Synthesis and structural X-ray analysis of 1,1'-(naphthalene-1,8-diyl)-3, 3'-dibenzoyl-bisthiourea and its use as anion-binding receptor

Article abstract of DOI:10.3906/kim-1201-12

A novel artificial receptor, 1,1'-(naphthalene-1,8-diyl)-3,3'-dibenzoyl- bisthiourea, based on a 1,8-naphthalene skeleton bearing bisthiourea groups was prepared and characterized by IR and ¹H-NMR, ¹³C-NMR, and MS spectroscopic techn

Full text of DOI:10.3906/kim-1201-12

Turk J Chem
36 (2012) , 764 – 777.
¨
˙
c
ꢀ TUBITAK
doi:10.3906/kim-1201-12
Synthesis and structural X-ray analysis of
1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea
and its use as anion-binding receptor
2
1
Fatma AYDIN1,∗, Nazan TUNOGLU , Dog˘an AYKAC¸
˘
Nahide Burcu ARSLAN3, Canan KAZAK3
1Department of Chemistry, C¸anakkale Onsekiz Mart University, TR-17100, C¸anakkale-TURKEY
e-mails: faydin@comu.edu.tr, dogan aykac@hotmail.com
2Department of Chemistry, Hacettepe University, 06532, Beytepe, Ankara-TURKEY
e-mail: nazan@hacettepe.edu.tr
3Department of Physics, Ondokuz Mayıs University, TR-55139 Kurupelit, Samsun-TURKEY
e-mails: nburcu@gmail.com, ckazak@omu.edu.tr
Received: 11.01.2012
A novel artificial receptor, 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea, based on a 1,8-naphtha-
lene skeleton bearing bisthiourea groups was prepared and characterized by IR and 1 H-NMR, 13 C-NMR,
and MS spectroscopic techniques. The compound proved to be an efficient and selective naked-eye detector
for the fluoride, cyanide, and hydroxide ions in DMSO. The crystal structure of the title compound was
examined by using X-ray crystallographic techniques and found to be crystallized in the monoclinic space
˚
˚
˚
group P − 1 with the unit cell parameters: a = 8.1556(8) A, b = 12.0127(11) A, c = 13.2081(11) A, α =
109.510(7)◦ , β = 95.390(7)◦ , γ = 103.660(7)◦ , Z = 2. The intramolecular N-H· · ·O hydrogen bonding
interactions between the N-H and the oxygen atom of C=O groups support a 1,1’-(naphthalene-1,8-diyl)-
3,3’-dibenzoyl-bisthiourea framework. Moreover, the combinations of N—H···S bonds produce R22 (8)rings.
Key Words: 1,1’-(Naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea, anion-binding receptor, crystal struc-
ture, bisthiourea
Introduction
Studies of N-aryl-N-benzoyl-thiourea compounds have attracted increasing attention due to their potential use
in agriculture for their insecticidal, herbicidal, and pesticidal activities;1−4 in medicine for their antibacterial
∗Corresponding author
764

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
and antimicrobial activities;5,6 and in analytical chemistry for extraction and separation.7,8 The bioactivities
of many acyl thiourea compounds have a promoting effect on plant growth.9 Furthermore, aroyl and acyl
thiourea derivatives are attractive model compounds for studies in solid-state chemistry due to their tendency
to form intra- and intermolecular hydrogen bonds of the N-H proton-donor groups to sulfur and carbonyl oxygen
atoms.10−13
Anions are of crucial importance in a range of biological, chemical, medical, and environmental processes.
Therefore, synthetic molecular receptors for anions have received considerable attention in recent years.14
These receptors are usually based on macrocyclic ammonium/guanidinium,15 amides,16 urea/thiourea,17−19
functionalized calixarenes,20 aromatics such as pyrroles,21 carbazoles and indoles,22 and phenylhydrazones.23,24
They exhibit such an obvious color change when anion is added that they can be detected by the naked eye
without the need to resort to spectroscopic instrumentation.25 Many synthetic receptors have been reported,
especially for F− anion in the presence of Cl− , Br− , and I− ions.26 Recently, among a variety of possible
hydrogen bond donor groups, systems employing thiourea moieties have been proven to be very efficient in the
design of neutral anion binding receptors.27,28
In this work, we present the synthesis (Scheme 1), X-ray analysis, and characterization and structural
analysis of 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea. Its structure was confirmed by several spec-
troscopic techniques, namely IR, 1 H-NMR, and 13 C-NMR spectroscopy and mass analysis. Its structure was
also confirmed by single crystal X-ray diffraction structural analysis. The location of the group on the bis-
thiourea moiety regarding intra- and intermolecular hydrogen bonding interactions between molecules in its
crystal structure has been discussed. In addition, this compound exhibited a distinct color change in the pres-
ence of fluoride anions, and showed no response to the other halide anions. It also responded to cyanide (CN−)
and hydroxide (OH−) ions.
NH2 NH2
O
O
S
C
S
NH
H
HN
H
S
KSCN
Cl
N
2
2
acetone
reflux
N
N
O
O
1
2
3
Scheme 1. Synthesis of 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea.
Experimental section
Apparatus
Melting points were measured on an Electro Thermal IA 9100 apparatus using a capillary tube. The 1 H- and
13 C-NMR spectra were obtained on a Bruker NMR spectrometer operating at 400 and 101.6 MHz. The UV-
Visible spectra were recorded using a Perkin-Elmer WinLab-25 series spectrophotometer with a quartz cuvette
(path length: 1 cm). Infrared absorption spectra were obtained by a Perkin Elmer BX II spectrometer as KBr
disks and were reported in cm−1 units. MS spectra were recorded on an Agilent 5973 Inert Mass Selective
Detector equipped with a direct insertion probe.
765

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
Reagents
All reagents for synthesis were obtained commercially and were used without further purification. In the
titration experiments, all the anions were added in the form of tetra-n-butylammonium (TBA) salts, which
were purchased from Merck Chemical Co. and Acros Organics, stored in a vacuum desiccator containing self-
indicating silica and fully dried before use. Dimethyl sulfoxide was dried with calcium hydride and then distilled
at reduced pressure.
Synthesis of the compound
A mixture of benzoyl chloride (2.32 mL, 20 mmol) and KSCN (1.94 g, 20 mmol) in 20 mL of acetone was
refluxed under stirring for 1 h; then a solution of 1.58 g (10 mmol) of 1,8-diaminonaphthalene in 20 mL of
acetone was added dropwise to benzoyl isothiocyanate over 0.5 h at ambient temperature. When the solution
was added completely, the resulting solution was then mixed for 5 h at ambient temperature and the progress
of the reaction was controlled by TLC. After the reaction was completed, the solution was poured into a beaker
containing an ice-water mixture. The white precipitate was filtered and washed with distilled water several
times and then dried under vacuum. Recrystallization of the crude product in tetrahydrofurane gave pure
colorless crystals.
Characterization
Analytical and spectral data
Yield: 3.85 g, 80%. colorless crystal, mp 222-224 ◦ C; IR (KBr pellet), (cm−1): 3394, 3186 (N − H), 3120,
3045 (Carom -H), 1685 (C = O), 1256 (N − C =S, thioureido), 712 (C = S); 1 H-NMR (CDCl3): δ ppm:
12.52 (s, 2H, N-H), 11.49 (s, 2H, N-H), 8.82-7.27 (8H, symmetric Ar-H); 13 C-NMR (CDCl3) δ ppm: 183.4
(C=S); 169.0 (C=O), 143.4, 133.7, 130.3, 129.3, 128.9, 126.7 (CAr.); MS (EI): (m/z) = 484 (M+1).
Absorption titration studies
All anions such as F− , Cl− , Br− , I− , CN− , and OH− were added in the form of tetrabutylammonium salts
to 5 × 10−5 M solutions of the title host compound in DMSO. The binding properties of the title compound
toward F− were explored with UV-Vis titration (Figure 3) and the 1 H-NMR experiment (Figure 4).
Results and discussion
The title compound, 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea, was characterized by MS analysis,
IR, and 1 H-NMR and 13 C-NMR spectroscopic techniques as well as single crystal X-ray diffraction analysis.
Spectroscopic studies
The IR spectrum of the title compound exhibited 2 N-H stretching bands at 3186 and 3394 cm−1 in the high
energy region. C-H stretching vibrations from aromatic groups such as phenyl and naphthalene are observed in
766

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
the 3120 and 3045 cm−1 range. In the 700-1700 cm−1 region, a strong absorbance band in the IR spectra of
the compound appears at about 1685 cm−1 , apparently decreasing in frequencies compared with the ordinary
carbonyl absorption (1700 cm−1). This is interpreted as being a result of its conjugated resonance with the
phenyl rings and the possible formation of hydrogen bonding with N-H. The strong bands observed at 1255 and
713 cm−1 were respectively assigned to thioureido N-C=S and C=S stretching vibrations29 (see Figure 7).
The experimental 1 H-NMR data of the title compound correspond to those of similar compounds.11−13
In the NMR spectra of the title compound, 2 signals were noted as singlets at 12.52 and 11.49 ppm, assigned
to the NH proton. The resonance values of the N-H protons are interpreted as being a result of conjugated
resonance with the carbonyl and thiocarbonyl, respectively. The resonance values of the aromatic protons for
naphthalene-1,8-diyl ring and phenyl rings were 8.82-8.05 ppm and 7.14-7.21 ppm as expected, respectively.
The most deshielded in the 13 C-NMR signals correspond to C=O and C=S groups. The carbon atom of
carbonyl appears at 169 ppm, while the carbon atom of thiocarbonyl appears at 183 ppm due to the lower
excitation energy π − π *. Formation of intramolecular hydrogen bonding, the increasing electronegativity of
oxygen and sulfur atoms, and different environments such as phenyl and naphthalene-1,8-diyl conformations
cause a deshielding effect for these signals. These data agree with the results reported by Arslan et al. 30
The mass spectral fragmentation pattern of the title compound is depicted in Scheme 2. Values of the
molecular ion peak at 484 and fragment ion peaks at 287, 244, 200, 164, and 105 confirmed the presence of
bisthiourea (see Figure 8).
+.
+.
+.
S
HN
O
S
S
NH
HN
O
m/z 164
m/z 244
C12H8N2S2
m/z 105
C7H5O
C8H6NOS
+.
+.
+.
S
S
NH HN
H
S
NH
H
HN
H
S
N
N
N
S
NH NH
O
m/z 287
C13H9N3S2O
O
O
m/z 200
C11H8N2S
m/z 484
C26H20N4O2S2
Scheme 2. The mass spectral fragmentation pattern of compound.
UV-Vis experiments
Firstly, the anion binding affinity of the present thiourea-based receptor was determined by UV-Vis absorption
spectroscopy in the absence and presence of different anions such as F− , Cl− , Br− , I− , CN− , and OH− (as
767

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
tetrabutylammonium salts). The experiment was performed by preparing 5 × 10−5 M solution of receptor in
DMSO solution followed by addition of particular tetrabutylammonium anionic salts separately. In the absence
of anions, the weak absorbance band at 287 nm was ascribed to π − π * transition of bisaroylthiourea. Upon
the addition of F− , CN− , and OH− to receptor, a prominent change was observed in UV-Vis absorption
spectra. In contrast, addition of an excess of tetrabutylammonium salt of Cl− , Br− , and I− did not cause
any notable spectrum changes (see Figure 1). The observed color changes in the presence of F− , OH− , and
CN− also could be detected by the naked eye (see Figure 2). Secondly, hydrogen binding ability of the receptor
for F− was investigated by UV-Vis spectrometry in DMSO using a constant host concentration (5 × 10−5
M) and increasing concentrations of the F− (0–5 equivalence). The UV-vis spectrum of the receptor (5 ×
10−5 M) in DMSO had a characteristic absorption peak at 287 nm. With the addition of more and more
doses of fluoride ions, the color of the receptor solution changed from colorless to yellow; at the same time, the
intensity of the absorbance band at 287 nm decreased gradually and that of the absorbance band at 335 nm
increasing gradually (see Figure 3). Obviously, a distinct isosbestic point at 308 nm was observed during the
titration process between the receptor and F− ion, which clearly indicated the formation of complex between
receptor and F− ion.26 By increasing the fluoride ion concentrations, the corresponding changes in absorbance
intensities at 335 nm were plotted against anion concentrations. The binding constant of the complex formed
between receptor and F− ion was calculated by nonlinear fitting of the spectroscopic titration curve31 as log
Kass 3.95
0.13 (Figure 3).
2.10
2.0
Host 3
1.8
Cl-
1.6
Br-
I-
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0.00
OH-
CN-
F-
A
260.0 280
300
320
340
360
380
NM
400
420
440
460
480
500.0
Figure 1. UV-vis spectra of 3 (5 × 10−5 mol L−1) after addition of different anions (none, F− , Cl− , Br− , I− , CN−
,
OH−) in DMSO.
1 H-NMR experiments
There are 2 kinds of NH proton signals for the free compound, designated as CONH (12.51 ppm) and CSNH
(11.49 ppm) (as shown in Scheme 1 and Figure 4). The hydrogen binding of F− ion to the free compound
768

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
was investigated by monitoring the changes in the 1 H-NMR spectra of DMSO-d6 solution of the receptor upon
addition of F− (1, 2 equiv.). The thiourea N–H signals at 12.51 and 11.49 ppm disappeared with the addition
of 1.0 equiv. F− ion solution and a new broad and small band at 10.88 ppm appeared. However, this new band
completely disappeared with the addition of 2.0 equiv. of the ion solution (Figure 4). The results indicate that
there are 2 steps in anion recognition: anion hydrogen bonds with receptor and deprotonation of it takes place
due to fluoride ion, which is a strong base with a high charge density and small size.32
Figure 2. Color changes in 3 (5 × 10−5 mol L−1) after addition of different anions (none, F− , Cl− , Br− , I− , CN−
,
OH−) in DMSO, from left to right.
1.98
1.2
1.8
1.0
0.8
1.6
0.6
0.4
1.4
335 nm
2.0
0.2
0.0
1.2
1.0
0.8
0.6
0.4
0.2
0.00
-
0.0
1.0
3.0
F
equiv.
A
280
300
320
340
360
380
NM
400
420
440
460
480 500.0
260.0
Figure 3. Titration of 5 × 10−5 mol L−1 solution of 3 in DMSO with a standard solution of F− (as tetrabutylam-
monium salt) in DMSO at 298.2
0.1 K.
769

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
Figure 4. Partial 1 H-NMR (400 MHz) spectra of the receptor (5 × 10−5 mol L−1) in DMSO-d6; in the absence and
in the presence of 1 and 2 equiv. of [(t−Bu)4 N]F.
X-ray crystallography
A suitable colorless prism-shaped crystal sample of size 0.51 × 0.38 × 0.21 mm was chosen for the crys-
tallographic study and then carefully mounted first on a glass fiber and then on the goniometer of a STOE
770

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
diffractometer with an IPDS(II) image plate detector. All diffraction measurements were performed at room
˚
temperature (296 K) using graphite monochromated Mo Kα radiation (λ = 0.71073 A). Reflection data were
recorded in rotation mode using the ω scan technique by using X-AREA33 software. Unit cell parameters
were determined from least-squares refinement of setting angels with θ in the range 1.7 ≤ θ ≤ 27.2. The
structure was solved by direct methods using SHELXS-9734 implemented in the WinGX35 program suite. The
refinement was carried out by full-matrix least-squares method on the positional and anisotropic temperature
parameters of the nonhydrogen atoms, or equivalently corresponding to 307 crystallographic parameters, using
SHELXL-97.36 All H atoms were positioned geometrically and treated using a riding model, fixing the bond
˚
lengths at 0.86 and 0.93 A for NH and CH atoms, respectively. The displacement parameters of the H atoms
were fixed at Uiso (H) = 1.2 Ueq of their parent atoms. Data collection: X-AREA; cell refinement: X-AREA;
data reduction: X-RED32.37
Figure 5. Molecular structure of the title compound showing the atomic labeling.
Crystal structure and conformations
Details of crystal structure crystal data collection and refinement of the title compound are summarized in
Table 1. The selected bond lengths and bond angles for the title compound are listed in Tables 2 and 3. The
ORTEP and molecular packing diagrams are displayed in Figures 5 and 6.
771

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
Figure 6. Packing diagram for the title compound with hydrogen bonds as dotted lines.
Figure 7. Infrared spectrum of 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea.
772

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
The molecule crystallized in the triclinic space group P-1. The molecule consists of 2 N-(carbamothioyl)
benzamide groups bonded to 1,8 positions of the naphthalene molecule. These groups are in trans positions
to each other. N-C bond distances are slightly different for these groups. While at the group of 1 position,
˚
˚
˚
N1-C11= 1.331 A and C11-N2 = 1.393 A, at 8 position these distances are N3-C19 = 1.316 A and C19-N4
˚
= 1.395 A. This difference was probably due to intramolecular hydrogen bonding interaction forming a 6-
member ring between the keto (C=O) group and the amine (–NH–) nitrogen. C-S bond distances reveal the
˚
˚
character of the bonds as double bonds with 1.655 A and 1.659 A for C11-S1 and C19-S2, respectively. The
geometry of the molecule moiety is stabilized by N—H···O type intramolecular hydrogen bonds with atoms N3—
H33···O2 and N1—H11···O1. In the crystal structure, the molecules are linked by N4—H44···S2ii [H44.. . S2=
◦
˚
˚
2.61A, N4—S2 = 3.454(2) A and N4—H44.. . S2 = 167.4 with symmetry code (-x, -y, -z)] intermolecular
hydrogen bonds to form centro symmetric dimers. This molecular interaction is consistent with similar related
i
compounds.12,13 Intermolecular hydrogen bonds also occur between with N1—H11· · ·O1 [H11. . . O1= 2.66 A,
˚
◦
˚
N1—O1= 3.196(3) A and N1—H11. . . O1= 122 with symmetry code (-x + 1, -y, -z)]. The crystal structure
also has C-H. . . π stacking. This C-H. . . π interaction occurs between C14 atoms Cg1 (the centroid of the
˚
C1-C6 ring of naphthalene) and its symmetry equivalent at (1 – x, 2 – y, –z), with distances of H. . . Cg1 2.75 A
˚
a centroid to centroid distance of 3.531(4) A as seen in Table 3. The combinations of N—H· · ·S bonds produce
R22 (8) rings.
Figure 8. Mass spectrum of 1,1’-(naphthalene-1,8-diyl)-3,3’-dibenzoyl-bisthiourea.
773

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
Table 1. Crystal data and structure refinement for the title compound.
F(000) = 504
C26H20N4O2S2
Mr = 484.58
Z = 2
Triclinic, P
Dx = 1.383 Mg m−3
Hall symbol: -P 1
Melting point: 496 K
˚
˚
a = 8.1556 (8) A
Mo Kα radiation, λ = 0.71073 A
Cell parameters from 10540 reflections
θ = 1.7 − 27.2◦
˚
b = 12.0127 (11) A
˚
c = 13.2081 (11) A
α = 109.510 (7)◦
β = 95.390 (7)◦
γ = 103.660 (7)◦
μ = 0.26 mm−1
T = 293 K
Prism, colorless
3
˚
V = 1163.92 (18) A
0.51 × 0.38 × 0.21 mm
4555 independent reflections
STOE IPDS 2 diffractometer
Radiation source: sealed X-ray tube,
12 × 0.4 mm long-fine focus
plane graphite
1911 reflections with I > 2σ(I)
Rint = 0.119
Detector resolution: 6.67 pixels mm−1 θmax = 26.0◦, θmin = 1.7◦
rotation method scans
Absorption correction: integration
X-RED32 (Stoe & Cie, 2002)
Tmin = 0.926, Tmax = 0.973
16,571 measured reflections
Refinement on F 2
h = -10 10
k = -14 14
l = -16 16
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighboring sites
H-atom parameters constrained
Least-squares matrix : Full
R[F 2 > 2σ(F 2)] = 0.041
wR(F 2) = 0.057
w = 1/[σ2(Fo2) + (0.P )2] where P = (Fo2 + 2Fc2)/3
S = 0.69
(Δ/σ)max = 0.002
−3
˚
Δρmax = 0.18 e A
4555 reflections
−3
˚
Δρmin = -0.20 e A
307 parameters
◦
◦
˚
Table 2. Selected bond lengths (A), bond angles ( ), and torsion angles ( ).
S2- C19 1.659 (3) N2-C11
S1-C11 1.655 (3) N1-C2
1.393 (3) C10-N3-C19-N4 171.1 (1)
1.434 (3) C10-N3-C19-S2 -10.2 (4)
C20-O2 1.226 (3) C20-N4-C19 127.8 (1) C20-N4-C19-N3 2.6 (4)
O1-C12 1.218 (3) C2-C1-C10
N1-C11 1.331 (3) N1-C11-N2
127.5 (1) C20-N4-C19-S2 -176.2
115.3(3) C11-N2-C12-O1 -9.3
N2-C12 1.384 (3) C12-N2-C11 130.2(3) C19-N4-C20-O2 0.5(2)
774

Synthesis and structural X-ray analysis of..., F. AYDIN, et al.
Table 3. Hydrogen-bond geometry (A, ◦ ).
˚
D—H· · ·A
D—H H· · ·A D· · ·A
D—H· · ·A
N1—H11· · ·O1i 0.86
2.66
1.95
2.02
2.61
3.196 (3) 122
N3—H33· · ·O2
N1—H11· · ·O1
0.86
0.86
2.631 (3) 135
2.698 (3) 135
3.454 (1) 167
N4—H44· · ·S2ii 0.86
Symmetry codes: (i) -x + 1, -y, -z; (ii) -x, -y, -z.
Conclusions
We describe here a simple and easy way to prepare a bisthiourea-based receptor that allows naked-eye detection
of fluoride ions among halide anions such as chloride, bromide, and iodine anions. The crystal structure of
this compound revealed many significant structural phenomena, including inter- and intramolecular hydrogen
bonds, and π -π interactions between phenyl and naphthyl groups, respectively. This compound, as a receptor,
proves to be a colorimetric anion sensor that shows selective coloration for fluoride, hydroxide, and cyanide ions
in DMSO solutions. This compound can be used as a potential chromogenic for these anion probes.
Supplementary material
Crystallographic data for the title compound have been deposited with the Cambridge Crystallographic Data
Centre as supplementary publication No. CCDC 821335 for the structure reported in this article. These data
can be obtained free of charge via http://www.ccdc.cam.ac.uk/data request/cif, by e-mailing
data request@ccdc.cam.ac.uk or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road,
Cambridge CB2 1EZ, UK; fax: +44-1223-336033.
Acknowledgments
The financial support from C¸anakkale Onsekiz Mart University Grants Commission (Project Number: 2008/35)
is gratefully acknowledged. We thank Hacettepe University Department of Chemistry for the 1 H-NMR titration
experiments and mass analyses.
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