Structures of two N-{2-([(5-amino-1,3,4-thiadiazol-2-yl)difluoromethyl]-4- halophenyl}acetamides

Article abstract of DOI:10.1007/s10870-011-0016-8

The compounds, N-{2-[(5-amino-1,3,4-thiadiazol-2-yl)difluoromethyl]-4- chlorophenyl}acetamide (1: X = Cl) and N-{2([(5-amino-1,3,4-thiadiazol-2-yl) difluoromethyl]-4-bromo-phenyl}acetamide (1: X = Br), are isostructural. The molecules are near ''V'' shaped with the angles between the two aromatic planes ca. 84° in each case. The various intermolecular interactions, namely N-H???O, N-H???N, N-H???F, and C-H???N hydrogen bonds and C-H???π, C-Cl???π and C-O???π interactions, generate 3-D arrays. Compound (1: X = Cl) crystallizes in the monoclinic space group P21/c with a = 16.9032(7) A, 10.2193(4) A, c = 7.5227(4) A, β = 100.179(3)° and Z = 4. Compound (1: X = Br) crystallizes in the monoclinic space group P21/c with a = 17.2119(4) A, 10.2167(2) A, c = 7.5677(2) A, β = 100.326(2)° and Z = 4.

Full text of DOI:10.1007/s10870-011-0016-8

J Chem Crystallogr (2011) 41:874–879
DOI 10.1007/s10870-011-0016-8
ORIGINAL PAPER
Structures of two N-{2-([(5-amino-1,3,4-thiadiazol-2-yl)
difluoromethyl]-4-halophenyl}acetamides
•
Nubia Boechat Monica M. Bastos
•
´
ˆ
Lindalva C. Maciel Warner B. Kover
•
•
•
Solange M. S. V. Wardell James L. Wardell
Received: 2 December 2010 / Accepted: 31 January 2011 / Published online: 13 February 2011
Ó Springer Science+Business Media, LLC 2011
Abstract The compounds, N-{2-[(5-amino-1,3,4-thia-
diazol-2-yl)difluoromethyl]-4-chlorophenyl}acetamide (1:
X = Cl) and N-{2([(5-amino-1,3,4-thiadiazol-2-yl)difluo-
romethyl]-4-bromo-phenyl}acetamide (1: X = Br), are
isostructural. The molecules are near ‘‘V’’ shaped with the
angles between the two aromatic planes ca. 84° in each case.
The various intermolecular interactions, namely N–HÁÁÁO,
N–HÁÁÁN, N–HÁÁÁF, and C–HÁÁÁN hydrogen bonds and
C–HÁÁÁp, C–ClÁÁÁp and C–OÁÁÁp interactions, generate 3-D
arrays. Compound (1: X = Cl) crystallizes in the monoclinic
Keywords Thiadiazole Á Hydrogen bonds Á p interactions
Introduction
Interests of the Boechat group during the past few years have
been concerned with the synthesis, structures and biological
activities of compounds bearing fluoro substituents [1–9],
and on small ring heterocycles, including triazoles and thi-
adiazoles [10–15]. Recently we reported on the usefulness of
N-acyl-3,3-difluoro-2-oxoindoles as precursors of 1-(2-acet-
amidophenyl)-2,2-difluoroacetic acid derivatives, 1-(2-(2-acet-
amidophenyl)-2,2-difluoroacetyl)thiosemi-carbazides and
N-(2-((5-amino-1,3,4-thiadiazol-2-yl)difluoromethyl)-
4-phenyl)acetamides [9].
˚
space group P21/c with a = 16.9032(7) A, 10.2193(4) A,
˚
˚
c = 7.5227(4) A, b = 100.179(3)° and Z = 4. Compound
(1: X = Br) crystallizes in the monoclinic space group P21/c
˚
˚
˚
with a = 17.2119(4) A, 10.2167(2) A, c = 7.5677(2) A,
b = 100.326(2)° and Z = 4.
We now wish to report on two isostructural N-{2-[(5-
amino-1,3,4-thiadiazol-2-yl)difluoromethyl]-4-halophenyl}
acetamides (1: X = Cl and Br) prepared from N-acyl-3,
3-difluoro-2-oxoindoles, see Fig. 1.
N. Boechat Á M. M. Bastos Á L. C. Maciel
Fundac¸a˜o Oswaldo Cruz, Far-Manguinhos, Avenida Brasil, Rio
de Janeiro, RJ 21041-250, Brazil
Experimental
The compounds were prepared as reported [9].
X-ray Crystallography
M. M. Bastos Á W. B. Kover
´
Instituto de Quımica, Universidade Federal do Rio de Janeiro,
Ilha do Funda˜o, Rio de Janeiro, RJ 21941-590, Brazil
S. M. S. V. Wardell
CHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY,
Scotland, UK
Data for compounds (1: X = Cl and Br) were obtained at
120(2) K with Mo-Ka radiation by means of the Bruker-
Nonius 95 mm CCD camera on \k-goniostat of the EPSRC
crystallographic service, based at the University of
Southampton. Data collection was carried out under the
control of the program COLLECT [16] and data reduction
and unit cell refinement were achieved with the COLLECT
and DENZO [17] programs. No correction for absorption
J. L. Wardell (&)
´
´
Centro de Desenvolvimento Tecnologico em Saude (CDTS),
Fundac¸a˜o Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de
Manguinhos, Av. Brasil 4365, Rio de Janeiro,
RJ 21040-900, Brazil
e-mail: j.wardell@abdn.ac.uk
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J Chem Crystallogr (2011) 41:874–879
875
Fig. 1 Formation of 1 and
structure of compound 3
(1: R = Cl or Br)
3
Table 1 Crystal data and
structure refinement
Identification code
(1: X = Cl)
(1: X = Br)
C11H9BrF2N4OS
363.19
Empirical formula
Formula weight
Temperature (K)
C11H9ClF2N4OS
318.73
120(2)
120(2)
˚
Wavelength (A)
0.71073
0.71073
Crystal system
Space group
Monoclinic
P21/c
Monoclinic
P21/c
Unit cell dimensions:
˚
a (A)
16.9032(7)
10.2193(4)
7.5227(4)
100.179(3)
1279.01(10)
4
17.2119(4)
10.2167(2)
7.5677(2)
100.326(2)
1309.22(5)
4
˚
b (A)
˚
c (A)
( (o)
3
˚
Volume (A )
Z
Density (calculated) (Mg/m3)
Absorption coefficient (mm-1
F(000)
1.655
1.843
)
0.487
3.324
648
720
Crystal size (mm)
0.38 9 0.28 9 0.03
2.9 to 27.5
0.44 9 0.20 9 0.08
3.1 to 27.5
Theta range for data collection (°)
Index ranges
-21 B h B 21; -13 B
k B 13; -9 B l B 9
-22 B h B 22; -13 B
k B 13; -9 B l B 9
Reflections collected
Independent reflections
Reflections observed ([r)
Data completeness
16918
5796
2934 [R(int) = 0.073]
2183
2988 [R(int) = 0.021]
2668
0.999
0.997
Absorption correction
Refinement method
Multi-scan
Multi-scan
Full-matrix least-squares
on F2
Full-matrix least-squares
on F2
Data/restraints/parameters
Goodness-of-fit on F2
2934/0/191
1.04
2988/0/191
1.04
Final R indices [I [ 2r(I)]
R1 = 0.042
wR2 = 0.094
R1 = 0.068
wR2 = 0.104
0.33 and -0.33
R1 = 0.027
wR2 = 0.064
R1 = 0.033
wR2 = 0.067
0.40 and -0.64
R indices (all data)
-3
˚
Largest diff. peak and hole, eA
was applied. The programs ORTEP-3 for Windows [18]
and MERCURY [19] were used in the preparation of the
figures. SHELXL97 [20] and PLATON [21] were used in
the calculation of molecular geometry.
program SHELXL-97 [20]. Difference map peaks provided
positions for the hydrogen atoms of the NH groups for
which the coordinates, along with isotropic displacement
parameters, were fully refined. All other hydrogen atoms
were placed in calculated positions. Crystal data and
structure refinement details are listed in Table 1.
The structures were solved by direct methods using
SHELXS-97 [22] and fully refined by means of the
123

876
J Chem Crystallogr (2011) 41:874–879
Fig. 2 a Atom numbering scheme and atom arrangement for (1:
X = Br). Numbering for (1: X = Cl), Cl1 replaces Br1. Probability
ellipsoids are drawn at the 50% level and hydrogen atoms are drawn
as spheres of arbitrary radii; b overlay of molecules (1: X = Cl), and
(1: X = Br); c View of the conformation of 1: X = Br) with the C–
O–pthiadiazole shown as a dashed red line: hydrogen atoms have been
omitted for clarity
Results and Discussion
S1–C5–C6–C7 torsion angle of 44.4 (3)° in each molecule.
The orientation of the thiadiazole and phenyl rings has the
S atom of the thiadiazole ring and the acetamido sub-
stituent of the phenyl ring placed on the same side of
the molecule, see Fig. 2c. This allows weak C(13)–
O(1)ÁÁÁp(thiadiazole) intramolecular interactions with O–
Molecular Structures
Compounds (1: X = Cl) and (1: X = Br) crystallize in the
monoclinic space group P21/c, and have similar cell
dimensions. Figure 2a shows the atom numbering system
and atom arrangements for (1: X = Br): the notation used
for (1: X = Cl) is similar except with Cl1 replacing Br1.
As shown in Fig. 2b, there is a very close overlay involving
the two molecular structures. Indeed the two isometric
compounds satisfy the criteria proposed by Kalman and
co-workers [23] for isotructural compounds, e.g., in terms of
orthogonized lattice parameters and isostructurality index.
Selected bond lengths and angles are listed in Table 2.
The data relating to the thiadiazole unit are in the ranges
generally found for 5-R-2-H2N-1,3,4-thiadiazoles (2: R =
alkyl or aryl) [24–33]. Weak intramolecular C6–H6ÁÁÁF2
hydrogen bonds are present in 1, see Table 2.
˚
Cg(thiadiazole) distances of 3.781(2) and 3.8045(17) A,
respectively for (1: X = Cl) and (1: X = Br).
A slightly smaller dihedral angle, 73.92(8)°, between the
thiadiazole and phenyl rings was earlier reported by us for
another substituted benzylated thiadiazole derivative,
namely 5-(3-nitrobenzyl)-1,3,4-thiadiazol-2-amine, 3. Of
interest, the thiadiazole S atom in 3 is also directed towards
the phenyl ring [23].
Crystal Structures
The supramolecular arrangements in each case is generated
from a combination of hydrogen bonds, N1–H1AÁÁÁO1, N1–
H1BÁÁÁN3, N2–H2ÁÁÁN4, N2–H2ÁÁÁF1 and C14–H14BÁÁÁN4,
and C–YÁÁÁp interactions, namely C11–H11ÁÁÁCg(1), and
C9–Cl1ÁÁCg(2): symmetry operations are listed in Table 3.
The amino groups act as double donors in N–HÁÁÁN and
N–HÁÁÁO hydrogen bonds, while the NH of the amido group
The essentially planar 1,3,4-thiadiazole and the aryl
rings are nearly orthogonal as shown by the angles between
the best planes though the aromatic rings of 83.7(3) and
83.8(3)° in (1: X = Cl) and (1: X = Br), respectively. A
twist between the aromatic group planes is indicated by the
Table 2 Selected geometric
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
parameters
S1–C2
N3–C2
N3–N4
N4–C5
S1–C5
1.750(2)
1.322(3)
1.386(3)
1.290(3)
1.734(2)
1.748(2)
1.323(3)
1.382(2)
1.291(3)
1.734(2)
C5–S1–C2
S1–C2–N3
C2–N3–N4
N3–N4–C5
N4–C5–S1
85.94(10)
114.31(16)
111.37(18)
113.09(18)
115.29(17)
85.98(10)
114.21(15)
111.53(17)
113.09(16)
115.19(16)
Intramolecular hydrogen bonds
Compound
D–HÁÁÁA
D–H
HÁÁÁA
D–A
D–HÁÁÁA
(1: X = Cl)
(1: X = Br)
C8–H8–F2
C8–H8–F2
0.95
0.95
2.34
2.33
2.680(3)
2.675(2)
101
101
123

J Chem Crystallogr (2011) 41:874–879
877
Fig. 3 a A zig-zag chain of
molecules, [C(11)], of (1:
X = Cl), formed from
N1–H1A–O1 hydrogen bonds
aligned along c; b Network of
molecules formed from
N1–H1A–O1, (red dash line),
N1–H1B–N3 (black), N2–H2–
N4 (blue) and N2–H2–F1
(green): symmetry codes are
listed in Table 3. Chlorine,
fluorine, oxygen, sulfur,
nitrogen, carbon and hydrogen
atoms are coloured bright green,
lime green, red, yellow, blue,
grey and white, respectively
(Color figure online)
˚
Table 3 Parameters (A, 8) for intermolecular contacts
(a) Intermolecular Hydrogen-bonds
Compound
D–HÁÁÁA
D–H
HÁÁÁA
D–A
D–HÁÁÁA
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
N1–H1AÁÁÁO1i
N1–H1AÁÁÁO1i
N6–H1BÁÁÁN3ii
N6–H1BÁÁÁN3ii
N2–H2ÁÁÁF1iii
0.89(3)
0.79(3)
0.85(3)
0.77(3)
0.83(3)
0.83(3)
0.85(3)
0.83(3)
0.98
1.97(3)
2.06(3)
2.32(3)
2.39(3)
2.52(3)
2.56(3)
2.33(3)
2.32(3)
2.58
2.801(3)
2.799(2)
3.147(3)
3.149(3)
3.021(2)
3.034(2)
3.156(3)
3.149(3)
3.358(3)
3.358(3)
156(2)
156(3)
173(3)
168(3)
119(2)
118(2)
164(2)
165(2)
137
N2–H2ÁÁÁF1iii
N2–H2ÁÁÁN4iii
N2–H2ÁÁÁN4iii
C14–H14BÁÁÁN4iii
C14–H14BÁÁÁN4iii
0.98
2.59
135
(b) X–Y–p interactions
Compound
C–HÁÁÁCg
HÁÁÁCg
Hperp
c
C–HÁÁÁCg
CÁÁÁCg
C–H, p
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
(1: X = Cl)
(1: X = Br)
C11–H11ÁÁÁCg(1i)
2.82
2.73
14.75
14.04
9.66
173
3.768(2)
3.789(2)
4.213(3)
4.490(2)
3.595(2)
3.615(2)
80
C11–H11ÁÁÁCg(1i)
C9–Cl1ÁÁÁCg(2ii)
C9–Cl1ÁÁÁCg(2iii)
C13–O1ÁÁÁCg(1iii)
C13–O1ÁÁÁCg(1iii)
2.84
2.76
173
80
3.5999(11)
3.7267(9)
3.781(2)
3.8024(17)
3.549
3.652
3.444
3.457
98.17(8)
100.95(6)
71.93(14)
71.90(12)
0.36
0.44
1.86
1.91
11.48
24.36
24.61
(a) Intermolecular Hydrogen-bonds: symmetry codes: (i) x, 3/2 - y, 1/2 ? z (ii) 1 - x, -1 - y, 2 - z; (iii) x, 1/2 - y, -1/2 ? z
(b) X–Y–p interactions: Cg(1) and Cg(2) are the centroids of the thiadiazole and phenyl rings, respectively. Gamma is the angle at H between the
vectors H–Cg and Hperp. C–H, p is an estimate of the significance of the interaction. Symmetry codes: (i) x, y, -1 ? z; (ii) 2 - x, 1 - y, 1 - z;
(iii) x, y, z
acts as a donor in N–HÁÁÁN hydrogen bonds, as well as in
weaker N–HÁÁÁF hydrogen bonds. The acetamido oxygen, as
well as the two nitrogen atoms in the thiadiazole ring, act as
strong acceptors.
hydrogen bonds lead to zig-zag chains, [C(11)], of mole-
cules aligned along the c axis, see Fig. 3a. Centrosymmetic
R22(8) dimers [14], are generated by paired N1–H1BÁÁÁN3
hydrogen bonds. The combination of the N2–H2ÁÁÁN4 and
N2–H2ÁÁÁF1 hydrogen bonds result in the formation of R125
rings. In addition, the combination of N1–H1AÁÁÁO1,
N1–H1BÁÁÁN3 [2 of these], and N2–H2ÁÁÁN4 hydrogen
The discussion of intermolecular interactions will con-
sider just the chloro compound, as the arrangement for (1:
X = Br) is essentially the same. The N1–H1AÁÁÁO1
123

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J Chem Crystallogr (2011) 41:874–879
Fig. 4 a Intermolecular connections involving X–Y–p interactions,
illustrated for (1: X = Cl). Blue, red and black dash lines represent
C11–H11–Cg(1), C13–O1–Cg(1) and C9–Cl1–Cg(2), respectively:
˚
symmetry codes are listed in Table 3. Values, in A, without esds, are
those calculated using the Y–Cg distances. Red and blue spheres are
centroids of the thiadiazole {Cg(1)} and phenyl [C7–C12] {Cg(2)}
rings; b Packing arrangement illustrated for (1: X = Cl). Chlorine,
fluorine, oxygen, sulfur, nitrogen, carbon and hydrogen atoms are
coloured bright green, lime green, red, yellow, blue, grey and white,
respectively (Color figure online)
bonds result in formation of [R44(18)] rings. The network
formed from these interactions is illustrated in Fig. 3b.
A PLATON analysis also recognized a weak C14–
H14BÁÁÁN4 hydrogen bond, which utilises a hydrogen of
the methyl group: this is not indicated but, if significant,
would further cement the network shown in Fig. 3b.
There are two intermolecular C–YÁÁÁp interactions,
namely C11–H11ÁÁÁpphenyl and C9–Cl1ÁÁÁpphenyl, in addition
to the intramolecular C13–O1ÁÁÁp(thiadiazole) intramolecular
interaction mentioned earlier. Chains of molecules are
formed by alternating C11–H11ÁÁÁpphenyl and C13–
O1ÁÁÁpthiadizole interactions. Such chains are linked by
symmetry related C9–Cl1ÁÁÁpphenyl interactions into double
columns. The combination of the three C–YÁÁÁp interactions
is illustrated in Fig. 4a: Cg(2)phenyl Cg(1)thiadiazole are the
centroids of the phenyl and thiadiazole rings respectively.
Altogether, all the intermolecular interactions result in a
3-D array: Fig. 4b shows the packing arrangement.
found in 2: R = 3-py) [34] and 2: R = 3-py) [35], and the
C–H–O hydrogen bonds detected in both 2: R = 2-F-4-
O2NC6H3) [36] and in 3 [24].
In compounds 1, while the hydrogen bonds involving
the amido O atom contribute significantly to the supra-
molecular arrangements, the centrosymmetric dimers gen-
erated from intermolecular N–H–N hydrogen bonds remain
major features.
Acknowledgments The use of the EPSRC X-ray crystallographic
service at Southampton and the valuable assistance of the staff there
are gratefully acknowledged. JLW thanks CAPES for financial
support.
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