Structure and Chemical Analysis of Major Specialized Metabolites Produced by the Lichen Evernia prunastri.

We performed comparative profiling of four specialized metabolites in the lichen Evernia prunastri, collected at three different geographic locations, California and Maine, USA, and Yoshkar Ola, Mari El, Russia. Among the compounds produced at high concentrations that were identified in all three specimens, evernic acid, usnic acid, lecanoric acid and chloroatranorin, evernic acid was the most abundant. Two depsidones, salazinic acid and physodic acid, were detected in the Yoshkar-Ola collection only. The crystalline structure of evernic acid (2-hydroxy-4-[(2-hydroxy-4-methoxy-6-methylbenzoyl)oxy]-6-methylbenzoate) (hmb) revealed two crystallographically and conformationally distinct hmb anions, along with two monovalent sodium atoms. One hmb moiety contained an exotetradentate binding mode to sodium, whereas the other exhibited an exohexadentate binding mode to sodium. Embedded edge-sharing {Na2 O8 }n sodium-oxygen chains connected the hmb anions into the full three-dimensional crystal structure of the title compound. The crystal used for single-crystal X-ray diffraction exhibited non-merohedral twinning. The data suggest the importance of the acetyl-polymalonyl pathway products to processes of maintaining integrity of the lichen holobiont community.

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-[(pyridin-4-yl)methanone]-4,4'-oxydi-benzoic acid (1/1).

In the title co-crystal, C25H32N4O2·C14H10O5, mol-ecules are connected into supra-molecular chains aligned along [102] by O-H⋯N hydrogen bonding. These aggregate into supra-molecular layers oriented parallel to (20-1) by C-H⋯O inter-actions. These layers then stack in an ABAB pattern along the c crystal direction to give the full three-dimensional crystal structure. The central chain in the dipyridylamide has an anti-anti conformation. The dihedral angle between the aromatic ring planes is 29.96 (3)°. Disorder is noted in some of the residues in the structure and this is manifested in two coplanar dispositions of one statistically disordered carb-oxy-lic acid group.

Poly[[di-aqua-[µ-1,4-bis(pyridin-4-ylmeth-yl)piperazine-κ(2) N:N']{µ-2,2'-[(1,4-phenyl-ene)bis(-oxy)]di-acetato-κ(2) O:O'}cobalt(II)] penta-hydrate].

In the title compound, {[Co(C10H8O6)(C16H20N4)(H2O)2]·5H2O} n , octa-hedrally coordinated Co(II) ions on crystallographic inversion centres are bound by trans O atoms belonging to two hydro-quinone-O,O'-di-acetate (hqda) anions {systematic name: 2,2'-[(1,4-phenyl-ene)bis-(-oxy)]di-acetate}, two trans-pyridine N-donor atoms from two bis-(pyridin-4-ylmeth-yl)piperazine (4-bpmp) ligands, and two trans aqua ligands. The exobidentate hqda and 4-bpmp ligands form [Co(hqda)(4-bpmp)(H2O)2] n coordination polymer layers parallel to (110) that are anchored into the full crystal structure by O-H⋯O hydrogen bonding between aqua ligands and ligated hqda O atoms. Disordered water mol-ecules of crystallization occupy incipient channels along [100]. However, these could not modeled reliably and so they were treated with SQUEEZE in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155]; the crystal data take the presence of these mol-ecules into account. The crystal under investigation was twinned by non-merohedry, the twin fraction of the components being 53.3% and 46.7%. Only data from the major twin component were used in the refinement.

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-[(pyridin-4-yl)methanone]-isophthalic acid (1/1).

In the crystal structure of the title co-crystal, C25H32N4O2·C8H6O4, isophthalic acid and [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-(pyridin-4-yl-methanone) mol-ecules are connected into supra-molecular chains aligned along the c axis by O-H⋯N hydrogen bonding. These aggregate into supra-molecular layers oriented parallel to the ac plane by C-H⋯O inter-actions. These layers then stack in an ABCD pattern along the b-axis direction by additional C-H⋯O inter-actions to give the full three-dimensional crystal structure. The central chain in the di-pyridyl-amide molecule has an anti-gauche conformation.

Bis(5-hy-droxy-isophthalato-κO (1))bis-[4-(pyridine-3-carboxamido-κN (3))pyridinium]copper(II) tetra-hydrate.

