Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures

Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).

Multipocket Cage Enables the Binding of High-Order Bulky and Drug Guests Uncovered by MS Methodology

Achieving high guest loading and multiguest-binding capacity holds crucial significance for advancement in separation, catalysis, and drug delivery with synthetic receptors; however, it remains a challenging bottleneck in characterization of high-stoichiometry guest-binding events. Herein, we describe a large-sized coordination cage (MOC-70-Zn8Pd6) possessing 12 peripheral pockets capable of accommodating multiple guests and a high-resolution electrospray ionization mass spectrometry (HR-ESI-MS)-based method to understand the solution host-guest chemistry. A diverse range of bulky guests, varying from drug molecules to rigid fullerenes as well as flexible host molecules of crown ethers and calixarenes, could be loaded into open pockets with high capacities. Notably, these hollow cage pockets provide multisites to capture different guests, showing heteroguest coloading behavior to capture binary, ternary, or even quaternary guests. Moreover, a pair of commercially applied drugs for the combination therapy of chronic lymphocytic leukemia (CLL) has been tested, highlighting its potential in multidrug delivery for combined treatment.

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Charge-Assisted Halogen Bonding in an Ionic Cavity of a Coordination Cage Based on a Copper(I) Iodide Cluster

The design of molecular containers capable of selectively binding specific guest molecules presents an interesting synthetic challenge in supramolecular chemistry. Here, we report the synthesis and structure of a coordination cage assembled from Cu₃ I₄ ^- clusters and tripodal cationic N-donor ligands. Owing to the localized permanent charges in the ligand core the cage binds iodide anions in specific regions within the cage through ionic interactions. This allows the selective binding of bromomethanes as secondary guest species within the cage promoted by halogen bonding, which was confirmed by single-crystal X-ray diffraction.

Identifying porous cage subsets in the Cambridge Structural Database using topological data analysis

As rationally designable materials, the variety and number of synthesised metal-organic cages (MOCs) and organic cages (OCs) are expected to grow in the Cambridge Structural Database (CSD). In this regard, two of the most important questions are, which structures are already present in the CSD and how can they be identified? Here, we present a cage mining methodology based on topological data analysis and a combination of supervised and unsupervised learning that led to the derivation of - to the best of our knowledge - the first and only MOC dataset of 1839 structures and the largest experimental OC dataset of 7736 cages, as of March 2022. We illustrate the use of such datasets with a high-throughput screening of MOCs and OCs for xenon/krypton separation, important gases in multiple industries, including healthcare.

Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State

Reactions between Zn(II) nitrate, pentaiodobenzoic acid (HPIBA) and different pyridines in dimethylformamide (DMF) result in the formation of the heteroleptic neutral complexes [Zn(3,5-MePy)2PIBA2] (1) and [Zn(DMF)3(NO3)PIBA] (2). Both compounds were isolated in pure form, as shown by the PXRD data. The features of specific non-covalent interactions involving halogen atoms (halogen bonding) were examined by means of DFT calculations (QTAIM analysis and the estimation of corresponding energies).

Correlations between ligand field Δ o, spin crossover T 1/2 and redox potential E pa in a family of five dinuclear helicates

A family of five new bis-bidentate azole-triazole Rat ligands (1,3-bis(5-(azole)-4-isobutyl-4H-1,2,4-triazol-3-yl)benzene), varying in choice of azole (2-imidazole, 4-imidazole, 1-methyl-4-imidazole, 4-oxazole and 4-thiazole), and the corresponding family of spin-crossover (SCO) and redox active triply bridged dinuclear helicates, [FeII 2L3]4+, has been prepared and characterised. X-ray crystal structures show all five Fe(ii) helicates are low spin at 100 K. Importantly, DOSY NMR confirms the intactness of these SCO-active dinuclear helicates in D3-MeCN solution, regardless of HS fraction: γ HS(298 K) = 0-0.81. Variable temperature 1H NMR Evans and UV-vis studies reveal that the helicates are SCO-active in MeCN solution. Indeed, the choice of azole in the Rat ligand used in [Fe2L3]4+ tunes: (a) solution SCO T 1/2 from 247 to 471 K, and (b) reversible redox potential, E m(FeII/III), from 0.25 to 0.67 V for four helicates, whilst one has an irreversible redox process, E pa = 0.78 V, vs. 0.01 M AgNO3/Ag. For the four reversible redox systems, a strong correlation (R 2 = 0.99) is observed between T 1/2 and E pa. Finally, the analogous Ni(ii) helicates have been prepared to obtain Δ o, establishing: (a) the ligand field strength order of the ligands: 4-imidazole (11 420) ∼ 1-methyl-4-imidazole (11 430) < 2-imidazole (11 505) ∼ 4-oxazole (11 516) < 4-thiazole (11 804 cm-1), (b) that Δ o ([NiII 2L3]4+) strongly correlates (R 2 = 0.87) with T 1/2 ([FeII 2L3]4+), and (c) interestingly that Δ o strongly correlates (R 2 = 0.98) with E pa for the four helicates with reversible redox, so the stronger the ligand field strength, the harder it is to oxidise the Fe(ii) to Fe(iii).

Confinement of Water-Soluble Cationic Substrates in a Cationic Molecular Cage by Capping the Portals with Tripodal Anions

The ability of a cationic coordination cage to encapsulate molecular guests is enhanced by non-covalent capping of the cage portals with tripodal anions. The capped cage provides new cation binding sites at the portals, which enable accommodation of cationic substrates within the cationic cage. In addition, non-covalent capping allows neutral guests in the cage to be exchanged for cationic ones on demand.

Interactions of Small-Molecule Guests with Interior and Exterior Surfaces of a Coordination Cage Host

Coordination cages are well-known to act as molecular containers that can bind small-molecule guests in their cavity. Such cavity binding is associated with interactions of the guests with the surrounding set of surfaces that define the cavity; a guest that is a good fit for the cavity will have many favourable interactions with the interior surfaces of the host. As cages have exterior as well as interior surfaces, possibilities also exist for ‘guests’ that are not well-bound in the cavity to interact with the exterior surface of the cage where spatial constraints are fewer. In this paper, we report a combined solid-state and solution study using an octanuclear cubic M8L12 coordination cage which illustrates the occurrence of both types of interaction. Firstly, crystallographic studies show that a range of guests bind inside the cavity (either singly or in stacked pairs) and/or interact with the cage exterior surface, depending on their size. Secondly, fluorescence titrations in aqueous solution show how some flexible aromatic disulfides show two separate types of interaction with the cage, having different spectroscopic consequences; we ascribe this to separate interactions with the exterior surface and the interior surface of the host cage with the former having a higher binding constant. Overall, it is clear that the idea of host/guest interactions in molecular containers needs to take more account of external surface interactions as well as the obvious cavity-based binding.

Two Orthogonal Halogen-Bonding Interactions Directed 2D Crystalline Supramolecular J-Dimer Lamellae

Dye assemblies exhibit fascinating properties and performances, both of which depend critically on the mutual packing arrangement of dyes and on the supramolecular architecture. Herein, we engineered, for the first time, an intriguing chlorosome-mimetic 2D crystalline J-dimer lamellar structure based on halogenated dyes in aqueous media by employing two distinct orthogonal halogen-bonding (XB) interactions. As the only building motif, antiparallel J-dimer was formed and stabilized by single π-stacking and dual halogen⋅⋅⋅π interactions. With two substituted halogen atoms acting as XB donors and the other two acting as acceptors, the constituent J-dimer units were linked by quadruple highly-directional halogen⋅⋅⋅halogen interactions in a staggered manner, resulting in unique 2D lamellar dye assemblies. This work champions and advances halogen-bonding as a remarkably potent tool for engineering dye aggregates with a controlled molecular packing arrangement and supramolecular architecture.

The role of non-covalent intermolecular interactions on the diversity of crystal packing in supramolecular dihalopyridine–silver(i) nitrate complexes

The crystal structures of six novel Ag⁺ complexes with NO₃⁻ and dihalopyridines revealed intriguing differences that were interpreted by DFT calculations.

Halogen Bonding in a Crystalline Sponge

Host-guest interactions are the key to the supramolecular chemistry and the further application of the receptors to study the structural details of the small guest molecules. Crystalline sponges as a kind of supramolecular receptor need to be investigated in terms of the binding ability with the guests. We found in this work that one guest with σ-hole donors and another with electron-donating species were separately entrapped in two distinct channels of the host framework via the crystalline sponge method. Halogen bonding and weak hydrogen bonding were detected between the host and the two guests, respectively. The ability of the crystalline sponge to absorb and sort guests of different types was unambiguously confirmed by X-ray crystallography.

Ultralow surface energy self-assembled monolayers of iodo-perfluorinated alkanes on silica driven by halogen bonding

Compact self-assembled monolayers (SAMs) of perfluorododecyl iodide (I-PFC12) of reproducible thickness (1.2 nm) are shown to form on silicon wafers. The SAMs have a high fluorine content (95%) and convey an extremely low surface energy to the silicon wafers (4.3 mN m-1), lower than previously reported in the literature for perfluorinated monolayers, and stable for over eight weeks. Shorter chain iodo-perfluorinated (I-PFC8) or bromo-perfluorinated molecules (Br-PFC10) led to less dense layers. The monolayers are stable to heating up to 60 °C, with some loss up to 150 °C. The I-PFC12 monolayer increases the work function of silicon wafers from 3.6 V to 4.4 eV, a factor that could be gainfully used in photovoltaic applications. The I-PFC12 monolayers can be transferred into patterns onto silica substrates by micro-contact printing. The NMR data and the reproducible thickness point to an upright halogen bonding interaction between the iodine in I-PFC12 and the surface oxygen on the native silica layer.

Proton in a Confined Space: Structural Studies of H+ ⊂Crypt-111 Iodide and Some Halogen-Bonded Derivatives

Experimental observations and modeling data are reported on the solid-state structural features of crypt- 111⋅HI (1) and the three-component co-crystals that 1 forms with α,ω-diiodoperfluoroalkanes 2 a-d. X-ray analyses indicate that, in all five systems and at low temperature, the caged proton is covalently bonded to a single nitrogen atom and is involved in a network of intramolecular hydrogen bonds. In contrast, room-temperature, solid-state ¹⁵ N NMR spectroscopy suggests magnetic equivalency of the two N atoms of crypt-111 in both 1 and co-crystals of 1 with diiodoperfluoroalkanes. Computational modelling confirms that the acidic hydrogen inside the cavity preferentially sits along the internitrogen axis and is covalently bonded to one nitrogen. The computed energy barriers suggest that the hopping of the encapsulated proton between the two N atoms of the cage can occur in the halogen-bonded co-crystals of 1⋅2, but it is hardly possible in the pure H⁺ ⊂crypt-111 iodide 1. These different pictures of the proton position and dynamics obtained by using different techniques and conditions confirm the unique characteristics of the confined space within the cavity of crypr-111 and the distinctive features of processes occurring therein.

Halogen effects on the solid-state packing of phenylalanine derivatives and the resultant gelation properties

Phenylalanine is an important amino acid both biologically, essential to human health, and industrially, as a building block of artificial sweeteners. Our interest in this particular amino acid and its derivatives lies with its ability to form gels in a number of solvents. We present here the studies of the influence of halogen addition to the aromatic ring on the gelation properties and we analyse the crystal structures of a number of these materials to elucidate the trends in their behaviour based on the halogen addition to the aromatic group and the interactions that result.

[Cd(H2O)6]@{Cd6Cl4(nico)12[Hg(Tab)2(μ-Cl)]2}: a heterometallic host–guest icosidodecahedron cage via hierarchical assembly

A reaction of [Hg(Tab)₂(nico)](PF₆) (Tab = 4-(trimethylammonio)benzenethiolate, nico = nicotinate) with equimolar CdCl₂·2.5H₂O afforded a unique heterometallic cage complex [Cd(H₂O)₆]@{Cd₆Cl₄(nico)₁₂[Hg(Tab)₂(μ-Cl)]₂}.

Diverse coordination polymers from a new bent dipyridyl-type ligand 3,6-di(pyridin-4-yl)-9H-carbazole

In the presence of different anions, Zn(ii) and a new bent dipyridyl-type ligand self-assemble to form unique structures.

Selective Co-Encapsulation Inside an M6 L4 Cage

There is broad interest in molecular encapsulation as such systems can be utilized to stabilize guests, facilitate reactions inside a cavity, or give rise to energy-transfer processes in a confined space. Detailed understanding of encapsulation events is required to facilitate functional molecular encapsulation. In this contribution, it is demonstrated that Ir and Rh-Cp-type metal complexes can be encapsulated inside a self-assembled M6 L4 metallocage only in the presence of an aromatic compound as a second guest. The individual guests are not encapsulated, suggesting that only the pair of guests can fill the void of the cage. Hence, selective co-encapsulation is observed. This principle is demonstrated by co-encapsulation of a variety of combinations of metal complexes and aromatic guests, leading to several ternary complexes. These experiments demonstrate that the efficiency of formation of the ternary complexes depends on the individual components. Moreover, selective exchange of the components is possible, leading to formation of the most favorable complex. Besides the obvious size effect, a charge-transfer interaction may also contribute to this effect. Charge-transfer bands are clearly observed by UV/Vis spectrophotometry. A change in the oxidation potential of the encapsulated electron donor also leads to a shift in the charge-transfer energy bands. As expected, metal complexes with a higher oxidation potential give rise to a higher charge-transfer energy and a larger hypsochromic shift in the UV/Vis spectrum. These subtle energy differences may potentially be used to control the binding and reactivity of the complexes bound in a confined space.

Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle

The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results.

Superfluorinated Ionic Liquid Crystals Based on Supramolecular, Halogen-Bonded Anions

Unconventional ionic liquid crystals in which the liquid crystallinity is enabled by halogen-bonded supramolecular anions [Cn F2 n+1 -I⋅⋅⋅I⋅⋅⋅I-Cn F2 n+1 ](-) are reported. The material system is unique in many ways, demonstrating for the first time 1) ionic, halogen-bonded liquid crystals, and 2) imidazolium-based ionic liquid crystals in which the occurrence of liquid crystallinity is not driven by the alkyl chains of the cation.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Novel hydrogen- and halogen-bonding anion receptors based on 3-iodopyridinium units

Iodopyridinium-based tripodal receptors strongly bind anionic species in their bowl-shaped cavity through the synergistic effect of hydrogen- and halogen-bonding interactions.

Coordination networks incorporating halogen-bond donor sites and azobenzene groups

A coordination network decorated with halogen-bond donor sites for specific guest binding.