Patterns of hydrogen bonding in mono- and di-substituted N-arylpyrazinecarboxamides

2008 ◽  
Vol 64 (1) ◽  
pp. 84-100 ◽  
Author(s):  
Solange M. S. V. Wardell ◽  
Marcus V. N. de Souza ◽  
Thatyana R. A. Vasconcelos ◽  
Marcelle de L. Ferreira ◽  
James L. Wardell ◽  
...  

The molecular and supramolecular structures of 18 N-arylpyrazinecarboxamides, Ar NHCO(C4H3N2), have been determined, including the stoichiometric monohydrate of N-(3-methoxyphenyl)pyrazinecarboxamide, and two polymorphs of N-(4-fluorophenyl)pyrazinecarboxamide having Z′ values of 1 and 4, respectively. The aryl groups were selected to include the geometric isomers for a compact range of substituents, namely methyl, trifluoromethyl, fluoro, chloro, methoxy and nitro groups, which exhibit markedly varied electronic properties and markedly varied behaviour as hydrogen-bond donors and acceptors. However, not all isomers in each group could be structurally investigated. A small number of derivatives containing disubstituted aryl groups have also been included in this study. The crystal structures of the solvent-free carboxamides reported here exhibit a wide range of direction-specific intermolecular forces, including N—H...N, N—H...O, C—H...N and C—H...O hydrogen bonds, and π...π stacking interactions, while the structure of N-(3-methoxyphenyl)pyrazinecarboxamide monohydrate also contains O—H...N and O—H...O hydrogen bonds. The resulting supramolecular structures can be zero-, one- or two-dimensional, although no three-dimensional supramolecular aggregation has been observed. In the finite, zero-dimensional structures, pairs of molecules are linked by hydrogen bonds to form cyclic centrosymmetric dimers. The one-dimensional structures include chains formed by the π-stacking of otherwise isolated molecules, simple chains generated by either C—H...O or C—H...N hydrogen bonds, and hydrogen-bonded chains of rings. The two-dimensional structures include examples of both π-stacked hydrogen-bonded chains and hydrogen-bonded sheets.

2003 ◽  
Vol 59 (2) ◽  
pp. 248-262 ◽  
Author(s):  
Katharine F. Bowes ◽  
George Ferguson ◽  
Alan J. Lough ◽  
Christopher Glidewell

The structures of seven salts formed by phosphonopropionic acid with organic diamines are reported; in these salts, the hydrogen-bonded substructures formed by the anions can be zero-, one- or two-dimensional, while the overall hydrogen-bonded supramolecular structures are three-dimensional. The 1:1 adduct, compound (1), formed between 1,2-bis(4′-pyridyl)ethene and phosphonopropionic acid is a salt, [{(C12H10N2)H2}2+]·[(C12H10N2)]·[(C3H6O5P)−]2, in which both diamine components lie across centres of inversion in space group P21/c. The anions form hydrogen-bonded head-to-head dimers, and these are linked by the two diamine units into sheets, which are themselves linked by C—H...O hydrogen bonds. With 2,2′-dipyridylamine the acid forms the hydrated salt [{(C10H9N3)H}+]·[(C3H6O5P)−]·H2O (2), in which all components are disordered with occupancy 0.5 in space group Fmm2. The anions form head-to-tail dimers, which are linked into sheets by the cations, and the sheets are linked into a three-dimensional framework by the water molecules. The piperazine salt [{(C4H10N2)H2}2+]·[(C3H5O5P)2−] (3) contains simple anion chains linked into a three-dimensional framework by the two independent cations, both of which are centrosymmetric. In the hydrated salt formed by N,N′-dimethylpiperazine, [{(MeNC4H8NMe)H2}2+]·[(C3H6O5P)−]2·(H2O)2 (4), head-to-tail anion chains combine with the water molecules to form a three-dimensional framework, which encloses voids that contain the cations. In the 4,4′-bipyridyl adduct [{(C10H8N2)H0.72}0.72+]·[{(H0.5O)3PCH2CH2COOH0.78}0.72−] (5), there is extensive disorder of the H atoms that are bonded to N and O atoms, and the anion chains are linked by the cations into sheets, which are themselves linked by C—H...O hydrogen bonds. In the 1:2 adduct formed with 1,2-bis(4′-pyridyl)ethane, [{(C12H12N2)H2}2+]·[(C3H6O5P)−]2 (6), where the cation lies across an inversion centre, the anions form molecular ladders. These ladders are linked into sheets by the cations, which are themselves linked by C—H...O hydrogen bonds. In the methanol-solvated salt formed with 2,6-dimethylpiperazine, [{(C6H14N2)H2}2+]·[(C3H6O5P)−]2· (CH4O)0.34 (7), the anions form sheets that are linked into a three-dimensional framework by the cations. The supramolecular structures are compared with those of analogous salts formed by phosphonoacetic acid.


2004 ◽  
Vol 60 (4) ◽  
pp. 472-480 ◽  
Author(s):  
Christopher Glidewell ◽  
John N. Low ◽  
Janet M. S. Skakle ◽  
Solange M. S. V. Wardell ◽  
James L. Wardell

Molecules of 2-iodo-N-(4-nitrobenzyl)aniline, 4-O2NC6H4CH2NHC6H4I-2′ (1) are linked into chains by C—H...O hydrogen bonds. In the isomeric compound 3-iodo-N-(4-nitrobenzyl)aniline (2) a combination of N—H...O and C—H...O hydrogen bonds and iodo...nitro and aromatic π...π stacking interactions links the molecules into a three-dimensional framework structure. The two-dimensional supramolecular structure of 4-iodo-N-(4-nitrobenzyl)aniline (6) is built from a combination of C—H...O and N—H...π(arene) hydrogen bonds and aromatic π...π stacking interactions. 2-Iodo-N-(2-nitrobenzyl)aniline (7) crystallizes with two molecules in the asymmetric unit and these molecules are linked into ladders by a combination of N—H...O and C—H...O hydrogen bonds and iodo...nitro and aromatic π...π stacking interactions. Comparisons are made between the supramolecular structures of these compounds and those of other isomers, in terms both of the types of direction-specific intermolecular interactions exhibited and the dimensionality of the resulting supramolecular structures.


Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.


2000 ◽  
Vol 56 (2) ◽  
pp. 273-286 ◽  
Author(s):  
Brian O'Leary ◽  
Trevor R. Spalding ◽  
George Ferguson ◽  
Christopher Glidewell

The structure of 1,1,3,3,5,5-hexaphenyltrisiloxane-1,5-diol–pyrazine (4/1), (C36H32O4Si3)4·C4H4N2 (1), contains finite centrosymmetric aggregates; the diol units form dimers, by means of O—H...O hydrogen bonds, and pairs of such dimers are linked to the pyrazine by means of O—H...N hydrogen bonds. In 1,1,3,3,5,5-hexaphenyltrisiloxane-1,5-diol–pyridine (2/3), (C36H32O4Si3)2·(C5H5N)3 (2), the diol units are linked into centrosymmetric pairs by means of disordered O—H...O hydrogen bonds: two of the three pyridine molecules are linked to the diol dimer by means of ordered O—H...N hydrogen bonds, while the third pyridine unit, which is disordered across a centre of inversion, links the diol dimers into a C 3 3(9) chain by means of O—H...N and C—H...O hydrogen bonds. In 1,1,3,3-tetraphenyldisiloxane-1,3-diol–hexamethylenetetramine (1/1), (C24H22O3Si2)·C6H12N4 (3), the diol acts as a double donor and the hexamethylenetetramine acts as a double acceptor in ordered O—H...N hydrogen bonds and the structure consists of C 2 2(10) chains of alternating diol and amine units. In 1,1,3,3-tetraphenyldisiloxane-1,3-diol–2,2′-bipyridyl (1/1), C24H22O3Si2·C10H8N2 (4), there are two independent diol molecules, both lying across centres of inversion and therefore both containing linear Si—O—Si groups: each diol acts as a double donor of hydrogen bonds and the unique 2,2′-bipyridyl molecule acts as a double acceptor, thus forming C 2 2(11) chains of alternating diol and amine units. The structural motif in 1,1,3,3-tetraphenyldisiloxane-1,3-diol–pyrazine (2/1), (C24H22O3Si2)2·C4H4N2 (5), is a chain-of-rings: pairs of diol molecules are linked by O—H...O hydrogen bonds into centrosymmetric R 2 2(12) dimers and these dimers are linked into C 2 2(13) chains by means of O—H...N hydrogen bonds to the pyrazine units. 1,1,3,3-Tetraphenyldisiloxane-1,3-diol–pyridine (1/1), C24H22O3Si2·C5H5N (6), and 1,1,3,3-tetraphenyldisiloxane-1,3-diol–pyrimidine (1/1), C24H22O3Si2·C4H4N2 (7), are isomorphous: in each compound the amine unit is disordered across a centre of inversion. The diol molecules form C(6) chains, by means of disordered O—H...O hydrogen bonds, and these chains are linked into two-dimensional nets built from R 6 6(26) rings, by a combination of O—H...N and C—H...O hydrogen bonds.


2006 ◽  
Vol 62 (4) ◽  
pp. o1529-o1531 ◽  
Author(s):  
Li-Ping Zhang ◽  
Long-Guan Zhu

In the crystal structure of the title organic proton-transfer complex, 2C12H11N2 +·C7H4O5S2−·3H2O, the cations form one-dimensional chains via intermolecular N—H...N hydrogen bonds and these chains, in turn, form a two-dimensional network through π–π stacking interactions. In addition, the anions and water molecules are connected into a two-dimensional hydrogen-bonded network through intermolecular O—H...O hydrogen bonds. The two motifs result in sheets of cations and anions stacked alternately.


Author(s):  
Songwuit Chanthee ◽  
Wikorn Punyain ◽  
Supawadee Namuangrak ◽  
Kittipong Chainok

The crystal structures of the building block tetramethylammonium (2,2′-bipyridine-κ2N,N′)tetracyanidoferrate(III) trihydrate, [N(CH3)4][Fe(CN)4(C10H8N2)]·3H2O, (I), and a new two-dimensional cyanide-bridged bimetallic coordination polymer, poly[[(2,2′-bipyridine-κ2N,N′)di-μ2-cyanido-dicyanido(μ-ethylenediamine-κ2N:N′)(ethylenediamine-κ2N,N′)cadmium(II)iron(II)] monohydrate], [CdFe(CN)4(C10H8N2)(C2H8N2)2]·H2O, (II), are reported. In the crystal of (I), pairs of [Fe(2,2′-bipy)(CN)4]−units (2,2′-bipy is 2,2′-bipyridine) are linked together through π–π stacking between the pyridyl rings of the 2,2′-bipy ligands to form a graphite-like structure parallel to theabplane. The three independent water molecules are hydrogen-bonded alternately with each other, forming a ladder chain structure withR44(8) andR66(12) graph-set ring motifs, while the disordered [N(CH3)4]+cations lie above and below the water chains, and the packing is stabilized by weak C—H...O hydrogen bonds. The water chains are further linked with adjacent sheets into a three-dimensional networkviaO—H...O hydrogen bonds involving the lattice water molecules and the N atoms of terminal cyanide groups of the [Fe(2,2′-bipy)(CN)4]−building blocks, forming anR44(12) ring motif. Compound (II) features a two-dimensional {[Fe(2,2′-bipy)(CN)4Cd(en)2]}nlayer structure (en is ethylenediamine) extending parallel to (010) and constructed from {[Fe(2,2′-bipy)(CN)4Cd(en)]}nchains interlinked by bridging en ligands at the Cd atoms. Classical O—H...N and N—H...O hydrogen bonds involving the lattice water molecule and N atoms of terminal cyanide groups and the N—H groups of the en ligands are observed within the layers. The layers are further connectedviaπ–π stacking interactions between adjacent pyridine rings of the 2,2′-bipy ligands, completing a three-dimensional supramolecular structure.


2016 ◽  
Vol 72 (5) ◽  
pp. 442-450 ◽  
Author(s):  
Ammasai Karthikeyan ◽  
Packianathan Thomas Muthiah ◽  
Franc Perdih

The coordination chemistry of mixed-ligand complexes continues to be an active area of research since these compounds have a wide range of applications. Many coordination polymers and metal–organic framworks are emerging as novel functional materials. Aminopyrimidine and its derivatives are flexible ligands with versatile binding and coordination modes which have been proven to be useful in the construction of organic–inorganic hybrid materials and coordination polymers. Thiophenecarboxylic acid, its derivatives and their complexes exhibit pharmacological properties. Cobalt(II) and copper(II) complexes of thiophenecarboxylate have many biological applications, for example, as antifungal and antitumor agents. Two new cobalt(II) and copper(II) complexes incorporating thiophene-2-carboxylate (2-TPC) and 2-amino-4,6-dimethoxypyrimidine (OMP) ligands have been synthesized and characterized by X-ray diffraction studies, namely (2-amino-4,6-dimethoxypyrimidine-κN)aquachlorido(thiophene-2-carboxylato-κO)cobalt(II) monohydrate, [Co(C5H3O2S)Cl(C6H9N3O2)(H2O)]·H2O, (I), andcatena-poly[copper(II)-tetrakis(μ-thiophene-2-carboxylato-κ2O:O′)-copper(II)-(μ-2-amino-4,6-dimethoxypyrimidine-κ2N1:N3)], [Cu2(C5H3O2S)4(C6H9N3O2)]n, (II). In (I), the CoIIion has a distorted tetrahedral coordination environment involving one O atom from a monodentate 2-TPC ligand, one N atom from an OMP ligand, one chloride ligand and one O atom of a water molecule. An additional water molecule is present in the asymmetric unit. The amino group of the coordinated OMP molecule and the coordinated carboxylate O atom of the 2-TPC ligand form an interligand N—H...O hydrogen bond, generating anS(6) ring motif. The pyrimidine molecules also form a base pair [R22(8) motif]viaa pair of N—H...N hydrogen bonds. These interactions, together with O—H...O and O—H...Cl hydrogen bonds and π–π stacking interactions, generate a three-dimensional supramolecular architecture. The one-dimensional coordination polymer (II) contains the classical paddle-wheel [Cu2(CH3COO)4(H2O)2] unit, where each carboxylate group of four 2-TPC ligands bridges two square-pyramidally coordinated CuIIions and the apically coordinated OMP ligands bridge the dinuclear copper units. Each dinuclear copper unit has a crystallographic inversion centre, whereas the bridging OMP ligand has crystallographic twofold symmetry. The one-dimensional polymeric chains self-assembleviaN—H...O, π–π and C—H...π interactions, generating a three-dimensional supramolecular architecture.


2014 ◽  
Vol 70 (3) ◽  
pp. 315-319 ◽  
Author(s):  
Graham Smith

The structures of ammonium 3,5-dinitrobenzoate, NH4+·C7H3N2O6−, (I), ammonium 4-nitrobenzoate dihydrate, NH4+·C7H4NO4−·2H2O, (II), and ammonium 2,4-dichlorobenzoate hemihydrate, NH4+·C7H3Cl2O2−·0.5H2O, (III), have been determined and their hydrogen-bonded structures are described. All three salts form hydrogen-bonded polymeric structures,viz.three-dimensional in (I) and two-dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph setR43(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′-carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O-carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O-atom acceptors. With structure (II), the primary inter-species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen-bonding motifs,viz.R43(10) (one cation, an O,O′-carboxylate group and two water molecules) and centrosymmetricR42(8) (two cations and two water molecules). The structure of (III) also has conjoinedR43(10) and centrosymmetricR42(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′-carboxylate group, an O-carboxylate group and one water molecule, and the second motif involves two cations and two O-carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two-dimensional layered arrays through conjoined hydrogen-bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three-dimensional structure of (I) is inconsistent with that trend.


1998 ◽  
Vol 54 (2) ◽  
pp. 129-138 ◽  
Author(s):  
G. Ferguson ◽  
C. Glidewell ◽  
R. M. Gregson ◽  
P. R. Meehan

Phenylphosphonic acid–4,4′-bipyridyl (1/1), (1), C6H7O3P.C10H8N2, triclinic, P1¯, a = 6.9026 (8), b = 9.7086 (9), c = 12.201 (2) Å, α = 77.138 (9), β = 74.345 (10), γ = 75.477 (8)°, with Z = 2, is a salt, C10H9N2 +.[C6H5PO2(OH)]−, containing singly protonated 4,4′-bipyridyl cations: the cations and anions are linked by N—H...O and C—H...O hydrogen bonds in an R^{2}_{2}(7) motif and these aggregates are linked into centrosymmetric R^{2}_{2}(8) dimers by O—H...O hydrogen bonds; the dimer units are linked into chains by C—H...O hydrogen bonds. Phenylphosphonic acid–piperazine (2/1), (C6H7O3P)2.C4H10N2 (2), monoclinic, P21/n, a = 6.0042 (9), b = 19.746 (3), c = 8.651 (2) Å, β = 105.63 (2)°, with Z = 2, is a salt, C4H12N2 2+. [{C6H5PO2(OH)}−]2, containing doubly protonated piperazine: the anions are linked by O—H...O hydrogen bonds into centrosymmetric R^{2}_{2}(8) dimers and these dimers are linked to the centrosymmetric cations by N—H...O hydrogen bonds: each cation is hydrogen-bonded to four different anion dimers and each anion dimer is hydrogen-bonded to four different cations; the overall structure consists of two-dimensional sheets built from R^{4}_{6}(16) and R^{4}_{4}(18) rings. Phenylphosphonic acid–1,4-diazabicyclo[2.2.2]octane (2/1), (3), (C6H7O3P)2.C6H12N2, monoclinic, P21/n, a = 6.3607 (3), b = 21.8300 (11), c = 14.5965 (9) Å, β = 92.558 (6)°, with Z = 4, is a salt in which one nitrogen of the diamine is fully protonated and the other is partially protonated: the anionic components are linked into C(4) chains by O—H...O hydrogen bonds, and these chains are cross-linked via the diamines by means of N—H...O and O—H...N hydrogen bonds. The resulting sheets built from R^{8}_{8}(34) rings are linked by C—H...O hydrogen bonds into a three-dimensional framework.


2017 ◽  
Vol 73 (9) ◽  
pp. 674-681 ◽  
Author(s):  
Zouaoui Setifi ◽  
Daniel Zambon ◽  
Fatima Setifi ◽  
Malika El-Ghozzi ◽  
Rachid Mahiou ◽  
...  

Three photoluminescent complexes containing either ZnII or CdII have been synthesized and their structures determined. Bis[4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole-κ2 N 1,N 5]bis(dicyanamido-κN 1)zinc(II), [Zn(C12H10N6)2(C2N3)2], (I), bis[4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole-κ2 N 1,N 5]bis(dicyanamido-κN 1)cadmium(II), [Cd(C12H10N6)2(C2N3)2], (II), and bis[4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole-κ2 N 1,N 5]bis(tricyanomethanido-κN 1)cadmium(II), [Cd(C12H10N6)2(C4N3)2], (III), all crystallize in the space group P\overline{1}, with the metal centres lying on centres of inversion, but neither analogues (I) and (II) nor CdII complexes (II) and (III) are isomorphous. A combination of N—H...N and C—H...N hydrogen bonds and π–π stacking interactions generates three-dimensional framework structures in (I) and (II), and a sheet structure in (III). The photoluminescence spectra of (I)–(III) indicate that the energies of the π–π* transitions in the coordinated triazole ligand are modified by minor changes of the ligand geometry associated with coordination to the metal centres.


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