Comprehensive studies of non-covalent interactions within four new Cu(ii) supramolecules

Article abstract of DOI:10.1039/c2ce26442k

This work investigates the supramolecular aggregation of Cu(ii) complexes based on a combination of the heterocyclic N-donor ligand 2-aminopyrimidine (2-apym) and a variety of different carboxylate ligands, like salicylic acid (H₂SAL), maleic a

Full text of DOI:10.1039/c2ce26442k

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PAPER
Comprehensive studies of non-covalent interactions within four new Cu(II)
supramolecules{
M. Mirzaei,*a H. Eshtiagh-Hosseini,a M. Chahkandi,*b N. Alfi,a A. Shokrollahi,c N. Shokrollahic
and A. Janiakd
Received 5th September 2012, Accepted 17th September 2012
DOI: 10.1039/c2ce26442k
This work investigates the supramolecular aggregation of Cu(II) complexes based on a combination
of the heterocyclic N-donor ligand 2-aminopyrimidine (2-apym) and a variety of different carboxylate
ligands, like salicylic acid (H2SAL), maleic acid (H2MAL), and glycine (HGLY). Four new Cu(II)
complexes [Cu(HSAL)2(2-apym)2] (I), [Cu(HSAL)2(2-apym)2]?(H2SAL)2(2-apym) (I9), {(H2-
apym)[Cu(GLY)(m-Cl)2Cl]}n (II) and [Cu(m-MAL)(2-apym)]n (III) have been synthesized and
characterized by elemental analyses, FT-IR spectra, and X-ray structural analyses. I and I9 appear as
molecular clusters whereas II is a 1-D coordination polymer with weak axial Cu–Cl interactions.
However the last one shows a 2-D coordination polymer with trigonal bipyramidal geometry for
Cu(II) ion. The two last cases have no molecular fragments packed with non-covalent interactions. In
these new supramolecular compounds, existent species join together with the cooperation of multiple
…
…
…
inter/intra-molecular classical O–H O/N, N–H O/N, and non-classical N–H Cl hydrogen bonds
…
…
…
(H-bonds), offset face to face p p, edge to face C/N–H p, and lp p stacking interactions in the
form of various homo/hetero-synthons leading to architecturally different structures. DFT
calculations were used to estimate the binding energy of the involved non-covalent interactions and
whole stabilization energy of related network of I, I9, and II. Theoretical calculations facilitate the
…
comparison of intermolecular interactions, which demonstrate that for all of I–II, N–H N and N–
…
H
O H-bonds govern the network formation. The equilibrium constants for the three proton-
transfer systems including SAL/2-apym, GLY/2-apym, MAL/2-apym, the stoichiometry and stability
of complexation of these systems with Cu2+ ion in aqueous solution were investigated by
potentiometric pH titration method. The stoichiometries of the most complex species in solution was
compared to the crystalline Cu2+ ion complexes with the cited proton-transfer systems.
were firstly recognized by van der Waals in the 19th century1 and
helped to reformulate the equation of state for real gases.
Introduction
In modern chemistry non-covalent interactions are determining
in the field of supramolecular chemistry and molecular recogni-
tion. Non-covalent interactions led to the formation of
molecular clusters while covalent interactions led to classical
molecules. Formation of a non-covalent cluster does affect
properties of the subsystems, and these changes are important
for the detection of cluster formation. Non-covalent interactions
…
…
Hydrogen bonds (H-bonds), p p stacking, cation p, and a
…
new type of van der Waals interactions namely the anion p (for
…
short lp p) as non-covalent interactions form the backbone of
supramolecular chemistry. H-bonds that play a central role in
the structure, function, and dynamics of chemical and biological
systems,2 cation p interactions which are supposed to be
…
3
decisive in the ion selectivity of potassium channels, anion
…
p
interactions that support the theoretical prediction and promis-
ing proposal for use of anion receptors in molecular recognition4
aDepartment of Chemistry, Ferdowsi University of Mashhad, 917791436,
Mashhad, Iran. E-mail: mirzaeesh@um.ac.ir
5
…
and p p interactions presence in the folding of proteins in the
structure of DNA as well as in its interaction with small
molecules, are used in crystal engineering for the design of
functional materials.6 Molecular functionalities, e.g. amino,
hydroxyl, carboxylate, play essential roles in studying the spatial
relationship between adjacent fragments resulting in repetitive
van der Waals patterns or supramolecular synthons.2 Many of
the synthons in crystal networks of metal–organic compounds
contain classical and non-classical H-bonds as well as stacking,
bDepartment of Chemistry, Hakim Sabzevari University, Sabzevar,
96179-76487, Iran. E-mail: chahkandimohammad@gmail.com
cDepartment of Chemistry, Yasouj University, Yasouj, Iran
dDepartment of Chemistry, Adam Mickiewicz University,
Grunwaldzka 6, Poznan˜, 64-510, Poland
{ Electronic supplementary information (ESI) available: Pertinent
figures of frameworks formation of I, I9, II, and III compounds via
different H-bonding and stacking interactions together with stabilization
and formation calculated energies. CCDC 893822, 893823, 827999, and
893821. For ESI and crystallographic data in CIF or other electronic
format see DOI: 10.1039/c2ce26442k
8468 | CrystEngComm, 2012, 14, 8468–8484
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Table 1 Crystal data and data collection, refinement parameters for the complexes
I
I9
II
III
Empirical formula
FW
Temp/K
C22H20CuN6O6
527.98
294.0(1)
0.71073
Monoclinic
P21/n
0.38 6 0.30 6 0.07
9.9258(2)
12.0698(3)
20.1039(6)
90.00
97.815(3)
90.00
2386.13(10)
4
1.470
C58H54CuN12O18
1270.67
295.5(1)
0.71073
Triclinic
C6H10Cl2CuN4O2
304.62
120(2)
0.71073
Orthorhombic
Pbca
0.40 6 0.20 6 0.20
12.4940(6)
7.5099(4)
22.6355(11)
90.00
90.00
90.00
2123.86(18)
8
1.905
C8H7Cu1N3O4
272.70
150 (2)
1.54184
Monoclinic
P21/c
0.22 6 0.20 6 0.14
10.0366 (7)
9.1255 (7)
10.2985 (7)
90.00
95.832 (5)
90.00
938.35 (12)
4
1.930
˚
l/A
Cryst. syst.
¯
P1
Space group
Cryst. size/mm3
0.55 6 0.30 6 0.20
7.6075(2)
9.9472(4)
20.8858(8)
81.235(3)
82.268(3)
72.818(3)
1485.61(9)
1
˚
a/A
˚
b/A
˚
c/A
a/u
b/u
c/u
3
˚
V/A
Z
dcalcd/mg m23
1.420
0.45
Abs coeff/mm21
0.97
2.54
3.32
h/u
2.96, 28.91
211 ¡ h ¡ 13
216 ¡ k ¡ 16
226 ¡ l ¡ 17
0.0412
2.97, 30.71
210 ¡ h ¡ 10
214 ¡ k ¡ 14
229 ¡ l ¡ 29
0.0216
3.15, 27.53
28 ¡ h ¡ 14
28 ¡ k ¡ 4
226 ¡ l ¡ 21
0.0356
6.57, 66.64
29 ¡ h ¡ 19
210 ¡ k ¡ 10
211 ¡ l ¡ 12
0.0386
h
k
l
Rint
GOF
Final R1, wR2 [I . 2s (I)]
1.03
0.0508, 0.0960
1.05
0.0374, 0.00991
0.85
0.0302, 0.0601
1.07
0.031, 0.083
˚
Table 2 Selected experimental and calculated atomic distances (A) and angles (u) for I–III
Experimental
Calculated
Experimental
Calculated
I
Cu1–O1
Cu1–O2
Cu1–O11
Cu1–O12
Cu1–N21
Cu1–N31
O1–C1
1.779(3)
1.780(3)
2.392(3)
2.384(3)
2.325(3)
2.359(3)
2.546(3)
1.276(6)
1.292(6)
1.730
1.741
2.282
2.275
2.339
2.291
2.479
1.252
1.237
O3–C3
O13–C13
1.349(4)
1.354(3)
177.38(8)
87.80(9)
90.64(9)
91.52(9)
90.12(9)
177.61(9)
1.354
1.286
178.20
88.13
90.37
90.65
91.24
176.70
O11–Cu1–O1
O11–Cu1–N21
O1–Cu1–N21
O11–Cu1–N31
O1–Cu1–N31
O2–Cu1–N21
O11–C11
O12–C11
I9
Cu1–O1
Cu1–O2
Cu1–N11
O1–C1
1.9887(9)
1.780(3)
2.0104(11)
1.2610(15)
1.889
1.691
1.910
1.198
O1–Cu1–O1
180.0
179.31
89.54
91.03
178.4
O1–Cu1–N11
O1–Cu1–N11
N11–Cu1–N11
87.14(4)
92.86(4)
180.00(3)
II
Cu1–N1
Cu1–O1
Cu1–Cl2
Cu1–Cl1
O1–C1
O2–C1
1.980(4)
1.982(2)
2.255(11)
2.2725(11)
1.269(4)
1.249(4)
1.881
1.883
2.164
2.174
1.235
1.196
N1–Cu1–O1
N1–Cu1–Cl2
N1–Cu1–Cl1
O1–Cu1–Cl2
O1–Cu1–Cl1
83.12(13)
91.21(1)
169.28(11)
166.49(8)
88.25(7)
85.71
90.24
169.80
165.3
87.81
III
Cu1–O4
Cu1–O3i
Cu1–O2ii
Cu1–O1i
Cu1–N11
O1–C1
O2–C1
O3–C3
O4–C3
O1i–Cu1–N11
1.9388(16)
1.9512(16)
1.9728(18)
2.0562(16)
2.1462(19)
1.260(3)
1.250(3)
1.256(3)
1.264(3)
98.92(7)
—
—
—
—
—
—
—
—
—
—
O4–Cu1–O3i
O4–Cu1–O2ii
O3i–Cu1–O2ii
O4–Cu1–O1i
O3i–Cu1–O1i
O2ii–Cu1–O1i
O4–Cu1–N11
O3i–Cu1–N11
O2ii–Cu1–N11
176.23(7)
96.07(7)
87.60(7)
90.31(7)
87.76(7)
133.27(7)
90.34(7)
86.76(7)
127.17(7)
—
—
—
—
—
—
—
—
—
Symmetry codes: (i) 2x, y 2 1/2, 2z + 1/2; (ii) 2x, 2y + 1, 2z.
