Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Fun HK

PROVIDER: S-EPMC3089143 | biostudies-other | 2011 May

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

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

Fun Hoong-Kun HK Chantrapromma Suchada S Salae Abdul Wahab AW Razak Ibrahim Abdul IA Karalai Chatchanok C

Acta crystallographica. Section E, Structure reports online 20110407 Pt 5

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 ...[more]

PMID: 21754362

Similar Datasets

Crystal structure and absolute configuration of preaustinoid A1.

Project description:The absolute structure of the title compound preaustinoid A1 [systematic name: (5aR,7aS,8R,10S,12R,13aR,13bS)-methyl 10-hy-droxy-5,5,7a,10,12,13b-hexa-methyl-14-methyl-ene-3,9,11-trioxohexa-deca-hydro-8,12-methano-cyclo-octa-[3,4]benzo[1,2-c]oxepine-8-carboxyl-ate], C26H36O7, has been determined by resonant scattering using Cu Kα radiation [Flack parameter = 0.07 (15)]. The structure is consistent with that reported previously [Stierle et al. (2011). J. Nat. Prod. 74, 2272-2277], determined by detailed analysis of MS and NMR data. The mol-ecule consists of a fused four-ring arrangement. The seven-membered oxepan-2-one ring has a chair conformation, as do the central cyclo-hexane rings, while the outer cyclo-hexa-1,3-dione ring has a boat conformation. In the crystal, mol-ecules are linked via O-H⋯O hydrogen bonds, forming helical chains propagating along [100].

| S-EPMC4571416 | biostudies-literature

Total synthesis, structure revision, and absolute configuration of (-)-brevenal.

Project description:Total synthesis of structure 1 originally proposed for brevenal, a nontoxic polycyclic ether natural product isolated from the Florida red tide dinoflagellate, Karenia brevis, was accomplished. The key features of the synthesis involved (i) convergent assembly of the pentacyclic polyether skeleton based on our developed Suzuki-Miyaura coupling chemistry and (ii) stereoselective construction of the multi-substituted (E,E)-dienal side chain by using copper(I) thiophen-2-carboxylate (CuTC)-promoted modified Stille coupling. The disparity of NMR spectra between the synthetic material and the natural product required a revision of the proposed structure. Detailed spectroscopic comparison of synthetic 1 with natural brevenal, coupled with the postulated biosynthetic pathway for marine polyether natural products, suggested that the natural product was most likely represented by 2, the C26 epimer of the proposed structure 1. The revised structure was finally validated by completing the first total synthesis of (-)-2, which also unambiguously established the absolute configuration of the natural product.

| S-EPMC2575246 | biostudies-literature

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

Project description: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.

| S-EPMC6362671 | biostudies-other

A Revised Structure and Assigned Absolute Configuration of Theissenolactone A.

Project description:Antimicrobial bioassay-guided fractionation of Microcera larvarum led to the isolation of a ?-lactone with a furo[3,4-b]pyran-5-one bicyclic ring system (1) and three known compounds, (3S,4R)-4-hydroxymellein (2), (3S,4S)-4-hydroxymellein (3) and 7-hydroxy-3-(1-hydroxyethyl)isobenzofuran-1(3H)-one (4). Structure elucidation was conducted by NMR spectroscopic methods. Absolute configuration of 1 (2R, 3S, 5S, 7S, 8R) was established using the chiral derivatizing agent MPA and was fully supported by calculated specific rotation and ECD spectra. The spectroscopic data observed for 1 were identical to those previously reported for theissenolactone A (7), necessitating a correction of the latter (from C-5/C-8 trans ring fusion to cis). Compounds 1-4 were evaluated for antimicrobial activity against a panel of pathogens.

| S-EPMC7587954 | biostudies-literature

Redetermined structure of oxaline: absolute configuration using Cu K? radiation.

Project description:In the title compound, C(24)H(25)N(5)O(4), the stereogenic C atom bonded to three N atoms and one C atom has an S configuration and its directly bonded neighbour has an R configuration. An intra-molecular N-H?O hydrogen bond supports the near coplanarity of the two C(3)N(2)-five-membered rings [dihedral angle = 5.64?(10)°]. In the crystal, mol-ecules are linked by N-H?N hydrogen bonds, forming a C(8) chain propagating in [001]. The chains are connected by C-H?O inter-actions, generating a three-dimensional network. The previous study [Nagel et al. (1974 ?). Chem. Commun. pp. 1021-1022] did not establish the absolute structure and no atomic coordinates were published or deposited.

| S-EPMC3379231 | biostudies-literature

Absolute configuration of odorine.

