Jump To Section:

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 22:16:07 UTC

Update Date

2022-03-07 02:55:09 UTC

HMDB ID

HMDB0037026

Secondary Accession Numbers

HMDB37026

Metabolite Identification

Common Name

3,4-Dimethyl-1,2-cyclopentanedione

Description

3,4-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. 3,4-Dimethyl-1,2-cyclopentanedione is a sweet, anise, and balsam tasting compound. 3,4-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 3,4-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 3,4-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-3,4-dimethyl-2-cyclopenten-1-one	HMDB
3,4-Dimethyl-1,2-cyclopentadione	HMDB
FEMA 3268	HMDB

Chemical Formula

C₇H₁₀O₂

Average Molecular Weight

126.1531

Monoisotopic Molecular Weight

126.068079564

IUPAC Name

3,4-dimethylcyclopentane-1,2-dione

Traditional Name

3,4-dimethylcyclopentane-1,2-dione

CAS Registry Number

13494-06-9

SMILES

CC1CC(=O)C(=O)C1C

InChI Identifier

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

InChI Key

WGAVDEVFJDQIMZ-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

Sweet

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0037026)

Source

Endogenous

Endogenous (HMDB: HMDB0037026)

Plant

Coffea (HMDB: HMDB0037026)

Exogenous

Food

Food (HMDB: HMDB0037026)

Coffee and coffee product

Coffee

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

Coffee and coffee products (FooDB: FOOD00861)

Exogenous (HMDB: HMDB0037026)

Process

Naturally occurring process

Biological process

Cellular process

Cell signaling (HMDB: HMDB0037026)

Role

Biological role

Energy source (HMDB: HMDB0037026)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0037026)

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0037026)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	71 - 72 °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	22.7 g/L	ALOGPS
logP	1.03	ALOGPS
logP	1.72	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	16.71	ChemAxon
pKa (Strongest Basic)	-8.6	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	33.51 m³·mol⁻¹	ChemAxon
Polarizability	13.2 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]+	128.784	31661259
DarkChem	[M-H]-	123.67	31661259
DeepCCS	[M+H]+	131.394	30932474
DeepCCS	[M-H]-	128.63	30932474
DeepCCS	[M-2H]-	165.487	30932474
DeepCCS	[M+Na]+	140.41	30932474
AllCCS	[M+H]+	126.4	32859911
AllCCS	[M+H-H2O]+	121.8	32859911
AllCCS	[M+NH4]+	130.7	32859911
AllCCS	[M+Na]+	131.9	32859911
AllCCS	[M-H]-	125.8	32859911
AllCCS	[M+Na-2H]-	128.0	32859911
AllCCS	[M+HCOO]-	130.5	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.	3.12 minutes	32390414
Predicted by Siyang on May 30, 2022	12.2558 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.64 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1661.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	444.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	148.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	267.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	105.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	445.3 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	540.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	93.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	917.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	333.2 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	1101.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	260.7 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	414.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	382.5 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	62.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,4-Dimethyl-1,2-cyclopentanedione	CC1CC(=O)C(=O)C1C	1732.4	Standard polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione	CC1CC(=O)C(=O)C1C	1020.1	Standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione	CC1CC(=O)C(=O)C1C	1079.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,4-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)CC1C	1228.9	Semi standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(=O)CC1C	1189.7	Standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #2	CC1C=C(O[Si](C)(C)C)C(=O)C1C	1249.7	Semi standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TMS,isomer #2	CC1C=C(O[Si](C)(C)C)C(=O)C1C	1205.2	Standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,2TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=CC1C	1374.6	Semi standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,2TMS,isomer #1	CC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)=CC1C	1393.8	Standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)CC1C	1478.9	Semi standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #1	CC1=C(O[Si](C)(C)C(C)(C)C)C(=O)CC1C	1416.7	Standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #2	CC1C=C(O[Si](C)(C)C(C)(C)C)C(=O)C1C	1483.1	Semi standard non polar	33892256
3,4-Dimethyl-1,2-cyclopentanedione,1TBDMS,isomer #2	CC1C=C(O[Si](C)(C)C(C)(C)C)C(=O)C1C	1435.3	Standard non polar	33892256
3,4-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)=CC1C	1853.7	Semi standard non polar	33892256
3,4-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)=CC1C	1762.5	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6r-9100000000-1497b7ff09debc96483e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-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 - 3,4-Dimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-004i-2900000000-5c24366c60b870acaba3	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-056r-9500000000-3aca1df1ff900bf41aea	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-0zfr-9000000000-108636ad5f3a92d28bbf	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-004i-0900000000-d406083cb1baecbcdb02	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-004i-1900000000-9814cce09bcc5c236f10	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-0pvl-9100000000-726367b03709009b462d	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 10V, Negative-QTOF	splash10-004i-0900000000-e8a652cde2a23224db30	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 20V, Negative-QTOF	splash10-004i-9600000000-5bf72d607e8eac0619f2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 40V, Negative-QTOF	splash10-01bc-9200000000-969a706cf6604e54ee81	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 10V, Positive-QTOF	splash10-004i-6900000000-1fba1a01be746a6302f8	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 20V, Positive-QTOF	splash10-066u-9000000000-9ae7707cdd35387b89f5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Dimethyl-1,2-cyclopentanedione 40V, Positive-QTOF	splash10-00kf-9000000000-11c26c9e2bd838092365	2021-09-24	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
Membrane

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

FDB016006

KNApSAcK ID

Not Available

Chemspider ID

55541

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

61633

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1012731

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 3,4-Dimethyl-1,2-cyclopentanedione (HMDB0037026)

MOL for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

3D MOL for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

3D SDF for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

3D-SDF for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

PDB for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

3D PDB for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

SMILES for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

INCHI for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

Structure for HMDB0037026 (3,4-Dimethyl-1,2-cyclopentanedione)

3D Structure for HMDB0037026 (3,4-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