4,4-disubstituted cyclohexyl bridged heptamethine cyanine dyes and uses thereof

A fluorescent compound represented by Formula

• or a salt thereof, wherein:
• X1 and X2 are each independently O, S, Se, or C(C1-4 alkyl)2;
• W1 and W2 are a benzo, naphtha, or pyridyl ring;
• R1 and R2 are independently hydrogen or —C1-C10 alkyl optionally substituted with one or two substituents independently selected from the group consisting of halogen, —SO3H, —SO2−, —COOH, —CO2−, and —OH;
• R3, R4, R13 and R14 are each independently H, —C1-C22 alkylene-X3, —SO3H, SO2−, —SO2N(R12)-alkylene-X3, halogen, or —NO2;
• X3 represents independently for each occurrence H, halogen, —CH3, —SO3H, —COOH, —CO2−, —NCS, —NCO, N-hydroxysuccinimidyl ester, N-hydroxysulfosuccinimidyl ester, —OH, —SH, maleimide, phthalimide, —NHCO—(CH2)m-(halogen), —CONHNH2, —CN, —NH2, —NO2, —CON(H)R13, alkynyl, —N3, a polyethyl glycol, optionally substituted aryl, or optionally substituted heterocyclyl;
• R9 and R10 are hydrogen, halogen, or alkyl, or R1 and R9 or R2 and R10 are taken together with their interconnecting atoms to form a 5-, 6- or 7-membered ring;
• R11 and R12 are each independently alkyl, haloalkyl, aryl, aralkyl, cyano, halogen, nitro, —COOH, —C(O)-haloalkyl, —C(O)-aryl, —C(O)OR15, —CON(H)R15, —(CH2)nC(O)OR15, —(CH2)nCONHR15, —CO(CH2)nR15, —(CH2)nSO3H, or —(CH2)nSO3−,
• R13 represents independently for each occurrence hydrogen or alkyl;
• R15 represents independently for each occurrence H, —COOH, —SO3H, —NH2, —SH, alkyl, a polyethylene glycol, or aryl which may be optionally substituted with X3 and/or a polyethylene glycol;
• m represents independently for each occurrence 0, 1, 2, 3, or 4;
• and
• n represents independently for each occurrence 1-10.

A fluorescent compound represented by Formula II:

• or a salt thereof, wherein:
• R1 and R2 are independently hydrogen or —C1-C10 alkyl optionally substituted with one or two substituents independently selected from the group consisting of halogen, —SO3H, —SO3−, —COOH, —CO2−, and —OH;
• R5, R6, R7 and R8 are each independently H or —C1-C22 alkylene-X3;
• R3, R4, R13 and R14 are each independently H, —C1-C22 alkylene-X3, —SO3H, —SO3−, —SO2N(R12)-alkylene-X3, halogen, or —NO2;
• X3 represents independently for each occurrence H, halogen, —CH3, —SO3H, —SO3−, —COOH, —CO2−, —NCS, —NCO, N-hydroxysuccinimidyl ester, N-hydroxysulfosuccinimidyl ester, —OH, —SH, maleimide, phthalimide, —NHCO—(CH2)m-(halogen), —CONHNH2, —CN, —NH2, —NO2, —CON(H)R12, alkynyl, —N3, a polyethyl glycol, optionally substituted aryl, or optionally substituted heterocyclyl;
• R9 and R10 are hydrogen, halogen, or alkyl, or R1 and R9 or R2 and R10 are taken together with their interconnecting atoms to form a 5-, 6- or 7-membered ring;
• R12 represents independently for each occurrence hydrogen or alkyl;
• m represents independently for each occurrence 0, 1, 2, 3, or 4;
• and
• n represents independently for each occurrence 1-10.

Fluorescent compounds represented by the following structural formula, Formula I

• Wherein, when X═R═CO—NR5R7 (Formula Ia);
• when X═CO—NR5R7 and R═R11 (Formula Ib);
• X═R═CO-Ph-X3 (Formula Ic) as shown below:
• Wherein X1 and X2 are independently chosen from O, S, Se, C(CH2R3CH2R4);
• R1, R2, R5, R6, R2 and R8 are each independently chosen from:
• H, (CH2)nX3, wherein n=1-20;
• R3, R4, R13 and R14 are each independently chosen from:
• H, (CH2)nX3, wherein n=0-20;
• X3 is independently chosen from:
• H, halogen, CH3, SO3H, SO3—, COOH, NCS (isothiocyanate), NCO (isocyanate), N-hydroxy succinimidyl (NHS) ester, N-hydroxysulfosuccinimidyl (NHSS) ester, hydroxy (OH), thiol (SH), maleimide, phthalimide, iodoacetamide, CONHNH2 (hydrazide), CN, NH2, CONHR, alkyne, azide (N3), SO2NX3R7, aryl that is optionally further substituted with X3;
• R9 and R10 are H or halogen or alkyl group;
• R1 and R9 or R2 and R10 optionally taken together form a 5 or 6 or 7 membered ring;
• W1 and W2 are the atoms necessary to form aryl rings including benzo or naphtho or pyridyl;
• R11 is independently chosen from:
• COOH, CN, F, NO2, COCF3, CF3, COOR, CONHR, CO(CH2)nR, wherein R is H or COOH or SO3H, or NH2 or SH or alkyl or aryl which is optionally further substituted with X3, or polyethylene glycol (PEG) units

A biocompatible fluorescent molecule represented by the formula III

• [BM]n—Fm, Formula III
• wherein BM is a biomolecule, F is a fluorophore represented by formulae Ia, Ib or Ic, and n=1 to 4;
• m=1 to 100
• Wherein X1 and X2 are independently chosen from O, S, Se, C(CH2R3CH2R4);
• R1, R2, R5, R6, R7 and R8 are each independently chosen from:
• H, (CH2)nX3, wherein n=1-20;
• R3, R4, R13 and R14 are each independently chosen from:
• H, (CH2)nX3, wherein n=0-20;
• X3 is independently chosen from:
• H, halogen, CH3, SO3H, SO3—, COOH, NCS (isothiocyanate), NCO (iscocyanate), N-hydroxy succinimidyl (NHS) ester, N-hydroxysulfosuccinimidyl (NHSS) ester, hydroxy (OH), thiol (SH), maleimide, phthalimide, iodoacetamide, CN, NH2, CONHR, alkyne, azide (N3), SO2NX3R7, aryl that is optionally further substituted with X3;
• R9 and R10 are H or halogen or alkyl group;
• R1 and R9 or R2 and R10 optionally taken together form a 5 or 6 or 7 membered ring;
• W1 and W2 are the atoms necessary to form aryl rings including benzo or naphtho or pyridyl;
• R11 is independently chosen from:
• COOH, CN, F, NO2, COCF3, CF3, COOR, CONHR, CO(CH2)nR, wherein R is H or COOH or SO3H, or NH2 or SH or alkyl or aryl which is optionally further substituted with X3, or polyethylene glycol (PEG) units