Self-assembly of a [2]Pseudorotaxane Composed of Cucurbit[6]uril into Linear Pseudopolyrotaxanes by N–H···O, C–H···O and π···π Interactions

The [2]pseudorotaxane of cucurbit[6]uril (Q6) with 1,6-bis(imidazol-1-yl)hexane dihydrobromide was synthesized and its crystal structure was described. The structure of [2]pseudorotaxane was mainly stablized by host–guest C–H···O interactions. Self-assembly of the [2]pseudorotaxane produces infinite one-dimensional chains with intermolecular N–H···O, C–H···O, and π···π interactions; thus, a linear non-covalent pseudopolyrotaxane is formed.     

Supramolecular architectures with ladder and lamellar topologies using metal-ligand coordination units via C–H···Cl and O–H···Cl hydrogen bonding

New Mn^II/Cu^II/Zn^II complexes [(L¹)MnCl₂] (1), [(L²)CuCl₂]·0.5H₂O (2) and [(L²)ZnCl(H₂O)][ClO₄] (3), containing (2-pyridyl)alkylamine ligands, N-methyl-N,N-bis(2-pyridylmethyl)amine (L¹) and methyl[2-(2-pyridyl)ethyl](2-pyridylmethyl)amine (L²), have been prepared and characterized, including X-ray crystallography. The most striking feature of the structures of these complexes is the formation of molecular ladder and lamellar topology through the crystal packing arrangement, determined by both strong O–H···Cl and weak (however, multiple) C–H···Cl hydrogen-bonding interactions, to maintain the neutral/cationic metal-ligand coordination units linked to each other. In 3, additional secondary interactions are observed involving coordinated solvent and the counter-ion. The results presented here demonstrate that (i) the choice of organic ligands to provide flexibility and inherent potential to participate in hydrogen-bonding interactions, (ii) the coordination geometry preferences of metal ions, (iii) the number of metal-bound chloride ion and (iv) the presence of solvent/counter-anion have a great influence on supramolecular network topology.     

Hydrogen-bonded supramolecular motifs in crystal structures of trimethoprim barbiturate monohydrate (I) and 2-amino-4,6-dimethylpyrimidinium barbiturate trihydrate (II)

In the present study, we report the crystal structures of two organic salts, namely 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidinium (TMP) barbiturate monohydrate (TMPBAR) (I), 2-amino-4,6-dimethylpyrimidinium (AMPY) barbiturate trihydrate (AMPYBAR) (II). In both complexes, one ring nitrogen of TMP and AMPY are protonated as a result of proton transfer from the−CH₂ group of barbituric acid. In compound (I), the TMP cation and barbiturate anion are paired through twoN−H···O and one N−H···N hydrogen bonds. This pair further self-organizes through N−H···O hydrogen bonds to generate an array of six hydrogen bonds. These arrays are further cross-linked by N−H···O hydrogen bonds forming a sheet-like structure. The water molecule is also embedded in the sheet via O−H···O and C−H···O hydrogen bonds, forming a rosette-like supramolecular motif. TMP cations are also bridged by alternating water molecules via C−H···O and O−H···N hydrogen bonds. In compound (II), the symmetrical barbiturate anions self-organize on both sides through N−H···O hydrogen bonds generating a supramolecular chain. These chains are cross-linked by the three water molecules. A pair of barbiturate anions and two water molecules constitute an array of four hydrogen bonds (DADA quadruple array). These arrays are cross-linked by another water molecule. 2-Amino-4,6-dimethylpyrimidine cations are paired through N−H···N hydrogen bonds. These pairs are bridged by three water molecules generating a supramolecular ribbon. The barbiturate chains and base pairs are arranged in an alternate manner via N−H···O and O−H···O hydrogen bonds to generate a 3-D network.     

On the relationships between molecular conformations and intermolecular contacts toward crystal self-assembly of mono-, di-, tri-, and tetra-oxygenated xanthone derivatives

Oxygenated xanthones have been extensively investigated over the years, but there are few reports concerning their crystal structure. Our chemical investigations of Brazilian plants resulted in the isolation of four natural products named 1-hydroxyxanthone (I), 1-hydroxy-7-methoxyxanthone (II), 1,5-dihydroxy-3-methoxyxanthone (III), and 1,7-dihydroxy-3,8-dimethoxyxanthone (IV). The structures of these compounds were established on the basis of single crystal X-ray diffraction. The xanthone nucleus conformation is essentially planar with the substituents adopting the orientations less sterically hindered. In addition, classical intermolecular hydrogen bonds (O–H···O) present in III and IV give rise to infinite ribbons. However, the xanthone I does not present any intermolecular hydrogen bonds, meanwhile the xanthone II presents only a non-classical one (C–H···O). The crystal packing of all xanthone structures is also stabilized by π–π interactions. The fingerprint plots, derived from the Hirshfeld surfaces, exhibited significant features of each crystal structures.     

Azabicyclo[3.3.1]nonanone: a case when weak interactions are preferred over strong hydrogen bonds

Derivatives of azabicyclo[3.3.1]nonanone tend to prefer for weak interactions in the crystal over strong N–H···O hydrogen bonds. The main stabilizing forces in the investigated azatricyclo[7.3.1.0^2,7]trideca-trienone derivatives are C–H···O, N–H···π and C–H···π interactions, leading to interesting structural patterns. The azabicyclo[3.3.1]nonanone ring adopts chair-envelope conformation having exo-C2,C4-aromatic substituents. Amino NH is in trigonal pyramidal configuration. The interesting stereochemistry of azabicyclo[3.3.1]nonanone, driving exceptional preference for weaker interactions over strong hydrogen bonds serves a useful example toward engineering and design strategy, and structure prediction methodologies.     

Synthesis of some cyclopentenones and crystal structure of 4-hydroxy-3,4-bis(4-methoxyphenyl)-5,5-dimethyl-2-cyclopenten-1-one

Abstract  

Sodium-hydroxide-catalyzed condensation of di-p-methyl- and di-p-methoxybenzil with acetone derivatives was investigated in methanol. Di- and trisubstituted products were obtained as cyclopentenones, while tetraaryl-substituted systems were isolated as cyclopentadienones. The structures of the products were identified by elemental analysis, infrared (IR), nuclear magnetic resonance (¹H NMR), and mass spectroscopy. The solid-state structure of 4-hydroxy-3,4-bis(4-methoxyphenyl)-5,5-dimethyl-2-cyclopenten-1-one was further studied by single-crystal X-ray diffraction analysis. The title compound crystallizes in an orthorhombic space group and intermolecular O–H···O and C–H···O hydrogen bonds stabilize the crystal lattice.     

Four complexes with a bulky carboxylate ligand: syntheses,crystal structures,and luminescent properties

Abstract  

Four complexes of 3,3-diphenylpropanoate (L) and 4,4′-bipyridine as auxiliary bridging ligands were synthesized and characterized, namely [Zn(L)₂(4bpy)(EtOH)₂]_∞ (1), [Co(L)₂(4bpy)(EtOH)₂]_∞ (2), [Ni(L)₂(4bpy)(EtOH)₂]_∞ (3), and [Cu(L)₂(4bpy)(H₂O)]_∞ (4) (4bpy = 4,4′-bipyridine). X-ray single-crystal diffraction analyses show that complexes 1–4 all take one-dimensional (1D) fishbone-like structures incorporating bridging 4bpy ligands. The complexes show different supramolecular frameworks interlinked via intermolecular hydrogen bonds, π···π stacking, and/or C–H···π supramolecular interactions. Complex 3 only has a simple one-dimensional fishbone-like chain, whereas complexes 1 and 2 show two-dimensional supramolecular structures by interchain C–H···O hydrogen bonds. Complex 4 is assembled into two-dimensional layers and then an overall three-dimensional framework by a combination of interchain O–H···O hydrogen bonds and C–H···π supramolecular interactions. The luminescent properties of the ligands and their complexes were investigated.     

X-ray crystal structures of halogen containing nucleobase derivatives in unsolvated and DMSO solvated forms

A series of halogenated nucleobase derivatives 1–4 is reported to yield solvent-free (2) and DMSO solvated crystals (1, 3, 4) on the crystallization from DMSO with one of them (4) containing an additional molecule of water. The molecular and crystal structures are described and comparatively discussed with reference to previous results on related compounds. The molecule of 1 is planar, molecules of 2 and 3 show syn alignment with reference to the heterocyclic ring and common C2′-endo conformation of the ribose residue, while 4 is also syn aligned but C4′-exo in the sugar conformation. The packing structures reveal typical aggregations created via networks of hydrogen bonds. These involve conventional N–H···N, N–H···O and O–H···O interactions between nucleobase and ribose units as well as solvent molecules, additionally supported by weak C–H···O contacts but excluding the participation of halogen···halogen interactions as well as halogen···heteroatom contacts in the supramolecular structure formation.     

Synthesis,crystal structure and other properties of the complexes of Er(III), Yb(III) and Lu(III) with 4,4′-bipyridine and dichloroacetates

A novel mixed-ligand complexes of Er(III), Yb(III) and Lu(III) with title ligands were prepared and characterized by chemical and elemental analysis and IR spectroscopy, conductivity (in methanol, dimethyloformamide and dimethylsulphoxide). The thermal properties of complexes in the solid state were studied. The mode of metal–ligand coordination was discussed. The title compounds are isomorphic and isostructural in solid state. All atoms in studied compounds lie in general positions but occurrence of inversion on the midpoint of the bond linking two pyridine rings leads to existence in asymmetric unit one complex molecule and half of outer coordination sphere 4-bpy molecule. All chelating carboxylate groups are symmetrically bonded to the metal cations. The molecules of studied compounds are connected to the three dimensional network via O–H···O and O–H···N intermolecular hydrogen bonds. In the structures also exist C–H···O, C–H···Cl weak hydrogen bonds and π····π stacking interactions.     

Intramolecular S···O chalcogen bond in thioindirubin

Results of X-ray diffraction study and quantum-chemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C–H···O and S···O interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (σ-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C–S bonds. One of these σ-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of σ-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using “Atoms in Molecules” (AIM) theory. Energies of the C–H···O hydrogen bond and the S···O σ-hole bond derived from AIM and NBO theories are very close.