Synthesis, characterization and crystal structure of 6-Chloro-4,4′-dimethyl-2,2′-bipyridine and 4,4′-Dimethyl 2,2′-bipyridine N-Oxide

Article abstract of DOI:10.1016/j.molstruc.2015.11.054

The synthesis, the NMR characterization and the crystal structure of 6-Chloro 4,4′-dimethyl 2,2′-bipyridine and of the reaction intermediate 4,4′-Dimethyl 2,2′-bipyridine N-Oxide are here reported. The target compound crystallizes in the orthorhombic system while the intermediate is monoclinic. In both structures, the molecules are linked by weak interactions. The structure of the reaction intermediate N-oxide is characterized by a dihedral angle between the two phenyl rings of 161.77° while the other is almost planar with a dihedral angle of 179.15°. The crystal packing was investigated, also with the aid of Hirshfeld surface analysis. In the N-oxide reaction intermediate the packing is governed by CH-O interactions, while in the product the packing is simply driven by minimizing the voids and thus maximizing the density, with a prevalence of H???H and C???H contacts, as indicated by fingerprint decomposition analysis.

Full text of DOI:10.1016/j.molstruc.2015.11.054

Accepted Manuscript
Synthesis, characterization and crystal structure of 6-Chloro-4,4′-dimethyl-2,2′-
bipyridine and 4,4′-Dimethyl 2,2′-bipyridine N-Oxide
Eleonora Conterosito, Claudio Magistris, Claudia Barolo, Gianluca Croce, Marco
Milanesio
PII:
S0022-2860(15)30458-0
10.1016/j.molstruc.2015.11.054
MOLSTR 22004
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 6 October 2015
Revised Date: 20 November 2015
Accepted Date: 20 November 2015
Please cite this article as: E. Conterosito, C. Magistris, C. Barolo, G. Croce, M. Milanesio Synthesis,
characterization and crystal structure of 6-Chloro-4,4′-dimethyl-2,2′-bipyridine and 4,4′-Dimethyl 2,2′-
bipyridine N-Oxide, Journal of Molecular Structure (2015), doi: 10.1016/j.molstruc.2015.11.054.
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ACCEPTED MANUSCRIPT
Synthesis, characterization and crystal structure of 6-Chloro-
4,4’-dimethyl-2,2’-bipyridine and 4,4’-Dimethyl 2,2’-bipyridine
N-Oxide
Eleonora Conterosito,a Claudio Magistris,b Claudia Barolo,b Gianluca Crocea* and Marco Milanesio,a*
aDipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121,
Italy
bDipartimento di Chimica, NIS Interdepartmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino, 10125, Italy
Correspondence email: marco.milanesio@uniupo.it
Abstract
The synthesis, the NMR characterization and the crystal structure of 6-Chloro 4,4’-dimethyl 2,2’-bipyridine
and of the reaction intermediate 4,4’-Dimethyl 2,2’-bipyridine N-Oxide are here reported. The target
compound crystallizes in the orthorhombic system while the intermediate is monoclinic. In both structures,
the molecules are linked by weak interactions. The structure of the reaction intermediate N-oxide is
characterized by a dihedral angle between the two phenyl rings of 161.77° while the other is almost planar
with a dihedral angle of 179.15°. The crystal packing was investigated, also with the aid of Hirshfeld surface
analysis. In the N-oxide reaction intermediate the packing is governed by CH-O interactions, while in the
product the packing is simply driven by minimizing the voids and thus maximizing the density, with a
prevalence of H•••H and C•••H contacts, as indicated by fingerprint decomposition analysis.
1. Introduction
2,2’-Bipyridines have enjoyed considerable success as ligands in metal complexes, thanks to their ability to
coordinate a variety of metal ions in different oxidation states.[1] Their simple structure favoured the
application of a wide range of synthetic strategies, in order to extend the π-conjugated system and tune their
physical and photochemical properties.[2–4] This resulted in a vast array of technological applications,
ranging from solar energy conversion[5] to redox electrocatalysis.[6]
Unsymmetrically substituted 2,2’-bipyridines, in particular, retain a considerable interest for the possibility
of tuning the electronic properties in donor-acceptor conjugated systems, as well as in the construction of
versatile metallo-supramolecular architectures.[7,8] In fact unsymmetrical substitution with a halogen

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represents a preferred route to metal-catalysed cross-coupling reactions, typically used to extend the π-
conjugation.
In this paper we report the synthesis and the structural determination of 6-chloro 4,4’-dimethyl 2,2’-
bipyridine (3) and its synthetic intermediate 4,4’-dimethyl-2,2’-bipyridine N-oxide (2) together with their
1
synthesis and characterization (MS, H and 13C NMR). 4,4’-Dimethyl-2,2’-bipyridine N-oxide (2), an
intermediate in the synthesis of 4-(aminomethyl)-4’-methyl-2,2’-bipyridin dihydrochloride hydrate3 and 4-
(bromomethyl)-4’-methyl-2,2’-bipyridine dihydrobromide,3 is usually synthesized by treatment of 4,4’-
dimethyl 2,2’-bipyridine (1) with 3-chloroperbenzoic acid.1,3 The synthesis of 6-Chloro 4,4’-dimethyl 2,2’-
bipyridine (3) has been reported either by chlorination with POCl3 of the N-oxide (2),[9] or through coupling
of 2-chloropicoline with 2-bromopicoline.[10] It is a useful building block in the synthesis of 6-phosphanyl
bipyridine ligands for electrochemical CO2 reduction,5 and tridentate azole-pyridine ligands for Co
complexes.[11]
O
O O
H
4'
3
3'
Cl
4
6
POCl3
2' 2
5'
5
N
N
N
N
N
N
CH3Cl
6'
Cl
O
1
2
3
Scheme 1 Synthesis route. 1st Step: oxidation of 4,4’-Dimethyl 2,2’-bipyridine (1) to 4,4’-Dimethyl 2,2’-
bipyridine N-Oxide (2); 2nd Step: chlorination of the N-Oxide to 6-Chloro 4,4’-dimethyl 2,2’-bipyridine (3).
2. Experimental
2.1. Reactants and Instrumentation
All the chemicals were purchased from Sigma Aldrich and used without further purification. GC-MS spectra
were recorded on a Thermo Finnigan Trace GC with a cross-linked methyl silicone capillary column,
coupled to a Thermo Finnigan Trace MS mass spectrometer equipped with an electronic impact source (EI).
1H NMR (200 MHz) and 13C NMR (50 MHz) spectra were recorded on a Bruker Avance 200 NMR
spectrometer.
2.2. Synthesis and crystallization

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4,4’-Dimethyl 2,2’-bipyridine N-Oxide (2). A solution of freshly crystallized 3-chloroperbenzoic acid
(31.30 g, 0.18 mol) in CHCl3 (1.2 L) was slowly dropped (3 h) into a solution of 4,4’-Dimethyl 2,2’-
bipyridine 1 (33.42 g, 0.18 mol) in CHCl3 (0.6 L) in ice bath, and let under stirring at r.t. for 48 h. The
solvent was evaporated and the residue neutralized with 1M K2CO3 and heated at 95 °C for 30 min, in order
to filter the unreacted 1; the solution was extracted with CHCl3, dried over Na2SO4 and evaporated. The
crude product (light brown solid, 27.97 g, η = 77%) was used in the following step; it was further purified by
chromatography (EtOAc/MeOH = 9/1) before proceeding to crystallization. [1,6]
1H-NMR (CDCl3): δ = 8.70 (t, J = 0.8 Hz, H3’), 8.54 (d, J = 5.0 Hz, H6’), 8.18 (d, J = 6.7 Hz, H6), 7.91 (d, J =
2.7, H3), 7.14 (dq, J5’,6’ = 5.0, J5’,3’ = 0.8 Hz, H5’), 7.04 (dd, J5,6 = 6.7, J5,3 = 2.7 Hz, H5), 2.41 (s, CH3), 2.36 (s,
CH3)[1,6]
13C-NMR (CDCl3): 149.7, 149.1, 147.6, 146.6, 140.1, 137.4, 128.4, 126.5, 126.59, 126.1, 125.3, 21.4, 20.5
GC-MS (EI): m/z (%) = 201 (41), 200 (77, M+), 199 (77), 184 (70), 183 (68), 172 (62), 171 (100), 157 (40),
156 (58), 144 (69), 142 (32), 132 (81), 119 (65), 93 (37), 92 (72)
6-Chloro 4,4’-dimethyl 2,2’-bipyridine (3). Freshly distilled POCl3 (50 mL) was carefully mixed with 2
(21.40 g, 0.11 mol) in ice bath, then let to room temperature under stirring and finally heated under reflux for
6 h. POCl3 was distilled and, after cooling, the solid was cautiously poured in a becher containing ice
(fumes); neutralized with Na2CO3 and extracted several times with CH2Cl2. The organic phase was dried
over Na2SO4 and evaporated; elution with PE/EtOAc = 8/2 gave the pure product as white solid, g 18.70 (η =
80%)[9]
1H-NMR (CDCl3): δ= 8.47 (d, J = 5.0 Hz, HAr), 8.18 (s, HAr), 8.12 (s, HAr), 7.11-7.07 (m, 2HAr), 2.38 (s,
CH3), 2.37 (s, CH3)[9,10]
13C-NMR (CDCl3): 156.5, 154.5, 151.3, 150.9, 149.0, 148.3, 125.2, 124.6, 124.6, 122.3, 120.6, 120.6, 21.2,
21.0
GC-MS (EI): m/z (%) = 220 (43), 219 (39), 218 (100, M+), 184 (38), 183 (93), 181 (37), 168 (35), 92 (44),
91 (33), 90 (34).
2.3. XRD data collection and refinement

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Single-crystal diffraction data were collected using an Oxford Xcalibur CCD area detector diffractometer
with graphite monochromator and Mo-Kα (λ =0.71069 Å) radiation. Data reduction and absorption
corrections were performed using CrysAlisPRO[12] 171.34.44. Single crystal structure solution was
performed by direct methods using SIR2011[13] and refinement with full-matrix least-squares employing
SHELXL-2013[14] with ShelXle GUI[15]. Crystal data, data collection and structure refinement details are
summarized in Table 1 and reported in details in Table S1-S4 and Table S5-S8 in the supplementary
information file. H atoms were originally found in the difference Fourier map and then inserted in the model.
All C-bound H atoms were then placed in the expected positions, with C-H = 0.97 (phenyl) or 0.95-1.00 Å
(methyl), and refined as riding atoms on their carrier atoms, with Uiso(HAr) = 1.2Ueq(C) for aromatic H atoms
and Uiso(HMe) 1.5Ueq(C) for methyl H atoms.‡ Structural illustrations have been drawn with CCDC
Mercury[16] and Crystal Explorer 3.1.[17] Crystal Explorer 3.1[17] was used to perform Hirshfeld surface
analysis.
Table 1: Relevant crystallographic data of crystal structures of 2 and 3.
Compound
2
3
Empirical formula
Formula weight
Temperature
Wavelength
C12 H12 N2 O
200.24
C12 H11 Cl N2
218.68
298 K
0.71073 Å
Crystal system
Space group
Monoclinic
P 21/n
Orthorhombic
P b c a
a = 7.3479(3) Å
b = 11.8541(5) Å
c = 12.0086(6) Å
β= 97.160(4)°
1037.83(8) Å3
4
a = 8.6128(8) Å
b = 11.976(1) Å
c = 21.591(3) Å
Unit cell dimensions
Volume
2227.1(4) Å3
8
Z
Density (calculated)
Absorption coefficient
F(000)
1.282 Mg/m3
0.084 mm-1
424
1.304 Mg/m3
0.310 mm-1
912
‡ Cif file of the structures of compound 2 and 3 were submitted to CCDC with numbers CCDC-1429846 and CCDC-
1429847 respectively

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Crystal size
0.4 x 0.3 x 0.2 mm3
4.432 to 29.479°.
0.2 x 0.2 x 0.4 mm3
4.251 to 29.546°.
2984 [R(int) = 0.0531]
99.6%
Theta range for data collection
Independent reflections
2696 [R(int) = 0.0204]
Completeness to theta = 25.242°
Data / restraints / parameters
Goodness-of-fit on F2
99.4 %
2696 / 0 / 138
2984 / 0 / 150
1.011
1.041
Final R indices [I>2sigma(I)]
R indices (all data)
R1 = 0.0541, wR2 = 0.1369
R1 = 0.0890, wR2 = 0.1589
R1 = 0.0688, wR2 = 0.1949
R1 = 0.1367, wR2 = 0.2447
2.4. Hirshfeld analyses
Hirshfeld surfaces were generated by the program Crystal Explorer 3.1[17] All bond lengths to hydrogen
were automatically modified to typical standard neutron values[18] (C-H = 1.083 Å, N-H = 1.009 Å and O-H
= 0.983 Å), while the CIF files of crystals 1-4 were read into the Crystal Explorer software program for
calculations. We are aware that this analysis has some limitations for very weak interactions, like H•••H and
C•••H contacts,[19] and the results were carefully checked by visual inspection of the crystal packing.
3. Results and discussion
6-Chloro 4,4'-dimethyl 2,2'-bipyridine (3) was synthesized as previously reported, through mono-oxidation
of 4,4’-Dimethyl 2,2’-bipyridine (1) with 3-chloroperbenzoic acid,[1,6] and selective chlorination of the
crude N-Oxide (2) with POCl3.[9] All the products were characterized through MS and NMR spectroscopy.
The crystal structures of 2 and 3 were solved (structures and crystal packing features are reported Figure 1
and Figure 2 respectively) and compared with relevant literature data. The conformational features of the
molecules and the packing of the molecule with (2) and without (3) the N-oxide moiety were analysed. The
reaction product 3 crystallizes in Pbca (Figure 2) space group while 2 crystallizes in P21/n (Figure 1).
The first difference is observed at the molecular level is on the conformation of the phenyl groups. The
dihedral angle between its two phenyl rings is close to 180° (179.15°) showing strong analogies with the
structure of 1.[20] Conversely, the intermediate compound 2 is not planar and the dihedral angle between the
two rings is of 161.77°. This originates in 2 a short contact interaction of 2.315Å between the O1 atom on
one molecule and the H15 and H9 atoms of two other molecules. It is possible to compare the structure of 2
with that of the symmetrical compound 4,4'-dimethyl-2,2'-bipyridine 1,1'-dioxide[21] (4) where the rotation

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between the two rings is more accentuated forming a dihedral angle of 117.55°. By comparing the pyridine
rings in the structures it is possible to see that, in both cases, they are planar but in the literature compound 4
the O atom of the N-oxide group is slightly out of the plane. Conversely, in our case it is almost in plane with
a displacement of 0.04Å only.
Figure 1 Crystal structure (A) and packing with relevant inter-molecular interactions (B) of compound 2.

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Figure 2 Crystal structure (A) and packing with relevant inter-molecular interactions (B) of compound 3.
The planarity and the presence of unconventional hydrogen bonds[22,23] can explain the different densities
of compounds 1, 2 ,3 and 4. Lower densities are associated to non-planar conformations and absence of
CH•••O bonds. The presence of the N-oxide group in 2 breaks the symmetry of the molecule, stabilizing the
non-planar conformation, and a less dense packing is observed (1.281 g/cm3) with respect to 1 (1.322 g/cm3),
showing a planar conformation. The final product 3 shows intermediate density (1.304 g/cm3), because it is

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planar but no CH•••O bonds are observed. It is worth noting that in 4 higher densities (1.396 g/cm3) are
observed because several unconventional CH•••O hydrogen bonds are formed.
To further confirm the crystal packing driving forces, the Hirshfeld surfaces were generated and are shown in
Figure 1 for the four compounds 1, 2, 3 and 4. The Hirshfeld surfaces (Figure 3) highlight the intermolecular
interactions better than the conventional packing pictures. The unique relevant contacts are the CH•••O
bonded[24] contacts in compound 2 and 4.
Figure 3 Hirshfeld surface (Isovalue 0.5) for 1 (A), 3 (B), 2 (C) and 4 (D). Neighbouring molecules associated with
close contacts are shown along with distances between the atoms involved.
Fingerprint plots, reported in Figure 4 (while their decomposition is reported in ESI file, Figure S1), are in
general rather flat without peculiar features (spots, densities in the low distances below 1.2 Å, asymmetrical
features), and this confirms the dominance of weak interactions. In particular, for compound 1 it is flat,

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symmetric and circular, with densities at the larger distances, and this indicates that the packing is driven by
minimization of voids. In general, all four patterns do not show the presence of clear and relevant π-stacking
interactions, that should be indicated by a red spot at the centre of the fingerprint plot, at about 1.8 Å, as can
be seen in Figure 4, usually present in phenyl-rich molecules. Only for compound 3 and 4 a weak spot in the
centre of Figure 4B and 4D suggests some degree of π-stacking, further confirmed by the inspection of
peculiar flat zones in the curvedness of the Hirshfeld surfaces[25] (Figure 3B and 3D) and of the crystal
packing. Conversely, Figure 2A and 2C do not show such flat portions in their surfaces. In compound 2 and
4, the CH•••O bonds are confirmed by the spikes at the low distances in Figure 2C. Conversely, in
compound 3 (Figure 4B) the absence of any significant feature indicates that the driving force of the packing
is in both cases the minimization of the empty space. Compound 3 is similar to the reactant 1 and compound
to 2 to compound 4, the symmetrical dioxide. The decomposition of the fingerprint plots (see Figure 5 and
Table S9 in ESI file for the numerical details) further confirms that the majority among the interactions are
weak H•••H and C•••H contacts (beyond 75% in compound 1 and 2, as expected from the chemical
formula).

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Figure 4 Fingerprint plots of 1 (A), 3 (B), 2 (C) and 4 (D).

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Figure 5 Distribution of intermolecular contacts from Hirshfeld surface analysis (%) for compound 1 – 4.
4. Conclusions
The comparison among compound 3, the reactant 1, the intermediate N-oxide (2) and the symmetrical
reference compound (4) allowed highlighting the features of the molecular interactions upon the change of
the functional groups and symmetry. The formation of CH•••O unconventional hydrogen bonds is favoured,
where possible, also by altering the molecule conformation (as in the oxidised compounds 2 and 4, where the
planarity of the molecule is broken), while in absence of these “not so weak” interactions the packing is
driven by the maximization of the density and of the inter-molecular contacts. In all the studied cases, these
CH•••O bonds and the minimization of empty spaces, with a predominance of H•••H and C•••H contacts
as indicated by fingerprint decompositions and confirmed by the visual inspection of the crystal structures,
are prevailing over π-stacking interactions. In compound 1, the driving force of the crystal packing is the
minimization of the empty space.
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Crystal structures of bipyridines ligands
Weak interaction analysis by Hirshfeld surface calculations and fingerprint decomposition
CH•••O bonds and the minimization of empty spaces are the prevailing interactions