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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 21:14:24 UTC

Update Date

2023-02-21 17:25:10 UTC

HMDB ID

HMDB0036179

Secondary Accession Numbers

HMDB36179

Metabolite Identification

Common Name

2-Methyl-1,3-dithiolane

Description

2-Methyl-1,3-dithiolane belongs to the class of organic compounds known as 1,3-dithiolanes. These are organic compounds containing a 1,3-dithiolane ring. 1,3-dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 3- ring positions. 2-Methyl-1,3-dithiolane is an alliaceous, savory, and smoky tasting compound. Based on a literature review very few articles have been published on 2-Methyl-1,3-dithiolane.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Methyl-1,3-dithiacyclopentane	HMDB
Acetaldehdye ethylene thioacetal	HMDB
FEMA 3705	HMDB

Chemical Formula

C₄H₈S₂

Average Molecular Weight

120.236

Monoisotopic Molecular Weight

120.006741636

IUPAC Name

2-methyl-1,3-dithiolane

Traditional Name

1,3-dithiolane, 2-methyl-

CAS Registry Number

5616-51-3

SMILES

CC1SCCS1

InChI Identifier

InChI=1S/C4H8S2/c1-4-5-2-3-6-4/h4H,2-3H2,1H3

InChI Key

CARJCVDELAMAEJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,3-dithiolanes. These are organic compounds containing a 1,3-dithiolane ring. 1,3-Dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dithiolanes

Sub Class

1,3-dithiolanes

Direct Parent

1,3-dithiolanes

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Cellular substructure

Extracellular (HMDB: HMDB0036179)
Cytoplasm (HMDB: HMDB0036179)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036179)

Source

Exogenous

Exogenous (HMDB: HMDB0036179)

Food

Food (HMDB: HMDB0036179)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0036179)

Biological role

Nutrient (HMDB: HMDB0036179)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	65.00 °C. @ 10.00 mm Hg	The Good Scents Company Information System
Water Solubility	1600 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.090 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.97 g/L	ALOGPS
logP	1.47	ALOGPS
logP	1.33	ChemAxon
logS	-2.1	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	34.24 m³·mol⁻¹	ChemAxon
Polarizability	12.78 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]+	122.779	31661259
DarkChem	[M-H]-	116.663	31661259
DeepCCS	[M+H]+	126.67	30932474
DeepCCS	[M-H]-	124.775	30932474
DeepCCS	[M-2H]-	160.209	30932474
DeepCCS	[M+Na]+	134.603	30932474
AllCCS	[M+H]+	119.3	32859911
AllCCS	[M+H-H2O]+	114.6	32859911
AllCCS	[M+NH4]+	123.7	32859911
AllCCS	[M+Na]+	125.0	32859911
AllCCS	[M-H]-	129.0	32859911
AllCCS	[M+Na-2H]-	132.8	32859911
AllCCS	[M+HCOO]-	137.1	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.	2.95 minutes	32390414
Predicted by Siyang on May 30, 2022	14.1198 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.17 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	119.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1815.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	423.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	116.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	271.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	72.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	292.4 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	550.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	112.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	752.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	298.6 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	997.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	258.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	250.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	473.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	326.5 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	121.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Methyl-1,3-dithiolane	CC1SCCS1	1494.6	Standard polar	33892256
2-Methyl-1,3-dithiolane	CC1SCCS1	978.0	Standard non polar	33892256
2-Methyl-1,3-dithiolane	CC1SCCS1	1021.5	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-Methyl-1,3-dithiolane GC-MS (Non-derivatized) - 70eV, Positive	splash10-05i3-9300000000-81c86a79c45d84fe5ac4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methyl-1,3-dithiolane 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-Methyl-1,3-dithiolane 10V, Positive-QTOF	splash10-00di-1900000000-270bdbc132a533523977	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Positive-QTOF	splash10-00fr-9600000000-cd469498fbc0e71eb0af	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Positive-QTOF	splash10-0006-9000000000-2c22c1e3069147695863	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Negative-QTOF	splash10-052f-9000000000-2ea3713d714bf8f9f464	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Negative-QTOF	splash10-0a4i-9000000000-296398224aa57bcea64d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Negative-QTOF	splash10-0a59-9000000000-0c60bdfdf4bedd2f36f0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Negative-QTOF	splash10-0a4i-9000000000-655cfc70bd113b960af1	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Negative-QTOF	splash10-052f-9000000000-b6cb2870ae74c26d2426	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Negative-QTOF	splash10-014l-9800000000-d4d75dc6c4cb1445d040	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Positive-QTOF	splash10-00di-3900000000-77700f7eae688c562d08	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Positive-QTOF	splash10-03di-9200000000-63fd31ccdb39062e420d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Positive-QTOF	splash10-0a4i-9000000000-4bdd61be5bd57eac4cd9	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View

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

FDB015033

KNApSAcK ID

Not Available

Chemspider ID

20518

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21828

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1037521

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-Methyl-1,3-dithiolane (HMDB0036179)

MOL for HMDB0036179 (2-Methyl-1,3-dithiolane)

3D MOL for HMDB0036179 (2-Methyl-1,3-dithiolane)

3D SDF for HMDB0036179 (2-Methyl-1,3-dithiolane)

3D-SDF for HMDB0036179 (2-Methyl-1,3-dithiolane)

PDB for HMDB0036179 (2-Methyl-1,3-dithiolane)

3D PDB for HMDB0036179 (2-Methyl-1,3-dithiolane)

SMILES for HMDB0036179 (2-Methyl-1,3-dithiolane)

INCHI for HMDB0036179 (2-Methyl-1,3-dithiolane)

Structure for HMDB0036179 (2-Methyl-1,3-dithiolane)

3D Structure for HMDB0036179 (2-Methyl-1,3-dithiolane)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra