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Hydrogen-bonding Motif (hydrogen-bonding + motif)
Selected AbstractsHydrogen-bonding motifs in 4-carboxyphenylammonium nitrate and perchlorate monohydrate, and in bis(4-carboxyphenylammonium) sulfateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2006S. Athimoolam In the title compounds, C7H8NO2+·NO3,, (I), C7H8NO2+·ClO4,·H2O, (II), and 2C7H8NO2+·SO42,, (III), the carboxyl planes of the 4-carboxyphenylammonium cations are twisted from the aromatic plane. A homonuclear C(8) hydrogen-bonding motif of 4-carboxyphenylammonium cations is observed in both (I) and (II), leading to `head-to-tail' layers. The cations in (III) form carboxyl group dimers, making a graph-set motif of R22(8). In all the structures, anions connect the cationic layers and an infinite chain running along the c axis is observed, having the C22(6) graph-set motif. Interestingly, in (II), the anions are connected through weak hydrogen bonds involving the water molecules, leading to a graph-set motif of R44(12). Alternate hydrophobic and hydrophilic layers are observed in all three compounds as a result of the column-like arrangement of the aromatic rings of the cations and the anions. Furthermore, in (I), head-to-tail N,H,O interactions and interactions linking the cations and anions form an R64(16) hydrogen-bonding motif, resulting in a pseudo-inversion centre at (, , 0). [source] Blind crystal structure prediction of a novel second polymorph of 1-hydroxy-7-azabenzotriazoleACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2006Harriott Nowell The commercially available peptide coupling reagent 1-hydroxy-7-azabenzotriazole has been shown to crystallize in two polymorphic forms. The two polymorphs differ in their hydrogen-bonding motif, with form I having an (10) dimer motif and form II having a C(5) chain motif. The previously unreported form II was used as an informal blind test of computational crystal structure prediction for flexible molecules. The crystal structure of form II has been successfully predicted blind from lattice-energy minimization calculations following a series of searches using a large number of rigid conformers. The structure for form II was the third lowest in energy with form I found as the global minimum, with the energy calculated as the sum of the ab initio intramolecular energy penalty for conformational distortion and the intermolecular lattice energy which is calculated from a distributed multipole representation of the charge density. The predicted structure was sufficiently close to the experimental structure that it could be used as a starting model for crystal structure refinement. A subsequent limited polymorph screen failed to yield a third polymorphic form, but demonstrated that alcohol solvents are implicated in the formation of the form I dimer structure. [source] S,S -1,2-Dicyclohexylethane-1,2-diol and its racemic compound: a striking exception to Wallach's ruleACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2006Brian O. Patrick The structures of enantiopure S,S -1,2-dicyclohexylethane-1,2-diol and its racemic compound (rac - S,S -1,2-dicyclohexylethane-1,2-diol) have been determined at 295 and 173,K. The crystals of the enantiopure material are more than 4% denser than the crystals of the racemic compound, but the melting points indicate that the crystals of the less dense racemic compound are considerably more stable than those of the racemic conglomerate. This apparent exception to the correlation of crystal density and melting point is explained. The enantiopure crystals have four molecules in the asymmetric unit (Z, = 4). Two of the molecules have the conformation observed for the one independent molecule of the racemic compound and two have a higher energy conformation; the overall P21 structure is a perturbed version of a P212121 structure with Z, = 2. The enantiopure and racemic crystals have the same hydrogen-bonding motif, but the motif in the former appears to be significantly strained. A reason why crystals of enantiopure material might be systematically less dense than crystals of its racemic compound and to be more likely to have Z, > 1 is suggested. [source] Hydrogen bonding in enantiomeric versus racemic mono-carboxylic acids; a case study of 2-phenoxypropionic acidACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2003Henning Osholm Sørensen The structural and thermodynamic backgrounds for the crystallization behaviour of racemates have been investigated using 2-phenoxypropionic acid (PPA) as an example. The racemate of PPA behaves normally and forms a racemic compound that has a higher melting point and is denser than the enantiomer. Low-temperature crystal structures of the pure enantiomer, the enantiomer cocrystallized with n -alkanes and the racemic acid showed that hydrogen-bonded dimers that form over crystallographic symmetry elements exist in all but the structure of the pure enantiomer. A database search for optically pure chiral mono-carboxylic acids revealed that the hydrogen-bonded cyclic dimer is the most prevalent hydrogen-bond motif in chiral mono-carboxylic acids. The conformation of PPA depends on the hydrogen-bond motif; the antiplanar conformation relative to the ether group is associated with a catemer hydrogen-bonding motif, whereas the more abundant synplanar conformation is found in crystals that contain cyclic dimers. Other intermolecular interactions that involve the substituent of the carboxylic group were identified in the crystals that contain the cyclic dimer. This result shows how important the nature of the substituent is for the crystal packing. The differences in crystal packing have been related to differences in melting enthalpy and entropy between the racemic and enantiomeric acids. In a comparison with the equivalent 2-(4-chlorophenoxy)-propionic acids, the differences between the crystal structures of the chloro and the unsubstituted acid have been identified and related to thermodynamic data. [source] Modulating the preferred O,H...O hydrogen-bonding motif in a conformationally constrained environment through hydroxy-group derivatizationACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010Goverdhan Mehta The crystal structures of three conformationally locked esters, namely the centrosymmetric tetrabenzoate of all-axial perhydronaphthalene-2,3,4a,6,7,8a-hexaol, viz.trans -4a,8a-dihydroxyperhydronaphthalene-2,3,6,7-tetrayl tetrabenzoate, C38H34O10, and the diacetate and dibenzoate of all-axial perhydronaphthalene-2,3,4a,8a-tetraol, viz. (2R*,3R*,4aS*,8aS*)-4a,8a-dihydroxyperhydronaphthalene-2,3-diyl diacetate, C14H22O6, and (2R*,3R*,4aS*,8aS*)-4a,8a-dihydroxyperhydronaphthalene-2,3-diyl dibenzoate, C24H26O6, have been analyzed in order to examine the preference of their supramolecular assemblies towards competing inter- and intramolecular O,H...O hydrogen bonds. It was anticipated that the supramolecular assembly of the esters under study would adopt two principal hydrogen-bonding modes, namely one that employs intermolecular O,H...O hydrogen bonds (mode 1) and another that sacrifices those for intramolecular O,H...O hydrogen bonds and settles for a crystal packing dictated by weak intermolecular interactions alone (mode 2). Thus, while the molecular assembly of the two crystalline diacyl derivatives conformed to a combination of hydrogen-bonding modes 1 and 2, the crystal packing in the tetrabenzoate preferred to follow mode 2 exclusively. [source] Hydrogen-bonding motifs in 4-carboxyphenylammonium nitrate and perchlorate monohydrate, and in bis(4-carboxyphenylammonium) sulfateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2006S. Athimoolam In the title compounds, C7H8NO2+·NO3,, (I), C7H8NO2+·ClO4,·H2O, (II), and 2C7H8NO2+·SO42,, (III), the carboxyl planes of the 4-carboxyphenylammonium cations are twisted from the aromatic plane. A homonuclear C(8) hydrogen-bonding motif of 4-carboxyphenylammonium cations is observed in both (I) and (II), leading to `head-to-tail' layers. The cations in (III) form carboxyl group dimers, making a graph-set motif of R22(8). In all the structures, anions connect the cationic layers and an infinite chain running along the c axis is observed, having the C22(6) graph-set motif. Interestingly, in (II), the anions are connected through weak hydrogen bonds involving the water molecules, leading to a graph-set motif of R44(12). Alternate hydrophobic and hydrophilic layers are observed in all three compounds as a result of the column-like arrangement of the aromatic rings of the cations and the anions. Furthermore, in (I), head-to-tail N,H,O interactions and interactions linking the cations and anions form an R64(16) hydrogen-bonding motif, resulting in a pseudo-inversion centre at (, , 0). [source] Supramolecular hydrogen-bonded networks in adeninediium hemioxalate chloride and adeninium semioxalate hemi(oxalic acid) monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Balasubramanian Sridhar In 9H -adenine-1,7-diium hemioxalate chloride, C5H7N52+·0.5C2O42,·Cl,, (I), adenine is doubly protonated, while in 7H -adenin-1-ium semioxalate hemi(oxalic acid) monohydrate, C5H6N5+·C2HO4,·0.5C2H2O4·H2O, (II), adenine and one oxalate anion are both monoprotonated. In (I), the adeninium cation forms R22(8) and R12(5) hydrogen-bonding motifs with the centrosymmetric oxalate anion, while in (II), the cation forms R21(6) and R12(5) motifs with the centrosymmetric oxalic acid molecule and R12(5)and R22(9) motifs with the monoprotonated oxalate anion. Linear hydrogen-bonded trimers are observed in (I) and (II). In both structures, the hydrogen bonds lead to the formation of two-dimensional supramolecular hydrogen-bonded sheets in the crystal packing. The significance of this study lies in the analysis of the interactions occurring via hydrogen bonds and the diversity seen in the supramolecular hydrogen-bonded networks as a result of such interactions. [source] Bis[2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium] dl -malateACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009S. Franklin Racemic malic acid and trimethoprim [5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine] form a 1:2 salt (monoclinic, P21/c), 2C14H19N4O3+·C4H4O52,, in which the malate component is disordered across a centre of inversion. The crystal structure of the salt consists of protonated trimethoprim residues and a malate dianion. The carboxylate group of the malate ion interacts with the trimethoprim cation in a linear fashion through pairs of N,H...O hydrogen bonds to form a cyclic hydrogen-bonded motif. This is similar to the carboxylate,trimethoprim cation interaction observed earlier in the complex of dihydrofolate reductase with trimethoprim. The structure of the salt of trimethoprim with racemic dl -malic acid reported here is the first of its kind. The present study investigates the conformations and the hydrogen-bonding interactions, which are very important for biological functions. The pyrimidine plane makes a dihedral angle of 78.08,(7)° with the benzene ring of the trimethoprim cation. The cyclic hydrogen-bonded motif observed in this structure is self-organized, leading to novel types of hydrogen-bonding motifs in supramolecular patterns. [source] | ||||||||||