Synthesis, electronic structure and spectroscopy of bridged pyrene-(CH2)n-aryl azide systems

Article abstract of DOI:10.1016/j.mencom.2008.09.016

The bridged systems containing pyrenyl and aryl azido residues have been synthesized for the first time, and the quenching of pyrene fluorescence on a picosecond time scale has been observed.

Full text of DOI:10.1016/j.mencom.2008.09.016

Mendeleev
Communications
Mendeleev Commun., 2008, 18, 273–275
Synthesis, electronic structure and spectroscopy
of bridged pyrene-(CH2)n-aryl azide systems
Igor I. Barabanov,a Elena A. Pritchina,a,b Tomohisa Takayac and Nina P. Gritsan*a,b
a Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences,
630090 Novosibirsk, Russian Federation. Fax: + 7 383 330 7350; e-mail: gritsan@kinetics.nsc.ru
b Novosibirsk State University, 630090 Novosibirsk, Russian Federation
c Department of Chemistry, The Ohio State University, 43210 Columbus, Ohio, USA
DOI: 10.1016/j.mencom.2008.09.016
The bridged systems containing pyrenyl and aryl azido residues have been synthesized for the first time, and the quenching of
pyrene fluorescence on a picosecond time scale has been observed.
The photoaffinity labeling of biopolymers1,2 is used to obtain
Me
I–
F
F
F
F
information on the higher order structure of RNA and RNA–
protein complexes.3,4 However, the aryl azido derivatives of
nucleic acids demonstrate sometimes low specificity and cross-
linking efficiency.3 Binary reagents were proposed to increase
the specificity of nucleic acid sequences.5 These systems consist
of two tandem oligonucleotides that are complementary to a target
sequence of nucleic acids. Each oligonucleotide is covalently
linked through its terminal phosphate group with photoreactive
or photosensitizing groups. Anthracene, pyrene and perylene
derivatives are used as sensitizers, and fluoro-substituted phenyl-
azides are used as photoreagents in binary systems.5,6 The
reaction mixture is irradiated with light, which is not absorbed
by aryl azide. Nevertheless, the azido group undergoes photo-
decomposition and forms a cross-link with protein either in or
at the active site.7 However, the mechanism of sensitization
remains unknown.
N
HO
O
Et3N
+
Cl
N3
– Et3N·HCl
6
1
OH
n
+ Et3N
I–
Me
N
F
F
F
F
4, 5
– Et3N·HI
O
N3
F
O
Recently,8 the quenching of pyrene fluorescence by aryl
azides, including 4-azido-2,3,5,6-tetrafluorobenzoic acid 1, has
been studied in solution using fluorescence spectroscopy and
nanosecond laser flash photolysis. The formation of the pyrene
cation was not detected, and quenching by energy transfer was
proposed.8 However, electron transfer followed by fast N–N bond
dissociation and charge recombination could not be excluded.
Bonding donor and acceptor residues will facilitate the quenching
and make it possible to distinguish between electron and energy
transfer mechanisms. Therefore, we have performed the synthesis
of bridged 1-[(4-azido-2,3,5,6-tetrafluorobenzoyloxy)methyl]-
F
N3
F
O
n
Me
O
F
N
+
O
2, 3
2, 4 n = 1
3, 5 n = 3
Scheme 1
pyrene
2 and 1-[3-(4-azido-2,3,5,6-tetrafluorobenzoyloxy)-
and 3-(pyren-1-yl)propan-1-ol 5,11 respectively. The preparative
one-stage synthesis of esters from carboxylic acids and alcohols
in the presence of Et3N was promoted by 1-methyl-2-chloro-
pyridinium iodide 6 (Mukaiyama reagent).12,13 The advantage
of this method (Scheme 1) is the absence of acidic catalysts and
the ambient temperature of synthesis, which is important for
very reactive and labile azido-derivatives.14
The esterification of pyrenylmethanol 4 at room temperature
was completed in 4.5 h. The esterification of 5 proceeded
more slowly and was completed in 46 h. After chromatographic
purification on silica gel and subsequent crystallization, the
yields of 2 and 3 were 58 and 42%, respectively.†
propyl]pyrene 3.
Pyrene derivatives 2 and 3 were synthesized using esterifica-
tion of azidotetrafluorobenzoic acid 19 by pyren-1-ylmethanol 410
F
F
F
F
O
O
N3
2
F
F
F
F
O
O
The structures of esters 2 and 3 were confirmed by high-
N3
1
resolution mass spectrometry, H NMR and IR spectroscopy.
The intense peaks of molecular ions at m/z 449 and 477 were
detected in the mass spectra of 2 and 3, respectively. The
3
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© 2008 Mendeleev Communications. All rights reserved.

Mendeleev Commun., 2008, 18, 273–275
(a)
800
(b)
(c)
50000
8.65 Å
7.86 Å
4.99 Å
400
0
A
B
C
f = 0.002
Figure 2 Structures of (a) the lowest energy conformer of 2 (A) and (b), (c)
two low-energy conformers of 3 (B, C) optimized using B3LYP/6-31G(d)
method.
360
390
420
l/nm
25000
A set of minima, corresponding to different conformations,
were localized§ at the potential energy surface (PES) of 2.
Figure 2(a) shows the structure corresponding to a global
minimum on the PES. According to the calculations,§ pyrenyl-
methanol 4 has a long wavelength transition at 347 nm (f = 0.317),
while bridged compound 2 [Figure 2(a)] has, besides a similar
band at 348 nm (f = 0.339), the transition at 417 nm with a
very low intensity (f = 0.002). This transition involves electron
excitation from the HOMO localized at the pyrene fragment to
LUMO localized at the aryl azide fragment (Figure 3). Therefore,
this excited state is the charge-transfer (CT) state. The contribu-
tion of this transition to the spectrum of 2 could explain the
above distinction at the red edge of the spectra (Figure 1, insert).
Note that taking into account the solvent using the PCM model16
has a minor effect on transitions and shifts the latter to the blue
region (408 nm in MeCN).
High-level RI-CC2 calculations,17 as well as early semi-
empirical ones,18,19 predict that the first excited singlet states
(S1) of phenyl azide and its simple derivatives [best characterised
as π ® (in plane, π*, azide) excitations] are dissociative toward
the formation of molecular nitrogen and the singlet nitrene.
Usually, these S0 ® S1 transitions manifest themselves as weak
long asymmetric tails,8,20 which is typical of the excitation to
the dissociative states. According to our calculations,§ the S0 ® S1
transition of azide 1 at 309 nm is also characterized as π ® (in
plane, π*, azide) excitation (HOMO ® LUMO + 1) and has a
very low oscillator strength (3×10–4).
f = 0.339
3
2
1
0
250
300
350
400
l/nm
Figure 1 UV-VIS spectra of (1) aryl azide 1, (2) pyren-1-ylmethanol 4
and (3) bridged system 2 in MeCN at room temperature. The calculated
long wavelength transitions in the spectrum of 2 are depicted as open bars.
1H NMR spectra of 2 and 3 consist of the signals typical of both
pyrene and methylene protons. However, the signals of CH2O
protons are shifted to the lower field as compared to those
of the same protons of pyrene alkanols 4 and 5 by ~0.815 and
~0.7 ppm,11 respectively. The IR spectra of 2 and 3 demonstrate
the presence of intense absorption bands of azido (~2120 cm–1)
and ester (~1720 cm–1) groups.
Figure 1 demonstrates that the electronic absorption spectrum
of bridged compound 2 is very close to the sum of the spectra
of pyrenylmethanol 4 and azide 1,‡ although the maxima of the
vibrational progression of 2 are slightly (1.5 nm) shifted to
the red region. The difference in the spectra of 2 and 4 is more
pronounced at the red edge (Figure 1, insert). Note that aryl
azide 1 has no noticeable absorption at this spectral region.
†
The 1H NMR spectra of 2 and 3 were recorded using a Bruker DPX 200
Figure 4 depicts the fluorescence decay kinetics of bridged
system 2 (curve 1).¶ This kinetics is well described by a two-
exponential function with time constants of t1 = 164 2 ps and
t2 = 6.9 0.2 ns. The contribution of the second term is very
small (A2/A1 ~ 0.06) and is, probably, due to the photoproduct.
The time constant of the fluorescence decay of pyrenylmethanol
4 was measured to be 200 10 ns. Therefore, the fluorescence
quantum yield of bridged system 2 is about three orders of
magnitude as low as that of 4. Thus, we failed to detect the
fluorescence spectrum of 2.
spectrometer in CDCl3 at room temperature. The high-resolution mass
spectra were measured using a Finnigan MAT 8200 spectrometer. The
IR spectra were recorded using a Bruker Vector 22 spectrometer. The course
of reaction and the purity of products were controlled using TLC monitoring
(Silufol UV 254; eluent, CHCl3–hexane).
Synthesis of 1-[(4-azido-2,3,5,6-tetrafluorobenzoyloxy)methyl]pyrene 2.
A solution of 91 mg (0.39 mmol) of 4-azido-2,3,5,6-tetrafluorobenzoic
acid 1,9 93 mg (0.36 mmol) of 1-methyl-2-chloropyridinium iodide 6,12,13
70 mg (0.30 mmol) of pyren-1-ylmethanol 4,10 and 73 mg (0.72 mmol,
0.1 ml) of Et3N in 3 ml of CH2Cl2 was stirred under N2 atmosphere at
20 °C for 4.5 h. The reaction mixture was separated by chromatography
on silica gel with a CH2Cl2 eluent. The effluent containing 2 was evaporated
in vacuo, the oily residue was blended with 5 ml of hexane, and the
crystals were filtered off and washed with 5 ml of hexane to give 79 mg
(58%) of compound 2, which was additionally recrystallized from CHCl3,
mp 188–190 °C. 1H NMR, d: 6.12 (s, 2H, CH2OCO), 7.95–8.40 (m,
9H). IR (CHCl3, n/cm–1): 1720 (C=O), 2120 (N3). HRMS, m/z: found,
449.07922; calc. for C24H11N3O2F4, 449.07873.
N
N
N
F
F
HOMO
LUMO
F
F
O
Synthesis of 1-[3-(4-azido-2,3,5,6-tetrafluorobenzoyloxy)propyl]pyrene 3.
Ester 3 was synthesized and purified similar to 2. The esterification
was completed in 46 h, the yield of crystalline 3 was 42%. Compound 3
was additionally recrystallized from CH2Cl2, mp 150.5–152.5 °C. 1H NMR,
d: 2.23–2.40 (m, 2H, CH2CH2CH2OCO), 3.50 [t, 2H, CH2(CH2)2OCO,
J 7.4 Hz], 4.45 [t, 2H, (CH2)2CH2OCO, J 6.0 Hz], 7.80–8.30 (m, 9H).
IR (CHCl3, n/cm–1): 1720 (C=O), 2130 (N3). HRMS, m/z: found, 477.10970;
calc. for C26H15N3O2F4, 477.11003.
H
H
Figure 3 Frontier MOs of 1-[(4-azido-2,3,5,6-tetrafluorobenzoyloxy)methyl]-
pyrene 2 calculated at the B3LYP/6-31(d) level.
§
The geometries of 2 and 3 were optimized by the B3LYP/6-31G(d)
method.21,22 All equilibrium structures were ascertained to be minima on
potential energy surfaces. The electronic absorption spectra (EAS) were
calculated by the time-dependent TD-B3LYP/6-31+G(d) technique.23
All calculations were performed with the Gaussian-0324 suite of programs.
The influence of the solvent on the EAS was taken into consideration by
the PCM16 models as implemented to Gaussian 03.
‡
Electronic absorption spectra were recorded on a UV-VIS Shimadzu 2401
spectrometer. Pyren-1-ylmethanol 410 was purified by chromatography
(silica gel; eluent, benzene), treated with activated carbon and finally
recrystallized from a benzene–hexane mixture. 4-Azido-2,3,5,6-tetra-
fluorobenzoic acid 1 from Aldrich was used.
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Mendeleev Commun., 2008, 18, 273–275
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This work was supported by the National Science Foundation
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¶
The fluorescence kinetics was measured using a time-correlated single-
photon counting (TCSPC) setup.25 The picosecond pulses at 336 nm were
used to excite solutions held in a 1 cm cuvette with OD ~ 0.3 at 336 nm.
Fluorescence was collected at 90°, directed through a double mono-
chromator (American Holographic), and detected by a microchannel-
plate photomultiplier tube (Hammamatsu). The instrument response
time was ~80 ps (fwhm). All fluorescence transients were recorded at
an emission wavelength of 360–380 nm. Lifetimes were determined
by iterative reconvolution of double- or three-exponential function with
instrument response.
Received: 21st April 2008; Com. 08/3129
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