Crystal structure determination and vibrational spectroscopic studies of terephthalate and 2-amino terephthalate complexes with the 1,10-di-amonium-decane cation

Article abstract of DOI:10.1016/j.molstruc.2019.127231

Recent advances in crystal engineering have shown an increasing trend in the promising employment of co-crystals obtained by benzene poly-carboxylic acids and polyamines. In this work, we present the synthesis and characterization of two “new” complexes c

Full text of DOI:10.1016/j.molstruc.2019.127231

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Crystal structure determination and vibrational spectroscopic studies of
terephthalate and 2-amino terephthalate complexes with the 1,10-di-amonium-
decane cation
A. Santoro, G. Bruno, F. Nicolò, G. Bella, G. Messina
PII:
S0022-2860(19)31340-7
DOI:
https://doi.org/10.1016/j.molstruc.2019.127231
MOLSTR 127231
Reference:
To appear in:
Journal of Molecular Structure
Received Date:
Accepted Date:
30 April 2019
13 October 2019
Please cite this article as: A. Santoro, G. Bruno, F. Nicolò, G. Bella, G. Messina, Crystal structure
determination and vibrational spectroscopic studies of terephthalate and 2-amino terephthalate
complexes with the 1,10-di-amonium-decane cation, Journal of Molecular Structure (2019),
https://doi.org/10.1016/j.molstruc.2019.127231
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Crystal structure determination and vibrational spectroscopic studies of
terephthalate and 2-amino terephthalate complexes with the 1,10-di-
amonium-decane cation
A Santoro*a, G. Brunoa, F. Nicolòa, G. Bellaa, G. Messina.b
a
Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of
Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy.
bDepartment of Information Engineering, Infrastructures and Sustainable Energy, University Mediterranea of
Reggio Calabria, Via Graziella, Loc. Feo di Vito, 89124 Reggio Calabria, Italy.
Abstract
Recent advances in crystal engineering have shown an increasing trend in the
promising employment of co-crystals obtained by benzene poly-carboxylic
acids and polyamines. In this work, we present the synthesis and
characterization of two “new” complexes coming from terephthalic derivates
and a long chain diamine (1,10-diaminodecane). We firstly report the X-ray
single crystal diffraction analysis and FT-IR results on two of these complexes.
We then assign the observed experimental vibrational modes by the support of
DFT analysis.
1. Introduction
The field of crystal engineering is primarily focused on predictably synthesizing
supramolecular structures from well-designed building-blocks[1]. The current
knowledge of weak chemical interactions[2] and the strong contribution of
computational chemistry often lead to evaluate the thermodynamic stability of
the crystal packing with good approximation. However, the real crystal packing
is strongly influenced by kinetically favored processes[3], which are more
difficult to predict. To date, the exact prediction of a molecular solid structure
still represents a big challenge in the field.
Indeed, for designing specific self-aggregated architectures, suitable
substructure should keep track of functional group to develop predefined
interactions[4, 5] (synthons[6, 7]); In this direction, different approaches have
been recently proposed. Planar (aromatic) molecules with carboxylic
groups[8-13] and/or with amine groups[14-16], are often used as building-
blocks[17, 18] to yield particular crystal lattices.
∗Corresponding author.
Email address: antonio.santoro@unime.it (Antonio Santoro)

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Because of the wide interest over this class of molecules, other studies have
been conducted on solid state structures of a planar molecule bearing both
carboxylic and amine groups: the 1,4–dicarboxy-2-amino-benzene or 2-amino-
therephtalic acid (H22a-TPT)[19-21].
In particular, several of the structurally characterized species of Hn2a-TPT2-n (n
= 0, 1, 2), present metal-organic-frameworks (MOF)[22] with attractive features
(magnetic or luminescence peculiar behaviors) and/or microporous
structures[23-28]. Remarkably, the simple terephthalic acid (ortho-benzene-
dicarboxylic acid) H2TPT represents “a versatile tool” for crystal designers due
to its capability to develop hydrogen bond motifs into opposite directions[9,
29]. Thanks to this topological feature, a lot of effort has been recently
dedicated to the specific recognition shown by accustomed ammonium cations
for H2TPT[30, 31] with subsequent biological implications[32]. Indeed, a
common structural feature of salts containing di-ammonium cations consists in
2
the ability of hydrogen bonds to be arranged in the R2 (8) type[14, 33]
supramolecular synthons. The presence of aromatic ring enhances the chances
of alternative hydrophobic intermolecular interactions. In this way, these
building blocks might be exploited as cocrystal in the obtainment of non-
centrosymmetric space-group with non-linear optic (NLO) properties[34].
Nowadays, the H2TPT attitude to develop intermolecular interactions is
witnessed by crystal structure resolution of a great number of organic and
inorganic complexes[33, 35-37]. Herein we have chosen as 2a-TPT and TPT
partner the base 1,10-di-aminodecane (1,10-D) Scheme 1, as it has shown an
important templating element in crystallization[38-40]. Nonetheless, to our
knowledge only one example of 1,10-D/carboxylic co-crystal is present in
literature[41].
HO
O
NH2
1)
H2N
HO
HO
O
O
NH2
2)
H2N
H2N
HO
O
Scheme 1: Two different dicarboxylic acids and the amine used for the synthesis of the two
complexes

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2. Experimental section
2.1 Materials
All chemicals and solvents used for the syntheses were of AR grade.
Terephthalic acid, 2-aminoterephthalic acid as well as the 1,10-diaminodecane
were purchased by Fluka and used without further purification.
2.2 Synthesis of (TPT)2-(H21,10-D)2+∙2H2O (1)
830 mg (5 mmol) of H2TPT and 862 mg (5 mmol) of 1,10-diaminodecane were
dissolved in a mixture water/ethanol. The resulting suspension was left to stir
overnight at RT. The transparent solution obtained was left to crystallize for
two days. The pure crystalline solid was collected and dried (yield 68%).
Calc. for C18H34N2O6: C 57.73; H 9.15; N 7.48.
Experimental: C 57.90; H 9.18; N 7.50%.
2.3. Synthesis of 2(H2a-TPT)-(H21,10-D)2+∙2H2O (2)
830 mg (5 mmol) of H2TPT and 434 mg (2.5 mmol) of 1,10-diaminodecane
were dissolved in a mixture water/ethanol. The resulting suspension was left to
stir overnight at RT. The solution obtained was left to crystallize for five days.
Afterward the obtained brownish-yellow crystals were collected and dried.
Calc. for C26H42N4O10: C 54.72; H 7.42; N 9.82.
Experimental: C 54.64; H 7.51; N 9.75 %.
2.4. Spectroscopic measurements
Elemental analyses (carbon, hydrogen and nitrogen) were performed with a
Perkin-Elmer 2400 II Elemental Analyser. The IR spectra were performed at
room temperature using a Perkin-Elmer RX-I FT-IR spectrophotometer, with
solid KBr discs, in the range of 4000–400 cm-1. Each spectrum consisted of 64
collected scans.
2.5. X-ray data collection and structure refinement processes
A good diffraction quality, colourless (for 1) and light-yellow (for 2) crystals
were mounted on a Bruker-Nonius X8 Apex II Kappa diffractometer equipped
with a CCD area detector using a molybdenum X-ray tube and graphite
monochromator (Mo-K = 0.71073 Å). The crystals showed almost no
decomposition under X-ray exposure during data collection. Frames were
integrated and corrected for Lorentz and polarization effects with SMART
Bruker utility[42]. The scaling and the global refinement of the crystal structure
were performed by SAINT[42]. The structures were solved by direct methods
with SIR04 [43] and then refined by least-square method on F2 [I/(I) > 2] with
SHELXS[44, 45]. All non-hydrogen atoms were successfully refined with

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anisotropic thermal parameters. The hydrogen atoms were placed in idealized
position with the “riding model technique”.
Additional refinement details are summarized in Table 1. All calculations and
graphical works were performed with WinGX software package [46].
2.6. Computational details
We used as starting geometries the one provided by x-ray analysis, to evaluate
dicarboxylic-diamines interactions on geometrical parameters and vibrational
spectroscopy. The complete geometry optimizations and normal modes analysis
were performed using the analytical gradient procedure implemented within
Gaussian 03 program[47]. All the calculations converged to an optimized
geometry which corresponds to a true energy minimum as revealed by the lack
of imaginary values in the calculated vibration frequencies. Vibration
frequencies were calculated by using B3LYP/6-31+G(d,p), and then scaled by
0.965 [48], by considering the complex acid-amine in gas phase without
dielectric simulation (in vacuum). Vibration mode assignments were made by
visual inspection of the eigenvectors, using the GaussianView program.
3. Results and Discussion
3.1 Fourier-Transform Infra-Red measured and computed spectra
The FT-IR spectra of 1 and 2 are consistent with the structural data.
For complex 1, characteristic bands at 3398 and 3348 cm-1 were assigned to
+
asymmetric and symmetric NH3 stretching respectively. The broad peak
between about 2966 and 2840 cm-1 was assigned to the stretching of C-H of the
amine. The high intensity peak at around 2700 cm-1 was assigned to the
stretching vibration of the hydrogen between the acid and the amine moieties.
The peak registered at 1654 cm-1 was assigned to the stretching of the
carboxylate group. The two absorption bands at 1617 and 1546 cm-1 were
assigned to C-C stretching of the aromatic ring. The four peaks at 1462, 1376,
1345 and 1302 cm-1 were assigned to different kind of C-H bending in the
amine moiety, with a contribution of the N-H bending in the peaks at 1376 and
1345 cm-1. The absorption band at 1275 cm-1 was due to the C-C stretching of
the carboxylic moiety with a contribution of C-H aromatic rocking and C-H
amine wagging. The peak at 1156 cm-1 was assigned to the out of plane bending
of O-H-N proton. The absorption peaks below 1000 cm-1, due to vibrational
“breathing” motions of the whole species, have not been assigned in specific.
Regarding complex 2, the absorption band at 3646 cm-1 was assigned to N-H
asymmetric stretching of the terephthalic amine group. The presence of the
band at 3437 cm-1 was due to N-H symmetric stretching of the terephthalic

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amine group with the contribution of the asymmetric N-H stretching of the
1,10-decandiamine group. The peak at 3320 cm-1 is attributed to a N-H
symmetric stretching. The absorption bands with maxima at 3174, 3042 and
3002 cm-1 were attributed to C-H asymmetric and symmetric stretching on the
aromatic ring. The band between 2960-2908 cm-1 and the one peaked at 2855
cm-1 were attributed to amino C-H symmetric and asymmetric stretching
respectively. The peak at 2679 cm-1 was assigned to the proton stretching
between the oxygen atom of the carboxylic moiety and the nitrogen of the 1,10-
decanediamine. The absorption band at 1646 cm-1 was assigned to a
combination of a C=O stretching, O-H-N wagging and N-H scissoring. The two
peaks at 1614 and 1533 cm-1 were attributed to both C-C stretching of the
aromatic ring and NH2 (linked to the aromatic ring) scissoring respectively. The
peak at 1463 cm-1 was assigned to N-H scissoring of the 1,10-decanediamine.
The peaks at 1378, 1301 and 1233 cm-1 were attributed to C-H bending of the
1,10-decanediamine, with a contribution of C-O stretching and C-H rocking
from the aromatic ring, on the 1301 cm-1 band. The absorption at 1155 cm-1 was
attributed to O-H-N out of plane bending and finally at C-C bending peak at
1015 cm-1. As for 1, the peaks below 1100 cm-1 are due to vibrational
“breathing” motions of the whole species. All the data are summarized in Table
2, while the IR spectra registered are showed in Figure 1 and Figure 2.
Figure 1: IR spectra registered for 1

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Figure 2: IR spectra registered for 2
3.2. Description of the crystal structures
The asymmetric unit of the solid state of 1 is constituted by a water molecule,
half of the TPT2- anionic group, and half of the 1,10-diammonium-decane
counterion (
Figure 3 top). The ionic groups are, indeed, placed on the crystallographic
inversion centres of the P-1 space group. As expected, the molecular units are
held together by strong hydrogen bonds network whose polar character and
strength is, in some cases, enhanced by the opposite electrostatic charges
located over the contact atoms.

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Figure 3: 1 (top) and 2 (bottom) respective ORTEP projections with the atom labelling scheme.
Non-hydrogen atoms of the asymmetric units are represented with 40% thermal ellipsoids.
Hydrogen atoms are represented as open circles, whereas dashed atoms are those obtained by
symmetry transformations.
It is worth mentioning that in the crystal obtained, the angle between the
carboxylic moieties and the aromatic ring in the anionic group is not completely
flat (C(8)-C(7)-C(10)-O(1)-19.95(0)°). In particular, the distortion that the

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carboxylic moiety assumes - compared to a fully planar system - partially
breaks the hyperconjugation of the system. In this way, the strength and number
of hydrogen bonds are maximized. As shown in Figure 4, the spatial
disposition of the system allows the formation of a further hydrogen bond for
each carboxylic group, therefore inducing a great energetic advantage.
Figure 4: hydrogen bonds of the carboxylic moiety.
The hydrogen interactions in the solid state allow the whole system to grow
along the same molecular plane. Indeed, the structural scaffold is made by
ribbon anionic arrays, running along the a crystallographic axis, flanked by
cationic ones in the stretched conformation (Figure 5a and Table 3). Notice
that such conformation, also known as trans zig-zag cation, has been observed
in similar crystals with a shorter chain used as nylon fibres precursors.[36, 37]
The 3D- packing is made by staggered supramolecular layers of alternate
hydrated TPT and 1,10-D ribbons. The inter-layer interactions (average distance
between the layers of 3,675(3) Å) are either hydrogen bonds between polar
heads (Table 4) or non-polar interactions occurring between the hydrophobic
molecular cores (Figure 5a).
Remarkably, water plays a key role in the structure reported. Its small size
allows it to be inserted between the anionic and cationic arrays stabilizing the
whole molecular packing.
Differently to the case 1, the stoichiometric ratio acid-amine in 2 is 2:1
respectively. Consequently it presents in the asymmetric unit one water
molecule, one Ha-TPT- anion and half of the H21,10-D2+ cation whose core is
obviously placed on one crystallographic inversion centre of the P21/n space
group (
Figure 3 bottom).

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Figure 5: Capped steaks representation of supramolecular layers generated within the solid
state of 1 and 2. Hydrogen interactions are displayed as cyan dashed lines. a) View along the b
axis for 1 shows single stranded ribbons of TPT2-, running along the a crystallographic axis and
flanked by 1,10-D arrays, flattened on the (0 1 -2) crystallographic plane. b) Orthogonal view
of 2 supramolecular layer evidences double stranded ribbons of H2a-TPT- running along the b
crystallographic axis and flanked by 1,10-D arrays, flattened down on the (1 0 2)
crystallographic plane.

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Similarly, the anionic site (deprotonated carboxylic moieties) is slightly out of
the plane described by the aromatic ring (C(8)-C(7)-C(10)-O(1)-25.0(3)°), in
order to make four hydrogen interactions. Differently, the angle between the
protonated acid moiety of the Ha-TPT- and the aromatic ring is almost flat
(C(13)-C(11)-C(14)-O(4)-7.0(3)°). This behaviour is due to the presence of the
amino group close to the acid moiety, which allows the formation of an
intramolecular hydrogen interaction, without breaking the conjugation with the
aromatic ring. We have already demonstrated the ability of 2a-TPT units to
develop self-intermolecular hydrogen interactions along the plane [19, 20];
here, once again, these interactions generate double stranded ribbons along the
b crystallographic axis. The stability role of water molecules is probably less
crucial then case 1. In this case there are only two hydrogen interactions which
involve a single water molecule, instead of the three showed in the structure of
1 (see Figure 6). As already seen for 1, the aromatic acid ribbons are flanked by
roughly coplanar cationic strands again in the total trans conformation, thus
generating a (slightly puckered) layer along the [301] crystallographic plane
(Figure 4b). Analogously to what observed in 1, the crystal 3D packing is due
to staggered layers interacting through hydrogen interactions and also by less
polar “hydrophobic” interactions (Figure 5b).
Figure 6: (left) Water hydrogen bonds in compound 1 crystal; (right) Water hydrogen bonds in
compound 2 crystal.
4. Conclusions
Because of the straightforward trend of poly-carboxylic aromatic substrates to
develop molecular layers supported by hydrogen interactions, clay mimics can
be possibly synthesized, by adding to these long chain alkyl di-ammonium
cations acting as spacers [41]. Unlike in a previous study [41], the structures
hereby analysed present pillared scaffold in which long chain cationic units are
included as part of the flat molecular layers. It also worth mentioning that in
both cases, the obtained crystals present solvent molecules (water) in the
packing. This is crucial, since the presence of water contributes towards the
crystal arrangement by making three and two hydrogen bonds each water

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molecule in 1 and 2 respectively. The vibrational modes of the two compounds
were assigned by the aid DFT-IR analysis.
Finally, CCDC 1912814 and 1912815 contains the supplementary
crystallographic data for the structure 1 and 2. These data are freely available
via www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge
Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax:
+44 1223 336033). Deposited data may be accessed by the journal and checked
as part of the refereeing process.
Table 1: Crystal data and structure refinement information for 1 and 2
1
2
Empiric formula
Formula weight
Temperature
Wavelength
Crystal system
Space group
C18H34N2O6
374.47
296(2) K
0.71073 Å
Triclinic
P-1
C26H42N4O10
570.64
296(2)K
0.71073 Å
Monoclinic
P21/n
Unit cell dimensions
a = 6.727(1) Å; α = 105.959(4)°
b = 7,351(1) Å β = 96.070(4)°
a = 11.2232(2)Å, α = 90°
b = 9.7204(2) Å, β = 97.377(1)°
c = 11.304(2) Å γ = 105.230(4)° c = 13.2111(2) Å γ = 90°
3
3
Volume
Z
508.0(1) Å
1
1429.32(4) Å
2
3
3
Density (calculated)
Absorption coefficient
F(000)
1.222 g/cm
1.326 Mg/m
-1
-1
0.091 mm
204
0.102 mm
612
3
3
Crystal size
0.40 x 0.35 x 0.20 mm
0.40 x 0.22 x 0.08 mm
2.61 to 25.42°.
Range for data collection (θ) 3.03 to 27.48°.
Index ranges
-8≤h≤8, -9≤k≤9, -14≤l≤13
-13≤h≤12, -11≤k≤11, -15≤l≤15
Reflections collected
Independent reflections
Completeness to theta
Absorption correction
Refinement method
5910
18176
2611 [R(int) = 0.0348]
0.991
None
2313 [R(int) = 0.0139]
0.99
None
2
2
Full-matrix least-squares on F
Full-matrix least-squares on F
Data / restraints / parameters 2313 / 0 / 122
2611 / 6 / 184
2
1.066
1.092
Goodness-of-fit on F
Final R indices [I>2sigma(I)] R1 = 0.0337, wR2 = 0.1012
R1 = 0.0549, wR2 = 0.1442
R1 = 0.0794, wR2 = 0.1615
R indices (all data)
R1 = 0.0364, wR2 = 0.1051
-3
-3
Largest diff. peak and hole
0.309 and -0.188 e.Å
0.571 and -0.263 e.Å

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Table 2: Observed (computed) vibrational absorption bands and their assignment
1(computed)/cm-1
3398 (3437)
3348 (3352)
Assignment
NH2** asymm stretching
NH2** symm. stretching
2966-2840 (2960-2913) CH2** asymm. and symm. stretching
2700 (2600)
2234-2140
OH* stretching
Overtone bands
1645 (1690)
1617 (1602)
1546 (1557)
1462 (1462)
1376 (1380)
1345 (1344)
1302 (1297)
1275 (1278)
1156 (1156)
CO* stretching
CC* stretching, NH2** scissoring
CC* stretching
CH2** scissoring
CH2** wagging, NH2** twisting
CH2** wagging, NH2** twisting
CH2** twisting
CO* stretching, CH* rocking, CH2** twisting
O-H-N bending out of plane
2(computed)/cm-1
3646 (3598)
3437 (3438)
3320 (3353)
3174 (3129)
3042 (3111)
Assignment
NH2* asymm. stretching
NH2* symm. stretching, NH2** asymm stretching
NH2** symm. stretching
CH* symm. stretching
CH* asymm. stretching
2960-2908 (2970-2920) CH2** asymm. stretching
2855 (2850)
2679 (2631)
1646 (1687)
1614 (1610)
1533 (1573)
1463 (1462)
1378 (1380)
1301 (1282)
1233 (1259)
1155 (1148)
1015 (1042)
797-776 (743)
CH2** symm. stretching
OH* stretching
CO* stretching, OH* wagging, NH2** scissoring
CC* stretching, NH2* scissoring
CC* stretching, NH2* scissoring
NH2** scissoring
CH2** wagging
CO* stretching, CH* rocking, CH2** twisting
CH2** wagging
O-H-N bending out of plane
C-C bending
CC* and CH* wagging
* Group on the 2-amino-tereftalic acid moiety
** Group on the 1,10-decanediamine moiety

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Table 3: Experimental (from X-ray data) and calculated bond lengths in Å and torsion angles in
degrees for 1 and 2
Parameters
C2-N1
C2-C3
C3-C4
C7-C10
C10-O1
C10-O2
C11-C14
C14-O3
C14-O4
C12-N15
X-ray (1)
1.489(1)
1.513(1)
1.520(1)
1.515(1)
1.254(1)
1.257(1)
-
X-ray (2)
1.478(3)
1.504(4)
1.521(4)
1.504(3)
1.255(3)
1.260(3)
1.504(3)
1.260(3)
1.255(3)
1.356(3)
Computed (1)
1.4781
1.5294
1.5342
1.4991
1.3321
1.2267
-
-
-
-
Computed (2)
1.4781
1.5294
1.5341
1.5009
1.3319
1.2267
1.4678
1.2291
1.3596
1.3636
-
-
-
O1-C10-O2
O3-C14-O4
C8-C7-C10-O1
C12-C11-C14-O4
124.2(1)
161.8(1)
124.3(2)
122.8(2)
154.9(2)
173.6(2)
123.46
120.07
179.00
-0.63
Table 4: Hydrogen interactions with geometrical parameters for 1 and 2 (distances in Å and
torsion angles in degrees)
Interaction type
D-H...A
D-H H...A
0.89 1.87
0.82 1.96
0.85 1.98
0.89 2.09
0.89 1.94
0.86 2.17
D...A
D-H-A
174.3
175.6
170.0
159.7
159.7
155.9
N1-H1A...O2#1
O1W-H1WB...O2
O1W-H1WA...O1#2
N1-H1B...O1
2.757(1)
2.771(1)
2.822(1)
2.937(1)
2.794(1)
2.9753)
Intra-layer
Interactions
of 1
Inter-layer
Interactions
of 1
Intramolecular
interactions
N1-H1C...O1W#3
N15-H15A...O3#1
0.89 1.95
0.89 2.01
0.82 1.77
0.86 2.07
0.89 1.95
0.95 1.81
0.95 2.68
2.790(3)
2.781(3)
2.586(2)
2.697(3)
2.828(3)
2.759(3)
3.509(4)
156.0
144.9
173.0
128.9
167.1
174.4
146.8
N1-H1A...O1W#2
N1-H1B...O1
O4-H4...O2#3
N15-H15B...O3
N1-H1C...O2#4
O1W-H1WA...O1#5
O1W-H1WB...N15#6
Intra-layer
Interactions
Inter-layer
interactions
Symmetry transformations used to generate equivalent atoms for structure 1: #1: -x+2,-y+1,-z; #2: x-
1,y,z ; #3: x+1,y+1,z.
Symmetry transformations used to generate equivalent atoms for structure 2: #1 -x+3/2,y-1/2,-z+3/2;
#2 x,y-1,z; #3 x,y+1,z; #4 -x+2,-y,-z+1; #5 -x+3/2,y+1/2,-z+1/2; #6 -x+2,-y+1,-z+1.
Herein is inserted O1W-H1WB...N15#6 dipolar interaction which is not mentionable as hydrogen-
interaction but is the best structural explanation of the water molecule orientation and position.

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X-ray analysis of 2-amino terephthalate salts;
Theorethical and experimental vibrational modes analysis;
Role of hydrogen bonds in solid state staggered layers formation