Interplay between steric and electronic factors in determining the strength of intramolecular N—H...O resonance-assisted hydrogen bonds in β-enaminones

2006 ◽  
Vol 62 (6) ◽  
pp. 1112-1120 ◽  
Author(s):  
Valerio Bertolasi ◽  
Loretta Pretto ◽  
Valeria Ferretti ◽  
Paola Gilli ◽  
Gastone Gilli
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Features ◽  
Membered Ring ◽  
Resonance Assisted Hydrogen Bond ◽  
Electronic Resonance ◽  
Hydrogen Bonded

The crystal structures of five β-enaminones are reported: (2Z)-3-(benzylamino)-1,3-diphenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(2-hydroxyphenyl)-1-phenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(4-methoxyphenyl)-1-(3-nitrophenyl)-prop-2-en-1-one, 2-{1-[(4-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione and 2-{1-[(3-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione. The structures were analysed and compared with those of similar compounds in order to establish which factors determine the range (2.53–2.72 Å) of N...O hydrogen-bond distances in intramolecularly hydrogen-bonded β-enaminones. It has been shown that, beyond electronic resonance-assisted hydrogen-bond effects modulated by substituents, the necessary requirements to produce very short N—H...O hydrogen bonding are steric intramolecular repulsions, including the embedding of an enaminonic C—C or C—N bond in an aliphatic six-membered ring. By considering the structural features it is possible to expect the strength of N—H...O hydrogen bonds adopted by specific β-enaminones.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

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.

N—H...S and N—H...O hydrogen bonds: `pure' and `mixed'R22(8) patterns in the crystal structures of eight 2-thiouracil derivatives

2014 ◽  
Vol 70 (2) ◽  
pp. 241-249 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Ernst Egert
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Crystal Structures ◽  
Thiouracil Derivatives ◽  
Bonding Patterns

The preferred hydrogen-bonding patterns in the crystal structures of 5-propyl-2-thiouracil, C7H10N2OS, (I), 5-methoxy-2-thiouracil, C5H6N2O2S, (II), 5-methoxy-2-thiouracil–N,N-dimethylacetamide (1/1), C5H6N2O2S·C4H9NO, (IIa), 5,6-dimethyl-2-thiouracil, C6H8N2OS, (III), 5,6-dimethyl-2-thiouracil–1-methylpyrrolidin-2-one (1/1), C6H8N2OS·C5H9NO, (IIIa), 5,6-dimethyl-2-thiouracil–N,N-dimethylformamide (2/1), 2C6H8N2OS·C3H7NO, (IIIb), 5,6-dimethyl-2-thiouracil–N,N-dimethylacetamide (2/1), 2C6H8N2OS·C4H9NO, (IIIc), and 5,6-dimethyl-2-thiouracil–dimethyl sulfoxide (2/1), 2C6H8N2OS·C2H6OS, (IIId), were analysed. All eight structures containR22(8) patterns. In (II), (IIa), (III) and (IIIa), they are formed by two N—H...S hydrogen bonds, and in (I) by alternating pairs of N—H...S and N—H...O hydrogen bonds. In contrast, the structures of (IIIb), (IIIc) and (IIId) contain `mixed'R22(8) patterns with one N—H...S and one N—H...O hydrogen bond, as well asR22(8) motifs with two N—H...O hydrogen bonds.

scholarly journals Hydrogen bonding in the crystal structure of the molecular salt of pyrazole–pyrazolium picrate

2016 ◽  
Vol 72 (6) ◽  
pp. 861-863 ◽  
Author(s):  
Ping Su ◽  
Xue-gang Song ◽  
Ren-qiang Sun ◽  
Xing-man Xu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Organic Salt ◽  
Asymmetric Unit ◽  
Molecular Salt ◽  
Hydrogen Bonded

The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-trinitrophenolate–1H-pyrazole (1/1)], H(C3H4N2)2+·C6H2N3O7−, consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N—H...N hydrogen bond is disordered over both symmetry-unique pyrazole molecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N—H...(O,O) hydrogen bonds. In addition, weak C—H...O hydrogen bonds link inversion-related chains, forming columns along [100].

Crystal structures of 7-azaindole, an unusual hydrogen-bonded tetramer, and of two of its methylmercury(II) complexes

1990 ◽  
Vol 68 (1) ◽  
pp. 193-201 ◽  
Author(s):  
Pascal Dufour ◽  
Yves Dartiguenave ◽  
Michèle Dartiguenave ◽  
Nathalie Dufour ◽  
Anne-Marie Lebuis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Membered Ring ◽  
Pyridine Nitrogen Atom ◽  
Nitrate Ions ◽  
Pyridine Nitrogen ◽  
Independent Molecules ◽  
Hydrogen Bonded

Crystals of 7-azaindole ([Formula: see text], a = 11.312(4), b = 14.960(6), c = 15.509(5) Å, α = 102.86(3), β = 108.78(3), γ = 90.71(3)°, Z = 16, R = 0.052) contain tetrameric units of approximate S4 symmetry, in which the molecules are associated by means of four complementary N—H … N hydrogen bonds. [CH3Hg(7-azaindole)]NO3 ([Formula: see text], a = 7.818(3), b = 7.884(3), c = 9.135(4) Å, α = 97.89(3), β = 109.13(3), γ = 103.28(3)°, Z = 2, R = 0.039) contains well-separated nitrate ions and complex cations in which the methylmercury group is linearly bonded to the pyridine nitrogen atom, whereas the five-membered ring remains protonated. In the neutral [CH3Hg(azaindolate)] complex ([Formula: see text], a = 10.926(10), b = 11.333(8), c = 11.647(10) Å, α = 92.13(8), β = 104.83(9), γ = 111.86(7)°, Z = 6, R = 0.048), methylmercury groups have substituted the N—H proton in the five-membered ring for the three symmetry-independent molecules. Intermolecular secondary Hg … N bonds are found with pyridine nitrogens. Keywords: azaindole, methylmercury, crystal structure.

Hydrogen bonding in enantiomeric versus racemic mono-carboxylic acids; a case study of 2-phenoxypropionic acid

2003 ◽  
Vol 59 (1) ◽  
pp. 132-140 ◽  
Author(s):  
Henning Osholm Sørensen ◽  
Sine Larsen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Carboxylic Acids ◽  
Crystal Packing ◽  
Cyclic Dimer ◽  
Optically Pure ◽  
Pure Enantiomer ◽  
Hydrogen Bonded

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.

A Comparison of the Enamino Carbonyl Conjugation Efficiency for Hydrogen Bonding Formation in Pyridone and Dihydropyridone Systems

2000 ◽  
Vol 55 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Teresa Borowiak ◽  
Irena Wolska ◽  
Artur Korzański ◽  
Wolfgang Milius ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds

The crystal structures of two compounds containing enaminone heterodiene systems and forming intermolecular hydrogen bonds N-H·O are reported: 1) 3-ethoxycarbonyl-2-methyl-4-pyridone (hereafter ETPY) and 2) 3-ethoxycarbonyl-2-phenyl-6-methoxycarbonyl-5,6-di-hydro-4-pyridone (hereafter EPPY). The crystal packing is controlled by intermolecular hydro­ gen bonds N-H·O = C connecting the heteroconjugated enaminone groups in infinite chains. In ETPY crystals the intermolecular hydrogen bond involves the heterodienic pathway with the highest π-delocalization that is effective for a very short N·O distance of 2.701(9) Å (average from two molecules in the asymmetric unit). Probably due to the steric hindrance, the hydrogen bond in EPPY is formed following the heterodienic pathway that involves the ester C = O group, although π-delocalization along this pathway is less than that along the pyridone-part pathway resulting in a longer N·O distance of 2.886(3) Å

The hydrogen-bonded complex bis(tert-butylammonium) 2,6-dichlorophenolate 2,4-dichlorophenol–2,4-dichlorophenolate tetrahydrofuran disolvate containing a chiralR53(10) hydrogen-bonded ring as a supramolecular synthon

2016 ◽  
Vol 72 (10) ◽  
pp. 720-723 ◽  
Author(s):  
Xiao-Qing Cai ◽  
Bei Tian ◽  
Jian-Nan Zhang ◽  
Zhi-Min Jin
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Functional Groups ◽  
High Probability ◽  
Internal Symmetry ◽  
Supramolecular Synthon ◽  
Π Interactions ◽  
Graph Set ◽  
Hydrogen Bonded

A fixed hydrogen-bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen-bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen-bonding motifR53(10) was observed previously in a cocrystal of 2,4,6-trichlorophenol, 2,4-dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C4H12N+·C6H3Cl2O−·(C6H3Cl2O−·C6H4Cl2O)·2C4H8O, five components, namely twotert-butylammonium cations, one 2,4-dichlorophenol molecule, one 2,4-dichlorophenolate anion and one 2,6-dichlorophenolate anion, are bound by N—H...O and O—H...O hydrogen bonds to form a hydrogen-bonded ring, with the graph-set motifR53(10), which is further associated with two pendant tetrahydrofuran molecules by N—H...O hydrogen bonds. The hydrogen-bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6-dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4-dichlorophenol, dicyclohexylamine and 2,4,6-trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen-bonded rings, along and across thecaxis, and successive pairs of rings are associated with each other through C—H...π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.