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which provide the requisite robustness and reproducibility to
create novel solid-state structures. In this work, glycine, maleic,
and salicylic acids have been used for synthesizing new
complexes because they can hold together interactive functional
groups for the formation of a variety of one-dimensional (1-D),
two-dimensional (2-D), and three-dimensional (3-D) architec-
tures based on multiple non-covalent interactions. Indeed, these
sophisticated spatial directions within related complexes result-
ing in different contacts with neighboring molecules would be
useful tools in new structure designing within crystal engineering
concepts. Modern ab initio quantum chemistry has been very
successful in describing the electronic structure of isolated
molecules in agreement with experimental results. The stronger
non-covalent interaction causes larger changes in the properties
of the subsystem. The majority of molecular clusters are non-
rigid systems, and hence, the potential energy surface represents
their primary property. Structures of global and local minima of
the surface are found by optimizing the stabilization energy and
not the total energy. Therefore, stabilization energy plays central
role in non-covalent interactions.7 Successes and failures of DFT
(density functional theory) in studies of H-bonded and stacked
structures have been demonstrated on DNA base pairs and
amino acid pairs. DFT calculations are much faster than
correlated WFT (wave function theory) calculations and do
not depend so heavily on the basis set size; furthermore,
additional speedups can be gained by using GGA functional
(like BLYP, BP86, etc.) A very promising approach entails a
combination of DFT-D (dispersion energy corrected). This
procedure is fast and can even be used in on-the-fly ab initio
(DFT-D) molecular dynamics simulations. This technique is a
very promising tool for studies of the dynamic properties of
small and medium non-covalent complexes.8 In recent years, the
design of systematic pathways to obtain supramolecular net-
works such as metal–organic frameworks (MOFs), coordination
polymers (CPs), and other geometries due to their diverse
potential applications, unprecedented architectures, and various
topologies are great of attention and rapidly growing the novel
research area.9–17 From crystal engineering view point, O-, N-,
and S-donor organic multifunctional ligands are the best
candidates for possible infinite expansion of supramolecular
architectures having different dimensionality.18–21 Over the past
decade, our research group has been interested in the syntheses,
structural features, and crystal engineering of the coordination
compounds obtained via proton-transfer mechanism between
organic ligands.22 Rational selection of appropriate acidic and
basic ligands having DpKa (pKa (D–H) 2 pKa (A–H+)) greater
than 2 or 3 has obvious significance. In general, versatile
functional organic ligands can establish strong coordination
ability, H-bonding, and stacking which are driving forces for
supramolecular networks.23–26 Theoretical calculations can
respond to the request to determine the optimized structure of
the cluster, its stabilization energy, its (intermolecular) vibra-
tional frequencies and the potential and free energy surfaces.27
For understanding the role of the latter contacts with diverse
distance ranges and directionalities on crystal network forma-
tion, using ligands of salicylic acid, maleic acid, glycine, and
heterocyclic N-donor 2-aminopyrimidine high level theoretical
calculations were carried out for better clarification of the
˚
Table 3 H-bond parameters (A, u)
…
…
…
D–H
A
d(D–H)
d(H A)
d(D A)
,(DHA)
˚
Table 4 The non-covalent interactions distances (A), angles (u), and
I
O3–H3 O1
binding energies (kcal mol21) calculated with B3LYP-D/triple-f6-
311+G(d,p)
…
…
0.99
1.00
0.86
0.97
0.90
0.93
0.93
1.61
1.65
2.24
2.32
2.09
2.28
2.46
2.546(3)
2.572(3)
3.086(3)
3.185(3)
2.989(3)
3.106(3)
3.208(3)
157
151
170
148
176
147
137
O13–H13 O12
1
2
…
N22–H22A N33
…
d(H A)
,(DHA)
Binding energy
…
…
N22–H22B O2
I
N32–H32 N23
N32–H32A N23
…
…
1.880
2.019
2.299
3.092
175.67
174.36
152.64
135.43
259.73
255.60
246.98
236.42
3
…
N32–H32B O13
N22–H22 N33
…
N32–H32B O12
…
C25–H25
…
C6–H6
p
p
I9
O3–H3 O2
…
0.90
0.88
0.81
0.88
0.97
0.89
0.90
0.87
0.88
1.68
2.13
2.28
1.79
1.70
1.76
1.73
2.10
2.15
2.5269(14)
3.0161(16)
3.0062(17)
2.658(2)
2.584(2)
2.638(2)
2.586(2)
2.950(2)
3.012(2)
156
179
149
175
151
171
157
166
166
I9
O32–H32 N41
4
…
…
N12–H12A N13
…
…
1.582
1.599
1.607
1.887
1.919
1.933
3.047
3.053
3.093
3.151
3.166
3.239
3.325
3.430
171.03
178.19
173.89
166.84
177.66
166.38
126.17
97.02
170.54
154.02
142.51
137.72
138.58
75.62
271.28
270.21
269.87
259.51
258.50
256.73
237.08
236.78
236.30
235.69
235.46
234.67
233.78
231.80
5
N12–H12B O3
O32–H32 N42
6
…
O22–H22 N43
…
O22–H22 N43
…
O23–H23 O21
…
N42–H42A O21
7
…
O32–H32 N41
…
N12–H12A N13
…
O33–H33 O31
…
N42–H42B O31
8
…
…
N42–H42A O21
…
C35–H35
N42–H42A
p
…
7
N42–H42B O31
p
…
C
36–H36
p
p
p
II
N1–H1N1 Cl1
…
…
C34–H34
44–H44
9
…
…
0.91(5)
0.77(4)
0.82(4)
0.77(5)
0.77 (4)
2.35(5)
2.66(4)
2.18(4)
2.12(4)
1.89(5)
3.244(4)
3.335(4)
2.988(5)
2.873(4)
2.645(4)
167(4)
147(4)
172(5)
169(5)
166(5)
C
C6–H6
10
N1–H1N2 Cl1
…
p
…
11
…
…
N4–H4N1 N2
N4–H4N2 O1
C
45–H45
p
…
N42–H42B
p
…
N3–H3N O2
II
N4–H4 O1
III
N12–H122 N13
…
…
1.581
1.801
1.773
2.396
2.697
3.452
177.03
168.18
167.29
145.25
145.25
180.00
278.98
274.82
263.37
246.98
241.63
-32.53
12
…
0.853
2.24(3)
3.077(4)
171(3)
N3–H3 O2
…
Symmetry codes: (1) x + 1, y, z; (2) x 2 1, y, z; (3) 2x + 1, 2y, 2z +
1; (4) 2x + 1, 2y + 1, 2z + 1; (5) x + 1, y, z; (6) x + 1, y 2 1, z; (7)
2x, 2y + 1, 2z; (8) x 2 1, y + 1, z; (9) 2x + 1/2, y 2 1/2, z; (10) x +
1/2, y, 2z + 1/2; (11) 2x, 2y + 1, 2z + 1(3); (12) 2x + 1, 2y, 2z.
N4–H4 N2
…
N4–H4 Cl1
…
N1–H1 Cl1
…
p
p
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essential roles of used functional groups in the final stabilization
gained by the titled crystal networks.
capacity Metrohm piston burette. The pH meter-electrode
system was calibrated to read 2log [H+].
Preparation
Experimental section
Preparation of complexes. [Cu(HSAL)2(2-apym)2] (I) and
[Cu(HSAL)2(2-apym)2]?(H2SAL)2(2-apym) (I9). These two new
complexes are obtained from solution containing H2SAL (0.22
mmol, 0.03 g), 2-apym (0.42 mmol, 0.04 g) and aqueous solution
of CuCl2?6H2O (0.04 mmol, 0.01 g). After 24 h, by recrystalliza-
tion of the first observed purple crystals, two types of
appropriate purple plate-like (I) and dark-blue block-shape
crystals (I9) was collected for X-ray studies (yield: 38.2% and
30.5% for I and I9 respectively based on H2SAL). Elem. Anal.
Calc. for C22H20 CuN6O6 (I): C, 50.00; H, 3.79; N, 15.90. Found:
C, 50.12; H, 3.83; N, 16.15%. Elem. Anal. Calc. for
C58H54N12O18Cu (I9): C, 54.77; H, 4.25; N, 13.22. Found: C,
Materials and general methods
All reagents were purchased from Merck Chemicals and used
without further purification. Infrared spectra were recorded on a
Bomem B-154 Fourier transform spectrometer using KBr discs.
Elemental analyses were performed with a Thermo Finnigan
Flash-1112EA microanalyzer. A Model 794 Metrohm Basic
Titrino was attached to an extension combined glass-calomel
electrode mounted in an air-protected, sealed, thermostated
jacketed cell maintained at 25.0 ¡ 0.1 uC by circulating water,
from a constant-temperature bath Fisherbrand model FBH604,
LAUDA, Germany, equipped with a stirrer and a 10.000 mL-
Fig. 1 Coordination environments of Cu(II) ions in I (a), I9 (b), II (c), and III (d) with the atom numbering scheme for complexes (50% probability
criterion for the thermal ellipsoids).
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54.28; H, 4.37; N, 13.37%. IR (KBr pressed pellet, cm21, (I):
3400(s), 3300(w), 3200(w), 1665(w), 1645(w), 1610(w), 1570(s),
1480(s), 1465(w), 1400(w), 1365(w), 1340(s), 1255(w), 1170(w),
1150(s), 865(s), 820(s), 770(s), 425(w). IR (KBr pressed pellet,
X-ray crystallography
The single crystal X-ray diffraction data were collected with
Xcalibur, Eos (I and I9), Xcalibur, Sapphire 2, large Be window
(II), and Rigaku Rapid II (III) diffractometers. The structures
were solved by direct methods and refined with a full-matrix
least-squares technique based on F2 with the SHELXL-97
crystallographic software package.28 Carbon bound hydrogen
atoms were positioned geometrically and refined as riding atoms
with their Uiso set to 1.2 Ueq of their parent atoms. Nitrogen
cm21
, (I9): 3400(s), 3350(w), 3200(sh), 1660(sh), 1600(w),
1550(w), 1480(s), 1465(w), 1400(s), 1360(w), 1300(s), 1255(w),
1250(s), 1160(s), 860(s), 860(s), 820(s), 755(s), 530(s), 465(w).
{(H2-apym)[Cu(GLY)(m-Cl)Cl]}n (II). Blue needle like crystals
of II were obtained after slow evaporation of the solution
containing HGLY (0.39 mmol, 0.03 g), 2-apym (0.39 mmol, 0.04
g), and CuCl2?6H2O (0.13 mmol, 0.03 g) which refluxed for 6 h at
333 K. The isolated crystals were subjected to X-ray studies
(yield: 41.7% for II based on GLY). Elem. Anal. Calc. for
C6H10Cl2N4O2Cu: C, 23.64; H, 3.28; N, 22.4. Found: C, 24.09;
H, 3.76; N, 22.2%. IR (KBr pressed pellet, cm21): 3130(br),
2800(br), 1680(w), 1480(w), 1410(w), 1355(s), 1120(s), 1060(m),
1035(w), 910(s), 705(w), 639(s), 520(w), 475(s).
bound hydrogen atoms were located in a difference Fourier map
2
and refined with fixed isotropic parameters of Uiso = 0.05 A for
˚
compounds II and III and the remaining compounds were
located geometrically and refined as riding model. Details of
crystallography data are given in Table 1. The selected bond
distances and angles together with the H-bond geometry are
listed in Tables 2 and 3, respectively.
Computational details
[Cu(m-MAL)(2-apym)]n (III). This compound was prepared in a
similar manner as described for II by refluxing of H2MAL (0.26
mmol, 0.03 g), 2-apym (0.52 mmol, 0.05 g), and CuCl2?6H2O (0.06
mmol, 0.015 g) (yield: 34.7% for III based on MAL). Elem. Anal.
Calc. for C8H7N3O4Cu: C, 35.2; H, 2.58; N, 15.40; Found: C,
35.62; H, 2.57; N, 15.67%. IR data (cm21): 3370(w), 3190(w),
1650(m), 1605(w),1660(vs), 1332(s), 1260(w), 1100(w), 753(w).
Periodic quantum calculations were executed in a Linux
environment employing the Gaussian 0929 software with
experimentally observed crystal geometry as input. For full
DFT geometry optimization calculations the hybrid functional
B3LYP30–32 was used with the LANL2DZ basis set for the
copper atom and the triple-f6-311+G(d,p) basis set for all other
atoms. We have considered high spin density for the Cu(II) atom
Fig. 2 A partial crystal packing diagram for I viewed parallel to the ac plane formed via H-bond interactions (H atoms have been omitted for clarity).
…
(a) Illustration of the arrangement of complexes in I. (b) View of two kinds of C–H p interactions.
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Table 4 we summarize and compare the finding non-covalent
interaction energies and related equilibrium distances and angles
of any network.
for the calculations of all compounds. B3LYP method has been
proved to provide accurate geometries and harmonic vibrational
frequencies for a wide variety of hydrogen-bonded systems.33
Binding energy calculations with correction for the basis set
superposition error (BSSE) using the Boys–Bernardi counter-
poise technique34 were also performed using the B3LYP-D35
functional as dispersion-corrected DFT. At first the structure of
the smallest independent fragment of any complexes as monomer
(Imon, I9mon, and IImon, Fig. 6–9) with the same molecular
formula as the respective CIF has been optimized. In the
following, for finding intermolecular interaction energies and
geometry optimization, the smallest structures of network
containing a number of corresponding monomers bearing all
possible non-covalent interactions have been optimized. In
Solution studies procedure
The details are described in ref. 36–39. The concentration of all
ligands including SAL, GLY, MAL and 2-apym was 2.50 6
1023 M for the potentiometric pH titrations of them in the
absence and presence of 1.25 6 1023 M Cu2+ ion in binary and
ternary systems. A standard carbonate-free NaOH solution
(0.09300 M) was used in all titrations. The ionic strength was
adjusted to 0.1 M with NaNO3. Before measuring of an
experimental point (pH), sufficient time was allowed for the
establishment of equilibrium. Protonation constants of ligands
Fig. 3 A view of sheet-like in I9 along the ab plane, formed via H-bond interactions. (a) Partial view of the arrangement of complex species (non
… …
coordinated molecules have been omitted for clarity). (b) View of two kinds of N–H p and C–H p interactions between adjacent species.
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and stability constants of proton-transfer systems and their
metal ion complexes were evaluated using BEST program
described by Martell and Motekaitis.40 The value of Kw = [H+]
[OH2] used in the calculations according our previous works.36–38
intra/intermolecular H-bond interactions led to the formation of
2
one type of N–H N homosynthon R2 (8) besides C15–H15 p,
…
…
…
…
…
C24–H24 p, C6–H6 p, and C16–H16 p interactions (average
˚
distances = 3.193 A), respectively which resulted in the expansion
as double chain-like architectures. In this regard, it is convenient
to consider the intramolecular interaction which leads to the
1
creation of an S1 (6) interaction ring between coordinated
Results and discussion
Solid-state characterization. Crystal structure of complexes
carboxylate oxygens (O1 and O12) as acceptors and non-
coordinated O3–H3 and O13–H13 groups belonging to HSAL
…
The molecular structure of I is shown in Fig. 1a with the atom
numbering scheme. The single crystal X-ray diffraction analysis
reveals that [Cu(HSAL)2(2-apym)2] crystallizes in the monoclinic
system with P21/n space group with an asymmetric unit
containing one crystallographically independent Cu(II) cation,
one 2-apym, and one HSAL ligand. The Cu(II) atom is
coordinated by nitrogen atoms of two 2-apym ligands [Cu1–
ligand. This resulted in establishing a O–H O H-bond that was
…
cooperatively stabilized by the participation in C1LO1
p
…
˚
˚
(3.846 A) and C11LO11 p (3.691 A) interactions. The interac-
tions between two neighboring complexes led to a crystalline
network (Fig. 2). The energies of the interactions associated with
the formation of this chain-like structure will be further studied
and discussed in the theoretical part. Single crystal X-ray
diffraction analysis shows that compound I9, [Cu(HSAL)2(2-
apym)2]?(H2SAL)2(2-apym), crystallizes in the triclinic system
˚
N31 = 1.998(2) A] and four oxygen atoms from two HSAL
ligands [Cu1–O1 = 1.9702(2), Cu1–O11 = 1.948(2), Cu1–O12 =
˚
2.606(2), and Cu1–O2 = 2.523(2) A] in which Cu1–O12 and
¯
with space group P1. The environment around the centrosym-
Cu1–O2 are in axial positions affected by the Jahn–Teller
distortion in the equatorial plane. Regarding bond angles in an
ideal octahedral geometry, the severely distorted chelate rings
within the octahedral geometry with N2O4Cu bounding set also
demonstrate this effect. In the crystalline network of I,
cooperation of combination of various non-covalent interactions,
metric Cu(II) complex, N2O4Cu bound set, can be described as the
same as the coordination geometry of I except that I9 comprises of
intact and non-coordinated two symmetrically independent
H2SAL and one 2-apym molecules. The asymmetric unit is
decorated by half of the Cu(II) complex, one 2-apym, and two
symmetrically independent H2SAL molecules (Fig. 1b). The
Fig. 4 A view of ladder-like in II, formed via H-bond interactions. (a) Partial view of the arrangement of complex species without non coordinated
…
molecules. (b) View of kinds of N–H O, p p, N–H p, C–H p, and N–H Cl interactions between adjacent species.
…
…
…
…
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˚
3.775 A. In the polymer, there are classical and one non-classical
existent of various intermolecular H-bond interactions results in a
grid-like structure of this complex (Fig. 3). Non-coordinated
molecules which are well exploited in crystalline architectures
contribute to generate non-flat zigzag sheets, which are connected
…
…
H-bond interactions, such as NH Cl along with p p stacking
interactions which cause more consolidation and assemble the
supramolecular network. Moreover, the carboxyl–pyrimidine
hydrogen bonded synthon and pyrimidine–pyrimidine hydrogen
bonded synthon form R22 (8) rings. Each of the non-coordinated
H2-apym cations is an effective factor to formation of these
by the carboxyl–amine and hydroxy–pyrimidine heterosynthon,
2
[O–H N and N–H O, R2 (8)], finally causing formation of an
…
…
acid–base motif. In our knowledge the hydrogen bond interac-
6
tions by the creation of a heterosynthon as R6 (34), besides
… …
synthons via N3–H3N O2, N4–H4N2 O1, and N4–
… …
H4N1 N2 H-bonds and p p stacking interactions, leading to
stacking interactions between two noncoordinated 2-apym
…
…
˚
molecules, N12–H12A p (3.503 A), C14–H14 p (2.607 A),
˚
the supramolecular network. They play a connector role between
…
…
…
˚
˚
N42–H42A p (3.392 A) and N42–H42B p (3.743 A) could play
crucial roles in the further stabilization of I9 (See Fig. 3). Similar to
three discrete chains by interconnecting N–HN O and N–
…
HN Cl contacts. It is interesting to point out that in the title
…
1
compound I, one can also see S1 (6) ring interaction along with
structure a rare non-classical H-bond in the form of N–HN Cl
…
…
˚
intramolecular C1LO1 p (3.698 A) interaction. Compound II as
a 1-D coordination polymer, {(H2-apym)[Cu(GLY)(m-Cl)2Cl]}n,
crystallizes in the orthorhombic system with space group Pbca.
The crystallographic analysis indicates that the title compound
consists of a discrete polymeric chain [Cu(GLY)(m-Cl)2Cl]2, and a
cationic fragment (H2-apym)+. Each Cu(II) ion is surrounded by
two bridged chloride ions (m-Cl)2, one terminal Cl2, and one GLY
ligand creating chelate ring which leads to the Cu(II) centre
arranged in square pyramidal fashion. The Cu–Cu distance is
and N–H p stacking interaction exist, which cooperatively
controls crystal growth of the structure. The chelating ring caused
by coordinative N- and O- donor atoms of glycine molecules
distributed in c direction lies alternately on opposite sides (see
Fig. 4). When flexible the H2MAL ligand was used instead of
HGLY, compound III was formed. X-ray crystallographic data
show that [Cu(m-MAL)(2-apym)]n crystallizes in the monoclinic
system with space group P21/c, and its asymmetric unit consists of
one crystallographically dependent Cu(II) ion, one MAL, and one
…
Fig. 5 (Top) A packing diagram of III along ac plane. (Bottom) Partial view of C–H p interactions between adjacent species.
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2-apym as coordinated ligands (Fig. 1d). The crystal structure of
III reveals a 2-D coordination arrangement. Each H2MAL ligand
acts as a tridentate ligand showing m3-bridge mode by carboxylate
groups O1–C1–O2 and O3–C3–O4 and uniform m2-g1:g1 bridging
and chelating modes. As depicted in Fig. 1d, the coordination
environment around the Cu(II) is portrayed as appreciably
distorted NO4Cu trigonal bipyramidal geometry. The Cu(II) is
surrounded by four oxygen atoms from carboxylate groups
through (O1, O3) and (O2, O4) from two symmetrically
independent MAL ligands and one nitrogen atom (N11) from a
coordinated 2-apym in which the Cu–O and Cu1–N11 distances
not been discussed from a theoretical point of view. Actually,
this 2-D network has been expanded via Cu–O–C covalent bonds
and finding independent monomers with connection to other
ones via non-covalent interactions is indeed impossible.
Comparison of geometrical features of these compounds shows
good agreement between the optimized and experimental
structures (Table 2). Various dispersive interactions, classical
…
…
and non-classical H-bonds, p p stacking, C–H p, and N–
…
H
p contacts stabilize the relative network of compounds I9
…
and II (Table 4). p p Stacking was only found in the network of
compound II (IInet). The calculated non-covalent interactions
represent the following stabilization sequence: H-bond . N–
˚
˚
˚
range from 1.9388(16) A to 2.562(16) A and 2.1462(19) A,
respectively. The overall structure defines a robust intriguing 2-D
architecture in which MAL ligands are considered as linkers which
hinge the Cu(II) ions as nodes. Indeed, the four central fragments
… … …
p . C–H p . p p (Table 4). In compound I, two N32–
H
…
…
˚
H32 N23 (1.880 A), two N22–H22 N33 (2.019 A) H-bonds, and
˚
…
C–H p of 2-apym with HSAL ring (2.299 A) and vice versa
˚
˚
(3.092 A) govern formation of network of compound I (Inet) and
…
are further connected by two N12–H122 N13 intermolecular
its fragments (I-fragment1, I-fragment2, see ESI,{ Fig. 1S)
(Fig. 6). The interaction energy associated with these contacts
was estimated using the formation energy of the pentamer from 5
monomers, calculated to be 2361.05 kcal mol21. This total
energy obtained by the network is indeed the sum of the 259.73,
H-bonds in two nearly perpendicular planes related to planes of
the pyrimidine ring and its amino group. These fragments create
2
R2 (8) homosynthon shown in the packing diagram of III and
…
H-bond interactions with C–H p in Fig. 5. It is interesting to
note that 2-apym within the complex deviates from the plane
(222), perhaps for steric reasons.
255.60, 246.98, and 236.42 kcal mol21 for N32–H32 N23,
…
…
…
N22–H22 N33, and C–H p of 2-apym ring with HSAL and vice
versa, respectively (Table 4). Inet contains 5 monomers (Imon
)
Network non-covalent interaction studies by DFT
bearing all these stabilizing non-covalent interactions that
participated in network formation (Fig. 6). Actually the network
…
Herein, the non-covalent interactions using DFT calculations
have fully been considered to evaluate their binding energies
governed by the crystal packing and probable interplaying of
them. For all complexes the network formation energies (nfe)
(Enfe = Enetwork 2 nEmonomer) are negative, indicating the
network formation with non-covalent interactions is favorable.
But it should be mentioned, since there are no non-covalent
interactions in formation of the compound III network, it has
formation is governed by two double N–H N H-bonds. The C–
…
H
H
p stacking of HSAL with 2-apym ring and vice versa and N–
…
N bonds show interplay with each other that causes
weakness of these interactions in Inet (Fig. 6 and Fig. 1S,
ESI{). The monomer of compound I9 (I9mon) due to having two
…
O32–H32 N42 of HSAL with 2-apym ring and vice versa
…
intramolecular H-bonds (1.599 A), four C–H2-apym pHSAL
˚
˚
Fig. 6 Formation energy of Inet (distances are given in A).
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˚
Fig. 7 Stabilization energy of I9mon compared to Imon (distances are given in A).
…
˚
bonds (3.325, 3.166 A) and two C44–H44,HSAL pHSAL bonds
stabilization of I-fragment (Fig. 1S, ESI{). We are looking for all
involved non-covalent interactions and their stabilization ener-
gies for I9net formation. For this purpose considering all
constraining parts of I9mon is not avoidable. In the next step,
two 2-apym molecules of I9mon are considered, demonstrating
they participate with two other 2-apym and four HSAL
molecules in the stabilization of I9-fragment2 (Fig. 3S, ESI{).
(3.239 A) stabilizes 2348.26 kcal mol21 more than Imon (Fig. 7).
˚
For more clarity, here, we try to classify different types of non-
covalent interactions and their binding energies among consti-
tuents of crystal lattice for stabilizing of the network of I9 (I9net).
…
˚
At first, the double N–H2-apym N2-apym (1.919 A) H-bonds are
considered, which contribute to the stabilization of I9net in 234.0
kcal mol21 (Fig. 2S, ESI{), comparable to the contribution in
…
In this system two sets of double O–HHSAL N2-apym (1.582,
˚
Fig. 8 Formation energies of I9net (A).
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˚
Fig. 9 Formation energies of IInet1 (top) and IInet2 (bottom) (distances are given in A).
Fig. 10 Potentiometric titration curves of SAL (a), GLY (b), MAL (c) and 2-apym (d) in the absence and presence of Cu2+ ion with NaOH 0.09300 M
in aqueous solution at 25 ¡ 0.1 uC and m = 0.1 M NaNO3.
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Table 5 Overall stability and stepwise protonation constants of SAL, GLY, MAL and 2-apym and recognition constants for interaction between
SAL/GLY/MAL and 2-apym in aqueous solution at 25 ¡ 0.1 uC and m = 0.1 M NaNO3
System
Stoichiometry
SAL/2-apym
logb
Equilibrium quotient
logK
Maximum%
pH
2-apym
SAL
GLY
MAL
H
0
0
1
1
1
1
1
0
1
1
0
0
0
0
0
0
0
0
0
0
1
2
1
1
3
13.22
16.08
3.39
16.40
22.85
13.22
2.86
3.39
3.18
3.38
100.0
90.40
96.08
58.36
62.45
.5.0
2.0
2.0
.4.6
2.0
[2-apymSALH]/[2-apym][SALH]
[2-apymSALH3]/[2-apymH][SALH2]
GLY/2-apym
MAL/2-apym
0
0
1
1
0
0
0
0
1
1
1
1
0
0
0
0
1
2
1
2
10.22
12.89
13.91
17.07
10.2
2.67
3.69
3.46
4.18
3.62
99.96
82.12
75.16
30.1
4.7–8.2
2.0
4.4–9.9
3.0
[2-apymGLYH]/[2-apym][GLYH]
[2-apymGLYH2]/[2-apymH][GLYH]
[2-apymGLYH2]/[2-apym][GLYH2]
[2-apymGLYH3]/[2-apymH][GLYH2]
1
0
1
0
3
19.90
62.36
2.0
0
0
1
0
0
0
0
0
0
1
1
1
1
2
1
5.98
8.40
9.94
5.98
2.42
3.96
6.55
3.29
96.76
72.68
80.36
4.2
2.0
4.1–5.6
[2-apymMALH]/[2-apym][MALH]
[2-apymMALH]/[2-apymH][MAL]
[2-apymMALH3]/[2-apymH][MALH2]
0
0
0
1
3
15.08
55.72
2.0
…
…
˚
(3.047, 3.093, 3.151 and 3.239 A), and two C–H2-apym pHSAL
˚
1.599 A), four N–H2-apym
˚
OHSAL (1.993 A), two
…
C–H2-apym pHSAL (3.166 A), and four sets of double
˚
˚
(3.325 A) for stabilization of I9net (Fig. 8 and Fig. 4S, ESI{). The
…
˚
N–H2-apym p2-apym (3.053, 3.430 A) govern the formation of
I9-fragment2 (Fig. 3S, ESI{, Table 4). In the last step, addition of
the remaining parts of I9mon (two HSAL molecules) to
I9-fragment2 causes to involve two more 2-apym and two more
formation energy of I9net trimer associated with all of these contacts
(21702.9 kcal mol21) has been estimated through similar route used
for compound I. The calculated interaction energies show that near
three fifths (21002.7 kcal mol21) of network stabilization energy
comes from H-bonds (Table 4). For compound II, species IImon as
selected monomer was employed for starting calculations (Fig. 9). In
…
HSAL molecules exhibiting two O–HHSAL N2-apym (1.607 A), two
˚
…
N–H2-apym OHSAL (1.887 A), four sets of double C–HHSAL p2-apym
…
˚
Fig. 11 Distribution diagrams of SAL(L) (a), GLY(L9) (b), MAL(L99) (c) and 2-apym (Q) (d).
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…
this inner-sphere complex, N3–H3 O2 (1.582 A) and N4–
˚
Solution studies
…
˚
H4 O1 (1.801 A) intramolecular interactions stabilize its
conformation in the solid state. Paying attention to different
non-covalent interactions of the network of compound II, we
could choose two species (IInet1, IInet2, Fig. 9). Comparing to
In this section primarily, the fully protonated forms of SAL(L),
GLY(L9), MAL(L99) and 2-apym(Q) were titrated with a
standard NaOH solution (Fig. 10a–d) in order to obtain their
protonation constants as the building blocks of the SAL/2-apym,
GLY/2-apym, MAL/2-apym adducts. The protonation constants
of SAL, GLY, MAL and 2-apym were calculated by fitting the
volume–pH data to BEST program. The results are summarized
in Table 5. It is noteworthy that the resulting protonation
constant values are in satisfactory agreement with those reported
in the literature.43–46 Distribution diagrams for all ligands are
shown in Fig. 11a–d. The evaluation of the equilibrium constants
for the interaction of SAL/GLY/MAL with 2-apym in different
protonation forms was accomplished through comparison of the
calculated and experimental pH profiles obtained with SAL/2-
apym, GLY/2-apym or MAL/2-apym present.36,47,48 The results
are shown in Table 5. The corresponding species distribution
diagrams for SAL/2-apym, GLY/2-apym, MAL/2-apym are
shown in Fig. 12a–c. The binding constants for the binary
species formed from SAL/2-apym, GLY/2-apym and MAL/2-
apym are listed in Table 5. The most abundant proton-transfer
species for SAL/2-apym present at pH . 4.6 (58.36%) and 2.0
…
˚
IImon, for IInet1, p2-apym p2-apym stacking (3.452 A), and N1–
…
˚
H1 Cl1 non-classical H-bond (2.697 A) and for IInet2, non-
…
classical N1–H1 Cl1 (2.697 A), and double N4–H4 N2
…
˚
21
˚
(1.773 A) H-bonds cause 274.16 and 2168.37 kcal mol
…
stabilization energy, respectively (Table 4). The title p
p
˚
interaction results in a N–centroid2-apym distance of 3.452 A
which reflects a moderate interaction of the N atom of the top
ring with the p cloud of bottom ring and vice versa (indeed a
strong interaction is characterized by a separation distance
41
below 3.03 A). Comparing IInet1 and IInet2 (Fig. 9) indicates
˚
…
that the N1–H1 Cl1 bond displayed a little interplaying on N4–
…
H4 Cl1, which causes weakness of the latter in IInet2. For
compound II some weak and not real non-covalent contacts
…
…
˚
˚
(N2–H1 Cl2, 2.984 A, N1–H1 Cl2, 3.042 A) having no
important effect in related network formation are not considered
in the theoretical point of view. Generally, the comparison of all
of these H-bond and stacking non-covalent interaction distances
…
…
…
show stabilization order as: O–H N . N–H O . N–H N .
