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Showing metabocard for Diethyl malonate (HMDB0029573)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:31:13 UTC
Update Date2023-02-21 17:18:49 UTC
HMDB IDHMDB0029573
Secondary Accession Numbers
  • HMDB29573
Metabolite Identification
Common NameDiethyl malonate
DescriptionDiethyl 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0029573 (Diethyl malonate)

  Mrv1652305271900092D          

 11 10  0  0  0  0            999 V2000
   -2.1771    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0949    0.8213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4376    1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6981    0.0004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4376   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1771    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0415    1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6981    0.8213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6981    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
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3D MOL for HMDB0029573 (Diethyl malonate)

HMDB0029573
     RDKit          3D
Diethyl malonate
 23 22  0  0  0  0  0  0  0  0999 V2000
   -4.1967    0.1157    0.0851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0496    1.0546   -0.1842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9016    0.3834   -0.6567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -0.5948    0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6619   -0.9330    1.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0419   -1.2324   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1917   -0.6281    0.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0815    0.2918    0.8663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4606   -1.0244   -0.3508 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6288   -0.4705    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7877    1.0004   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8989   -0.9549    0.0080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5776    0.2958    1.1072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0464    0.2499   -0.6188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8274    1.6905    0.7163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3686    1.7637   -0.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0673   -2.3140   -0.2754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0210   -1.1663   -1.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5275   -1.0362   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5984   -0.6044    1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9858    1.5601    0.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7438    1.3061    0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8929    1.2470   -1.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
 11 22  1  0
 11 23  1  0
M  END
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3D SDF for HMDB0029573 (Diethyl malonate)

  Mrv1652305271900092D          

 11 10  0  0  0  0            999 V2000
   -2.1771    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0949    0.8213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4376    1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6981    0.0004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4376   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1771    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0415    1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6981    0.8213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6981    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -1.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029573

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C7H12O4

> <MOLECULAR_WEIGHT>
160.1678

> <EXACT_MASS>
160.073558872

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.951087561820216

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-diethyl propanedioate

> <ALOGPS_LOGP>
0.93

> <JCHEM_LOGP>
0.6742867529999996

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.359424246273893

> <JCHEM_PKA_STRONGEST_BASIC>
-6.846154885175358

> <JCHEM_POLAR_SURFACE_AREA>
52.6

> <JCHEM_REFRACTIVITY>
38.02320000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.44e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diethyl malonate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0029573 (Diethyl malonate)

HMDB0029573
     RDKit          3D
Diethyl malonate
 23 22  0  0  0  0  0  0  0  0999 V2000
   -4.1967    0.1157    0.0851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0496    1.0546   -0.1842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9016    0.3834   -0.6567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -0.5948    0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6619   -0.9330    1.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0419   -1.2324   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1917   -0.6281    0.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0815    0.2918    0.8663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4606   -1.0244   -0.3508 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6288   -0.4705    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7877    1.0004   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8989   -0.9549    0.0080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5776    0.2958    1.1072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0464    0.2499   -0.6188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8274    1.6905    0.7163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3686    1.7637   -0.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0673   -2.3140   -0.2754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0210   -1.1663   -1.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5275   -1.0362   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5984   -0.6044    1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9858    1.5601    0.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7438    1.3061    0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8929    1.2470   -1.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
 11 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0029573 (Diethyl malonate)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -4.064   0.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.910   1.533   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.684   2.300   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       1.303   0.001   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.684  -0.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.064   0.001   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.077   2.300   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.303   1.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.303   0.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.076  -0.766   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.076  -2.300   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    8                                                       
CONECT    4    5   10                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    8                                                            
CONECT    8    3    7    9                                                  
CONECT    9    8   10                                                       
CONECT   10    4    9   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0029573 (Diethyl malonate)

COMPND    HMDB0029573
HETATM    1  C1  UNL     1      -4.197   0.116   0.085  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.050   1.055  -0.184  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.902   0.383  -0.657  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.240  -0.595   0.047  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.662  -0.933   1.187  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.042  -1.232  -0.551  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.192  -0.628   0.013  1.00  0.00           C  
HETATM    8  O3  UNL     1       1.082   0.292   0.866  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.461  -1.024  -0.351  1.00  0.00           O  
HETATM   10  C6  UNL     1       3.629  -0.471   0.166  1.00  0.00           C  
HETATM   11  C7  UNL     1       3.788   1.000  -0.082  1.00  0.00           C  
HETATM   12  H1  UNL     1      -3.899  -0.955   0.008  1.00  0.00           H  
HETATM   13  H2  UNL     1      -4.578   0.296   1.107  1.00  0.00           H  
HETATM   14  H3  UNL     1      -5.046   0.250  -0.619  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.827   1.690   0.716  1.00  0.00           H  
HETATM   16  H5  UNL     1      -3.369   1.764  -0.975  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.067  -2.314  -0.275  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.021  -1.166  -1.642  1.00  0.00           H  
HETATM   19  H8  UNL     1       4.527  -1.036  -0.169  1.00  0.00           H  
HETATM   20  H9  UNL     1       3.598  -0.604   1.278  1.00  0.00           H  
HETATM   21  H10 UNL     1       2.986   1.560   0.411  1.00  0.00           H  
HETATM   22  H11 UNL     1       4.744   1.306   0.421  1.00  0.00           H  
HETATM   23  H12 UNL     1       3.893   1.247  -1.161  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   15   16
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7   17   18
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   19   20
CONECT   11   21   22   23
END
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SMILES for HMDB0029573 (Diethyl malonate)

CCOC(=O)CC(=O)OCC
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INCHI for HMDB0029573 (Diethyl malonate)

InChI=1S/C7H12O4/c1-3-10-6(8)5-7(9)11-4-2/h3-5H2,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC7H12O4
Average Molecular Weight160.1678
Monoisotopic Molecular Weight160.073558872
IUPAC Name1,3-diethyl propanedioate
Traditional Namediethyl malonate
CAS Registry Number105-53-3
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 KeyIYXGSMUGOJNHAZ-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic 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 FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-50 °CNot Available
Boiling Point199.00 to 200.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility23.2 mg/mL at 37 °CNot Available
LogP0.96Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000728
KNApSAcK IDNot Available
Chemspider ID13863636
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiethyl malonate
METLIN IDNot Available
PubChem Compound7761
PDB IDNot Available
ChEBI ID391281
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1004331
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .