Metallosupramolecular zinc and cadmium complexes of Bis[4-(2-pyridyl)pyrimidinylthiomethyl]benzenes

Article abstract of DOI:10.1016/j.molstruc.2008.03.054

Reactions of L¹ and L² (L¹ = 1,4-bis[4-(2-pyridyl)pyrimidinylthiomethyl] benzene; L² = 1,3-bis[4-(2-pyridyl)pyrimidinylthiomethyl]benzene) with CdI₂, ZnI₂ and Cd(NO₃)₂

Full text of DOI:10.1016/j.molstruc.2008.03.054

Journal of Molecular Structure 891 (2008) 266–271
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Metallosupramolecular zinc and cadmium complexes
of Bis[4-(2-pyridyl)pyrimidinylthiomethyl]benzenes
Huaze Dong b, Haibin Zhu a, Taifeng Tong a,1, Shaohua Gou a,b,
*
a School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 211189, China
b School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
a r t i c l e i n f o
a b s t r a c t
Reactions of L1 and L2 (L1 = 1,4-bis[4-(2-pyridyl)pyrimidinylthiomethyl] benzene; L2 = 1,3-bis[4-(2-pyri-
dyl)pyrimidinylthiomethyl]benzene) with CdI2, ZnI2 and Cd(NO3)2 led to the formation of two discrete
bimetallic complexes and one single-handed helix, respectively. Conformation changes of ligands after
interactions with metal salts were found due to the positional isomerism of xylyl groups and the effect
of anions.
Article history:
Received 17 January 2008
Accepted 25 March 2008
Available online 11 April 2008
Keywords:
Ó 2008 Elsevier B.V. All rights reserved.
Dinuclear complexes
Metallosupramolecule
Single-handed helix
Structure elucidation
1. Introduction
As our continuing study, herein reported are metallosupramo-
lecular zinc and cadmium complexes of bis[4-(2-pyridyl)pyr-
A class of multi-armed organic ligands with a generalized
formula (Scheme 1a) has been frequently used for constructing
supramolecular architectures in recent years. Within these mol-
ecules, heterocyclic donors containing N atoms are attached to
the central linking aryl core via the –SCH2-spacer. Several re-
ports on metallosupramolecular complexes assembled from
these organic ligands reveal some common features [1–7]: (i)
Attached arms within these molecules can be arranged in vari-
ous conformations when interacting with different metal ions.
(ii) Not only N atoms from heterocyclic donors but also S atoms
of the thioether spacer are capable of binding metal ions with
preference for the soft metal ions such as Cu(I) and Ag(I) ions.
(iii) Discrete and polymeric structures with 1D, 2D and 3D
dimensions have been obtained with these organic ligands. (iv)
Apart from the metal ions, counterions also exert a significant
impact on the final assembly outcome. In our previous study,
we have reported an intriguing Cu4S4 cluster resulted from C–
imidinylthiomethyl]benzenes (Scheme 1c, L1 and L2), two of
which are discrete dinuclear complexes and one is a single-handed
helix.
2. Experimental
All solvents were in analytic grade used as commercially avail-
able. Infrared spectra were performed on a Bruker Vector 22 spec-
trophotometer with KBr pellets in the 400–4000 cmꢀ1 1H NMR
.
spectra were recorded on a Bruker DRX 500 MHz spectrometer.
Electrospray ionization (ESI) mass spectra were performed
employing a Finnigan MAT SSQ 710 mass spectrometer in a scan
range 100–1200 amu.
2.1. Synthesis of L1 and L2
Both L1 and L2 were made by a similar way as following. To the
solution of 4-(2-pyridinyl)pyrimidine-2-thiol (3.78 g, 20 mmol)
and sodium hydroxide(0.80 g, 20 mmol) in dry ethanol (300 mL),
1,4-bis(bromomethyl)benzene or 1,3-bis(bromomethyl)benzene
(2.64 g, 10 mmol) in CCl4 (30 mL) was added. The mixture was stir-
red and refluxed for 8 h. After cooled, precipitates were filtered,
washed by water and ethanol, and dried in vacuum. For L1: yield
54.3%, m.p. 173–174 °C. Anal. Calcd for C26H20N6S2: C, 64.98; H,
4.19; N, 17.49%. Found: C, 64.61; H, 4.52; N, 17.39 %. IR (KBr,
cmꢀ1): 1605 (w), 1557 (s), 1538 (s), 1471 (m), 1418 (s), 1346 (s),
1243 (m), 1194 (s), 1080 (w), 1042 (w), 829 (w), 797 (w),
S
cleavage of 2,6-bis((4-(pyridine-2-yl)pyrimidin-2-ylthio)-
methyl)-4-chlorophenol (Scheme 1b) in the presence of copper
(I) chloride [8]. In contrast, a discrete dinuclear cobalt complex
has been generated from the assembly with cobalt nitrate in our
following work [9].
* Corresponding author. Address: School of Chemistry and Chemical Engineering,
Southeast University, Nanjing, Jiangsu 211189, China.
E-mail address: sgou@seu.edu.cn (S. Gou).
On leave from China Pharmaceutical University.
1
0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2008.03.054

H. Dong et al. / Journal of Molecular Structure 891 (2008) 266–271
267
Scheme 1.
765(m). ESI-MS: 503.0 (100%) [L+Na]+, 481.3 (25%) [L+H]+. 1H NMR
(CDCl3): d 8.71 (d, 2H, pyridyl-H), 8.64 (d, 2H, pyrimidyl-H), 8.44
(d, 2H, pyrimidyl-H), 8.00 (d, 2H, pyridyl-H), 7.86 (t, 2H, pyridyl-
H), 7.66 (s, 1H, aryl-H), 7.40 (m, 5H, pyridyl-H (2H) and aryl-H
(3H)), 4.52 (s, 4H, methylene-H). For L2: yield 74.6%, m.p. 110–
111 °C. Anal. Calcd for C26H20N6S2: C, 64.98; H, 4.19; N, 17.49%.
Found: C, 64.57; H, 4.37; N, 17.42%. IR (KBr, cmꢀ1): 1591 (w),
1562 (vs), 1531 (s), 1476 (w), 1421 (s), 1334 (s), 1289 (w), 1243
(w), 1215 (m), 1198 (m), 1023 (w), 832 (w). ESI-MS: 503.0
(100%) [L+Na]+, 481.3 (10%) [L+H]+. 1H NMR (CDCl3): d 8.74 (d,
2H, pyridyl-H), 8.69 (d, 2H, pyrimidyl-H), 8.46 (d, 2H, pyrimidyl-
H), 8.10 (d, 2H, pyridyl-H), 7.89 (t, 2H, pyridyl-H), 7.45 (s, 6H, pyr-
idyl-H (2H) and aryl-H(4H)), 4.52 (s, 4H, methylene-H). Single crys-
tals of L1 and L2 suitable for X-ray diffraction were grown from
each methanol solution by slow evaporation in air at room
temperature.
tubes and diffused with ether. Colorless crystals were obtained.
(yield: 47%). Anal. Calcd for C26H20CdN8O6S2: C, 43.55; H,
2.814; N, 15.63%. Found: C, 43.59; H, 2.78; N, 15.58%. IR (KBr,
cmꢀ1): 1652 (w), 1563 (m), 1546 (m), 1478 (w), 1415 (s),
1384 (vs), 1339 (m), 1296 (w), 1211 (w), 824 (w), 797 (w),
764 (w).
2.3. X-ray crystallography
Single crystal data for organic ligands, L1 and L2, together
with complexes 1–3 were collected at 291(2) K on a Bruker
SMART CCD-4K diffractometer employing graphite-monochro-
mated MoKa radiation (k = 0.71073 Å). The data were collected
using SMART and reduced by the program SAINT [10]. All the
structures were solved by direct methods and refined by the
full-matrix least squares method on F2obs by using SHELXTL-PC
software package [11]. Non-hydrogen atoms were placed in geo-
metrically calculated positions. The crystallographic data and se-
lected bonds length and angles are listed in Tables 1 and 2,
respectively.
2.2. Preparation of zinc and cadmium complexes
2.2.1. Synthesis of [Cd2L1I4] (1)
To a suspension of L1 (24.0 mg, 0.050 mmol) in chloroform
(5 mL) in a tube, a solution of CdI2 (18.3 mg, 0.05 mmol) in meth-
anol (5 mL) was very slowly dropped on the top of the ligand solu-
tion. Crystals formed after 10 days. (yield: 40%). Anal. Calcd for
C26H20I4N6S2Cd2: C, 25.74; H, 1.66; N, 6.93%. Found: C, 32.20; H,
2.27; N, 10.78%. IR (KBr, cmꢀ1): 1597 (w), 1561 (s), 1547 (s),
1476 (w), 1416 (m), 1338 (vs), 1217 (m), 1198 (m), 1106 (w),
1016 (w), 821 (w).
3. Results and discussion
3.1. Description of crystal structures of L1 and its cadmium complex 1
A perspective view of L1 with the atom-numbering scheme is
shown in Fig. 1. L1 crystallizes in the monoclinic space group
P21/n. It adopts a trans conformation with two arms on the oppo-
site sides of the central phenyl ring. Both pyridyl and pyrimidinyl
rings at the end of each arm are not coplanar with a deviation of
6.95°. It is worthwhile to note that N1 and N3 donor atoms in each
arm are not situated in chelating positions but with a large torsion
angle N3–C5–C4–N1of 173.45°. The mean plane across the pyri-
midinyl ring is inclined to that of linking phenyl ring at the angle
of 66.43°.
2.2.2. Synthesis of [Zn2L2I4] (2)
2 was made in the same way as that of 1 except that ZnI2
(16.0 mg, 0.05 mmol) and L2 (20.9 mg, 0.05 mmol) were used.
Crystals formed after six days. (yield: 42%). Anal. Calcd for
C26H20I4N6S2Zn2: C, 27.91; H, 1.80; N, 7.51%. Found: C, 27.93; H,
1.82; N, 7.49%. IR (KBr, cmꢀ1): 1602 (w), 1561 (s), 1544 (s), 1478
(m), 1446 (w), 1414 (s), 1335 (s), 1210 (m), 1166 (w), 1085 (w),
828 (w), 791 (w), 760 (m).
However, reaction of CdI2 resulted in significant conformation
changes in L1. As depicted in Fig. 2a, each ligand connects two
ˆ
identical Cd ions in NN chelation modes to form a discrete dinu-
2.2.3. Synthesis of [CdL2(NO3)2]n (3)
clear cadmium coordination complex 1, which crystallizes in the
monoclinic space group P21/n. The coordination geometry
around each Cd atom is a distorted tetrahedron completed by
L2 was treated with Cd(NO3)2 in DMF in ration 1:1 at room
temperature. The solution was introduced into crystallization

268
H. Dong et al. / Journal of Molecular Structure 891 (2008) 266–271
Table 1
Crystal and structure refinemental data for ligand and complexes 1–3
Complex
L1
1
L2
2
3
Formula
Formula weight
Crystal size (mm)
Crystal system
Space group
a (Å)
b (Å)
c (Å)
a (°)
b (°)
C26H20N6S2
480.62
0.10 ꢁ 0.20 ꢁ 0.60
Monoclinic
P21/n
4.1704(13)
16.407(5)
16.275(5)
90
90.000
90
1113.6(6)
2
C26H20Cd2I4N6S2
1213.00
0.04 ꢁ 0.20 ꢁ 0.10
Monoclinic
P21/c
7.6879(15)
17.822(3)
12.652(3)
90
103.519(4)
90
1685.5(6)
2
C26H20N6S2
480.62
0.40 ꢁ 0.60 ꢁ 0.80
Triclinic
P ꢀ 1
C26H20I4N6S2Zn2
1119.00
C26H20CdN8O6S2
717.05
0.10 ꢁ 0.20 ꢁ 0.40
0.10 ꢁ 0.20 ꢁ 0.40
Triclinic
Monoclinic
P ꢀ 1
P21/c
15.837(3)
9.808(2)
18.661(4)
9.241(2)
11.281(3)
11.546(3)
79.827(4)
87.086(4)
72.829(4)
1131.9(5)
2
11.6667(14)
12.6015(15)
12.8564(16)
114.148(2)
98.539(2)
90.164(2)
1701.4(4)
2
90
107.746(4)
90
2760.7(10)
4
c (°)
V (Å3)
Z
T (K)
291(2)
1.433
0.268
500
291(2)
2.390
5.075
1116
291(2)
1.407
0.264
498
291(2)
2.184
5.188
1044
291
1.725
1.001
1440
Dcalcd (mg/m3)
l (mmꢀ1
F(000)
)
Ref. collected/unique
Parameters
5441/1943 (Rint = 0.097)
154
0.0543,
0.1088,
0.78
8300/2961 (Rint = 0.063)
181
0.0550,
0.0922,
0.92
5654/3925 (Rint = 0.035)
307
0.0586
0.1603
0.96
8466/5868 (Rint = 0.049)
361
0.0446
0.1224
0.95
13,957/5142 (Rint = 0.089)
388
0.0517
0.0885
0.75
ꢀ0.34/0.61
a
R1
wR2
b
GOF
Min/max Dq (e Åꢀ3
)
ꢀ0.21/0.20
ꢀ0.56/0.83
ꢀ0.47/0.37
ꢀ1.57/1.17
P
P
a
R1
wR2
¼
kFoj ꢀ jFck= jFoj.
h
i
1=2
P
P
2
2
½wðF2o ꢀ F2c Þ ꢂ= wðFo2Þ
.
b
¼
Table 2
(dC–I = 3.818(11), \C–H. . .I = 153.1°; symmetry code: 1 ꢀ x, 1 ꢀ y,
ꢀz), giving a chain-like structure.
Selected bonds length (Å) and angles (°)
Complex 1
Cd1–I1
Cd1–N1
I1–Cd1–I2
I1–Cd1–N3
I2–Cd1 –N1
2.6535(15)
2.318(7)
123.94(4)
111.6(2)
119.7(2)
Cd1–I2
Cd1–N3
I1–Cd1–N1
N1–Cd1–N3
I2–Cd1–N3
2.6469(14)
2.298(8)
108.4(2)
71.0(3)
3.2. L2 and its zinc (2) and cadmium complexes (3)
Fig. 3 shows a perspective view of L2 with the atom-numbering
1
ꢀ
109.9(2)
scheme. It crystallizes in the triclinic space group P1. Like L , two N
donor atoms belonging to two different heterocyclic rings in each
arm are not arranged in a chelation mode, with the torsion angle
N–C–C–N of 169.98° and 178.50°, respectively. Two pyrimidinyl
rings of each arm are inclined to the central phenyl ring at the an-
gles of 67.67° and 75.28°, respectively. Despite that the thioether
spacers are arrayed in a trans conformation, each arm is pointed to-
ward the same direction.
Attempt to assemble with CdI2 fails to obtain single crystals
suitable for X-ray crystallography. Replacement of ZnI2 affords a
discrete dinuclear zinc complex 2 analogous to complex 1. Similar
to the situation in L1, coordination of zinc atom promotes the pyr-
idyl ring to rotate to chelation positions. More importantly, metal
chelation significantly alters the whole conformation of organic li-
gand L2. On one hand, space arrangement of two arms distinctly
varies from in trans to in cis conformation. On the other hand,
the dihedral angle of two pyrimidinyl rings with respect to the cen-
tral phenyl ring changed to 72.34° and 82.39°, respectively (see
Fig. 4).
Complex 2
I1–Zn1
Zn1–N1
I3–Zn2
Zn2–N4
I1–Zn1–I2
I1–Zn1–N3
I2–Zn1–N3
I3–Zn2–I4
I3–Zn2–N6
I4–Zn2–N6
2.5139(14)
2.103(7)
2.5262(13)
2.072(8)
123.04(5)
107.4(2)
117.5(2)
120.54(5)
107.6(2)
114.4(2)
I2–Zn1
Zn1–N3
I4–Zn2
Zn2–N6
I1–Zn1–N1
I2–Zn1–N1
N1–Zn1–N3
I3–Zn2–N4
I4–Zn2–N4
N4–Zn2–N6
2.5265(12)
2.074(8)
2.5234(15)
2.023(8)
119.2(2)
103.2(2)
78.2(3)
115.7(2)
111.3(2)
80.5(3)
Complex 3
Cd1–O1
Cd1–O4
Cd1–N3
Cd1–N6
O1–Cd1–N1
O1–Cd1–N4
O2–Cd1–O4
N1–Cd1–N4
N3–Cd1–N4
O4–Cd1–N4
O4–Cd1–N3
2.369(6)
2.335(7)
2.320(5)
2.299(5)
111.1(2)
158.35(18)
155.6(2)
80.02(18)
119.70(19)
75.2(2)
Cd1–O2
Cd1–N1
Cd1–N4
2.755(7)
2.423(6)
2.525(5)
108.9(2)
81.95(19)
91.33(19)
125.12(17)
115.74(19)
173.2(2)
96.37(19)
127.0(2)
O1–Cd1–O4
O1–Cd1–N3
O1–Cd1–N6
O2–Cd1–N4
N1–Cd1–N6
N3–Cd1–N6
O4–Cd1–N6
O4–Cd1–N1
Treatment of Cd(NO3)2 with L2 generates a polymeric complex 3
rather than the discrete one. The compound crystallizes in the
space group P21/n, consisting of one Cd atom, one ligand and two
nitrate. The coordination environment around the Cd atom is a dis-
torted octahedron, equatorially coordinated by three N atoms from
two arms and one O atom from one nitrate and apically occupied
by one N atom and one O atom. It is noted that two nitrate anions
are different in coordination modes. One is unidentate with Cd–O
bond length of 2.335 Å and the other is semi-bidentate with one
exceptional longer Cd–O distance of 2.755 Å apart from normal
Cd–O bond length of 2.369 Å. Each ligand bridges two Cd atoms
via N–N chelation to produce a single-handed helix with a
period of 18.661 Å. Furthermore, as shown in Fig. 5b, helices are
joined together via C–H. . .O hydrogen bonds (dC–O = 3.305(9), \C–
84.77(19)
two N atoms from one arm and two I atoms. The average Cd–N
and Cd–I bond lengths are 2.308 Å and 2.650 Å, respectively.
Notably, the pyridyl ring in each arm is obliged to rotate to che-
lation sites along C4–C5 bond axis due to the metal coordination,
whilst the dihedral angle between the two heterocyclic rings of
each arm is decreased to 3.36° compared with that in a free li-
gand. In addition, the mean plane of pyrimidinyl ring is nearly
perpendicular to that of central phenyl ring in sharp contrast
with the situation in the free ligand. As shown in Fig. 2b, com-
plex 1 is further joined together via C–H. . .I hydrogen bonds

H. Dong et al. / Journal of Molecular Structure 891 (2008) 266–271
269
Fig. 1. Perspective view of L1 with the atom-numbering scheme (30% probability ellipsoids).
Fig. 2. (a) Perspective view of cadmium complex 1 with the atom-numbering scheme (30% probability ellipsoids). (b) View of the packing structure of complex 1 along a axis.
Fig. 3. Perspective view of L2 with the atom-numbering scheme (30% probability
Fig. 4. Perspective view of complex 2 with the atom-numbering scheme (30% pr-
ellipsoids).
obability ellipsoids).

270
H. Dong et al. / Journal of Molecular Structure 891 (2008) 266–271
Fig. 5. (a) Perspective view of asymmetric unit of complex 3 with the atom-numbering scheme (30% probability ellipsoids). (b) View of helix in complex 3 (top), perspective
view of the helices held by hydrogen bonds (bottom).
H. . .O = 146.0°; symmetry code: 2 ꢀ x, 1/2 + y, 3/2 ꢀ z) between the
5. Supplementary
adjacent helical chains with opposite chirality.
In addition, L2 in 3 adopts a trans conformation to open its two
Crystallographic data for the structural analysis have been
heterocyclic arms to connect metal ions, which are on the opposite
side of the central phenyl ring. The pyrimidinyl and pyridyl rings
are not parallel each other with a dihedral angle of 14.92° and
12.31°, respectively. The dihedral angle of two pyrimidinyl rings
with respect to the central phenyl ring changed to 76.93° and
67.61°, respectively.
deposited at the Cambridge Crystallographic Data Center with
CCDC deposition numbers 673988–673992 for organic ligands L1,
L2 and for metal complexes 1–3, respectively. Copies of this infor-
mation may be obtained free of charge from the CCDC, 12 Union
Road, Cambridge, CB2 1EZ, UK (fax: +44 1223 336 033; e-mail: de-
posit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk).
Acknowledgements
4. Conclusions
The authors are grateful to the financial support from National
Natural Science of Foundation of China (Project No. 20271026) and
Postdoctoral Research Fund of China (20070411010).
In this study, three novel complexes with different architec-
tures, [Cd2L1I4] (1), [Zn2L2I4] (2), [CdL2(NO3)2]n (3) were con-
structed from L1 and L2, respectively. In contrast to that in a free
ligand, the pyridyl ring in each arm in the complexes is forced to
rotate to connect metal ions. L1 kept the same configuration in 1
with that of the free ligand, while in the structures of 2 and 3, L2
takes different configurations, i.e. two arms are distinctly in a cis
conformation in 2 and adopt a trans conformation in 3. The present
study demonstrates that the nature of positional isomerism and
geometric needs of metal atoms as well as the effect of anions play
an important role in the crystal packing of MOFs.
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