Molecular architectonics of stereochemically constrained π-complementary functional modules

Article abstract of DOI:10.1002/ejoc.201300677

The elucidation of the complex factors that govern recognition events at the molecular level represents a daunting challenge in our quest to master the art of pre-programmed molecular assemblies. In this context, we present the molecular architectonics of thoughtfully designed amino acid appended functional molecules 1-5. Naphthalenediimide (NDI and pyrene were employed as functional modules due to their unusual topological shape similarity as well as complementary π-acidic and π-basic character, respectively. In addition, we show that dyads of such unusual functional modules energetically favour alternate assembly in contrast to the predominant self-sorted assembly observed for single-component systems. Moreover, by incorporating minute structural mutations into the amino acid side-chains of 1-5, we successfully tailored their assemblies into well-defined supramolecular architectures, namely supercoiled helices, twisted nanoribbons, nanobelts, comb-edged nanoflakes and nanosheets. A detailed analysis with the aid of experimental and theoretical studies has generated interesting insights into the factors that govern the recognition events at the molecular level. In a quest to master pre-programmed molecular assemblies, we show that alternate stacking over self-sorting of functional aromatic modules can be energetically controlled by smarter molecular design. Furthermore, by introducing structural mutations into the side-chain of amino acid auxiliaries, the molecular assemblies form tailored well-defined 1D and 2D supramolecular nanoarchitectures. Copyright

Full text of DOI:10.1002/ejoc.201300677

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Molecular Programming
M. B. Avinash, P. K. Samanta,
K. V. Sandeepa, S. K. Pati,
T. Govindaraju* ............................... 1–11
Molecular Architectonics of Stereochem-
ically
Constrained
π-Complementary
Functional Modules
Keywords: Charge transfer
/ Molecular
programming / Molecular architectonics /
Amino acids / Self-assembly
In a quest to master pre-programmed mo-
lecular assemblies, we show that alternate
stacking over self-sorting of functional aro-
matic modules can be energetically con-
trolled by smarter molecular design. Fur-
thermore, by introducing structural mu-
tations into the side-chain of amino acid
auxiliaries, the molecular assemblies form
tailored well-defined 1D and 2D supramo-
lecular nanoarchitectures.
0000, 0–0
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T. Govindaraju et al.
FULL PAPER
DOI: 10.1002/ejoc.201300677
Molecular Architectonics of Stereochemically Constrained π-Complementary
Functional Modules
M. B. Avinash,[a] Pralok K. Samanta,[b] K. V. Sandeepa,[a] Swapan K. Pati,[b] and
T. Govindaraju*[a]
Keywords: Charge transfer / Molecular programming / Molecular architectonics / Amino acids / Self-assembly
The elucidation of the complex factors that govern recogni-
tion events at the molecular level represents a daunting chal-
lenge in our quest to master the art of pre-programmed mo-
lecular assemblies. In this context, we present the molecular
architectonics of thoughtfully designed amino acid appended
functional molecules 1–5. Naphthalenediimide (NDI) and
pyrene were employed as functional modules due to their
unusual topological shape similarity as well as complemen-
tary π-acidic and π-basic character, respectively. In addition,
we show that dyads of such unusual functional modules en-
ergetically favour alternate assembly in contrast to the pre-
dominant self-sorted assembly observed for single-compo-
nent systems. Moreover, by incorporating minute structural
mutations into the amino acid side-chains of 1–5, we success-
fully tailored their assemblies into well-defined supramolec-
ular architectures, namely supercoiled helices, twisted nano-
ribbons, nanobelts, comb-edged nanoflakes and nanosheets.
A detailed analysis with the aid of experimental and theoreti-
cal studies has generated interesting insights into the factors
that govern the recognition events at the molecular level.
lecular recognition events, and the resulting supramolecular
architectures are governed by the stereochemical con-
straints of the functionalities. The process of custom-
designing and/or molecularly engineering assemblies is con-
ceptualized as molecular architectonics.
Introduction
Nature’s archetypal molecular engineering with specific
structure–property correlations has inspired researchers to
design novel biomimics for advanced functional applica-
tions, and also to unravel the progressive evolution of self-
organization towards complex matter.[1] To construct such
complex molecular systems, various weak non-covalent in-
teractions have to be harnessed synchronously. This obliga-
tion of harvesting tricky intermolecular interactions coop-
eratively makes supramolecular engineering a challenging
and intriguing endeavour.[2] To achieve this daunting task,
several primitive yet elegant molecular designs involving hy-
drogen-bonding, metal coordination and/or aromatic inter-
actions either in solution or at an interface (liquid/liquid,
solid/air etc.) have been attempted in the recent past.[3]
However, the supramolecular engineering of designed func-
tional molecular modules to tailor-made architectures en-
compassing a detailed relationship between structural infor-
mation and functional property has rarely been explored.[4]
With this premise, we report our designer molecules 1–5
(Figure 1) comprising NDI and pyrene modules in which
the molecular assembly is engineered by tailoring the mo-
In this work we have employed NDI as the functional
module, which is one of the most versatile and fascinating
classes of molecules with a wide variety of potential appli-
cations in fields ranging from biomedicine to electronics.[5]
Because the performance of electroactive molecular materi-
als is essentially dependent on their molecular ordering, it
is extremely important to develop novel modular ap-
proaches for tailoring their assemblies. Interestingly, NDI is
a highly π-acidic planar molecule with an estimated molec-
ular quadrupole moment (Qzz) of +18.6 B (Bucking-
hams).[6] This π-acidic behaviour of NDI, which is in the
range of explosive TNT, is an attractive property, because
most aromatic compounds are π-basic, for example, benz-
ene has a Qzz of –8.5 B, and pyrene has a Qzz of –13.8 B.
Thus, NDI and pyrene exemplify a unique molecular (elec-
tron donor–acceptor) pair due to their complementary π
character and also the unusual topological shape and the
similarity of their molecular structures. However, the antici-
pated preferential alternate stacking of NDI and pyrene
(when part of distinct molecular components), in contrast
to their self-sorted assemblies, are rarely realized due to
their relatively weak non-covalent interaction energies.[7] On
the other hand, exploitation of such donor/acceptor alter-
nate stacking induced charge-transfer complexation (if ex-
tended to long-range order) is instrumental for obtaining
excellent conduction through inherent doping as well as for
[a] Bioorganic Chemistry Laboratory, New Chemistry Unit,
Jawaharlal Nehru Centre for Advanced Scientific Research,
Jakkur P. O., Bangalore 560064, India
E-mail: tgraju@jncasr.ac.in
Homepage: http://www.jncasr.ac.in/tgraju/
[b] Theoretical Sciences Unit, Jawaharlal Nehru Centre for
Advanced Scientific Research,
Jakkur P. O., Bangalore 560064, India
Supporting information for this article is available on the
WWW under http://dx.doi.org/10.1002/ejoc.201300677.
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Molecular Architectonics of π-Complementary Functional Modules
auxiliaries for tailoring the molecular assemblies were cho-
sen on the basis of the phenomenal molecular/chiral re-
cognition and distinctive sequence-specific self-assembling
properties embodied in them as a result of over a billion
years of stringent natural selection.[1e] Specifically, by intro-
ducing minute molecular structural mutations in the side-
chain of the amino acid auxiliary (Figure 1), striking varia-
tions in the supramolecular architectures, namely su-
percoiled helices, twisted nanoribbons, nanobelts, comb-
edged nanoflakes and nanosheets, were realized.
Results and Discussion
A detailed procedure for the synthesis of our functional
molecules 1–5 with l-alanine, l-valine, l-isoleucine, l-phen-
ylalanine and d-phenylalanine methyl ester derivatives,
respectively, is given in the Exp. Sect. Briefly, 1-pyrenemeth-
ylamine and the respective amino acid methyl ester were
condensed with 1,4,5,8-naphthalenetetracarboxylic dian-
hydride at 110 °C in N,N-dimethylformamide in the pres-
ence of N,N-diisopropylethylamine to obtain the corre-
sponding desired products 1–5. To understand the nature
of the molecular assembly, we first subjected our functional
molecules 1–5 to photophysical studies. The UV/Vis ab-
sorption spectra of 1 in dimethyl sulfoxide exhibits typical
absorption bands in the region of 270–400 nm due to char-
acteristic π–π* transitions polarized along the z and y axes
of the NDI and pyrene chromophores (Figure 2a).[9] Upon
incremental addition of water to the DMSO solution of 1,
a decrease in absorption intensity as well as broadening of
the band were observed, which indicates molecular aggrega-
tion. Up to 30% aqueous DMSO, only a decrease in the
Figure 1. Molecular structures of designer functional molecules 1–
5. Blue colour signifies the topological shape similarity of naphth-
alenediimide (NDI) and pyrene. Electrostatic potential surfaces of
(a) π-acidic NDI and (b) π-basic pyrene with their respective com-
puted axial quadrupole moments Qzz. (c) Energy-minimized struc-
tures of NDI–NDI, pyrene–pyrene and NDI–pyrene stacking.
(d) Schematic representation depicting the probable self-sorting or
alternate stacking for hypothetical dyads of NDI and pyrene. The
estimated interaction energies, E in kcalmol–1, are shown in (c) and
(d).
the recently shown remarkable room-temperature ferroelec- absorption intensity was observed without any appreciable
tric property.[8] Thus, to extend the envisioned ordering changes in the absorption maxima (λmax). Interestingly,
from the molecular level to well-defined supramolecular with a further increase in water content in the DMSO solu-
architectures on a microscopic scale and also to explore sys- tion of 1, a bathochromic shift of around 3 nm with respect
tematic molecular structural mutation induced structure– to the band at 330 nm (λmax), as well as an increase in the
property correlations, we have designed amino acid func- absorption intensity, was observed. Thus, these absorption
tionalized dyads of NDI and pyrene (1–5). The amino acid characteristics of 1 suggest the formation of two different
Figure 2. (a) UV/Vis absorption spectra of a 200 μm solution of 1 in aqueous DMSO containing various percentages of water. (b) Absorp-
tion spectra of a 1 mm solution of 1–5 in 30% aqueous DMSO showing the charge-transfer band. The inset shows the characteristic
brick-red free-floating aggregates formed in 1 mm solutions of 1–5 (1A–5A) in 30% aqueous DMSO within a few hours of sample
preparation. 1D is a solution of 1 in DMSO alone.
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kinds of aggregates at 30 and 80% aqueous DMSO, which scription of molecular chirality from the l-isoleucine methyl
are termed as AGG1 and AGG2 (AGG = aggregate), ester is extended to the pyrene unit through the covalently
respectively (see below). Similar spectral features were ob- interlinked NDI, which can be ascribed to the domino ef-
served for 2–5 in aqueous DMSO, which suggests identical fect. The band at 278 nm, which is due to S0–S3 transitions
molecular aggregation behaviour.[9] In addition, the fluores- in pyrene, shows a negative bisignated couplet centred at
cence emission of both the pyrene and NDI units in 1–5 280 nm, consistent with an M-type helical arrangement of
was found to be quenched in DMSO as well as in aqueous adjacent pyrene transition dipoles within the assembly.
DMSO.[9] Interestingly, in aqueous DMSO, brick-red free- Furthermore, at 80% aqueous DMSO very weak CD sig-
floating aggregates of 1–5 were found to form within a cou- nals are observed for 3, which can be attributed to effective
ple of hours of sample preparation, which suggests a prob- charge-transfer-induced CD silencing. Thus, the observed
able alternate stacking of NDI and pyrene (1A–5A; inset in distinct CD spectral features of 3 in 30 and 80% aqueous
Figure 2b). Note that neither NDI nor pyrene are coloured DMSO are consistent with the two kinds of aggregates
in the visible region when dissolved individually (not (AGG1 and AGG2; Figure 2a and Figure S2 in the Sup-
shown) nor the dyad dissolved in only DMSO (1D; inset in porting Information) found in absorption studies. Identical
Figure 2b). Furthermore, the UV/Vis spectra of 1–5 clearly CD spectral characteristics were also observed for 1, 2 and
show the characteristic broad absorption band in the region 4 (Figure 3 and Figure S4) in DMSO as well as in aqueous
of 400–600 nm, which confirms the charge-transfer com- DMSO. However, 5 shows a complementary Cotton effect
plexation of NDI and pyrene (Figure 2b). The differences with a right-handed (P-type) supramolecular helicity as the
in the intensities of the charge-transfer bands for 1–5 can transcription of chirality is from d-phenylalanine methyl es-
be ascribed to the steric and geometrical constraints in the ter (Figure 3c). Furthermore, we subjected the two enantio-
complexes formed by NDI and pyrene.
mers 4 and 5 to a majority-rules experiment to evaluate
To gain further insights into their mode of aggregation the amplification of chirality. The non-linear plot of CD
and also to detail the relationship between chirality and amplitude versus enantiomeric excess indeed shows appreci-
function, circular dichroism (CD) studies were performed. able amplification in the majority-rules experiment (Fig-
A DMSO solution of 3 did not show any CD features, ure 3d). Powder X-ray diffraction patterns of 1–5 (Fig-
which indicates the absence of excitonic coupling between ure S7) show reflections at around 3.36 Å, which corre-
the chromophores (Figure 3a). However, 3 in 30% aqueous sponds to the interplanar distances between stacked NDI
DMSO exhibits a bisignated Cotton effect in the region of and pyrene.[9] In addition, the reflection at around 21 Å in
270–400 nm, which corresponds to characteristic π–π* tran- the small-angle region correlates well with the calculated
sitions of NDI and pyrene. The negative sign of the first end-to-end length of dimers of the functional molecules (ca.
Cotton effect indicates a left-handed (M-type) supramolec- 21 Å) and can thus be ascribed to the distance between
ular helical organization of 3. More interestingly, the tran- their centres in two laterally assembled structures.
Figure 3. CD spectra of (a) 3, (b) 4 and (c) 5 in aqueous DMSO containing various percentages of water. (d) Results of majority-rule
experiments for 4/5 monitored at 350 and 386 nm in 30% aqueous DMSO.
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The free-floating self-assembled aggregates of 1–5 range of 50–100 nm. The 1D belts of 2 are a few hundreds
formed in aqueous DMSO were subjected to morphological of microns long with their widths in the range of 50–
studies. The two kinds of aggregates, namely AGG1 and 300 nm.
AGG2, formed from 1–5 in 30 and 80% aqueous DMSO,
On the other hand, 1D twisted ribbons are observed for
respectively, were investigated extensively under electron l-isoleucine methyl ester appended functional molecule 3 in
and scanning probe microscopes. The l-alanine methyl ester 30% aqueous DMSO (Figure 4e). Moreover, the free-float-
appended functional molecule 1 in 30% aqueous DMSO ing aggregates of 3 formed in 80% aqueous DMSO were
shows 2D sheet architectures (Figure 4a). Typically, these also found to be 1D twisted ribbons (Figure 4f). These
sheets have lengths of up to around 2 μm and widths in the twisted ribbons have widths of 50–125 nm, topographical
range of 0.2–1.4 μm. The 2D sheet architecture emphasizes thicknesses of 35–60 nm and lengths of several microns. In
the fact that the tendency for molecular assembly (strength addition, the pitch of the helix was found to be around
of intermolecular interactions) of 1 along its length and 200 nm. Interestingly, l-phenylalanine methyl ester ap-
breadth is nearly equal. Although there is no clear demar- pended functional molecule 4 shows 1D supercoiled helix
cation between sheets and short belt-like architectures, we structures in both 30 and 80% aqueous DMSO (Figure 4g).
had earlier proposed that an aspect ratio (length to breadth) Similarly, 1D supercoiled helix structures are observed for
of Յ10 corresponds to sheets, based on reports in the litera- d-phenylalanine methyl ester appended functional molecule
ture.[2b] Atomic force microscopy (AFM) revealed that the 5 (Figure 4h). The resultant supercoiled helix structures of
topographical thickness (height) of these sheets is in the 4 and 5 exhibit left- and right-handed helical signatures,
range of 20–50 nm.[9] However, 1 in 80% aqueous DMSO which is consistent with the CD studies. The widths of these
shows 1D belts with lengths in the order of several microns supercoiled helices were found to be around 100 nm,
(Figure 4b). Interestingly, the widths of these belts are be- whereas the helical pitches are around 120 nm and the
tween 100 and 500 nm, and their heights are 15–80 nm.[9] heights from 4 to 20 nm (Figure 4i–l). Although the photo-
Thus, it appears that in 80% aqueous DMSO, enhanced physical studies of 3–5 showed the existence of two different
hydrophobic force induced aromatic stacking predominates kinds of aggregates (AGG1 and AGG2 in 30 and 80%
along the length of the belt in contrast to the van der Waals aqueous DMSO, respectively), the absence of appreciable
force driven lateral association of 1 along its breadth. Simi- differences in their morphologies is believed to be a result
larly, the l-valine methyl ester appended functional mole- of variations in structural organization that make minimal
cule 2 was found to assemble into 2D comb-edged flakes contributions to the overall supramolecular architecture.
(Figure 4c) and 1D belts (Figure 4d) in 30 and 80% aque- Subsequently, we carried out further studies to gain an un-
ous DMSO, respectively. The 2D comb-edged flakes are 1– derstanding of the nature of the supramolecular architec-
2 μm in length with widths of 0.5–1 μm and heights in the ture upon mixing 4 and 5 in a majority-rules experiment.
Figure 4. Field emission scanning electron microscopy images of (a) 1 in 30% aqueous DMSO, (b) 1 in 80% aqueous DMSO, (c) 2 in
30% aqueous DMSO, (d) 2 in 80% aqueous DMSO, (e) 3 in 30% aqueous DMSO, (f) 3 in 80% aqueous DMSO, (g) 4 in 30% aqueous
DMSO and (h) 5 in 30% aqueous DMSO. The insets in (g) and (h) are high-resolution micrographs of the left- and right-handed
supercoiled helices of 4 and 5, respectively. (i) Atomic force microscopy (AFM) image of 4 in 30% aqueous DMSO and (j) the correspond-
ing height profile along the dashed black line in (i). (k) AFM image of 5 in 30% aqueous DMSO and (l) the corresponding height profile
along the dashed black line in (k).
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This study showed the existence of both left- and right-han- NDI–DHN have interaction energies of –17.39 and
ded supercoiled helices in the mixed sample, and in addition –19.85 kcalmol–1, respectively (Figure 5). Consequently, an
non-helical 1D belts were also observed. The formation of interaction energy difference of around 6 kcalmol–1 be-
non-helical nanobelts is most likely due to the mixing of tween the hetero-stacks of NDI–pyrene (–23.35 kcalmol–1)
oppositely helical 4 and 5 into a single 1D architecture that and NDI–Nap (–17.39 kcalmol–1) can be ascribed to the
nullifies the net helical contributions from 4 and 5.[9]
topological shape similarity of NDI and pyrene. Unsurpris-
The above-discussed 1D or 2D supramolecular architec- ingly, in the literature, molecular NDI is most commonly
tures, namely nanobelts, twisted nanoribbons, supercoiled found in a self-sorted assembly when mixed with donors
helices, comb-edged nanoflakes and nanosheets, formed by like dialkoxynaphthalene (DAN) at room temperature.[13]
our functional molecules are a result of the information On the other hand, mixing an oligomer/polymer of NDI
stored in their molecular structure, which ultimately gov- with another oligomer/polymer of a donor like pyrene or
erns the recognition events at the molecular level. The pho- DAN was found to facilitate charge-transfer complex-
tophysical studies indeed confirmed that the NDI and pyr- ation.[14] However, it should be noted that in the latter case,
ene units of the functional modules form stacks, supposedly a 1:1 co-assembly of all NDI and pyrene/DAN units may
due to the envisioned topological shape similarity and π- not be feasible, and in addition a well-defined supramolec-
complementarity. However, to gain greater insights into the ular architecture has not been realized to the best of our
energetics as well as stereochemical and geometrical con- knowledge. Alternatively, a smarter design involving a dyad
straints of the functional molecules, ab initio DFT studies of NDI and pyrene should facilitate mixed stacking rather
were performed by using the Gaussian 09 package.[10] For than a self-sorted assembly (Figure 1). Logically, the self-
the DFT calculations, we employed the B3LYP exchange sorting of a hypothetical dyad of NDI–pyrene accounts for
correlation functional with the 6-31+g(d,p) basis set for all an interaction energy of –43.62 kcalmol–1 [–(27.17 +
atoms.[11] For the optimization of the dimer formed by 16.45) kcalmol–1], whereas alternate stacking results in
homo- or hetero-stacking of two functional modules, we –46.7 kcalmol–1 [–(23.35 + 23.35) kcalmol–1]. To further
used the ωB97XD exchange correlation functional, which validate our hypothesis, we first obtained energy-minimized
includes empirical dispersion and long-range correlation structures of our functional molecules, which, as expected,
with the 6-31g(d) basis set.[12] In general, when two different revealed V-shaped structures due to the presence of the
chromophores like NDI and pyrene are mixed, the result methylene linker between the NDI and pyrene units. The
could be either a self-sorted (NDI–NDI and pyrene– characteristic V-shaped geometric structures of the func-
pyrene) or alternate (NDI–pyrene) assembly. To predict the tional molecules allows four modes (I–IV) of dimerization
outcome of such a scenario, we estimated the interaction (Figure 6a). Of these, mode IV has the most stable struc-
energies of hetero- and homo-stacked NDI and pyrene ture; the three remaining modes, I–III, are not so stable
(Figure 1 and Table 1). The interaction energies for NDI– due to energetically unfavourable aromatic interactions and
NDI, pyrene–pyrene and NDI–pyrene complexes are steric repulsions. The geometry optimizations of the dimers
–27.17, –16.45 and –23.35 kcalmol–1, respectively, which of 4 and 5 show alternate stacking of NDI and pyrene with
suggests that molecular self-sorting (driven mainly by the interaction energies of –52.10 and –53.62 kcalmol–1, respec-
stacking of two π-acidic NDIs, which would experience re- tively (Figure 6b,c). In addition, computational studies
duced electrostatic repulsions) is most likely to predominate showed the charge-transfer interaction of NDI and pyrene
over alternate assembly unless aided by an additional mo- units with λmax = 519 nm (Figure 7).
lecular interaction.
Table 1. Computed interaction energies (E) of homo- and hetero-
stacked functional modules.
Functional modules
E [kcalmol–1]
NDI–NDI[a]
Pyrene–pyrene
Nap–Nap[b]
DHN–DHN[c]
NDI–pyrene
NDI–Nap
–27.17
–16.45
–8.43
–10.05
–23.35
–17.39
–19.85
NDI–DHN
[a] NDI = naphthalenediimide. [b] Nap = naphthalene. [c] DHN =
1,5-dihydroxynaphthalene.
Figure 5. Energy-minimized structures of naphthalene–naphthal-
ene (Nap–Nap), 1,5-dihydroxynaphthalene–1,5-dihydroxynaphth-
alene (DHN–DHN), naphthalenediimide–naphthalene (NDI-Nap)
and naphthalenediimide–1,5-dihydroxynaphthalene (NDI–DHN)
Alternatively, interaction energies of –8.43 and
–10.05 kcalmol–1 were obtained for homo-stacked naphth-
alene (Nap) and 1,5-dihydroxynaphthalene (DHN), respec-
tively (Figure 5), whereas hetero-stacked NDI–Nap and stacking with their respective estimated interaction energies (E).
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Having understood the origin and nature of the primary semblies of our functional molecules, namely, nanosheets
molecular interactions in our functional modules, that is, and nanobelts from alanine derivative 1, comb-edged nano-
charge-transfer complexation, we performed additional flakes and nanobelts from valine derivative 2, twisted nano-
analyses to account for the observed supramolecular archi- ribbons from isoleucine derivative 3 and supercoiled helices
tectonics. The resulting differences in the molecular as- from phenylalanine derivatives 4 and 5, can all be ascribed
to molecular structural mutations in the side-chain of the
amino acid (Figure 8 and Table 2). The side-chains of alan-
ine, valine, isoleucine and phenylalanine possess an esti-
mated hydrophobicity of 1.0, 2.2, 2.7 and 2.3 kcalmol–1,
respectively, whereas their non-polar surface areas (exclud-
ing the methyl ester functionality) vary from 86 to 194 Å2
(Table 2).[15] At the same time, the hydrophobic nature of
the amino acid residues plays an equally important role by
facilitating hydrophobic interactions in aqueous solutions.
Moreover, based on our earlier experience we believe that
the conversion of the carboxylic acid group of the amino
acids into the methyl ester is necessary to eliminate any
probable counter hydrophilic interactions in aqueous solu-
tion.[16] Although the steric bulkiness of the side-chain in-
creases by a factor of 1.57 from alanine (86 Å2) to valine
(135 Å2), it is believed that it is still below the threshold
for inducing helicity into the supramolecular architecture.
However, the greater steric repulsion rendered by the side-
chains of isoleucine (155 Å2; 1.80 times that of alanine) and
phenylalanine (194 Å2; 2.25 times that of alanine) is
thought to result in twisted belts and supercoiled helices,
respectively. Moreover, the left- and right-handed su-
Figure 6. (a) Schematic representation of four plausible modes of
dimerization for functional molecules 1–5. (b,c) Energy-minimized
structures of dimers of 4 and 5, respectively.
Figure 7. Molecular orbital diagrams depicting the charge-transfer interaction between NDI and pyrene in 4. The value of 519 nm is the
wavelength of the absorption maxima predicted by using time-dependent density functional theory (TD-DFT) as implemented in the
Gaussian 09 package. The B3LYP exchange correlation was used for the TD-DFT calculations.
Figure 8. Schematic representation of the molecular organization of (a) 1, (b) 2, (c) 3, (d) 4 and (e) 5 in aqueous DMSO. The energy-
optimized structures obtained by using the B3LYP exchange correlation functional with the 6-31+g(d,p) basis set were employed to arrive
at the proposed molecular packing models.
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with chemical shifts reported in ppm (in [D6]DMSO with tet-
ramethylsilane as internal standard). Mass spectra were obtained
with an HRMS 6200 series TOF/6500 series spectrometer (Agilent
Technologies). Elemental analysis was carried out with a Thermo-
Scientific FLASH 2000 Organic Element Analyzer.
percoiled helical architectures of 4 and 5 arise from the
transcription of chirality from the l- and d-phenylalanine
methyl ester functionalities, respectively.
Table 2. Hydrophobicity and surface areas of the amino acid func-
tionalities.
Absorption Spectroscopy: UV/Vis spectra were recorded with a Per-
kin–Elmer Model Lambda 900 spectrophotometer. Samples
(200 μm/1 mm) were analysed in quartz cuvettes of 1 mm
pathlength.
Functionality
Hydrophobicity[a]
[kcalmol–1]
Surface area[b] [Å2]
Alanine
Valine
Isoleucine
Phenylalanine
1.0
2.2
2.7
2.3
86
135
155
194
Fluorescence Spectroscopy: Fluorescence spectra were recorded
with a Perkin–Elmer Model LS 55 spectrophotometer. Samples
(200 μm) were analysed in quartz cuvettes of 1 mm pathlength with
excitation at 330 nm.
[a] Estimated hydrophobicity of the side-chain of the respective
amino acid. [b] Non-polar surface area (excluding methyl ester
functionality) of the respective amino acid.
Circular Dichroism (CD) Spectroscopy: CD measurements were
performed with a Jasco J-815 spectrometer under nitrogen. The
sensitivity, time constant and scan rate were chosen appropriately.
Samples (400 μm) were analysed in quartz cuvettes of 1 mm
pathlength.
Conclusions
Field-Emission Scanning Electron Microscopy (FESEM): FESEM
micrographs were acquired by using a FEI Nova nanoSEM-600
microscope equipped with a field-emission gun operating at 5 kV.
Samples were prepared by drop-casting the free-floating aggregates
on Si(111) substrate and allowing them to dry under ambient con-
ditions.
We have designed and developed amino acid appended
functional molecules 1–5 comprising NDI and pyrene mod-
ules. These functional molecules are unique in terms of
their design as they comprise topologically matching π-
complementary modules. Such a design was envisioned to
be the structural analogue of the lock-and-key model. Inter-
estingly, the functional molecules 1–5 assembled into free-
floating aggregates in aqueous DMSO due to enhanced
hydrophobic forces in aqueous solutions. Moreover, we
Atomic Force Microscopy (AFM): AFM micrographs were acquired
under ambient conditions with an Innova (Veeco) atomic force
microscope in dynamic force (tapping) mode. The sample was pre-
pared by drop-casting the free-floating aggregates on Si(111) sub-
have shown that this design strategy was instrumental to strate and allowing them to dry under ambient conditions. AFM
section analysis was carried out offline.
exploit the intermolecular charge-transfer complexation of
NDI and pyrene unlike the predominant self-sorted as-
sembly observed for single-component systems. With the
aid of DFT calculations we have shown that the alternate
stacking of functional aromatic modules could be energeti-
cally controlled by smarter molecular designs. In addition,
by incorporating systematic structural mutations into the
side-chains of the amino acid auxiliaries, we have shown
that the molecular assemblies can be tailored effectively to
give well-defined 1D and 2D supramolecular nanoarchitec-
tures. In particular, supercoiled helices, twisted nanorib-
bons, nanobelts, comb-edged nanoflakes and nanosheets
were realized through minute structural mutations in 1–5.
We further hope that this work will inspire the design and
development of novel as well as improved molecular sys-
tems in an enduring effort to master the art of molecular
programming and to decipher the role of molecular struc-
ture in complex biochemical processes through the intri-
guing systems-chemistry approach.
Powder X-ray Diffraction (PXRD): PXRD patterns were recorded
with a Rigaku-99 (Miniflex) diffractometer by using Cu-Kα radia-
tion (λ = 1.5406 Å). The free-floating self-assembled aggregates of
1–5 were placed in a Petri dish and allowed to dry under ambient
conditions. The solvent-free aggregates thus obtained were trans-
ferred to a glass slide to collect the diffraction data.
Synthesis of 1
Synthesis of L-Alanine Methyl Ester Hydrochloride: Anhydrous
methanol (50 mL) was placed in a 100 mL 2-necked round-bottom
flask fitted with a reflux condenser and an additional dropping
funnel, cooled to ice temperature. Acetyl chloride (3 mL) was
added dropwise through the dropping funnel. After 15 min, l-ala-
nine (3 g) was added, and the reaction mixture was refluxed at
70 °C for 24 h ensuring complete conversion of the carboxylic acid
to the methyl ester. The reaction mixture was vacuum-dried with
successive co-evaporation with toluene to obtain the pure l-alanine
methyl ester hydrochloride. 1H NMR (400 MHz, D2O): δ = 4.26
(q, 1 H, α-carbon proton), 3.86 (s, 3 H, methyl ester protons), 1.59
(d, J = 8 Hz, 3 H, methyl protons) ppm.
1,4,5,8-Naphthalenetetracarboxylic
dianhydride
(200 mg,
0.74 mmol), l-alanine methyl ester hydrochloride (104 mg
0.74 mmol) and 1-pyrenemethylamine hydrochloride (200 mg,
0.74 mmol) together with N,N-dimethylformamide (DMF) (20 mL)
and N,N-diisopropylethylamine (1 mL) were heated at 110 °C for
36 h. Herein, mainly three products could be expected, viz. naphth-
alenediimide with l-alanine methyl ester as the imide substituents
on both sides (denoted as Ala-NDI-Ala); naphthalenediimide with
1-pyrenemethylamine as the imide substituents on both sides (de-
noted as Py-NDI-Py); naphthalenediimide with l-alanine methyl
ester and 1-pyrenemethylamine as the imide substituent on either
Experimental Section
Materials and Methods: 1,4,5,8-Naphthalenetetracarboxylic dian-
hydride, 1-pyrenemethylamine hydrochloride and N,N-diisopropy-
lethylamine were obtained from Sigma–Aldrich. l-Isoleucine, l-al-
anine, l-valine, l-phenylalanine, d-phenylalanine and acetyl chlor-
ide were obtained from Spectrochem Pvt. Ltd. Mumbai, India. All
other reagents and solvents were of reagent- and spectroscopy-
grade and used without further purification. 1H and 13C NMR
spectra were recorded at 298 K with a Bruker AV-400 spectrometer
8
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© 0000 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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Pages: 11
Molecular Architectonics of π-Complementary Functional Modules
sides (expected product 1). The product pyrene-NDI-pyrene is in-
soluble in most of the solvents supposedly due to lack of any chem-
ical functionality to facilitate solubility. The product Ala-NDI-Ala
is highly soluble in non-polar organic solvents like chloroform,
while the expected product 1 (pyrene-NDI-Ala) possess limited sol-
ubility (ca. 1 mg/mL) in solvents like DMF and dimethyl sulfoxide
(DMSO). The resulting reaction mixture containing a precipitate
was filtered, and the filtrate was dried under vacuum and then sub-
jected to thorough washing with chloroform and methanol to ob-
tain the expected product 1. Yield 10%. 1H NMR (400 MHz, [D6]-
DMSO): δ = 8.75 (br., 4 H, NDI aromatic protons), 8.66 (br., 1 H,
pyrene aromatic proton), 8.34 (br., 3 H, pyrene aromatic protons),
8.15 (br., 4 H, pyrene aromatic protons), 7.98 (br. , 1 H, pyrene
aromatic proton), 6.06 (s, 2 H, methylene protons), 5.62 (br., 1 H,
α-carbon proton), 3.65 (s, 3, H, methyl ester protons), 1.61 (d, J =
8 Hz, 3 H, methyl protons) ppm. HRMS (ESI): calcd. for
C35H23N2O6 [M + H]+ 567.1556; found 567.1522. C35H22N2O6
(566.15): calcd. C 74.20, H 3.91, N 4.94; found C 74.15, H 3.95, N
4.93.
successive co-evaporation with toluene to obtain the pure l-iso-
leucine methyl ester hydrochloride. 1H NMR (400 MHz, D2O): δ =
4.17 (d, J = 4 Hz, 1 H, α-carbon proton), 3.89 (s, 3 H, methyl ester
protons), 2.17–2.07 (m, 1 H, β-carbon proton), 1.57–1.47 (m, 1 H,
γ-carbon proton), 1.43–1.32 (m, 1 H, γ-carbon proton), 1.06 (d, J
= 8 Hz, 3 H, methyl protons), 0.98 (t, 3 H, methyl protons) ppm.
1,4,5,8-Naphthalenetetracarboxylic
dianhydride
(200 mg,
0.74 mmol), l-isoleucine methyl ester hydrochloride (135 mg
0.74 mmol) and 1-pyrenemethylamine hydrochloride (200 mg,
0.74 mmol) together with of DMF (20 mL) and of N,N-diisoprop-
ylethylamine (1 mL) were heated at 110 °C for 36 h. Here also three
main products could be expected as described above. The resulting
reaction mixture containing a precipitate was filtered, and the fil-
trate was dried under vacuo and then subjected to thorough wash-
ing with chloroform and methanol to obtain the expected product
3. Yield 13%. 1H NMR (400 MHz, [D6]DMSO): δ = 8.76–8.71 (m,
4 H, NDI aromatic protons), 8.63 (d, J = 8 Hz, 1 H, pyrene aro-
matic proton), 8.34–8.28 m, 3 H, (pyrene aromatic protons), 8.16–
8.07 (m, 4 H, pyrene aromatic protons), 7.95 (d, 1 H, J = 8 Hz,
pyrene aromatic proton), 6.05 (s, 2 H, methylene protons), 5.25 (d,
J = 8 Hz, 1 H, α-carbon proton), 3.61 (s, 3 H, methyl ester pro-
tons), 2.73–2.71 (m, 1 H, β-carbon proton), 1.33–1.27 (m, 1 H, γ-
carbon proton), 1.22 (d, J = 8 Hz, 3 H, methyl protons), 0.98–0.92
(m, 1 H, γ-carbon proton), 0.76 (t, 3 H, methyl protons) ppm.
HRMS (ESI): calcd. for C38H29N2O6 [M + H]+ 609.2026; found
609.1996. C38H28N2O6 (608.19): calcd. C 74.99, H 4.64, N 4.60;
found C 74.95, H 4.68, N 4.57.
Synthesis of 2
Synthesis of L-Valine Methyl Ester Hydrochloride: Anhydrous meth-
anol (50 mL) was placed in a 100 mL 2-necked round-bottom flask
fitted with a reflux condenser and an additional dropping funnel,
cooled to ice temperature. Acetyl chloride (3 mL) was added drop-
wise through the dropping funnel. After 15 min, l-valine (3 g) was
added, and the reaction mixture was refluxed at 70 °C for 24 h
ensuring complete conversion of the carboxylic acid to the methyl
ester. The reaction mixture was vacuum-dried with successive co-
evaporation with toluene to obtain the pure l-valine methyl ester
Synthesis of 4
1
hydrochloride. H NMR (400 MHz, D2O): δ = 4.05 (d J = 4 Hz, 1
Synthesis of L-Phenylalanine Methyl Ester Hydrochloride: Anhy-
drous methanol (50 mL) was placed in a 100 mL 2-necked round-
bottom flask fitted with a reflux condenser and an additional drop-
ping funnel, cooled to ice temperature. Acetyl chloride (3 mL) was
added dropwise through the dropping funnel. After 15 min, l-phe-
nylalanine (3 g) was added, and the reaction mixture was refluxed
at 70 °C for 24 h ensuring complete conversion of the carboxylic
acid to the methyl ester. The reaction mixture was vacuum-dried
with successive co-evaporation with toluene to obtain the pure l-
phenylalanine methyl ester hydrochloride. 1H NMR (400 MHz,
D2O): δ = 7.50–7.33 (m, 5 H, phenyl aromatic protons), 4.49 (t, 1
H, α-carbon proton), 3.89 s, 3 H, (methyl ester protons), 3.41 (dd,
J = 8, 8 Hz, 1 H, methylene proton), 3.30 (dd, J = 8, 8 Hz, 1 H,
methylene proton) ppm.
H, α-carbon proton), 3.87 (s, 3 H, methyl ester protons), 2.41–2.33
(m, 1 H, β-carbon proton), 1.06 (dd, J = 4, 4 Hz, 6 H, methyl
protons) ppm.
1,4,5,8-Naphthalenetetracarboxylic
dianhydride
(200 mg,
0.74 mmol), l-valine methyl ester hydrochloride (125 mg
0.74 mmol) and 1-pyrenemethylamine hydrochloride (200 mg,
0.74 mmol) together with of DMF (20 mL) and of N,N-diisoprop-
ylethylamine (1 mL) were heated at 110 °C for 36 h. Here also three
main products could be expected as described above. The resulting
reaction mixture containing a precipitate was filtered, and the fil-
trate was dried under vacuum and then subjected to thorough
washing with chloroform and methanol to obtain the expected
1
product 2. Yield 12%. H NMR (400 MHz, [D6]DMSO): δ = 8.68
(br., 4 H, NDI aromatic protons), 8.60 (d, J = 8 Hz, 1 H, pyrene
aromatic proton), 8.31–8.25 (m, 3 H, pyrene aromatic protons),
8.14–8.04 (m, 4 H, pyrene aromatic protons), 7.95–7.90 (m, 1 H,
pyrene aromatic proton), 6.00 (s, 2 H methylene protons), 5.16 (d,
J = 8 Hz, 1 H,α-carbon proton), 3.63 (s, 3 H, methyl ester protons),
2.73–2.67 (m, 1 H, β-carbon proton), 1.25 (d J = 4 Hz, 3 H, methyl
protons), 0.76 (d, J = 8 Hz, 3 H, methyl protons) ppm. HRMS
(ESI): calcd. for C37H27N2O6 [M + H]+ 595.1869; found 595.1838.
C37H26N2O6 (594.18): calcd. C 74.74, H 4.41, N 4.71; found C
74.76, H 4.44, N 4.69.
1,4,5,8-Naphthalenetetracarboxylic
dianhydride
(200 mg,
0.74 mmol), l-phenylalanine methyl ester hydrochloride (160 mg
0.74 mmol) and 1-pyrenemethylamine hydrochloride (200 mg,
0.74 mmol) together with of DMF (20 mL) and of N,N-diisoprop-
ylethylamine (1 mL) were heated at 110 °C for 36 h. Here also three
main products could be expected as described above. The resulting
reaction mixture containing a precipitate was filtered, and the fil-
trate was dried under vacuum and then subjected to thorough
washing with chloroform and methanol to obtain the expected
product 4. Yield 13%. 1H NMR (400 MHz, [D6]DMSO): δ = 8.72–
8.61 (m, 5 H, NDI and pyrene aromatic protons), 8.36–8.30 (m, 3
H, pyrene aromatic protons), 8.16–8.08 (m, 4 H, pyrene aromatic
protons), 7.98 (d, 1 H, J = 8 Hz, pyrene aromatic proton), 7.19–
7.05 (m, 5 H, phenyl aromatic protons), 6.04 (br., 3 H, α-carbon
and methylene protons), 3.69 (s, 3 H, methyl ester protons), 3.66–
3.59 (m, 1 H, methylene proton), 3.44–3.37 (m, 1 H,methylene pro-
ton) ppm. HRMS (ESI): calcd. for C41H27N2O6 [M + H]+
643.1869; found 643.1836. C41H26N2O6 (642.18): calcd. C 76.63, H
4.08, N 4.36; found C 76.61, H 4.12, N 4.33.
Synthesis of 3
Synthesis of L-Isoleucine Methyl Ester Hydrochloride: Anhydrous
methanol (50 mL) was placed in a 100 mL 2-necked round-bottom
flask fitted with a reflux condenser and an additional dropping
funnel, cooled to ice temperature. Acetyl chloride (3 mL) was
added dropwise through the dropping funnel. After 15 min, l-iso-
leucine (3 g) was added, and the reaction mixture was refluxed at
70 °C for 24 h ensuring complete conversion of the carboxylic acid
to the methyl ester. The reaction mixture was vacuum-dried with
Eur. J. Org. Chem. 0000, 0–0
© 0000 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
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/KAP1
Date: 23-07-13 17:24:13
Pages: 11
T. Govindaraju et al.
FULL PAPER
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Synthesis of 5
Synthesis of D-Phenylalanine Methyl Ester Hydrochloride: Anhy-
drous methanol (50 mL) was placed in a 100 mL 2-necked round-
bottom flask fitted with a reflux condenser and an additional drop-
ping funnel, cooled to ice temperature. Acetyl chloride (3 mL) was
added dropwise through the dropping funnel. After 15 min, d-
phenylalanine (3 g) was added, and the reaction mixture was re-
fluxed at 70 °C for 24 h ensuring complete conversion of the car-
boxylic acid to the methyl ester. The reaction mixture was vacuum-
dried with successive co-evaporation with toluene to obtain the
pure d-phenylalanine methyl ester hydrochloride. 1H NMR
(400 MHz, D2O): δ = 7.51–7.33 (m, 5 H, phenyl aromatic protons),
4.48 (t, 1 H, α-carbon proton), 3.88 (s, 3 H, methyl ester protons),
3.41 (dd, J = 8, 8 Hz, 1 H, methylene proton), 3.31 (dd, J = 8,
8 Hz, 1 H, methylene proton) ppm.
[4]
1,4,5,8-Naphthalenetetracarboxylic
dianhydride
(200 mg,
0.74 mmol), d-phenylalanine methyl ester hydrochloride (160 mg
0.74 mmol) and 1-pyrenemethylamine hydrochloride (200 mg,
0.74 mmol) together with of DMF (20 mL) and of N,N-diiso-
propylethylamine (1 mL) were heated at 110 °C for 36 h. Here also
three main products could be expected as described above. The
resulting reaction mixture containing a precipitate was filtered, and
the filtrate was dried under vacuum and then subjected to thorough
washing with chloroform and methanol to obtain the expected
product 5. Yield 12%. 1H NMR (400 MHz, [D6]DMSO): δ = 8.74–
8.60 (m, 5 H, NDI and pyrene aromatic protons), 8.36–8.30 (m, 3
H, pyrene aromatic protons), 8.17–8.07 m, 4 H, (pyrene aromatic
protons), 7.98 (d, J = 8 Hz, 1 H, pyrene aromatic proton), 7.19–
7.06 (m, 5 H, phenyl aromatic protons), 6.03 (br., 3 H, α-carbon
and methylene protons), 3.69 (s, 3 H, methyl ester protons), 3.66–
3.58 (m, 1 H, methylene proton), 3.44–3.37 (m, 1 H, methylene
proton) ppm. HRMS (ESI): calcd. for C41H27N2O6 [M + H]+
643.1869; found 643.1832. C41H26N2O6 (642.18): calcd. C 76.63; H
4.08, N 4.36; found C 76.64, H 4.10, N 4.38.
[5]
Supporting Information (see footnote on the first page of this arti-
cle): Absorption, emission, CD, LD, FESEM, AFM and CV data.
Acknowledgments
The authors thank Prof. C. N. R. Rao, FRS for constant support
and encouragement, the Jawaharlal Nehru Centre for Advanced
Scientific Research, the Department of Biotechnology (Innovative
Young Biotechnologist Award) and the Department of Science and
Technology, Government of India for financial support, Prof. G. U.
Kulkarni for access to the FESEM facility, VINL for the AFM
facility, and Selvi, Basavaraja and Mahesh for technical aid in vari-
ous measurements. P. K. S. thanks the CSIR, Government of India
for a senior research fellowship.
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/KAP1
Date: 23-07-13 17:24:13
Pages: 11
Molecular Architectonics of π-Complementary Functional Modules
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Received: May 8, 2013
Published Online: ᭿
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