Project description:The title compound, known as odorine or roxburghiline {systematic name: (S)-N-[(R)-1-cinnamoylpyrrolidin-2-yl]-2-methyl-butanamide}, C(18)H(24)N(2)O(2), is a nitro-genous compound isolated from the leaves of Aglaia odorata. The absolute configuration was determined by refinement of the Flack parameter with data collected using Cu Kα radiation showing positions 2 and 2' to be S and R, respectively. The pyrrolidine ring adopts an envelope conformation. In the crystal, mol-ecules are linked into chains along [010] by inter-molecular N-H⋯O hydrogen bonds.

| S-EPMC3007931 | biostudies-literature

Absolute configuration of isoeichlerialactone.

Project description:The title seco-dammarane triterpenoid, C(27)H(42)O(4) (systematic name: 3-{(3S,3aR,5aR,6S,7S,9aR,9bR)-6,9a,9b-trimethyl-3-[(R)-2-methyl-5-oxotetra-hydro-furan-2-yl]-7-(prop-1-en-2-yl)dodeca-hydro-1H-cyclo-penta-[a]naphthalen-6-yl}propanoic acid), has been isolated for the first time from the seeds of Aglaia forbesii. The mol-ecule has three fused rings and all rings are in trans-fused. The two cyclo-hexane rings are in standard chair conformations and the cyclo-pentane ring adopts an envelope conformation. Its absolute configuration was determined by the refinement of the Flack parameter to 0.26 (17). In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds.

| S-EPMC2984085 | biostudies-literature

Absolute configuration of micromelin.

Project description:The title compound {systematic name: 7-meth-oxy-6-[(1R,2R,5R)-5-methyl-4-oxo-3,6-dioxabicyclo-[3.1.0]hexan-2-yl]-2H-chromen-2-one}, C(15)H(12)O(6), is a coumarin, which was isolated from the roots of Micromelum glanduliferum. There are two mol-ecules in the asymmetric unit with slight differences in bond angles. In both mol-ecules, the furan ring adopts a flattened envelope conformation. In the crystal, mol-ecules are linked by weak C-H?O inter-actions into chains along the a axis. Aromatic ?-? stacking inter-actions with centroid-centroid distances in the range 3.6995?(11)-3.8069?(11)?Å and C?O short contacts [3.030?(2)-3.171?(3)?Å] also occur.

| S-EPMC3151812 | biostudies-other

Absolute configuration of dolichol.

Project description:A derivative of dolichol was formed and then chemically degraded to a small fragment containing the sole centre of asymmetry of the original molecule. Polarimetric comparison of this derivative with a standard prepared from (R)-citronellol showed dolichol to have an S-configuration at C-3. To determine the optical purity of dolichol a diastereoisomeric derivative was prepared and compared with standard diastereoisomers, which could be resolved by high-pressure liquid chromatography. Dolichols from pig liver, human liver and hen oviduct were analysed by this procedure and were all found to be greater than 95% S-configuration.

| S-EPMC1162022 | biostudies-other

Isolation, Structure Elucidation, and Absolute Configuration of Germacrane Isomers from Carpesium divaricatum.

Project description:Five sets of germacrane isomers (1/8/17, 2/7/10/11/13/16/18, 3/4/5/14/20, 6/12/15, and 9/19) with different skeletal types, including seven new ones (1-3, 8-9, and 15-16) were isolated from the whole plant of Carpesium divaricatum. Among them, there are six pairs of stereoisomers (1/8, 2/13, 4/14, 6/12, 7/11 and 10/11). The planar structures and relative configurations of the new compounds were elucidated by detailed spectroscopic analysis. The absolute configurations of 4, 10, 11, and 17 were established by circular dichroism (CD) spectra and X-ray crystallographic analyses, and the stereochemistry of the new compounds 1-3, 8-9, and 15-16 were determined by similar CD spectra with 4, 10, 11, and 17, respectively. The confusion in the literature about subtypes I and II of germacranolides was clarified in this paper. The NMR data of 10-11, and the absolute configurations of the known compounds 4-6, 13-14, and 17-20 were reported for the first time. Compounds 13, 17, and 18 showed cytotoxicity against human cervical (HeLa), colon (LoVo) and stomach cancer (BGC-823) cell lines with IC50 values in the range 4.72-13.68 μM compared with the control cis-platin (7.90-15.34 μM).

| S-EPMC6102216 | 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