Synthesis, characterization, crystal structure, and theoretical studies on Schiff-base compound 6-[(5-Bromopyridin-2-yl)iminomethyl]phenol

Article abstract of DOI:10.1007/s11224-009-9554-5

The title Schiff-base compound, 6-[(5-Bromopyridin-2-yl)iminomethyl]phenol (1), has been synthesized and characterized by elemental analyses, FT-IR, UV-Vis and ¹H-NMR spectroscopy, and X-ray single crystal diffraction. In the gas phase four iso

Full text of DOI:10.1007/s11224-009-9554-5

Struct Chem (2010) 21:153–157
DOI 10.1007/s11224-009-9554-5
ORIGINAL RESEARCH
Synthesis, characterization, crystal structure,
and theoretical studies on Schiff-base compound
6-[(5-Bromopyridin-2-yl)iminomethyl]phenol
•
Aliakbar Dehno Khalaji Alireza Najafi Chermahini
•
•
Karla Fejfarova Michal Dusek
Received: 31 August 2009 / Accepted: 10 November 2009 / Published online: 21 November 2009
Ó Springer Science+Business Media, LLC 2009
Abstract The title Schiff-base compound, 6-[(5-Bromo-
pyridin-2-yl)iminomethyl]phenol (1), has been synthesized
and characterized by elemental analyses, FT-IR, UV–Vis
metal complexes [5–8]. This activity increases by coordi-
nating a ligand to the metal ion, such as catalyst [9] and
interaction with DNA [10, 11]. Among the variety of
Schiff-base ligands, Salen derivatives have been studied
widely [5, 11–13]. In this article, we have succeeded in the
synthesis of new Schiff-base compound 6-[(5-Bromopyri-
din-2-yl)iminomethyl]phenol (1) and its characterization
by elemental analyses, FT-IR, UV–Vis and 1H-NMR
spectroscopy, and X-ray single crystal diffraction (Fig. 1).
1
and H-NMR spectroscopy, and X-ray single crystal dif-
fraction. In the gas phase four isomers were found for title
compound. Density functional (DFT) calculations have
been carried out and it was found that the A isomer is the
most stable one. The protonated imine N atom is involved
in intra- and inter-molecular hydrogen bonds with the
phenoxide group and H aromatic atoms, respectively.
The title compound displays a trans configuration about the
C=N double bond.
Experimental
Keywords Schiff-base compound Á Single crystal Á
Monoclinic Á Spectroscopy Á DFT
Physical techniques and materials
All reagents and solvents for synthesis and spectroscopic
studies were commercially available and used as received
1
without further purification. H-NMR spectra were mea-
Introduction
sured with a BRUKER DRX-500 AVANCE spectrometer
at 500 MHz and all chemical shifts are reported in d units
downfield from TMS. The infrared spectrum was recorded
on a JASCO 680 plus FT-IR spectrophotometer as a KBr
pellet.
Schiff-base compounds exhibit a wide range of biological
activities [1], anti-HIV [2, 3], anti-tumor activities [4], and
they play an important role in the synthesis of transition
Synthesis of 6-[(5-Bromopyridin-2-
A. D. Khalaji (&)
yl)iminomethyl]phenol (1)
Department of Chemistry, Faculty of Science,
Golestan University, Gorgan, Iran
e-mail: alidkhalaji@yahoo.com
Salicylaldehyde (36.6 mg, 0.3 mmol) and 5-bromo-2-ami-
nopyridine (51.9, 0.3 mmol) were dissolved in methanol
(10 mL). The mixture was stirred at room temperature for
30 min to give a clear yellow solution. Suitable crystals of
the title compound for X-ray study were formed by slow
evaporation of the solvent over 3 days at room temperature
(63 mg, yield 76%). Yellow crystals. IR (KBr pellet,
A. N. Chermahini
Department of Chemistry, Yasouj University,
Yasouj, Iran
K. Fejfarova Á M. Dusek
Institute of Physics of the ASCR, Na Slovance 2,
182 21 Prague 8, Czech Republic
123

154
Struct Chem (2010) 21:153–157
He
O
Hd
Hb
Table 1 Crystallographic and structure refinement for 1
Hh
Hi
N
Hg
Hf
Empirical formula
Formula weight
Crystal system, space group
T (K)
C12H9BrN2O
277.1
Hc
Br
N
Monoclinic, P21/c
120
N
Ha
˚
a (A)
5.7979(2)
8.5662(5)
21.7821(9)
91.584(3)
1081.42(9)
4
A
˚
b (A)
B
6
H
˚
c (A)
H
N
7
6
2
N 1
b (deg)
1
N
Br
3
V (A )
Br
˚
3
8
2
1
H
O
O
1
1
Z
H
l (mm-1
)
3.78
Crystal size (mm3)
0.28 9 0.16 9 0.10
0.502
C
D
H
N
H
N
Tmin
Tmax
0.690
Br
Br
Measured reflections
Independent reflections
Reflection with I [ 3r(I)
Parameters
4843
H
O
N
O
N
1822
H
1445
149
Fig. 1 Chemical structure and selected numbering of four conform-
ers considered in the gas phase of the title compound 1 with its
labeling
Rint
0.028
S
1.33
R[F2 [ 3r(F2)]
0.031
wR(F2)
0.076
cm-1): 2850–3080 (m, C–H aromatic and aliphatic), 1605
(s, C=N), 1490–1570 (m, C=C and C=N aromatic).
1H-NMR (CDCl3, d(ppm)): 6.94–6.97 (1H, t, Hd), 7.01–
7.03 (1H, d, Hb), 7.20–7.21 (1H, d, Hf), 7.26 (CDCl3),
7.39–7.43 (1H, td, He), 7.47–7.49 (1H, dd, Hc), 7.85–7.87
(1H, dd, Hh), 8.53 (1H, d, Hg), 9.39 (1H, s, Hi), 13.20
(1H, s, Ha).
-3
˚
Dqmax (e A
)
0.56
-3
)
˚
Dqmin (e A
-0.40
˚
Table 2 Selected bond lengths (A) and angles (°) optimized and
experimental of conformers 1 in the gas phase obtained at the DFT/6-
31?G(d) level of theory
X-ray data collection and structure determination
DFT/6-31?G(d)
Exp
A
B
C
D
Crystallographic measurements were done with four circle
CCD diffractometer Geminy of Oxford diffraction, Ltd.,
with graphite monochromated Mo Ka radiation (k =
N2–C3
N2–C6
C6–C7
C7–C8
C8–O1
O1–H1
C3–N1
N1–C2
C2–C1
C1–Br1
H1–N2
C3–N2–C6
N2–C3–N1
a
1.405
1.299
1.445
1.425
1.344
0.998
1.342
1.333
1.398
1.900
1.756
120.2
120.4
1.406
1.287
1.461
1.419
1.359
0.971
1.345
1.332
1.398
1.902
–
1.402
1.293
1.447
1.425
1.343
0.996
1.342
1.333
1.397
1.899
1.773
121.4
115.0
1.399
1.280
1.464
1.417
1.357
0.971
1.344
1.333
1.397
1.901
–
1.423
1.296
1.433
1.411
1.352
0.820a
1.338
1.333
1.398
1.896
1.873
119.1
119.1
˚
0.71073 A). The crystal structures was solved by direct
methods using program SIR2002 [14] and refined with the
Jana2006 program package [15] by full-matrix least-
squares technique on F2. The molecular structure plots
were prepared by using the ORTEP III [16]. Crystallo-
graphic data and details of the data collection and structure
refinements are listed in Table 1. Selected bond distances
and angles are listed in Table 2.
Computational details
118.7
121.6
119.4
115.8
Density functional theory (DFT) [17] calculations were
performed using Gaussian 98 program [18]. Geometries of
all species were optimized using 6-31G(d) and 6-31?G(d)
basis sets at the HF and DFT levels. Vibrational frequency
calculations were used to characterize all stationary
points as minima (the number of imaginary frequencies
Restrained to 0.82 A
(NIMAG = 0). All calculations were performed on a
Pentium IV Processor personal computer without any
constraint on the geometry.
123

Struct Chem (2010) 21:153–157
Results and discussions
Synthesis and spectroscopy
155
The bond angles C7–C6–N2 and C6–N2–C3 are 121.9(3)8
and 119.1(3)8, respectively, which is consistent with the sp2
hybrid character of C6 and N2 atoms. The two aromatic rings
in the roughly planar molecule of 1 (Fig. 3) are bridged by the
–C=N– fragment double bonds, with the distance between
The title compound 1 was obtained in yields 76%. It is air-
stable in the solid state for about 3–5 months. The stability
of dissolved compound is much shorter than in the solid
state and depends on the nature of the solvent. The title
compound is stable in methanol and acetonitrile solution at
room temperature for about 4 days and at 273 K for
9 days. Also, it remains unchanged in chloroform and
dichloromethane for about 1 day at room temperature and
3 days at 273 K. The title compound is slightly soluble in
common organic solvents such as acetonitrile and methanol
but completely soluble in chloroform and dichloromethane.
The strong bands at 1,605 cm-1 FT-IR spectra is
assigned to the C=N stretching vibration. The spectrum of
1 also shows several weak bands corresponding to aromatic
and aliphatic C–H stretching (2,850–3,080 cm-1), and
aromatic C=C or C=N stretching (1,490–1,570 cm-1). The
1H-NMR spectra of 1 is shown in Fig. 2, and display nine
different signals for nine hydrogen (Ha to Hi) (see
‘‘Experimental’’ section and Fig. 2).
˚
aromatic rings of ca 3.687 A. The title compound 1, exhibits
intramolecular O1–H1o–N2 hydrogen bond (Table 3).
Theoretical studies
In the gas phase the four conformers for the compound 1
were found. The structure and selected numbering of these
isomers are presented in the Fig. 1. In the conformer A the
hydroxyl group and imine nitrogen participate in an inter-
molecular hydrogen bonding and pyridine nitrogen is in the
other side of the N1–C7 bond. Isomer B was obtained with
rotation of hydroxyl group around C4–O5 bond while
rotation around N1–C7 yields the rotamer C. In this isomer
internal hydrogen bonding between hydroxyl hydrogen and
imine nitrogen is clear. With a rotation of hydroxyl group
around C4–O5 bond isomer D was obtained.
The results of calculated total energies and relative
stabilities of four conformers of title compound are pre-
sented in the Table 4. In consistence with results obtained
in the solid state, DFT calculations predict that in the gas
phase isomer A is the most stable ones. It is clear that
hydrogen bonding stabilizes the isomer of A but similar
stabilization for the isomer C has not been confirmed. The
order of stability predicted by DFT methods was found as:
A [ C [ B [ D. In addition, based on DFT results a
planar structure for the conformers was found.
Crystal structure
The title compound 1 crystallizes in the monoclinic system
with space group P21/c. The molecular structure of 1 with the
atom numbering scheme is given in Fig. 3. All bond distances
and angles are normal and in good agreement with
those reported in similar Schiff-base compounds [19, 20].
Fig. 2 1H-NMR spectra
of 1 in CDCl3
123

156
Struct Chem (2010) 21:153–157
Fig. 3 ORTEP view of 1,
showing the crystallographic
numbering scheme
˚
Moreover, the pyridine ring in the isomers A and B is
planar with C6=N2 bond, while in the isomer D pyridine
ring and phenyl rings were deviated by 132.7 (DFT)
degrees from each other. Interestingly DFT calculation
predict that pyridine ring is deviated by 145.0 degree from
C=N bond.
Table 3 Hydrogen-bond geometry (A, °)
D–HÁÁÁA
D–H
HÁÁÁA
DÁÁÁA
D–HÁÁÁA
O1–H10ÁÁÁN2
0.820
1.873
3.974
149.690
Table 4 Calculated total energies and relative stabilities of four
conformers of the title compound at various levels of the theory
A
B
C
D
Conclusion
DFT/6-31G(d)
-3219.1316623a
0b
13.93
13.22
4.29
4.27
17.85
17.39
In summary, the new Schiff-base compound 1 was syn-
thesized and single crystals were successfully character-
ized. FT-IR and 1H-NMR spectroscopy confirms the
functional groups, particularly –HC=N imine groups, of
the compound. The single crystal X-ray diffraction has
revealed a monoclinic structure, space group P21/c. The
molecules form 3D network via weak C–HÁÁÁO, C–HÁÁÁBr,
and C–HÁÁÁp interactions. In the gas phase, four isomers of
the title compound 1 were found. Density functional (DFT)
calculations have been carried. They have confirmed the A
isomer being the most stable one.
DFT/6-31?G(d)
-3219.1805441
0
a
Total energies in Hartree
b
Relative stabilities in kcal/mol
The optimized bond lengths and selected bond angles
for the preferred geometries of conformers A–D deter-
mined at B3LYP/6-31?G(d) levels are presented in
Table 2 in accordance with the atom numbering scheme of
the molecule shown in Fig. 3. A close looked at shows that
the results of DFT calculation are in good agreement with
those obtained from experimental data. For example DFT
calculated N2–C3 bond length differs from the experi-
mental value by 0.0179. In addition for N2–C6 bond length
in the isomer A, difference between DFT calculation with
experimental data was found as 0.0026.
Supplementary data
Crystallographic data (excluding structure factors) for the
structure reported in this paper has been deposited with the
Cambridge Crystallographic Center, CCDC Nos. 739030.
Copies of the data can be obtained free of charge on
application to The Director, CCDC, 12 Union Road,
Cambridge CB2 1EZ, UK, fax: ?44 1223 336 033, e-mail:
deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk.
It was observed that the influence of the internal
hydrogen bonding on the molecular parameters, particu-
larly in the C–C bond distance in phenyl rings, seems to be
negligibly small except for C7–C8. The results of calcu-
lated bond angles of four isomers of the title compound are
collected in the Table 2. It is clear that there is very good
agreement between calculated and experimental data. In
addition, the calculations show that hydroxyl group in the
all isomers is located in the plane of the phenyl ring.
Acknowledgments We thank Golestan University (GU) and Yasouj
University (YU) for partial support of this work. The institutional
research plan No. AVOZ10100521 of the Institute of Physics and the
project Praemium Academiae of the Academy of Sciences of the
Czech Republic is also gratefully acknowledged.
123

Struct Chem (2010) 21:153–157
157
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