Home About us Contact
|
Home About us Contact | ||
|
|
||
Hydrogen-bonded Chains (hydrogen-bonded + chain)
Kinds of Hydrogen-bonded Chains Selected AbstractsN -(3- tert -Butyl-1-phenyl-1H -pyrazol-5-yl)- N -(4-methoxybenzyl)acetamide: a hydrogen-bonded chain of centrosymmetric ringsACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010Juan C. Castillo The molecule of the title compound, C23H27N3O2, adopts a conformation having no internal symmetry so that the compound exhibits conformational chirality. The molecules are linked by a combination of C,H...O and C,H...,(arene) hydrogen bonds into a chain of rings in which two types of centrosymmetric ring alternate. [source] A simple hydrogen-bonded chain in (3Z)-3-{1-[(5-phenyl-1H -pyrazol-3-yl)amino]ethylidene}-4,5-dihydrofuran-2(3H)-one, and a hydrogen-bonded ribbon of centrosymmetric rings in the self-assembled adduct (3Z)-3-{1-[(5-methyl-1H -pyrazol-3-yl)amino]ethylidene}-4,5-dihydrofuran-2(3H)-one,6-(2-hydroxyethyl)-2,5-dimethylpyrazolo[1,5- a]pyrimidin-7(4H)-one (1/1)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2010Jairo Quiroga (3Z)-3-{1-[(5-Phenyl-1H -pyrazol-3-yl)amino]ethylidene}-4,5-dihydrofuran-2(3H)-one, C15H15N3O2, (I), and the stoichiometric adduct (3Z)-3-{1-[(5-methyl-1H -pyrazol-3-yl)amino]ethylidene}-4,5-dihydrofuran-2(3H)-one,6-(2-hydroxyethyl)-2,5-dimethylpyrazolo[1,5- a]pyrimidin-7(4H)-one (1/1), C10H13N3O2·C10H13N3O2, (II), in which the two components have the same composition but different constitutions, are formed in the reactions of 2-acetyl-4-butyrolactone with 5-amino-3-phenyl-1H -pyrazole and 5-amino-3-methyl-1H -pyrazole, respectively. In each compound, the furanone component contains an intramolecular N,H...O hydrogen bond. The molecules of (I) are linked into a chain by a single intermolecular N,H...O hydrogen bond, while in (II), a combination of one O,H...N hydrogen bond, within the selected asymmetric unit, and two N,H...O hydrogen bonds link the molecular components into a ribbon containing alternating centrosymmetric R44(20) and R66(22) rings. [source] A novel trinuclear zinc(II) cluster with a tetrahedral ZnO4 coreACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Orde Q. Munro The reaction of 0.67 molar equivalents of the O,N,O,-tridentate zwitterionic Schiff base (2Z,4E)-4-[(2-hydroxyphenyl)iminio]pent-2-en-2-olate (H2L) with one equivalent of zinc(II) acetate in methanol affords a novel trinuclear ZnII cluster, di-,-acetato-1:2,2O:O,;2:3,2O:O,-dimethanol-1,O,3,O -bis{,-2-[(2E,3Z)-4-oxidopent-3-en-2-ylideneamino]phenolato}-1:2,4O2,N,O4:O4;2:3,4O4:O2,N,O4 -trizinc(II), [Zn3(C11H11NO2)2(C2H3O2)2(CH4O)2], (I), in which two bridging acetate ligands link the terminal square-based pyramidal ZnII ions to the approximately tetrahedral ZnII ion at the core of the cluster. The ZnO4 coordination group of the central ZnII ion is established by two bridging phenolate and two bridging acetate O atoms. The remaining four coordination sites of each terminal ZnII ion are occupied by methanol and deprotonated H2L. Furthermore, the Zn-bound methanol hydroxyl groups are involved in complementary hydrogen bonding with the Zn-bound enolate O atom of a neighbouring molecule, about an inversion centre in each case. The structure of (I) is therefore best described as an extended one-dimensional hydrogen-bonded chain of trinuclear ZnII clusters. [source] Conformational and configurational disorder in 6-(3,4,5-trimethoxyphenyl)-6,7-dihydro-5H -1,3-dioxolo[4,5- g]quinolin-8(5H)-one and 6-(1,3-benzodioxol-5-yl)-6,7-dihydro-5H -1,3-dioxolo[4,5- g]quinolin-8-one: a hydrogen-bonded chain of rings and ,-stacked hydrogen-bonded chainsACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Paola Cuervo In 6-(3,4,5-trimethoxyphenyl)-6,7-dihydro-5H -1,3-dioxolo[4,5- g]quinolin-8(5H)-one, C19H19NO6, (I), the six-membered heterocyclic ring adopts a conformation intermediate between envelope and half-chair forms; it is disordered over two enantiomeric configurations, with occupancies of 0.879,(3) and 0.121,(3), leading to positional disorder of the 3,4,5-trimethoxyphenyl unit. In 6-(1,3-benzodioxol-5-yl)-6,7-dihydro-5H -1,3-dioxolo[4,5- g]quinolin-8-one, C17H13NO5, (II), the molecules are similarly disordered, with occupancies of 0.866,(4) and 0.134,(4). The molecules in (I) are linked by one three-centre N,H...(O)2 hydrogen bond and one two-centre C,H...O hydrogen bond to form a complex chain of rings whose formation is reinforced by two independent aromatic ,,, stacking interactions. In (II), a single N,H...O hydrogen bond links the molecules into a simple chain, and pairs of chains are linked by a single aromatic ,,, stacking interaction. [source] Reversible phase transition of pyridinium-3-carboxylic acid perchlorateACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Heng-Yun Ye Pyridinium-3-carboxylic acid perchlorate was synthesized and separated as crystals. Differential scanning calorimetry (DSC) measurements show that this compound undergoes a reversible phase transition at ,,135,K with a wide hysteresis of 15,K. Dielectric measurements confirm the transition at ,,127,K. Measurement of the unit-cell parameters versus temperature shows that the values of the c axis and , angle change abruptly and remarkably at 129,(2),K, indicating that the system undergoes a first-order transition at Tc = 129,K. The crystal structures determined at 103 and 298,K are all monoclinic in P21/c, showing that the phase transition is isosymmetric. The crystal contains one-dimensional hydrogen-bonded chains of the pyridinium-3-carboxylic acid cations, which are further linked to perchlorate anions by hydrogen bonds to form well separated infinite planar layers. The most distinct differences between the structures of the higher-temperature phase and the lower-temperature phase are the change of the distance between the adjacent pyridinium ring planes within the hydrogen-bonded chains and the relative displacement between the hydrogen-bonded layers. Structural analysis shows that the driving force of the transition is the reorientation of the pyridinium-3-carboxylic acid cations. The degree of order of the perchlorate anions may be a secondary order parameter. [source] Precursor effects of the orthorhombic to monoclinic phase transition in benzocaine form (II) revealed by X-ray diffuse scatteringACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010E. J. Chan We described the development of a Monte Carlo computer model for the room-temperature form (II) polymorph of benzocaine that incorporates, on a local scale, structural features derived from the low-temperature form (III) polymorph. The introduction of this extra information convincingly reproduces those observed diffraction features that an earlier harmonic model was unable to achieve. In both form (I) and form (II) the hydrogen-bonded chains of molecules that extend along the respective a axes tend to slide backward and forward along their lengths. While in form (I) the motion is well modelled by a harmonic potential in form (II) there is a degree of anharmonicity that means that some intermolecular contact vectors, which are identical in the average structure, are distributed bimodally with either longer or shorter vectors being preferred to the average. Moreover there is a tendency for these deviations from average to be correlated to give short-range ordered domains that are the precursors of the two twinned variants of the long-range ordered low-temperature form (III) structure. [source] Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2000W. D. Samuel Motherwell The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of ,,,,, 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If , approaches ,60° and , 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks. [source] 1-(6-Amino-1,3-benzodioxol-5-yl)-3-(2-oxo-1,2-dihydroquinolin-3-yl)prop-2-enone: a sheet built by ,-stacking of hydrogen-bonded chains of ringsACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2010Rodrigo Abonía The bond distances in the molecule of the title compound, C19H14N2O4, provide evidence for electronic polarization in the aminoarylpropenone fragment and for bond fixation in the quinolinone unit. Molecules are linked by N,H...O and C,H...O hydrogen bonds into chains in which centrosymmetric rings of R22(8) and R22(18) types alternate, and these chains are linked into sheets by a single aromatic ,,, stacking interaction. [source] Hydrogen bonding and ,,, interactions in 1-benzofuran-2,3-dicarboxylic acid and its 1:1 cocrystals with pyridine, phenazine and 1,4-phenylenediamineACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009Hatem M. Titi The structure of 1-benzofuran-2,3-dicarboxylic acid (BFDC), C10H6O5, (I), exhibits an intramolecular hydrogen bond between one ,COOH group and the other, while the second carboxyl function is involved in intermolecular hydrogen bonding to neighbouring species. The latter results in the formation of flat one-dimensional hydrogen-bonded chains in the crystal structure, which are ,,, stacked along the normal to the plane of the molecular framework, forming a layered structure. 1:1 Cocrystallization of BFDC with pyridine, phenazine and 1,4-phenylenediamine is associated with H-atom transfer from BFDC to the base and charge-assisted hydrogen bonding between the BFDC, monoanion and the corresponding ammonium species, while preserving, in all cases, the intramolecular hydrogen bond between the carboxyl and carboxylate functions. The pyridinium 2-carboxylato-1-benzofuran-3-carboxylic acid, C5H6N+·C10H5O5,, (II), and phenazinium 3-carboxylato-1-benzofuran-2-carboxylic acid, C12H9N2+·C10H5O5,, (III), adducts form discrete hydrogen-bonded ion-pair entities. In the corresponding crystal structures, the two components are arranged in either segregated or mixed ,,, stacks, respectively. On the other hand, the structure of 4-aminoanilinium 2-carboxylato-1-benzofuran-3-carboxylic acid, C6H9N2+·C10H5O5,, (IV), exhibits an intermolecular hydrogen-bonding network with three-dimensional connectivity. Moreover, this fourth structure exhibits induction of supramolecular chirality by the extended hydrogen bonding, leading to a helical arrangement of the interacting moieties around 21 screw axes. The significance of this study is that it presents the first crystallographic characterization of pure BFDC, and manifestation of its cocrystallization with a variety of weakly basic amine molecules. It confirms the tendency of BFDC to preserve its intramolecular hydrogen bond and to prefer a monoanionic form in supramolecular association with other components. The aromaticity of the flat benzofuran residue plays an important role in directing either homo- or heteromolecular ,,, stacking in the first three structures, while the occurrence of a chiral architecture directed by multiple hydrogen bonding is the dominant feature in the fourth. [source] Four differently substituted 2-aryl-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepines: hydrogen-bonded structures in one, two and three dimensionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Sandra L. Gómez In (2RS,4SR)-7-chloro-2- exo -(2-chloro-6-fluorophenyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C16H12Cl2FNO, (I), molecules are linked into chains by a single C,H...,(arene) hydrogen bond. (2RS,4SR)-2- exo -(2-Chloro-6-fluorophenyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C16H13ClFNO, (II), is isomorphous with compound (I) but not strictly isostructural with it, as the hydrogen-bonded chains in (II) are linked into sheets by an aromatic ,,, stacking interaction. The molecules of (2RS,4SR)-7-methyl-2- exo -(4-methylphenyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C18H19NO, (III), are linked into sheets by a combination of C,H...N and C,H...,(arene) hydrogen bonds. (2S,4R)-2- exo -(2-Chlorophenyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C16H14ClNO, (IV), crystallizes as a single enantiomer and the molecules are linked into a three-dimensional framework structure by a combination of one C,H...O hydrogen bond and three C,H...,(arene) hydrogen bonds. [source] Seven 5-benzylamino-3- tert -butyl-1-phenyl-1H -pyrazoles: unexpected isomorphisms, and hydrogen-bonded supramolecular structures in zero, one and two dimensionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009Juan C. Castillo 5-Benzylamino-3- tert -butyl-1-phenyl-1H -pyrazole, C20H23N3, (I), and its 5-[4-(trifluoromethyl)benzyl]-, C21H22F3N3, (III), and 5-(4-bromobenzyl)-, C20H22BrN3, (V), analogues, are isomorphous in the space group C2/c, but not strictly isostructural; molecules of (I) form hydrogen-bonded chains, while those of (III) and (V) form hydrogen-bonded sheets, albeit with slightly different architectures. Molecules of 3- tert -butyl-5-(4-methylbenzylamino)-1-phenyl-1H -pyrazole, C21H25N3, (II), are linked into hydrogen-bonded dimers by a combination of N,H...,(arene) and C,H...,(arene) hydrogen bonds, while those of 3- tert -butyl-5-(4-chlorobenzylamino)-1-phenyl-1H -pyrazole, C20H22ClN3, (IV), form hydrogen-bonded chains of rings which are themselves linked into sheets by an aromatic ,,, stacking interaction. Simple hydrogen-bonded chains built from a single N,H...O hydrogen bond are formed in 3- tert -butyl-5-(4-nitrobenzylamino)-1-phenyl-1H -pyrazole, C20H22N4O2, (VI), while in 3- tert -butyl-5-(3,4,5-trimethoxybenzylamino)-1-phenyl-1H -pyrazole, C23H29N3O3, (VII), which crystallizes with Z, = 2 in the space group P, pairs of molecules are linked into two independent centrosymmetric dimers, one generated by a three-centre N,H...(O)2 hydrogen bond and the other by a two-centre N,H...O hydrogen bond. [source] 3-{[4-Amino-6-methoxy-2-(methylsulfanyl)pyrimidin-5-yl]amino}-1,2,-biindenylidene-1,,3,-dione dimethyl sulfoxide solvate: ,-stacked sheets of hydrogen-bonded chains of edge-fused ringsACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Fabián Orozco In the title compound, C24H18N4O3S·C2H6OS, the biindenylidene component shows evidence of polarization of the electronic structure. The dimethyl sulfoxide solvent molecules are disordered over two sites, and they are linked to the biindenylidenedione components via N,H...O and C,H...O hydrogen bonds. A combination of N,H...N and N,H...O hydrogen bonds links the nonsolvent components into a chain of edge-fused centrosymmetric R22(8) and R22(22) rings, and these chains are linked into sheets by a single aromatic ,,, stacking interaction. [source] Zero-, one- and two-dimensional hydrogen-bonded structures in the 1:1 proton-transfer compounds of 4,5-dichlorophthalic acid with the monocyclic heteroaromatic Lewis bases 2-aminopyrimidine, nicotinamide and isonicotinamideACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Graham Smith The structures of the anhydrous 1:1 proton-transfer compounds of 4,5-dichlorophthalic acid (DCPA) with the monocyclic heteroaromatic Lewis bases 2-aminopyrimidine, 3-(aminocarbonyl)pyridine (nicotinamide) and 4-(aminocarbonyl)pyridine (isonicotinamide), namely 2-aminopyrimidinium 2-carboxy-4,5-dichlorobenzoate, C4H6N3+·C8H3Cl2O4,, (I), 3-(aminocarbonyl)pyridinium 2-carboxy-4,5-dichlorobenzoate, C6H7N2O+·C8H3Cl2O4,, (II), and the unusual salt adduct 4-(aminocarbonyl)pyridinium 2-carboxy-4,5-dichlorobenzoate,methyl 2-carboxy-4,5-dichlorobenzoate (1/1), C6H7N2O+·C8H3Cl2O4,·C9H6Cl2O4, (III), have been determined at 130,K. Compound (I) forms discrete centrosymmetric hydrogen-bonded cyclic bis(cation,anion) units having both R22(8) and R12(4) N,H...O interactions. In (II), the primary N,H...O-linked cation,anion units are extended into a two-dimensional sheet structure via amide,carboxyl and amide,carbonyl N,H...O interactions. The structure of (III) reveals the presence of an unusual and unexpected self-synthesized methyl monoester of the acid as an adduct molecule, giving one-dimensional hydrogen-bonded chains. In all three structures, the hydrogen phthalate anions are essentially planar with short intramolecular carboxyl,carboxylate O,H...O hydrogen bonds [O...O = 2.393,(8),2.410,(2),Å]. This work provides examples of low-dimensional 1:1 hydrogen-bonded DCPA structure types, and includes the first example of a discrete cyclic `heterotetramer.' This low dimensionality in the structures of