SM(d18:1/24:1(15Z)) (13-11-9) Physical and Chemical Properties
SM(d18:1/24:1(15Z))
A very‑long‑chain sphingomyelin (d18:1/24:1) used as a lipid standard and membrane component for lipidomics, analytical method development and membrane biophysics research.
| CAS Number | 13-11-9 |
| Family | Sphingomyelins (sphingolipids) |
| Typical Form | Powder or crystalline solid |
| Common Grades | BP, EP |
SM(d18:1/24:1(15Z)) is a ceramide phosphocholine (sphingomyelin) species: a phosphosphingolipid with an \(\mathrm{d18:1}\) sphingoid base backbone N-acylated by a (15Z)-tetracosenoyl (\(\mathrm{C_{24:1}}\)) fatty chain. Structurally it combines a polar phosphocholine headgroup, a secondary amide linking the long N-acyl chain to the sphingoid base, and two long aliphatic hydrocarbon segments (sphingoid and N-acyl chains) that dominate hydrocarbon volume and impart strong amphiphilicity. The molecule contains two defined stereocenters and two C=C double bonds with defined geometry (including a \((15Z)\) olefin in the N-acyl chain), and it is a zwitterionic inner-salt in physiological contexts due to the charged phosphate–trimethylammonium headgroup balanced internally.
Key electronic and physicochemical attributes: molecular formula C47H93N2O6P and computed molecular weight 813.2 (see table below for other computed descriptors). The headgroup confers significant polarity and hydrogen-bonding capacity (hydrogen-bond donors = 2; acceptors = 6; topological polar surface area = 108 \(\text{Å}^2\)), while the very long hydrocarbon chains produce a high calculated lipophilicity (XLogP = 15.7) and extremely large hydrophobic surface area. The net formal charge is 0 for the neutral covalent structure, but the phosphocholine moiety produces a permanent internal charge separation that governs membrane association and interactions with cations and cholesterol.
In practical terms this combination gives behavior typical of membrane sphingomyelins: strong partitioning into lipid bilayers and ordered domains, low aqueous solubility, and thermal/enzymatic mobilities dictated by acyl chain length and unsaturation. The presence of a single cis double bond at the 15-position in the acyl chain reduces acyl-chain packing relative to the fully saturated homolog but retains high ordering compared with shorter-chain sphingomyelins. Enzymatic hydrolysis (e.g., sphingomyelinases, phospholipases) and oxidative attack at unsaturated sites are the principal biochemical transformation routes. Functionally, members of this class are widely recognized as membrane structural lipids, contributors to lipid-raft formation and modulators of signaling via ceramide generation.
Common commercial grades reported for this substance include: BP, EP.
Molecular Overview
Molecular Weight and Composition
- Molecular formula: C47H93N2O6P
- Molecular weight: 813.2 \(\mathrm{g}\,\mathrm{mol}^{-1}\)
- Exact mass: 812.67712569 (reported exact/monoisotopic mass)
- Monoisotopic mass: 812.67712569
The high molecular weight and extensive hydrocarbon content yield a bulky amphiphile that is essentially non-volatile and will partition strongly into nonpolar phases or membranes. The exact/monoisotopic mass is consistent with the listed elemental composition and is the appropriate value for high-resolution mass spectrometric confirmation.
Charge, Polarity, and LogP
- Formal charge: 0
- Topological polar surface area (TPSA): 108 \(\text{Å}^2\)
- Hydrogen-bond donor count: 2
- Hydrogen-bond acceptor count: 6
- XLogP3-AA (computed): 15.7
Although the formal covalent charge is neutral, the phosphocholine headgroup produces a localized ion pair (positively charged trimethylammonium and negatively charged phosphate) that determines aqueous interfacial behavior. The TPSA and H-bonding counts reflect a polar headgroup capable of hydration and hydrogen bonding, whereas the very high computed XLogP indicates dominant hydrophobic character driven by the two long aliphatic chains; consequently, aqueous solubility is negligible and partitioning into lipid membranes and nonpolar solvents is pronounced.
Biochemical Classification
- Chemical class: Lipids -> Sphingolipids -> Phosphosphingolipids [SP03] -> Ceramide phosphocholines (sphingomyelins) [SP0301]
- IUPAC name (computed): [(E,2S,3R)-3-hydroxy-2-[[(Z)-tetracos-15-enoyl]amino]octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate
This compound is a sphingomyelin species (commonly abbreviated SM), specifically an \(\mathrm{d18:1/24:1(15Z)}\) sphingomyelin. As a phosphosphingolipid it is classed with membrane phospholipids that have a sphingoid base rather than glycerol backbone.
Chemical Behavior
Stability and Degradation
Physical description: Solid.
Conformer generation for 3D modeling may be problematic for highly flexible, large lipids; for this compound conformer generation is disallowed due to size and flexibility. As with related sphingomyelins, chemical stability under neutral conditions is high; thermal degradation requires elevated temperatures. The unsaturated acyl chain introduces susceptibility to oxidative degradation (lipid peroxidation) at the cis double bond under aerobic, radical-promoting conditions. Hydrolytic stability is moderate in neutral aqueous buffers but decreases under acidic or alkaline extremes; elevated temperature and strong acids or bases will promote cleavage of the phosphoester and amide linkages.
Hydrolysis and Transformations
Biochemically, the principal transformation is enzymatic: hydrolysis of the phosphocholine headgroup by sphingomyelinases generates ceramide and a phosphocholine derivative, while sphingomyelin synthases interconvert ceramide and sphingomyelin in metabolic pathways. Phospholipases and nonspecific esterases may act on the phosphate linkage under harsh conditions. Nonenzymatic cleavage of the amide bond requires more forcing conditions (strong acid or base and heat). The single cis double bond at C-15 of the N-acyl chain is the primary site for oxidative attack leading to peroxidation products; such oxidative modifications alter membrane packing and can be recognized by cellular repair or signaling systems.
Biological Role
Functional Role and Pathways
SM(d18:1/24:1(15Z)) functions as a structural lipid in membranes and as a metabolic precursor/reservoir for ceramide-mediated signaling. Sphingomyelins participate in the formation of ordered membrane microdomains (lipid rafts) through favorable interactions with cholesterol and saturated sphingolipid chains; the long \(\mathrm{C_{24:1}}\) acyl chain contributes to interleaflet interactions and membrane thickness modulation. Enzymatic hydrolysis by sphingomyelinases releases ceramide, a bioactive lipid involved in apoptosis, cell differentiation, and stress responses. This species therefore sits at the intersection of membrane biophysics and sphingolipid metabolic pathways.
Pathways: central to sphingolipid metabolism and turnover; interconversion with ceramide and complex sphingolipids via sphingomyelinases and synthases is expected.
Physiological and Cellular Context
Cellular locations reported: extracellular; membrane. Tissue location reported: placenta. Additional organismal reports note presence of C24:1 sphingomyelin in Trypanosoma brucei and Ailuropoda melanoleuca. In cellular membranes this sphingomyelin species will preferentially localize to the outer leaflet and to ordered domains, influencing membrane curvature, rigidity, and protein partitioning. Clinical associations have been reported in diverse contexts (e.g., metabolic and inflammatory conditions); changes in sphingomyelin species distributions are frequently observed in pathophysiological lipidomic studies.
Identifiers and Synonyms
Registry Numbers and Codes
- CAS number: 13-11-9
- ChEBI ID: CHEBI:74535
- ChEMBL ID: CHEMBL4545046
- HMDB ID: HMDB0012107
- LIPID MAPS ID (LM_ID): LMSP03010007
- Metabolomics Workbench ID: 30732
- Wikidata: Q27144714
- InChIKey: WKZHECFHXLTOLJ-QYKFWSDSSA-N
- InChI: InChI=1S/C47H93N2O6P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-26-27-29-31-33-35-37-39-41-47(51)48-45(44-55-56(52,53)54-43-42-49(3,4)5)46(50)40-38-36-34-32-30-28-19-17-15-13-11-9-7-2/h20-21,38,40,45-46,50H,6-19,22-37,39,41-44H2,1-5H3,(H-,48,51,52,53)/b21-20-,40-38+/t45-,46+/m0/s1
- SMILES: CCCCCCCCCCCCC/C=C/C@HO
(Identifiers are presented exactly as supplied; SMILES, InChI and InChIKey are shown as plain text.)
Synonyms and Biological Names
Reported synonyms (depositor-supplied and common names): - SM(d18:1/24:1(15Z)) - N-(15Z-tetracosenoyl)-sphing-4-enine-1-phosphocholine - RefChem:1098598 - C24:1 Sphingomyelin - 94359-13-4 - N-Nervonoyl-D-erythro-sphingosylphosphorylcholine - 24:1 SM - [(E,2S,3R)-3-hydroxy-2-[[(Z)-tetracos-15-enoyl]amino]octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate - N-[(15Z)-tetracosenoyl]sphing-4-enine-1-phosphocholine - Additional systematic and depositor-supplied name variants as provided by suppliers and lipidomic annotations
Safety and Handling Overview
High-level guidance for handling this class of biochemical substances: - Physical state: solid; non-volatile under ambient conditions. - Primary hazards arise from the material being an organic biochemical reagent: skin and eye contact should be avoided (use nitrile gloves, safety glasses), and standard laboratory PPE should be used when handling powders or solutions. - Because of negligible volatility, inhalation risk from vapors is low, but dust generation should be controlled to prevent respiratory irritation and contamination of analytical workflows. - The long-chain unsaturated acyl group is susceptible to oxidative degradation; store protected from air and light for long-term stability. - For detailed hazard, transport and regulatory information, users should refer to the product-specific Safety Data Sheet (SDS) and local legislation.
Handling and Storage of Biochemical Materials
- Storage: recommended at low temperature (refrigerated or frozen) and in a desiccated, dark environment to minimize hydrolysis and oxidative rancidity. For long-term storage, inert atmosphere (e.g., argon) or antioxidants may be used to reduce oxidative degradation; avoid repeated freeze–thaw cycles which can promote aggregation or hydrolysis.
- Solubility and formulation: essentially insoluble in water; dissolve or disperse in appropriate organic solvents (e.g., chloroform, methanol mixtures) or lipid-compatible buffers with care to avoid hydrolysis. When preparing dispersions for biological assays, use sonication or established lipid reconstitution procedures to form vesicles or micelles as required.
- Compatibility: avoid strong acids/bases and prolonged exposure to elevated temperatures; these conditions accelerate cleavage of phosphoester and amide linkages.
- Waste and disposal: collect contaminated materials as organic laboratory waste and dispose of per institutional hazardous-waste procedures.
Analytical notes: collision cross section (CCS) values and mass spectrometric data useful for identification are available for this compound and its adducts; see spectral data below for reference.
- Collision cross sections (reported): 305.1 \(\text{Å}^2\) [M+HCOO]- (DT, N2, zebrafish sample); 304.5 \(\text{Å}^2\) [M+H]+ (DT, N2, human plasma sample); 307.6 \(\text{Å}^2\) [M+CH3COO]- (DT, N2, human BALF sample).
- Representative MS/MS precursor and spectral information: precursor m/z (MS2, [M+H]+) = 813.6844; common fragment peaks include m/z 795.7, 736.6, 630.7. Several LC–MS experimental MS2 spectra and qTOF negative-mode precursor data (e.g., precursor m/z 797.653, top peak 797.651306) are reported for analytical confirmation.
