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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-07-25 00:10:05 UTC

Update Date

2021-09-14 15:47:38 UTC

HMDB ID

HMDB0012931

Secondary Accession Numbers

HMDB12931

Metabolite Identification

Common Name

Dopachrome o-semiquinone

Description

Dopachrome o-semiquinone belongs to the class of organic compounds known as indolecarboxylic acids. Indolecarboxylic acids are compounds containing a carboxylic acid group linked to an indole. Based on a literature review very few articles have been published on Dopachrome o-semiquinone.

Structure

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

      
  Mrv1652303102016472D          

 14 15  0  0  1  0            999 V2000
   12.9563  -12.4297    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   13.6708  -12.0172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3854  -12.4297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0999  -12.0172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8845  -12.2721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3689  -11.6047    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.8845  -10.9374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.0999  -11.1923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3854  -10.7798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6708  -11.1923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9563  -10.7798    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1939  -11.6046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6063  -10.8901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6064  -12.3191    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  2 10  2  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 12  1  1  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  1  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012931

> <DATABASE_NAME>
hmdb

> <SMILES>
[O]C1=C(O)C=C2N[C@H](CC2=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H8NO4/c11-7-2-4-1-6(9(13)14)10-5(4)3-8(7)12/h2-3,6,10,12H,1H2,(H,13,14)/t6-/m1/s1

> <INCHI_KEY>
YHAPBGUGQAHLME-ZCFIWIBFSA-N

> <FORMULA>
C9H8NO4

> <MOLECULAR_WEIGHT>
194.1641

> <EXACT_MASS>
194.045332749

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
18.111933224809608

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(2R)-2-carboxy-6-hydroxy-2,3-dihydro-1H-indol-5-yl]oxidanyl

> <ALOGPS_LOGP>
1.10

> <JCHEM_LOGP>
0.6101999999999997

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.150245268106089

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0841756577883355

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2954218802517934

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
59.90340000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-carboxy-6-hydroxy-2,3-dihydro-1H-indol-5-yloxidanyl

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  O   UNK     0      24.185 -23.202   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      25.519 -22.432   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.853 -23.202   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.186 -22.432   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.651 -22.908   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      30.555 -21.662   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      29.651 -20.416   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      28.186 -20.892   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      26.853 -20.122   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      25.519 -20.892   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      24.185 -20.122   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      32.095 -21.662   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      32.865 -20.328   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      32.865 -22.996   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    3   10    1                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    4    7    9                                                  
CONECT    9    8   10                                                       
CONECT   10    2    9   11                                                  
CONECT   11   10                                                            
CONECT   12    6   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
DCSQ	HMDB
Leukodopachrome O-semiquinone radical	HMDB

Chemical Formula

C₉H₈NO₄

Average Molecular Weight

194.1641

Monoisotopic Molecular Weight

194.045332749

IUPAC Name

[(2R)-2-carboxy-6-hydroxy-2,3-dihydro-1H-indol-5-yl]oxidanyl

Traditional Name

(2R)-2-carboxy-6-hydroxy-2,3-dihydro-1H-indol-5-yloxidanyl

CAS Registry Number

1246035-97-1

SMILES

[O]C1=C(O)C=C2N[C@H](CC2=C1)C(O)=O

InChI Identifier

InChI=1S/C9H8NO4/c11-7-2-4-1-6(9(13)14)10-5(4)3-8(7)12/h2-3,6,10,12H,1H2,(H,13,14)/t6-/m1/s1

InChI Key

YHAPBGUGQAHLME-ZCFIWIBFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolecarboxylic acids. Indolecarboxylic acids are compounds containing a carboxylic acid group linked to an indole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolecarboxylic acids and derivatives

Direct Parent

Indolecarboxylic acids

Alternative Parents

Substituents

Indolecarboxylic acid
Alpha-amino acid
Alpha-amino acid or derivatives
D-alpha-amino acid
Dihydroindole
1-hydroxy-2-unsubstituted benzenoid
Secondary aliphatic/aromatic amine
Aralkylamine
Benzenoid
Amino acid or derivatives
Amino acid
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Secondary amine
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Amine
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Solid

