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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:41:48 UTC

Update Date

2023-02-21 17:20:10 UTC

HMDB ID

HMDB0031242

Secondary Accession Numbers

HMDB31242

Metabolite Identification

Common Name

Dihydro-3(2H)-thiophenone

Description

Dihydro-3(2H)-thiophenone belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom. Dihydro-3(2H)-thiophenone is a buttery, clam, and garlic tasting compound. Dihydro-3(2H)-thiophenone has been detected, but not quantified in, several different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, nuts, and robusta coffees (Coffea canephora). This could make dihydro-3(2H)-thiophenone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Dihydro-3(2H)-thiophenone.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-oxo-2,3,4, 5-Tetrahydrothiophene	HMDB
3-oxo-2,3,4,5-Tetrahydrothiophene	HMDB
3-Oxotetrahydrothiophene	HMDB
3-Tetrahydrothiophenone	HMDB
3-Thiacyclopentanone	HMDB
3-Thiolanone	HMDB
3-Thiophanone	HMDB
4,5-dihydro-3(2H)Thiophenone	HMDB
dihydro-3-(2H)-Thiophenone	HMDB
dihydro-3-(2H)-Thiophenone (tetrahydrothiophen-3-one)	HMDB
Dihydrothiophen-3(2H)-one	HMDB
FEMA 3266	HMDB
tetrahydro-Thiophen-3-one	HMDB
Tetrahydrothiophen-3-one	HMDB
Tetrahydrothiophene-3-one	HMDB
Thiolan-3-one	HMDB

Chemical Formula

C₄H₆OS

Average Molecular Weight

102.155

Monoisotopic Molecular Weight

102.013935504

IUPAC Name

thiolan-3-one

Traditional Name

thiolan-3-one

CAS Registry Number

1003-04-9

SMILES

O=C1CCSC1

InChI Identifier

InChI=1S/C4H6OS/c5-4-1-2-6-3-4/h1-3H2

InChI Key

DSXFPRKPFJRPIB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Thiolanes

Sub Class

Not Available

Direct Parent

Thiolanes

Alternative Parents

Substituents

Thiolane
Cyclic ketone
Ketone
Dialkylthioether
Thioether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Cellular substructure

Extracellular (HMDB: HMDB0031242)
Cytoplasm (HMDB: HMDB0031242)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031242)

Source

Endogenous

Endogenous (HMDB: HMDB0031242)

Plant

Plant (HMDB: HMDB0031242)
Coffea (HMDB: HMDB0031242)

Exogenous

Food

Food (HMDB: HMDB0031242)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Coffee and coffee products (FooDB: FOOD00861)

Nut

Nuts (FooDB: FOOD00869)

Exogenous (HMDB: HMDB0031242)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0031242)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	175.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	192400 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.222 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	38.4 g/L	ALOGPS
logP	-0.1	ALOGPS
logP	0.55	ChemAxon
logS	-0.43	ALOGPS
pKa (Strongest Acidic)	18.41	ChemAxon
pKa (Strongest Basic)	-7.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	26.86 m³·mol⁻¹	ChemAxon
Polarizability	10.17 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]+	118.255	31661259
DarkChem	[M-H]-	112.164	31661259
DeepCCS	[M+H]+	126.78	30932474
DeepCCS	[M-H]-	124.722	30932474
DeepCCS	[M-2H]-	160.204	30932474
DeepCCS	[M+Na]+	134.587	30932474
AllCCS	[M+H]+	118.5	32859911
AllCCS	[M+H-H2O]+	113.5	32859911
AllCCS	[M+NH4]+	123.2	32859911
AllCCS	[M+Na]+	124.5	32859911
AllCCS	[M-H]-	125.8	32859911
AllCCS	[M+Na-2H]-	129.5	32859911
AllCCS	[M+HCOO]-	133.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dihydro-3(2H)-thiophenone	O=C1CCSC1	1523.7	Standard polar	33892256
Dihydro-3(2H)-thiophenone	O=C1CCSC1	931.1	Standard non polar	33892256
Dihydro-3(2H)-thiophenone	O=C1CCSC1	956.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Dihydro-3(2H)-thiophenone,1TMS,isomer #1	C[Si](C)(C)OC1=CSCC1	1222.1	Semi standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TMS,isomer #1	C[Si](C)(C)OC1=CSCC1	1209.3	Standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TMS,isomer #2	C[Si](C)(C)OC1=CCSC1	1216.7	Semi standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TMS,isomer #2	C[Si](C)(C)OC1=CCSC1	1211.6	Standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CSCC1	1434.8	Semi standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CSCC1	1432.5	Standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CCSC1	1436.0	Semi standard non polar	33892256
Dihydro-3(2H)-thiophenone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CCSC1	1417.2	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dihydro-3(2H)-thiophenone GC-MS (Non-derivatized) - 70eV, Positive	splash10-06vl-9000000000-8920a03b7f602925528c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dihydro-3(2H)-thiophenone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dihydro-3(2H)-thiophenone 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 - Dihydro-3(2H)-thiophenone 10V, Positive-QTOF	splash10-0udr-7900000000-d57d2cdd3d0696b386d4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 20V, Positive-QTOF	splash10-0udi-5900000000-a741a9b25e6b72552b40	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 40V, Positive-QTOF	splash10-000i-9000000000-67d262f4d56bb8ebe811	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 10V, Negative-QTOF	splash10-0uk9-9700000000-a789186f119cc8dc97a5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 20V, Negative-QTOF	splash10-0zmi-9300000000-4852f51e992b471ea1d4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 40V, Negative-QTOF	splash10-0abc-9000000000-aa29fcae8cafcad89af6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 10V, Positive-QTOF	splash10-0udi-2900000000-de6a9b91fefe92c19186	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 20V, Positive-QTOF	splash10-0006-9100000000-e3567016322e7e5ca27d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 40V, Positive-QTOF	splash10-0006-9000000000-78ed59499ffbdf7655ba	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 10V, Negative-QTOF	splash10-0uyi-9400000000-ac091bff34a35585516b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 20V, Negative-QTOF	splash10-001i-9000000000-d508959c4a3b196a9a8e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dihydro-3(2H)-thiophenone 40V, Negative-QTOF	splash10-001i-9000000000-716139e2de81bc94af5f	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)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	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

FDB003269

KNApSAcK ID

Not Available

Chemspider ID

55193

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

61252

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1005811

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 Dihydro-3(2H)-thiophenone (HMDB0031242)

MOL for HMDB0031242 (Dihydro-3(2H)-thiophenone)

3D MOL for HMDB0031242 (Dihydro-3(2H)-thiophenone)

3D SDF for HMDB0031242 (Dihydro-3(2H)-thiophenone)

3D-SDF for HMDB0031242 (Dihydro-3(2H)-thiophenone)

PDB for HMDB0031242 (Dihydro-3(2H)-thiophenone)

3D PDB for HMDB0031242 (Dihydro-3(2H)-thiophenone)

SMILES for HMDB0031242 (Dihydro-3(2H)-thiophenone)

INCHI for HMDB0031242 (Dihydro-3(2H)-thiophenone)

Structure for HMDB0031242 (Dihydro-3(2H)-thiophenone)

3D Structure for HMDB0031242 (Dihydro-3(2H)-thiophenone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra