This compound belongs to the class of organic compounds known as sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.
1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.
Zertifikate (CoA, COO, BSE/TSE und Analyse-Diagramm)
C of A & Other Certificates(BSE/TSE, COO):
Analytical Chart:
Chemische und physikalische Eigenschaften
Molekulargewicht
302.360 g/mol
XLogP3
1.400
Hydrogen Bond Donor Count
3
Hydrogen Bond Acceptor Count
6
Rotatable Bond Count
8
Exact Mass
302.173 Da
Monoisotopic Mass
302.173 Da
Topological Polar Surface Area
96.200 Ų
Heavy Atom Count
21
Formal Charge
0
Complexity
343.000
Isotope Atom Count
0
Defined Atom Stereocenter Count
5
Undefined Atom Stereocenter Count
0
Defined Bond Stereocenter Count
1
Undefined Bond Stereocenter Count
0
The total count of all stereochemical bonds
1
Covalently-Bonded Unit Count
1
Lösungsrechner
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Application Protocols
No vendor-validated protocols are provided for this item. The following general, literature-style workflows can help design experiments; they are offered as examples only and are not product specifications.
C. elegans plate assay (aggregation/dauer cues):
Prepare a 10–50 mM DMSO stock of ascaroside C9.
Spot 1–10 µL of diluted working solution onto seeded NGM agar to achieve the desired surface dose (e.g., low pmol–nmol range per plate, per literature); allow solvent to absorb/evaporate.
Add synchronized worms; score behavior/development after defined intervals. Include vehicle-only controls at matched DMSO.
LC-MS calibration curve for metabolomics:
Prepare serial dilutions in 50:50 water:MeOH (0.1% formic acid if analyzing in positive mode, or ammonium acetate for negative mode).
Spike into matrix blanks (worm extract) to construct matrix-matched standards.
Analyze by reversed-phase LC (C18) with a water/MeOH gradient; monitor exact masses and diagnostic fragments.
Aqueous dosing solution for liquid culture:
Dilute DMSO stock into M9 or minimal buffer to ≤0.5% DMSO.
Mix vigorously; filter-sterilize if required.
Use promptly or store cold, protected from light.
Always optimize concentration ranges empirically, as effects are highly concentration-dependent. Record solvent percentages and plate/buffer composition for reproducibility.
Biological Roles
General/literature overview (for research context; not a medical/clinical claim):
Pheromonal signaling: Ascaroside C9 belongs to the ascaroside family of small-molecule signals produced by nematodes, notably Caenorhabditis elegans. These molecules integrate environmental cues (population density, food availability) into behavioral and developmental decisions.
Dauer and development: In C. elegans, specific ascarosides modulate dauer entry/exit via G protein–coupled receptors (GPCRs) expressed on sensory neurons. Side-chain length and headgroup substitutions fine-tune potency and receptor selectivity. C9-length ascarosides are among the most studied benchmarks in this context.
Social/foraging behaviors: Ascaroside blends affect aggregation, avoidance, mating, and foraging, often in a concentration-dependent and synergistic manner. C9 motifs commonly serve as essential components of attractive or repellent blends, providing a reference point in SAR studies.
Metabolism/biogenesis: Biosynthesized from peroxisomal β-oxidation of long-chain fatty acids, coupled to the deoxy sugar ascarylose through glycosylation pathways; side-chain truncation to C9 reflects iterative β-oxidation steps.
Cross-species ecology: Ascarosides act as interspecies cues among nematodes and potentially microbes, shaping community dynamics in soil microhabitats.
Experimental implications:
Precise dosing and solvent controls are crucial, as effects can invert with concentration.
Matrix interactions (agar, plasticware) can sequester amphiphiles; pre-equilibration and adsorption controls improve reproducibility.
Use chemically defined stocks (purity, isomer ratio) to deconvolute biological responses.
Buffer Applications
This product is not a buffer or buffering reagent. However, it is frequently dosed into biological buffers for assays. The following general guidance is provided for practical laboratory use (literature-based; not product specifications):
Stock preparation: Dissolve in anhydrous DMSO or methanol to 10–50 mM. For aqueous systems, dilute the organic stock into buffer with vigorous mixing; final organic solvent content typically kept ≤0.5% v/v to limit solvent effects on organisms or enzymes.
Compatible buffers: Phosphate-buffered saline (PBS), M9, MOPS, HEPES, and other neutral buffers commonly used in C. elegans culture. Maintain pH 7.0–7.4 to minimize glycosidic hydrolysis and preserve enone integrity.
Solubilization aids: A minimal amount of Tween-20 (≤0.01%) or cyclodextrin may improve dispersion at very low organic cosolvent, but evaluate for biological inertness in your system.
Filtration: If visible particulates occur upon dilution, clarify with a 0.22 µm PTFE or PVDF syringe filter; avoid cellulose esters if using high organic content.
Storage of working solutions: Prepare fresh daily for sensitive bioassays; for multi-day use, refrigerate buffers containing the compound and protect from light. Monitor for precipitation.
Note: Buffer capacity, ionic strength, and additives (e.g., peptone in NGM media) can affect adsorption and apparent potency. Include vehicle-only and matrix-only controls.
Green Alternatives
Because ascaroside C9 is typically handled as a standard or bioactive reference, the main green chemistry lever is solvent choice and minimization of waste during solution preparation and analysis.
Replace high-toxicity aprotic solvents where possible. For initial dissolution, DMSO is common; for dilutions, switch to aqueous buffers with ≤0.5% DMSO to reduce solvent load.
For workups/purification in synthesis, consider 2-methyltetrahydrofuran (2-MeTHF) or cyclopentyl methyl ether (CPME) instead of dichloromethane or THF when compatible with the glycoside and enone functionality.
Use ethanol or isopropanol instead of acetonitrile for certain LC methods if sensitivity allows; however, note viscosity and backpressure tradeoffs.
Small comparison (general guidance):
DMSO: high bp, low volatility; worker exposure lower; difficult to remove; generally greener than DMF/NMP in acute toxicity profile.
MeOH/EtOH: renewable routes available; flammable; readily biodegradable; effective for dissolution but evaporative losses can cause concentration drift.
2-MeTHF/CPME: bio-based (2-MeTHF), low peroxide formation relative to ethers like THF, water-tolerant; check for compatibility with sugar-containing molecules and avoid strong acid conditions that may hydrolyze glycosides.
Operational best practices:
Prepare concentrated stock once, aliquot into microvials to reduce repeated solvent use.
Adopt micro-scale bioassays and LC injections to minimize consumption.
Evaluate solid-phase extraction (SPE) with aqueous-compatible eluents to reduce chlorinated solvent usage in sample cleanup.
Pharmaceutical Uses
No pharmacopeial status, excipient role, or manufacturing use is specified for this item. This product is offered strictly for research use only.
General context (literature):
Ascarosides are natural signaling metabolites from nematodes and are not typical pharmaceutical excipients.
In drug discovery research, ascaroside standards can be used to study GPCR signaling pathways and chemosensory biology in model organisms, supporting target deconvolution or phenotypic screening workflows. These activities are preclinical and exploratory in nature.
Formulation considerations for research use: If formulating dosing solutions for in vivo model organisms (e.g., nematode plates or liquid culture), the compound is commonly delivered via solvent-spiked media or spotted onto agar. Excipient-like solubilizers (e.g., cyclodextrins) may be explored for improving aqueous dispersion but must be validated for biological neutrality.
Regulatory note: No claims are made regarding suitability for human or veterinary use. Do not use in diagnostic procedures or clinical applications. For any regulated application, consult your institutional guidelines and do not proceed without appropriate validation and approvals.
Physical Properties
Item-specific specifications (this product):
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Formula: Not specified for this item; refer to CoA/Spec Sheet.
Refractive index / UV cutoff / metal content / water content: Not specified for this item; refer to CoA/Spec Sheet.
General/literature characteristics for ascaroside-type C9 molecules (informational, not product specifications):
Physical state: typically solid to waxy solid at ambient temperature due to amphiphilic structure and hydrogen bonding in the sugar headgroup.
Solubility profile (literature): good in DMSO and methanol; moderate in ethanol and acetonitrile; limited in pure water without cosolvent; very low in nonpolar hydrocarbons. Aqueous solubility can be enhanced by minimal DMSO (≤1–2% v/v), cyclodextrins, or mild base if the carboxyl group is free.
Acid–base: if the terminal carboxyl is present, pKa typically ~4–5 (literature range for aliphatic carboxylic acids), favoring anionic form at neutral pH.
LogP/logD (literature expectations): intermediate due to sugar head (lowers logP) and C9 tail (raises logP); ionization at neutral pH will further reduce logD.
Thermal behavior: decomposition/softening before sharp melting may occur for glycosylated amphiphiles; avoid prolonged heating.
Note: Use these literature values only for planning; consult the item’s CoA for lot-specific physical data.
Quality and Grades
Item-specific grade/purity for SKU A1008203: Not specified for this item; refer to CoA/Spec Sheet.
Guidance on interpreting grades for small-molecule standards (general):
Research/biological standard grade: typically emphasizes identity confirmation (1H/13C NMR, HRMS) and defined purity by HPLC/UPLC and/or qNMR, suitable for bioassays and analytical calibration.
Chromatography/HPLC grade (if offered): low non-volatile residue and defined UV background—useful when the compound is used as a reference in LC-UV/LC-MS.
Synthetic grade: fit-for-purpose purity for chemical transformations where downstream purification is anticipated.
Identity and impurity considerations for ascarosides (general best practices):
Diastereomeric/isomeric purity: ascarosides can exist as E/Z isomers across the enone; verify isomer ratio by NMR or LC-MS. The sugar configuration (L-ascarylose, α-linkage) should be established by NMR coupling constants and optical rotation.
Counter-ions/salt form: free acid vs salt will affect solubility and mass balance; confirm on CoA.
Residual solvents and water: amphiphilic materials can retain alcohols/water; Karl Fischer and residual solvent profiles may be provided on CoA when applicable.
Documentation: For this specific item, consult the lot-specific Certificate of Analysis for purity method (e.g., HPLC area%), acceptance criteria, and any stabilizers or form (free acid, ester, or salt).
Reaction and Applications
Manufacturer Applications (catalog): For research use only. No specific application text was provided in the listing.
Expanded research context (literature/general):
Chemical ecology and behavior: Ascaroside C9 is a core member of the C. elegans pheromone blend used in studies of dauer formation, aggregation, mating, and interspecies signaling. It is commonly employed as a defined reference standard in behavioral bioassays and metabolomics.
Analytical calibration: Used as a standard in LC-MS/MS and GC-MS (after derivatization) workflows to quantify endogenous ascarosides in nematode extracts and environmental samples.
Structure–activity relationship (SAR): Employed to probe side-chain length effects (C7–C13 series), sugar modifications, and head-group alterations on receptor activation and behavioral outputs.
Chemical synthesis benchmarking: Serves as a target for method development in glycosylation, stereoselective formation of 4-hydroxy-2-enoate motifs, and protecting-group strategies on deoxy sugars.
Practical tips (general):
Stock solutions: Prepare in dry DMSO or methanol at 10–50 mM; store aliquots to minimize freeze–thaw and solvent evaporation. Validate concentration by UV or quantitative NMR where precision is required.
Adsorption: Amphiphiles can adsorb to plastics; use low-binding polypropylene or glass vials. For low-nanomolar assays, pre-rinse surfaces with diluted working solution.
Stability: Avoid prolonged exposure to strong acid/base and high temperatures; monitor for E/Z isomerization or hydrolysis by LC-MS.
Note: These are general research applications; consult primary literature for organism-specific dosing and assay conditions.
Reaction Conditions
No reaction conditions are specified for this catalog item. The following generalized conditions summarize common transformations used in the preparation or modification of ascaroside C9 (literature guidance; not product specifications):
Glycosylation to assemble the ascaroside:
Donor: ascarylose trichloroacetimidate or thioglycoside; Acceptor: C9 hydroxy-acid derivative.
Activators: TMSOTf, BF3·Et2O, or NIS/TfOH (for thio donors).
Solvents: CH2Cl2, toluene, or Et2O/CH2Cl2 mixtures; temperatures −78 to 0 °C to control α-selectivity.
Side-chain construction:
Wittig/Horner–Wadsworth–Emmons to install the 2-enoate from an aldehyde precursor; solvents THF or toluene; bases NaHMDS or K2CO3 depending on the reagent; temperatures −78 to room temperature; E/Z ratio tuned by reagent choice.
Aldol variants to introduce the 4-hydroxy functionality, followed by oxidation/elimination.
Protecting-group manipulations:
Benzyl ether hydrogenolysis (H2, Pd/C, EtOH/EtOAc) at ambient temperature; avoid over-reduction of the enone by careful monitoring.
Silyl ether deprotection with TBAF in THF at 0–25 °C; brief exposure minimizes enone isomerization.
Coupling at the carboxylate:
Esterification (e.g., MeOH/HCl(g) or DCC/DMAP) and amide formation (HATU/DIPEA, DMF or NMP alternatives like NBP/EtOAc) for probe synthesis.
Yields: Highly route- and substrate-dependent; multi-step sequences commonly deliver 20–40% overall from sugar and side-chain precursors. Always validate on small scale.
Safety and Handling
Authoritative safety information is provided in the product SDS. The following are general laboratory precautions for small-molecule glycoside pheromones and carboxylated amphiphiles.
GHS classification, signal word, pictograms, H-statements: Not specified for this item; refer to SDS.
Likely hazards (general): low volatility organic solid; may cause irritation to eyes/skin if contacted; ingestion/inhalation hazards typical of organic research chemicals. Not known to be highly flammable in solid form, but combustible—keep away from ignition sources.
Personal protective equipment (PPE): laboratory coat, safety glasses or goggles, and appropriate chemical-resistant gloves (e.g., nitrile). Use in a fume hood when weighing or preparing solutions to avoid dust or aerosol exposure.
Handling tips:
Avoid moisture introduction if performing microgram-scale bioassays that require accurate dosing; hygroscopicity can vary.
Prepare stock solutions in dry DMSO or methanol; cap tightly to prevent solvent evaporation and concentration drift.
If the free acid form is present, avoid strong bases/acids that may trigger hydrolysis of the glycosidic bond.
Incompatibilities (general): strong oxidizers; strong acids/bases (can hydrolyze glycosidic linkages); prolonged exposure to high heat and light may cause degradation (E/Z isomerization or oxidation of the enone side chain).
First aid (overview; see SDS):
Skin/eye contact: rinse with water for 15 minutes; remove contaminated clothing; seek medical evaluation if irritation persists.
Inhalation: move to fresh air; seek medical advice if symptoms occur.
Ingestion: rinse mouth; do not induce vomiting; seek medical attention.
Spill/cleanup: collect solids by gentle sweeping; for solutions, absorb with inert material; dispose according to institutional chemical waste protocols.
Solvent Selection
This compound is an amphiphilic glycoside with a C9 aliphatic tail and polar sugar headgroup. Solvent choice should balance dissolution, stability of the glycosidic linkage, and compatibility with downstream bioassays.
Highly effective solvents: DMSO, methanol. These provide rapid dissolution at mg/mL to tens of mg/mL for many ascarosides.
Moderately effective: ethanol, acetonitrile, isopropanol; warming (≤40 °C) and sonication can help.
Aqueous buffers: limited solubility as a free acid; small amounts of co-solvent (0.1–2% DMSO or MeOH) or mild basification (e.g., pH 7.4–8.0) can aid dissolution. Avoid strong base that may hydrolyze the glycosidic bond over time.
Poor solvents: alkanes (hexane, heptane); solubility is typically insufficient due to the polar headgroup.
Polarity context (literature):
Amphiphilic behavior can lead to micelle-like aggregation above certain concentrations in water; filtration through 0.22 µm PTFE can clarify stocks.
Comparison (general):
DMSO vs methanol: DMSO maximizes aqueous compatibility via serial dilution and minimizes evaporation; methanol offers low viscosity and rapid drying for plating assays but evaporates readily (risk of concentration drift).
Buffer compatibility: For C. elegans assays on agar plates or liquid culture, prepare concentrated DMSO stocks (e.g., 10–50 mM) and dilute into media to ≤0.5% DMSO final to avoid solvent effects (typical practice in literature).
Shipped In: Not specified for this item; refer to CoA/Spec Sheet.
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
General guidance for this compound class (literature/best practice; not product specifications):
Long-term storage: Keep the solid tightly sealed in a dry, inert atmosphere (desiccator with desiccant). Protect from prolonged exposure to light to minimize potential degradation of the unsaturated side chain.
Reconstitution: Dissolve in anhydrous DMSO or methanol to prepare concentrated stocks (e.g., 10–50 mM). Mix gently or sonicate briefly if needed. Filter through 0.22 µm PTFE for particle removal if preparing analytical standards.
Aliquoting: Divide stock solutions into single-use aliquots (amber vials or foil-wrapped microtubes) to avoid repeated freeze–thaw or evaporation. Cap promptly to prevent solvent loss.
Aqueous dilutions: Prepare immediately before use; maintain neutral pH (≈7) and minimize exposure to strong acids/bases that can hydrolyze the glycosidic bond. Limit final DMSO/MeOH content to levels tolerated by your assay system.
Stability checks: For critical work, verify concentration by qNMR or LC-UV upon reconstitution and after storage. Monitor for E/Z isomerization or hydrolysis by LC-MS.
Disposal: Dispose of unused solutions and waste according to institutional chemical waste procedures. Always consult the product’s SDS for authoritative handling and storage instructions.
Structure and Identity
Brief description: Ascaroside C9 is a nematode small-molecule pheromone consisting of an ascarylose (3,6-dideoxy sugar) glycosidically linked to a short-chain fatty acid–derived side chain with nine carbons ("C9").
SKU: A1008203
Product Name: ascaroside C9
CAS: 946524-26-1 (item-specific)
PubChem CID: 16066476 (item-specific)
InChIKey (as provided): 230180 — note: this appears non-standard/truncated; consult CoA/SDS for the full identifier.
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Formula: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Weight: Not specified for this item; refer to CoA/Spec Sheet.
Structural features (general literature description):
Core sugar: ascarylose (3,6-dideoxy-β-L-mannose) typically α-linked to the aglycone at C1.
Aglycone: a 4-hydroxy-2-enoic acid (or related oxoenoate) bearing a linear aliphatic side chain of nine carbons (C9 ascaridic side chain), often terminating in a carboxylate (free acid or ester forms appear across the family).
Functional groups: glycosidic ether, secondary alcohol(s) on the sugar ring, conjugated enone or hydroxyenoate in the side chain, terminal carboxylic acid (typical for isolated ascarosides).
2D description in words: a six-membered deoxy sugar ring bearing multiple axial/equatorial hydroxyls is connected via its anomeric center to an unsaturated, oxygenated C9 fatty-acid–like chain ending with a carboxyl group; overall amphiphilic, with a polar sugar head and a hydrophobic aliphatic tail.
Stereochemistry (literature): defined configuration on ascarylose (L-series); the glycosidic linkage is typically α. Exact stereochemical descriptors for this item’s batch are not specified; refer to CoA.
Synthetic Utility
While often used as a biological standard, ascaroside C9 also serves as a valuable synthetic target and intermediate in method development.
Key functional elements (general literature):
Glycosidic linkage on a deoxy sugar (ascarylose), enabling studies of stereoselective α-glycosylation with neighboring-group participation control absent (due to deoxy pattern).
Conjugated 4-hydroxy-2-enoate (or oxoenoate) side chain, allowing E/Z geometry control, conjugate addition, and selective oxidation/reduction.
Terminal carboxylic acid functionality that supports esterification, amidation, and salt formation.
Synthetic approaches (general):
Modular assembly: Prepare the C9 side-chain fragment (e.g., via Wittig/HWE olefination or aldol) and couple to a protected ascarylose donor/acceptor.
Glycosylation tactics: Trichloroacetimidate, glycosyl bromide/silver salts, or thioglycoside activation under mild Lewis acids to secure α-selectivity; careful protecting-group layout (e.g., benzyl vs silyl) facilitates late-stage deprotection without isomerizing the enone.
Final elaboration: Global deprotection (hydrogenolysis or fluoride-mediated) with conditions tuned to preserve the enone; optional conversion between free acid and methyl/ethyl esters for purification and stability.
Utility in derivatization:
Click handles or reporter tags can be introduced at the carboxylate (amide/ester) for pull-downs and imaging in chemical biology.
Isotopologues (13C, 2H) can be prepared at defined positions for quantitative metabolomics.
Note: These are literature-based strategies; for this catalog item, no specific synthetic route or impurity profile is claimed—consult CoA for identity and purity data.
Target Specificity
This section typically applies to biologics (e.g., antibodies) and targeted affinity reagents. Ascaroside C9 is a small-molecule pheromone standard, not an antibody or targeted biologic.
Specific receptor targets and binding constants in biological systems are organism- and receptor-dependent and are not specified for this item.
For studies in C. elegans, literature implicates several chemosensory GPCRs responsive to ascaroside motifs; however, precise target profiles vary with structural context and assay conditions.
Item-specific target/receptor data: Not specified for this item; refer to primary literature and your assay validation.
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