Photophysical studies and submicron ring formation of morpholino U-nucleoside monomers

Article abstract of DOI:10.1039/c3cc45082a

Synthesis, photophysical properties and submicron ring formation of functionalized uracil morpholino monomers have been reported. A series of characterization techniques indicated that the rings are formed by the inter-molecular hydrogen bonding of the uracil nucleus having a trityl-protected morpholino moiety. This is the smallest nucleoside unit known to date for submicron size ring formation.

Full text of DOI:10.1039/c3cc45082a

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Photophysical studies and submicron ring formation of
morpholino U-nucleoside monomers†
Cite this: Chem. Commun., 2013,
4
9, 11278
a
b
a
a
Sibasish Paul, Santanu Jana, Jhuma Bhadra and Surajit Sinha*
Received 6th July 2013,
Accepted 10th October 2013
DOI: 10.1039/c3cc45082a
www.rsc.org/chemcomm
26
27,28
Synthesis, photophysical properties and submicron ring formation of in nanotechnology and surface hybridization.
Though the photo-
functionalized uracil morpholino monomers have been reported. physical properties of nucleoside monomers are known in the
5
A series of characterization techniques indicated that the rings are literature, the same is not reported in the case of morpholino
formed by the inter-molecular hydrogen bonding of the uracil nucleus monomers. As a part of our project toward the synthesis of
2
9,30
31
having a trityl-protected morpholino moiety. This is the smallest morpholino monomers
and morpholino oligomers, herein
nucleoside unit known to date for submicron size ring formation.
we report the synthesis, photophysical studies and self-assembly into
submicron rings of functionalized uracil morpholino monomers
During the past decades, organic materials have attracted wide- which, to the best of our knowledge, is the first report. In addition, we
spread attention due to their exceptional optical and electronic reveal some insight into the mechanism of the formation of rings. It
properties, though most of the studies are focused on macro- is also important to mention that submicron ring formation using
1
–3
molecules.
There has been notable interest in nucleosides such a small molecular scaffold has hardly been described before.
Nucleoside monomers 3, 4, 5 and 6 were synthesized from 1
where the base unit has been modified (especially uracil nucleo-
sides) to study the fluorescence properties. Interests are also through Sonogashira coupling with appropriate aryl alkynes
growing for the use of nucleobase pairs from the field of according to our reported procedure in good to excellent yields
4
,5
6
–9
29
materials research and nanosciences. Topologically important (Scheme 1).
structures like Borromean rings, catenanes, and other shapes or
patterns have already been built either by chemical synthesis
The UV-Vis absorption spectra of compounds 3 to 6 were
measured in chloroform (Fig. 1a). The absorption band of all the
1
0,11
1
2–14
or using DNA.
by several groups
Formation of DNA minicircles was reported compounds falls in between 300 and 400 nm, which belongs to
1
5–18
including the controlled synthesis of the gap between the HOMO and LUMO of all compounds. In the
minicircles through the introduction of a customized sequence case of compound 4 the HOMO–LUMO gap decreases due to the
18
into the template. Formation of protein nanorings with diameters presence of an electron accepting group whereas compounds
ranging from 8 to 20 nm has been described by the Wagner having an electron donating group show a higher band gap. The
1
9
group. Small organic molecules containing both hydrogen photoluminescence (PL) spectra are shown in Fig. 1b. Compounds
bonding and hydrophobic parts are able to self-assemble to 3, 5 and 6 show very bright blue luminescence (digital pictures are
2
0–22
form objects of different morphology.
shown in the inset of Fig. 1b, the excitation wavelength is 365 nm),
Uracil functionalized single-walled carbon nanotubes were also
known to self-assemble with a diameter of 50–70 nm to form regular
23
nanorings. DNA-mediated self-assembly of single-walled carbon
nanotubes into nanorings using DNA hybridization has also been
24
studied. Morpholino nucleoside-containing oligomers are now
gaining interest due to their biological activity, which were initially
introduced by Summerton and Weller as steric-blocking antisense
25
reagents. More recently, these have also found growing applications
a
Department of Organic Chemistry, Indian Association for the Cultivation of
Science, Jadavpur, Kolkata 700 032, India. E-mail: ocss5@iacs.res.in;
Fax: +91 33 2473 2805; Tel: +91 33 2473 4971
b
Department of Material Science, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata 700 032, India
†
Electronic supplementary information (ESI) available. See DOI: 10.1039/c3cc45082a
Scheme 1 Synthesis of 5-substituted uracil morpholino monomers.
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Fig. 2 AFM images of uracil morpholino monomers in CHCl
3
solution drop-casted
À3
on a silicon wafer at 3 Â 10 M concentration: (a) compound 3, (b) cross sectional
analysis of compound 3 along the white line, (c) 3D AFM image (X B length,
Y B width and Z B height) of microrings showing the height from the silicon
wafer surface, (d) compound 6, (e) height–diameter profile of rings for compound
Fig. 1 (a) UV-visible absorption spectra of compounds 3, 4, 5, 6 in chloroform.
6
and (f) 3D profile of compound 6.
(
b) Corresponding photoluminescence (PL) spectra of these compounds. (c) Excited
state PL lifetime of compounds 3, 4 and 5.
rings are different from each other. Similar AFM images were
also noticed in the case of compounds 4 and 5.
whereas compound 4 failed to show any emission after excitation.
The lack of emission of compound 4 might be attributable to the
n–p* excitation of the nitro group of this compound and also likely
to have – I (electron withdrawing) effect of the nitro group which
affects the overall conjugation of the system with a quenching
effect. The emission maxima for all compounds are B420 nm and
the nature of the spectra depends upon the structure of the
compound. The full width at half maximum (FWHM) varied from
Ring formation was not only noticed in the case of 5-alkynylated
uracil morpholino monomers but the formation was also noticed in
the case of compounds 1 and 5-unsubstituted morpholino mono-
mers 7 (Fig. S5, ESI†). When compound 6 was spin-coated (800 rpm)
on a silicon wafer similar observations were noticed (Fig. 3a) as in the
case of drop-casting. The bearing ratio of compound 6 (Fig. 3c) shows
that B50% of the surface is covered with rings of height B30 nm.
Fig. 3e shows the AFM images of compound 5 when drop-casted on a
75–80 nm. The excited state lifetime (Fig. 1c) was measured for all
À3
silicon wafer at 4 Â 10 M concentration. HRTEM analysis of these
the compounds. Higher lifetime was observed in the case of
compound 3 due to the presence of an electron donating group,
whereas lesser lifetime was noticed in the case of compound 4.
The quantum yield (QY) of all compounds (Table S1, ESI†) is
calculated with respect to quinine sulphate dye, compound 6
shows maximum QY (B50%). A decrease in PL intensity was
noticed with raising temperature for all the compounds, whereas
UV-Vis spectra remained unaffected with temperature variation
compounds also provided similar ring-like architecture (Fig. S6, ESI†).
We were interested to find out the minimum structural scaffold
required for the formation of such rings. Accordingly, compounds 7
to 10 were synthesized (Fig. 4). The aliphatic primary alcohol has
no role in such ring formation, since silyl protected morpholino
monomer 7 also provided similar AFM images. Replacement of the
trityl group by an acetyl group in 8 failed to produce similar images
during AFM spectroscopy. The bulky trityl group on the cyclic six
membered morpholino ring may be responsible for the compounds
to adopt such circular curvature. Presence of a uracil base was
found to be important as compound 9 failed to assemble into rings.
(Fig. S1, ESI†). Upon changing from a polar to nonpolar solvent a
red shift in the absorption spectrum (Fig. S2, ESI†) was observed
in the case of compounds 5 and 6 whereas PL spectra remained
unaltered upon changing the solvent under similar conditions.
To understand the stability of the compounds (Fig. 1c) we
irradiated all the compounds using a 365 nm UV lamp (6 mW).
Compound 5 is much more stable than 3 and 6; the stability was
noticed for up to 48 h and the TGA data show that all these
monomers are quite stable up to 250 1C (Fig. S3a and b, ESI†).
Fig. 2 displays atomic force microscopy (AFM) images of
compounds 3 (Fig. 2a and b) and 6 (Fig. 2d and e). The
macrostructures formed by 3 and 6 in chloroform were drop-
casted on a clean silicon wafer substrate. Both the specimens
À3
were prepared at 3 Â 10 M concentration.
AFM images show that the compounds form ring-like archi-
tecture in solution. From the height profile of compound 3
(
Fig. 2c) it is clear that the diameter of the ring is B500 nm and
Fig. 3 (a) AFM images of compound 6 when spincasted on a silicon wafer,
the height of the ring is B60 nm. Ring structures were also
seen on the mica surface of compound 6 (diameter 2 mm and
height B60 nm) (Fig. S4, ESI†). AFM images and the height
(b) bearing profile, (c) 3D profile (X B length, Y B width and Z B height), (d) AFM
images of compound 5 dropcasted on silicon wafer, (e) height–diameter profile of
microrings along white line in the case of compound 5 and (f) 3D image showing
profiles clearly indicate that the height and diameters of the the height of the rings in the case of compound 5.
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In conclusion, photophysical studies of 5-alkynylated uracil
morpholino monomers have been reported. Some of these alkynyl-
ated monomers exhibited blue emission during excitation using a
UV lamp, and spectral data suggest that they can be treated as
organic semiconductors. These uracil morpholino monomers are
able to form submicron rings through supramolecular assembly.
Fig. 4 Determination of the minimum structural scaffold necessary for ring formation. Although there are some reports on the formation of nanorings
using larger building blocks, however, submicron ring formation
using such a small nucleoside monomeric scaffold has been
reported for the first time. We are trying to apply the current
molecular design to create various p-conjugated functional
architectures of defined size and shape. These circular struc-
tures can be used for electronic and biomedical applications.
This work has been supported by CSIR, India (grant number
Formation of rings was not noticed in the case of compound 10
where the active hydrogen of the uracil base was replaced by a methyl
group. However, addition of adenosine (equimolar) did not affect the
ring structure perhaps because adenosine is not able to form a
Watson–Crick base pair with the uracil morpholino under these
conditions. The presence of a morpholine moiety was also found to
play a key role, since uracil itself or N-tritylated uracil failed to
produce such mini architecture. From the above discussion we
realized that the presence of a tritylated morpholine moiety along
with a uracil nucleus is necessary for the formation of such rings.
Leading intermolecular interactions such as hydrogen bonds, p–p
interactions, and van der Waals interactions are found to play an
important role in the formation of organic nano structures with
unusual shapes. Among them H-bond is found to be efficient in
determining the morphology of the structures. To confirm the pre-
02(0012)/11/EMR-II). S. P. and S. J. thank CSIR, J. B. thanks the
Institute for their fellowship. We acknowledge Dr Somobrata
Acharya for his help during manuscript preparation.
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1280 Chem. Commun., 2013, 49, 11278--11280
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