1,1-Difluoro-3-aryl(heteroaryl)-1: H -pyrido[1,2- c] [1,3,5,2]oxadiazaborinin-9-ium-1-uides: Synthesis; Structure; and photophysical, electrochemical, and BSA-binding studies

Article abstract of DOI:10.1039/c7nj04032f

This paper presents a series of six examples of 1,1-difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1-uides (2) - in which aryl(heteroaryl) = phenyl, 4-MeC₆H₄, 4-N(CH₃)₂C₆H<

Full text of DOI:10.1039/c7nj04032f

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T. P. Calheiro, B. A. Iglesias, T. Acunha, S. Franceschini, A. Ketzer, A. R. Meyer, L. V. Rodrigues, P. A.
Nogara, J. B. T. Rocha, M. A. P. Martins and N. Zanatta, New J. Chem., 2017, DOI: 10.1039/C7NJ04032F.
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PAPER
Jason B. Benedict et al.
The role of atropisomers on the photo-reactivity and fatigue of
diarylethene-based metal–organic frameworks
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1,1-Difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uides: Synthesis; structural
characterization; and photophysical, electrochemical, and BSA-
binding studies
17Received 00th January 20xx,
Accepted 00th January 20xx
DOI: 10.1039/x0xx00000x
Helio G. Bonacorso,a* Tainara P. Calheiro,a Bernardo A. Iglesias,b* Thiago V. Acunha,b Steffany Z.
Franceschini,a Alex Ketzer,a Alexandre R. Meyer,a Letícia V. Rodrigues,a Pablo A. Nogara,c João B. T.
Rocha,c Nilo Zanatta,a and Marcos A. P. Martins a
www.rsc.org/
This paper presents a series of six examples of 1,1-difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-
ium-1-uides (2) — in which aryl(heteroaryl) = phenyl, 4-MeC6H4, 4-N(CH3)2C6H4, 4-NO2C6H4, 2-naphthyl, and 2-thienyl — as
pyridine-based boron heterocycles with variable ligand structures. The heterocycles 2 were easily synthesized at yields of
51–70 % from reactions — at room temperature for 24 h — of simple N-(pyridin-2-yl)benzamides (1) with BF3·Et2O, and
they were fully characterized by 1H-, 13C-, 19F-, and 11B-NMR, GC–MS, and X-ray diffractometry. The optical and
electrochemical properties of 2 (UV–vis, fluorescence, quantum yield calculations, Stokes shift, redox potential, and DFT
calculations) were determined and discussed. BSA-binding experiments and molecular docking studies of new complexes 2
were
performed
and
correlated
between
each
other.
pyridine (I, II), quinoxalines (III), and 1,8 naphthyridines (IV)
have also been explored in the synthesis of similar compounds
(Figure 1).
Introduction
Fluorescent organoboron compounds have been extensively
explored in recent years, and their photophysical properties
have been utilized in many fields of current research. Among
boron complexes, boron-dipyrromethene (BODIPY) and its
derivatives have excellent fluorescence properties; for
example, outstanding fluorescence quantum yields, sharp
absorption and fluorescence spectra, and high chemical
stability.1
Fig 1. Examples of compounds containing a BF2 core.
The optical and physical properties of boron complexes and
their derivatives have been explored in energy conversion
devices (organic light-emitting diodes and organic
Compounds like the ones shown in Figure 1 have widespread
applications; for example, in chemosensors,9 biomolecular
labeling,10 and photodynamic therapy.11 Recent research has
also described the use of these structures as fluorescence
lifetime probes for DNA interactions.12 Additionally, bovine
serum albumin (BSA) has been used as a model protein in
research, due to its high stability, low cost, and similar
structure to human serum albumin. The interaction between
dyes and BSA changes the fluorescent signal of dyes, thus
providing a convenient method to achieve the detection of
BSA.13
Recently Grabarz14 and Bednarska15 reported the synthesis of
similar pyridine systems using cyclic and acyclic unsaturated
chains, as π-conjugated spacer moieties, binding a dimethyl
amino group to the difluoroboranyl structures in order to
evaluate their photochemical properties. However, there is a
lack for understanding of the electronic effects on the
photovoltaics),2–4
energy
transport
devices,5
solar
concentrators,6 and NIR-absorbing systems.7 All these features
are beneficial for the spectroscopic properties inducing well-
defined and sharp absorption and emission transitions, high
quantum yields, and suitable excited-state lifetimes.8
Additionally, many nitrogenated heterocyclic scaffolds like
a.Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química,
Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil. E-mail:
helio.bonacorso@ufsm.br
b.Departamento de Química, Universidade Federal de Santa Maria, Santa Maria, RS
97105-900, Brazil. E-mail: bernardopgq@gmail.com
c. Laboratório de Bioquímica Toxicológica, Departamento de Bioquímica e Biologia
Molecular, Universidade Federal de Santa Maria, 97105-900, Santa Maria-RS,
Brazil
†
Electronic Supplementary Information (ESI) available: [details of any
supplementary information available should be included here]. See
DOI: 10.1039/x0xx00000x
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photophysical and electrochemical properties, as well as BSA- In Table 1 it can be seen that the best yields for the series of
binding studies for specific 3-aryl(heteroaryl)-substituted 2a–f were obtained for complexes containing a substituent
scaffolds. In this way, we firstly developed the synthesis under with a strong electron-withdrawing group (–R) — for example,
mild conditions (room temperature) for a series of fluoro- 2d (R = 4-NO2C6H4 at 70% yield); while the lowest yield was
organoboron compounds (
starting from BF3OEt2 and selected N-(pyridin-2-yl)benzamides group (+R) — that is, 2f (R = 2-thienyl at 51% yield).
). Amide
were previously described by Devi16 as simple but Specific details of the experimental procedures and complete
useful building blocks. After the synthesis of the fluorinated data for structural characterization via NMR and GC–MS are
heterocycles , we conducted studies to evaluate the optical described in the supplementary material.
and electrochemical properties, as well as theoretical The new structures of were confirmed and characterized by
calculations. Additionally, BSA binding assays and a molecular 1H-, 13C-, 11B-, and 19F-NMR, and their purity was evaluated
2) containing the pyridine ring, observed for the complex containing the electron-donating
(
1
1
2
2
docking study were done.
from CHN elemental analysis. The structural assignments for
1
synthesized benzamides 1a–f are consistent with the H- and
13C-NMR spectra described in the literature for these
compounds.16 Thus, upon comparing the 1H- and 13C-NMR data
Results and discussion
of the benzamide precursors
1 with the new oxadiazaborinin
Synthesis
derivatives 2, no significant differences were seen in the
chemical shift values.
The
1,1-difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uides (2a–f) were prepared
1
A comparison between the H-NMR data of compounds 2a–f
using the N-(pyridine-2-yl)benzamides
(
1a–f
)
previously
and 1a–f showed that the major evidence for the formation of
synthesized in accordance with the procedure described in the
literature.16 The benzamides (1a–f) were obtained from the
reaction of 2-aminopyridine with the respective aldehydes,
using aqueous hydrogen peroxide and water. Subsequently,
starting from the procedures previously described in the
literature,17,18 the benzamides 1a–f were subjected to the
compounds
2 was the signal disappearance of the hydrogen
atom bonded to the nitrogen atom (N-H) in
ppm.
1, at 8.60–8.84
Also, in order to demonstrate the formation of the BF2
complexes, 19F- and 11B-NMR experiments were performed. In
the CDCl3 spectra for compounds 2a–f, the 19F-NMR showed a
distorted quartet for each compound, with a broad base on
average at -138.80 ppm (-139.62 to -137.95 ppm), which is in
agreement with similar compounds described in the
literature.17,19 In the 11B-NMR spectra, the 11B signals for the
series of compounds appear as a well-defined triplet for each
compound, due to the coupling with the two 19F nuclei. The
chemical shifts for the boron atoms were observed on average
at 0.50 ppm (0.37 to 0.65 ppm), with a coupling constant
average of 13 Hz, which is due to the coupling between the
atoms of boron and fluorine.
.
optimized reaction conditions, with BF3 Et2O in anhydrous
chloroform at room temperature for 24 h, using triethylamine
as base, which furnished the desired fluorine–boron
compounds 2a–f at satisfactory to good yields (51–70 %). The
synthetic route, yields, and the structures of the synthesized
four-coordinated organo-boron compounds
Table 1.
2 are shown in
Table 1 Synthesis of 1,1-difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uides.a,b
Finally, and in order to determine the real molecular structure
of the compounds of series
2 in solid state, a single crystal X-
ray diffraction measurement was performed for the BF2
compound 2b (Figure 2).
Fig 2. ORTEP and selected lengths and bond angles of
organoboron compound 2b (CCDC 1529635).20 Displacement
ellipsoids are drawn at the 50% probability level, and H atoms
are represented by circles with arbitrary radii.
The new organoboron compounds 2a–f were obtained without
decomposition, as yellow or white air-stable solids, with
melting points in the range of 142–145 °C (2f) to 200–202 °C
(
2e).
2 | J. Name., 2012, 00, 1-3
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The crystals of compound 2b were obtained by slowly 340 nm (an average of the absorption bands between 330-350
evaporating a dichloromethane solution at room temperature. nm). In general, the organoboron compounds exhibited
Compound 2b was crystallized in a monoclinic lattice without emissions in the purple-blue region (400–460 nm range). As
solvates. The central B-atom has
a slightly distorted already observed in the ground state, they had locations
tetrahedron geometry, with B-F, B-N, and B-O distances of comparable with the emission maxima, which indicates that
1.352, 1.567 and 1.440 Å, respectively, and bond angles different organic moieties in the organoboron complexes 2a–f
around the B-atom ranging from 108.54° (F1-B1-N9) to 110.41° did not play a fundamental role in the excited state of these
(F1-B1-F2). These values for bond lengths and bond angles are compounds. When the nature of the pyridyl-BF2-type
normal for similar fluoro-organoboro heterocycles.21
molecules in the excited state was compared, the same
The dihedral angle between the atoms N(4)-C(3)-C(31)-C(32) behaviour was observed in the emission spectra (Figure 4).
had a torsion angle of 1.9 (2)°, which suggests that the These results can probably also be attributed to the nature of
oxazaborinine ring and the p-toluoyl substituent are almost in the π→π* intraligand electronic transition, which indicates
a periplanar orientation. The detailed crystallographic data are that these compounds allow better electronic delocalization in
summarized in the supplementary material.
the excited state.16,19
General absorption and emission properties of organoboron
compounds 2a–f
The comparative absorption spectra of compounds 2a–f, using
chloroform as solvent, are shown in Figure 3. The optical
properties are listed in Table 2. The absorption in the
organoboron derivatives
300 nm in the UV region, which can be attributed to the
transition band of the intraligand *; and the other at 310–
410 nm, which can be attributed to the n→ * transition. It can
2 indicates bands as follows: at 260–
Fig. 4. Comparative emission spectra of organoboron
complexes 2a–f containing different substituent groups in
π→π
CHCl3 solutions at λexc = 340 nm.
π
The Stokes shifts observed in the excited state for these
molecules indicate that boron derivatives show some charge
separation (50–90 nm), which can be attributed to the
intramolecular charge transfer character (ICT) in the excited
state (Table 2).
be seen that the band shifts occur due to the electronic
properties of the substituents present in the molecules. As an
example, for compounds with substituent R = 4-NMe2C6H4
(e.g., 2c), a red shift is seen, contrary to what is observed for
derivative 2a (R = C6H5) and 2d (R = 4-NO2C6H4 — see Figure 3).
These facts can be attributed to: the withdrawing effect of the
Table 2. UV–vis and emission analysis data for compounds 2a–
f.
1
c
Comp.
2a
λ
,
nm
(
ε
, M-
λem
,
Φfl
Stokes
shifts
(nm)d
87
cm-1)a
nmb
π-electronic conjugation and the internal resonance (2d as a
nitro group).
266 (1711), 324
(sh), 335 (2869),
351 (sh)
422
0.003
2b
2c
2d
2e
271 (2740), 339
(5577), 353 (sh)
293 (622), 317
(459), 403 (3074)
274 (sh), 336
(3237)
409
454
423
404
0.140
0.217
70
51
87
63
< 0.001
0.167
262 (3666), 286
(sh), 341 (3814),
362 (sh)
Fig 3. Comparative electronic UV-vis absorption spectra of
organoboron complexes 2a–f containing different substituent
groups in CHCl3 solutions.
2f
271 (1540), 351
(4429)
411
0.176
60
sh = shoulder; aMeasured in chloroform; bIn chloroform
(
λexc
Φfl
=
=
340 nm); c9,10-Diphenylanthracene in CHCl3 as standard
(
The emission fluorescence spectra were recorded in N2
saturated chloroform solution obtained by exciting the
0.65); dꢀλ
= λem – λabs.
compounds 2a-f at the absorption maxima wavelength of λexc
=
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The BF2-derivatives 2a–f had lower fluorescence quantum LUMO densities distributed internally throughout each
yields when compared to the 9,10-Diphenylanthracene molecule; however, for compounds 2c and 2e it was seen that
quencher standard (Table 2). This suggests that the presence the HOMO density is located on the dimethylaminophenyl and
of the boron atom seems to be a non-efficient and non- naphthyl substituents, respectively. The theoretical UV-Vis
radiative deactivation channel in these pyridyl-structure types. spectra and related data (Table S3 and Figure S13
supplementary material) are in agreement with the
experimental values.
Electrochemical behavior of organoboron complexes 2a–f
Table 3. Energy and HOMO-LUMO density plots for 2a-f.
Cyclic voltammetry analysis of derivatives 2a–f was recorded in
0.1 M TBAPF6 CH3CN solution with a glassy carbon electrode,
Comp.
HOMO
LUMO
Energy
(eV)
using a platinum wire with a pseudo-reference electrode in
acetonitrile, within a range of -1.50 to +2.00 V versus SHE
(Figure 5 and Table 4). The CV data is referenced to the
standard internal Fc/Fc+ (0.49 V vs. SHE in CH3CN).
3.867
2a
In general, the electrochemical behavior of the organoboron
compounds 2a–f indicates a reduction process in the -0.60 to -
1.20 V range in the cathodic region, which can be attributed to
the fact that the reduction in the core of the organoboron
complexes in all of the structures probably forms
π-anion
radical species.22 In almost all cases, the re-oxidation of the
organoboron complexes is not observed, except for compound
2d (R = 4-C6H4NO2), which indicates the decomposition of the
pyridine unit upon reduction.
2b
2c
2d
2e
3.781
3.070
3.440
3.340
In the positive range (anodic region), oxidation peaks were
observed in compounds 2a–f, within the +0.70 to +1.50 V
potential range, which can be attributed to the π-radical cation
species formation in the organoboron complexes.23,24
2f
3.653
Fig. 5. Comparative redox potentials of compounds 2a–f using
TBAPF6 as supporting electrolyte.
DFT calculations
BSA binding assays
For a better insight into the frontier orbitals of 2a–f, DFT
calculations were performed for these compounds with the
Gaussian 09 package of programs.25
The electronic spectra of BSA in the absence and presence of
the organoboron derivatives 2a–f are shown in Figure 7 and in
the Supplementary data. For free BSA, the peak observed at
280 nm corresponds to the absorption of tryptophan and
tyrosine residues.26 The enhancement, upon addition of the
boron-complexes, in the BSA’s absorption band at 280 nm
indicated that these compounds bind to the protein.
All geometrical structures were optimized at the SCRF(PCM)-
B3LYP/cc-pVTZ level of theory, with the single point energies
and molecular orbitals calculated at the TD-DFT-B3LYP/cc-pVTZ
level of theory.
The data in Table 3 show the HOMO and LUMO density of
compounds 2a–f. Most of the compounds had the HOMO and
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Table 4. Electrochemical data for compounds 2a–f.
ARTICLE
d
Comp.
2a
R
E0-0
HOMOe
-5.552
-5.555
-5.953
-5.633
-5.839
-5.559
LUMOf
-2.298
-2.111
-2.656
-2.421
-2.405
-2.105
Ε1 (V)
-0.970a
-0.917a
-1.013a
-0.638c
-0.931a
-0.828a
Ε2 (V)
+0.752b
+0.755b
+1.153b
-0.930a
-1.197c
+0.759b
Ε3 (V)
+1.353b
+1.309b
+1.266b
+0.833b
+1.039b
+1.299b
Ε4 (V)
-----
C6H4
3.254
3.444
3.297
3.212
3.434
3.454
2b
4-CH3C6H4
4-NMe2C6H4
4-NO2C6H4
2-Naphtyl
2-Thienyl
-----
2c
+1.406b
+1.448b
-----
2d
2e
2f
-----
aEpc = cathodic peak; bEpa = anodic peak; cE1/2 = Epc + Epa / 2; dDetermined from the interception of the normalized
absorption and emission spectra (E0-0 = 1240/λintercp in eV); eEHOMO = - [4.8 + 1stEox (vs. SHE)]eV; fELUMO = [EHOMO + E0-0]eV
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Comp.
Κ
SV (M-1)
Κ
b (M-1)
n
6.03 x 103
8.59 x 103
1.16 x 104
5.24 x 104
2.54 x 105
1.80 x 105
8.10 x 102
1.37 x 103
1.51 x 104
1.46 x 104
1.99 x 104
1.77 x 104
0.27
0.21
0.38
0.25
0.32
0.21
The electronic spectral change of BSA upon incremental
addition of these molecules may reflect the change in the
environment of the amino acid residues; that is, the
conformational changes that occur upon binding with these
compounds. Such a significant variation in the electronic
spectra of BSA indicates that these compounds bind to BSA to
form a complex, which induces conformational changes in the
BSA molecule.
2a
2b
2c
2d
2e
2f
Molecular docking of BSA
The equilibrium (Kb) and quenching (KSV) constants were
evaluated from the linear plots of emission intensities versus
organoboron complex concentration — the values obtained
are shown in Table 5. The relatively high quenching (104 M−1
range) and binding constant values (104 to 105 M−1 range)
obtained for the organoboron complexes suggests that there is
a good interaction between the compounds and the BSA
structure. As an example, compound 2e exhibited the highest
binding and quenching constant values (Figure 6). The number
of binding sites n is close to 1, which suggests the presence of
a single binding site for the compounds in the BSA molecule.
All the BSA emission assays are shown in the Supplementary
data.
The blind docking simulation showed that most of the
conformers of compounds interact in the region close to
2
Trp134. Thus, a local semi-flexible docking was done in the
region around the Trp34 residue, with the lateral chain of the
residues Arg185, Lys136, Lys131, Trp134, Tyr137 and Tyr160
flexible, in order to increase the interactions between ligand
and protein.
The semi-flexible docking showed that the compounds that
have the benzene ring (2a–2d) bind between two α-helix,
interacting weakly with the Trp134. However, compounds 2e
and 2f interact directly with the Trp134 residue, via π-π
stacking between the imidazole ring of Trp134 and the 2-
naphtyl and 2-thienyl substituents of the respective
compounds 2 (Figure 7).
Fig. 6. Fluorescence quenching emission spectra of BSA in the
absence and presence of compound 2e (BSA = 1.0
0 – 100 M).
ꢁM and 2e =
ꢁ
Fig. 7. Binding sites of the organoboron complexes with the
BSA.
A conformation pattern was observed for compounds 2a–d
,
which indicates that the substituents in the benzene ring do
not change the orientation of the molecules in the BSA
protein. On the other hand, compounds 2e and 2f — which
have naphthalene and thiophene rings, respectively — interact
with the Trp134.
Table 5. Stern–Volmer quenching constant (KSV), binding
constant (Kb), and the number of binding sites (n) for the
interactions of compounds with BSA.
Thus, correlating the values determined by the Stern-Volmer
quenching and binding constants and the molecular docking, it
could be seen that both experiments show the more
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pronounced interaction of tryptophan with compounds 2e and atoms were calculated for idealized positions. The structures
2f. It is believed that this increased interaction occurs because were solved with SHELXS-2013 by using direct methods and
of the stereochemistry of these compounds.
refined with SHELXL-2013 on F2 for all reflections.
The molecular graph was prepared using ORTEP-3 for
Windows.29 The crystallographic data for the structure of 2b
have been deposited with the Cambridge Crystallographic Data
Centre and allocated the deposition number CCDC 1529635.
Copies of the data can be obtained free of charge upon
application to: CCDC, 12 Union Road, Cambridge CB2 1EZ, UK
(fax: +44 1223336033 or deposit@ccdc.com.ac.uk).
Conclusions
In summary, we firstly described the easy synthesis of 1,1-
difluoro-3-aryl(heteroaryl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uides
(
2)
—
from very
are
accessible benzamides 1 — at good yields. Compounds
2
UV-vis absorption spectra were recorded on a Shimadzu
UV2600 spectrophotometer, using chloroform as solvent.
Emission spectra of samples in CHCl3 and DMSO/PBS mixture
solutions were measured with a Varian Cary 50 Eclipse
fluorescence spectrophotometer (emission; slit 2.0 mm), and
were corrected in accordance with the manufacturer’s
solid, air-stable, easy to handle, and could be fully
1
characterized by H-, 13C-, 11B- and 19F-NMR spectroscopy and
X-ray diffractometry. The pyridinyl-boron complexes showed
small differences in emission fluorescence values for both
electron-donating and electron-accepting groups. The DFT
calculations showed HOMO and LUMO densities distributed
throughout each molecule; however, compounds 2c and 2e
instructions. Fluorescence quantum yields (Φfl) of the
compounds 2a–f in solutions were determined by comparing
had
HOMO
densities
and
distributed
2-naphthyl
over
the
4-
the corrected fluorescence spectra with that of 9,10-
dimethylaminophenyl
substituents,
Diphenylanthracene in chloroform
standard.30
(Φfl = 0.65) as the
respectively. The results of the BSA-binding studies for
compounds 2e (2-naphthyl substituted) and 2f (2-thienyl
substituted) indicated that the greatest interaction was with
the tryptophan site.
Cyclic voltammograms were recorded on an AutoLab
EcoChimie PGSTAT 32N potenciostat/galvanostat system, at
room temperature under argon atmosphere, using dry
acetonitrile solution (Sigma-Aldrich). Electrochemical grade
tetrabutylammonium hexafluorophosphate (0.1 M, TBAPF6,
Sigma-Aldrich) was used as supporting electrolyte. These
Experimental section
Unless otherwise indicated, all common reagents and solvents
were used as obtained from commercial suppliers, without
further purification. 1H- and 13C-NMR spectra were acquired on
Bruker Avance III 400 MHz spectrometers for one-dimensional
experiments, with 5 mm sample tubes, 298 K, and digital
resolution of 0.01 ppm, in CDCl3 as solvent and using TMS as
the internal reference. The 19F- and 11B-NMR spectra were
acquired on a Bruker Avance III (19F at 564 MHz and 11B at 192
MHz), equipped with a 5 mm PABBO probe, 5 mm sample
tubes at 298 K, digital resolution of 0.01 ppm, in CDCl3, and
experiments were performed using
a standard three-
component system: a glassy carbon working electrode, a
platinum wire auxiliary electrode, and a platinum wire pseudo-
reference electrode. For monitoring of the reference
electrode, the Fc/Fc+ couple was used as an internal reference
(E1/2 = 0.46 V vs. NHE). All measurements were performed at
room temperature (298 K).31
All theoretical calculations were performed with the Gaussian
09 package of programs.25 The structures of the compounds
were full optimized without any constrain at the B3LYP/cc-
pVTZ level of theory. The PCM model was used for account the
acetonitrile solvent effect. Harmonic frequencies calculations
were performed with de aim to confirm that the geometries
are on minimum of potential energy. UV-vis spectroscopic
properties were obtained by TD-DFT single point calculations
at the B3LYP/cc-pVTZ level and the acetonitrile solvent effects
were accounted by the PCM model.
.
using CFCl3 and BF3 OEt2, respectively, as the external
reference.
All results are reported with the chemical shift (δ), multiplicity,
integration, and coupling constant (Hz). The following
abbreviations were used to explain multiplicities: s = singlet, d
= doublet, t = triplet, q = quartet, m = multiplet, and dd =
double doublet. All NMR chemical shifts are reported in parts
per million, relative to the internal reference. All melting
points were determined using coverslips on a Microquímica
MQAPF-302 apparatus and are uncorrected. The CHN
elemental analyses were performed on a Perkin–Elmer 2400
CHN elemental analyzer (University of São Paulo, Brazil).
The reflections for the X-ray diffractometry were measured by
using a D8 Venture, Bruker Photon CMOS Detector (MoKα
radiation: λ = 0.71073 Å)27 up to a resolution of (sin u/l)max =
0.60 Å1, at a temperature of 293 K. The structures were solved
with SHELXS-201328 by using direct methods, and they were
refined with SHELXL-201326 on F2 for all reflections. Non-
hydrogen atoms were refined by using anisotropic
displacement parameters. The positions of the hydrogen
The 3D structure of BSA was obtained from the Protein Data
Bank (http://www.rcsb.org/pdb/) with the following code:
4f5s.32 The Chimera 1.8 software33 was used to remove the
chain B, waters, and other molecules, and also to add
hydrogens to the BSA protein. The ligands were built in the
Avogadro 1.1.1 software,34 following the semi-empirical PM635
geometry optimization, using the MOPAC2012 program.36 The
ligands and protein were generated in the pdbqt format by
Auto Dock Tools — the ligands were considered to be flexible
(with PM6 charges) and the enzyme rigid (with Gasteiger
charges).37
The Auto Dock Vina 1.1.1 program was used for the blind
docking,38 using a gridbox of 92 x 62 x 86 and the coordinates x
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Journal Name
= 9.457, y = 23.359, and z = 98.149, with an exhaustiveness of 1,1-difluoro-3-(p-tolyl)-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-
50. Due to the Auto Dock not recognizing the B atom, it was ium-1-uide (2b)
replaced by C, in the pdbqt file. The semi-flexible docking was
Physical state: white solid. Melting point: 184–186 °C. Yield:
1
58%. NMR H (400 MHz, CDCl3) : δ = 8.36 (d, J = 5 Hz, 1H-Py),
done in the region involving the Trp134 residue, with a gridbox
of 30 x 30 x 35 and the coordinates x = 20.324, y = 33.690, and
8.26 (d, J = 8 Hz, 2H-Ph), 8.07 (t, J = 8 Hz, 1H-Py), 7.50 (d, J = 8
z = 97.801. The lateral chain of the residues Arg185, Lys136,
Hz, 1H-Py), 7.36 (t, J = 7 Hz, 1H-Py), 7.31 (d, J = 8 Hz, 2H-Ph),
2.46 (s, 3H- CH3). NMR 13C (100 MHz, CDCl3): δ = 165.7 (C-3),
Lys131, Trp134, Tyr137, and Tyr160 was considered flexible
during the docking, in order to increase the interactions
154.6 (C-4a), 144.2 (C-Py), 143.7 (C-Py), 138.5 (C-Py), 129.7 (C-
between ligand and protein. The conformer that interacts
Ph), 129.5 (C-Ph), 129.2 (C-Ph), 123.4 (C-Py), 120.3 (C-Py) 21.8
1
(C- CH3). NMR 19F (564 MHz, CDCl3): δ = -138.68 (q, JB-F = 14
most closely with the Trp134 residue was selected. The results
Hz) (BF2). NMR 11B (192 MHz, CDCl3): δ = 0.56 (t, 1JB-F = 13 Hz).
from the docking were analyzed using the Accelrys Discovery
Studio 3.5 software.39
GC–MS (EI, 70 (eV): m/z (rel.int.) 259 (55) [M – H ]+, 241 (6) [M
-
F]+, 91 (100) [M C6H4BF2N2O]+. Anal. Calcd. for
–
General procedure for the synthesis of N-(pyridin-2-yl)benzamides
C13H11BF2N2O: C, 60.04; H, 4.26; N, 10.77. Found:t C,58.98 ; H,
4.18; N,10.59.
(1a–f)
The N-(pyridin-2-yl) benzamides were synthesized in
accordance with the procedure described in the literature.16
3-(4-(dimethylamino)phenyl)-1,1-difluoro-1H-
pyrido[1,2c][1,3,5,2]oxadiazaborinin-9-ium-1-uide (2c)14
General procedure for the synthesis of 1,1-difluoro-3-
Physical state: yellow solid (orange powder).14 Melting point:
aryl(heteroaryl)-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1- 165–168 °C (Mp 167−169 °C).14 Yield: 52 %. NMR 1H (400 MHz,
uides (2a–f)
CDCl3) δ = 8.25 – 8.22 (m, 2H-Ph), 7.97 (t, J = 7 Hz, 1H-Py), 7.40
(d, J = 7 Hz, 1H-Py), 7.23 (t, J = 7 Hz, 1H-Ph), 6.70 (d, J = 8 Hz,
2H-Ph), 3.09 (s, 6H- CH3). NMR 13C (100 MHz, CDCl3): δ = 166.1
(C-3), 155.2 (C-4a), 153.9 (C-Ph), 142.9 (C-Py), 138.1 (C-Py),
131.7 (C-Ph), 131.1 (C-Ph), 123.0 (C-Py), 118.8 (C-Py), 110.9 (C-
Ph) 39.9 (C- CH3). NMR 19F (564 MHz, CDCl3): δ = - 139.58 (q,
1JB-F = 14 Hz) (BF2). NMR 11B (192 MHz, CDCl3): δ = 0.51 (t, 1JB-F
= 13 Hz). GC–MS (EI, 70 (eV): m/z (rel.int.) 289 (81) [M]+, 288
(58) [M – H]+, 148 (100) [M – C6H4BF2N2O]+. Anal. Calcd. for
C14H14BF2N3O: C, 58.17; H, 4.88; N, 14.54. Found: C, 58.08; H,
4.70 ; N,14.88.
The BF2 complexes
2 were synthesized using a procedure
similar to that described in the literature.17,18 Solutions of the
respective N-(pyridin-2-yl)benzamides 1a–f (3 mmol), BF3·Et2O
(6.0 mL, 49 mmol), and anhydrous triethylamine (4.5 mL, 32
mmol) in anhydrous chloroform (60 mL) were magnetically
stirred for 24 h at room temperature. At the end of the
reactions (TLC), the resulting mixtures were extracted with
dichloromethane (3 x 20 mL) and water (3 x 20 mL). The
organic phase of each reaction was dried over anhydrous
Na2SO4, and the solvent was evaporated under reduced
pressure. The crude products 2a–f were purified by column 1,1-difluoro-3-(4-nitrophenyl)-1H-pyrido[1,2-
chromatography on silica gel 60, using dichloromethane as the c][1,3,5,2]oxadiazaborinin-9-ium-1-uide (2d)
eluent.
Physical state: yellow solid. Melting point: 198–202 °C. Yield:
1
70 %. NMR H (400 MHz, CDCl3) δ = 8.54 (d, J = 8 Hz, 2H-Ph),
8.46 (m, 1H-Py), 8.34 (d, J = 8 Hz, 2H-Ph), 8.20 (t, J = 7 Hz, 1H-
Py), 7.62 (d, J = 8 Hz, 1H-Py), 7.52 (t, J = 7 Hz, 1H-Py). NMR 13C
(100 MHz, CDCl3): δ = 163.2 (C-3), 153.9 (C-4a), 150.6 (C-Ph),
144.3 (C-Py), 139.1 (C-Py), 137.9 (C-Ph), 130.5 (C-Ph), 128.9 (C-
Ph) 123.5 (C-Py), 121.7 (C-Py). NMR 19F (564 MHz, CDCl3): δ = -
1,1-difluoro-3-phenyl-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-
ium-1-uide (2a)
1
137.98 (q, JB-F = 13 Hz) (BF2). NMR 11B (192 MHz, CDCl3): δ =
1
Physical state: yellow solid. Melting point: 144–145 °C. Yield:
1
54%. NMR H (400 MHz, CDCl3): δ = 8.37- 8.35 (m, 3H, Ph and
0.56 (t, JB-F = 13 Hz). GC–MS (EI, 70 (eV): m/z (rel.int.) 291
(100) [M]+, 272 (5) [M – F]+, 150 (69) [M – C6H4BF2N2O]+. Anal.
Calcd. for C12H8BF2N3O3: C, 49.53; H, 2.77; N, 14.44. Found: C,
49.53; H, 2.88; N, 14.25.
H-Py), 8.08 (t, J = 7 Hz, 1H-Py), 7.59 (t, J = 7 Hz, 1H-Py), 7.54 (d,
J = 8 Hz, 1H-Py), 7.48 (t, J = 8 Hz, 2H, Ph), 7.38 (t, J = 7 Hz, 1H-
Py). NMR 13C (100 MHz, CDCl3): δ = 165.7 (C-3), 154.6 (C-4a),
143.8 (C-Py), 138.6 (C-Py), 133.2 (C-Ph), 132.3 (C-Ph), 129.6 (C-
Ph), 128.4 (C-Ph), 123.5 (C-Py) 120.5 (C-Py). NMR 19F (564 MHz,
1,1-difluoro-3-(naphthalen-2-yl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uide (2e)
1
CDCl3): δ = -138.52 (q, JB-F = 14 Hz) (BF2). NMR 11B (192 MHz,
1
Physical state: yellow solid. Melting point: 200–202 °C. Yield:
1
64 %. NMR H (400 MHz, CDCl3) δ = 8.94 (s, 1H- naph), 8.41 –
CDCl3): δ (ppm): 0.59 (t, JB-F = 13 Hz). GC–MS (EI, 70 (eV): m/z
(rel.int.) 246 (78) [M]+, 245 (100) [M – H ]+, 227 (5) [M - F]+, 169
(1) [M – C6H5]+. Anal. Calcd. for C12H9BF2N2O: C, 58.58; H, 3.69;
N, 11.39. Found: C,58.76; H, 3.92 ; N,11.16.
8.38 (m, 2H- Py and Naph), 8.13 (t, J = 7 Hz, 1H-Py), 8.02 (d, J =
7 Hz, 1H-Py), 7.92 (t, J = 7 Hz, 1H-Naph), 7.64 – 7.65 (m, 1H-
Naph), 7.43 (t, J = 7 Hz, 1H-Py). NMR 13C (100 MHz, CDCl3): δ =
165.6 (C-3), 154.5 (C-4a), 143.9 (C-Py), 138.7 (C-Py), 135.8 (C-
8 | J. Name., 2012, 00, 1-3
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ARTICLE
Naph), 132.6 (C- Naph), 131.3 (C-Naph), 129.6 (C-Naph), 128.5
(C-Naph) 128.1 (C-Naph), 127.9 (C-Naph), 126.7 (C-Naph),
125.1 (C-Naph), 123.6 (C-Py), 120.7 (C-Py) .NMR 19F (564 MHz,
7
8
9
G. Ulrich, S. Goeb, A. De Nicola, P. Retailleau and R. Ziessel,
J. Org. Chem., 2011, 76, 4489.
D. Frath, J. Massue, G. Ulrich and R. Ziessel, Angew. Chem.,
2014, 53, 2290.
1
CDCl3): δ = - 138.53 (q, JB-F = 14 Hz) (BF2). NMR 11B (192 MHz,
1
CDCl3): δ = 0.64 (t, JB-F = 13 Hz).GC–MS (EI, 70 (eV): m/z
(rel.int.) 296 (32) [M]+, 127 (100) [M – C6H4BF2N2O]+. Anal.
E. Okutan, S. O. Tumay and S. Yeşilot, J Fluoresc., 2016, 6,
2333.
Calcd. for C16H11BF2N2O: C, 64.91; H, 3.74; N, 9.46. Found: C, 10 V. I. Martynov, A. A. Pakhomov, N. V. Popova, I. E. Deyev,
64.72; H, 3.70; N, 9.88.
and A. G. Petrenko, Acta Naturae, 2016,
11 A. Kamkaew, S. H. Lim, H. B. Lee, L. V. Kiew, L. Y. Chungc
and K. Burgess, Chem. Soc. Rev., 2013, , 77.
4, 33.
1,1-difluoro-3-(thiophen-2-yl)-1H-pyrido[1,2-
c][1,3,5,2]oxadiazaborinin-9-ium-1-uide (2f)
1
12 D. Dziuba, P. Jurkiewicz, M. Cebecauer, M. Hof and M.
Hocek, Angew. Chem., 2016, 55, 174.
Physical state: yellow solid. Melting point: 142–145 °C. Yield:
51 %. NMR 1H (400 MHz, CDCl3) δ = 8.33 (s, 1H-Py), 8.07 - 8.03
(m, 2H-Py and Thienyl), 7.64 (d, J = 5 Hz, 1H- Thienyl), 7.46 (d, J
= 8 Hz, 1H-Py), 7.35 (t, J = 7 Hz, 1H-Py), 7.15 (t, J = 4 Hz, 1H-
Thienyl). NMR 13C (100 MHz, CDCl3): δ = 161.8 (C-3), 154.5 (C-
4a), 143.7 (C-Py), 138.7 (C-Py), 136.7 (C- Thienyl), 133.8 (C-
Thienyl), 133.7 (C- Thienyl), 128.4 (C- Thienyl), 123.2 (C-Py),
13 K. Jurek, J. Kabatc and K. Kostrzewska, Color. Technol.,
2017, 133, 170.
14 A. M. Grabarz, A. D. Laurent, B. Jędrzejewska, A.
Zakrzewska, D. Jacquemin, and B. Osmiałowski, J. Org.
Chem., 2016, 81, 2280.
15 J. Bednarska, R. Zalesny, M. Wielgus, B. Jedrzejewska, R.
Puttreddy, K. Rissanen, W. Bartkowiak, H. Ågren and B.
Osmiałowski, Phys. Chem. Chem. Phys., 2017, 19, 5705.
16 E. S. Devi, A. Alanthadka, A. Tamilselvi, S. Nagarajan, V.
Sridharana and C. U. Maheswaria, Org. Biomol. Chem.,
2016, 35, 8228.
120.2 (C-Py). NMR 19F (564 MHz, CDCl3): δ = - 139.05 (q, 1JB-F
=
13 Hz) (BF2). NMR 11B (192 MHz, CDCl3): δ = 0.37 (t, JB-F = 13
Hz). GC–MS (EI, 70 (eV): m/z (rel.int.) 252 (68) [M]+, 233 (5) [M
– F]+, 111 (100) [M – C6H4BF2N2O]+.
1
Anal. Calcd. for C10H7BF2N2OS: C, 47.65; H, 2.80; N, 11.11.
Found: C,47.95; H, 2.75; N,11.01.
17 H.G. Bonacorso, T. P. Calheiro, B. A. Iglesias, I. R. C. Berni, E.
N. da Silva Júnior, J. B. T. Rocha, N. Zanatta and M. A. P.
Martins, Tetrahedron Lett., 2016, 57, 5017.
18 Y-Y. Wu, Y. Chen, G-Z. Gou, W-H. Mu, X. J. Lv, M. L. Du and
W-F Fu, Org. Lett., 2012, 20, 5226.
Conflicts of interest
There are no conflicts to declare.
19 X. Xie, Y. Yuan, R. Krüger and M. Bröring, Magn. Reson.
Chem., 2009, 47, 1024.
20 The crystallographic data for the structure of 2b have been
deposited with the Cambridge Crystallographic Data Centre
and allocated the deposition number CCDC 1529635.
Copies of the data can be obtained free of charge, on
application to CCDC, 12 Union Road, Cambridge CB2 1EZ,
UK (fax: +44 1223336033 or deposit@ccdc.com.ac.uk).
21 S. Hachiya, T. Inagaki, D. Hashizume, S. Maki, H. Niwa and
T. Hirano, Tetrahedron Lett., 2010, 51, 1613.
Acknowledgments
The authors thank the Coordination for Improvement of
Higher Education Personnel (CAPES) for the fellowships, and
the National Council for Scientific and Technological
Development (CNPq) for financial support (Process numbers
306.883/2015-5 and 402.075/2016-1 CNPq/Universal).
22 A. Harriman, L. J. Mallon, G. Ulrich and R. Ziessel,
Supplementary material
ChemPhysChem., 2007, 8, 1207.
Supplementary material associated with this article can be 23 K. Krumova, G. Cosa, J. Am. Chem. Soc., 2010, 132, 17560.
found, in the online version, at…
24 J. Bartelmess, W. W. Weare, N. Latortue, C. Duongb and D.
S. Jones, New J. Chem., 2013, 37, 2663.
25 Gaussian 09, Revision A.02, M. J. Frisch, G. W. Trucks, H. B.
Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G.
Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M.
Caricato, A. Marenich, J. Bloino, B. G. Janesko, R.
Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F.
Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F.
Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T.
Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N.
Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R.
Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O.
Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery,
Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E.
Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R.
Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C.
References and notes
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Journal Name
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New fluorinated pyridine-based boron heterocycles showing optical properties were
easy prepared and fully characterized. BSA-binding and molecular docking studies
indicated strong interactions with the tryptophan site.
N
R
N
F
O
B
F
06 examples,
up to 70% yield