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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:48:46 UTC

Update Date

2022-03-07 02:56:32 UTC

HMDB ID

HMDB0040279

Secondary Accession Numbers

HMDB40279

Metabolite Identification

Common Name

2,4,5-Trimethyl-1,3-dioxolane

Description

2,4,5-Trimethyl-1,3-dioxolane belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3. 2,4,5-Trimethyl-1,3-dioxolane has been detected, but not quantified in, several different foods, such as alcoholic beverages, apples (Malus pumila), blackberries (Rubus), evergreen blackberries (Rubus laciniatus), and pulses. This could make 2,4,5-trimethyl-1,3-dioxolane a potential biomarker for the consumption of these foods. 2,4,5-Trimethyl-1,3-dioxolane 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 very few articles have been published on 2,4,5-Trimethyl-1,3-dioxolane.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₆H₁₂O₂

Average Molecular Weight

116.1583

Monoisotopic Molecular Weight

116.083729628

IUPAC Name

2,4,5-trimethyl-1,3-dioxolane

Traditional Name

2,4,5-trimethyl-1,3-dioxolane

CAS Registry Number

3299-32-9

SMILES

CC1OC(C)C(C)O1

InChI Identifier

InChI=1S/C6H12O2/c1-4-5(2)8-6(3)7-4/h4-6H,1-3H3

InChI Key

HLEXJAVJCZLRTH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxolanes

Sub Class

1,3-dioxolanes

Direct Parent

1,3-dioxolanes

Alternative Parents

Substituents

Meta-dioxolane
Oxacycle
Acetal
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dioxolane (CHEBI:87572 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040279)
Cytoplasm (HMDB: HMDB0040279)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040279)

Source

Exogenous

Exogenous (HMDB: HMDB0040279)

Food

Food (HMDB: HMDB0040279)

Fruit

Pome

Apple (FooDB: FOOD00105)

Berry

Evergreen blackberry (FooDB: FOOD00901)
Blackberry (FooDB: FOOD00906)

Pulse

Pulses (FooDB: FOOD00867)

Beverage

Alcoholic beverage

Alcoholic beverages (FooDB: FOOD00854)

Endogenous

Plant

Fabaceae (HMDB: HMDB0040279)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040279)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	115.00 to 117.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	16140 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.154 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	55.7 g/L	ALOGPS
logP	0.86	ALOGPS
logP	1.08	ChemAxon
logS	-0.32	ALOGPS
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	18.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	30.58 m³·mol⁻¹	ChemAxon
Polarizability	13.12 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]+	125.29	31661259
DarkChem	[M-H]-	120.742	31661259
DeepCCS	[M+H]+	130.714	30932474
DeepCCS	[M-H]-	128.679	30932474
DeepCCS	[M-2H]-	164.483	30932474
DeepCCS	[M+Na]+	139.165	30932474
AllCCS	[M+H]+	127.0	32859911
AllCCS	[M+H-H2O]+	122.3	32859911
AllCCS	[M+NH4]+	131.4	32859911
AllCCS	[M+Na]+	132.7	32859911
AllCCS	[M-H]-	125.8	32859911
AllCCS	[M+Na-2H]-	128.6	32859911
AllCCS	[M+HCOO]-	131.7	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.	2.79 minutes	32390414
Predicted by Siyang on May 30, 2022	13.5749 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.37 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	27.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1824.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	489.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	161.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	295.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	94.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	427.5 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	623.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	110.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1007.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	368.1 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	1114.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	353.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	342.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	458.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	433.6 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	49.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,4,5-Trimethyl-1,3-dioxolane	CC1OC(C)C(C)O1	918.3	Standard polar	33892256
2,4,5-Trimethyl-1,3-dioxolane	CC1OC(C)C(C)O1	741.2	Standard non polar	33892256
2,4,5-Trimethyl-1,3-dioxolane	CC1OC(C)C(C)O1	729.4	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 - 2,4,5-Trimethyl-1,3-dioxolane GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fi3-9100000000-b7df0dc953069948786b	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 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 - 2,4,5-Trimethyl-1,3-dioxolane 10V, Positive-QTOF	splash10-014i-1900000000-912ad8384336ba8b9e42	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 20V, Positive-QTOF	splash10-014i-3900000000-8fd1278a4d23daa45f75	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 40V, Positive-QTOF	splash10-0adi-9100000000-4d3312bfa6f4f3482885	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 10V, Negative-QTOF	splash10-014i-0900000000-06e98e6eccea522fe8ba	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 20V, Negative-QTOF	splash10-014i-4900000000-0c9ddb4cd15cab111aa0	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 40V, Negative-QTOF	splash10-014l-9000000000-36f6c29c1bef798eda22	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 10V, Negative-QTOF	splash10-00ku-9100000000-ea2307d4735d95ed2178	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 20V, Negative-QTOF	splash10-0006-9000000000-bc38631d963596327baa	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 40V, Negative-QTOF	splash10-0006-9000000000-00d21970abd391a58634	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 10V, Positive-QTOF	splash10-00dj-9100000000-43a42d0bced396437b06	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 20V, Positive-QTOF	splash10-0aba-9000000000-b883bfed6494c76d3f32	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,4,5-Trimethyl-1,3-dioxolane 40V, Positive-QTOF	splash10-052k-9000000000-579009f2d061890c5c6f	2021-09-23	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

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

FDB019998

KNApSAcK ID

C00058083

Chemspider ID

93019

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102967

PDB ID

Not Available

ChEBI ID

87572

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1484701

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 2,4,5-Trimethyl-1,3-dioxolane (HMDB0040279)

MOL for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

3D MOL for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

3D SDF for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

3D-SDF for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

PDB for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

3D PDB for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

SMILES for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

INCHI for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

Structure for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

3D Structure for HMDB0040279 (2,4,5-Trimethyl-1,3-dioxolane)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra