2-[6-(dimethylamino)-3-(dimethyliminiumyl)-3H-xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate

• ChemBase ID: 155959
• Molecular Formular: C29H25N3O7
• Molecular Mass: 527.5247
• Monoisotopic Mass: 527.16925016
• SMILES: CN(C)c1ccc2c(c1)oc1cc(=[N+](C)C)ccc1c2c1ccc(cc1C(=O)[O-])C(=O)ON1C(=O)CCC1=O
• Canonical SMILES: O=C1CCC(=O)N1OC(=O)c1ccc(c(c1)C(=O)[O-])c1c2ccc(=[N+](C)C)cc2oc2c1ccc(c2)N(C)C
• InChI: InChI=1S/C29H25N3O7/c1-30(2)17-6-9-20-23(14-17)38-24-15-18(31(3)4)7-10-21(24)27(20)19-8-5-16(13-22(19)28(35)36)29(37)39-32-25(33)11-12-26(32)34/h5-10,13-15H,11-12H2,1-4H3
• InChIKey: VWFRSNKRTNUMET-UHFFFAOYSA-N

NAMES AND DATABASE IDS

Names

• IUPAC name: 2-[6-(dimethylamino)-3-(dimethyliminiumyl)-3H-xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate
• IUPAC Traditional name: 2-[3-(dimethylamino)-6-(dimethyliminio)xanthen-9-yl]-5-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}benzoate
• Synonyms: "4-Carboxytetramethylrhodamine N-succinimidyl ester"; 5-TAMRA; 5-Carboxy-tetramethylrhodamine N-succinimidyl ester

Database IDs

• CAS Number: 150810-68-7
• MDL Number: MFCD03453223
• PubChem SID: 162250097; 24877749
• PubChem CID: 2762600

CALCULATED PROPERTIES

• Acid pKa: 3.6780312
• H Acceptors: 7
• H Donor: 0
• LogD (pH = 5.5): 0.13623959
• LogD (pH = 7.4): 0.14210227
• Log P: -0.76182264
• Molar Refractivity: 177.5728 cm^3
• Polarizability: 53.672615 Å^3
• Polar Surface Area: 119.29 Å^2
• Rotatable Bonds: 5
• Lipinski's Rule of Five: false

PROPERTIES

Physical Property

• Solubility: acetonitrile: soluble; DMF: soluble
• Fluorescence: λex 543 nm; λem 578 nm in 0.1 M phosphate pH 7.0

Safety Information

• German water hazard class: 3
• Personal Protective Equipment: Eyeshields, Gloves, type N95 (US), type P1 (EN143) respirator filter
• Storage Temperature: -20°C

Product Information

• Suitability: suitable for fluorescence
• Product Line: BioReagent
• Empirical Formula (Hill Notation): C29H25N3O7

DETAILS

Sigma Aldrich - 53048

Other Notes
Fluorescent labeling of DNA and RNA1