NP-MRD: Showing NP-Card for 5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium (NP0267428)

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Record Information

Version

1.0

Created at

2022-09-08 12:12:19 UTC

Updated at

2022-09-08 12:12:19 UTC

NP-MRD ID

NP0267428

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium

Description

4-[(2S)-2-amino-2-carboxyethyl]-5-{[(3R,5S,10R)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]Docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-3-methyl-1H-imidazol-3-ium belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on 4-[(2S)-2-amino-2-carboxyethyl]-5-{[(3R,5S,10R)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]Docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-3-methyl-1H-imidazol-3-ium.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082214122D          

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M  CHG  1   2   1
M  END

     RDKit          2D

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M  CHG  1   2   1
M  END


  Mrv1652309082214122D          

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 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
  8 28  1  1  0  0  0
 28 29  1  0  0  0  0
 17 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
 22 30  1  0  0  0  0
  5 31  2  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
NP0267428

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+]1=CNC(SC2[C@H]3N4CCC5=CN=C6C5=C4C4=C(N[C@H]5C[C@]24C(S5)=CC3=O)C6=O)=C1C[C@H](N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H22N6O4S2/c1-30-8-28-23(11(30)4-10(26)24(34)35)37-22-19-12(32)5-13-25(22)6-14(36-13)29-18-16(25)20-15-9(2-3-31(19)20)7-27-17(15)21(18)33/h5,7-8,10,14,19,22H,2-4,6,26H2,1H3,(H2,27,29,33,34,35)/p+1/t10-,14+,19-,22?,25+/m0/s1

> <INCHI_KEY>
ARYKGGHKIXVLJL-YIAFZJLRSA-O

> <FORMULA>
C25H23N6O4S2

> <MOLECULAR_WEIGHT>
535.62

> <EXACT_MASS>
535.121672013

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
68.6664966822971

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2S)-2-amino-2-carboxyethyl]-5-{[(3R,5S,10R)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1^{3,10}.0^{2,12}.0^{3,8}.0^{5,20}.0^{17,21}]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-3-methyl-1H-imidazol-3-ium

> <JCHEM_LOGP>
-6.749589786391849

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
9.652311942029723

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4179518122420651

> <JCHEM_PKA_STRONGEST_BASIC>
8.559660073623428

> <JCHEM_POLAR_SURFACE_AREA>
144.76

> <JCHEM_REFRACTIVITY>
142.172

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-[(2S)-2-amino-2-carboxyethyl]-4-{[(3R,5S,10R)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1^{3,10}.0^{2,12}.0^{3,8}.0^{5,20}.0^{17,21}]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3H-imidazol-1-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.656  -4.474   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.119  -4.566   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0      -3.142  -3.376   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -1.708  -3.938   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.799  -5.475   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0      -0.542  -6.512   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0       0.836  -5.886   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.319  -7.110   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.271  -7.555   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.135  -9.223   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.538  -6.529   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.249  -4.927   0.000  0.00  0.00           C+0
HETATM   13  S   UNK     0      -2.057  -3.453   0.000  0.00  0.00           S+0
HETATM   14  C   UNK     0      -0.979  -2.167   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.301  -3.216   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.319  -4.522   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.817  -3.897   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.968  -2.307   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.540  -1.476   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       3.440  -1.766   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       3.754  -0.160   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.711  -2.679   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       6.263  -2.479   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       6.934  -3.887   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.814  -5.023   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.657  -6.603   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.252  -7.293   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       2.887  -6.483   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       3.091  -4.872   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.487  -4.216   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.289  -5.863   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.409  -7.191   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -3.887  -8.639   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      -2.371  -8.911   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      -4.880  -9.816   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -4.357 -11.265   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -6.396  -9.545   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   31                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   16                                                  
CONECT    8    7    9   28                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   12    7   17                                             
CONECT   17   16   18   29                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18   14                                                       
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   30                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27    8   29                                                  
CONECT   29   28   17   30                                                  
CONECT   30   29   25   22                                                  
CONECT   31    5    2   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   88    0
END

View in JSmol

Synonyms

Value	Source
4-[(2S)-2-Amino-2-carboxyethyl]-5-{[(3R,5S,10R)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1,.0,.0,.0,.0,]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulphanyl}-3-methyl-1H-imidazol-3-ium	Generator

Chemical Formula

C₂₅H₂₃N₆O₄S₂

Average Mass

535.6200 Da

Monoisotopic Mass

535.12167 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[N+]1=CNC(SC2[C@H]3N4CCC5=CN=C6C5=C4C4=C(N[C@H]5C[C@]24C(S5)=CC3=O)C6=O)=C1C[C@H](N)C(O)=O

InChI Identifier

InChI=1S/C25H22N6O4S2/c1-30-8-28-23(11(30)4-10(26)24(34)35)37-22-19-12(32)5-13-25(22)6-14(36-13)29-18-16(25)20-15-9(2-3-31(19)20)7-27-17(15)21(18)33/h5,7-8,10,14,19,22H,2-4,6,26H2,1H3,(H2,27,29,33,34,35)/p+1/t10-,14+,19-,22?,25+/m0/s1

InChI Key

ARYKGGHKIXVLJL-YIAFZJLRSA-O

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Histidine and derivatives

Alternative Parents

Substituents

Histidine or derivatives
1,7-phenanthroline
Diazanaphthalene
L-alpha-amino acid
Naphthyridine
Azaspirodecane
Alpha-amino acid
Indole or derivatives
Aryl thioether
Cyclohexenone
Aralkylamine
Alkylarylthioether
Tetrahydropyridine
Vinylogous thioester
Piperidine
N-substituted imidazole
Heteroaromatic compound
Thiolane
Imidazole
Azole
Amino acid
Tertiary aliphatic amine
Thioenolether
Tertiary amine
Ketone
Ketimine
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Hemithioaminal
Thioether
Secondary amine
Monocarboxylic acid or derivatives
Enamine
Secondary aliphatic amine
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Imine
Carbonyl group
Amine
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

57641944

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163191637

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium (NP0267428)

MOL for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

3D MOL for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

3D SDF for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

3D-SDF for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

PDB for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

3D PDB for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

SMILES for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

INCHI for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

Structure for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)

3D Structure for NP0267428 (5-[(2s)-2-amino-2-carboxyethyl]-4-{[(3r,5s,10r)-6,13-dioxo-9-thia-11,15,20-triazaheptacyclo[12.6.1.1³,¹⁰.0²,¹².0³,⁸.0⁵,²⁰.0¹⁷,²¹]docosa-1(21),2(12),7,14,16-pentaen-4-yl]sulfanyl}-1-methyl-3h-imidazol-1-ium)