Amidothiourea as a potential receptor for organic bases by resonance assisted low barrier hydrogen bond formation: Structure and Hirshfeld surface analysis

Article abstract of DOI:10.1039/c2ce06541j

The complexes (1-3) of an amidothiourea receptor L with three different types of organic bases have been synthesized, and their crystal structures were solved using single crystal X-ray diffraction data. A detailed structural analysis of the complexes reveals that the complexes are primarily stabilized by a strong hydrogen bonding interaction between the amide oxygen of the deprotonated receptor and N-H proton of the protonated bases. Close inspection of the hydrogen bond parameters of the complexes shows that the receptor significantly forms a low barrier hydrogen bond with imidazole and hexamine, whereas no obvious low barrier hydrogen bond has been found in case of triethylamine. The Hirshfeld surface and fingerprint plot analysis of the complexes have been carried out, and reveal that the complexes are stabilized O-H...O, C-H...O, N-H...S and N-H...O, hydrogen bonds. Additionally, the nitro groups of the receptor are involved in different types of charge transfer or electron donor acceptor interactions, which also have a prominent effect in the solid state stabilization of the complexes (1-3). The Royal Society of Chemistry 2012.

Full text of DOI:10.1039/c2ce06541j

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PAPER
Amidothiourea as a potential receptor for organic bases by resonance assisted
low barrier hydrogen bond formation: Structure and Hirshfeld surface
analysis†
*
Arghya Basu and Gopal Das
Received 17th November 2011, Accepted 15th February 2012
DOI: 10.1039/c2ce06541j
The complexes (1–3) of an amidothiourea receptor L with three different types of organic bases have
been synthesized, and their crystal structures were solved using single crystal X-ray diffraction data. A
detailed structural analysis of the complexes reveals that the complexes are primarily stabilized by
a strong hydrogen bonding interaction between the amide oxygen of the deprotonated receptor and
N–H proton of the protonated bases. Close inspection of the hydrogen bond parameters of the
complexes shows that the receptor significantly forms a low barrier hydrogen bond with imidazole and
hexamine, whereas no obvious low barrier hydrogen bond has been found in case of triethylamine. The
Hirshfeld surface and fingerprint plot analysis of the complexes have been carried out, and reveal that
the complexes are stabilized O–H/O, C–H/O, N–H/S and N–H/O, hydrogen bonds.
Additionally, the nitro groups of the receptor are involved in different types of charge transfer or
electron donor acceptor interactions, which also have a prominent effect in the solid state stabilization
of the complexes (1–3).
directly used as corrosion inhibitors and adhesion promoters.7,8
Introduction
These interesting features make organic bases important target
analytes for recognition in both the solid and solution state.
Strong hydrogen bonds appear in the literature under various
names such as ‘‘short-strong’’ hydrogen bonds (SSHB)9 or ‘‘low-
barrier’’ hydrogen bonds (LBHB).10 The formation of SSHB or
LBHB can stabilize intermediates and/or transition states of
enzymatic reactions.9b,11 The catalytic triad of a serine protease is
primarily governed by the formation of LBHB between aspartate
and histidine, which is present in the tetrahedral intermediate.12
In the LBHB structure the formal charges are dispersed between
the Asp-His residue relative to a localized Aspꢀ/H–His+
form.11a Therefore, it will always be a challenge to stabilize
histidine or imidazole in their low-barrier hydrogen bonding or
short-strong hydrogen bonding form.
Organic bases usually include amines and nitrogen-containing
heterocyclic compounds which are capable of accepting protons.
Amines are widespread in nature and are not often benign.
Amine recognition is of particular importance1 because both
aliphatic and aromatic amines can induce toxicological responses
at low concentrations.2 Aliphatic amines are found in many
waste water effluents from industry, agriculture, pharmaceuti-
cals, and food processing,3 and their easy detection and separa-
tion are valuable for environmental4 and industrial monitoring,
food quality control, etc.5 Nitrogen containing heterocyclic
compounds such as imidazole are important alkaloids present in
a large number of natural products and pharmacologically active
molecules. The imidazole ring is present in amino acid histidine
and also in its decarboxylated form histamine. It also acts as
a ligand toward transition metal ions in a number of biologically
important molecules.6 The substituted imidazole derivatives and
benzimidazole are well known in the treatment of many systemic
fungal infections. Imidazole and some of its derivatives are
Amidothiourea compounds have attracted considerable
attention recently as they function as selective colorimetric and
fluorescent anion sensors through hydrogen bonding complex
formation or by deprotonation of the one N–H proton of the
thiourea group.13 Moreover, reports on the recognition of
organic bases by using the highly acidic N–H protons of ami-
dothiourea type compounds have not yet been reported. Herein
we explore the complexation behavior of an amidothiourea
based receptor L with different organic bases both in the solid
and solution state (Scheme 1). A detailed crystal structure
analysis of the complexes reveals that resonance assisted strong
hydrogen bond formation between the acidic receptor (L)
and basic guests plays a key role toward stabilization of the
Department of Chemistry, Indian Institute of Technology Guwahati,
Guwahati, 781039, Assam, India. E-mail: gdas@iitg.ernet.in; Fax: +91
03612582349; Tel: +91 361 258231
† Electronic supplementary information (ESI) available: 1H and 13C
NMR, ESI-MS and FT-IR specta, synthesis and figures. CCDC
reference numbers 814617, 818087 and 844827. For ESI and
crystallographic data in CIF or other electronic format see DOI:
10.1039/c2ce06541j
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Synthesis of complex 1
Upon addition of an equimolar imidazole solution (in CHCl3) to
the suspended solution of the receptor in the same solvent, the
colorless suspended solution of the receptor instantly turns
orange and a dark orange precipitate starts to appear. The
precipitate was collected by filtration, washed 2–3 times with
CHCl3, and finally dried in vacuum over silica gel (yield 81%).
1
Mp 162 ꢁC, H-NMR(400 MHz, d6-DMSO) d (ppm): 10.17(s,
1N–H), 10.00(s, 1N–H), 9.12(s, 2H), 8.98(s, 1H), 7.95(m, 2H),
7.85(d, 1H) 7.79(s, 1H), 7.55(d, 3H), 7.41(s, 1H) and 7.086(s, 2H).
13C-NMR(100 MHz, d6-DMSO) d (ppm): 120.79, 121.24, 123.36,
125.29, 125.90, 126.79, 127.82, 130.46, 133.58, 134.9, 135.43,
136.26, 147.82, 161.89, and 181.16. IR (KBr, cmꢀ1): 3341(N–H),
3105(N–H), 1543(C]0) and 718(C]S). ESI mass spectrometry:
411.06 and 822.15.
Scheme 1 Structure of the receptor and three different organic bases.
receptor–guest complexes in the solid state. Furthermore, close
inspection of the crystal structure of the receptor–guest
complexes reveals that the receptor L forms a low-barrier
hydrogen bond with imidazole and hexamine, where as in the
case of triethylamine the receptor guest hydrogen bond is beyond
the range of the low barrier hydrogen-bond.
Synthesis of complex 2
Same as complex 1. Mp 163 ꢁC, 1H-NMR (400 MHz, d6-
DMSO) d (ppm): 10.19(s, 1N–H), 9.9(s, 1N–H), 9.08(s, 2H),
8.92 (s, 1H), 7.97(m, 2H), 7.82(d, 1H) 7.79(s, 1H), 7.55(m, 2H),
7.48(s, 1H) and 4.51(s, 12H). IR (KBr, cmꢀ1): 3425(N–H),
1547(C]0) and 780(C]S). ESI mass spectrometry: 411.06 and
822.15.
Experimental
All reagents were obtained from commercial sources and used as
received. Solvents were distilled freshly following standard
procedures.
Synthesis of complex 3
Same as complex 1. Mp 168 ꢁC, 1H-NMR (400 MHz, d6-DMSO)
d (ppm): 9.94(s, 1N–H), 9.69(s, 1N–H), 9.16(s, 2H), 8.78(s, 1H),
7.96(m, 2H), 7.82(d, 1H) 7.70(s, 1H), 7.54(m, 3H), 2.94(q, 2H)
and 1.13(t, 3H). IR (KBr, cmꢀ1): IR (KBr, cmꢀ1): 3339(N–H),
3108(N–H), 1547(C]0) and 714(C]S). ESI mass spectrometry:
411.06 and 822.15.
Instrumentation
The IR spectra were recorded on a Perkin Elmer-Spectrum One
FT-IR spectrometer with KBr disks in the range 4000–400 cmꢀ1
.
UV-Vis spectra were recorded with Perkin-Elmer Lambda-25
UV-Vis spectrophotometer. NMR spectra were recorded on
a Varian FT-400 MHz instrument. The chemical shifts were
recorded in parts per million (ppm) on the scale using a solvent
peak as reference. ESI-MS spectra were recorded in WATERS
LC-MS/MS system, Q–Tof Premier at the Central Instrument
Facility (CIF) of IIT Guwahati.
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-Ka radiation (l ¼ 0.71073 A) at 298 K, with
increasing u (width 0.3ꢁ per frame) at a scan speed of 6s/frame.
The SMART software was used for data acquisition. Data
integration and reduction were undertaken with SAINT and
XPREP software.14 Multi scan empirical absorption corrections
were applied to the data using the program SADABS.15 The
structures were solved by direct methods using SHELXS-97 and
refined with full-matrix least-squares on F2 using SHELXL-97.16
All non-hydrogen atoms were refined anisotropically. Hydrogen
atoms attached to all carbon atoms were geometrically fixed
while the hydrogen atoms connected to the nitrogen atom were
located from the difference Fourier maps. All X–H bonds were
subsequently normalized with standard neutron diffraction
values and the positional and temperature factors were refined
isotropically. The structural illustrations were drawn with
ORTEP-317a and MERCURY17b Windows. A summary of the
crystal data and relevant refinement parameters are given in
Table 1. CCDC 814617 (1), 818087 (2) and 844827 (3) are con-
tained the supplementary crystallographic data for this paper.†
These data can be obtained free of charge from the Cambridge
Synthesis of the compounds
Synthesis of receptor L
Receptor L was easily synthesized by stirring 4-(1-naphthyl)-3-
thiosemicarbazide 0.217 g (1 mmol) in presence of 3,5–dini-
trobenzoyl chloride 0.230 g (1 mmol) in dry CHCl3 for 6 h. The
precipitate was collected by filtration, washed 2–3 times with cold
EtOH, and finally dried in vacuum over silica gel (yield 87%). Mp
ꢁ
1
169 C, H-NMR (400 MHz, d6-DMSO) d (ppm): 11.45(s, 1N–
H), 10.21(s, 1N–H), 10.04(s, 1N–H), 9.14(s, 2H), 9.024(s, 1H),
7.95(m, 2H), 7.88(d, 1H) 7.54(d, 3H) and 7.40(s, 1H). 13C-NMR
(100 MHz, d6-DMSO) d (ppm): 121.46, 123.68, 125.48, 126.12,
126.633, 127.13, 127.97, 128.25, 130.75, 133.78, 135.55, 148.04,
162.88, and 182.69. IR (KBr, cmꢀ1): 3277(N–H), 3099(N–H),
1544(C]0) and 784(C]S) ESI mass spectrometry: calcd for
412.07. [M + H+]; found 412.07 [M + H+].
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Table 1 Crystal data and structure refinement parameters for complexes (1–3)
Compound
Complex 1
Complex 2
Complex 3
Formula
C22H21N7O6S
511.53
Triclinic
P-1
9.1908(5)
11.6347(6)
12.4736(7)
100.591(4)
111.361(3)
101.380(4)
1169.06(11)
2
C24H27N9O6S
569.61
Monoclinic
P21/c
8.3350(7)
12.3287(10)
25.638(3)
90.00
100.345(7)
90.00
2591.7(4)
4
298(2)
0.185
1.460
C24H28N6O5S
512.59
Monoclinic
P21/c
12.6988(14)
15.4250(18)
14.7893(18)
90.00
118.108(8)
90.00
2555.3(5)
4
298(2)
0.174
1.322
Formula weight
Crystal system
Space group
ꢀ
a/A
ꢀ
b/A
ꢀ
c/A
a (ꢁ)
b (ꢁ)
g (ꢁ)
ꢀ
V (A)
Z
T/K
m/cmꢀ1
dcal (g cmꢀ3
298(2)
0.193
)
1.453
0.32 ꢂ 0.29 ꢂ 0.27
Cryst dimensions (mm3)
No. of reflns collected
No. of unique reflns
No. of params
R1; wR2(I > 2s(I))
R(int)
0.31 ꢂ 0.26 ꢂ 0.23
0.30 ꢂ 0.26 ꢂ 0.24
5875
5752
343
6440
6410
362
6402
6385
333
0.0511, 0.1669
0.0897
0.875
0.0498, 0.1709
0.1278
0.906
0.0541, 0.2588
0.1127
0.958
GOF (F2)
CCDC No.
814617
818087
844827
Crystallographic Data Centre via www.ccdc.cam.ac.uk/
data_request/cif.
Hirshfeld surface analysis
The Hirshfeld surfaces18,19 in the crystal structure are
constructed based on the electron distribution calculated as the sum
of spherical atom electron densities.20 For a given crystal structure
and set of spherical atomic electron densities, the Hirshfeld surface
is unique,21 and suggests the possibility of achieving both qualita-
tive and quantitative insight into the intermolecular interaction of
molecular crystals. The Hirshfeld surface surrounding a molecule is
defined by points where the contribution to the electron density
from the molecule of interest is equal to the contribution from all
the other molecules. For each point on that isosurface two
distances are defined: de, the distance from the point to the nearest
nucleus external to the surface, and di the distance to the nearest
nucleus internal to the surface. The normalized contact distance
(dnorm) based on both de and di, and the vdW radii of the atom,
given by eqn (1) facilitates effective detection of the regions of
particular importance to intermolecular interactions.18 The value of
dnorm is negative or positive when intermolecular contacts are
shorter or longer than vdW separations, respectively. Because of
the symmetry between de and di in the expression for dnorm, where
two Hirshfeld surfaces touch, both will be marked with a red spot
identical in color intensity as well as size and shape. The combi-
nation of de and di in the form of a 2D fingerprint plot22 gives
detailed information of intermolecular interactions in the crystal.18
The Hirshfeld surfaces are mapped with dnorm, and 2D fingerprint
plots presented in this paper were generated using Crystal
Explorer 2.1.23
di ꢀ rivdw de ꢀ revdw
Fig. 1 (a) Molecular structure of the receptor–imidazole complex (1)
with an atom numbering scheme. (b) Intermolecular dimeric hydrogen
bonding interaction between two receptors in complex 1. Nonacidic
hydrogens and a solvent molecule are omitted for clarity.
dnorm
¼
þ
(1)
rivdw
revdw
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receptor exits in its deprotonated form and the hexamine is
present in its mono-protonated form and the complex is princi-
pally stabilized by low barrier hydrogen bond formation10 (N6–
Results and discussion
The structure of complex 1 was established unambiguously by
X-ray diffraction of single crystals. Orange color block shaped
crystals of the receptor-imidazole complex were grown by slow-
driven crystallization from dilute solution of acetonitrile and
methanol mixture (8 : 2). It crystallized in the space group P-1
with Z ¼ 2. The structure determination shows that the receptor
and imidazole formed 1 : 1 complex stoichiometry with a crys-
tallized methanol molecule, and the complex is principally
stabilized by a low barrier hydrogen bond10 formation (N6–H/
ꢀ
H/O1 distance 2.651(4) A) between the deprotonated receptor
and the protonated hexamine (Fig. 2a). This hydrogen bond is
comparative larger than complex 1, presumably the cage likes
bulky structure of hexamine. The CH protons of hexamine unit
and the oxygen atoms of the nitro group of the next receptor
molecule forms two different types of ring motifs R22(6) and R22(8)
through C–H/O hydrogen bonds (Fig. 2b). Additionally, the
lattice water molecule and protonated hexamine forms R22(6) ring
motif by the participation of C23–H23A/O6 and C21–H21A/
O6 hydrogen bonds. This ring motif is further attached to the
next hexamine unit through O6–H20/N8 hydrogen bond and
eventually forms hexamine (protonated)–water–hexamine
(protonated) one-dimensional chain along the a-axis (Fig. 2c).
Two deprotonated receptor molecules form a R22(11) ring motif
(Fig. 2b) by the involvement of C5–H/O1 and C6H/O2
hydrogen-bonds which subsequently form 1D polymeric exten-
sion along the b-axis (ESI, Fig. S19).† In association with
significant lone-pair/p interactions between the oxygen atom of
the nitro group (O3) and the napthyl ring of the next receptor,
a molecule is observed with a notable O3/centroid distance
ꢀ
O1 distance 2.622(4) A) between the deprotonated receptor and
the protonated imidazole (Fig. 1). The crystallized methanol
molecule forms a strong hydrogen-bond (O6–H6O/O1) with
the amide oxygen atom (O1) of the deprotonated receptor
accompanied by a weak interaction (C19–H19/O6) with acidic
C19–H19 proton of protonated imidazole ring. These two
interactions lead to the formation of a dimeric ring R66(14)
between two nearby complex molecules, where the two crystal-
lized methanol molecules play a bridging role (ESI, Fig. S14).†24
In addition to that, two deprotonated receptors form centro-
symmetric dimer R22(8) by the participation of two N(2)–H/S(1)
hydrogen bonds (Fig. 1b). Interestingly, the nitro groups of the
receptor are involved in different types of charge transfer inter-
actions including a lone-pair/p interaction which provides
added stabilization to the receptor imidazole complex.25–28 In this
regard recently Gilli and co-worker nicely explained in detail the
electron donor acceptor interactions involving nitro groups in
a series of picric acid complexes with different nitrogen con-
taining bases.29
ꢀ
3.326 A (ESI, Fig. S20).†
The crystals of complex 3 were obtained from dilute acetoni-
trile solution as a red thin block crystallizing in P21/c space
group. The asymmetric unit contains one molecule each of the
receptor and triethylamine. The molecular structure of the
complex 3 is shown in Fig. 3(a) along with proper atom
numbering. Similar to complexes 1 and 2 here also the amide N–
H proton of the receptor undergoes deprotonation by triethyl-
amine. Interestingly, the hydrogen bond distance between the
protonated triethylamine and the deprotonated receptor is quite
high as compared to complexes 1 and 2 and is beyond the low
barrier hydrogen bonding range. This is probably due to the
higher pKa value of triethylamine as compared to imidazole and
Crystals of complex 2 were grown by isothermal slow evapo-
ration of dilute acetonitrile solution. It crystallized in the space
group P21/c with Z ¼ 4. The asymmetric unit is composed of one
unit each of receptor and hexamine molecules along with
a crystallized water molecule. Similar to complex 1 the crystal
structure of the hexamine receptor complex reveals that the
Fig. 2 (a) Molecular structure of the receptor–hexamine complex with an atom numbering scheme. Non-acidic hydrogen atoms are removed for clarity
(b) A perspective of different hydrogen bonding synthons in complex 2. (c) Hexamine (protonated)–water–hexamine(protonated) one dimensional
hydrogen bonding chain along the a-axis. Non interacting hydrogens are removed for clarity.
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intensity indicating the relative strength of the interactions. Two-
dimensional fingerprint plots complement these surfaces, quan-
titatively summarizing the nature and type of intermolecular
contacts experienced by the molecules in the crystal. The two-
dimensional fingerprint plots can also be broken down to give the
relative contribution to the Hirshfeld surface area from each type
of interactions present, quoted as the ‘‘contact contribution’’.30
The Hirshfeld surfaces of the title complexes are illustrated in
Fig. 4, showing surfaces that have been mapped over dnorm (ꢀ0.5
ꢀ
to 1.5 A). It is clear that the information present in Table S3
(ESI)† is summarized effectively in these spots, with the large
circular depressions (deep red) visible on the surfaces indicative
of strong N–H/O interactions.
In the case of complex 1 The N–H/O intermolecular
interactions appear as two distinct spikes in the 2D fingerprint
plots (Fig. 4a). The proportion of O/H/H/O interactions
comprises 23.4% of the total Hirshfeld surfaces. The O/H
interactions are represented by a sharp large spike (di ꢀ 0.976
and de ꢀ 0.626) in the fingerprint plot (Fig. 4b), indicating the
formation of a low barrier hydrogen bond with protonated
imidazole along with a moderate hydrogen bond with the
solvent (methanol) molecule. The H/O interactions are rep-
resented by a comparatively small spike (di ꢀ 1.067 and de ꢀ
1.367), these oxygen-based interactions represent the closest
contacts in the structures and can be viewed as three dark red
spots on the dnorm surface (Fig. 4). Beside this dark spots the
presence of faint red spots of the Hirshfeld surface can be
assigned to S/H/H/S interactions with two moderate spikes
ꢀ
having (de + di) z 2.7 A. The proportion of S/H interactions
comprises 7.5% of the total Hirshfeld surfaces. This comprising
is due to the formation of the centrosymmetric dimer through
N(2)–H/S(1) hydrogen bonds between two deprotonated
receptor molecules along with the S/H–N(7) hydrogen bond
interaction of the protonated imidazole. Apart from that the
presence of significant C–H/p interactions is observed, with
C/H close contacts contributing 22.1% of the total Hirshfeld
Fig. 3 (a) Molecular structure of the receptor–triethylamine complex
with a proper atom numbering scheme. Non-acidic hydrogen atoms are
removed for clarity. (b) Intermolecular centrosymmetric dimeric
hydrogen bonding interaction between two receptors in complex 3.
surfaces. The H/H interactions also have
a significant
contribution towards the solid state stabilization of complex 1.
It contributes 19.6% of the total Hirshfeld surfaces and is
reflected in the distribution of scattered points in the 2D
fingerprint plot. The inspection of contacts between other atom
types pointed out that there are also specific features in the C/
O/O/C fingerprint plot for complex 1. The plot shows the
characteristic ‘‘wings’’ in the upper left and lower right of the
hexamine. Here also the two deprotonated receptors form
a centrosymmetric dimer R22(10) through a pair of N(2)–H/O(1)
hydrogen bonds. Additionally the deprotonated receptors also
form one dimensional polymeric chain along the b-axis via C–
H(nap)/O(nitro) hydrogen bond (ESI, Fig. S24).† In both
complexes 1 and 2 the receptors are completely planar but,
interestingly, in complex 3 the deprotonated receptor is not
planar, the dinitro phenyl ring is twisted slightly relative to the
napthyl ring, the angle between the planes of the two rings is
27.54ꢁ (ESI, Fig. S22).†
ꢀ
plot with (de + di) z 3.1 A. These correspond to lone-pair
(oxygen atoms of the nitro groups)/p interactions and
significantly cover 8.9% of the total Hirshfeld surfaces
(Table S3).†
Fig. 4(a) displays the Hirshfeld surfaces mapped with dnorm for
the receptor segments in complex 2. Similar to complex 1, the N–
H/O intermolecular interactions appear as two distinct spikes in
the 2D fingerprint plots and the proportion of O/H/H/O
interactions is covering 25.7% of the entire Hirshfeld surfaces. The
strong O/H hydrogen bond interactions between the protonated
hexamine unit and the deprotonated receptor molecule is repre-
sented by a sharp large spike (di ꢀ 1.000 and de ꢀ 0.641), whereas
H/O interaction is represented by a spike (di ꢀ 0.841 and de ꢀ
1.192) in the bottom left region of the fingerprint plot, indicating
a hydrogen bonding interaction between the N(2)–H proton of the
It is worth mentioning here that we also tried to crystallize the
receptor molecule in presence of other different basic guests
having different pKa values, but despite our several attempts we
were unable to grow good quality single crystals from them.
The contribution of the strong N–H/O hydrogen bonds in
the above described complexes can also be visualised by the
Hirshfeld surfaces, which is a useful tool for describing the
surface characteristics of the molecules.20 Hirshfeld surfaces
facilitate a novel method of visualizing intermolecular interac-
tions by colour-coding short or long contacts, the colour
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Fig. 4 (a) Hirshfeld surface analysis of the receptor segments in complexes 1, 2 and 3. (b) Two-dimensional fingerprint plots with the N–H/O
interactions highlighted in color.
respectively (Table S3).† The other significant interaction present
in complex 2 is the lone pair/p interaction, involving the oxygen
atoms of the nitro groups and the p electron cloud of the aromatic
rings. The proportion of C/O/O/C interactions comprising
7.1% of the total Hirshfeld surfaces and the fingerprint plot shows
characteristic ‘‘wings’’ in the upper left and lower right of the plot
with pseudosymmetry on either side of the diagonal where de ¼ di.
The Hirshfeld surfaces mapped with dnorm for the deproto-
nated receptor segments in the supramolecular complex 3 are
illustrated in Fig. 5(a). Similar to complexes 1 and 2, here also the
significant N–H/O intermolecular interactions appear as two
distinct spikes in the 2D fingerprint plots and the proportion of
O/H/H/O interactions contributing 28.7% of the total
Hirshfeld surfaces (Table S3).† The O/H interactions are rep-
resented by a sharp large spike (di ꢀ 0.976 and de ꢀ 0.626) in the
finger print plot, indicating the existence of a strong hydrogen
bond between the protonated triethylamine and the deproto-
nated receptor along with a centrosymmetric dimeric interaction
between two deprotonated receptors involving amide oxygen and
Fig. 5 UV-Vis titration profile of the receptor (4.6 ꢂ 10ꢀ5M) upon an
the N(2)–H proton of the thiourea group. Whereas H/O
incremental addition of (a) imidazole (1.05 ꢂ 10ꢀ1 M), (b) hexamine
(8.2 ꢂ 10ꢀ2 M), (c) triethyl amine (1.25 ꢂ 10ꢀ2 M), (d) tetrabutylammo-
nium hydroxide (5 ꢂ 10ꢀ3 M).
interaction is represented by a spike (di ꢀ 0.841 and de ꢀ 1.192) in
the bottom left region of 2D fingerprint plot. These oxygen-based
interactions can be visualized as three dark red spots on the dnorm
surface. Besides these hydrogen bonding interactions the C/H
close contacts and H/H interactions have also contributed
18.3% and 25.7% of the total Hirshfeld surfaces, respectively. As
compared to complexes 1 and 2 the C/O/O/C interaction
comprising less contribution in complex 3. It only covers 3.3% of
the total Hirshfeld surfaces. This suggests that in complex 3 the
thiourea group and the water molecule. These oxygen-based
interactions can be viewed as a pair of dark red spots on the dnorm
surface. Additionally in complex 2 the C–H/p close contact and
H/H comprises 14.2% and 26.6% of the total Hirshfeld surfaces,
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lone pairs of the oxygen atoms of the nitro groups are compar-
atively less involved in the lone pair/ p interactions.
We have looked at the effect on the UV-Vis spectra, recorded
in acetonitrile (CH3CN), of various structurally different organic
bases. The addition of organic bases to a solution of receptor L
has a profound effect on the electronic spectra. Upon incre-
mental addition of different organic bases the UV-Vis spectra of
L show the growth of absorbance at 433 nm with a generation of
a new band at 335 nm (Fig. 5). The change in the absorption
spectra at 433 nm could be applied to detect the receptor-organic
bases interaction process by the naked eye (ESI, Fig. S25).† The
colourless receptor instantly forms orange coloured complexes
upon addition of different bases. For the quantitative analysis of
the receptor–guest association in solution, the spectrophoto-
metric absorbance changes were treated by the Benesi–Hilde-
brand procedure. On the basis of the change in absorbance at
433 nm associated with gradual addition of the bases, the asso-
ciation constant of the studied organic bases was calculated.31
The calculated binding constants along with the pKa value of the
guest amines are given in Table 2. The deprotonation tendencies
of amidothiourea type of compounds in presence of basic anions
such as fluoride, acetate, etc, are quite common in literature.13c,e
Therefore, the spectral change of the receptor L upon addition of
different organic bases might be a deprotonation phenomenon,
which is readily verified by titrating the receptor L with OHꢀ
(tetrabutylammonium hydroxide) in acetonitrile (Fig. 5d).
However, the titration profile is exactly similar to that observed
for organic bases. As the spectral change is due to the amine
induced deprotonation of the receptor, therefore, the compara-
tively higher binding constant of triethylamine can be attributed
to the higher basicity (pKa value) of triethylamine as compared to
imidazole and hexamine.
Fig. 6 (A) 1H-NMR spectrum of receptor L in d6-DMSO. (B) 1H–NMR
spectrum of complex 1 in d6-DMSO at 298 K.
deprotonation of amide N–H of the receptor is due to the close
proximity of the highly electron deficient 3,5-dinitrophenyl ring
and the greater electron negativity of the oxygen than sulfur
make the amide N–H proton more acidic as compared to N–H
protons assigned to the thiourea part present in the receptor L.
Comparative 1H-NMR spectra of the free receptor and
receptor–imidazole complex are shown in the Fig. 6, where the
1H-NMR spectra of complexes 2 and 3 are given in the ESI
(Fig. S9 and S1).† The significant disappearance of amide N–H
proton signal in all the complexes convincingly ascertains that
the position of the amide N–H proton is not the same as the free
receptor. Furthermore, it is well known in literature that the
formation of a strong hydrogen bond can be assigned far
downfield 1H-NMR chemical shift in the N–H proton, but we are
unable to assign any signal corresponding to the formation of
a strong hydrogen bond in the case of complexes 1 and 2. These
results indicate that in solution the receptor is present in its
deprotonated anionic form and the guests (imidazole and hex-
amine) are present in their protonated cationic form and there is
no significantly strong hydrogen bond present between the
deprotonated receptor and the protonated guests (imidazole and
hexamine) in solution.
The nature of the interaction between receptor L and the
organic bases has also been confirmed by the 1H-NMR titration
of receptor L with imidazole in d6-DMSO (ESI, Fig. S26 and
S27).† We have chosen imidazole instead of other organic bases
because the solid state crystal structure of the complexes shows
that the receptor forms the strongest hydrogen bond with imid-
azole. The disappearance of amide N–H proton resonance occurs
at d ¼ 11.45 ppm with as little as 0.1 equiv of the imidazole
present. This is probably due to imidazole inducing deprotona-
tion of the amide N–H proton of receptor L. Consequently, the
deprotonation process was been confirmed by monitoring the
almost similar spectral changes of receptor L in presence of OHꢀ
(tetrabutylammonium hydroxide) (ESI, Fig. S27).†
The ESI-mass spectrum in a positive ion mode of complexes in
acetonitrile is well consistent with the 1H-NMR experiment (ESI,
Fig. S7).† The signal at m/z ¼ 411.06 indicates that the receptor is
present in its deprotonated anionic form. However, the
signal corresponding to m/z ¼ 822.15 clearly demonstrates the
1
Interestingly, the results from H-NMR experiments suggest
an imidazole induced deprotonation of amide N–H proton of the
receptor, which is quite unusual for amidothiourea type of
compounds. Generally one N–H proton of thiourea groups
undergoes deprotonation in presence of basic guests.13c,e The
formation of
a dimeric interaction between two anionic
receptor molecules.The detail ESI-mass spectra analysis of the
complexes also supports the formation of stable charge separated
species in solution. The absence of any signal corresponding
to the receptor–guest complex indicates that there is no appre-
ciably strong hydrogen bonding interaction present between
the deprotonated receptor and the protonated guests in
solution. Probably the efficient solvation of cationic
guests prevents it from forming a strong hydrogen bonding
adduct with the deprotonated receptor, although it is quite
prominent in their solid state crystal structure of complexes 1
and 2.
Table 2 Binding constants of the receptor with the studied organic bases
Binding constant
(Mꢀ1
)
Guest
pKa
Imidazole
Hexamine
Triethyl amine
6.8
6.4
10.75
506
498
1056
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This journal is ª The Royal Society of Chemistry 2012

View Article Online
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Conclusions
We have demonstrated the detailed complexation behavior of an
amidothiourea based receptor L with different organic bases
such as imidazole, hexamine and triethylamine both in the solid
and solution state. In presence of basic guests the amide N–H
proton of receptor L undergoes deprotonation. A thorough
structural investigation of the complexes reveals that the strong
hydrogen bonding interaction between the amide oxygen of the
deprotonated receptor and N–H hydrogen of the protonated
guest plays a key role towards the stabilization of the receptor–
guest complexes in the solid state. Close inspection of the
hydrogen bond parameters of the receptor–guest complexes
reveals that the receptor significantly forms low barrier hydrogen
bonds with imidazole and hexamine, whereas no obvious low
barrier hydrogen bond has been found in case of triethylamine.
The Hirshfeld surface and fingerprint plot analysis provide
a rapid quantitative insight into the intermolecular interactions
in complex molecular solids. The Hirshfeld surfaces and finger-
print plots prove to be particularly suitable for comparing the
molecular environments in the title structures. The Hirshfeld
surface and fingerprint plot analysis of the complexes show that
close contacts are dominated by O/H, H/H and C/H
contacts and these relatively weak interactions have prominent
signatures in the fingerprint plots.
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Finally, it is worth mentioning that apart from the strong
receptor guest hydrogen bonding interactions in complexes 1 and
2 the oxygen atoms of the nitro groups of the receptor are
actively involved in lone-pair/p interactions, whereas no
significant lone-pair/p interaction is observed in the case of
complex 3. This is also reflected in the Hirshfeld surface analysis
of the C/O close contact contribution of complexes (1–3).
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Acknowledgements
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single crystal X-ray diffraction facility. A.B. thanks IIT
Guwahati for fellowship.
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31 The binding constants of the amine guests with receptor L were
calculated by plotting [1/(A ꢀ A0)] as a function of the inverse of
amine (guest) concentration fits a linear relationship, indicating 1 : 1
stoichiometry of receptor/amine complex. The ratio for the intercept
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in the absence of guest, A is the absorbance recorded in the
presence of added guest.
3314 | CrystEngComm, 2012, 14, 3306–3314
This journal is ª The Royal Society of Chemistry 2012