Synthesis and structural characterization of first adenine containing organosilicon nucleobase for the recognition of Cu2+ ion

Article abstract of DOI:10.1016/j.ica.2018.04.019

This work reports the synthesis and structural characterization of a new adenine based organosilicon nucleobase using an efficient and biocompatible Click approach. Synthetic procedure included the preparation of a new N-acetylinic linked propyl silatrane 3 whose structure was confirmed through Single crystal X-ray crystallography. The designed silatrane L is found to be highly selective and sensitive for detection of Cu²⁺ with a color change from colourless to yellowish orange. The stoichiometry ratio of L + Cu²⁺ was obtained 1:1 by Job's Plot. The binding of copper ions to the chemosensor was studied over wide pH range and the results demonstrated that the sensor worked well in the physiological range 6–9. Furthermore, the sensing of Cu²⁺ was found to be reversible upon addition of EDTA. These results widen the scope of adenine based derivatives in the field of colorimetric probes. The newly synthesized silatrane 3 and the receptor L were successfully characterized by various spectroscopic techniques [IR, NMR (¹H, ¹³C) and Mass] and elemental analysis.

Full text of DOI:10.1016/j.ica.2018.04.019

Accepted Manuscript
Research paper
Synthesis and Structural Characterization of first Adenine containing Organo-
2
+
silicon Nucleobase for the recognition of Cu ion
Gurjaspreet Singh, Geetika Sharma, Pooja Kalra, Sanchita, Vikas Verma, V.
Ferretti
PII:
S0020-1693(18)30033-1
https://doi.org/10.1016/j.ica.2018.04.019
ICA 18210
DOI:
Reference:
To appear in:
Inorganica Chimica Acta
Received Date:
Revised Date:
Accepted Date:
6 January 2018
11 April 2018
12 April 2018
Please cite this article as: G. Singh, G. Sharma, P. Kalra, Sanchita, V. Verma, V. Ferretti, Synthesis and Structural
2
+
Characterization of first Adenine containing Organosilicon Nucleobase for the recognition of Cu ion, Inorganica
Chimica Acta (2018), doi: https://doi.org/10.1016/j.ica.2018.04.019
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Synthesis and Structural Characterization of first Adenine containing Organosilicon
2
+
Nucleobase for the recognition of Cu ion
*a
a
a
a
b
c,*
Gurjaspreet Singh , Geetika Sharma , Pooja Kalra , Sanchita , Vikas Verma , V. Ferretti,
a
Department of Chemistry, Panjab University, Chandigarh 160014, India
b
Guru Jhambeshwar University of Science and Technology, Hisar 125001, India
c
Center for Structural Diffractometry and Department of Chemical and Pharmaceutical Sciences,
University of Ferrara, via Fossato di Mortara 17-27, I-44100, Ferrara, Italy.
*
Corresponding Authors
1
. Dr. Gurjaspreet Singh
Associate Professor,
Department of Chemistry, Panjab University, Chandigarh
India
+91-0172-2534428
Email: gjpsingh@pu.ac.in
2
. V. Ferretti,
Center for Structural Diffractometry and Department of Chemical and Pharmaceutical Sciences,
University of Ferrara, via Fossato di Mortara 17-27, I-44100, Ferrara, Italy.
1

Abstract
This work reports the synthesis and structural characterization of a new adenine based
organosilicon nucleobase using an efficient and biocompatible Click approach. Synthetic procedure
included the preparation of a new N-acetylinic linked propyl silatrane 3 whose structure was
confirmed through Single crystal X-ray crystallography. The designed silatrane L is found to be
2
+
highly selective and sensitive for detection of Cu with a color change from colourless to yellowish
2
+
orange. The stoichiometry ratio of L+Cu was obtained 1:1 by Job’s Plot. The binding of copper
ions to the chemosensor was studied over wide pH range and the results demonstrated that the
2
+
sensor worked well in the physiological range 6-9. Furthermore, the sensing of Cu was found to
be reversible upon addition of EDTA. These results widen the scope of adenine based derivatives in
the field of colorimetric probes. The newly synthesized silatrane 3 and the receptor L were
1
13
successfully characterized by various spectroscopic techniques [IR, NMR ( H, C) and Mass] and
elemental analysis.
2
+
Keywords: Adenine, Triazole, Organosilicon nucleobase, Cu sensing
1
. Introduction
Adenine is an essential naturally occurring nitrogen heterocycle purine base present in the nucleic
acids. Biomolecules containing adenine are known to act as catalyst for several biochemical processes
1,2]. With its versatile skeleton that offers multiple interactive sites, it can support varied
[
coordination geometries [3-8]. Such multifaceted roles of the adenine framework are the motivation
behind addressing research problems, extending from classical coordination chemistry to the
construction of new materials.
2

In addition, triazole containing nucleosides have received a lot of attention by virtue of their
diverse biological roles [9]. Stability of 1,2,3-triazoles to metabolic degradations and harsh
oxidation/reduction conditions makes them a suitable connecting unit to different motifs to obtain
new bio-conjugates [10]. The introduction of a triazole moiety into a receptor induces an increase in
its complexation ability by offering more coordination sites [11-15]. Silatranes comprise of another
important class of scaffolds that have been frequently reviewed by many research groups owing to
their significance in different fields such as in biology, material science, sol–gel chemistry,
pharmaceutics, agriculture and medicine [16,17]. The modification of silatranes at the exocyclic
position with different groups is a significant trend as the resultant compounds preserve the activities
of silatranes as well as of the substituted groups [18,19]. Keeping the above perspectives in mind, we
have designed this adenine linked triazole allied silatrane that can efficiently act as a colorimetric
metal recognition probe because of the electron rich adenine triazole pocket and an additional
silatrane unit, a useful linker with applicability in nanoscience [20].
Amidst various transition metal ions, copper ion is one preeminent metal ion present in the
foundation of numerous categories of plant and animals [21-22]. Copper occupies third rank as a
crucial pollutant and the third most important in human biology. Production of dopamine, gene
expression, bone development, regulation of nerve function and the functional and structural
enhancement of proteins are some of the roles played by copper in biological processes [23-24].
Further, the role of copper ion is implicated in several physiological responses such as in accelerating
the healing of broken bones during the convalescence period [25], repairing of injured human skin
tissues [26] and increasing the production of hair pigments [27]. On the other hand, its higher
concentration can activate the production of reactive oxygen species (ROS) which would disturb the
cellular metabolism [28]. Additionally, it’s over accumulation in human can cause serious pernicious
3

effects such as Menke’s disease, Wilson’s and Alzheimer’s diseases, gastrointestinal disturbance,
kidney damage and Indian Childhood Cirrhosis (ICC) [29–31]. Therefore, the detection of copper ion
in various media has become an important consideration for the environment and human health.
Atomic absorption spectroscopy, Inductively coupled plasma emission, X-ray photoelectron
spectroscopy, surface-plasmon resonance detector and voltammetry are some of the customary
methods applied for the determination of copper ion at trace quantity levels [32-34]. However,
because of the sophisticated instrumentation required, these techniques are less favourable. Lately,
much effort has been dedicated to the construction of fluorescent chemosensors. Despite their high
sensitivity, selectivity and fast response as efficient fluorescent probes, the fluorescent based
techniques suffer a major drawback in case of copper sensing. Reports in literature have confirmed
2
+
that paramagnetic heavy metal ions like Cu ion are well–known fluorescent quenchers [35].
Presently, naked-eye detection methods are generally favored over fluorimetric methods because
colorimetric sensors are easily prepared and show easy detection without the help of instruments [36].
The design of such chemosensors that are simple to use and naked eye diagnostic tools are the
current areas of research interest. In particular, our shift focuses to synthesis of those chemosensors
that are prepared easily employing an efficient biocompatible route. Click Chemistry is one powerful
tool that allows synthetic chemists to obtain modular, high yield and excellent selectivity in product
formation [37-41].
The present research focuses on synthesis of a new Adenine linked triazole functionalized
silatrane through click approach. This new ternary act as selective chromogenic probe for the naked
eye detection of copper ion and to the best of our knowledge this is the first study of an organosilicon-
based nucleobase for the recognition of Copper (II) ion.
4

2
. Experimental Section
.1. Materials and Methods
Adenine (Avra), 1,2-dibromoethane
Trimethoxysilyl)propyl]aniline (Aldrich), Propargyl Bromide (80% in toluene., Aldrich),
potassium carbonate (Thomas) and Bromotris(triphenylphosphine)Copper(I), (CuBr(PPh3)3
Aldrich) were used directly as received. Compounds 2, 5 and 6 were synthesized from the
2
(Avra),
Sodium
Azide
(Avra),
N-[3-
(
(
1
13
previously known literature [42-44]. H and C NMR spectra were recorded on a JEOL
AL 400 MHz) spectrometer using CDCl as an internal reference and chemical shifts were
(
3
reported relative to tetramethylsilane, values are given in Hz. The infrared spectra were recorded
as neat spectra on a Thermo Scientific NICOLET IS50 spectrophotometer. Electronic spectral
measurements were carried out using JASCO V-530 UV-Vis spectrophotometer. Mass spectral
measurements (TOF MS ESþ 1.38 eV) were carried out on Waters QQeTOF micro Mass
Spectrometer. Melting points were measured in a Mel Temp II device using sealed capillaries
and were uncorrected
2
.2. Single X-ray Crystallography
A single crystal of 3 was carefully selected under polarizing microscope in order to perform its
structural analysis by X-ray diffraction. Diffraction data were collected on a Nonius Kappa
diffractometer equipped with a CCD detector with graphite-monochromatized MoKα radiation
(k = 0.71069 Å). Intensities were corrected for Lorentz, polarization and absorption effects [45].
The structure was solved by direct methods with the SIR97 suite of programs [46] and
2
refinements were performed on F by full-matrix least-squares methods with all non-hydrogen
atoms anisotropic. Hydrogens were included on calculated positions, riding on their carrier
atoms. All calculations were performed using SHELXL-2014/7 [47] implemented in the WINGX
5

system of programs [48]. The crystal data are reported in Table 1. The drawings were made with
Diamond [49] and ORTEPIII [50]. Crystallographic data for the structural analysis of 3 have
been deposited at the Cambridge Crystallographic Data Centre, CCDC No 1567199. These data
can be obtained free of charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html, or from the
CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK: fax: (+44) 01223-336-033; e-mail:
deposit@ccdc.cam.ac.
Table 1. Experimental details for compound 3
Crystal data
Chemical formula
Mr
C H N O Si
18 26 2 3
346.50
Crystal system, space group
Temperature (K)
a, b, c (Å)
Monoclinic, P2 /c
1
295
12.7048 (7), 11.3656 (6), 14.2006 (5)
β (°)
114.790 (3)
1861.58 (16)
4
3
V (Å )
Z
-1
μ (mm )
0.14
Crystal size (mm)
0.35 × 0.29 × 0.11
20346, 4028, 2830
No. Of measured, independent and
6

observed [I > 2σ(I)] reflections
Rint
0.070
2
2
2
R[F > 2σ(F )], wR(F ), S
0.072, 0.222, 1.06
4028
No. of reflections
No. of parameters
217
-3
Δρmax, Δρmin (e Å )
0.68, -0.36
2
.3. Hydrolytic stability study
To a dry aluminium sheet, 30 mg of starting material that is trimethoxysilane 2 and the final
product silatrane L was uniformly spread out under inert atmosphere. The sheet was then let
open in room temperature and moisture absorption by the silane and silatrane respectively was
monitored with time through Infra Red Spectroscopy.
2
.4. Synthesis
2
.4.1 N-(4-(2,8,9-trioxa-5-aza-1-sila-bicyclo[3.3.3]undecan-1-yl)butyl)-N-(prop-2-ynyl) benzenamine (3)
To a round-bottomed two-necked flask, 2 (1 g, 3.24 mmol) was dissolved in dry DMF (30 ml)
o
followed by the addition of K CO (0.67 g, 4.86 mmol) and stirred at 25 C for 30 minutes under
2
3
nitrogen atmosphere. To this, propargyl bromide (0.48 g, 4.05 mmol) was subsequently added
dropwise over a period of 10 min under stirring and the resulting mixture was allowed to stir at
o
2
5 C for 48 h. The reaction was monitored by TLC and on completion reaction was quenched
by ice cold water. The organic layer was extracted with chloroform, followed by washing of the
organic layer by water (3×15 ml). The organic layer was separated and dried (anhyd Na SO )
2
4
and evaporated under reduced pressure to give viscous oil which upon addition of diethyl ether
7

o
gave orange coloured crystals. Yield: 69%, M.P.: 86-87 C. Anal. Calcd. C H N O Si: C,
1
8
26
2
3
-
1
6
1
2
2.39; H, 7.56; N, 8.08. Found: C, 62.31; H, 7.48; N, 8.01. IR (Neat cm ): 579 (N→Si), 773,
1
093 (Si-O), 908 (C-C), 2120 (v C≡C), 3281 (v C≡C-H). H NMR (400MHz,CDCl ): δ 0.40 (m,
3
H, -SiCH -), 1.70 (m, 2H, -CCH C-), 2.13 (t, J = 2.3 Hz, 1H, -C≡C-H), 2.78 (t, J = 5.8 Hz, 6H,
2
2
-
NCH -), 3.29 (m, 2H, Ar-NCH ), 3.76 (t, J = 5.8 Hz, 6H, -OCH -), 4.02 (d, J = 2.3 Hz, 2H,
2 2 2
CH -C≡C-H), 6.69 (t, J = 7.3 Hz, 1H, H2), 6.83 (d, J = 8.0 Hz, 2H, H4 and H6), 7.21 (dd, J =
2
1
3
8
3
.7, 7.3 Hz, 2H, H1 and H3). C NMR (101 MHz, CDCl ): δ 13.2 (Si-CH ), 22.81 (-CCH C),
3 2 2
9.72 (CH -C≡C), 51.06 (NCH ), 54.76 (Ar-NCH ), 57.76 (OCH ), 71.14 (C≡C-H), 80.79
2
2
2
2
(C≡C-H), 113.16 (C4, C6), 116.63 (C2), 128.98 (C1, C3), 148.38 (C5).
2
.4.2. Ligand L
Acetylinic silatrane 3 (0.5g, 1.44 mmol) was added to 1:1 THF/Et N solvent mixture taken in a
3
two-neck round bottomed flask and the mixture was stirred for 15 min at room temperature
under nitrogen. Slow addition of 6 (0.295g, 1.44 mmol) was done followed by catalyst
o
[
CuBr(PPh ) ] (0.01 mmol/alkyne function) loading. The mixture was stirred at 60 C for 5 h.
3
3
The reaction was then brought to room temperature. The solvents were evaporated under reduced
pressure followed by the addition of diethyl ether. The contents were left for overnight stirring
after which the product was isolated as a light orange solid which was filtered under nitrogen and
o
dried under vacuum. Light orange solid. Yield: 66%, M.P.: Charring after 220 C. Anal. Calcd.
-1
C H N O Si: C, 54.23; H, 6.22; N, 25.43. Found: C, 54.21; H, 6.17; N, 25.38. IR (Neat cm ):
25
34 10
3
1
5
84 (N→Si), 773, 1057 (Si-O), 909 (C-C), 1670 (C=N), 3350 (-NH ). H NMR (400 MHz,
2
DMSO- d6) δ 0.15 (m, 2H, -SiCH -), 1.51 (m, 2H, -CCH C-), 2.77 (t, J = 5.8 Hz, 6H, -CH N-),
2
2
2
3
.16(m, 2H, Ar-NCH ), 3.61 (t, J = 5.8 Hz, 6H, -OCH CH -), 4.41 (s, 2H, -CH Tz-), 4.58 (t, 2H,
2 2 2 2
CH CH Tz), 4.76 (t, J = 7.6 Hz, -CH CH Tz), 6.51 (t, J = 7.2 Hz, 2H, H11, H15), 6.62 (d, J =
2,
2
2
2
8

1
3
8
.2 Hz, 1H, H13), 7.05 (m, 2H, H12, H14), 7.64 (s, 1H, H6, Tz-H), 8.19 (s, 1H, H8). C NMR
(
(
(
101 MHz, DMSO- d6): δ 13.15 (Si-CH ), 22.81 (-CCH C), 46.68 (-CH Tz), 48.84
2
2
2
CH CH Tz), 51.09 (-NCH ), 54.75 (Ar-NCH ), 57.74 (OCH ), 112.19 (C11, C15), 115.82
2
,
2
2
2
2
C13), 122.75 (C3. Tz-C), 129.09 (C12, C14), 147.43 (C4 and C16), 148.05 (C8), 153.25 (C2).
+
MS m/z (relative abundance (%), assignment): 551.49 (100, (M + H) ).
3
.
Results and Discussion
3
.1. Synthetic aspects
We have designed our ligand L taking into consideration the efficient binding capability of three
significant moieties, namely adenine, triazole and silatrane which have been stitched together to
obtain an efficient chemosensor L. A simple methodology was chosen to tether Adenine with
materially important amino functionalized silatrane so as to derive our required receptor L. The
synthesis of L has been accomplished by a five step synthetic pathway as outlined in Scheme 1.
The intermediates 2, 5 and 6 were prepared following the literature methods [42-44]. N-(3-
(trimethoxysilyl)propyl)benzenamine was chosen as the starting material for the synthesis of new
N-acetylinic organopropylsilatrane 3. The swiftness in hydrolysis rate of free alkoxy groups of
silanes renders them unstable towards advance applications. Silatranes are favoured over
trialkoxysilanes owing to the controlled adherence to diverse materials like glass slides or optical
fibers as a chemical linker generating various types of sensors. Therefore, transetherification
reaction of trimethoxysilane 1 was carried out by triethanolamine, so as to cap silicon in a
position to preclude the chances of hydrolysis. The N-H group of the silatrane was
nucleophilically substituted with propargyl group using propargyl bromide, resulting into N-
1
13
alkylated product 3 which has been well characterized by IR, H and C NMR and elemental
analysis. Further the structure of 3 has been confirmed by Single X-ray Crystallography. The
9

newly synthesized acetylinic silatrane 3 undergoes a [3+2] cycloaddition reaction with Adenine
azide 6 in the presence of THF/Et N solvent system and bromotris(triphenylphosphine)copper (I)
3
catalyst to generate the corresponding Adenine appended triazole allied organopropyl silatrane L
1
13
in good yield and is suitably characterized by IR, NMR ( H and C) and mass spectrometry. The
advantage of the presence of silicon in the receptor lies in the augmentation of this receptor
system to silica based nanoparticles that can further replicate its significance in fabricated
2
+
nanomaterials. The essence of this ternary lies in the efficient sensing of Cu ions through naked
eye.
1
0

(a) Synthesis of the new N-acetylinic silatrane 3
O
Si
O
Si
O
N
O
Si
O
O
N
(i)
(ii)
N
N
H
O
N
O
O
H
3
2
1
(b) Synthesis of Adenine ligand L
O
O
N
N
N
N
N
N
3
Si
N
N
N
N
(iv)
(
iii)
N
N
N
O
(
v) H N
2
H N
N
H N
H N
2
N
2
NH
2
N
N
N
N
N
Br
N3
L
6
4
5
Scheme 1. Synthesis of Adenine based ligand L. Reagents and conditions. (i) Triethanolamine,
Toluene, KOH, 5 h. (ii) Propargyl bromide, DMF, K CO , R.T, 48 h. (iii) 1,2-dibromoethane,
2
3
o
o
DMF, K CO , R.T, 48 h. (iv) NaN , DMF, 80 C, 4 h (v) CuBr(PPh ) Et N, THF, 60 C, 6 h.
2
3
3
3 3,
3
3
.2. Characterization aspects
1
13
All the newly synthesized compounds were characterized by IR, H and C NMR, low
resolution mass spectroscopy and elemental analysis. Compound 3 has also been characterized
by single crystal X-ray crystallography. The FT-IR spectra of the newly synthesized compounds
-1
were recorded as neat spectra in the range 4000-400 cm . The absorption frequencies recorded
were found to be in close agreement with the structure of the synthesized compounds. The newly
1
1

synthesized acetylinic silatrane 3 exhibited the characteristic bands of the silatranyl group which
are assigned on the basis of literature. The incidence of symmetric deformational vibration peak
-1
of the silatranyl framework possessing transannular N
Si bond is observed at 583 cm
-1
whereas, the Si-O stretching vibration appears at 1094 cm for 3. Furthermore, the typical bands
-1
-1
observed for terminal alkynes appeared near 2153 cm and 3293 cm corresponding to C≡C and
-1
C≡C-H bonds. The absence of C≡C stretching vibrations in the region 2100 cm in the receptor
L proves the cyclization of the alkynyl moiety into triazole unit. In addition to this, the
-1
symmetric stretching vibrations of C=N and N-H of the adenine unit at 1658 and 3338 cm
confirms the inclusion of adenine into N-acetylinic silatrane through cycloaddition. The
prominent contribution from the transannular N→Si bond and Si-O is evident in the region
-1
-1
1
13
5
80–590 cm and 1079-1099 cm respectively. The multinuclear ( H and C) NMR spectra are
1
in accordance with the structure of the newly synthesized compounds. In H NMR, atranyl
moiety of compound 3 consists of sharp triplets due to NCH and OCH protons at 2.78 and 3.76
2
2
ppm respectively. The confirmation of the propargylic group in 3 is depicted by the presence of
two singlet peaks at 2.13 and 4.02 ppm corresponding to -C≡C-H and CH -C≡C-H respectively.
2
After cycloaddition, emergence of peak at δ 7.65-7.70 ppm due to triazole proton confirms the
cyclization of alkynyl moiety into triazole unit in the receptor L. Furthermore, shift in NCH2
proton of the alkynyl group in 3 from δ 4.02 to 4.41 ppm validates the formation of the cyclized
proton. Similar shifting is observed in the carbon spectrum of the compounds. The triplets at δ
1
3
2
.77-2.70 and δ 3.59-3.62 are evident of the atranyl framework in L. In the C NMR spectra of
the synthesized compound 3 as highly de-shielded carbon in the region carbons of alkynyl
moiety appear in the range of δ 71.1–80.7 ppm. The distinguishing peaks for the atranyl moiety
appeared at δ 51.06 and 57.16 ppm. In the cyclized compound (Ligand L), appearance of triazole
1
2

carbons at around δ 121.0–122.9 ppm and δ 132.8–143.2 ppm confirms the cyclization of alkyne
to triazole unit.
3
.2.1. X-ray crystallographic study
The ORTEPIII [50] view of compound 3 is shown in Figure 1 and a selection of bond distances
and angles is reported in Table 2. The coordination polyhedron of the silicon atom can be
described as a trigonal bipyramid with N1 and C7 atom occupying the apical positions
(N1 - Si - C7=178.8(1)°). The Si-N distance lies in the range 1.96-2.32 Å found in related
silatrane compounds (CSD search, 237 values) confirming the existence of this transannular
bond. The silicon atom is displaced by 0.22 Å towards C7 from the equatorial plane defined by
the three oxygen atoms. The distortion of the coordination polyhedron can be quantified by
using the τ parameter, which is defined in terms of the angles α ( mean O-Si-O angle) and β (C-
Si-N angle). τ = (β − α)/60, such that in the ideal square pyramid τ = 0, while in the ideal
trigonal bipyramid τ = 1; in the present case, the τ value is 1.01 which undoubtedly indicates a
regular polyhedron. Due to the absence of good hydrogen bonding donors, the molecules are
held together mainly by very weak C-H…O/N intermolecular hydrogen bonds, besides van der
Waals interactions. It is however noteworthy that the ethynyl hydrogen is involved in a short C-
H...π interaction with the phenyl ring to give the dimeric moiety shown in Figure 2. The
geometrical parameters of the main intermolecular interactions are given in Table 3.
1
3

Fig 1. A view of the asymmetric unit in the crystal structure of 3 showing the atom numbering
scheme and displacement ellipsoids drawn at the 40% probability level.
Fig 2. C-H...π interactions (dashed bonds) in compound 3
1
4

3
.2.2. Structural Descriptions
The bond lengths and the bond angles of the compound 3 were compared with the theoretical
calculations. The GAUSSIAN-03 Revision C.01 program package [52] was used for theoretical
calculations. The structure of compound 3 was optimized using DFT calculations carried out at
B3LYP/6-31G(d) level of theory. The optimized structure is presented in Figure S1. As can be
seen from Table 2, all the bond lengths and bond angles of the compound 3 from the
crystallographic data are in accordance with the Gaussian results. The measured N Si bond
length is 2.199 Å that is much shorter than the computed bond length that is 2.977 Å showing the
strength of this coordinate bond.
Table 2.
Selected bond distances and angles (Å ) for Compound 3
Measured
Computed
Bond length (Å)
Si1-O1
1.648
1.645
1.869
1.654
2.199
1.72
1.71
1.87
1.72
2.97
Si1-O2
Si1-C7
Si1-O3
Si1-N1
Bond Angles
O1-Si1-O2
O1-Si1-O3
O1-Si1-C7
O2-Si1-C7
117.0
118.6
97.6
112.11
111.58
107.23
107.33
98.6
1
5

O3-Si1-C7
O2-Si1-N1
O1-Si1-N1
O2-Si1-O3
O3-Si1-N1
96.7
82.4
82.3
119.1
82.3
108.90
73.73
71.12
109.50
71.7
Table 3. Intermolecular interaction parameters (Å, °) for compound 3 (Cg= centroid)
D-H…A
D-H
D…A
3.549(5)
H…A
D-H…A
i
C2 -H...O3
0.97
2.71
144
ii
C4-H ...O2
0.97
0.97
3.414(5)
3.293(5)
2.67
2.54
133
134
iii
C4-H...O1
C-H...π interaction
iv
C18-H…Cg(C1-C15)
0.93
3.46
167
Equivalent positions: (i) x,1/2-y,z-1/2; (ii) 1-x,-y,-z; (iii) 1-x,y-1/2,-z-1/2; (iv) 2-x,1-y,1-z
3
.2.3. Hydrolytic stability study
The hydrolytic instability of trialkoxysilanes results from the attack of water molecules on the
vacant d orbital of the Si atom and the higher mobility of OR group that facilitates the removal of
1
6

alkoxy groups. Replacement of alkoxy groups by hydroxyl group results in formation of silica
thereby reducing the utility of silanes. However, this tendency is reduced by their conversion to
silatranes which are capped structures that prevent any attack on the Si atom.
The greater stability of the silatrane L as compared to the starting material
trimethoxysilane 1 was affirmed through time dependent Infrared Spectroscopy technique which
clearly signified water gain with time (Figure 3). It can be seen from the spectra (Fig 3a) that the
starting material trimethoxysilane was quite susceptible to moisture attack. There can be two
probable reasons for its faster hydrolysis, firstly as a result of extensive intermolecular hydrogen
bonding of –OCH groups with water molecules, the vacant d orbital on Silicon atom becomes
3
more vulnerable to nucleophilic attack by water molecules, secondly since the starting material
silane is a amino functionalised silane, being a amine it has tendency to form hydrogen bond
with water molecules. Thus capping of silicon atom as well as functionalization of amine became
necessary. Next, the synthesized silatrane L was subjected to hydrolytic study, it was observed
that no significant change was noticed in the spectra upon repeated exposure to moisture
(Fig 3b). Its lesser susceptibility to moisture attack can be accounted from the fact that the
construction of the silatrane L comprises of three aromatic units namely adenine, triazole and
benzene unit because of which aromatic π stacking dominates which averts its interaction with
water. Additionally the silatrane unit further increase its resistance to water. These points also
explain the partial solubility of our silatrane in water.
1
7

5
1
2
3
4
min
0 min
0 min
0 min
0 min
1
500
2000
2500
3000
3500
4000
-
Wavenumber (cm )
1
(
a)
5
min
10 min
20 min
30 min
40 min
1
500
2000
2500
3000
3500
4000
-
1
Wavenumber (cm )
(
b)
Figure 3: IR monitored time dependent spectrum of silane 1 and silatrane L (time dependent hydrolysis)
1
8

3
.2.4. UV-Vis Spectral Study
To have a clear insight about the electronic transitions and geometrical confirmation of the
prepared compound, its UV–vis spectrum was recorded. Ligand concentration was fixed at
-6
1
0 M in all titration experiments. The absorption spectrum recorded in acetonitrile reveals a
higher energy band at 259 nm and a lower energy band at 307 nm, which are assigned to π-π*
and n-π* electronic transitions, respectively (Figure 4).
2
+
3
.2.5.Chromogenic recognition of Cu ion
The chromogenic character of receptor L was investigated in the presence and absence of Copper
2
+
ion in CH CN. Figure 4 depicts the change in absorption spectra upon addition of Cu as its
3
chloride salt. The solution of the receptor appeared colorless in the absence of copper ions and
exhibited sharp absorption bands in the UV region centered at 259 and 307 nm. Upon addition of
2
+
Cu ions, two new peaks at 314 nm and 457 nm were observed. The peak at 259 nm did not
undergo a major shift but the peak at 307 nm was red shifted to 314 nm along with a
hyperchromic shift. A new peak at 457 nm appeared which is indicative of the complexation
2
+
between Cu and L. The color of the solution changed from transparent to yellow orange. This
change is evident from the fact that the new peak at 457 nm lies in visible range.
1
9

2
+
Fig 4: Change in UV-vis absorption spectra upon addition of Cu
2+
Figure 5 depicts the spectra upon concomitant additions of Cu to the above solution.
2
+
With the sequential additions of Cu ions (0 to 3 equiv.) to the CH CN solution of receptor L
3
-6
(
1 ×10 M), an incessant increase in the absorption intensity along with a red shift in absorption
wavelength was observed. The absorption intensity of the bands at 259 nm and 314 nm increased
gradually with every addition. The band at 457 nm developed gradually on each addition.
2
0

3.0
2.5
2.0
1.5
1.0
0.5
0.0
2
+
Addition of Cu
250
300
350
400
450
500
550
600
Wavelength(nm)
2
+
Fig 5: Change in UV–vis absorption spectrum of L upon addition of increasing amounts of Cu (0.2, 0.4, 0.6, 0.8,
1
.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0 equiv., respectively) in CH CN solution.
3
The stoichiometry of the complex was evaluated using Job's continuous variation
method, the maxima at 0.5 suggested that the stoichiometry of the complex formed between L
and Cu(II) would be 1:1 (Fig. S2). To further explore the binding mechanism, the graphical
method proposed by Benesi and Hildebrand (B–H) was employed which indicated that
2
+
stoichiometry of complexation of the receptor with Cu ion is 1:1. The association constant (K ),
a
a gauge of the strength of interaction of the receptor with copper ions, was determined from the
5
-1
B–H plot (Fig. S3). A significant value of K (i.e. 3.55×10 M ) was obtained which illustrates
a
the strong binding ability of the prepared chemosensor. The probable binding mode of the ligand
with the copper ion is illustrated in Scheme 2. Further the binding ability of the prepared
chemosensor was compared with some recently reported sensors in literature (Table S4). Data
2
1

revealed that the synthesized sensor has enhanced affinity for copper ion than these known
colorimetric and fluorescent probes. These observations pave the way for more such adenine
derived sensors.
An effort was made to calculate the limit of detection of the designed receptor L towards
2
+
Cu . For the said purpose, a calibration curve was constructed for the quantitative determination
2
+
of Cu by L (Fig. S5). The curve exhibited a good linear relationship between absorbance of L
2
+
2
and Cu concentration (1.00-30.00 µM) with a correlation coefficient of R =0.995. The limit of
detection as calculated from the standard deviation of responses and slope of the curve came out
2
+
to be 2.92 µM that is below the limit assigned by WHO for Cu ion (20 µM). Scheme 2 depicts
the probable binding mode of Copper ion.
O
O
O
Si
O
N
Si
N
O
Cu2+
N
N
N
O
N
N
Cu2+
N
N
N
N
N
N
H N
N
N
2
H N
2
N
N
N
2+
Scheme 2: Proposed binding of Cu with the Ligand L
Since effect of pH is of utmost significance as far as practical facet of sensing is concerned, the
2
+
effect of pH on the absorption response of receptor L to Cu ions was investigated in the
the highly acidic and basic pH range and the pH values were adjusted with the 0.1N NaOH and
0
.1N HCl solution. As shown in Fig. 6, at lower pH (<6) the absorbance values were relatively
lower indicating that the protonated form coordinated less effectively with copper ion. As the pH
increases to neutral, the absorbance values rises indicating deprotonation and thereby increased
2
+
binding affinity with Cu ion. The best binding results were obtained in the pH range 6-9. At pH
2
2

above 10, there is a sharp fall in absorbance values which may be due to the formation of copper
ion to copper hydroxide ion which inhibits binding with ligand. Thus from the results it can be
concluded that the receptor L worked well in the environmentally and physiology relevant pH
range.
0.16
0.12
0.08
0.04
0.00
2
4
6
8
10
12
pH
2+
Figure 6: Effect of pH on L-Cu complexation
2
+
A significant trait of the receptor L is its high selectivity toward Cu ions over other competitive
species. For the selectivity study 2 equiv. of each metal ions were separately added to the 1µM
solution (in CH CN) of receptor L. Among all the tested metal ions from the following group of
3
2
+
2+
2+
3+
2+
+
2+
+
2+
2+
+
2+
2+
cations, Ba , Cd , Co , Cr , Fe , Ag , Hg , K , Mg , Mn , Na , Ni and Zn , the
significant alteration was observed only upon addition of Cu(II) ions as can be seen from the
spectra of Ligand L with different cations (Figure 7a). In addition to this, visual color change
2
3

2
+
was observed only upon addition of Cu to the receptor solution, while, no other metal ion gave
any color to the receptor solution (Figure 7b). These results indicate that ligand L is highly
2
+
selective towards Cu among a number of metal ions. The relative absorbance of L with
different metal ions is depicted in Figure S5, which further demonstrates it high selectivity
2
+
towards Cu ion.
(
a)
2.0
1.5
1.0
0.5
0.0
2
+
L+Cu
2
+
2+
2+
2+
3+
2+
2+
+
L+Ba +Cd +Co +Cr +Fe +Ag
2+
+
2+
+
2+
Hg +K +Mg +Mn +Na +Ni +Zn
250
300
350
400
450
500
550
Wavelength (nm)
(
b)
2
+
2+
2+
3+
2+
2+
+
2+
+
2+
2+
+
2+
2+
Ba
Cd Co Cr
Fe
Cu
Ag Hg
K
Mg Mn Na Ni Zn
Fig 7: (a) Variations in absorption spectrum of receptor solution in the presence of different metal ions (b) Visual
color changes upon addition of different metal ions in the receptor solution
2
4

Reversibility is an important characteristic of a good practical sensor. Reusability of the
sensor is a crucial factor kept in mind while constructing a good sensor so as to increase its
applicability. Reversibilty of the receptor L was checked using disodium salt of EDTA.
2
+
Scheme 3 depicts the reversible reaction of the receptor L upon addition of Cu and EDTA .
O
O
Si
O
O
N
O
N
N
Si
N
N
O
N
N
N
Cu2+
N
EDTA
N
N
N
N
Cu2+
H N
N
2
N
N
H N
N
2
N
2+
Scheme 3. Reaction of the receptor L upon addition of Cu and EDTA
Reversibility study was performed by recording absorption spectra of receptor L (1 µM) in
2
+
CH CN. The receptor L is colourless initially. Upon addition of 3 equiv. amount of Cu to the
3
receptor solution, the colour changes from transparent to yellowish orange (Figure 8). Further in
the absorption spectra, a new band emerged at 457 nm indicating complexation between receptor
2
+
2+
L and Cu ion. On addition of Na EDTA (3 equiv.) to the mixture of L and Cu , the band at
2
4
57 nm slowly disappeared and the solution again became colourless, signifying that the receptor
2
+
L has been regenerated presumably due to the formation of a stronger EDTA-Cu complex
Fig 9). Furthermore, the colour changes were found to be reversible after several cycles with the
(
2
+
sequential addition of Cu and EDTA (Figure 10). This revival makes the molecular sensor
2
+
reusable and attractive for real-time applications to sense Cu ion.
2
5

2
+
2+
Cu
EDTA
Cu
Fig 8. Colour change upon sequential addition of Copper ion and EDTA
L
L+Cu
2
2
+
+
3
L+Cu +EDTA
2
L+Cu +EDTA+Cu
+
2+
2
1
0
250
300
350
400
450
500
550
600
Wavelength (nm)
2+
Fig 9. Absorption response of L and L + Cu with and without EDTA solution.
0
0
0
0
0
0
0
.30
.25
.20
.15
.10
.05
.00
1
2
3
4
5
6
Number of addition
2+
Fig 10. Reversible changes in absorbance of L at 457 nm after the sequential addition of Cu and EDTA.
2
6

Further insights into the complexation of Copper ion with adenine sensor and changes in
absorption spectra of L upon addition of copper ion were studied using Quantum chemical
2
+
calculations at DFT level. L-Cu complex was subjected to energy optimization by using
B3LYP in combination with 6-31+G(d,p) basis set for H, C, N and O atoms and LANL2DZ
2
+
basis set for Cu atom. The energy minimized structure for L–Cu complex is shown in
Figure 11.
2
+
Fig 11: Energy minimized structure of L+Cu complex
2
+
It is evident from Fig. 11 that the energy minimized structure of L-Cu afforded a macrocyclic
framework incorporating copper ion resulting from the preorganization of ligating sites viz.
2
+
electronically richer N atom (from triazole and adenine group) for binding to Cu ions. We have
also evaluated the frontier molecular orbitals at the same level of theory. From the energy level
diagram (Figure 12), it can be perceived that addition of the copper ion leads to the stabilization
of the HOMO and LUMO of the receptor L. From the computed results, energy levels of HOMO
and LUMO of L decreased after addition of copper ion when compared with that the free L. In
2
7

addition, the energy gap between HOMO and LUMO in case of complex is lowered by 0.029 eV
as compared with the parent receptor L .This may be the reason behind the red-shift phenomenon
of the absorption spectrum. Furthermore, it can be seen from the molecular diagram of receptor
L, electron density at HOMO is distributed over triazole ring, whereas LUMO is located over
2
+
2+
silatrane part. Similarly for L-Cu complex, the HOMO is now distributed over Cu complex
while LUMO is located over silatranes. This signifies that this is a metal to ligand transfer, which
2
+
is evident from a low absorption band at 457 nm in spectra of L upon addition of Cu ion.
2
+
Fig. 12. Energy diagrams of HOMO and LUMO orbitals of L and Cu +L complex calculated
on the DFT level using a B3LYP/6-31G* basis set.
ΔE= 0.036eV
2
+
LUMO of L+Cu (E =-0.11641 eV)
LUMO of L (E = -0.11907 eV)
ΔE = 0.0077 eV
2
+
HOMO of L (E = -0.15770 eV)
HOMO of L+Cu ( E= -0.12420 eV)
2
8

3
.3. Performance in Real water samples
To test the applicability of our prepared chemosensor in real water samples, choice of
appropriate aqueous solvent system was necessary. Due to the partial solubility of our compound
in water, mixed solvent system was chosen. Studies on the UV-absorption studies revealed that
the compound was selective for copper ion in CH CN: H O (9:1 v/v) solvent system. The
3
2
practical application of the chemosensor L was then employed in detecting copper ion in tap
water, distilled water and river water. These samples were first filtered to remove insoluble
substances. Absorption spectra results revealed that the chosen samples were free of copper ion
(Figure S14).
Conclusions
In conclusion, a new Adenine allied triazole linked silatrane was successfully synthesized and
characterized. It was found that the designed compound L acted as remarkable chromogenic
2
+
2+
probe for the selective detection of Cu ion. The recognition of Cu gave rise to color changes
from colorless to yellowish orange that was clearly visible to the naked eye. From the Job’s plot
and B-H plot, its stoichiometry for binding was found to be 1:1, with a high value of association
5
-1
constant (3.55×10 M ). The sensor worked well in the physiological pH range 6-9. Further its
recyclability was confirmed upon titration with EDTA. These results widen the scope of adenine
based derivatives in the field of colorimetric probes.
Acknowledgements
The authors are grateful to UGC, DST-PURSE II, DST-SERB and CSIR, New Delhi for
providing necessary financial assistance.
2
9