In the title compound, [Cu(C11H10N3O)2(C8H4O5)2]·4H2O, the Cu(II) ion, located on a crystallographic inversion center, is coordinated in a square-planar environment by two trans-O atoms belonging to two monodentate 5-hy-droxy-isophthalate (hip) dianions and two trans nicotinamide pyridyl N-donor atoms from monodentate protonated pendant N-(pyridin-4-yl)nicotinamide (4-pnaH) ligands. The protonated 4-pyridyl-amine groups engage in N-H(+)⋯O(-) hydrogen-bond donation to unligated hip O atoms to construct supra-molecular chain motifs parallel to [100]. Water mol-ecules of crystallization, situated between the chains, engage in O-H⋯O hydrogen bonding to form supra-molecular layers and the overall three-dimensional network structure.

Poly[[(µ3-adamantane-1,3-di-acetato)[µ-N-(pyridin-3-yl)isonicotinamide]-nickel(II)] monohydrate], a layered coordination polymer with triangular (3,6) topology.

The title compound, {[Ni(C14H18O4)(C11H9N3O)]·H2O}n, contains octa-hedrally coordinated NiII ions ligated by 1,3-adamantanedi-acetato (ada) ligands and N-(pyridin-3-yl)isonicotinamide (3-pina) ligands, to form coordination polymer layers with a triangular (3,6) grid topology based on [Ni2(OCO)2] dimeric units. The diperiodic layer motifs stack in an ABAB pattern mediated by C-H⋯O supra-molecular inter-actions between ada ligands and water mol-ecules of crystallization to form the full triperiodic crystal structure of the title compound.

Poly[[[µ-1,4-bis-(pyridin-4-ylmeth-yl)piperazine][µ-4-(2-carboxyl-atoeth-yl)benzoato]copper(II)] monohydrate], a coordination polymer with twofold inter-penetrated cds topology networks.

The title compound, {[Cu(C10H8O4)(C16H20N4)]·H2O}n, contains square-planar coordinated CuII ions linked by 4-(carboxyl-atoeth-yl)benzoato (ceb) and 1,4-bis-(pyridin-4-ylmeth-yl)piperazine (bpmp) ligands into a tri-periodic coordination polymer with twofold inter-penetrating 658 cds topology. Positional crystallographic disorder among the copper atoms, the ethyl-carb-oxy group of the ceb ligands, and the water mol-ecules of crystallization exists in a refined 0.655 (6)/0.345 (6) ratio.

Poly[[(µ-aqua)[µ4-4-(carboxyl-atometh-yl)ben-zo-ato]cobalt(II)] hemi[1,4-bis-(pyridin-4-ylmeth-yl)piper-azine] hemihydrate].

In the title com-pound, {[Co(C9H6O4)(H2O)]·0.5C16H20N4·0.5H2O}n, two-di-men-sional coordination polymer slabs are held together in the three-dimensional crystal structure by means of O-H⋯N hydrogen bonding between bound water mol-ecules and pyridyl N atoms of cocrystallized 1,4-bis-(pyridin-4-yl-meth-yl)piperazine mol-ecules.

Poly[[bis-[µ4-3-(2-carboxyl-atophen-yl)propionato]{N-[2-(pyridine-3-amido)-eth-yl]nicotinamide}-dicopper(II)] penta-hydrate].

In the title compound, {[Cu2(C10H8O4)2(C14H14N4O2)]·5H2O}n, the CuII cations are coordinated in a square-pyramidal fashion, with four 3-(2-carb-oxy-phen-yl)propionate (cpp) carboxyl-ate O-atom donors in the basal plane, along with an N-atom donor from a N-[2-(pyridin-3-yl-amino)-eth-yl]nicotinamide (pen) ligand in the apical position. [Cu2(cpp)2]n coordination polymer layer motifs with embedded {Cu2(OCO)4} paddlewheel clusters are thereby constructed. These layer motifs are connected into a three-dimensional [Cu2(cpp)2(pen)]n coordination polymer network by tethering pen ligands. Treating the {Cu2(OCO)4 paddelwheel clusters as 6-connected nodes reveals an underlying cross-pillared self-penetrated rob network with 48668 topology. The water mol-ecules of crystallization are held to the coordination polymer network by N-H⋯O and O-H⋯O hydrogen-bonding patterns.

Poly[[µ-1,3-bis-(pyridin-3-yl)urea]bis-(µ4-glutarato)dicopper(II)].

The title compound, [Cu2(C5H6O4)2(C11H10N4O)]n, contains square-pyramidally coordinated CuII ions linked by anti-gauche conformation glutarate (glu) ligands into [Cu2(glu)2]n di-periodic coordination polymer layers with embedded [Cu2(OCO)4] paddlewheel clusters. In turn, the layer motifs are connected by 1,3-di(pyridin-3-yl)urea (3-dpu) linkers to form a [Cu2(glu)2(3-dpu)]n tri-periodic coordination polymer network. Treating the [Cu2(OCO)4] clusters as 6-connected nodes reveals an underlying 41263 pcu topology according to TOPOSPRO software [Blatov et al. (2014 ▸). Cryst. Growth Des. 14, 3576-3586].

Poly[[[µ-1,4-bis-(pyridin-4-ylcarbon-yl)piperazine-κ2N:N'][µ-2-(2-carboxyl-atoeth-1-en-1-yl)benzoato-κ2O:O2]zinc(II)] 2.5 hydrate]: a tri-periodic coordination polymer with a dimer-based six-connected pcu topology.

The title compound, {[Zn(C10H6O4)(C16H16N4O2]·2.5H2O}n, contains five-coordinate ZnII ions inter-mediate between square-pyramidal and trigonal-bipyramidal coordination environments. The ZnII ions are connected by 2-carb-oxy-cinnamate (cca) ligands and N,N'-bis-(pyridine-4-carboxamido)-piperazine (4-pcap) ligands to construct a non-inter-penetrated, tri-periodic coordination polymer with embedded [Zn2(OCO)2] dimeric units. Treating these as six-connected nodes reveals an overall (41263) pcu topology. One of the 4-pcap piperazinyl rings is disordered equally over two sets of crystallographic positions.

Poly[[µ-1,3-bis-(pyridin-3-yl)urea]bis-(µ4-succinato)dicopper(II)], a ribbon-like coordination polymer.

In the title com-pound, [Cu2(C4H4O4)2(C11H10N4O)]n, mono-periodic coordination polymer ribbons are held into the crystal structure by means of N-H⋯O hydrogen bonding and crystal packing forces.

Poly[di-aqua-[µ-1,4-bis-(pyridin-4-ylmeth-yl)pip-era-zine][µ-4-(carboxyl-atoeth-yl)benzoato]nickel(II)].

The title compound, [Ni(C10H8O4)(C16H20N4)(H2O)2]n, contains NiII cations octa-hedrally surrounded within an [O4N2] coordination set. The cations are linked by 4-(carb-oxy-eth-yl)benzoate (ceb) and 1,4-bis-(pyridin-4-ylmeth-yl)piperazine (bpmp) ligands into tri-periodic diamondoid (dia) networks. The fivefold inter-penetrated dia networks are held into the crystal structure by means of O-H⋯O hydrogen bonding between bound water mol-ecules and unligated carboxyl-ate O atoms of the ceb ligands.

catena-Poly[[di-aqua-bis-(1,3-di-hydro-3-oxo-isobenzo-furan-1-acetato)-copper(II)]-µ-N,N'-(ethane-1,2-di-yl)dinicotinamide].

The title compound, {[Cu(C10H7O4)2(C14H14N4O2)(H2O)2]n, contains octa-hed-rally coordinated CuII ions ligated by two bis-(1,3-di-hydro-3-oxo-1-isobenzo-furan-acetate (dibf) ligands and two trans water mol-ecules, linked by N,N'-(ethane-1,2-di-yl)dinicotinamide (edn) ligands into mono-periodic coordination polymer chains. The dibf ligands exhibit a pseudo-mirror positional disorder over two positions in a 89.2 (3)/10.8 (3) ratio; the central amide groups of the edn ligands are disordered pseudo-rotationally in the same ratio. These mono-periodic chain motifs are held into supra-molecular di-periodic supra-molecular layers by means of N-H⋯O hydrogen bonding between edn amide groups and unligated dibf carboxyl-ate O atoms. In turn, the supra-molecular layers are held by crystal packing forces into the full crystal structure of the title compound.

Poly[[(µ3-adamantane-1,3-di-carboxyl-ato)aqua-[µ-N-(pyridin-3-yl)isonicotinamide]-nickel(II)] monohydrate], a layered coordination polymer with (4,4) topology.

The title com-pound, {[Ni(C12H14O4)(C11H9N3O)(H2O)]·H2O}n, contains octa-hedrally coordinated NiII ions ligated by adamantane-1,3-di-carboxyl-ate (adc) and N-(pyridin-3-yl)isonicotinamide (3-pina) ligands forming coordination polymer layers with a (4,4) grid topology. These diperiodic layer motifs aggregate in an AAA pattern mediated by supra-molecular C-H⋯O inter-actions to form the full triperiodic crystal structure of the title com-pound.

Poly[[aqua-[µ2-1,3-bis-(pyridin-4-yl)urea-κ2N4:N4']bis-(µ3-5-tert-butyl-isophthalato-κ3O1:O1':O3)dizinc(II)] trihydrate], a double-strand coordination polymer.

In the title compound, {[Zn2(C12H12O4)2(C11H10N4O)(H2O)]·3H2O}n, monoperiodic coordination polymer double strands are held into the triperiodic crystal structure by means of N-H⋯O hydrogen-bonding patterns between the amide groups of the 1,3-di(pyridin-4-yl)urea ligands and unligated O atoms belonging to 5-tert-butyl-isophthalate ligands. One of the Zn atoms displays a tetra-hedral coordination environment, while the other Zn atom adopts a five-coordinate geometry inter-mediate between square pyramidal and trigonal bipyramidal. Additionally, O-H⋯O hydrogen-bonding patterns involving the water mol-ecules of crystallization serve as a structure-stabilizing element by aggregating the double-strand motifs.

Poly[[[µ3-3-(2-carboxyl-atophen-yl)propionato][µ2-N,N'-(ethane-1,2-di-yl)bis-(pyridine-4-carbox-amide)]copper(II)] monohydrate], a layered coordination polymer with (4,4) topology.

In the title compound, {[Cu(C10H8O4)(C14H14N4O2)]·H2O}n, the CuII cations are coordinated in a square-pyramidal fashion, with trans pyridyl-N donor atoms from two N-(2-(pyridin-3-yl-amino)-eth-yl)isonicotinamide (pein) ligands in the basal plane. The other three coordination sites are taken up by carboxyl-ate O-atom donors from three different 3-(2-carb-oxy-phen-yl)propionate (cpp) ligands. The central ethyl-enedi-amine segments of the pein ligands are disordered equally over two sets of positions. {Cu2O2} rhomboid clusters are connected into [Cu(cpp)(pein)]n (4,4) coordination polymer grids by the full span of the cpp and pein ligands. Individual layer motifs stack in an AAA pattern along the a axis by means of inter-layer hydrogen-bonding inter-actions.

Poly[[µ-1,4-bis-(pyridin-4-ylmeth-yl)piperazine]bis-[µ3-4-(2-carboxyl-atoeth-yl)benzoato]dicopper(II)].

In the title coordination polymer, [Cu2(C9H6O4)2(C16H20N4)]n, the CuII atoms in {NO4} square-pyramidal coordination environments are conjoined into diperiodic coordination polymer slabs by the full span of the bridging 1,4-bis-(pyridin-4-ylmeth-yl)piperazine (bpmp) and 4-(carboxyl-eth-yl)benzoate (ceb) ligands. The slab motifs are expanded into the full crystal structure by means of longer-range C-H⋯O attractive inter-actions.

Poly[bis-[µ2-1,3-bis-(pyridin-4-yl)urea-κ2N4:N4']bis-(µ2-5-methyl-isophthalato-κ2O1:O3)dizinc(II)], a parallel inter-penetrated slab-like coordination polymer with {3.648}{326.728} 4,4-connected binodal topology.

In the title compound, [Zn2(C9H6O4)2(C11H10N4O)2]n, diperiodic coordination polymer slabs with {3.648}{326.728} 4,4-connected binodal topology are held into a parallel inter-penetrated triperiodic crystal structure by means of N-H⋯O hydrogen-bonding patterns.

catena-Poly[[aquabis[N-(pyridin-3-yl)isonicotinamide-κN (1)]copper(II)]-µ-fumarato-κ(2) O (1):O (4)].

In the title compound, [Cu(C4H2O4)(C11H9N3O)2(H2O)] n , Cu(II) ions on crystallographic twofold rotation axes are coordinated in a square pyramidal environment by two trans O atoms belonging to two monodentate fumarate anions, two trans isonicotinamide pyridyl N-donor atoms from monodentate, pendant 3-pyridyl-isonicotinamide (3-pina) ligands, and one apical aqua ligand, also sited on the crystallographic twofold rotation axis. The exobidentate fumarate ligands form [Cu(fumar-ate)(3-pina)2(H2O)] n coordination polymer chains that are arranged parallel to [001]. In the crystal, these polymeric chains are anchored into supra-molecular layers parallel to (100) by O-H⋯O hydrogen bonds between aqua ligands and unligating fumarate O atoms, and N-H⋯O(=C) hydrogen bonds between 3-pina ligands. In turn, the layers aggregate by weak C-H⋯N and C-H⋯O hydrogen bonds, affording a three-dimensional network.