Graded IR Filters: Distinguishing Between Single and Multipoint NO2···I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons)
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The NO2···I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2···I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2···I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and R and in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.Keywords:
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Two new supramolecular compounds, [(H4aobtc)0.5(H2O)0.5] (1) and [(H3aobtc)(H2bipy)0.5] (2) (H4aobtc = azoxybenzene-3,3′,4,4′-tetracarboxylic acid), were synthesized and characterized. Compound 1 has a complicated three-dimensional hydrogen bonding network with 4-connected {33.62.7} topology. Compound 2 also shows a three-dimensional supramolecular motif with hexagonal topology. The result indicated that hydrogen bonding interactions from different molecular synthons take important roles in the formation of supramolecular architectures.
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2-Amino-6-hydroxymethylpyridine (1) and 2-pivaloylamino-6-hydroxymethylpyridine (2) are important hydrogen bonding synthons as they are the very useful substrates which can be used for the synthesis of designed receptors in the field of molecular recognition [1] and supramolecular chemistry [2]. Here we report the compounds 1 and 2 as simple designers to create polymeric supramolecular three-dimensional assembly and self-complementary dimer respectively in solid-state crystal engineering. Keywords: Hydrogen bonding synthons, supramolecular assembly, dimerisation and polymerization
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Iodination of Ph 2 Te 2 Se by molecular iodine is directed towards the Te atom and yields {diiodo[(phenyltellanyl)selanyl]-λ 4 -tellanyl}benzene, PhTeSeTeI 2 Ph or C 12 H 10 I 2 SeTe 2 . The molecule can be considered as a chimera of PhTeSe R , PhTeSeTePh and R ′TeI 2 Ph fragments. The crystal structure features a complex interplay of the supramolecular synthons Te...π(Ph), Se...Te and I...Te, combining molecules into a three-dimensional framework. Their combination affords long-range supramolecular synthons which are fused in a way resembling the mythological chimera and could be defined as chimeric supramolecular synthons . The energies of the intermolecular interactions have also been calculated and analyzed.
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A series of organic salts derived from various dicarboxylic acids and two α,ω-diamines, namely, 1,3-diaminopropane and 1,4-diaminobutane, were prepared and characterized by various physicochemical techniques, including single-crystal X-ray diffraction, with the aim of extending the well-studied 2D primary ammonium dicarboxylate (PAD) supramolecular synthon in the context of supramolecular gelation. Single crystal structures of 9 out of 14 diprimary ammonium dicarboxylate (DPAD) salts were determined. The results showed that none of the salts displayed the expected 2D DPAD synthon; instead, all of them self-assembled into a 3D hydrogen-bonded network. Consequently, only two salts, namely, B3FA and B4SA, appeared to show gelation behavior producing weak gels—a finding that corroborated well with the current understanding of gelation.
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It has been 20 years since the concept of supramolecular synthon was introduced with the purpose of rational supramolecular synthesis. While this concept has been greatly successful in employing a retrosynthetic approach in crystal engineering, the past few years have seen a continuous evolution of supramolecular synthons from being a synthetic subunit to a basic unit for understanding the dynamics of crystallization. This review attempts to give a glimpse of such developments.
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An effective method for the synthesis of novel adenine amides was developed and successfully implemented, leading to 4-propyloxy-N-(9H-purin-6-yl)benzamide (1) and 4-dodecyloxy-N-(9H-purin-6-yl)benzamide (2). The compounds were fully characterised by means of spectroscopic (1H NMR, 13C NMR, FT-IR) and thermal (TG, DSC) analysis. The crystallographic analysis revealed that the formation of supramolecular chains relies on hydrogen bonding between amide functionalities. All supramolecular synthons found in the crystal structure of 1 were confirmed with the temperature-dependent IR method. The temperature-dependent IR method is useful in determining supramolecular interactions for compound 2, for which the crystal structure could not be obtained. A detailed analysis of temperature-dependent FT-IR spectra was used for the first time to identify the hydrogen bonds that exist in the solid state of our compounds; it can therefore be considered a promising method for the pattern recognition of hydrogen bonding in supramolecular chemistry.
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Analysis of the strengths and directionality of intermolecular interactions in the crystals containing only one type of supramolecular synthon allows the suggestion of a general classification of molecular crystals depending on type of their basic structural motifs. All crystals may be divided on four classes namely (I) crystals with isotropic packing of the building units; (II) columnar crystals where the basic structural motif (BSM) is a chain/column; (III) layered crystals with layers as the BSM; (IV) columnar-layered crystals containing chains/columns as the primary basic structural motif and layers as the secondary BSM. Taking into account the participation of different supramolecular synthons in the formation of different levels of the organization of molecular crystals, they may be considered as basic (responsible for the formation of molecular complexes as building units of crystals), primary, secondary and auxiliary, which are involved in the agglomeration of molecules in primary or secondary basic structural motifs or in the packing of these motifs, respectively. The ranking of supramolecular synthons depends on values of energies of intermolecular interactions and it is individual for each crystal.
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The theme of supramolecular synthons runs through all disciplines of crystal engineering. The concept of supramolecular synthons has received ever increasing attention in various fields since it was defined and introduced in 1997. This trend is manifest in the exploding number of articles published, and not only in the specialised journals, Crystal Growth and Design and CrystEngComm. Attention is being given both to supramolecular synthons, which involve strong intermolecular interactions, and to weak intermolecular interactions, for instance C–X⋯CN, C–H⋯N, C–H⋯F or X⋯X, in the interpretation and understanding of molecular aggregation in the solid state. This highlight article will give a picture of the rapid development of interest in supramolecular synthons in the last ten years together with a discussion about the boundaries of this concept.
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