Conformation of the azo bond and its influence on the molecular and crystal structures, IR and Raman spectra, and electron properties of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine – Quantum chemical DFT calculations

Article abstract of DOI:10.1016/j.saa.2017.10.053

The crystal and molecular structures of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine have been determined by X-ray diffraction and quantum chemical DFT calculations. The crystal is monoclinic, space group Cc (No. 9) with Z = 4 with the unit cell parameters: a = 12.083(7), b = 12.881(6), c = 8.134(3) ? and β = 97.09(5)°. The azo-bridge appears in the trans conformation in which C2-N2-N2′-C1′ torsion angle takes a value ? 178.6(3)°, whereas the dihedral angle between the planes of the phenyl and pyridine rings is 3.5(2)°. The IR and Raman spectra measured in the temperature range 80–350 K and quantum chemical calculations with the use of B3LYP/6-311G(2d,2p) approach confirmed the trans configuration of the azo-bridge as the most stable energetically and allowed determination of the energy other virtual structures. The observed effects were used in the discussion of vibrational dynamics of the studied compound. The energy gap between cis and trans conformers equals to 1.054 eV (0.03873 Hartree). The electron absorption and emission spectra have been measured and analyzed on the basis of DFT calculations. The life time of the excited state is 12 μs and the Stokes shift is close to 5470 cm^{? 1}.

Full text of DOI:10.1016/j.saa.2017.10.053

Accepted Manuscript
Conformation of the azo bond and its influence on the molecular
and crystal structure, IR and Raman spectra, and electron
properties
of
6-methyl-3,5-dinitro-2-[(E)-
phenyldiazenyl]pyridine – Quantum chemical DFT calculations
J. Michalski, I. Bryndal, J. Lorenc, K. Hermanowicz, J. Janczak,
J. Hanuza
PII:
DOI:
Reference:
S1386-1425(17)30858-2
doi:10.1016/j.saa.2017.10.053
SAA 15559
Spectrochimica Acta Part A: Molecular and Biomolecular
Spectroscopy
To appear in:
Received date: 27 January 2017
Revised date:
Accepted
date:
14 October 2017
19 October 2017
Please cite this article as: J. Michalski, I. Bryndal, J. Lorenc, K. Hermanowicz, J. Janczak,
J. Hanuza , Conformation of the azo bond and its influence on the molecular and crystal
structure, IR and Raman spectra, and electron properties of 6-methyl-3,5-dinitro-2-[(E)-
phenyldiazenyl]pyridine – Quantum chemical DFT calculations. The address for the
corresponding author was captured as affiliation for all authors. Please check if
appropriate. Saa(2017), doi:10.1016/j.saa.2017.10.053
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1
Conformation of the azo bond and its influence on the molecular and crystal structure,
IR and Raman spectra, and electron properties of
6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine –
quantum chemical DFT calculations
J. Michalski (1)*, I. Bryndal(1), J. Lorenc(1), K. Hermanowicz(2), J. Janczak (2), J. Hanuza (2)
(1) Department of Bioorganic Chemistry, Institute of Chemistry and Food Technology,
Faculty of Engineering and Economics, Wrocław University of Economics, Wrocław,
Poland
(2) Institute of Low Temperature and Structure Research, Polish Academy of Sciences,
Wrocław, Poland
Abstract
The
crystal
and
molecular
structures
of
6-methyl-3,5-dinitro-2-[(E)-
phenyldiazenyl]pyridine have been determined by X-ray diffraction and quantum chemical
DFT calculations. The crystal is monoclinic, space group Cc (No. 9) with Z = 4 with the unit
cell parameters: a = 12.083(7), b = 12.881(6), c = 8.134(3) Å and  = 97.09(5)°. The azo-
bridge appears in the trans conformation in which C2-N2-N2’-C1’ torsion angle takes a value
-178.6(3)º, whereas the dihedral angle between the planes of the phenyl and pyridine rings is
3.5(2)°. The IR and Raman spectra measured in the temperature range 80 – 350 K and
quantum chemical calculations with the use of B3LYP/6-311G(2d,2p) approach confirmed
the trans configuration of the azo-bridge as the most stable energetically and allowed
determination of the energy other virtual structures. The observed effects were used in the
discussion of vibrational dynamics of the studied compound. The energy gap between cis and
trans conformers equals to 1.054 eV (0.03873 Hartree). The electron absorption and emission
spectra have been measured and analyzed on the basis of DFT calculations. The life time of
the excited state is 12 µs and the Stokes shift is close to 5470 cm-1.
Keywords: 6-methyl-3,5-dinitro-2-(phenyldiazenyl)pyridine; azo-bond conformation;
temperature dependence of IR and Raman spectra; characteristic normal modes of the azo-
bond; DFT quantum chemical calculations; theoretical and experimental energy levels of the
studied complex
 Corresponding author. Tel.: +48 71 368 0299; fax: +48 71 368 0292.
E-mail address: jacek.michalski@ue.wroc.pl (J. Michalski)

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1. Introduction
Azo compounds constitute a very important class of synthetic dyes and pigments.
They belong to the group of the most versatile pigments and therefore they are called FD&C
dyes due to their use in the food, drug, and cosmetics industry. The majority of their industrial
applications represents nearly 60 % of the world production of dyes [1,2]. They are also used
to coloring fibers [3,4], in printing systems [5,6], optical storage equipment [7-9],
photoelectronic devices and analytical substances [10,11] as well as polymer additives [12].
There were attempts to use them as a molecular memory storage, nonlinear optical elements
and photoconductors [13,14]. Their biological activity was reported due to their inflammatory
[15,16], anticancer [17,18] properties. Their reversible interconversion of the cis and trans
isomers and protonation and deprotonation processes in aqueous solutions leading to color
changes is the main factor that determines such wide applications of azo compounds.
The spectroscopic properties of the azobenzenes are well recognized. Vibrational
spectra of the monomeric and polymeric azo-compounds were recorded [19-23] and analyzed
in term of DFT calculations [21,22]. However, the number of papers on the systems in which
the azo bond joints the pyridine and benzene rings or two pyridine rings is significantly lower.
In our previous works 2,2’-azobipyridine and 4,4’-dimethyl-3,3’-dinitro-2,2’-azobipyridine
[24], 2-phenylazo-5-nitro-6-methyl-pyridine [25], dimethyl-dinitro-azo-pyridines [26], 3,3’-
dinitro-2,2’-azo-bipyridine and its 4,4’(or 5,5’ or 6,6’)-dimethyl-derivatives [27] were
studied. Their crystal and molecular structures, vibrational spectra and DFT quantum
chemical calculations were reported. These data were used in the discussion of the results
presented in this work, this allows us to generalize several statements on the structure and
spectroscopic properties of azopyridines and azobenzenopyridines. Besides, the influence of
different substituents and the place of their substitution in the pyridine rings as well as the
formation of the hydrogen bonds on the properties of the whole molecule and crystallographic
unit cell should be recognized.
The electron absorption spectrum of azobenzene consists of two characteristic bands. The
* transition is observed in the near UV region, whereas the n* transition appears in the
visible region. The latter originates in the presence of the unshared electron pairs of nitrogen
atoms [28]. For the trans isomer the * absorption band is very intense and the * band
is significantly weaker. For the cis isomer the former band is shifted towards shorter
wavelenghts with decreasing intensity, whereas the latter band gains its intensity [29]. The

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structural, spectroscopic and electronic properties of selected azo dyes were studied by
Jayabharathi et al. on the basis of DFT calculations [30]. The light induced cis-trans
isomerization of some azo compounds was studied by Grebenkin and Bolshakov using the
results of UV-VIS measurements. [31]
The aim of the present work was to characterize the structural and spectroscopic
properties of a new phenylazopyridine 6-methyl-3,5-dinitro-2-(phenyldiazenyl)pyridine
(6M3,5NPAP) in the solid state. The influence of the temperature change on the IR spectra of
this compound was also studied. The spectral measurements and quantum chemical
calculations were undertaken to determine the energies of azo-bridge conformations, i.e. the
possibility of reversible interconversion between cis and trans isomers (see Fig. 1). Besides,
because 2-phenylazo-3,5-dinitro-6-methylpyridine is a new black-brown azo-dye, it is
important to define its spectral range of absorbing light. These parameters can answer the
question if this material can serve as photochromic system.
Fig. 1
2. Experimental details
2.1. Synthesis of the studied phenylazopyridine
The way of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine (6M3,5NPAP)
synthesis was published by us many years ago in a Polish journal [32]. The presented here
method was modified allowing obtaining single crystals suitable for XRD studies. The
synthesis was performed in two steps. In the first step 2-fluoro-3,5-dinitro-6-methylpyridine
was transformed into 2-phenylhydrazo-3,5-dinitro-6-methylpyridine and this intermediate
product was changed into the final dye.
The first step: 0.01 moles of 2-fluoro-3,5-dinitro-6-methylpyridine were dissolved in
10 cm3 of methanol and next 0.02 moles of phenylhydrazine were added. This mixture was
heated for 1-2 minutes at 60 °C and kept for 24 h at room temperature. Then, the solvent was
vacuum distilled off and the residue was extracted using hot chloroform. The insoluble
phenylhydrazine fluorohydrate was filtered and washed with hot chloroform. The
chloroformic extract was distilled off and washed with a small amount of extraction naphtha
in order to remove the rest of phenylhydrazine. The insoluble final product was filtered, dried
and re-crystallized from acetonitrile. The yield of the reaction: 42.6%. The obtained 2-
phenylhydrazo-3,5-dinitro-6-methylpyridine is nearly black and its melting point is 164 °C.

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The chemical content for C12H11N5O4 formula and M = 289.24: calculated 49.82% C, 3.83%
H, 24.21% N and experimental 50.20% C, 3.83% H, 24.21% N.
The second step: 1 g of 2-phenylhydrazo-3,5-dinitro-6-methylpyridine was gradually
added to heated at 50 °C nitric acid (1.4 g/cm3 density). The reaction is exothermic and during
this process nitrogen oxides release. The red solution was heated for 5 minutes at 50-60 °C,
kept for 2 hours at room temperature, diluted with water, and recrystallized from methanol.
The obtained 2-phenylazo-3,5-dinitro-6-methylpyridine is dark-brown and its melting point is
138 °C. The yield of the reaction: 71.2%. The chemical content for C12H9N5O4 formula and
M = 287.13: calculated 50.19% C, 3.16% H, 24.38% N; experimental 50.48% C, 3.00% H,
24.70% N. In this paper the following abbreviation was used: 6M5NPAP - 6-methyl-5-nitro-
2-[(E)-phenyldiazenyl]pyridine.
2.2. X-ray data collection
X-ray diffraction intensity data for the studied crystal were collected at 130(2) K using
graphite monochromatic MoK radiation on a Xcalibur PX automated four-circle
diffractometer with Ruby CCD camera. No correction on the relative intensity variations was
necessary. Data collection, cell refinement, and data reduction and analysis were carried out
with CrysAlisCCD and CrysAlisRED, respectively [33]. The structure was solved by the
direct methods using SHELXS-97 and refined using SHELXL-97 programs [34]. All H atoms
were found in difference Fourier maps. In the final refinement cycles, the C-bonded H atoms
were treated as riding atoms in geometrically optimized positions, with C–H = 0.95–1.00 Å,
and with Uiso(H) = 1.2Ueq(C) for CH or 1.5Ueq(C) for CH3. The final difference Fourier maps
showed no peaks of chemical significance. The largest peaks on the final  map were
+0.126 and –0.154 eÅ-3. Visualisation of the structure was made with the Diamond 3.0
program [35]. Crystal data for the studied compound: C12H9N5O4, red: 0.40  0.15  0.05
mm, M = 287.24, monoclinic, space group Cc, a = 12.083 (7), b = 12.881 (6), c = 8.134 (3)
Å,  = 97.09 (5)°, V = 1256.3 (11) Å3, Z = 4, T = 130(2) K, 2741 measured reflections, 2066
independent reflections, 1677 reflections with I > 2σ(I), S = 1.07, θmin = 3.2°, θmax = 30.7°,
R[F2 > 2σ(F2)] = 0.050, wR(F2) = 0.099, Δρmax = 0.28 e Å−3, Δρmin = −0.20 e Å−3. CCDC-
1448287 contains the supplementary crystallographic data for this article. These data can be
obtained free of charge from The Cambridge Crystallographic Data Centre via
www.ccdc.cam.ac.uk/data_request/cif.

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2.3. Raman and IR measurements
IR spectra in the 4000 – 40 cm-1 range were recorded at room temperature in Nujol and
Fluorolube suspensions and KBr pellet with a FTIR Biorad 575C spectrometer. They were
identical in the ranges where the bands of Nujol or Fluorolube are absent, so the IR spectra
measured in KBr are shown in this paper. The resolution was 2.0 cm-1.
Raman spectra in the 4000 – 80 cm-1 range were measured in back scattering geometry
with a FT Bruker 110/S spectrometer. The resolution was 2.0 cm-1. The YAG:Nd (excitation
wavelength 1064 nm) laser was used as an excitation source.
Temperature dependence of FTIR spectra was also measured in the 30 – 4000 cm-1
range with the resolution of 2 cm-1 in the temperature range 4-298 K using a Janis ST100
Cryostat and BIORAD 575C spectrophotometer. The spectra were measured using pressed
KBr and Nujol mulls techniques in the MIR region and Nujol suspension on the polyethylene
plates in the FTIR region.
2.4. Spectroscopic studies
The electronic absorption spectra of the studied compounds were measured in Nujol
suspension using a JASCO V-570 UV/VIS spectrophotometer with the resolution of 0.5 nm.
The emission spectra were measured by a highly sensitive spectrofluorymeter NIR-
VIS PTI (Photon Technology International) working in T-configuration and equipped with a
photon-counting system (range 200 - 1000 nm).
2.5. Quantum chemical calculations
The geometry optimisation of the molecular structure of the studied compound was
performed for the monomeric unit with the use of Gaussian 03 programme package [36]. All
calculations were performed using density functional three-parameters hybrid (B3LYP)
methods [37-39] with the 6-311G(2d,2p) [40,41] basis set starting from the X-ray geometry.
The calculated and experimental values were compared using scaling factors to correct the
evaluated wavenumbers for vibrational anharmonicity and deficiencies inherent to the used
computational level. The Potential Energy Distribution (PED) of the normal modes among the
respective internal coordinates was calculated for 6M3,5NPAP using the BALGA [42]
program. The atomic coordinates from the X-ray studies were used as the input data in the
optimization procedure and the data from optimization were introduced to the BALGA
program. The IR and Raman wavenumbers were calculated for a single molecule.

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The vector displacements of the atoms from their equilibrium positions during the
vibration and the pictures of these displacements were prepared using the ANIMOL program
that also visualizes particular modes in an animated way [43].
A linear correlation was used for scaling the theoretical wavenumbers to compare them
with the experimental values [44]. The mean square deviation between the experimental
and calculated unscaled wavenumbers for 6M3,5NPAP was 8.6 cm-1 for the IR
and the Raman spectra. The scaling of the calculated wavenumbers improves this result
to 2.4 cm-1 for the IR and the Raman spectra. 0.965 scaling factor was used for the whole
range of the spectra.
The theoretical Raman intensities were calculated using the RAINT computer program
[45,46] and DFT calculated Raman scattering coefficients.
3. Results and discussion
3.1. Crystal structure
6-Methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine crystallizes in monoclinic, Cc =
C1 (No. 9) space group, with one molecule in the asymmetric unit (Fig. 2). The primitive unit
cell is built of four molecules. Selected geometrical parameters are presented in Table 1. They
are compared with the geometrical data obtained from the DFT calculations. The phenyl
moiety and pyridine ring are nearly planar. The N2, N3 and N5 lie approximately in the
pyridine ring plane with deviations of 0.013(6), -0.017(6) and 0.059(7) Å, respectively,
whereas the C7 and N2’ atoms are shifted by -0.095(6) and -0.107(7) Å, respectively, from
the corresponding ring plane. Both nitro groups are twisted in respect to the pyridine ring
plane; the dihedral angle between these planes is 89.7(2)° and 19.9(2)°, respectively, for NO2
group attached to C3 and C5 atoms. The nitro group attached to the C3 atom is twisted in a
higher extent in respect to the pyridine ring plane than in the previously described
compounds. For instance, the twisting angle of the NO2 group is < 10º in 2-amino-3-
nitropyridine compounds [1-6], and as large as 55º in 2-amino-4-methyl-3-nitropyridininium
trifluoroacetate [7]. The azo-bridge appears in the trans conformation in which C2-N2-N2’-
C1’ torsion angle takes a value of -178.6(3)º. The dihedral angles between the planes of the
pyridine ring and the phenyl ring is 3.5(2)°. Similar conformation with the corresponding
value of 4.8(3)º was previously observed in a similar compound, 6-methyl-5-nitro-2-[(E)-
phenyldiazenyl]pyridine (6M5NPAP) [25].
Table 1

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Fig. 2.
The crystal structure of the title compound is stabilized by weak C−H···O, C−H···N
and also - stacking interactions (Table 2, Fig. 3). The molecules are linked by a C−H···O
hydrogen bond involving the aromatic C4 atom (as a hydrogen bond donor) and the nitro O1
atom (as a hydrogen bond acceptor) of the adjacent molecule at (x, −y+1, z+1/2). This
hydrogen-bond motif, which can be described as C(5), generates a zigzag chain. Furthermore,
there is also an aromatic - stacking interaction between the pyridine ring at (x, y, z) and the
phenyl ring of adjacent molecule at (x, y, z+1) forming a chain. The distance between the
centroids of N1-C6 ring at (x ,y, z) and C1’-C6’ ring at (x, y, z+1) is 3.637(5) Å with an
interplanar spacing of 3.474(5) Å and a centroid offset of 1.16 Å, respectively. The angle
between the planes of these rings is 6.4(2). The adjacent chains are interconnected by a weak
C−H···N interaction between the C7 atom of the methyl group and the N1 pyridine atom of
an adjacent molecule at (x, −y, z+1/2), so forming a corrugated layer (Fig. 3). The three-
dimensional connectivity of this structure is completed by an additional aromatic - stacking
interaction between the pyridine ring at (x, y, z) and the phenyl ring of adjacent molecule at
(x-1/2, -y+1/2, z+1/2) of adjacent layers. The distance between the centroids of the N1-C6
ring at (x, y, z) and the C1’-C6’ ring at (x-1/2, -y+1/2, z+1/2) is 3.622(5) Å, an interplanar
spacing is 3.467(5) Å, a centroid offset is 1.1 Å and the angle between the planes of these
rings is 3.3(2)º, respectively.
Fig. 3
Table 2
3.2. Vibrational characteristics and DFT calculations
The monoclinic Cc (Cs4) (No. 9) primitive unit cell of the studied compound contains two
formula units giving rise to the 180 degree of freedom (2 x 30 = 60 atoms). Among them,
2A’+A” representation describes acoustic phonons and remaining 88A’+89A” are optical
modes. From the correlation between the C1 local symmetry of the single unit and Cs factor of
the group symmetry it follows that the unit cell modes corresponding to the internal vibrations
are described by the relation: C1  Cs A  A’ + A”. Comparing the theoretical data with the
number of the experimentally observed IR and Raman bands it is seen that the effect of the
interactions between two molecules in the unit cell is not visible in the spectra. For the studied

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compound, 74 bands are observed in the IR spectrum and 69 lines in the Raman one. Because
84 bands should be observed both in the IR and Raman spectra for a single molecule in local
C1 symmetry, the Ci molecular symmetry is sufficient in our case. This agreement between
the theoretical and experimental data proves that the intermolecular interactions do not
influence the number of the observed bands.
The experimental and calculated IR and Raman spectra obtained for the studied compound
are shown in Fig. 4. Calibration plots derived from the observed and calculated wavenumbers
are presented in Fig. 5. They show good correlation between the experimental and theoretical
values. The assignment of the IR and Raman bands to the respective normal modes is
proposed in Table 3.
Fig. 4
Fig. 5
Table 3
The calculated and experimental wavenumbers listed in Table 3 fit well those reported
in our earlier publication [25]. Moreover, the normal modes of the methyl, nitro, azo and rings
vibrations fall into similar energy ranges. Therefore, it is unnecessary to repeat the presented
earlier discussion about these data because the assignment of the modes is sufficiently
presented in Table 3. However, some regularities can be seen while comparing the observed
here IR and Raman band wavenumbers to those previously reported for another azo-
compound [6M5NPAP] having only two chromophores: nitro-group in 5 position and methyl-
group in 6 position of the pyridine ring. For this derivative new DFT calculations were
performed in the present work using the same 6-311(2d, 2p) functional and B3LYP basis set.
Table 4
The small differences between the values listed in Table 4 originate from a small
deviation of the structural parameters of the both compared compounds. It can be seen when
the geometry of the C-N=N-C bridge system is compared in Table 5 (C and C - carbon
atoms of the pyridine and phenyl rings, respectively).
Table 5
It means, that the introduction of an additional nitro group to the pyridine ring noticeably
influences the change of the C-N-distances as well as flat and dihedral angles. These

