Molecular recognition of 2-alkylbenzimidazole: Photophysical and structural studies

Article abstract of DOI:10.1016/j.jphotochem.2010.01.021

2-Alkylbenzimidazole (L_1-3) forms organic salt co-crystals with several electron-deficient aromatic as well as aliphatic polycarboxylic acids. Electron-rich benzimidazole shows dramatic quenching of fluorescence in presence of electron-deficient acidic guest molecules. Higher selectivity was found towards pyromellitic acid. Substituted benzimidazole forms organic salt co-crystals with different acids of general composition [L_nH⁺·A^-] (where, A is the acid molecule). The non-covalent interactions between carboxylic acids and L_1-3 were investigated by UV-vis, fluorescence and ¹H NMR spectroscopic methods in solution and by single crystal X-ray diffraction in solid state.

Full text of DOI:10.1016/j.jphotochem.2010.01.021

Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
Contents lists available at ScienceDirect
Journal of Photochemistry and Photobiology A:
Chemistry
journal homepage: www.elsevier.com/locate/jphotochem
Molecular recognition of 2-alkylbenzimidazole: Photophysical
and structural studies
Bimlesh Ojha, Gopal Das∗
Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781 039, India
a r t i c l e i n f o
a b s t r a c t
Article history:
2-Alkylbenzimidazole (L1–3) forms organic salt co-crystals with several electron-deficient aromatic as
well as aliphatic polycarboxylic acids. Electron-rich benzimidazole shows dramatic quenching of fluo-
rescence in presence of electron-deficient acidic guest molecules. Higher selectivity was found towards
pyromellitic acid. Substituted benzimidazole forms organic salt co-crystals with different acids of general
composition [LnH+·A−] (where, A is the acid molecule). The non-covalent interactions between carboxylic
acids and L1–3 were investigated by UV–vis, fluorescence and 1H NMR spectroscopic methods in solution
and by single crystal X-ray diffraction in solid state.
Received 1 August 2009
Received in revised form
30 December 2009
Accepted 29 January 2010
Available online 16 March 2010
Keywords:
Organic salt
© 2010 Elsevier B.V. All rights reserved.
Co-crystal
Electron-deficient compound
Electron-rich compound
Supramolecular chemistry
Fluorescence
1. Introduction
Within the field of supramolecular chemistry, the non-covalent
interactions between a ␲-electron-rich donor molecules and a ␲-
The development of new hosts capable to form hydrogen
bonding with guest molecules in solution and their use in the
construction of new chemosensors for the selective recognition
of important anions is of great interest in the field of host–guest
recognition chemistry. In this aspect, aromatic acids are impor-
tant target anions. It is well established that the weak C–H· · ·O
hydrogen bonds extensively exist just like their strong counter-
parts [1,2] and are found widely in proteins and many organic
crystals [3–5]. Although it is much weaker in comparison to the
usual strong hydrogen bond, X–H· · ·Y (X, Y = N, O, F), this kind of
interactions have aroused significant interest in recent times. In this
aspect, reports concerning the occurrence of weak C–H· · ·O inter-
actions in solution are still rare [6,7]. Although the idea of such
C–H· · ·O interactions are familiar [8], more recently their existence
and importance as a weak, but forceful, secondary interactions
have been widely accepted [9]. In molecular recognition processes
the non-covalent interactions such as hydrogen bonding, aromatic
␲-stacking and weak intermolecular interactions (viz. C–H· · ·␲
and C–H· · ·O) play the crucial role [9]. Intermolecular interactions
involving aromatic rings are important in both biological [10] and
non-biological processes [11]. Much of the works have been done in
the field of directed synthesis of novel host with specific properties.
electron-deficient acceptor moiety through hydrogen bond and/or
cooperative aromatic ␲–␲ interactions have attracted much atten-
tion in recent years [12].
Strong classical hydrogen bonds, such as O–H· · ·N and O–H· · ·O,
are ideal to rationalize and systemize the relationship between
hydrogen bond acceptor and donor molecules. Because of the pre-
dictable supramolecular properties and the ability to form strong
and directional hydrogen bonds, dicarboxylic acids were frequently
chosen as building blocks for crystal engineering [13–15], and
numerous heterodimers composed of carboxylic acids and a vari-
ety of basic building blocks such as amines, dipyridines, pyrazines,
and their analogues have been documented recently [16–19]. The
hydrogen bonding between hydroxyl of carboxylic acids and het-
erocyclic nitrogen atoms has been proved to be a useful and
powerful organizing force and utilized for the formation of variety
of supramolecular 3D architectures. Depending on the difference
in the pKa value of the acidic and basic organic unit, they may
form organic salt or co-crystal in solution or in solid state [20,21].
Benzimidazole and its derivatives are ubiquitous in biology. Their
structures and functions are important in various biochemical pro-
cesses. They are also important class of molecules in the field
of drugs and pharmaceuticals [22–26] and have attracted special
attention in the construction of some interesting 3D framework
in recent years [22–26]. It is also conceivable that great efforts
have been directed towards the development of organic molec-
ular crystals containing a variety of benzimidazole architectures
∗
Corresponding author. Tel.: +91 361 258 2313; fax: +91 361 258 2349.
E-mail address: gdas@iitg.ernet.in (G. Das).
1010-6030/$ – see front matter © 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.jphotochem.2010.01.021

B. Ojha, G. Das / Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
177
melting point and were found to be in good agreement with the
reported data (Supporting information) [39–41].
2.3. Synthesis of organic salts
Equivalent amounts of acids and ligands (L1–3) were dis-
solved in acetonitrile and methanol mixture at room temperature
with constant stirring for
a period of 3–5 h. The result-
ing solution was kept at room temperature for 3–7 days
without any mechanical disturbance to obtain the single crys-
tals of the corresponding salts suitable for X-ray diffraction.
The organic salts isolated are: [HL1][Malonate] (1); [HL1][p-
toluenesulphonate] (2); [HL1][Pyromellitate] (3); [HL2][Malonate]
(4); [HL2][Pyromellitate], (5); and [HL3][p-toluenesulphonate] (6).
Scheme 1. Chemical Structures of L1, L2, L3 and acids.
[22–26]. Non-ionic surfactants belonging to 2-alkylbenzimidazole
are widely used in industrial and medical applications [27]. Benz-
imidazole head group has several advantages viz. it can act as both
hydrogen bond donor and acceptor [28–31], it has both acid and
base character [32], it has intrinsic fluorescence properties [33] and
it is well-known ligand for metal ions [22–26].
We are interested to explore the scope of various weak
non-covalent interactions in molecular recognition processes by
designing new ligands [34–38]. In this paper, we report the molecu-
lar recognition of electron-deficient aromatic acid by electron-rich
2-alkylbenzimidazole molecules (L1–3). We have determined the
single crystal X-ray structure of the ligands (L1–3) and their organic
salts in presence of different acidic molecules viz. oxalic acid (OA);
malonic acid (MA); pyromellitic acid (PA) and p-toluenesulphonic
acid (PTSA) to have an idea of different types of non-covalent inter-
molecular interactions in the solid state (Scheme 1). We have also
studied the interactions of these amphiphilic molecules in solu-
tion with various other acids and their derivatives using UV-visible,
steady state fluorescence and NMR spectroscopy.
2.4. X-ray crystallography
The intensity data were collected using a Bruker SMART APEX-
II CCD diffractometer, equipped with a fine focus 1.75 kW sealed
tube Mo K␣ radiation (ꢀ = 0.71073 Å) at 298(2) K, with increas-
ing ω (width of 0.3◦ per frame) at a scan speed of 3 s/frame. The
SMART software was used for data acquisition. Data integration and
reduction were undertaken with SAINT and XPREP [42] software.
Multi-scan empirical absorption corrections were applied to the
data using the program SADABS [43]. Crystal and molecular struc-
tures were solved by direct methods using SHELXS-97 and refined
with full-matrix least squares on F2 using SHELXL-97 [44]. All non-
hydrogen atoms were refined anisotropically. The hydrogen atoms
were located from the difference Fourier maps and refined isotrop-
ically. Structural illustrations have been drawn with ORTEP-3 for
Windows [45].
2. Experimental
3. Results and discussion
2.1. Materials and methods
3.1. Supramolecular interactions in solution phase
Commercially available o-phenylenediamine and aliphatic acids
were obtained from Sigma, USA. Other chemicals were of reagent
grade and used without further purification. The absorption spectra
were recorded on a Perkin Elmer Lambda-25 UV–vis spectropho-
tometer using 10 mm path length quartz cuvettes at 298 0.1 K,
in the range of 230–350 nm wavelengths. Fluorescence measure-
ments were made on a Carry eclipse spectrofluorometer using
10 mm path length quartz cuvettes with slit width of 5 nm at
298 0.1 K. NMR spectra were recorded on a Varian FT-400 MHz
instrument. The chemical shifts were recorded in parts per mil-
lion (ppm) scale using tetramethylsilane (TMS) as a reference at
298 K. Optical fluorescence micrograph images of air-dried sam-
ples on a glass micro slide were taken using a Zeiss-Axio Cam-MRc
microscope fitted with a digital camera. Scanning electron micro-
graph (SEM) images of samples glued on an aluminum stub
and gold sputtered were obtained by means of a LEO-1430 VP
electron microscope. For spectral studies, the ligands and acid
stock solutions were prepared in acetonitrile. In a 3 mL solu-
tion of the ligands, different concentrations of the acid were
added ranging from 0.05 to 0.56 mM. After proper mixing of
the solution the spectra were recorded on the spectrophotome-
ter.
Aromatic compounds usually have electron-deficient or
electron-rich hydrophobic moieties, and therefore, aromatic
molecules capable to form weak complexes via ␲–␲ stacking
interactions are extremely attractive. Formation of organic salt
co-crystal is an important field of research in pharmaceutical
chemistry. Construction of different 3D network via variety of
non-covalent interactions between organic anion and cation is a
challenge to the crystal engineering. Presence of electron-rich basic
benzimidazole unit in ligands (L1–3) allows us to study this phe-
nomenon with a large variety of electron-deficient aromatic or
aliphatic acids and their derivatives in solution as well as in solid
state. Fig. 1a shows the UV–vis absorption spectra of the ligands in
acetonitrile. The three characteristics absorptions at 243, 273 and
280 nm were observed [46,47] for the ligands in neutral medium
(Fig. 1a). The UV–vis spectra of the compounds do not show any
significant changes with the variation of solvent polarity as well as
with alkyl chain length.
The absorption maximum of L1–3 does not show any spectral
shift or appearance of a new peak when titrated with oxalic acid,
malonic acid, phthalic acid and phthalic anhydride (Supporting
information, Figs. S3–S5). Fig. 1b shows the UV–vis absorption spec-
tra of ligand L1, with increasing concentrations of pyromellitic acid
in acetonitrile. It can be seen from the figure that the absorbance of
ligand increases with increasing concentrations of the acid, while
the acid has one absorption at around 292 nm, showed gain in
intensityupon complexation with the ligand. A reasonable explana-
tion for the two evidences may come from the complex formation
between ligand and pyromellitic acid. Similar result has been
obtained with pyromellitic anhydride too (Supporting information,
Fig. S3). As the acids are not soluble in non-polar solvents, we are
2.2. Synthesis of L1, L2 and L3
2-Alkylbenzimidazoles (L1–3) were prepared by the conden-
sation of o-phenylenediamine and corresponding aliphatic acids
according to the literature method [39,40]. The compounds were
purified by re-crystallization from methanol. The compounds were
also characterized by single crystal X-ray along with NMR, IR and

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the fluorophores and hence, the ligands have very similar chemical
and physical properties [46,47]. The emission spectra of the ligands
are found to be independent of solvent polarity and the intensity
increases with increasing concentrations without appearance of
any new peak at higher wavelengths (Supporting information, Fig.
S10). The air-dried sample of L1 on glass surface showed blue flu-
orescence, when observed under optical fluorescence microscope
in solid state (Fig. 2a inset). In contrast to the emission spectra in
presence of inorganic acid (H2SO4), the changes in the fluorescence
emission spectra of ligands (L1–3) in presence of organic acids are
very different. When solution of ligands prepared in acetonitrile
(5 mM) were titrated with different types of organic acids and their
anhydrides, the fluorescence intensity was quenched to varying
degrees depending on the nature of the added acid molecules with-
out appearance of any peak at 365 nm (Fig. 2b). To investigate the
selectivity and sensitivity of these electron-rich ligands towards
the above mentioned acidic guest molecules, the changes in fluores-
cence intensity of L1 has been plotted as a function of concentration
of the guest molecules (Fig. 2c). Upon addition of pyromellitic
acid and pyromellitic anhydride to the ligands (L1–3), the inten-
sity of emission band at ∼297 nm gradually decreased without any
spectral change (no spectral shifts or appearance of new emission
bands) as shown in Fig. 2b. In a similar way to that described above
the fluorescence intensity were not substantially change due to
the addition of phthalic acid/anhydride, p-toluenesulphonic acid,
oxalic acid and malonic acid to the ligands (Supporting information,
Fig. S11). The maximum quenching of fluorescence intensity was
obtained due to the addition of pyromellitic acid and pyromellitic
anhydride to L1–3 (Fig. 2d). Fig. 2d clearly showed that L1–3 exhibits
relatively higher selectivity towards pyromellitic acid and its anhy-
dride over other electron-deficient aromatic as well as aliphatic
acids in term of quenching percentage. Pyromellitic anhydride
quenches the fluorescence emission by ∼82%, whereas for pyromel-
litic acid the quenching was much more pronounced (∼90%). The
difference in quenching behaviour can be rationalized by the differ-
ence in complex forming ability of these guest molecules with the
ligands (L1–3). In the absence of organic acid, intrinsic fluorescence
of the ligands displayed typical emission spectrum with emission
maxima around at 297 nm, while pyromellitic acid, pyromellitic
anhydride and phthalic acid shows an intense absorption in the UV
region at around 292 and 280 nm, respectively. As shown in Fig. 1c
the absorption spectrum of pyromellitic acid and anhydride exten-
sively overlaps with the emission spectra of the ligands. Altogether,
these results indicate that the quenching of ligand fluorescence
was due to a non-radiative energy transfer between pyromellitic
acid/anhydride and ligands. In case of ligands and pyromellitic
acid/anhydride the spectral overlap is quite large compared to
phthalic acid and PTSA where, the spectral overlap is very less
(Supporting information, Fig. S6). Thus, resonance energy trans-
fer is enhanced in case of pyromellitic acid/anhydride compare
to other acids used. The larger overlap between emission spectra
of ligands and absorbance spectra of pyromellitic acid/anhydride
compared to other acids indicate that pyromellitic acid/anhydride
should show more fluorescence-quenching effect. This indeed was
the observation as shown in Fig. 2, where fluorescence of the lig-
and was quenched more in presence of pyromellitic acid/anhydride
than in presence of other acids (Supporting information, Fig. S12).
Electron-deficient pyromellitic acid can form non-covalent interac-
Fig. 1. (a) Absorbance spectra of L1−3 (5 mM) in acetonitrile and (b) Absorbance
spectra of L1 (5 mM) with increasing concentrations of pyromellitic acid in the
range of 0–0.25 mM and (c) emission spectra of ligand L1 (1), absorbance spectra of
pyromellitic acid (2) and pyromellitic anhydride (3) showing the spectral overlap.
unable to do the experiment in non-polar solvents to examine the
formation of a weak ␲-complex. Thus, these results confirmed that
there are some significant ground state interactions between the
ligands (L1–3) and the pyromellitic acid/anhydride.
Fig. 2a shows the emission spectra of ligands (L1–3) in ace-
tonitrile at room temperature. The ligands shows a locally excited
monomer emission at ∼297 nm when excited at 270 nm, at neu-
tral pH [46,47]. However, in presence of inorganic acid (H2SO4), i.e.
at acidic pH, the molecules showed two emission bands at ∼297
and 365 nm, respectively, when activated at 270 nm (Supporting
information, Fig. S7), where the peak at 365 nm is due to the for-
mation of benzimidazolium cation [46,47]. There is no appreciable
change in the peak position due to variation of alkyl chain length,
as there is a very little change in the excited state behaviour of
tions like hydrogen bonding with electron-rich basic ligands (L1–3
)
and also have aromatic ␲–␲ stacking interactions (Fig. 3), whereas
electron-deficient pyromellitic anhydride can have only the lat-
ter interactions. Thus, it can be concluded that quenching is the
cumulative effect of both acid–base and aromatic ␲–␲ stacking
interactions as shown in Fig. 3.
On the basis of the relationship between quenching of excited
states of benzimidazole and the quencher concentration, the

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179
Fig. 2. (a) Emission spectra of L1–3 in acetonitrile (inset: fluorescence microscope image of L1); (b) emission spectra of L1 with increasing concentrations of pyromellitic acid
and (c) changes in the fluorescence emission intensity at 297 nm of L1 upon addition of different acids and (d) Stack plot showing the extent of quenching by different acid
molecules; where pyromellitic acid (1), pyromellitic anhydride (2), phthalic acid (3), phthalic anhydride (4), malonic acid (5), p-toluene sulphonic acid (6) and oxalic acid
(7); [L1]: 5 mM and [acid]: 0–0.56 mM.
Stern–Volmer equation is given by [48]
following equation was employed for the determination of binding
constant or association constant (KA) and binding sites (n) [49,50]:
F0
ꢀ
ꢁ
= 1 + KSV [Q]
(1)
F − Fmin
Fmax − F
F
log
= n log[Q] − log KA
(2)
where F0 and F are the relative fluorescence intensity in absence
and presence of quencher, respectively and [Q] is the concentra-
tion of the quencher. KSV is the Stern–Volmer quenching constant
which measures the efficiency of quenching. Fig. 4a shows the
Stern–Volmer plots of F0/F versus concentration of quencher. The
figure clearly shows that the degree of fluorescence quenching var-
ied with the type of acid molecules used. It also shows that the
Stern–Volmer plots are linear for oxalic acid, malonic acid, phthalic
acid/anhydride and PTSA. With increasing concentrations of the
guest molecules the plots do not deviate from linearity, while those
of pyromellitic acid and its anhydride deviate from linearity, reveal-
ing that their interactions with L1–3 are stronger compared to the
other acids used. In Table 1, the binding constants obtained from
the Stern–Volmer method are listed for different guest molecules.
The highest value of KSV was found for the pyromellitic acid, which
also showed the maximum quenching of fluorescence intensity. For
the static quenching process, under the assumption that benzimi-
dazole head group has the same and independent binding sites, the
Fig. 4b shows the plot of log[(F − Fmin)/(Fmax − F)] versus log[Q].
To determine KA and n via a Hill plot, the expression on the left
hand side of Eq. (2) is plotted as a function of log of quencher con-
centration. From the slope of this linear graph, a value for n can
be derived, while the intersection with the abscissa corresponds
to (log KA)/n. The obtained binding constants KA and number of
binding sites n were shown in Table 1. The association constants
calculated for the ligand-acid/anhydride suggest low binding affin-
ity. However lower binding constants (104–105 M−1) were recently
reported for several other complexes using the fluorescence spec-
troscopic method which correlates with our results [51–54]. Thus,
it was found that the binding constant for pyromellitic acid is larger
than other acid/anhydride molecules used. The number of binding
sites obtained for pyromellitic acid and pyromellitic anhydride is
more than one, while for other acids it is close to one. The binding
Table 1
Stern–Volmer (KSV
) and binding constant (KA) of L1 with the different
acid/derivatives molecules.
Sample
KSV (M−1
)
KA (M−1
)
n
L
L
L
L
L
L
L
1 + pyromellitic acid
1 + pyromellitic anhydride
1 + phthalic acid
1 + phthalic anhydride
1 + PTSA
5.64 × 103
3.50 × 103
1.67 × 103
1.32 × 103
0.82 × 103
0.75 × 103
0.53 × 103
3.05 × 103
2.50 × 103
0.07 × 103
0.05 × 103
0.04 × 103
0.01 × 103
0.02 × 103
1.7
1.6
1.3
1.2
1.3
1.5
1.4
1 + malonic acid
1 + oxalic acid
Fig. 3. Schematic illustration showing the fluorescence quenching of the ligands by
pyromellitic acid due to aromatic interactions.

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B. Ojha, G. Das / Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
Fig. 5. 1H NMR spectra (400 MHz, CD3OD, 298 K) of L1 (A) and Salt 3 (B).
litic acid, the morphology remains same as that of L1 (Fig. 6b).
However, at 1:5 ratios the morphology is governed by the guest
molecule and it changes to sharp needles of average thickness
25 ␮m (Fig. 6c). At very high concentration of acid, only bulk pre-
cipitates (Fig. 6d) appears, no crystalline nature was observed. It is
very clearly evident from the SEM images that the molecule has a
very effective structure directing agent and the L1/acid ratio plays
a major role in the formation of various types of microcrystalline
structures.
3.2. Supramolecular interactions in solid state
Some of our main concerns have been to ascertain the 3D organi-
zation of the organic cation and anion of an organic salt in the solid
state and the consequences of weak intermolecular forces between
them on the 3D network structures. Single crystal structural anal-
ysis [55] confirmed the 3D supramolecular self-organization of
the organic salts formed between basic ligands (L1–3) and differ-
ent aliphatic and aromatic polycarboxylic acids. ORTEP plots of
these amphiphilic ligands (L1–3) are shown in Fig. 7a. We antici-
pated that the crystals was formed by slow evaporation of solvent,
constructed by strong charge assisted N–H· · ·O rather than less
energetically favorable N· · ·H–O interactions in neutral complexes.
The schematic representations of the hydrogen bond synthons and
non-bonded interactions in these ligands and their salts are listed
in Supporting information (Tables S1 and S2).
Fig. 4. (a) Stern–Volmer plot for the ligands-guest acid/derivatives complex and (b)
plot of log[(F − Fmin)/(Fmax − F)] vs. log the concentration of acid/anhydride, where
pyromellitic acid (1), pyromellitic anhydride (2), phthalic acid (3), phthalic anhy-
dride (4), malonic acid (5), PTSA (6) and oxalic acid (7).
Benzimidazole unit can act both as a hydrogen bond donor
and acceptor. In all three ligands the benzimidazole head group
is intermolecularly hydrogen bonded with the neighboring benz-
imidazole unit via strong N–H· · ·N hydrogen bond. The strength of
the hydrogen bond is almost comparable in all three cases. They
form an infinite hydrogen bonded 1D-chain along b axis and the
aromatic rings in the superstructures are arranged in an alternate
fashion along the 1D-chain (Fig. 7b). L1 and L3 also form weak
intermolecular C–H· · ·␲ non-covalent interactions in solid state,
where as similar type of interaction is absent in L2. Planar head
group in each of these molecules form a V-shaped pattern, which
propagates in a zigzag fashion (Supporting information, Fig. S20).
However, with increasing hydrophobic chain length, the thickness
of the hydrophobic layer has increased considerably, which in turn
separate the V-shaped hydrophilic layer to a greater extent. L2 and
L3 packed in the crystal lattice with distinct alternating hydropho-
bic and hydrophilic layer because of comparatively longer chain
length compared to L1 (Fig. 7c), where the hydrophobic layer is not
so prominent (Supporting information, Fig. S21).
constant values of these acids and their derivatives with L2 and L3
were also evaluated by fluorescence titration methods considering
the change in emission at ∼297 nm and showed similar trends to
those obtained for L1.
To investigate the binding interactions and stoichiometries of
the adduct formation in solution, we recorded 1H NMR of L1 and
its 1:1 adduct with pyromellitic acid in CD3OD (Fig. 5). In solu-
tion the carboxyl protons of pyromellitic acid have transferred to
the benzimidazole unit of the ligand molecule, resulting in the
formation of benzimidazolium-pyromellitate salts in which the
hydrogen-bonding donors and acceptors reside separately on the
cations and anions. The chemical shifts of four H atoms of ben-
zimidazole ring showed downfield shifts because of the cation
formation. Especially, the Bz-NH, Bz-5H, Bz-6H and methylene-CH
have shifts from 4.95 to 5.00, 7.47 to 7.52, 7.16 to 7.25 and 2.87
to 2.94 ppm, respectively. Surprisingly, the other methylene pro-
tons do not show any change in its chemical shift values thereby
indicating its non-involvement in adduct formation in solution.
The morphologies of the crystalline materials were recorded
using scanning electron microscope, and SEM images of the sam-
ples are given in Fig. 6. L1 alone shows the formation of micron sized
rectangular stacked plates (Fig. 6a) and at 1:1 ratio with pyromel-
Crystallization of L1–3 in presence of various organic acids
results in the formation of organic salts. Structural analysis of these
salts reveals that benzimidazole head group is mono protonated to
form cation while carboxylic acid is de-protonated to form anion,

B. Ojha, G. Das / Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
181
Fig. 6. (a–d) SEM images of microcrystalline L1 with various ratio between L1 and pyromellitic acid.
where the hydrogen bond donors and acceptors reside separately
on the cations and anions (Scheme 2), respectively. In the next sec-
tion we have described the crystal structures of the six salts formed
by the various combinations of basic amphiphilic ligands with dif-
ferent organic acids. The various types of non-bonded interactions
present in the salts are listed in Supporting information (Table S2).
[HL1]Malonate (Salt 1) crystallizes in monoclinic Cc space group
with mono de-protonated malonate in the crystal lattice (Fig. 8a).
In solid-state benzimidazolium cations and malonate anions are
self-assembled to form an infinite 1D N–H· · ·O hydrogen bonded
chain along the diagonal of ac plane. It also has C–H· · ·O interac-
tions in the solid state. Along b axis, HL1+ forms an inter-connecting
zigzag chain which leaves a hexagonal honey comb channel run-
ning through a axis (Supporting information, Figs. S22 and S14),
filled with a pair of malonate anions, while the alkyl chain of L1 is
clipping the pairs of anions together (Fig. 8a).
[HL1]p-Toluenesulphonate (Salt 2) crystallizes in orthorhom-
bic Fdd2 space group, where the protonated benzimidazole head
group forms strong N–H· · ·O hydrogen-bonding interactions with
sulphonate group (Fig. 8b). The infinite 1D hydrogen bonded chain
propagates along the diagonal of ac plane, while the methyl group
in the para position of the anion forms C–H· · ·␲ interactions with
␲-electron clouds of the cationic benzimidazole unit. Sulphonate
anion also forms C–H· · ·O non-covalent interactions with the neigh-
boring cationic head group of the ligand (Supporting information,
Fig. S23). The hydrophobic alkyl group of cations and tolyl group
of anions are packed in the same region of the crystal lattice and
formed a thick hydrophobic layer, where polar part of the anions
and cations are aligned in a thin layer that results in the formation
of a channel like architecture along a axis (Fig. 8b).
and two doubly de-protonated pyromellitate anions (Supporting
information, Fig. S16). Benzimidazole N–H proton forms strong
N–H· · ·O hydrogen bonds with the adjacent carboxylate group of
the anions. However, some of the N–H protons are involved in the
formation of two such types of hydrogen bonds simultaneously,
which results in the formation of a 2D hydrogen bonded sheet along
the diagonal of bc plane (Supporting information, Fig. S24). Here
the anions exits in a pair of pockets surrounded by the protonated
L1 (Fig. 9b) and the elliptical channel is running along c axis and
the adjacent pockets are separated by protonated ligands (Fig. 9b).
However, due to displacement of the aromatic rings, no ␲-stacking
interaction is observed in the solid state.
Unlike Salt 1, [HL2]Malonate (Salt 4) crystallizes in symmet-
ric triclinic P-1 space group, where mono de-protonated malonate
anion forms strong hydrogen bond at both ends, with both N–H of
the protonated ligand (Supporting information, Fig. S17). The salt
forms an infinite 1D hydrogen bonded chain along b axis, which
are interlinked among themselves via several C–H· · ·O interactions,
while the alkyl chains in the adjacent layers are oriented in an
opposite direction. The protonated ligand is stacked in a head-to-
head and tail-to-tail fashion and the alternate hydrophobic and
hydrophilic layers are formed in the crystal lattice (Supporting
information, Fig. S25).
Like Salt 3, [HL2]Pyromellitate (Salt 5) also crystallizes in triclinic
P-1 space group and the asymmetric unit contains four HL2+ cations
and two doubly de-protonated pyromellitate anions (Supporting
information, Fig. S18). The N–H protons of HL2+ cations form strong
N–H· · ·O hydrogen bonds with the adjacent carboxylate anions of
the acid, which results in the formation of a 2D hydrogen bonded
sheet (Supporting information, Fig. S26), where the pyromellitate
anions exits in a pair of hydrophilic pockets surrounded by the pro-
tonated ligands. This circular channel runs along c axis and the
[HL1]Pyromellitate (Salt 3) crystallizes in triclinic P-1 space
+
group, where the asymmetric unit contains four HL1 cations

182
B. Ojha, G. Das / Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
Scheme 2. Hydrogen-bond synthons of ligand (L1) with pyromellitic acid.
Fig. 7. (a) ORTEP plots of L1−3 with atom numbering scheme at 50% ellipsoids prob-
ability level and hydrogen atoms have been removed for simplicity; (b) 1D hydrogen
bonded chain in L1 and (c) packing diagram L3 with alternating hydrophobic and
hydrophilic layers.
adjacent pockets are oriented in a zigzag fashion (Fig. 9d). How-
ever, unlike Salt 3, the pyromellitate anions in Salt 5 are stacked
together through aromatic ␲–␲ interactions (3.638 Å).
Unlike Salt 2, [HL3]p-Toluenesulphonate (Salt 6) crystallizes in
monoclinic C2/c space group with a water molecule incorporated
in the asymmetric unit (Supporting information, Fig. S19), where
the protonated benzimidazole head group forms square hydro-
gen bonded networks through strong N–H· · ·O interactions with
sulphonate group of anions. The sulphonate anions also form strong
hydrogen-bonding interactions with water molecules (Supporting
information, Fig. S27). However, the methyl group in the para
position of the anion does not form C–H· · ·␲ interactions with ␲-
electron clouds of the cationic benzimidazole unit unlike Salt 2,
probably because of the increase in the alkyl chain length, which
hindered the approach of benzimidazole unit from the back side to
the anion. Similar to Salt 2, the hydrophobic part of both anions and
cations are stacked in the crystal lattice and form a thick hydropho-
bic layer (Supporting information, Fig. S19). Hydrophilic part of the
ligand aligned as a thin layer along a axis, which results in the for-
mation of hydrophilic channel similar to Salt 2. But, in this case
the channel is filled with water molecules. Overall the network
has several N–H· · ·O and C–H· · ·O interactions, where the anions
are oriented in the subsequent layers in a face-to-face and tail-to-
tail fashion. The increased hydrophobic chain length helps to form
Fig. 8. Packing diagram of (a) Salt 1 along c axis and (b) Salt 2 along c axis.

B. Ojha, G. Das / Journal of Photochemistry and Photobiology A: Chemistry 211 (2010) 176–184
183
Fig. 9. (a and b) Packing diagram of Salt 3 along c axis; (c and d) packing diagram of Salt 5 along a axis.
denser and thicker hydrophobic layer in the lattice as compared to
Salt 2 (Supporting information, Fig. S19).
signaling systems for other organic molecules are currently in
progress.
Acknowledgements
4. Conclusions
We thank CSIR (01-2235/08/EMR-II) and DST (SR/S1/IC-
01/2008), New Delhi, India for financial support. We also thank
DST-FIST for single crystal X-ray diffractometer facility. BO thanks
IIT Guwahati for the fellowship.
In summary, we have synthesized 2-alkyl benzimidazole ligands
of various chain lengths (L1–3) which are basic and electron-rich
molecules with intrinsic fluorescence property. We have found
that fluorescence properties of these ligands were highly affected
by organic acids to different extent. Fluorescence-quenching effi-
ciency of these molecules depends on the extent of electron
deficiency of the guest molecules coupled with their acidic nature.
Guest molecules having protected acid group with similar extent
of electron deficiency can also quench the fluorescence to a similar
extent. Electron-rich L1–3 can form strong intermolecular interac-
tions with aromatic acid bearing a stronger electron-withdrawing
group in solution. Thus, it has been suggested that fluorescence
quenching of these molecules is a cumulative effect of both
acid–base and aromatic interactions in solution. Solid-state struc-
tures of these molecules give a clue to the types of non-covalent
supramolecular interactions that play role in self-assembly. We
have also shown structurally, the formation of organic salts in
the solid state between these basic molecules (L1–3) and the dif-
ferent types of acid molecules. The 3D self-assembled structures
exhibit a number of weak non-covalent interactions in addition
to conventional hydrogen bonding. Additionally, this study shows
that benzimidazole unit is a good supramolecular building mod-
ule that can produce bimolecular co-crystals, and its modular
nature makes it possible to select a comfortable configuration
in the course of formation of hydrogen bonds with acids. As
expected, the N atom of benzimidazole ring always acts as an excel-
lent hydrogen-bonding donor or acceptor by the formation of a
strong O–H· · ·N or ionic N–H· · ·O hydrogen bond. In our labora-
tory designing of supramolecular architectures and fluorescence
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.jphotochem.2010.01.021.
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R
R
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R
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wR2 = 0.2146. Salt 4: C19H28N2O4, CCDC #736548; M = 348.43, triclinic,
a = 5.3488(4), b = 9.5569(7), c = 19.1994(16) Å, V = 963.43(13) Å3, space group P-
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R indices: R1 = 0.0607 [I > 2ꢂ(I)], wR2 = 0.1251; R indices (all data): R1 = 0.0942,
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a = 12.8838(4), b = 16.4270(5), c = 19.2316(5) Å, V = 4024.0(2) Å3, space group
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R1 = 0.0801, wR2 = 0.2440. Salt 6: C50H72N4O7S2, CCDC #736550; M = 905.26,
monoclinic, a = 16.2311(11), b = 9.0989(7), c = 36.055(3) Å, V = 5308.4(7) Å3,
space group C2/c, Z = 4, T = 298(2) K, ꢁ (Mo-K␣) = 0.148 mm−1, F(0 0 0) = 1912,
GOF = 1.0649; final R indices: R1 = 0.0659 [I > 2ꢂ(I)], wR2 = 0.2168; R indices (all
data): R1 = 0.0822, wR2 = 0.2332. The crystallographic data for the complexes
have been deposited with the Cambridge Crystallographic Data Centre. Copies
of this information may be obtained free of charge from the Director, CCDC,
12 Union Road, Cambridge, CB2 1EZ, UK (fax: +44 1223 336033, e-mail:
deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk).