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Showing metabocard for Dimethyl carbonate (HMDB0029580)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:31:16 UTC
Update Date2023-02-21 17:18:50 UTC
HMDB IDHMDB0029580
Secondary Accession Numbers
  • HMDB29580
Metabolite Identification
Common NameDimethyl carbonate
DescriptionDimethyl carbonate is used for cold sterilisation of beverages. Effective against typical beverage-spoiling microorganisms, like yeasts and fermentative bacteria Dimethyl carbonate, often abbreviated DMC, is a flammable clear liquid boiling at 90 °C. It has recently found use as a methylating reagent. Its main benefit over other methylating reagents such as iodomethane and dimethyl sulfate is its lesser toxicity and its biodegradability. Also, it is now prepared from catalytic oxidative carbonylation of methanol with carbon monoxide and oxygen, instead of from phosgene making its production non-toxic and environmentally friendly. This allows dimethyl carbonate to be considered a green reagent
Structure
Data?1676999930
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0029580 (Dimethyl carbonate)


  Mrv0541 02241215442D          

  6  5  0  0  0  0            999 V2000
   -0.7015   -1.0314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015   -0.2064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.2057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.0314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -0.2064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -1.0314    0.0000 C   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  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0029580 (Dimethyl carbonate)

HMDB0029580
     RDKit          3D
Dimethyl carbonate
 12 11  0  0  0  0  0  0  0  0999 V2000
    2.4705    0.0142   -0.0364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2335    0.0007   -0.7121 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0058   -0.0137   -0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0110   -0.0147    1.1899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2097   -0.0269   -0.7203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4563   -0.0415   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509    0.2220   -0.8227 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7186   -0.9279    0.4636 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5154    0.8915    0.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1996    0.3640   -0.8108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5143    0.6130    0.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8037   -1.0805    0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  6 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0029580 (Dimethyl carbonate)


  Mrv0541 02241215442D          

  6  5  0  0  0  0            999 V2000
   -0.7015   -1.0314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015   -0.2064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.2057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.0314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -0.2064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -1.0314    0.0000 C   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  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029580

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O3/c1-5-3(4)6-2/h1-2H3

> <INCHI_KEY>
IEJIGPNLZYLLBP-UHFFFAOYSA-N

> <FORMULA>
C3H6O3

> <MOLECULAR_WEIGHT>
90.0779

> <EXACT_MASS>
90.031694058

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
8.301328505774375

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dimethyl carbonate

> <ALOGPS_LOGP>
0.03

> <JCHEM_LOGP>
0.5418394776666665

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-5.535508108684515

> <JCHEM_POLAR_SURFACE_AREA>
35.53

> <JCHEM_REFRACTIVITY>
19.0364

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.25e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethyl carbonate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0029580 (Dimethyl carbonate)

HMDB0029580
     RDKit          3D
Dimethyl carbonate
 12 11  0  0  0  0  0  0  0  0999 V2000
    2.4705    0.0142   -0.0364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2335    0.0007   -0.7121 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0058   -0.0137   -0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0110   -0.0147    1.1899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2097   -0.0269   -0.7203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4563   -0.0415   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509    0.2220   -0.8227 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7186   -0.9279    0.4636 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5154    0.8915    0.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1996    0.3640   -0.8108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5143    0.6130    0.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8037   -1.0805    0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  6 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

PDB for HMDB0029580 (Dimethyl carbonate)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -1.309  -1.925   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.309  -0.385   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.076   0.384   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.076   1.925   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.309  -0.385   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.309  -1.925   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0029580 (Dimethyl carbonate)

COMPND    HMDB0029580
HETATM    1  C1  UNL     1       2.470   0.014  -0.036  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.233   0.001  -0.712  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.006  -0.014  -0.072  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.011  -0.015   1.190  1.00  0.00           O  
HETATM    5  O3  UNL     1      -1.210  -0.027  -0.720  1.00  0.00           O  
HETATM    6  C3  UNL     1      -2.456  -0.041  -0.066  1.00  0.00           C  
HETATM    7  H1  UNL     1       3.251   0.222  -0.823  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.719  -0.928   0.464  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.515   0.892   0.644  1.00  0.00           H  
HETATM   10  H4  UNL     1      -3.200   0.364  -0.811  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.514   0.613   0.805  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.804  -1.081   0.137  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6
CONECT    6   10   11   12
END
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SMILES for HMDB0029580 (Dimethyl carbonate)

COC(=O)OC
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INCHI for HMDB0029580 (Dimethyl carbonate)

InChI=1S/C3H6O3/c1-5-3(4)6-2/h1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Carbonic acid, dimethyl esterChEBI
DMCChEBI
Methyl carbonateChEBI
Carbonate, dimethyl esterGenerator
Methyl carbonic acidGenerator
Dimethyl carbonic acidGenerator
Carbonic acid dimethyl ester, 9ciHMDB
CH3OCOOCH3HMDB
Dimethyl ester OF carbonic acidHMDB
e242HMDB
Methyl carbonate ((meo)2co)HMDB
Methyl carbonate, 11C-labeledHMDB
Methyl carbonate, hexachloroantimonate (1-)HMDB
Methyl carbonate, hexachloroantimonate (1-) (2:1)HMDB
Chemical FormulaC3H6O3
Average Molecular Weight90.0779
Monoisotopic Molecular Weight90.031694058
IUPAC Namedimethyl carbonate
Traditional Namedimethyl carbonate
CAS Registry Number616-38-6
SMILES
COC(=O)OC
InChI Identifier
InChI=1S/C3H6O3/c1-5-3(4)6-2/h1-2H3
InChI KeyIEJIGPNLZYLLBP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carbonic acid diesters. Carbonic acid diesters are compounds comprising the carbonic acid diester functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassCarbonic acid diesters
Direct ParentCarbonic acid diesters
Alternative Parents
Substituents
  • Carbonic acid diester
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point0.5 °CNot Available
Boiling Point90.00 to 91.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility78590 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.070 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility225 g/LALOGPS
logP0.03ALOGPS
logP0.54ChemAxon
logS0.4ALOGPS
pKa (Strongest Basic)-5.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area35.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity19.04 m³·mol⁻¹ChemAxon
Polarizability8.3 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+117.12931661259
DarkChem[M-H]-111.29431661259
DeepCCS[M+H]+131.50530932474
DeepCCS[M-H]-128.74330932474
DeepCCS[M-2H]-164.84730932474
DeepCCS[M+Na]+139.91330932474
AllCCS[M+H]+127.232859911
AllCCS[M+H-H2O]+123.032859911
AllCCS[M+NH4]+131.232859911
AllCCS[M+Na]+132.432859911
AllCCS[M-H]-125.032859911
AllCCS[M+Na-2H]-129.832859911
AllCCS[M+HCOO]-135.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Dimethyl carbonateCOC(=O)OC866.7Standard polar33892256
Dimethyl carbonateCOC(=O)OC542.5Standard non polar33892256
Dimethyl carbonateCOC(=O)OC599.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Dimethyl carbonate EI-B (Non-derivatized)splash10-015a-9000000000-e030547c5837144d92012017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethyl carbonate EI-B (Non-derivatized)splash10-05nb-9000000000-a91772bfccbb956b63532017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethyl carbonate EI-B (Non-derivatized)splash10-015a-9000000000-e030547c5837144d92012018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethyl carbonate EI-B (Non-derivatized)splash10-05nb-9000000000-a91772bfccbb956b63532018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethyl carbonate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-447264e4562bc93a92622017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethyl carbonate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 10V, Positive-QTOFsplash10-0006-9000000000-d6394b7c8007fe101e942016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 20V, Positive-QTOFsplash10-0006-9000000000-86d32ff334e1f921b0272016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 40V, Positive-QTOFsplash10-001i-9000000000-6121c86e8ccc73c321062016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 10V, Negative-QTOFsplash10-000i-9000000000-571a361989c8785cd4712016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 20V, Negative-QTOFsplash10-000i-9000000000-a11417e54fd89fbc91002016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 40V, Negative-QTOFsplash10-0a4r-9000000000-50fcebbdd13c6d94e1c22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 10V, Negative-QTOFsplash10-000i-9000000000-b586cb8f053eb4465b4e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 20V, Negative-QTOFsplash10-000i-9000000000-b586cb8f053eb4465b4e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 40V, Negative-QTOFsplash10-001i-9000000000-8071a59ff1eb417f4a9a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 10V, Positive-QTOFsplash10-0006-9000000000-6f1149e85cd0e0e20ac72021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 20V, Positive-QTOFsplash10-06r6-9000000000-635c32887e493a62d6842021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethyl carbonate 40V, Positive-QTOFsplash10-0a4i-9000000000-07e977e6b65b7f3e03362021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
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 IDFDB000737
KNApSAcK IDNot Available
Chemspider ID11526
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDimethyl_carbonate
METLIN IDNot Available
PubChem Compound12021
PDB IDNot Available
ChEBI ID36596
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1019981
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .