Pentafluorophenyl dipyrrin as probe for transition metal ion detection and bioremediation in: Bacillus subtilis and Bacillus cereus

Article abstract of DOI:10.1039/c7nj02157g

We report a highly sensitive and selective "turn-on" fluorescent/colorimetric probe, 5-(pentafluorophenyl)dipyrrin (1), for selected transition metal ions in aqueous medium at biological pH. The limit of detection for Zn(ii), Hg(ii), Cu(ii) and Ni(ii) is

Full text of DOI:10.1039/c7nj02157g

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ISSN 1144-0546
PAPER
Jason B. Benedict et al.
The role of atropisomers on the photo-reactivity and fatigue of
diarylethene-based metal–organic frameworks
rsc.li/njc

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Pentafluorophenyl dipyrrin as probe for transition metal ion detection and its
bioremediation in Bacillus subtilis and Bacillus cereus
Dijo Prasannan and Chellaiah Arunkumar*
Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut,
Kozhikode, Kerala, India - 673 601; E-mail: arunkumarc@nitc.ac.in
Abstract:
We report the highly sensitive and selective ‘‘turn-on’’ fluorescent / colorimetric probe,
5ꢀ(pentafluorophenyl)dipyrrin (1) for selected transition metal ions in aqueous medium at
biological pH. The limit of detection for Zn(II), Hg(II), Cu(II) and Ni(II) is found to be as 0.18
µM, 0.28 µM,13.01 µM and 18.31 µM respectively. Mechanism of complexation is confirmed as
1:2 ratio of metal to ligand by Job’s plot and mass spectrometry. The practical application of the
probe in bioremediation of metal ions by B. subtilis (BS) and B. cereus (BC) has been
demonstrated and the tolerance level of microorganisms against metal ions is identified. The
emission peak centered at a long wavelength of 548 to 558 nm indicates the potential application
of this probe in bioꢀimaging Zn(II) and Hg(II) by fluorescence microscopy. Thus, it is possible to
track the ions absorbed by BS and BC.
Keywords: Pentafluorophenyl dipyrrin, Colorimetric, Fluorescent Probing, Crystal structure,
Electrochemistry, Bioremediation.
______________________________________________________________________

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Introduction
Metal ions play a vital role in the chemistry of life and their concentration has to be
maintained within an acceptable range to ensure normal biochemical functions.1 As redox
cofactor of metalloenzymes, zinc, copper and nickel perform assorted physiological functions
and they involved in gene transcription, protein metabolism, DNA replication, etc.2,3 These metal
ions are added as an environmental impurity during numerous industrial activities such as
extraction, metal plating, steel processing, coal / waste combustion, etc. Their effect on
environmental issues are regularly reviewed and extensively studied because of various chronic
hazards on living organisms.4,5 The typical methods of removal of toxic metals from
environment via precipitation, filtration, ion exchange, flotation, evaporative recovery, using
hierarchical or nano structures, etc are often inefficient or expensive.6–10 As microorganisms
develop resistance to toxic metal pollutants, bioremediation11,12 is considered as one of the most
efficient, specific and economic metal ion removal methods. Bacillus sp. are used as an
inexpensive, effective and easily cultivable biosorbent for the removal of metal ions.13,14 Such
bioaccumulations are mostly determined by cell dry weighing, scanning electron microscopy,
atomic absorption spectroscopy etc.
Rational design and synthesis of chemosensors and ion probing molecules for metal ions
are thus important in both biology and environmental chemistry.4,15 The metal ion recognition
based on intramolecular16 or metalꢀligand charge transfer17–23
,
chelationꢀenhanced
fluorescence24–26, nonꢀcovalent interactions27, electrochemical properties28, quantum dots29–31 etc
with application in medical diagnosis32–34 are of special interest. The past few decades have
introduced molecules like BODIPY35, imidazole36, quinoline37, anthracene38, coumarin39,
Schiffbase26 etc for probing Zn(II), Cu(II), Ni(II) and Hg(II).40–45 However, some require
complicated syntheses and some are insoluble in aqueous medium. Currently, efforts to develop
sensors with improved sensitivity, selectivity, fast response time and multiple analyte
recognition26,46,47,48 by colorimetric48 / fluorometric49 methods are being focused.
Herein, we report the pentafluorophenyl dipyrrin probe which function as a “turnꢀon”
fluorescent probe for Zn(II)/Hg(II); which also displays recognizable colour change from yellow
to orange / pink respectively upon binding Ni(II)/Cu(II). The dipyrrin molecule rapidly
complexed with metal ions in aqueous medium at physiological pH and allows mapping at
cellular level. Although architectures based on dipyrrinato metal complexes and their application

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in ratiometric sensing / cell imaging are reported in the literature50,51, their use in monitoring
metal bioaccumulation in B. subtilis and B. cereus is unknown; and we are the first one to
monitor the bioremediation in Bacillus Sp using a dipyrrin ligand to the best of our knowledge.
The potential biological application of the dipyrrin was evaluated for in vitro detection of Zn(II)
and Hg(II) ions.
Results and discussion
Synthesis
The dipyrrin ligand, 1 was synthesized by the 2,3ꢀdichloroꢀ5,6ꢀdicyanoꢀ1,4ꢀbenzoquinone
(DDQ) oxidation of mesoꢀ(2,3,4,5,6ꢀpentafluorophenyl)dipyrromethane52 obtained from TFA
catalyzed condensation of pyrrole with 2,3,4,5,6ꢀpentafluorobenzaldehyde for 4 h in THF
medium under inert atmosphere at room temperature (Scheme 1).53
F
F
F
F
F
F
F
F
F
F
CHO
i) TFA, RT,
N2, 10 min.
DDQ, THF,
RT, N2, 4 hrs
F
F
F
F
+
N
H
ii) NaOH
HN
HN
PFDPM; 60 %
N
NH
F
PFDPMe; 1, 85 %
Scheme 1. Synthesis of dipyrrin, 1.
The purified dark brownish yellow powder of dipyrrin was yielded in 85 % after
1
separation on silica gel column using 1:1 chloroform / hexane. H NMR spectrum showed four
types of protons out of which three signals correspond to two hydrogen intensity and a pyrrolicꢀ
NH signal as broad singlet at 7.25 ppm, which confirms the structure (Figure S1). Further, IR
stretching and bending vibrations of -NH is observed at 3226 and 1650 cm−1 respectively. The βꢀ
H of pyrrole ring was observed near 768 cm−1; CꢀN bond appears at 1348 cm−1 and aryl fluorides
at 1255 and 1115 cm−1 (Figure S2). Above all, the single crystal XRD analysis confirms the
dipyrrin structure which is discussed later in this section.
Spectral properties
The photophysical properties of dipyrrin ligand, 1 were studied in solvents of varying
polarity and the data are listed in table S1. UVꢀVisible and emission spectra of dipyrrin in
various solvents are shown in figure S3. As anticipated, the π → π* transition of the dipyrrin

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chromophore appears as a broad band centered at 435 nm for most of the solvents except few.
Also, dipyrrin ligands do exhibit very weak fluorescence than its BODIPY counter parts.54 As
evident from the emission spectra, dipyrrin shows a very weak emission in organic solvents (508
to 533 nm), but no emission was observed in aqueous solution at biological pH 7.4 .
Single crystal X-ray diffraction analysis
Pentafluorophenyl dipyrrin, 1 was crystallized as single crystals of suitable XRD quality
in chloroform by slow evaporation at room temperature over a period of one week. The solid
state structure of 1 in orthorhombic crystal system with P212121 space group (Table 1) explored
by single crystal XRD technique; the crystallographic data and selected geometrical parameters
are presented in table 2.
Table 1. Crystal data and structure refinement parameters of pentafluorophenyl dipyrrin, 1.
Parameters
Molecular formula
Formula weight
CCDC number
Temperature / K
Crystal system
Space group
λ / Å
a / Å
b / Å
c / Å
α, (°)
1
C15H7F5N2
310.23
980776
293(2) K
Orthorhombic
P212121
0.71073
9.1606(9)
9.1763(10)
15.3777(19)
90
β (°)
90
γ (°)
90
1292.7(2)
4
1.594
624
Volume / Å3
Z
Densitycalcd/ mg mꢀ3
F(000)
θ range (°)
e data / unique
Rint
2.58 ꢀ 24.99
7128 / 2276
0.0471
Data
/
restraints
/
2276 / 14 / 204
parameters
GOF on F2
1.081
a
R1 , wR2b [I > 2σ(I)]
0.0378, 0.0989
aR1 = Σ||Fo|–|Fc||/Σ|Fo|; Io> 2σ (Io); bwR2 = [Σ w(Fo –Fc2)2/Σw(Fo ) ] .
2
2 2 1/2
Table 2. Intermolecular distances (in Å) for 1.
Interactionsa
(pyr)CꢁꢁꢁF
1b
3.130ꢀ3.155 (6)

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(ph)CꢁꢁꢁF
2.954 (2)
2.819 (2)
2.483 (2)
(pyr)CꢁꢁꢁH(pyr)
(pyr)HꢁꢁꢁF
(ph)HꢁꢁꢁH(pyr)
FꢁꢁꢁF
2.391 (2)
2.606ꢀ2.795 (4)
aDifferent types. bValue in parenthesis givesthe number of interactions of each types per molecule.
Figure 1. (a) ORTEP diagramof 1; (b) crystal packing diagram of 1 viewed down ‘c’ axis; (c) Hirshfeld surfaces
with normalized contact distance from ꢀ0.16 Å (red) to 1.28 Å (blue); (d) 2D fingerprint plots of all the
intermolecular contacts with di and de ranging from 1 to 2.56 Åand (e) Pie diagram showing the percentage of
interactions present.
The ORTEP and molecular crystal packing diagram viewed along ‘c’ axis are shown in
figure 1. As per the earlier report, the solid state structure of mesoꢀsubstituted dipyrrin exists as
dimer in (Z)ꢀsyn conformation formed through intramolecular hydrogenꢀbonding between iminoꢀ
N and aminoꢀNH atoms.55 Interestingly, there is no such intramolecular hydrogenꢀbonding
present in 1. Moreover, the interactions involving fluorine (FꢁꢁꢁC/H/F) is the key factor in
stabilizing the crystal structure as shown in figure 1b.
Nonꢀcovalent interactions present in the crystal structure are quantified by Hirshfeld
surface analysis. The Hirshfeld surfaces (HS) and 2D fingerprint plot (FP) is as shown in figure
1c, d. The pie diagram, figure 1e displays percentage distribution of individual intermolecular
interactions based on the results of HS analysis for the dipyrrin molecule. The contributions of

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CꢁꢁꢁF, CꢁꢁꢁH and FꢁꢁꢁF interactions are comparable and the interactions involving fluorine
(FꢁꢁꢁC/H/F) contribute maximum (57 %) for the crystal packing.
Chromogenic detection of Zn(II), Hg(II), Cu(II) and Ni(II) ions
The chromogenic ability of 1 in detecting various metals ions namely Ba2+, Ca2+, Cd2+,
Co2+, Cr3+, Fe3+, K+, Na+, Mg2+, Hg2+, Ni2+, Cu2+, Zn2+, Mn2+, Sn2+ and Al3+ was performed.
About 1 equiv. addition of each metal ion to 1, only Ni2+, Cu2+, Zn2+ and Hg2+ ions produced a
distinct colour change while other metal ions did not show any colour change even after the
addition of 100 equivalents (Figure 2b).
(a)
1.0
0.8
0.6
0.4
0.2
0.0
1 + Ni(II)
1 + Zn(II)
1
1 + Hg(II)
1 + Cu(II)
400
500
600
700
Wavelength (nm)
(b)
Figure 2. (a) Absorption changes of 1 (21 ꢂM) upon addition of 1 equiv. of different metal salts in PBS 1X buffer ꢀ
CH3OH mixture (99.33:0.67, v/v); (b) Color changes observed for 1 (21 ꢂM) upon the addition of various metal ions
(1 equiv.) under visible light.
These colour changes for the complexes [Ni(II)ꢀ1: orange; Cu(II)ꢀ1:pink; Zn(II)ꢀ1: pink
and Hg(II)ꢀ1: orange] are also reflected in consistent with the absorption spectral changes for
Ni2+ (486 nm), Cu2+ (480ꢀ534 nm), Zn2+ (526 nm) and Hg2+ (520 nm) ions while other metal ions
showed no change in the absorption spectra relative to 1 (Figure 2a). This observation indicates
that the receptor 1 could serve as a promising candidate of colorimetric probe for the detection of
Ni2+, Cu2+, Zn2+ and Hg2+ ions.

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Further, the binding affinity of dipyrrin with selective metal ions was quantitatively
studied by UVꢀVisible titration experiments. For instance, with incremental addition of Zn(II)
ions (0ꢀ2 equiv.) to a solution of 1, the absorption band corresponding to dipyrrin at 435 nm was
gradually decreased and a concomitant increase of new absorption band centered at 526 nm with
an isosbestic point at 468 nm is observed (Figure 3a).
0.5
0.5 (a)
(b)
2 equiv.
0.4
0.3
0.2
0.1
0.4
0.3
0.2
0.1
0.0
Zn2+
0 equiv.
200
300
400
500
600
700
0.0
(d)
0.5
1.0
1.5
2.0
[Zn2+] / [L]
Wavelength (nm)
0.5
0.4
0.3
0.2
0.1
0.0
(c)
0.5
L
Cu(II)
Ni(II)
Zn(II)
Hg(II)
0.4
0.3
0.2
0.1
0.0
300
400
500
600
700
Cu2+Al3+ Ba2+Ca2+Cd2+ Cr3+ K+ Mg2+Mn2+ Na+ Fe3+Co2+Sn2+ Ni2+ Zn2+Hg2+
Zn2+Zn2+Zn2+Zn2+Zn2+ Zn2+Zn2+Zn2+ Zn2+ Zn2+Zn2+ Zn2+Zn2+Zn2+ Zn2+
Wavelength (nm)
Figure 3. (a) Absorption spectra of 1 (21 ꢂM) after addition of increasing amounts of Zn(II) ions (0 to 2 equiv.) in
PBS 1X bufferꢀCH3OH (99.33:0.67, v/v) at room temperature; (b) Absorbance at 526 nm versus the number of
equivalents of Zn(II): Optical density as a function of concentration of Zn(II). (c) Absorbance of Zn(II) complex
with 1 in the presence of various metal ions and its (d) absorption spectra.
Further addition of Zn(II) ions, the absorption spectrum remained nearly a plateau
(Figure 3b) which doubtlessly imply the conversion of 1 to the corresponding zinc(II) complex
and the saturation level is observed at 0.5 equivalents of zinc. The binding property of 1 with
other metal ions, Cu(II), Ni(II) and Hg(II)ions were also studied (Figure S4, S5, S6); new peaks
were observed as 480ꢀ534 nm, 486 nm and 520 nm respectively and the saturation levels were
found as 0.4, 1 and 1 equivalents respectively. Interestingly, the absorption maxima as well as
the nature of the peaks of all complexes are different from each other.

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The strong absorptions in the region of 480ꢀ535 nm can be assigned to the characteristic
ligand to metal (LMCT) and π → π* charge transfer transitions; and the shoulder peaks in the
range of 302ꢀ368 nm possibly due to the metal perturbed intra ligand charge transfer (ILCT)
transitions.56
Fluorogenic detection of Zn(II) and Hg(II) ions
Though dipyrrin exhibits distinct emission properties in various organic solvents, it
displays little fluorescence intensity under the experimental conditions (PBS bufferꢀCH3OH
mixture). The fluorescence response of 1 (λex: 480 nm) was examined upon treating it with
various metal ions, all ions except Zn(II) and Hg(II) showed no appreciable increase in
fluorescence intensity (Figure 4a). Remarkably, a 440ꢀfold increase in emission intensity was
observed by the addition of one equivalent of Zn(II) ions which can be described as chelationꢀ
enhanced fluorescence (CHEF) effect acquired via complexation which can impart rigidity,
planarity and hence the stability for the dipyrrin group upon coordinating to Zn(II).51,57 This
intensity enhancement often brings the selective offꢀon type of fluorescent signaling behavior of
zinc(II)ꢀ1 complex.58 It was also noted that the intensity of the zinc(II)ꢀ1 complex is about three
times higher than mercury(II)ꢀ1 complex. The normalized fluorescence intensities are shown in
figure 4b clearly indicating that mercury(II)ꢀ1 emits at 548 nm and zinc(II)ꢀ1 at 558 nm. Thus,
the difference in emission intensity can be taken as an advantage to distinguish Hg(II) and
Zn(II)ions.
The fluorescence quantum yield measurements were done using fluorescein (Φf = 0.90)
as reference. The nominal fluorescence of 1 in presence of Hg(II) ions (Φf = 0.0012) does not
interfere the detection of Zn(II) ions (Φf = 0.0056). The emission efficiency is better than the
Zn(II)ꢀdipyrrin complex reported recently.59 It has to be marked that not only the coordinated
metal ion, but also the mode of coordination, the associated anion, the nature of solvent and the
substituents on the mesoꢀphenyl ring affects the quantum yield.60 Though the small size of
fluorine atoms may impose steric constraints on intramolecular rotations that restrain the nonꢀ
radiative energy loss of the excited state leading to the observed fluorescence ‘‘turn on’’.61 The
better selectivity of Zn(II) ion is also associated with the coordination preference ascribed to the
suitable size. Figure 4c shows the relative emission intensity of 1 (λex: 480 nm) upon treatment

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with different metal ions and the coordination of Zn(II) afforded an appreciable fluorescence
turnꢀon.
500
5
1.0
(b)
(a)
1 + Zn2+
4
3
2
1
0
400
300
200
100
0
0.8
0.6
0.4
0.2
0.0
Hg(II)
Zn(II)
450
500
550
600
650
700 750
1 + Hg2+
Wavelength (nm)
Dipyrrin and
other metal ions
500
550
600
650
700
750
500
550
600
650
700
Wavelength (nm)
Wavelength (nm)
500
400
300
200
100
0
500
400
300
200
100
0
(d)
(c)
Hg2+Al3+ Cr3+ K+ Na+ Ca2+Fe3+Mn2+Ni2+Sn2+Ba2+Cd2+Co2+Mg2+Cu2+ Zn2+
Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+Zn2+
L
Ba2+Ca2+Cd2+Co2+Cr3+Cu2+Fe2+Hg2+K+ Mg2+ Mn2+ Na+ Ni2+Sn2+ Zn2+Al3+
Figure 4. (a) Fluorescence spectra of 1 (21 ꢂM) in presence of various metal salts (21 ꢂM) in PBS 1X bufferꢀ
CH3OH; an inset image (zoomed in) of fluorescence spectra of the dipyrrin and with other metal ions; (b)
Normalized fluorescence intensities of Hg(II) and Zn(II) ions in presence of 1; (c) Bar graph shows the relative
emission intensity of 1 upon treatment with various metal ions; (d) Relative fluorescence of 1 (21 ꢂM) and its
complexation with Zn(II) (21 ꢂM) in the presence of various metal ions (λex= 480 nm).
Moreover, the selectivity of Zn(II) ion was tested on the fluorescence spectra of 1 with
Zn(II) in presence of other competing ions. The relative fluorescence of 1 and its complexation
with Zn(II) in the presence of various metal ions is shown in figure 4d. As observed, there is a
drop in fluorescence intensity of zinc(II)ꢀ1 in presence of metal cations like nickel, copper and
mercury ions which means 1 do not bind with Zn(II) with the same affinity as before,
independently of the presence of zinc / other competitive ions; still sufficient turnꢀon ratio is
observed for the detection of Zn(II).

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Fluorescence titration was performed on 1 with Zn(II) ions (0 to 1.2 equiv.) at pH 7.4
(Figure 5a). Upon gradual addition of Zn(II) metal ions to 1, a steady fluorescence turnꢀon with
no shift in emission maximum was noticed. The fluorescence intensity was increased till 0.5
equivalents after which it decreased or almost leveled off (Figure 5b); at a concentration of
Zn(II) greater than 8.4 µM, the emission intensity reached virtually a plateau. Earlier reports
suggest that dipyrrin ligand initially forms heteroleptic zinc complexes in the form of MLX (M =
Zn(II), L = dipyrrin ligand and X = Cl−) and shows fluorescent behavior, followed by the
formation of homoleptic ML2 complex due to the presence of excess dipyrrins.54 But, the initial
fluorescence itself sense Zn(II) ions so that the dipyrrin can be used as an effective “turn on”
probe for Zn(II) or Hg(II). For the quantitative application of the Zn(II)L2 complex, a
working curve24 was obtained, based on the fluorescence intensity at 558 nm vs. change in
concentrations of Zn(II) (Figure. S10a). The curve showed a good linear relationship between
the fluorescence intensity and zinc concentration suggesting that the quantitative detection of
Zn(II) is possible with 1.
200
150
100
50
200
160
120
80
1.2 equiv.
Zn2+
0 equiv.
40
0
510
540
570
600
630
660
690
0.0
0.2
0.4
0.6
0.8
1.0
1.2
[Zn2+] / [1]
Wavelength (nm)
Figure 5. (a) Fluorescence spectra of dipyrrin (20 ꢂM, λex = 480 nm) after addition of increasing amounts of Zn(II)
ions in PBS bufferꢀCH3OH at room temperature; (b) Intensity at 558 nm versus the number of equivalents of Zn(II),
Fluorescence intensity as a function of concentration of Zn(II).
The fluorescence titration of 1 with Hg(II) ions was also carried out and the emission
intensity increased gradually as the concentration of Hg(II) increases till 0.7 equivalents, after
which saturation was observed. The working curve shown in figure S10b for Hg(II) also suggests
that dipyrrin ligand could be used to measure the amount of mercuric ions unless zinc interferes,
as dipyrrin has greater affinity to zinc than to mercuric ions. Once Hg(II) complexes with

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dipyrrin moiety, the fluorescence intensity is less which indicates that the nonꢀradiative decay
channels are enhanced here compared to zinc.62,63 Recently, Chen et al. has reviewed molecular
sensors for Hg(II) promoted via formation of HgꢀN bonds.4 However, Cu(II) is likely to quench
fluorescence by mechanisms inherent to paramagnetic species which has been useful here to
differentiate it from zinc dipyrrinato complex.40 Nickel complexes are also fluorescent quenchers
due to the occurrence of low energy electronic absorptions in the visible region.64
It has been observed that 1 is selective and sensitive to Zn(II) ions in presence of
millimolar concentrations of other ions [Na(I), K(I), Ca(II), and Mg(II)] which are present in
biological systems in substantial amount. The emission property of Zn(II)L2 is useful to spot out
it in presence of copper ions. Zn(II) with its d10 electronic configuration weaken the
photoinduced electron transfer (PET) and provide fluorescence turnꢀon upon coordination with
dipyrrin.41 The ligand is photoꢀstable and provides rapid detection of Zn(II) at physiological pH.
So, it has been anticipated that the dipyrrin ligand 1 can provide good spatial and temporal
resolution to sense Zn(II) in biological samples.
Mechanism of complexation
The coordination chemistry of dipyrrins to form complexes with metal ions is well
reported.62,63 and as anticipated the metal ions [Zn(II), Cu(II) Ni(II) or Hg(II)] with dipyrrin
forms homoleptic ML2 crystal structures.51,55,56,65ꢀ68 The free ligand absorbs at 435 nm which can
be ascribed to S0 → S1 of dipyrrin moiety.69 The complexation with a M(II) ions have induced
bathochromic shift in this π → π* band and can be attributed to the intermolecular interactions
which effectively decreases the energy gap. The absorption spectra of all the complexes in
methanol show both spinꢀallowed π → π* ligandꢀcentered (LC) and metal to ligand charge
transfer (MLCT) between 200 to 400 nm. These are observed at 307, 385 nm in Cu complex,70
303, 368 nm in zinc complex; 302 nm in mercury complex and 303 in Ni complex. These high
energy absorptions are due to metal perturbed intra ligand charge transfer (ILCT) transitions
associated with the dipyrrin.56 The shoulder bands at wavelength greater than 500 nm is assigned
as the π → π* ligandꢀcentered transition of the dipyrrinato ligand or LMCT,56 as displayed at
524 nm in nickel complex.
The intensity and wavelength is comparable to boronꢀ and metalꢀdipyrrinato dyes. The
emission peak maxima for zinc and mercury complex fall in the range of 548 to 558 nm, similar

