Halogen Bonding in Supramolecular Chemistry

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

The first example of halogen-bonded fluorescent liquid crystals based on the interaction of iodofluorobenzene derivatives with nitro-cyanostilbenes is reported. The systematic variation of the fluorination degree and pattern indicates the relevance of the halogen bond strength for the induction of liquid crystalline properties. The modular self-assembly approach enables the efficient tuning of the fluorescence behaviour and mesomorphic properties of the assemblies.

Fast transport of HCl across a hydrophobic layer over macroscopic distances by using a Pt(II) compound as the transporter: micro- and nanometric aggregates as effective transporters

Bis-(diethyl-dithioxamidate)platinum(ii) is able to transport HCl from the donor aqueous phase to the receiving one over a mean distance of 12 cm in about 3 minutes across an organic membrane in the bulk, without stirring of the organic phase, i.e. at a rate far exceeding the unidirectional macroscopic diffusion coefficient. The way in which this surprising phenomenon can happen is linked to the behaviour of HCl which, because of dynamic interactions with [Pt(HEt2C2N2S2)2] (in which HCl is hosted as a tight ion pair [Pt(H2Et2C2N2S2)2][Cl]2) and chloroform molecules, gives rise to observable nanometric and micrometric domains, more dense than the surrounding bulk, whose formation and disaggregation processes accelerate the unidirectional macroscopic diffusion of HCl. Thermodynamic parameters obtained from the study of acid-base behaviour of the system Pt(ii) species/HCl/CHCl3 also agree with the proposed mechanism of HCl transport.

Neutral Chiral Tetrakis-Iodo-Triazole Halogen-Bond Donor for Chiral Recognition and Enantioselective Catalysis

Halogen bonding represents a powerful tool in the field of noncovalent interactions. However, applications in enantioselective recognition and catalysis remain almost nonexistent, due in part to the distinct features of halogen bonds, including long covalent and noncovalent bond distances and high directionality. Herein, this work presents a novel chiral tetrakis-iodo-triazole structure as a neutral halogen bond donor for both chiral anion-recognition and enantioinduction in ion-pair organocatalysis. NMR-titration studies revealed significant differences in anion affinity between the halogen bonding receptor and its hydrogen bonding parent. Selective recognition of chiral dicarboxylates and asymmetric induction in a benchmark organocatalytic reaction were demonstrated using the halogen bond donor. Inversions in the absolute sense of chiral recognition, enantioselectivity, and chiroptical properties relative to the related hydrogen donor were observed. Computational modeling suggested that these effects were the result of distinct anion-binding modes for the halogen- versus hydrogen-bond donors.

Synthesis and characterization of N-heterocyclic carbene-MOEt2 complexes (M = Cu, Ag, Au). Analysis of solvated auxiliary-ligand free [(NHC)M]+ species

We report the synthesis, characterization and computational analysis of coinage metal-ether complexes supported by N-heterocyclic carbenes (NHC), SIPr and Et2CAAC. The related water adducts are also included. The [(NHC)M]+(M = Cu, Ag, Au) species show the noteworthy ability to bind Et2O and H2O. This interaction towards Et2O and H2O is partly ascribed to a σ-hole bonding with an almost linear disposition, taking advantage of the enhanced σ-hole potential evaluated for such [(NHC)M]+ species. This enhanced ability is larger than those found for non-covalent interactions involving main group species.

Halogen-Bonded BODIPY Frameworks with Tunable Optical Features*

The ability to tune the optical features of BODIPY materials in the solid state is essential for their photorelated application and requires efficient control of the crystal packing. In this study, such control of BODIPY supramolecular assemblies was achieved by deliberate design and synthesis of a BODIPY containing a strong halogen-bond (XB) acceptor (-NO₂ ) and donor (I, Br) to mediate XB interactions. The di-halogenated structures formed isostructural mono-coordinate motif B3, B4 (1D tubular structure) and symmetric bifurcated motif B4-II (1D zigzag chains structure) through N-O⋅⋅⋅I, Br XB interactions. These XB interactions promote singlet-to-triplet intersystem crossing and triplet-to-singlet reverse intersystem crossing due to partial delocalization of oxygen electrons onto Br and I, which leads to unexpected fluorescence enhancement of B4-II. Finally, the indirect optical band gaps of B3, B4 and B4-II were amenable to tuning in the range of 1.85-2.50  eV by XB-driven crystal packings.

Halogen bonding vs. π-stacking interactions in new bis(acenaphthylene)dione semiconductors

A series of new halogenated bis(acenaphthylene)dione (BAN) derivatives was synthesized, and the effect of halogen bonding on both molecular and crystal structure, and charge transport in n-type thin film transistors was investigated.

Molecular salts of quinine: a crystal engineering route to enhance the aqueous solubility

Salts of quinine, with α,ω-aliphatic dicarboxylic acids, and aromatic coformers, show superior aqueous solubility. The structural, thermal and microscopy data provide structural, compositional, and stability profiles of the salts.

Intermolecular interactions in hydrates of 4-methylpiperidine and 4-chloropiperidine – a structural and computational study

The highest hydrates of 4-methylpiperidine and 4-chloropiperidine are trihydrates, which are very similar but not isostructural and contain water layers of the L4(6)5(7)6(8) type.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.

Interplay of halogen and hydrogen bonding in a series of heteroleptic iron(iii) complexes

The impact of the halogen substituent on supramolecular preferences that influence packing is explored in a series of heteroleptic iron(iii) complexes.

Single-crystal to single-crystal transformation of a coordination chain to a two-dimensional coordination network through a photocycloaddition reaction

UV irradiation of a unique ladder-like coordination polymer affords a two-dimensional coordination network through single-crystal to single-crystal photocycloaddition reaction.

Intermolecular binding preferences of haloethynyl halogen-bond donors as a function of molecular electrostatic potentials in a family of N-(pyridin-2-yl)amides

In order to explore how σ-hole potentials, as evaluated by molecular electrostatic potential (MEP) calculations, affect the ability of halogen atoms to engage in structure-directing intermolecular interactions, we synthesized four series of ethynyl halogen-substituted amide containing pyridines (activated targets); (N-(pyridin-2-yl)benzamides (Bz-act-X), N-(pyridin-2-yl)picolinamides (2act-X), N-(pyridin-2-yl)nicotinamides (3act-X) and N-(pyridin-2-yl) isonicotinamides (4act-X), where X = Cl/Br/I. The molecules are deliberately equipped with three distinctly different halogen-bond acceptor sites, π, N(pyr), and O[double bond, length as m-dash]C, to determine binding site preferences of different halogen-bond donors. Crystallographic data for ten (out of a possible twelve) new compounds were thus analyzed and compared with data for the corresponding unactivated species. The calculated MEPs of all the halogen atoms were higher in the activated targets in comparison to the unactivated targets and were in the order of iodine ≈ chloroethynyl < bromoethynyl < iodoethynyl. This increased positive σ-hole potential led to a subsequent increase in propensity for halogen-bond formation. Two of the four chloroethynyl structures showed halogen bonding, and all three of the structurally characterized bromoethynyl species engaged in halogen bonding. The analogous unactived species showed no halogen bonds. Each chloroethynyl donor selected a π-cloud as acceptor and the bromoethynyl halogen-bond donors opted for either π or N(pyr) sites, whereas all halogen bonds involving an iodoethynyl halogen-bond donor (including both polymorphs of Bz-act-I) engaged exclusively with a N(pyr) acceptor site.

Understanding the impact of anticancer halogenated inhibitors and various functional groups (X = Cl, F, CF3, CH3, NH2, OH, H) of casein kinase 2 (CK2)

Main focus of study is to understand potency of halogen (X = Br) atom that exists in tetrabromobenzotriazole (TBB) derivatives of crystal CK2 ligand along with hinge region amino acids (VAL45, PHE113, GLU114, VAL116, ASN118) through interaction energy analysis. In turn to attain profound insight on nature of stabilization of core CK2 ligands: 1ZOE-L1, 1ZOG-L2, 1ZOH-L3, 2OXX-L4, 2OXY-L5, 3KXG-L6, 3KXH-L7 -L7 and 3KXM-L8, having four bromine atoms, we attempted to mutate all bromine (X = Br) atoms by various functional groups (X = Cl, F, CF₃, CH₃, NH₂, OH, H) and binding strength along with amino acids was calculated. Most stable ligands exist in mutated NH₂ functional groups: 1ZOG-L2, 1ZOH-L3, 2OXX-L4, 3KXM-L8 having interaction energy as -5.21, -14.87, -6.69 and -11.72 kcal/mol respectively, revealing strong binding strength. Second most stable mutated Cl functional group ligands also play a major role in 1ZOH-L3, 2OXX-L4 and 3KXM-L8 having interaction energy as -6.89, -5.37, and -10.48 kcal/mol respectively. Overall, this study will pave way for crystal growth and medicinal chemist to have cleared perceptive about structural properties of CK2 halogenated ligands with new insight on CK2 mutated functional group ligands. Further, it insists us to reuse existing CK2 crystal ligand with more preferable suggested binding contacts in course of new functional groups that lead to anticancer affinity.Communicated by Ramaswamy H. Sarma.

Effects of n → π* Orbital Interactions on Molecular Rotors: The Control and Switching of Rotational Pathway and Speed

The role of n → π* orbital interactions in the rotational pathway and barrier of biaryl-based molecular rotors was elucidated through a combined experimental and computational study. The n → π* interaction in the transition state can lead to the acceleration of rotors. The competition between the n → π* interaction and hydrogen bonding further enabled the reversal of the pathway and greasing/braking the rotor in response to acid/base stimuli, thereby creating a switchable molecular rotor.

Intermolecular Interactions Involving Heavy Alkenes H2Si=TH2 (T = C, Si, Ge, Sn, Pb) with H2O and HCl: Tetrel Bond and Hydrogen Bond

The intermolecular interactions between the heavy alkenes H₂Si=TH₂ (T = C, Si, Ge, Sn, Pb) and H₂O or HCl have been explored at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level. The various hydrogen bond (HB) and tetrel bond (TB) complexes can be located on the basis of molecular electrostatic potential maps of the isolated monomers. The competition between TB and HB interactions has been investigated through the relaxed potential energy surface scan. The results indicate that the HB complexes become more and more unstable relative to the TB complexes with the increase of the T atomic number, and cannot even retain as a minimum in some cases, for H₂Si=TH2···H₂O systems. In contrast, the HB complexes are generally more stable than TB complexes, and the TB complexes exhibit rather weak binding strength, for H₂Si=TH₂···HCl systems. The majority of the TB complexes formed between H₂Si=TH₂ and H₂O possesses very strong binding strength with covalent characteristics. The noncovalent TB complexes can be divided into two types on the basis of the orbital interactions: π-hole complexes, with binding angles ranging from 91 to 111°, and hybrid σ/π-hole complexes, with binding angles ranging from 130 to 165°. The interplay between different molecular interactions has been explored, and an interesting result is that the covalent TB interaction is significantly abated and becomes noncovalent because of the competitive effect.

Toward N,P-Doped π-Extended PAHs: A One-Pot Synthesis to Diannulated 1,4,2-Diazaphospholium Triflate Salts

A novel method for the one-pot synthesis of diannulated 1,4,2-diazaphospholium triflate salts by a Me₃SiOTf-mediated self-condensation of dichlorophosphaneyl aza-(poly)cyclic aromatic hydrocarbons (aza-(P)AHs; namely, pyridine, quinoline, phenanthridine, and benzo[d]thiazole) is reported. The diannulated 1,4,2-diazaphospholium triflate salts are characterized by multinuclear NMR spectroscopy, X-ray analysis, as well as their calculated NICS values, underlining their aromatic character. Quantum mechanical calculations shed light on the intermolecular reaction mechanism. Follow up chemistry, such as the halogenation reaction with XeF₂ or SO₂Cl₂ with the dipyridinium derivative selectively yields the respective dihalo-σ⁴,λ⁵- and tetrahalo-σ⁵,λ⁶-diazaphospholium triflate salts. The dihalo-σ⁴,λ⁵-diazaphospholium triflate salt serves well as a surrogate for the introduction of the cationic 2-(1,2'-bipyridin)-1-iumyl ligand (1,2'-bipyl), the monocationic structural isomer of the prototypical 2,2'-bipyridine ligand (2,2'-bipy).

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

Dissecting the electric quadrupolar and polarization effects operating in halogen bonding through electron density analysis with a focus on bromine

The form of the electron density change (or difference) is usable as a kind of fingerprint of the electronic structural origin or mechanism that gives rise to intermolecular interactions. Here, this method is applied to halogen-bonding brominated systems to dissect the electric quadrupolar effect (arising from the anisotropic distribution of the valence electrons and intrinsic to the s²p_x ²p_y ²p_z electronic configuration) and the polarization effect (induced by a partial negative charge of the halogen-bond accepting atom). It is shown that a suitable location of the "extra point" for placing a partial positive charge to represent the former is crucial and is clearly found from the electron density difference from the spherically isotropic Br^- ion, while the latter consists of the dipolar polarization of the Br atom and the delocalized polarization of the whole molecule. A practical way for application to molecular dynamics simulations, etc., to represent these two factors is discussed.

Activating Chalcogen Bonding (ChB) in Alkylseleno/Alkyltelluroacetylenes toward Chalcogen Bonding Directionality Control

Activation of a deep electron-deficient area on chalcogen atoms (Ch=Se, Te) is demonstrated in alkynyl chalcogen derivatives, in the prolongation of the (C≡)C-Ch bond. The solid-state structures of 1,4-bis(methylselenoethynyl)perfluorobenzene (1Se) show the formation of recurrent chalcogen-bonded (ChB) motifs. Association of 1Se and the tellurium analogue 1Te with 4,4'-bipyridine and with the stronger Lewis base 1,4-di(4-pyridyl)piperazine gives 1:1 co-crystals with 1D extended structures linked by short and directional ChB interactions, comparable to those observed with the corresponding halogen bond (XB) donor, 1,4-bis(iodoethynyl)-perfluorobenzene. This "alkynyl" approach for chalcogen activation provides the crystal-engineering community with efficient, and neutral ChB donors for the elaboration of supramolecular 1D (and potentially 2D or 3D) architectures, with a degree of strength and predictability comparable to that of halogen bonding in iodoacetylene derivatives.

Photo-switchable Fluorescence in Hydrogen-Bonded Liquid Crystals

A series of hydrogen-bonded liquid crystals showing switchable fluorescence is reported. The fluorescence behavior results from the unique combination of hydrogen bonding, liquid crystallinity, and photobasicity. Thus, the molecular mobility in the mesophase is essential for the reversible photo-initiated proton transfer switching on the fluorescence of the assemblies. The application potential of the materials for photo-patterning was demonstrated.

The X-ray constrained wavefunction of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions

The synthesis and X-ray structure determination of the [Mn(CO)₄{(C₆H₅)₂P-S-C(Br₂)-P(C₆H₅)₂}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.

Das Ytterbium(III)-Oxidbromid-Oxidotellurat(IV) Yb3O2Br[TeO3]2

The ytterbium(III) oxide bromide oxidotellu-rate(IV) Yb3O2Br[TeO3]2 was obtained from a mixture of Yb2O3, YbBr3 and TeO2 in a molar ratio of 2:1:2 along with an excess of KBr as fluxing agent in evacuated fused silica ampoules after 10 days at T = 800 °C and subsequent slow cooling to room temperatures as colorless, plate-shaped single crystals. Its triclinic crystal structure (a = 663.97(5), b = 697.46(5), c = 1080.15(8) pm, α = 105.102(3), β = 90.931(3), γ = 100.034(3)°; Z = 2, space group: P 1 ‾ $&#x203e;{1}$ ) displays three crystallographically different Yb3+ cations with coordination numbers of six, seven and eight. Six out of eight distinct oxygen atoms belong to two independent ψ1-tetrahedral [TeO3]2−anions, whereas the other two represent O2− anions in tetrahedral coordination of four Yb3+ cations each, not having any contact to tellurium. Condensed via common vertices and edges, these [OYb4]10+ tetrahedra form cationic layers ∞ 2 ${}_{\infty }{}^{2}$ {[O2Yb3]5+}, which spread out parallel to the (001) plane. Two discrete [TeO3]2− groups and one Br− anion per formula unit take care of their three-dimensional interconnection along [001] and the overall charge balance of Yb3O2Br[TeO3]2. Remarkable interactions between the lone pair of electrons at the Te4+ cations of the ψ1-tetrahedral [TeO3]2− anions and those at the Br− anions are discussed.

Comparison between Chlorine-Shared and π-Halogen Bonds Involving Substituted Phosphabenzene and ClF Molecules

Ab initio MP2/aug-cc-pVTZ calculations have been carried out in order to study the nature of P···Cl halogen bonding interaction between a phosphorus atom in an aromatic ring in para-substituted phosphabenzene (PPBZ) and ClF molecule. The interaction of PPBZ with ClF results in two different types of complexes: (i) complex formation through the chlorine-shared halogen bond (T1-X-PPBZ·ClF) and (ii) complex formation via halogen-π interaction (T2-X-PPBZ·ClF). T1-X-PPBZ·ClF complexes are found to be more stable than the T2-X-PPBZ·ClF complexes. This work also presents a general criterion to distinguish a chlorine-shared halogen bond from a traditional halogen bond and sheds light on the formation of the chlorine-shared halogen bond. The binding energy of T1-X-PPBZ·ClF complexes correlates well with the negative electrostatic potential of the P atom and PA value of the substituted PPBZ. The properties of both T1-X-PPBZ·ClF and T2-X-PPBZ·ClF complexes are analyzed using atom-in-molecule, natural bond orbital, and symmetry-adapted perturbation theory calculations. The variation of the Cl-F bond distances and the redshifts of the ν(ClF) vibration resulting from the interaction with PPBZs are discussed.

Unconventional Type III Halogen···Halogen Interactions: A Quantum Mechanical Elucidation of σ-Hole···σ-Hole and Di-σ-Hole Interactions

Herein, two unconventional type III halogen···halogen interactions, namely, σ-hole···σ-hole and di-σ-hole interactions, were reported in a series of halogenated complexes. In type III, the A-halogen···halogen angles are typically equal to 180°, and the occurrence of σ-hole on halogen atoms is mandatory. Using diverse quantum mechanical calculations, it was demonstrated that the occurrence of such interactions with binding energies varied from -0.35 to -1.30 kcal/mol. Symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) revealed that type III interactions are dominated by dispersion forces, while electrostatic forces are unfavorable. Cambridge Structure Database (CSD) survey unveiled the experimental evidence for the manifestation of σ-hole···σ-hole interactions in crystal structures. This work might be deemed as a foundation for a vast number of forthcoming crystal engineering and materials science studies.

F-Halogen Bond: Conditions for Its Existence

The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp², or sp³ C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O₂NF, FOF, ClF, BrF, SiF₄, or GeF₄, but F₂ is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a V_s,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.

Halogen-Bonded Assemblies of Arylene Imides and Diimides: Insight from Electronic, Structural, and Computational Studies

Halogen-bonding interactions in electron-deficient π scaffolds have largely been underexplored. Herein, the halogen-bonding properties of arylene imide/diimide-based electron-deficient scaffolds were studied. The influence of scaffold size, from small (phthalimide) to moderately sized (pyromellitic diimide or naphthalenediimides) to large (perylenediimide), axial-group modification, and number of halo substituents on the halogen bonding and its self-assembly was probed in a set of nine compounds. The structural modification leads to tunable optical and redox properties. The first reduction potential E 1 / 2 1 ranges between -1.09 and -0.17 V (vs. SCE). Two of the compounds, that is, 6 and 9, have deep-lying LUMOs with values reaching -4.2 eV. Single crystals of all nine systems were obtained, which showed Br⋅⋅⋅O, Br⋅⋅⋅Br, or Br⋅⋅⋅π halogen-bonding interactions, and a few systems are capable of forming all three types. These interactions lead to halogen-bonded rings (up to 12-membered), which propagate to form stacked 1D, 2D, or corrugated sheets. A few outliers were also identified, for example, molecules that prefer C-H⋅⋅⋅O hydrogen bonding over halogen bonding, or noncentrosymmetric rather than centrosymmetric organization. Computational studies based on Atoms in Molecules and Natural Bond Orbital analysis provided further insight into the halogen-bonding interactions. This study can lead to a predictive design tool-box to further explore related systems on surfaces reinforced by these weak directional forces.

Probing cooperativity in C-H⋯N and C-H⋯π interactions: Dissociation energies of aniline⋯(CH4)n (n = 1, 2) van der Waals complexes from resonant ionization and velocity mapped ion imaging measurements

Recent studies of the weakly bound anisole⋯CH₄ complex found a dual mode of binding, featuring both C/H⋯π and C/H⋯O noncovalent interactions. In this work, we examine the dissociation energies of related aniline⋯(CH₄)_n (n = 1, 2) van der Waals clusters, where both C/H⋯π and C/H⋯N interactions are possible. Using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity-mapped ion imaging (VMI), we derive the dissociation energies of both complexes in the ground (S₀), excited (S₁), and cation radical (D₀) states. As the amide group is non-planar in the ground state, the optimized ground state geometry of the aniline⋯CH₄ 1:1 complex shows two isomers, each with the methane positioned above the aniline ring. The observed redshift of the electronic origin from the aniline monomer is consistent with TDDFT calculations for the more stable isomer, where the methane sits on the same face as the amino hydrogens. The dissociation energies of the 1:1 complex, obtained from 2CAP measurements, are in good agreement with the calculated theoretical values from selected density functional theory methods. VMI data for the 1:1 complex gave a binding energy value overestimated by ∼179 cm^-1 when compared to the 2CAP results, indicating that dissociative ionization selectively populates an excited vibrational level of the aniline cation radical. Given that the electron donating ability of aromatic substituents trends as -NH₂ > -OCH₃ > -CH₃, it is noteworthy that the strength of methane binding also trends in this order, as found by experiment (dissociation energies in kJ/mol: 6.6 > 5.8 > 4.5) and predicted by theory (PBE0-D3/def2-QZVPPD, in kJ/mol: 6.9 > 6.0 > 5.0). For the 1:2 complex of aniline and methane, calculations predict that the more stable conformer is the one where the two methane molecules lie on opposite faces of the ring, consistent with the observed redshift of the electronic origin. Unlike the anisole-methane 1:2 complex, which shows an enhanced dissociation energy for the loss of one methane in comparison with the 1:1 complex, here, we find that the energy required to remove one methane from the ground state aniline-methane 1:2 complex is smaller than that of the 1:1 complex, consistent with theoretical expectations.

Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study

In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.

Charge Anisotropy of Nitrogen: Where Chemical Intuition Fails

For more than half a century computer simulations were developed and employed to study ensemble properties of a wide variety of atomic and molecular systems with tremendous success. Nowadays, a selection of force-fields is available that describe the interactions in such systems. A key feature of force-fields is an adequate description of the electrostatic potential (ESP). Several force-fields model the ESP via point charges positioned at the atom centers. A major shortcoming of this approach, its inability to model anisotropies in the ESP, can be mitigated using additional charge sites. It has been shown that nitrogen is the most problematic element abundant in many polymers as well as large molecules of biological origin. To tackle this issue, small organic molecules containing a single nitrogen atom were studied. In performing rigorous scans of the surroundings of these nitrogen atoms, positions where a single extra charge can enhance the ESP description the most were identified. Significant improvements are found for ammonia, amines, and amides. Interestingly, the optimal location for the extra charge does not correlate with the chemically intuitive position of the nitrogen lone pair. In fact, the placement of an extra charge in the lone-pair location does not lead to significant improvements in most cases.

Activation of a Metal-Halogen Bond by Halogen Bonding

In recent years, the non-covalent interaction of halogen bonding (XB) has found increasing application in organocatalysis. However, reports of the activation of metal-ligand bonds by XB have so far been limited to a few reactions with elemental iodine or bromine. Herein, we present the activation of metal-halogen bonds by two classes of inert halogen bond donors and the use of the resulting activated complexes in homogenous gold catalysis. The only recently explored class of iodolium derivatives were shown to be effective activators in two test reactions and their activity could be modulated by blocking of the Lewis acidic sites. Bis(benzimidazolium)-based halogen bonding activators provided even more rapid conversion, while the non-iodinated reference compound showed little activity. The role of halogen bonding in the activation of metal-halogen bonds was further investigated by NMR experiments and DFT calculations, which support the mode of activation occurring via halogen bonding.

π covalency in the halogen bond

Halogen bonds are a highly directional class of intermolecular interactions widely employed in chemistry and chemical biology. This linear interaction is commonly viewed to be analogous to the hydrogen bond because hydrogen bonding models also intuitively describe the σ-symmetric component of halogen bonding. The possibility of π-covalency in a halogen bond is not contemplated in any known models. Here we present evidence of π-covalency being operative in halogen bonds formed between chloride and halogenated triphenylamine-based radical cations. We reach this conclusion through computational analysis of chlorine K-edge X-ray absorption spectra recorded on these halogen bonded pairs. In light of this result, we contend that halogen bonding is better described by analogy to metal coordination bonds rather than hydrogen bonds. Our revised description of the halogen bond suggests that these interactions could be employed to influence the electronic properties of conjugated molecules in unique ways.

Building Shape-Persistent Arylene Ethynylene Macrocycles as Scaffolds for 1,4-Diiodobutadiyne

Two shape-persistent arylene ethynylene macrocycles have been designed and synthesized as scaffolds to bind the nonpolar molecule 1,4-diiodobutadiyne. Binding via halogen bonding interactions between the pyridine moieties of the macrocycle and 1,4-diiodobutadiyne is predicted by density functional theory calculations and has been demonstrated in solution by ¹³C NMR titrations. The binding constant for the macrocycle-monomer complex (K = 10.5 L mol^-1) is much larger than for other comparable halogen bonds, strongly supporting cooperative binding of both ends of the diyne. These results demonstrate a fully inserted geometry of 1,4-diiodobutadiyne in the complex.

The role of the halogen bond in iodothyronine deiodinase: Dependence on chalcogen substitution in naphthyl-based mimetics

The effects on the activity of thyroxine (T4) due to the chalcogen replacement in a series of peri-substituted naphthalenes mimicking the catalytic function of deiodinase enzymes are computationally examined using density functional theory. In particular, T4 inner-ring deiodination pathways assisted by naphthyl-based models bearing two tellurols and a tellurol-thiol pair in peri-position are explored and compared with the analogous energy profiles for the naphthalene mimic having two selenols. The presence of a halogen bond (XB) in the intermediate formed in the first step and involved in the rate-determining step of the reaction is assumed to facilitate the process increasing the rate of the reaction. The rate-determining step calculated energy barrier heights allow rationalizing the experimentally observed superior catalytic activity of tellurium containing mimics. Charge displacement analysis is used to ascertain the presence and the role of the electron density charge transfer occurring in the rate-determining step of the reaction, suggesting the incipient formation or presence of a XB interaction. © 2019 Wiley Periodicals, Inc.