Symmetry of three-center,four-electron bonds

Three-center, four-electron bonds provide unusually strong interactions; however, their nature remains ununderstood. Investigations of the strength, symmetry and the covalent versus electrostatic character of three-center hydrogen bonds have vastly contributed to the understanding of chemical bonding, whereas the assessments of the analogous three-center halogen, chalcogen, tetrel and metallic -type long bonding are still lagging behind. Herein, we disclose the X-ray crystallographic, NMR spectroscopic and computational investigation of three-center, four-electron [D–X–D]⁺ bonding for a variety of cations (X⁺ = H⁺, Li⁺, Na⁺, F⁺, Cl⁺, Br⁺, I⁺, Ag⁺ and Au⁺) using a benchmark bidentate model system. Formation of a three-center bond, [D–X–D]⁺ is accompanied by an at least 30% shortening of the D–X bonds. We introduce a numerical index that correlates symmetry to the ionic size and the electron affinity of the central cation, X⁺. Providing an improved understanding of the fundamental factors determining bond symmetry on a comprehensive level is expected to facilitate future developments and applications of secondary bonding and hypervalent chemistry.

The factors determining the symmetry and the fundamental nature of the three-center, four-electron bonds are assessed.     

Symmetry of [N-X-N]+ halogen bonds in solution

The first investigation of halogen bond symmetry is presented. In contrast to related hydrogen bonds, the iodous halogen bond is symmetric in solution and in the crystal. The bromous analogue is symmetric in solution, but shows asymmetry in the solid state. NMR results are in agreement with DFT predictions.     

Counterion influence on the N–I–N halogen bond

A detailed investigation of the influence of counterions on the [N–I–N]⁺ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N–I–N]⁺ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in the solid state by single crystal X-ray crystallography. Molecular systems encompassing weakly coordinating counterions behave similarly to the corresponding silver(i) centered coordination complexes. In contrast, systems possessing moderately or strongly coordinating anions show a distinctly different behavior. Such silver(i) complexes are converted into multi-coordinate geometries with strong Ag–O bonds, whereas the iodine centered systems remain linear and lack direct charge transfer interaction with the counterion, as verified by ¹⁵N NMR and DFT computation. This suggests that the [N–I–N]⁺ halogen bond may not be satisfactorily described in terms of a pure coordination bond typical of transition metal complexes, but as a secondary bond with a substantial charge-transfer character.     

Mechanochemical Preparations of Anion Coordinated Architectures Based on 3-Iodoethynylpyridine and 3-Iodoethynylbenzoic Acid

The halogen bond has previously been explored as a versatile tool in crystal engineering and anion coordination chemistry, with mechanochemical synthetic techniques having been shown to provide convenient routes towards cocrystals. In an effort to expand our knowledge on the role of halogen bonding in anion coordination, here we explore a series of cocrystals formed between 3-iodoethynylpyridine and 3-iodoethynylbenzoic acid with halide salts. In total, we report the single-crystal X-ray structures of six new cocrystals prepared by mechanochemical ball milling, with all structures exhibiting C≡C−I⋅⋅⋅X⁻ (X=Cl, Br) halogen bonds. Whereas cocrystals featuring a pyridine group favoured the formation of discrete entities, cocrystals featuring a benzoic acid group yielded an alternation of halogen and hydrogen bonds. The compounds studied herein were further characterized by ¹³C and ³¹P solid-state nuclear magnetic resonance, with the chemical shifts offering a clear and convenient method of identifying the occurrence of halogen bonding, using the crude product obtained directly from the mechanochemical ball milling. Whereas the ³¹P chemical shifts were quickly able to identify the occurrence of cocrystallization, ¹³C solid-state NMR was diagnostic of both the occurrence of halogen bonding and of hydrogen bonding.     

Construction of halogen and hydrogen bond‐based multicomponent nanostructures at liquid‐solid interface

The cooperative effect of hydrogen and halogen bonds on the 2‐dimensional molecular arrangement of highly oriented pyrolytic graphite has been studied by scanning tunneling microscopy. The scanning tunneling microscopy observations demonstrate that the self‐assembled hydrogen‐bonded molecular chicken‐wire networks of trimesic acid have been significantly transformed after annealing and the introduction of tribromobenzene guest molecules. Bromine atoms and carboxyl groups were found to form 2 different multicomponent structures via hydrogen and halogen bonds. Owing to the effect of halogen and hydrogen bonds, tribromobenzene with trimesic acid formed the 3‐fold symmetry networks.     

Effects of solvent on weak halogen bonds: Density functional theory calculations

In recent years, many applications of solution‐phase halogen bonding in anion recognition, catalysis, and pseudorotaxane formation have been reported. Moreover, a number of thermodynamic data of halogen bonding interactions in organic solution are now available. To obtain detailed information of the influence of the surrounding medium on weak halogen bonds, a series of dimeric complexes of halobenzene (PhX) with three electron donors (H₂O, HCHO, and NH₃) were investigated by means of DFT/PBE calculations in this work. The PCM implicit solvation approach was utilized to include the effects of three solvents (cyclohexane, chloroform, and water) as representatives for a wide range of dielectric constant. In some cases, halogen‐bond distances are shown to shorten in solution, accompanied by concomitant elongation of the C? X bonds. For the remaining systems, the intermolecular distances tend to increase or remain almost unchanged under solvent effects. In general, the solvent has a slight destabilizing effect on weak halogen bonds; the strength order of halogen bonds observed in vacuum remains unchanged in liquid phases. Particularly, the interaction strength attenuates in the order I > Br > Cl in solution, consistent with the experimental measurements of weak halogen bond door abilities. The similarities between halogen and hydrogen bonding in solution were also elucidated. The results presented herein would be very useful in future applications of halogen bonding in molecular recognition and medicinal chemistry. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Source of Cooperativity in Halogen‐Bonded Haloamine Tetramers

Inspired by the isostructural motif in α‐bromoacetophenone oxime crystals, we investigated halogen–halogen bonding in haloamine quartets. Our Kohn–Sham molecular orbital and energy decomposition analysis reveal a synergy that can be traced to a charge‐transfer interaction in the halogen‐bonded tetramers. The halogen lone‐pair orbital on one monomer donates electrons into the unoccupied σ*_N?X orbital on the perpendicular N?X bond of the neighboring monomer. This interaction has local σ symmetry. Interestingly, we discovered a second, somewhat weaker donor–acceptor interaction of local π symmetry, which partially counteracts the aforementioned regular σ‐symmetric halogen‐bonding orbital interaction. The halogen–halogen interaction in haloamines is the first known example of a halogen bond in which back donation takes place. We also find that this cooperativity in halogen bonds results from the reduction of the donor–acceptor orbital‐energy gap that occurs every time a monomer is added to the aggregate.     

Spectroscopic and Crystallographic Characterization of the R3N+−C−H⋅⋅⋅X Interaction

As appreciation for nonclassical hydrogen bonds has progressively increased, so have efforts to characterize these interesting interactions. Whereas several kinds of C−H hydrogen bonds have been well-studied, much less is known about the R₃N⁺−C−H⋅⋅⋅X variety. Herein, we present crystallographic and spectroscopic evidence for the existence of these interactions, with special relevance to Selectfluor chemistry. Of particular note is the propensity for Lewis bases to engage in nonclassical hydrogen bonding over halogen bonding with the electrophilic F atom of Selectfluor. Further, the first examples of ¹H NMR experiments detailing R₃N⁺−C−H⋅⋅⋅X (X=O, N) hydrogen bonds are described.     

Calix

Chiral calix[4]arene derivatives with four O-(N-acetyl-PhgOMe), (1), (Phg denotes R-phenylglycine), or O-(N-acetyl-LeuOMe) (2) strands have been synthesised. Both compounds exist in chloroform in stable cone conformations with a noncovalently organised cavity at the lower rim that is formed by circular interstrand amidic hydrogen bonds. Such organisation affects both the selectivity and extraction/transport properties of 1 and 2 toward metal cations. Calix[4]arene derivatives with one OCH2COPhgOMe strand (3), two OCH2COPhgOMe strands (5) and with 1,3-OMe-2,4-(O-CH2COPhgOMe) substituents (4) at the lower rim have also been prepared. For 3, a conformation stabilised by a circular hydrogen-bond arrangement is found in chloroform, while 4 exists as a time-averaged C2 conformation with two intramolecular NH ...OCH3 hydrogen bonds. Compound 5 has a unique hydrogen-bonding motif in solution and in the solid state with two three-centred NH-.. O and two OH...O hydrogen bonds at the lower rim. This motif keeps 5 in the flattened cone conformation in chloroform. The X-ray structure analysis of 1 revealed a molecular structure with C2 symmetry; this structure is organised in infinite chains by intra- and intermolecular H bonds. The solid-state and solution structures of the [1-Na]ClO4 complex are identical, C4 symmetric cone conformations.     

S···X halogen bonds and H···X hydrogen bonds in H2CS-XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes: cooperativity and solvent effect

Using ab initio calculations, we have studied the structures, properties, and nature of halogen bonds in H(2)CS-XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes. The results show that the ring-shaped complexes are formed by a halogen bond (S···X) and a secondary hydrogen bond (H···X). We also analyzed the H(2)CS-ClF-ClF and FCl-H(2)CS-ClF complexes to investigate the cooperative and diminutive halogen bonding. The cooperative effect of halogen bonding is found in the former, while the diminutive effect is present in the latter. We finally considered the solvent effect on the halogen bond in H(2)CS-BrCl complex and found that the solvent has a prominent enhancing effect on it. The complexes have also been analyzed with natural bond orbital, atoms in molecules, and symmetry adapted perturbation theory method.     

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.     

Theoretical study of the interaction of fluorinated dimethyl ethers and the ClF and HF molecules. Comparison between halogen and hydrogen bonds

A theoretical study of the halogen‐bonded complexes formed between fluorinated dimethyl ethers (n_F = 0–4) and ClF is carried out using the wB97XD method combined with the 6‐311++G(d,p) basis set. The properties of the complexes are compared with the corresponding properties of the hydrogen‐bonded complexes formed between the same electron donors and HF. The optimized geometries, the interaction energies, relevant natural bonding orbital characteristics along with some vibrational data are calculated. The analyzed properties also include the symmetry adapted perturbation theory decomposition of the energies along with the atoms‐in molecule analysis. For both the halogen and hydrogen bonds, the interaction energies are ruled by the intermolecular hyperconjugation energies. In contrast, the correlations between the binding energies and the basic properties of the ethers or the charge transfer are different for the halogen and hydrogen bonds. The applicability of the Bent's rule to these systems is discussed. © 2016 Wiley Periodicals, Inc.     

Pushing the limits of the hydrogen bond enhanced halogen bond—the case of the C–H hydrogen bond

C–H hydrogen bonds have remarkable impacts on various chemical systems. Here we consider the influence of C–H hydrogen bonds to iodine atoms. Positioning a methyl group between two iodine halogen bond donors of the receptor engendered intramolecular C–H hydrogen bonding (HBing) to the electron-rich belt of both halogen bond donors. When coupled with control molecules, the role of the C–H hydrogen bond was evaluated. Gas-phase density functional theory studies indicated that methyl C–H hydrogen bonds help bias a bidentate binding conformation. Interaction energy analysis suggested that the charged C–H donors augment the halogen bond interaction—producing a >10 kcal mol⁻¹ enhancement over a control lacking the C–H⋯I–C interaction. X-ray crystallographic analysis demonstrated C–H hydrogen bonds and bidentate conformations with triflate and iodide anions, yet the steric bulk of the central functional group seems to impact the expected trends in halogen bond distance. In solution, anion titration data indicated elevated performance from the receptors that utilize C–H Hydrogen Bond enhanced Halogen Bonds (HBeXBs). Collectively, the results suggest that even modest hydrogen bonds between C–H donors and iodine acceptors can influence molecular structure and improve receptor performance.

C–H hydrogen bonds to iodine halogen bond donors are shown to improve halogen bonding and molecular preorganization.     

Some measures for making halogen bonds stronger than hydrogen bonds in H2CS-HOX (X = F, Cl, and Br) complexes

The properties and applications of halogen bonds are dependent greatly on their strength. In this paper, we suggested some measures for enhancing the strength of the halogen bond relative to the hydrogen bond in the H(2)CS-HOX (X = F, Cl, and Br) system by means of quantum chemical calculations. It has been shown that with comparison to H(2)CO, the S electron donor in H(2)CS results in a smaller difference in strength for the Cl halogen bond and the corresponding hydrogen bond, and the Br halogen bond is even stronger than the hydrogen bond. The Li atom in LiHCS and methyl group in MeHCS cause an increase in the strength of halogen bonding and hydrogen bonding, but the former makes the halogen bond stronger and the latter makes the hydrogen bond stronger. In solvents, the halogen bond in the Br system is strong enough to compete with the hydrogen bond. The interaction nature and properties in these complexes have been analyzed with the natural bond orbital theory.     

Ionic liquid based on α-amino acid anion and N7,N9-dimethylguaninium cation ([dMG][AA]): theoretical study on the structure and electronic properties

The interactions between five amino acid based anions ([AA](-) (AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaninium cation ([dMG](+)) have been investigated by the hybrid density functional theory method B3LYP together with the basis set 6-311++G(d,p). The calculated interaction energy was found to decrease in magnitude with increasing side-chain length in the amino acid anion. The interaction between the [dMG](+) cation and [AA](-) anion in the most stable configurations of ion pairs is a hydrogen bonding interaction. These hydrogen bonds (H bonds) were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of hydrogen bonds and interaction energy as well as vibrational frequencies in the most stable configurations of ion pairs have been checked.     

Comparison of Hydrogen and Gold Bonding in [XHX]−, [XAuX]−, and Isoelectronic [NgHNg]+, [NgAuNg]+ (X=Halogen,Ng=Noble Gas)

Quantum chemical calculations at the MP2/aug‐cc‐pVTZ and CCSD(T)/aug‐cc‐pVTZ levels have been carried out for the title compounds. The electronic structures were analyzed with a variety of charge and energy partitioning methods. All molecules possess linear equilibrium structures with D_∞h symmetry. The total bond dissociation energies (BDEs) of the strongly bonded halogen anions [XHX]^? and [XAuX]^? decrease from [FHF]^? to [IHI]^? and from [FAuF]^? to [IAuI]^?. The BDEs of the noble gas compounds [NgHNg]⁺ and [NgAuNg]⁺ become larger for the heavier atoms. The central hydrogen and gold atoms carry partial positive charges in the cations and even in the anions, except for [IAuI]^?, in which case the gold atom has a small negative charge of ?0.03 e. The molecular electrostatic potentials reveal that the regions of the most positive or negative charges may not agree with the partial charges of the atoms, because the spatial distribution of the electronic charge needs to be considered. The bonding analysis with the QTAIM method suggests a significant covalent character for the hydrogen bonds to the noble gas atoms in [NgHNg]⁺ and to the halogen atoms in [XHX]^?. The covalent character of the bonding in the gold systems [NgAuNg]⁺ and [XAuX]^? is smaller than in the hydrogen compound. The energy decomposition analysis suggests that the lighter hydrogen systems possess dative bonds X^?→H⁺←X^? or Ng→H⁺←Ng while the heavier homologues exhibit electron sharing through two‐electron, three‐center bonds. Dative bonds X^?→Au⁺←X^? and Ng→Au⁺←Ng are also diagnosed for the lighter gold systems, but the heavier compounds possess electron‐shared bonds.     

Halogen‐ and Hydrogen‐Bonding Catenanes for Halide‐Anion Recognition

Halogen‐bonding (XB) interactions were exploited in the solution‐phase assembly of anion‐templated pseudorotaxanes between an isophthalamide‐containing macrocycle and bromo‐ or iodo‐functionalised pyridinium threading components. ¹H NMR spectroscopic titration investigations demonstrated that such XB interpenetrated assemblies are more stable than analogous hydrogen bonding (HB) pseudorotaxanes. The stability of the anion‐templated halogen‐bonded pseudorotaxane architectures was exploited in the preparation of new halogen‐bonding interlocked catenane species through a Grubbs’ ring‐closing metathesis (RCM) clipping methodology. The catenanes’ anion recognition properties in the competitive CDCl₃/CD₃OD 1:1 solvent mixture revealed selectivity for the heavier halides iodide and bromide over chloride and acetate.     

Triangular Halogen Bond and Hydrogen Bond Supramolecular Complex Consisting of Carbon Tetrabromide,Halide, and Solvent Molecule： A Theoretical and Spectroscopic Study

The theoretical calculation and spectroscopic experiments indicate a kind of triangular three bonding supramolecular complexes CBr4…X^-…-H-C, which consist of carbon tetrabromide, halide, and protic solvent molecule （referring to dichloromethane, chloroform and acetonitrile）, can be formed in solution. The strength of halogen and hydrogen bonds in the triangular complexes using halide as common acceptor obeys the order of iodide〉bromide〉chloride. The halogen and hydrogen bonds work weak-cooperatively. Charge transfer bands of halogen bonding complexes between CBra and halide are observed in UV-Vis absorption spectroscopy in three solvents, and then the stoichiometry of 1：1, formation constants K and molar extinction coefficients ε of the halogen bonding complexes are obtained by Benesi-Hildebrand method. The K and ε show a dependence on the solvent dielectric constant and, on the whole, obey an order of iodide〉bromide〉chloride in the same solvents. Furthermore, the C-H vibrational frequencies of solvent molecules vary obviously with the addition of halide, which indicates the C-H…X- interaction. The experimental data indicate that the halogen bond and hydrogen bond coexist by sharing a common halide acceptor as predicted by calculation.     

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.     

Noncovalent paramagnetic complexes: detection of halogen bonding in solution by ESR spectroscopy

Halogen-bonded complexes between aliphatic and aromatic iodoperfluorocarbons and persistent nitroxide radicals have been detected by ESR spectroscopy in solution. Quantitative data indicate that nitroxides behave as strong electron donors in halogen bonding, giving rise to interactions whose strength is close to that of strong hydrogen bonds. These results point to a novel design of supramolecular paramagnetic species.