Adenine supported hydroxyl-bridged dicopper core as a catalytically competent unit for phenol oxidation

Article abstract of DOI:10.1016/j.poly.2012.05.013

This communication describes crystallographic investigation of a dicopper complex of modified adenine nucleobase containing a Cu₂O₂ core. This arrangement is remarkably similar to active sites present in some copper-containing redox enzymes. Interestingly, this complex is also competent in catalyzing redox reactions, suggesting the possibility of catalytically competent primitive metal-nucleobase systems.

Full text of DOI:10.1016/j.poly.2012.05.013

Polyhedron 52 (2013) 1385–1390
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Polyhedron
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Adenine supported hydroxyl-bridged dicopper core as a catalytically competent
unit for phenol oxidation
⇑
Ashutosh Kumar Mishra, Rajneesh Kumar Prajapati, Sandeep Verma
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Available online 30 May 2012
This communication describes crystallographic investigation of a dicopper complex of modified adenine
nucleobase containing a Cu2O2 core. This arrangement is remarkably similar to active sites present in
some copper-containing redox enzymes. Interestingly, this complex is also competent in catalyzing redox
reactions, suggesting the possibility of catalytically competent primitive metal-nucleobase systems.
Ó 2012 Elsevier Ltd. All rights reserved.
Dedicated to 100th Anniversary of the 1913
Nobel Prize in Chemistry to Alfred Werner
Keywords:
Propyladenine
Dicopper core
Phenol oxidation
1. Introduction
ladenine (1), containing a hydroxyl-bridged dicopper core and its
ability to catalyze phenol oxidation reactions.
Studies involving metal–adenine interactions have attracted
considerable attention owing to the presence of heterocyclic ring,
which can support coordination leading to the formation of varied
motifs with potential applications in generating metal–nucleobase
frameworks and aiding catalysis of certain reactions [1]. The het-
erocyclic ring of adenine can be dissected into two unequal halves
of six- and five-membered rings. The former supports Watson–
Crick hydrogen bonding, while the five membered ring invoked
for the Hoogsteen base-pairing resembles imidazole side-chain of
histidine amino acid offering a nucleophilic site and general
acid–base framework [2]. Thus, adenine has been implicated in
synthetic metalated motifs exhibiting catalytic actions such as cat-
alase-like activity for hydrogen peroxide disproportionation [3],
and phosphate ester hydrolysis reaction [4], to name a few. Sys-
tematic studies conducted by us to explore silver coordination
chemistry of substituted adenine nucleobase have resulted in the
formation of several novel frameworks [5,6]. In this process, we
have discovered that N9-alkyl substituents display a marked pref-
erence for silver metallaquartets [5a,b,j]; a carboxyl substituent
supports silver containing hexamer formation [5e]; a cyanoethyl
substituent yields an interconnected metal-nucleobase framework
[5i]; while a thiocyanatoethyl substituent leads to CuI aggregates
[5l]. In addition, our earlier studies had also revealed interesting
catalytic activities [4b–e,6]. The present report describes synthesis
and crystallographic investigation of copper complex of 9-propy-
2. Material and methods
N,N-dimethylformamide was distilled prior to use. 1H and 13C
NMR were recorded on JEOL-JNM LAMBDA 400 model operating
at 400, 100 MHz, respectively. HRMS mass spectra for the ligand
and metalated complexes were recorded at IIT Kanpur, India, on
Waters, Q-Tof Premier Micromass HAB 213 mass spectrometer
using capillary voltage 2.6–3.2 kV. Solvents were evaporated using
rotary evaporator under reduce pressure. NaH was purchased from
sd fine chemicals Pvt. Ltd. Mumbai, India, n-propyl bromide was
purchased from Spectrochem Pvt. Ltd. Mumbai; 6-chloropurine
was purchased from SRL, India and used without further purifica-
tion. All solvents were distilled prior to use using standards
procedures.
2.1. Synthesis of 9-propyladenine (9-PA)
Synthesis of 9-PA was carried out by a previously reported pro-
cedure [5b]. In brief, adenine (2.0 g, 14.8 mmol) was dissolved in
DMF (10 mL), followed by addition of NaH (0.71 g as 60% in paraf-
fin, 17.7 mmol) and stir under nitrogen atmosphere for 30 min.
After this n-propyl bromide (1.33 mL, 14.0 mmol) is added and stir
overnight under nitrogen atmosphere. After this time, DMF is
evaporated under high vacuum and compound is separated by col-
umn chromatography (1.05 g, 40% yield). FABMS: (M+ + 1) = 178;
M.P. = 167 °C. 1H NMR: (400 MHz, CDCl3, 22 °C, TMS) d (ppm)
0.88–0.92 (t, 3H), 1.84–1.91 (m, 2H), 4.09–4.12 (t, 2H), 6.14 (s,
⇑
Corresponding author.
E-mail address: sverma@iitk.ac.in (S. Verma).
0277-5387/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.poly.2012.05.013

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A.K. Mishra et al. / Polyhedron 52 (2013) 1385–1390
Scheme 1. Schematic representation of different substrates used.
Table 1
Table 2
Crystallographic data for 9-propyladenine (9-PA) and its copper complex (1).
Selected hydrogen bond distances (Å) and bond angles (°) in 1.
Identification code
9-PA
9-PA copper complex
Complex 1
Empirical formula
Mr
Crystal system
Space group
a (Å)
C8H11N5
177.22
monoclinic
P 21/c
8.4744 (9)
14.2188 (14)
14.3922 (14)
90
92.091 (2)
90
1733.0 (3)
1.358
8
0.091
752
C64H104Cl12Cu4N40O56
3009.43
monoclinic
P 21/n
18.274 (3)
14.433 (3)
21.692 (4)
90
100.46 (3)
90
5626.2 (18)
1.776
D–Hꢂ ꢂ ꢂAa
dHꢂ ꢂ ꢂA
dDꢂ ꢂ ꢂA
angle
N1–H1ꢂ ꢂ ꢂOW2
1.92
2.08 (4)
2.14
2.15
1.96
2.15
2.04(4)
2.10
2.11
2.18
2.73(4)
2.89(4)
2.88(4)
2.89(4)
2.74(4)
2.89(4)
2.85(4)
2.85(4)
2.95(4)
2.98(4)
2.91(4)
2.96(4)
2.92(4)
3.09(4)
3.01(4)
3.02(4)
3.10(4)
3.90(4)
2.94(4)
3.35(5)
3.43(5)
3.15(5)
3.27(5)
3.26(5)
3.37(5)
3.26(5)
3.29(5)
3.42(5)
3.37(5)
3.28(5)
158
171(4)
146
145
152
145
166(6)
146
166
155
143
143
168
161
146(3)
131(4)
131(4)
161(4)
157(3)
169
O1–H10ꢂ ꢂ ꢂO14i
N6B–H6B1ꢂ ꢂ ꢂO18ii
N1A–H1Aꢂ ꢂ ꢂO18ii
N1C–H1Cꢂ ꢂ ꢂOW1ii
N1D–H1Dꢂ ꢂ ꢂO22
O2–H20ꢂ ꢂ ꢂO24iii
N6B–H6B2ꢂ ꢂ ꢂO2
N6C–H6C1ꢂ ꢂ ꢂO15ii
N6C–H6C2ꢂ ꢂ ꢂO3
N6D–H6D1ꢂ ꢂ ꢂO22
N6D–H6D2ꢂ ꢂ ꢂO1
N6–H6Aꢂ ꢂ ꢂO20
b (Å)
c (Å)
a
(°)
b (°)
k (°)
V (A3)
Dcalc (mg mꢁ3
)
2.17
2.24
2.08
2.27
Z
8
l
(Mo K
F (000)
2h range
a
) (mmꢁ1
)
1.147
3072
2.14–26.0
31070
N6–H6Bꢂ ꢂ ꢂO7
2.01–28.30
11326
OW1–H1W1ꢂ ꢂ ꢂO17
OW2–H1W2ꢂ ꢂ ꢂO21
OW2–H1W2ꢂ ꢂ ꢂO11i
OW1–H2W1ꢂ ꢂ ꢂO19i
OW2–H2W2ꢂ ꢂ ꢂO16i
C2A–H2Aꢂ ꢂ ꢂO9iv
C2D–H2Dꢂ ꢂ ꢂO5v
C8–H8ꢂ ꢂ ꢂO25i
2.27
Reflection measured
Independent reflection
Reflection observed
(I > 2r(I))
Parameters
Final R1, wR2 (observed
data)
Goodness-of-fit (observed
data)
2.38 (4)
2.47(4)
2.07(3)
2.15(3)
2.44
2.52
2.33
2.44
2.54
2.56
2.54
2.48
2.54
2.42
2.33
4266; [Rint = 0.0631] 11010; [Rint = 0.0593]
2519
7559
235
813
R1 = 0.0651;
wR2 = 0.1218
1.069
R1 = 0.0523;
wR2 = 0.1232
1.002
168
148
150
135
146
135
141
153
C8A–H8Aꢂ ꢂ ꢂOW2vi
C8C–H8Cꢂ ꢂ ꢂO13
C8D–H8Dꢂ ꢂ ꢂOW1
C8C–H8Cꢂ ꢂ ꢂO13
C14–H14Aꢂ ꢂ ꢂN3Civ
C14–H14Bꢂ ꢂ ꢂO21vi
C21–H21Bꢂ ꢂ ꢂN3v
C23–H23Aꢂ ꢂ ꢂO8i
CCDC number⁄
659665
789919
170
172
2H, D2O exchange), 7.75 (s, 1H), 8.30 (s, 1H). 13C NMR (100 MHz,
DMSO-d6, 20.9 °C, TMS); d (ppm) 10.94, 22.78, 44.51, 118.76,
140.93, 149.58, 152.38, 155.97. Anal. Calc for C8H11N5; C, 54.22;
H, 6.26; N, 39.52; found C, 54.17; H, 6.22; N, 39.58.
a
Symmetry of A: (i) 1/2ꢁx,1/2+y,1/2ꢁz; (ii) ꢁx,1ꢁy,1ꢁz; (iii) ꢁ1+x,y,z; (iv) ꢁ1/
2ꢁx,1/2+y,1/2ꢁz; (v) 1/2ꢁx,ꢁ1/2+y,1/2ꢁz; (vi) ꢁx,1ꢁy, ꢁz.
2.4. Phenol oxidation assay
2.2. Procedure for metalation of 1
A spectrophotometric assay for 1 with three substrates, cate-
chol, 4-hydroxyanisole, and 4-t-butylcatechol, along with a natural
9-PA (0.1 g, 0.145 mmol) was dissolved in methanol (3 mL), fol-
lowed by addition of methanolic solution of copper chloride
(0.04 g, 0.3 mmol) and stir for 30 min. After this, solvent is evapo-
rated and the greenish solid thus obtained is washed with water
(4 ꢀ 5 mL) and methanol (4 ꢀ 5 mL) to remove any traces of unre-
monophenolic and diphenolic substrate, tyrosine and
L-DOPA
respectively (Scheme 1), was used to evaluate the catalytic behav-
iour of 1 towards phenol oxidation. 0.1 mM solution of 1 prepared
in methanol was used for assay. Detailed procedure for each sub-
strate is shown as under:
acted metal salt and ligand. After this, 20 lL of perchloric acid was
added and left for 1 h. The solvent is evaporated and product so ob-
tained is dried under high vacuum. HRMS: [4L+2Cu+2O+CH3OH]+
calculated: 882.2861, found 882.5978.
2.3.1. Catechol oxidation
Solutions of catechol (0.04–0.1 mM) were prepared in 50% aq.
methanol. 1% MBTH solution was prepared in methanol. The for-
mation of MBTH–quinone adduct was monitored at 500 nm
(e
= 3.25 ꢀ 104 Mꢁ1 cmꢁ1) [7].
2.3. EPR studies for 1
EPR spectra were recorded with a Varian E-109 C spectrometer
fitted with a quartz dewar for measurements at 120 K. The spectra
were calibrated with the help of DPPH (g = 2.0037).
2.3.2. 4-Hydroxyanisole (4HA) oxidation
Solutions of 4-HA (2–8 mM) were prepared in 50% aq. methanol
containing 2% DMF to ensure the solubility of MBTH-adduct. The

A.K. Mishra et al. / Polyhedron 52 (2013) 1385–1390
1387
Fig. 1. ORTEP diagram of the asymmetric unit of 1 [Cu2(LH+)4(OH)ꢁ2(ClO4)ꢁ6(H2O)2] with 35% ellipsoid probability.
Fig. 4. Representation of dihedral angle in 1 for adenine moieties positioned in cis
fashion in the dinuclear tetrameric motif. (a) When present on same copper ion. (b)
When present at different copper.
followed as described above. The quinone–MBTH adduct was mon-
itored at 494 nm (
e
= 3.25 ꢀ 104 Mꢁ1 cmꢁ1) [7].
2.3.4.
Solution of
N-ethylmorpholine buffer (pH 7.5, prepared in 80% aq. methanol).
10 L of hydrogen peroxide (30% w/v) was added just before the
L
-DOPA oxidation
Fig. 2. Hydrogen bonding interaction between N6H and N1H with solvent
molecules and anions connecting two discrete units.
L-DOPA (0.2–0.8 mM) were prepared in 0.01 M
l
MBTH adduct was monitored at 492 nm (
[8].
e
= 3.13 ꢀ 104 Mꢁ1 cmꢁ1
)
addition of catalyst. The formation of MBTH–quinone adduct was
monitored at 500 nm (
e
= 1.34 ꢀ 104 Mꢁ1 cmꢁ1) [9].
2.3.3. 4-t-Butylcatechol oxidation
2.3.5. Tyrosine oxidation
Solutions of 4-t-butylcatechol (5–20 mM) were prepared in 50%
Solution of tyrosine (0.4–1.0 mM) were prepared in 0.01 M
aq. methanol, containing 10% DMF. Similar assay conditions were
N-ethylmorpholine buffer (pH 7.5, prepared in 80% aq. methanol).
Fig. 3. (a) Representation of discrete unit in 1 where the highlighted portion reveals the presence of Cu2O2 entity. (b) and (c) Pictorial representation of important bond
distances and angles, respectively, in Cu2O2 entity as observed in crystal lattice of 1.

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A.K. Mishra et al. / Polyhedron 52 (2013) 1385–1390
Table 3
Comparison of bond distances (Å) and angles (°) of Cu2O2 core unit in 1 and met-II
form of copper-bound tyrosinase enzyme [7e].
Bond distance (Å)
Bond angle (°)
Atoms
Cu–Cu
1
Enzyme
Atoms
1
Enzyme
2.92
3.13
ꢃ2.05
ꢃ2.27
Cu–
N–Cu–
O–Cu–
N–Cu–N
lO–Cu
ꢃ97.3
ꢃ94.7
ꢃ82.6
ꢃ90.8
ꢃ99.74
ꢃ93.68
ꢃ76.28
ꢃ90.62
Cu–
lO
ꢃ1.94
lO
lO
Cu–N
ꢃ2.00
l
Scheme 3. Schematic representation of Cu2O2 core unit in: (a) met-II form of
copper-bound tyrosinase enzyme [7e]. (b) in 1.
10 lL of hydrogen peroxide (30% w/v) was added just before the
addition of catalyst. The formation of MBTH–quinone adduct was
Table 4
monitored at 500 nm (
e
= 1.34 ꢀ 104 Mꢁ1 cmꢁ1) [9].
Kinetic data for the catalytic activity of 1 towards phenol oxidation.
Tyrosine
4-Hydroxyanisole
1.71
38.46
0.90
2.37 ꢀ 10ꢁ4
2.28 ꢀ 10ꢁ4
3.94 ꢀ 10ꢁ4
2.62 ꢀ 10ꢁ4
2.53 ꢀ 10ꢁ4
4.37 ꢀ 10ꢁ4
2.3.6. X-ray crystallography
Single Crystal of 9-PA and 1 were coated with light hydrocarbon
oil and mounted in the 100 K dinitrogen stream of a Bruker SMART
APEX CCD diffractometer equipped with CRYO Industries low-tem-
perature apparatus and intensity data were collected using graph-
L-Dopa
Catechol
4-t-Butylcatechol
0.08
30.30
1.34 ꢀ 10ꢁ4
1.72 ꢀ 10ꢁ3
1.49 ꢀ 10ꢁ4
1.91 ꢀ 10ꢁ3
ite-monochromated Mo Ka radiation. The data integration and
reduction were processed with the SAINT software [10]. An absorp-
tion correction was applied [11]. Structures were solved by the di-
rect method using SHELXS-97 and refined on F2 by a full-matrix
least-squares technique using the SHELXL-97 program package
[12]. Non-hydrogen atoms were refined anisotropically. In the
refinement, hydrogens were treated as riding atoms using the SHEL-
XL default parameters. Crystal structure refinement parameters are
given in Table 1 whereas H-bonding parameters are provided in
Table 2.
A closer inspection of the crystal lattice revealed hydrogen
bonding interactions between N6H and protonated N1H of the ade-
nine moiety with perchlorate anions and water molecules, leading
to the formation of an extended lattice structure. The protonated
N1 nitrogen of one adenine moiety interacts with percholorate
oxygen; the N1H of the other adenine interacts with a water mol-
ecule, which is further hydrogen bonded to a percholorate anion.
In-space hydrogen bonding interactions between N6H and N1H
with perchlorate and water entities permits extended connection
of discrete units (Fig. 2).
The hallmark of this structure is the presence of a Cu2O2 core
unit, where each copper ion exhibits a distorted square pyramidal
3. Results and discussion
geometry, as indicated by corresponding
equatorial coordination sites are occupied by two N7 nitrogen
atoms from the adenine moieties and two -hydroxy oxygen
atoms, while the apical position is occupied by the oxygen atom
from perchlorate anion (Fig. 3).
s value being 0.23. The
Crystals suitable for X-ray diffraction study for 1 were grown in
a month by mixing methanolic solution of ligand with the metha-
nolic solution of copper chloride, in the presence of a few drops of
perchloric acid. Crystal analysis of 1 revealed a monoclinic system
with P21/n (No. 1401) as the space group. The asymmetric unit
l
It is notable that while N7 nitrogen of adenine residues, copper
consisted of two copper ions, bridged together through two l-hy-
ions and
l-hydroxy groups lie in one plane, the two perchlorate
droxyl groups, four N1 protonated adenine moieties coordinated to
metal center through N7 nitrogen, six perchlorate counter anions
and two water molecules, thereby resulting in a discrete dinuclear
motif (Fig. 1).
oxygen atoms are directed towards the opposite ends of the plane.
The steric demand of accommodating two adenine moieties at
each copper ion does not permit favorable stacking interactions
Scheme 2. Schematic representation of the formation of o-quinone–MBTH adduct.

A.K. Mishra et al. / Polyhedron 52 (2013) 1385–1390
1389
between adjacent adenine moieties, as evident from higher dihe-
dral angle between the planes passing through N1, N3, N7 and
N9 nitrogen atoms of adjacent nucleobases present in cis fashion
(ꢃ83–89°) (Fig. 4).
However, efforts were not made to fully optimize reaction con-
ditions or for the scale up of products.
A time-dependent formation of corresponding chromogenic
MBTH-adduct (formed as a result of reaction between MBTH and
the oxidation product, o-quinone) was monitored at their respec-
tive kmax values (Scheme 2). The adduct formation with the sub-
strates suggested the possibility of both monophenolase and
diphenolase catalytic activities for 1. Table 4 shows the Km, Vmax
and Kcat values for the monophenolic and diphenolic substrates
used, as determined from corresponding Lineweaver–Burk plots
(Fig. 5). It must be emphasized that exogenous oxidant was not
used for synthetic substrates in these reactions. In comparison,
the Michaelis–Menten parameters, Km, and Vmax for commercial
tyrosinase enzyme, using catechol as substrate, were reported as
3.88 mM and 5.29 ꢀ 10ꢁ4 mM minꢁ1, respectively [8].
We were aware of the fact that dinuclear copper motifs, bridged
by oxygen atoms, are integral part of tyrosinase enzyme active site,
as well as other type-3 copper enzymes. These enzymes bind oxy-
gen in a ‘side-on’ fashion, thereby activating it for the enzymatic
reaction [13]. Each copper ion present in the active site is also coor-
dinated to three histidine residues, thereby affording a trigonal
bipyrimidal geometry around the copper center. It is important to
mention that type-3 copper enzymes are EPR inactive [13]. Interest-
ingly, complex 1 was also found to be EPR-silent at 120 K, which
suggests for a strong coupling between the two copper atoms and
is consistent with doubly bridged structures previously reported
[14]. This led us to further compare salient structural details of
the copper center in present in redox copper enzymes and 1.
The dinuclear copper unit present in 1 was compared with the
dicopper present in the active site of met-II form of tyrosinase. It is
interesting to note that three histidiyl imidazole rings coordinate
to the copper center, to afford a penta-coordinated environment
(Scheme 3a), whereas perhaps owing to the bulk of adenine rings
only two ligands were accommodated around the copper center,
while perchlorate anion coordinates to the copper ions (Scheme
3b). Table 3 displays selected bond distances and bond angles in
1 and the met-II form of copper-bound tyrosinase enzyme [13e],
indicating remarkable similarities between the two copper centers.
Considerable studies focusing on synthetic models of dinuclear
copper core have been designed and tested for the mimicry of cat-
alytic activity present protein enzymes, with much success [15].
Thus, the structural similarity described above provided us an
impetus to analyse the catalytic potential of 1 for the oxidation
of monophenolic and diphenolic substrates. Three different mono-
phenolic and diphenolic substrates, such as catechol, 4-t-butyl-
catechol and 4-hydroxyanisole were employed, along with their
Low Km values were observed for simple diphenols namely cat-
echol and L-DOPA suggesting preferential binding of diphenols to 1.
Introduction of a bulky t-butyl group probably hinders the binding
interaction with 1, thus 4-t-butylcatechol exhibits higher Km value.
On the other hand 4-hydroxyanisole, a monophenol shows least
binding preferences when compared to other diphenols. However,
these binding preferences cannot be correlated with observed
velocities, thereby making it difficult to establish an unequivocal
relationship between binding preferences and the rate of reactions.
We decided to further confirm the oxidation of 4-hydroxyani-
sole by 1 via an alternate method. In this reaction, the oxidized
o-diquinone product was reacted with 1,2-phylenediamine
in situ and the appearance of resulting adduct was confirmed by
mass spectral analysis, thus once again indirectly proving oxida-
tion of a monophenol (ESI).
4. Conclusions
In conclusion, we have presented crystallographic features of
copper complex of 9-propyladenine exhibiting a discrete dicopper
center around Cu2O2 core, an arrangement remarkably similar to
natural analogues, tyrosine and L-DOPA.
Fig. 5. Lineweaver–Burk plot for Tyrosine,
L
-DOPA, Catechol, t-butylcatechol and 4-hydroxyanisole.

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A.K. Mishra et al. / Polyhedron 52 (2013) 1385–1390
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nol oxidation thus raising a possibility of catalytically competent
metal-nucleobase systems which perhaps preceded protein en-
zymes [16].
[12] G.M. Sheldrick, SHELXL-97, Program for Crystal Structure Refinement, University
of Göttingen, Göttingen, Germany, 1997.
Acknowledgment
[13] (a) A.G. Martin, F. Depoix, M. Stohr, U. Meissner, S. Hagner-Holler, K.
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We thank Single Crystal CCD X-ray facility at IIT-Kanpur. This
work is financially supported by an Indo-Spain project supported
by DST, India.
(b) T. Klabunde, C. Eicken, J.C. Sacchettini, B. Krebs, Nat. Struct. Biol. 5 (1998)
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Appendix A. Supplementary data
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Crystallogr., Sect. F66 (2010) 1101–1103.;
CCDC 659665 and 789919 contain the supplementary crystallo-
graphic data for this paper. 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: de-
posit@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.2012.05.013.
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