Influence of ligand substituent on structural assembly and coordination geometry

Article abstract of DOI:10.1039/c2ce25898f

In this study, N-(aryl)-2-pyrazinecarboxamide ligands with two different aryl groups (o-anisidyl, L^OMe, and o-phenitidyl, L^OEt, groups) have been employed for the synthesis of six Hg(ii) complexes, [HgCl ₂(L^OMe)₂]_n, 1, [HgBr ₂(L^OMe)]_n, 2, [HgI₂(L ^OMe)]_n, 3, [Hg₃Cl₆(L ^OEt)₃·HgCl₂(L^OEt)], 4, [HgBr₂(L^OEt)], 5, and [HgI₂(L^OEt)], 6, in order to get insights into the substituent effects on the molecular architecture of complexes. Structural analysis of mercury(ii) halides containing L^OMe ligand demonstrated that the assembly process produced an infinite 1D linear chain, 1D double chain and 1D ladder chain in 1, 2 and 3 respectively. Structural analysis showed that compounds 4-6 have non-polymeric structures. 4 resulted in a trimeric/monomeric motif while isostructural 5 and 6 compounds formed a discrete three coordinated mercury compound. Our results show that when compared to the L^OMe substituent, the steric properties of the L^OEt group significantly alter the molecular architecture and coordination sphere of complexes. This journal is

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PAPER
Influence of ligand substituent on structural assembly and coordination
geometry{
Hamid Reza Khavasi,* Maryam Mehdizadeh Barforoush{ and Mahmood Azizpoor Fard{
Received 5th June 2012, Accepted 6th August 2012
DOI: 10.1039/c2ce25898f
In this study, N-(aryl)-2-pyrazinecarboxamide ligands with two different aryl groups (o-anisidyl,
LOMe, and o-phenitidyl, LOEt, groups) have been employed for the synthesis of six Hg(II) complexes,
[HgCl2(LOMe)2]n, 1, [HgBr2(LOMe)]n, 2, [HgI2(LOMe)]n, 3, [Hg3Cl6(LOEt)3?HgCl2(LOEt)], 4,
[HgBr2(LOEt)], 5, and [HgI2(LOEt)], 6, in order to get insights into the substituent effects on the
molecular architecture of complexes. Structural analysis of mercury(II) halides containing LOMe
ligand demonstrated that the assembly process produced an infinite 1D linear chain, 1D double chain
and 1D ladder chain in 1, 2 and 3 respectively. Structural analysis showed that compounds 4–6 have
non-polymeric structures. 4 resulted in a trimeric/monomeric motif while isostructural 5 and 6
compounds formed a discrete three coordinated mercury compound. Our results show that when
compared to the LOMe substituent, the steric properties of the LOEt group significantly alter the
molecular architecture and coordination sphere of complexes.
the classical13 and non-classical hydrogen bonds and p–p14 and
Introduction
C–H
15 interactions have also been investigated.
…
p
In the frame of a research line about p-stacking16a and the effect
The construction of the structures of crystalline coordination
compounds1 depends on a number of experimental variables such
as the solvent,2 time of reaction,3 reagent ratio,4 temperature,5 pH,6
guest molecules and counterions.7 In this regard, the chemical
structure of the organic ligand8 – even the site of the substitute
position – and preferred coordination geometry of the metal9 play
an important role on the formation of different molecular
architecture in the complexes in the assembly processes. To make
progress in controlling specific interactions in the solid state of
coordination compounds, requires systematic investigations of the
effects of different factors on the final structures. Despite their
potential utility, there has been little attention paid to systematic
studies that examine the effect of the substituent variation of the
ligand on the supramolecular aggregation of coordination com-
plexes. Controlling the supramolecular aggregation by steric groups
on the ligand in several series of zinc-triad dithiolate compounds has
been systematically studied by Tiekink and co-workers.10 Recently,
systematic investigation of the influence of the substituent groups of
benzimidazoles on the formation of coordination frameworks of
zinc and cadmium has been reported.11 In Mondal and co-worker’s
paper, the role of the steric bulk and angular dispersion of the
coordination site of benzene polycarboxylic acids on the crystal
engineering of zinc MOFs have been shown.12 Substituent effects on
16b
…
of C–H
p
interaction on the crystal packing of mercury
coordination compounds containing pyrazine carboxamide
ligands, that the authors are developing, the effect of ligand
substituent on coordination geometry and three-dimensional
supramolecular architecture have been reported here. In this
study, two N-(aryl)-2-pyrazinecarboxamide ligands carrying a
different aryl groups have been employed for the synthesis of
mercury(II) complexes in order to get insights into the steric effects
of aryl on the structural assembly of the complexes. We selected
flexible ligands, N-(o-anisidyl)-2-pyrazinecarboxamide, LOMe, and
N-(o-phenitidyl)-2-pyrazinecarboxamide, LOEt, in which the free-
dom C–C and C–N single bond rotations give rise to variable
conformations and the pyrazine and aryl rings can freely twist to
meet the requirements of the coordination geometries of metal
atoms in the assembly process. Six Hg(II) complexes of these
ligands, [HgCl2(LOMe)2]n, 1, [HgBr2(LOMe)]n, 2, [HgI2(LOMe)]n,
3, [Hg3Cl6(LOEt)6?HgCl2(LOEt)2], 4, [HgBr2(LOEt)], 5, and
[HgI2(LOEt)], 6, have been prepared by the reaction of equimolar
quantities of mercury halides (chloride, bromide and iodide) in
methanol solutions, Scheme 1. The structural details show that the
N-aryl group significantly influences the structural assembly and
coordination geometry of the resulting mercury(II) complexes.
Department of Chemistry, Shahid Beheshti University, G. C., Evin,
Tehran, 1983963113, Iran. E-mail: h-khavasi@sbu.ac.ir;
Fax: +98 21 22431663
{ CCDC reference numbers 865862 (1), 865863 (2), 865861 (3), 865866
(4), 865865 (5) and 865864 (6). For crystallographic data in CIF or other
electronic format see DOI: 10.1039/c2ce25898f
Experimental section
General
All chemicals were purchased from Aldrich or Merck and used
without further purification. The synthesis and recrystallization
{ These authors contributed equally.
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Synthesis of N-(o-phenitidyl)-2-pyrazinecarboxamide, LOEt
This compound was prepared by using the previously reported
method.19
Synthesis of mercury(II) complexes; [HgCl2(LOMe)2]n, 1,
[HgBr2(LOMe)]n, 2, [HgI2(LOMe)]n, 3,
[Hg3Cl6(LOEt)6?HgCl2(LOEt)2], 4, [HgBr2(LOEt)], 5, and
[HgI2(LOEt)], 6
To a solution of 0.2 mmol mercury(II) halide (HgX2, X = Cl, Br
and I) in 5 mL methanol, a solution of 0.2 mmol of L in 5 mL
methanol was added while stirring. The mixture was heated at
40 uC for about 30 min and then filtered. Upon slow evaporation
of the filtrate at room temperature, suitable complexes for X-ray
analysis were obtained after several days. It is notable that using
1 : 2 molar ratio of HgCl2 to LOMe and LOEt ligands resulted in
the same product as when using 1 : 1 molar ratio.
Scheme 1 Synthetic route of 1–6.
of LOMe and LOEt, and compounds 1–6 were carried out in air.
Infrared spectra (4000–250 cm21) of solid samples were taken as
1% dispersions in CsI pellets using a BOMEM-MB102 spectro-
meter. Elemental analysis was performed using a Heraeus CHN–
O Rapid analyzer. 1H NMR spectrum was recorded on a Bruker
AC-300 MHz spectrometer at ambient temperature in CD3OD.
All chemical shifts are quoted in parts per million (ppm) relative
to tetramethylsilane. Melting point was obtained by a Bamstead
Electrothermal type 9200 melting point apparatus and corrected.
Ligand N-(o-anisidyl)-2-pyrazinecarboxamide, LOMe, was pre-
pared according to the reported procedure.17
1. Mp: 188 uC. Anal. Calcd for C24H22Cl2HgN6O4: C, 39.45;
H, 3.01; N, 11.51. Found: C, 39.55; H, 3.06; N, 11.58. IR (CsI
pellet, cm21): 3360s, 2960, 1667s, 1600, 1527, 1459s, 1246, 1108,
1020, 910,756. 1H NMR (CD3OD, d from TMS): 9.33(s,
1H-pyrazine), 8.83(s, 1H-pyrazine), 8.73(s, 1H-pyrazine),
8.43(d, 1H-phenyl), 7.17–6.97(m, 3H-phenyl), 3.97(s, 3H–CH3).
2. Mp: 145 uC. Anal. Calcd for C12H11Br2HgN3O2: C, 24.42;
H, 1.87; N, 7.12. Found: C, 24.48; H, 1.92; N, 7.17. IR (CsI
pellet, cm21): 3356s, 3072, 1690s, 1598, 1540, 1457s, 1248, 1132,
1022, 908, 752. 1H NMR (CD3OD, d from TMS): 9.35(s,
1H-pyrazine), 8.83(s, 1H-pyrazine), 8.72(s, 1H-yrazine), 8.42(d,
1H-phenyl), 7.13–6.98(m, 3H-phenyl), 3.97(s, 3H–CH3).
3. Mp: 152 uC. Anal. Calcd for C24H22Hg2I4N6O4: C, 21.06;
H, 1.61; N, 6.14. Found: C, 21.12; H, 1.68; N, 6.20. IR (CsI
pellet, cm21): 3360s, 3056, 1686s, 1598, 1542, 1457s, 1250, 1132,
1022, 900,753. 1H NMR (CD3OD, d from TMS): 9.35(s,
1H-pyrazine), 8.83(s, 1H-pyrazine), 8.73(s, 1H-pyrazine),
8.43(d, 1H-phenyl), 7.14–6.98(m, 3H-phenyl), 3.96(s, 3H–CH3).
4. Mp: 188 uC. Anal. Calcd for C26H26Cl2HgN6O4: C, 41.16; H,
3.43; N, 11.08. Found: C, 41.20; H, 3.49; N, 11.13. IR (CsI pellet,
cm21): 3342s, 2980, 1680s, 1600, 1526, 1453s, 1251, 1129, 1042,
901,760. 1H NMR (CD3OD, d from TMS): 9.38(s, 1H-pyrazine),
8.85(s, 1H-pyrazine), 8.74(s, 1H-pyrazine), 8.45(d, 1H-phenyl),
7.17–6.98(m, 3H-phenyl), 4.21(q, 2H–CH2) and 1.52(t, 3H–CH3).
5. Mp: 145 uC. Anal. Calcd for C13H13Br2HgN3O2: C, 25.84; H,
2.15; N, 6.96. Found: C, 25.91; H, 2.19; N, 7.00. IR (CsI pellet,
cm21): 3343s, 2937, 1690s, 1593, 1534, 1452s, 1250, 1129, 1037,
903, 752. 1H NMR (CD3OD, d from TMS): 9.39(s, 1H-pyrazine),
8.86(s, 1H-pyrazine), 8.76(s, 1H-pyrazine), 8.46(d, 1H-phenyl),
7.18–7.00(m, 3H-phenyl), 4.22(q, 2H–CH2) and 1.52(t, 3H–CH3).
6. Mp: 152 uC. Anal. Calcd for C13H13HgI2N3O2: C, 22.36; H,
1.86; N, 6.02. Found: C, 22.41; H, 1.93; N, 6.10. IR (CsI pellet,
cm21): 3340s, 2975, 1686s, 1593, 1535, 1451s, 1249, 1128, 1038,
900,754. 1H NMR (CD3OD, d from TMS): 9.36(s, 1H-pyrazine),
8.83(s, 1H-pyrazine), 8.72(s, 1H-pyrazine), 8.42(d, 1H-phenyl),
7.12–6.96(m, 3H-phenyl), 4.19(q, 2H–CH2) and 1.49(t, 3H–CH3).
Single crystal diffraction studies
X-ray data for compounds 1–6 were collected on a STOE IPDS-
II diffractometer with graphite monochromated Mo-Ka radia-
tion. For [HgCl2(LOMe)2]n (1),
a colorless needle crystal,
for [HgBr2(LOMe)]n (2), [Hg3Cl6(LOEt)6?HgCl2(LOEt)2] (4),
[HgBr2(LOEt)] (5), and [HgI2(LOEt)] (6), yellow block crystals
and for [HgI2(LOMe)]n (3), a yellow plate crystal was chosen
using a polarizing microscope and they were mounted on a glass
fiber which was used for data collection. Cell constants and an
orientation matrix for data collection were obtained by least-
squares refinement of the diffraction data from 3261, 4073,
4426, 14729, 4369 and 4664 unique reflections for complexes
1–6, respectively. Data were collected at a temperature of
120(2) K for 1 and 4 and 298(2) K for 2, 3 and 5–6 to a
maximum 2h value of 58.58u, 58.48u, 58.42u, 58.48u, 58.38u and
58.62u for 1–6, respectively, in a series of v scans in 1u
oscillations and integrated using the Sto¨e X-AREA18a software
package. A numerical absorption correction was applied using
the X-RED18b and X-SHAPE18c software. The data were
corrected for Lorentz and Polarizing effects. The structures
were solved by direct methods18d and subsequent different
Fourier maps and then refined on F2 by a full-matrix least-
square procedure using anisotropic displacement parameters.
All hydrogen atoms were added at ideal positions and
constrained to ride on their parent atoms, with Uiso(H) =
1.2Ueq. All refinements were performed using the X-STEP32
crystallographic software package.18e Crystallographic data for
complexes 1–6 are listed in Table 1. Selected bond distances and
angles are summarized in Table 2.
Results and discussion
Synthesis
The ligands LOMe and LOEt were prepared by simply mixing of
the same equivalents of ortho-anisidine or ortho-phenitidine and
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Table 1 Structural data and refinement for compounds 1–6
1
2
3
Formula
FW
˚
l/A
T/K
Cryst. system
Space group
C
729.97
0.71073
120
Orthorhombic
Pbna
24H22Cl2HgN6O4
C12H11Br2HgN3O2
589.63
0.71073
298
Triclinic
C24H22Hg2I4 N6O4
1367.26
0.71073
298
Triclinic
¯
P1
¯
P1
˚
a/A
6.7123(6)
13.9195(17)
26.783(3)
7.9158(9)
8.1142(8)
13.4426(17)
98.167(9)
94.158(10)
115.388(8)
763.49(15)
2.565
2
15.316
540
58.48
6.9418(11)
7.9241(11)
16.6673(19)
82.282(10)
82.029(11)
66.661(11)
830.5(2)
2.734
1
12.987
612
58.42
˚
b/A
˚
c/A
a (u)
b (u)
c (u)
3
˚
V/A
2502.4(5)
1.938
4
6.409
1416
58.58
0.0990
1.120
0.0616
0.1810
Dc/Mg m23
Z
m/mm21
F(000)
2h/u
R (int)
GOOF
R1a(I . 2s(I))
wR2b(I . 2s(I))
0.0959
1.146
0.0942
0.1882
0.0847
1.149
0.0617
0.1521
4
5
6
Formula
FW
˚
l/A
C26H26Cl2HgN6O4
758.02
0.71073
C13H13Br2HgN3O2
603.65
0.71073
C13H13HgI2N3O2
697.65
0.71073
T/uC
Cryst. system
120
Monoclinic
P21/c
14.662(3)
28.360(6)
14.515(3)
298
Triclinic
¯
P1
298
Triclinic
¯
P1
Space group
˚
a/A
˚
7.7934(10)
8.7382(12)
12.4967(14)
93.388(10)
96.104(10)
103.975(10)
817.98(18)
2.451
2
14.299
559
58.38
7.9431(7)
8.9284(8)
12.9309(12)
93.369(7)
97.228(7)
104.449(7)
877.10(14)
2.642
2
12.300
628
58.62
b/A
˚
c/A
a (u)
b (u)
cu
114.78(3)
3
˚
V/A
5480.0(2)
1.838
8
5.857
2960
58.48
0.0667
1.147
0.0535
0.1089
2
Dcalc/Mg.m23
Z
m/mm21
F(000)
2h/u
R (int)
GOOF
0.0895
1.182
0.0626
0.1554
0.1004
1.098
0.0598
0.1602
R1a(I . 2s(I))
wR2b(I . 2s(I))
a
R1 = S||Fo| 2 |Fc||/S|Fo|. wR2 = [S(w(Fo 2 Fc2)2)/Sw(Fo2)2]1/2
.
b
pyrazinecarboxylic acid in pyridine in the presence of triphenyl
phosphite (colorless block crystals, 75% and 85% yield for LOMe
and LOEt respectively). Reaction of equimolar amounts of these
ligands and HgX2 (X = Cl, Br and I) in methanol gave the
corresponding complexes. Slow evaporation of the solvent
resulted in the air-stable colorless needle crystals of 1, yellow
block crystals of 2 and 4–6 and yellow plate crystals of 3, after a
few days.
deviation of angles fom 90u is ¡1.5u) with two N atoms and two
O atoms from LOMe ligands and two Cl atoms (Hg–Cl: 2.304(2)
˚
A, Table 2).
˚
The Hg–N and Hg–O distances of 2.812(5) A and Hg–O
˚
2.922(5) A, are slightly longer than the other Hg–N and Hg–O
distances previously reported but a search on Hg–N/O distances
using the Cambridge Structural Database (CSD), resulted in
more than 40 and 100 hits which have a longer bond distance
20
˚
˚
than 2.800 A for Hg–N and 3.000 A for Hg–O. Coordination
geometry around the Hg(II) center in compounds 2 and 3 are
square-based pyramid (SBP), Fig. 1(b) and 1(c), respectively,
with trigonality indexes (t)21 of 0.30 and 0.00 respectively. In
both structures of 2 and 3, the plane of square-based pyramid is
occupied by halogen anions (Hg–Br: 2.455(1), 2.472(2) and
Structural analysis of 1–3
A simple reaction between HgX2 and LOMe in methanol afforded
well-formed crystals of 1–3. The asymmetric unit of 1 consists of
a half crystallographically independent Hg2+ ion, one N-
(o-anisidyl)-2-pyrazinecarboxamide, LOMe, and one chloride
ion. As depicted in Fig. 1(a), in this compound, the Hg(II) ion
adopts an octahedral (Oh) coordination geometry (maximum
˚
˚
3.112(1) A and Hg–I: 2.611(1), 2.632(1), 3.501(1) and 3.542(1) A,
Table 2). The apical position in both structures is occupied by a
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˚
Table 2 Selected bond distances (A) and angles (u) for complexes 1–6
Complex
Bond distance
Hg–X
1
2.304(2)
2
3
4
5
2.413(1)
6
2.586(1)
2.455(1)
2.472(2)
3.112(1)e
2.611(1)
2.632(1)
3.501(1)g
3.542(1)g
2.513(7)
2.315(2)
2.316(2)
2.319(2)
2.312(2)
2.658(5)
2.760(6)
2.723(6)
2.713(5)
2.944(6)
2.445(1)
2.538(7)
2.608(1)
2.561(7)
Hg–N
2.812(5)
2.447(1)
Hg–O
Bond angle
X–Hg–X
2.922(5)a
180.0b
—
—
—
—
155.7(1)
172.5(1)e
93.8(1)e
89.3(1)e
93.2(1)f
85.5(1)f
160.6(1)
160.6(1)g
94.5(1)g
94.5(1)h
88.5(1)g
88.5(1)h
101.8(2)
97.6(2)
178.3(1)
162.3(1)
160.0(1)
180.0i
180.0j
X–Hg–N
90.6(1) 89.4(1)b
90.7(1)
90.8(1)
90.2(1)
89.8(1)
91.0(1)
87.4(1)
91.9(1)
88.1(1)
—
100.8(2)
95.9(2)
—
100.2(2)
98.0(2)
—
106..3(3)
97.9(3)
82.7(2)g
79.0(2)h
87.1(3)e
88.4(3)f
Hg–X–Hg
—
90.7(1)e
86.8(1)f
160.5(1)g
91.5(1)g
91.2(1)h
—
X–Hg–O
O–Hg–N
CLO–Hg
88.5(1)
91.5(1)b
90.3(1)b
89.7(1)c
104.1(4)d
b
—
—
90.3(1)
90.9(1)
75.0(1)
118.1(2)
118.7(4)
—
—
—
—
—
—
—
—
c
—
Symmetry codes:a 21 + x, y, z. 2x, 1 2 y, 2 2 z. 1 2 x, 1 2 y, 2 2 z. 1 + x, y, z. 2x + 1, 2y, 2z. 2 2 x, 2y, 2z. 2x, 2 2 y, 21 2 z.
d
e
f
g
h
i
1 2 x, 2 2 y, 21 2 z. 2x, 2 2 y, 2z. 1 2 x, 1 2 y, 2z.
j
nitrogen atom from the pyrazine ring of the LOMe ligand at a
CLO H–Cpyz non-classical hydrogen bonds and from the other
side by the weak C–H...Oether intermolecular interactions,
…
˚
normal distance of 2.447(1) and 2.513(7) A for 2 and 3
respectively. As is clear from the t values and geometrical
parameters around the central metal atoms, Table 2, in 2, the
Hg(II) has a distorted SBP environment while in 3, the
coordination geometry around Hg(II) is almost perfect SBP.
In 1, the o-anisidyl and pyrazine rings are in-plane with the
carbonyl CLO group (the maximum deviation from mean plane
Table 3.
Within the asymmetric unit of 2, each mercury coordinates the
a nitrogen donor atom of the pyrazine ring of the LOMe ligand,
while each bromine atom in the basal plane bridges two adjacent
metal centers to generate a 1D double chain motif in the
a-direction, Fig. 3(a). In this chain, the Br atom is dicoordinated.
The planar organic ligands stack along both sides of the HgBr
˚
through o-anisidyl and pyrazine ring is less than 0.125 A). In this
˚
skeleton and the distance between their mean planes is 7.916 A,
compound, the formation of parallel p–p stacks of the adjacent
ligands influences the CLO–Hg angles. The o-anisidyl ring
involved in the intramolecular p–p stacking interaction with the
adjacent pyrazine and phenyl rings, is arranged in such a way
that the angle between the plane (containing C–CO–N fragment)
normal and the O–Hg vector (for geometrical definition see
Fig. 3(a).
In 3, the arrangement of the asymmetric units defines the well-
known double-stranded stair motif, Fig. 3(b). In this stair 1D
polymer, the translation axis is parallel to the a-direction.
Although many halide-bridged mercury-based structures have
been reported in the literature,22 but such a stair 1D polymer
containing a Hg–I moiety is rare and there is only one reported
[HgI(L)]n stair which contains an imidazolium thiolate ligand.23
…
reference 16a), is about 13.85u. In the pphen ppyz interactions,
˚
the centroid–centroid distance is 3.511 A. Such p–p interaction
effects on the primary structure which direct the coordination
geometry around Hg(II) containing similar ligands with those
discussed in this paper have been reported previously in detail.16a
Thus, adjacent mercury atoms are linked by CLO–Hg bonds to
form a 1D linear polymeric chain spanning along the a-axis,
Fig. 2(a). The interchain distance of the neighboring mercury
˚
In 3, the Hg–I bond distances of 3.501(1) and 3.542(1) A are
˚
comparable to that previously reported (3.377 A) by Popovic
et al.23 The iodide anion in the stair is tricoordinated in a highly
iii
…
˚
= 4.369 A). The
distorted pyramidal geometry (diagonal I
I
organic ligand moieties approximately preserve their planarity
and stack along both sides of the HgI skeleton; the distance
atoms bridged by LOMe ligands, is about 6.712 A. As shown in
˚
˚
between their main planes being 6.942 A, Fig. 3(b). This 1D
Fig. 2(b), these 1D linear chains are further linked to each other
…
from one side by head-to-tail dimeric C–Hpyz Cl–Hg and
double chain in 2 and double-stranded stair chain in 3, are
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Fig. 2 Representation of 1D linear polymeric chain in 1 viewed down
[010], (a), and a side view representation of 1 in a-direction showing the
association of the adjacent molecules in the chain, through an additional
…
…
head-to-tail dimeric C–Hpyz Cl–Hg and CLO H–Cpyz non-classical
hydrogen bonds and C–H Oether intermolecular interactions, (b).
Fig. 1 Portion of the structure of coordination polymers formed
between LOMe and HgCl2, 1, (a), HgBr2, 2, (b), and HgI2, 3, (c), showing
coordination geometry around central metal. Symmetry codes; (a) i) 2x,
1 2 y, 2 2 z, ii)21 + x, y, z, iii) 1 2 x, 1 2 y, 2 2 z, (b) i) 2 2 x, 2y, 2z,
ii) 1 2 x, 2y, 2z and (c) i) 2x, 2 2 y, 21 2 z, ii) 1 2 x, 2 2 y, 1 2 z.
…
Different colours show different adjacent linear chains.
chloride ions, and three neutral LOEt ligands, Fig. 5(a).
Therefore, for this complex, Table 2 shows three sets of values.
In part 4A, Hg1 is in a slightly distorted square-based pyramidal
geometry (SBP), with trigonality index (t) of 0.19, coordinated by
two LOEt ligands and two Cl atoms in the basal plane and in cis
position and one carbonyl oxygen atom of the third LOEt ligand at
the vertex. The recent LOEt ligand, acts as an angular bridge via
carbonyl oxygen and pyrazine nitrogen atoms to link Hg1 and
Hg2 ions, meanwhile, the Hg2 atom, in a square-planar geometry,
is also bonded to two Cl atoms in the cis position and to another
bridged LOEt ligand between Hg2 and Hg1i (symmetry code: 2x,
2 2 y, 2z), to form a three-nuclear complex. Part 4B complex,
features slightly distorted square-planar (SP) geometry. The
Cl–Hg–Cl and N–Hg–N axis are constrained to linearity by
crystallographic symmetry, Table 2. The angles of Cl–Hg–N range
from 88.1(1) to 91.9(1)u. It is notable that there is a very weak
further linked to adjacent chains from one side by head-to-tail
…
…
dimeric C–Hphen OLC and C–Hmethyl Oether non-classical
hydrogen bonds in 2 and 3, respectively, and from the other
…
…
side by the intermolecular C–Hpyz Br–Hg and C–Hphen I–Hg
interactions, respectively, Fig. 4(a) and 4(b), Table 3.
Planar organic ligand moieties along both sides of the HgX
…
pphen interactions
skeleton in adjacent chains are liked by CLO
˚
with C(carbonyl)–centroid(phen) distances of 3.651 and 3.581 A
for 2 and 3 respectively, Table 3, Fig. 4(c) and 4(d). It is notable
…
that in 2, ppyz pphen (with centroid–centroid distance of
…
˚
3.696 A) cooperates with this CLO pphen interactions in the
stabilization of the packing, Fig. 4(c), Table 3.
Structural analysis of 4–6
…
Hg O interaction between the Hg3 atom and the two adjacent
iii
…
˚
carbonyl oxygen atoms (Hg3 O3 = 3.206 A, symmetry code:
(iii) 1 2 x, 2K + y, K 2 z) in the part 4B coordination center.
In isostructural compounds 5 and 6 the mercury atom is
located in a three coordination environment, Fig. 5(b) and 5(c),
chelating with two halogen atoms and one pyrazine nitrogen
atom from ligand LOEt with bond lengths of Hg–X = 2.413(1)
Compound 4 consists of two different three-nuclear, part 4A,
and mono-nuclear, part 4B, mercury complexes. This compound
displays 2/m point symmetry in the solid state, making half of the
three-nuclear and mono-nuclear part of this compound crystal-
lographically unique. Thus, in 4, each asymmetric unit consists
of 2.5 crystallographically independent Hg(II) centers, four
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Table 3 Significant intermolecular interactions (interatomic distance
˚
(A) and bond angles (u)) found in the structures of 1–6
…
…
…
…
D–H A
D–H
A
D–H
H
A
D
A
compound 1
a
…
C11pyz–H11 Cl1–Hg
0.930
0.930
0.970
2.864 3.793(12) 177
b
…
C12pyz–H12 O2LC
C3phen–H3 Oether
compound 2
2.421 3.282(9)
2.740 3.688(7)
154
165
c
…
d
…
C12pyz–H12 Br2–Hg
0.930
0.930
—
3.031 3.716(11) 132
2.639 3.507(12) 156
e
…
C6phen–H6 O2LC
f
…
Cg(pphen)
…
C8LO
Cg(pphen
—
—
3.651
3.696
—
—
g
Cg(ppyz
compound 3
)
)
—
h
…
C4pyz–H4 I1–Hg
0.930
0.960
—
3.037 3.800(10) 140
2.550 3.452(13) 156
i
…
C1methyl–H1C O1ether
j
…
Cg(pphen)
compound 4
C8LO
—
3.581
—
k
…
C51methyl–H51A Cl2–Hg
0.970
0.930
0.930
0.930
0.930
0.930
0.930
0.930
0.930
—
2.740 3.688(7)
2.320 2.917(8)
2.520 3.204(8)
2.360 2.937(8)
2.420 3.157(8)
2.350 2.935(8)
2.500 3.222(8)
2.320 2.910(9)
2.460 3.145(8)
165
121
131
120
136
121
134
121
130
—
…
C7phen–H7 O1LC
l
…
…
…
…
…
…
…
C10phen–H10 O3LC
C20phen–H20 O3LC
m
C23phen–H23 O1LC
Fig. 3 Representation of a 1D double chain in 2, (a), and stair 1D
polymer in 3, (b), in b-direction.
C33phen–H33 O5LC
n
C36phen–H36 O7LC
C46phen–H46 O7LC
o
C49phen–H49 O5LC
Influence of ligand substituent on molecular architecture
p
…
Cmethyl–H52B Cg(pphen
)
—
2.854(7)
2.846(7)
3.597(3)
3.606(4)
3.791(4)
q
…
Cmethyl–H13A Cg(pphen
)
—
—
—
—
—
—
—
—
—
—
—
—
Understanding and controlling the structural assemblies in the
solid state requires investigations on families of materials which
have been designed in such a way as to systematically delineated
the effects of different factors on the resultant supramolecular
and structural properties.
q
…
…
…
Cg(pphen
Cg(pphen
Cg(pphen
)
)
)
Cg(ppyz
Cg(ppyz
Cg(ppyz
)
)
)
q
r
compound 5
C13methyl–H13C O1LC
s
…
0.960
—
—
2.430 3.373(14) 169
t
…
Cg(ppyz
…
)
Hg1 Cg(pphen
Cg(pphen
)
)
—
—
3.710
3.501
—
—
f
In this regard, the effect of the ligand substituent and the effect
of different halogen anions, on the coordination geometry and
three-dimensional supramolecular architecture of the six coordi-
nation compound of mercury(II) has been studied. In the
following discussion, we will focus on similarities and differences
between the various coordination compounds.
compound 6
u
…
C13methyl–H13C O1LC
0.960
—
—
2.560 3.501(15) 168
v
…
Cg(ppyz
…
)
Hg1 Cg(pphen
Cg(pphen
)
)
—
—
3.790
3.540
—
—
w
Symmetry codes:a 2x, K + y, z. b 1 2 x, 1/2 + y, z. c 1/2 + x, y, 3/2 2 z.
2 2 x, 1 2 y, 2z. 1 2 x, 2y, 1 2 z. 1 2 x, 1 2 y, 1 2 z. 2 2 x, 1
d
e
f
g
h
i
j
2 y, 1 2 z. 1 2 x, 1 2 y, 2z. 2x, 3 2 y, 2z. 1 2 x, 2 2 y, 2z.
k
1
Much of the difference in structural motifs can be explained by
the changing of the steric environment of the ligands, but the role
of the different halogen anions should not be neglected. In the
first series, in compounds 1–3 where the carboxamide ligand is
similar, our results clearly show that the coordinated anion has a
remarkable effect on the coordination geometry as well as the
structural motif of the resulting one-dimensional polymers. The
coordination geometry around the Hg(II) center in compound 1
adopts an Oh coordination geometry. The situation for
compounds 2 and 3 (where X is Br and I anions respectively),
is quite different from that of compound 1, both in the
coordination geometry of the Hg(II) centers and in the kind of
1D polymeric structures. By replacing coordinated anions from
chloride to bromide or iodide, the coordination geometry
changed from Oh to SBP. It is notable, that although the
structural motif in compounds 1–3 are different, the structural
analysis show that in all three structures, 1D coordination
polymers have resulted, Table 4.
l
m
n
+ x, y, z. 2x, 2K + y, K 2 z. 1 2 x, K + y, K 2 z. x, 3/2 2 y,
K + z. o 1 + x, 3/2 2 y, 2K + z. p 21 + x, 3/2 2 y, 21/2 + z. q 21 + x,
y, z. 2x, K + y, K 2 z. 21 + x, 21 + y, z. t 2x, 1 2 y, 1 2 z. 1 +
r
s
u
x, 1 + y, z. v 2 2 x, 2 2 y, 1 2 z. w 1 2 x, 2 2 y, 1 2 z.
˚
˚
and 2.445(1) A for 5 and 2.586(1) and 2.608(1) A for 6 and Hg–N
= 2.538(7) and 2.561(7) for 5 and 6 respectively, Table 2. The
X–Hg–X angle of 162.3(1) and 160.0(1)u for 5 and 6, respec-
tively, shows that the geometry around the metal center is
slightly distorted T-shape.
As shown in Fig. 6, in 4, monomeric and trimeric molecules
… …
are linked to adjacent molecules by pphen
…
ppyz, C–Hmethyl
Cl–Hg, C–Hmethyl pphen interactions, Table 3. As depicted in
Fig. 6, these intermolecular interactions act as cooperative
…
factors with several C–Hmethyl OLC interactions to generate
three dimensional packing.
The non-classical hydrogen bonds in 5 and 6, which are those
between C–Hmethyl donor and carbonyl oxygen acceptor, form a
one dimensional chain, Fig. 7(a) and 7(b), respectively. These 1D
It is interesting to compare the coordination core and
structural assembly of the present complexes with respect to
the growing steric bulk of the aryl group on the phenyl ring.
When compared to the LOMe substituent, the steric properties of
the LOEt group significantly alter the molecular architecture and
coordination sphere of complexes containing N-(aryl)-2-pyrazi-
necarboxamide ligand. For the HgCl2 adduct, from 1 to 4, the
…
chains are further linked by Hg p and head-to-tail dimeric
…
pphen ppyz interactions in the other direction, Table 3. For the
…
pphen ppyz interactions, the centroid–centroid distance and for
…
the Hg p, the metal–centroid distance is about 3.710 and
˚
3.501 A, for 5 and 3.790 and 3.540 A for 6, respectively.
˚
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Fig. 5 Structure of coordination compound formed between LOEt and HgCl2,
4, (a), HgBr2, 5, (b), and HgI2, 6, (c), showing coordination geometry around the
central metal. Symmetry codes; i) 2x, 2 2 y, 2z, ii) 1 2 x, 1 2 y, 2z.
Fig. 4 A side view representation of 2, (a), and 3, (b), in a-direction
showing the association of the adjacent molecules in the chains, through
…
…
head-to-tail dimeric C–Hphen OLC and C–Hpyz Br–Hg in 2 and head-
…
…
to-tail dimeric C–Hmethyl Oether and C–Hphen I–Hg non-classical
hydrogen bonds in 3. Different colours show different adjacent linear
chains. A representation of part of 2 and 3 showing the cooperation of
…
…
…
CLO pphen and ppyz pphen interactions in 2, (c), and CLO pphen
interactions in 3, (d), in generation of three dimensional packing.
coordination sphere changes from Oh to SBP-SP. For HgX2
adducts (while X = Br and I), the coordination geometry around
the central atom has been changed from SBP for 2 and 3 to
T-shape for 5 and 6. As listed in Table 4, for the second series,
compounds 4–6 have non-polymeric structures. In 4 the trimeric/
monomeric motif resulted while in isostructural 5 and 6
Fig. 6 A side view representation of 4 showing the cooperation of
…
…
…
…
pphen
ppyz, C–Hmethyl Cl–Hg, C–Hmethyl pphen and C-Hmethyl OLC
interactions in generation of three dimensional packing.
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structural assemblies and coordination geometries from LOMe to
LOEt. The difference in structural motifs can thus be explained by
the changing of the steric properties of the ligands. The role of
the size and nature of the halogen anions can also affect the
nature of the mercury coordination sphere. Based on these
results, we tentatively propose that the most important factors
dictating polymeric or non-polymeric structures are the steric
properties of the ligands surrounding the mercury atom. These
steric properties affects the nature of the intermolecular
interactions in these complexes and therefore indirectly affect
the structural assemblies and coordination geometries indirectly.
The crystal packing patterns of 1–3 were analyzed in terms of
…
…
CLO p and p p in some cases and non-classical weak
…
…
intermolecular interactions such as C–H O and C–H X–Hg
(X = halogen) in all three compounds. The analysis shows that
the changing of the steric profile of the ligands from o-anisidyl to
o-phenitidyl, successfully changed some of the synthons seen in
the 1–3 packings and that the new compounds, specially
compounds 5 and 6 adopt other packing strategies, based on
Fig. 7 A representation of part of the unit cell contents of 5, (a) and 6,
…
…
…
Hg p contacts.
(b), showing the non-classical C–Hmethyl OLC hydrogen bonds, Hg
p
…
and head-to-tail dimeric pphen ppyz interactions.
Conclusion
compounds, discrete three coordinated mercury compounds
were formed.
We have shown that by varying the steric profile of N-(aryl)-2-
pyrazinecarboxamide ligands, the nature of the structural
assemblies and coordination geometries of mercury coordination
polymers can be tuned. Structural analysis of mercury(II) halides
containing the N-(o-anisidyl)-2-pyrazinecarboxamide ligand
demonstrated that the assembly process produced an infinite
1D linear chain, 1D double chain and 1D ladder chain in
chloride, bromide and iodide adducts respectively. When
compared to the o-anisidyl substituent, the steric properties of
the N-(o-phenitidyl)-2-pyrazinecarboxamide ligand significantly
alter the molecular architecture and coordination sphere of the
complexes. For the HgCl2 adduct, the coordination sphere
changes from Oh to square-based pyramid/square-planar (SBP/
SP). For the HgX2 adducts (while X = Br and I), the
coordination geometry around the central atom has been
changed from SBP to T-shape. For the second series, discrete
These later three structures, together with the HgX2 adduct
with LOEt, clearly add further evidence that even in the case of
simple and monodentate ligands such as N-(aryl)-pyrazinecar-
boxamide, the substituents on the organic ligand can influence
the structural motif by its steric properties. It is proper to
consider why such a drastic substituent effect is induced. The
most significant feature is the similar electronic properties of the
ligands chosen for this study, with respect to the donating
pyrazine nitrogen atom. The same pyrazine–CONH–aryl moiety
is presented in the two ligands. The small angle between the
pyrazine–phenyl main planes (less than 8.46u), shows the
coplanarity of the ligands in all six compounds. In spite of this
similarity and molecular rigidity, the difference in the steric
properties of the ligands is quite remarkable in the changes of
Table 4 Coordination geometries and list of intermolecular interactions controlling the packing of polymeric and non-polymeric compounds 1–6
Complex
Coordination geometry
Main factors controlling the packing
Polymeric/non-polymeric
1D linear chain
1, [HgCl2(LOMe)2]n
Oh
…
C–Hpyz Cl–Hg
…
C–Hphen Oether
…
CLO H–Cpyz
C–Hpyz Br–Hg
2, [HgBr2(LOMe)]n
SBP
1D double chain
…
…
C–Hphen OLC
…
CLO pphen
ppyz pphen
…
3, [Hg2I4(LOMe)]n
SBP
C–Hphen I–Hg
1D ladder chain
…
…
C–Hmethyl Oether
…
CLO pphen
C–Hmethylene Cl–Hg
4, [Hg3Cl6(LOEt)3]?[HgCl2(LOEt)]
SBP-SP-SBP/SP
Trimmer/Monomer
…
…
C–Hphen OLC
pphen ppyz
…
…
C–Hmethyl pphen
5, [HgBr2(LOEt)]
6, [HgI2(LOEt)]
T-shape
T-shape
Hg pphen
…
C–Hmethyl OLC
ppyz pphen
Monomer
Monomer
…
…
…
Hg pphen
…
ppyz pphen
…
C–Hmethyl OLC
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non-polymeric coordination compounds have been formed.
While substituents on the terminal phenyl rings do not influence
the planarity of the N-(aryl)-2-pyrazinecarboxamide, they do
significantly influence the intermolecular stacking arrangements
for these compounds in the solid state. A combination of several
weak and medium intermolecular interactions, including
…
…
…
…
…
CLO p, p p, C–H O, Hg p and C–H X–Hg (X =
halogen) interactions determine the structural assemblies and
coordination geometries in these compounds.
Acknowledgements
We would like to thank the Graduate Study Councils of Shahid
Beheshti University, General Campus and the Iran National
Science Foundation (grant No. 87041984) for financial support.
11 S.-L. Li, Y.-Q. Lan, J.-C. Ma, J.-F. Ma and Z.-M. Su, Cryst. Growth
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