The present review is aimed to compare crystal packing interactions contributing to stacking arrangements of primarily nonaromatic systems referring only briefly to classical aromatic stacking. The ...classical aromatic stacking is mainly based on weak dispersion interactions (E ≤ 1 kcal mol–1) whereas heteroaromatics reveal more electrostatic (or specifically dipolar) contributions (E = 5–10 kcal mol–1). Based mainly on our charge density studies and DFT calculations, the results show that (i) all planar rings stack, regardless of aromaticity (or delocalization of π electrons) and (ii) stacking interactions cover a wide continuum ranging from weak, mainly dispersion interactions (E < 5 kcal mol–1) to unlocalized two-electron multicentric (2e/mc) covalent bonds (“pancake bonds”, E > 15 kcal mol–1). Our recent studies showed that quinones form face-to-face stacks and the energies of interactions exceed 10 kcal mol–1; ours and other authors’ results indicate that interactions between planar radicals involve a significant contribution of covalent bonding. Thus, π-interactions cover a broad range of energies, ranging from ≤1 to ≥20 kcal mol–1, and the interactions span from weak dispersion to multicentric covalent bonding. Therefore, development of a universal model of stacking is needed. In this respect, stacking can be compared to hydrogen bonding, which also ranges between dispersion (weakest hydrogen bonds, such as C–H···S and C–H···Cl) and two-electron/three-centric covalent bonding (the strongest “symmetrical” hydrogen bonds).
The crystal structure of 4‐damp)2Cl4Q3 (4‐damp=4‐dimethylamino‐N‐methylpyridinium, Cl4Q=tetrachloroquinone) salt is built up from slipped columnar stacks of quinoid rings composed of closely bound ...trimers with the intra‐trimer separation distance of 2.84 Å and total charge of −2 whereas the inter‐trimer distance is 3.59 Å. The individual rings exhibit partial negative charges that are distributed unevenly among the three Cl4Qs in the trimer. The strong interactions within a trimer (Cl4Q)32− have a partially covalent character with two‐electron/multicentered bonding, that is extended over three rings, plausibly termed as “pancake bonding”. The electron pairing within this multicentre bond leads to the fact that the crystals are diamagnetic and act as insulators. The studies of the structure and nature of bonding are based on X‐ray charge density analysis and density functional theory.
Bonding over breakfast? Partially covalent pancake bonding in a trimer of partially charged tetrachloroquinone molecules (total charge −2) is studied by a combination of X‐ray charge density analysis and DFT calculations. Separation distance between the rings in a trimer is 2.84 Å.
An X-ray charge density study of 4-cyano-N-methylpyridinium salt of 5,6-dichloro-2,3-dicyanosemiquinone radical anion (4-CN-N-MePy+DDQ−) revealed fine details of two-electron multicenter (2e/mc) ...covalent bonding within stacked dimers of DDQ anion radicals with a short separation distance of 2.87 Å. Since the electron pair is not localized but rather spread over a large area between two semiquinoid rings (28 atoms), the maximum electron density is 0.085 e Å–3; the electron density value is consistent with the existence of a nonlocalized electron pair. However, the presence of multiple bond (3,–1) critical points and a local electron density minimum (which is usually found in cage-like moieties, such as adamantyl) between the rings point to a 3D shape of frontier orbitals, consistent with the presence of a 2e/mc bond.
X-ray charge density was determined and analyzed for two polymorphs of the N-methylpyridinium salt of the tetrachlorosemiquinone radical anion and its analogous closed-shell relatives, ...tetrachloroquinone (chloranil) and tetrachlorohydroquinone. The study, which was combined with calculations of electron delocalization, electrostatic potentials, and aromaticity, presents details of electronic structure of the semiquinoid ring. This comparative study reveals that the negative charge is delocalized over the entire semiquinone radical and that the chlorine substituents play a crucial role in its stabilization through induction effect. In general, the semiquinoid ring has partially delocalized π-electrons and is approximately halfway between a quinoid and an aromatic ring. In the orthorhombic polymorph with stacks of equidistant radicals electron density between the rings of almost 0.05 e Å–3 and four (3,–1) saddle points between the contiguous rings were found. In the diamagnetic triclinic polymorph, comprising strongly bound radical dimers (with significant covalent character“pancake bond”), maximum electron density between the rings exceeds 0.095 e Å–3, and multiple (3,–1) critical points are found. However, only negligible electron density is observed between the dimers. Thus, in the radical anion stacks spin coupling, along with dispersive and polarization effects, defines interplanar distance and magnetic behavior, whereas intermolecular electrostatic potential determines the ring offset.
First anion···π contacts with quinoid rings have been described in novel co-crystals of tetrabromo- and tetrachloroquinone with iodide salts of substituted N-methylpyridinium cations. In seven ...crystal structures of these co-crystals, a centrosymmetric unit I–···quinone···I– is observed involving close contacts between iodide anions and electron-depleted carbon skeletons of the quinoid rings. However, the salt with N-methyl-4-methylcarboxypyridinium base crystallizes in two polymorphs characterized by OC···quinone···CO interaction instead of I–···quinone···I– one. A possible charge transfer, suggested by the black color of the crystals, is probed by solid-state NMR and IR spectroscopies and analyzed by DFT calculations.
Herein, we present a detailed X-ray charge density study of the electron delocalization in five species of chloranilic acid: neutral molecule, mono- and dianion, and two chelating modes: bidendate ...and (bis)bidentate. The experiments provide the electron density at the bond critical points, which yields an accurate measure of bond order (and therefore electron delocalization), and complement previous literature and our data on bond lengths extracted from crystal structures and infrared spectra. Mapping of the electrostatic potential indicates electron-rich and electron-poor areas in the molecule, corresponding to single (electron-poor), double, and delocalized bonds (electron-rich) that can explain stacking interactions of quinoid rings in crystal packing.
SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few ...lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A1 from Streptomyces albidoflavus (PDB: 4HYQ). The structure reveals the Rossmann-like 3-layer αβα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···OC-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG ⧧ ENZ = 17.9 kcal mol–1, being in reasonable agreement with the experimental value of 14.5 kcal mol–1, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.
A series of six novel mononuclear, binuclear and linear one-dimensional (1D) compounds of copper( ii ) with chloranilic acid (3,6-dichloro-2,5-dihydroxybenzoquinone, H 2 CA) is prepared and a design ...strategy for the preparation of such complexes is discussed. Four described compounds are linear 1D coordination polymers Cu(CA) n , whereas another two involve a binuclear and a mononuclear, Cu 2 (CA) 3 and Cu(CA) 2 , core unit. A linear polymer incorporating bulky aromatic imidazole has been synthesized as a result of investigation of the influence of pH on the reaction mixture. Two coordination modes of the chloranilate dianion are observed. The bridging (bis)bidentate mode generates linear 1D polymeric species. Among these one reveals square-pyramidal coordination of Cu 2+ , whereas the three polymers contain Cu 2+ in an octahedral arrangement. However, the combination of both, terminal bidentate ( ortho -quinone) and bridging (bis)bidentate modes of coordination produces a binuclear complex anion, which comprises a square-pyramidal coordination of Cu 2+ complex anions forming a supramolecular honeycomb-like network encapsulating 4,4′-bipyridine cations. When the chloranilate dianion coordinates the Cu 2+ atom only in a terminal bidentate mode, a mononuclear complex with an octahedral environment of the metal centre is formed. The presence of the bulky ancillary ligand imidazole produces an unprecedented packing involving chiral (racemic) and achiral ( meso -compound) coordination polymers in the same crystal. Electron spin resonance spectroscopy of polycrystalline samples determined g-tensor parameters of copper( ii ) ions in different coordination geometries and revealed weak exchange interactions (| J | < 1 cm −1 ) in linear metal-complex polymers and dimeric species.
Two salts of tetrachloro- (chloranil, Cl4Q) and tetrabromosemiquinone (bromanil, Br4Q) radical anions with an organic cation N-methylpyridinium (N-MePy), displaying a variety of tunable electrical ...and magnetic properties, are characterized. These systems comprise π-stacks of equidistant semiquinone radical anions, without Peierls deformation and diamagnetic spin coupling. Both are stable up to 150 and 120 °C in air, respectively, and are semiconductors with conductivities of 10–6–10–7 (Ω cm)−1 in the single crystals. The room-temperature concomitant crystallization of two polymorphs with different magnetic properties (antiferromagnetic and Peierls-distorted diamagnetic) has been observed for Cl4Q·N-MePy. The semiquinone radical organic salts represent a novel class of potential (multi)functional materials with tunable properties.
The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical ...calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (
quinones) than those involving delocalized systems (
aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding ('pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.
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