Supramolecular assembly of a new series of copper-l-arginine Schiff bases

Article abstract of DOI:10.1039/c0ce00444h

A series of copper-l-arginine complexes has been synthesized and characterized by spectroscopic and single-crystal X-ray diffraction analyses. The l-arginine Schiff bases invariably show [ONO] tridentate coordination on a mononuclear Cu(ii) sphere. [Cu(RN

Full text of DOI:10.1039/c0ce00444h

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PAPER
Supramolecular assembly of a new series of copper-L-arginine Schiff bases†
a
Siu Yee New, Yude Thio, Lip Lin Koh, T. S. Andy Hor
a
a
ab
a
*
*
and Feng Xue
Received 23rd July 2010, Accepted 22nd November 2010
DOI: 10.1039/c0ce00444h
A series of copper-L-arginine complexes has been synthesized and characterized by spectroscopic and
single-crystal X-ray diffraction analyses. The L-arginine Schiff bases invariably show [ONO] tridentate
coordination on a mononuclear Cu(II) sphere. [Cu(RNap)(OAc)]$2H2O, 1 (RNap ¼ N-(2-hydroxy-1-
naphthalidene) L-arginine), obtained from Cu(OAc)2$2H2O and HRNap, gives two stereochemically
different molecules in the crystal unit cell, with each of them showing different acetate binding modes. It
exhibits a channel structure with disordered water molecules filling the cavity. Complexation of
N-(2-hydroxy-5-nitro-1-salicylidene) L-arginine (HRNO2) with Cu(ClO4)2$6H2O yields the intriguing
triclinic crystal structure of 2. Its unit cell consists of a neutral molecule [Cu(RNO2)Cl(H2O)], an ion
pair [Cu(RNO2)(H2O)2]ClO4 and three water molecules of crystallization. Complexation of HRMe
(RMe ¼ N-(2-hydroxy-5-methyl-1-salicylidene) with Cu(OAc)2$2H2O gives [Cu(RMe)(OAc)]$5H2O,
3, whose crystal packing shows a zeolite-like network with a water cluster residing in the hydrophilic
channel, thus facilitating the hydrogen bonding interaction.
fused-rosette layers using guanidinium with various
Introduction
oxoanions.11–14 Similarly, Yamauchi et al. have demonstrated
impressive supramolecular assemblies using arginine as building
block.15–18 These show that the topology outcomes can be
appropriately influenced by factors such as framework chirality
and counterions.17,18
A salient feature of arginine amongst the 20 amino acids is its
guanidinium moiety which plays a functional and structural role
in a range of biological activities. Owing to its high pKa value
(ꢀ12.5), the guanidinium group tends to retain its protonation
state over a wide range of pH media. Consequently, it is partic-
ularly amenable to both electrostatic and hydrogen bond inter-
actions with various anionic substrates.1,2 Numerous examples
found in nature clearly elucidate the significant interaction of
arginine with carboxylate,3 phosphate,1,3–7 guanine,8,9 and
superoxide (e.g. Cu, Zn-superoxide dismutase, SOD).10 Hence,
there have been considerable efforts directed in designing
guanidinium-based drugs and artificial receptors over the
decades.1,2 One example is thrombin inhibitors, which typically
contain a benzamidine or arginine moiety to establish crucial
electrostatic interaction with Asp189. Crystallographic results
revealed that the guanidinium moiety could orientate the
substrate by two parallel hydrogen bonds, ultimately elaborating
the non-covalent network.2 Utilizing this peculiar binding
capability, Mak et al. have constructed a series of interesting
In view of the synthetic utility of Schiff bases in coordination
chemistry,19–21 we are interested in the construction of supra-
molecular architectures using arginine Schiff bases. Although
numerous studies have been directed at supramolecular assembly
of many amino acid Schiff bases, they are mainly devoted to
simple amino acids such as glycine,22–26 valine,26,27 phenylala-
nine,26,28–30 etc. Comparatively, studies involving functional
amino acids are significantly less explored.31–33 One of the recent
studies done by Khatua et al. showed the self-assembly of
copper-lysine Schiff bases which generated a 3D hydrogen bond
network via interaction of the lysine side chain with carboxylate
groups.31 It is interesting to observe the formation of octanuclear
water clusters and water chains and their interaction with these
networks. Ray et al. have constructed a novel molecular capsule
using a copper-histidine reduced Schiff base which is capable of
trapping up to four pyridines in the cavity.32 These studies
demonstrated the potential of functional amino acid Schiff bases
in directing novel assembly architectures.
aDepartment of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543. E-mail: andyhor@nus.edu.sg; xuefeng@nus.
edu.sg
The present work studies the assembly outcomes of L-arginine
Schiff bases by systematically varying the ring substituent
(tuning the p system with polarization or ring enlargement) and
oxyanions. Three crystal structures of copper(II)-L-arginine
Schiff bases together with a ligand are herein reported. Within
two of them, there are two structurally different molecules in the
unit cells. To the best of our knowledge, arginine Schiff bases
bInstitute of Materials Research and Engineering, Agency for Science,
Technology and Research, 3 Research Link, Singapore 117602
† Electronic supplementary information (ESI) available: Images of
superimposition of complexes, NMR spectra for Schiff base ligands,
CD, TGA, UV-visible, ESI-MS and simulated isotopic spectra for
compound 1, 2 and 3. CCDC reference numbers 786079–786082. For
ESI and crystallographic data in CIF or other electronic format see
DOI: 10.1039/c0ce00444h
2114 | CrystEngComm, 2011, 13, 2114–2122
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have not yet been studied crystallographically34–36 although other
amino acid Schiff bases are common.
Results and discussion
The Schiff base ligands
A Schiff base can be prepared by simple condensation of amino
acid with aldehyde. The synthesis of N-(2-hydroxy-1-naph-
thalidene) L-arginine (HRNap) was reported in 1947 by McIntire
in a moderate yield (70%), which required pretreatment with
Ag2CO3 under a moisture-free environment and longer reaction
time (1–2 days).34 In this work, HRNap was obtained in high
yield (94%), following a simpler method reported by Chow and
Ebel.36,37
Typically, an amino acid Schiff base with an o-hydroxyaryl
moiety enables its isolation due to intramolecular stabilization by
hydrogen bonding.34 As an attempt to elucidate the effect of
para-substituent to –OH of hydroxyaryl, nitro and methyl are
chosen as electron withdrawing and donating groups
respectively. Two new L-arginine ligands, N-(2-hydroxy-5-nitro-
1-salicylidene) L-arginine (HRNO2) and N-(2-hydroxy-5-methyl-
1-salicylidene) L-arginine (HRMe) have been successfully
synthesized in moderate yields (55 and 68%) (Scheme 1). The
scheme of the complexation of these ligands with Cu(II) is shown
in the Electronic Supplementary Information.† The complexes
can be obtained either by one-pot synthesis wherein the ligand is
not isolated but reacted in situ with the metal precursor or by
reacting the pre-formed Schiff base with a metal salt.
Single crystals of HRNap were obtained by slow evaporation
of methanolic solution of the sample. We herein report the
crystal structure of the first example of an arginine Schiff base,
from which we can gain new insights into the self-assembled
patterns of arginine derivatives. HRNap crystallizes in triclinic
P1 with two water molecules of crystallization in an asymmetric
unit (Fig. 1a). Notably, the bond order of C2–O1 and C22–O4 is
estimated to be close to two, as depicted by their relatively
ꢀ
shorter bond lengths of 1.279(4) and 1.277(4) A (given the
ꢀ
normal aryl C–O bond in phenol ¼ 1.362 A and C]O ¼
38
1.222 A). In addition, the bond lengths of C3–C4 (1.339(5) A)
ꢀ
ꢀ
ꢀ
and C23–C24 (1.342(5) A) are shorter than the other aromatic
C–C of the same ring, which proves that the pseudo aromatic
system exists in a quinoid form.39 This quinoid effect of the N-
aryl Schiff bases shifts the phenol proton to the imine nitrogen,
causing HRNap to exist as a zwitterion. This is supported by the
longer N1–C11 and N5–C31 bond lengths, which are 1.306(3)
Fig. 1 (a) ORTEP diagram (30% probability of thermal ellipsoid) of
HRNap within crystal lattice. All hydrogen atoms except imine C]N–H
have been omitted for clarity. The intramolecular hydrogen bond is
depicted as pink dotted lines. (b) Hydrogen bond interaction (cyan dotted
lines) in a layer structure of HRNap viewed along a axis. (c) Intercon-
nection between the parallel 2D layers of HRNap via hydrogen bonding
between phenolate and guanidinium.
ꢀ
and 1.304(4) A respectively (a typical C]N bond length is
38
ꢀ
1.279 A). Extensive intra- and intermolecular hydrogen
bonding was found, with the interaction between the phenolate
and guanidinium (N7–H7A/O1vi 3.13, N8–H8B/O1vi 2.85,
ii
ii
ꢀ
N3–H3A/O4 3.17 and N4–H4B/O4 2.79 A; symmetry codes
(vi): ꢁ1 + x, 1 + y, z; (ii): x, ꢁ1 + y, z) interconnects the 2D layers
(Fig. 1b and 1c, Table 1). This interconnection results in the short
Scheme 1 Synthetic scheme of two new L-arginine-based Schiff bases,
HRNO2 and HRMe.
This journal is ª The Royal Society of Chemistry 2011
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Table 1 Hydrogen bond parameters for HRNap ligand.a
<DHA/ꢂ
ꢀ
ꢀ
D–H/A
d(H/A)/A
d(D/A)/A
O1W–H1WA/O3i
N1–H1N/O1
1.89(3)
1.97
2.11
1.88(3)
2.07(4)
2.22
2.48
2.30
2.55
1.97(4)
1.99
1.96
1.99
2.12
2.41
2.24
2.41
1.99
2.729(4)
2.574(4)
2.916(4)
2.762(4)
2.713(4)
2.887(4)
3.172(4)
3.043(4)
3.237(4)
2.821(4)
2.815(4)
2.793(4)
2.577(4)
2.876(4)
3.133(4)
2.784(4)
3.166(4)
2.826(4)
2.849(4)
153(3)
137
153
164(3)
128(3)
133
137
143
137
157(3)
158
159
134
145
141
130
146
162
N2–H2/O3ii
O1W–H1WB/O2
O2W–H2WA/O6iii
N3–H3A/O2Wii
N3–H3A/O4ii
N3–H3B/O1Wiv
N3–H3B/O3ii
O2W–H2WB/O5
N4–H4A/O5ii
N4–H4B/O4ii
N5–H5N/O4ii
N6–H6A/O6v
N7–H7A/O1vi
N7–H7A/O1Wv
N7–H7B/O2Wvi
N8–H8A/O2
N8–H8B/O1vi
2.03
158
a
Symmetry codes: (i) ꢁ1 + x, y, z; (ii) x, ꢁ1 + y, z; (iii) 1 + x, y, z; (iv) 1 +
x, ꢁ1 + y, z; (v) x, 1 + y, z; (vi) ꢁ1 + x, 1 + y, z.
ꢀ
contact of C4/C29 at 3.345 A. Weak p–p interaction between
the naphthalene rings was also observed in a parallelism pattern,
with the range of centroid–centroid distances40 in the region of
ꢀ
4.51–6.93 A.
[Cu(RNap)(OAc)]$2H2O, 1
The complexation of HRNap with Cu(OAc)2$2H2O results in
the isolation of 1, containing 1a and 1b that differ by the coor-
dination modes of acetate (Fig. 2a). The former adapts a square
planar geometry with the coordination sphere completed by
a tridentate RNap [ONO] donation and unidentate attachment
of acetate. 1b shows a distorted square pyramidal geometry
(structural indices s41 ¼ 0.17) with an additional oxygen donor
from the semi-chelating acetate. The basal plane of 1b is signifi-
cantly more distorted than 1a, with O6–Cu2–O7 and O9–Cu2–
N5 angles of 157.7(2)ꢂ and 167.7(2)ꢂ respectively (Table 2). The
larger deviation in 1b may be attributed to the semi-coordina-
tion42 of axial acetate ligand at a distance of 2.674(7) A, which is
ꢀ
43,44
ꢀ
in the region (ꢀ2.6 A) of weak Cu/O interactions.
Viewing along the a axis, these Cu(II) units form a channel
3
structure with void volume ca. 771.2 A (17.1%). The dimension
ꢀ
ꢀ
ꢀ
of the channel is small (approximately 8 A ꢃ 9 A), indicating the
tight packing in 1. A schematic diagram of the channel formation
is illustrated in Fig. 2c, with 1a and 1b shown as green and blue
blocks respectively. Complex 1b forms 1D chains (projecting
along the a axis) that interact with each other by hydrogen
bonding (N6–H6A/O5iii 2.99, N7–H7A/O6iv 2.98, N7–H7B/
Fig. 2 (a) ORTEP diagram (30% probability of thermal ellipsoid) of 1
contains two geometrically different Cu(II) units. All hydrogen atoms
have been omitted for clarity. (b) Packing diagram of 1 in stick model
(colored by symmetry equivalence), in the projection along a axis. 1a and
1b units are shown in green and blue respectively. Water molecules in the
channel are shown as red balls, with O1W and O2W located close to
framework, and O3W and O4W in the middle. (c) A schematic diagram
of 1 illustrates the formation of the channel-like structure. Packing of 1b
units (blue block) gives continuous 1D chains, which are interconnected
by 1a (green block) that act as linkers.
O4iii 2.88, N8–H8A/O9iv 2.83 and N8–H8B/O3iv 2.83 A;
ꢀ
symmetry codes (iii): 1/2 ꢁ x, 2 ꢁ y, 1/2 + z; (iv): ꢁ1 + x, y, z)
(Table 3). The neighboring 1a species then act as linkers, holding
two neighboring 1b chains in a perpendicular pattern. There is
also evidence of p–p stacking in the channel. Aromatic stacking
was observed between naphthalene rings of Cu2 and Cu1–chelate
proximities from the channel wall (Fig. 2b). O1W and O2W are
relatively less disordered than O3W and O4W, and located closer
to the wall of the channel. All hydrogen atoms of water molecules
were not included in the refinement due to distortion.
ring,45 with centroid–centroid distance at 3.587 A. Four disor-
ꢀ
dered water molecules fill up the small cavity with different
2116 | CrystEngComm, 2011, 13, 2114–2122
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Table 3 Hydrogen bond parameters for the Cu(II) complexes.a
ꢂ
ꢀ
Table 2 Selected bond lengths [A] and angles [ ] for the complexes
ꢀ
ꢀ
Complex 1
1a
Cu1–O1
Cu1–N1
Cu1–O4
Cu1–O2
D–H/A
d(H/A)/A
d(D/A)/A
<DHA/ꢂ
1b
Cu2–N5
Cu2–O6
Cu2–O9
Cu2–O7
Cu2–O10
N5–Cu2–O6
N5–Cu2–O9
O6–Cu2–O9
N5–Cu2–O7
O6–Cu2–O7
O9–Cu2–O7
1.872(4)
1.906(5)
1.928(4)
1.955(4)
1.897(5)
1.902(5)
1.936(5)
1.952(5)
2.674(7)
93.3(2)
167.7(2)
93.6(2)
84.18(19)
157.7(2)
93.2(2)
Complex 1
N2–H2/O8i
2.13
2.02
2.09
2.12
2.08
2.12
2.18
2.05
2.03
2.10
2.985(6)
2.882(6)
2.904(7)
2.982(6)
2.898(7)
2.989(7)
2.982(7)
2.884(7)
2.830(8)
2.828(6)
167
170
155
169
157
176
153
160
153
141
N3–H3A/O7i
N3–H3B/O3i
N4–H4A/O2i
N4–H4B/O1Wii
N6–H6A/O5iii
O1–Cu1–N1
O1–Cu1–O4
N1–Cu1–O4
O1–Cu1–O2
N1–Cu1–O2
O4–Cu1–O2
Complex 2
2a
Cu1–O1
Cu1–N1
Cu1–O2
Cu1–O1W
Cu1–Cl1
N1–Cu1–O2
O1–Cu1–O1W
N1–Cu1–O1W
O2–Cu1–Cl1
O1–Cu1–Cl1
O1–Cu1–N1
O1–Cu1–O2
O2–Cu1–O1W
N1–Cu1–Cl1
O1W–Cu1–Cl1
Complex 3
Cu1–O1
Cu1–O2
Cu1–O5
O1–Cu1–N1
N1–Cu1–O2
N1–Cu1–O4
93.73(19)
91.70(18)
173.19(19)
169.1(2)
84.69(18)
90.73(18)
N7–H7A/O6iv
N7–H7B/O4iii
N8–H8A/O9iv
N8–H8B/O3iv
Complex 2
2b
Cu2–O6
Cu2–N6
Cu2–O7
Cu2–O3W
Cu2–O2W
O6–Cu2–N6
N6–Cu2–O7
O6–Cu2–O7
O6–Cu2–O3W
O7–Cu2–O2W
N6–Cu2–O2W
O3W–Cu2–O2W
N6–Cu2–O3W
O3W–Cu2–O7
O6–Cu2–O2W
O1W–H1WA/O8
N2–H2/O8v
1.89(3)
1.95
1.86(3)
1.96(2)
2.15
2.21(3)
1.88(3)
2.03(4)
2.18
2.56(4)
2.14
2.14
2.10
2.27
2.54
2.33
2.06(3)
1.97(3)
2.25(3)
2.42
2.32(2)
2.74
2.31(3)
2.699(4)
2.801(4)
2.658(4)
2.772(3)
2.989(4)
2.920(4)
2.677(4)
2.816(4)
2.829(4)
3.386(4)
2.980(4)
2.979(4)
2.828(6)
3.032(4)
3.226(5)
3.016(4)
2.793(4)
2.748(4)
3.097(4)
3.226(4)
3.110(3)
3.479(3)
3.116(3)
168(3)
171
174(3)
172(4)
167
144(3)
177(5)
154(4)
132
170(4)
166
166
141
147
138
137
150(4)
152(3)
167(4
157
161(4)
144
166(4)
1.920(2)
1.941(2)
1.957(2)
2.033(2)
2.5028(9)
83.26(10)
91.37(10)
147.33(10)
92.02(7)
94.80(7)
93.42(10)
173.17(10)
88.28(9)
120.18(8)
91.53(7)
1.915(2)
1.931(3)
1.956(2)
1.955(3)
2.283(3)
93.10(10)
83.74(10)
169.76(10)
89.44(11)
97.93(10)
106.30(11)
87.40(12)
165.94(13)
91.34(11)
92.31(9)
O1W–H1WB/O5Wi
O2W–H2WA/O2iv
N3–H3B/O14v
O2W–H2WB/O4vi
O3W–H3WB/O6Wvii
O4W–H4WA/O5Wviii
N7–H7A/O4Wviii
O4W–H4WB/O3W
N8–H8A/O6ix
N8–H8B/O13x
N8–H8B/O3iv
N9–H9A/O2Wix
N9–H9A/O3Wix
N9–H9B/O1Wviii
O5W–H5WB/O10xi
O6W–H6WA/O3
O6W–H6WB/O5x
N4–H4A/Cl1ix
1.881(2)
1.940(2)
2.575(2)
95.24(10)
84.00(10)
168.61(11)
Cu1–N1
Cu1–O4
1.917(2)
1.978(2)
O3W–H3WA/Cl1iv
N3–H3A/Cl1ix
O1–Cu1–O2
O1–Cu1–O4
O2–Cu1–O4
175.39(10)
92.80(10)
88.62(10)
O5W–H5WA/Cl1iv
Complex 3
O1W–H1WA/O5Wxii
N2–H2/O3Wv
2.09(4)
1.98
2.20(4)
2.14
2.16
2.03(4)
2.03
2.39
1.98(4)
2.01(3)
2.27(6)
2.00(6)
1.93(2)
2.18(2)
2.904(4)
2.836(4)
2.785(4)
3.002(3)
2.992(4)
2.785(5)
2.871(4)
3.064(4)
2.795(3)
2.821(4)
3.044(5)
2.776(7)
2.774(3)
2.989(4)
160(6)
166
127(4)
170
160
152(4)
162
135
166(3)
164(4)
160(7)
155(6)
175(4)
158(4)
O2W–H2WA/O3xiii
N3–H3A/O3xiv
N3–H3B/O5W
O2W–H2WB/O1W
N4–H4A/O2xiv
N4–H4B/O3Wxiii
O3W–H3WA/O4xii
O3W–H3WB/O2W
O4W–H4WA/O4xv
O4W–H4WB/O1W
O5W–H5WA/O5
O5W–H5WB/O50xvi
[Cu(RNO2)Cl(H2O)]${[Cu(RNO2)(H2O)2](ClO4)}$3H2O, 2
In order to examine the geometric effect of Cu(II) in the absence
of additional coordination from acetate, we have studied the
complexation of HRNO2 with Cu(ClO4)2$6H2O which gives
product 2. The crystal lattice also contains two Cu(II) units, 2a
and 2b with different coordination environments (Fig. 3a). Both
contain square pyramidal Cu(II) (s2a ¼ 0.43; s2b ¼ 0.06) with
a common basal plane comprising the RNO2 [ONO] donors and
aqua oxygen. They differ in the axial ligand being Cl in 2a and
aqua in 2b. The Clꢁ source probably originates from L-arginine
hydrochloride. Our efforts to obtain crystals using chloride-free
arginine did not yield suitable crystals. There is no direct coor-
dination of perchlorate but it participates in a hydrogen bonding
network with guanidinium moieties and in a different fashion
from chloride. The perchlorates connect to both 2a and 2b in an
anti-parallel pattern (N3–H3B/O14v 2.99 and N8–H8B/O13x
a
Symmetrycodes: (i) 1 ꢁ x, 1/2 + y, 3/2ꢁ z;(ii) 1 ꢁ x, 1/2+ y, 3/2 ꢁ z; (iii) 1/
2ꢁ x, 2 ꢁy, 1/2+ z;(iv) ꢁ1+ x, y, z; (v)1 + x, y, z;(vi) ꢁ1 +x, y, ꢁ1 + z;(vii)
ꢁ1 + x, ꢁ1 + y, z; (viii) x, 1 + y, z; (ix) 1 + x, 1 + y, z; (x) x, y,ꢁ1 + z; (xi) x, y,
1 + z; (xii) ꢁ1/2 + x, ꢁ1/2 + y, z; (xiii) x, ꢁy, 1 ꢁ z; (xiv) 1/2 + x, 1/2 ꢁ y, 1 ꢁ
z; (xv) 1/2 ꢁ x, ꢁ1/2 + y, 1/2 ꢁ z; (xvi) 1 ꢁ x, y, 1/2 ꢁ z.
nitro-containing aromatic rings with the centroid–centroid
ꢀ
distance being 3.766 A.
ꢀ
2.98 A; symmetry codes (v): 1 + x, y, z; (x) x, yꢁ1 + z). In
contrast, the chloride anion of 2a is hydrogen bonded to lattice
water and three Cu(II) units (N4–H4A/Cl1ix 3.23, O3W–
H3WA/Cl1iv 3.11, N3–H3A/Cl1ix 3.48 and O5W–H5WA/
[Cu(RMe)(OAc)]$5H2O, 3
iv
ꢀ
Cl1 3.12 A; symmetry codes (ix) 1 + x, 1 + y, z; (iv) ꢁ1 + x, y, z)
(Fig. 3a and Table 3). The combination of these interactions
leads to the formation of a comb-like structure with perchlorates
sitting inside the cavities (Fig. 3c). Apart from hydrogen bond
interaction, there are aromatic stackings between the
The crystal structure of 3 reveals a single Cu(II) unit in square
pyramidal geometry, with s ¼ 0.11. Similar to complex 1, strong
coordinating acetate anion tends to bind to the metal centre, but
with no hydrogen bond interaction with the guanidinium moiety.
ꢀ
The axial oxygen is also weakly bonded to copper (2.575(2) A).
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Notably, guanidinium and carboxylate groups form eight-
membered hydrogen bonded rings, which give 1D zig zag chains
along the b axis (N3–H3A/O3xiv 3.00 and N4–H4A/O2xiv
ꢀ
2.87 A; symmetry code (xiv): 1/2 + x, 1/2 ꢁ y, 1 ꢁ z) (Table 3).
Facilitated by the hydrogen bond interaction of H2O(5W), these
supramolecular chains then crosslink with each other in
a complementary pattern (Fig. 4d). As shown in Fig. 4b, two
H2O(5W) connect a pair of C2-symmetry-related molecules of 3
via O5 and N3 (O5W–H5WA/O5 2.77, O5W–H5WB/O50xvi
2.99, O1W–H1WA/O5Wxii 2.90 and N3–H3B/O5W 2.99 A;
ꢀ
symmetry codes (xvi): 1 ꢁ x, y, 1/2 ꢁ z; (xii): ꢁ1/2 + x, ꢁ1/2 + y,
z) (Table 3). Collectively these hydrogen bonds help to give rise
to a tightly-packed 2D structure. Stacking of the aryl–metal
chelate ring and aryl-planar guanidinium is also observed, with
45,46
ꢀ
centroid–centroid distances at 3.474 and 3.780 A respectively.
Packing along the c axis gives a zeolite-like structure with water
molecules trapped in the distinctive hydrophilic channels
(Fig. 4c). This gives a zeolite-like structure with the ratio of
hydrophobic to hydrophilic channels of approximately 1 : 2. The
3
ꢀ
cavity size of 3 is larger than 1, with void volume 1105.0 A
(23.4%) (with O5W retained). The O5W is located in the 2D
layers. In comparison, O1W positions close to the cavity wall and
interconnects O5W with other water molecules which are located
in the middle of the channel (Fig. 4c).
Comparison of copper-L-arginine crystal structures
All the copper complexes and HRNap ligand crystallize in
a chiral space group, with a Flack parameter close to zero
(Table 4). Our circular dichroism (CD) results also correlate well
to the absolute configuration from the Flack parameter (see
Electronic Supplementary Information†). All complexes display
an appreciable negative Cotton effect at 300–400 nm and a weak
negative band at 600–800 nm.16–18
The orientation of L-arginine side chains among the copper(II)
complexes was compared by superimposing their crystal struc-
tures (Figure S2–S4 in Electronic Supplementary Information†).
This is done by overlapping the rigid portion of the aryl ring,
phenoxy O and imine C]N, while keeping the remaining parts
flexible. The different orientation is within expectation. In fact,
different rotameric states of arginine side chains are well known
in proteins.47 The superimposition of both Cu(II) units in 1 and 2
are substantially different, with the side chains in 1 much more
deviated from each other (Figure S2†). The side chains of 1a are
oriented perpendicular to the naphthalene rings whereas those of
1b form the wall of the cavity. The different pattern may be
attributed to the orientation of acetate anions. The acetates in
both units are tilted, especially in 1b, presumably due to the weak
coordination of axial acetate. In contrast, both Cu(II) units in 2
give similar orientation, with the carboxylate of 2a more
protruded out of the basal plane.
Fig. 3 (a) ORTEP diagram (30% probability of thermal ellipsoid) of 2
with hydrogen bond interaction indicated as cyan dotted lines. Perchlo-
rate and water molecules of crystallization are disordered. Only hydrogen
atoms involved in hydrogen bonding are shown for clarity. (b) Packing
diagram of 2 viewed along b axis (colored by symmetry equivalence)
resembling a comb-like structure. 2a and 2b units are shown in green and
blue stick models respectively. Perchlorate and water molecules are
shown in yellow and red respectively. (c) A schematic diagram of 2
illustrates the formation of comb-like structure. 2a and 2b are represented
as green and blue blocks, whereas perchlorates are shown as yellow ovals.
The mononuclear Cu(II) unit in 3 was used as a template for
thorough comparison with other complexes (Figure S3 and S4†).
Overlaid structures of square pyramidal 1b and 3 reveal that the
axial Cu–O (OAc) bond in 3 is more perpendicular to the basal
plane. The plane angles between the axial acetate oxygen and
basal coordination plane in 1b and 3 are 70.1ꢂ and 88.6ꢂ
respectively. Also, it is noteworthy that the basal planes of 2b and
3 are apparently much more deviated than 2a and 3. This is due
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to the free O of carboxylate in 2 (O3 and O8) being involved in
different hydrogen bonding (Table 3), resulting in different
orientation.
Physicochemical studies
All the Schiff base ligands show HC]N peaks with dH ꢀ 8.4–9.0
ppm. The assignment of the peaks in the aromatic region is
1
further confirmed by COSY and H-13C HMQC NMR (Elec-
tronic Supplementary Information†). The HRNO2 ligand is
insoluble in common organic solvents except basic methanol
(doped with base) and hence its 13C NMR analysis of this ligand
is unsatisfactory. Its 1H NMR analysis shows the existence of two
geometrically different isomers, presumably anti and syn isomers
with ratio 5 : 1. The IR spectra of all free ligands revealed that
the sharp n(N–H) peaks are shifted to lower wavelength upon
coordination.48 All complexes exhibit 260–280 cmꢁ1 difference
for nasym(COO) and nsym(COO) indicating terminal and semi-
chelating coordination of carboxylate groups.49,50 Those nitro-
containing samples show two strong n(N]O) stretching bands at
ꢀ1600 and 1310 cmꢁ1 51
. The solution properties of the complexes
were studied using ESI-MS and UV-visible spectroscopy. A clean
dominant peak of [Cu(ligand)(MeOH)]+ was observed in positive
mode ESI-MS spectra for most of the Cu(II) complexes.
