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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 22:16:10 UTC

Update Date

2022-03-07 02:55:09 UTC

HMDB ID

HMDB0037027

Secondary Accession Numbers

HMDB37027

Metabolite Identification

Common Name

3,5-Dimethyl-1,2-cyclopentanedione

Description

3,5-Dimethyl-1,2-cyclopentanedione belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety. 3,5-Dimethyl-1,2-cyclopentanedione is a sweet, caramel, and maple tasting compound. 3,5-Dimethyl-1,2-cyclopentanedione has been detected, but not quantified in, a few different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, and robusta coffees (Coffea canephora). This could make 3,5-dimethyl-1,2-cyclopentanedione a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3,5-Dimethyl-1,2-cyclopentanedione.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Hydroxy-3,5-dimethyl-2-cyclopenten-1-one, 9ci	HMDB
3,5-Dimethyl-1,2-cyclopentadione	HMDB
3,5-Dimethylcyclopentane-1,2-dione	HMDB
FEMA 3269	HMDB
Caramel	MeSH

Chemical Formula

C₇H₁₀O₂

Average Molecular Weight

126.1531

Monoisotopic Molecular Weight

126.068079564

IUPAC Name

3,5-dimethylcyclopentane-1,2-dione

Traditional Name

3,5-dimethylcyclopentane-1,2-dione

CAS Registry Number

13494-07-0

SMILES

CC1CC(C)C(=O)C1=O

InChI Identifier

InChI=1S/C7H10O2/c1-4-3-5(2)7(9)6(4)8/h4-5H,3H2,1-2H3

InChI Key

MIDXCONKKJTLDX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclic ketones

Alternative Parents

Substituents

Cyclic ketone
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Organoleptic effect

Taste

Sweet

Odor

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0037027)
Cytoplasm (HMDB: HMDB0037027)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0037027)

Source

Exogenous

Exogenous (HMDB: HMDB0037027)

Food

Food (HMDB: HMDB0037027)

Coffee and coffee product

Coffee

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

Coffee and coffee products (FooDB: FOOD00861)

Endogenous

Plant

Coffea (HMDB: HMDB0037027)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0037027)

Biological role

Nutrient (HMDB: HMDB0037027)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	91 - 92 °C	Not Available
Boiling Point	187.37 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	121100 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.796 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	23.6 g/L	ALOGPS
logP	1.11	ALOGPS
logP	1.97	ChemAxon
logS	-0.73	ALOGPS
pKa (Strongest Acidic)	16.43	ChemAxon
pKa (Strongest Basic)	-8.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	34.14 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	33.54 m³·mol⁻¹	ChemAxon
Polarizability	13.25 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]+	127.426	31661259
DarkChem	[M-H]-	123.186	31661259
DeepCCS	[M+H]+	130.198	30932474
DeepCCS	[M-H]-	127.133	30932474
DeepCCS	[M-2H]-	163.874	30932474
DeepCCS	[M+Na]+	138.828	30932474
AllCCS	[M+H]+	125.8	32859911
AllCCS	[M+H-H2O]+	121.1	32859911
AllCCS	[M+NH4]+	130.2	32859911
AllCCS	[M+Na]+	131.4	32859911
AllCCS	[M-H]-	126.0	32859911
AllCCS	[M+Na-2H]-	128.2	32859911
AllCCS	[M+HCOO]-	130.6	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.	3.04 minutes	32390414
Predicted by Siyang on May 30, 2022	12.7654 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.0 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1681.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	460.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	155.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	281.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	116.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	466.9 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	549.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	106.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	965.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	339.0 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	1148.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	276.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	323.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	432.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	397.7 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	74.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,5-Dimethyl-1,2-cyclopentanedione	CC1CC(C)C(=O)C1=O	1706.8	Standard polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione	CC1CC(C)C(=O)C1=O	1004.8	Standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione	CC1CC(C)C(=O)C1=O	1050.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,5-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)C(C)C1	1197.5	Semi standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)C(C)C1	1187.7	Standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,2TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(C)C1	1381.1	Semi standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,2TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=C(C)C1	1460.7	Standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C(C)C1	1453.4	Semi standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C(C)C1	1404.0	Standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,2TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=C(C)C1	1853.0	Semi standard non polar	33892256
3,5-Dimethyl-1,2-cyclopentanedione,2TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=C(C)C1	1832.0	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione GC-MS (Non-derivatized) - 70eV, Positive	splash10-056r-9100000000-eac1e203afcdaaa9a69f	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 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 - 3,5-Dimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-004i-1900000000-31cd31914cd9466f6d9c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-004i-8900000000-5de4f0ab6ecf92c2dc45	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-00kf-9000000000-dd57a8e6cd878b6d1ab4	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-004i-0900000000-fcb80cbfcdb8990d044a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-004i-1900000000-8ab89b622c9ad83858e1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-0aor-9100000000-7e2c4ac28ab6e6fb0c95	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-004i-1900000000-32756250330f6211ba73	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-014i-9100000000-3a66eb05d9e211ce6bc3	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-0aor-9100000000-c977b2b533b159464348	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-004i-5900000000-b0ab93dccd778cb0ac92	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-00kf-9100000000-129a6c91b5b319814ca5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5-Dimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-00kf-9000000000-138d4f3db820ad834278	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart 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

FDB016007

KNApSAcK ID

Not Available

Chemspider ID

55542

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

61634

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1012741

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 3,5-Dimethyl-1,2-cyclopentanedione (HMDB0037027)

MOL for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

3D MOL for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

3D SDF for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

3D-SDF for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

PDB for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

3D PDB for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

SMILES for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

INCHI for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

Structure for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

3D Structure for HMDB0037027 (3,5-Dimethyl-1,2-cyclopentanedione)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra