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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:21:49 UTC

Update Date

2023-02-21 17:27:12 UTC

HMDB ID

HMDB0039826

Secondary Accession Numbers

HMDB39826

Metabolite Identification

Common Name

xi-2-Methyl-1,3-oxathiane

Description

xi-2-Methyl-1,3-oxathiane belongs to the class of organic compounds known as oxathianes. Oxathianes are compounds containing an oxathiane moiety, which consists of a saturated aliphatic six-member ring with one oxygen atom, a sulfur atom, and four carbon atoms. Isomers of oxaphospholane include 1,2-oxathiane, 1,3-oxathiane,and 1,4-oxathiane. xi-2-Methyl-1,3-oxathiane has been detected, but not quantified in, several different foods, such as red onion, green onion, welsh onions (Allium fistulosum), garden onions (Allium cepa), and garden onion (var.). This could make XI-2-methyl-1,3-oxathiane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on xi-2-Methyl-1,3-oxathiane.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₅H₁₀OS

Average Molecular Weight

118.197

Monoisotopic Molecular Weight

118.045235632

IUPAC Name

2-methyl-1,3-oxathiane

Traditional Name

2-methyl-1,3-oxathiane

CAS Registry Number

Not Available

SMILES

CC1OCCCS1

InChI Identifier

InChI=1S/C5H10OS/c1-5-6-3-2-4-7-5/h5H,2-4H2,1H3

InChI Key

VKZBKCJAWXBYBF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxathianes. Oxathianes are compounds containing an oxathiane moiety, which consists of a saturated aliphatic six-member ring with one oxygen atom, a sulfur atom, and four carbon atoms. Isomers of oxaphospholane include 1,2-oxathiane, 1,3-oxathiane,and 1,4-oxathiane.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxathianes

Sub Class

Not Available

Direct Parent

Oxathianes

Alternative Parents

Substituents

1,3-oxathiane
Monothioacetal
Oxacycle
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0039826)
Cytoplasm (HMDB: HMDB0039826)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039826)

Source

Exogenous

Exogenous (HMDB: HMDB0039826)

Food

Food (HMDB: HMDB0039826)

Herb and spice

Herb

Welsh onion (FooDB: FOOD00241)

Vegetable

Onion-family vegetable

Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Endogenous

Plant

Plant (HMDB: HMDB0039826)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039826)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	9.11 g/L	ALOGPS
logP	1.38	ALOGPS
logP	0.91	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	9.23 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	32.77 m³·mol⁻¹	ChemAxon
Polarizability	12.89 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	124.088	31661259
DarkChem	[M-H]-	118.908	31661259
DeepCCS	[M+H]+	130.627	30932474
DeepCCS	[M-H]-	128.635	30932474
DeepCCS	[M-2H]-	164.253	30932474
DeepCCS	[M+Na]+	138.892	30932474
AllCCS	[M+H]+	122.0	32859911
AllCCS	[M+H-H2O]+	117.1	32859911
AllCCS	[M+NH4]+	126.5	32859911
AllCCS	[M+Na]+	127.8	32859911
AllCCS	[M-H]-	128.3	32859911
AllCCS	[M+Na-2H]-	131.5	32859911
AllCCS	[M+HCOO]-	135.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	2.89 minutes	32390414
Predicted by Siyang on May 30, 2022	12.8149 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.34 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	45.3 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1642.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	471.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	170.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	319.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	172.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	492.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	551.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	140.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1042.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	340.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1084.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	370.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	321.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	481.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	470.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	98.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
xi-2-Methyl-1,3-oxathiane	CC1OCCCS1	1346.0	Standard polar	33892256
xi-2-Methyl-1,3-oxathiane	CC1OCCCS1	934.7	Standard non polar	33892256
xi-2-Methyl-1,3-oxathiane	CC1OCCCS1	926.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - xi-2-Methyl-1,3-oxathiane GC-MS (Non-derivatized) - 70eV, Positive	splash10-0706-9000000000-e71e1ee0dce3827b5af1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-2-Methyl-1,3-oxathiane GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-2-Methyl-1,3-oxathiane GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 10V, Positive-QTOF	splash10-014i-1900000000-f2961677f151f2f3ef8f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 20V, Positive-QTOF	splash10-0wor-9400000000-f7394b09221ff407001a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 40V, Positive-QTOF	splash10-0006-9000000000-f22ae4c36d3354f6090c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 10V, Negative-QTOF	splash10-014i-9800000000-60d86965befd02db6445	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 20V, Negative-QTOF	splash10-0a4i-9000000000-3bd1217b782854ba6bcc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 40V, Negative-QTOF	splash10-0a4i-9000000000-f8a4c04facb9918b604d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 10V, Positive-QTOF	splash10-01b9-9600000000-244c7bb57c1c248b64b2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 20V, Positive-QTOF	splash10-00di-9100000000-40aff4e3296a038ec37a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 40V, Positive-QTOF	splash10-006t-9000000000-d085344f4622b45f45cf	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 10V, Negative-QTOF	splash10-0bt9-9000000000-00b2264f306b5228b3d8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 20V, Negative-QTOF	splash10-05i3-9000000000-141ebc7e671696736c47	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-2-Methyl-1,3-oxathiane 40V, Negative-QTOF	splash10-00di-9000000000-64d8b95641ef9a0fff7e	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB019479

KNApSAcK ID

Not Available

Chemspider ID

472581

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

542685

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for xi-2-Methyl-1,3-oxathiane (HMDB0039826)

MOL for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

3D MOL for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

3D SDF for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

3D-SDF for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

PDB for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

3D PDB for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

SMILES for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

INCHI for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

Structure for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

3D Structure for HMDB0039826 (xi-2-Methyl-1,3-oxathiane)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra