The fluorescent chemodosimeter RT based on
rhodamine derivative for detection of mercury ions
was studied, including the synthesis process,
characteristics and applications. The optimized
geometry and the electron properties of RT and RG
were identified at the B3LYP/LanL2DZ level of
theory with a combination of AIM and NBO
analysis. The obtained results showed that the
presence of spirolactam ring in RT led to break the
π-bond conjugated system of rhodamine fluorophore
at C10 atom, causing the fluorescence quenching of
RT. Meanwhile, the formation of guanidine ring and
spirolactam ring-opening in RG restored the π-bond
conjugated system of rhodamine fluorophore,
leading to the strong fluorescence in RG. As a
result, RT could be used as an OFF-ON fluorescent
chemodosimeter for detection of Hg(II) ions
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Vietnam Journal of Chemistry, International Edition, 55(2): 139-147, 2017
DOI: 10.15625/2525-2321.2017-00433
139
A fluorescent chemodosimeter based on rhodamine derivative for
detection of Hg(II) ions studied by using the density functional theory
Phan Tu Quy
1,2
, Nguyen Khoa Hien
3
, Truong Quy Tung
4
, Duong Tuan Quang
5*
1
Department of Chemistry - Hue University of Sciences - Hue University, Hue City, 84-54, Vietnam
2
Tay Nguyen University, Buon Ma Thuot City, 84-50, Vietnam
3
Mientrung Institute for Scientific Research - Vietnam Academy of Science and Technology, Hue City, 84-54, Vietnam
4
Hue University, Hue City, 84-54, Vietnam
5
Department of Chemistry - Hue University of Education - Hue University, Hue City, 84-54, Vietnam
Received 7 November 2016; Accepted for publication 11 April 2017
Abstract
The synthesis, characteristics and applications of the rhodamine derivative-based fluorescent chemodosimeter RT
for detection of mercury ions have been studied at the B3LYP/LanL2DZ level of theory. The calculated results
confirmed the presence of spirolactam ring in RT molecule. The Hg(II) ions reacted with RT to form RG, accompanied
by the formation of guanidine ring and the spirolactam ring-opening in RG, turning on the fluorescence of RG. These
results were in a good agreement with experimental investigations. It indicated that the quantum chemical calculations
could be used well for the design, synthesis of the fluorescent chemodosimeter.
Keywords. Fluorescence, chemodosimeter, rhodamine, mercury, DTF, TD-DFT.
1. INTRODUCTION
The fluorescent sensors (chemodosimeter and
chemosensor) are molecular sensors based on the
transforms of fluorescence signal resulting in the
interaction of the analytes with sensors. The first
chemodosimeter based on spirolactam ring-opening
process of rhodamine B derivative for the detection
of Cu(II) ions was reported by Czarnik (1992) [1].
The publications of new fluorescent sensors have
rapidly increased since 2005. Nowadays, new
fluorescent sensors have been reported almost every
week in the world [2]. This is due to the fact that the
fluorescent sensors are often sensitive to
the analytes, easy to carry out, and less expensive
[3]. The fluorescent sensors are studied and applied
for detecting many different objects, especially
heavy metal ions.
A great number of fluorescent sensors have
recently been reported and can be used to selectively
detect many different heavy metals ions, such as
Hg(II), Cu(II), Fe(II), Fe(III), and Al(III) [4-8].
Many fluorescent sensors can detect metal ions in
living cells like Fe(III) in Hepatic cells, Cu(II) in
HepG2 cells [4], Hg(II) in PC3 cells [7], etc.
However, the development of new fluorescent
sensors for detection of trace heavy metal ions in
various objects is currently receiving considerable
attention due to their increasingly serious pollution.
Scientists still continue to develop new fluorescent
sensors to improve the detection limit, the
selectivity, the solubility, the pH working range, the
excitation and emission wavelength, etc [9-13].
The reported fluorescent sensors for the
detection of heavy metal ions, biothiols and other
analytes are studied mainly by experimental
methods (including the design, synthesis, and
application) and based on the researcher's experience
[14, 15].
Currently, quantum chemical calculation can
predict or explain many important properties of
chemical systems [16, 17]. Using the quantum
chemical calculation to study the synthesis and
applications of fluorescent sensors is very useful,
helping us to understand the nature of processes to
provide a basis for research and development of
new sensors. In this work, following the previously
reported experimental studies [12], the synthesis
process, characteristics and applications of a
fluorescent chemodosimeter based on a rhodamine
derivative for detection of Hg(II) ions were studied
VJC, 55(2), 2017 Duong Tuan Quang et al.
140
at the B3LYP/LanL2DZ level of theory with a
combination of AIM and NBO analysis.
2. MATERIALS AND METHODS
2.1. Instruments
1
H NMR spectra were obtained on Bruker-400
instrument (400 MHz); mass spectra were acquired
on Finnigan 4021C MS-spectrometer; elemental
analysis was carried out on Flash EA 1112
instrument; UV-Vis spectra and fluorescence spectra
were performed on Shimadzu UV-1800 UV-Vis
spectrophotometer and Shimadzu RF-5301 PC series
fluorescence spectrometer, respectively.
2.2. Reagents
4-nitrophenyl isothiocyanate, rhodamine 6G,
ethylenediamine, and all cations (Zn
2+
, Cu
2+
, Cd
2+
,
Pb
2+
, Ag
+
, Fe
2+
, Cr
3+
, Co
3+
, Ni
2+
, Ca
2+
, Mg
2+
, K
+
and
Na
+
) were obtained from Aldrich. Acetonitrile,
ethanol, and all other solvents were HPLC-grade
reagents without fluorescent impurity.
2.3. Computational methods
Geometry optimization and single point energy
calculations of molecules were carried out using
density functional theory (DFT) with the Gaussian
09 program. The B3LYP density function was
applied using the LanL2DZ basis set [17-19].
The variation of enthalpy (ΔH298) and variation
of Gibbs free energy (ΔG298) of reactions (at 1.0
atmosphere and 298K) are calculated based on the
difference between the total energy of the reaction
products and the total energy of the reactants, with
the following equations [19]:
H298 = (0 +Hcorr)products - (0 +Hcorr)reactants
H298 = (0 +Gcorr)products - (0 +Gcorr)reactants
Where 0 is total energies of the molecule, Hcorr and
Gcorr are the thermal correction to enthalpy and the
thermal correction to Gibbs free energy.
The excited state and time-dependent factors
were investigated using time-dependent density
functional theory (TD-DFT) at the same level of
theory [11]. Topological properties of electron
density were probed using the AIM 2000 software
for the atom-in-molecule (AIM) theory. The
characteristics of each bond critical point (BCP) and
bond ring critical point (RCP) considered in this
study included the electron density (ρ(r)), its
Laplacian (2(ρ(r)) [11, 20-21]. Those theoretical
calculations were carried out on a supercomputer
operating system with a 32-cores processor and 72-
gigabytes memory at the laboratory of
computational chemistry and modelling of Quy
Nhon University.
3. RESULTS AND DISCUSSION
3.1. The survey on the calculation method
To use the B3LYP/LanL2DZ level of theory for
research compounds, a comparison between the
calculated results and the experimental structure of
rhodamine (fluorophore) has been carried out. The
optimized geometry of rhodamine with the
numbering scheme of the atoms is shown in Fig. 1.
The calculated and experimental bond lengths in
rhodamine were listed in table 1.
Table 1: The calculated and experimental bond
lengths in rhodamine (Å)
Bond lengths Exp [23] B3LYP
C1-C2 1.442 1.419
C1-C6 1.341 1.390
C1-C21 1.502 1.510
C2-C3 1.409 1.401
C2-N22 1.325 1.408
C3-C4 1.361 1.387
C4-C5 1.419 1.406
C4-O7 1.368 1.363
C5-C6 1.430 1.407
C5-C10 1.388 1.448
C10-C15 1.491 1.495
C15-C16 1.400 1.412
C15-C20 1.381 1.402
C16-C17 1.392 1.402
C16-C29 1.475 1.501
C17-C18 1.361 1.388
C18-C19 1.370 1.393
C19-C20 1.373 1.392
N22-C27 1.455 1.473
C27-C28 1.493 1.523
C29-O30 1.193 1.212
C29-O31 1.333 1.342
O31-C33 1.462 1.453
C32-C33 1.470 1.519
VJC, 55(2), 2017 A fluorescent chemodosimeter based on
141
Figure 1: The optimized geometry of rhodamine at
the B3LYP/LanL2DZ level of theory
The paired t-test method in the statistical test
was used for comparison between the calculated
values and experimental values [23]. For the bond
length, the calculated value of |t| of 0.54 is less than
the critical value of |t| of 2.07 (f = n-1 = 23 degrees
of freedom, P = 0.05). These results indicate that the
difference between the calculated and experimental
values is insignificant. Therefore, the selected level
of theory is possible to apply to the research system
with reliable results.
3.2. The synthesis and characterization of sensor
The sensor RT (rhodamine-ethylenediamine-
nitrothiourea conjugate) was synthesized via two
reactions. The synthetic procedure of the RT is
shown in figure 2. The calculated enthalpies (∆H298)
and free energies (∆G298) of reactions at the
B3LYP/LanL2DZ level are summarized in table 2.
The obtained results indicate that the enthalpies and
free energy of these reactions are quite negative.
This indicates that the reactions (1) and (2) are
energetically favorable.
Figure 2: Synthetic procedure of the RT
Table 2: The calculation results of enthalpies and
free energies of reactions at the B3LYP/LanL2DZ
level (kcal.mol
-1
)
Reaction ∆H298 ∆G298
(1) -757.9 -765.1
(2) -25.1 -6.3
The synthesis of RT was studied and presented
in our previous publication [12]. Accordingly, the
chemodosimeter RT was synthesized from the
reaction of the rhodamine 6G and ethylenediamine,
followed by the reaction with 4-nitrophenyl
isothiocyanate in ca. 39.5 % overall yield. The
structures of intermediate and final products were
confirmed by
1
H NMR and mass spectra. The
structure of RT was obtained as shown in figure 2.
The optimized geometry of RT with the
numbering scheme of the atoms is identified at the
B3LYP/LanL2DZ level of theory and is shown in
figure 3. The theoretical structural parameters such
as bond lengths, bond angles and dihedral angles of
RT are shown in table 3. The obtained results show
that the majority of the atoms in the RT molecule is
distributed on two perpendicular planes. The C2–
C12–N19–C25 dihedral angle in RT is 85.20. One of
them contains the C1, C2, C3, C4, C5, C6, N7, C8,
C9, C10, C11, C12, C13, C14, C15, N16, N17, and
C18 atom. The other one contains the N19, C20,
C21, C22, C23, C24, C25 and C26 atoms.
Figure 3: The optimized geometry of RT with the
numbering scheme of the atoms at the
B3LYP/LanL2DZ level of theory
The C5–C9–N19–C22 dihedral angle in RT is
73.1
0
. The C5–C10–C9, C5–C10–C22, C9–C10–
N19, C9–C10–C22 angles are 110.20, 112.20, 110.60,
112.0
0
,
respectively. The C5–C10–C9, C5–C10–
C22, C9–C10–N19, C9–C10–C22 angles are 110.20,
112.2
0
, 110.6
0
, 112.0
0
,
respectively. The C5–C10,
C9–C10, C22–C10 bond lengths are 1.522 Å, 1.525
VJC, 55(2), 2017 Duong Tuan Quang et al.
142
Å, 1.530 Å, nearly the same as the C–C single bond
(1.5 Å). The C10–N19 bond length is 1.496 Å,
nearly the same as the C–N single bond (1.5 Å). The
results show that the C10 atom acquires sp
3
hybrid
state.
The N19, N34, N36, N44 atoms acquire sp
3
hybrid state, but the N19–C10–C20–C32, N34–
C33–C35–H77, N36–C35–C37–H78, N44–C40–
O45–O46 dihedral angles are 3.60, 6.80, 6.30, 0.10,
respectively, different from the N-H-H-H dihedral
angle of 35
0
in NH3.
The structure of RT was again confirmed by the
results obtained from AIM analysis. The calculated
values of (r) and 2(ρ(r)) at the BCPs of RT are
listed in table 4. The topological properties of the
BCPs are summarized in Fig. 4a.
The results obtained from AIM analysis also
indicate the presence of the BCPs in each of the
intermolecular contacts in RT, especially at the new
bonds formed. A RCP is found in the central area of
the C10, N19, C20, C21 and C22 atom, indicating
the presence of spirolactam ring in RT. The
molecular structure of RT obtained from the
theoretical investigations agrees well with
experimental results as shown in figure 2.
Figure 4: The topological properties of RT (a) and
RG (b), at the Bond Critical Points (BCPs) and Ring
Critical Point (RCPs): Bond Critical Points (BCPs)
denoted by red color, Ring Critical Points (RCPs)
denoted by yellow color
Table 3: The structural parameters of RT, bond lengths in angstrom, angles in degrees
Bond lengths B3LYP Bond angles B3LYP Dihedral angles B3LYP
C1–C2 1.425 C1–C2–C3 118.9 C1–C2–C3–C4 -0.1
C2–C3 1.396 C4–O7–C8 118.9 C3–C4–O7–C8 179.9
C4–N7 1.373 C5–C10–C9 110.2 C5–C10–C9–C14 -178.6
N7–C8 1.370 C9–C10–N19 110.6 O7–C8–C11–C12 -179.7
C8–C9 1.392 C5–C10–C22 112.2 C4–C5–C10–N19 121.3
C9–C10 1.525 C22–C10–N19 100.1 C9–C10–C22–C26 -63.8
C5–C10 1.522 C10–N19–C20 114.3 C9–C10–N19–C20 -116.5
C8–C11 1.395 N19–C20–O27 125.4 C10–N19–C20–C21 -1.8
C10–N19 1.496 C21–C20–O27 128.5 C10–N19–C20–O27 178.1
C10–C22 1.530 C22–C21–C23 121.8 O27–C20–N19–C32 3.8
C20–N19 1.373 C20–N19–C32 121.3 C20–N19–C32–C33 -78.0
C20–C21 1.486 N19–C32–C33 112.1 N19–C32–C33–N34 167.0
C21–C22 1.390 C32–C33–N34 112.3 C32–C33–N34–C35 87.5
C20–O27 1.224 C33–N34–C35 125.6 C33–N34–C35–N36 176.1
N19–C32 1.451 N34–C35–N36 111.4 C33–N34–C35–S43 -1.5
C32–C33 1.541 N34–C35–S43 123.5 N34–C35–N36–C37 170.0
C33–C34 1.458 S43–C35–N36 125.1 C35–N36–C37–C38 154.2
N34–C35 1.360 C35–N36–C37 130.8 C37–C38–C39–C40 0.3
C35–S43 1.670 C37–C38–C39 121.0 C39–C40–N44–O45 -179.3
C35–N36 1.391 C40–N44–O45 117.8 C39–C40–N44–O46 0.7
VJC, 55(2), 2017 A fluorescent chemodosimeter based on
143
Bond lengths B3LYP Bond angles B3LYP Dihedral angles B3LYP
N36–C37 1.401 C40–N44–O46 117.8 C4–C3–C2–N16 -178.4
C37–C38 1.406 O45–N44–O46 124.4 C8–C11–C12–N17 177.0
C40–N44 1.468 C2–N16–C30–C31 -175.8
N44–O45 1.227 C12–N17–C28–C29 179.4
N44–O46 1.228
Table 4: Electron density (ρ(r), in au) and the Laplacian (2(ρ(r)), in au) of RT and RG at the
B3LYP/LanL2DZ level of theory
3.3. The application of sensor
The previously published experimental results
indicated that RT could be used as a fluorescent
chemodosimeter for selective detection of Hg(II)
ions in water media in the presence of the competing
metal ions. The addition of Hg(II) ions to the
aqueous solution of the chemodosimeter RT caused
an irreversible fluorescence OFF-ON response with
a remarkable visual color change from colorless to
pink. The experimental results suggested that the
addition of Hg(II) induced a desulfurization reaction
and cyclic guanylation of thiourea moiety followed
by the ring-opening of rhodamine spirolactam in
RT, finally, a new rearrangement product RG was
formed as shown in figure 5. This led to the change
in fluorescence signal [12].
Figure 5: The proposed mechanism of the reaction
between RT and Hg(II) ions
To shed light on the cause of the fluorescence
signal changes in the reaction between Hg(II) ions
and RT to form RG, the theoretical investigation on
the optimized geometry of the ground state, excited
states, AIM and NBD analysis have been conducted
for both RT and RG.
The optimized geometry of RG (with the
numbering scheme of the atoms) is identified at the
B3LYP/LanL2DZ level of theory and is shown in
figure 6. The calculated values of (r) and 2(ρ(r))
at the BCPs of RG are listed in table 3. The
topological properties of the BCPs are summarized
in figure 4b. The results obtained from AIM analysis
confirms the presence of bonds through the presence
of the BCPs in each of the intermolecular contacts in
RG, especially at the new bonds formed or the new
Figure 6: The optimized geometry of RG with the
numbering scheme of the atoms at the
B3LYP/LanL2DZ level of theory
Compound Bond (r) 1 2 3
2
((r))
Critical Point
RT N34C35 0.300 4.544 -1.278 -3.239 0.249 BCP
C10N19C20C21C22 0.042 -5.676 -0.178 -3.566 0.163 RCP
RG N22C23 0.272 -1.019 -1.188 -3.153 0.249 BCP
N22C23N24C25C26 0.045 0.133 -1.029 -4.565 0.163 RCP
VJC, 55(2), 2017 Duong Tuan Quang et al.
144
bonds cleaved. The results obtained from AIM
analysis show the presence of a RCP in the central
area of the N22, C23, N24, C25, and C26 atom.
There is not any RCP in the central area of the C10,
C15, C16, C21, N22 and O27 atom in RG,
suggesting the presence of guanidine ring, and the
absence of spirolactam ring in RG. These theoretical
investigations agree well with experimental results
as shown in figure 5.
The UV-Vis spectra, the electronic and
fluorescent properties of RT and RG were
calculated using the TD-DFT method at the same
level optimized structure. Fig. 7 shows that RT
exhibits a characteristic absorption band at 543.6 nm
with a insignificant oscillation strength of 0.0003.
Meanwhile, RG exhibits a characteristic absorption
band at 476.5 nm with strong oscillation strength of
0.5727. These calculated results are quite similar to
the experimental investigations.
Figure 7: The UV-Vis spectra of RT (a) and RG (b) at the B3LYP/LanL2DZ level of theory
The UV-Vis experimental spectra of RT (c) and RG (d).
Table 5: Calculated excitation energy (E), wavelength (λ), and oscillator strength (f) for low-laying singlet
state of RT and RG
Compound Main orbital
transition
TD-DFT/B3LYP/LanL2DZ
CIC
a
E(eV) (nm) f
RT S0 S1 163 164 0.7065 2.13 581.79 0.0003
S0 →S2 162 164 0.7064 2.28 548.63 0.0003
S0 →S3 160 164 0.6106 2.52 492.60 0.0002
RG S0 S1 159 160 0.7060 1.79 691.58 0.0009
S0 →S2 155 161 0.1255 2.60 476.55 0.5727
159 161 0.5797
S0 →S3 159 162 0.7018 2.69 460.23 0.0102
aCI expansion coefficients for the main orbital transitions.
(a)
(b)
450 500 550 600 650
0,0
0,1
0,2
0,3
0,4
A
b
so
rb
a
n
ce
Wavelength (nm)
450 500 550 600 650
0,0
0,1
0,2
0,3
0,4
A
b
so
rb
a
n
ce
Wavelength (nm)
(c) (d)
VJC, 55(2), 2017 A fluorescent chemodosimeter based on
145
The main orbital transitions were calculated
using TD-DFT at the B3LYP/LanL2DZ level of
theory and presented in table 5, Figs. 8 and 9. The
oscillator strength of all singlet electronic transition
of RT is insignificant, f < 0.01, indicating that RT is
not a fluorescent compound [24]. The singlet
electronic transition of RG is mainly contributed by
the S0→S2 transitions with the strongest oscillation
strength of 0.5727, and is composed of the
transitions from MO-155→MO-161 and MO-
159→MO-161. The transition from MO-155 to MO-
161 does not cause the fluorescence. This is due to
the fact that MO-155 belongs to receptor, but MO-
161 belongs to fluorophore (Fig. 8), therefore the
space distance between them is large, preventing the
fluorescence. It is similar to the Förster Resonance
Energy Transfer (FRET) - based sensors [25]. The
transition from MO-159 to MO-161 is an important
transition to cause the fluorescence in RG. Here, the
PET process from receptor to fluorophore does not
occur in RG because there is not any MO belonging
to the receptor with energy level between MO-159
and MO-161 (Fig. 9).
NBO analysis results in table 6 provide more
thorough insight into the bond properties and
intermolecular orbital interaction, and therefore
make clearer the fluorescent properties of RT and
RG. The results further confirm the presence of
spirolactam ring in RT molecule. The π-bond
conjugated system of rhodamine fluorophore is
broken at C10 atom and this causes the fluorescence
quenching of RT. Meanwhile, the formation of
guanidine ring and spirolactam ring-opening in RG
restore the π-bond conjugated system of rhodamine
fluorophore, causing the strong fluorescence in RG.
Figure 9: Frontier orbital energy diagram of free
fluorophore, receptor and chemosimeter RT and RG
(The energy levels are relative, not in proportion)
Figure 8: Molecular orbital plots of RT and RG at the B3LYP/LanL2DZ level. C, N, S, and H atoms
denoted as gray, blue, yellow, and white atoms, respectively
VJC, 55(2), 2017 Duong Tuan Quang et al.
146
Table 6: Significant second-order interaction energies (E
(2)
, in kcal mol
-1
) between donor and acceptor
orbitals in RT and RG (at the B3LYP/LanL2DZ level of theory)
Donor NBO (i) Acceptor NBO (j) E
(2)
Donor NBO (i) Acceptor NBO (j) E
(2)
RT RG
π(C1–C6) π*(C2–C3) 21.22 π(C1–C6) π*(C2–C3) 20.68
π(C1–C6) π*(C4–C5) 16.53 π(C1–C6) π*(C4–C5) 16.45
π(C2–C3) π*(C1–C6) 15.84 π(C2–C3) π*(C1–C6) 16.67
π(C2–C3) π*(C4–C5) 26.99 π(C2–C3) π*(C4–C5) 28.09
π(C4–C5) π*(C1–C6) 21.63 π(C4–C5) π*(C1–C6) 22.26
π(C4–C5) π*(C2–C3) 14.91 π(C4–C5) π*(C2–C3) 18.04
π(C8–C9) π*(C11–C12) 16.63 π(C4–C5) π*(C9–C10) 17.75
π(C8–C9) π*(C13–C14) 21.57 π(C8–C11) π*(C9–C10) 16.20
π(C11–C12) π*(C8–C9) 25.78 π(C8–C11) π*(C12–C17) 17.79
π(C11–C12) π*(C13–C14) 16.72 π(C9–C10) π*(C4–C5) 13.65
π(C13–C14) π*(C8–C9) 18.03 π(C9–C10) π*(C8–C11) 17.79
π(C13–C14) π*(C11–C12) 22.24 π(C9–C10) π*(C13–C14) 15.54
π(C12–N17) π*(C8–C11) 12.39
π(C12–N17) π*(C13–C14) 10.65
π(C13–C14) π*(C9–C10) 17.95
π(C13–C14) π*(C12–N17) 17.69
4. CONCLUSION
The fluorescent chemodosimeter RT based on
rhodamine derivative for detection of mercury ions
was studied, including the synthesis process,
characteristics and applications. The optimized
geometry and the electron properties of RT and RG
were identified at the B3LYP/LanL2DZ level of
theory with a combination of AIM and NBO
analysis. The obtained results showed that the
presence of spirolactam ring in RT led to break the
π-bond conjugated system of rhodamine fluorophore
at C10 atom, causing the fluorescence quenching of
RT. Meanwhile, the formation of guanidine ring and
spirolactam ring-opening in RG restored the π-bond
conjugated system of rhodamine fluorophore,
leading to the strong fluorescence in RG. As a
result, RT could be used as an OFF-ON fluorescent
chemodosimeter for detection of Hg(II) ions.
Acknowledgment. This research was funded by the
Vietnam National Foundation for Science and
Technology Development (NAFOSTED) under grant
number 104.04-2014.35 (DTQ).
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Corresponding author: Duong Tuan Quang
College of Education - Hue University, Hue City, Vietnam
No. 34, Le Loi, Hue City, Thua Thien Hue
E-mail: duongtuanquang@dhsphue.edu.vn; Telephone number: 0914050126.
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