Benzopyrylium compounds

A method of labeling at least one biomolecule, the method comprising combining a composition comprising a compound according to any of general formula Ia

• general formula Ib
• general formula Ic
• general formula Id
• general formula Ie
• general formula If
• general formula Ig
• general formula Ih
• general formula IIa
• general formula IIb
• general formula IIc
• general formula IId
• general formula IIe
• general formula IIf
• general formula IIg
• or general formula IIh
• wherein
• each of R1, R2, R3, R4, R5, R6, R11, and R12 is the same or different and is independently selected from H, SO3, Z, L-Z, a PEG group P-L-Z where P is an ethylene glycol group, a diethylene glycol group, or a polyethylene glycol group, where the polyethylene glycol group is (CH2CH2O)s, where s is an integer from 3-6 inclusive, a sulfonamide group -L-SO2NH—P-L-Z, a carboxamide group -L-CONH—P-L-Z, hydrogen, alkyl-, tert-alkyl, aryl-, carboxyaryl-, dicarboxyaryl, heteroaryl-, cycloalkyl-, heterocycloalkyl-, alkyloxy-, alkylmercapto- with alkyl and cycloalkyl including olefin linkage residues, aryloxy-, arylmercapto-, heteroaryloxy-, heteroarylmercapto-, hydroxy-, nitro-, a carboxylic acid, an amino group, or cyano residues;
• where L is a divalent linear (—(CH2)t—, t=0 to 15), branched, or cyclic alkane group that can be substituted by at least one atom of oxygen, nitrogen, substituted nitrogen, and/or sulfur;
• where Z is H, CH3, alkyl group, sulfoalkyl, heteroalkyl group, NH2, —COO−, —COOH, —COSH, CO—NH—NH2, —COF, —COCl, —COBr, —COI, —COO-Su (succinimidyl/sulfosuccinimidyl), —COO-STP (4-sulfo-2,3,5,6-tetrafluorophenyl), —COO-TFP (2,3,5,6-tetrafluorophenyl), —COO-benzotriazole, —CO-benzotriazole, —CONR′—CO—CH2—I, —CONR′R″, —CONR′-biomolecule, —CONR′-L-COO−, —CONR′-L-COOH, —CONR′-L-COO-Su, —CONR′-L-COO-STP, —CONR′-L-COO-TFP, —CONR′-L-CONR″2, —CONR′-L-CO-biomolecule, —CONR′-L-CO—NH—NH2, —CONR′-L-OH, —CONR′-L-O-phosphoramidite, —CONR′-L-CHO, —CONR′-L-maleimide, or —CONR′-L-NH—CO—CH2—I;
• each of R′ and R″ is selected from H, aliphatic group, or heteroaliphatic group;
• X is selected from —OH, —SH, —NH2, —NH—NH2, —F, —Cl, —Br, I, —NHS (hydroxysuccinimidyl/sulfosuccinimidyl), —O-TFP (2,3,5,6-tetrafluorophenoxy), —O-STP (4-sulfo-2,3,5,6-tetrafluorophenoxy), —O-benzotriazole, -benzotriazole, —NR-L-OH, —NR-L-O-phosphoramidite, —NR-L-SH, —NR-L-NH2, —NR-L-NH—NH2, —NR-L-CO2H, —NR-L-CO—NHS, —NR-L-CO-STP, —NR-L-CO-TFP, —NR-L-CO-benzotriazole, —NR-L-CHO, —NR-L-maleimide, or —NR-L-NH—CO—CH2—I, where R is —H or an aliphatic or heteroaliphatic group;
• each of R10, R13, and R14 is the same or different and is independently selected from aliphatic, heteroaliphatic, sulfoalkyl group, carboxyalkyl group, heteroaliphatic with terminal SO3, Z, L-Z, PEG group P-L-Z where P is an ethylene glycol group, a diethylene glycol group, or a polyethylene glycol group where the polyethylene glycol group is (CH2CH2O)s, where s is an integer from 3-6 inclusive, a sulfonamide group -L-SO2NH—P-L-Z, or a carboxamide group -L-CONH—P-L-Z;
• each of R7 and R9 is the same or different and is independently hydrogen, aliphatic group, heteroaliphatic group, or PEG group P-L-Z where P is selected from an ethylene glycol group, a diethylene glycol group, or a polyethylene glycol group where the polyethylene glycol group is (CH2CH2O)s, where s is an integer from 3-6 inclusive;
• or R7 and R9 together form a cyclic structure where R3 and R4 are joined using a divalent structural element selected from —(CH2)q—, —(CH2)qO(CH2)q′—, —(CH2)qS(CH2)q′—, —(CH2)qCH═CH—, —OCH═CH— where each of q and q′ is the same or different and is a integer from 1 to 6 inclusive;
• and
• R8 is selected from hydrogen, alkyl, sulfoalkyl, fluorine, chlorine, bromine, and PEG group P-L-Z where P is selected from an ethylene glycol group, a diethylene glycol group, or a polyethylene glycol group, where the polyethylene glycol group is (CH2CH2O)s, where s is an integer from 3-6 inclusive;
• each of R1 and R2, R2 and R3, R3 and R4, R5 and R6, R5 and R8, R9 and R10, R11 and R12, or R12 and R13 may form one or more aliphatic, heteroaliphatic or aromatic rings, and where the resultant ring(s) is optionally substituted by at least one alkyl-, sulfoalkyl, tert-alkyl, aryl-, carboxyaryl-, dicarboxyaryl, heteroaryl-, cycloalkyl-, heterocycloalkyl-, alkyloxy-, alkylmercapto- with alkyl and cycloalkyl including olefin linkage residues, aryloxy-, arylmercapto-, heteroaryloxy-, heteroarylmercapto-, hydroxy-, nitro-, sulfonic acid, a carboxylic acid, an amino group, or cyano residues;
• at least one of R1-R14 contains at least one PEG and optionally an additional solubilizing, or ionized substituent selected from SO3−, PO32−, CO2H, OH, NR3+, cyclodextrins or sugars providing hydrophilic characteristics;
• the substituents optionally linked to chromophore by an aliphatic or heteroaliphatic or cyclical spacer;
• Kat is a number of Na+, K+, Ca2+, ammonia, or other cation(s) needed to compensate the negative charge(s);
• n is 0, 1, 2, or 3;
• o is an integer from 0 to 12 inclusive;
• and p is an integer from 1 to 6 inclusive, in an effective concentration to the at least one biomolecule under conditions sufficient for labeling the biomolecule with the compound.