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Hydrogen-bonded Structures (hydrogen-bonded + structure)
Selected AbstractsPhenyl-ring rotational disorder in the two-dimensional hydrogen-bonded structure of the 1:1 proton-transfer salt of the diazo-dye precursor 4-(phenyldiazenyl)aniline (aniline yellow) with l -tartaric acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Graham Smith In the structure of the 1:1 proton-transfer compound from the reaction of l -tartaric acid with the azo-dye precursor aniline yellow [4-(phenyldiazenyl)aniline], namely 4-(phenyldiazenyl)anilinium (2R,3R)-3-carboxy-2,3-dihydroxypropanoate, C12H12N3+·C4H5O6,, the asymmetric unit contains two independent 4-(phenyldiazenyl)anilinium cations and two hydrogen l -tartrate anions. The structure is unusual in that all four phenyl rings of the two cations have identical rotational disorder with equal occupancy of the conformations. The two hydrogen l -tartrate anions form independent but similar chains through head-to-tail carboxyl,carboxylate O,H...O hydrogen bonds [graph set C(7)], which are then extended into a two-dimensional hydrogen-bonded sheet structure through hydroxy O,H...O hydrogen-bonded links. The anilinium groups of the 4-(phenyldiazenyl)anilinium cations are incorporated into the sheets and also provide internal hydrogen-bonded extensions, while their aromatic tails are layered in the structure without significant association except for weak ,,, interactions [minimum ring centroid separation = 3.844,(3),Å]. The hydrogen l -tartrate residues of both anions exhibit the common short intramolecular hydroxy,carboxylate O,H...O hydogen bonds. This work provides a solution to the unusual disorder problem inherent in the structure of this salt, as well as giving another example of the utility of the hydrogen tartrate anion in the generation of sheet substructures in molecular assembly processes. [source] An ice-like water hexamer with symmetry in the hydrogen-bonded structure of 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Huan Xu An ice-like hexameric water cluster, stabilized by the flexible bis-imidazolyl compound 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene (Fbix), is found in the trigonal R crystal structure of the title compound, C14H10F4N4·2H2O or Fbix·2H2O. The Fbix molecule lies about an inversion centre with one water molecule in the asymmetric unit in a general position. A cyclic chair-like hexameric water cluster with symmetry is generated with a hydrogen-bonded O...O distance within the hexamer of 2.786,(3),Å. The Fbix molecule adopts a trans conformation, where the imidazole ring makes a dihedral angle of 70.24,(11)° with the central tetrafluorinated aromatic ring. Each water hexamer is connected by six Fbix molecules through intermolecular O,H...N hydrogen bonds [N...O = 2.868,(3),Å] to yield a three-dimensional supramolecular network with primitive cubic (pcu) topology. Large voids in each single pcu network lead to fourfold interpenetrated aggregates of Fbix·2H2O. [source] Directed anisotropy in bis(acetato-,2O,O,)diaquazinc(II) at 110 and 250,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009Martin Lutz The molecule of the title compound, [Zn(C2H3O2)2(H2O)2], is located on a twofold axis in the crystal structure. The displacement parameters and the thermal expansion of the crystal show significant anisotropy. This is explained by the two-dimensional hydrogen-bonded structure, with only very weak interactions perpendicular to it. Besides the overall molecular motion, there are internal vibrations, which cause the Zn,O(carboxylate) bonds to fail the Hirshfeld rigid-bond test. It is shown that this can be interpreted in terms of the steric strain in the four-membered chelate ring due to the bidentate carboxylate coordination. [source] Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water,BIOPOLYMERS, Issue 2 2005Earle Stellwagen Abstract The free solution mobilities of single- and double-stranded DNA molecules of various molecular weights have been measured by capillary electrophoresis in solutions of constant ionic strength containing a common anion and fifteen different monovalent cations. In solutions with the same ionic composition, the mobilities of different DNA molecules can vary by up to 20%, depending on molecular weight, the number of strands, and the presence or absence of A-tracts, runs of four or more contiguous adenine residues. Importantly, the mobilities observed for the same DNA sample can vary by up to 40% in solutions containing different cations. The mobility differences observed for the same DNA in solutions containing different cations cannot be rationalized by differences in the anhydrous radii or intrinsic conductivities of the various cations, or by the sequence-dependent binding of certain cations to A-tracts. Instead, the observed mobilities are linearly correlated with the average number of water,water hydrogen bonds that are present in solutions containing different cations. The mobilities are also correlated with the viscosity B coefficients of the various cations and with the rotational correlation times frictional coefficients observed for water molecules in solutions containing different cations. Hence, monovalent cations modify the free solution mobility of DNA primarily by perturbing the hydrogen-bonded structure of water, affecting the friction experienced by the migrating DNA molecules during electrophoresis. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 62,68, 2005 [source] Low-dimensional hydrogen-bonded structures in the 1:1 and 1:2 proton-transfer compounds of 4,5-dichlorophthalic acid with the aliphatic Lewis bases triethylamine, diethylamine, n -butylamine and piperidineACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Graham Smith The structures of the proton-transfer compounds of 4,5-dichlorophthalic acid (DCPA) with the aliphatic Lewis bases triethylamine, diethylamine, n -butylamine and piperidine, namely triethylaminium 2-carboxy-4,5-dichlorobenzoate, C6H16N+·C8H3Cl2O4,, (I), diethylaminium 2-carboxy-4,5-dichlorobenzoate, C4H12N+·C8H3Cl2O4,, (II), bis(butanaminium) 4,5-dichlorobenzene-1,2-dicarboxylate monohydrate, 2C4H12N+·C8H2Cl2O42,·H2O, (III), and bis(piperidinium) 4,5-dichlorobenzene-1,2-dicarboxylate monohydrate, 2C5H12N+·C8H2Cl2O42,·H2O, (IV), have been determined at 200,K. All compounds have hydrogen-bonding associations, giving discrete cation,anion units in (I) and linear chains in (II), while (III) and (IV) both have two-dimensional structures. In (I), a discrete cation,anion unit is formed through an asymmetric R12(4),N+,H...O2 hydrogen-bonding association, whereas in (II), chains are formed through linear N,H...O associations involving both aminium H-atom donors. In compounds (III) and (IV), the primary N,H...O-linked cation,anion units are extended into a two-dimensional sheet structure via amide,carboxyl N,H...O and amide,carbonyl N,H...O interactions. In the 1:1 salts (I) and (II), the hydrogen 4,5-dichlorophthalate anions are essentially planar with short intramolecular carboxyl,carboxyl O,H...O hydrogen bonds [O...O = 2.4223,(14) and 2.388,(2),Å, respectively]. This work provides a further example of the uncommon zero-dimensional hydrogen-bonded DCPA,Lewis base salt and the one-dimensional chain structure type, while even with the hydrate structures of the 1:2 salts with the primary and secondary amines, the low dimensionality generally associated with 1:1 DCPA salts is also found. [source] 5-Amino-1-benzoyl-3-methylpyrazole: complex sheets built from N,H...N, C,H...O and C,H...,(arene) hydrogen bondsACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Jairo Quiroga Molecules of the title compound [systematic name: (5-amino-3-methylpyrazol-1-yl)(phenyl)methanone], C11H11N3O, contain an intramolecular hydrogen bond. The molecules are linked into sheets by a combination of N,H...N, C,H...O and C,H...,(arene) hydrogen bonds. Comparisons are made with the hydrogen-bonded structures of some related compounds. [source] Three-dimensional hydrogen-bonded structures in the 1:1 proton-transfer compounds of l -tartaric acid with the associative-group monosubstituted pyridines 3-aminopyridine, 3-carboxypyridine (nicotinic acid) and 2-carboxypyridine (picolinic acid)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2010Graham Smith The 1:1 proton-transfer compounds of l -tartaric acid with 3-aminopyridine [3-aminopyridinium hydrogen (2R,3R) -tartrate dihydrate, C5H7N2+·C4H5O6,·2H2O, (I)], pyridine-3-carboxylic acid (nicotinic acid) [anhydrous 3-carboxypyridinium hydrogen (2R,3R)-tartrate, C6H6NO2+·C4H5O6,, (II)] and pyridine-2-carboxylic acid [2-carboxypyridinium hydrogen (2R,3R)-tartrate monohydrate, C6H6NO2+·C4H5O6,·H2O, (III)] have been determined. In (I) and (II), there is a direct pyridinium,carboxyl N+,H...O hydrogen-bonding interaction, four-centred in (II), giving conjoint cyclic R12(5) associations. In contrast, the N,H...O association in (III) is with a water O-atom acceptor, which provides links to separate tartrate anions through Ohydroxy acceptors. All three compounds have the head-to-tail C(7) hydrogen-bonded chain substructures commonly associated with 1:1 proton-transfer hydrogen tartrate salts. These chains are extended into two-dimensional sheets which, in hydrates (I) and (III) additionally involve the solvent water molecules. Three-dimensional hydrogen-bonded structures are generated via crosslinking through the associative functional groups of the substituted pyridinium cations. In the sheet struture of (I), both water molecules act as donors and acceptors in interactions with separate carboxyl and hydroxy O-atom acceptors of the primary tartrate chains, closing conjoint cyclic R44(8), R34(11) and R33(12) associations. Also, in (II) and (III) there are strong cation carboxyl,carboxyl O,H...O hydrogen bonds [O...O = 2.5387,(17),Å in (II) and 2.441,(3),Å in (III)], which in (II) form part of a cyclic R22(6) inter-sheet association. This series of heteroaromatic Lewis base,hydrogen l -tartrate salts provides further examples of molecular assembly facilitated by the presence of the classical two-dimensional hydrogen-bonded hydrogen tartrate or hydrogen tartrate,water sheet substructures which are expanded into three-dimensional frameworks via peripheral cation bifunctional substituent-group crosslinking interactions. [source] Different hydrogen-bonded structures in three 2-thienyl-substituted tetrahydro-1,4-epoxy-1-benzazepinesACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Maria C. Blanco The molecules of (2RS,4SR)-2- exo -(5-bromo-2-thienyl)-7-chloro-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C14H11BrClNOS, (I), are linked into cyclic centrosymmetric dimers by C,H...,(thienyl) hydrogen bonds. Each such dimer makes rather short Br...Br contacts with two other dimers. In (2RS,4SR)-2- exo -(5-methyl-2-thienyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C15H15NOS, (II), a combination of C,H...O and C,H...,(thienyl) hydrogen bonds links the molecules into chains of rings. A more complex chain of rings is formed in (2RS,4SR)-7-chloro-2- exo -(5-methyl-2-thienyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C15H14ClNOS, (III), built from a combination of two independent C,H...O hydrogen bonds, one C,H...,(arene) hydrogen bond and one C,H...,(thienyl) hydrogen bond. [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] Different hydrogen-bonded structures in the isomeric solvates 2-amino-6-anilino-4-methoxy-5-[(E)-4-nitrobenzylideneamino]pyrimidine dimethyl sulfoxide solvate and 2-amino-6-[methyl(phenyl)amino]-5-[(E)-4-nitrobenzylideneamino]pyrimidin-4(3H)-one dimethyl sulfoxide solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Ricaurte Rodríguez The title solvates, (I) and (II), both C18H16N6O3·C2H6OS, are isomeric. The conformations adopted by the 6-substituent are significantly different, with the 6-aminophenyl unit remote from the nitrophenyl ring in methoxypyrimidine (I) but adjacent to it in pyrimidinone (II). Pairs of pyrimidine molecules in (I) are linked by N,H...N hydrogen bonds to form cyclic centrosymmetric dimers from which the dimethyl sulfoxide molecules are pendent, while in (II) a combination of three independent N,H...O hydrogen bonds links the components into a chain containing both R22(8) and R42(8) rings, in which the dimethyl sulfoxide component acts as a double acceptor of hydrogen bonds. The significance of this study lies in its observation of different conformations for the pyrimidine components in (I) and (II), and different hydrogen-bonded structures, apparently dominated by the different roles adopted by the dimethyl sulfoxide components. [source] | ||||||||||