2-Hydroxyisophthalic acid: hydrogen-bonding patterns in the monohydrate and the tetraphenylphosphonium salt. An instance of dramatic acidity enhancement by symmetric, internally hydrogen-bonded anion stabilization

2004 ◽  
Vol 60 (4) ◽  
pp. 438-446 ◽  
Author(s):  
Shaleen Bawa ◽  
Marie L. Coté ◽  
Patrick Dubois ◽  
Roger A. Lalancette ◽  
Hugh W. Thompson
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Negative Charge ◽  
Static Disorder ◽  
Dioic Acid ◽  
Factors Affecting ◽  
Planar Conformation ◽  
Phenol Oxygen ◽  
Hydrogen Bonded

The monohydrate of the title phenolic diacid (C8H6O5·H2O, 2-hydroxybenzene-1,3-dioic acid or 3-carboxysalicylic acid) adopts a planar conformation, with the phenol hydrogen internally hydrogen-bonded to the carbonyl of one highly ordered carboxyl, which, in turn, donates a hydrogen bond to the oxygen of water. The second carboxyl is disordered and hydrogen-bonded both to water and to the disordered carboxyl of a centrosymmetrically related neighbor in a static disorder arrangement extending over two full asymmetric units. The water accepts either one or two hydrogen bonds and donates a long bifurcated hydrogen bond shared equally by O atoms of the phenol and the disordered carboxyl. The hydrogen bonding includes no standard carboxyl pairing and is entirely two-dimensional. The resulting planar ribbons stack translationally at a distance of 3.413 (8) Å, in an offset arrangement having non-translational interplanar distances of 0.821 (5) and 2.592 (6) Å. This structure is compared with two previously reported for this compound. The title compound forms a monoanion, whose tetraphenylphosphonium salt is described (C32H25O5P, tetraphenylphosphonium 2,6-dicarboxyphenolate, tetraphenylphosphonium 2-oxidoisophthalic acid or tetraphenylphosphonium 3-carboxysalicylate). The phenol oxygen is the site of formal negative charge on the anion, which is stabilized in a planar arrangement by symmetrical hydrogen bonds from both ortho-carboxyl groups. The energetics of this arrangement, the phenol and carboxyl acidities, and factors affecting those acidities and providing anion stabilization are discussed.

Ferrocene Mono- and Di-Sulfonates as Building Blocks in Hydrogen-Bonded Networks

2007 ◽  
Vol 60 (8) ◽  
pp. 578 ◽  
Author(s):  
Jingli Xie ◽  
Brendan F. Abrahams ◽  
Tobias J. Zimmermann ◽  
Arindam Mukherjee ◽  
Anthony G. Wedd
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Crystalline State ◽  
Building Blocks ◽  
The Individual ◽  
Secondary Bonding ◽  
Hydrogen Bonded

The structure directing influence of a variety of hydrogen-bonding cations on the arrangement of ferrocene mono- and di-sulfonate anions within the crystalline state is reported. The crystal structures of four different networks of composition A[Fe(η5-C5H5)(η5-C5H4SO3)] (A = imidazolium or N-methylimidazolium) and B2[Fe(η5-C5H4SO3)2] (B = imidazolium or pyridinium) are presented. The imidazolium ions are able to act as hydrogen bond bridges in the generation of layer-type structures similar to those found for guanidinium analogues. Secondary bonding interactions exert a powerful structure-directing influence within these networks even though the individual interactions appear to be rather weak.

Extensive analysis of N—H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

2017 ◽  
Vol 73 (3) ◽  
pp. 287-297 ◽  
Author(s):  
Farahnaz Hamzehee ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Duane Choquesillo-Lazarte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Neutral Hydrogen ◽  
The Other ◽  
Phosphorus Compounds ◽  
Database Study ◽  
Extensive Analysis ◽  
Structural Database

The N—H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N′-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P− or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P− or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N—H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation–anion compounds. The overall tendencies of N...O distances in neutral and cation–anion compounds were compared. The N—H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

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