Exploring hydrogen bonding and weak aromatic interactions induced assembly of adenine and thymine functionalised naphthalenediimides

Article abstract of DOI:10.1039/c3nj00060e

Adenine and thymine functionalised naphthalenediimide (NDI) conjugates and complementary peptide nucleic acid (PNA) dimers are designed to exploit complementary hydrogen bonding and aromatic interactions for controllable molecular organization. These nucleobase appended NDIs organized into well-defined fibers, nanoribbons, porous spheres, belts and petal-like 2D sheets.

Full text of DOI:10.1039/c3nj00060e

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Exploring hydrogen bonding and weak aromatic
interactions induced assembly of adenine and thymine
Cite this: DOI: 10.1039/c3nj00060e
functionalised naphthalenediimides†
Received (in Montpellier, France)
1
4th January 2013,
Nagarjun Narayanaswamy, M. B. Avinash and T. Govindaraju*
Accepted 12th March 2013
DOI: 10.1039/c3nj00060e
www.rsc.org/njc
5
Adenine and thymine functionalised naphthalenediimide (NDI) science and biomedicine. This communication complements
conjugates and complementary peptide nucleic acid (PNA) dimers the bio-inspired molecular engineering approach reported by
are designed to exploit complementary hydrogen bonding and our group and also the pioneering studies on DNA templated
6
–8
aromatic interactions for controllable molecular organization. assembly.
In addition, complementary peptide nucleic acid
These nucleobase appended NDIs organized into well-defined (PNA) dimers were employed as templates for the molecular
fibers, nanoribbons, porous spheres, belts and petal-like 2D sheets. assembly of nucleobase modified NDIs. PNAs are the DNA
mimics with nucleobases attached to the pseudopeptide back-
9
One of the most fascinating aspects of biological systems is bone. PNAs form complexes with complementary nucleobase
their selectivity and specificity, emphasizing their grandeur in sequences with greater affinity and strength than natural
1
,2
9
structure–property correlations. This unparalleled character- oligonucleotides. Furthermore, this work represents a unique
istic of natural systems could be exemplified by the elegant example of constructing supramolecular polymers by exploiting
2
,3
molecular design and functioning of nucleic acids. These Watson–Crick and Hoogsteen type hydrogen bonding of the
polynucleotides with their specific sequence of nucleobases adenine base. As a consequence of unusual hydrogen bonding
facilitate coding and encoding of genetic information and are of adenine and thymine besides weak aromatic interactions
3
also known to form a variety of complex molecular assemblies.
(NDI-core), adenine–NDI–adenine (NDA–AA) organised into well-
It is this intriguing property of nucleobases to form hydrogen defined nanoribbons by solution processing, whereas comple-
bonded molecular structures that inspired us to explore their mentary PNA–TT templating resulted in 2D microstructures.
efficacy to achieve controllable molecular assemblies. Such a While thymine–NDI–thymine (NDA–TT) conjugates assemble
concept in the name of DNA nanotechnology was evoked by into porous spheres, tapes and petal-like 2D sheets with
Nadrian C. Seeman and it has been an area of active research complementary PNA–AA templating. The obtained nano- and
4
for the past two decades. However, when aiming for a solution micro-structures find importance from a fundamental science
processable controlled molecular assembly of p-conjugated perspective as well as in technological implications.
organic molecules, DNA nanotechnology in its original form
Nucleobase appended NDI–AA and NDI–TT were prepared
8
would be impractical. Therefore, in a minimalistic approach, as shown in Scheme 1. We incorporated an ethylene linker
one could envision p-conjugated molecules appended with spacer between nucleobases and the NDI-core to reduce
nucleobases as an attractive alternative. Herein, we report the the dominating role of aromatic p–p interaction by taking
synthesis and molecular assembly of adenine and thymine advantage of its flexibility via C–C bond rotation and hence
functionalised naphthalenediimides (NDIs). NDI is one of the the terminal nucleobases will facilitate the assembly of NDI
most promising n-type organic semiconductors with a wide conjugates through dominating hydrogen bonding inter-
range of applications in the fields of electronics, materials actions. Boc-protected adeninyl-9-ethyl amine (1) was prepared
9
in good yield by N-alkylation of adenine (N -H) using 1-(butyloxy-
carbonyl)-2-bromo ethylamine and sodium hydride as base in
Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for
Advanced Scientific Research, Jakkur, Bangalore 560064, India.
DMF at 65 1C. Similarly Boc-protected thyminyl-1-ethyl amine (2)
E-mail: tgraju@jncasr.ac.in; Fax: +91 8022082627
Electronic supplementary information (ESI) available: Synthesis and character-
1
was synthesized by the N-alkylation of thymine (N -H) with
-(butyloxycarbonyl)-2-bromo ethylamine and potassium carbonate
as base in DMF at 65 1C. Boc-deprotected 1 and 2 were condensed
†
1
ization of compounds, experimental procedures, UV-Vis absorption and NMR
spectra and temperature dependent study data. See DOI: 10.1039/c3nj00060e
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Fig. 1 UV-vis absorption spectra of NDI-conjugates. (A) NDI–AA in the DMSO–
water system. (B) NDI–TT in the DMSO–water system.
in the absorption band (300–400 nm region). However upon
further increasing the CH CN percentage to 90% a new band
3
was observed at 403.5 nm (Fig. S1B, ESI†). This clearly suggests
the improved aromatic p-stacking interactions among NDI–TT
3
molecules in the 90% CH CN–DMSO solvent system.
Next we studied the effect of PNA templates viz. PNA–TT
100 mM) and PNA–AA (100 mM) on the molecular aggregation of
(
NDI–AA and NDI–TT respectively. Room temperature UV-vis
absorption studies did not show any detectable spectral
changes for both NDI–AA and NDI–TT with the addition of
Scheme 1 Synthesis and molecular structures of NDI–AA, NDI–TT, PNA–AA respective complementary PNA dimers. Interestingly, tempera-
and PNA–TT.
ture dependent absorption studies provided more insight into
the interaction among individual NDI–AA or NDI–TT and with
with 1,4,5,8-naphthalenetetracarboxylic dianhydride (NDA) in their respective complementary PNA dimers. Surprisingly, in
the presence of triethylamine (TEA) in DMF to obtain the the case of NDI–AA absorption in the 300–400 nm region
corresponding nucleobase appended NDI–AA and NDI–TT gradually decreases with an increase in temperature from
conjugates in good yield (Scheme 1). PNA–TT and PNA–AA were 20 1C to 80 1C (Fig. S2A, ESI†). This can be ascribed to
9
prepared according to the procedure reported in the literature.
disruption of hydrogen bonding among the adenine bases
We investigated the molecular interactions of NDI–AA and at higher temperature and subsequent strengthening of
NDI–TT in solution using UV-vis absorption spectroscopy. It aromatic p-staking interactions between NDI chromophores.
should be noted that NDI–AA is sparingly soluble in most of the Interestingly, distinct spectral features were observed for NDI–TT.
organic solvents due to strong aromatic and hydrogen bonding The J-type aggregation band at B405 nm gradually decreased
interactions; however trace amounts of trifluoroacetic acid while experiencing hyperchromic effects with respect to the
(TFA) rendered increased solubility in DMSO. The UV-vis absorption band at 300–400 nm as the temperature increased
absorption spectra of NDI–AA (100 mM) and NDI–TT (100 mM) from 20 1C to 80 1C (Fig. S2B, ESI†). The gradual decrease in the
in DMSO exhibited absorption bands in the 300–400 nm region intensity of the J-type aggregation band at higher temperature
due to characteristic p–p* transitions of NDI chromophores indicates the transformation of the aggregated system to a
polarized along the z-axis. The absorption spectra of NDI–AA in molecularly dissolved state due to disruption of hydrogen
water–DMSO (Fig. 1A) did not show any significant spectral bonding and aromatic interactions in NDI–TT. There was no
changes. Interestingly, the intensity of the absorption band significant change in the absorption band at 300–400 nm
(
300–400 nm region) of NDI–TT in DMSO gradually decreases for NDI–AA/PNA–TT (Fig. S2C, ESI†). However in the case of
with addition of water and a new absorption band appeared at NDI–TT/PNA–AA the absorption band at 405 nm decreases
04.5 nm with an appreciable bathochromic shift of 25 nm gradually with a blue shift of 2 nm as a function of increasing
Fig. 1B). This spectral change is attributed to J-type aggrega- temperature from 20 1C to 80 1C and there was no change in
4
(
tion of the aromatic core and the molecules arranged in an the 300–400 nm spectral region (Fig. S2D, ESI†). Overall the
edge to edge fashion to attain the minimum free energy for observed changes in absorption spectra of NDI–AA and NDI–TT
stability. In DMSO–acetonitrile (CH CN) solvent system NDI–AA in the presence and absence of respective complementary PNA
3
exhibited a blue shift in the absorption band with enhanced templates suggest the crucial role of hydrogen bonding of
absorption intensity (Fig. S1A, ESI†). This enhancement in nucleobases and relatively weaker p–p interactions of the
the intensity of the absorption band is attributed to weakening NDI-core in their molecular aggregation.
of p-stacking interactions as a consequence of probable
strengthening of intermolecular (adenine–adenine) hydrogen NDI–AA and NDI–TT using microscopy techniques by drop casting
bonding interactions. Increasing the CH CN percentage from their respective solution onto silicon (111) substrates. FESEM
to 70% in DMSO solution of NDI–TT also lead to a blue shift (field emission scanning electron microscopy) micrographs
We investigated the morphology of supramolecular structures of
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To understand the aggregation of NDI–AA and NDI–TT
and the role of nucleobases, we have analyzed temperature
1
dependent H-NMR and 2D-NOESY spectra. At ambient
temperature (25 1C), two separate broad signals were observed
for NH2 protons (Ha and H ) of adenine (NDI–AA) in the
b
downfield region of 8.5 to 10 ppm. This clearly suggests that
a b
the two N–H protons (H and H ) of adenine possess different
1
1
hydrogen bonding environments. Upon increasing the tem-
perature from 25 1C to 60 1C, these two N–H signals merge to a
single broad peak as a consequence of disruption of hydrogen
bonds and hence the two N–H protons become equivalent
8
at higher temperature (Fig. 4A). Two C–H protons (C -H and
c
2
C -H ) at 8.535 and 8.185 ppm undergo an upfield shift
d
(0.03 and 0.05 ppm respectively) with an increase in tempera-
ture from 25 1C to 60 1C. Therefore temperature dependent
1
H-NMR spectra confirmed the involvement of two distinct
Fig. 2 FESEM micrographs of (A) fibers obtained from NDI–AA in 100% DMSO
solution, (B) nanoribbons obtained from NDI–AA in 90% CH
3
CN–DMSO solution,
(
C) porous spheres obtained from NDI–TT in 100% DMSO solution, and (D)
3
bundles of belts obtained from NDI–TT in 90% CH CN–DMSO solution.
revealed the formation of a fibrous network by NDI–AA in
pure DMSO (Fig. 2A). While NDI–AA in 90% acetonitrile–
DMSO assembled into ribbons with relatively uniform length
(410 mm) and width (1–1.5 mm) throughout the sample
(Fig. 2B). AFM (atomic force microscopy) measurements
revealed that these ribbons have a topographical thickness in
the range of 50–60 nm (Fig. S3B, ESI†). Interestingly a solution
of NDI–TT in pure DMSO formed porous sphere-like structures
(
Fig. 2C). In contrast, a solution of NDI–TT in 90% acetonitrile–
DMSO resulted in belt-like structures with high aspect ratios
5–10 mm length and 500 nm width) (Fig. 2D). Next, we studied
(
the effect of PNA–TT template on the morphology of NDI–AA.
The annealed solution NDI–AA + PNA–TT (1 : 1) was drop cast
onto a silicon (111) substrate. The FESEM image showed the
formation of rectangular 2D microstructures (Fig. 3A), whereas
petal-like 2D sheets were observed for NDI–TT + PNA–AA (1 : 1)
(Fig. 3B). Thus, PNA–TT and PNA–AA templates reengineer the
morphological structures of NDI–AA and NDI–TT from 1D to
1
0
extended 2D structures.
Fig. 3 (A) FESEM micrographs of NDI–AA
+
PNA–TT (1 : 1) rectangular
2
D microstructures obtained from DMSO–water solution. (B) FESEM micrographs
Fig. 4 Partial molecular structures of NDI–AA and PNA–TT with proton assignment.
1
of NDI–TT
+
PNA–AA (1 : 1) petal-like 2D sheets obtained from DMSO–
(A) Temperature dependent H-NMR spectra of NDI–AA in DMSO-d
6
. (B) Temperature
1
water solution.
6
dependent H-NMR spectra of NDI–AA/PNA–TT (1 : 1) in DMSO-d .
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hydrogen bonds of N and N of the adenine base. Further, the progress in our laboratory to extend this strategy to other
imide proton (N–H ) of thymine in PNA–TT/NDI–AA also molecular systems to develop functional molecular materials.
e
appeared in the downfield region (11.3 ppm) due to its parti-
cipation in hydrogen bonding. This was further confirmed by
Experimental section
the upfield shift (0.2 ppm) of the imide N–H proton of thymine
e
at higher temperature (Fig. 4B). The 2D-NOESY studies further NMR spectroscopy, mass spectroscopy and elemental analysis
revealed the interaction between the adenine bases of NDI–AA
Fig. S4A, ESI†). Further, 2D-NOESY spectra of PNA–TT tem-
plated NDI–AA showed the absence of spatial coupling between
N–H and N–H of adenine (Fig. S4B, ESI†). While the appear-
ance of a new set of spatial interactions for N–H and N–H
1
13
H, 2D-NOESY and C NMR spectra were recorded on a Bruker
AV-400 spectrometer with chemical shifts reported in ppm
in CDCl –DMSO-d , tetramethylsilane as internal standard)
at 20 1C. The variable-temperature NMR spectra were recorded
by monitoring the temperature with Æ1 1C variation. Mass spectra
were obtained on Shimadzu GC–MS 2010 and Bruker Ultraflex II
MALDI/TOF spectrometers. Elemental analysis was carried on a
ThermoScientific FLASH 2000 Organic Elemental Analyzer.
(
(
3
6
a
b
a
b
(NDA–AA) with N–He of thymine (PNA–TT) proved the cross
hydrogen bonding between the two nucleobases.
1
10
Normally, involvement of N and N -H of adenine indicates
7
Watson–Crick type hydrogen bonding, while that of N and
1
0
N -H suggests Hoogsteen type hydrogen bonding. In conven- UV-vis spectroscopy
tional Watson–Crick hydrogen bonding between adenine and
thymine, N - and N -H of adenine yield a hydrogen bonded
The UV-vis absorption spectra were recorded on a Perkin Elmer
Model Lambda 900 spectrophotometer. 100 mM solution of the
sample was analyzed in a quartz cuvette of 1 mm path length.
1
10
eight membered ring. However, for Hoogsteen type hydrogen
7
10
bonding, N and N -H of adenine are involved in the formation
of a hydrogen bonded nine membered ring. Surprisingly, in the
case of NDI–AA N , N and N -H (H and H ) are all involved in
a b
Field emission scanning electron microscopy (FESEM)
1
7
10
FESEM imaging of the samples was carried out using FESEM,
FEI Nova nanoSEM-600. Freshly prepared solutions were drop
cast on a clean one side polished surface of silicon(111). These
samples were thoroughly dried under vacuum and imaging was
carried out by operating the field emission gun at 5 kV.
hydrogen bonding as discussed earlier. This unusual hydrogen
bonding among NDI–AA molecules through adenine and
relatively weak aromatic interaction of the NDI-core as
indicated by the UV-vis absorption studies are believed to be
the major driving force for the formation of 1D fibers and
1
7
10
nanoribbons. Moreover, the participation of N , N and N -H
of adenine in hydrogen bonding interactions indicates that the
adenine nucleobase binds to thymine in PNA–TT by either
Watson–Crick or Hoogsteen type complementary hydrogen
bonding (Fig. S5, ESI†). However, the flexibility of the ethylene
linker and the relative orientation of thymine functionalities in
the PNA dimer are also believed to be the major determinants
for the assembly of NDI–AA/PNA–TT to rectangular 2D micro-
structures. Similarly, the hydrogen bonding of the thymine
base and weak aromatic interaction of the NDI-core play
a crucial role in the formation of porous spheres, belts from
NDI–TT and petal-like 2D sheets from NDI–TT/PNA–AA. Never-
theless, the marked difference in the molecular assembly to
form 1D fibres, 1D nanoribbon, belts to 2D microstructures
and petal-like 2D sheets clearly emphasizes the role of com-
plementary PNA dimers as effective templates.
Transmission electron microscopy (TEM)
TEM micrographs were obtained by drop casting the sample
solution on a 200 mesh holey carbon supported copper grid
and dried at 40 1C. The images were recorded using a JEOL,
JEM 3010 instrument operating at 300 kV.
Atomic force microscopy (AFM)
AFM measurements were performed on an Innova (Veeco) AFM
instrument in the tapping mode. The samples were prepared by
drop casting the sample solutions on the silicon(111) surface.
Acknowledgements
The authors thank Prof. C. N. R. Rao. FRS for constant support
and encouragement, VIN lab and Basavaraj for AFM, JNCASR
In summary, we have developed a new strategy for control- and DBT-IYBA, Govt. of India, and CSIR (SRF to NN), New Delhi,
ling the morphology of NDI-chromophores by conjugating with for financial support.
nucleobases. These NDI–nucleobase conjugates self-assembled
into well-defined fibres, nanoribbons, porous spheres, belts, 2D
microstructures, and petal-like 2D sheets based on hydrogen
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