Influence of the metal salt on the self-assembly of isophthaloylbis-β-alanine and Cu(II) ion

Article abstract of DOI:10.1016/j.poly.2015.01.023

The initial employment of the new pseudopeptidic ligand isophthaloylbis-β-alanine (H₂IBbA, H₂L) with Cu^II ion affords a one dimensional (1D) [Cu₂L₂(H₂O)(CH₃OH)]·2H₂O·C

Full text of DOI:10.1016/j.poly.2015.01.023

Polyhedron 89 (2015) 313–321
Contents lists available at ScienceDirect
Polyhedron
journal homepage: www.elsevier.com/locate/poly
Influence of the metal salt on the self-assembly of isophthaloylbis-
b-alanine and Cu(II) ion
Smaragda Lymperopoulou a,b, Vassiliki N. Dokorou a,c, Athanassios C. Tsipis b, Peter G. Weidler d,
John C. Plakatouras b, Annie K. Powell a,e, George E. Kostakis a,
⇑
a Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
b Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, 451 10 Ioannina, Greece
c X-ray Unit, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
d Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
e Institute of Inorganic Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 15, 76131 Karlsruhe, Germany
a r t i c l e i n f o
a b s t r a c t
Article history:
The initial employment of the new pseudopeptidic ligand isophthaloylbis-b-alanine (H2IBbA, H2L) with
CuII ion affords a one dimensional (1D) [Cu2L2(H2O)(CH3OH)]ꢀ2H2OꢀCH3OH (1) and a two dimensional
(2D) [Cu2L2(H2O)4]ꢀ6H2O (2) compound, respectively, illustrating the important influence of the metal
salt and the solvent system used in determining the motif of the final product. Infrared spectroscopy,
thermal, adsorption and theoretical studies of these compounds are also discussed.
Ó 2015 Elsevier Ltd. All rights reserved.
Received 7 November 2014
Accepted 23 January 2015
Available online 3 February 2015
Keywords:
Coordination polymers
Copper
Pseudopeptidic ligands
Self-assembly
Theoretical studies
1. Introduction
acids, have been reported and show interesting properties [6]. In
this direction, we and others have shown that placing amino acid
Amino acids held together via amide bonds to form peptides
and proteins serve vital biological functions [1], however in recent
years such biomolecules have emerged as building blocks for con-
structing nanoporous Coordination Polymers (CPs) and Metal
Organic Frameworks (MOFs) [2]. This class of ligands presents
multiple possible coordination modes and it is also possible to
form H-bonds through their non-coordinating heteroatoms. For
example, the FeIII gallate, fumarate or muconate MOFs show either
rigid small pore structures or structures built from a highly flexible
porous matrix [3]. In addition, porous zinc dipeptide based MOFs
exhibiting flexible frameworks capable of accommodating CO2
have also been reported [4].
On the other hand, particular attention has been paid to utiliz-
ing ligands based on amino acids attached to aromatic or aliphatic
backbones. For example, N-protected amino acids have been
extensively used to form complexes in order to better understand
the active site of biological systems [5]. Furthermore, several metal
coordination compounds, derived from reduced Schiff base ligands,
obtained by reducing the C@N bond in the Schiff bases formed by
the condensation of aldehyde and various natural/unnatural amino
groups on aromatic scaffolds yields pseudopeptidic ligands which
in turn can be used along with various metal centres to synthesize
CPs [7,8]. From the structural point of view, the reactions of tereph-
thaloylbisglycine (H2TBG, Scheme 1 upper) and isophthaloyl-
bisglycine (H2IBG, Scheme 1 middle) along with CuII ion results
in a non-porous 2-fold interpenetrated three dimensional (3D) CP
formulated as [Cu(
CP formulated as [Cu(
l
-TBG)(
l
-H2O)(H2O)2] 2(H2O) [7a,b] and a 2D
-H2O)(H2O)2]ꢀ2(H2O) [7d], respec-
l
-IBG)(
l
tively. In both cases, the product has the same molecular formula
and each CuII centre has the same coordination environment but
the different positions of the two (CONHCH2COO) units in the aro-
matic ring result in compounds with different dimensionality.
From the crystal engineering point of view, such pseudopeptidic
ligands are of great interest because they can give access to the
synthesis of pseudo polymorphs [7c,e] as well to 2D + 2D ? 3D
parallel polycatenated structures [7e].
2. Experimental
2.1. Materials and instrumentation
All chemicals and solvents used for synthesis were obtained
from commercial sources and used as received without further
purification. All reactions were carried out under aerobic
⇑
Corresponding author at: Department of Chemistry, School of Life Sciences,
University of Sussex, Brighton BN1 9QJ, United Kingdom.
E-mail addresses: george.kostakis@kit.edu, G.Kostakis@sussex.ac.uk (G.E. Kostakis).
http://dx.doi.org/10.1016/j.poly.2015.01.023
0277-5387/Ó 2015 Elsevier Ltd. All rights reserved.

314
S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
conditions. The 1H NMR and 13C NMR spectra were recorded on a
Bruker AMX 500 MHz spectrometer. All spectra were recorded
using commercially available d6-DMSO or D2O (Aldrich) of 99.6%
isotopic purity or better and referenced to a residual solvent. The
elemental analyses (C, H and N) were carried out at the Institute
of Nanotechnology, Karlsruhe Institute of Technology, using an
ElementarVario EL analyzer. Fourier transform IR spectra
(4000–400 cmꢁ1) were measured on a Perkin–Elmer Spectrum
GX spectrometer with samples prepared as KBr discs. Thermo-
gravimetric analysis (TGA) curves were measured using a Netzsch
STA 409C Thermal Analyzer under nitrogen flow (30 mL minꢁ1) at
a scan rate of 5 °C minꢁ1 from 25 to 800 °C.
temperature for 30 min and then filtered and left undisturbed.
Slow evaporation yielded green crystals after almost 3 weeks.
The crystals were collected by filtration and washed with Et2O.
Yield: 190 mg, 92% based on Cu. Anal. Calc. for C29H38Cu2N4O16
(found): C, 42.18 (42.04); H, 4.64 (4.78); N, 6.79 (6.71)%. Selected
IR data (KBr disc, cmꢁ1): 3468, 3389, 2959, 1656, 1605, 1540,
1475, 1445, 1424, 1319, 1281, 1076, 715, 683.
2.2.3. Synthesis of [Cu2L2(H2O)4]ꢀ6H2O (2)
H2L (154 mg, 0.500 mmol) and Et3N (69 ll, 0.500 mmol) were
dissolved in H2O (40 mL) with stirring. Cu(NO3)2 2.5 H2O
(116 mg, 0.500 mmol) was dissolved in MeOH (10 mL) and then
added to the aqueous solution. The final solution was stirred at
room temperature for 30 min and then filtered and left undis-
turbed. Slow evaporation yielded light blue crystals after almost
2 weeks. The crystals were collected by filtration and washed with
Et2O. Yield: 210 mg, 92% based on Cu. Anal. Calc. for C28H48Cu2N4
O22 (found): C, 36.56 (36.34); H, 5.26 (5.38); N, 6.09 (6.11)%. Select-
ed IR data (KBr disc, cmꢁ1): 3399, 3286, 1662, 1626, 1574, 1433,
1407, 1316, 1295, 1262, 1205, 1080, 727.
2.2. Synthesis of the compounds
2.2.1. Synthesis of isophthaloyl-bis-b-alanine (H2L)
b-Alanine (7.127 g, 0.080 mol) and NaOH (4.80 g, 0.120 mol)
were dissolved in water (50 mL) with stirring in a round-bottomed
flask in an ice bath. After the solution cooled to below 10 °C, a solu-
tion of isophthaloylchloride (8.12 g, 0.040 mol) dissolved in toluene
(50 mL) was added drop wise. The reaction mixture was stirred for
one hour, after which the aqueous phase was separated from the
organic phase and collected. The aqueous phase was acidified with
35% HCl until the pH was approximately 1. The white product was
collected by vacuum filtration and dried in a vacuum oven overnight
at 50 °C. Yield: 12.33 g, 100%. Anal. Calc. for C14H16N2O6 (found): C,
54.54 (54.22); H, 5.23 (5.20); N, 9.09 (8.98)%. 1H NMR (ppm): 2.55
(t, 4H), 3.48 (m, 4H), 7.55 (t, 1H), 7.98 (dd, 2H), 8.40 (s, 1H) 8.79
(t, 2H), 12.32 (s, 2H). 13C NMR (ppm): 33.70, 35.58, 126.14, 128.29,
129.76, 134.39, 165.79, 172.81. Selected IR data (KBr disc, cmꢁ1):
3345, 3080, 2956, 2662, 2531, 1727, 1630, 1581, 1545, 1481, 1433,
1400, 1381, 1371, 1313, 1279, 1202, 1082, 1037, 1000, 932, 914,
879, 858, 826, 798, 729, 706, 686.
2.3. Computational details
All calculations were performed using the GAUSSIAN09 suite of
programs [9] employing the M05-2X [10a] functional combined
with the Def2-TZVP basis set [10b] for copper and the Pople’s
6-31G(d,p) basis set for the non metal atoms. Single point calcula-
tions were performed on the building blocks of the 1D and 2D CPs
using the geometries determined by X-ray crystallography. The
geometry of the dianionic pseudopeptidic isophthaloyl-bis-b-
alanine ligand (IBba2ꢁ) was fully optimized at the M05-2X/
6-31G(d,p) level in aqueous solution employing the universal con-
tinuum solvation model based on solute electron density called
SMD [11] starting from both the syn- and anti-conformations of
the IBba2ꢁ ligand. The interconversion of the syn- and anti-confor-
mations of the IBba2ꢁ ligand in aqueous solution was investigated
by calculating the potential energy surface for the adiabatic rota-
tion of the b-alanine moiety around the C–C bond employing the
M05-2X/6-31G(d,p) computational protocol. The natural bond
orbital (NBO) population analysis was performed using Weinhold’s
methodology [12,13]. The ELF (Electron Localization Function)
plots were obtained by employing the Multiwfn software version
2.2.1 [14].
2.2.2. Synthesis of [Cu2L2(H2O)(CH3OH)]ꢀ2H2OꢀCH3OH (1)
H2L (154 mg, 0.500 mmol) and Et3N (69 ll, 0.500 mmol) were
dissolved in MeOH (30 mL) with stirring. Cu(OAc)2 H2O (100 mg,
0.500 mmol) was dissolved in H2O (20 mL) and then added to the
methanolic solution. The final solution was stirred at room
2.4. X-ray crystallographic study
Data for 1–2 were collected at 180 K on a Stoe IPDS II area
detector diffractometer using graphite-monochromated Mo K
a
radiation. Semi-empirical absorption corrections were applied
using XPREP in SHELXTL [15a]. The structures were solved using direct
methods, followed by
a full-matrix least-squares refinement
against F2 (all data) using SHELXTL [15a]. Anisotropic refinement
was used for all ordered non-hydrogen atoms; organic hydrogen
atoms were placed in calculated positions, while atomic
coordinates of hydroxo hydrogen and amine hydrogen atoms were
either placed in calculated positions or located from the difference
Fourier map and then constrained to ride on their parent atom
with Uiso = 1.5 Ueq (parent atom). Hydrogen atoms of the water of
crystallization and methanol molecules in the structure of 1 could
not be located from difference Fourier maps and their positions
were calculated with CALCOH implemented into WinGX [15b].
The crystal data and the parameters of the structure refinement
are listed in Table 1.
Scheme 1. Pseudopeptidic ligands used in previous and present works.

S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
315
strand running along the b axis. The asymmetric unit (Fig. 1) of 1
comprises of two CuII centres, two organic ligands, one ligated
water and one ligated methanol molecule, and two water and
one methanol as solvent of crystallization. The two CuII centres
possess the well-known paddle – wheel motif and are ligated to
four carboxylate groups belonging to four different organic ligands
with the axial positions being occupied by one water molecule
(on Cu2) and one methanol molecule (on Cu1). Each organic ligand
is coordinated to four CuII centres (coordination mode I, Scheme 2)
belonging to two different paddle wheels, while all carboxylate and
peptidic groups are planar in trans arrangement. This way the
strand extends with alternating rings formed by two paddle-
wheels and two ligands (Fig. 1). The molecular conformation is also
characterized by the NCamidoCarylCaryl torsion angles (see Table 2)
which clearly indicate that the planar amide groups are placed in
the plane of the benzene ring, resulting in a planar arrangement
for the CH2NHCO(m-C6H4)CONHCH2 residue (max deviations from
least squares planes are 0.22 Å for N2 in ligand C1–C14 and 0.14 Å
for N4 in ligand C15–C28).
3. Results and discussion
3.1. Synthesis
Both compounds were prepared under normal atmospheric
conditions in aqueous–methanolic solutions. Although the
preparation of the two compounds looks quite straightforward,
the isolation of pure and homogeneous samples, especially for 1
(Fig. S1), proved rather tedious.
We started our synthetic attempts utilizing 1:1 aque-
ous:methanolic solutions of CuII salts and the pseudopeptidic
ligand. In most of the experiments, light blue microcrystalline
solids were isolated which eventually proved to be compound 2
(Fig. S2). Using different CuII salts such as nitrate, chloride, perchlo-
rate, sulfate and freshly prepared hydroxide in the reaction results
in the isolation of compound 2. When Cu(OAc)2ꢀH2O was used as
CuII source, we isolated a mixture of green and light blue crystals
which eventually proved to correspond to compounds 1 and 2,
respectively. Reactions, with an excess either of the metal salt or
the ligand, with metal-to-ligand ratio spanning the range 2: 1 to
1: 2, led to the formation of 2 with all the salts except the acetate
which led to mixtures of 1 and 2. In order to rationalize the influ-
ence of the solvent on the final product and its purity, several
experiments were carried out changing solvents and the degree
of the solvent hydration. When MeOH was replaced with heavier
alcohols (such as EtOH or iPrOH), acetone or DMF we isolated
solids formulated as 2 but with different solvation properties.
Scanning MeOH:water ratios in the reaction system, we found
out that we could increase the amount of the green crystals in
the crystalline mixture by increasing the amount of MeOH. We
manage to isolate pure 1 (Fig. S1) using a 3:2 MeOH:water system.
Compound 1 can be isolated in pure form utilizing MeOH:water
ratios up to 5:1. Both coordination polymers are stable and retain
their crystallinity in air, but 2 dehydrates easily upon gentle
heating or storing in a desiccator.
The Cu atoms belonging to the same ring are essentially
co-planar. Adopting the nomenclature described before [7d],
the first ligand (C1–C14) adopts an atata conformation while
the other ligand (C15–C28) adopts
a btatb conformation.
Alternatively, the metal-atom plane is an approximate mirror
plane in the ring or bisects the angle formed by the two ligands
planes (122.60°), therefore both ligands can be described as
having atata conformations. When the solvent molecules are
removed, narrow channels appear into the 1D zig–zag strands.
The void space is 6.5% of the cell volume (234.1 Å3) as calculat-
ed with Platon.
There is an extended hydrogen bonding network stabilizing the
crystal structure of 1. The geometrical characteristics of all
H-bonds can be found in Table T1. It is worth noting that all solvent
of crystallization are held on the inner side of the ‘tube’ formed
along the 1D strands, while each strand interacts with four neigh-
bouring strands via the amide bond pointing out from the strand,
i.e., the two N2–H2N and N4–H4N hydrogen atoms and the two
C4–O3 and C18–O9 carbonyl oxygen atoms. The complete H-bond
pattern is presented in Fig. 2.
3.2. Crystal structure description
The green crystals of compound 1 crystallize in the monoclinic
space group P21/c with Z = 4. The crystal structure of 1 reveals a 1D
Table 1
Crystal data and structure refinement for 1 and 2.
Empirical formula
Formula weight
C30H42Cu2N4O17
857.76
C28H48Cu2N4O22
919.78
T (K)
180(2)
180(2)
k (Å)
Crystal system
Space group
0.71073
monoclinic
P21/c
0.71073
monoclinic
Pc
Unit cell dimensions
a (Å)
b (Å)
c (Å)
16.7550(10)
8.7603(5)
29.3760(16)
123.360(8)
3601.3(4)
4
1.582
1.262
1776
15.978(3)
7.1089(8)
16.458(3)
99.110(14)
1845.8(5)
2
1.655
1.247
956
b (°)
V (Å3)
Z
Calculated density (Mg/m3)
Absorption coefficient (mmꢁ1
F(000)
)
Crystal size (mm)
Theta range for data collection (°)
Limiting indices
Reflections collected/unique
Completeness to h = 25.00
Maximum and minimum transmission
Refinement method
0.10 ꢂ 0.08 ꢂ 0.05
0.20 ꢂ 0.12 ꢂ 0.07
1.66–25.71
1.29–25.72
ꢁ20 6 h 6 20, ꢁ9 6 k 6 10, ꢁ35 6 l 6 35
22595/6780 [Rint = 0.1258]
99.8%
ꢁ19 6 h 6 19, ꢁ8 6 k 6 8, ꢁ19 6 l 6 19
22382/6925 [Rint = 0.0716]
99.9%
0.9396 and 0.8842
0.9178 and 0.7886
full-matrix least-squares on F2
6780/12/495
full-matrix least-squares on F2
6925/26/530
Data/restraints/parameters
Goodness-of-fit on F2
0.943
0.952
Final R indices [I > 2
R indices (all data)
r
(I)]
R1 = 0.0774, wR2 = 0.1898
R1 = 0.1527, wR2 = 0.2143
2.470 and ꢁ0.831
R1 = 0.0386, wR2 = 0.0673
R1 = 0.0563, wR2 = 0.0706
0.528 and ꢁ0.477
Largest difference peak and hole (e Aꢁ3
)

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S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
Scheme 2. Coordination modes found in compounds 1 (mode I) and 2 (mode II).
Table 2
Selected torsion angles (°) for compounds 1 and 2.
1
2
N1C4C5C10
N2C11C7C8
N3C18C19C24
N4C25C21C22
177.4(9)
ꢁ11.5(14)
178.8(8)
4.5(12)
N1C4C5C10
N2C11C7C8
N3C18C19C24
N4C25C21C22
29.5(16)
39.3(15)
36.6(15)
27.6(15)
of CuII dimers (Cu. . .Cu 3.407 Å) linked by the organic ligands into
an infinite 2D network. The asymmetric unit of 2 consists of two
CuII centres, two organic ligands, four ligated and six water of crys-
tallization molecules. Both CuII centres are five coordinate possess-
ing a square pyramidal geometry; O7, O13, O14, O110 and O2, O15,
O16, O50 form the basal planes for Cu1 and Cu2, respectively, while
O2 and O110 occupy the axial positions for Cu1 (2.366(3) Å) and
Cu2 (2.402(3) Å), respectively. Thus, the two CuII centres are only
bridged through two carboxylate oxygen atoms O2 and O110
(Cu1–O2–Cu2 104.07(13)° and Cu1–O110–Cu2 102.21(12)°). Analy-
sis of the shape determining angles using the approach of Addison,
Reedijk et al. [16] yields a value for trigonality index, s, of 0.17 for
Cu1 and 0.16 for Cu2 suggesting square pyramidal geometries
(s = 0 and 1 for perfect sp and tbp geometries, respectively).
Interestingly, this motif, i.e., a dimer formed by two five coordi-
nated aqua carboxylate complexes sharing an edge, is unexpected-
ly rare in transition metal chemistry. A search in CSD [17] revealed
only eight examples; one MnII [18a], two ZnII [18b,c] and five
CuII complexes [18d–h] and none of them in a coordination poly-
mer, therefore it can be characterized as a new SBU in MOF
chemistry.
Each organic ligand is coordinated to three CuII centres (coordi-
nation mode II, Scheme 2), while all carboxylate and peptidic
groups are planar. The NCcarbnylCarylCaryl torsion angles (see Table 2)
clearly indicate that the planar amide groups are displaced out the
plane of the benzene ring which is in contrast to compound 1. The
reason for this non-planarity appears to be the strong hydrogen
bonds between the peptide moieties of adjacent ligands (detailed
geometrical characteristics are presented in Table T4). Moreover
the first ligand (C1–C14) adopts an atsta conformation while the
other ligand (C15–C28) adopts a btstb conformation [7d]. The CuII
dimers are linked by the organic ligands to form a 2D coordination
polymer (Fig. 3). From the topological point of view, considering
each metal centre and each ligand as a node then the 2D net
possessing a fes topology is formed while considering each CuII
dimer as a node then an sql network is formed.
Fig. 1. (Upper) the asymmetric unit of 1, extended to show the coordination of the
ligand and the coordination sphere of the metal ions. (Middle) perspective view of
the strand in 1, running parallel to b and (lower) down to ac plane. CH hydrogen
atoms and solvent molecules have been omitted for clarity.
The blue crystals of compound 2 crystallize in a monoclinic
space group Pc with Z = 2. The crystal structure of 2 is composed
There is an extended network of hydrogen bonds which pro-
vides extra stabilizing interactions. The asymmetric unit of 2 also

S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
317
Fig. 2. A packing diagram of 1, indicating the intra- and inter-chain H-bonding interactions stabilizing the crystal structure, shown down to ac plane. CH hydrogen atoms
have been omitted for clarity.
contains six water of crystallization molecules which are located
between the layers and held in the architecture with H-bonds.
Generally, all the H-bonds of the structure can be separated into
three distinct groups: (a) the intra-layer H-bonds, which include
two of the amide moieties {N2–H2Nꢀ ꢀ ꢀO10 and N3–H3Nꢀ ꢀ ꢀO3
(x, y + 1, z)} and two coordinated water molecules which are
H-bonded to the coordinated carboxylates {O14–H141ꢀ ꢀ ꢀO1
(x, y + 1, z), O14–H142ꢀ ꢀ ꢀO6(x ꢁ 1, ꢁy + 1, z + 1/2), O15–
H151ꢀ ꢀ ꢀO8(x, y ꢁ 1, z) and O15–H152ꢀ ꢀ ꢀO12(x ꢁ 1, ꢁy, z + 1/2)} as
donors; (b) the inter-layer H-bonds, which include the other two
amide moieties which are H-bonded as donors to a carboxylate
group {N1–H1Nꢀ ꢀ ꢀO8(x, ꢁy + 1, z ꢁ 1/2) and to a coordinated water
molecule {N4–H4Nꢀ ꢀ ꢀO16(x + 1, y + 1, z)}; and (c) the water of crys-
tallization molecule H-bonds. The latter water molecules act as
bridges between the layers reinforcing the overall architecture.
The amide NH H-bonds are depicted in Fig. 4. The interlayer
H–bonds {i.e. N1–H1Nꢀ ꢀ ꢀO8(x, ꢁy + 1, z ꢁ 1/2) and {N4–H4Nꢀ ꢀ ꢀ
O16(x + 1, y + 1, z)} are responsible for the polarity of the space
group (Pc) for 2, since they are pointing to the same direction
parallel to c axis [19].
one step at 120 °C (calculated 19.57%, experimental 19.38%). The
decomposition of both compounds starts at 220 °C resulting in
CuO metal oxide as the final residue according to weight loss
calculations.
Having in mind the different thermal behaviour of 1 and 2 and
the possibility that these two compounds can be interconverted,
several experiments were performed [20]. Samples of both com-
pounds were heated at 150 °C under vacuum, to remove all solvent
molecules, and then the desolvated samples were placed in H2O or
MeOH or H2O/MeOH solutions to check the possibility that 1 can
be transformed to 2 or vise versa (Figs. S5–S7). The IR data of the
desolvated samples indicate that in both compounds the organic
molecules retain their initial coordination modes. However, the
comparison of the IR data of the initial, heated and resolvated sam-
ples (Figs. S6 and S7), indicate that the structural transformation of
1 to 2 or 2 to 1 is impossible. Furthermore, efforts to recrystallize
compounds
1 and 2 to form 2 and 1, respectively, were
unsuccessful.
3.4. Theoretical studies
3.3. Thermal and structural studies
At first we investigated the conformational preference of the
dianionic IBbA2ꢁ ligand in aqueous solution by optimizing the geo-
metry of the dianion at the M05-2X/6-31G(d,p) level employing
the universal continuum solvation model based on solute electron
density (SMD) starting from both the anti- and syn-conformations
of the amide carbonyl groups. The optimized equilibrium geome-
tries are shown in Fig. 6.
The experimental powder XRD patterns of the bulk material of
both compounds (Figs. S1 and S2) fit well with the theoretical pow-
der XRD pattern. Thermogravimetric analysis (TGA) was carried
out on both compounds (Fig. 5). In compound 1, the solvent of
crystallization was removed step wise; part of the crystallization
solvent is removed at 120 °C and 180 °C (calculated 7.93%,
experimental 7.38%). In compound 2, the thermal behaviour differs
to that of 1; all the water molecules were successfully removed in
The IBbA2ꢁ ligand with the anti-conformation of the carbonyl
groups is slightly more stable than that with the syn-conformation
(DE = 0.6 kcal/mol at the M05-2X/6-31G(d,p) level in aqueous

318
S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
Fig. 3. (Upper) the asymmetric unit of 2, extended to show the coordination of the ligand and the coordination sphere of the metal ions. CH hydrogen atoms and solvent
molecules have been omitted for clarity. Label scheme is complete and the atoms are at the 50% probability level. Symmetry operations to generate equivalent atoms: #1,
x ꢁ 1,ꢁy + 1, z + 1/2; #2, x ꢁ 1,ꢁy, z + 1/2; #3, x + 1,ꢁy, z ꢁ 1/2; #4, x + 1,ꢁy + 1, z ꢁ 1/2. (Lower) a view of the 2D thick layer formed in 2, indicating the intra-layer H-bonding
interactions stabilizing the crystal structure. CH hydrogen atoms and water of crystallization molecules have been omitted for clarity.
Fig. 4. A packing diagram of 2 shown down to b axis. Intra-layer H-bonds are drawn in red while inter-layer in green. CH hydrogen atoms and water of crystallization
molecules have been omitted for clarity. (Color online.)

S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
319
The interconversion of the syn- and anti-conformations of the
IBbA2ꢁ ligand in aqueous solution is characterized by a low rota-
tional barrier (around 5.0 kcal/mol) as shown from the calculated
potential energy surface for the adiabatic rotation of the b-alanine
moiety around the C–C bond depicted schematically in Fig. 6. It is
also noteworthy that both the b-alanine moieties in the crystal
structure of 2 are not co-planar with the aromatic benzene ring.
In the syn-conformer the OCCO dihedral angle is 79.5° (93.3° in
vacuum at the M05-2X/6-311+G(d,p) level), with the C@O groups
of the two b-alanine moieties pointing towards opposite directions
with respect to the benzene ring. The same holds true in the
anti-conformer, see compound 1, where both the b-alanine
moieties are also not co-planar with the aromatic benzene ring;
the OCCO dihedral angle is ꢁ123.6° (162.7° in vacuum at
the M05-2X/6-311+G(d,p) level) and the C@O groups of the two
b-alanine substituents point towards opposite directions with
respect to the ring plane. In both conformers the carboxyl moieties,
C(O)O, acquire negative natural atomic charges of ꢁ0.89 |e| and
have similar proton affinities estimated to be 361.7 kcal/mol in
vacuum at the M05-2X/6-311+G(d,p) level.
Temperature (oC)
Fig. 5. TGA graphs of compound 1 (orange line) and 2 (blue line). (Color online.)
The influence of the metal salt on the self-assembly of isoph-
thaloyl-bis-b-alanine and CuII ions could be explained by consider-
ing the substitution reactions that yield compounds 1 and 2.
Cu(OAc)2 in solid state and in aqueous solution possesses the
well-known [Cu(OAc)2(L)]2 paddle – wheel motif where the CuII
centres syn,syn-bridged by four acetate groups, while the two axial
positions are occupied by water and/or methanol ligands [21].
Therefore, compound 1 is the product of substitution of the acetate
ligands by the IBbA2ꢁ ligand, thus maintaining the paddle – wheel
solution and 1.6 kcal/mol at the M05-2X/6-311+G(d,p) level in
vacuum). It is noteworthy that the syn-conformation of the
IBba2ꢁ ligand shown in Fig. 6 was obtained even starting from
the geometry of the coordinated IBba2ꢁ ligand in 2. The latter
corresponds to a third order saddle point on the potential energy
surface, but only 3.2 kcal/mol higher in energy than the global
minimum and therefore could be accessible upon coordination
with the CuII metal centres. It is obvious that the two conformers
of the IBbA2ꢁ ligand coexist in equilibrium in aqueous solution.
Fig. 6. Equillibrium geometries of the IBba2ꢁ ligand along with the potential energy surface for the adiabatic rotation of the b-alanine moiety around the C–C bond calculated
at the M05-2X/6-31G(d,p) level.

320
S. Lymperopoulou et al. / Polyhedron 89 (2015) 313–321
0
found in 1 and 2. This leads to the conclusion that the coordination
abilities of the carboxylate group of the N-protected b-alanine moi-
ety are not altered by being incorporated into an aromatic scaffold.
In addition, the theoretical studies presented herein indicate that
compounds 1 and 2 are the thermodynamically most favourable
products; therefore the possibilities of obtaining a large variety
of products under specified synthetic conditions are highly
restricted. With this in mind, in order to give an explanation of
the different coordination modes of the H2IBbA ligand, we assume
that the paddle wheel motif of [Cu(OAc)2L]2 is retained in the solu-
tion and therefore compound 1 is the product of substitution of the
acetate ligands by carboxylate groups of the IBbA2ꢁ ligand. In this
case, the IBbA2ꢁ ligand adopts the most favourable anti-conforma-
tion as could be substantiated from the theoretical studies. For 2, it
is well known that the salts Cu(NO3)2, CuCl2, Cu(ClO4)2, Cu(SO4) in
aqueous solutions yield hydrated CuII ions, existing mainly as
square planar [Cu(H2O)4]2+ and/or octahedral [Cu(H2O)6]2+ species
and in this case the dimeric unit in 2, also found to be the most
stable conformation from the theoretical studies, is formed upon
complexation with the ligand.
structure. Notice that the intermetallic Cu–Cu distance 2.604 ÅA in 1
is comparable to that of 2.617 Å in the [Cu(OAc)2(L)]2 dimer. On the
other hand, the copper nitrate, chloride, perchlorate and sulfate
salts in aqueous solutions exist mainly as square planar
[Cu(H2O)4]2+ and/or octahedral [Cu(H2O)6]2+ species. Therefore,
substitution of the water ligands by the IBba2ꢁ ligands yields the
five coordinated CuII in compound 2. The estimated proton
affinities of the IBba2ꢁ and acetate ligands in vacuum were found
to be 361.7 and 344.5 kcal/mol, respectively, at the M05-2X/
6-311+G(d,p) level indicating that the IBbA2ꢁ ligand is a slightly
stronger nucleophile than acetate, thus accounting for the substi-
tution of acetate in the [Cu2(OAc)4(H2O)2] complex yielding 1. It
is interesting to note that the CuII atoms acquire lower positive
natural atomic charges in the [Cu2(OAc)4(H2O)2] complex than in
1, thus reducing the repulsive electrostatic interactions between
the CuII atoms and renders the intermetallic Cuꢀ ꢀ ꢀCu separation
distance shorter. It is worth noting that, according to the estimated
Wiber Bond Index (WBI) value of 0.08, the covalent intermetallic
interactions are negligible.
In order to throw light on the conformational preferences of
compounds 1 and 2 we performed single point calculations on
the crystal structures of the complexes involving the IBba2ꢁ ligands
either in the anti- or the syn-conformation. It was found that com-
pound 1 with the IBbA2ꢁ ligands in the anti-conformation is more
stable (by 15.2 kcal/mol) than the structure with the IBbA2ꢁ
ligands in the syn-conformation in line with experiment. On the
other hand compound 2 with the IBbA2ꢁ ligands in the syn-confor-
mation is more stable (by 5.3 kcal/mol) than the structure with the
IBbA2ꢁ ligands in the anti-conformation in line with experiment.
To see whether steric interactions are responsible for the con-
formational preferences in compounds 1 and 2 we truncated the
CH2CH2C(O)O end of each IBbA2ꢁ ligand affording the coordinated
O(O)C(CH2)2NHC(O)C6H4C(O)NH2 ligands. It was found that in
compound 1 with the IBba2ꢁ ligands in the anti-conformation the
truncated CH2CH2C(O)O end contributes to repulsive steric interac-
tions by 5.3 kcal/mol. Similarly in compound 2 with the IBba2ꢁ
ligands in the syn-conformation the truncated CH2CH2C(O)O end
contributes to repulsive steric interactions by 9.3 kcal/mol. Thus
even with this truncation the conformational observed geometries
4. Conclusion
We presented herein an extension of our systematic study on
pseudopeptidic ligands. In this work, we have shown that the
self-assembly of isophthaloylbis-b-alanine and CuII ions is radically
depended on the nature of the CuII starting material. Theoretical
studies showed that compounds 1 and 2 are the thermodynamical-
ly most favourable products. Having gained this knowledge from
this study and having in mind that structural motifs for such kinds
of pseudopeptidic ligands can be readily reproducible [7a,d], we
will focus our following efforts to synthesize porous CPs using such
pseudopeptidic ligands and to characterize those compounds not
only through single crystal X-ray, but also though powder diffrac-
tion studies using Rietveld refinements. Our major focus will be on
optimising the production of highly porous compounds.
Acknowledgments
The authors would like to thank Sven Stahl from the Institute of
Nanotechnology at the Karlsruhe Institute of Technology for per-
forming the elemental analysis and differential thermal analysis
experiments. S.L. acknowledges Erasmus Placement for a 3 month
research visit in Institute of Nanotechnology at the Karlsruhe
Institute of Technology.
remain more stable. The repulsive steric interactions in
2
are further corroborated by the energy release (estimated to be
9.6 kcal/mol) that accompanies the complete separation of the
two 1D chains of 2.
3.5. Discussion
Appendix A. Supplementary data
In the present study the coordination abilities of the pseu-
dopeptidic ligand H2IBbA along with various CuII salts were inves-
tigated. The different coordination behaviour of the ligand
observed in compounds 1 and 2 can be attributed to the different
CuII starting material and solvent used. This is the first report of
this ligand in the literature and therefore, due to the semi-flexibil-
ity of the ligand, any prediction for the final product is not valid. A
literature survey indicates that b-alanine has been widely
employed for the synthesis of finite and infinite structures [22]
either being chelated to a metal centre [22e] or being coordinated
only through the carboxylic group [22a–d]. Interestingly, N-acetyl-
b-alanine (Ac-b-alaH), a ligand which is very close structurally
related to H2IBbA, reacts with freshly prepared Cu(OH)2 to give a
mononuclear compound formulated as Cu(Ac-b-ala)2ꢀ2H2O, while
a recrystallization of the latter gives a dinuclear compound formu-
lated as [Cu(Ac-b-ala)2ꢀH2O]ꢀ2H2O possessing a paddle wheel motif
[5]. The coordination modes of Ac-b-alaH reported in the latter
study are very closely related to the coordination modes of H2IBbA
CCDC 977089 and 977090 contains the supplementary crystal-
lographic data for 1 and 2. These data can be obtained free of
charge via http://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 336 033; or e-mail:
deposit@ccdc.cam.ac.uk. Supplementary data associated with this
article can be found, in the online version, at http://dx.doi.org/10.
1016/j.poly.2015.01.023.
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