C-H...N hydrogen bonds mediated solid state structures of 2,2′-bis(4-pyridylsulfanylmethyl)-1,1′-biphenyl and 9-(4-pyridylsulfanyl)phenanthrene

Article abstract of DOI:10.1016/j.molstruc.2009.08.020

Solid state structure elucidation of sulfanyl ligands, 2,2′-bis(4-pyridylsulfanylmethyl)-1,1′-biphenyl, L₁ and 9-(4-pyridylsulfanyl)phenanthrene, L₂ are reported. In the structures L₁ and L₂, the molecules are s

Full text of DOI:10.1016/j.molstruc.2009.08.020

Journal of Molecular Structure 937 (2009) 81–84
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Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
C–H. . .N hydrogen bonds mediated solid state structures of 2,20-bis
(4-pyridylsulfanylmethyl)-1,10-biphenyl and 9-(4-pyridylsulfanyl)phenanthrene
*
Ketaki Upadhye, J. PrakashaReddy, V.R. Pedireddi
Solid State & Supramolecular Structural Chemistry Lab, Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
a r t i c l e i n f o
a b s t r a c t
Solid state structure elucidation of sulfanyl ligands, 2,20-bis(4-pyridylsulfanylmethyl)-1,10-biphenyl, L1
and 9-(4-pyridylsulfanyl)phenanthrene, L2 are reported. In the structures L1 and L2, the molecules are
self-assembled through C–H. . .N hydrogen bonds, yielding ensembles of cyclic and helical networks.
Ó 2009 Elsevier B.V. All rights reserved.
Article history:
Received 30 July 2009
Received in revised form 17 August 2009
Accepted 19 August 2009
Available online 23 August 2009
Keywords:
Supramolecular assemblies
Noncovalent interactions
Hydrogen bonds
1. Introduction
9-(4-pyridylsulfanyl)phenanthrene have been prepared. In this
process, the native structures of these ligands are found to
Design and synthesis of organic and metal–organic assemblies
with exotic supramolecular architectures utilizing various nonco-
valent interactions, in particular, hydrogen bonds, are of current
research interest due to the potential applications of these assem-
blies in the areas of separation technology, catalysis, pharmaceu-
be not known in the literature, so we carried out structure determi-
nation of these pyridylsulfanyl ligands by single crystal X-ray
diffraction methods. Herein, we report the salient features of solid
state structures of 2,20-bis(4-pyridylsulfanylmethyl)-1,10-biphenyl
and 9-(4-pyridylsulfanyl)phenanthrene, which form different
types of networks in the crystal lattices (see Chart 1).
tics, etc. [1–11]. Thus, numerous reports of
a myriad of
supramolecular assemblies utilizing different types of organic li-
gands possessing varied functionalities like carboxylates, aza-do-
nor groups etc., are well known in the recent literature [12–15].
However, development of novel supramolecular assemblies is
always a challenging, especially choosing co-crystal former with
required functional moieties. Since most of the assemblies are
generally associated with rigid molecules [16–18], exploration of
supramolecular structures through molecules substituted with
functional moieties associated with topology, properties, etc., of
the conformational flexibility would provide a lot of advantages
for tuning the ultimate supramolecular assemblies [19–22]. For
this purpose, thio-based pyridylsulfanylmethyl derivatives, with
multi-armed tripodal geometry have now used as novel ligands
for the evaluation in organic and metal–organic assemblies. In this
regard, earlier, we reported [23] a systematic study of coordination
assemblies of 1,3,5-tris(4-pyridylsulfanylmethyl)-2,4,6-trimethyl-
benzene, with different mercuric halides. In continuation of our
endeavors to prepare such assemblies with other pyridylsulfanyl
compounds, 2,20-bis(4-pyridylsulfanylmethyl)-1,10-biphenyl and
2. Results and discussion
Refluxing a methanol solution of 2,20-bis(bromomethyl)-1,10-
biphenyl with pyridine-4-thiol (also exists as pyridinethione)
[24–26] at 35 °C, obtained a product 2,20-bis(4-pyridylsulfanyl-
methyl)-1,10-biphenyl but the same reaction mixture refluxing at
80 °C for 48 h, however, gave ligand, 9-(4-pyridylsulfanyl)phenan-
threne (Chart 2). Both the compounds upon purification, by recrys-
tallization, gave good quality single crystals, suitable for the
structure elucidation by X-ray diffraction methods.
2.1. Structure of 2,20-bis(4-pyridylsulfanylmethyl)-1,10-biphenyl, L1
Block type single crystals of L1 obtained by diffusion of petro-
leum ether into ethyl acetate, at ambient conditions. X-ray diffrac-
tion analysis reveals that L1 is found to be crystallized into triclinic
ꢀ
space group, P1; unit cell parameters and other pertinent crystallo-
graphic details are given in Table 1. In the crystal structure of L1,
molecules are fully ordered and the asymmetric unit is shown in
Fig. 1. The two phenyl moieties of biphenyl core are twisted such
that they got arranged almost perpendicular to each other. These
* Corresponding author. Fax: +91 20 25902629.
E-mail address: vr.pedireddi@ncl.res.in (V.R. Pedireddi).
0022-2860/$ - see front matter Ó 2009 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2009.08.020

