Novel amide-type ligand bearing bis-pyridine cores: Synthesis, spectral characterizations and X-ray structure analyses

Article abstract of DOI:10.1016/j.molstruc.2016.04.012

The novel salicylamide-type ligand containing bis-pyridine moieties, i.e. 2-((6-chloropyridin-3-yl)methoxy)-N-(2-((6-chloropyridin-3-yl)methylthio)phenyl)benzamide, which has been successfully synthesized and characterized by typical spectroscopic techniques mainly including IR, ¹H NMR and ESI-MS. The structure of target compound was further determined by single crystal X-ray diffraction method and which crystallized in the monoclinic system with space group P2(1)/c.

Full text of DOI:10.1016/j.molstruc.2016.04.012

Journal of Molecular Structure 1118 (2016) 91e97
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: http://www.elsevier.com/locate/molstruc
Novel amide-type ligand bearing bis-pyridine cores: Synthesis,
spectral characterizations and X-ray structure analyses
Shaoyong Ke
National Biopesticide Engineering Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan,
430064, People's Republic of China
a r t i c l e i n f o
a b s t r a c t
Article history:
The novel salicylamide-type ligand containing bis-pyridine moieties, i.e. 2-((6-chloropyridin-3-yl)
methoxy)-N-(2-((6-chloropyridin-3-yl)methylthio)phenyl)benzamide, which has been successfully syn-
thesized and characterized by typical spectroscopic techniques mainly including IR, 1H NMR and ESI-MS.
The structure of target compound was further determined by single crystal X-ray diffraction method and
which crystallized in the monoclinic system with space group P2(1)/c.
Received 14 February 2016
Received in revised form
5 April 2016
Accepted 5 April 2016
Available online 7 April 2016
© 2016 Elsevier B.V. All rights reserved.
Keywords:
Amide
Ligand
Synthesis
Spectral characterizations
Crystal structure
1. Introduction
have been demonstrated to present widely medicinal activities
such as EGFR PTK inhibitors [17], antiviral activity [18], anti-
Carboxamide scaffolds have been known for a few decades,
which attracted great attention as versatile ligands in numerous
applications. Many carboxamide derivatives have been widely used
in the field of coordination chemistry, and most of which can
interact with various biologically important ions [1e4]. Meanwhile,
many synthetic carboxamides have also been applied in material
chemistry, and the broad biological activities of carboxamide-type
derivatives have also been known for a long time [5e15]. Nowa-
days, many carboxamides derivatives have been developed as
commercial medicines (such as BMS-354825, Finasteride, Dura-
steride, and Lacosamide) and agrochemicals (such as Flonicamid,
Tolfenpyrad, Chlorantraniliprole, Cyantraniliprole, Niclosamide,
Penthiopyrad, Isotianil, Tiadinil, Mandipropamid, Mefenacet, and
Propisochlor) (Fig. 1), and so which have played significantly
important role in drug design and agrochemical industry.
tuberculosis activity [19], antibacterial activity [20], anti-
inflammatory activities [21], antimycobacterial activity [22], cer-
caricidal activity [23], and aldose reductase inhibitors [24].
Thus, there is a great demand for the development of novel
synthetic ligands capable of selective interaction with biomolecules
or biologically important ions. In the present study, we focus on the
synthesis and characterization of neotype salicylamide ligand
bearing bis-pyridine moieties as shown in Scheme 1. Its structure
was confirmed by typical spectroscopic methods mainly including
IR, 1H NMR, ESI-MS spectra, and single crystal X-Ray diffraction
structural analysis has also been applied for further study on its
detail structural information.
2. Experimental
Among these carboxamide skeletons, especially those multi-
substituted salicylamide skeletons arouse many researchers' in-
terest, which have been demonstrated to be important structural
unit with diverse use in various biochemical process and coordi-
nation chemistry [16]. Up to now, many salicylamide derivatives
2.1. Materials and general methods
All melting points (m.p.) were obtained using a digital model X-
5 apparatus and are uncorrected. Infrared (IR) spectra in potassium
bromide (KBr) were recorded on a Thermo Nicolet FT-IR Avatar 330
instrument. 1H NMR spectra were recorded on a Bruker spec-
trometer at 600 MHz with CDCl3 as the solvent and TMS as the
E-mail addresses: keshaoyong@163.com, shaoyong.ke@nberc.com.
internal standard. Chemical shifts are reported in d (parts per
http://dx.doi.org/10.1016/j.molstruc.2016.04.012
0022-2860/© 2016 Elsevier B.V. All rights reserved.

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S. Ke / Journal of Molecular Structure 1118 (2016) 91e97
Fig. 1. Representative structure of drugs and pesticides containing amide units.
Scheme 1. Reagents and conditions: a. MeOH, Conc. H2SO4; b. 2-Chloro-5-(chloromethyl)pyridine, K2CO3, MeCN, r.t. to reflux for 10e12 h; c. NaOH, methanol/H2O, rt to 50 ꢀC for
5e7 h; d. SOCl2, reflux for 4e6 h; e. 2-Chloro-5-(chloromethyl)pyridine, K2CO3, MeCN, r.t.; f. Et3N, DMAP, DCM, r.t. for 2e5 h.
million) values. Coupling constants nJ are reported in Hz. Mass
spectra were performed on a WATERS ACQUITY UPLC® H-CLASS
PDA (Waters®) instrument. Analytical thin-layer chromatography
(TLC) was carried out on precoated plates, and spots were visual-
ized with ultraviolet light. All chemicals or reagents used for syn-
theses were commercially available, were of AR grade, and were
used as received. All anhydrous solvents were dried according to
standard methods. All other solvents and reagents were analytical
reagent and used directly without purification.
K2CO3 (1.52 g, 11 mmol) in MeCN (25 mL) was added 2-chloro-5-
(chloromethyl)pyridine (1.62 g, 10 mmol). The resultant mixture
was stirred at room temperature for sever hours, which was
detected by TLC. Then the mixture was charged with water and
extracted with ethyl acetate, the organic phase was separated and
dried over anhydrous Na2SO4. After filtered and concentrated, the
organic residue is purified by silica gel column-chromatography.
2.2.3. General synthetic procedure for the target compound 8
The typical process of synthesis of novel salicylamide derivative
containing 2-chloro-5-pyridyl moiety 8 is shown as following: The
2.2. Syntheses of target molecule 8
freshly formed acylchloride
dichloromethane was added dropwise to
5
(2.2 mmol) dissolved in dry
solution of the
2.2.1. General synthetic procedure for 2-((6-chloropyridin-3-yl)
methoxy)benzoic acid 4 and 2-((6-chloropyridin-3-yl)methoxy)
benzoyl chloride 5
The key intermediate 2-((6-chloropyridin-3-yl)methoxy)ben-
zoic acid 4 and 2-((6-chloropyridin-3-yl)methoxy)benzoyl chloride
5 was routinely prepared via multi-steps according to document
method [25,26].
a
substituted aniline 7 (2 mmol), Et3N (2.5 mmol), and catalytic
amount of DMAP in dry dichloromethane under ice-bath. The
resultant solution was stirred at room temperature for 2e5 h,
which was detected by TLC. Then the mixture was washed to
neutral with water and dried via anhydrous Na2SO4. After filtered
and concentrated, the organic residue is purified by silica gel
column-chromatography (ethyl acetate/petroleum ether) or
recrystallization to give white solid or crystal. Their phys-
icoechemical properties and the spectra data are as follows: 2-((6-
chloropyridin-3-yl)methoxy)-N-(2-((6-chloropyridin-3-yl)
2.2.2. General synthetic procedure for 2-((6-chloropyridin-3-yl)
methylthio)aniline 7
To a solution of 2-aminobenzenethiol (1.25 g, 10 mmol) and

S. Ke / Journal of Molecular Structure 1118 (2016) 91e97
93
Table 1
Crystal data and structure refinement for target compound 8.
Parameter
Data
Empirical formula
Formula weight
C25H19Cl2N3O2S
496.39
Crystal system
Space group
Monoclinic
P2(1)/c
Unit cell dimensions
Volume
Z, Density (calculated)
Absorption coefficient
F(000)
Crystal size
Theta range for data collection
Index ranges
Reflections collected
Independent reflections
Completeness to theta ¼ 28.29ꢀ
Max. and min. transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I > 2sigma(I)]
R indices (all data)
Largest diff. peak and hole
a ¼ 15.1485(9) Å,
2320.9(2) Å3
4, 1.421 Mg/m3
0.398 mmꢁ1
1024
a
¼ 90ꢀ b ¼ 7.7630(5) Å,
b
¼ 97.7130(10)ꢀ c ¼ 19.9163(12) Å,
g
¼ 90ꢀ
0.16 ꢂ 0.12 ꢂ 0.10 mm3
2.06e28.29ꢀ
ꢁ20 ꢃ h ꢃ 20e10 ꢃ k ꢃ 10e26 ꢃ l ꢃ 26
27650
5741 [R(int) ¼ 0.0406]
99.4%
0.9613 and 0.9390
Full-matrix least-squares on F2
5741/0/301
1.143
R1 ¼ 0.0602, wR2 ¼ 0.1518
R1 ¼ 0.0659, wR2 ¼ 0.1558
0.333 andꢁ0.250 e.Åꢁ3
methylthio)phenyl)benzamide: yellowish crystal, yield 83%, m.p.
112e114 ꢀC; IR (nmax, KBr, cmꢁ1): 3281.77,1662.75,1586.26,1574.49,
1562.71, 1526.43, 1457.74, 1197.71, 1009.32, 820.93, 758.95, 747.34;
determination was obtained from a mixed solution of acetone and
alcohol. The resultant crystals were separated from the solution by
decanting. Yellowish crystal of 8 (0.16 mm ꢂ 0.12 mm ꢂ 0.10 mm)
were counted on a quartz fiber with protection oil. Cell dimensions
and intensities were measured at 298 K on a Bruker SMART CCD
1H NMR (600 MHz, CDCl3)
d
10.44 (s, 1H, NH), 8.57 (d, J ¼ 7.2 Hz, 1H,
PyeH), 8.46 (s, 1H, PyeH), 8.26 (d, J ¼ 7.8 Hz, 1H, PyeH), 8.01 (s, 1H,
PyeH), 7.70 (d, J ¼ 8.4 Hz, 1H, PyeH), 7.50e7.00 (m, 9H, PyeH and
Ph-H), 5.34 (s, 2H, OCH2), 3.73 (s, 2H, SCH2); ESI-MS: m/z 496.3
(M þ H)þ, 518.2 (M þ Na)þ, calcd for C25H19Cl2N3O2S m/z ¼ 495.1.
area detector diffractometer with graphite monochromated Mo K
a
radiation (
l
¼ 0.71073 Å); qmax ¼ 28.29; 27,650 measured re-
flections; 5741 independent reflections (Rint ¼ 0.0406). Data were
corrected for Lorentz and polarization effects and for absorption
(Tmin ¼ 0.9390; Tmax ¼ 0.9613). The structure was solved by direct
methods using SHELXS-2001 [27]; all other calculations were per-
formed with Bruker SAINT System and Bruker SMART programs
2.3. X-ray crystallography
Crystals of target molecule 8 suitable for X-ray crystal structure
Fig. 2. The IR spectra analyses of compound 8.

94
S. Ke / Journal of Molecular Structure 1118 (2016) 91e97
Fig. 3. The 1H NMR spectra analyses of compound 8.
[28]. Full-matrix least-squares refinement based on F2 using the
displacement parameters have been deposited as Supporting In-
formation, and the crystallographic and refinement data of 8 is
shown in Table 1.
weight of 1/[
R ¼ 0.0602,
s
2(Fo2) þ (0.0849P)2 þ 0.0555P] gave final values of
R ¼ 0.1518, and GOF(F) ¼ 1.143. The fractional co-
u
ordinates, all bond lengths and angles, and the anisotropic
Fig. 4. The ESIMS spectra analyses of compound 8.

S. Ke / Journal of Molecular Structure 1118 (2016) 91e97
95
Table 3
Hydrogen bond geometry (Å,ꢀ).
D-H/A
d(D-H)
d(H/A)
d(D/A)
<(DHA)
N(2)eH(2A) /O(3)
C(27)eH(27)/N(1)#1
0.80(3)
0.93
1.92(3)
2.43
2.618(2)
3.347(3)
145(3)
169.8
Symmetry transformations used to generate equivalent atoms: #1 -x þ 1, y þ 1/2,
-z þ 1/2.
analyses. The IR spectra was measured with a Thermo Nicolet FT-IR
Avatar 330 spectrophotometer using KBr pellets and shown in
Fig. 2. As we can find that the IR spectra for target molecule showed
obvious signals of NH, which presented a band at 3281.77 cmꢁ1. The
obvious adsorption signal at 1662.75 cmꢁ1 in the IR spectra of
compound 8 was assigned to the carbonyl of amide as shown in the
following spectra. For compound 8, the bands that appeared in its
IR spectra such as 1586.26, 1574.49, 1562.71, 1562.43 and
1457.74 cmꢁ1 were attributed to the typical carbonecarbon
stretching vibrations of heteroaromatic rings. The bands observed
at 1197.71 and 1009.32 cmꢁ1 in the IR spectrum are assigned to CeO
bending vibration for title compound. The wavenumbers observed
at 820.93, 758.95, and 747.34 cmꢁ1 have been assigned to the
typical aromatic ring vibrational modes.
Fig. 5. The ORTEP diagram of 8, showing the atom-labeling scheme. Displacement
ellipsoids are drawn at the 50% probability level.
The 1H NMR spectra showed distinctive signals of methylene
between oxygen/sulfur and pyridine ring, which presented a
singlet at 5.34 and 3.73 ppm, respectively. The broad singlet at
10.44 ppm in the 1H NMR spectra of compounds 8 was assigned to
the NH proton of amide as shown in the representative spectra
(Fig. 3). For compound 8, the signals that appeared in its 1H NMR
spectra in the ranges 8.57e7.50 ppm were attributed to the typical
protons of pyridine heterocycles.
The electron spray impact mass spectra (ESI-MS) for compound
8 was measured with a Mass spectra were performed on a WATERS
ACQUITY UPLC® H-CLASS PDA (Waters®) instrument, and the ion
peak or adduct ions of the synthesized compound were investi-
gated as shown in Fig. 4. Experimentally, in the positive ion mode,
the ESI-MS of compound 8 exhibit the obvious molecular peak
[M þ H]þ appeared at m/z 496.8 with high abundance (100%), and
the peak appears at m/z 518.2 was assigned to the corresponding
sodium adduct ions (15e20%). The medium abundance peaks at m/
z 246.3 presented in the ESI mass spectra were assigned to the
cleavage fragments [M e NHR]þ. The lowest abundance peaks at m/
z 126.3 were assigned to further cleavage fragments [ClPyCH2]þ.
3. Results and discussion
3.1. Synthesis of salicylamide derivative containing bis-pyridine
moieties
In the present study, a novel amide ligand derived from salicylic
acid was synthesized by reacting functionalized salicylic acid with
substituted-amine. The general methods for the preparation of
target molecule containing bis-pyridine moieties 8 are outlined in
Scheme 1.
The low-cost salicylic acid was selected as raw materials, which
was routinely transferred to the corresponding intermediates 4 via
three steps according to document method [25,26]. Activation of
the substituted carboxylic acid 4 with thionyl chloride provides the
corresponding acid chloride 5, which was further used to couple
with newly prepared amine 7 to give the ligand 8. The target
molecule 8 gave satisfactory chemical analyses, and all the IR, 1H
NMR, ESI-MS spectra were consistent with the assigned structure.
Furthermore, the crystal of target molecule has been obtained by
recrystallization method, and the single-crystal structure was
determined by X-Ray diffraction.
3.3. Crystal structure determination of compound 8
3.2. Spectroscopic studies on compound 8
In order to explore the possible molecule structure and
hydrogen-bonding systems, the crystal structure of molecule 8 has
also been studied. Compound 8 is crystallized in monoclinic crystal
system with P2(1)/c space group, unit cells a ¼ 15.1485(9) Å,
The structure of target molecule 8 was confirmed by its IR, 1H
NMR spectra and electron spray impact mass spectra (ESI-MS)
Table 2
Selected bond lengths (Å), bond angles (ꢀ) and torsion angles (ꢀ) for compound 8.
Bond lengths (Å)
Bond angles (ꢀ)
Torsion angles (ꢀ)
C(1)eN(1)
C(1)eC(2)
C(1)eCl(1)
C(5)eN(1)
C(7)eS(1)
C(21)eO(3)
C(20)eO(3)
C(8)eS(1)
C(14)eO(2)
C(14)eN(2)
C(13)eN(2)
1.307(3)
1.374(3)
1.743(2)
1.337(3)
1.799(2)
1.437(2)
1.371(3)
1.7645(19)
1.213(2)
1.354(3)
1.413(3)
N(1)eC(1)eC(2)
N(1)eC(1)eCl(1)
N(1)eC(5)eC(4)
N(1)eC(5)eH(5)
O(3)eC(21)eC(22)
O(3)eC(20)eC(15)
C(20)eO(3)eC(21)
S(1)eC(7)eH(7A)
C(9)eC(8)eS(1)
C(8)eS(1)eC(7)
O(2)eC(14)eN(2)
124.7(2)
116.23(18)
124.5(2)
C(3)eC(4)eC(7)eS(1)
C(5)eC(4)eC(7)eS(1)
C(4)eC(7)eS(1)eC(8)
C(9)eC(8)eS(1)eC(7)
C(8)eC(13)eN(2)eC(14)
C(12)eC(13)eN(2)eC(14)
C(13)eC(8)eS(1)eC(7)
C(15)eC(14)eN(2)eC(13)
O(3)eC(21)eC(22)eC(23)
O(3)eC(21)eC(22)eC(27)
C(15)eC(20)eO(3)eC(21)
ꢁ91.5(2)
83.9(3)
178.40(16)
ꢁ21.4(2)
117.8
112.81(19)
117.09(17)
120.49(17)
110.9
123.74(17)
106.04(10)
122.4(2)
145.3(2)
ꢁ37.4(3)
159.65(17)
ꢁ177.51(18)
ꢁ35.8(3)
145.8(2)
179.17(19)

96
S. Ke / Journal of Molecular Structure 1118 (2016) 91e97
Fig. 6. Packing diagram of target compound 8, and the dashed lines denote intermolecular hydrogen bonds.
b ¼ 7.7630(5) Å, c ¼ 19.9163(12) Å and
b
¼ 97.7130(10)ꢀ. An Ortep
ESI-MS spectra. The further X-ray diffraction analyses demon-
strated the target ligand exhibits monoclinic crystal system. To our
best knowledge, this is the first investigate the structure features of
pyridine-functional salicylamide ligand, which is promising po-
tential compound for developing novel amide ligand for broad
applications in the coordination chemistry. Further application and
properties about the designed novel amide ligand are well ongoing
in our laboratory.
view of the target compound is shown in Fig. 5, and the crystallo-
graphic and refinement data of 8 is listed in Table 1.
The title molecule can be described as being built from planar
fragments, mainly including phenyl ring A (C8/C9/C10/C11/C12/
C13), B (C15/C16/C17/C18/C19/C20), and pyridine ring C (C1/C2/C3/
C4/C5/N1) and D (C22/C23/C24/C25/N3/C27) linking by eCONHe,
eOCH2- and eSCH2- groups, respectively. The pyridine ring C and D
are essentially parallel, however, the phenyl ring A and B are not
parallel, and there exist an obvious dihedral angle (17.545ꢀ) be-
tween them. This is undoubtedly due to the hydrogen bong inter-
action from amide bond between these two phenyl rings.
Meanwhile, the phenyl ring B and pyridine ring D is nearly
perpendicular (88.944ꢀ), however, a dihedral angle (25.558ꢀ) exists
between the phenyl ring A and pyridine ring C, which are a result of
the different electron withdrawing effects of sulfur and oxygen
atoms.
Acknowledgment
This work was financially supported by the Projects from Hubei
Agricultural Science Innovation Centre (2012-620-008-002, 2015-
620-003-001) and the Key Laboratory of Integrated Pest Manage-
ment in Crops in Central China, Ministry of Agriculture and Key
Laboratory for Crop Diseases, Insect Pests and Weeds Control in
Hubei Province (2015ZTSJJ9).
Appendix A. Supplementary data
3.4. Intermolecular interactions and packing relations
Supplementary data related to this article can be found at http://
dx.doi.org/10.1016/j.molstruc.2016.04.012.
The typical bond length and angles for compound 8 are pre-
sented in Table 2, and most of which are in good agreement with
the reasonable range of standard values. The bond lengths C14eN2
(1.354(3)Å) are shorter than the normal CeN (1.472 Å) bond length
because of the partial double bond character for amide bond. These
can also be attributed to the presence of resonance in this fragment
and forming a planar six-membered ring with N2eH2A/O3
hydrogen bond (Table 3). Furthermore, the bond angles for C(20)-
O(3)-C(21) and C(8)-S(1)-C(7) are 120.49(17)ꢀ and 106.04(10)ꢀ,
respectively, which are a result of the different steric effects of a
lone-pair electron for sulfur and oxygen atoms.
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conveniently synthesized, and fully characterized by IR, 1H NMR,

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