However, 1 and 2 which contain two different Cu(II) species in
the crystal lattice show the presence of dinuclear species,
[2Cu(RNap) + Na]+ at m/z 803.0 and [2Cu(RNO2)]+ at m/z 768.9
respectively. UV-visible spectra for all complexes show weak
d–d transitions at the 650–670 nm region, which is typical for
square pyramidal and square planar Cu(II) compounds.52 The
thermal stability of the complexes was analyzed using thermo-
gravimetric analysis (TGA). All complexes show the loss of water
molecules of crystallization below 150 ꢂC. Notably, crystals of 3
lost three water molecules at ambient conditions upon removal
from the mother liquor, as evidenced from the TGA data and the
ꢂ
lost of crystallinity. All complexes decompose below 225 C.
Experimental
All syntheses were carried out in an air atmosphere. The chem-
icals were obtained from commercial sources and used without
further purification. All the solvents used were of reagent grade.
NMR spectra were recorded with Bruker AMX 500 spectrometer
using CD3OH as internal standard (3.31 ppm in 1H and 49.0 ppm
in 13C NMR). Infrared spectra (4000–400 cmꢁ1) were recorded on
a Perkin-Elmer 1600 FTIR spectrophotometer with KBr pellets.
The electronic transmittance spectra were recorded on a Shi-
madzu UV-2450 in MeOH. Electrospray ionization mass spectra
(ESI-MS) were measured on a Finnigan MAT 731 LCQ spec-
trometer using manual injector (Rheodyne). The peak identifi-
cation was based on m/z values and isotopic matching patterns.
Circular dichroism was measured in a 1 mm path length cell
using a Jasco J-810 spectropolarimeter. Elemental analyses were
performed on a Perkin-Elmer PE 2400 elemental analyzer in the
Micro Analytical Laboratory of the Department of Chemistry at
the National University of Singapore. Water present in the
compounds was determined using ꢂa SDT 2960 TGA Thermal
Analyzer with a heating rate of 10 C per min.
Fig. 4 (a) ORTEP diagram (30% probability of thermal ellipsoid) 3 with
acetateanion coordinated tocopper. All hydrogen atoms have been omitted
for clarity. (b) Two C2-symmetry-related molecules of 3 H-bonded with two
O5W. (c) Packing diagram along c axis shows alternating arrangement of
water chain in 3. Water molecules are shown as red balls. (d) A schematic
diagram of 3 illustrates the formation of the channel structure.
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Table 4 Crystal data and structure refinement details
HRNap
1
2
3
Molecular formula
C17H20N4O3$H2O
C19H22CuN4O5$2H2O
(C13H18ClCuN5O6)$(C13
H20ClCuN5O11)$3H2O
1014.68
293(2) K
ꢀ
0.71073 A
C
16H22CuO5N4$ 5H2O
M
346.39
223(2) K
ꢀ
0.71073 A
485.98
223(2) K
ꢀ
0.71073 A
504.00
223(2) K
0.71073 A
Orthorhombic
C2221
Temperature
Wavelength
Crystal system
Space group
Unit cell dimensions
ꢀ
Triclinic
P1
Orthorhombic
P212121
Triclinic
P1
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
a ¼ 6.9339(5) A
a ¼ 11.7518(9) A
a ¼ 8.2119(8) A
a ¼ 11.7263(10) A
b ¼ 8.4735(6) A
b ¼ 16.3475(12) A
b ¼ 8.7239(9) A
b ¼ 19.1424(10) A
ꢀ
ꢀ
c ¼ 15.3249(10) A
c ¼ 23.4131(18) A
c ¼ 14.2024(14) A
c ¼ 21.0208(14) A
a ¼ 75.124(2)ꢂ
b ¼ 82.496(2)ꢂ
g ¼ 80.882(2)ꢂ
a ¼ 90ꢂ
b ¼ 90ꢂ
g ¼ 90ꢂ
a ¼ 90.923(2)ꢂ
b ¼ 96.679(2)ꢂ
g ¼ 99.903(2)ꢂ
a ¼ 90ꢂ
b ¼ 90ꢂ
g ¼ 90ꢂ
3
3
3
3
ꢀ
ꢀ
ꢀ
ꢀ
Volume
Z
Density (calculated)
Absorption coefficient
Reflns collected
Independent reflections
855.41(10) A
2
4498.0(6) A
8
994.82(17) A
2
4718.5(6) A
8
1.345 Mg mꢁ3
0.098 mmꢁ1
11184
1.435 Mg mꢁ3
1.017 mmꢁ1
31714
1.694 Mg mꢁ3
1.296 mmꢁ1
12676
1.419 Mg mꢁ3
0.981 mmꢁ1
16649
7760
[R(int) ¼ 0.0304]
10372
[R(int) ¼ 0.0824]
9021
[R(int) ¼ 0.0270]
5400
[R(int) ¼ 0.0548]
Gof
Final R indices [I > 2s(I)]
1.049
1.073
1.010
1.034
R1 ¼ 0.0617
wR2 ¼ 0.1327
0.1053
R1 ¼ 0.0782
wR2 ¼ 0.1750
0.0246
R1 ¼ 0.0382
wR2 ¼ 0.0832
0.0234
R1 ¼ 0.0461
wR2 ¼ 0.1010
0.0317
Flack parameter
(esd 1.1653)
(esd 0.0187)
(esd 0.0076)
(esd 0.0133)
Preparation of ligands: N-(2-hydroxy-1-naphthalidene)
L-arginine (HRNap)
N]Osym (1312), C–O (1227). 1H NMR dH (500 MHz, CD3OD +
NaOH) 1.61 (m, 2H, H11), 1.90 (m, 2H, H10), 3.16 (m, 2H, H12),
3.75 (m, 1H, H8), 6.49 (d, JHH ¼ 9.45, 1H, H3), 7.94 (dd, JHH
¼
A mixture of L-arginine (523 mg, 3 mmol) and 2-hydroxy-1-
naphthaldehyde (517 mg, 3 mmol) in MeOH (120 mL) was
refluxed at 65 ꢂC for 45 min. The bright yellow solution was then
filtered, concentrated on a rotovap and precipitated out with
a large amount of acetone to give the resultant yellow powder.
Slow evaporation of HRNap in methanol afforded yellow plate
crystals. Yield: 978 mg (2.8 mmol, 94%). Decomposition point:
205 ꢂC. Found: C, 60.0; H, 6.4; N, 16.9; C17H20N4O3$H2O
9.45, JHH ¼ 3.15, 1H, H4), 8.41 (s, 1H, H7), 8.45 (d, JHH ¼ 3.15,
1H, H6).
N-(2-hydroxy 5-methyl-1-salicylidene) L-arginine (HRMe)
HRMe was prepared in a similar way to HRNap by using 2-
hydroxy-5-methylbenzaldehyde in a relatively smaller quantity
(55 mg, 0.4 mmol). Light yellow product was precipitated out
upon distilling off the solvent and subsequently washed with
Et2O and vacuum dried.ꢂ Yield: 84 mg (0.3 mmol, 68%).
Decomposition point: 200 C. Found: C, 53.5; H, 7.0; N, 18.1;
C14H20O3N4$H2O (310.35) requires C, 54.2; H, 7.2; N, 18.1%. IR
(KBr, nmax/cmꢁ1: O–H (3391), N–H (3173), C]Oasym (1642),
(346.39) requires C, 59.0; H, 6.4; N, 16.2%. IR (KBr, nmax/cmꢁ1
:
O–H (3350), N–H (3168), C]Oasym (1629), C]N (1543),
1
C]Osym (1354), C–O (1183). H NMR dH (500 MHz, CD3OD)
1.73 (m, 2H, H15), 2.03 (m, 2H, H14), 3.24 (t, JHH ¼ 6.9 Hz, 2H,
H16), 4.25 (m, 1H, H12), 6.76 (m, 1H, H4), 7.19 (m, 1H, H6), 7.41
(m, 1H, H7), 7.57 (m, 1H, H5), 7.71 (m, 1H, H3), 7.99 (m, 1H,
H5), 8.95 (s, 1H, H11). 13C NMR dC (125 MHz, CD3OD, ppm):
26.1 (C15), 32.5 (C14), 42.3 (C16), 66.3 (C12), 107.5 (C1), 119.3
(C8), 123.6 (C6), 126.6 (C4), 127.2 (C10), 129.4 (C7), 130.1 (C5),
136.1 (C9), 139.8 (C3), 158.5 (C2), 158.7 (C11), 176.4 (C17), 181.3
(C13).
1
C]N (1568), C]Osym (1371), C–O (1277). H NMR dH (500
MHz, CD3OD) 1.65 (m, 2H, H11), 1.95 (m, 2H, H10), 2.25 (s, 3H,
H14), 3.22 (m, 2H, H12), 3.92 (m, 1H, H8), 6.73 (m, 1H, H3), 7.11
(m, 1H, H4), 7.12 (m,1H, H6), 8.35 (s, 1H, H7). 13C NMR dC (125
MHz, CD3OD, ppm): 20.3 (C14), 26.6 (C11), 32.5 (C10), 42.2
(C12), 74.1 (C8), 118.5 (C3), 119.4 (C1), 128.0 (C5), 132.9 (C4),
135.1 (C6), 158.7 (C13), 162.9 (C2), 166.3 (C7), 178.4 (C9).
N-(2-hydroxy-5-nitro-1-salicylidene) L-arginine (HRNO2)
[Cu(RNap)(OAc)]$2H2O, 1
HRNO2 was synthesized in a similar way to HRNap by using 2-
hydroxy-5-nitrobenzaldehyde (501 mg, 3 mmol). The ligand was
obtained as yellow precipitate without distilling off the solvent.
The yellow powder was insoluble in normal organic solvent,
except basic methanol (doped with basꢂe). Yield: 537 mg (1.7
mmol, 55%). Decomposition point: 227 C. Found: C, 48.1; H,
5.4; N, 21.7; requires C13H17O5N5 (325.31) C, 48.3; H, 5.3; N,
21.7%. IR (KBr, nmax/cmꢁ1: O–H (3433), N–H (3068), C]Oasym
(1650), N]Oasym (1606), C]N (1544), C]Osym (1368),
To the methanol solution (4 mL) of HRNap (69 mg, 0.2 mmol),
an equimolar amount of Cu(OAc)2$2H2O (40 mg) in water
(2 mL) was added and the solution was stirred for 3 h. Greenish
plate crystals suitable for X-ray diffraction studies were obtained
after one week by diffusing acetone into the resulting green
solution at 5 ꢂC. The same product was obtained by in situ
reaction of L-arginine, 2-hydroxy-1-naphthaldehyde and
Cu(OAc)2$2H2O in similar condition. Yield: 48 mg (0.1 mmol,
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49%). Found: C, 46.0; H, 5.0; N, 11.3; C19H22CuN4O5$2H2O
(485.98) requires C, 47.0; H, 5.4; N, 11.5%. UV-vis lmax(MeOH)/
nm 316 (3/dm3 molꢁ1 cmꢁ1 10500), 388 (9250), 661(100). IR (KBr,
nmax/cmꢁ1: O–H (3366), N–H (3183), C]Oasym (1677, 1623),
C]N (1577), C]Osym (1393, 1340), C–O (1185). ESI-MS
(MeOH) m/z 421.5 ([Cu(RNap)(MeOH)]+, 100%), 803.0
([2(Cu(RNap) + Na]+, 50%). TGA: weight loss (%) calcd. for 2
H2O: 7.4, found 8.7. meff (298 K) ¼ 1.54 B.M.
absorption correction.54 All structures were solved by direct
methods and refined on |F|2 by full-matrix least squares using
SHELXTL.55 Unless otherwise stated, all non-hydrogen atoms
were refined anisotropically whereas hydrogen atoms were
placed in their ideal positions and refined isotropically. The void
volumes were calculated using PLATON program.56 H1n and
H5n of HRNap ligand were identified from the electron density
map. O3W and O3W0 in 1 are disordered with 60 : 40 site
occupancy, similarly for O4W and O4W0.