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K. Upadhye et al. / Journal of Molecular Structure 937 (2009) 81–84
N
N
S
S
S
N
2,2'-bis(4-pyridylsulfanyl-methyl)-1,1'-biphenyl (L1)
9-(4-pyridylsulfanyl)phenanthrene (L2)
Chart 1.
reflux, 35 oC, 24 h
reflux, 80 oC, 48 h
Compound L1
Compound L2
BrH2C
CH2Br
KOH
N
SH
+
CH3OH
Chart 2.
Table 1
Crystallographic data of ligands L1 and L2.
L1
L2
Formula
Fw
C24H20N2S2
400.54
Blocks
C19H13N1S1
287.36
Blocks
Colorless
Monoclinic
P21
9.223(4)
5.517(2)
14.147(6)
90
105.20(1)
90
694.7(5)
2
1.374
298
Crystal shape
Crystal color
Crystal system
Space group
a (Å)
Colorless
Triclinic
ꢀ
P1
9.337(5)
9.923(5)
12.939(6)
110.52(1)
94.01(1)
113.29(1)
1000.5(9)
2
b (Å)
c (Å)
a
(deg)
b (deg)
c
(deg)
V (Å3)
Z
Dcalc (g cmꢀ3
T (K)
)
1.330
298
Mo-K
l
a
0.71073
0.278
0.71073
0.224
(mmꢀ1
)
2h range (deg)
46.70
46.74
F (000)
420
300
No. reflns. measured
No. unique reflns. [R (int)]
No. reflns used
No. parameters
GOF on F2
4232
2844 [0.0349]
2332
333
1.144
5846
2001[0.0466]
1916
185
1.214
Fig. 1. ORTEP drawing of asymmetric unit in the crystal structure of L1.
Flack parameter
–
0.13(14)
0.0506
0.1110
R1 [I > 2
r
(I)]
0.0717
0.1595
2.2. Structure of 9-(4-pyridylsulfanyl)phenanthrene, L2
wR2
Compound L2 crystallizes in a non-centrosymmetric and chiral
space group (P21), unlike L1. The salient features of the crystal
structure parameters are given in Table 1. In the crystal structure
of L2, the pyridyl moiety exists like a pendant group on the phen-
anthrene moiety, as shown in Fig. 3. Further, in accordance with
the chiral space group arrangement, the molecules in the crystal
structure of L2, self-assembled through C–H. . .N hydrogen bonds
(H. . .N, 2.64 Å) into right-handed helical pattern. The hydrogen
bonds are formed between pyridyl N atom and –CH group of the
phenanthrene group, as shown in Fig. 4.
molecules interact with the surrounding ones through C–H. . .N
hydrogen bonds (H. . .N, 2.46 Å).
However, in the structure of L1, the hydrogen bonds are formed
between pyridyl N atoms and –CH group of pyridyl moieties. Thus,
cyclic networks of dimers are present in the crystal structure of L1
as shown in Fig. 2a. Such dimeric units are further held together
through C–H. . .N bonds (H. . .N, 2.69 Å) using methylene hydrogen
atoms and pyridyl N atoms constituting a bracelet network, as
shown in Fig. 2b.

K. Upadhye et al. / Journal of Molecular Structure 937 (2009) 81–84
83
Fig. 2. (a) Dimers of molecules of L1 formed through C–H. . .N hydrogen bonds. (b) Packing of cyclic moieties in the extended structure, within the crystal lattice L1.
4. Experimental
4.1. Synthesis of 2,20-bis(4-pyridylsulfanylmethyl)-1,10-biphenyl, L1
Pyridine-4-thiol (222 mg, 2 mmol) and KOH (560 mg, 10 mmol)
were stirred in methanol at 0 °C. To the above mixture 2,20-bis(bro-
momethyl)-1,10-biphenyl (340 mg, 1 mmol) was added slowly and
stirred for about 24 h at room temperature. The mixture was
poured into ice-cold water, filtered the crude product and pure
product was separated by column chromatography to give pure
colorless microcrystalline solid. Yield: 75%, melting point: 137–
139 °C. Crystals of L1, suitable for single crystal X-ray diffraction,
were obtained by diffusion of petroleum ether into a solution of
ethyl acetate.
4.2. Synthesis of 9-(4-pyridylsulfanyl)phenanthrene, L2
The same procedure, as that of the preparation of ligand L1, was
followed for the preparation of L2 as well except that the mixture
was refluxed at 80 °C. The solution was poured into ice-cold water,
filtered the crude product and separated by column chromatogra-
phy to give pure colorless microcrystalline solid. Yield: 70%, melt-
ing point: 185–187 °C. Single crystals of L2 suitable for X-ray
diffraction were obtained from chloroform solution after 2 days.
Fig. 3. ORETP drawing of the asymmetric unit in the crystal structure of L2.
The structures of both L1 and L2 indeed signify the effectiveness
of weak hydrogen bonds like C–H. . .N towards stabilizing the
molecular aggregation in the solid state. Also the cyclic network
observed in L1, could be evaluated for the possible incorporation
of guest species by increasing the dimensions of the empty space
through co-crystallization of it with appropriate receptors.
4.3. Crystal structure determination
Good quality single crystals of L1 and L2, grown as described
above were carefully chosen with the aid of polarized optical
microscope and glued to glass fiber to mount on an X-ray diffrac-
tometer goniometer equipped with CCD area detector [27]. The
data collection proceeded without any complication and processed
using the Bruker suite of software. The structures were determined
and refined using SHLEXTL suite of programmes, and absorption
3. Conclusion
We have reported two solid structures of the pyridylsulfanyl
compounds L1 and L2, mediated by C–H. . .N hydrogen bonds with
different topological arrangement, in the form of cyclic and helical
networks.

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K. Upadhye et al. / Journal of Molecular Structure 937 (2009) 81–84
Fig. 4. (left) Hydrogen bonds between the adjacent molecules in a helix formed in the crystals of L2. (right) Representation of a typical helical arrangement.
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We thank DST for the generous funding. One of us (J.P.) thanks
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