the 1:1 aromatic Lewis base salts of the parent acid is generally associated with the planar DCPA anion species. [source] Halide salts of antimigraine agents eletriptan and naratriptanACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2008K. Ravikumar Molecules of eletriptan hydrobromide monohydrate (systematic name: (1S,2R)-1-methyl-2-{5-[2-(phenylsulfonyl)ethyl]-1H -indol-3-ylmethyl}pyrrolidinium bromide monohydrate), C22H27N2O2S+·Br,·H2O, (I), and naratriptan hydrochloride (systematic name: 1-methyl-4-{5-[2-(methylsulfamoyl)ethyl]-1H -indol-3-yl}piperidinium chloride), C17H26N3O2S+·Cl,, (II), adopt conformations similar to other triptans. The C-2 and C-5 substituents of the indole ring, both of which are in a region of conformational flexibility, are found to be oriented on either side of the indole ring plane in (I), whilst they are on the same side in (II). The N atom in the C-2 side chain is protonated in both structures and is involved in the hydrogen-bonding networks. In (I), the water molecules create helical hydrogen-bonded chains along the c axis. In (II), the hydrogen bonding of the chloride ions results in macrocyclic R42(20) and R42(24) ring motifs that form sheets in the bc plane. This structural analysis provides an insight into the molecular structure,activity relationships within this class of compound, which is of use for drug development. [source] Azetidine, pyrrolidine and hexamethyleneimine at 170,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2008Andrew D. Bond The crystal structures of the cyclic amines azetidine (C3H7N), pyrrolidine (C4H9N) and hexamethyleneimine (homopiperidine, C6H13N), of the series (CH2)nNH, with n = 3, 4 and 6, respectively, have been determined at 170,K, following in situ crystallization from the melt. These structures provide crystallographic data to complete the homologous series of cyclic amines (CH2)nNH, for n = 2,6. Azetidine and pyrrolidine contain chains propagating along 21 screw axes, in which the molecules are linked by co-operative N,H...N hydrogen bonds. Azetidine has two molecules in its asymmetric unit, while pyrrolidine has only one. Hexamethyleneimine contains tetrameric hydrogen-bonded rings formed about crystallographic inversion centres, with two molecules in its asymmetric unit. The observation of crystallographically distinct molecules in the hydrogen-bonded chains of azetidine and cyclic hydrogen-bonded motifs in hexamethyleneimine is consistent with expectations derived from comparison with monoalcohols forming chains or rings by co-operative O,H...O hydrogen bonds. The next member of the cyclic amine series, heptamethyleneimine, forms a cubic plastic phase on cooling from the melt. [source] Does the Surface Matter?CHEMPHYSCHEM, Issue 17 2008Hydrogen-Bonded Chain Formation of an Oxalic Amide Derivative in a Two-, Three-Dimensional Environment Abstract We report on a multi-technique investigation of the supramolecular organisation of N,N -diphenyl oxalic amide under differently dimensioned environments, namely three-dimensional (3D) in the bulk crystal, and in two dimensions on the Ag(111) surface as well as on the reconstructed Au(111) surface. With the help of X-ray structure analysis and scanning tunneling microscopy (STM) we find that the molecules organize in hydrogen-bonded chains with the bonding motif qualitatively changed by the surface confinement. In two dimensions, the chains exhibit enantiomorphic order even though they consist of a racemic mixture of chiral entities. By a combination of the STM data with near-edge X-ray absorption fine-structure spectroscopy, we show that the conformation of the molecule adapts such that the local registry of the functional group with the substrate is optimized while avoiding steric hindrance of the phenyl groups. In the low coverage case, the length of the chains is limited by the Au(111) reconstruction lines restricting the molecules into fcc stacked areas. A kinetic Monte Carlo simulated annealing is used to explain the selective assembly in the fcc stacked regions. [source] | ||||||||||