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deviations are small, but are reflected in the band wavenumebers. The following conclusions
can be drawn from these comparisons.
1. The azo-bond in two compared 6M3,5NPAP and 6M5NPAP compounds appears in the
trans-configuration.
2. The (N=N) vibrations of the former compound is observed in the Raman spectrum at
1490 cm-1 but for the latter at 1469 cm-1 with 53% and 44% contribution of the N=N
stretching, respectively. This tendency agrees with the shorter N=N bond length in the
6M3,5NPAP derivative. The (C-N) and (C-N) vibrations of the C-NN-C bridge are
observed at 1199 and 1193 cm-1, respectively, both in the IR and Raman spectra. They
are denoted as 29 and 30 modes in Table 3. The small difference between these values
reflect the small deviation between the C-N (1.426 Å) and C-N (1.430 Å) bond lengths
well. These data are similar in both compared phenyl- azopyridine. The vibrational
pattern, characteristic for the trans-phenylo-azopyridines, contains a strong Raman band
with a weak IR counterpart in the range 1460-1490 cm-1 and a weak IR and Raman
doublet in the range 1180 -1240 cm-1. These bands are sensitive to the chromophores type
and their substitution place in the pyridine ring.
3. The other characteristic vibrations of the trans-azo bridge are observed in the 1265 –
1210 and 1195 – 1180 cm-1 ranges and correspond to the stretching vibrations of two C-N
bonds of this system as as(CNNC) and s(CNNC) modes. The contribution of the C-N
stretch to these modes is of the order of 15 – 45%. These modes are coupled with the ()
and () modes of the pyridine ring. The other characteristic bands of the azo-bond are as
follows:
 in-plane bending as(CNNC)
 in-plane bending s(CNNC)
 out-of-plane bending (CNNC)
 torsions (CNNC)
at
at
at
at
975 - 910 cm-1,
640 - 610 cm-1,
139 - 119 cm-1,
100 - 30 cm-1.
It should be noted that the contribution of the –N=N- bond vibrations to the bands in the
far-IR region is very large due to participation of the azo-bridge in the mutual vibrations
of the large fragments of the molecule. The energetic position and the assignment of the
main IR and Raman bands are compatible with the data reported in the earlier works of
other Authors [19-23] and our own studies [24-27].
4. The nitro-groups bonded to C6 and C3 atoms of the pyridine ring, i.e. in the para and
ortho positions in respect to the azo-bond, are denoted as (NO2)A and (NO2)B,

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respectively. The wavenumbers of their as(NO2) vibrations clearly differ. The
contribution of the para-located group vibrations in the studied here 6M3,5NPAP
derivative appears for the modes: 11(20%) = 1591 cm-1 (RS), 14(31%) = 1547 cm-1
(IR,RS) and 15(27%) = 1525 (IR), 1524 (RS) cm-1. On the other hand, the vibrations of
the B nitro-group in the ortho-position contribute to the following modes: 12(19%) =
1584 cm-1(IR,RS), 13(33%) = 1570 cm-1 (IR,RS) and 14(43%) = 1547 cm-1 (IR,RS). A
reverse trend appears for the symmetric s(NO2) vibrations the calculated wavenumbers
of which are following: 24 = 1333 and 25 = 1317 cm-1 for the B and A groups with the
contribution 72 and 87%, respectively. The experimental wavenumbers of these
vibrations are observed at 1335 cm-1 (IR,RS) and 1311 (IR) and 1313 (RS) cm-1. It should
be noted that the bending (NO2) vibrations of both groups are coupled with each other.
The DFT calculations prove that in the 46 mode the coupling of 32% B and 20% A
group vibrations appears, but the 48 mode originates from the 48% A and 38% B group
vibrations. Generalizing these data it could be stated that the wavenumber of these bands
could be used for identification of the number and substitution place of the nitro-group in
the pyridine ring.
5.
The possibility of a hydrogen bond formation in the studied compound is suggested by
the X-ray studies since the 3.2 – 3.4 Å close contacts between the adjacent molecules
appear in the unit cell. The IR and Raman spectra do not confirm the existence of any
significant intra- or inter-molecular hydrogen bond type interactions in it. It is the reason
why its IR and Raman spectra can be interpreted on the basis of group theory applied for
the isolated molecule. Therefore the DFT calculations of the vibrational and electron
energy levels were performed for the isolated molecule. The weak interactions between
the adjacent molecules could be taken into account in the DFT approach for the dimer
system, however, the long distance between the interacting atoms of the
donorHacceptor system of the 2.2 - 2.4 Å order could not be defined in the used here
procedure. For these reasons the PED calculations were performed for the isolated
molecule in which the HB intermolecular interactions could not be taken into account.
In the discussion of the obtained results it should be taken into account that the DFT
calculations were performed for isolated molecules not confined in the crystal lattice. In the
solid state the azo-bond as well as phenyl and pyridine rings of the studied compound appear
in the quasi planar conformation. This could not be true for the isolated molecule in gas and

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liquid states. Therefore, the potential energy curves as a function of the torsion angles around
the –N=N- azo bond were determined. Fig. 6 shows this dependence. The course of this
relationship indicates that the most stable configuration of the studied phenylazopyridine
molecule appears when the C2-N2-N2’-C1’ torsion angle is -180 or 180, i.e. when the azo-
bond lies in the same plane in trans-configuration. This nearly appears for this compound in
the solid state and should be realized in the gas phase. This also follows from the good
accordance between the XRD data and geometrical parameters obtained from the DFT
procedure.
In the DFT calculations the molecular energies were calculated for all possible
conformations of the studied compound. Fig. 6 presents graphically such a relation between
the molecular energy and rotation angle of the azo bond and other functional groups. The
respective conformations are shown in this figure for all the energetic minima and maxima.
From this dependence follows that trans – configuration is the most stable for the azo bond in
the studied compound because the energy gap between these conformers equals to 1.054 eV
(0.03873 Hartree).
Fig. 6
The effect of the temperature change on the IR spectra of 6M3,5NPAP was studied in
the range 80 – 350 K. It is well known that decreasing temperature causes an increase of band
wavenumbers and an increase in band intensity. These changes are particularly visible for the
vibrations of the substituents involved in the inter- and intra-molecular interactions or those
with possibility of their rotation for which the band contours become significantly narrower.
Such effects are observed in the low-temperature spectra of the studied compound (Fig. 7).
Fig. 7
The shifts of the bands from the range 650 – 1000 cm-1 are insignificant and do not
exceed a few cm-1. Comparing these data with the results of the DFT calculations the
respective bands were mainly assigned to the vibrations of the phenyl and pyridine rings.
Clear changes of the spectral contour and shape are observed at low temperature for
the IR bands appearing at RT at 1584 cm-1 νθ + νas(NO2), 1570 cm-1 νas(NO2), 1438 cm-1
δas(CH3), 1376 cm-1 δs(CH3), 1311 cm-1 νs(NO2), 1039 cm-1 ρ(CH3). These bands also show a
shift exceeding 10 cm-1. These changes indicate a structural ordering of the whole molecule at
low temperature. The above-mentioned bands correspond to the vibrations of the CH3 and

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NO2 groups with a possibility of an internal rotation It should also be pointed out that the
bands at 1488, 1199 and 1193 cm-1 corresponding to the ν(NN) vibrations of the azo-bond
practically do not change their wavenumber and shape, which confirms that the conformation
of this bridge is stable both at low (to 80 K) and high (to 350 K) temperature.

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3.3 Electron absorption and emission spectra
The absorption spectrum of 6M3,5NPAP in the polycrystalline state is shown in Fig. 8a. It
contains two clear contours: the strong band at 323 nm, the shoulder at about 240 nm on the
slope of a strong transition at about 180 – 250 nm and the very broad band (shoulder) that
expands from 400 to 1000 nm. Such a spectral pattern agrees with that reported for trans-
azobenzenes [28,47-50]. A comparison of the absorption and luminescence spectra of
6M3,5NPAP in the polycrystalline state and the lifetime of its excited state is shown in Fig.
8a-c.
Fig. 8 a, b and c
The results of DFT calculations performed for electron levels of the studied dye are
shown in Table 6. The singlet states fall in the range 290 – 520 nm and the energy of the
triplet levels ranges from 400 to 570 nm. These values show a good agreement with the
position of the observed bands (Fig. 8). However, the calculated oscillator strengths of the
singlet transitions at 294 nm (No. 9) and in the range 420 – 520 nm (No. 1,2) take the greatest
values showing the shift from the greatest intensity band with he maximum at 323 nm
.
Table 6
The observed bands should be assigned to the following transitions: 200-289 nm -  
* of the phenyl and pyridine rings, the HOMO-LUMO transition observed in the range 280 –
400 nm and above 400 nm - n  * of the azo-bond. Due to the substitution of the nitro
groups simultaneously in the ortho and para-position of the azo-bridge, the observed bands
are shifted towards red.
It should be noted that mechanical milling of polycrystalline samples changes their color
(from violet to deep-red) and shape of its spectrum. Two contours of the initial spectrum stick
together into a very strong contour with the maximum at 289 nm and clear shoulders at 397
and 464 nm (see Fig. 8a). These changes could be explained as the isomerization to the cis-
form of this compound or its decomposition caused by mechanical milling.
The emission spectra of the studied material (Fig. 8b) contain two bands: one of a great
intensity at about 700 nm and the second, clearly weaker and narrower, at 625 nm. Depending
on the wavelength of the used for the excitation line the former band is somewhat shifted

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towards blue. The observed bands should be assigned to the following transitions: the former
band to the *n transition of the azo bond and the latter band to the *n transition
between the nitro-group and pyridine ring. The lifetime of the excited state is 12 s (Fig. 7c).
Comparison of the absorption and emission spectra allows us to state that the Stokes shift for
the measured sample is close to 5470 cm-1.
4. Conclusions
 2-phenylazo-3,5-dinitro-6-methylpyridine (6M3,5NPAP) is a new black-brown azo-dye
absorbing light at about 31,000 cm-1.
 The X-ray diffraction at 130 K and also at room temperature suggests that 6M3,5NPAP
appears in trans configuration in which C2-N2-N2’-C1’ torsion angle takes a value of
-178.6(3)º, whereas the dihedral angle between the planes of the phenyl and pyridine rings
is 3.5(2)°. The DFT calculations confirm that the trans – configuration of the azo bond in
the studied compound is the most stable because the energy gap between cis and trans
conformers equals to 1.054 eV (0.03873 Hartree).
 Both nitro groups are twisted with respect to the pyridine ring plane; the dihedral angle
between these planes is 89.7(2)° and 19.9(2)°, for NO2 group attached to C3 and C5
atoms, respectively. The nitro group attached to C3 atom is twisted in a higher extent in
respect to the pyridine ring plane than in the previously described compounds.
 In the crystal structure, the molecules are linked by a combination of C(sp2)−H···O and
C(sp3)−H···N hydrogen bonds and also - stacking interactions.
 The (N=N) vibrations of the studied 6M3,5NPAP dye are observed in the Raman
spectrum at 1490 cm-1 and at 1469 cm-1 with 53% and 44% contribution of the N=N
stretching, respectively.
6. The as(NO2) vibrations of the nitro-groups bonded to C6 and C3 atoms of the pyridine
ring, i.e. in the para and ortho positions in respect to the azo-bond, clearly differ both in
their wavenumbers and PED contribution. The wavenumber of these bands could be used
for identification of the number and substitution place of the nitro-group in the pyridine
ring.
7. The possibility of a hydrogen bond formation in the studied compound is suggested by
the X-ray studies since the 3.2 – 3.4 Å close contacts between the adjacent molecules

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appear in the unit cell. The IR and Raman spectra do not confirm the existence of any
significant intra- or inter-molecular hydrogen bond type interactions in it.
8. The emission spectra of the studied material contain two bands: at about 700 and 625 nm.
The observed bands should be assigned to the *n transition of the azo bond and the
*n transition between the nitro-group and pyridine ring, respectively. The life time of
the excited state is 12 s and the Stokes shift is close to 5470 cm-1.

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Acknowledgement: The present work was partly supported by Polish National Centre of
Science under the grant No. 2014/15/B/ST5/04730.
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List of figures
Fig. 1. Possible configurations of 6-methyl-3,5-dinitro-2-(phenyldiazenyl)pyridine.
Fig. 2. Molecular conformation of the studied compound showing the atom numbering
scheme. Displacements ellipsoids are drawn at the 50% probability level and H atoms
are shown as small spheres of arbitrary radii.
Fig. 3. A packing diagram of the title compound showing molecules organized via
C-H···O hydrogen bonds (black dashed lines), C-H···N (orange dashed lines) and -
 stacking (green dashed lines) interactions. Symmetry codes as in Table 2.
Fig. 4. The experimental and calculated IR and Raman spectra obtained for the studied
compound.
Fig. 5. Calibration plots showing the correlation between experimental and theoretical (IR,
Raman) wavenumners.
Fig. 6. The potential energy curve of the azo-bond in 6M3,5NPAP as a function of the torsion
C2-N2-N2’-C1’ angle (see Fig. 2).
Fig. 7. The temperature dependence of the IR spectra of 6M3,5NPAP in the ranges: 3150 –
2800 (A), 1650 – 675 (B), cm-1.
Fig. 8. The absorption spectra of 6M3,5NPAP in the polycrystalline state (a); The
luminescence spectra of 6M3,5NPAP in the polycrystalline state (b); The lifetime of
6M3,5NPAP excited state (c).

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Figure 1

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Figure 2

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Figure 3

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A

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B

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C

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D
Figure 4

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Figure 5

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Figure 6

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Figure 7