[Cu(RNO2)Cl(H2O)].{[Cu(RNO2)(H2O)2](ClO4)}$3H2O, 2
Conclusions
L-Arginine hydrochloride (211 mg, 1 mmol) and NaOH (40 mg, 1
mmol) were dissolved in an ethanol–water mixture (1 : 1, v/v)
This study unveiled the combinative effect of the rigidity of Schiff
base and flexibility of L-arginine side chain in producing different
assemblies both at the local metal geometric and the crystal
architectural and packing levels. Complexation of HRNap and
HRMe with Cu(OAc)2$2H2O afforded channel structures with
different cavity sizes influenced by the subtle changes in aryl
moieties. The acetate ligands (in 1) exhibit unidentate and semi-
chelation modes in two different molecules. The uncoordinating
perchlorate anion (in 2) acts as linker between two different
Cu(II) units, giving rise to a comb-like structure hosting the
perchlorate ions. Comparison of these Cu(II) complexes suggests
that the orientation of arginine side chain plays an important role
in determining the outcome of the assemblies, which resembles
the influence of rotameric side chains in the protein structures.
These crystallographic studies of the Cu(II) supramolecular
assemblies of L-arginine Schiff bases will help the exploration of
their potential application as thrombin inhibitors. Our prelimi-
nary docking results indicated that these complexes displayed
similar binding mode to copper(II) and iron(III) Schiff bases
reported by Toyota et al.57,58 Apart from the crucial interaction
with key residue Asp189, the hydrophobic part of the aromatic
rings is also fixed well into the hydrophobic P- and D-pocket of
the enzyme.
ꢂ
and heated to about 65 C. A suspension of 2-hydroxy-5-nitro-
benzaldehyde (167 mg, 1 mmol) in ethanol (4 mL) was then
added to the solution, affording yellow precipitate.
Cu(ClO4)2$6H2O (371 mg, 1 mmol) in water (2 mL) was added
after 1 h, resulting in clear bluish green solution. The reaction
was continuously heated for 2 h and filtered after cooling to
room temperature. The solution was then filtered and left for
slow evaporation to give green crystals after three days. Yield:
320 mg (0.3 mmol, 32%). Found: C, 30.6; H, 4.5; N, 13.4; Cl 6.9;
(C13H18ClCuN5O6)$(C13H20ClCuN5O11)$3H2O
requires C, 30.8; H, 4.4; N, 13.8; Cl 7.0%. UV-vis lmax (MeOH)/
nm 362 (3/dm3 molꢁ1 cmꢁ1 29188), 670(304). IR (KBr, nmax/cmꢁ1
(1014.68)
:
O–H (3364), N–H (3215), C]Oasym (1647), N]Oasym (1604),
C]N (1554), C]Osym (1383), N]Osym (1318), C–O (1110).
ESI-MS (MeOH) m/z 385.0 ([Cu(RNO2)]+, 40%), 416.5 ([Cu-
(RNO2)(MeOH)]+, 100%), 768.9 ([2Cu(RNO2)]+, 20%). TGA:
weight loss (%) calcd. for 3 water of crystallization: 5.3, found
6.9; calcd. for 3 coordinated H2O: 5.3, found 4.3. meff (298 K) ¼
1.20 B.M.
[Cu(RMe)(OAc)]$5H2O, 3
To a mixture of 4 mL ethanol and 3 mL water, L-arginine (35 mg,
0.2 mmol) and 2-hydroxy-5-methylbenzaldehyde (27 mg,
0.2 mmol) in ethanol were added and stirred for one hour to give
a yellow cloudy solution. Cu(OAc)2$2H2O (40 mg, 0.2 mmol)
was then added to yield a clear green solution and stirred over-
night at room temperature. The mixture of water and ethanol
deposited green needle crystals upon slow evaporation at room
temperature. The same product was obtained by using equimolar
of L-arginine hydrochloride and NaOH as substitution to L-
arginine. Yield: 31 mg (0.07 mmol, 34%). Found: C, 43.3; H: 5.6;
N, 12.2; C16H22CuO5N4$2H2O (450.00) requires C, 42.7; H, 5.8;
N, 12.5%. UV-vis lmax (MeOH)/nm 374 (3/dm3 molꢁ1 cmꢁ1 6040)
and 646 (106). IR (KBr, nmax/cmꢁ1: O–H (3377), N–H (3202),
C]Oasym (1637), C]Osym (1364), C–O (1285). ESI-MS (MeOH)
m/z 385.5 ([Cu(RMe)(MeOH)]+, 100%). TGA: weight loss (%)
calcd. for 2H2O: 8.0, found 7.5. meff (298 K) ¼ 2.05 B.M. at 25 ꢂC.
Acknowledgements
This research was supported by National University of
Singapore (NUS) (Grant R143-050-288-101 and R143-000-415-
112). We thank G. K. Tan and Y. Hong (NUS), and Dr. Danielle
Gray (UIUC) for assistance with the crystallographic analysis.
We acknowledge Prof. Yi Lu (UIUC) and Prof. Michael
McGlinchey (UC Dublin) for helpful discussions. S. Y. New
thanks Dr Shiqiang Bai and Hang Xing for suggestions in the
preparation of the manuscript.
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