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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 19:49:48 UTC

Update Date

2023-02-21 17:24:29 UTC

HMDB ID

HMDB0034901

Secondary Accession Numbers

HMDB34901

Metabolite Identification

Common Name

2-Vinyl-4H-1,3-dithiine

Description

2-Vinyl-4H-1,3-dithiine belongs to the class of organic compounds known as dithiins. Dithiins are compounds comprising a dithiin ring, which is an unsaturated six-member heterocycle containing four carbon atoms, two sulfur atoms and two double bonds. 2-Vinyl-4H-1,3-dithiine is found, on average, in the highest concentration within soft-necked garlics (Allium sativum L. var. sativum). 2-Vinyl-4H-1,3-dithiine has also been detected, but not quantified in, several different foods, such as garden onions (Allium cepa), green onion, garlics (Allium sativum), onion-family vegetables, and garden onion (var.). This could make 2-vinyl-4H-1,3-dithiine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2-Vinyl-4H-1,3-dithiine.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Ethyltridecyl 3-bromobenzoate	HMDB
2-Ethenyl-4H-1,3-dithiin	HMDB
2-Ethenyl-4H-1,3-dithiine, 9ci	HMDB
2-Vdtii	HMDB
2-Vinyl-(4H)-1,3-dithiine	HMDB
2-Vinyl-4(H)-1,3-dithiin	HMDB
2-Vinyl-4H-1,3-dithiin	HMDB
2-Vinyl-4H-1,3-dithin	HMDB
2-Vinyl-[4H]-1,3-dithin	HMDB
3-Bromobenzoic acid, 3-pentadecyl ester	HMDB
4H-1,3-Dithiin, 2-ethenyl	HMDB

Chemical Formula

C₆H₈S₂

Average Molecular Weight

144.258

Monoisotopic Molecular Weight

144.006741636

IUPAC Name

2-ethenyl-2,4-dihydro-1,3-dithiine

Traditional Name

2-ethenyl-2,4-dihydro-1,3-dithiine

CAS Registry Number

80028-57-5

SMILES

C=CC1SCC=CS1

InChI Identifier

InChI=1S/C6H8S2/c1-2-6-7-4-3-5-8-6/h2-4,6H,1,5H2

InChI Key

XUKBDTUPIIADOP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dithiins. Dithiins are compounds comprising a dithiin ring, which is an unsaturated six-member heterocycle containing four carbon atoms, two sulfur atoms and two double bonds.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dithiins

Sub Class

Not Available

Direct Parent

Dithiins

Alternative Parents

Substituents

1,3-dithiin
Thioacetal
Thioenolether
Dialkylthioether
Thioether
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

an organosulfur compound (CPD-9295 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0034901)
Cytoplasm (HMDB: HMDB0034901)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034901)

Source

Exogenous

Exogenous (HMDB: HMDB0034901)

Food

Food (HMDB: HMDB0034901)

Herb and spice

Herb

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: HMDB0034901)

Process

Not Available

Role

Biological role

Industrial application

Agriculture

Pesticide (HMDB: HMDB0034901)

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	203.9 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.16 g/L	ALOGPS
logP	2.1	ALOGPS
logP	2.37	ChemAxon
logS	-3	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	43.22 m³·mol⁻¹	ChemAxon
Polarizability	15.31 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]+	127.44	31661259
DarkChem	[M-H]-	123.144	31661259
DeepCCS	[M+H]+	131.009	30932474
DeepCCS	[M-H]-	128.946	30932474
DeepCCS	[M-2H]-	164.51	30932474
DeepCCS	[M+Na]+	138.78	30932474
AllCCS	[M+H]+	125.9	32859911
AllCCS	[M+H-H2O]+	121.3	32859911
AllCCS	[M+NH4]+	130.1	32859911
AllCCS	[M+Na]+	131.4	32859911
AllCCS	[M-H]-	129.2	32859911
AllCCS	[M+Na-2H]-	131.8	32859911
AllCCS	[M+HCOO]-	134.6	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.	3.37 minutes	32390414
Predicted by Siyang on May 30, 2022	12.8384 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.3 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1497.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	327.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	93.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	215.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	60.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	258.6 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	374.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	229.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	739.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	277.9 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	942.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	226.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	242.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	449.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	285.1 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	113.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Vinyl-4H-1,3-dithiine	C=CC1SCC=CS1	1872.6	Standard polar	33892256
2-Vinyl-4H-1,3-dithiine	C=CC1SCC=CS1	1168.1	Standard non polar	33892256
2-Vinyl-4H-1,3-dithiine	C=CC1SCC=CS1	1197.1	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 - 2-Vinyl-4H-1,3-dithiine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0076-9300000000-427ec03e23132d179c77	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Vinyl-4H-1,3-dithiine 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 - 2-Vinyl-4H-1,3-dithiine 10V, Positive-QTOF	splash10-0002-0900000000-3e4031f35064cbb84c6c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Positive-QTOF	splash10-0002-9400000000-3f55c8c9bcb5d7f640b8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Positive-QTOF	splash10-00di-9200000000-b8c078f742906e31bf23	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Negative-QTOF	splash10-0k97-7900000000-d5450a6d81360c9060b7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Negative-QTOF	splash10-00di-9000000000-4f1ad5366369dc5b28f9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Negative-QTOF	splash10-00di-9000000000-63208c7fa296fbcdcd5a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Negative-QTOF	splash10-006x-5900000000-aee8163659956229a887	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Negative-QTOF	splash10-00dl-9400000000-990c5bd04132b963aca6	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Negative-QTOF	splash10-00dl-9800000000-4bcdcb7bb21fc0af6075	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Positive-QTOF	splash10-0002-3900000000-e3821642d6b887647ed2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Positive-QTOF	splash10-007a-9200000000-27e6f3875eaaa018745f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Positive-QTOF	splash10-05g0-9000000000-f8425ec58d9ee201de03	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

FDB013480

KNApSAcK ID

C00058205

Chemspider ID

117630

KEGG Compound ID

Not Available

BioCyc ID

CPD-9295

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

133337

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1846241

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 2-Vinyl-4H-1,3-dithiine (HMDB0034901)

MOL for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

3D MOL for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

3D SDF for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

3D-SDF for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

PDB for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

3D PDB for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

SMILES for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

INCHI for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

Structure for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

3D Structure for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra