Preparation of diverse BODIPY diesters

Article abstract of DOI:10.1016/j.tetlet.2018.07.054

The synthesis and properties of a variety of substituted BODIPY diesters is presented. We find that certain substitution patterns afford appreciable yields of the target compounds and that electronic effects result in predicable differential fluorescent behavior. Challenges to further water solubilize these dyes and/or provide new points of attachment for biological tagging remain, these strategies are discussed.

Full text of DOI:10.1016/j.tetlet.2018.07.054

Accepted Manuscript
Preparation of Diverse BODIPY Diesters
Sewwandi Abeywardana, Annabelle L. Cantu, Teodora Nedic, Michael P.
Schramm
PII:
S0040-4039(18)30935-3
https://doi.org/10.1016/j.tetlet.2018.07.054
TETL 50163
DOI:
Reference:
Tetrahedron Letters
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Accepted Date:
25 May 2018
23 July 2018
Please cite this article as: Abeywardana, S., Cantu, A.L., Nedic, T., Schramm, M.P., Preparation of Diverse BODIPY
Diesters, Tetrahedron Letters (2018), doi: https://doi.org/10.1016/j.tetlet.2018.07.054
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Sewwandi Abeywardana, Annabelle L. Cantu, Teodora Nedic
and Michael P. Schramm

1
Tetrahedron Letters
Preparation of Diverse BODIPY Diesters
a,
Sewwandi Abeywardana, Annabelle L. Cantu, Teodora Nedic and Michael P. Schramm 
aDepartment of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, U.S.A.
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
The synthesis and properties of a variety of substituted BODIPY diesters is presented. We find
that certain substitution patterns afford appreciable yields of the target compounds and that
electronic effects result in predicable differential fluorescent behavior. Challenges to further
water solubilize these dyes and/or provide new points of attachment for biological tagging
remain, these strategies are discussed.
Available online
2009 Elsevier Ltd. All rights reserved.
Keywords:
Dipyrrolemethane
BODIPY
fluorophores
Fluorescence
combinatorial
The synthesis of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
(after referred to as BODIPY) dyes has a rich history with room
for further exploration. Improvement to existing synthetic
strategies as well as peripheral modification to provide means of
attachment to biological molecules are a central focus to their
further deployment towards pressing areas. BODIPY dyes have
numerous favorable properties that make them suitable for
biological applications.1-2 They are small molecules that absorb
light in the UV-visible range, their absorbance and emission
peaks are relatively sharp and they have high molar extinction
coefficients as well as typically high quantum yields of
fluorescence.3 BODIPY dyes are uncharged, relatively
insensitive to solvent polarity and reasonably stable under
physiological conditions.
Figure 1: The dipyrrolemethane precursor 1 and BODIPY motif 2 and
selected examples 3-5 (description of utility discussed in text).
Additionally, we are very interested in applications where
BODIPYs are directly applied to biological problems. Several
compelling examples exist that utilize some of the above
mentioned features.12-13 We previously published a report en
route to BODIPYS as we developed a modular methodology of
diverse dipyrrolemethane preparation.14 Within this initial study
we recognized that modular routes afforded critical modifications
around the core that would ultimately allow for photochemical
tuning should the dipyrrolemethanes be converted to BODIPY,
some examples are shown (Figure 2). Of the three scaffolds
shown, we produced several variations for each. The final
condensation of 2 pyrrole molecules with an aldehyde was
universal, but the syntheses of the pyrroles was different for each
substitution pattern.
To our knowledge BODIPY 2 was first reported in 1968
(Figure 1)4 and reviews demonstrate its extensive study5
including tuning from green to near-IR.6 In general the
dipyrrolemethane scaffold 1 provides a facile retrosynthetic
target, subsequent oxidation and insertion of BF2 completes the
forward sequence. These final steps, however are not without
peril. Advances continue despite synthetic challenges as this
motif has potential as a near-infrared emitter 37 as well as a
selective chemical sensor compatible with cells 4.8 Most
applicable to the work we present include BODIPYS with
carboxy groups attached to the pyrrole components (e.g. 5).9-11
———
 Corresponding author. e-mail: michael.schramm@csulb.edu

2
Tetrahedron
Figure 2: 3 variations on a theme, dipyrrolemethanes prepared from the
substituted pyrroles with aldehydes in DCM with catalytic p-
toluenesulfonic acid provides a reliable and high-yielding route
to these compounds (Figure 4).14, 16 Of the six permutations we
report (19-24), they range in yield from 72% to quantitative.
Dipyrrolemethanes 19 and 20 we previously reported.14 These
reactions yield material that is very pure, typically extraction
followed by either evaporation of excess aldehyde or trituration
with diethyl ether gives compounds with greater than 95%
analytical purity. The compounds are also readily purified by
silica gel chromatography. For this work benzaldehyde and 4-
formyl benzoic acid were employed. Other aldehydes work with
similar efficacy. Of note at this stage is that 4-formyl benzoic
acid17 after condensation places a carboxylic acid group onto our
BODIPY framework. This group survives subsequent steps and
ultimately could provide a means of covalent attachment to
biological molecules via well-known amide coupling reactions. A
similar functional group with an alkyl tether has been used to
attach cholesterol.18
condensation of pyrrole with aldehyde. For 6, 7 and 8 however, the individual
pyrrole building blocks required different routes.
Knowing that BODIPYS posses low toxicity, directed us
towards conversion of these dipyrrolemethanes into functional
BODIPYS, as we envisioned points of attachment allowing for
the development of new probes for biological applications. The
modular synthesis also provides options to improve water
solubility. Currently, there are only a few BODIPY dyes
commercially available to use as imaging probes and thus the
development of new chemistry remains relevant to fully utilize
these molecules.
Results and Discussion
We began our study with dipyrrolemethanes based on
compounds 6 and 7 and their analogs. A variety of conditions
were unsuccessful in converting these compounds into their
BODIPY counterparts. Standard conditions for oxidation include
DDQ or chloranil, conventional or microwave heating, stepwise
isolation of dypprolemethenes or direct addition of BF3. A vast
screen of these reactions never gave promising results, even
though starting material was consumed by TLC. We decided to
examine the more heavily substituted scaffolds such as found in
compound 8. The fully substituted pyrrole components ultimately
provided a course for development. We describe in detail
exclusively the results with this scaffold.
Figure 4: Preparation of dipyrrolemethanes from tri-substituted pyrrole
building blocks and isolated yields .
The subsequent conversion to BODIPYs 25-30, is more
perilous however (Figure 5). The conditions that we explored
revealed one combination that was better than the rest. For
certain scaffolds a two-step procedure where the
dipyrrolemethene (not illustrated) is isolated before insertion of
boron was reported to be preferable.19 We find that combination
of dipyrrole with DDQ in degassed DCM under microwave
irradiation gave clean conversion of dipyrrolemethane to
dipyrrolemethene after 5-7 minutes. TLC was used after 5
minutes and if starting material remained, an additional 2 minutes
was sufficient to exhaust it. Isolation of the dipyrrolemethene
was desirable to us, but in practical terms was not possible due to
resulting degradation on chromatography. We thus proceeded by
adding TEA and BF3 and allowing the mixture to stir overnight.
Under these conditions, the resulting TLCs showed lots of
colored and streaking material, but in all cases, one clean and
fluorescent spot was observed. Subsequent silica gel
Figure 3: Preparation of tri-substituted pyrrole building blocks used in
this study. Yields are reported for the overall process starting from a variety
of aldehydes, production of 10 grams of compound via this route is
straightforward.
We began by preparing tri-substituted pyrroles. Using a
procedure15 that we previously employed for the preparation of
13 and 14,14 we were able to vary the electronics of the pyrrole
building block with the preparation of new p-methoxy (15) and
p-nitro (16) pyrroles (Figure 3). Starting with a variety of
aliphatic and aromatic aldehydes, reaction with nitroethane and
subsequent reaction with acetic anhydride produces a mix of
nitro-acetate stereoisomers 10. Additionally, the presence of (E)-
alkene isomers (via loss of acetate) were sometimes noted as
previously reported.15 These details, while complicating
characterization of 10 didn’t interfere with subsequent steps.
After reaction with ethylisocyanoacetate, pyrroles 12 were easily
isolated on 10 gram scale. Pyrroles 15 and 16 were newly
prepared for this work and demonstrate that the yields are
consistent across a variety of motifs. While low yielding for a
two step process, the ready availability and variability of
aldehydes 9 makes this an incredibly powerful strategy for the
rapid preparation of diverse pyrroles 12.
chromotography afforded adducts in 90% or higher analytical
purity as determined by H NMR. Isolated yields vary
tremendously for these compounds, but in all cases enough
material was isolated to fully characterize UV and fluorescent
properties. It remains to be understood why substitution of the
phenyl group R (which is attached to the pyrrole ring) would
have such a drastic effect on yield. Indeed both p-methoxy (28,
29) and p-nitro (30) groups for now are not well tolerated. The
reported yields are after several attempts. Pentyl was acceptable
(25) but phenyl was superior (26, 27).
Having completed the preparation of a series of pyrroles, we
next condensed them with aldehydes to construct the BODIPY
precursor, dipyrrolemethanes (Figure 4). The reaction of tri-

3
has a carboxylic acid group incorporated into the back of the
BODIPY core. This should provide ample peptide coupling
opportunities for this compound to be added to biological
molecules of importance. This work also aimed to convert the
Figure 5: Preparation of diverse BODIPY diesters.
flanking ester groups into carboxylic acids; after which coupling
to other molecules would be possible. As has been reported,
BODIPY is very sensitive to strong base, and in our hands
neither base nor acid could give the corresponding BODIPY
diacids that we originally desired. When we took a
dipyrrolemethane precursor and prepared a diacid from it, the
subsequent oxidation and incorporation of BF2 failed. With think
other protecting group strategies could lead to BODIPYS with
free carboxylic acids flanking the core, but for now other
researchers can contemplate those challenges. We have presented
methods to produce a variety of dipyrrolemethanes that will lead
to BODIPYS. The challenging yields in the later stages remain
empirical. The dipyrrolemethane syntheses using heavily
substituted pyrroles like 13-16 however are very robust.
Additionally, the preparation of 13-16 is also versatile,
We carried out uv-visible and fluoresce measurement of
newly synthesized BODIPY in order to understand photophysical
properties in relation to their structure. It is found that electron
donating groups generally shift the absorbance and emission
maxima of BODIPY to higher wavelength (red shift) while
electron withdrawing groups shifts those to lower wavelength
(blue shift).
Table 1: Absorbance and Fluorescent maxima (in Chloroform)
Compound λabs (nm)
λems (nm)
25
26
27
28
29
30
537
535
538
541
547
530
557
576
586
620
628
558
straightforward and economical. When these building blocks are
crossed with either benzaldehyde or its para-carboxylic acid
analog, many new compounds can be prepared and isolated with
ease. Having mapped out a small set of 6 compounds’
absorbance and emissions properties provides a straightforward
path for subsequent work in the area. Our ultimate goal to deploy
compounds 27 and 29 towards bio-labeling is undergoing.
Acknowledgments
We would like to thank Research Corporation for a Single
Investigator Cottrell College Science Award that made this work
possible. We also thank Woman and Philanthropy (A.C.) and
NIH RISE (NIH 2R25GM071638-09A1) (A.C., T.N.) for
significant student support. NMR instrumentation was provided
by the National Science Foundation (MRI CHE-1337559). The
content is solely the responsibility of the authors and does not
necessarily represent the views of Research Corporation, the
National Institutes of Health nor the National Science
Foundation.
Figure 6: Normalized emission spectra for compounds 25-30. Excitation
was carried out at compounds’ absorbance maxima.
Supplementary Material
First we replaced the pentyl substituent in 25 with phenyl
groups in 26. While absorbance maxima remain the same (Table
1), we see a slight red shift in emission consistent with the
increased donating ability of phenyl into the BODIPY core
(Table 1, Figure 6). We followed with addition of a carboxylic
acid group to the central phenyl ring 27. Absorbance remained
largely insensitive throughout the whole series, but with 27
further red shift occurred. 28 and 29 were prepared and p-
methoxy groups were now introduced and gave the most drastic
red-shifts to the emission spectra. Indeed both donation in the
form of the para-methoxy AND incorporation of a para-
carboxylic acid group on the central ring gave 29 with our
highest emissions of 628 nm. The remaining compound with
para-nitro groups, 30 displayed expected blue shifts, further to
the left of the phenyl variant 26.
Experimental procedures for the preparation of all new
compounds as well as H, C, MS, UV-Vis Absorbance and
Fluorescence spectra are included .
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