Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY-X···X-Z(B)m] Type (X = Cl, Br, I)

Facile heterolytic bond splitting of molecular chlorine upon reactions with Lewis bases: Comparison with ICl and I2

Formation of molecular complexes and subsequent heterolytic halogen-halogen bond splitting upon reactions of molecular Cl2 with nitrogen-containing Lewis bases (LB) are computationally studied at M06-2X/def2-TZVPD and for selected compounds at CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz levels of theory. Obtained results are compared with data for ICl and I2 molecules. Reaction pathways indicate, that in case of Cl2∙LB complexes the activation energies for the heterolytic Cl-Cl bond splitting are lower than the activation energies of the homolytic splitting of Cl2 molecule into chlorine radicals. The heterolytic halogen splitting of molecular complexes of X2∙Py with formation of [XPy2]+…X 3 - contact ion pairs in the gas phase is slightly endothermic in case of Cl2 and I2, but slightly exothermic in the case of ICl. Formation of {[ClPy2]+…Cl 3 - }2 dimers makes the overall process exothermic. Taking into account that polar solvents favor ionic species, generation of donor-stabilized Cl+ in the presence of the Lewis bases is expected to be favorable. Thus, in polar solvents the oxidation pathway via donor-stabilized Cl+ species is viable alternative to the homolytic Cl-Cl bond breaking.

Charge-Assisted Anion-π Interaction and Hydrogen Bonding Involving Alkylpyridinium Cations

Competition and cooperation of charge-assisted anion-π interactions and hydrogen bonding were explored in the solid state and in solutions of 1-ethyl-4-carbomethoxypyridinium iodide, the compound utilized by Kosower to calculate solvent polarity Z-indices. X-ray structural analysis of this salt revealed multiple short contacts of iodide anions with hydrogen atoms and aromatic rings of pyridinium cations. Geometric characteristics, quantum theory of atoms in molecules (QTAIM), and noncovalent interaction (NCI) analysis of these contacts indicated comparable interaction energies of the anion-π and hydrogen bonding between iodide and pyridinium cation. 1H NMR (indicating the presence of the hydrogen-bonded complexes) and UV-vis measurements (which were consistent with the formation of anion-π associations) pointed out that both these supramolecular interactions also coexist in solutions. The comparable interaction energies (ΔE) of these modes were confirmed by the DFT computations. Also, while the variations of ΔE with the dielectric constant of the solvents for the complexes of iodide with the neutral π-acceptors were related to the increase of the effective radii of hydrogen- or anion-π bonded iodides, the changes in ΔE for the complexes with pyridinium followed interaction energies between two unit charges. However, the distinction of the bonding in hydrogen-bonded and anion-π complexes of iodide with pyridinium led to a switch of their relative energies with an increase of the polarity of the medium.

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.

Roles of Hydrogen, Halogen Bonding and Aromatic Stacking in a Series of Isophthalamides

The synthesis and spectroscopic characterisation of six bis(5-X-pyridine-2-yl)isophthalamides (X = H, F, Br, Cl, I, NO2) are reported, together with five crystal structure analyses (for X = H, F to I). The isophthalamides span a range of conformations as syn/anti (H-DIP; I-DIP), anti/anti- (F-DIP; Br-DIP) and with both present in ratio 2:1 in Cl-DIP. The essentially isostructural F-DIP and Br-DIP molecules (using strong amide…amide interactions) aggregate into 2D molecular sheets that align with either F/H or Br atoms at the sheet surfaces (interfaces), respectively. Sheets are linked by weak C-H⋯F contacts in F-DIP and by Br⋯Br halogen bonding interactions as a ‘wall of bromines’ at the Br atom rich interfaces in Br-DIP. Cl-DIP is an unusual crystal structure incorporating both syn/anti and anti/anti molecular conformations in the asymmetric unit (Z’ = 3). The I-DIP•½(H2O) hemihydrate structure has a water molecule residing on a twofold axis between two I-DIPs and has hydrogen and N⋯I (Nc = 0.88) halogen bonding. The hydrate is central to an unusual synthon and involved in six hydrogen bonding interactions/contacts. Contact enrichment analysis on the Hirshfeld surface demonstrates that F-DIP, Cl-DIP and Br-DIP have especially over-represented halogen···halogen interactions. With the F-DIP, Cl-DIP and Br-DIP molecules having an elongated skeleton, the formation of layers of halogen atoms in planes perpendicular to the long unit cell axis occurs in the crystal packings. All six DIPs were analysed by ab initio calculations and conformational analysis; comparisons are made between their minimized structures and the five crystal structures. In addition, physicochemical properties are compared and assessed.

σ-Hole interactions in organometallic catalysts: the case of methyltrioxorhenium(VII)

Methyltrioxorhenium(VII) (MTO) is a widely employed catalyst for metathesis, olefination, and most importantly, oxidation reactions. It is often preferred to other oxometal complexes due to its stability in air and higher efficiency. The seminal papers of K. B. Sharpless showed that when pyridine derivatives are used as co-catalysts, MTO-catalyzed olefin epoxidation with H₂O₂ as oxidant, a particularly useful reaction, is accelerated, with pyridine speeding up catalytic turnover and increasing the lifetime of MTO under the reaction conditions. In this paper, combined experimental and theoretical results show that the occurrence of σ-hole interactions in catalytic systems extends to MTO. Four crystalline adducts between MTO and aliphatic and heteroaromatic bases are obtained, and their X-ray analyses display short Re⋯N/O contacts opposite to both O-Re and C-Re covalent bonds with geometries consistent with σ-hole interactions. Computational analyses support the attractive nature of these close contacts and confirm that their features are typical of σ-hole interactions. The understanding of the nature of Re⋯N/O interactions may help to optimize the ligand-acceleration effect of pyridine in the epoxidation of olefins under MTO catalysis.

Non-covalent interactions in the monohydrated complexes of 1,2,3,4-tetrahydroisoquinoline

The eleven monohydrates of 1, 2, 3, 4-tetrahydroisoquinoline (THIQ) are analyzed through natural bond orbital (NBO) analysis and QTAIM methods employing M06-2X functional in DFT and MP2 methods. Here, the role of OH bonds as an acceptor and donor is critically analyzed. The role of lone pairs of O is critically monitored in two of the complexes, where N-H···O hydrogen bonds are present. The relative contributions of rehybridisation and hyperconjugation are compared in detail. Popelier criteria are satisfied in all the complexes barring a few exceptions involving weak hydrogen bonds. At the bond critical points (BCP), four monohydrates show higher values of electron density (ρ_C) and negative values of total electron energy density (H_C), while Laplacian [Formula: see text] remains positive. These complexes satisfy the criteria of partial covalency. All these are O-H⋅⋅⋅N-type bonds. Remaining h-bonds are weaker in nature. These are also confirmed by the smaller values of ρ_C at the respective BCP. The variation of potential energy density (V_C) among the complexes seems to be the most important factor in determining the nature of non-covalent interactions.

Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study

A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.

Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions

Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.

The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond

The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.

Halogen bonding in cadmium(II) MOFs: its influence on the structure and on the nitroaldol reaction in aqueous medium

A solvothermal reaction of Cd(II) with the dicarboxyl-functionalized arylhydrazone pro-ligands, 5-(2-(2,4,6-trioxotetrahydro-pyrimidin-5(2H)-ylidene)hydrazineyl)isophthalic acid (H₅L¹) and 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)isophthalic acid (H₃L²), or their halogen bond donor centre(s) decorated analogs 2,4,6-triiodo-5-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)isophthalic acid (H₅L³) and 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)-2,4,6-triiodoisophthalic acid (H₃L⁴), leads to the formation of known [Cd(H₃L¹)(H₂O)₂]_n (1) and new {[Cd(HL²)(H₂O)₂(DMF)]·H₂O}_n (2), [Cd(H₃L³)]_n (3) and {[Cd₂(μ-H₂O)₂(μ-H₂L⁴)₂(H₂L⁴)₂]·2H₂O}_n (4) coordination compounds, respectively. The aggregation of mononuclear units via Cd-OC and Cd-OH₂ coordination and C_Ar-I⋯I types of intramolecular halogen bonds lead to a dinuclear tecton 4. Both C_Ar-I⋯O and C_Ar-I⋯I types of intermolecular halogen bonds play a fundamental role in the supramolecular architectures of the obtained metal-organic frameworks 3 and 4. Theoretical (DFT) calculations confirmed the presence of the C_Ar-I⋯O and C_Ar-I⋯I halogen bonds in 3 and 4 and allowed their characterisation. The formation of intermolecular noncovalent interactions between the attached iodine substituents to the hydrazone ligands and polar solvent (water or methanol) molecules promoted, at least in part, the solubility of the corresponding complexes (3 and 4), which act as homogeneous catalyst precursors in the Henry reaction between aldehydes and nitroethane. The corresponding β-nitroalkanol products were obtained in good yields (66-79%) and with good diastereoselectivity (threo/erythro ca. 72 : 28) in water at room temperature.

Molecular Electrostatic Potential and Noncovalent Interactions in Derivatives of Group 8 Elements

This communication reports experimental and theoretical evidences of σ‐hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements. Cocrystals between pyridine or pyridine N‐oxide derivatives and osmium tetroxide are characterized through various techniques and rationalized as σ‐hole interactions using DFT calculations and several other computational tools. We propose the term “osme bond” (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile. The word osme is the transcription of ὀσμή, the ancient Greek word for smell that was used to name the heaviest group 8 element in relation to the smoky odor of its tetroxide.

Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller-Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (E_int(BSSE)) was determined using a supramolecular approach. The E_int(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.

Strength of the [Z-I···Hal]- and [Z-Hal···I]- Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z-I···Hal]- and [Z-Hal···I]- types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06-4.76 kcal/mol.

Polycentric binding in complexes of trimethylamine-N-oxide with dihalogens

Dihalogens readily interact with trimethylamine-N-oxide under ambient conditions. Accordingly, herein, stable 1 : 1 adducts were obtained in the case of iodine chloride and iodine bromide. The crystal and molecular structure of the trimethylamine-N-oxide-iodine chloride adduct was solved. Furthermore, the geometry and electronic structure of the trimethylamine-N-oxide-dihalogen complexes were studied computationally. Only molecular ensembles were found in the global minimum for the 1 : 1 stoichiometry. The O⋯X-Y halogen bond is the main factor for the thermodynamic stability of these complexes. Arguments for electrostatic interactions as the driving force for this noncovalent interaction were discussed. Also, the equilibrium structures are additionally stabilised by weak C-H⋯X hydrogen bonds. Consequently, formally monodentate ligands are bound in a polycentric manner.

Attractive halogen···halogen interactions in crystal structure of trans-dibromogold(III) complex

A synthesis of the trans-dibromogold(III) t-Bu-Xantphos complex and its self-assembly into infinite 1-dimensional chain in the solid state is reported. The new complex characterized using elemental analyses (C, H, N), ESI-MS, 1H and 13C NMR techniques and X-ray diffraction analysis. Results of DFT calculations followed by the topological analysis of the electron density distribution within the framework of QTAIM method at the ωB97XD/DZP-DKH level of theory reveal that strength of attractive intermolecular non-covalent interactions Br···Br in the crystal is 1.2–1.6 kcal/mol.

Exploring the Polymorphism of Drostanolone Propionate

2α-Methyl-4,5α-dihydrotestosterone 17β-propionate, known as drostanolone propionate or masteron, is a synthetic anabolic-androgenic steroid derived from dihydrotestosterone. The crystal structures of two polymorphs of drostanolone propionate have been determined by single crystal X-ray diffraction and both crystallizes in the monoclinic crystal system. One is belonging to the P21 space group, Z = 2, and has one molecule in the asymmetric unit while the second belongs to the I2 space group, Z = 4, and contains two molecules in the asymmetric unit. Another polymorph has been investigated by an X-ray powder diffraction method and solved by Parallel tempering/Monte Carlo technique and refined with the Rietveld method. This polymorph crystallizes in the orthorhombic P212121 space group, Z = 4 having one molecule in the asymmetric unit. The structural configuration analysis shows that the A, B, and C steroid rings exist as chair geometry, while ring D adopts a C13 distorted envelope configuration in all structures. For all polymorphs, the lattice energy has been computed by CLP (Coulomb-London-Pauli), and tight-binding density functional theory methods. Local electron correlation methods were used to estimate the role of electron correlation in the magnitude of the dimer energies. The nature of the intermolecular interactions has been analyzed by the SAPT0 energy decomposition methods as well as by Hirshfeld surfaces.

Peculiarities of Br⋯Br bonding in crystal structures of polybromides and bromine solvates

Analysis of supramolecular associates formed by Br⋯Br interactions in crystals of 204 polybromide and bromine-containing compounds has been carried out.

Metal-Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy

Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y₂)(NC₅H₄X-3)₂ with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC₅H₄X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.