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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-08-28 16:58:09 UTC

Update Date

2021-09-26 22:47:35 UTC

HMDB ID

HMDB0242209

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(-)-Cytisine

Description

7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one. Based on a literature review very few articles have been published on 7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). (-)-cytisine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (-)-Cytisine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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


  Mrv1533004171523482D          

 14 16  0  0  0  0            999 V2000
   -0.8328    2.0583    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7736    1.2354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4567    0.7727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3975   -0.0502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6553   -0.4104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0277    0.0523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6514   -0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4743   -0.4286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0143    0.1951    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9552    1.0180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3315    1.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7357    0.6202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5086    1.4989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0314    0.8752    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  2 14  1  0  0  0  0
  6 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0242209

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1C=CC=C2C3CNCC(C3)CN12

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N2O/c14-11-3-1-2-10-9-4-8(5-12-6-9)7-13(10)11/h1-3,8-9,12H,4-7H2

> <INCHI_KEY>
ANJTVLIZGCUXLD-UHFFFAOYSA-N

> <FORMULA>
C11H14N2O

> <MOLECULAR_WEIGHT>
190.246

> <EXACT_MASS>
190.110613079

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.19550133162881

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one

> <ALOGPS_LOGP>
1.06

> <JCHEM_LOGP>
-0.27985360699999995

> <ALOGPS_LOGS>
-1.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.823392598653696

> <JCHEM_POLAR_SURFACE_AREA>
32.34

> <JCHEM_REFRACTIVITY>
56.9283

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
citizin

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0      -1.555   3.842   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.444   2.306   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.719   1.442   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.609  -0.094   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.223  -0.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.052   0.098   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.216  -0.910   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.752  -0.800   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.760   0.364   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.650   1.900   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.485   2.908   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.373   1.158   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.949   2.798   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.059   1.634   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11    7                                                       
CONECT   13   11   14                                                       
CONECT   14   13    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

COMPND    HMDB0260297
HETATM    1  O1  UNL     1       2.253   2.558   0.272  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.122   1.299   0.187  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.273   0.560   0.368  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.211  -0.817   0.291  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.967  -1.362   0.031  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.838  -0.590  -0.145  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.920   0.731  -0.067  1.00  0.00           N  
HETATM    8  C6  UNL     1      -0.196   1.635  -0.233  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.464   0.958  -0.614  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.281   0.691   0.626  1.00  0.00           C  
HETATM   11  N2  UNL     1      -2.545  -0.729   0.794  1.00  0.00           N  
HETATM   12  C9  UNL     1      -1.269  -1.413   0.874  1.00  0.00           C  
HETATM   13  C10 UNL     1      -0.472  -1.255  -0.424  1.00  0.00           C  
HETATM   14  C11 UNL     1      -1.209  -0.312  -1.367  1.00  0.00           C  
HETATM   15  H1  UNL     1       4.243   1.002   0.572  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.104  -1.434   0.429  1.00  0.00           H  
HETATM   17  H3  UNL     1       1.909  -2.439  -0.032  1.00  0.00           H  
HETATM   18  H4  UNL     1      -0.322   2.156   0.754  1.00  0.00           H  
HETATM   19  H5  UNL     1       0.075   2.462  -0.952  1.00  0.00           H  
HETATM   20  H6  UNL     1      -2.028   1.637  -1.307  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.253   1.251   0.546  1.00  0.00           H  
HETATM   22  H8  UNL     1      -1.788   1.090   1.544  1.00  0.00           H  
HETATM   23  H9  UNL     1      -3.045  -1.085  -0.043  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.473  -2.490   1.089  1.00  0.00           H  
HETATM   25  H11 UNL     1      -0.666  -1.024   1.729  1.00  0.00           H  
HETATM   26  H12 UNL     1      -0.323  -2.247  -0.909  1.00  0.00           H  
HETATM   27  H13 UNL     1      -2.089  -0.756  -1.822  1.00  0.00           H  
HETATM   28  H14 UNL     1      -0.492  -0.076  -2.192  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    4   15
CONECT    4    5   16
CONECT    5    6    6   17
CONECT    6    7   13
CONECT    7    8
CONECT    8    9   18   19
CONECT    9   10   14   20
CONECT   10   11   21   22
CONECT   11   12   23
CONECT   12   13   24   25
CONECT   13   14   26
CONECT   14   27   28
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Cytisine hydrochloride	MeSH, HMDB
3-Hydroxy-11-norcytisine	MeSH, HMDB
Cytisine dihydrochloride, trihydrate	MeSH, HMDB
Cytisine hydrochloride, hydrate	MeSH, HMDB
Cytisine tetrahydrochloride, trihydrate	MeSH, HMDB
Cytiton	MeSH, HMDB
Tsitizin	MeSH, HMDB
Cystisin	MeSH, HMDB
Tabex	MeSH, HMDB
Citizine	MeSH, HMDB

Chemical Formula

C₁₁H₁₄N₂O

Average Molecular Weight

190.246

Monoisotopic Molecular Weight

190.110613079

IUPAC Name

7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one

Traditional Name

citizin

CAS Registry Number

Not Available

SMILES

O=C1C=CC=C2C3CNCC(C3)CN12

InChI Identifier

InChI=1S/C11H14N2O/c14-11-3-1-2-10-9-4-8(5-12-6-9)7-13(10)11/h1-3,8-9,12H,4-7H2

InChI Key

ANJTVLIZGCUXLD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Lupin alkaloids

Sub Class

Cytisine and derivatives

Direct Parent

Cytisine and derivatives

Alternative Parents

Substituents

Cytisine
Aralkylamine
Pyridinone
Piperidine
Pyridine
Heteroaromatic compound
Lactam
Secondary aliphatic amine
Azacycle
Organoheterocyclic compound
Secondary amine
Amine
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Quinolizidine alkaloids (C10763 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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
logP	1.06	ALOGPS
logP	-0.28	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Basic)	9.82	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.34 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	56.93 m³·mol⁻¹	ChemAxon
Polarizability	20.2 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DeepCCS	[M-2H]-	178.212	30932474
DeepCCS	[M+Na]+	153.75	30932474
AllCCS	[M+H]+	141.4	32859911
AllCCS	[M+H-H2O]+	137.2	32859911
AllCCS	[M+NH4]+	145.4	32859911
AllCCS	[M+Na]+	146.6	32859911
AllCCS	[M-H]-	145.2	32859911
AllCCS	[M+Na-2H]-	145.3	32859911
AllCCS	[M+HCOO]-	145.6	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(-)-Cytisine,1TMS,isomer #1	C[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	1979.2	Semi standard non polar	33892256
(-)-Cytisine,1TMS,isomer #1	C[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	2103.4	Standard non polar	33892256
(-)-Cytisine,1TMS,isomer #1	C[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	2448.3	Standard polar	33892256
(-)-Cytisine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	2232.7	Semi standard non polar	33892256
(-)-Cytisine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	2359.4	Standard non polar	33892256
(-)-Cytisine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CC2CC(C1)C1=CC=CC(=O)N1C2	2651.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Cytisine GC-MS (Non-derivatized) - 70eV, Positive	splash10-03dj-4900000000-39e9ec91f667264d22e0	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Cytisine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Cytisine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Cytisine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (-)-Cytisine 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 - (-)-Cytisine 10V, Positive-QTOF	splash10-0006-0900000000-478c29bdf6674a2ea905	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Cytisine 20V, Positive-QTOF	splash10-0006-0900000000-478c29bdf6674a2ea905	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Cytisine 40V, Positive-QTOF	splash10-0007-9700000000-da466d006adeed3adfb7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Cytisine 10V, Negative-QTOF	splash10-000i-0900000000-737a601f9d97628ca508	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Cytisine 20V, Negative-QTOF	splash10-000i-0900000000-ee3c51c2e80badac3911	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (-)-Cytisine 40V, Negative-QTOF	splash10-07bf-2900000000-5fe2ec7f16531a8a8a30	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

21030

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for (-)-Cytisine (HMDB0242209)

MOL for HMDB0242209 ((-)-Cytisine)

3D MOL for HMDB0242209 ((-)-Cytisine)

3D SDF for HMDB0242209 ((-)-Cytisine)

3D-SDF for HMDB0242209 ((-)-Cytisine)

PDB for HMDB0242209 ((-)-Cytisine)

3D PDB for HMDB0242209 ((-)-Cytisine)

SMILES for HMDB0242209 ((-)-Cytisine)

INCHI for HMDB0242209 ((-)-Cytisine)

Structure for HMDB0242209 ((-)-Cytisine)

3D Structure for HMDB0242209 ((-)-Cytisine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra