Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages

Stereoselective Processes Based on σ-Hole Interactions

The σ-hole interaction represents a noncovalent interaction between atoms with σ-hole(s) on their surface (such as halogens and chalcogens) and negative sites. Over the last decade, significant developments have emerged in applications where the σ-hole interaction was demonstrated to play a key role in the control over chirality. The aim of this review is to give a comprehensive overview of the current advancements in the use of σ-hole interactions in stereoselective processes, such as formation of chiral supramolecular assemblies, separation of enantiomers, enantioselective complexation and asymmetric catalysis.

Reliable prediction of association (free) energies of supramolecular complexes with heavy main group elements – the HS13L benchmark set

We introduce a set of 13 supramolecular complexes featuring diverse non-covalent interactions with heavy main group elements (Zn, As, Se, Te, Br, I), high charges (−2 up to +4), and large systems with up to 266 atoms (HS13L).

The mechanism of the selective binding ability between opiate metabolites and acyclic cucurbit[4]uril: an MD/DFT study

Subtle changes in molecular structure often lead to significant differences in host-guest interactions, which result in different host-guest recognition capabilities and dynamics behaviours in complex formation. Herein, we reveal the influence of the guest substituents on host-guest molecular recognition by molecular dynamics (MD) simulation and density functional theory (DFT) approaches. The results suggest that the binding energy barrier of acyclic cucurbit[4]uril (ACB[4]) with opiate metabolites gradually decreases. The methyl group in morphine (MOR) and morphine-3-glucuronide (M3G) strengthens the hydrophobicity of the guest, while depressing the energy loss of the desolvation of polar groups (e.g. hydroxyl) inside the ACB[4] cavity. However, in M3G, the 3-glucuronide group located outside the ACB[4] host cavity effectively alleviates the unfavourable desolvation effect of the hydroxyl and increases the binding constant by two orders of magnitude (compared with normorphine (NMOR)). Our findings stressed the essentiality of the binding mode and intermolecular noncovalent interactions in the host-guest selective binding ability.

Supramolecular architectures sustained by delocalised C–I⋯π(arene) interactions in molecular crystals and the propensity of their formation

A survey of delocalised C–I⋯π(chelate ring) interactions is presented.

Molecular Recognition and Cocrystallization of Methylated and Halogenated Fragments of Danicalipin A by Enantiopure Alleno-Acetylenic Cage Receptors

Enantiopure (P)₄- and (M)₄-configured alleno-acetylenic cage (AAC) receptors offer a highly defined interior for the complexation and structure elucidation of small molecule fragments of the stereochemically complex chlorosulfolipid danicalipin A. Solution (NMR), solid state (X-ray), and theoretical investigations of the formed host-guest complexes provide insight into the conformational preferences of 14 achiral and chiral derivatives of the danicalipin A chlorohydrin core in a confined, mostly hydrophobic environment, extending previously reported studies in polar solvents. The conserved binding mode of the guests permits deciphering the effect of functional group replacements on Gibbs binding energies ΔG. A strong contribution of conformational energies toward the binding affinities is revealed, which explains why the denser packing of larger apolar domains of the guests does not necessarily lead to higher association. Enantioselective binding of chiral guests, with energetic differences ΔΔG_293 K up to 0.7 kcal mol^-1 between diastereoisomeric complexes, is explained by hydrogen- and halogen-bonding, as well as dispersion interactions. Calorimetric studies (ITC) show that the stronger binding of one enantiomer is accompanied by an increased gain in enthalpy ΔH but at the cost of a larger entropic penalty TΔS stemming from tighter binding.

Intensified C≡C Stretching Vibrator and Its Potential Role in Monitoring Ultrafast Energy Transfer in 2D Carbon Material by Nonlinear Vibrational Spectroscopy

In this work, an intensity-enhanced C≡C stretching infrared (IR) absorption is observed in hexakis[(trimethylsilyl)ethynyl]benzene (HTEB), whose IR transition dipole magnitude becomes comparable to that of a typical C═O stretch, and the enhancement is believed to be due to a joint effect of π-π conjugation and hyperconjugation associated with a terminal trimethylsilyl group. Using dynamical time-dependent two-dimensional infrared (2D IR) spectroscopy, a picosecond intramolecular energy redistribution process is observed between two nondegenerate C≡C stretching modes, whose symmetry breaking is attributed to a noncovalent halogen-bonding interaction between HTEB and solvent CH₂Cl₂. The rigid structure of HTEB and limited structural dynamics are also inferred from the insignificant initial spectral diffusion value extracted from the 2D IR spectra. This work provides the first nonlinear infrared investigation of the conventionally weak C≡C stretch. The methods outlined are particularly important for detailed understanding of the structure-related processes such as vibrational energy transfer in novel C≡C species containing materials such as graphdiyne.

Larger Substituents on Amide Cavitands Induce Bigger Cavities

A series of quinoxaline cavitands bearing pendant amide groups with various substituent sizes (Et, ⁱPr, ^tBu) were synthesized, and their cavity size/structure were investigated by X-ray and NMR analyses. In the case of the Et or ⁱPr amide cavitand, the conformation of the molecule was in the vase form, while the bulky ^tBu amide cavitand gave the kite conformation at room temperature. X-ray crystal structures of Et and ⁱPr cavitands clearly showed the intramolecular H-bondings to influence the conformation and the cavity sizes dependent on the bulkiness of functional groups. The ¹H NMR spectrum revealed that the Et cavitand can encapsulate an adamantane guest compound with slow exchange.

A self-assembled nanotube supported by halogen bonding interactions

Upper-rim halogenation of a calix[4]arene modulates the packing of self-assembled nanotubes through the formation of complementary halogen bonding interactions.

Synthesis of an open-cage fullerene-based unidirectional H-bonding network and its coordination with titanium

Hydroxyl groups formed a unidirectional H-bond network on the rim of an orifice and showed a weak interaction with a water molecule trapped inside a fullerene cage.

Cycloalkanes and cycloalkenes in dispersive force oriented inclusion crystals by a functionalized acyclic host molecule

The complexation of alicyclic compounds with a functionalized acyclic host gave inclusion crystals. Guest molecules were enclathrated within the cavity of the cyclic dimer of host molecules.

Can Combined Electrostatic and Polarization Effects Alone Explain the F···F Negative-Negative Bonding in Simple Fluoro-Substituted Benzene Derivatives? A First-Principles Perspective

The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry in molecular assemblies are presented in a brief review of the field. Emphasis has been placed to show that type-I and -II halogen-centered F···F long-ranged intermolecular distances viable between the entirely negative fluorine atoms in some fluoro-substituted dimers of C6H6 can be regarded as the consequence of significant non-covalent attractive interactions. Such attractive interactions observed in the solid-state structures of C6F6 and other similar fluorine-substituted aromatic compounds have frequently been underappreciated. While these are often ascribed to crystal packing effects, we show using first-principles level calculations that these are much more fundamental in nature. The stability and reliability of these interactions are supported by their negative binding energies that emerge from a supermolecular procedure using MP2 (second-order Møller-Plesset perturbation theory), and from the Symmetry Adapted Perturbation Theory, in which the latter does not determine the interaction energy by computing the total energy of the monomers or dimer. Quantum Theory of Atoms in Molecules and Reduced Density Gradient Non-Covalent Index charge-density-based approaches confirm the F···F contacts are a consequence of attraction by their unified bond path (and bond critical point) and isosurface charge density topologies, respectively. These interactions can be explained neither by the so-called molecular electrostatic surface potential (MESP) model approach that often demonstrates attraction between sites of opposite electrostatic surface potential by means of Coulomb’s law of electrostatics, nor purely by the effect of electrostatic polarization. We provide evidence against the standalone use of this approach and the overlooking of other approaches, as the former does not allow for the calculation of the electrostatic potential on the surfaces of the overlapping atoms on the monomers as in the equilibrium geometry of a complex. This study thus provides unequivocal evidence of the limitation of the MESP approach for its use in gaining insight into the nature of reactivity of overlapped interacting atoms and the intermolecular interactions involved.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

Coupling Metaloid-Directed Self-Assembly and Dynamic Covalent Systems as a Route to Large Organic Cages and Cyclophanes

The synthesis of large cyclic and caged disulfide structures was achieved by pnictogen-assisted iodine oxidation starting from self-assembled pnictogen thiolate complexes. The directing behavior of pnictogen enables rapid and selective syntheses of many discrete disulfide assemblies over competing oligomers/polymers, ranging from structures that are small and strained to those that are large and multifaceted, including 3D cages. Traditional cyclization reactions carried out under kinetic control are generally low-yielding, which often results in the formation of insoluble oligomers and polymers as unwanted side products. The prospect of self-assembling organic structures efficiently under thermodynamic control adds an attractive tool for the synthesis of cyclophanes and other large cage compounds. This method of metaloid-directed self-assembly within a dynamic covalent system allows for the rapid and discriminant self-assembly of disulfide cyclophanes without the consequences sometimes seen in traditional cyclophane syntheses such as poor yields, long reaction times, low ring-closing selectivity, and extensive purifications. The present paper provides an overview of this approach, explores the role of the pnictogen additive and solvent in this reaction, begins to test the limits of this strategy in complex 3D molecule formation, and extends our strategy to include one-pot syntheses that do not require the use of a pnictogen additive. This Viewpoint also includes an extended introduction to serve as a minireview highlighting the utility of a self-assembly approach to create organic cage structures. From a practical standpoint, the cyclophanes isolated from this method can serve as precursors in the production of insulating plastics (e.g., through the widely used parylene polymerization process, which uses derivatives of paracyclophane as monomers) or as potential hosts for molecular separations or capture.