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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 23:52:51 UTC

Update Date

2023-02-21 17:26:38 UTC

HMDB ID

HMDB0038557

Secondary Accession Numbers

HMDB38557

Metabolite Identification

Common Name

xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran

Description

xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran, also known as 4-methyl-2-(2-methyl-1-propen-1-yl)-3,6-dihydro-2H-pyran or neryl oxide, belongs to the class of organic compounds known as pyrans. Pyrans are compounds containing a pyran ring, which is a six-member heterocyclic, non-aromatic ring with five carbon atoms, one oxygen atom and two ring double bonds. xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran is a celery, cortex, and diphenyl oxide tasting compound. xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran has been detected, but not quantified in, a few different foods, such as black elderberries (Sambucus nigra), gingers (Zingiber officinale), and white wine. This could make XI-3,6-dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran a potential biomarker for the consumption of these foods. xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran.

Structure

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

COMPND    HMDB0038557
HETATM    1  C1  UNL     1       3.603   1.100  -0.140  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.451   0.182  -0.170  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.664  -1.285  -0.154  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.214   0.645  -0.212  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.024  -0.254  -0.242  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.912   0.202   0.824  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.331  -0.084   0.556  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.326  -0.359   1.646  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.707  -0.090  -0.716  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.707   0.183  -1.746  1.00  0.00           C  
HETATM   11  O1  UNL     1      -0.456  -0.288  -1.509  1.00  0.00           O  
HETATM   12  H1  UNL     1       4.061   1.026   0.874  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.290   2.149  -0.288  1.00  0.00           H  
HETATM   14  H3  UNL     1       4.322   0.852  -0.941  1.00  0.00           H  
HETATM   15  H4  UNL     1       2.244  -1.653   0.821  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.740  -1.550  -0.255  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.098  -1.734  -0.985  1.00  0.00           H  
HETATM   18  H7  UNL     1       1.042   1.736  -0.224  1.00  0.00           H  
HETATM   19  H8  UNL     1       0.391  -1.265   0.031  1.00  0.00           H  
HETATM   20  H9  UNL     1      -0.826   1.314   0.980  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.665  -0.246   1.813  1.00  0.00           H  
HETATM   22  H11 UNL     1      -4.307   0.085   1.346  1.00  0.00           H  
HETATM   23  H12 UNL     1      -2.978   0.006   2.617  1.00  0.00           H  
HETATM   24  H13 UNL     1      -3.470  -1.449   1.689  1.00  0.00           H  
HETATM   25  H14 UNL     1      -3.743  -0.293  -1.005  1.00  0.00           H  
HETATM   26  H15 UNL     1      -1.656   1.292  -1.877  1.00  0.00           H  
HETATM   27  H16 UNL     1      -2.059  -0.221  -2.734  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    4
CONECT    3   15   16   17
CONECT    4    5   18
CONECT    5    6   11   19
CONECT    6    7   20   21
CONECT    7    8    9    9
CONECT    8   22   23   24
CONECT    9   10   25
CONECT   10   11   26   27
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran	ChEBI
3,6-Dihydro-4-methyl-2-(2-methylpropen-1-yl)-2H-pyran	ChEBI
3,6-Dihydro-4-methyl-2-(2-methylpropenyl)-2H-pyran	ChEBI
4-Methyl-2-(2-methyl-1-propen-1-yl)-3,6-dihydro-2H-pyran	ChEBI
4-Methyl-2-(2-methylprop-1-enyl)-3,6-dihydro-2H-pyran	ChEBI
Neryl oxide	ChEBI
Nerol oxide	MeSH

Chemical Formula

C₁₀H₁₆O

Average Molecular Weight

152.2334

Monoisotopic Molecular Weight

152.120115134

IUPAC Name

4-methyl-2-(2-methylprop-1-en-1-yl)-3,6-dihydro-2H-pyran

Traditional Name

4-methyl-2-(2-methylprop-1-en-1-yl)-3,6-dihydro-2H-pyran

CAS Registry Number

Not Available

SMILES

CC(C)=CC1CC(C)=CCO1

InChI Identifier

InChI=1S/C10H16O/c1-8(2)6-10-7-9(3)4-5-11-10/h4,6,10H,5,7H2,1-3H3

InChI Key

FRISMOQHTLZZRP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrans. Pyrans are compounds containing a pyran ring, which is a six-member heterocyclic, non-aromatic ring with five carbon atoms, one oxygen atom and two ring double bonds.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrans

Sub Class

Not Available

Direct Parent

Pyrans

Alternative Parents

Substituents

Pyran
Oxacycle
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0038557)

Source

Endogenous

Endogenous (HMDB: HMDB0038557)

Plant

Plant (HMDB: HMDB0038557)

Exogenous

Food

Food (HMDB: HMDB0038557)

Beverage

Fermented beverage

White wine (FooDB: FOOD00917)

Herb and spice

Spice

Ginger (FooDB: FOOD00206)

Fruit

Berry

Black elderberry (FooDB: FOOD00166)

Process

Naturally occurring process

Biological process

Cellular process

Cell signaling (HMDB: HMDB0038557)

Role

Biological role

Energy source (HMDB: HMDB0038557)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0038557)

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0038557)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	201.00 to 202.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	77.23 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	2.984 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.4 g/L	ALOGPS
logP	3.17	ALOGPS
logP	2.43	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	9.23 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	49.19 m³·mol⁻¹	ChemAxon
Polarizability	18.66 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]+	136.348	31661259
DarkChem	[M-H]-	131.791	31661259
DeepCCS	[M+H]+	134.82	30932474
DeepCCS	[M-H]-	131.011	30932474
DeepCCS	[M-2H]-	168.455	30932474
DeepCCS	[M+Na]+	143.853	30932474
AllCCS	[M+H]+	130.7	32859911
AllCCS	[M+H-H2O]+	126.1	32859911
AllCCS	[M+NH4]+	135.0	32859911
AllCCS	[M+Na]+	136.2	32859911
AllCCS	[M-H]-	135.1	32859911
AllCCS	[M+Na-2H]-	136.6	32859911
AllCCS	[M+HCOO]-	138.3	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.	5.6 minutes	32390414
Predicted by Siyang on May 30, 2022	13.7809 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.42 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2325.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	426.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	173.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	252.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	69.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	477.5 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	522.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	64.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1164.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	464.4 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	996.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	415.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	371.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	410.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	486.6 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	14.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran	CC(C)=CC1CC(C)=CCO1	1425.3	Standard polar	33892256
xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran	CC(C)=CC1CC(C)=CCO1	1103.8	Standard non polar	33892256
xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran	CC(C)=CC1CC(C)=CCO1	1130.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran EI-B (Non-derivatized)	splash10-014i-9000000000-c7728956a05defa6ddc5	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran EI-B (Non-derivatized)	splash10-014i-9000000000-c7728956a05defa6ddc5	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran GC-MS (Non-derivatized) - 70eV, Positive	splash10-0py0-9500000000-f3d29d3d5c62599d2c0a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 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 - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 10V, Positive-QTOF	splash10-0udi-1900000000-368a69826e2649ef9845	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 20V, Positive-QTOF	splash10-0uyj-9500000000-354b9b1ed1b49bee9201	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 40V, Positive-QTOF	splash10-0gb9-9000000000-0b3a09563832b518f44d	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 10V, Negative-QTOF	splash10-0udi-1900000000-44e765cd2daec5bef6c7	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 20V, Negative-QTOF	splash10-0udi-5900000000-8df464ef69bfcc97c688	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 40V, Negative-QTOF	splash10-067i-9100000000-7599f12f73eed131a3e1	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 10V, Positive-QTOF	splash10-0hft-9600000000-3fd3ea10d3d866324b8a	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 20V, Positive-QTOF	splash10-0aor-9000000000-8b15d65ba863a573bcf2	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 40V, Positive-QTOF	splash10-014l-9000000000-bcdd6d965b814b14515c	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 10V, Negative-QTOF	splash10-0udi-0900000000-c373c9eea3cebf186f53	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 20V, Negative-QTOF	splash10-0udi-2900000000-a60813a4e90968d64c3f	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran 40V, Negative-QTOF	splash10-014i-9200000000-1741d255b40beefc00fe	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

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

FDB020082

KNApSAcK ID

C00056008

Chemspider ID

55214

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

61275

PDB ID

Not Available

ChEBI ID

144705

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1001891

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 xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran (HMDB0038557)

MOL for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

3D MOL for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

3D SDF for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

3D-SDF for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

PDB for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

3D PDB for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

SMILES for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

INCHI for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

Structure for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

3D Structure for HMDB0038557 (xi-3,6-Dihydro-4-methyl-2-(2-methyl-1-propenyl)-2H-pyran)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra