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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:22:15 UTC

Update Date

2023-02-21 17:27:13 UTC

HMDB ID

HMDB0039831

Secondary Accession Numbers

HMDB39831

Metabolite Identification

Common Name

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

Description

6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 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. 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine is a burnt, earthy, and nutty tasting compound. 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine has been detected, but not quantified in, several different foods, such as breakfast cereal, coffee and coffee products, nuts, cocoa beans (Theobroma cacao), and arabica coffees (Coffea arabica). This could make 6,7-dihydro-2,5-dimethyl-5H-cyclopentapyrazine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,5-Dimethyl-6,7-dihydro-(5H)-cyclopentapyrazine	HMDB
2,5-Dimethyl-6,7-dihydro-5H-cyclopenta[b]pyrazine	HMDB

Chemical Formula

C₉H₁₂N₂

Average Molecular Weight

148.205

Monoisotopic Molecular Weight

148.100048394

IUPAC Name

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

Traditional Name

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

CAS Registry Number

38917-61-2

SMILES

CC1CCC2=C1N=CC(C)=N2

InChI Identifier

InChI=1S/C9H12N2/c1-6-3-4-8-9(6)10-5-7(2)11-8/h5-6H,3-4H2,1-2H3

InChI Key

CTFGVWCFSGCLHZ-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

Cellular substructure

Extracellular (HMDB: HMDB0039831)
Cytoplasm (HMDB: HMDB0039831)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039831)

Food (HMDB: HMDB0039831)

Cereal and cereal product

Cereal product

Breakfast cereal (FooDB: FOOD00270)

Cereals and cereal products (FooDB: FOOD00858)

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)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039831)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	110.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Boiling Point	222.08 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	719 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.794 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	11.5 g/L	ALOGPS
logP	1.83	ALOGPS
logP	0.97	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Basic)	1.75	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	42.94 m³·mol⁻¹	ChemAxon
Polarizability	17.07 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]+	132.628	31661259
DarkChem	[M-H]-	130.094	31661259
DeepCCS	[M+H]+	134.493	30932474
DeepCCS	[M-H]-	130.665	30932474
DeepCCS	[M-2H]-	168.033	30932474
DeepCCS	[M+Na]+	143.572	30932474
AllCCS	[M+H]+	132.0	32859911
AllCCS	[M+H-H2O]+	127.5	32859911
AllCCS	[M+NH4]+	136.3	32859911
AllCCS	[M+Na]+	137.5	32859911
AllCCS	[M-H]-	134.5	32859911
AllCCS	[M+Na-2H]-	135.6	32859911
AllCCS	[M+HCOO]-	136.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine	CC1CCC2=C1N=CC(C)=N2	1659.9	Standard polar	33892256
6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine	CC1CCC2=C1N=CC(C)=N2	1168.9	Standard non polar	33892256
6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine	CC1CCC2=C1N=CC(C)=N2	1223.8	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-2,5-dimethyl-5H-cyclopentapyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-001j-2900000000-c1e83c8d2e97432002a8	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6,7-Dihydro-2,5-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-2,5-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-b4c5580d24ab87d771fa	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-1900000000-481f96962d72558f84b3	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-0kcr-9600000000-c34ab3e7e7465bfd9d37	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-276f718afdf772401b48	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-a469551d404672368100	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-014l-4900000000-55ff7fded4e49a96f936	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-2ef1a63f0d174650da9c	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-1900000000-392e18cabc33199fe354	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-005c-9200000000-0a5cda27313684a9b33b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-aff21bfca25e06c85423	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-4127051532b1d57df8b2	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-014l-5900000000-f5a9d7cb47a3f7a9f9c1	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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

FDB019484

KNApSAcK ID

C00054445

Chemspider ID

462010

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

530404

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1595401

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-2,5-dimethyl-5H-cyclopentapyrazine (HMDB0039831)

MOL for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

3D MOL for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

3D SDF for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

3D-SDF for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

PDB for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

3D PDB for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

SMILES for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

INCHI for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

Structure for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

3D Structure for HMDB0039831 (6,7-Dihydro-2,5-dimethyl-5H-cyclopentapyrazine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra