Oxidative Halogenation with “Green” Oxidants: Oxygen and Hydrogen Peroxide

It is difficult to imagine organic chemistry without organo‐halogen compounds and the molecular halogens needed for their preparation. The halogens have very different reactivity, with iodine usually requiring some form of activation, while others are reactive and hazardous chemicals. To avoid their use, various modified reagents have been discovered (N‐bromo‐ and N‐chlorosuccinimide, Selectfluor…?), but halogens are used to prepare these reagents and when they are used the atom economy is poor. A better approach, which is based on biomimetric research on oxidative halogenation in nature, consists of generating the halogenating reagent in situ under acidic conditions from a halide salt. The result of such a reaction has been halogenation with 100 % halogen atom economy. Suitable oxidants for the oxidation of halides are hydrogen peroxide and oxygen.     

Intramolecular halogen bonds in 1,2-aryldiyne molecules: a theoretical study

Intramolecular halogen bonds have been the subject of several current experimental and theoretical studies. In this work, intramolecular halogen bonds in a series of 1,2-aryldiyne molecules were investigated using density functional theory calculations at the M06-2x level of theory. For comparison, some dimeric complexes between halogenated aryldiynes and quinolinyl compounds were also considered. The calculated interatomic distances and interaction angles of intramolecular halogen bonds compare fairly well with those determined experimentally, and the triangle motifs retain almost perfectly planar in all the studied molecules. Many of the well-known properties of conventional halogen bonds are reproduced in intramolecular halogen bonds: the interaction strength tends to increase with the enlargement of the atomic radius of halogens (I > Br > Cl); the attachment of electron-withdrawing moieties to halogens leads to much stronger intramolecular halogen bonds; the X···N (quinolinyl) interactions are stronger than the X···O (carbonyl) halogen bonds. On the basis of the shorter interatomic distances and the larger values of electron densities at the bond critical points, intramolecular halogen bonds become stronger in strength than corresponding intermolecular halogen bonds. However, these interactions have similar structural, energetic, atoms in molecules (AIM), and noncovalent interaction index (NCI) characteristics to traditional halogen bonds. Therefore, these interactions can be recognized as halogen bonds that are primarily electrostatic in nature. Particularly, the formation of intramolecular halogen bonds gives rise to the essential coplanarity of the molecules, whereas the two subunits in the dimeric complexes deviate from planarity to a large degree. In addition, a small number of crystal structures containing intramolecular halogen bonds were retrieved from the Cambridge Structural Database (CSD), to provide more insights into these interactions in crystals. This work not only will extend the knowledge of noncovalent interactions involving halogens as electrophilic centers but also could be very useful in molecular design and synthetic chemistry.     

Die rolle der elektronenaffinität der halogene in der chemischen analyse

On the basis of their study on the analysis of halogens and their combinations (including the halogen cyanides), the authors have made the following observations: 1. The electronic structure of molecules, in particular the arrangement of active electrons in a covalent linkage, can not be considered as static, because it depends on the conditions of the surroundings (such as, pH, temperature, etc.). It is necessary to distinguish between the “reactive capacity” (affinity of the electrons) and the “reactive disposition” (speed of reaction) depending on the affinity of the electrons. This conception may also serve in the consideration of the “electronere” phenomena. 2. Halogen halides (including the halogen cyanides) react in aqueous solution giving up always the halogen which possesses the greatest electron-affinity.     

Using halogen bonds to address the protein backbone: a systematic evaluation

Halogen bonds are specific embodiments of the sigma hole bonding paradigm. They represent directional interactions between the halogens chlorine, bromine, or iodine and an electron donor as binding partner. Using quantum chemical calculations at the MP2 level, we systematically explore how they can be used in molecular design to address the omnipresent carbonyls of the protein backbone. We characterize energetics and directionality and elucidate their spatial variability in sub-optimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. By deriving simple rules, we aid medicinal chemists and chemical biologists in easily exploiting them for scaffold decoration and design. Our work shows that carbonyl-halogen bonds may be used to expand the patentable medicinal chemistry space, redefining halogens as key features. Furthermore, this data will be useful for implementing halogen bonds into pharmacophore models or scoring functions making the QM information available for automatic molecular recognition in virtual high throughput screening.     

The Reactions of Phosphorus Selenonoesters, > P(Se)OR,with Halogens. New Five-Co-Ordinate and Phosphonium Intermediates Containing P-Se Bond

Abstract

As a continuation of our investigation on the chemistry of thiono- and selenonophosphorus acid esters, the reactions of phosphoroselenoates with various halogens were studied (1). Depending on the structure of selenonophosphoryl compound and on the nature of halogen these reactions involve the formation of different type of intermediates like:     

Rational Modification of the Hierarchy of Intermolecular Interactions in Molecular Crystal Structures by Using Tunable Halogen Bonds

A family of 16 isomolecular salts (3‐XpyH)₂[MX′₄] (3‐XpyH=3‐halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X′=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X‐ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non‐covalent interactions: N? H???X′? M hydrogen bonds, C? X???X′? M halogen bonds and π–π stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C? X???X′? M halogen bonds, whereas an analogous change of the inorganic halogen (X′) weakens both halogen bonds and N? H???X′? M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C? F???X′? M) halogen bonds are absent. The structure is directed by N? H???X′? M hydrogen bonds and π‐stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X′), long (weak) C? X???X′? M interactions are observed with type I halogen–halogen interaction geometries (C? X???X′ ≈ X???X′? M ≈155°), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X′), stronger halogen bonds are formed with a type II halogen–halogen interaction geometry (C? X???X′ ≈180°; X???X′? M ≈110°) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.     

Palladium‐catalysed room‐temperature Suzuki–Miyaura coupling in water extract of pomegranate ash,a bio‐derived sustainable and renewable medium

An agro waste‐derived, ‘water extract of pomegranate ash’ (WEPA), has been utilized for the first time as a renewable medium for Pd(OAc)₂‐catalysed Suzuki–Miyaura cross‐coupling at room temperature. This method offers a simple and sustainable synthesis of biaryls from aryl halides and arylboronic acids under ligand‐ and external base‐free aerobic and ambient conditions. This method has been found effective for both activated and unactivated aryl halides in the production of biaryls with moderate to nearly quantitative yields. The protocol shows high chemoselectivity over identical/similar reactive sites in aryl halides (i.e. selectivity over identical halogens or different halogens of aryl halides). This method exhibits high regioselectivity, i.e. the selective reactivity of a halogen over other identical halogens at different positions on the aromatic nucleus. Therefore, we disclose here a clean, benign, substantial chemo‐ and regioselective and highly economic alternative method for the palladium‐assisted synthesis of biaryls using an agro waste‐derived medium.     

Gas-phase molecular halogen formation from NaCl and NaBr aerosols: when are interface reactions important?

Unique interface reactions at the surface of sea-salt particles have been suggested as an important source of photolyzable gas-phase halogen species in the troposphere. Many factors influence the relative importance of interface chemistry compared to aqueous-phase chemistry. The Model of Aerosol, Gas, and Interfacial Chemistry (MAGIC 2.0) is used to study the influence of interface reactions on gas-phase molecular halogen production from pure NaCl and NaBr aerosols. The main focus is to identify the relative importance of bulk compared to interface chemistry and to determine when interface chemistry dominates. Results show that the interface process involving Cl-(surf) and OH(g) is the main source of Cl2(g). For the analogous oxidation of bromide by OH, gaseous Br2 is formed mainly in the bulk aqueous phase and transferred across the interface. However, the reaction of Br-(surf) with O3(g) at the interface is the primary source of Br2(g) under dark conditions. The effect of aerosol size is also studied. Potential atmospheric implications and effects of interface processes on aerosol pH are discussed.     

Sodium halides as the source of electrophilic halogens in green synthesis of 3-halo- and 3,n-dihalobenzo[b]thiophenes

A convenient methodology for the synthesis of mono- and di-halogenated benzo[b]thiophenes is described herein, which utilizes copper(II) sulfate pentahydrate and various sodium halides in the presence of substituted 2-alkynylthioanisoles. The proposed method is facile, uses ethanol as a green solvent, and results in uniquely substituted benzo[b]thiophene structures with isolated yields up to 96%. The most useful component of this methodology is the selective introduction of bromine atoms at every available position (2–7) around the benzo[b]thiophene ring, while keeping position 3 occupied by a specific halogen atom such as Cl, Br or I. Aromatic halogens are useful reactive handles; therefore, the selective introduction of halogens at specific positions would be valuable in the targeted synthesis of bioactive molecules and complex organic materials via metal-catalyzed cross coupling reactions. This work is a novel approach towards the synthesis of dihalo substituted benzo[b]thiophene core structures, which provides a superior alternative to the current methods discussed herein.     

Characterization of At species in simple and biological media by high performance anion exchange chromatography coupled to gamma detector

Astatine is a rare radioelement belonging to the halogen group. Considering the trace amounts of astatine produced in cyclotrons, its chemistry cannot be evaluated by spectroscopic tools. Analytical tools, provided that they are coupled with a radioactive detection system, may be an alternative way to study its chemistry. In this research work, high performance anion exchange chromatography (HPAEC) coupled to a gamma detector (γ) was used to evaluate astatine species under reducing conditions. Also, to strengthen the reliability of the experiments, a quantitative analysis using a reactive transport model has been done. The results confirm the existence of one species bearing one negative charge in the pH range 2–7.5. With respect to the other halogens, its behavior indicates the existence of negative ion, astatide At⁻. The methodology was successfully applied to the speciation of the astatine in human serum. Under fixed experimental conditions (pH 7.4–7.5 and redox potential of 250 mV) astatine exists mainly as astatide At⁻ and does not interact with the major serum components. Also, the method might be useful for the in vitro stability assessment of ²¹¹At-labeled molecules potentially applicable in nuclear medicine.     

Superhalogens as Building Blocks of Halogen‐Free Electrolytes in Lithium‐Ion Batteries

Most electrolytes currently used in Li‐ion batteries contain halogens, which are toxic. In the search for halogen‐free electrolytes, we studied the electronic structure of the current electrolytes using first‐principles theory. The results showed that all current electrolytes are based on superhalogens, i.e., the vertical electron detachment energies of the moieties that make up the negative ions are larger than those of any halogen atom. Realizing that several superhalogens exist that do not contain a single halogen atom, we studied their potential as effective electrolytes by calculating not only the energy needed to remove a Li⁺ ion but also their affinity towards H₂O. Several halogen‐free electrolytes are identified among which Li(CB₁₁H₁₂) is shown to have the greatest potential.     

Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules

The net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom-centered point-charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley & Sons, Inc.     

Halogen Bonding: An Interim Discussion

Halogen bonding is a noncovalent interaction that is receiving rapidly increasing attention because of its significance in biological systems and its importance in the design of new materials in a variety of areas, for example, electronics, nonlinear optical activity, and pharmaceuticals. The interactions can be understood in terms of electrostatics/polarization and dispersion; they involve a region of positive electrostatic potential on a covalently bonded halogen and a negative site, such as the lone pair of a Lewis base. The positive potential, labeled a σ hole, is on the extension of the covalent bond to the halogen, which accounts for the characteristic near‐linearity of halogen bonding. In many instances, the lateral sides of the halogen have negative electrostatic potentials, allowing it to also interact favorably with positive sites. In this discussion, after looking at some of the experimental observations of halogen bonding, we address the origins of σ holes, the factors that govern the magnitudes of their electrostatic potentials, and the properties of the resulting complexes with negative sites. The relationship of halogen and hydrogen bonding is examined. We also point out that σ‐hole interactions are not limited to halogens, but can also involve covalently bonded atoms of Groups IV–VI. Examples of applications in biological/medicinal chemistry and in crystal engineering are mentioned, taking note that halogen bonding can be “tuned” to fit various requirements, that is, strength of interaction, steric factors, and so forth.     

Global inorganic source of atmospheric bromine

A few bromine molecules per trillion (ppt) causes the complete destruction of ozone in the lower troposphere during polar spring and about half of the losses associated with the "ozone hole" in the stratosphere. Recent field and aerial measurements of the proxy BrO in the free troposphere suggest an even more pervasive global role for bromine. Models, which quantify ozone trends by assuming atmospheric inorganic bromine (Bry) stems exclusively from long-lived bromoalkane gases, significantly underpredict BrO measurements. This discrepancy effectively implies a ubiquitous tropospheric background level of approximately 4 ppt Bry of unknown origin. Here, we report that I- efficiently catalyzes the oxidation of Br- and Cl- in aqueous nanodroplets exposed to ozone, the everpresent atmospheric oxidizer, under conditions resembling those encountered in marine aerosols. Br- and Cl-, which are rather unreactive toward O3 and were previously deemed unlikely direct precursors of atmospheric halogens, are readily converted into IBr2- and ICl2- en route to Br2(g) and Cl2(g) in the presence of I-. Fine sea salt aerosol particles, which are predictably and demonstrably enriched in I- and Br-, are thus expected to globally release photoactive halogen compounds into the atmosphere, even in the absence of sunlight.     

Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods

This article analyzes the ability of semiempirical quantum-mechanical methods (PM6 and PM7) and self-consistent charge density-functional tight-binding (SCC-DFTB) method DFTB3 to describe halogen bonds. Calculations of the electrostatic potential on the surface of molecules containing halogens show that the σ-hole could be described well in modified neglect of diatomic overlap-based methods. The situation is more complex in the case of DFTB3 where a simpler model is used for the electrostatics, but short-ranged effects are covered in the Hamiltonian. All these methods can thus capture the effects that, for example, define the geometry of halogen bonds. The interaction energies are, however, affected by generally underestimated repulsion, which has been addressed earlier by standalone empirical corrections. Another approach to correcting this issue in DFTB3 is presented here—a modification of the energies of d-orbitals on halogens yields better results than the empirical correction in DFTB3-D3X, although it remains difficult to describe halogen and hydrogen bonds simultaneously. © 2019 Wiley Periodicals, Inc.     

Selenium-catalyzed oxidative halogenation

Organoselenides catalyze the oxidation of halides by H₂O₂. Furthermore, these selenides catalyze the transfer of oxidized halogens from N-halosuccinimides to olefins and ketones. Thus, organoselenides catalyze oxidative halogenation reactions including halolactonization, α-halogenation of ketones, and allylic halogenation. The ability of selenium to undergo reversible 2e⁻ oxidation-reduction chemistry facilitates halogenation through selenium-bound halogen intermediates.     

New Halogen-Containing Drugs Approved by FDA in 2021: An Overview on Their Syntheses and Pharmaceutical Use

This review describes the recent Food and Drug Administration (FDA)-approved drugs (in the year 2021) containing at least one halogen atom (covalently bound). The structures proposed throughout this work are grouped according to their therapeutical use. Their synthesis is presented as well. The number of halogenated molecules that are reaching the market is regularly preserved, and 14 of the 50 molecules approved by the FDA in the last year contain halogens. This underlines the emergent role of halogens and, in particular, of fluorine and chlorine in the preparation of drugs for the treatment of several diseases such as viral infections, several types of cancer, cardiovascular disease, multiple sclerosis, migraine and inflammatory diseases such as vasculitis.     

Design and verification of halogen-bonding system at the complex interface of human fertilization-related MUP PDZ5 domain with CAMK’s C-terminal peptide

Calmodulin-dependent protein kinase (CAMK) is physiologically activated in fertilized human oocytes and is involved in the Ca²⁺ response pathways that link the fertilization calmodulin signal to meiosis resumption and cortical granule exocytosis. The kinase has an unstructured C-terminal tail that can be recognized and bound by the PDZ5 domain of its cognate partner, the multi-PDZ domain protein (MUP). In the current study, we reported a rational biomolecular design of halogen-bonding system at the complex interface of CAMK’s C-terminal peptide with MUP PDZ5 domain by using high-level computational approaches. Four organic halogens were employed as atom probes to explore the structural geometry and energetic property of designed halogen bonds in the PDZ5–peptide complex. It was found that the heavier halogen elements such as bromine Br and iodine I can confer stronger halogen bond but would cause bad atomic contacts and overlaps at the complex interface, while fluorine F cannot form effective halogen bond in the complex. In addition, the halogen substitution at different positions of peptide’s aromatic ring would result in distinct effects on the halogen-bonding system. The computational findings were then verified by using fluorescence analysis; it is indicated that the halogen type and substitution position play critical role in the interaction strength of halogen bonds, and thus the PDZ5–peptide binding affinity can be improved considerably by optimizing their combination.     

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4?O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4?O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4?O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4?O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.     

Carbon-13 NMR spectra of polybromoalkanes and polychlorobromoalkanes. Structural increments of halogens in polyhalogenated groups

The ¹³C NMR spectra of 48 polychlorobromoalkanes have been studied. Unlike the ¹³C signals of chlorine-containing groups (38–105 ppm), those of bromine-containing fragments, with the exception of CBr₂ (60–70 ppm), appear in a rather narrow range (25–50 ppm) and are shifted to higher field in relation to similar chlorine-containing groups. The spin–spin coupling constants in similar bromine- and chlorine-containing groups practically coinciEN. Calculation of the chemical shifts for the polyhaloalkanes under study according to the additivity scheme, as previously observed for polychloroalkanes, renders values which are in considerable discord with experimental values (up to –32 ppm for CBr₃). These discrepancies may be compensated for by corrections for the binary interaction of halogen atoms by grouping the halogen-containing fragments according to the geminal, vicinal, 1,3-, 1,3,5- and 1,2,3-arrangement of halogen atoms, and by introducing an increment for the position of the halogen at the secondary atom. It is established that as compared to 1-monohaloalkanes: (a) in the case of the geminal arrangement of halogen atoms the α- and γ-effects diminish (Δ α from –3.2 to –8 ppm; Δγ = 2.6 ppm), while the β-effect increases slightly (from 0 to 1.2 ppm); (b) in the case of a vicinal arrangement both the α- and β-effects diminish (by about –3.5 ppm) and the γ-effect remains constant, as if the vicinal system of the halogens was topologically insulated; (c) for the 1,3- and 1,3,5-arrangement of halogens their mutual influence is weak (about –0.5 ppm for each halogen atom in the α- and γ-positions); (d) the 1,2,3 system (serial arrangement of halogen atoms) is the sum of two vicinal fragments and hardly deviates from the additivity scheme; (e) the arrangement of a halogen at the secondary C atom enhances the α-effect (Δα = 2.8 and 1.0 for methyl and methylene, respectively, in the case of Cl, and 3.5 and 3.7 ppm in the case of Br); the variation of the β-effect has a different sign in relation to CH₃ and CH₂ groups (+1.2 and –1.7 for Cl, and +2.5 and –1.0 for Br). More distant effects of halogens (δ and ?) were not considered. The determined increments (Δα, Δβ and Δγ) for the α-, β- and γ-effects of chlorine and bromine atoms allow the prediction of the 13^C chemical shifts in polyhaloalkanes with an accuracy up to ±1.5 ppm. Some deviations of up to ±5 ppm may be connected with the influence of a three particle interaction of halogen atoms, which was taken into account only in the case of a geminal arrangement of halogen atoms.