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to dipyrrinato metal complexes reported earlier.69 All these photophysical facts reflect the
position of metal coordinated to ligand.69 The dipyrrin ligand and the fluorine atoms act as
electronꢀdonating and withdrawing groups respectively. When probe interacts with metal ion in
buffer, a 1:2 or 1:1 (M to L) type of complex may be formed with electronꢀdonating nitrogen of
dipyrrin group.71,72 The internal charge transfer (ICT) results in fluorescence emission at 614 and
640 nm.50 Owing to the quenching nature, the nickel and copper complexes of 1 exhibit zero
luminescence whereas zinc and mercury complexes displayed an emission band at 558 nm and
548 nm respectively because of chelationꢀenhanced fluorescence (CHEF) effect.
Job’s plot measurements
The formation of stable dipyrrinato complexes of Zn(II), Cu(II), Ni(II) and Hg(II) in solid
state and its crystal structures are reported earlier.65–68 The Job plot investigation stipulates the
mechanistic analysis on the exact photophysics of dipyrrin complexes in solution phase. Here, it
is assumed that MnLm complex is the only one formed and so this is solely responsible for the
observed absorbance or emission intensity. The value of mole fraction of metal ion for which the
Job’s plot presents the maximum deviation gives the stoichiometry of the inclusion complex; if
the mole fraction of ion was at 0.5, it implicit a 1:1 metal to ligand complexation. Moreover, if it
lies between 0.29 to 0.63, the stoichiometry73,74 can be assumed to be either of 1:1 or 1:2
depending on the combinations of mole fractions of metal and ligand used. Here, the maximum
deviation of mole fraction of dipyrrin appeared at 0.58 (Figure 6) for zinc complex in both
fluorescence and absorption studies indicates the presence of either 1:1 or 1:2 metal to ligand
complexation which is similar to the reported value by Ulatowski et al75. Hence, dipyrrin ligand
may form stable L2Zn(II) complex in solution state and gives a stoichiometry of 1:2 metal to
ligand under this experimental conditions (PBS 1X buffer ꢀ CH3OH (99.33 : 0.67, v/v), pH = 7.4)
which is responsible for the observed photophysics to sense the metal ion.
In the case of Cu(II) to pentafluorophenyldipyrrin, the maxima is spotted at 0.53 which
clearly demonstrates a combined stoichiometry of 1:1 and 1:2. The broadness of absorption peak
also throws light to this fact. For nickel and mercury complexes, the maxima deviation were
found respectively at 0.55 and 0.58 mole fractions of pentafluorophenyl dipyrrin and therefore
the ratio of metal to ligand is 1:1 or 1:2. In all the above mentioned cases, there is a composite
stoichiometry between metal ion and ligands.

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350
(b)
300
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
(a)
250
200
150
100
50
0
0.0
0.2
0.4
0.6
0.8
1.0
0.0
0.2
0.4
0.6
0.8
1.0
[L] / {[L]+[Zn(II)]}
[L] / {[L]+[Zn(II)]}
Figure 6. Job’s plot for the determination of stoichiometry of dipyrrin with Zn(II); (a) Absorbance at 526 nm and
(b) Emission intensity at 558 nm were plotted against molar ratio [L]/{[L]+[Zn(II)]}.
The right stoichiometric ratio of metal to ligand can be further confirmed by mass
spectral analysis. For example, 12ꢀHg2+ complex was confirmed by ESIꢀmass spectral analysis.
The positive ion mode mass spectrum indicated that the 1:2 binding model between Hg2+ and 1
[m/z: 821.09 (found), 820.06 (calcd.)] as shown in figure 7.
F
F
F
F
F
F
F
N
N
N
N
Hg
F
F
F
(m/z: 820.06)
Figure 7. ESIꢀmass spectrum (positiveꢀion mode) of 1 (1.0 x 10−5 M) upon addition of 1 equiv. of Hg2+ (0.5 x 10−5
M) in MeOH.
Similarly, for 12ꢀNi2+ [m/z: 677.06 (found), 677.12 (calcd.)], 12ꢀCu2+ [m/z: 681.04
(found), 681.02 (calcd.)] and 12ꢀZn2+ [m/z: 683.03 (found), 682.03 (calcd.)] complexes were also
confirmed by mass analysis (Figure S7, S8, S9). Based on Job plot and ESIꢀmass data analysis,

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we propose that the two nitrogen atoms of 1 might bind to M2+ ion to have the tetra coordination
to form a stable complex as reported.76
One of the most important parameters in cation sensing is the detection limit. Dipyrrin
ligand with sensitivity and selectivity in the low to mid microꢀmolar range to Zn(II) are reported
previously.50 For many practical purposes, it is important to sense cations at extremely low
concentrations. Thus, based on the fluorescence titration measurements, the detection limit was
found using the formula 3σ/m where m is the slope and σ, the standard deviation. The limit of
detection for dipyrrin as a fluorescent sensor for Zn(II) was determined from the plot of
fluorescence intensity as
a
function of zinc concentration. It was found that
pentafluorophenyldipyrrin has a limit of detection of 0.18 µM for Zn(II) ions. Likewise for
mercury the detection limit is 0.28 µM. Similarly, detection limits were studied for Cu(II) and
Ni(II) complexes from the plot of absorption versus ion concentration, and were found to be
respectively, 13.01 µM and 18.31 µM.
Electrochemical studies
The electrochemical redox studies of dipyrrin ligand 1 along with metal ions [Ni(II),
Cu(II), Zn(II) and Hg(II)] were carried out using cyclic voltammetric and differential pulse
voltammetric techniques in presence of tetrabutylammonium hexafluorophosphate (NBu4PF6) as
supporting electrolyte and the results were listed in table 3. Dipyrrin ligands can undergo both
irreversible oneꢀelectron oxidation and reduction and the reversibility of the redox events depend
on the specific functionality at its periphery. Here, 1 displays two irreversible oxidation and two
quasiꢀreversible reduction peaks; number of reductions are more since the ligand is electron
deficient.77,78 The quasi reversible one electron reduction wave in the cyclic voltammogram of
free dipyrrin ligand 1, at ꢀ0.87 V indicates the formation of stable radical anion (Figure S11).
This stability is imparted by electron withdrawing fluorine atoms.59And, another quasi reversible
one electron reduction is observed at ꢀ1.17 V. The irreversible oxidation process is detected at
1.28 V at the anodic side. These potential values are comparable with the values reported by
Ducloiset et al.59 It has been reported that the dipyrrin based imine like pyrrole possess an
inherent basicity which may strongly influence the electroꢀactivity of pyrrole based cation
radicals and the observed irreversible oxidation peaks ensue from this. The oxidation waves also
results from nonꢀoxidized isolated pyrrole or on the dipyrrin fragment.79

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The addition of metal ions has effects on the redox potentials of 1. The metal complexes
also exhibited quasiꢀreversible peaks in cyclic voltammetry displaying their electron deficient
nature as well as stability of the complexes formed.62,63 The reduction waves are showing the
positive shift in metalꢀcomplex systems; ꢀ0.87 V for free ligand to ꢀ0.65 V, ꢀ0.57 V and ꢀ0.66 V
in copper, nickel and mercury complexes respectively. This reduction potential wave
disappeared upon complexation to zinc(II). Among the four ions coordinated, Ni(II) complex
showed most cathodic shift in potential compared to 1, ꢀ0.57 V. The complexation of metal ions
also produced a significant increase in current intensity.
The oxidation waves of the metal complexes are also showing the positive shifts in
potentials; 1.28 V for free ligand to 1.05 V, 0.96 V, 1.02 V and 1.16 V in copper, nickel, zinc
and mercury complexes respectively. Overall, the observed positive shift in redox potentials for
the metalꢀcomplex system over ligand indicates the electron deficient nature of dipyrrin core
upon complexation as well as the stability of complexes formed.62
Table 3. Comparison of halfꢀwave potentials (in V) for L and L2M complexes in CH3OH using 0.1 M NBu4PF6 at
25 °C.
Oxidation
Reduction
Compound
I
II
III
I
II
III
ꢀ1.17
ꢀ1.18
ꢀ
ꢀ1.12
ꢀ0.97
ꢀ
Dipyrrin, L
L2Cu
0.64
0.34
ꢀ
ꢀ
ꢀ
1.28
1.05
0.96
1.02
ꢀ0.30
ꢀ0.44
ꢀ0.30
ꢀ0.30
ꢀ0.06
ꢀ0.87
ꢀ0.65
ꢀ0.57
ꢀ
ꢀ
ꢀ
ꢀ
L2Ni
L2Zn
L2Hg
1.16
1.60
ꢀ0.66
Metal ion uptake by B. cereus and B. subtilis
Both Bacillus species showed active growth in 33 µg/mL of Zn(II), Cu(II) and Ni(II)
while with Hg(II), no growth was observed. The organisms tolerated up to 700 µg/mL of
Cu(II)/Ni(II), 33 µg/mL of Zn(II), and 25 µg/mL of Hg(II). Complete removal of Hg(II) and
Cu(II)/Ni(II), was achieved by Bacillus sps within 24 hours for concentration respectively, 25
and 33 µg/mL which strongly suggests them as candidates for bioremediation.

