Crystallographic signatures of N6-methoxyadenine imino tautomer-silver complexes

Article abstract of DOI:10.1021/cg300231r

Detailed crystallographic analysis of four silver complexes of N9-benzyl-N⁶-methoxyadenine, 1, on the basis of three different counteranions and silver ion stoichiometry, is discussed in this article. 1 is a rare tautomer of adenine, which exhibits promutagenic behavior as it partly mimics hydrogen bond donor and acceptor properties of guanine and mispairs with cytosine. Complexes 2 and 4 exhibit discrete Ag₂L₂ dimer, while complex 3 shows two AgL₂ units in addition to a Ag ₂L₂ dimer, all in a head-to tail fashion. Complex 5, on the other hand, shows four AgL₂ units coordinated in a head-to-head fashion affording a three-dimensional lattice stabilized by CH??? F interactions. Various noncovalent interactions such as hydrogen bonding, CH-π interactions, argentophilic interactions, and Ag-π interactions stabilize these complexes.

Full text of DOI:10.1021/cg300231r

Article
pubs.acs.org/crystal
6
Crystallographic Signatures of N -Methoxyadenine Imino
Tautomer−Silver Complexes
Shruti Khanna and Sandeep Verma*
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016 (UP), India
*
S Supporting Information
6
ABSTRACT: Detailed crystallographic analysis of four silver complexes of N9-benzyl-N -methoxyadenine, 1, on the basis of
three different counteranions and silver ion stoichiometry, is discussed in this article. 1 is a rare tautomer of adenine, which
exhibits promutagenic behavior as it partly mimics hydrogen bond donor and acceptor properties of guanine and mispairs with
cytosine. Complexes 2 and 4 exhibit discrete Ag L dimer, while complex 3 shows two AgL units in addition to a Ag L dimer,
2
2
2
2 2
all in a head-to tail fashion. Complex 5, on the other hand, shows four AgL units coordinated in a head-to-head fashion affording
2
a three-dimensional lattice stabilized by CH···F interactions. Various noncovalent interactions such as hydrogen bonding, CH-π
interactions, argentophilic interactions, and Ag-π interactions stabilize these complexes.
6
INTRODUCTION
N -methoxyadenine derivative crystallizes out in its imino form,
mimicking a guanine base, while maintaining an amino−imino
equilibrium in solution. This change in structure explains its
ambiguous base pairing capacity with thymine and cytosine
leading to pyrimidine transition mutation, which incidentally is
■
Prototropic tautomerism in purine and pyrimidine nucleobases of
DNA has relevance in understanding DNA mutations and
1
ensuing phenotypic effects. Such mutations are a critical area of
concern for chemists, biochemists, and biologists alike as it is
estimated that human cells may experience considerable DNA
damage amounting to at least 2000−10000 times per day, but are
quickly repaired by protective cellular mechanisms. According
to the Watson−Crick base pairing rules, it is well-known that
adenine binds to thymine/uracil, while guanine pairs with
cytosine through hydrogen bonding interactions; however, the
formation of “rare tautomers” may cause deviation from the usual
base pairing schemes.
nucleobase complexes has revealed concerted intramolecular 1,3-
proton shift from exocylic N-atom to ring N-atoms. In addition,
several physical and quantum mechanical studies have been
reported in the literature investigating physicochemical properties
such as acidity and basicity, stability, hydration, and ionization
energies of nucleobase tautomeric forms resulting from metal ion
6
observed in DNA polymerase III readout when N -methox-
7
yadenine is present in the template strand during replication.
2
These experiments also suggest that anti-imino tautomer of
6
N -methoxyadenine predominates in B-DNA. Moreover, studies
of corresponding adenosine derivatives have also confirmed
3
8
promutagenic behavior of such tautomers.
We have extensively studied metalated purine nucleobases
and explored their novel supramolecular architectural motifs,
polymeric matrices and surface patterning using atomic
1b,4
X-ray crystal analysis of certain metal-
9
force microscopy. Herein, we report a modified synthesis of
6
N9-benzyl-N -methoxyadenine (Scheme 1), structure of its
10
imino tautomer in the solid state (Figure 1). This article
presents crystallographic studies concerning Ag(I)-stabilized
rare tautomer, where the multiple structures originate on the
basis of the nature of counteranions and silver stoichiometry.
4b,5
coordination and substitutions.
6
The choice of substitution at the adenine N position may
contribute to the formation of the rare imino tautomer.
Electron-donating groups such as amino, hydroxyl, and methoxy
at the exocyclic amino group shift the equilibrium toward a
Received: February 16, 2012
Revised: April 21, 2012
Published: April 24, 2012
6
higher ratio of imino tautomer favoring this tautomerism. The
©
2012 American Chemical Society
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Crystal Growth & Design
Scheme 1. Synthesis of N9-Benzyl N -Methoxyadenine (1)
Article
6
EXPERIMENTAL SECTION
■
6
1
. Synthesis of N9-Benzyl-N -methoxyadenine (1). Ligand 1
was synthesized in two steps starting from 6-chloropurine by the
following procedure (Scheme 1).
