Study of hydrogen bonding in N'-(4,6-disubstituted-pyrimidin-2-yl)-N-[2-(2, 4-dichlorophenoxypropionyl)]thiourea

Article abstract of DOI:10.1007/s10870-010-9719-5

Two of N'-N'-(4,6-disubstituted-pyrimidin-2-yl)- N-[2-(2,4- dichlorophenoxypropionyl)]thiourea (4a-4b) had been synthesized and their crystal structures had been determined by X-ray diffraction method. 4a crystallizes in the triclinic space group P-1, wit

Full text of DOI:10.1007/s10870-010-9719-5

J Chem Crystallogr (2010) 40:675–680
DOI 10.1007/s10870-010-9719-5
ORIGINAL PAPER
Study of Hydrogen Bonding in N0-(4,6-disubstituted-pyrimidin-
2-yl)-N-[2-(2,4-dichlorophenoxypropionyl)]thiourea
•
Guo-Hua Liu Chuan-Shou Sun
•
•
Yun-Ning Xue Mei Yao Han Yu
•
Received: 13 August 2006 / Accepted: 16 January 2010 / Published online: 2 February 2010
Ó Springer Science+Business Media, LLC 2010
Abstract Two of N0-N0-(4,6-disubstituted-pyrimidin-2-yl)-
N-[2-(2,4-dichlorophenoxypropionyl)]thiourea (4a-4b) had
been synthesized and their crystal structures had been deter-
mined by X-ray diffraction method. 4a crystallizes in the
and stalk for dicotyledon weeds [13], while N-(4,6-dis-
ubstituted-pyrimidin-2-yl)-2-fluro-6-chlorobenzoylthiourea
and N0-(4,6-disubstituted-pyrimidin-2-yl)-N-[3-methyl-2-
(4-chlorophenyl)butyryl]thiourea exhibit highly herbicidal
activities against root and stalk for monocotyledon weeds
[14, 15]. However, although these thiourea derivatives have
been synthesized and some of crystal structures have been
described [16], so far, relatively few reports on study of role
of the weak hydrogen bond using sulfur atom as hydrogen-
bonding acceptor is available.
˚
triclinic space group P-1, with a = 8.053(12) A, a =
˚
102.84(2)°, b = 10.541(16) A, b = 106.99(2)°, c = 12.461
3
˚
(19) A, c = 94.615(19)°, and Dc = 1.470 mg/m for Z = 2.
4b crystallizes in the triclinic space group P-1, with a =
˚
˚
7.939(5) A, a = 105.302(10)°, b = 10.183(7) A, b =
˚
105.729(9)°, c = 12.764(9) A, c = 90.698(11)°, and Dc =
1.517 mg/m3 for Z = 2.
As an extension of our previous studies, we herein report
the crystal structures of two phenoxyl thiourea derivatives and
their applications in herbicidal activity. This research focuses
on investigation of weak hydrogen bonding using sulfur atom
as hydrogen-bond acceptor, which will provide a potential
opportunity to explore the structure–activity relationship.
Keywords Thiourea ꢀ Crystal structure ꢀ
Hydrogen bonding
Introduction
As a kind of important biologically active molecule, thiourea
and its derivatives are well-known as herbicides [1–3] and
pesticides [4–6] in agrochemical industry. In order to eluci-
date relationship between their structure and activity, a
variety of structural studies have appeared in literature
[7–12]. In particular, thiourea derivatives containing pyrim-
idine ring show highly herbicidal activities. Recently, we
have reported a series of thiourea derivatives containing the
pyrimidine ring and their applications in herbicidal research.
N0-(4,6-disubstituted-pyrimidin-2-yl)-N-b-(c-)pyridinecar-
bonyl thiourea shows highly inhibitory activities against root
Experimental
Instrumentation
The melting points were determined an XT4A digital
melting point apparatus. IR was recorded on a Niclet
AVATAR-37ODTGS Spectrophotometer in the region
4,000–400 cm-1 KBr discs. 1H NMR spectra were recorded
on a Bruker Avance-400 superconduct nuclear magnetic
resonance instrument. Chemical shift values are reported in
ppm (d) relative to TMS as internal standard. EI Mass
spectra were obtained on an HP-5998A-high performance
liquid chromatography-mass spectrometer-computer. Ele-
mental analysis was performed with an Elemental VARIO
EL apparatus. 2-(2,4-dichlorophenoxy)propionic acid 1 and
2-(2,4-dichlorophenoxy)propionyl isothiocyanate 2 was
synthesized according to reported method [17, 18].
G.-H. Liu (&) ꢀ C.-S. Sun ꢀ Y.-N. Xue ꢀ M. Yao ꢀ H. Yu
Department of Chemistry, College of Life and Environmental
Science, Shanghai Normal University, 200234 Shanghai,
People’s Republic of China
e-mail: ghliu@shnu.edu.cn
123

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J Chem Crystallogr (2010) 40:675–680
Structure Determinations
Table 2 Selected bond angles (°) of 4a and 4b
4a
4b
Suitable crystals for X-ray diffraction were obtained
through slow evaporation the mixture solution in DMF/
C2H5OH/H2O (v/v/v = 1:5:1) at room temperature for 4a
and in ethyl acetate/hexane(v/v = 5:1) for 4b. Crystals
were mounted on a glass fiber in a Bruker SMART APEX
CCD diffractometer (4a and 4b). Intensity data were col-
C9–N1–C10
C10–N2–C11
C4–O1–C7
O1–C7–C9
O1–C7–C8
C9–C7–C8
O2–C9–N1
O2–C9–C7
N1–C9–C7
N2–C10–N1
N2–C10–S1
N1–C10–S1
C14–O3–C15
129.58(18)
130.65(18)
118.66(17)
107.61(18)
112.3(2)
C9–N1–C10
C10–N2–C11
C4–O1–C7
O1–C7–C9
O1–C7–C8
C9–C7–C8
O2–C9–N1
O2–C9–C7
N1–C9–C7
N2–C10–N1
N2–C10–S1
N1–C10–S1
C14–O3–C15
130.5(3)
129.9(3)
119.5(2)
106.9(2)
112.1(3)
111.0(3)
123.8(3)
120.0(3)
116.2(3)
112.5(3)
129.5(2)
118.0(2)
116.8(3)
˚
lected with MoKa radiation (k = 0.71073 A). Preliminary
109.5(2)
data revealed the crystal system. A hemisphere routine was
used for data collection and determination of lattice con-
stants. The space group was identified, and the data were
processed using the Bruker SAINT program and corrected
for absorption using SADABS [19]. All refinements and
geometry calculations were performed with the program
packages SHELXL [20]. The selected bond lengths are
Table 1 and the bond angles in Table 2, the hydrogen
bonding distance and angles in Table 3. Crystallographic
data and details of the data collections and structure
refinements are listed in Table 4. The crystal structure and
packing diagram of the title compound of 4a and 4b are
shown in Figs. 1, 2, 3, and 4 respectively.
124.3(2)
119.8(2)
115.98(18)
112.9(2)
129.55(17)
117.58(16)
116.9(2)
on silica gel (petroleum ether:acetic ether = 3:1, v/v) to
gave 4a (0.52 g, 1.21 mmol) as yellow solids. Yield 67%;
m.p. 117–118 °C; IR (KBr): 3,374, 3,158, 3,109, 2,990,
2,949, 1,695, 1,610, 1,580, 1,474, 1,323, 1,213, 918, 816,
698 cm-1; 1H-NMR (DMSO-d6, 400 MHz) d: 12.23, 12.31
(s, 2H, NH), 7.62 (s, 1H, Ph-H), 7.38–7.40 (d, 1H, Ph-H),
7.01–7.04 (d, 1H, Ph-H), 7.62–7.61 (d, J = 2.4 Hz,1H, Ph-
H), 7.41–7.38 (q, J1 = 2.4 Hz, J2 = 8.8 Hz,1H, Ph-H),
7.04–7.01 (d, J = 8.8 Hz,1H, Ph-H), 6.05 (s, 1H, Py-H),
5.17–5.22 (q, J = 6.4 Hz,1H, CHCH3), 3.86 (s, 3H,
OCH3), 1.57–1.58 (d, J = 6.4 Hz,3H, CHCH3); MS(EI)
(70 eV) m/z (%): 432 (1.25) [M ? 2]?, 430 (1.94) [M]?,
268 (100), 197 (61.89), 154 (30.22), 125 (30.84),
68(40.49), 44 (40.66); Anal. Calcd. for C16H16Cl2N4O4S:
C, 44.56; H, 3.74; N, 12.99. Found: C, 44.63; H, 3.88%, N,
12.62.
General Synthetic Procedures of 4a and 4b
To a stirred solution of 2 (0.50 g, 1.82 mmol) in acetoni-
trile (10 mL) was slowly added a solution of 4,6-dime-
thoxyl-2-amino-pyrimidine (0.28 g, 0.82 mmol) in dry
acetonitrile (10 mL) over 30 min at room temperature
under nitrogen. Then the mixture was refluxed and stirred
for 2 h. After evaporation of most of the solvent, the res-
idue was cooled to room temperature and water (5 mL)
was added to quench the reaction. Then the residue was
repeatedly extracted with 50 mL of diethyl ether. The
combined organic layer was washed with water and brine,
and then dried over Na2SO4. After evaporation of solvent,
the residue was further purified by column chromatography
Date for 4b
According to above procedure, the resulting residue was
purified by column chromatography on silica gel (petro-
leum ether:acetic ether = 5 : 1, v/v) to give 4b as yellow
solids. Yield 53%; m.p. 160–161 °C; IR (KBr): 3,370,
3,154, 3,088, 2,990, 2,945, 1,695, 1,593, 1,564, 1,482,
˚
Table 1 Selected bond lengths (A) of 4a and 4b
4a
4b
N1–C9
1.368(3)
1.402(3)
1.652(3)
1.334(3)
1.326(3)
1.353(3)
1.399(3)
1.223(3)
1.429(3)
1.367(3)
1.389(3)
N1–C9
1.364(4)
1.398(4)
1.637(3)
1.330(4)
1.329(4)
1.358(4)
1.390(4)
1.225(3)
1.439(4)
1.367(4)
1.392(5)
N1-C10
S1–C10
N4–C12
N4–C11
N2–C10
N2–C11
O2–C9
N1–C10
S1–C10
N4–C12
N4–C11
N2–C10
N2–C11
O2–C9
1,315, 1,241, 714, 637 cm-1
;
1H-NMR (DMSO-d6,
400 MHz) d: 12.19, 12.40 (s, 2H, NH), 7.55 (s, 1H, Ph-H),
7.31, 7.33 (d, 1H, Ph-H), 7.01, 7.03 (d, 1H, Ph-H), 7.55–
7.54 (d, J = 2.4 Hz,1H, Ph-H), 7.33–7.31 (q, J1 = 2.4 Hz,
J2 = 8.8 Hz, 1H, Ph-H), 7.03–7.01 (d, J = 8.8 Hz,1H, Ph-
H), 6.82 (s, 1H, Py-H), 5.04–5.10 (q, J = 6.4 Hz,1H,
CHCH3), 2.49 (s, 3H, OCH3),1.52–1.54 (d, J = 6.4 Hz,
3H, CHCH3); MS(EI) (70 eV) m/z (%): 436 (11.63)
[M ? 2]?, 434 (11.24) [M]?, 362 (56.94), 272 (100), 201
(45.65), 129 (25.53), 44 (33.55); Anal. Calcd. for
O1–C7
O1–C7
O1–C4
O1–C4
C13–C14
C13–C14
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J Chem Crystallogr (2010) 40:675–680
677
Table 3 Hydrogen bonding
˚
distance (A) and angles
Compd. D–HꢀꢀꢀA
d(D–H) d(HꢀꢀꢀA) d(DꢀꢀꢀA) \(DHA) Symmetry code
(°) of 4a and 4b
4a
N1–H1AꢀꢀꢀO1
N2–H2BꢀꢀꢀO2
C15–H15AꢀꢀꢀS1
C15–H15AꢀꢀꢀO4
0.86
0.86
0.96
0.96
2.09
1.94
2.94
2.96
2.95
2.72
2.88
2.92
2.34
2.06
1.93
2.96
2.67
2.89
2.96
2.40
2.552(4) 112.8
2.655(3) 140.1
3.830(5) 155.6
3.753(5) 144.9
3.505(5) 116.9
3.486(5) 136.9
3.790(5) 164.9
3.529(4) 121.1
3.186(4) 143.8
2.533(3) 113.8
2.657(3) 141.0
3.688(5) 133.5
3.435(5) 137.5
3.837(4) 171.3
3.545(4) 119.6
3.281(4) 149.6
-x, -y ? 1, -z ? 2
x - 1, ?y, ?z
C13–H13AꢀꢀꢀC11 0.93
x, ?y - 1, ?z ? 1
C8–H8BꢀꢀꢀO3
C6–H6AꢀꢀꢀO4
C7–H7AꢀꢀꢀS1
C7–H7AꢀꢀꢀO2
N1–H1AꢀꢀꢀO1
N2–H2BꢀꢀꢀO2
C15–H15CꢀꢀꢀN2
C8–H8CꢀꢀꢀO3
C8–H8BꢀꢀꢀS1
C7–H7AꢀꢀꢀS1
C7–H7AꢀꢀꢀO2
0.96
0.93
0.98
0.98
0.86
0.86
0.96
0.96
0.96
0.98
0.98
-x ? 1, -y ? 1, -z ? 2
-x ? 2, -y ? 2, -z ? 2
–x ? 1, -y ? 2, -z ? 2
–x ? 2, -y ? 2, -z ? 2
4b
-x ? 2, -y ? 2, -z
-x ? 2, -y ? 2, -z
x - 1, y, z
-x ? 2, -y ? 1, -z
-x ? 1, -y ? 1, -z
Table 4 Crystal data
for 4a and 4b
4a
4b
Empirical formula
Formula weight
C16H16Cl2N4O4S
431.29
C15 H13Cl3N4O3S
435.70
CCDC deposit no.
290740
296648
˚
Wavelength(A)
0.71073
0.71073
Crystal size (mm)
Temperature (K)
Crystal system
0.35 9 0.30 9 0.25
298(2)
0.15 9 0.15 9 0.05
298(2)
Triclinic
Triclinic
Space group
P-1
P-1
˚
a = 8.053(12) A
˚
a = 7.939(5) A
Unit cell dimensions
a = 102.84(2)°
b = 10.541(16) A
a = 105.302(10)°
˚
b = 10.183(7) A
˚
b = 106.99(2)°
c = 12.461(19) A
b = 105.729(9)°
˚
c = 12.764(9) A
˚
c = 94.615(19)°
974(3)
c = 90.698(11)°
954(11)
2
3
˚
Volume (A )
Z
2
Density (Mg/m3)
Absorption coefficient (mm-1
F(000)
1.470
0.470
444
1.517
)
0.613
444
Theta range for data collection(°)
Limiting indices
1.77–26.01
1.73–25.01
-9 B h B 9, -12 B k
B 12, -9 B l B 15
-9 B h B 8, -8 B
k B 12, -15 B l B 13
Reflections collected
Independent reflections
Completeness to theta
Goodness-of-fit on F2
Final R indices [I [ 2r(I)]
R indices (all data)
4433
3289
3723 [R(int) = 0.0250]
26.01, 97.4%
2056 [R(int) = 0.0294]
25.01, 98.0%
1.021
0.924
R1 = 0.0461, wR2 = 0.1231
R1 = 0.0583, wR2 = 0.1334
0.376 and -0.423
R1 = 0.0517, wR2 = 0.1254
R1 = 0.0818, wR2 = 0.1385
0.352 and -0.347
-3
)
˚
Largest diff. peak and hole (e A
123

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J Chem Crystallogr (2010) 40:675–680
Fig. 1 Molecular structure of 4a. The intramolecular hydrogen bonds
are shown as dashed lines
Fig. 4 The packing diagram viewed down the a axis for 4b.
Hydrogen bonds are shown as dashed lines
C15H13Cl3N4O3S: C, 41.35; H, 3.01; N, 12.86; Found: C,
41.46; H, 3.23, N, 12.98.
Results and Discussion
Synthesis and Spectral Analyses
Compounds 4a and 4b were synthesized according to our
previous reported [13–16]. The synthetic routes were out-
lined in Scheme 1. Firstly, 2-(2,4-dichlorophenoxy)propi-
onic acid was readily prepared following the literature
procedures from commercially available 2,4-dichlorophe-
nol. Then 2,4-dichlorophenoxypropionic acid was acylated
by SOCl2 followed by the reactions of potassium isothio-
cyanate to give 2 in 95% reaction yield. Finally, the cou-
pling 2 with 4,6-disubstituted-2-amino-pyrimidine 3 was
successfully carried out to afford thiourea 4a and 4b in
moderate reaction yields. 4a and 4b were characterized by
Fig. 2 The packing diagram viewed down the a axis for 4a.
Hydrogen bonds are shown as dashed lines
CH
CH
SOCl
3
3
2
Cl
O
CHCONCS
Cl
O
CHCOOH
KSCN
Cl
Cl
1
2
X
N
X
H2N
N
O
C
N
N
Y
Cl
O
CH
CH
NH C NH
S
3: 3a~3b
3
Cl
Y
3
4
4a: X,Y = OCH ; 4b: X = Cl, Y = OCH
3
Fig. 3 Molecular structure of 4b. The intramolecular hydrogen bonds
are shown as dashed lines
Scheme 1 Synthesis of 4a and 4b
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J Chem Crystallogr (2010) 40:675–680
679
1
IR, H NMR, GC/MS and Elemental analysis. All results
More importantly, 4a can be stabilized by two intra-
molecular hydrogen bonds, forming a six-member
were in full agreement with the proposed structures. Taking
4a as an example, IR spectrum gave the strong stretching
vibration at 1,695 cm-1 for carbonyl group and at 3,370
and 3,154 cm-1 for N–H group. Two singlet signal at
˚
N2–H2BꢀꢀꢀO2 [2.655(3) A, 140.1°]) and an five-member
˚
ring N1–H1AꢀꢀꢀO1 [2.552 (4) A, 112.8°]). The intermo-
lecular hydrogen bonds can consolidate obviously the
crystal lattices as shown in Table 3. Each layer is consisted
of many thiourea ribbons (only one layer and two ribbons
were drawn in Fig. 5a). Each ribbon include three indepen-
dent thiourea molecules and form four hydrogen bonds of
C–HꢀꢀꢀS in Fig. 5b, in which two independent thiourea mol-
ecule are arranged in a parallel and overlapping fashion and
third thiourea molecule in opposite orientation in a parallel
and bordering fashion. In comparison with 4a, these similar
hydrogen-bonding patterns in the 4b are also observed.
In particular, the sulphur in the 4a is involved in
bifurcated hydrogen bonding with the hydrogen of methyne
(CHCH3) group and the hydrogen of the terminal methyl of
methoxy group in the thiourea moiety. As shown in Fig. 6,
one of linkage mode is that two independent thiourea
molecule is bonded together via two same types of
hydrogen bonds of C–HꢀꢀꢀS (C7A–H7AAꢀꢀꢀS1E and C7E–
H7AEꢀꢀꢀS1A) with a parallel manner in opposite orienta-
tion (Fig. 6a), while the another mode is bonded via two
same hydrogen bonds of C–HꢀꢀꢀS (C15I–H15ZꢀꢀꢀS1AE and
C15E–H15MꢀꢀꢀS1AJ) with shoulder to shoulder manner in
a coplanar behavior (Fig. 6b). These hydrogen-bonding
patterns demonstrate clearly the role of linkage modes of
C–HꢀꢀꢀS hydrogen bonds in such a thiourea molecule,
which indicate the versatility of C–HꢀꢀꢀS hydrogen bonds in
the construction of novel crystal lattices. Table 3 shows a
1
12.31 and 12.23 ppm in H NMR spectrum ascribed NH
protons and a singlet signal at 6.05 ppm for proton in
pyrimidine ring. In addition, MS matched the calculated
values to show [M]? ions as 430.
Crystal Structure
A single crystal X-ray structure determination (Fig. 1, the
selected bond distances in Table 1 and the angles and in
Table 2) shows that the molecular structure of 4a consists
of a phenoxypropionyl moiety and a pyrimidine moiety in
approximate opposite direction around the bridge of thio-
urea, where the both moiety are almost in the same
plane. Configuration of 4a with S–O distance [S1–C10
˚
1.652(3) A] and the N2–C10–S1 angle [129.55(17)°] is
strongly similar with the molecular structure of N0-(4-
Chloro-6-methoxypyrimidin-2-yl)-N-(2-(2,4-dichlorophen-
oxy)propionyl)thiourea with S–O distance [S1–C10 in
˚
1.637(3) A] and the N2–C10–S1 angle of [129.5(2)°] [21].
In comparison with 4a, 4b gives similar bond patterns of
˚
CONH bond with C=O [O2–C9 of 1.223(3) A and of
˚
˚
1.225(3) A] and C–N distance [N1–C9 of 1.368(3) A and
˚
of 1.364(4) A] as shown in Fig. 3 and in Tables 1 and 2. In
addition, both bond distances of C–Cl are in the expected
single-bonds range although slight difference.
(a)
(b)
Fig. 5 Perspective view of the layer structure of 4a. a Presenting the unit of layer, b linkage modes of self-assembled hydrogen-bonded ribbons
123

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J Chem Crystallogr (2010) 40:675–680
from the Cambridge Crystallographic Data Centre(CCDC),
12 Union Road, Cambridge CB2 1EZ, UK; fax: ?44(0)
1223-336033; e-mail:deposit@ccdc.cam.ac.uk].
(a)
Acknowledgments We are grateful to China National Natural
Science Foundation (No. 20543007), Shanghai Leading Academic
Discipline Project (projects No. S30406, 08YZ71 and DZL807) for
financial support and the Shanghai Branch of National Pesticide R&D
South Center for the preliminary Biological Test.
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