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0.5
0.4
0.3
0.2
0.1
0.0
1.00
0.95
0.90
0.85
0.80
0.75
0.70
0.65
BC-Cu
BS-Cu
BC-Ni
BS-Ni
Dipyrrin, L
0 h
4 h
8 h
24 h
48 h
0
10
20
30
40
50
60
70
300
400
500
600
Time (h)
Wavelength (nm)
Figure 8. (a) Absorption spectra of supernatant of BC maintained with Zn(II) in presence of dipyrrin ligand. (b)
Normalized absorbance at 486 nm of ligand 1 in presence of Ni(II) and Cu(II) treated with BC and BS.
The samples were removed at regular intervals and the supernatants obtained after
centrifugation were analyzed by absorption / fluorescence spectroscopy for residual metal
concentration. After 48 hours of incubation, the amount of Zn(II) ions incubated with BC
diminished and the spectra show the presence of free ligand [Figure 8(a)]. Quicker absorption of
Zn(II) was observed with BS cells compared to that of BC cells; the presence of free ligand is
observed from 8 hours onwards. Alternatively, the uptake of Zn(II) and Hg(II) could be
monitored by fluorescence spectroscopy (Figure S12). It was observed that, BC up took 59.2 %
of copper, 57 % of nickel whereas BS up took 62 and 50 % of nickel and copper respectively.
This proves that the ligand 1 can be used for the detection of metal ions in different levels of
biosorption. Hence, pentafluorophenyl dipyrrin can be used as an effective probe among the
molecules studied in UVꢀvisible / fluorescent spectroscopic methods.
Fluorescence microscopic studies
Dipyrrins have already been reported as selective turnꢀon probe for zinc ions in neuronal
vesicles.50 The uptake of Zn(II) and Hg(II) by BS and BC were imaged using fluorescence
microscopy. The dipyrrin ligand is cell permeable and it coordinated with the Zn(II) or Hg(II)
ions within the bacterial cells resulting in fluorescence (Figure 9). It has to be noted that the
metal ions should be in their +2 oxidation state within the bacterial environment for the probe to
detect its presence. As we were able to accomplish the fluorescence imaging of Zn(II) and Hg(II)
ion within the cell, it is clear that the ions are present as detectable forms. The strains of BS and
BC showed good absorption potential with Zn(II) and Hg(II) ions. The practical utility of the

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probe is examined by bioꢀimaging the analyte, both Zn(II) and Hg(II) specifically in living cells
without the interference of any other intercellular matter and was confirmed that the probe is
biocompatible in nature and detects metal ions rapidly.
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Figure 9. Uptake of ligand 1, by bacterial cells: Cells treated with metal ions, Zn(II) / Hg(II) were incubated with 1
for 30 min and processed for microscopic analysis. (a) untreated cells of B. cereus (b) bright field image of B. cereus
(c) B. cereus in presence of Zn(II) (d) B. cereus in presence of Hg(II) (e) untreated cells of B. subtilis (f) bright field
image of B. subtilis (g) B. cereus in presence of Zn(II) (h) B. subtilis in presence of Hg(II).
Conclusions
In conclusion, we report the easily synthesized 5ꢀ(pentafluorophenyl) dipyrrin as a dual
probe; a strong “turnꢀon” fluorescent probe for the detection of Zn(II)/Hg(II) ions and
colorimetric detection of Cu(II)/Ni(II) ions. The probe offers selectivity and fast response for
micro molar concentration of metal ions. Little effect was observed with competing alkali and
alkaline earth metal ions which are present abundantly in biological systems. The emission peak
centered at a long wavelength of 640 nm indicates the potential application of dipyrrin probe in
bioꢀimaging. Our venture has been to monitor bioremediation by spectroscopic techniques and it
is successful. Thus, dipyrrin 1 may be further established as a potential tool for the detection of
metal ions in environmental and biological samples. Current investigations including the exact
cellular compartment where the ions have been accumulated and its exact mechanism of action
are underway.

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Supplementary Data
Crystallographic data of pentafluorophenyl dipyrrin, 1 has been deposited with the
Cambridge Crystallographic Data Centre, CCDC reference number is 980776. Copy of this
information may be obtained free of charge from The Director, CCDC, 12 Union Road,
Cambridge, CB2 1EZ, UK (fax: + 44 1233336 033; eꢀmail: deposit@ccdc.cam.ac.uk).
Acknowledgements
CA (SB/EMEQꢀ016/2013) thanks DST, New Delhi for the financial support. We would
like to thank Dr. Babu Varghese, SAIF, IIT Madras for the single crystal data collection,
structure solution and refinement. We also thank Dr. Suchithra, T. V, Mrs. Sareena. C and Ms.
Anna. S. Kynadi, School of Biotechnology, NIT Calicut for their help in acquiring the biological
data. We thank School of Environmental Sciences, MG University, Kottayam for mass
spectrometric analysis.
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Pentafluorophenyl dipyrrin as probe for transition metal ion detection
and its bioremediation in Bacillus subtilis and Bacillus cereus
Dijo Prasannan and Chellaiah Arunkumar*
Recognition of transition metal ions and bioaccumulation in B. subtilis and B. cereus
were examined using pentafluorophenyl dipyrrin probe