Synthesis of bisisoindolomethene dyes bearing anisole or ethylthiophene residues for red and near-IR fluorescence

Article abstract of DOI:10.1055/s-2007-982557

New difluorobora-diisoindolomethenes dyes were synthesized from carbohydrazide and o-hydroxy-acetophenone derivatives bearing phenyl, p-anisole or ethylthiophene substituents. The nature of the substituents allows modulating the fluorescence from 650 nm t

Full text of DOI:10.1055/s-2007-982557

LETTER
1517
Synthesis of Bisisoindolomethene Dyes Bearing Anisole or Ethylthiophene
Residues for Red and Near-IR Fluorescence
S
ynthesis of Bisiso
i
indolo
l
m
ethen
l
e
D
ye
s
es Ulrich,*a Sébastien Goeb,a Antoinette De Nicola,a Pascal Retailleau,b Raymond Ziessel*a
a
LCM, ECPM/ULP, CNRS, 25 Rue Becquerel, 67087 Strasbourg Cedex 02, France
E-mail: gulrich@chimie.u-strasbg.fr; E-mail: ziessel@chimie.u-strasbg.fr
b
Laboratoire de Cristallochimie, ICSN – CNRS, Bât 27 – 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, Cedex, France
Received 27 March 2007
sensing purposes.11 Here, we describe some new tandem
molecules derived from E-Bodipy (E for ethynyl) species
with a common absorption center but displaying red or
NIR emissions depending on the nature of the core sub-
Abstract: New difluorobora-diisoindolomethenes dyes were syn-
thesized from carbohydrazide and o-hydroxy-acetophenone deriva-
tives bearing phenyl, p-anisole or ethylthiophene substituents. The
nature of the substituents allows modulating the fluorescence from
650 nm to 780 nm. Replacement of the fluoro ligands by ethynyl- stituents. The difluorobora-diisoindolomethenes 4a–c
aryl residues is feasible using Grignard reagents. Standard fluores-
necessary for red emission were inspired from literature
procedures (Scheme 1).12 This method was preferred to
cence studies prove that very efficient energy transfer, from the
pyrene moiety linked to the boron center to the boradiazaindacene,
the procedure developed by Ono et al., using a retro-Di-
is effective in providing large virtual Stokes shifts.
els–Alder reaction of bicyclo[2.2.2]octadiene.13 The R1
and R2 substituents, which have directly an influence on
Key words: diisoindolomethene, ethynyl-boron, pyrene, fluores-
cence, energy transfer
the diazaboraindacene absorption and emission wave-
lengths, are introduced on the starting carbohydrazide and
o-hydroxy-acetophenone derivatives. Condensation of
both compounds in refluxing propanol gives 1a–c in ac-
To take full advantage of the absorption window in blood
between 650 and 900 nm1 (where both hemoglobin and
water/lipid absorptions are low and autofluorescence is
minimal) for fluorescence imaging and mapping deeper
tissues or DNA,2 the engineering of new red emitters is
necessary. Both strong emission in this spectral region
and excitation through absorption at high energies are de-
sirable. Most common organic dyes show small Stokes
shifts in emission, meaning there is only a small differ-
ence in excitation and emission energies, but Stokes shifts
can be dramatically increased in tandem dyes where a
high-energy chromophore is linked to a low-energy emit-
ter.2 One absorbing center can then be coupled to various
emitters to produce multichromatic fluorescent tags, as
exploited in DNA sequencing based on fluorescent deriv-
atives of A, T, G, and C bases.3,4 The efficiency of the in-
termolecular energy transfer in these dyes largely depends
upon dipole–dipole interactions.5
ceptable yields. A rearrangement in presence of lead(IV)14
salt resulting in the replacement of the phenolic hydroxyl
by the acyl substituent led to the diketone 2a–c precursor
in high yield. The diisoindolemethene 3a–c were obtained
by condensation of the diketone with ammonium salt.
This step likely produces a diisoindolomethane intermedi-
ate after formaldehyde elimination by a retro-aldol mech-
anism. Air oxidation of the diisoindolomethane to the
diisoindolomethene derivatives affords the pivotal com-
pounds 3a–c.15 These diisoindolemethenes compounds
were subsequently deprotonated and stabilized in the
presence of boron trifluoride etherate leading to the highly
stable deep-blue (4a, 4b) or deep-green (4c) F-Bodipy
dyes.
To obtain enhanced Stokes’ shifts, we opted for the use of
pyrene residues a strongly absorbing chromophore around
370 nm.10 Replacement of fluoride in an F-Bodipy by an
ethynyl group, to generate E-Bodipys, can be readily
achieved using ethynyl-Grignard reagents (Scheme 2).16
The homosubstituted compounds 5a–c and 6b,c were iso-
lated in excellent yields. Unfortunately, the bis(ethynyl-
pyrene) derivative 6a was extremely insoluble and diffi-
cult to characterize. Thus, to study intramolecular pyrene-
to-diisoindolomethene energy transfer along this series
and to increase the solubility, the ethyl-mono(pyrenyl-
ethynyl) compound 7a was synthesized by reaction of
equimolar quantities of ethylmagnesium bromide and
pyrene ethynyl magnesium bromide with the F-Bodipy 4a
(Scheme 3). The resulting three components (homo- and
heterocoupling compounds) of the product mixture being
easily separated by column chromatography. In the 11B
NMR spectra, the characteristic triplet at d = 5.1 ppm (t,
Known red and near IR organic emitters include
rhodamines, cyanines and some F-Bodipy (difluoro-bora-
diazaindacene) fluorophores.6 In the last family, extension
of the p-system of the central cyanine unit, for example by
introduction of vinyl7 or phenyl8 substituents adjacent to
the aza centers, is a tool to obtain low-energy emission, as
is true for aza-Bodipy dyes as well.9
Our first work10 showed the remarkable efficiency of the
energy transfer from pyrene to the yellow/orange emitting
Bodipy. Lately we developed green-absorbing fluoro-
phores bearing various oligopyridine-based platforms for
SYNLETT 2007, No. 10, pp 1517–1520
1
8
.0
6
.2
0
0
7
Advanced online publication: 07.06.2007
DOI: 10.1055/s-2007-982557; Art ID: G08907ST
© Georg Thieme Verlag Stuttgart · New York
J
BF = 32 Hz) for compounds 4a–c disappeared after

1518
G. Ulrich et al.
LETTER
O
O
R1
H
N
R2
H
R2
R1
N
NH2
a
c
b
N
O
R1
O
R2
O
HN
N
R2
OH
R1
R1
1a–c
2a–c
3a–c
R2
OH
R1
Ph
R2
R2
R2
a
b
c
H
OMe
Et
d
OMe
OMe
N
N
B
R1
R1
F
F
S
4a–c
Scheme 1 Reagents and conditions: a) for compounds a and b: 1-PrOH, reflux, 66–88%), for compound c no solvent 75 °C, 87%; b)
Pb(OAc)4, THF, 60–95%; c) for compounds a and b: NH4OH, MeCOOH, MeOH, r.t., 60–65%; for compound c: NH4OAc, NH4Cl, MeCOOH,
EtOH, reflux, 50%.
fluorine substitution, a singlet appearing at ca. d = –6.3 to the sterically hindered boron center. The bond lengths of
–7.3 ppm, depending on the nature of R3, for 5a–c, 6b,c the indacene framework are characteristic of boradiazain-
and at d = 1.1 ppm for 7a.
dacene, reflecting the entire delocalization of the cyanine.
A slight distortion of the planarity of the diisoindolo-
methene core is observed as previously described for F-
Bodipy possessing bulky substituent at the nitrogens
ortho position.20 This deformed system can be described
as a ‘butterfly’ conformation; the single ‘wings’ consist-
ing of two planes B–N1–C1–C2–C4–C9 and B–N2–C5–
C6–C7–C9. The dihedral angle between both planes is
8.6° for 4a, 9.0° for 5a and 12.3° for 6a. In the case of 7a
the boron is pointing in the ethynyl substituent direction.
A tilt between the phenyl group and the indacene core is
observed and seems to be dependent of the congestion in-
duced by the boron substituent: average dihedral angles
between the mean planes are 57° for 4a, 60° for 5a and
68° for 7a with the larger angle facing the bulky ethyl
group.
Crystal structure determinations for 4a (Figure 1),17 5a
(Figure 2),18 and 6a (Figure 3)19 first confirm the stoichio-
metry and connectivity deduced from the NMR spectra.
All structures reflect the almost tetrahedral geometry for
R2
R2
a
N
N
B
R1
R1
F
F
4a–c
R2
R2
R1
Ph
R2
N
N
a
b
c
H
B
R1
R1
OMe
Et
R3
R4
OMe
5a–c R3 = R4 = p-tolyl
6b–c R3 = R4 = pyrene
OMe
S
Scheme 2 Reagents and conditions: a) R3–≡–MgBr (2 equiv) for
5a–c and 6b–c; THF, 60 °C, 41–62%.
N
N
B
a
N
N
B
F
F
Figure 1 ORTEP view of compound 4a (50% probability), all
hydrogen atoms were removed for the sake of clarity. B–N1, B–N2,
B–F1, B–F2 are 1.569(5) Å, 1.570(4) Å, 1.395(4) Å, 1.367(4) Å, re-
spectively, with angles N1–B–N2, F1–B–F2, N1–B–F1 and N2–B–
F2 of 107.95(11)°, 110.94(12)°, 108.12(11)°, and 108.05(11)°,
respectively.
7a
Scheme 3 Reagents and conditions: a) Et–≡–MgBr (1 equiv) +
pyrene–≡–MgBr (1 equiv), THF, 60 °C, 50%.
Synlett 2007, No. 10, 1517–1520 © Thieme Stuttgart · New York

LETTER
Synthesis of Bisisoindolomethene Dyes
1519
Table 1 Optical Properties in CH2Cl2 at Room Temperature
Compd
4a
l
abs (nm)
l
em (nm) DS (cm–1) e (M–1 cm–1) F (%)a
634
673
727
632
666
707
658
704
780
656
700
746
575
654
934
579
729
740
108400
118600
100000
82500
85000
90000
88
49
20
57
58
36
4b
4c
5a
5b
5c
6b
667
370
702
702
748
12780
88500
111000
56
32
6c
7a
720
371
754
758
626
13762
90000
140000
33
24
Figure 2 ORTEP view of compound 5a (50% probability), all
hydrogen atoms were removed for the sake of clarity. B–N1, B–N2,
B–C1¢ are 1.598(18) Å, 1.595(7) Å, 1.563(7) Å, respectively, while
B–C1¢¢ is 1.597(24) Å, with angles N1–B–N2, C1¢–B–C1¢¢, N1–B–
C1¢¢, and N2–B–C1¢ of 106.62(13)°, 118.39(15)°, 106.56(15)°, and
109.00(19)°, respectively.
614
370
643
643
734
11475
78300
42000
65
64
a Relative quantum yields determined using Cresyl violet as shown in
ref. 21 (F = 0.51%, lexc = 578 nm).21 For compounds 4–6c, com-
pound 7a was used as reference. The estimated error is fairly large in
the 700–800 nm region due to apparatus sensitivity.
induced by steric effects that moderate electronic delocal-
ization of the cyanine. Compounds 4b, 5b, and 6b exhibit
relatively strong fluorescence (quantum yields ca. 50%)
around 700 nm. Selected spectroscopic data are gathered
in Table 1.
Compounds 4–5c are weaker emitters (f 20–30%) in the
750–780 nm region, the hypsochromic shifts resulting in
5c from fluorine substitution possibly reflecting steric ef-
fects of the boron substituent on the delocalization to the
ethylthiophene group. When excited in the pyrene absorp-
tion band, 5–6c show only near-IR fluorescence, with no
residual pyrene emission. In these cases the energy trans-
fer is not quantitative (60% and 70%, respectively), de-
spite the fact that no residual pyrene fluorescence is
observed. For compound 7a, photons absorbed by the
pyrene subunit are channeled to the Bodipy unit, which ef-
ficiently luminesces, leading to an almost quantitative in-
tramolecular energy transfer. The virtual Stokes shift is
estimated to be 11,500 cm–1 for 7a and up to 13,800 cm–1
for 6c. The high quantum yields and short excited-state
lifetimes (tflu = 7.0–9.0 ns) in dichloromethane at room
temperature, and insensitivity to the presence of oxygen,
are in keeping with emission from a singlet excited state.
Figure 3 ORTEP view of compound 7a (50% probability), all
hydrogen atoms were removed for the sake of clarity. B–N1, B–N2,
B–C1¢, and B–C1¢¢ are 1.579(13) Å, 1.603(30) Å, 1.583(11) Å, and
1.577(24)Å, respectively, with angles N1–B–N2, C1¢–B–C1¢¢, N1–
B–C1¢¢, and N2–B–C1¢ of 106.60(29)°, 117.82(33)°, 105.00(32)°,
and 110.44(29)°, respectively.
All dyes exhibit very high absorption in the visible
(labs = 614–634 nm for 4a–5a and 7a, labs = 666–673 nm
for 4b–6b and labs = 707–727 nm for 4c–6c), assigned to
the S0→S1 (p–p*) transition, of the Bodipy fragment.
Additional high-energy absorption bands are observed for
compounds 4a–c and 5a–c in the 360–410 nm region, e =
approx. 20,000 to 40,000 M–1cm–1, likely due to the
cyanine framework. Other intense absorptions are found
at 352 nm and 372 nm (e = 40,000 M–1cm–1 and 50,000
M–1cm–1 per pyrene unit for 6b–c and 7a), assigned to the
absorption of the pyrene (Figure 4). Solution lumines-
cence is strong for all the novel dyes in the red-near IR
window, diminishing near 800 nm (Table 1). Quantum
yields are slightly less for 5a and 7a than for the strongly
red-luminescent 4a. For 7a, a significant hypsochromic
shift is observed in absorption and emission, probably
Clearly, tuning of the optical properties of these tandem
dyes is synthetically facile by first synthesizing the bisin-
dolomethene core and then by replacing the fluoro ligands
with ethynylaryl fragments. An added advantage of the
presently described compounds is the variation in charac-
teristics associated with the substituted alkynyl ligands on
boron. These compounds have particularly useful charac-
teristics in regard to application as fluorescent labels.
They absorb and emit at exceptionally long wavelengths
when compared to previously studied Bodipy species and
the quantum yields remain satisfactory given the low
Synlett 2007, No. 10, 1517–1520 © Thieme Stuttgart · New York

1520
G. Ulrich et al.
LETTER
(12) Kang, H. C.; Haugland, R. P. US 5,433,896, 1995.
(13) Wada, M.; Ito, S.; Uno, H.; Murashime, T.; Ono, N.; Urano,
T.; Urano, Y. Tetrahedron Lett. 2001, 42, 6711.
(14) Katritzky, A. R.; Harris, P. A. J. Org. Chem. 1991, 56, 5049.
(15) Maekawa, E.; Suzuki, Y.; Sugiyama, S. Chem. Ber. 1968,
101, 847.
(16) General Procedure for Fluorine Replacement
A Schlenk flask was charged with the ethynyl derivative and
anhyd THF. A solution of EtMgBr (1 M in THF) was then
added dropwise and the mixture was stirred at 50 °C for 2 h.
The mixture was then added at 25 °C via a cannula to a
solution of 4a–c in anhyd THF. The mixture was stirred at
70 °C for 16 h and the solvent was removed by rotary
evaporation. The residue was treated with H2O and extracted
with CH2Cl2. The organic extracts were washed with H2O,
and dried over MgSO4. The solvent was removed, and the
residue was purified by chromatography.
Figure 4 Absorption (full line) and emission (dotted line) of 7a
(black), 6b (red) and 6c (blue).
Compound 5a
Prepared following general procedure from 4a (100 mg, 0.22
mmol), 1-ethynyltoluene (104 mg, 0.9 mmol), EtMgBr (0.41
mL, 0.41 mmol, 1 M in THF), THF (8 mL). Chromatography
(silica gel, CH2Cl2–cyclohexane, 30:70 to 50:50) gave 5a as
a blue crystalline powder (60 mg, 42%). 1H NMR (CDCl3,
300 MHz): d = 8.20 (d, 4 H, J = 6.6 Hz), 7.96 (d, 4 H, J = 6.0
Hz), 7.92 (s, 1 H), 7.61–7.39 (m, 11 H), 7.22–7.18 (m, 1 H),
6.88 (AB system, 8 H, JAB = 8.0 Hz, DdAB = 24.3 Hz),
2.27 (s, 6 H). 13C NMR (CDCl3, 75 MHz): d = 151.2, 136.8,
133.7, 132.4, 131.3, 130.9, 130.3, 128.3, 128.1, 127.7,
127.6, 124.6, 123.0, 122.4, 121.7, 118.4, 115.8, 98.6, 21.3.
11B NMR (CDCl3, 128 MHz): d = –7.14 (s). UV/Vis
(CH2Cl2): l (e, M–1 cm–1) = 632 (82500), 588 (27000, sh),
269 (12000) nm. MS (ES): m/z (nature of the peak, relative
intensity) = 637.1 (100) [M + H]+. Anal. Calcd for
C47H33BN2: C, 88.68; H, 5.23; N, 4.40. Found: C, 88.40; H,
4.95; N, 4.18.
energy of the emission. We contend that the present work
paves the way for the development of a new generation of
stable, functionalized luminophores. For bioanalytical
applications, a functional group suitable for their grafting
onto biomolecules is necessary. Chemistry at boron to
meet this requirement is currently under active develop-
ment.
Acknowledgment
The authors thank the CNRS and ULP for partial funding. GU
thanks the ANR ‘Borsupstokes’ project JC05-4228 for financial
support.
References and Notes
(17) Crystal Data for 4a at 293 K: C29H19BF2N2, M = 444.27,
triclinic, space group P–1, a = 7.310 (5) Å, b = 11.771 (5) Å,
c = 13.336 (5) Å, a = 86.84 (0)°, b = 79.14 (0)°, g = 89.79
(0)°, V = 1125.2 (10) Å3, Z = 2, l = 0.7107 Å, Dc = 1.311 g
cm–3, m = 0.057 mm–1, 24014 reflections collected with
q £ 26.0°, 4363 unique, R(int) = 0.0202, and 3343 observed
reflections [ I ≥ 2s(I)], 308 parameters, R1 = 0.0396,
wR2 = 0.1012 refined on F2. CCDC 637684.
(18) Crystal Data for 5a at 293 K: C47H33BN2, M = 636.56,
triclinic, space group P–1, a = 11.119 (4) Å, b = 11.674 (3)
Å, c = 15.572 (4) Å, a = 78.73 (2)°, b = 73.51 (2)°, g = 66.73
(2)°, V = 1772.5 (9) Å3, Z = 2, l = 0.7107 Å, Dc = 1.193 g
cm–3, m = 0.068 mm–1, 12226 reflections collected with q <
27.5°, 8071 unique, R(int) = 0.0241, and 5025 observed
reflections [ I ≥ 2s(I)], 453 parameters, R1 = 0.0571,
wR2 = 0.1438 refined on F2. CCDC 623954.
(1) Weissleder, R. Nature Biotech. 2001, 19, 316.
(2) (a) Farkas, E.; Hilbert, M.; Ketskemety, I.; Gati, L. Acta
Phys. Chem. 1985, 31, 711. (b) Tian, H.; Tang, Y.; Chen, K.
Dyes Pigm. 1994, 26, 159. (c) Ju, J.; Ruan, C.; Fuller, C. W.;
Glazer, A. N.; Mathies, R. Proc. Natl. Acad. Sci. U.S.A.
1995, 92, 4347. (d) Langhals, H.; Saulich, S. Chem. Eur. J.
2002, 8, 5630. (e) Wan, C.-W.; Burghart, A.; Chen, J.;
Bergström, F.; Johanson, L. B.-A.; Wolford, M. F.; Kim, T.
G.; Topp, M. R.; Hochstrasser, R. M.; Burgess, K. Chem.
Eur. J. 2003, 9, 4430.
(3) (a) Berti, L.; Xie, J.; Medintz, I. L.; Glazer, A. N.; Mathies,
R. A. Anal. Biochem. 2001, 292, 188. (b) Kim, T. G.;
Castro, J. C.; Loudet, A.; Jiao, J. G.-S.; Hochstrasser, R. M.;
Burgess, K.; Topp, M. R. J. Phys. Chem. A 2006, 110, 20.
(4) Glazer, A. N.; Mathies, R. A. Curr. Opin. Biotech. 1997, 8,
94.
(5) Forster, T. Discuss. Faraday Soc. 1959, 27, 7.
(6) The Handbook: A Guide to Fluorescent Probes and
Labeling Technologies, 10th ed.; Haughland, R. P., Ed.;
Invitrogen/Molecular Probes: Eugene, OR, 2005.
(7) (a) Kang, H. C.; Haughland, R. P. US 5,274,113, 1993.
(b) Rurack, K.; Kollmansberger, M.; Daub, J. New J. Chem.
2001, 25, 289. (c) Dost, Z.; Atilgan, S.; Akkaya, E. U.
Tetrahedron 2006, 62, 8484.
(19) Crystal Data for 6a at 293 K: [C49H33BN2, 0.5 × (C6H12,
C2H3N)], M = 723.19, triclinic, space group P–1, a = 11.294
(4) Å, b = 13.299 (3) Å, c = 14.735 (4) Å, a = 101.78 (2)°,
b = 110.03 (2)°, g = 102.17 (2)°, V = 1938.4 (10) Å3, Z = 2,
l = 0.7107 Å, Dc = 1.239 g cm–3, m = 0.071 mm–1, 10488
reflections collected with q < 22.4°, 4585 unique,
R(int) = 0.0351, and 3135 observed reflections [ I ≥ 2s(I)],
470 parameters, R1 = 0.0649, wR2 = 0.1879 refined on F2.
SQUEEZE macro within PLATON was used to take
disordered solvent molecules (half a molecule of
cyclohexane and half a molecule of MeCN in the
asymmetric unit) into account during the structure
refinement process. CCDC 623955.
(8) Chen, J.; Burghart, A.; Derecskei-Kavocs, A.; Burgess, K.
J. Org. Chem. 2000, 65, 2900.
(9) Zhao, W.; Carreira, E. M. Angew. Chem. Int. Ed. 2005, 117,
1705.
(10) Ulrich, G.; Goze, C.; Guardigli, M.; Roda, A.; Ziessel, R.
Angew. Chem. Int. Ed. 2005, 44, 3694.
(11) Goeb, S.; Ziessel, R. Org. Lett. 2007, 9, 737.
(20) Shen, Z.; Röhr, H.; Rurack, K.; Uno, H.; Spieles, M.; Schulz,
B.; Reck, G.; Ono, N. Chem. Eur. J. 2004, 10, 4853.
(21) Olmsted, J. III J. Phys. Chem. 1979, 83, 2581.
Synlett 2007, No. 10, 1517–1520 © Thieme Stuttgart · New York

Copyright of Synlett is the property of Georg Thieme Verlag Stuttgart and its content may not
be copied or emailed to multiple sites or posted to a listserv without the copyright holder's
express written permission. However, users may print, download, or email articles for
individual use.