Hydrogen-bonded 3D network of d10-metal halide coordination polymer containing N-(3-pyridinyl) nicotinamide: influence of ligand conformation, halide anions and solvent

Article abstract of DOI:10.1039/c9ce00107g

In this study, four new d¹⁰-metal halide coordination polymers (CPs), namely [HgCl₂ (3-pna)]_n (1), [HgBr₂(3-pna)]_n (2), [HgI₂(3-pna)]_n CH₃OH (3) and [CdI₂(3-pna)]_n (4), (3-pna = N-(3-pyridinyl)nicotinamide) were prepared through the reaction of mercury(ii) or cadmium(ii) salts with 3-pna by a solution-based method and structurally characterized via single-crystal X-ray diffraction. Moreover, X-ray crystal structure determination of 3-pna is reported for the first time. From the viewpoint of green chemistry, solid state reactivity of the starting materials of compounds 1 and 2 was investigated by mechanochemical and thermal synthesis methods under solvent-free conditions. Powder X-ray diffraction (PXRD) patterns of the reaction mixture upon grinding of the starting reactant and powders isolated from heating the reactant materials were successfully matched with simulated PXRD patterns of the compounds. According to single-crystal X-ray analysis, all compounds 1-4 are isostructural CPs as one-dimensional (1D) zigzag chains based on the anti conformation of the ligand. The accompanying halogen ions are observed to form C/N-HX (X = Cl, Br, I) hydrogen bonds resulting in 3D supramolecular architectures. The presence of solvent molecules in the mercury iodide complex expands the packing structure with the change of halogen-based interactions to N-HO_solvent and C-HO_amide interactions. Conformational dependence of ligand interactions was investigated on the reported 3-pna complexes in the Cambridge Structural Database (CSD). The results revealed that supramolecular synthons of the amide skeleton of the ligand as well as the polymeric architecture of the complex are significantly influenced by the anti/syn conformation of the ligand.

Full text of DOI:10.1039/c9ce00107g

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Tiddo J. Mooibroek, Antonio Frontera et al.
Towards design strategies for anion–π interactions in crystal engineering
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DOI: 10.1039/C9CE00107G
Journal Name
ARTICLE
1
0
Hydrogen-Bonded 3D Network of d -Metal Halide Coordination
Polymer Containing (N-(3-pyridinyl) nicotinamide: Influence of
Ligand Conformation, Halide Anions and Solvent
Received 00th January 20xx,
Accepted 00th January 20xx
a
a
a
b
Zahra Nezhadali Baghan, Alireza Salimi,* Hossein Eshtiagh-Hosseini and Allen G. Oliver
DOI: 10.1039/x0xx00000x
1
0
In this study, four new d -metal halide coordination polymers (CPs), namely [HgCl
2 n 2 n 2
(3-pna)] (1), [HgBr (3-pna)] (2), [HgI (3-
www.rsc.org/
pna)] . CH OH (3) and [CdI (3-pna)] (4), (3-pna = N-(3-pyridinyl)nicotinamide) were prepared through reaction of mercury(II)
n
3
2
n
or cadmium(II) salts with 3-pna by solution-based method and structurally characterized via single-crystal X-ray diffraction.
Moreover, X-ray crystal structure determination of 3-pna has been reported for the first time. In view point of green
chemistry, solid state reactivity of starting materials of compounds 1 and 2 was investigated by mechanochemical and
thermal synthesis methods under solvent-free conditions. Powder X-ray diffraction (PXRD) patterns of the reaction mixture
upon grinding of starting reactant and powders isolated from heating the reactant materials were successfully matched with
simulated PXRD pattern of compounds. According to single-crystal X-ray analysis, all compounds 1-4 are isostructural CPs as
one-dimensional (1D) zigzag chains based on anti conformation of ligand. The accompanying halogen ions are observed to
form C/N−H∙∙∙X (X= Cl, Br, I) hydrogen bonds resulting in 3D supramolecular architectures. Presence of solvent molecule in
mercury iodide complex expands the packing structure with the change of halogen-based interactions to N−H∙∙∙Osolvent and
C−H∙∙∙Oamide interactions. Conformational dependence of ligand interactions was investigated on the reported 3-pna
complexes in the Cambridge Structural Database (CSD). The results revealed that supramolecular synthons of amide skeleton
of ligand as well as polymeric architecture of complex are significantly influenced by anti / syn conformation of ligand.
supramolecular network of CPs depends on the number and
nature of hydrogen bonding moieties of ligand structure. In the
synthesis of coordination networks an intriguing strategy for
Introduction
It has been well recognized that intermolecular interactions
play a crucial role in the self-assembly process for construction
of supramolecular architectures. In the recent years,
remarkable progress in the field of crystal engineering has been
achieved by design approaches reported by different research
groups for prediction and construction of a wide range of
the design of CPs is utilization of different metal center and
organic ligands with a variety in coordination geometries,
functional groups, spacer groups, coordination sites and
9
flexibility. Different spacers allow the ligands to participate in
different non-covalent interaction and/or in coordination
environment, so can significantly effect on the crystal structure
of the compounds.
1
coordination compounds. Coordination polymers (CPs) are an
2
important class of coordination compounds with magnetic ,
Impact of these factors on the architecture control can be
explored using different synthetic methodologies. In this
regard, design and synthesis of new CPs with structural diversity
under different synthetic conditions has been also
3
4
luminescent and antibacterial properties and with extensive
5
6
applications in various area such as catalysis , gas adsorption
and selective adsorption of organic dyes . In this regard,
numerous coordination polymer with wide variety of metals
7
1
0
investigated. A principal challenge for synthetic chemists is to
develop alternative methods for materials synthesis in which
problems related to the solvent such as purification, pollution
and risk be resolved. Mechanochemical methods without bulk
solvents in chemicals synthesis have attracted the chemists to
perform these techniques as environmentally friendly synthetic
8
(such as: Ag, Mn, Fe, Co, Ni, Cu, Zn, Cd, Hg) and organic linkers
have been reported with infinite covalent frameworks of one,
two, and three dimensions. Recently, the design of organic
linkers has attracted great attention to gain reproducible
assembly strategies especially through hydrogen bonds for the
coordination networks. The propagation of 1D, 2D and 3D
1
1
routes. Mechanosynthetic Methods are now a clean and
practical alternative to conventional solution-based methods
and have provided a green route for the preparation of various
compounds including, cocrystals, and pharmaceutical
a. Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad,
Mashhad, Iran
b.
Molecular Structure Facility, Department of Chemistry and Biochemistry, University
1
2
13
cocrystals , metal-organic frameworks (MOFs) , zeolitic
of Notre Dame, Notre Dame, Indiana 46556, USA
1
4
15
imidazolate frameworks (ZIFs) , inorganic complexes , Host–
Guest compounds , nanoparticles
Electronic Supplementary Information (ESI) available: [details of any supplementary
information available should be included here]. See DOI: 10.1039/x0xx00000x
16
17
and coordination
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1
8
polymers . In addition to advantages related to lack of solvent
in these techniques, these methods reduce the required time
View Article Online
DOI: 10.1039/C9CE00107G
1
9
and energy for reactions and products are in remarkable yield.
Comp.
In the present study crystal structure of conformationally
flexible N-(3-pyridinyl) nicotinamide ligand (3-pna) with CONH
spacer for the first time is investigated. Compounds containing
bis-(3-pyridyl) ligands with different spacer group such as
M/X
1
2
3
Hg
I
4
Cd
I
M
X
Hg
Cl
Hg
Br
2 2
CH NH, CH-N(imine), CONH(amide), N (diazene) and alkyl
2
0
group have also been reported by reseachers. An attractive
feature observed in bis-(3-pyridyl) ligands is the ability to adopt
different anti/syn conformation resulted in ligating topologies.
Singha and co-workers explored molecular conformation of 3-
pna in solution.21 Kumar and co-workers investigated gelation
Scheme 1. Schematic representation of complex [HgCl
HgI (L)]n (3) and[CdI (L)]n (4)
2
(L)]n (1), [HgBr
2
(L)]n (2)
[
2
2
2
2
properties and ligating topologies of 3-pna. However, to the
best of our knowledge no report has been yet made on
crystalline structure of 3-pna and the comparison of amide
backbone interactions of ligand with metal complexes to
explore the effect of directional interactions on the stabilization
of crystal packing. Furthermore, typical solution-based
synthesis of four one-dimensional CPs derived from 3-pna also
are reported. Conformational dependence of ligand
interactions, hydrogen bonding capability of amide backbone of
suite. Intensities were integrated and absorption corrections
applied using numerical correction methods. The structures
2
3
were solved using SHELXS, all of the structures were refined
against F in SHELXL using WINGX.25a All of the non-hydrogen
atoms were refined anisotropically. The H atoms, on carbon and
nitrogen atoms were placed at calculated positions using a
riding model with Uiso(H) = 1.2Ueq(C or N). For L, Intensity data
revealed twinning by merohedry. The twin law was found by
2
24
3
-pna in self-assembly process and important role of hydrogen-
bonding in the final crystalline structure, these compounds are
explored. All prepared structures are isostructural that in three
of them, accompanying halogen ions are involved in C/N−H∙∙∙X
2
5b
using TwinRotMat implemented in PLATON.
Due to the
moderate quality of the data for 1 and 2, two and four EADP
constraints had to be used to equalize the guest atoms,
respectively. Crystal structure and refinement data are given in
Table 1.
(X= Cl, Br, I) hydrogen bonding to form 3D supramolecular
architectures (Scheme 1). Presence of solvent molecules in the
solid state of a fourth compound led to the change of halogen-
based interactions to include N−H∙∙∙Osolvent and C−H∙∙∙Oamide
interactions. In these complexes, an anti conformation of
pyridyl nitrogen atoms of the 3pna ligand, resulted in zigzag
polymeric chains. To explore the impact of reaction conditions
on the synthesized CPs, solid-state reactivity of starting
materials in solvent-free condition using thermal and
Synthesis of (N-(3-pyridinyl) nicotinamide ligand, L.
Various methods have been reported for the synthesis of well-
2
1,22
known (N-(3-pyridinyl) nicotinamide ligand.
However, no
report has yet been made on crystalline structure of this ligand.
In this work, we tried to prepare suitable single crystals for the
X-ray single crystallography analysis. Oily solution obtained
from reaction between 3-aminopyridine and nicotinic acid, was
sprayed in dichloromethane solvent. Resulting powder were
filtered and were washed with methanol. Colourless single
crystals were isolated after slow evaporation of products in
methanol solvent after several days. (yield: 68%). M.P = 189-191
mechanochemical reactions of
pyridinyl)nicotinamide ligand with HgCl
was also investigated. Except in the case of HgI
has no reaction with ligand, mixing the ligand with HgCl
HgBr
a
mixture of N-(3-
2
, HgBr
2
, HgI
2
and CdI
2
2
and CdI
2
which
2
and
2
under solvent-free reaction conditions successfully
produced pure compound in high yield.
-1
°
C. IR (cm ): 3243.5, 3066.8, 1678.5s, 1608.7, 1587.7, 1548.8s,
Experimental section
1482.3, 1428.2s, 1332.3, 1293.7s, 1152.2, 1022.6, 815.7,713
All the reagents and solvents for syntheses and analyses were
purchased from either Aldrich or Merck and used without
-1
2 2 2 3
further purification. Infrared spectra (4000– 250 cm ) of solid Synthesis of [HgCl (L)]n (1), [HgBr (L)]n (2), [HgI (L)]n .CH OH (3)
sample were taken as 1% dispersion in KBr pellets using a and [CdI
BOMEM-MB102 spectrometer. Elemental analysis was
performed using a Heraeus CHN-O Rapid analyzer. Melting
2
(L)]n (4)
Solution Method:
point was obtained by a Bamstead Electrothermal type 9200
melting point apparatus and corrected. X-ray diffraction
experiments were performed at 120 K on a Bruker Apex-II
For synthesis of compound 1, to a solution of 3-pna (0.02 g, 0.1
mmol) in 7.0 mL methanol, mercury (II) chloride (0.027 g, 0.1
diffractometer using Mo-Kα radiation (λ = 0.71073 Å). Data mmol) in 3.0 mL methanol was added with stirring. The mixture
collections were performed with the Bruker APEX-3 software
was heated to 70 °C for 50 min and the resulting solution
filtered. Upon slow evaporation at room temperature, colorless
2
| J. Name., 2012, 00, 1-3
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crystals for suitable X-ray analysis were obtained after several Complex (4) synthesized by layering an ethanolicVsieowluArttiicolenO(n5li.n0e
-1
DOI: 10.1039/C9CE00107G
days. Mp 278-279 °C, IR data (KBr pellet, cm ): 693, 800, 1052, mL) of 3-pna (0.02 g, 0.1 mmol) over a 5.0 mL aqueous solution
121, 1290, 1333, 1426s, 1485, 1529s, 1584, 1603, 1681s, 3332. of CdI (0.037 g, 0.1 mmol). After two weeks, single crystals
1
2
Anal. Calcd for C11
C, 28.13; H, 1.79; N, 9.08.
H
9
HgCl
2
N
3
O: C, 28.07; H, 1.93; N, 8.93 Found: suitable for X-ray analysis were obtained. Mp 315-318 °C, IR
data (KBr pellet, cm-1): 693, 802, 1052, 1122, 1293s, 1335,
A similar procedure was performed for the preparation of
compound 2, except that mercury (II) bromide (0.036 g, 0.1
mmol) instead of mercury (II) chloride was added to ligand
1
429s, 1484, 1532s, 1585, 1605, 1684s, 3338. Anal. Calcd. for
C11H9CdI2N3O: C, 23.37; H, 1.60; N, 7.43 Found: C, 23.49; H,
.52; N, 7.85.
1
-1
solution. Mp 268-269 °C, IR data (KBr pellet, cm ): 693, 800,
052, 1120, 1288, 1426s, 1482, 1528s, 1584, 1682s, 3344. Anal.
Calcd for C11 HgBr O: C, 23.61; H, 1.62; N, 7.51 Found: C,
3.87; H, 1.43; N, 7.67.
In addition, mechanochemical and thermal synthesis procedures
applied for 1 and 2 which is described in Supporting Information.
1
H
9
2 3
N
2
Computational methods
The most stable (probable) syn and anti conformations for title
3
Slow evaporation of solution obtained from heating of mixture
of mercury (II) iodide and 3-pna at 70°C resulted in compound
in which amide moiety was disordered. So, for preparation of
compound 3, to a solution of 3-pna (0.02 g, 0.10 mmol) in 7.0
mL methanol, mercury (II) iodide (0.045 g, 0.10 mmol) in 3.0 mL
methanol was added with stirring at room temperature and
then mixture was left in refrigerator for several days. After this
time, suitable single crystals were isolated. Mp 202-204 °C, IR
-pna were obtained via full optimization using DFT calculations
(B3LYP method with the 6-311+G(d,p) basis set) without any
restriction condition, and the frequency analysis showed the
absence of imaginary frequencies in any state. The electrostatic
surface potential (ESP) for conformational forms was obtained
based on the full optimized structures. Energy of CH∙∙∙X and,
NH∙∙∙X interactions for compounds 1, 2 and 4 were calculated
using M062X method with the 6-311G (d, p) basis set for C, H, N
atoms and Lanl2DZ basis set for metal and halogen atoms. The
interaction energies were corrected for the basis set
superposition error (BSSE) in all the complexes. All the
-1
data (KBr pellet, cm ): 697, 802, 1048, 1125, 1195, 1334, 1426s,
1
C
481s, 1549s, 1590s, 1663s, 3268. Anal.Calcd for
HgI O.CH OH: C, 21.02; H, 1.91; N, 6.13 Found: C, 21.22;
H
11 9
N
2 3
3
H, 1.72; N, 6.71.
Table1. Crystallographic data, data collection and refinement for 1-4
Compound L
Compound 1
Hg Cl
Compound 2
HgBr
Compound 3
Compound 4
2 3
CdI N O
formula
C
11
H
9
N
3
O
C
11
H
9
2
N
3
O
C
11
H
9
2
N
3
O
C
12 2 3
H13HgI N O
2
C
11
H
9
Formula weight
199.21
120(2)
470.70
120(2)
559.62
120(2)
685.64
120(2)
565.41
120(2)
T/K
λ/Å
0.71073
0.71073
Monoclinic
P2 /n
7.9213(6)
0.71073
Monoclinic
P2 /n
0.71073
0.71073
Monoclinic
P2 /n
crystal.system
Monoclinic
C c
Monoclinic
P2 /n
space group
1
1
1
1
a/Å
3.8737(3)
21.9191(16)
10.6759(8)
90
7.9879(14)
13.791(2)
12.334(2)
90
10.9713(3)
12.5068(3)
12.1087(3)
90
8.0392(7)
14.4602(12)
12.4285(10)
90
b/Å
13.4161(10)
11.9553(9)
90
c/Å
α/°
β/°
95.751(2)
90
95.349(2)
90
93.939(2)
90
90.4760(10)
90
92.449(2)
90
γ/°
V/Å3
901.91(12)
1264.99(16)
1355.5(4)
1661.45(7)
1443.5(2)
Z
Density
2
4
4
4
4
1.467 g.cm-3
0.099
2.472 g.cm-3
12.579
872
2. 742 g.cm-3
17.240
2. 741 g.cm-3
12.984
2. 602 g.cm-3
5.781
μ/mm-1
F(000)
416
1016
1232
1032
θ range for data collection
2.67 to 28.21
2.29 to 26.46
2.22 to 28.54
2.34 to 27.12
2.16 to 28.38
GOOF
1.054
1.528
1.421
1.370
1.177
Final R indices
R
1
= 0.0346,wR
0.0789
2
=
=
R
1
= 0.0926 ,wR
0.2072
2
=
=
R
1
= 0.0817, wR2 =0.
0.1776
R
1
= 0.0552,wR
0.1217
2
=
=
R
R
1
1
= 0.0601,wR
0.1187
2
=
=
[
I>2σ(I)]
R indices (all data)
CCDC No.
R
1
= 0.0408, wR
2
R
1
= 0.0952 , wR
0.2081
2
R
1
= 0.0846 , wR
0.1787
2
=
R
1
= 0.0587, wR
0.1229
2
= 0.0698,wR
0.1242
2
0
.0817
1889063
1855821
1855820
1855819
1855822
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calculations were performed using the GAMESS program
package.26
View Article Online
DOI: 10.1039/C9CE00107G
Results and discussion
X-ray single crystal diffraction analysis of 3-pna demonstrates and iodide anions, successively. In the asymmetric unit of 3 in
that L crystallizes in the monoclinic crystal system with Cc space addition to the one ligand, one metal ion, and two iodides, there
group. Asymmetric unit of this compound consists of one is one methanol solvent molecule. Coordination geometry
molecule. Molecular structure of 3-pna indicates that this around the metal center in compounds 1-4 is similar. According
2
7
compound adopt an anti conformation. The dihedral angle to τ4 index defined by Houser and co-workers , metal center
between two pyridine rings is 22.42(8)° indicate to the non- adopts a distorted tetrahedral geometry with τ value of 0.78
planar anti conformation. Dihedral angle for 3-pna are listed in 0.79, 0.75 and 0.86, successively. In these compounds, 3-pna act
TableS3. Crystal packing structure of 3-pna as depicted in Fig.1, as µ2-bridging ligand and each metal center is four-coordinate.
1
indicates that hydrogen bonding 푅
(6) motifs of C8-H8…N2 and The coordination sphere of metal ion is occupied by two halide
(7) motifs of C1-H1…N2 anions, two pyridine nitrogen atoms from two different
2
N3H3A…N2 and hydrogen bonding 푅1
2
and N3H3A…N2 exist between molecules. Moreover, C5H5…O1 carboxamide ligand. In the case of compound 4, Cd-N and Cd-I
hydrogen bonding occurs between CH pyridine ring from one distances of 2.251(9), 2.275(8) Å and 2.677(1), 2.688(1) Å are in
molecule and CO amide group from adjacent molecule. As the range of previously reported covalent bond for similar
2
8
expected, participation of amide spacer group as a good cadmium complexes. Also in the case of compounds 1, 2 and
hydrogen bonding acceptor and donor has a remarkable role in 3 Hg-N and Hg-X (X = halogen atom) distances are in the range
2
9
the formation of these interaction. Hydrogen bonding of covalent bond in mercury coordination compounds.
parameters for 3-pna are listed in Table 2. Furthermore, π-π Selected bond distances and angles are listed in Table S1.
stacking interactions with centroid to centroid distance of Structural analysis of complexes 1, 2, 3 and 4, demonstrates
3
.874(3) Å exist between two pyridine rings.
that self-assembly process in these similar compounds creates
X-ray crystallographic analyses for compounds 1-4 reveal that one-dimensional zigzag chains extending along the b-axis. In the
these compounds crystallize in monoclinic P21/n space group compounds 1, 2 and 3, 1D coordination polymers generated
(Table 1). The asymmetric unit of 1, 2 and 4 consist of one from mercury-bridged extending in b-direction. As shown in Fig.
carboxamide ligand, one metal ion, and two chloride, bromide
Fig. 1 Representation of crystal packing of 3-pna showing NH∙∙∙N, CH∙∙∙N, and CH∙∙∙O hydrogen bonding interactions and π-π stacking interactions with
This journal is © The Royal Society of Chemistry 20xx
4
| J. Name., 2012, 00, 1-3
centroid to centroid distance of 3.874(3) Å between pyridine rings.
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DOI: 10.1039/C9CE00107G
interactions occurs between pyridine rings in adjacent chains.
2
connection between the 1D chains in compounds 1, 2 and 4 This causes more stability in the crystal packing of these
2
2
similarly occurs through R
(12) motifs of C−H∙∙∙X, 푅 (16) compounds. As shown in Fig. 4a, in these compounds πpy-C∙∙∙πpy-
2
2
motifs of N−H∙∙∙X (X=Cl, Br, I) and C−H∙∙∙π hydrogen bonds in ac
N
stacking interactions occurs between pyridine ring directly
plane. In the case of compound 3, polymeric chains are connected to amide C=O group (here after for short Py–C) and
2
connected to each other through 푅 (14) motifs of C−H…O pyridine ring directly connected to amide N–H group (here after
2
hydrogen bond between amide oxygen atom from one chain for short Py–N) with centroid to centroid distance of 3.720(2),
and pyridine hydrogen atom of the other ligand in the adjacent 3.816(4) and 3.893(2) Å for compounds 1, 2 and 4, successively.
chain. Furthermore, presence of methanol solvent molecules in It seems that CH group of Py-C orientated toward Py–N ring to
1
compound 3 generate 푅
(7) motifs N−H∙∙∙O and C−H∙∙∙O create C−H∙∙∙π interaction while N−H amide group form N−H∙∙∙X
2
hydrogen bonds between methanol oxygen atom and amide hydrogen bonding with halide anion (Cl or Br) (Fig. 4b). As
hydrogen and pyridine hydrogen atoms, respectively and shown in Fig. 4c, π–π interactions in compound 3 is occurred
O−H∙∙∙I hydrogen bond between methanol and iodine atom (Fig. between two similar Py-C rings so that Py-N rings don’t
3
and Table 2).
participate in π–π interactions. Centroid to centroid distance of
Among the different non-covalent interactions, π– based Py-C rings for compound 3 is 3.545(1) Å and angle of mean
interactions such as anion∙∙∙π, cation∙∙∙π, lone–pair∙∙∙ π, XH∙∙∙π (X planes equal zero (Table S2). To further study the interactions
=
B, C, N, O) and π–π interactions have an important role in the of the pyridine rings of these compounds, we used Harmonic
planning and designing of final crystal packing of compounds. Oscillator Model of Aromaticity (HOMA) index to determine
The term “π–π stacking interactions” refers to attractive local aromaticity of the pyridine rings. HOMA indices for the
intermolecular interactions between aromatic molecules with pyridine rings directly connected to C=O amide group (Py–C)
parallel-stacked, parallel-displaced, edge-to-face or T-shaped for compounds 1, 2, 3 and 4 are 0.857, 0.921, 0.951 and 0.916,
geometries. π–π interactions have been studied extensively in successively. The HOMA indices for the Py–N rings are 0.609,
molecular recognition, catalysis, supramolecular and 0.985, 0.971 and 0.951, successively. These results indicated
3
0
biomolecular systems.
that in the case of compound 1, (HOMA) index value and
Structural analyses of compounds 1, 2 and 4 clearly show that subsequently aromaticity is less than the compounds 2 and
the intermolecular parallel-displaced head-to-tail π∙∙∙π stacking
Fig. 2 Representation of 1-D zigzag chains extending along the b-axis in 1, 2 and 4 (a) NH∙∙∙Cl (b) CH∙∙∙Br and (c) CH∙∙∙π hydrogen bonding interactions between resulting
chains in bc plane in 1, 2 and 4. For clarity, only one synthon was shown for each compound.
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DOI: 10.1039/C9CE00107G
Fig. 3 (a) Spacefill representation of methanol molecules between 1-D zigzag chains in 3. (b) CH∙∙∙O and NH∙∙∙O hydrogen bonding interactions
in 3. (c) Hirshfeld surface mapped with dnorm and (d) two-dimensional fingerprint plot showing CH∙∙∙O and NH∙∙∙O contacts.
which NH or CO amide group act as hydrogen-bonding donor or
4
. This localization in pyridine ring can be related to the stronger acceptor. Among them, CO contribution is only 2 out of 31
1
C–H∙∙∙π hydrogen bond in this compound which leads to variety cases. 퐷
(2) synthon has the largest contribution (18 out of 31
1
of bond distances in π acceptor pyridine ring (Fig. S2) (C-C/C-N cases (51%)). In these cases, NH amide group act as hydrogen
bond distances of pyridine ring are 1.297(28), 1.42(3), 1.302 bond donor (in 30 cases guest molecule (H O) act as acceptor)
25), 1.37(3), 1.38(3) and 1.38(3) Å). and only 3 cases create ring synthon. Interestingly, in our
A main difference in the molecular geometry of compound 3 in compounds 1, 2 and 4 all of amide NH…X hydrogen-bonds show
2
(
2
comparison with compounds 1, 2 and 4 is significant angle of
푅 (16) synthon. In order to get further insight about the nature
2
Py–N ring to amide plane (44.2 (6)°) and dihedral angle between of these interactions, we theoretically investigated the pair of
Py–N and Py–C rings (38.1(3)°) which are the largest observed molecules containing the NH∙∙∙X and CH∙∙∙X interactions of
(Table S3). Corresponding Py–N and amide angles for compound 1, 2 and 4 by DFT-D method. The calculated energies
compounds 1, 2 and 4 are in the range of 28.2(9)°- 32.7(12)° for NH∙∙∙X interactions in compounds 1, 2 and 4 are -20.15, -
-1
while dihedral angle between two pyridine rings for compounds 15.72 and -17.47 kcalmol and for CH∙∙∙X interaction are -4.79,
-1
1
, 2 and 4 are 4.6(6)°, 8.2(5)° and 13.5(3)° respectively. Such -3.82 and -2.18 kcalmol , respectively.
deviation in compound 3 may be explained by N–H∙∙∙O Interestingly, conformational dependence of 3-pna is also
hydrogen bonding between amide NH group and methanol considered as an important factor in the final crystalline
while no guest molecules were observed in 1, 2 and 4.
architecture of these compounds. Indeed, 3-pna can adopt
Cambridge Structural Database (CSD) analysis of previously different conformations as well as structural diversity in its
reported compounds containing 3-pna clearly illustrated great complexes. Different possible conformations of titled ligand are
tendency of these compounds for guest molecules such as shown in Fig. 5. In order to gain more insight into the
solvent and counterions. These moieties are commonly located interactional behaviour of four probable conformations, the
in such way to participate in hydrogen bond with amide moiety computational study on electrostatic surface potential (ESP)
as a good hydrogen-bonding donor and acceptor. These results was performed (Fig. 5). The full optimization results showed
show the important role of spacer amide group in the that anti
compounds including titled ligand (Table S4). It is noteworthy
that, 31 out of 42 cases have hydrogen bonding synthon in
6
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DOI: 10.1039/C9CE00107G
Table 2. Hydrogen bonding parameters for 1-4
Compound
D-H∙∙∙A (Å)
N3–H3A∙∙∙N2
C1–H1∙∙∙ N2
C8–H8∙∙∙ N2
C10–H10∙∙∙ N1
C5–H5∙∙∙O1
D-H(Å)
0.88
0.95
0.95
0.95
0.95
0.95
0.88
0.95
0.95
0.95
0.88
0.95
0.95
0.95
0.95
0.88
0.95
0.84
0.95
0.88
0.95
0.95
H
∙∙∙A(Å)
2.23
2.48
2.56
2.59
2.70
2.81
2.48
3.06
2.30
2.96
2.65
3.20
2.52
2.33
2.41
1.96
2.46
2.02
3.15
2.86
3.44
2.34
D
∙∙∙A(Å)
<D-H∙∙∙
164
146
143
156
175
153
155
171
110
151
149
168
100
113
162
155
159
164
149
138
169
113
A
Symmetry
L
3.086(2)
3.310(3)
3.368(3)
3.477(3)
3.650(3)
3.686(18)
3.30(2)
-1/2+x, 3/2-y, -1/2+z
-1/2+x, 3/2-y, -1/2+z
-1/2+x, 3/2-y, -1/2+z
3/2+x, 3/2-y, 1/2+z
-1+x, 1-y, -1/2+z
-x, 1-y, 1-z
[
HgCl
2
(L)]
n
(1)
C4–H4∙∙∙Cl2
N3–H3A∙∙∙Cl1
C3–H3∙∙∙πPy–N
C11–H11∙∙∙O1
C4–H4∙∙∙Br2
N3–H3A∙∙∙Br1
C3–H3∙∙∙ πPy–N
C3–H3∙∙∙O1
1-x, 1-y, 2-z
3.999(24)
2.78(3)
-1/2+x, 3/2-y, -1/2+z
[
HgBr
2
(L)]
n
(2)
3.82(2)
1-x, 2-y, 1-z
1-x, 1-y, 1-z
3.438(16)
4.14(2)
-1/2+x, 1/2-y, -1/2+z
2.84(2)
C11–H11∙∙∙O1
C9–H9∙∙∙O1
2.84(2)
[
HgI
2
(L)]
n
.meth(3)
3.330(16)
2.783(16)
3.365(19)
1-x, 1-y, 1-z
N3–H3A∙∙∙O2
C3–H3∙∙∙O2
O2–H2A∙∙∙O1
C4–H4∙∙∙I1
2.835(13)
3.989(11)
3.558(10)
4.38(1)
1/2-x, -1/2+y, 1/2-z
-x, 1-y, 1-z
[
CdI
2 n
(L)] (4)
N3–H3A∙∙∙I2
C3–H3∙∙∙πPy–N
C11–H11∙∙∙O1
-x, -y, 1-z
-1/2+x, 1/2-y, -1/2+z
2.849(13)
a
b
c
Fig. 4 (a) Representation of π∙∙∙π stacking interactions of πpy-C∙∙∙πpy-N (black dashed line), and (b) C3H3∙∙∙π interactions between πpy-C (red) and πpy-N (blue)
rings in 1, 2 and 4 (c) showing π∙∙∙π interactions between πpy-C (red) rings and C3H3∙∙∙O2, N3H3A∙∙∙O2 hydrogen bonding in 3.
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conformations are more stable than syn geometries which is
consistent with the abundance of 57% for anti decoration in CSD
analysis. Orientation of nitrogen atom of Py–C ring to the amide
CO group can take two modes described as cis and trans
geometry to differentiate the two forms of anti or syn
conformations. Statistical analysis of amide backbone
interactions as the total number of N–H∙∙∙A (A= any hydrogen
bond acceptor) and C=O∙∙∙D (D= any hydrogen bond donor) in
all 3-pna complexes revealed that anti/cis form has the most
frequent hydrogen bond and the syn/cis is the least.
View Article Online
DOI: 10.1039/C9CE00107G
In the compounds 1-4 two pyridyl nitrogen atoms are located in
anti conformation and therefore favourable polymeric zigzag
chains are created. Moreover, 3-pna in compound 3 has cis
geometry and display anti/cis decoration while ligand shows
anti/trans decoration in compounds 1, 2 and 4. (Fig. 7). Another
feature observed in CSD analysis is the disorder structure of
amide backbone in 3-pna for some of compounds. It is
interesting to note that we also observed the disorder amide
structure for compound 3. The structure partially solved from
low quality x-ray diffraction data of single crystal obtained by
slow evaporation in room temperature. Surprisingly we
successfully prepared suitable single crystal of this compound
by crystallization in low temperature in which no amide
disorder as well as solvent molecule is investigated in the crystal
structure. One other interesting comparison with the CSD is that
there are very few examples of 3-pna that are part of a complex
where the metal center is four-coordinate. Most of the
structures have metal centers that are six coordinate, with
some five-coordinate metal centers and about 5 that have four-
coordinate metal centers.
Fig. 5 Representation of different possible conformations of (N-(3-pyridinyl)
nicotinamide ligand (3-pna), as well as their related electrostatic surface potentials
(ESP) with total number of amide backbone amide hydrogen bonds observed in CSD
compounds.
Intermolecular interactions in titled compounds were
quantified using molecular Hirshfeld surfaces calculations as a
useful tool for visualizing, exploring, and analysing
intermolecular interactions applying the program Crystal
Explorer. Three dimensional pictures show close contact in the
crystal structure with red-white-blue colour, where white
colour indicates contacts with distances equal to the sum of van
der Walls radii of involved atoms and red and blue regions are
referred to shorter and longer contacts respectively. dnorm value
for red, white and blue regions is negative, zero and positive
respectively (dnorm is the normalized contact distance based on
close contacts of H∙∙∙H, H∙∙∙X, C∙∙∙O, O∙∙∙H. In this regard, the H∙∙∙H
contact is most significant interaction in compounds 3-pna and
1
-3 with contributions of 42.4, 24.5, 22.2 and 24.2%
respectively. However, the H∙∙∙I contact has the largest
contribution of 20.8% in 4, H∙∙∙X contact for 1 and 2 is in second
order (20% and 20.6% respectively) and for 3 has proportion of
1
1.2%. In the case of 3-pna, N…H contact is in second order
(18%). The C–H∙∙∙X and N–H∙∙∙X hydrogen bonds refer to
aforementioned contacts in fingerprint plots that N–H∙∙∙X
hydrogen bond is shown as a sharp spike and C–H∙∙∙X is shown
as wings. Also, larger proportion of O∙∙∙H contact in compound
d
e
i i e
and d and the vdW radii of the atom where the d and d are
3
related to others is referring to N–H∙∙∙O and C–H∙∙∙O
distances from the surface to the nearest nucleus inside and
interaction in this compound. Comparing histogram of
percentage contributions of compounds 1-4 is shown in Fig. 8.
Further investigation to identify aromatic π∙∙∙π stacking
interactions were performed with the shape index and
curvedness in which shape index is the measurement of “which
shape” and curvedness is the measurement of “how much
3
1
outside the surface respectively). On the dnorm surface of 3-
pna red area as shown in Fig. S1, indicates CH…N and NH…N
hydrogen bond and for compounds 1, 2 and 3 reported here,
red area as seen in Fig. S3 indicates N–H∙∙∙X (X= I, Cl and Br)
hydrogen bond which is one of the most significant contacts in
these compound due to the presence of amide group.
3
3
shape”. The presence of alternating adjacent red (concave
regions) and blue (convex regions) triangles on the same region
of shape index of these compounds are correspond to the π∙∙∙π
stacking interactions between pyridine rings. Moreover, large
flat green areas separated from each other by dark blue outline
on the Hirshfeld surface mapped with the curvedness
correspond to the π∙∙∙π stacking interactions in these
The two-dimensional fingerprint plots complement to the
surfaces, can be provide summary of nature and type of various
intermolecular interaction in the crystal structures. These plots
showing quantitative contribution of close contacts and it can
be decomposed to give relative contribution of each type of
interactions for better understanding of intermolecular
contacts.32 The Hirshfeld surface analysis for compounds 3-pna
and 1-4 show the significant contributions of some important
3
4
compounds. The Hirshfeld surfaces mapped with shape index
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-1
Figure 6. Molecular pairs (a, b) for compounds 1, 2 and 4 with corrected interaction energy (in Kcalmol )
and curvedness and decomposed 2D finger print plots for In order to investigate the effect of reaction condition on the
compounds 3-pna and 1-4 are shown in Fig. S1 and Fig. S4 final structure of titled compounds, we synthesized compounds
respectively. The results clear that in compound 3, only one ring [HgCl2(L)] (1), [HgBr2(L)] (2) using mechanochemical and
n n
of Py–C participates in π∙∙∙π stacking interactions. As mentioned thermal methods in solvent-free condition. Powder X-ray
above, crystal structure analysis of compounds 1, 2 and 4 clearly diffraction has been utilized to investigate the structure of
demonstrate that the accompanying anion affect the 3D products. The results indicated that PXRD patterns of the solid
supramolecular networks result from the cooperation of reaction mixture of mentioned compounds similar to simulated
C/N−H∙∙∙X (X= Cl, Br, I) hydrogen bonds to link resulting 1-D PXRD pattern derived from single crystal structure of these
zigzag chains. The comparison of compound 3 with these compounds. The same results obtained for powders isolated
compounds clearly shows that amide (CO–NH) group in from thermal synthetic method (Fig. 9).
presence of solvent molecule has a key role in the formation of
N−H∙∙∙Osolvent and C−H∙∙∙Oamide interactions instead of halogen-
based interactions.
Fig.7 Superimposed asymmetric units of 1(green), 2(brown), 3(purple) and 4(yellow)
showing different conformation of 3-pna ligand in 3. (Solvent molecule in the case of 3 is
omitted for clarity)
Fig. 8 Relative contributions to the Hirshfeld surface area for intermolecular contacts
in L and 1-4.
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Khavasi and M. Esmaeili, CrystEngComm., 201V4ie,w 1Ar6ti,cle8O4n7li9ne-
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DOI: 10.1039/C9CE00107G
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1
and 2 from bottom to up.
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017,46, 471-482; f) H. R. Khavasi and N. Rahimi, Cryst.
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To summarize, we have presented the synthesis and structural
1
0
analysis of four new d -metal halide coordination polymers
containing conformationally flexible N-(3-pyridinyl)
4
19.
9
a) N. N. Adarsh, A. Chakraborty, M. Tarres, S. Dey, F. Novio, B.
Chattopadhyay, X. Ribas and D. Ruiz-Molina, New J. Chem.,
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compounds are determined as one-dimensional (1D) zigzag
chains derived from anti conformation of ligand which contact
to each other by C/N−H∙∙∙X (X= Cl, Br, I) hydrogen bonds and
π∙∙∙π interactions to form 3D supramolecular architectures.
Presence of solvent molecule in mercury iodide complex causes
that amide (CO–NH) group form N−H∙∙∙Osolvent and C−H∙∙∙Oamide
Interactions instead of halogen-based interactions. Cambridge
Structural database study of complexes including 3-pna
revealed that non-covalent interactions of amide skeleton of
ligand is significantly influenced by different forms of
conformation of ligand. The Hirshfeld surfaces analysis clearly
showed that hydrogen bonded 3D network of titled compounds
is due to the specific interaction of amide backbone in these
compounds.
2
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The authors respectfully acknowledge the Ferdowsi University
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