Self-assembly of seven diamide-containing pyridinium salts via nonconventional C-H...O hydrogen bonding catemers

Article abstract of DOI:10.1039/c2ce06448k

A series of 1-(2-amino-2-oxoethyl)-3-carbamoylpyridin-1-ium salts with different anions (Cl^-, Br^-, BF₄^-, NO₃^-, OTf^-, PF₆^- and BPh₄^-) have been synthesized and characterized by single crystal X-ray diffraction. The results demonstrate that the L-shaped diamide pyridinium cations can aggregate convergently to form a tubular structure or divergently to form a one-dimensional ribbon structure or two-dimensional brick, grid and sheet structures via different hydrogen bonding catemer motifs, including conventional N-H...O type (BPh₄^- (7)), the nonconventional N-H...O types (Cl^- (1)) and, the mixed N-H...O/C-H...O type (OTf (5) and PF₆^- (6)), and the interesting pure C-H...O types (Cl^- (1), Br^- (2) and BF₄^- (3)).

Full text of DOI:10.1039/c2ce06448k

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PAPER
Self-assembly of seven diamide-containing pyridinium salts via
nonconventional C–H/O hydrogen bonding catemers†
*
An-Kai Wu and Kwang-Ming Lee
Received 30th October 2011, Accepted 8th February 2012
DOI: 10.1039/c2ce06448k
A series of 1-(2-amino-2-oxoethyl)-3-carbamoylpyridin-1-ium salts with different anions (Clꢀ, Brꢀ,
BF4ꢀ, NO3ꢀ, OTfꢀ, PF6ꢀ and BPh4ꢀ) have been synthesized and characterized by single crystal X-ray
diffraction. The results demonstrate that the L-shaped diamide pyridinium cations can aggregate
convergently to form a tubular structure or divergently to form a one-dimensional ribbon structure or
two-dimensional brick, grid and sheet structures via different hydrogen bonding catemer motifs,
including conventional N–H/O type (BPh4ꢀ (7)), the nonconventional N–H/O types (Clꢀ (1)) and,
the mixed N–H/O/C–H/O type (OTf (5) and PF6ꢀ (6)), and the interesting pure C–H/O types
(Clꢀ (1), Brꢀ (2) and BF4ꢀ (3)).
bonding is a well known supramolecular synthon in crystal
Introduction
engineering.35 Generally, there are four possible amide hydrogen
bonding motifs, including the simple dimer, the syn- and anti-
oriented N–H/O catemers and a dimer–catemer mixed motif
(Scheme 1).36 Recently, we reported a series of pyridinium salts
with both N-acetamido and ethyl acetate functional groups.37
The L-shaped cations could form well-defined structures via
different synthons. The conventional N–H/O hydrogen
bonding dimer or catemer motifs could be formed only when the
anions were BF4ꢀ or PF6ꢀ, but these motifs were disturbed when
Brꢀ or OTfꢀ were used. In other words, the results demonstrated
that the amide motifs are significantly affected by the hydrogen
bonding acceptor abilities of the anionic species. Here, we report
the subsequent results achieved by changing the ethyl acetate to
Nonconventional C–H/X (X ¼ O, N and anions) hydrogen
bonding1–6 has received attention due to its importance in
supramolecular structures,7–18 biological structures,19–27 and
anion receptors.28–33 Although the structural characteristics of C–
H/X interactions are relatively well documented, the role of the
C–H/X hydrogen bond in crystal packing is still not clear,
especially the roles that C–H/X hydrogen bonds play when they
coexist with other conventional, strong, hydrogen bonding
groups, such as amide, carboxylic acid and ester groups. For
example, the C–H group exists in the presence of these other
strong hydrogen bonding groups in amino acids, proteins,
protein–ligand complexes and acyl-enzyme species.34 Therefore,
it would be helpful to investigate C–H/X hydrogen bonding by
using small molecules to simplify the system. For example, using
charge-enhanced C–H donor cationic molecules would increase
the proton donor ability of the C–H moiety, and a series of weak
or strong hydrogen bond acceptors, such as carbonyl groups or
Xꢀ anions, would aid in the investigation of the competition for
weak hydrogen bonding between these hydrogen bond acceptors
and the associated hydrogen bond donors. Meanwhile, it is
helpful to understand how the anions tune the hydrogen bonding
interactions involving the cationic moieties within the C–H
donor-rich environment of the crystal structure. In fact, anionic
species play important roles in biological structures, supramo-
lecular chemistry and crystal engineering due to the great variety
of their shapes, sizes, charges and basicities. The primary amide
group (–C(]O)NH2) with intermolecular N–H/O hydrogen
Department of Chemistry, National Kaohsiung Normal University, 62,
Shen-Shung Road, Kaohsiung 824, Taiwan. E-mail: kmlee@nknu.edu.tw;
Fax: +886-7-6051083; Tel: +886-7-7172930 ext 7119
Scheme 1 Conventional amide hydrogen bonding dimer and catemer
† CCDC reference numbers 838304–838310. For crystallographic data in
CIF or other electronic format see DOI: 10.1039/c2ce06448k
motifs and the space requirement for the R groups.
3424 | CrystEngComm, 2012, 14, 3424–3432
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3
an amide group to form a series of diamide-functionalized pyr-
idinium salts with seven anions, including Clꢀ, Brꢀ, BF4ꢀ, NO3
9.08–9.06 (d, 1H, J ¼ 5.8 Hz, –N–CH–CH), 9.00–8.97 (d, 1H,
ꢀ
,
3J ¼ 8.1 Hz, –CH–CH–C–CO), 8.55, 7.73 (s, 1H, N–CH–C–CO–
ꢀ
ꢀ
3
OTfꢀ, PF6 and BPh4
.
NH2), 8.31–8.26 (t, 1H, J ¼ 7.12 Hz, –N–CH–CH–CH–), 8.15,
The results demonstrate that the different types of hydrogen
bonding catemer motifs formed in six salts except the NO3ꢀ salt;
however, the conventional pure N–H/O hydrogen bonding
8.05 (s, 1H, –N–CH2–CO–NH2), 5.47 (s, 2H, –N–CH2–CO–
NH2).
ꢀ
catemer is formed only in the BPh4 salt. When the anions are
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium
tetra-
Brꢀ and BF4ꢀ, the conventional N–H/O hydrogen bonding
catemers are disturbed, and the pure C–H/O]C type catemers
are formed instead. However, in the structures of Clꢀ, OTfꢀ and
fluoroborate (3). A solution of compound 1 (1.0057 g, 4.66 mmol)
in D.I. water (25 ml) was added to a 25 ml H2O/MeOH solution
of AgBF4 (0.9443 g, 4.85 mmol). The resultant solution was
filtered, and the product was collected with a yield of 0.7600 g
(2.85 mmol) or 61%. Needle-shaped crystals suitable for single
crystal X-ray diffraction were obtained by recrystallization of the
product (0.1024 g) from a H2O (1 ml)–MeOH (30 ml) solution via
vapor diffusion of diethyl ether. 1H-NMR (300 MHz, d6-DMSO,
ppm): 9.39 (s, 1H, –N–CH–CCO–), 9.07–9.05 (d, 1H, 3J ¼
5.1 Hz, –N–CH–CH), 8.98–8.95 (d, 1H, 3J ¼ 8.1 Hz, –CH–CH–
C–CO), 8.53, 7.71 (s, 1H, N–CH–C–CO–NH2), 8.29–8.25 (t, 1H,
3J ¼ 6.9 Hz, –N–CH–CH–CH–), 8.13, 8.03 (s, 1H, –N–CH2–
CO–NH2), 5.45 (s, 2H, –N–CH2–CO–NH2).
ꢀ
PF6 salts, the mixed C–H/O/N–H/O types of hydrogen
bonding catemers are observed. From these catemer and dimer
motifs, the different packing structures, including tubular,
ribbon, brick and sheet-like structures, form depending on the
shapes and sizes of the anion species. This study will help clarify
how the amide motifs and the packing structures of the diamide-
containing cationic molecules are affected by different anion
species, and it provides useful information for the application of
these motifs in the field of crystal engineering.
Experimental
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium nitrate (4).
A solution of compound 1 (1.0064 g, 4.67 mmol) in D.I. water
(25 ml) was added to a 25 ml H2O/MeOH solution of AgNO3
(0.8299 g, 4.89 mmol). The resultant solution was filtered, and
the product was collected with a yield of 0.7287 g (3.01 mmol) or
64%. Plate-shaped crystals suitable for single crystal X-ray
diffraction were obtained by recrystallization of the product
(0.1043 g) from a H2O (1 ml)–MeOH (30 ml) solution via vapor
diffusion of diethyl ether. 1H-NMR (300 MHz, d6-DMSO, ppm):
9.39 (s, 1H, –N–CH–CCO–), 9.08–9.06 (d, 1H, 3J ¼ 6.1 Hz, –N–
CH–CH), 8.98–8.96 (d, 1H, 3J ¼ 8.2 Hz, –CH–CH–C–CO), 8.54,
7.71 (s, 1H, N–CH–C–CO–NH2), 8.30–8.25 (t, 1H, 3J ¼ 7.1 Hz,
–N–CH–CH–CH–), 8.14, 8.04 (s, 1H, –N–CH2–CO–NH2), 5.46
(s, 2H, –N–CH2–CO–NH2).
General materials and methods
The 1-(2-amino-2-oxoethyl)-3-carbamoylpyridin-1-ium chloride
(1) and bromide (2) salts were synthesized first by the reaction of
nicotinamide with 2-chloroacetamide and 2-bromoacetamide,
respectively. The BF4 (3), NO3 (4), OTfꢀ (5), PF6 (6), and
ꢀ
ꢀ
ꢀ
ꢀ
BPh4 (7) salts were obtained by the reaction of 1 with AgBF4,
AgNO3 or AgOTf or by the metathesis reactions with NH4PF6 or
NaBPh4 salts, respectively.
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium chloride (1).
A solution of nicotinamide (2.0034 g, 16.40 mmol) and 2-chlor-
oacetamide (1.5953 g, 17.06 mmol) was refluxed in acetonitrile
for 32 h. After cooling, the white-yellow precipitated powder was
collected and recrystallized from H2O/methanol (1 : 3) solution
via layering with diethyl ether to give the product 1 with a yield of
2.9385 g (13.63 mmol) or 83%. Column-shaped crystals suitable
for single crystal X-ray diffraction were obtained by recrystalli-
zation of the product (0.1103 g) from a H2O (1 ml)–DMF (7 ml)
mixed solution via vapor diffusion of THF. 1H-NMR (300 MHz,
d6-DMSO, ppm): 9.56 (s, 1H, –N–CH–CCO–), 9.13–9.11 (d, 1H,
3J ¼ 7.2 Hz, –N–CH–CH), 9.11–9.08 (d, 1H, 3J ¼ 9.5 Hz, –CH–
CH–C–CO), 8.82, 7.72 (s, 1H, N–CH–C–CO–NH2), 8.29–8.24 (t,
1H, 3J ¼ 3.5 Hz, –N–CH–CH–CH–), 8.23, 8.15 (s, 1H, –N–CH2–
CO–NH2), 5.51 (s, 2H, –N–CH2–CO–NH2).
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium
tri-
fluoromethanesulfonate (5). A solution of compound 1 (1.0005 g,
4.63 mmol) in D.I. water (25 ml) was added to a 25 ml H2O/
MeOH solution of AgOTf (1.2296 g, 4.79 mmol). The resultant
solution was filtered, and the product was collected with a yield
of 0.8717 g (2.65 mmol) or 57%. Column-shaped crystals suitable
for single crystal X-ray diffraction were obtained by recrystalli-
zation of the product (0.1024 g) from a MeOH (15 ml) solution
1
via vapor diffusion of diethyl ether. H-NMR (300 MHz, d6-
DMSO, ppm): 9.40 (s, 1H, –N–CH–CCO–), 9.08–9.06 (d, 1H,
3J ¼ 6.1 Hz, –N–CH–CH), 9.00–8.97 (d, 1H, 3J ¼ 8.1 Hz, –CH–
CH–C–CO), 8.54, 7.72 (s, 1H, N–CH–C–CO–NH2), 8.31–8.26 (t,
3
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium bromide (2).
A solution of nicotinamide (2.0015 g, 16.38 mmol) and 2-bro-
moacetamide (2.3514 g, 17.04 mmol) was refluxed in acetonitrile
for 18 h. After cooling, the white precipitated powder was
collected and recrystallized from H2O/methanol (1 : 3) solution
via layering with diethyl ether to give the white product 2 with
a yield of 3.8360 g (14.75 mmol) or 90%. Column-shaped crystals
suitable for single crystal X-ray diffraction were obtained by
recrystallization of the product (0.1076 g) from a H2O (0.5 ml)–2-
1H, J ¼ 7.14 Hz, –N–CH–CH–CH–), 8.14, 8.04 (s, 1H, –N–
CH2–CO–NH2), 5.47 (s, 2H, –N–CH2–CO–NH2).
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium
hexa-
fluorophosphate (6). A solution of compound 1 (1.0042 g,
4.66 mmol) in D.I. water (25 ml) was added to a 25 ml aqueous
solution of NH4PF6 (0.7895 g, 4.84 mmol). The resultant solu-
tion was filtered, and the product was collected with a yield of
1.4679 g (4.52 mmol) or 83%. Column-shaped crystals suitable
for single crystal X-ray diffraction were obtained by recrystalli-
zation of the product (0.1011 g) from a H2O (9 ml)–DMF (1 ml)
1
propanol(10 ml) mixed solvent via vapor diffusion of THF. H-
NMR (300 MHz, d6-DMSO, ppm): 9.41 (s, 1H, –N–CH–CCO–),
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mixed solution via vapor diffusion of THF. 1H-NMR (300 MHz,
d6-DMSO, ppm): 9.40 (s, 1H, –N–CH–CCO–), 9.08–9.06 (d, 1H,
3J ¼ 5.8 Hz, –N–CH–CH), 9.00–8.97 (d, 1H, 3J ¼ 7.7 Hz, –CH–
CH–C–CO), 8.56, 7.73 (s, 1H, N–CH–C–CO–NH2), 8.30–8.26 (t,
1H, 3J ¼ 7.1 Hz, –N–CH–CH–CH–), 8.15, 8.05 (s, 1H, –N–CH2–
CO–NH2), 5.46 (s, 2H, –N–CH2–CO–NH2).
and three F atoms were disordered with two independent
orientations having occupancies of 0.73 and 0.27. The non-
hydrogen atoms were refined with anisotropic thermal parame-
ters. For the H-atoms, a riding model was employed, except that
of salt 7, in which all the atoms were refined with anisotropic
thermal parameters. The details of the crystal parameters, data
collection and structure refinements are summarized in Table 1.
1-(2-Amino-2-oxoethyl)-3-carbamoylpyridin-1-ium
tetraphe-
nylborate (7). A solution of compound 1 (1.0037 g, 4.67 mmol) in
D.I. water (25 ml) was added to a 25 ml aqueous solution of
NaBPh4 (1.6577 g, 4.84 mmol). The resultant solution was
filtered, and the product was collected with a yield of 1.9977 g
(4.00 mmol) or 86%. Plate-shaped crystals suitable for single
crystal X-ray diffraction were obtained by recrystallization of the
product (0.1051 g) from a THF (15 ml) solution via layering of n-
hexane. 1H-NMR (300 MHz, d6-DMSO, ppm): 9.41 (s, 1H, –N–
CH–CCO–), 9.03–9.01 (d, 1H, 3J ¼ 5.94 Hz, –N–CH–CH), 8.98–
Results and discussion
For the convenience of their description and discussion, all of
the types of hydrogen bonding motifs adopted in salts 1 to 7 are
depicted in Scheme 2. All of the cationic moieties of salts 1 to 7,
1-(2-amino-2-oxoethyl)-3-carbamoylpyridin-1-ium,
exhibit
L-shaped structures (Fig. 1(a)). Due to steric hindrance, the
acetamide planes are not coplanar with the pyridinium planes,
and they adopt torsional angles of 61–120ꢁ (q1). Notably, the
nicotinamide groups of salts 1, 2, 3, 5 and 6 adopt a U-shaped
arrangement, and the q2 twist angles are less than 38ꢁ (Fig. 1(b)
3
8.96 (d, 1H, J ¼ 8.1 Hz, –CH–CH–C–CO), 8.55, 7.73 (s, 1H,
3
N–CH–C–CO–NH2), 8.26–8.21 (t, 1H, J ¼ 7.1 Hz, –N–CH–
ꢀ
ꢀ
and (d)). However, the NO3 (4) and BPh4 (7) salts adopt an
N-shaped conformation with torsional angles of 155ꢁ and 157ꢁ,
respectively (Fig. 1(c)). In the crystal structure of the Clꢀ salt
(1), there is a twist angle of 38ꢁ (q2) between the amide plane of
the nicotinamide moiety and the pyridinium ring. Two L-sha-
ped cations are bonded to each other via N1–H1A/
O2#1(Fig. 2(a)) to form a centrosymmetric dimer. Meanwhile,
the dimers stack to form a tubular structure involving two types
of hydrogen bonding catemers. One is a C–H/O catemer
which is formed by two C–H/O]C hydrogen bonds (C3–
H3/O1#2 and C2–H2A/O1#2, red and blue dashed lines
respectively in Fig. 2(b)) with the carbonyl O atom serving as
a bifurcate acceptor. The other is a N–H/O]C hydrogen
bonded catemer which is formed by N1–H1A/O2#1 and
CH–CH–), 8.16, 8.04 (s, 1H, –N–CH2–CO–NH2), 7.20 (t, 8H,
3J ¼ 6.8 Hz, –B–CH–CH–CH), 6.96–6.91 (t, 8H, 3J ¼ 7.2 Hz, –B–
CH–CH–CH), 6.82–6.77 (t, 4H, 3J ¼ 6.8 Hz, –B–CH–CH–CH),
5.45 (s, 2H, –N–CH2–CO–NH2).
X-Ray crystallographic analyses and computation methods
Single-crystal X-ray diffraction data were collected with Mo-Ka
ꢀ
radiation (l ¼ 0.71073 A) in F and u scan modes using a Bruker
APEX-II diffractometer equipped with a CCD array detector
with a graphite monochromator. All structures were solved by
the direct method and refined (based on F2 using all independent
data) using full-matrix least-squares methods (Bruker
SHELXTL 97). In salt 5, several atoms including one C, three O
Table 1 Crystal data and structure refinement for salts 1 to 7
1
2
3
4
5
6
7
Empirical formula
Formula weight
Crystal system
T/K
C8H10ClN3O2 C8H10BrN3O2 C8H10BF4N3O2 C8H10N4O5
C9H10F3N3O5S C8H10F6N3O2P C32H30BN3O2
215.64
Monoclinic
100
260.10
267.00
242.20
Triclinic
296
329.26
Triclinic
100
325.16
499.40
Monoclinic
100
P21/n
Monoclinic
100
P21/c
Orthorhombic
100
Pbca
Orthorhombic
100
Pca21
ꢁ
P1
ꢁ
ꢁ
Space group
ꢀ
P1
P1
a/A
ꢀ
5.3951(4)
8.1557(7)
11.4412(9)
80.447(2)
84.791(2)
72.016
471.77(7)
2
1.518
10.3283(8)
8.1976(7)
12.3290(9)
90
114.243(3)
90
951.81(13)
4
1.815
11.5624(4)
8.3426(4))
12.2163(5)
90.00
116.412
90.00
1055.39(8)
4
1.680
5.4520(3)
6.1264(3)
15.5624(8)
99.478
92.657(3)
99.407(3)
504.38(5)
2
8.4003(2)
8.9153(2)
10.3151(3)
101.5700(10)
103.4520(10)
111.6400(10)
662.40(3)
2
13.2470(10)
11.2054(10)
15.5055(14)
90
90
90
2301.6(3)
8
1.877
9.7596(3)
15.6860(5)
16.8530(5)
90
90
90
2580.01(14)
4
1.286
b/A
ꢀ
c/A
a/deg
b/deg
g/deg
3
ꢀ
V/A
Z
Dcalc./g cmꢀ3
m/mmꢀ1
q/deg
1.595
0.134
1.651
0.307
0.382
4.296
0.165
0.327
0.080
1.81 to 26.53
ꢀ6 to 6
ꢀ10 to 10
ꢀ13 to 14
7994
3.08 to 26.36
ꢀ8 to 12
ꢀ10 to 10
ꢀ15 to 15
7935
1.97 to 26.38
ꢀ14 to 14
ꢀ10 to 10
ꢀ14 to 15
8738
1.33 to 26.45
ꢀ6 to 6
ꢀ7 to 7
ꢀ19 to 19
8320
2.14 to 26.51
ꢀ10 to 10
ꢀ8 to 11
ꢀ12 to 12
10 291
2.72 to 26.40
ꢀ16 to 16
ꢀ13 to 14
ꢀ19 to 19
17 454
1.30 to 26.40
ꢀ10 to 12
ꢀ19 to 19
ꢀ20 to 21
20 147
Range h
Range k
Range l
Reflns collected
Unique reflns
1933
1937
1937/0/127
2137
2137/0/163
2060
2060/0/154
2702
2702/0/190
2356
5121
Data/restraints/parameters 1933/0/127
2356/0/181
0.0290, 0.0714
0.0383, 0.0775
1.053
5121/1/343
0.0343, 0.0862
0.0425, 0.1102
1.153
R1, wR2 [I > 2s(I)]
R1, wR2 (all data)
GOF
0.0258, 0.0679 0.0168, 0.0416 0.0309, 0.0783
0.0268, 0.0687 0.0182, 0.0420 0.0332, 0.0805
0.0338, 0.1044 0.0336, 0.0358
0.0382, 0.1196 0.0832, 0.0847
1.068
838304
1.049
838305
1.075
838306
1.930
838307
1.056
838308
CCDC number
838309
838310
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Scheme 2 (a) There are two conformations formed by nicotinamide groups. One conformation is the U-shaped conformation, and the other is the N-
shaped conformation (green lines). (b) The hydrogen bonding dimer and catemer motifs of the seven salts in this study.
N1#3–H1B#3/O2 (green dashed lines in Fig. 2(b)). Notably,
this N–H/O]C catemer is formed by carbonyl O atoms of
nicotinamide (bifurcate acceptors) and NH2 groups of acet-
amide alternatively (Fig. 2(b) and Scheme 2(b)). The Clꢀ anions
are located between the cationic tubular structures, and they
form two N–H/Clꢀ and two C–H/Clꢀ hydrogen bonds
(Fig. 2(c)). In the crystal structure of the Brꢀ salt (2), the amide
plane in the nicotinamide moiety is also not coplanar with the
pyridinium ring and has a twist angle of 28ꢁ (q2). However,
unlike the tubular structures in 1, the cationic moieties of 2
stack in an interdigitated fashion to form a two dimensional
brick packing structure via a mixed C–H/O/N–H/O type of
catemer (C2#2–H2A#2/O1 and N2#2–H1B#2/O1 bonds in
Fig. 3(a)).
ꢀ
Fig. 1 (a) ORTEP drawing of the 1-(2-amino-2-oxoethyl)-3-carbamoylpyridin-1-ium cation moiety of PF6 salt 6 with atomic numbering and the
definitions of the two torsional angles q1 and q2. (b) and (c) Superposition of the cations with side views of the pyridinium rings and a view along the C6/
N2–C2 direction. (b) 1 (Clꢀ, red), 2 (Brꢀ, yellow), 3 (BF4ꢀ, green), 5 (OTfꢀ, pale blue) and 6 (PF6ꢀ, pink). (c) 4 (NO3ꢀ, purple) and 7 (BPh4ꢀ, orange). The
nicotinamide groups of both salts adopt an N-shaped conformation. (d) The torsion angle of q1 (C3–N2–C2–C1) and q2 (C3–C4–C5–O2) of salts 1–7.
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Fig. 2 The hydrogen bonding motif and packing of the Clꢀ salt (1). (a) The dimer building block (Symm. Op. #1 ¼ 1 ꢀ x, 1 ꢀ y, 2 ꢀ z), (b) double
catemer motifs (Symm. Op. #2 ¼ ꢀ1 + x, y, z; #3 ¼ ꢀx, 1 ꢀ y, 2 ꢀ z) and (c) the arrangement of the cationic tubular structures that surround the Clꢀ
anions in the packing (Symm. Op. #4 ¼ 1 + x, ꢀ1 + y, z; #5 ¼ ꢀx, 1 ꢀ y, 1 ꢀ z; #6 ¼ 1 ꢀ x, 1 ꢀ y, 1 ꢀ z; #7 ¼ ꢀ1 + x, y, z). The detailed hydrogen
bonding data are listed in Table 2.
Table 2 Hydrogen bonding details of salt 1
Table 3 Hydrogen bonding details of salt 2
D–H/A H/A/A D/A/A :D–H/A/ꢁ
D–H/A
D–H/A H/A/A D/A/A :D–H/A/ꢁ
ꢀ ꢀ ꢀ
ꢀ
ꢀ
ꢀ
D–H/A
N1–H1A/O2#1
C3–H3/O1#2
0.88
0.95
0.99
0.88
0.99
0.95
0.95
2.16
2.34
2.44
2.26
2.49
2.84
2.52
2.29
2.36
3.03
3.06
3.27
3.26
3.37
3.64
3.38
3.17
3.21
166
132
141
138
148
143
151
172
162
C2–H2A/O1#1
N1#2–H1B#2/
O2#3
C2#4–H2B#4/Br1
N1#5–H1A#5/Br1
N3#6–H3A#6/Br1
C7#7–H7#7/Br1
C8#8–H8#8/Br1
N3#8–H3B#8/Br1
0.99
0.88
2.36
2.28
3.31
3.06
161
147
C2–H2A/O1#2
N1#3–H1B#3/O2
C2–H2B/O2#4
C7#6–H7#6/Cl1
C8#7–H8#7/Cl1
0.99
0.88
0.88
0.95
0.95
0.88
2.86
2.70
2.78
3.03
3.03
5/20
3.67
3.51
3.59
3.82
3.68
3.35
140
153
153
142
127
164
N3#4–H3A#4/Cl1 0.88
N3#5–H3B#5/Cl1 0.88
The Brꢀ anions are located between two pyridinium rings
(Fig. 3(b)) and form six hydrogen bonds, including two C–H/
O]C, one Ca–H/O]C and three N–H/O]C hydrogen
bonds, which are shown in Fig. 3(c). A comparison of the
structures of salts 1 and 2 indicates that the hydrogen bonding
catemers formed by the acetamide groups are syn-orientated in 1
and anti-orientated in 2. This difference is likely a result of the
size of the anions because the distance between two neighboring
indicates that the latter could serve as an alternative to the N–H
ꢀ
donor in the crystal packing. In the crystal structure of the BF4
salt (3), a two-dimensional brick packing structure is formed.
The amide plane of the nicotinamide moiety is not coplanar with
the pyridinium ring and has a twist angle of 31ꢁ (q2). Fig. 4(a)
depicts the two-dimensional brick packing structure of 3 which
contains one more N–H/O]C hydrogen bonded dimer motif
(N1#2–H1A#2/O1#1) when compared to the brick structure
of the Brꢀ salt. Like the Brꢀ anions in 2, the BF4ꢀ anions of 3 are
located between two pyridinium rings and form six hydrogen
bonds, including two Cring–H/F, one Ca–H/F and three N–
H/F hydrogen bonds, which are shown in Fig. 4(c). Fig. 5
depicts the ribbon building block of the NO3ꢀ salt (4). The amide
ꢀ
acetamide groups on the same side of the structure is 8.198 A,
which would allow the larger Brꢀ anion to fit in a condensed
packing arrangement. It is worth noting that the hydrogen
bonding catemers in 1 and 2 consist of conventional N–H/O]
C and nonconventional C–H/O]C hydrogen bonds, which
Fig. 3 The hydrogen bonding motif and packing of the Brꢀ salt (2). (a) Catemer motifs (Symm. Op. #1 ¼ 1 ꢀ x, 1 ꢀ y, 2 ꢀ z; #2 ¼ 1/2 ꢀ x, 1/2 + y, 3/2 ꢀ
z; #3 ¼ 1/2 ꢀ x, 1/2 + y, 3/2 ꢀ z, ꢀ1/2 + x, 3/2 ꢀ y, ꢀ1/2 + z). (b and c) The arrangement of the cationic brick structure with the intercalated Brꢀ anions in
the packing (Symm. Op. #4 ¼ 1/2 ꢀ x, 1/2 + y, 3/2 ꢀ z; #5 ¼ 1/2 + x, 3/2 ꢀ y, 1/2 + z; #6 ¼ 3/2 ꢀ x, 1/2 + y, 5/2 ꢀ z; #7 ¼ 1 + x, y, z; #8 ¼ 1/2 + x, 3/2 ꢀ y,
ꢀ1/2 + z). The detailed hydrogen bonding data are listed in Table 3.
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Fig. 4 The hydrogen bonding motif and packing of the BF4ꢀ salt (3). (a) The dimer building block (Symm. Op. #1 ¼ 2 ꢀ x, 1/2 + y, 3/2 ꢀ z; #2 ¼ x, 1/2
ꢀ y, ꢀ1/2 + z), (b) catemer motifs and (c) the arrangement of the cationic brick structure with the intercalated BF4ꢀ anions in the packing (Symm. Op. #3
¼ x, 1 + y, z; #4 ¼ 1 ꢀ x, 1 ꢀ y, ꢀz; #5 ¼ 1 ꢀ x, 1 ꢀ y, 1 ꢀ z; #6 ¼ x, 1/2 ꢀ y, ꢀ1/2 + z). The detailed hydrogen bonding data are listed in Table 4.
Table 4 Hydrogen bonding details of salt 3
Table 5 Hydrogen bonding details of salt 4
D–H/A H/A/A D/A/A :D–H/A/ꢁ
D–H/A
H/A/A
D/A/A
:D–H/A/ꢁ
ꢀ
ꢀ
ꢀ
ꢀ
D–H/A
ꢀ
ꢀ
D–H/A
C2–H2A/O1#1
N1#2–H1B#2/O2
N1#2–H1A#2/
O1#1
N3#3–H3B#3/F2
N3#3–H3B#3/F4
N3#4–H3A#4/F1
C2#5–H2B#5/F3
C8#5–H8#5/F3
C7#6–H7#6/F2
0.99
0.88
0.88
2.61
2.21
2.26
3.60
2.98
3.06
172
146
151
C8–H8/O4
0.93
0.93
0.93
0.86
0.97
0.97
0.86
0.86
0.86
2.34
2.18
2.65
2.10
2.50
2.15
2.26
2.40
2.19
3.14
3.08
3.27
2.95
3.43
2.98
2.95
3.25
2.99
143
165
124
168
160
163
138
167
155
C3#3–H3#3/O3
C7#1–H7#1/O2
N3#2–H3A#2/O2
C2#6–H2A#6/O5
N1#4–H1A#4/O5
N1#5–H1B#5/O3
N1#5–H1B#5/O5
N3#3–H3B#3/O4
0.88
0.88
0.88
0.99
0.95
0.95
2.60
2.16
2.13
2.34
2.56
2.41
3.42
2.94
2.95
3.07
3.28
3.18
155
148
155
131
133
138
H8/O4, and C3#3–H3#3/O3), one Ca–H/O]C (C2#6–
H2B#6/O5) and four N–H/O]C hydrogen bonds (N3#3–
H3B#3/O4, N1#5–H1B#5/O3, N1#5–H1B#5/O5 and
N1#3–H1B#3/O5), which are shown in Fig. 5(b). In the crystal
structure of the OTfꢀ salt (5), the amide plane of the nicotin-
amide moiety is coplanar with the pyridinium ring (q2 ¼ 0). A
linear tape building block is formed by two alternative dimer
motifs; one such building block is formed via a N–H/O type
(N1–H1B/O2#1) bonding interaction, and the other is formed
via a C–H/O type (C–H7/O1#2) interaction as depicted in
Fig. 6(a). The acetamide group of salt 5 possesses a twist angle of
112ꢁ relative to the pyridinium ring and bonds to the other amide
groups of the cations in the neighboring tape with bond distances
group of the nicotinamide moiety adopts a N-shaped confor-
mation, which is the opposite arrangement of the U-shaped
conformation (Scheme 2(a)); in other words, the directions of the
C]O and NH2 groups are exchanged, and the C]O group
adopts a large twist angle of 155ꢁ relative to the plane of the
pyridinium ring. The C]O groups serve as bifurcate hydrogen
bonding acceptors and form alternative C–H/O (C7#1–
H7#1/O2) and N–H/O (N3#2–H3A#2/O2) hydrogen
bonding dimer motifs. The continuous dimer motifs result in
a ribbon building block (Fig. 5(a)).
ꢀ
The NO3 anions are located between the ribbons and
form seven hydrogen bonds, including two Cring–H/O]C (C8–
Fig. 5 The hydrogen bonding motif and packing of the NO3ꢀ salt (4) (Symm. Op. #1 ¼ 1 ꢀ x, ꢀy, 1 ꢀ z; #2 ¼ 2 ꢀ x, ꢀ1 ꢀ y, 1 ꢀ z; #3 ¼ ꢀ1 + x, 1 + y, z;
#4 ¼ 2 ꢀ x, 1 ꢀ y, 2 ꢀ z, #5 ¼ 1 ꢀ x, 1 ꢀ y, 2 ꢀ z, #6 ¼ x, 1 + y, z). (a) The ribbon building block and (b) the arrangement of the cationic ribbon structure
and the intercalated NO3ꢀ anions in the packing. The detailed hydrogen bonding data are listed in Table 5.
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Fig. 6 The hydrogen bonding motif and packing of the OTfꢀ salt (5). (a) The tape building block formed by the dimer/catemer mixed motif (Symm. Op.
#1 ¼ 1 ꢀ x, 2 ꢀ y, 1 ꢀ z; #2 ¼ 1 ꢀ x, ꢀ1 ꢀ y, ꢀz) and (b) the dimer motif serves as an inter-tape linkage (Symm. Op. #3 ¼ 1 ꢀ x, 1 ꢀ y, 1 ꢀ z; #4 ¼ x, y,
ꢀ1 + z). (c and d) show the arrangement of the cationic tape structure and the intercalated OTfꢀ anions in the packing (Symm. Op. #5 ¼ x, y, 1 + z; #6 ¼
1 ꢀ x, 2 ꢀ y, 1 ꢀ z; #7 ¼ ꢀ1 + x, ꢀ1 + y, 1 + z; #8 ¼ ꢀx, 1 ꢀ y, 1 ꢀ z). The detailed hydrogen bonding data are listed in Table 6.
ꢀ
Table 6 Hydrogen bonding details of salt 5
which are shown in Fig. 6(d). In the crystal structure of the PF6
salt (6), the amide plane of the nicotinamide moiety is nearly
coplanar with the pyridinium ring (q2 ¼ 0). Fig. 7 depicts the two-
dimensional sheet packing structure of the PF6ꢀ salt 6. Notably,
the hydrogen bonding catemers via pure amide groups are
formed by the alteration of nicotinamide and acetamide moieties
via two sets of hydrogen bonding interactions. The first set of
interactions is the N–H/O]C (N3#2–H3B#2/O1#1) and C–
H/O]C (C6#2–H6#2/O1#1) hydrogen bonding interac-
tions, and the second set is the N–H/O]C (N1#1–H1B#1/
D–H/A
D–H/A H/A/A D/A/A :D–H/A/ꢁ
ꢀ ꢀ ꢀ
N1–H1B#1/O2
C7–H7/O1#2
N1#1–H1A#1/
O1#3
0.88
0.95
0.88
2.03
2.38
2.06
2.88
3.31
2.92
162
165
167
C2#5–H2A#5/O5
C6#6–H6#6/O4
N3#7–H3A#7/O3
C8#8–H8#8/F1
C2#8–H2B#8/O3
C2#8–H2B#8/O4
N3#6–H3B#6/O4
0.99
0.95
0.88
0.95
0.99
0.99
0.88
2.70
2.34
2.18
2.62
2.65
2.41
2.08
3.41
3.27
2.96
3.57
3.47
3.28
2.94
137
166
147
174
141
146
164
ꢀ
O2#3) hydrogen bonding interaction. The PF6 anions, like
ꢀ
those in the Brꢀ and BF4 salts, are located between two pyr-
idinium rings and form seven hydrogen bonds, including two C–
H/O]C (C7#2–H7#2/F3 and C8#6–H8#6/F1), two Ca–
H/O]C (C2#3–H2A#3/F2 and C2#6–H2B#6/F6) and two
N–H/O]C hydrogen bonds (N1#1–H1A#1/F3 and N3#4–
H3A#4/F2), which are shown in Fig. 7. In the crystal structure
of the BPh4ꢀ salt (7), as in the NO3ꢀ salt (4), the amide plane of
the nicotinamide moiety adopts a large twist angle relative to the
pyridinium ring (q2 ¼ 157ꢁ). Fig. 8(a) depicts the two-dimen-
sional sheet packing structure of the BPh4ꢀ salt 7. However, the
types of hydrogen bonding amide hydrogen bonding catemers in
salt 7 differ from those in salt 6. Two hydrogen bonding catemers
in salt 7 are formed by pure nicotinamide or acetamide groups
with N–H/O]C hydrogen bonding respectively (N1#2–
H1B#2/O1 and N3–H3B/O2#1 Fig. 8(a)). The amide plane of
the nicotinamide moiety adopts an opposite conformation like
ꢀ
of 2.06 A (N1#1–H1A#1/O1#3, Fig. 6(b)). This typical amide
dimer motif serves as a linkage between the tapes to form a two-
dimensional grid structure. The OTfꢀ anions are located within
the cavities of the grid (Fig. 6(c)) and form two Cring–H/O
hydrogen bonds (C6#6–H6#6/O4 and C8#8–H8#8/F1),
three Ca–H/O hydrogen bonds (C2#5–H2A#5/O5, C2#8–
H2B#8/O3 and C2#8–H2B#8/O4) and two N–H/O
hydrogen bonds (N3#7–H3A#7/O3 and N3#6–H3B#6/O4),
ꢀ
that observed in the NO3 salt 4 (Fig. 5(a) and Scheme 1). The
Table 7 Hydrogen bonding details of salt 6
D–H/A
D–H/A H/A/A D/A/A :D–H/A/ꢁ
ꢀ ꢀ ꢀ
N3#2–H3B#2/
O1#1
0.88
2.04
2.90
163
C6#2–H6#2/O1#1
N1#1–H1B#1/
O2#3
0.95
0.88
2.38
2.10
3.30
2.94
162
157
ꢀ
Fig. 7 The hydrogen bonding motif and packing of the PF6 salt (6).
The sheet structure is formed by alternating nicotinamide and acetamide
C7#2–H7#2/F3
C8#6–H8#6/F1
C2#3–H2A#3/F2
C2#6–H2B#6/F6
N1#1–H1A#1/F3
N3#4–H3A#4/F2
0.95
0.95
0.99
0.99
0.88
0.88
2.47
2.49
2.51
2.46
2.34
2.16
3.38
3.38
3.48
3.43
3.10
3.00
160
156
165
167
145
160
moieties via C–H/O/N–H/O hydrogen bonding catemers. The anti-
oriented catemer arrangement with the intercalated PF6 anions in the
ꢀ
packing (Symm. Op. #1 ¼ ꢀx, 1/2 + y, 1/2 ꢀ z; #2 ¼ 1/2 ꢀ x, 2 ꢀ y, ꢀ1/2
+ z, #3 ¼ 1/2 ꢀ x, 1/2 + y, z; #4 ¼ 1 ꢀ x, 1/2 + y, 1/2 ꢀ z; #5 ¼ 1/2 + x, 1 +
y, 1/2 ꢀ z; #6 ¼ 1/2 + x, y, 1/2 ꢀ z). The detailed hydrogen bonding data
are listed in Table 7.
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Fig. 8 The hydrogen bonding motifs in the packing structure of the BPh4ꢀ salt (7). (a) The sheet structure formed by the N–H/O hydrogen bonding
catemer motif. (b) The formation of the C–H/p interactions by cations and BPh4ꢀ anions. (c) The BPh4ꢀ anions are intercalated between the cationic
sheet structures (Symm. Op. #1 ¼ ꢀ1/2 + x, 2 ꢀ y, z; #2 ¼ 1/2 + x, 1 ꢀ y, z; #3 ¼ 1 + x, y, ꢀ1 + z; #4 ¼ 1/2 ꢀ x, y, ꢀ1/2 + z). The detailed hydrogen
bonding data are listed in Table 8.
with the smallest anion (Clꢀ), but they form anti-oriented
Table 8 Hydrogen bonding details of salt 7
hydrogen bonding catemers in the other four salts. This
H/A/A D/A/A :D–H/A/ꢁ
ꢀ ꢀ
ꢀ
D–H/A
D–H/A
observation can be explained by the large separation of anti-
oriented hydrogen bonding catemer that is suitable for large
ꢀ
N1#2–H1B#2/O1
N3–H3B/O2#1
C8#3–H8#3/ R1
C3#4–H3#4/ R2
C2#4–H2B#4/ R3
C2#4–H2B#4/C10
0.90(3) 2.23(3)
0.86(3) 2.35(3)
0.94(2) 2.51
0.90(2) 2.71
0.95(2) 2.57
1.02(2) 2.81(2)
2.977(2)
2.839(2)
3.34
3.35
3.26
127(2)
128(2)
147
128
130
anions. Intriguingly, the cationic moieties of the NO3 and
ꢀ
BPh4 salts adopt the N-shaped conformation. One reason for
ꢀ
this phenomenon is the tendency of the NO3 salt to achieve
ꢀ
the maximum number of hydrogen bonds with the NO3
3.394(3)
121(2)
anions, which would overcome the energy lost by adopting the
ꢀ
N-shaped conformation. As for the BPh4 salts, the confor-
mation may be a result of the size effect simply because the
BPh4ꢀ anions are located between sheets and form four C–H/p
hydrogen bonds, including two C–H/p (C8#3–H8#3/ R1 and
C3#4–H3#4/ R2) and two Ca–H/p (C2#4–H2B#4/R3 and
C2#4–H2B#4/C10) hydrogen bonds, which are shown in
Fig. 8(b) and (c). The C–H/p hydrogen bonds are similar to
those in the pyridinium BPh4ꢀ salt.38
ꢀ
ꢀ
BPh4 anion is very large in size. Additionally, BPh4 is a very
weak hydrogen bond acceptor. Therefore, to be compatible
with the anion size, the cationic moieties adopt the N-shaped
conformation and form a sheet structure to maximize the space
that could be occupied by an anion. Notably, the sheet formed
ꢀ
in the BPh4 salt is different from the smaller sheet structure
ꢀ
On the basis of the crystal structures of salts 1 to 7, we drew
the following conclusions: (1) The diamide pyridinium salts
may aggregate convergently to form tubular structures (Clꢀ (1))
or divergently to form a one-dimensional ribbon structure
observed in the structure containing the PF6 anion (Fig. 7) in
which the U-shaped structure is adopted.
ꢀ
ꢀ
(NO3 (4)) or two-dimensional brick (Brꢀ (2) and BF4 (3)),
Conclusions
grid (OTfꢀ (5) and PF6 (6)) and sheet structures (BPh4 (7)).
(2) The hydrogen bonding catemer motifs via the amide C]O
acceptor are reliable building units for all of the salts with
ꢀ
ꢀ
Here we reported a series of diamide-containing pyridinium salts.
The L-shaped cations could aggregate convergently to form
a tubular structure or divergently to form a one-dimensional
ribbon structure or two-dimensional brick, grid and sheet
structures via variable hydrogen bonding catemers. Additionally,
the size of the anion plays a significant role in determining the
types of hydrogen bonding catemer motifs that form. These
results not only imply the importance of C–H/O]C hydrogen
bonding, which is able to serve as an alternative to the N–H/
O]C hydrogen bonding in hydrogen bonding catemer motifs,
but also allow us to design better, new supramolecular
architectures.
ꢀ
spherical or regular polyhedral anions, Clꢀ (1), Brꢀ (2), BF4
ꢀ
ꢀ
(3), PF6 (6) and BPh4 (7). These motifs include the conven-
ꢀ
tional N–H/O type (BPh4 (7)), the nonconventional N–H/
O types (Clꢀ (1)) and, the mixed N–H/O/C–H/O type (OTf
(5) and PF6 (6)), and the interesting pure C–H/O types (Clꢀ
ꢀ
(1), Brꢀ (2) and BF4 (3)). These results clearly demonstrate
ꢀ
that the charge-enhanced C–H group is able to bond to
carbonyl O atoms and is also robust enough to be an alterna-
tive hydrogen bond donor in the construction of C–H/O
hydrogen bonding catemers. Thus, this finding could also
expand the flexibility of the amide group in variable hydrogen
bonding catemer motifs. (3) It appears that the size of the
anions plays a significant role in the type of hydrogen bonding
catemer, because these N–H/O types were only observed in
Acknowledgements
The work was supported by the National Science Council of
Taiwan, Republic of China (NSC-100-2113-M-017-001) and
National Kaohsiung Normal University. We are grateful to the
National Center for High-performance Computing for computer
time and facilities.
ꢀ
ꢀ
the species with relatively larger anions (PF6 (6) and BPh4
(7)). Additionally, the type of four typical motifs (Scheme 1) is
also affected by the size of anion species, thus the syn-oriented
hydrogen bonding catemers were only observed in the species
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