Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inter-molecular inter-actions in a phenol-substituted benzimidazole.

ABSTRACT: Hydrogen bonding plays an important role in the design of solid-state structures and gels with desirable properties. 1-(4-Hydroxybenzyl)-2-(4-hydroxyphenyl)-5,6-dimethyl-1H-benzimidazole was isolated as the acetone disolvate, C22H20N2O2·2C3H6O. O-H⋯N hydrogen bonding between benz-imidazole mol-ecules results in chains parallel to [010]. One of the acetone solvate mol-ecules participates in O-H⋯O hydrogen bonding with the benzimidazole derivative. C-H⋯π inter-actions are observed in the extended structure. Hirshfeld surface analysis was used to explore the inter-molecular inter-actions and density functional theory was used to estimate the strength of the hydrogen bonds.

SUBMITTER: Geiger DK

PROVIDER: S-EPMC6362671 | biostudies-other | 2019 Feb

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Inter-molecular inter-actions in a phenol-substituted benzimidazole.

Geiger David K DK Geiger H Cristina HC Moore Shawn M SM

Acta crystallographica. Section E, Crystallographic communications 20190129 Pt 2

Hydrogen bonding plays an important role in the design of solid-state structures and gels with desirable properties. 1-(4-Hydroxybenzyl)-2-(4-hydroxyphenyl)-5,6-dimethyl-1H-benzimidazole was isolated as the acetone disolvate, C22H20N2O2·2C3H6O. O-H⋯N hydrogen bonding between benz-imidazole mol-ecules results in chains parallel to [010]. One of the acetone solvate mol-ecules participates in O-H⋯O hydrogen bonding with the be ...[more]

PMID: 30800466

Similar Datasets

An exploration of O-H?O and C-H?? inter-actions in a long-chain-ester-substituted phenyl-phenol: methyl 10-[4-(4-hydroxyphenyl)phenoxy]decanoate.

Project description:An understanding of the driving forces resulting in crystallization vs organogel formation is essential to the development of modern soft materials. In the mol-ecular structure of the title compound, methyl 10-[4-(4-hydroxyphenyl)phen-oxy]decanoate (MBO10Me), C23H30O4, the aromatic rings of the biphenyl group are canted by 6.6?(2)° and the long-chain ester group has an extended conformation. In the crystal, mol-ecules are linked by O-H?O hydrogen bonds, forming chains along [10[Formula: see text]]. The chains are linked by C-H?O hydrogen bonds, forming layers parallel to the ac plane. The layers are linked by C-H?? inter-actions, forming a three-dimensional supra-molecular structure. The extended structure exhibits a lamellar sheet arrangement of mol-ecules stacking along the b-axis direction. Each mol-ecule has six nearest neighbors and the seven-mol-ecule bundles stack to form a columnar superstructure. Inter-action energies within the bundles are dominated by dispersion forces, whereas inter-columnar inter-actions have a greater electrostatic component.

| S-EPMC5947469 | biostudies-literature

Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

Project description:The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ?). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H?O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H?O hydrogen bonds and weak C-H?O inter-actions. The packing also features C?O [3.131?(3)?Å] short contacts.

| S-EPMC3089143 | biostudies-other

Oxidative condensations to form benzimidazole-substituted potassium organotrifluoroborates.

Project description:A library of benzimidazole-substituted potassium organotrifluoroborates was prepared via the condensation of various potassium formyl-substituted aryl- and heteroaryltrifluoroborates with aromatic 1,2-diamines under oxidative conditions. The efficient Suzuki-Miyaura cross-coupling of products thus formed to various aryl and heteroaryl bromides was achieved in good yields. The method allows the facile preparation of benzimidazole-containing triaromatic products in two steps from simple potassium formyl substituted aryl- or heteroaryltrifluoroborates.

| S-EPMC3428750 | biostudies-literature

Redetermined structure of diphenyl-phospho-nimidotriphenyl-phospho-rane: location of the hydrogen atoms and analysis of the inter-molecular inter-actions.

Project description:The title compound, C(30)H(25)NOP(2), is a bulky phosphazene derivative. Its previous crystal structure [Cameron et al. (1979 ?). Acta Cryst. B35, 1373-1377] is confirmed and its H atoms have been located in the present study. The formal P=N double bond is about 0.05?Å shorter than the P-N single bond and the large P=N-P bond angle reflects the steric strain in the mol-ecule. An intra-molecular C-H?O inter-action occurs. In the crystal, short C-H?O contacts connect the mol-ecules into chains propagating in [011], which are cross-linked via C-H?? inter-actions, generating a three-dimensional network. Aromatic ?-? stacking also occurs [shortest centroid-centroid separation = 3.6012?(11)?Å].

| S-EPMC3089147 | biostudies-literature

Hydrogen-bond inter-actions in morpholinium bromide.

Project description:In the title compound, C(4)H(10)NO(+)·Br(-), which was synthesized by dehydration of diethano-lamine with HBr, morpholinium and bromide ions are linked into chains by N-H?Br hydrogen bonds describing a C(2) (1)(4) graph-set motif. Weaker bifurcated N-H?Br inter-actions join centrosymmetrically related chains through alternating binary graph-set R(4) (2)(8) and R(2) (2)(4) motifs, to form ladders along [100]. In addition, C-H?O inter-actions between centrosymmetric morpholinium cations link ladders, via[Formula: see text](8) motifs, to yield sheets parallel to (101), which in turn are crosslinked by weak C-H?O inter-actions, related across a glide plane, to form a three-dimensional network.

| S-EPMC3201370 | biostudies-literature

Crystal structures of 6-chloro-indan-1-one and 6-bromo-indan-1-one exhibit different inter-molecular packing inter-actions.

Project description:The two title compounds are analogs of 1-indanone that are substituted at the 6-position with chlorine and bromine. Although very similar in mol-ecular structure, the crystal structures are not isomorphous and reveal that 6-chloro-indan-1-one, C9H7ClO (I), and 6-bromo-indan-1-one, C9H7BrO (II), exhibit unique inter-molecular packing motifs. The mol-ecules of the chloro analog (I) pack with a herringbone packing motif of C-H?O inter-actions, whereas the bromo derivative (II) packs with offset face-to-face ?-stacking, C-H?O, C-H?Br and Br?O inter-actions. Compound (II) was refined as a two-component non-merohedral twin, BASF 0.0762?(5).

| S-EPMC5095827 | biostudies-other

The crystal structures of three disordered 2-substituted benzimidazole esters.

Project description:The crystal structures of three benzimidazole esters containing aryl or heterocyclic substituents at position 2 are reported, and all three exhibit disorder of mol-ecular entities. In ethyl 1-methyl-2-[4-(prop-2-yn-oxy)phen-yl]-1H-benzimidazole-5-carboxyl-ate, C20H18N2O3, (I), the prop-2-yn-1-oxyphenyl unit is disordered over two sets of atomic sites having effectively equal occupancies, 0.506 (5) and 0.494 (5). The propyl substituent in ethyl 1-propyl-2-(pyren-1-yl)-1H-benzimidazole-5-carboxyl-ate, C29H24N2O2, (II), is disordered over two sets of atomic sites having occupancies 0.601 (8) and 0.399 (8), and the ester unit in ethyl 1-methyl-2-(5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1H-benzimidazole-5-carboxyl-ate, C21H19ClN4O2 (III), is disordered over two sets of atomic sites having occupancies 0.645 (7) and 0.355 (7). In each of the C-H⋯π(arene) hydrogen bonds in (I), the donor and acceptor form parts of different disorder components, so that no continuous aggregation is possible. The mol-ecules of (II) are linked by a single C-H⋯O hydrogen bond into C(10) chains, which are linked into sheets by a π-π stacking inter-action, whereas those of (III) are just linked into C(13) chains, again by a single C-H⋯O hydrogen bond. Comparisons are made with the structures of some related compounds.

| S-EPMC8100276 | biostudies-literature

Three closely related 1-[(1,3-benzodioxol-5-yl)methyl]-4-(halobenzo-yl)piperazines: similar mol-ecular structures but different inter-molecular inter-actions.

Project description:In each of the compounds 1-[(1,3-benzodioxol-5-yl)methyl]-4-(3-fluoro-benzo-yl)piperazine, C19H19FN2O3 (I), 1-[(1,3-benzodioxol-5-yl)methyl]-4-(2,6-di-fluoro-benzo-yl)piperazine, C19H18F2N2O3 (II), and 1-[(1,3-benzodioxol-5-yl)methyl]-4-(2,4-di-chloro-benzo-yl)piperazine, C19H19Cl2N2O3 (III), the piperazine rings adopt a chair conformation with the (1,3-benzodioxol-5-yl)methyl substituent occupying an equatorial site: the five-membered rings are all slightly folded across the O?O line leading to envelope conformations. The dihedral angle between the planar amidic fragment and the haloaryl ring is 62.97?(5)° in (I) but 77.72?(12)° and 75.50?(5)° in (II) and (III), respectively. Despite their similarity in constitution and conformation, the supra-molecular inter-actions in (I)-(III) differ: in (I), a combination of C-H?O and C-H??(arene) hydrogen bonds links the mol-ecules into a three-dimensional framework structure, but there are no hydrogen bonds of any sort in either (II) or (III), although the structure of (III) contains a short Cl?Cl contact between inversion-related pairs of mol-ecules.

| S-EPMC6362650 | biostudies-literature

Substituted Benzimidazole Analogues as Potential α-Amylase Inhibitors and Radical Scavengers.

Project description:Benzimidazole scaffolds are known to have a diverse range of biological activities and found to be antidiabetic and antioxidant. In this study, a variety of arylated benzimidazoles 1-31 were synthesized. Except for compounds 1, 6, 7, and 8, all are new derivatives. All compounds were screened for α-amylase inhibitory, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities. In vitro screening results revealed that all molecules demonstrated significant α-amylase inhibition with IC50 values of 1.86 ± 0.08 to 3.16 ± 0.31 μM as compared to standard acarbose (IC50 = 1.46 ± 0.26 μM). However, compounds showed significant ABTS and DPPH radical scavenging potentials with IC50 values in the range of 1.37 ± 0.21 to 4.00 ± 0.10 μM for ABTS and 1.36 ± 0.09 to 3.60 ± 0.20 μM for DPPH radical scavenging activities when compared to ascorbic acid with IC50 values of 0.72 ± 0.21 and 0.73 ± 0.05 μM for ABTS and DPPH radical scavenging potentials, respectively. Structure-activity relationship (SAR) was established after critical analysis of varying substitution effects on α-amylase inhibitory and radical scavenging (ABTS and DPPH) potentials. However, molecular docking was also performed to figure out the active participation of different groups of synthetic molecules during binding with the active pocket of the α-amylase enzyme.

| S-EPMC8427641 | biostudies-literature

Host-guest supra-molecular inter-actions between a resorcinarene-based cavitand bearing a -COOH moiety and acetic acid.

Project description:The cavitand 5,11,17,23-tetra-methyl-4,24:6,10:12,16:18,22-tetra-kis-(methyl-enedi-oxy)resorcin[4]arene functionalized at the upper rim with a carb-oxy-lic acid group, CavCOOH-in, of chemical formula C37H32O10, was synthesized in order to study its supra-molecular inter-actions with acetic acid in the solid state. Crystals suitable for X-ray diffraction analysis were obtained by slow evaporation of a di-chloro-methane-acetone solution of CavCOOH-in, to which glacial acetic acid had been added. The resulting compound, C37H32O10·2C2H4O2 (1) crystallizes in the space group P and its asymmetric unit consists of one mol-ecule of cavitand and two mol-ecules of acetic acid, one of which is encapsulated inside the aromatic cavity and disordered over two positions with a refined occupancy ratio of 0.344?(4):0.656?(4). The guest inter-acts with the host primarily through its methyl group, which (in both orientations) forms C-H?? inter-actions with the benzene rings of the cavitand. The crystal structure of 1 is dominated by O-H?O and C-H?O hydrogen bonding due to the presence of acetic acid and of the carb-oxy-lic group functionalizing the upper rim. Further stabilization is provided by offset ?-? stacking inter-actions between the aromatic walls of adjacent cavitands [inter-centroid distance = 3.573?(1)?Å].

| S-EPMC6399691 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data