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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-03-20 21:18:03 UTC

Update Date

2023-02-21 17:29:38 UTC

HMDB ID

HMDB0059936

Secondary Accession Numbers

HMDB0037146
HMDB37146
HMDB59936

Metabolite Identification

Common Name

5-Pentyl-1,4-dioxan-2-one

Description

5-Pentyl-1,4-dioxan-2-one belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4. 5-Pentyl-1,4-dioxan-2-one is slightly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Pentyl-1,4-dioxan-2-one, along with 6-pentyl-1,4-dioxan-2-one, are mixed isomers used in food flavouring (FEMA 2076; CAS 65504-96-3). Both have a fruity-winey, somewhat ethereal odour.

Structure

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

HEADER    PROTEIN                                 20-MAR-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-13         0                                  
HETATM    1  C   UNK     0     -11.031   0.882   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -11.031  -0.659   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -9.701  -1.429   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -8.368  -0.659   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.368   0.882   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -9.701   1.645   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0     -12.369  -1.429   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -7.038   1.645   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.700   0.882   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.370   1.645   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.033   0.882   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.702   1.645   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    1    5                                                       
CONECT    7    2                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

COMPND    HMDB0059936
HETATM    1  C1  UNL     1       3.857   0.619  -0.159  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.585   1.385  -0.004  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.423   0.554   0.454  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.122  -0.560  -0.518  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.045  -1.363  -0.019  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.294  -0.570   0.142  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.380  -1.509   0.649  1.00  0.00           C  
HETATM    8  O1  UNL     1      -3.452  -0.646   1.065  1.00  0.00           O  
HETATM    9  C8  UNL     1      -3.513   0.565   0.401  1.00  0.00           C  
HETATM   10  O2  UNL     1      -4.041   1.584   0.895  1.00  0.00           O  
HETATM   11  C9  UNL     1      -2.922   0.635  -0.954  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.711  -0.000  -1.058  1.00  0.00           O  
HETATM   13  H1  UNL     1       4.321   0.472   0.842  1.00  0.00           H  
HETATM   14  H2  UNL     1       3.779  -0.298  -0.753  1.00  0.00           H  
HETATM   15  H3  UNL     1       4.575   1.285  -0.714  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.312   1.790  -1.015  1.00  0.00           H  
HETATM   17  H5  UNL     1       2.758   2.209   0.700  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.528   1.219   0.461  1.00  0.00           H  
HETATM   19  H7  UNL     1       1.533   0.182   1.489  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.991  -1.264  -0.582  1.00  0.00           H  
HETATM   21  H9  UNL     1       0.973  -0.131  -1.516  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.242  -1.752   0.992  1.00  0.00           H  
HETATM   23  H11 UNL     1      -0.224  -2.246  -0.645  1.00  0.00           H  
HETATM   24  H12 UNL     1      -1.179   0.209   0.941  1.00  0.00           H  
HETATM   25  H13 UNL     1      -2.725  -2.174  -0.186  1.00  0.00           H  
HETATM   26  H14 UNL     1      -1.988  -2.105   1.472  1.00  0.00           H  
HETATM   27  H15 UNL     1      -2.831   1.706  -1.286  1.00  0.00           H  
HETATM   28  H16 UNL     1      -3.696   0.203  -1.651  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   16   17
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6   22   23
CONECT    6    7   12   24
CONECT    7    8   25   26
CONECT    8    9
CONECT    9   10   10   11
CONECT   11   12   27   28
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
FEMA 2076	HMDB

Chemical Formula

C₉H₁₆O₃

Average Molecular Weight

172.2215

Monoisotopic Molecular Weight

172.109944378

IUPAC Name

5-pentyl-1,4-dioxan-2-one

Traditional Name

5-pentyl-1,4-dioxan-2-one

CAS Registry Number

93263-93-5

SMILES

CCCCCC1COC(=O)CO1

InChI Identifier

InChI=1S/C9H16O3/c1-2-3-4-5-8-6-12-9(10)7-11-8/h8H,2-7H2,1H3

InChI Key

AYJJZBHSZOCJJX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxanes

Sub Class

1,4-dioxanes

Direct Parent

1,4-dioxanes

Alternative Parents

Substituents

Para-dioxane
Lactone
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0059936)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	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	2.45 g/L	ALOGPS
logP	2.19	ALOGPS
logP	1.85	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	35.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	44.64 m³·mol⁻¹	ChemAxon
Polarizability	19.28 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	140.582	31661259
DarkChem	[M-H]-	135.79	31661259
DeepCCS	[M+H]+	145.302	30932474
DeepCCS	[M-H]-	141.884	30932474
DeepCCS	[M-2H]-	179.448	30932474
DeepCCS	[M+Na]+	154.542	30932474
AllCCS	[M+H]+	138.9	32859911
AllCCS	[M+H-H2O]+	134.7	32859911
AllCCS	[M+NH4]+	142.9	32859911
AllCCS	[M+Na]+	144.1	32859911
AllCCS	[M-H]-	142.1	32859911
AllCCS	[M+Na-2H]-	143.3	32859911
AllCCS	[M+HCOO]-	144.8	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 √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	4.27 minutes	32390414
Predicted by Siyang on May 30, 2022	15.1286 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.39 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2210.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	498.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	188.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	306.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	335.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	632.9 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	720.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	95.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1282.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	447.6 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	1421.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	439.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	397.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	536.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	473.4 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	38.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Pentyl-1,4-dioxan-2-one	CCCCCC1COC(=O)CO1	2154.1	Standard polar	33892256
5-Pentyl-1,4-dioxan-2-one	CCCCCC1COC(=O)CO1	1379.4	Standard non polar	33892256
5-Pentyl-1,4-dioxan-2-one	CCCCCC1COC(=O)CO1	1513.8	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 - 5-Pentyl-1,4-dioxan-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-0ab9-9200000000-356f8de032c8feef5d35	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 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 - 5-Pentyl-1,4-dioxan-2-one 10V, Positive-QTOF	splash10-00fr-4900000000-328150c678a34c7b5d0a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 20V, Positive-QTOF	splash10-0002-9300000000-d311991ea7169354260d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 40V, Positive-QTOF	splash10-0a4l-9000000000-ba732dbfc02e332f6f77	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 10V, Negative-QTOF	splash10-00di-0900000000-f0a84cc882ca17f13a80	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 20V, Negative-QTOF	splash10-0ab9-9300000000-2f87107560ebe7efeedd	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Pentyl-1,4-dioxan-2-one 40V, Negative-QTOF	splash10-052f-9000000000-fab23aa7c95b5f170431	2017-10-06	Wishart Lab	View Spectrum

NMR Spectra

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

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

Not Available

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53435896

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 5-Pentyl-1,4-dioxan-2-one (HMDB0059936)

MOL for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

3D MOL for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

3D SDF for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

3D-SDF for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

PDB for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

3D PDB for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

SMILES for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

INCHI for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

Structure for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

3D Structure for HMDB0059936 (5-Pentyl-1,4-dioxan-2-one)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra