Proton-transfer supramolecular salts resulting from 3,5-dinitrobenzoic acid and aminomethyl pyridine

Article abstract of DOI:10.1039/c2nj40252a

Three hydrogen-bonding three-dimensional (3D) networks of ammonium carboxylate salts formed between 3,5-dinitrobenzoic acid and aminomethyl pyridine (2-, 3-, 4-) are described here. During solution crystallization, the hydrogen atom transfers from the carboxylic acid to the amine to yield ammonium carboxylate salts, which feature three charge-separated N⁺- H...O^- hydrogen bonds to afford two types of one-dimensional (1D) hydrogen-bonding columns. Of the three structures, ((2-pyridylmethyl) ammonium) (3,5-dinitrobenzoate) (1) shows a hydrogen-bonding column which consists of alternating R12(4) and R24(8) rings whereas ((3-pyridylmethyl) ammonium) (3,5-dinitrobenzoate) (2) results in a hydrogen-bonding column which comprises repeating R34(10) rings. ((4-pyridylmethyl)ammonium) (3,5-dinitrobenzoate) (3) bears a unique shape of Chinese knot among four cations instead of the column constructed by rings. From this we can gather information about the possible position effects of functional groups on the overall packing.

Full text of DOI:10.1039/c2nj40252a

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Proton-transfer Supramolecular Salts Resulted from 3,5-Dinitrobenzoic Acid
and Aminomethyl Pyridine
Xue-Hua Ding, Lin-Fang Cui, Yong-Hua Li,* Shi Wang and Wei Huang*
Key Laboratory for Organic Electronics & Information Displays (KLOEID) and
Institute of Advanced Materials (IAM), Nanjing University of Posts
Telecommunications, Nanjing 210046, China
&
* Corresponding authors. Tel/Fax: +86 25 85866396 (Y. H. Li); +86 25 85866008 (W.
Huang)
Eꢀmail addresses: iamyhli@njupt.edu.cn (Y. H. Li), weiꢀhuang@njupt.edu.cn (W.
Huang)
Abstract
Three hydrogenꢀbonding threeꢀdimensional (3D) networks of ammonium carboxylate
salts formed between 3,5ꢀdinitrobenzoic acid and aminomethyl pyridine (2ꢀ, 3ꢀ, 4ꢀ)
are described here. During solution crystallization, the hydrogen atom transfers from
the carboxylic acid to the amine to yield ammonium carboxylate salts, which feature
three chargeꢀseparated N+–H…O– hydrogen bonds to afford two types of
oneꢀdimensional (1D) hydrogenꢀbonding columns. Of the three structures,
((2ꢀpyridylmethyl)ammonium) ꢁ (3,5ꢀdinitrobenzoate) (1) shows a hydrogenꢀbonding
1
2
column which consists of alternating
(4) and
(8) rings whereas
R
R
2
4
((3ꢀpyridylmethyl)ammonium)
ꢁ
(3,5ꢀdinitrobenzoate) (2) results in
a
3
hydrogenꢀbonding column which comprises repeating
(10)
rings.
R
4
((4ꢀpyridylmethyl)ammonium) ꢁ (3,5ꢀdinitrobenzoate) (3) bears a unique shape of
Chinese knot among four cations instead of the column constructed by rings. From
this we can gather clues about the possible position effects of functional groups on the
overall packing.
1

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Introduction
Since JeanꢀMarie Lehn’s famous description of supramolecular chemistry,
supramolecular synthesis as a rapidly growing field is still in its formative stages.1ꢀ6
Crystal engineering offers a rational approach to the design and construction of
multicomponent supermolecules or supramolecular arrays.7 By the judicious choice of
the supramolecular synthons, various supramolecular assemblies can be generated by
the effective selfꢀassembly of organic and inorganic molecules. Neutral coꢀcrystals
and molecular salts have aroused great interest, because they have the potential to
alter and optimize physical properties such as crystalline form, solubility and
stability.8
As an organic chemist employs the covalent bond in the design of target
molecules, nonꢀcovalent bonds can be exploited in the design of supramolecular
compounds.9,10 Nonꢀcovalent interactions include hydrogen bonding, ionic
interactions, van der Waals, π–π stacking and electrostatic interactions. Dominant
among such molecular interactions is hydrogen bonding due to its strength and
directional properties.11ꢀ14 Currently, Hꢀbonding interactions have been of widespread
interest in the realm of crystal engineering,15,16 supramolecular chemistry,4,17 material
science18 and biological recognition19. Since hydrogen bonds may be considered the
partially activated precursors, a very close relationship exists between hydrogen
bonding and protonꢀtransfer reactions.20 Chargeꢀassisted hydrogen bonds are
considered to be strong and possibly a more robust hydrogenꢀbonding synthon than
the same interaction between neutral molecules.21,22 Whenever the hydrogenꢀbonding
associations result in complete proton transfer, an ionic compound is produced and the
nonꢀcovalent interactions between hydrogenꢀbonding groups are reinforced.23
Supramolecular salts of multifarious topological structures have been constructed
through hydrogenꢀbonding interactions, such as oneꢀdimensional (1D) tapes,
twoꢀdimensional (2D) sheets and threeꢀdimensional (3D) networks.24ꢀ33 The facile
way is to select the supramolecular synthons with complementary hydrogenꢀbonding
functional groups. Carboxylic acid and amine bear the important functional group
2

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–COOH and –NH2 for crystal engineering. If the two components with the correct
difference in pKas are combined in solution, the proton is transferred from the
carboxylic acid to the amine and three potential chargeꢀassisted N+–H…O– hydrogen
bonds can form.34 Supramolecular ammonium carboxylate salts of general formula
+
–
(R–NH3 ) ꢁ (R′–CO2 ) can be achieved by the assembly of deprotonated carboxylic
group with four potential hydrogenꢀbonding acceptors (two lone pairs on each of the
two O atoms) and protonated ammonium group with threeꢀfold hydrogenꢀbonding
donors.34,35 Kinbara et al. observed that the hydrogenꢀbonding pattern afforded
2
different types of translational hydrogen bonded units, a column of repeating
(8)
,
R
4
(12) rings etc.36,37
R
3
4
(10) or
R
4
4
In this context, our attention has been attracted by the protonꢀtransfer
supramolecular salts 1-3, constructed by 3,5ꢀdinitrobenzoic acid and aminomethyl
pyridine (2ꢀ, 3ꢀ, 4ꢀ) (Scheme 1). The aim of this work is to try to explore the possible
position effect of the aminomethyl group in the pyridine ring and compare the
1
architectures of the resulting supramolecular system. A column of alternating
(4)
R
2
2
3
and
2).
(8) rings is found in salt 1, yet that of repeating
(10) rings in 2 (Scheme
R
R
4
4
Scheme 1 Structures of the protonꢀtransfer ammonium carboxylate salts.
3

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Scheme 2 Two types of the hydrogenꢀbonding chains in ammonium carboxylate salts
1 and 2, respectively. The nomenclature is adopted from Kinbara et al.34
Results and Discussion
We performed a systematic screen for supramolecular salts 1-3, resulting from
3,5ꢀdinitrobenzoic acid and the set of aminomethyl pyridine (2ꢀ, 3ꢀ, 4ꢀ). Salt 1
crystallizes in the monoclinic space group P21/c and contains one crystallographically
independent (2ꢀpyridylmethyl)ammonium cation and one 3,5ꢀdinitrobenzoate anion in
the asymmetric unit (Fig. 1). The deprotonated carboxylate group and positively
charged amino group are linked together forming a twoꢀcomponent complex via
COO–…H3N+ hydrogen bonds. The values of these contacts are within a normal range
(1.93, 2.52, 2.15 and 1.93 Å, respectively). Anions and cations form a 2D layered
structure through hydrogen bonds parallel to the bcꢀplane (Fig. 2a). Every one
3,5ꢀdinitrobenzoate anion layer is followed by two (2ꢀpyridylmethyl)ammonium
cation layers, however, total number are consistent. As in the pink shadow, a declining
cross
is
shaped
through
hydrogenꢀbonding
interactions
of
two
(2ꢀpyridylmethyl)ammonium cations and two 3,5ꢀdinitrobenzoate anions. For more
4

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simplicity and better clarification, schematic representation is given (Fig. 2b), in
which arrow diagram refers to (2ꢀpyridylmethyl)ammonium cation and the other is its
counterion. The orientation of the cations in the same layer is consistent, yet
antiparallel to that of the adjacent cation layer. In contrast to cations,
3,5ꢀdinitrobenzoate anions in the identical layer are arranged alternately and every
other anion is homoꢀorientated and parallel.
The declining cross, mentioned above, can be as a primary building block and
linked by another via the hydrogen bond N4–H4A…O2 in the top view (Fig. 3a).
1
2
From the side view, a column of alternating
(4) and
(8) rings is observed.
R
R
2
4
The rings alternate with H(4B) common to both rings. Two such double crosses are
connected to form a quadrangular grid through the hydrogen bond C9–H9AꢁꢁꢁO3 in
the golden background. By effective packing along the aꢀaxis, two types of these
grids, colored as light pink and light green, result in a 3D network (Fig. 3b), which are
just like doubleꢀzigzag chains.
Salt
2
contains
one
crystallographically
independent
(3ꢀpyridylmethyl)ammonium cation and one 3,5ꢀdinitrobenzoate anion in the
asymmetric unit and crystallizes in the orthorhombic space group P212121 (Fig. 4).
Anions and cations form a 2D layered structure through hydrogen bonds parallel to
the bcꢀplane, constructed by the alternate 3,5ꢀdinitrobenzoate anion and
(2ꢀpyridylmethyl)ammonium cation layers (Fig. 5a). As in the pink shadow, one
unique hydrogenꢀbonding ring is formed by two anions and two cations via
COO–…H3N+ hydrogen bonds. Viewed from the schematic representation, the
orientation of ions is arranged alternately in either cationic or anionic layers and every
other ion is homoꢀorientated and parallel (Fig. 5b).
Four molecules in the pink background, mentioned above, can be as a primary
synthon and connected with other fourꢀmolecule units along the aꢀaxis in the top view
3
(Fig. 6a). From the side view, a column of repeating
(10) rings forms. The unique
R
4
hydrogenꢀbonding ring consists of two ammonium groups, one benzoate anion using
both O(1) and O(2) as acceptors and one benzoate anion using only O(1). The ring is
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repeated with H(4B) common to adjacent rings to afford the hydrogenꢀbonding
columns. The neighbouring columns are linked by C13–H13B…O4 interactions along
the bꢀaxis and a 3D network forms (Fig. 6b).
Interestingly, the analysis of the crystal structure reveals that 3 contains two
crystallographically independent (4ꢀpyridylmethyl)ammonium cations and two
3,5ꢀdinitrobenzoate anions in the asymmetric unit and crystallizes in the triclinic
space
group
P−1
(Fig.
7).
3,5ꢀDinitrobenzoate
anion
and
(4ꢀpyridylmethyl)ammonium cation layers alternate and form a 2D layered structure
through hydrogen bonds (Fig. 8a). By comparison with salts 1 and 2, the arrangement
of anions in complex 3 is more disordered and anomalous (Fig. 8b). In the cation layer,
the adjacent ions as a pair retain its orientated assembly but run antiparallel to the
neighbouring ones.
Hydrogen bonds are extraordinarily extensive in 3 viewed along the aꢀaxis that
range from N–H…O, N–H…N to C–H…O. The 3D network forms between anions
and cations via these hydrogenꢀbonding interactions (Fig. 9a). For better investigation
to cations, part of (4ꢀpyridylmethyl)ammonium packing diagram is draw out along the
aꢀaxis (Fig. 9b). Viewed along the bꢀaxis, the shape of Chinese knot is observed
among four (4ꢀpyridylmethyl)ammonium molecules through hydrogen bonds
N6–H6A…N7 and N6–H6C…N5.
Summarizing, the vast number of possible structures with carboxylic and amine
functional groups make this heterosynthon potentially limitless. This makes it an ideal
system to study the influence of molecular structure on the supramolecular assemblies.
+
–
Work on ammonium carboxylate salts of general formula (R–NH3 ) ꢁ (R′–CO2 ) has
afforded many hydrogenꢀbonded columns consisting of different hydrogenꢀbonded
2
3
4
rings, such as
(8)
,
(10) and
(12)
. For example, Lemmerer et al. choose a
R
R
R
4
4
4
similar series of cyclic hydrocarbon rings with a single amine group and two different
hydrocarbons with a carboxylic acid functional group.34 Although hydrogenꢀbonded
3
2
4
patterns of both – (10) – and – (8)
–
(12) – form, it seems that large groups
R
R
R
4
4
4
drive or promote the formation of the former. The type of hydrogenꢀbonded columns,
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either the former or latter, is possibly dependent on subtle variations of the
ammonium cations and independent of the steric size of the anions. 34
To explore the influence of ammonium cations, we employ the same carboxylic
acid and a series of amines that have NH2 groups in different positions of the pyridine
ring, resulting in the formation of salts 1ꢀ3. Among them, salts 1 and 2 afford two
1
types of 1ꢀD hydrogenꢀbonded columns, constructed by alternating
(4) and
R
2
2
3
(8) rings and repeating
(10) rings, respectively. Interestingly, salt 3 does not
R
R
4
4
form any of the recognized types of assemblies between cations and anions. Therefore,
although cations are smilar both in shape and size, three different supramolecular
architectures are obtained. It could mean that different positions of the NH2 groups
play an important role in determining the final crystal structures. Importantly, salts 1
and 2 both contain one crystallographically independent pyridylmethyl ammonium
cation and one 3,5ꢀdinitrobenzoate anion in the asymmetric unit while two pairs of the
ions are found in salt 3. It seems probable that more crystallographical molecules in
the asymmetric unit lead to more disorder in the close packing. This disorder
alternates cation–anion arrangement, and inhibits the formation of 1D
hydrogenꢀbonded columns.
Conclusions
The formation of a salt between amine and carboxylic acid with a suitable difference
in pKas leads to a family of 3D supramolecular architectures by robust and predictable
1
2
hydrogenꢀbonding interactions. In the three cases, alternating
(4) and
(8)
R
R
2
4
3
rings are observed in salt 1 and repeating
(10) rings in 2. In despite of no this
R
4
column constructed by rings, the unique shape of Chinese knot exists among four
cations in 3. A description of the geometrical arrangement of the hydrogenꢀbonding
columns in the solid state will be useful in analysing the suparamolecular structures.
Protonꢀtransfer salts 1ꢀ3 crystallize in different space groups (P21/c, P212121 and P–1,
respectively). It is worth mentioning that 2 adopts a polar point group P212121, which
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is associated with the point group C2, one of the 10 polar point groups (C1, C2, Cs, C2ν,
C4, C4ν, C3, C3ν, C6, C6ν) required for ferroelectric behavior.
In future studies, a more substantial investigation could shed light on potential
ferroelectric property in the complex 2. Though under similar reaction conditions,
large discrepancy has been found among these compounds.
Acknowledgment
The authors gratefully acknowledge financial support from the Natural Science
Foundations of China (20901016, 20901042 and 51173082), the National Basic
Research Program of China (2009CB930601) and the Starting Fund from Nanjing
University of Posts and Telecommunications (NY211027 and NY211135). We also
thank our coꢀworkers for their distinct contributions and helpful discussions.
Experimental Section
Synthesis
The chemicals and solvents used in this work are of analytical grade and available
commercially and were used without further purification. Stoichiometric amounts (1:1)
of 3,5ꢀdinitrobenzoic acid and aminomethyl pyridine (2ꢀ, 3ꢀ, 4ꢀ) were dissolved in
methanol. After stirring for a few minutes, the solution was filtered and left standing
at room temperature for several days. Colorless crystals 1-3 were isolated by slow
evaporation. Elemental analysis confirms the identity of the bulk materials and are
tabulated in the ESI. Other crystallization conditions were not tested during this study,
and the possibility for polymorphism has not been extensively considered.
X-ray crystallography
Data collections were made by using graphite monochromated MoꢀKα diffraction (λ=
0.71073 Ǻ) at 293K. The structures were solved by direct methods using the
SHELXS97 (Sheldrick, 1990) program and refined by a fullꢀmatrix least squares
technique based on F2 using the SHELXL97 (Sheldrick, 1997) program. Primary
atoms were refined by structureꢀinvariant direct methods; secondary atoms were
8

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located from Difference Fourier maps and hydrogen site location was inferred from
neighbouring sites.
Crystal data for 1: C7H3N2O6, C6H9N2, formula weight 320.27, monoclinic, space
group P21/n, a = 6.5494(13), b = 9.1960 (18), c = 23.512 (5) Å, β = 90.39 (3)°, V =
1416.0 (5) Å3, Z = 4, Dx = 1.502 Mg mꢀ3. In the final leastꢀsquaresrefinement cycles
on F2, the model converged at Rint = 0.045, R[F2 > 2σ(F2)] = 0.055, wR2 = 0.148 for
14201 data (3246 independent), 208 parameters, and 0 restrains. CCDC 873913.
Crystal data for 2: C7H3N2O6, formula weight 320.27, C6H9N2, orthorhombic, space
group P212121, a = 6.8770 (14), b = 9.2116 (18), c = 22.056 (4) Å, β = 90°, V =
1397.2 (5) Å3, Z = 4, Dx = 1.522 Mg mꢀ3. In the final leastꢀsquaresrefinement cycles
on F2, the model converged at Rint = 0.041, R[F2 > 2σ(F2)] = 0.039, wR2 = 0.092 for
14505 data (3190 independent), 208 parameters, and 0 restrains. CCDC 873914.
Crystal data for 3: 2(C7H3N2O6, C6H9N2), formula weight 640.53, triclinic, space
group P−1, a = 7.4234 (15), b = 11.738 (2), c = 17.698 (4) Å, β = 100.52 (3)°, V =
1431.8 (5) Å3, Z = 2, Dx = 1.486 Mg mꢀ3. In the final leastꢀsquaresrefinement cycles
on F2, the model converged at Rint = 0.063, R[F2 > 2σ(F2)] = 0.062, wR2 = 0.167 for
14831 data (6511 independent), 416 parameters, and 0 restrains. CCDC 873915.
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Figures and Figure captions:
Figure 1 View of the asymmetric unit for 1 with the labeled atoms.
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Figure 2 (a) View of the 2D layer crystal structure in 1 parallel to the bcꢀplane, in
which hydrogen bonds are shown by dashed lines in green. The declining cross as a
primary building block is shown in the pink background. (b) The schematic
representation of the anion and cation layered structure; the blue rhombus, red circle
and blue arrowhead stand for the arranging orientation of nitryl, carboxyl and
amidogen, respectively.
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Figure 3 (a) The declining cross is linked by another through the hydrogen bond
1
2
N4–H4A…O2 to form a column of alternating
(4) and
(8) rings in 1. Two
R
R
2
4
these crosses are connected to form a quadrangular grid through the hydrogen bond
C9–H9AꢁꢁꢁO3 in the golden background. (b) The 3D network by effective packing
parallel to the bcꢀplane, where two types of grids are colored as light pink and light
green.
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Figure 4 View of the asymmetric unit for 2, showing the crystallographic numbering
scheme.
Figure 5 (a) View of the 2D layer crystal structure in 2 parallel to the bcꢀplane, in
which hydrogen bonds are shown by dashed lines in green. The four molecules as a
primary building block are shown in the pink background. (b) The schematic
representation of the anion and cation layered structure; the blue rhombus, red circle
and blue arrowhead stand for the arranging orientation of nitryl, carboxyl and
amidogen, respectively.
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Figure 6 (a) Four molecules as a primary synthon are connected with other units
3
through hydrogen bonds to form a column of repeating
(10) rings in 2. (b) The
R
4
3D packing diagram of the salt 2, parallel to the bcꢀplane.
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Figure 7 View of the asymmetric unit for 3, showing the crystallographic numbering
scheme.
Figure 8 (a) View of the 2D layer crystal structure in 3, in which hydrogen bonds are
shown by dashed lines in green. (b) The schematic representation of the anion and
cation layered structure; the blue rhombus, red circle and blue arrowhead stand for the
arranging orientation of nitryl, carboxyl and amidogen, respectively.
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Figure 9 (a) View of the 3D supermolecule networks in 3. (b) Top: part of
(4ꢀpyridylmethyl)ammonium packing diagram along the aꢀaxis. Bottom: part of
(4ꢀpyridylmethyl)ammonium packing diagram along the bꢀaxis, where the shape of
Chinese knot is observed among four cations through hydrogen bonds N6–H6A…N7
and N6–H6C…N5.
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New Journal of Chemistry
Page 18 of 18
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Different hydrogen-bonding patterns of two heterosynthons are observed in
ammonium carboxylate salts.