Step 1: In a typical procedure, 6-chloropurine (2 g, 1 equiv) was
dissolved in DMSO (25 mL), which was followed by the addition of
K CO (2.15 g, 1.2 equiv). To the reaction mixture, dropwise benzyl
2
3
bromide (1.5 mL, 0.95 equiv) was added and stirred at room
temperature for 10 h. Reaction mixture was then concentrated under
vacuum and the crude reaction mass was purified by silica-gel column
chromatography using 10−20% EtOAc: petroleum ether yielding 1.5 g
+
(
48%) of pure compound as white powder. HRMS: (M + H) =
1
calculated: 245.0594, observed: 245.0953. H NMR: (500 MHz,
CDCl , 25 °C, TMS) δ (ppm) 5.45 (s, 2H, CH ), 7.32 (d, 2H, Ar−H),
3
2
1
3
7
.36 (t, 3H. Ar−H), 8.09 (s, 1H, C8−H), 8.79 (s, 1H, C2−H). C
NMR (125 MHz, CDCl , 25 °C, TMS); δ (ppm) 47.86, 127.90,
3
1
28.86, 129.25, 131.46, 134.45, 144.93, 151.11, 151.81, 152.15.
Step 2: N9-benzyl-6-chloropurine (4 g, 1 equiv) was suspended in
butanol (50 mL). To this were then added O-methyl hydroxylamine
9
6
Figure 1. Prototropic tautomerism of N -benzyl-N -methoxyadenine
1. (a) Amino and imino tautomers; (b) syn- and anti-imino tautomers.
hydrochloride (6.82 g, 5 equiv) and triethyl amine (13 mL, 5.75 equiv).
1
Figure 2. H NMR of ligand 1. Inset displaying the imino−amino ratio difference for the chemical shift values of 5.23 and 5.37.
3
026
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Article
Table 1. Crystal Structure Refinement Parameters for 1−5
identification code
ligand 1
complex 2
complex 3
complex 4
complex 5
empirical formula C H N O
C H Ag N O
C H Ag N O
C H Ag Cl N O
C H AgF N O P
26 28 6 10 3
1
3
13
5
26 26
2
12
8
78 86
4
34 22
26 26
2
2
10 10
Mr
255.28
850.33
2281.27
925.21
781.42
crystal system
space group
triclinic
triclinic
monoclinic
P1 21/n1
22.321(4)
12.638(3)
31.194(4)
90
triclinic
tetragonal
P42/n
30.163(5)
30.163(5)
6.574(5)
90
P1
̅
P1
̅
P1
̅
9.915(2)
́
a (Å)
10.0702(19)
11.277(2)
11.358(2)
88.658(4)
87.650(4)
77.547(3)
1259.2(4)
4
7.2331(10)
7.9989(11)
13.7505(18)
79.317(2)
78.741(2)
71.096(2)
731.74(17)
1
́
b (Å)
9.942(2)
́
c (Å)
16.461(3)
101.292(5)
98.813(4)
93.590(3)
1565.4(6)
2
α (deg)
β (deg)
γ (deg)
95.07(4)
90
90
90
́
3
volume (Å )
8765.2(29)
4
5981(5)
8
Z
D (Mg m−3)
1.347
1.930
1.729
1.963
1.736
3152
x
F(000)
μ (mm−1)
536
424
4616
920
0.092
1.412
0.975
1.496
0.814
θ range for data
collection (deg)
2.47−26.0
2.72−28.38
4.09−25.03
2.09−28.34
4.11−25.03
limiting indices
−12 → h → 12, −13 → k −9 → h → 9, −10 → k −25 → h → 26, −14 → k −13 → h → 12, −13 → k −24 → h → 35, −35 → k
→
12, −14 → l → 11
→ 6, −18 → l → 15
4752
→ 15, −37 → l → 28
44855
→ 12, −18 → l → 21
10296
→ 35, −7 → l → 7
29846
reflections
collected
6999
unique reflections 4787
R(int) 0.0219
completeness to θ = 25.00, 97.8
3430
15396
7354
5250
0.0178
0.0772
0.0311
0.1342
= 25.00, 97.5
0.7752/0.7372
3430/0/218
= 25.00, 99.5
0.8440/0.8068
15396/9/1273
= 28.34, 94.0
0.7745/0.7247
7354/0/429
= 25.00, 99.4
0.8673/0.8348
5250/3/432
Tmax/Tmin
0.9855/0.9819
4787/0/345
data/restraints/
parameters
GOF on F2
1.172
1.260
1.024
1.116
1.033
R1 and R2
0.0518, 0.1392
0.0484, 0.1037
0.0589, 0.1296
0.0667, 0.1594
0.0704, 0.1735
[
I > 2σ(I)]
R1 and R2
all data)
0.0684, 0.1740
0.0749, 0.1725
0.0935, 0.1514
0.1096, 0.2420
0.1161, 0.2075
(
largest diff peak
and hole (e·A−3)
0.489 and −0.506
2.184 and −2.900
2.299 and −0.762
2.015 and −2.009
1.928 and −0.693
The reaction mixture was refluxed at 120 °C and the progress of the
reaction was monitored. Heating was stopped after 6 h and solvent
was removed under a vacuum. The solid so obtained was washed with
water (2 × 50 mL) and extracted into ethyl acetate (3 × 100 mL). The
organic layer was collected, dried, and concentrated for further purifi-
3. Synthesis of Complex 3 [C H Ag N O ]. The complex
78 86 4 34 22
was grown by slow evaporation of ligand 1 (1 equiv) and AgNO
3
(2 equiv) solutions in methanol. Violet colored crystals were obtained
+
in a month’s time (yield: 30%). HRMS: [L + H] : 256.1226 (Calcd.:
+
+
2
6
56.1198), [L + Ag] : 362.0172 (Calcd.: 362.0171) and [2 L + Ag] :
17.1243 (Calcd.: 617.1291).
cation using silica-gel column chromatography with CHCl . Pure
3
4
. Synthesis of Complex 4 [C H Ag Cl N O ]. The
26 26 2 2 10 10
compound 1 was obtained as a white powder. Yield: 3.5 g (84%).
+
equimolar reaction of AgClO (1 equiv) and ligand 1 (1 equiv) in
4
HRMS: (M + H) = calculated: 256.1198, observed: 256.1196. m.p.:
MeOH gave the violet colored solution which under slow evaporation
Decomposes with melting at 227−229 °C.
for 2−3 weeks gave crystals of complex 4 (yield: 50%). HRMS: [L +
NMR. Solution state amino-imino tautomerism in N9-substituted
+
+
H] : 256.1191 (Calcd.: 256.1198), [L + Ag] : 362.0191 (Calcd.:
6
N -alkoxyadenines has been studied previously by proton nuclear
+
3
62.0171) and [2L + Ag] : 617.1299 (Calcd.: 617.1291).
. Synthesis of Complex 5 [C H AgF N O P]. The reaction
6,10,14
14c
magnetic resonance,
and ultraviolet and infrared spectroscopy,
5
26
28
6
10
3
clearly indicating domination of imino tautomer in polar solvents such
of freshly prepared AgPF (1 equiv) solution with ligand 1 (1 equiv) in
6
6,14c
as DMSO or water.
Such observations were also made in the case
MeOH and subsequent slow evaporation afforded brown crystals
+
of 1 by determining differences in chemical shift values and integrals
of the two tautomeric forms (Figure 2). The peak ratio of 4:1 for the
protons of the imino tautomer with respect to the amino tautomer
of complex 5 (yield: 42%). HRMS: [L + H] : 256.1118 (Calcd.:
+
256.1198) and [2L + Ag] : 617.1293 (Calcd.: 617.1291).
1
as observed in H NMR spectra indicates its greater stability and
CRYSTAL STRUCTURE DETERMINATION AND
REFINEMENT
There was distinct color in most of the crystals of complexes
■
1
predominance. H NMR (DMSO-d ) 11.16 (br s, 0.95 H, H -N1),
6
i
1
1
0
0.90 (br s, 0.23 H, H -N6), 8.34 (s, H -2), 8.28 (s, H -8), 7.92 (s,
a a a
.0 H, H8), 7.53 (br s, 1.1 H, H 2), 7.28 (m, 6.83 H, Ar−H), 5.37 (s,
i
i
2
−5. This observed coloration could be attributed to silver ion
.5 H, a-CH ), 5.23 (s, 2.03 H, i-CH ), 3.73 (s, 0.85 H, a-OMe), 3.71
2
2
complexation of neutral imino tautomer. UV−vis titrations
(
s, 3.08 H, i-OMe) (i: imino, a: amino).
. Synthesis of Complex 2 [C H Ag N O ]. Block-shaped
−4
were conducted using 10 M solution of ligand 1 in methanol
2
26
26
2
12
8
+
against Ag ions. An increase in absorbance (λ = ∼465 nm) was
violet color crystals of the complex were obtained in a week’s time
from their methanolic solution by dissolving stoichiometric amounts
+
noted with the addition of increasing equivalents of Ag ions
of AgNO (1 equiv) and ligand 1 in methanol (yield: 63%). HRMS:
(Figure S1, Supporting Information).
Crystals were coated with light hydrocarbon oil and mounted
in the 100 K dinitrogen stream of a Bruker SMART APEX
3
+
+
[
L + H] : 256.1173 (Calcd.: 256.1198), [L + Ag] : 362.0120 (Calcd.:
+
362.0171) and [2 L + Ag] : 617.1165 (Calcd.: 617.1291).
3
027
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Crystal Growth & Design
Article
Figure 3. (a) ORTEP diagram of 1 at 30% probability level; (b) syn-imino tautomer; (c) ribbon formation in 1 as viewed along the a-axis showing
two crystallographically independent units.
1
3
program package. Non-hydrogen atoms were refined
anisotropically. In the refinement, hydrogens were treated as
riding atoms using the SHELXL default parameters. In the case
of 3 and 5, water molecules were found trapped in the lattice
and the hydrogen atoms of these water molecules are located
on the Fourier map and constraints were applied to fix the
O−H distance and H−O−H angle. Crystal structure refinement
parameters are given in Table 1. All of these software packages
were the integrated WINGX software package. CCDC Nos.
8
56027, 856028, 856029, 856030 contain the supplementary
crystallographic data for this paper. Copies of this information
can be obtained free of charge upon application to CCDC,
1
3
2 Union Road, Cambridge CB21EZ, U.K. (fax +44−1223/
36−033; e-mail deposit@ccdc.cam.ac.uk).
RESULTS AND DISCUSSION
Crystal Structure Analysis of 1. The crystal structure of
ligand 1 has already been reported in the literature; however,
a brief description of its solid state structure is discussed here
to provide a background of the present work. Crystals suit-
able for X-ray crystallographic analysis were obtained by slow
evaporation of methanolic solution of 1. Refinement data
■
Figure 4. (a) ORTEP diagram of 2 showing the asymmetric unit of
the cell at 30% probability level; (b) representation of tetra-
coordinated geometry around silver ion and Ag···Ag interaction with
a distance of 2.92 Å.
10
CCD diffractometer equipped with CRYO Industries low-
temperature apparatus and intensity data were collected using
graphite-monochromated Mo−Kα radiation. The data integra-
̅
suggest that 1 crystallized in a triclinic unit cell (P1) consisting
of two crystallographically independent molecules (Figure 3a).
The distinction between these two molecules lies in the
difference of orientation of the benzyl rings at the N9 position
11
tion and reduction were processed with SAINT software. An
12
absorption correction was applied. Structures were solved
2
10
by the direct method using SHELXS-97 and refined on F by
(Figure 3c). The crystal structure of 1 clearly reveals the
a full-matrix least-squares technique using the SHELXL-97
occurrence of the syn-imino tautomer stabilized by the
3
028
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Crystal Growth & Design
Article
Figure 5. (a) Hydrogen bonded lattice of 2, also depicting π−π interactions (benzyl rings are removed for clarity); (b) part of crystal lattice
depicting CH···π stacking interactions (nitrate ions are omitted for clarity).
6
intramolecular hydrogen bonding between N −OMe and
N1−H (Figure 3b). The bond distances of 1.39 Å between
6
N1 and C6 and 1.29 Å between N and C6 suggest a single
bond character for N1−C6 and a double bond character for
6
the N −C6 bond. It is known that syn orientation of imino
6
6,10,15
tautomer dominates in N9-substitued-N -alkoxyadenines.
The crystal lattice of 1 is composed of neatly packed adenine
ribbons with alternately arranged two crystallographically
independent molecules, which are stabilized by three hydrogen
bonds through both Watson−Crick and Hoogsteen faces. These
unusual hydrogen bonding interactions result from prototropic
6
tautomerism where N −H shifts to the N1 ring nitrogen,
thereby creating altered donor and acceptor sites. This anomalous
hydrogen bonding scheme causes slight differences in the H-bond
distances between atoms (Table 3). Interestingly, the orientation
of the syn-imino tautomer remains intact even in metal com-
plexes, where the coordinating silver ion is positioned in an anti-
orientation in four crystal structures.
Figure 6. ORTEP diagram of the asymmetric unit of complex 3 at 20%
probability illustrating six ligand molecules coordinated to four silver
ions neutralized by four nitrate counteranions and four unbound water
molecules.
The preponderance of amino to imino tautomer, in the
neutral form of adenine nucleobase, estimated in the range of
4
5
1
0 −10 , could be modulated in the presence of coordinating
16
metal ions. So far, there have been a limited number of
reports concerning solution or solid state structure of neutral
adenine tautomer exhibiting interaction with metal ions.
17
On the basis of prior observations and our ongoing work on
adenine−silver interactions, we decided to elucidate solid state
6
structures of N9-benzyl-N -methoxyadenine (1) in the
presence of silver ions. These studies were also intended to
6
provide evidence for the importance of N , N7 coordination in
4a
stabilizing the adenine neutral imino tautomer.
Crystal Structure Analysis of Complex 2. Block-shaped
violet colored crystals, suitable for single crystal X-ray analysis,
were grown in a week by slow evaporation from the methanolic
solution of ligand 1 (1 equiv) and AgNO (1 equiv). Crystal
3
data refinement suggested that 2 [C H Ag N O ] crystallizes
26
26
2
12
8
̅
in a triclinic space group “P1”. The asymmetric unit of the cell
is composed of one ligand coordinated to a silver ion which is
neutralized by a nitrate ion (Figure 4a). A closer inspection of
crystal lattice revealed that the ligand 1 supports a bidentate
6
coordination mode, where N and N7 ring nitrogens coordinate
to silver ions in a head-to-tail fashion resulting in a dinuclear
dimeric species (Figure 4b).
The coordination geometry around the tetra-coordinated
silver ions may be described as distorted tetrahedron wherein
Ag(I) was found coordinated to N of one ligand (2.216 Å),
N7 of other ligand (2.295 Å), and to the two oxygen atoms of
nitrate counteranion (2.527 Å, 2.546 Å respectively). However,
Figure 7. Part of crystal lattice of 3 illustrating the weak out-of-plane
coordination of Ag1 and Ag2 to N7C and N7B in AgL unit thereby
2
6
resulting in a distorted tetrahedral geometry around these silver ions as
shown in the highlighted region. Linear coordination of Ag3 and Ag4
is also shown.
3
029
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Article
Table 2. Selected Bond Lengths (Å) and Bond Angles (°) for Complex 3
Bond Lengths (Å)
Ag(1)−N(6A)
Ag(1)−N(6B)
Ag(1)−N(7B)
Ag(1)−N(7C)
2.21(48)
2.19(47)
2.85(47)
2.81(48)
Ag(2)−N(6C)
Ag(2)−N(6D)
Ag(2)−N(7B)
Ag(2)−N(7C)
2.22(48)
2.22(48)
2.70(46)
2.73(48)
Bond Angles (deg)
Ag(1)−N(7B)−Ag(2)
Ag(1)−N(7C)−Ag(2)
N(6A)−Ag(1)−N(7C)
81.37(137)
81.53(137)
84.36(156)
N(6B)−Ag(1)−N(7B)
N(6C)−Ag(2)−N(7C)
N(6D)−Ag(2)−N(7B)
72.14(155)
73.62(161)
87.15(161)
water molecules (Figure 6). However, as seen in the ORTEP
diagram, hydrogens for O2W have not been assigned as they
are not unequivocally located on the Fourier map due to weakly
diffracting crystal. Detailed crystal structure analysis of complex
3
revealed an unusual coordination of nitrogen atoms to silver
ions as described below.
The remarkable feature of complex 3 is the presence of two
sets of crystallographically unique silver ions (Ag1, Ag2 and
Ag3, Ag4). ORTEP diagram reveals an interesting coordination
pattern: two discrete AgL units are present, coordinated in a
2
6
head-to-tail fashion via N purine nitrogen, in addition to an
Ag L unit. The latter resembles complex 2; however, geometry
2
2
around the silver ions is slightly different with the presence of
non-interacting nitrate ions, resulting in a linear geometry. This
6
F
discrete dimer is defined by distance parameters of Ag(3)−N :
6
E
2
.112 Å, Ag(3)−N7E: 2.121 Å, Ag(4)−N : 2.108 Å and
6F
Ag(4)−N7F: 2.110 Å, and angle parameters of N −Ag(3)−
6E
N7E: 169.7° and N −Ag(4)−N7F: 171.1°. Further, the observed
Figure 8. Part of the crystal lattice of 3 displaying a columnar structure
arising out of extensive hydrogen bonding network between N1
hydrogens of purine and nitrate ions and water molecules (black
dotted line), C8 hydrogens with nitrate ions only (pink dotted line)
and between nitrate ions and water molecules.
Ag···Ag interaction at 2.809 Å is stronger compared to complex
2
at 2.919 Å.
Two AgL units coordinate each other through weak, out-of-
2
plane interactions of silver ions to N7 nitrogens of purine
(
shown in dotted lines in Figure 7). These silver ions can be
6
A
assumed to adopt a linear geometry with angles N −Ag(1)−
the presence of strong Ag···Ag interactions with a distance of
6B
6C
6D
N : 169.33° and N −Ag(2)−N : 166.14°, while the bond-
2
.919 Å, much less than the sum of their van der Waals radii
6A
6B
2+
ing distances are Ag(1)−N : 2.207 Å, Ag(1)−N : 2.188 Å,
(
3.40 Å), results in an interesting argentophilic (Ag ) dimers
2
18
6C
6D
Ag(2)−N : 2.222 Å, and Ag(2)−N : 2.221 Å. However, two
N7 nitrogens, N7B and N7C, found in proximity to silver ions,
are able to establish weak interactions with the distances
Ag(1)−N7B: 2.850 Å, Ag(1)−N7C: 2.810 Å, Ag(2)−N7B:
formed by the two silver ions.
The crystal lattice is further stabilized due to intermolecular
hydrogen bonding interactions between N1H and O2 of the
nitrate counteranion and C8H and O3 of the nitrate
counteranion, as confirmed by hydrogen-bonding parameters
given in Table 3. Significant π interactions are also implicated
for the reinforcement and overall stability of the crystal lattice.
Complex 2 exhibits face-to-face π−π interactions between
modified adenine rings with a centroid-to-centroid distance of
2
.699 Å, and Ag(2)−N7C: 2.732 Å, which are shorter than the
sum of their van der Waals radii of 3.27 Å. This results in
a long-range, out-of-plane coordination leading to a distorted
tetrahedral geometry around silver ions. Selected bond distances
and bond angles of complex 3 are given in Table 2.
The crystal structure of complex 3 illustrates the critical
role played by hydrogen bonding in stabilizing overall crystal
packing. The two units in the lattice, AgL and Ag L ,
are represented in two different color codes for distinct
visualization of hydrogen bonding patterns (Figure 8). These
interactions mainly occur via purine N1−H and C8−H
hydrogens with nitrate ions and water molecules. N1 hydrogens
of all six purines are involved in hydrogen bonding with both
nitrate ions and water molecules (black dotted line), and C8
hydrogens are exclusively involved in hydrogen bonding
interactions with nitrate ions (pink dotted line) (Figure 8).
Both nitrate ions and water molecules in turn also indulge in
hydrogen bonding among themselves. Isolated oxygen atom
also shows short contact with the nitrate ion (2.57−3.04 Å).
Such myriad network of hydrogen bonding interactions across
the crystal lattice could be visualized as a columnar structure,
20
3.341 Å (Figure 5a). Additionally, the presence of intermo-
lecular CH···π interaction (2.59 Å), via methyl in the methoxy
group of one unit to the phenyl rings of the other unit, is
observed within acceptable interacting distances with a C−H−
X angle of 174.46°, where X is the centroid of the phenyl ring
2 2 2
1
9
(
Figure 5b).
Crystal Structure Analysis of Complex 3. Role of the
metal-to-ligand ratio on the coordination behavior of the ligand
was probed by varying the M:L stoichiometry. Complex 3
was prepared by employing 2:1 stoichiometry of 1:AgNO and
3
violet-colored crystals were obtained through a slow evapo-
ration process in few weeks' time. X-ray crystallographic
analysis revealed that complex 3 [C H Ag N O ] crystal-
7
8
86
4
34 22
lizes in a monoclinic space group “P1 21/n1”. The asymmetric
unit consists of six ligand molecules coordinated to four Ag(I)
ions, neutralized by four nitrate ions, and four non-coordinated
3
030
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Crystal Growth & Design
Table 3. Hydrogen Bonding Table for Ligand 1 and Complexes 2−5
Article
a
a
D−H···A
symmetry of A
D−H
H···A
D−A
∠D−H···A
Ligand 1
N(1)−H(1)···N(7′)
N(1′)−H(1′)···N(7)
C(2)−H(2)···N(6′)
C(2′)−H(2′)···N(6)
1 − x, −y, 1 − z
0.86
0.86
0.93
0.93
2.10
2.07
2.51
2.50
2.935
2.884
3.380
3.351
165
159
156
152
1 − x, −y, −z
1 − x, −y, 1 − z
1 − x, −y, −z
Complex 2
Complex 3
N(1)−H(1)···O(2)
C(8)−H(8)···O(3)
1 − x, 1 − y, −z
−1 + x, y, z
0.86
0.93
2.19
2.51
2.854
3.232
133
135
N(1A)−H(1A)···O(1W)
N(1B)−H(1B)···O(21)
N(1C)−H(1C)···O(14)
N(1D)−H(1D)···O(3W)
N(1E)−H(1E)···O(2W)
N(1F)−H(1F)···O(4W)
O(1W)−H(1W1)···O(13)
O(1W)−H(1W1)···O(23)
O(1W)−H(2W1)···O(34)
O(4W)−H(1W4)···O(12)
O(4W)−H(1W4)···O(22)
O(4W)−H(2W4)···O(31)
O(3W)···H(1W3)···O(22)
O(3W)−H(1W3)···O(22)
O(3W)−H(2W3)···O(11)
C(8A)−H(8A)···O(32)
C(8B)−H(8B)···O(13)
C(8B)−H(8B)···O(33)
C(8C)−H(8C)···O(31)
C(8D)−H(8D)···O(24)
C(8E)−H(8E)···O(12)
C(8F)−H(8F)···O(34)
1 − x, 1 − y, −z
1/2 − x, −1/2 + y, 1/2 − z
−x, 1 − y, 1 − z
1/2 − x, 1/2 + y, 1/2 − z
−1/2 + x, 1/2 − y, 1/2 + z
1/2 − x, −1/2 + y, 1/2 − z
0.86
0.86
0.86
0.86
0.86
0.86
0.84
0.84
0.85
0.84
0.84
0.83
0.83
0.83
0.85
0.93
0.93
0.93
0.93
0.93
0.93
0.93
1.94
1.96
2.00
2.03
1.97
1.92
2.01
2.50
2.03
2.19
2.42
2.09
2.20
2.24
2.04
2.52
2.57
2.32
2.33
2.30
2.23
2.52
2.746
2.762
2.802
2.826
2.648
2.695
2.826
3.125
2.853
2.976
3.109
2.918
2.884
3.036
2.876
3.263
3.248
3.189
3.187
3.159
3.108
3.364
157
156
155
153
134
149
165
132
164
156
140
170
139
162
170
137
130
155
154
152
157
151
1/2 − x, 1/2 + y, 1/2 − z
1/2 − x, 1/2 + y, 1/2 − z
1/2 − x, 1/2 + y, 1/2 − z
1/2 − x, −1/2 + y, 1/2 − z
1/2 − x, −1/2 + y, 1/2 − z
1/2 − x, −1/2 + y, 1/2 − z
1/2 − x, −1/2 + y, 1/2 − z
−1/2 + x, 3/2 − y, −1/2 + z
1 − x, 2 − y, 1 − z
1 − x, 1 − y, 1 − z
Complex 4
N(1)−H(1)···O(2′)
N(1′)−H(1′)···O(2)
C(2′)−H(2′)···O(4)
C(8)−H(8)···O(3)
C(8′)−H(8′)···O(4′)
1 − x, 1 − y, −z
1 − x, −y, 1 − z
1 − x, −y, 1 − z
0.86
0.86
0.93
0.93
0.93
2.28
2.08
2.58
2.35
2.44
2.963
2.890
3.364
3.206
3.124
137
156
142
153
130
−1 + x, y, z
Complex 5
N(1)−H(1)···F(3)
−y, −1/2 + x, 1/2 + z
x, y, −1 + z
y, 1/2 − x, 1/2 − z
0.86
0.86
0.86
0.86
0.93
0.93
0.93
0.96
2.30
1.98
2.01
2.09
2.50
2.41
2.30
2.46
2.993
2.794
2.857
2.952
3.286
3.157
3.195
3.375
138
156
165
177
143
137
161
160
N(1′)−H(1′)···O(1W)
O(1W)−H(1W)···F(2)
O(1W)−H(2W)···N(6′)
C(8)−H(8)···F(1)
C(8)−H(8)···F(4)
C(8′)−H(8′)···F(1)
C(16′)−H(16B)···F(3)
1/2 − x, 1/2 − y, z
1/2 − x, 1/2 − y, z
1/2 − x, 1/2 − y, z
−y, −1/2 + x, −1/2 + z
a
Where D is donor and A is acceptor, the bond lengths are in Å and angles are in deg.
where the outer periphery is composed of water molecules and
nitrate anion, while the inner core comprises of silver-
coordinated hydrophobic purine bases (Figure 8). The signifi-
cant hydrogen bonding parameters are given in Table 3.
The stability of crystal lattice is further enhanced by
remarkable Ag···π interactions encountered in the complex
containing AgL and Ag L units show an interplanar separation
2 2 2
of 3.36 Å (yellow and orange plane) and 2.99 Å (orange and
purple plane), suggesting close contact and lattice stabilization
(Figure 9b).
Crystal Structure Analysis of Complex 4. Replacement
of counteranion was probed for its effect on the coordina-
tion behavior of ligand 1 in this complex. Mixing equimolar
2
1
(
Figure 9a). These interactions bring two crystallographically
different subunits, AgL and Ag L , close to each other thereby
methanolic solution of AgClO (1 equiv) and 1 (1 equiv)
2
2
2
4
reinforcing lattice stability. It is observed that Ag2 and Ag3
are in proximity to the adjacent purine imidazole rings, at
respective distances of 3.66 Å and 3.46 Å, as can be seen in
Figure 9a. It is also worth mentioning here that the planes
resulted in a violet-colored solution, which under slow evapora-
tion for a few weeks afforded crystals of complex 4
[C H Ag Cl N O ]. Careful inspection of the crystal data
26
26
2
2
10 10
̅
confirmed triclinic space group “P1”. The asymmetric unit of
3
031
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Crystal Growth & Design
Article
Figure 9. Part of the crystal lattice of 3 depicting (a) Ag···π interactions; (b) interplanar separation.
Figure 10. (a) ORTEP diagram of 4 showing asymmetric unit of the cell at 30% probability level; (b) linear geometry of silver ions with a Ag···Ag
distance 2.803 Å.
Figure 11. Part of crystal lattice of 4 depicting (a) hydrogen bonding interactions forming a 1D-polymeric sheet (benzyl groups are omitted for
clarity); (b) π−π stacking interactions between centroids of adenine rings and also between benzyl rings and six-membered ring of the adenine
moiety.
the lattice comprises of two crystallographically unique units
wherein two ligand molecules coordinate to two silver ions,
neutralized by perchlorate anions (Figure 10a). Crystallo-
graphic analysis revealed a bidentate coordination mode via
The stability of the crystal lattice is enhanced due to inter-
molecular hydrogen bonding interactions of purine N1, C8, and
C2 hydrogens. These interactions, mediated through bridg-
ing perchlorate ions, result in a one-dimensional polymeric
sheet along the a-axis (Figure 11a). Moreover, extensive π−π
stacking interactions are observed between adjacent purines
with a centroid distance of 3.59 Å and between the benzyl
substituent and six-membered ring of the purine, with a centroid
distance of 3.51 Å (Figure 11b). The important H-bond parameters
are summarized in Table 3.
6
purine N and N7 nitrogens, leading to Ag L dimeric units
2
2
similar to complex 2. However, unlike complex 2, complex 4
exhibited stronger argentophilic interactions with an unusually
shorter Ag···Ag interaction distance of 2.803 Å. The silver ions
in complex 4 display linear coordination, similar to the Ag L
2
2
6
subunit in complex 3, through N7′ (2.114 Å) and N nitrogen
(
(
2.130 Å), without participation of perchlorate counteranions
Figure 10b).
Crystal Structure Analysis of Complex 5. Complex 5,
−
containing PF , differs from the above complexes in terms of
6
3
032
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Crystal Growth & Design
Article
Figure 12. (a) Part of the 3-D crystal lattice of complex 5; (b) enlarged view of (a) illustrating hydrogen bonding and π−π interactions (color code:
P: pink, F: green).
bifurcated hydrogen bonding with C8H of the other ligand
(
Figure 12b). Purine N1 hydrogens and water also participate
in intermolecular hydrogen bonding interactions through
fluoride ions of PF . Moreover, π-interactions between the
−
6
benzyl ring and six-membered ring of the adjacent purine also
contribute to lattice stability (Figure 12b).
Each discrete AgL unit further extends along the c-axis
2
forming an infinite 1D-coordination polymeric chain via
6
N1H···OH and HOH···N hydrogen bonding. Additionally,
2
π−π interactions between five-membered rings of the purine
framework stabilize the polymeric chain as shown in Figure 13a.
Interestingly, like in complex 3, these polymeric chains display
unique intermolecular Ag···π interactions but with six-membered
rings of the purine framework with distances 3.48 and 3.84 Å
21,22a
(
Figure 13b).
These noncovalent interactions cumulatively
Figure 13. (a) Part of the crystal lattice of complex 5 showing 1D-
reinforce the overall supramolecular organization of 5.
coordination band through H-bonds between N1−H···OH and
2
6
These crystallographic studies highlight the absolute
HOH···N and π−π interactions; (b) Ag···π interactions between Ag
and six-membered rings of purine framework in two AgL2 units
6
preference of silver complexes toward N −Ag−N7 bidentate
6
(
benzyl rings are removed for clarity).
coordination over the N −Ag−N1 case. In an exhaustive
́
computational study, Schreiber and Gonzalez described that
the affinity of silver ions for N7 coordination in terms of gas
phase energy calculations. It was found that silver ion affinity
non-coordinating behavior of its counteranion. 5 [C H AgF -
26
28
6
N O P] belonged to the tetragonal system in “P42/n” space
10
3
6
9
for the N ,N -unsustituted neutral adenine imino tautomer is
∼75 kcal/mol, which is ∼24 kcal/mol higher compared to
group and exists as a AgL complex in the crystalline state.
2
6
Silver ions bridge two ligand molecules through linear N
5b
other possible canonical tautomeric complexes. Notably, the
−Ag−N7 connectivity, in a head-to-head fashion exhibiting
Ag−N7 distance in all four cases (2−5), described in this paper,
a two-coordinated linear geometry around the silver ion.
The asymmetric unit of lattice consists of an unbound PF6−
counterion and a free water molecule, both playing an
important role in determining overall stability of the crystal
lattice. The extensive hydrogen bonding interactions due to the
presence of strong donor and acceptor groups in the purine
ring, PF6− and water molecules, give rise to a complex three-
dimensional (3-D) framework (Figure 12a). Further analysis of
6
was longer compared to Ag−N distances, suggesting that the
latter is a highly stable coordination. This variance matches well
with the calculated distances for silver-neutral adenine imino
5b
complexes, and, more importantly, it could be inferred that a
6
stable bidentate N −Ag−N7 coordination augments stability of
imino tautomer upon silver ion complexation.
CONCLUSION
the lattice revealed that AgL units are held together in the
■
2
6
crystal lattice by CH···F interactions between inorganic fluoride
ions of PF6− and the purine C8 and methoxy group hydrogens,
within the acceptable limit of 2.6 Å for CH···F interactions
In summary, affinity of N9-benzyl-N -methoxyadenine toward
tautomerization and its complexation with silver were studied
by X-ray crystallography. Diverse crystallographic patterns were
obtained by varying the stoichiometry and counteranions of the
corresponding silver salt. We have presented a detailed analysis
of these complexes and the significant role played by
2
2
(
see Table 3). Interestingly, C8−H also exhibits bifurcated
hydrogen bonding with two different fluorine atoms of a PF ¯
group, while one of these fluorine atoms in turn displays a
6
3
033
dx.doi.org/10.1021/cg300231r | Cryst. Growth Des. 2012, 12, 3025−3035

Crystal Growth & Design
Article
noncovalent interactions such as hydrogen bonding, π-stacking,
and argentophilic interactions. An interesting complexation
behavior was also observed in complex 3, where six ligand
molecules coordinated to four silver ions to give Ag L and two
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2
2
AgL structures. Such a complexation behavior when translated
2
in a biological scenario may provide valuable insights into the
mutagenic behavior of these rare tautomers.
Verma, S. Inorg. Chim. Acta 2009, 362, 855−860. (i) Mishra, A. K.;
Purohit, C. S.; Verma, S. Cryst. Eng. Comm. 2008, 10, 1296−1298.
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ASSOCIATED CONTENT
Supporting Information
X-ray crystallographic data in CIF format and additional
experimental data for the complexes. This information is
available free of charge via the Internet at http://pubs.acs.org/.
CCDC contains the supplementary crystallographic data for
this paper with a deposition number of CCDC 856027
complex 2), 856030 (complex 3), 856028 (complex 4) and
56029 (complex 5). Copies of this information can be
obtained free of charge on application to CCDC, 12 Union
Road, Cambridge CB21EZ, UK. [Fax: +44−1223/336−033;
E-mail: deposit@ccdc.cam.ac.uk].
■
*
S
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AUTHOR INFORMATION
Corresponding Author
E-mail: sverma@iitk.ac.in.
■
*
(
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Notes
(
The authors declare no competing financial interest.
(
2
ACKNOWLEDGMENTS
■
We acknowledge the Single Crystal CCD X-ray facility at
IIT-Kanpur; CSIR, for SRF (S.K.). This work is supported by
an Indo-Spain DST project, India (S.V.).
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