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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:12:23 UTC

Update Date

2023-02-21 17:25:07 UTC

HMDB ID

HMDB0036142

Secondary Accession Numbers

HMDB36142

Metabolite Identification

Common Name

6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine

Description

6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine is found in animal foods. 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine is formed from cysteine and rhamnose under roasting conditions. 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine is found in beef, coffee, cocoa, earth almond (Cyperus esulentus), roast almonds, walnut and hazelnut. 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine is a flavouring ingredien

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,3-Dimethyl-6,7-dihydro-5H-cyclopentapyrazine	HMDB
FEMA 3917	HMDB

Chemical Formula

C₉H₁₂N₂

Average Molecular Weight

148.205

Monoisotopic Molecular Weight

148.100048394

IUPAC Name

2,3-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

Traditional Name

2,3-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

CAS Registry Number

38917-63-4

SMILES

CC1=NC2=C(CCC2)N=C1C

InChI Identifier

InChI=1S/C9H12N2/c1-6-7(2)11-9-5-3-4-8(9)10-6/h3-5H2,1-2H3

InChI Key

AIKNQWWUQFXNAZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0036142)
Cytoplasm (HMDB: HMDB0036142)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036142)

Source

Exogenous

Exogenous (HMDB: HMDB0036142)

Food

Food (HMDB: HMDB0036142)

Coffee and coffee product

Coffee

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

Coffee and coffee products (FooDB: FOOD00861)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Cocoa and cocoa products (FooDB: FOOD00860)

Nut

Nuts (FooDB: FOOD00869)

Not Available

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0036142)

Biological role

Nutrient (HMDB: HMDB0036142)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	25 - 27 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	8.76 g/L	ALOGPS
logP	1.83	ALOGPS
logP	0.56	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Basic)	1.93	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	25.78 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.96 m³·mol⁻¹	ChemAxon
Polarizability	17.24 Å³	ChemAxon
Number of Rings	2	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]+	131.586	31661259
DarkChem	[M-H]-	128.369	31661259
DeepCCS	[M+H]+	134.351	30932474
DeepCCS	[M-H]-	131.675	30932474
DeepCCS	[M-2H]-	167.766	30932474
DeepCCS	[M+Na]+	143.065	30932474
AllCCS	[M+H]+	131.8	32859911
AllCCS	[M+H-H2O]+	127.2	32859911
AllCCS	[M+NH4]+	136.0	32859911
AllCCS	[M+Na]+	137.3	32859911
AllCCS	[M-H]-	133.5	32859911
AllCCS	[M+Na-2H]-	134.6	32859911
AllCCS	[M+HCOO]-	135.9	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.	2.62 minutes	32390414
Predicted by Siyang on May 30, 2022	8.4986 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.5 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	302.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	412.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	285.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	97.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	170.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	58.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	299.9 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	227.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	762.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	614.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	64.7 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	941.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	172.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	186.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	665.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	583.4 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	333.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine	CC1=NC2=C(CCC2)N=C1C	1775.2	Standard polar	33892256
6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine	CC1=NC2=C(CCC2)N=C1C	1195.5	Standard non polar	33892256
6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine	CC1=NC2=C(CCC2)N=C1C	1271.9	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 - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-0900000000-44d097e4e4d85931ef64	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 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 - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-9de68a09059d340b18a3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-0900000000-a07e8a28364e3a7e5722	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-066u-9400000000-66cd6b9f9728e235f62e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-1b1c396de2b758edf13e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-a985875692e5cf0700f3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-0a59-1900000000-d5a2598aaef6607ebd2f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-aff21bfca25e06c85423	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-13f22a3dcd89162f8b55	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-001m-2900000000-4999ab2dcdfb40b9a5b1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-2ef1a63f0d174650da9c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-2900000000-40f61c41d317e14a87f8	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-00lr-9100000000-82420d910ae03d09fbb9	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

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

FDB014993

KNApSAcK ID

C00054447

Chemspider ID

4934180

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6428802

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

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 6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine (HMDB0036142)

MOL for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

3D MOL for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

3D SDF for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

3D-SDF for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

PDB for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

3D PDB for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

SMILES for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

INCHI for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

Structure for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

3D Structure for HMDB0036142 (6,7-Dihydro-2,3-dimethyl-5H-cyclopentapyrazine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra