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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:31:13 UTC

Update Date

2023-02-21 17:18:49 UTC

HMDB ID

HMDB0029573

Secondary Accession Numbers

HMDB29573

Metabolite Identification

Common Name

Diethyl malonate

Description

Diethyl malonate, also known as dicarbethoxymethane or ethyl propanedioate, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Diethyl malonate is a sweet, apple, and fruity tasting compound. Diethyl malonate has been detected, but not quantified, in a few different foods, such as alcoholic beverages, evergreen blackberries, and fruits. Like other esters, this compound can undergo bromination at the alpha position. Fischer esterification gives diethyl malonate: One of the principal uses of this compound is in the malonic ester synthesis. It occurs naturally in grapes and strawberries as a colourless liquid with an apple-like odour, and is used in perfumes. Malonic acid is a rather simple dicarboxylic acid, with the two carboxyl groups close together. The hydrogen atoms on a carbon adjacent to two carbonyl groups are even more acidic because the carbonyl groups help stabilize the carbanion resulting from the removal of that proton. Like many other esters, this compound can undergo the Claisen ester condensation. This alkylated 1,3-dicarbonyl compound (3) readily undergoes decarboxylation with loss of carbon dioxide, to give a substituted acetic acid, using Sodium ethoxide as the preferred base. The use of aqueous sodium hydroxide may give the base hydrolysis products: sodium malonate and ethanol.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Diethyl malonic acid	Generator
Carbethoxyacetic ester	HMDB
Dicarbethoxymethane	HMDB
Diethyl propanedioate	HMDB
Diethyl propanedioate, 9ci	HMDB
Ethyl malonate	HMDB
Ethyl methanedicarboxylate	HMDB
Ethyl propanedioate	HMDB
FEMA 2375	HMDB
Malonic acid diethyl ester	HMDB
Malonic acid, diethyl ester	HMDB
Malonic ester	HMDB
Methanedicarboxylic acid, diethyl ester	HMDB
Propanedioic acid, 1,3-diethyl ester	HMDB
Propanedioic acid, diethyl ester	HMDB
1,3-Diethyl propanedioic acid	Generator
Diethyl malonate	MeSH
Diethylmalonate	MeSH

Chemical Formula

C₇H₁₂O₄

Average Molecular Weight

160.1678

Monoisotopic Molecular Weight

160.073558872

IUPAC Name

1,3-diethyl propanedioate

Traditional Name

diethyl malonate

CAS Registry Number

105-53-3

SMILES

CCOC(=O)CC(=O)OCC

InChI Identifier

InChI=1S/C7H12O4/c1-3-10-6(8)5-7(9)11-4-2/h3-5H2,1-2H3

InChI Key

IYXGSMUGOJNHAZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Dicarboxylic acids and derivatives

Direct Parent

Dicarboxylic acids and derivatives

Alternative Parents

Substituents

1,3-dicarbonyl compound
Dicarboxylic acid or derivatives
Carboxylic acid ester
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Sweet

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029573)
Cytoplasm (HMDB: HMDB0029573)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029573)

Source

Endogenous

Endogenous (HMDB: HMDB0029573)

Plant

Plant (HMDB: HMDB0029573)

Exogenous

Food

Food (HMDB: HMDB0029573)

Fruit

Fruits (FooDB: FOOD00871)

Berry

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

Beverage

Alcoholic beverage

Alcoholic beverages (FooDB: FOOD00854)

Exogenous (HMDB: HMDB0029573)

Process

Not Available

Role

Not Available

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	-50 °C	Not Available
Boiling Point	199.00 to 200.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	23.2 mg/mL at 37 °C	Not Available
LogP	0.96	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	24.4 g/L	ALOGPS
logP	0.93	ALOGPS
logP	0.67	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	12.36	ChemAxon
pKa (Strongest Basic)	-6.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	38.02 m³·mol⁻¹	ChemAxon
Polarizability	15.95 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	136.362	31661259
DarkChem	[M-H]-	132.178	31661259
DeepCCS	[M+H]+	134.115	30932474
DeepCCS	[M-H]-	131.528	30932474
DeepCCS	[M-2H]-	168.198	30932474
DeepCCS	[M+Na]+	143.196	30932474
AllCCS	[M+H]+	137.6	32859911
AllCCS	[M+H-H2O]+	133.7	32859911
AllCCS	[M+NH4]+	141.2	32859911
AllCCS	[M+Na]+	142.2	32859911
AllCCS	[M-H]-	136.1	32859911
AllCCS	[M+Na-2H]-	138.2	32859911
AllCCS	[M+HCOO]-	140.5	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. Predicted by Afia on May 17, 2022.	5.14 minutes	32390414
Predicted by Siyang on May 30, 2022	12.7837 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.39 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1739.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	402.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	137.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	246.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	90.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	458.2 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	550.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	127.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	973.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	374.7 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	1251.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	335.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	294.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	516.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	373.8 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	101.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Diethyl malonate	CCOC(=O)CC(=O)OCC	1657.1	Standard polar	33892256
Diethyl malonate	CCOC(=O)CC(=O)OCC	1003.0	Standard non polar	33892256
Diethyl malonate	CCOC(=O)CC(=O)OCC	1108.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-016u-9400000000-adc51f2543836992b5a7	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00pl-9100000000-686a923858ceb77f2ab3	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00ou-9300000000-baedf40984817543fb55	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00ou-9300000000-ca6a39f537696bdd1204	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-017i-9800000000-b9f129ca3341a0dc4057	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-016u-9400000000-adc51f2543836992b5a7	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00pl-9100000000-686a923858ceb77f2ab3	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00ou-9300000000-baedf40984817543fb55	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-00ou-9300000000-ca6a39f537696bdd1204	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Diethyl malonate EI-B (Non-derivatized)	splash10-017i-9800000000-b9f129ca3341a0dc4057	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Diethyl malonate GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9200000000-521aa9a304ed814bfb1d	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Diethyl malonate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Diethyl malonate 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Diethyl malonate 20V, Positive-QTOF	splash10-0006-9000000000-f5ad3eda53f3b99fc2ed	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Diethyl malonate 10V, Positive-QTOF	splash10-00kf-9700000000-ecca8ff833198def45b7	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Diethyl malonate 40V, Positive-QTOF	splash10-016u-9300000000-2589b4ca78c97b95c191	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 10V, Positive-QTOF	splash10-03di-2900000000-0dcf20fb7a7668f4991f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 20V, Positive-QTOF	splash10-0292-9700000000-ebd4c59ff9ec0aa6674e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 40V, Positive-QTOF	splash10-02g5-9000000000-c3d6ded5e3f0148b1eff	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 10V, Negative-QTOF	splash10-0bt9-3900000000-cacc99a9a8f1cd451446	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 20V, Negative-QTOF	splash10-06rj-9500000000-78842db871bcfa2f2842	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 40V, Negative-QTOF	splash10-052g-9000000000-bcad04b3aebdaff62cfb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 10V, Negative-QTOF	splash10-0a4i-4900000000-7de68f92e6a8d0d22cab	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 20V, Negative-QTOF	splash10-01w0-9200000000-2baec930662daf8d0390	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 40V, Negative-QTOF	splash10-052e-9000000000-ce6ba549218977c8766c	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 10V, Positive-QTOF	splash10-015i-4900000000-1e726b2f9dc40b5f16fc	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 20V, Positive-QTOF	splash10-0007-9100000000-26d1b01554b94a4c765d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Diethyl malonate 40V, Positive-QTOF	splash10-006w-9000000000-f0bf526552ec6cd9298b	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)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	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

FDB000728

KNApSAcK ID

Not Available

Chemspider ID

13863636

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Diethyl malonate

METLIN ID

Not Available

PubChem Compound

7761

PDB ID

Not Available

ChEBI ID

391281

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1004331

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Chevanet C, Besson F, Michel G: Effect of various growth conditions on spore formation and bacillomycin L production in Bacillus subtilis. Can J Microbiol. 1986 Mar;32(3):254-8. [PubMed:3011233 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Diethyl malonate (HMDB0029573)

MOL for HMDB0029573 (Diethyl malonate)

3D MOL for HMDB0029573 (Diethyl malonate)

3D SDF for HMDB0029573 (Diethyl malonate)

3D-SDF for HMDB0029573 (Diethyl malonate)

PDB for HMDB0029573 (Diethyl malonate)

3D PDB for HMDB0029573 (Diethyl malonate)

SMILES for HMDB0029573 (Diethyl malonate)

INCHI for HMDB0029573 (Diethyl malonate)

Structure for HMDB0029573 (Diethyl malonate)

3D Structure for HMDB0029573 (Diethyl malonate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra