Synthesis and structure of a silver(I) complex {[Ag5(L) 2(NO3)4](NO3)(CHCl3) 2}n [L = 2,3-bis(pyrimidine-2-thiomethyl)quinoxaline]

Article abstract of DOI:10.1007/s10870-008-9382-2

The reaction of the dithioether ligand, 2,3-bis(pyrimidine-2-thiomethyl) quinoxaline (L) with AgNO₃, leads to the formation of a novel complex {[Ag₅(L)₂(NO₃)₄](NO ₃)(CHCl₃)₂}n 1, which has been characterized by single-crystal X-ray diffraction analysis: monoclinic, space group C2/c, with a = 34.741(7), b = 9.930(2), c = 17.004(4) A, β = 106.497(6)° and V = 5625(2) A³. Complex 1 consists of 2D {[Ag ₅(L)₂(NO₃)₄]⁺}n cations, uncoordinated NO₃^- anions and CHCl₃ solvent molecules. In 1, there exist three crystallographic independent Ag^I centers, which adopt different coordination geometries. There exist π-π stacking interactions in the complex and these weak interactions further stabilize the crystal structure in the solid state. The coordination feature of the ligand has been investigated by DFT calculations.

Full text of DOI:10.1007/s10870-008-9382-2

J Chem Crystallogr (2008) 38:749–753
DOI 10.1007/s10870-008-9382-2
ORIGINAL PAPER
Synthesis and Structure of a Silver(I) Complex
{[Ag5(L)2(NO3)4](NO3)(CHCl3)2}n [L = 2,3-bis
(pyrimidine-2-thiomethyl)quinoxaline]
Chao-Yan Zhang Æ Qian Gao Æ Ya-Bo Xie Æ
Jian-Bo Feng
Received: 19 October 2007 / Accepted: 27 March 2008 / Published online: 15 April 2008
Ó Springer Science+Business Media, LLC 2008
Abstract The reaction of the dithioether ligand, 2,3-
bis(pyrimidine-2-thiomethyl)quinoxaline (L) with AgNO3,
leads to the formation of a novel complex {[Ag5(L)2
(NO3)4](NO3)(CHCl3)2}n 1, which has been characterized
by single-crystal X-ray diffraction analysis: monoclinic,
approach is attractive because the flexibility and conforma-
tion freedoms of such ligands offer the possibility for the
construction of unprecedented frameworks with tailored
properties and functions. Due to the multiformity of coor-
dination geometry of AgI ion, the complexes of AgI with
organic ligands were widely investigated in the past decades
[10–14]. In this paper, a multi-dentate dithioether ligand
containing a aromatic spacers, 2,3-bis(pyrimidine-2-thio-
methyl)quinoxaline (L), and a AgI complex of this ligand,
{[Ag5(L)2(NO3)4](NO3)(CHCl3)2}n 1, have been synthe-
sized and characterized. We report herein the crystal
structure of the AgI coordination polymer, and the coordi-
nation feature of the ligand has also been investigated by
DFT calculations (Chart 1).
space group C2/c, with a = 34.741(7), b = 9.930(2),
3
˚
˚
c = 17.004(4) A, b = 106.497(6)° and V = 5625(2) A .
Complex 1 consists of 2D {[Ag5(L)2(NO3)4]+}n cations,
uncoordinated NOÀ3 anions and CHCl3 solvent molecules. In
1, there exist three crystallographic independent AgI centers,
which adopt different coordination geometries. There exist
p–p stacking interactions in the complex and these weak
interactions further stabilize the crystal structure in the
solid state. The coordination feature of the ligand has been
investigated by DFT calculations.
Experimental
Keywords Crystal structure Á Dithioether ligand Á
Silver(I) complex Á Coordination feature of ligand
Materials and General Methods
All the reagents for syntheses were commercially available
and employed without further purification or purified by
standard methods prior to use. Elemental analyses were
performed on a Perkin-Elemer 240C analyzer and IR
spectra were measured on a 170SX (Nicolet) FT-IR spec-
Introduction
The generation of coordination architectures depends on the
combination of several factors like the coordination geom-
etry of metal ions, the nature of the ligands and the reaction
conditions. The suitable organic ligands favoring structure-
specific self-assembly are the basis for the construction of
coordination architectures. Recently, increasing attention
has been paid to the use of flexible bridging units in the
construction of supramolecular architectures [1–9], and this
1
trometer with KBr pellets. H NMR spectra were recorded
on a Bruker AC-P500 spectrometer (300 MHz) at 25 °C in
CDCl3 with tetramethylsilane as the internal reference.
Preparation of L and
{[Ag5(L)2(NO3)4](NO3)(CHCl3)2}n (1)
The ligand L was prepared according to Scheme 1. 1,4-
Dibromo-2,3-butanedione was synthesized by the adoption
of a literature procedure [15]. 2,3-Bis(bromomethyl)quin-
oxaline was prepared by the condensation reaction of an
C.-Y. Zhang Á Q. Gao Á Y.-B. Xie (&) Á J.-B. Feng
College of Environmental and Energy Engineering,
Beijing University of Technology, Beijing 100022, China
e-mail: xieyabo@bjut.edu.cn
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J Chem Crystallogr (2008) 38:749–753
Table 1 Crystal data and structure refinement summary for 1
CCDC deposit no.
Empirical formula
Formula weight
Crystal system
Space group
CCDC-272331
38H30Ag5Cl6N17O15S4
C
N
N
1845.08
N
N
N
N
Monoclinic
C2/c
S
S
˚
Unit cell dimensions (A, °)
a = 34.741(7)
b = 9.930(2)
c = 17.004(4)
b = 106.497(6)
5625(2)
L
Chart 1
3
˚
equimolar amount of 1,4-dibromo-2,3-butanedione and
1,2-diaminobenzene in ethanol at reflux for ca. 2 h. The
reaction of 2,3-bis(bromomethyl)quinoxaline with the
appropriate 2-mercaptopyrimidine in the presence of KOH
gave the ligand with a yield of 78%, and the product was
Volume (A )
Z
4
Dcalcd (g/cm3)
2.179
l (mm-1
)
2.224
F (000)
3592
1
characterized by H NMR and elemental analyses. Anal.
Range of h, k, l
-27/41, -11/11, -20/14
12448/4943
0.0651
Found: C, 56.84; H, 3.91; N, 22.43. Calcd. for C18H14N6S2:
1
C, 57.02; H, 3.73; N, 22.21. H NMR (CDCl3): d 5.00
(s, 4H, –SCH2–), 6.96*8.51 (m, 12H, Ar–H).
Reflections collected/unique
R(int)
Max. and min. transmission
Data/restraints/parameters
Goodness-of-fit on F2
R and Rw
1.0000 and 0.5388
4943/91/422
1.012
The complex 1 was prepared by the method described as
follow. The solution of AgNO3 (17 mg, 0.1 mmol) in
MeOH was carefully layered on top of a solution of L
(38 mg, 0.1 mmol) in CHCl3 in a test-tube. After 2 weeks
at room temperature, colorless block single crystals suit-
able for X-ray investigation appeared at the boundary
between MeOH and CHCl3. IR (KBr pellet, cm-1): 3441w,
3003w, 2918w, 1561s, 1547s, 1488w, 1382vs, 1355s,
1292m, 1205m, 1180m, 763s. Anal. Found: C, 24.51; H,
1.83; N, 13.05. Calcd. for C38H30Ag5Cl6N17O15S4: C,
24.74; H, 1.64; N, 12.91.
0.0469 and 0.1234
0.961 and -0.744
3
Largest diff. Peak and hole (e/A )
˚
The final refinements were performed by full-matrix least-
squares methods on F2 by SHELXL-97 program package
[18]. Hydrogen atoms were included in calculated positions
and refined with fixed thermal parameters riding on their
parent atoms. The crystallographic data and experimental
details for structural analyses are summarized in Table 1.
CCDC-272331 contains the supplementary crystallo-
graphic data for the complex 1. These data can be obtained
from the Cambridge Crystallographic Data Centre, 12
Union Road, Cambridge CB2 1EZ, UK; Fax: +44-1223-
336033; E-mail: deposit@ccdc.cam.ac.uk.
X-ray Crystallographic Study of the Complex 1
The single crystal X-ray diffraction measurement was
carried out on a Bruker Smart 1000 CCD area detector.
Intensities of reflections were measured using graphite-
˚
monochromatized MoKa radiation (k = 0.71073 A) with x
scan mode at 293(2) K in the range of 1.22 \ h \ 25.00°.
Unit cell dimensions were obtained with least-squares
refinements and semi-empirical absorption corrections
were applied using SADABS program [16]. The structure
was solved by direct method [17] and non-hydrogen atoms
were obtained in successive difference Fourier syntheses.
Results and Discussion
The IR spectra of complex 1 show absorption bands resulting
from the skeletal vibrations of aromatic rings in the 1,400–
1,650 cm-1 region, and the strong absorption band of
Scheme 1
SH
NH2
N
N
O
O
O
O
NH2
Br2
L
N
N
KOH
BrH2C
CH2Br
H3C
CH3
BrH2C
CH2Br
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751
˚
Table 2 Selected bond lengths [A] and angles [°] for complex 1
Ag(1)–N(1)
2.220(5)
2.520(6)
2.323(5)
2.406(6)
2.55(4)
Ag(1)–N(4)i
Ag(1)–S(2)i
2.304(5)
2.844(2)
2.730(2)
2.32(3)
Ag(1)–O(1)
Ag(2)–N(3)
Ag(2)–O(2)ii
Ag(2)–S(1)
Ag(2)–O(4)
Ag(2)–O(5)
Ag(3)–N(5)
2.221(5)
115.4(2)
117.57(15)
80.28(17)
96.3(11)
94.7(9)
N(1)–Ag(1)–N(4)i
N(4)i–Ag(1)–O(1)
N(4)i–Ag(1)–S(2)i
O(4)–Ag(2)–N(3)
N(3)–Ag(2)–O(5)
O(4)–Ag(2)–S(1)
N(3)–Ag(2)–S(1)
156.4(2)
85.9(2)
74.01(14) O(1)–Ag(1)–S(2)i
135.0(11) O(4)–Ag(2)–O(2)ii
N(1)–Ag(1)–O(1)
N(1)–Ag(1)–S(2)i
123.0(7)
81.5(5)
74.62(14) O(2)ii–Ag(2)–S(1)
O(2)ii–Ag(2)–O(5)
O(5)–Ag(2)–S(1)
124.8(5)
114.11(16)
N(5)iii–Ag(3)–N(5) 146.4(3)
Symmetry codes (i): x, -y + 1, z - 1/2; (ii) x, y - 1, z; (iii) -x, y,
-z + 3/2
Fig. 1 (a) View of the coordination geometry of AgI, and (b) the
coordination mode of L
complex 1 have three states: chelated, bridged and free
state with 2:2:1 rate. The basic repeat unit of the
2D {[Ag5(L)2(NO3)4]+}n network is centrosymmetrical
[Ag10(L)4(NO3)8]2+ structure (Fig. 2a). In the basic unit,
the two pyrimidine rings at the symmetric positions are
parallel to each other with the centroid–centroid separation
*763 cm-1 can be assigned to the C-Sstretching vibration.
Complex 1 consists of 2D {[Ag5(L)2(NO3)4]+}n cations,
uncoordinated NOÀ3 anions and CHCl3 solvent molecules.
The crystal structure of {[Ag5(L)2(NO3)4]+}n shows three
crystallographic independent AgI centers (Fig. 1a). Ag(1) is
coordinated by two nitrogen atoms (a pyrimidine nitrogen
and a quinoxaline nitrogen from different ligands), a sulfur
and an oxygen atom of NOÀ3 showing tetrahedral coordina-
tion geometry with the bond angles around Ag(1) being in the
range of 74.0(1)–156.4(2)° (Table 2). The Ag–N and Ag–O
bonds fall in the expected ranges for such coordination
bonds, while the Ag–S bond is slightly longer than those in
the AgI complexes with thioether ligands. Ag(2) forms afive-
coordination geometry coordinated by a quinoxaline nitro-
gen, a sulfur atom from the same ligand as well as three
oxygen atoms from two different NOÀ3 anions. Ag–N and
Ag–O bonds are in the normal range, while the length of
Ag(2)–S is slightly shorter than that of Ag(1)–S. Ag(3) is
coordinated by two pyrimidine nitrogen atoms from different
ligands showing linear coordination geometry with the
N–Ag–N bond angle of 146.4(3)°.
The ligand in 1 adopts N4S2 hexadentate coordination
mode (Fig. 1b). Each ligand uses its quinoxaline nitrogen
and adjacent sulfur atom chelating AgI cations forming two
five-membered rings, and use the nitrogen atoms of ter-
minal pyrimidine rings bridging two AgI centers. Only a
nitrogen atom of terminal pyrimidine ring takes part in
coordination to AgI atom. Two terminal pyrimidine rings
almost are vertical to central quinoxaline ring and lie in the
two sides of the quinoxaline ring. The NOÀ3 anions in
˚
of ca. 3.650 A, indicating the presence of face-to-face p–p
stacking interactions [19, 20]. The basic units are linked by
NOÀ3 anions to form a 2D network (Fig. 2b)
In 1, although the terminal groups (pyrimidine ring) of
the ligand contain four potential coordination atoms, the
quinoxaline N atom prefer still to cooperate with S atom
chelating AgI atom forming five-member ring, while ter-
minal pyrimidine N atoms bridge other AgI atoms. In order
to investigate the coordination feature of the dithioether
ligand, the single-point energy calculations based on the
geometry of the coordinated ligand was carried out by the
DFT (density functional theory) method using the b3lyp/3-
21g basis set in the Gaussian 94 program [21, 22]. The
charge distributions of the coordination atoms of the ligand
are described as Fig. 3. The calculated results show that all
N atoms of the ligand bear negative charge, while all S
atoms possess positive charge, indicating that the coordi-
nation ability of N atom of ligands is stronger than S atom.
In addition, the quinoxaline N atoms of the ligand bear
more negative charge than the N atoms of terminal groups,
which indicates that the quinoxaline N atoms possess
stronger coordination ability than the N atoms of terminal
groups. In L, the two N atoms of each terminal pyrimidine
ring bear unequal negative charge, indicating that the two
pyrimidine N atoms have unequal coordination ability. In
the complexes of pyrimidine thioether ligands, it is general
phenomenon that only a nitrogen atom of pyrimidine ring
takes part in coordinating.
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J Chem Crystallogr (2008) 38:749–753
Fig. 2 (a) The basic unit of the
2D network, and (b) the 2D
structure of 1
Inconclusion, thecoordinationchemistry ofthe dithioether
ligandwithAgNO3 hasbeeninvestigatedbyexperimentaland
calculation methods. In such complexes, in addition to the
strong coordination bonds, there also exist p–p stacking
interactions. These weak interactions play a crucial role in the
self-organization of supramolecular polymer as well as the
stabilization of the complex structure in the solid state.
Acknowledgments This work was supported by the Funding Pro-
ject for Academic Human Resources Development in Institutions of
Higher Learning under the Jurisdiction of Beijing Municipality.
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