…
…
…
…
(62.45%) are: [2-apym][HSAL] (logK
= 3.18) and [H2-
N–H Cl . C–H p . N–H p . p p (Table 4). It is
noteworthy to say that the energy values reported in this work
have good agreement with experimental data similar to the
previously reported theoretical research in literature.42
apym][H2SAL] (logK = 3.38); for GLY/2-apym present at pH
4.4–9.9 (75.16%), 3.0 (30.1%) and 2.0 (62.36) are: [2-
apym][HGLY] (logK = 3.69), {[H2-apym][HGLY](logK = 3.46),
Fig. 12 Distribution diagrams for the proton-transfer interaction between SAL(L)/2-apym(Q) (a), GLY(L9)/2-apym(Q) (b) and MAL(L99)/2-apym(Q)
(c) in all probability protonated forms.
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Fig. 13 Distribution diagrams of M/SAL(L) (a), M/GLY(L9) (b), M/MAL(L99) (c) and M/2-apym (Q) (d) binary systems MLCu2+
.
[2-apym][H2GLY] (logK = 4.18)} and [H2-apym][H2GLY] (logK
= 3.62); for MAL/2-apym present at pH 4.1–5.6 (80.36%) and 2.0
(55.72%) are: {[2-apym][HMAL] (logK = 3.96), [H2-apym][MAL]
(logK = 6.55)} and [H2-apym][H2MAL] (logK = 3.29). In order to
evaluate the stoichiometry and stability of Cu2+ ion complexes
with SAL/2-apym, GLY/2-apym and MAL/2-apym proton-transfer
systems in aqueous solution, the equilibrium potentiometric pH
titration profiles of SAL, GLY, MAL, 2-apym and their 1 : 1
mixture were obtained in the absence and presence of the Cu2+ ion.
The resulting pH profiles are shown in Fig. 10a–d and Fig. 14 (a–c).
It is seen from Fig. 10d that the titration of 2-apym in the presence of
Cu2+ ion was stopped when the formation of precipitate in solution
was observed. It was found that 2-apym forms weak complexes with
the Cu2+ ion and the potentiometric titration curves SAL/2-apym,
GLY/2-apym and MAL/2-apym mixtures are depressed consider-
ably in the presence of the cited metal ion. The results are shown in
Table 6. The calculated values are in agreement with previous
reports.45,49,50 The cumulative stability constants of MmLlQqHh,
Table 6 Overall stability constants of 2-apym/SAL, GLY or MAL/Cu
(Q/L, L9 or L99/M) binary and ternary systems in aqueous solution at 25
¡ 0.1 uC and m = 0.1 M NaNO3
System
M L L9 L99 Q H logb Maximum % pH
Cu/2-apym
1
1
1
0
0
0
0
0
0
0
0
0
1
1
1
0
1
3.98 89.76
7.12 90.4
5.1
2.0
.7.8
22 28.17 100.0
Cu/SAL
Cu/GLY
1
1
1
1
2
2
0
0
0
0
0
0
0
0
0
0
0
1
10.94 89.2
17.78 96.16
6.7–7.7
12.0
5.6–7.6
25.28
9.36
1
1
1
1
0
0
0
0
1
2
2
1
0
0
0
0
0
0
0
0
0
0
1
9.07 38.81
17.48 77.06
22.10 25.64
4.6
6.5–9.7
4.1
12.0
21 3.18 82.96
Cu/MAL
1
1
1
1
0
0
0
0
0
0
0
0
1
2
1
2
0
0
0
0
0
0
3.71 79.18
5.29 3.50
6.4
6.5–7.3
11.3–12
10.5–12.0
21 24.27 82.96
21 21.97 17.03
b
mlqh, are defined in our previous publications.36,37 They are M, L
(L9, L99), Q and H as metal ion, SAL (GLY, MAL), 2-apym and
proton, respectively, and m, l, q and h are the respective
stoichiometric coefficients. The cumulative stability constants were
evaluated by fitting the corresponding pH–volume data to BEST
program and the resulting values for the most likely complexed
species in aqueous solutions are also included in Table 6 and the
corresponding distribution diagrams are shown in Fig. 13a–d and
15a–c. These results revealed that the Cu2+ ions form relatively stable
Cu/SAL/2-apym
Cu/GLY/2-apym
1
1
1
1
2
2
0
0
0
0
0
0
1
2
2
1
1
2
19.73
33.98 26.78
40.79 70.43
8.75
2.9–3.9
7.2
4.2–5.2
1
1
0
0
1
1
0
0
1
1
0
1
13.23 39.52
16.67 26.8
5.4
3.7
Cu/MAL/2-apym 1
1
0
0
0
0
1
1
1
1
0
2
14.09 90.64
17.10 77.86
4.5–5.5
2.1
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Fig. 14 Potentiometric titration curves of SAL/2-apym (a), GLY/2-apym (b) and MAL/2-apym(c) in the absence and presence of Cu2+ ion with
NaOH 0.09300 M in aqueous solution at 25 ¡ 0.1 uC and m = 0.1 M NaNO3.
Fig. 15 Distribution diagrams of M/SAL(L)/2-apym (Q) (a), M/GLY(L9)/2-apym(Q) (b) and M/MAL(L99)/2-apym(Q) (c) ternary systems M = Cu2+
.
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complexes with SAL, GLY, MAL alone and mixed with 2-apym,
including SAL/2-apym, GLY/2-apym and MAL/2-apym systems,
but weak complexes with 2-apym. Fig. 13a–c and Table 6 show for
Cu/2-apym/SAL/GLY/MAL binary systems, the most likely
species are: CuQ, CuQH, CuQH22, CuL, CuL2, CuL2H, CuL9,
the computing centre of the Friedrich-Schiller Universita¨t Jena
(URZ), Jena, Germany for supplying their Cray XD1 (officer:
Sabine Irmer) for performing the computational research part.
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The authors gratefully acknowledge the financial support by the
Ferdowsi University of Mashhad, Mashhad, Iran. We also thank
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