic nitrogen-containing acceptors (4,4'-bipyridine, 1,2-bis(4-pyridyl)ethane, and 1,4-diazabicyclo[2.2.2]octane) in 1:1 and 2:1 stoichiometries were prepared by liquid-assisted grinding and crystallization from solution. Crystallographic analysis revealed bifunctional donor properties in both anilines. The dominant supramolecular interaction in four cocrystals of btfa is the N-H···Nacceptor hydrogen bond between btfa and acceptor molecules, while in the one remaining cocrystal, donor and acceptor molecules are connected via the N-H···Nacceptor hydrogen bond and the Br···Nacceptor halogen bond. In two cocrystals of itfa, the dominant supramolecular interaction is the I···Nacceptor halogen bond between itfa and acceptor molecules, while in the remaining four cocrystals, donor and acceptor molecules are additionally connected by the N-H···Nacceptor hydrogen bond. Periodic density-functional theory (DFT) calculations have been conducted to assess the formation energies of these cocrystals and the strengths of the established halogen and hydrogen bonds. Molecular DFT calculations on btfa and itfa indicate that the differences in electrostatic potential between the competing sites on the molecules are 261.6 and 157.0 kJ mol-1 e-1, respectively. The findings suggest that itfa, with a smaller electrostatic potential difference between donor sites, is more predisposed to act as a bifunctional donor.

Supramolecular assembly activated single-molecule phosphorescence resonance energy transfer for near-infrared targeted cell imaging

Pure organic phosphorescence resonance energy transfer is a research hotspot. Herein, a single-molecule phosphorescence resonance energy transfer system with a large Stokes shift of 367 nm and near-infrared emission is constructed by guest molecule alkyl-bridged methoxy-tetraphenylethylene-phenylpyridines derivative, cucurbit[n]uril (n = 7, 8) and β-cyclodextrin modified hyaluronic acid. The high binding affinity of cucurbituril to guest molecules in various stoichiometric ratios not only regulates the topological morphology of supramolecular assembly but also induces different phosphorescence emissions. Varying from the spherical nanoparticles and nanorods for binary assemblies, three-dimensional nanoplate is obtained by the ternary co-assembly of guest with cucurbit[7]uril/cucurbit[8]uril, accompanying enhanced phosphorescence at 540 nm. Uncommonly, the secondary assembly of β-cyclodextrin modified hyaluronic acid and ternary assembly activates a single intramolecular phosphorescence resonance energy transfer process derived from phenyl pyridines unit to methoxy-tetraphenylethylene function group, enabling a near-infrared delayed fluorescence at 700 nm, which ultimately applied to mitochondrial targeted imaging for cancer cells.

Direct observation of photoinduced sequential spin transition in a halogen-bonded hybrid system by complementary ultrafast optical and electron probes

A detailed understanding of the ultrafast dynamics of halogen-bonded materials is desired for designing supramolecular materials and tuning various electronic properties by external stimuli. Here, a prototypical halogen-bonded multifunctional material containing spin crossover (SCO) cations and paramagnetic radical anions is studied as a model system of photo-switchable SCO hybrid systems using ultrafast electron diffraction and two complementary optical spectroscopic techniques. Our results reveal a sequential dynamics from SCO to radical dimer softening, uncovering a key transient intermediate state. In combination with quantum chemistry calculations, we demonstrate the presence of halogen bonds in the low- and high-temperature phases and propose their role during the photoinduced sequential dynamics, underscoring the significance of exploring ultrafast dynamics. Our research highlights the promising utility of halogen bonds in finely tuning functional properties across diverse photoactive multifunctional materials.

Crystal structures of four gold(I) complexes [AuL 2]+[AuX 2]- and a by-product (L·LH+)[AuBr2]- (L = substituted pyridine, X = Cl or Br)

Bis(2-methyl-pyridine)-gold(I) di-bromido-aurate(I), [Au(C6H7N)2][AuBr2], (1), crystallizes in space group C2/c with Z = 4. Both gold atoms lie on twofold axes and are connected by an aurophilic contact. A second aurophilic contact leads to infinite chains of alternating cations and anions parallel to the b axis, and the residues are further connected by a short H⋯Au contact and a borderline Br⋯Br contact. Bis(3-methyl-pyridine)-gold(I) di-bromido-aurate(I), [Au(C6H7N)2][AuBr2], (2), crystallizes in space group C2/m with Z = 2. Both gold atoms lie on special positions with symmetry 2/m and are connected by an aurophilic contact; all other atoms except for one methyl hydrogen lie in mirror planes. The extended structure is closely analogous to that of 1, although the structures are formally not isotypic. Bis(3,5-di-methyl-pyridine)-gold(I) di-chlor-ido-aurate(I), [Au(C7H9N)2][AuCl2], (3) crystallizes in space group P with Z = 2. The cation lies on a general position, and there are two independent anions in which the gold atoms lie on inversion centres. The cation and one anion associate via three short H⋯Cl contacts to form a ribbon structure parallel to the b axis; aurophilic contacts link adjacent ribbons. Bis(3,5-di-methyl-pyridine)-gold(I) di-bromido-aurate(I), [Au(C7H9N)2][AuBr2], (4) is isotypic to 3. Attempts to make similar compounds involving 2-bromo-pyridine led instead to 2-bromopyridinium di-bromido-aurate(I)-2-bromo-pyridine (1/1), (C5H5BrN)[AuBr2]·C5H4BrN, (5), which crystallizes in space group P with Z = 2; all atoms lie on general positions. The 2-bromo-pyridinium cation is linked to the 2-bromo-pyridine mol-ecule by an N-H⋯N hydrogen bond. Two formula units aggregate to form inversion-symmetric dimers involving Br⋯Br, Au⋯Br and H⋯Br contacts.

Structural, computational and in silico studies of 4-bromo-3-flurobenzonitrile as anti-Alzheimer and anti-Parkinson agents

A novel dimer of the 4-bromo-3-fluorobenzonitrile was crystallized and studied using a spectroscopic method such as the scanning electron microscope method. The computational simulations substantiated the structural analysis findings. The Hirshfeld surface analysis has been performed for visualizing, exploring and quantifying the intra and inter-molecular interactions that stabilize the crystal packing of the compound. The NBO and QTAIM analyses were applied to study the nature and origin of the attractive forces involved in the crystal structure. Further, the pharmacokinetic properties of the compound were evaluated, indicating good brain-blood barrier and central nervous system penetration capability. Hence, in silico studies was carried out to explore the binding pattern of the titled compound against acetylcholinesterase and butyrylcholinesterase, and tumor necrosis factor-alpha converting enzyme proteins using molecular docking and molecular dynamics simulations approach. Further, the titled compound is compared with standard drugs through molecular docking studies. The in silico studies finally predicts that the compound under investigation may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may provide its therapeutic potential.Communicated by Ramaswamy H. Sarma.

Selective Gold Precipitation by a Tertiary Diamide Driven by Thermodynamic Control

The simple diamide ligand L was previously shown to selectively precipitate gold from acidic solutions typical of e-waste leach streams, with precipitation of gallium, iron, tin, and platinum possible under more forcing conditions. Herein, we report direct competition experiments to afford the order of selectivity. Thermal analysis indicates that the gold-, gallium-, and iron-containing precipitates present as the most thermodynamically stable structures at room temperature, while the tin-containing structure does not. Computational modeling established that the precipitation process is thermodynamically driven, with ion exchange calculations matching the observed experimental selectivity ordering. Calculations also show that the stretched ligand conformation seen in the X-ray crystal structure of the gold-containing precipitate is more strained than in the structures of the other metal precipitates, indicating that intermolecular interactions likely dictate the selectivity ordering. This was confirmed through a combination of Hirshfeld, noncovalent interaction (NCI), and quantum theory of atoms in molecules (QTAIM) analyses, which highlight favorable halogen···halogen contacts between metalates and pseudo-anagostic C-H···metal interactions in the crystal structure of the gold-containing precipitate.

A Charge-Charge Flux-Dipole Flux Analysis of Simple Molecular Systems with Halogen Bonds

The presence of halogen bonds (R-X···B; R = substituent group, X = halogen, and B = Lewis base) provides quite amazing molecular systems for electronic structure investigations, presenting unique characteristics of fundamental relevance to supramolecular chemistry among other areas. Here, we use a double-hybrid approach from Density Functional Theory and triple-ζ basis sets augmented with diffuse functions (B2PLYP/def2-TZVPD) to deal with a large group of simple molecular systems containing halogen bonds (XBs), focusing on geometrical structures, binding energies, harmonic vibrational frequencies, and fundamental infrared intensities. Next, the electron densities and their variations on vibrations are carefully studied with the Quantum Theory of Atoms in Molecules (QTAIM) formalism and the charge-charge flux-dipole flux (CCFDF) model. We notice that the R-X stretching mode usually shows vibrational frequency decrements and infrared intensifications during the XB formation. Such features were also observed in hydrogen bonds, although the explanation for the band strengthening is different. Surprisingly, the most important contribution to these intensity increments due to complexation is now the interaction term between the charge flux and dipole flux (CF × DF). Thus, the use of atomic dipoles is mandatory to fully understand this phenomenon. In fact, the huge charge flux contributions to changes in dipole moment derivatives of R-X stretchings on halogen bonding are no longer accompanied by opposite variations of similar magnitudes in polarizations described by atomic dipole fluxes, which provided nearly unaltered values during the XB formation. Thus, the electronic charge flux direction change that takes place in complexes (from B to R) now reinforces dipole moment derivative terms from such atomic polarizations (mainly from the X atom). This intermolecular charge flux seems to be responsible for the unusual features noticed in the R-X stretching mode with the CCDDF/QTAIM model.

Combination of Hydrogen and Halogen Bonds in the Crystal Structures of 5-Halogeno-1H-isatin-3-oximes: Involvement of the Oxime Functionality in Halogen Bonding

Various functional groups have been considered as acceptors for halogen bonds, but the oxime functionality has received very little attention in this context. In this study, we focus on the analysis of the hydrogen and halogen bond preferences observed in the crystal structures of 5-halogeno-1H-isatin-3-oximes. These molecules can be involved in various non-covalent interactions, and the competition between these interactions has a decisive influence on their self-organization. In particular, we were interested to see whether the crystal structures of 5-halogeno-1H-isatin-3-oximes, especially bromine- and iodine-substituted ones, are characterized by the presence of halogen bonds formed with the oxime functionality. The oxime group proved its ability to compete with the other strong donor and acceptor sites by participating in the formation of cyclic hydrogen-bonded heterosynthons oxime∙∙∙amide and Ooxime∙∙∙Br/I halogen bonds.

Elucidating the Role of Electron-Donating Groups in Halogen Bonding

Computational quantum chemical techniques were utilized to systematically examine how electron-donating groups affect the electronic and spectroscopic properties of halogen bond donors and their corresponding complexes. Unlike the majority of studies on halogen bonding, where electron-withdrawing groups are utilized, this work investigates the influence of electron-donating substituents within the halogen bond donors. Statistical analyses were performed on the descriptors of halogen bond donors in a prescribed set of archetype, halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond systems. The σ-hole magnitude, binding and interaction energies, and the vibrational X···N local force constant (where X = Cl, Br, I, and At) were found to correlate very well in a monotonic and linear manner with all other properties studied. In addition, enhanced halogen bonds were found when the systems contained electron-donating groups that could form intramolecular hydrogen bonds with the electronegative belt of the halogen atom and adjacent linker features.

Dioxygen-halogen bonding exemplified by crystalline peroxosolvates of N,N'-bis(haloacetyl) bispidines

The halogen bonding in molecular crystals and supramolecular assemblies has been widely investigated. Special attention is given to the molecular structures capable of simultaneously exhibiting different types of non-covalent interactions, including conventional hydrogen bonds and halogen bonds. This paper systematically analyzes crystalline peroxosolvates of bispidine-based bis-amide derivatives, containing haloacetic acid residues, namely previously reported 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodooethanone) peroxosolvate C13H20I2N2O2·H2O2 (1) and four new crystalline compounds, 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O2·H2O2 (2), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodoethanone) peroxosolvate C13H20I2N2O5·0.5H2O2 (3), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O5·H2O2 (4), and 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-chloroethanone) peroxosolvate C13H20Cl2N2O5·H2O2 (5). Compounds 2-5 were synthesized for the first time and their crystal structures were determined by single-crystal X-ray diffractometry (SCXRD). To the best of our knowledge, 3-5 are unprecedented crystalline hydrogen peroxide adducts of organic hydroperoxides (R-OOH). Short intermolecular contacts between halogen and hydroperoxo oxygen atoms were found in 1-3. The halogen bonding of C-I(Br) fragments with dioxygen species in compounds 1-3 as well as in the previously reported cocrystal of diacetone diperoxide with triodotrinitrobenzene (6) was identified through reduced density gradient analysis, Hirshfeld surface analysis, and Bader analysis of crystalline electron density. The interactions were quantified using the electron density topological properties acquired from the periodic DFT calculations and evaluated to lie in the range of 9-19 kJ mol-1. A distinctive spectral feature was revealed for this type of interaction, involving a red shift of the characteristic O-O stretching vibration by about 6 cm-1, which appeared in IR spectra as a narrow low-intensity band in the region 837-872 cm-1.

Crystal structures of five gold(I) complexes with methyl-piperidine ligands

In bis-(4-methyl-piperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl (1), the methyl groups are, as expected, equatorial at the piperidine ring, but the Au atom is axial; this is the case for all five structures reported here, as is the expected linear coordination at the Au atom. Hydrogen bonding of the form N-H⋯Cl-⋯H-N leads to inversion-symmetric dimers, which are further connected by C-H⋯Au contacts. Bis(4-methyl-piperidine-κN)gold(I) di-chlorido-aurate(I), [Au(C6H13N)2][AuCl2] (2), also forms inversion-symmetric dimers; these involve aurophilic inter-actions and three-centre hydrogen bonds of the form NH(⋯Cl)2. Bis(4-methyl-piperidine-κN)gold(I) di-bromido-aurate(I), [Au(C6H13N)2][AuBr2] (3), is isotypic to 2. The 1:1 adduct chlorido-(4-methyl-piperidine-κN)gold(I) bis-(4-methyl-piperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl·[AuCl(C6H13N)] (4), crystallizes as its di-chloro-methane solvate. The asymmetric unit contains two formula units, in each of which the chloride anion accepts a hydrogen bond from the cation and from the neutral mol-ecule, and the two Au atoms are linked via an aurophilic inter-action. A further hydrogen bond leads to inversion-symmetric dimers. The asymmetric unit of bis-(2-methyl-piperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl (5), contains two 'half' cations, in which the Au atoms lie on twofold axes, and a chloride ion on a general position. Within each cation, the relative configurations at the atoms N and C2 (which bears the methyl substituent) are R,S. The twofold-symmetric dimer involves two N-H⋯Cl-⋯H-N units and an aurophilic contact between the two Au atoms.

Exploring the Role of Metal in the Biointeraction of Metallacarboranes with C. elegans Embryos

Cobaltabis(dicarbollides), ferrabis(dicarbollide), and their halogenated derivatives are the most studied metallacarboranes with great medical potential. These versatile compounds and their iodinated derivatives can be used in chemotherapy, radiotherapy, particle therapy, and bioimaging when isotopes are used. These metallacarboranes have been evaluated in vitro and recently in vivo with complex animal models. Lately, these studies have been complemented using the invertebrate Caenorhabditis elegans (C. elegans), a nematode largely used in toxicology. When evaluated at the L4 stage, cobaltabis(dicarbollides), ([o-COSAN]- and [8,8'-I2 -o-COSAN]- ), exhibited a higher mean lethal dose (LD50 ) than ferrabis(dicarbollides) ([o-FESAN]- and [8,8'-I2 -o-FESAN]- ). In this work, we used the C. elegans embryos since they are a complex biological barrier with concentric layers of polysaccharides and proteins that protect them from the environment. We assessed if the metal atom changes their biointeraction with the C. elegans embryos. First, we assessed the effects on embryo development for metallacarboranes and their di-iodinated derivatives. We observed changes in color and in their surface structure. An exhaustive physicochemical characterization was performed to understand better this interaction, revealing a stronger interaction of ferrabis(dicarbollide) compounds with C. elegans embryos than the cobaltabis(dicarbollide) molecules. Unveiling the biological interaction of these compounds is of great interest for their future biomedical applications.

Study on the modulating effect of halogen atom substitution on the detection range of water content detection probes in organic solvents

Fluorescence probes based on the variations of aggregation state (Aggregation-Induced Emission (AIE) and Aggregation-Caused Quenching (ACQ)) have received widespread attention due to their simplicity, efficiency and intuitiveness. However, typical probes are highly sensitive to changes in polarity and slight variations in the external environment can cause a complete change in the aggregation state. With the aim of expanding the detection range of the molecular probe, this work adopts a different design strategy from adjusting the molecular backbone but regulates the fluorescence behavior of the Schiff base molecular backbone by introducing different halogen atoms. Systematic studies show that when chlorine serves as substitutional atoms (3,5-Cl Salen), the probe can achieve full-range detection of water content (0-100 vol%) in ethanol and DMF. To our knowledge, the 3,5-Cl Salen represents the best water content probe in organic molecules. Experimental and theoretical studies have shown that the adjustment of halogen atoms can linearly change the charge distribution on the benzene ring and precisely control the strength of intermolecular interactions. At the same time, we developed a fluorescent filter paper based on 3,5-Cl Salen and used smartphones for rapid, sensitive and precise on-site measurement of water content in organic solvents.

Crystal structures of sixteen phosphane chalcogenide complexes of gold(I) chloride, bromide and iodide

The structures of 16 phosphane chalcogenide complexes of gold(I) halides, with the general formula R 1 3- nR 2 nPEAuX (R 1 = t-butyl; R 2 = isopropyl; n = 0 to 3; E = S or Se; X = Cl, Br or I), are presented. The eight possible chlorido derivatives are: 1a, n = 3, E = S; 2a, n = 2, E = S; 3a, n = 1, E = S; 4a, n = 0, E = S; 5a, n = 3, E = Se; 6a, n = 2, E = Se; 7a, n = 1, E = Se; and 8a, n = 0, E = Se, and the corresponding bromido derivatives are 1b-8b in the same order. However, 2a and 2b were badly disordered and 8a was not obtained. The iodido derivatives are 2c, 6c and 7c (numbered as for the series a and b). All structures are solvent-free and all have Z' = 1 except for 6b and 6c (Z' = 2). All mol-ecules show the expected linear geometry at gold and approximately tetra-hedral angles P-E-Au. The presence of bulky ligands forces some short intra-molecular contacts, in particular H⋯Au and H⋯E. The Au-E bond lengths have a slight but consistent tendency to be longer when trans to a softer X ligand, and vice versa. The five compounds 1a, 5a, 6a, 1b and 5b form an isotypic set, despite the different alkyl groups in 6a. Compounds 3a/3b, 4b/8b and 6b/6c form isotypic pairs. The crystal packing can be analysed in terms of various types of secondary inter-actions, of which the most frequent are 'weak' hydrogen bonds from methine hydrogen atoms to the halogenido ligands. For the structure type 1a, H⋯X and H⋯E contacts combine to form a layer structure. For 3a/3b, the packing is almost featureless, but can be described in terms of a double-layer structure involving borderline H⋯Cl/Br and H⋯S contacts. In 4a and 4b/8b, which lack methine groups, Cmeth-yl-H⋯X contacts combine to form layer structures. In 7a/7b, short C-H⋯X inter-actions form chains of mol-ecules that are further linked by association of short Au⋯Se contacts to form a layer structure. The packing of compound 6b/6c can conveniently be analysed for each independent mol-ecule separately, because they occupy different regions of the cell. Mol-ecule 1 forms chains in which the mol-ecules are linked by a Cmethine⋯Au contact. The mol-ecules 2 associate via a short Se⋯Se contact and a short H⋯X contact to form a layer structure. The packing of compound 2c can be described in terms of two short Cmethine-H⋯I contacts, which combine to form a corrugated ribbon structure. Compound 7c is the only compound in this paper to feature Au⋯Au contacts, which lead to twofold-symmetric dimers. Apart from this, the packing is almost featureless, consisting of layers with only translation symmetry except for two very borderline Au⋯H contacts.

Bispidine as a Versatile Scaffold: From Topological Hosts to Transmembrane Transporters

The development of designer topological structures is a synthetically challenging endeavor. We present herein bispidine as a platform for the design of molecules with various topologies and functions. The bispidine-based acyclic molecule, which shows intriguing S-shape topology, is discussed. Single-crystal X-ray diffraction studies revealed that this molecule exists in the solid state as two conformational enantiomers. In addition, bispidine-based designer macrocycles were synthesized and investigated for ionophoric properties. Patch clamp experiments revealed that these macrocycles transport both anions and cations non-specifically with at least tenfold higher chloride conductance over the cations under the given experimental conditions. Ultramicroscopy and single-crystal X-ray crystallographic studies indicated that the self-assembling macrocycle forms a tubular assembly. Our design highlights the use of unconventional dihydrogen interactions in nanotube fabrication.

Crystal structures of the isotypic complexes bis-(morpholine)-gold(I) chloride and bis-(morpholine)-gold(I) bromide

The compounds bis-(morpholine-κN)gold(I) chloride, [Au(C4H9NO)2]Cl, 1, and bis-(morpholine-κN)gold(I) bromide, [Au(C4H9NO)2]Br, 2, crystallize isotypically in space group C2/c with Z = 4. The gold atoms, which are axially positioned at the morpholine rings, lie on inversion centres (so that the N-Au-N coordination is exactly linear) and the halide anions on twofold axes. The residues are connected by a classical hydrogen bond N-H⋯halide and by a short gold⋯halide contact to form a layer structure parallel to the bc plane. The morpholine oxygen atom is not involved in classical hydrogen bonding.

An Experimental and Theoretical Insight into I2 /Br2 Oxidation of Bis(pyridin-2-yl)Diselane and Ditellane

The reactivity between bis(pyridin-2-yl)diselane o Py2 Se2 and ditellane o Py2 Te2 (L1 and L2, respectively; o Py=pyridyn-2-yl) and I2 /Br2 is discussed. Single-crystal structure analysis revealed that the reaction of L1 with I2 yielded [(HL1+ )(I- )⋅5/2I2 ]∞ (1) in which monoprotonated cations HL1+ template a self-assembled infinite pseudo-cubic polyiodide 3D-network, while the reaction with Br2 yielded the dibromide Ho PySeII Br2 (2). The oxidation of L2 with I2 and Br2 yielded the compounds Ho PyTeII I2 (3) and Ho PyTeIV Br4 (6), respectively, whose structures were elucidated by X-ray diffraction analysis. FT-Raman spectroscopy measurements are consistent with a 3c-4e description of all the X-Ch-X three-body systems (Ch=Se, Te; X=Br, I) in compounds 2, 3, Ho PyTeII Br2 (5), and 6. The structural and spectroscopic observations are supported by extensive theoretical calculations carried out at the DFT level that were employed to study the electronic structure of the investigated compounds, the thermodynamic aspects of their formation, and the role of noncovalent σ-hole halogen and chalcogen bonds in the X⋅⋅⋅X, X⋅⋅⋅Ch and Ch⋅⋅⋅Ch interactions evidenced structurally.

Hole interactions of aerogen oxides with Lewis bases: an insight into σ-hole and lone-pair-hole interactions

σ-Hole and lone-pair (lp)-hole interactions of aerogen oxides with Lewis bases (LB) were comparatively inspected in terms of quantum mechanics calculations. The ZOn ⋯ LB complexes (where Z = Kr and Xe, n = 1, 2, 3 and 4, and LB = NH3 and NCH) showed favourable negative interaction energies. The complexation features were explained in light of σ-hole and lp-hole interactions within optimum distances lower than the sum of the respective van der Waals radii. The emerging findings outlined that σ-hole interaction energies generally enhanced according to the following order: KrO4 ⋯ < KrO⋯ < KrO3⋯ < KrO2⋯LB and XeO4⋯ < XeO⋯ < XeO2⋯ < XeO3⋯LB complexes with values ranging from -2.23 to -12.84 kcal mol-1. Lp-hole interactions with values up to -5.91 kcal mol-1 were shown. Symmetry-adapted perturbation theory findings revealed the significant contributions of electrostatic forces accounting for 50-65% of the total attractive forces within most of the ZOn⋯LB complexes. The obtained observations would be useful for the understanding of hole interactions, particularly for the aerogen oxides, with application in supramolecular chemistry and crystal engineering.

A Halogen-Bonded Organic Framework (XOF) Emissive Cocrystal for Acid Vapor and Explosive Sensing, and Iodine Capture

There is a strong and urgent need for efficient materials that can capture radioactive iodine atoms from nuclear waste. This work presents a novel strategy to develop porous materials for iodine capture by employing halogen bonding, mechanochemistry and crystal engineering. 3D halogen-bonded organic frameworks (XOFs) with guest-accessible permanent pores are exciting targets in crystal engineering for developing functional materials, and this work reports the first example of such a structure. The new-found XOF, namely TIEPE-DABCO, exhibits enhanced emission in the solid state and turn-off emission sensing of acid vapors and explosives like picric acid in nanomolar quantity. TIEPE-DABCO captures iodine from the gas phase (3.23 g g-1 at 75 °C and 1.40 g g-1 at rt), organic solvents (2.1 g g-1 ), and aqueous solutions (1.8 g g-1 in the pH range of 3-8); the latter with fast kinetics. The captured iodine can be retained for more than 7 days without any leaching, but readily released using methanol, when required. TIEPE-DABCO can be recycled for iodine capture several times without any loss of storage capacity. The results presented in this work demonstrate the potential of mechanochemical cocrystal engineering with halogen bonding as an approach to develop porous materials for iodine capture and sensing.

Crystal structures of five halido gold complexes involving piperidine or pyrrolidine as ligands or (protonated) as cations

In bromido-(pyrrolidine-κN)gold(I) bis-(pyrrolidine-κN)gold(I) bromide, [AuBr(pyr)]·[Au(pyr)2]Br (pyr = pyrrolidine, C4H9N), 2, alternating [AuBr(pyr)] mol-ecules and [Au(pyr)2]+ cations are connected by aurophilic contacts to form infinite chains of residues parallel to the b axis. The chains are cross-linked by three N-H⋯Br- hydrogen bonds and an Au⋯Br contact to form a layer structure parallel to the ab plane. Tri-chlorido-(piperidine-κN)gold(III), [AuCl3(pip)] (pip = piperidine, C5H11N), 3, consists of mol-ecules with the expected square-planar coordination at the gold atom, which are connected by an N-H⋯Cl hydrogen bond and an Au⋯Cl contact to form a layer structure parallel to the ac plane. The structures of bis-(piperidinium) tetra-chlorido-aurate(III) chloride, (pipH)2[AuCl4]Cl, 4, and bis-(pyrrolidinium) tetra-bromido-aurate(III) bromide, (pyrH)2[AuBr4]Br, 6, are closely related but not isotypic. Compound 6 crystallizes in space group Ibam; the Au and two Br atoms of the anion lie in the mirror plane x, y, 0, whereas the bromide ions occupy special positions 0, 0.5, 0 and 0, 0.5, 0.25, with site symmetry 2/m. The NH2 group forms a hydrogen bond to one bromide ion, and also a three-centre hydrogen bond to the other bromide atom and to a metal-bonded Br atom. The packing involves chains of hydrogen-bonded pyrrolidinium and bromide ions parallel to the c axis, combined with a layer structure of [AuBr4]- and bromide anions, parallel to the ab plane and involving Au⋯Br and Br⋯Br contacts. Compound 4, however, crystallizes pseudosymmetrically in space group Iba2; two chlorine atoms of the anion lie on the twofold axis 0.5, 0.5, z, and there are two independent cations. The packing is closely similar to that of 6, but there are no N-H⋯Cl hydrogen bonds to metal-bonded chlorines. The contact distances Au⋯Cl are appreciably longer than their Au⋯Br counterparts in 6, whereas the Cl⋯Cl contact is much shorter than Br⋯Br in 6. Tri-bromido-(piperidine-κN)gold(III) crystallizes as its di-chloro-methane solvate, [AuBr3(pip)]·CH2Cl2, 7. It too displays a square-planar coordination at the gold atom. The packing involves hydrogen bonds N-H⋯Br, stacking of neighbouring AuBr3 units by Au⋯Br contacts, and a short Br⋯Br contact; these combine to form a layer structure parallel to the ac plane.

Coverage-modulated halogen bond geometry transformation in supramolecular assemblies

Halogen bonding (HB) has emerged as a promising route for designing supramolecular assemblies due to its directional nature and versatility in modifying interactions through the choice of halogens and molecular entities. Despite this, methods for tuning these interactions on surfaces, particularly in terms of directionality, are limited. In this study, we present a strategy for tuning the directionality of self-assembly processes in homomolecular organic compounds on inert metal surfaces. A variety of halogen-halogen geometries can promote highly-extended one-dimensional or two-dimensional self-assembly depending on the molecular coverage. Our results indicate that under lower molecular coverage conditions, robust one-dimensional (1D) structures promote the self-assembly of halogen-bonded molecules on Au(111). At certain coverage, a transformation from type-I to synthon halogen bonding is observed, leading to an extended hexagonal pattern of molecular assembly. The atomistic details of the structures are experimentally studied using high-resolution atomic force microscopy and supported by first-principle calculations. We employed DFT to evaluate the interplay between electrostatics and dispersion forces driving both type-I and synthon assemblies. The results reveal a halogen-bond geometry transformation induced by a subtle balance of molecule-molecule interaction. Finally, we investigate the capability of the halogen-bonded supramolecular assembly to periodically confine electronic quantum states and single atoms. Our findings demonstrate the versatility of sigma-bonding in regulating molecular assembly and provide new insights for tailoring functional molecular structures on an inert metal substrate.

Asymmetric Trihalogenated Aromatic Lithium Salt Induced Lithium Halide Rich Interface for Stable Cycling of All-Solid-State Lithium Batteries

Solid polymer electrolytes (SPEs) are the key components for all-solid-state lithium metal batteries with high energy density and intrinsic safety. However, the low lithium ion transference number (t+) of a conventional SPE and its unstable electrolyte/electrode interface cannot guarantee long-term stable operation. Herein, asymmetric trihalogenated aromatic lithium salts, i.e., lithium (3,4,5-trifluorobenzenesulfonyl)(trifluoromethanesulfonyl)imide (LiFFF) and lithium (4-bromo-3,5-difluorobenzenesulfonyl)(trifluoromethanesulfonyl)imide (LiFBF), are synthesized for polymer electrolytes. They exhibit higher t+ values and better compatibility with Li metal than conventional lithium bis(trifluoromethanesulfonyl) imide (LiTFSI). Due to the trihalogenated aromatic anions, LiFFF- and LiFBF-based electrolytes are prone to generate an LiF- and LiBr-rich solid electrolyte interphase (SEI), therefore increasing the stability of the solid electrolyte/anode interface. Particularly, LiFBF could induce a LiF/LiBr hybrid SEI, where LiF shows a high Young's modulus and high surface energy for homogenizing Li ion flux and LiBr exhibits an extremely low Li ion diffusion barrier in the SEI layer. As a result, the Li/Li symmetric cells could remain stable for more than 1200 h without a short circuit and the LiFePO4/Li batteries showed superb electrochemical performance over 1200 cycles at 1 C. This work provides valuable insights from the perspective of lithium salt molecular structures for high-performance all-solid-state lithium metal batteries.

Supramolecular axial chirality in [N-I-N]+-type halogen bonded dimers

Axial chiral molecules are extensively used as skeletons in ligands for asymmetric catalysis and as building blocks of chiroptical materials. Designing axial chirality at the supramolecular level potentially endows a material with dynamic tunability and adaptivity. In this work, for the first time, we have reported a series of halogen-bonded dimeric complexes with axial chirality that were formed by noncovalent bonds. The [N-I-N]+-type halogen bond is highly directional and freely rotatable with good linearity and ultra-high bond energy; this bond was introduced to couple quinoline moieties with chiral substitutes. The resultant dimers were stable in solutions with thermo-resistance. Prominent steric effects from the 2' chiral pendant allowed the chirality to be transferred to aryl skeletons with induced preferred axial chirality and optical activities. Halogen-bonded complexation presented visible emissions to afford luminescent axial chiral materials, whereby circularly polarized fluorescence and phosphorescence were achieved. The [N-I-N]+-type halogen bond performed as a powerful tool to construct functional axial chiral compounds, enriching the toolbox for asymmetric synthesis and optics.

Halogen Bonding in Brominated BODIPY Crystals: a Crystallographic and Computational Study

The study of halogen bonds (XBs) has been a subject of great interest in recent years due to its clear application in catalysis, liquid crystals, and crystal engineering. In this study, we analyzed the intermolecular interactions, in particular halogen bonds in BODIPYs with an increasing number of bromine atoms. The computational study included analyses through three different methods: the first approach of close contacts provided by mercury, then the expanded approach of the electron density partition of the molecules in the crystals provided by the analysis of Hirshfeld surfaces, and finally, the approach of the Quantum Theory of Atoms in Molecules (QT-AIM) to characterize the non-covalent interactions through finding electron density critical points between atoms and between neighboring molecules. The use of different computational methods allowed to gain insight into the interactions directing the crystal packing as the number of bromine atoms increased in the BODIPY moiety. Monocoordinated and bifurcated halogen bonds involving halide/halide were found. The penta-brominated BODIPY showed four-center cyclic nodes where each node is linked via XBs. This kind of motif can be useful in supramolecular chemistry and self-assembly.

Investigation of the Effect of Solvents on the Synthesis of Aza-flavanone from Aminochalcone Facilitated by Halogen Bonding

It has been recognized that CBr4 can give rise to a noncovalent interaction known as halogen bond (XB). CBr4 was found to catalyze, in terms of XB formation, the transformation of 2'-aminochalcone to aza-flavanone through an intramolecular Michael addition reaction. The impact of XB and the resulting yield of aza-flavanone exhibited a pronounced dependence on the characteristics of the solvent. Notably, yields of 88% in ethanol and 33% in DMSO were achieved, while merely a trace amount of the product was detected in benzene. In this work, we use a computational modeling study to understand this variance in yield. The reaction is modeled at the level of density functional theory (based on the M06-2X exchange-correlation functional) with all-electron basis sets of triple-ζ quality. Grimme's dispersion correction is incorporated to account for the noncovalent interactions accurately. Harmonic frequency calculations are carried out to establish the character of the optimized structures (minimum or saddle point). Our calculations confirm the formation of an XB between CBr4 and the reacting species and its role in lowering the activation energy barrier. Stronger orbital interactions and significant lowering of the steric repulsion were found to be important in lowering the activation barrier. The negligible yield in the nonpolar solvent benzene may be attributed to the high activation energy as well as the inadequate stabilization of the zwitterionic intermediate. In ethanol, a protic solvent, additional H-bonding contributes to further lowering of the activation barrier and better stabilization of the zwitterionic intermediate. The combined effects of solvent polarity, XB, and H-bond are likely to give rise to an excellent yield of aza-flavanone in ethanol.

Fluoride Anions: Unexploited but Effective Halogen Bond Acceptors

Due to their high electron density, fluoride anions can be considered the most effective halogen bond (HaB) acceptors among the halides. However, under common experimental conditions, F- uncommonly acts as HaB acceptor, expectedly as it is present in hydrated form. Herein we report that under specific crystallization conditions a hydrogen bond-free F- functioning as donor of electron density can be obtained, with the formed HaBs constituting the driving force of the observed crystal packings. Computations confirm the strength of these HaBs compared to analogous interactions involving other halides.