Six-membered Hydrogen-bonded Ring Research Articles

Crystal, mol-ecular structure and Hirshheld surface analysis of 5-hy-droxy-3,6,7,8-tetra-meth-oxy-flavone.

The title compound (systematic name: 5-hydroxy-3,6,7,8-tetramethoxy-2-phenyl-4H-chromen-4-one), C19H18O7, is a flavone that was isolated from a butanol extract of the herb Scutellaria nepetoides M. Pop. The flavone mol-ecule is almost planar, with a dihedral angle between the planes of the benzo-pyran-4-one group and the attached phenyl ring of 6.4 (4)°. The 5-hy-droxy group forms a strong intra-molecular hydrogen bond with the carbonyl group, resulting in a six-membered hydrogen-bonded ring. The crystal structure has triclinic (P ) symmetry. In the crystal, the mol-ecules are linked by C-H⋯O hydrogen bonds into a two dimensional network parallel to the ab plane. The Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (53.9%) and H⋯O/O⋯H (20.9%) inter-actions.

Infrared photodissociation spectroscopy of D2-tagged CH3CO2 −(H2O)0−2 anions

ABSTRACT Infrared photodissociation spectroscopy of D2-tagged anions is used to obtain the vibrational spectra of microsolvated acetate, (n = 0–2), in the CH/OH stretching (∼4000–2500 cm−1) and fingerprint (∼1800–800 cm−1) spectral regions. These results are analysed by comparison to anharmonic IR spectra from MP2 calculations as well as Born-Oppenheimer molecular dynamics (BOMD) simulations. In agreement with prior work, we find that the first water molecule adds to the acetate anion by donating two hydrogen bonds, yielding a symmetrical structure involving a six-membered hydrogen-bonded ring. Two nearly degenerate binding motifs that differ in energy by less than 1 kJ/mol are identified for n = 2 anion, where the lowest-energy geometry has two ion-water hydrogen bonds as well as a water-water hydrogen bond. The molecular dynamics simulations confirm that this lower-energy structure is preferred over a slightly higher-lying configuration possessing three ion-water hydrogen bonds and no water-water interactions. Analysis of the molecular motion contributing to peaks in the BOMD spectra via a generalised normal mode approach provides assignment of all observed transitions to the lower-energy structure, and enables distinction of the vibrational signatures associated with ion-water and water-water intermolecular motions.

(Thio)phosphoryl-functionalized enaminoketones: Synthesis, structure, and complexing properties towards transition metal ions

P(X)-functionalized enaminoketones (X = O, S) 1a,b have been readily obtained by the condensation of o-(thio)phosphorylated anilines with sodium salt of benzoylacetaldehyde. The ligands derived exist in solution in the expected ketamino tautomeric form, but, unlike typical enaminoketones, tend to exist as cis-isomers in polar media, favored by the formation of the strong PO…HN intramolecular hydrogen bond. This six-membered hydrogen-bonded ring is also observed in the solid structure of 1a, which, nevertheless, features a trans-configuration of the enaminoketone fragment. Independent from the isomeric composition, the ligands obtained readily form κ3-X,N,O (X = O, S) complexes with a range of transition metal ions (Re(I), Pd(II), Cu(II), and Ni(II)) adopting in all cases the cis-configuration. The structures of the novel compounds are confirmed using multinuclear NMR and IR spectroscopy as well as X-ray crystallography.

4-Chloro-2-[(E)-(4-fluorophenyl)iminomethyl]phenol

In the title Schiff base mol­ecule, C13H9ClFNO, the benzene rings are twisted slightly with respect to each other, making a dihedral angle of 7.92 (2)°. An intra­molecular O—H⋯N hydrogen bond occurs. In the crystal, an infinite chain is formed along the c-axis direction by π–π stacking inter­actions between the phenyl rings and the six-membered hydrogen-bonded ring of neighboring Schiff base ligands [centroid–centroid distances of 3.698 (2) and 3.660 (3) Å]. Neighboring chains are linked into a three-dimensional supra­molecular structure by C—H⋯O and C—H⋯F hydrogen bonds.

The zwitterionic structure of 2-hydroxy-4-[(2-hydroxybenzylidene)amino]benzoic acid

The title compound, C₁₄H₁₁NO₄, exists in the solid phase in the zwitterionic form, 2-{[(4-carboxy-3-hydroxyphenyl)iminiumyl]methyl}phenolate, with the H atom from the phenol group on the 2-hydroxybenzylidene ring transferred to the imine N atom, resulting in a strong intramolecular N-H∙∙∙O hydrogen bond between the iminium H atom and the phenolate O atom, forming a six-membered hydrogen-bonded ring. In addition, there is an intramolecular O-H∙∙∙O hydrogen bond between the carboxylic acid group and the adjacent hydroxy group of the other ring, and an intermolecular C-H∙∙∙O contact involving the phenol group and the C-H group adjacent to the imine bond, connecting the molecules into a two-dimensional network in the (103) plane. π-π stacking interactions result in a three-dimensional network. This study is important because it provides crystallographic evidence, supported by IR data, for the iminium zwitterionic form of Schiff bases.

Ethyl (Z)-4′-(4-ethoxy-1-hydroxy-3,4-dioxobut-1-en-1-yl)-[1,1′-biphenyl]-3-carboxylate

The 1,3-diketone group of the title compound, C21H20O6, exists in a keto–enol form stabilized by a strong intra­molecular O—H⋯O hydrogen bond. As a result, a planar (mean deviation = 0.0099 Å) six-membered hydrogen-bonded ring is formed. The C—O and C—C bond lengths suggest significant electron delocalization in the ring. The dihedral angle between the six-membered hydrogen-bonded ring and its adjacent benzene ring is 8.78 (5)° and that between the benzene rings is 19.70 (5)°. In the crystal, mol­ecules are packed in a layered structure parallel to the b axis through C—H⋯O and π–π inter­actions [centroid–centroid distance between stacked benzene rings = 3.868 (2) Å].

5,6-Dihy-droxy-7,8-di-meth-oxy-flavone.

The title compound (systematic name: 5,6-dihy­droxy-7,8-dimeth­oxy-2-phenyl­chromen-4-one), C17H14O6, is a flavone that was isolated from the petroleum ether-soluble fraction of the rare traditional Chinese medicinal herb Saussurea involucrata. The flavone mol­ecule is almost planar, with a dihedral angle between the planes of the benzo­pyran-4-one group and the attached phenyl group of 1.89 (6)°. The 5-hy­droxy group forms a strong intra­molecular hydrogen bond with the carbonyl group, resulting in a six-membered hydrogen-bonded ring. The 6-hy­droxy group also forms an intra­molecular O—H⋯O contact. In the crystal, the molecules are linked by O—H⋯O and C—H⋯O hydrogen bonds and π–π inter­actions [3.37 (2)–3.39 (2) Å], which build up a three–dimensional network.

Structure of 4-methyl-N-{2-[2-alkylamino-5-nitrophenyliminomethyl]phenyl}benzenesulfonamides

The structures of Schiff bases prepared by the condensation of 2-tosylaminobenzaldehyde with 2-alkylamino-5-nitroanilines were studied by X-ray diffraction. The intramolecular N-H…N hydrogen bonds result in the closure of six-membered hydrogen-bonded rings, which are either planar or nonplanar depending on the substituent. According to the results of quantum-chemical calculations, the distortion of the hydrogen-bonded ring is associated with the character of molecular packing in the crystal.

6,6′-Dimethoxy-2,2′-{[(E,E)-hydrazine-1,2-diylidene]bis(methanylylidene)}diphenol methanol disolvate

The title compound, C16H16N2O4·2CH3OH, is a hydrazone in an E geometric arrangement, with an inversion centre at the mid-point of the N—N bond. A symmetry-related pair of six-membered hydrogen-bonded rings [graph-set motif S 1 1(6)] are present for the terminal vanillin–imine moieties. Two lattice methanol solvent mol­ecules are present per formula unit (Z′ = 1/2), which form hydrogen-bonded chains along [010] with two orientations due to disorder of the methanol H-atom.

Bis(2,2′-bipyridyl-κ2N,N′)bis(2-hydroxybenzoato)-κO1;κ2O1,O1′-cadmium(II) methanol solvate

The title compound, [Cd(C7H5O3)2(C10H8N2)2]·CH3OH, contains one monomeric seven-coordinate cadmium complex and one methanol solvate mol­ecule. The CdII atom is coordinated to two 2,2′-bipyridyl ligands via the N atoms and to two salicylate anions (Hsal−) via the carboxyl­ate O atoms, which act as monodentate ligand for the one and bidentate ligand for the second. The CdII atom exhibits a {6 + 1} environment, approximately described as a distorted capped octa­hedron with the apical positions occupied by one of the two N atoms belonging to one bipyridyl ligand and one of the two carboxyl­ate O atoms from the monodentate Hsal− ligand. Two intra­molecular six-membered hydrogen-bonded rings are present, generated from inter­actions between the carboxyl­ate and hydr­oxy groups of the salicylate ligands. There is one inter­molecular hydrogen-bonding inter­action involving the methanol solvent mol­ecule and the carboxyl­ate group from the monodentate Hsal− ligand. The crystal packing is governed by π–π stacking inter­actions [centroid–centroid distance = 3.783 (4) Å] which occur between bipyridyl ligands, by C—H⋯O and C—H⋯π inter­actions and by numerous van der Waals contacts.

Folding and self-assembling with β-oligomers based on (1R,2S)-2-aminocyclobutane-1-carboxylic acid

Improved methodologies are provided to synthesize (1R,2S)-2-aminocyclobutane-1-carboxylic acid derivatives and their incorporation into beta-peptides of 2-8 residues bearing different N-protecting groups. The conformational analysis of these oligomers has been carried out by using experimental techniques along with theoretical calculations. This study shows that these oligomers adopt preferentially a strand-type conformation in solution induced by the formation of intra-residue six-membered hydrogen-bonded rings, affording cis-fused [4.2.0]octane structural units that confer high rigidity on these beta-peptides. Moreover, all of them are prone to self-assemble producing nano-sized fibres, as evidenced by TEM, AFM and SPFM, and, in some instances, they also form gels. These techniques and molecular modelling allowed us to suggest an aggregation model for the assembly structures in which a parallel molecular-arrangement is preferred and the conformation is similar to that observed in solution. According to this model, both hydrogen-bonding and hydrophobic interactions would account for formation of the assemblies.

N'-[(E)-Benzyl-idene]-1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide.

In the title compound, C19H18N4O2, the 1,8-naphthyridine ring system is essentially planar [r.m.s. deviation = 0.011 (3) Å]. The dihedral angle between the naphthyridine ring system and the phenyl ring is 28.95 (7)°. The carbohydrazide H atom is involved in an intra­molecular N—H⋯O hydrogen bond, forming a six-membered hydrogen-bonded ring. In the crystal, the mol­ecules arrange themselves into centrosymmetric dimers by means of inter­molecular C—H⋯O hydrogen bonds.

1-Ethyl-N′-[(E)-4-hydroxybenzylidene]-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide

In the crystal structure of the title compound, C19H18N4O3, the fused-ring system is essentially planar [maximum deviation is 0.031 (2) Å] while the dihedral angle between the ring system and the benzene ring is 12.64 (6)°.The carbohydrazide H atom is involved in an intra­molecular N—H⋯O hydrogen bond, forming a six-membered hydrogen-bonded ring. The mol­ecules arrange themselves into centrosymmetric dimers by means of inter­molecular O—H⋯O hydrogen bonds.

Reinvestigation of the microwave spectrum of 2-methylmalonaldehyde

The molecule 2-methylmalonaldehyde (2-MMA) exists in the gas phase as a six-membered hydrogen-bonded ring [HO CH C(CH 3) CH O] and exhibits two large-amplitude motions, an intramolecular hydrogen transfer and a methyl torsion. The former motion is interesting because transfer of the hydrogen atom from the hydroxyl to the carbonyl group induces a tautomerization in the ring, which then triggers a 60° internal rotation of the methyl group attached to the ring. We present a new experimental study of the microwave spectra of the 2-MMA-d0 [HO CH C(CH 3) CH O] and 2-MMA-d1 [DO CH C(CH 3) CH O] isotopologs of the molecule. The new measurements were carried out by Fourier-transform microwave (FTMW) spectroscopy in the 8–24 GHz frequency range and by conventional absorption spectroscopy in the 49–149 GHz range. In the present work, we use a tunneling-rotational Hamiltonian based on a G 12 m group-theoretical formalism to carry out global fits of 2578 2-MMA-d0 transitions and 2552 2-MMA-d1 transitions to measurement uncertainty, obtaining a root-mean-square deviation of 0.015 MHz for both isotopologs. This represents a significant improvement in fitting accuracy over past attempts. Some problems associated with calculating barrier heights from the observed tunneling splittings and assumed tunneling paths are also considered.

Hydrogen-bonding patterns in enaminones: (2Z)-1-(4-bromophenyl)-2-(pyrrolidin-2-ylidene)ethanone and its piperidin-2-ylidene and azepan-2-ylidene analogues

The title compounds, namely (2Z)-1-(4-bromophenyl)-2-(pyrrolidin-2-ylidene)ethanone, C12H12BrNO, (I), (2Z)-1-(4-bromophenyl)-2-(piperidin-2-ylidene)ethanone, C13H14BrNO, (II), and (2Z)-2-(azepan-2-ylidene)-1-(4-bromophenyl)ethanone, C14H16BrNO, (III), are characterized by bifurcated intra- and intermolecular hydrogen bonding between the secondary amine and carbonyl groups. The former establishes a six-membered hydrogen-bonded ring, while the latter leads to the formation of centrosymmetric dimers. Weak C-H...Br interactions link the individual molecules into chains that run along the [011], [101] and [101] directions in (I)-(III), respectively. Additional weak Br...O, C-H...pi and C-H...O interactions further stabilize the crystal structures.

N-[2-(Aminocarbonyl)phenyl]-4-hydroxy-2H-1,2-benzothiazine-3-carboxamide 1,1-dioxide dimethyl sulfoxide solvate

The title compound, C16H13N3O5S·C2H6OS, is of interest as a precursor to biologically active (benzothiazin-3-yl)quinazolinones and its structure is reported here as the dimethyl sulfoxide (DMSO) solvate. The structure displays intramolecular N—H...O and O—H...O hydrogen bonding, giving rise to six-membered hydrogen-bonded rings, with head-to-tail intermolecular pairs of N—H...O hydrogen bonds linking pairs of neighbouring molecules and two independent N—H...O=S intermolecular hydrogen bonds to the DMSO molecule resulting in the pairs of molecules being linked into stepped chains parallel to a.

Ethyl (2E)-3-oxo-2-(pyrrolidin-2-ylidene)butanoate

The pyrrolidine ring in the title compound, C10H15NO3, adopts an envelope conformation. Both the secondary amine and acetyl groups participate in bifurcated intra- and inter­molecular hydrogen bonding; the former sets up a six-membered hydrogen-bonded ring, while the latter links the mol­ecules into centrosymmetric dimers.

Two-dimensional tunneling Hamiltonian treatment of the microwave spectrum of 2-methylmalonaldehyde

The molecule 2-methylmalonaldehyde (2-MMA) exists in the gas phase as a six-membered hydrogen-bonded ring [HO-CH=C(CH(3))-CH=O] and exhibits two large-amplitude motions, an intramolecular hydrogen transfer and a methyl torsion. The former motion is interesting because the transfer of the hydrogen atom from the hydroxyl to the carbonyl group induces a tautomerization in the ring, i.e., HO-CH=C(CH(3))-CH=O-->O=CH-C(CH(3))=CH-OH, which then triggers a 60 degrees internal rotation of the methyl group attached to the ring. The microwave spectra of 2-MMA-d0, 2-MMA-d1, and 2-MMA-d3 were studied previously by Sanders [J. Mol. Spectrosc. 86, 27 (1981)], who used a rotating-axis-system program for two-level inversion problems to fit rotational transitions involving the nondegenerate A(+) and A(-) sublevels to several times their measurement uncertainty. A global fit could not be carried out at that time because no appropriate theory was available. In particular, observed-minus-calculated residuals for the E(+) and E(-) sublevels were sometimes as large as several megahertz. In the present work, we use a tunneling-rotational Hamiltonian based on a G(12) (m) group-theoretical formalism to carry out global fits of Sanders' 2-MMA-d0 and 2-MMA-d1 [DO-CH=C(CH(3))-CH=O] spectra nearly to measurement uncertainty, obtaining root-mean-square deviations of 0.12 and 0.10 MHz, respectively. The formalism used here was originally derived to treat the methylamine spectrum, but the interaction between hydrogen transfer and CH(3) torsion in 2-MMA is similar, from the viewpoint of molecular symmetry, to the interaction between CNH(2) inversion and CH(3) torsion in methylamine. These similarities are discussed in some detail.

(2,2'-Bipyridyl-kappa2N,N')bis(salicylato-kappa2O,O')zinc(II).

The asymmetric unit of the title compound, [Zn(C7H5O3)2(C10H8N2)], contains one monomeric zinc complex. The Zn atom is coordinated to one 2,2′-bipyridyl ligand via both N atoms and to two salicyl­ate anions (Hsal−) in a bidentate chelating manner involving carboxyl­ate O-atom coordination. The complex exhibits a distorted octahedral geometry about the ZnII atom, with the `apical' positions occupied by one of the two N atoms of the bipyridyl ligand and an O atom from one Hsal− ligand; the Zn atom is 0.168 (1) Å out of the `basal' plane. Two intramolecular six-membered hydrogen-bonded rings are present, generated from interactions between the carboxyl and hydroxyl groups of the salicyl­ate ligands. The crystal packing is governed by weak C—H⋯O and C—H⋯π interactions.

Study of the sulfur atom as hydrogen bond acceptor in N(2)-pyridylmethyl-N -arylthioureas

The hydrogen acceptor capability of the sulfur atom in the biologically relevant N-2-pyridylmethyl-N′-arilthioureas was explored. N-2-Pyridylmethyl thioreas were selected to avoid the formation of intramolecular six-membered hydrogen-bonded ring. The compounds studied were N-2-pyridylmethyl-N′-phenylthiourea (1), N-2-pyridylmethyl-N′-2-methoxythiourea (2), N-2-pyridylmethyl-N′-4-methoxyphenylthiourea (3), and N-2-pyridylmethyl-N′-4-bromophenylthiourea (4). 1 crystallizes in the monoclinic space group P21/c, with a = 7.419(1) A, b = 18.437(2) A, c = 9.656(1) A, β = 106.277(6)°, V = 1267.8(3) A3, Z = 4. 2 crystallizes in the monoclinic space group P21/c, with a = 8.064(2) A, b = 18.382(7) A, c = 9.865(5) A, β = 97.81(3)°, V = 1448.8(11) A3, Z = 4. 3 crystallizes in the monoclinic space group P21/c, with a = 11.472(1) A, b = 13.520(1) A, c = 10.088(1) A, β = 112.60(1)°, V = 1444.5(2) A3, Z = 4. 4 crystallizes in the triclinic space group P-1, with a = 4.583(3) A, b = 10.263(3) A, c = 14.396(3) A, α = 77.92(2)°, β = 88.55(4)°, γ = 80.02(4)°, V = 652.1(5) A3, Z = 2. Both thiourea N–H groups form intermolecular hydrogen bonds, one with the thione sulfur atom and the other with the pyridine nitrogen atom but the H-bonding schemes are not the same maybe due to the flexibility of the molecules.