Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stereochemical revision of xylogranatin F by GIAO and DU8+ NMR calculations.

ABSTRACT: This manuscript describes predicted NMR shifts for the limonoid natural product xylogranatin F. The ¹ H and ¹³ C NMR shifts of four diastereomers were evaluated by GIAO and hybrid DFT/parametric DU8+ methods. The results of the ¹ H and ¹³ C NMR calculations for both the GIAO method and the DU8+ calculations suggest the revised structure that was recently reassigned by chemical synthesis. Furthermore, we show that while DU8+ provides superior accuracy with less computation time, GIAO points to the correct structure with more distinguishable data in this case study.

SUBMITTER: Liu Y

PROVIDER: S-EPMC8048713 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Coibacins A and B: total synthesis and stereochemical revision.

Project description:The interface between synthetic organic chemistry and natural products was explored in order to unravel the structure of coibacin A, a metabolite isolated from the marine cyanobacterium cf. Oscillatoria sp. that exhibits selective antileishmanial activity and potent anti-inflammatory properties. Our synthetic plan focused on a convergent strategy that allows rapid access to the desired target by coupling of three key fragments involving E-selective Wittig and modified Julia olefinations. CD measurements and comparative HPLC analyses of the natural product and four synthetic stereoisomers led to determination of its absolute configuration, thus correcting the original assignment at C-5 and unambiguously establishing those at C-16 and C-18. Additionally, we synthesized coibacin B on the basis of the assignment of configuration for coibacin A.

| S-EPMC3962765 | biostudies-literature

An enantioselective total synthesis and stereochemical revision of (+)-citrinadin B.

Project description:This manuscript describes an enantioselective synthesis of the naturally occurring alkaloid citrinadin B. The synthetic effort revealed an anomaly in the original structural assignment that has led to the proposal of a stereochemical revision. This revision is consistent with the structures previously reported for a closely related family of alkaloids, PF1270A-C. The synthesis is convergent and employs a stereoselective intermolecular nitrone cyloaddition reaction as a key step.

| S-EPMC6775640 | biostudies-literature

Enantioselective total synthesis of (-)-citrinadin A and revision of its stereochemical structure.

Project description:The first enantioselective total synthesis of (-)-citrinadin A has been accomplished in 20 steps from commercially available materials via an approach that minimizes refunctionalization and protection/deprotection operations. The cornerstone of this synthesis features an asymmetric vinylogous Mannich addition of a dienolate to a chiral pyridinium salt to set the initial chiral center. A sequence of substrate-controlled reactions, including a highly stereoselective epoxidation/ring-opening sequence and an oxidative rearrangement of an indole to furnish a spirooxindole, are then used to establish the remaining stereocenters in the pentacyclic core of (-)-citrinadin A. The successful synthesis of citrinadin A led to a revision of the stereochemical structure of the core substructure of the citrinadins.

| S-EPMC3748604 | biostudies-literature

DFT Calculations of 1H NMR Chemical Shifts of Geometric Isomers of Conjugated Linolenic Acids, Hexadecatrienyl Pheromones, and Model Triene-Containing Compounds: Structures in Solution and Revision of NMR Assignments.

Project description:A DFT study of the 1H NMR chemical shifts, δ(1H), of geometric isomers of 18:3 conjugated linolenic acids (CLnAs), hexadecatrienyl pheromones, and model triene-containing compounds is presented, using standard functionals (B3LYP and PBE0) as well as corrections for dispersion interactions (B3LYP-D3, APFD, M06-2X and ωB97XD). The results are compared with literature experimental δ(1H) data in solution. The closely spaced "inside" olefinic protons are significantly more deshielded due to short-range through-space H…H steric interactions and appear close to or even beyond δ-values of aromatic systems. Several regularities of the computational δ(1H) of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest-energy DFT-optimized single conformer for all functionals used and are in very good agreement with experimental δ(1H) in solution. Examples are provided of literature studies in which experimental resonance assignments deviate significantly from DFT predictions and, thus, should be revised. We conclude that DFT calculations of 1H chemical shifts of trienyl compounds are powerful tools (i) for the accurate prediction of δ(1H) even with less demanding functionals and basis sets; (ii) for the unequivocal identification of geometric isomerism of conjugated trienyl systems that occur in nature; (iii) for tackling complex problems of experimental resonance assignments due to extensive signal overlap; and (iv) for structure elucidation in solution.

| S-EPMC8201138 | biostudies-literature

Cryptocaryols A and B: total syntheses, stereochemical revision, structure elucidation, and structure-activity relationship.

Project description:The first total syntheses and structural elucidation of cryptocaryol A and cryptocaryol B were achieved in 23 and 25 linear steps, respectively. The synthesis relied on the use of a key pseudo-Cs symmetric pentaol intermediate, which in a stereochemically divergent manner was converted into either enantiomer as well as diastereomers. This synthetic effort enabled the first structure-activity relationships of this class of PDCD4 stabilizing natural products.

| S-EPMC3772640 | biostudies-literature

Enantioselective total syntheses of citrinadins A and B. Stereochemical revision of their assigned structures.

Project description:The concise, enantioselective total syntheses of (-)-citrinadin A and (+)-citrinadin B in a total of only 20 and 21 steps, respectively, from commercially available starting materials are described. Our strategy, which minimizes refunctionalization and protection/deprotection operations, features the highly diastereoselective, vinylogous Mannich addition of a dienolate to a chiral pyridinium salt to set the first chiral center. The absolute stereochemistry of this key center was then relayed by a sequence of substrate-controlled reactions, including a highly stereoselective epoxidation/ring opening sequence and an oxidative rearrangement of an indole to furnish a spirooxindole to establish the remaining stereocenters in the pentacyclic core of the citrinadins. An early stage intermediate in the synthesis of (-)-citrinadin A was deoxygenated to generate a dehydroxy compound that was elaborated into (+)-citrinadin B by a sequence of reaction identical to those used to prepare (-)-citrinadin A. These concise syntheses of (-)-citrinadin A and (+)-citrinadin B led to a revision of their stereochemical structures.

| S-EPMC4195386 | biostudies-literature

Magnetically Induced Alignment of Natural Products for Stereochemical Structure Determination via NMR.

Project description:Anisotropic NMR has gained increasing popularity to determine the structure and specifically the configuration of small, flexible, non-crystallizable molecules. However, it suffers from the necessity to dissolve the analyte in special media such as liquid crystals or polymer gels. Generally, small degrees of alignment are also caused by an anisotropic magnetic susceptibility of the molecule, for example, induced by aromatic moieties. For this mechanism, the alignment can be predicted via density functional theory. Here we show that both residual dipolar couplings and residual chemical shift anisotropies can be acquired from natural products without special sample preparation using magnetically induced alignment. On the two examples of the novel natural product gymnochrome G and the alkaloid strychnine, these data, together with the predicted alignment, yield the correct configuration with high certainty.

| S-EPMC7540557 | biostudies-literature

Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of (13)C chemical shifts.

Project description:In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of (13)C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of (13)C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

| S-EPMC3896268 | biostudies-literature

Oxygenated Theonellastrols: Interpretation of Unusual Chemical Behaviors Using Quantum Mechanical Calculations and Stereochemical Reassignment of 7α-Hydroxytheonellasterol.

Project description:A total of eight new oxygenated 4-exo-methylene sterols, 1-8, together with one artifact 9 and six known sterols 11-16, were isolated from the marine sponge Theonella swinhoei collected from the Bohol province in Philippines. Structures of sterols 1-8 were determined from 1D and 2D NMR data. Among the sterols, 8α-hydroxytheonellasterol (4) spontaneously underwent an allylic 1,3-hydroxyl shift to produce 15α-hydroxytheonellasterol (9) as an artifact; this was rationalized by quantum mechanical calculations of the transition state. In addition, the 1,2-epoxy alcohol subunit of 8α-hydroxy-14,15-β-epoxytheonellasterol (5) was assigned using the Gauge-Independent Atomic Orbital (GIAO) NMR chemical shift calculations and subsequent DP4+ analysis. Finally, comparison of the 13C chemical shifts of isolated 7α-hydroxytheonellasterol (6) with the reported values revealed significant discrepancies at C-6, C-7, C-8, and C-14, leading to reassignment of the C-7 stereochemistry in the known structure.

| S-EPMC7760259 | biostudies-literature

Concise total synthesis and stereochemical revision of (+)-naseseazines A and B: regioselective arylative dimerization of diketopiperazine alkaloids.

Project description:Concise and enantioselective total syntheses of (+)-naseseazines A and B are described. Our regioselective and directed dimerization of diketopiperazines provides their critical C3-C(sp(2)) linkages, an assembly with plausible biogenetic relevance. We revise the absolute stereochemistry of (+)-naseseazines A and B.

| S-EPMC3369503 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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