Intermolecular Hydrogen-bonding Patterns Research Articles

Synthesis and Crystal Structure Analysis of Some Aromatic Imines of Syringaldehyde

A series of syringaldehyde imines with para-substituted anilines have been synthesized in a good yield, and their crystal structures have been analyzed. The orientation of the syringaldehyde hydroxyl group plays in important role in the intermolecular hydrogen-bonding pattern of the molecules. The O–H…N hydrogen bonding interactions primarily determine the three-dimensional packing of the molecules, even though they make up a relatively small percentage of intermolecular interactions in the molecules. The three structures with the p-hydroxy group cis to the imine group give hydrogen-bonded zigzag chains in the monoclinic crystals, while the structure with a trans hydroxy group crystallize in a hexagonal space group (R3¯) and form hydrogen-bonded hexamers. The hexagonal structure also displays Br…Br interactions, forming additional hexameric clusters. The analysis of published p-hydroxyphenyl imine crystal structures from the Cambridge Crystallographic Database revealed patterns in the length of the hydrogen bonding interactions based on steric congestion around the hydroxyl group.

Mechanochemical synthesis and X-ray structural characterization of three 3-nitrophenol cocrystals with three aminal cage azaadamantanes: the role of the stereoelectronic effect on intermolecular hydrogen-bonding patterns.

The structures of the cocrystalline adducts of 3-nitrophenol (3-NP) with 1,3,5,7-tetraazatricyclo[3.3.1.13,7]decane [HMTA, (1)] as the 2:1:1 hydrate, 2C6H5NO3·C6H12N4·H2O, (1a), with 1,3,6,8-tetraazatricyclo[4.3.1.13,8]undecane [TATU (2)] as the 2:1 cocrystal, 2C6H5NO3·C7H14N4, (2a), and with 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane [TATD, (3)] as the 2:1 cocrystal, 2C6H5NO3·C8H16N4, (3a), are reported. In the binary crystals (2a) and (3a), the 3-nitrophenol molecules are linked via O-H...N hydrogen bonds into aminal cage azaadamantanes. In (1a), the structure is stabilized by O-H...N and O-H...O hydrogen bonds, and generates ternary cocrystals. There are C-H...O hydrogen bonds present in all three cocrystals, and in (1a), there are also C-H...O and C-H...π interactions present. The presence of an ethylene bridge in the structures of (2) and (3) defines the formation of a hydrogen-bonded motif in the supramolecular architectures of (2a) and (3a). The differences in the C-N bond lengths of the aminal cage structures, as a result of hyperconjugative interactions and electron delocalization, were analysed. These three cocrystals were obtained by the solvent-free assisted grinding method. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation from a mixture of hexanes.

Characteristic Hydrogen Bonding Observed in the Crystals of Aromatic Sulfonamides: 1D Chain Assembly of Molecules and Chiral Discrimination on Crystallization

N-Phenylbenzenesulfonamides exist preferentially in (+)- or (−)-synclinal conformations, which place the aromatic rings at both ends in the same direction with a twist. We have systematically analyzed the crystal structure of secondary aromatic sulfonamides bearing methyl, ethyl, and/or methoxy groups on the benzene rings. Intermolecular hydrogen bonding between the sulfonamide protons and sulfonyl oxygens was observed in 81 out of 85 crystals. The intermolecular hydrogen-bonding patterns could be classified into four types, i.e. Dimeric, Zigzag, Helical, and Straight patterns, with retention of the synclinal conformation of the sulfonamide moiety. We investigated the relationship between the hydrogen-bonding pattern and the proportion of the compounds that show chiral crystallization. On the basis of our classification of the intermolecular hydrogen bonds of aromatic sulfonamides, the crystals with Dimeric and Zigzag patterns, which both have enantiomeric synclinal conformers, intrinsically become achira...

Extremely short H···H distances and intermolecular hydrogen-bonding patterns of dialkyl α-aryl-α-(diphenylmethylamino)methanephosphonates

GRAPHICAL ABSTRACT

Intermolecular C—F...H—C contacts in the molecular packing of three isostructuralN-(fluorophenyl)mannopyranosylamines

Among the three compounds reported here, namely N-(4-fluorophenyl)-β-D-mannopyranosylamine, (I), N-(3-fluorophenyl)-β-D-mannopyranosylamine, (II), and N-(2-fluorophenyl)-β-D-mannopyranosylamine, (III), all with chemical formula C(12)H(16)FNO(5), (I) and (II) are isostructural, whereas (III) assumes the same packing arrangement as the unfluorinated analogue N-phenyl-β-D-mannopyranosylamine, (IV), which has been reported previously. Similarities with respect to the intermolecular hydrogen-bonding patterns exist across the series (I)-(III). A packing motif that distinguishes the shared packing arrangement of (I) and (II) from that of (III) is a C-F...H-C chain of graph set C(4) that is preserved in the formal exchange of F and H atoms at the 4- and 3-positions on the aromatic ring of (I) and (II), but is replaced by a different chain of graph set C(5) when the F atom is located at the 2-position of the aromatic ring in (III). The steric role of the F atom in (I)-(III) is ambiguous but is examined here in detail.

Methyl 4-O-β-D-galactopyranosyl α-D-mannopyranoside methanol 0.375-solvate

Methyl beta-D-galactopyranosyl-(1-->4)-alpha-D-mannopyranoside methanol 0.375-solvate, C(13)H(24)O(11).0.375CH(3)OH, (I), was crystallized from a methanol-ethanol solvent system in a glycosidic linkage conformation, with varphi' (O5(Gal)-C1(Gal)-O1(Gal)-C4(Man)) = -68.2 (3) degrees and psi' (C1(Gal)-O1(Gal)-C4(Man)-C5(Man)) = -123.9 (2) degrees , where the ring is defined by atoms O5/C1-C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the betaGalp and alphaManp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl alpha-lactoside [methyl beta-D-galactopyranosyl-(1-->4)-alpha-D-glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C61, o674-o677], where varphi' is -93.6 degrees and psi' is -144.8 degrees . An intermolecular hydrogen bond exists between O3(Man) and O5(Gal) in (I), similar to that between O3(Glc) and O5(Gal) in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl alpha-D-mannopyranoside, methyl alpha-D-glucopyranoside and methyl beta-D-galactopyranoside, revealing significant differences in the Cremer-Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen-bonding patterns.

Conformational Flexibility of Tetralactam Macrocycles and Their Intermolecular Hydrogen‐Bonding Patterns in the Solid State

Despite their rigid scaffold, tetralactam macrocycles (TLMs) display a remarkable degree of conformational flexibility, as revealed by analysis of the corresponding X-ray crystal structures. This flexibility is not limited to the rotatability of the TLM amide groups but also applies to the m-xylene rings, and it thus has a great impact on the overall shape of the macrocycle cavity. The conformational properties of the TLMs give rise to a broad variety of intermolecular hydrogen-bonding patterns, including infinite ladders, an interesting catemer motif, and short C-HO=C hydrogen bonds. These results are in accord with previous theoretical calculations, support a structural model proposed earlier for an interpretation of scanning tunneling microscopy images, and substantially contribute to the understanding of the adaptability of macrocyclic scaffolds, which is crucial for guest binding or templated syntheses with TLMs.

Two polymorphs of chlorpropamide: the δ-form and the high-temperature ∊-form

The epsilon-form of chlorpropamide [systematic name: 4-chloro-N-(propylaminocarbonyl)benzenesulfonamide], C(10)H(13)ClN(2)O(3)S, has been obtained as single crystals from solution (and not as a polycrystalline sample by heating the alpha-, gamma- or delta-forms). The results of anisotropic structure refinements for the epsilon- and delta-forms are reported. The density of the delta-polymorph is the highest, and that of the epsilon-polymorph the lowest, among the five known chlorpropamide polymorphs. The main intermolecular hydrogen-bonding pattern in polymorphs delta and epsilon is the same as in polymorphs alpha, beta and gamma, but the conformations differ. The densities of the polymorphs were found to depend on the molecular conformations.

Hydrogen-bond patterns and the structures of 1,4-cyclohexanediol: 2:1 cis:trans-1,4-cyclohexanediol

The structure of a co-crystal with both trans and cis isomers of 1,4-cyclohexanediol (1,4-CHD) is reported. The intermolecular hydrogen-bond patterns are described and compared with those of the all trans structure, using the graph-set model. A second crystal with possible cis/trans disorder is also described. The results of molecular modeling of the simple isomers and conformers are compared with the known structures.

Biosynthesis of bacterial cellulose/multi-walled carbon nanotubes in agitated culture

The morphology of bacterial cellulose (BC) is quite different in the static and agitated culture. In this study, the snow-like cellulose assemblies are synthesized in the agitated culture and the fibrous and rice-like cellulose assemblies are produced in the presence of multi-walled carbon nanotubes (MWNTs) in agitated culture. The microstructure of BC synthesized in agitated culture are investigated by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray diffractometry (XRD). The analysis results reveal that the crystallinity index, crystallite size and cellulose I α content for cellulose synthesized in agitated culture are lower than those for cellulose synthesized in static culture. The agitating stress influences the aggregation and crystallization of sub-elementary fibrils, further changes the intramolecular and intermolecular hydrogen bond patterns. The stress makes greater effect on BC synthesized in the absence of MWNTs than in the presence of MWNTs.

Schiff Base Macrocycles Containing Pyrroles and Pyrazoles

A double nucleophilic substitution reaction of 3,5-bis(chloromethyl)pyrazole with pyrroles generates a novel pyrrole-pyrazole hybrid building block, the pyrazole analogue to tripyrrane. Vilsmeier-Haack formylation produces the corresponding dialdehyde, which was used in the formation of a series of nonaromatic Schiff base macrocycles. NMR and UV/Vis spectroscopy and single-crystal diffractometry were used to characterize the novel macrocycles. The solid-state structures of select free bases and protonated members of this class of macrocycles display a range of intra- and intermolecular hydrogen-bonding patterns that suggest their use in molecular-recognition systems. They also contain an acid-sensitive chromophore. Their acid-base and anion-recognition properties were ascertained; alas, only modest anion-selective spectroscopic signatures could be detected by using UV/Vis and (1)H NMR spectroscopy. The macrocycles proved resistant toward oxidation to their aromatic congeners. The pyrrole-pyrazole building blocks presented are potentially useful for the synthesis of a range of pyrazole analogues of all-pyrrole macrocycles.

Preparation and crystalline analysis of high‐grade bamboo dissolving pulp for cellulose acetate

AbstractHigh grade bamboo dissolving pulp for cellulose acetate (named as acetate bamboo pulp) was prepared from bamboo Cizhu (Dendrocalamus affinnis) by oxygen‐alkali pulping, xylanase and DMD (an intermediate product of the reaction of oxone with acetone) delignification treatments, and H2O2 bleaching. Its properties and structures were investigated by different analytical techniques, and compared with those of high grade hardwood dissolving pulp for cellulose acetate (named as acetate wood pulp), viscose bamboo pulp, and bamboo fiber for textile. Most of its properties are comparable with those of acetate wood pulp except ash contents and DCM (dichloromethane) extractive that are slightly high. Crystallinities and crystalline allomorphs of acetate bamboo pulp and the three samples were determined by FTIR spectroscopy, X‐ray diffraction and solid state 13C NMR spectroscopy, and the results obtained by the three methods were coincident. Bamboo cellulose crystalline allomorphs are classified as Iβ‐dominant type, and a higher lateral order index and a larger crystallite size for acetate bamboo pulp were found in spite of its crystallinity similar to acetate wood pulp. Different intermolecular hydrogen bond patterns are likely be responsible for the predominant crystalline fibrils in acetate bamboo pulp. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008

Polymorphism of N,N′′‐Diacetylbiuret Studied by Solid‐State 13C and 15N NMR Spectroscopy, DFT Calculations, and X‐ray Diffraction

The molecular configuration and crystal structure of solid polycrystalline N,N''-diacetylbiuret (DAB), a potential nitrogen-rich fertilizer, have been analyzed by a combination of solid- and liquid-state NMR spectroscopy, X-ray diffraction, and DFT calculations. Initially a pure NMR study ("NMR crystallography") was performed as available single crystals of DAB were not suitable for X-ray diffraction. Solid-state 13C NMR spectra revealed the unexpected existence of two polymorphic modifications (alpha- and beta-DAB) obtained from different chemical procedures. Several NMR techniques were applied for a thorough characterization of the molecular system, revealing chemical shift anisotropy (CSA) tensors of selected nuclei in the solid state, chemical shifts in the liquid state, and molecular dynamics in the solid state. Dynamic NMR spectroscopy of DAB in solution revealed exchange between two different configurations, which raised the question, is there a correlation between the two different configurations found in solution and the two polymorphic modifications found in the solid state? By using this knowledge, a new crystallization protocol was devised which led to the growth of single crystals suitable for X-ray diffraction. The X-ray data showed that the same symmetric configuration is present in both polymorphic modifications, but the packing patterns in the crystals are different. In both cases hydrogen bonds lead to the formation of planes of DAB molecules. Additional symmetry elements, a two-fold screw in the case of alpha-DAB and a c-glide plane in the case of beta-DAB, lead to a more symmetric (alpha-DAB) or asymmetric (beta-DAB) intermolecular hydrogen-bonding pattern for each molecule.

Trans-Dichlorobis[diphenyl(p-tolyl)phosphine]palladium(II)

The centrosymmetric title compound, [PdCl2(C19H17P)2], crystallizes with a square-planar geometry about the PdII metal centre. The most important bond distances include Pd—P (trans P) of 2.3404 (9) Å and Pd—Cl (trans Cl) of 2.2977 (12) Å. Weak intra- and intermolecular hydrogen bonding is observed in the solid-state structure between the chloro and phenyl H atoms. This weak intermolecular hydrogen-bonding pattern forms a one-dimensional chain along the b axis.

Self-Assembling Characteristics of A New Nonionic Gemini Surfactant

A new class of unusual nonionic gemini surfactant, viz. the bis-amide p-phenylenediamine Boc-bis-glycamide, was synthesized for the first time in our laboratory. The bis-amide is insoluble in water. However, the evidence for micelle formation of this bis-amide in chloroform has been obtained from surface tension, Langmuir film balance, and UV−visible, IR, and fluorescence spectroscopy. The critical micelle concentration (cmc) of this bis-amide, obtained by these techniques, correlates well. Tensiometry gave the cmc value, surface activity, and Gibbs molecular surface area. Film studies on the bis-amide gemini gave limiting areas and collapse pressures. The results of film studies also suggest that the bis-amide forms a stable monolayer film even at low concentrations and the limiting areas obtained at high concentrations (above the cmc value) are in good agreement with the contact area estimated from the theoretically calculated Connolly surface treatments. Both theoretical and experimental results suggest that the bis-amide molecules at high concentrations (above the cmc value) prefer slightly tilted conformations rather than a fully extended conformation at the air/water interface. The aggregation numbers of the bis-amide have also been determined by using both steady-state and time-resolved fluorescence methods, and they are in good agreement with each other. The concentration dependence aggregation number for bis-amide micelles has also been observed, and the results suggest the formation of only small micelles, despite the potential to grow; this is similar to the case for many micellar geminis. Computer simulation techniques show that about 11 molecules of bis-amide can aggregate to form a cluster. The IR spectra of the bis-amide in pre- and postmicellar regions were analyzed; there is no significant change in the intensity of the intermolecular hydrogen-bonding pattern for the bis-amide in the monomeric and micellar states. However, the intensity of the solvent-exposed −N−H stretching band increased as a function of bis-amide concentration after the cmc value was obtained. The fluorescence intensity of ANS in chloroform increases on interaction with bis-amide micelles, suggesting that, even in apolar media, ANS binds to the bis-amide in a region of lower polarity than does the chloroform alone. The pyrene emission intensity ratio of the first vibronic band to the third band as a function of bis-amide concentration suggested the hydrophobic character of bis-amide micelles in chloroform. Since there is no trace amount of water present in the system and the aggregate formation of the bis-amide is in the presence of pure chloroform solvent only, the species may be considered an inverted micelle. Steady-state fluorescence results suggest that 66% of the total pyrene emission is accessible to quenching in bis-amide micelles in chloroform. On the basis of lifetime measurements, the bimolecular quenching rate constant of the pyrene by CPC quencher in bis-amide micelles was found to be (1.4 ± 0.3) × 107 M-1 s-1, which is due to collisional quenching by strongly partitioning quenchers.

Complementarity of halide-mediated hydrogen-bonding and alkyl substitution in the construction of two-dimensional rhombic (4,4) grids using bis(N-alkylamidino-O-alkylurea)copper(ii) halides

A series of hydrogen-bonded networks based on bis(N-alkylamidino-O-alkylurea)copper(II) cations, [CuL2]2+, bridged by either chloride or bromide have been synthesised, of which six have been structurally characterised by single crystal X-ray diffraction methods. The [CuL2]2+ cation acts as a four-connecting centre and forms 2-D rhombic (4,4) grids for the majority of the compounds studied. However, the grids do not adopt a common intermolecular hydrogen-bonding pattern. Three distinct systems can be differentiated: one mediated solely by halide anions, a second mediated by protic solvent molecules as well as halide anions, and a third with no intermolecular interactions. There is evidence for complementarity in (4,4) rhombic grids mediated solely by halide anions, as grid formation only occurs when there is a match between the size of the cavity formed within the grid and the space required by the pendant alkyl groups of the N-alkylamidino-O-alkylurea ligands. Such complementarity occurs for [Cu(Lmm)2]·2Cl (Lmm = N-methylamidino-O-methylurea) and [Cu(Lme)2]·2Br (Lme = N-methylamidino-O-ethylurea). Chloride bridges generate a cavity which can accommodate four juxtaposed methyl groups while bromide bridges generate a cavity large enough to accommodate two methyl and two ethyl groups. Rhombic (4,4) grid formation based on simple halide bridges does not take place for [Cu(Lmm)2]·2Br·2MeOH, [Cu(Lee)2]·2Cl·H2O (Lee = N-ethylamidino-O-ethylurea), [Cu(Lee)2]·2Br·MeOH or [Cu(L2m)2]·2Cl·2MeOH (L2m = N-benzylamidino-O-methylurea). The cavity generated by bromide bridges is too large for the four methyl groups of [Cu(Lmm)2]2+ cations. To overcome this problem and still form a (4,4) grid, the hydrogen-bonding assembly in [Cu(Lmm)2]·2Br·2MeOH incorporates a methanol molecule. The spatial requirements of the four ethyl groups of the [Cu(Lee)2]2+ cations are greater than can be provided by either of the grids generated by chloride or bromide bridges. Consequently, 1-D chains rather than 2-D rhombic (4,4) grids are formed. The cavity required to accommodate two benzyl groups and two methyl groups of the [Cu(L2m)2]2+ cations is far larger than can be provided by chloride bridges. Hence, although the disposition of copper(II) centres in [Cu(L2m)2]·2Cl·2MeOH is similar to those in [Cu(Lmm)2]·2Cl and [Cu(Lme)2]·2Br, the molecular units are not linked by hydrogen-bonding interactions. A common feature of the halide bridges is a hydrogen-bonded supramolecular synthon in which the anion acts as acceptor to two pairs of N–H donors thus forming two R12(6) motifs with a common halide anion.

Intramolecular Hydrogen Bonding and Intermolecular Dimerization in the Crystal Structures of Imidazole-4,5-dicarboxylic Acid Derivatives

Diamide and amide-ester derivatives of imidazole-4,5-dicarboxylic acid form reliable hydrogen-bonding motifs in the solid state. The crystal structures of symmetrically substituted and dissymmetrically substituted diamides as well as amide-ester combinations were analyzed in order to identify the intermolecular hydrogen-bonding patterns. An intramolecular seven-membered hydrogen-bonded conformation forms in all derivatives where the possibility existed due to the functionality present. The motifs observed for the diamides include intermolecular NH···O and NH···N hydrogen-bonded dimers, with the exceptions to these motifs occurring in compounds having benzylamine substituents. The amines with a higher classification (i.e., 3° > 2° > 1°) in the dissymmetrically substituted diamides are the intramolecular hydrogen bond donors in the solid state, consistent with the capacity of the alkyl group to stabilize developing carbocation character resulting from bond polarization. The amide-ester derivatives also form...

Patterns of hydrogen bonding in crystals of molybdenum carbonyl complexes

The solid-state structures of complexes of the type [HO–(N∩N′)]Mo(CO)3L (L = CO, THF, PPh3, CNtBu, CNCy) have been determined by X-ray crystallography. Two major types of multiple intermolecular hydrogen-bonding patterns involving the OH group and CH moieties as hydrogen donors and carbonyl groups and solvent molecules as hydrogen acceptors have been found and interpreted in terms of hydrogen bond strength, steric availability and dense packings. Discrimination between the two hydrogen-bonding patterns is also possible on the basis of unit cell dimensions and IR spectroscopy. DFT calculations support the interpretations.

(+/-)-2-Aza-3,9-dioxotricyclo[4.4.4.01,6]tetradecane: dimeric and catemeric hydrogen bonding in two polymorphs of a propellanoid keto lactam

The title compound, C 13 H 19 NO 2 , is the cyclized ringchain tautomer of the corresponding angularly substituted Δ 1(9) -2-octalone and exists in two crystalline polymorphs, (I) and (II), displaying fundamentally different intermolecular hydrogen-bonding patterns, neither of which involves the ketone. In (I), amide groups are paired by hydrogen bonding in non-centrosymmetric dimers (space group C2/c). In (II), hydrogen bonding proceeds from the NH of each molecule to the amide C=O of a screw-related neighbor, generating parallel, centrosymmetrically related, counterdirectional chains passing through the cell in the b direction (space group P2 1 /c). Several intermolecular C=O...H-C close contacts were found for both (I) and (II).

Conformation of the Amide Bond in Topographically Restricted Environment

Graph set methodology used for the group of di- and tetrazacoronands showed characteristic intra- and intermolecular hydrogen bond patterns stabillizing molecular conformation and crystal lattice.