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	11.4 g/L	ALOGPS
logP	1.1	ALOGPS
logP	0.61	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	3.08	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.56 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	59.9 m³·mol⁻¹	ChemAxon
Polarizability	18.11 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	147.737	31661259
DarkChem	[M-H]-	142.492	31661259
DeepCCS	[M+H]+	141.317	30932474
DeepCCS	[M-H]-	138.921	30932474
DeepCCS	[M-2H]-	172.278	30932474
DeepCCS	[M+Na]+	147.23	30932474
AllCCS	[M+H]+	142.1	32859911
AllCCS	[M+H-H2O]+	137.9	32859911
AllCCS	[M+NH4]+	146.1	32859911
AllCCS	[M+Na]+	147.2	32859911
AllCCS	[M-H]-	139.5	32859911
AllCCS	[M+Na-2H]-	139.7	32859911
AllCCS	[M+HCOO]-	140.0	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Dopachrome o-semiquinone,1TMS,isomer #1	C[Si](C)(C)OC1=CC2=C(C=C1[O])C[C@H](C(=O)O)N2	2140.9	Semi standard non polar	33892256
Dopachrome o-semiquinone,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O)C=C2N1	2063.3	Semi standard non polar	33892256
Dopachrome o-semiquinone,1TMS,isomer #3	C[Si](C)(C)N1C2=CC(O)=C([O])C=C2C[C@@H]1C(=O)O	2095.6	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C)C=C2N1	2109.7	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TMS,isomer #2	C[Si](C)(C)OC1=CC2=C(C=C1[O])C[C@H](C(=O)O)N2[Si](C)(C)C	2098.2	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O)C=C2N1[Si](C)(C)C	2078.4	Semi standard non polar	33892256
Dopachrome o-semiquinone,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C)C=C2N1[Si](C)(C)C	2108.8	Semi standard non polar	33892256
Dopachrome o-semiquinone,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C)C=C2N1[Si](C)(C)C	2102.3	Standard non polar	33892256
Dopachrome o-semiquinone,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C)C=C2N1[Si](C)(C)C	2252.0	Standard polar	33892256
Dopachrome o-semiquinone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2=C(C=C1[O])C[C@H](C(=O)O)N2	2401.5	Semi standard non polar	33892256
Dopachrome o-semiquinone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O)C=C2N1	2353.2	Semi standard non polar	33892256
Dopachrome o-semiquinone,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C2=CC(O)=C([O])C=C2C[C@@H]1C(=O)O	2382.9	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C(C)(C)C)C=C2N1	2587.7	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CC2=C(C=C1[O])C[C@H](C(=O)O)N2[Si](C)(C)C(C)(C)C	2655.6	Semi standard non polar	33892256
Dopachrome o-semiquinone,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O)C=C2N1[Si](C)(C)C(C)(C)C	2570.9	Semi standard non polar	33892256
Dopachrome o-semiquinone,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C(C)(C)C)C=C2N1[Si](C)(C)C(C)(C)C	2805.7	Semi standard non polar	33892256
Dopachrome o-semiquinone,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C(C)(C)C)C=C2N1[Si](C)(C)C(C)(C)C	2763.2	Standard non polar	33892256
Dopachrome o-semiquinone,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC([O])=C(O[Si](C)(C)C(C)(C)C)C=C2N1[Si](C)(C)C(C)(C)C	2622.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dopachrome o-semiquinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fk9-0900000000-14161f2f212d7f618988	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dopachrome o-semiquinone GC-MS (2 TMS) - 70eV, Positive	splash10-00r6-9862000000-48bde12fcf4b33d59d79	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dopachrome o-semiquinone 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 - Dopachrome o-semiquinone 10V, Positive-QTOF	splash10-002b-0900000000-b20012b2274681d12add	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 20V, Positive-QTOF	splash10-00dj-0900000000-c837b0952c9118b19617	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 40V, Positive-QTOF	splash10-00dj-3900000000-c08c219ad8015ee050bd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 10V, Positive-QTOF	splash10-0002-0900000000-d95cfc7e3a54a6f9a4a6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 20V, Positive-QTOF	splash10-0udi-0900000000-21cbd7b3c97ef0183c57	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 40V, Positive-QTOF	splash10-001l-4900000000-c16a28629a2b109bcf85	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 10V, Negative-QTOF	splash10-0002-0900000000-17f8e7f25df3a1f125cb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 20V, Negative-QTOF	splash10-0002-0900000000-436b7bee27cb61484cd8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dopachrome o-semiquinone 40V, Negative-QTOF	splash10-00dj-1900000000-a8a00903984a194ba494	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart 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

FDB029211

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

Not Available

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

Not Available

Showing metabocard for Dopachrome o-semiquinone (HMDB0012931)

MOL for HMDB0012931 (Dopachrome o-semiquinone)

3D MOL for HMDB0012931 (Dopachrome o-semiquinone)

3D SDF for HMDB0012931 (Dopachrome o-semiquinone)

3D-SDF for HMDB0012931 (Dopachrome o-semiquinone)

PDB for HMDB0012931 (Dopachrome o-semiquinone)

3D PDB for HMDB0012931 (Dopachrome o-semiquinone)

SMILES for HMDB0012931 (Dopachrome o-semiquinone)

INCHI for HMDB0012931 (Dopachrome o-semiquinone)

Structure for HMDB0012931 (Dopachrome o-semiquinone)

3D Structure for HMDB0012931 (Dopachrome o-semiquinone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra