Importance of halide involving interactions at Hoogsteen sites in supramolecular architectures of some coordination metal complexes of N(6)-benzyl/furfuryl adenine

A third polymorph of the zwitterionic complex trichlorido-((dimethylphosphoryl)methanaminium-κO)zinc(II)

By the reaction of (dimethylphosphoryl)methanamine (dpma) with one equivalent of zinc(II) chloride in a concentrated hydrochloric acid solution and subsequent slow evaporation of the solvent, the title compound (dpmaH)ZnCl3 was obtained in quantitative yield. The primary reaction product mainly consists of larger brick-shaped colorless and smaller cuboide colorless crystals. Long-time storage over several months of these crystals in the mother liquor yielded a third polymorph (P21/n; a = 9.6639(1); b = 10.0271(1); c = 11.2446(1) Å; β = 98.964(1)°) of this compound. Similar to the two other modifications, its crystal structure consists of a zwitterionic dpmaHZnCl3 complex containing the cationic dpmaH+ ligand, which coordinates the zinc atom through its oxygen atom. Hydrogen bonds connect neighboring zwitterionic complexes to a layered structure. The motif of a hydrogen bonded dimer, similar to that found in the chain structure of polymorph I, is also present, but in the title structure these dimers form hydrogen bonds in two dimensions.

Does H3O+ Really Act as a Ligand in the Solid State?

The evidence for the existence of metal complexes containing H₃O⁺ as a ligand in the solid state is examined. Each of the 68 examples in the Cambridge Structural Database in which H₃O⁺ is bound to a transition metal, lanthanoid, actinoid, or main group metal ion is detailed and critically appraised. It is concluded that none of the reported examples of complexes containing coordinated H₃O⁺ have been unequivocally characterized and that they result from either curation errors or misinterpretations of the crystallographic data. These conclusions are supported by computational techniques, which show that three purported H₃O⁺ complexes based on the 1,4,7,10,13,16,21,24-octa-azabicyclo(8.8.8)hexacosane azacryptand skeleton are better described as aqua complexes, with protonation occurring at the amine ligand.

Crystal structures of N6-modified-amino acid nucleobase analogs(iii): adenine–valeric acid, adenine–hexanoic acid and adenine–gabapentine

H-bonding networks, anion–π and π–π interactions in the crystal structures of N⁶-modified-amino acid adenine analogs are investigated by means of DFT calculations and X-ray crystallography analysis.

Crystal structures of N6-modified-amino acid related nucleobase analogs (II): hybrid adenine-β-alanine and adenine-GABA molecules

H-Bonding networks and anion–π interactions in the crystal structures of N⁶-modified-amino acid adenine analogs are investigated using X-ray crystallography and DFT calculations.

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine

Three new metal(II)-cytosine (Cy)/5-fluorocytosine (5FC) complexes, namely bis(4-amino-1,2-dihydropyrimidin-2-one-κN³)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI₂(C₄H₅N₃O)₂], (I), bis(4-amino-1,2-dihydropyrimidin-2-one-κN³)bis(nitrato-κ²O,O')cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO₃)₂(C₄H₅N₃O)₂], (II), and (6-amino-5-fluoro-1,2-dihydropyrimidin-2-one-κN³)aquadibromidozinc(II)-6-amino-5-fluoro-1,2-dihydropyrimidin-2-one (1/1) or (6-amino-5-fluorocytosine)aquadibromidozinc(II)-4-amino-5-fluorocytosine (1/1), [ZnBr₂(C₄H₅FN₃O)(H₂O)]·C₄H₅FN₃O, (III), have been synthesized and characterized by single-crystal X-ray diffraction. In complex (I), the Cd^II ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr₂(C₄H₅N₃O)₂] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. In compound (II), each of the two cytosine molecules coordinates to the Cd^II ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N-H...O hydrogen bond involving two cytosine molecules is also present. In compound (III), one zinc-coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The Zn^II atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)-H tautomer of 5FC mimics N(3)-protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R₂²(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a-axis direction, forming the rungs of a ladder motif, whereas Zn-Br bonds and N-H...Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O-H...O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound (III), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N-H...O, N-H...N, O-H...O, N-H...I and N-H...Br hydrogen bonds, and stacking interactions.

Crystal structures of N6-modified-aminoacid/peptide nucleobase analogs: hybrid adenine–glycine and adenine–glycylglycine molecules

Anion–π interactions in crystal structures of N⁶-modified-aminoacid and dipeptide adenine analogs are investigated using X-ray crystallography and DFT calculations.

Crystal structure of a compact three-dimensional metal-organic framework based on Cs+ and (4,5-di-cyano-1,2-phenyl-ene)bis-(phospho-nic acid)

A new metal-organic framework compound, poly[[μ7-dihydrogen (4,5-di-cyano-1,2-phenyl-ene)diphospho-nato]-(oxonium)caesium], [Cs(C8H4N2O6P2)(H3O)] n (I), based on Cs+ and the organic linker 4,5-di-cyano-1,2-phenyl-ene)bis-(phospho-nic acid, (H4cpp), containing two distinct coordinating functional groups, has been prepared by a simple diffusion method and its crystal structure is reported. The coordination polymeric structure is based on a CsO8N2 complex unit comprising a monodentate hydro-nium cation, seven O-atom donors from two phospho-nium groups of the (H2cpp)2- ligand, and two N-atom donors from bridging cyano groups. The high level of connectivity from both the metal cation and the organic linker allow the formation of a compact and dense three-dimensional network without any crystallization solvent. Topologically (I) is a seven-connected uninodal network with an overall Schäfli symbol of {417.64}. Metal cations form an undulating inorganic layer, which is linked by strong and highly directional O-H⋯O hydrogen-bonding inter-actions. These metallic layers are, in turn, connected by the organic ligands along the [010] direction to form the overall three-dimensional framework structure.

Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate

In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

Supramolecular hydrogen-bonding patterns in two cocrystals of the N(7)–H tautomeric form ofN6-benzoyladenine:N6-benzoyladenine–3-hydroxypyridinium-2-carboxylate (1/1) andN6-benzoyladenine–DL-tartaric acid (1/1)

Two novel cocrystals of the N(7)—H tautomeric form ofN6-benzoyladenine (BA), namelyN6-benzoyladenine–3-hydroxypyridinium-2-carboxylate (3HPA) (1/1), C12H9N5O·C6H5NO3, (I), andN6-benzoyladenine–DL-tartaric acid (TA) (1/1), C12H9N5O·C4H6O6, (II), are reported. In both cocrystals, theN6-benzoyladenine molecule exists as the N(7)—H tautomer, and this tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the benzoyl C=O group and the N(7)—H hydrogen on the Hoogsteen site of the purine ring, forming anS(7) motif. The dihedral angle between the adenine and phenyl planes is 0.94 (8)° in (I) and 9.77 (8)° in (II). In (I), the Watson–Crick face of BA (N6—H and N1; purine numbering) interacts with the carboxylate and phenol groups of 3HPA through N—H...O and O—H...N hydrogen bonds, generating a ring-motif heterosynthon [graph setR22(6)]. However, in (II), the Hoogsteen face of BA (benzoyl O atom and N7; purine numbering) interacts with TA (hydroxy and carbonyl O atoms) through N—H...O and O—H...O hydrogen bonds, generating a different heterosynthon [graph setR22(4)]. Both crystal structures are further stabilized by π–π stacking interactions.