Molecular and crystal structures, vibrational studies and quantum chemical calculations of 3 and 5-nitroderivatives of 2-amino-4-methylpyridine

Article abstract of DOI:10.1016/j.saa.2012.07.121

The crystal structures of 2-amino-4-methyl-3-nitropyridine (I), 2-amino-4-methyl-3,5-dinitropyridine (II) and 2-amino-4-methyl-5-nitropyridine (III) have been determined. The compounds crystallize in the monoclinic P2 ₁/n, triclinic P-1 and monoclinic C2/c space groups, respectively. These structures are stabilized by a combination of N-H···N and N-H···O hydrogen bonds and exhibit layered arrangement with a dimeric N-H···N motif in which the molecular units are related by inversion centre. The molecular structures of the studied compounds have been determined using the DFT B3LYP/6-311G(2d,2p) approach and compared to those derived from X-ray studies. The IR and Raman wavenumbers have been calculated from the optimized geometry of monomers and dimers formed in the unit cell and compared to the experimental values obtained from the spectra.

Full text of DOI:10.1016/j.saa.2012.07.121

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
Contents lists available at SciVerse ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
Molecular and crystal structures, vibrational studies and quantum chemical
calculations of 3 and 5-nitroderivatives of 2-amino-4-methylpyridine
a
a
a
b
a
a,c
I. Bryndal a,b, , E. Kucharska , W. Sa˛siadek , M. Wandas , T. Lis , J. Lorenc , J. Hanuza
⇑
a Department of Bioorganic Chemistry, Institute of Chemistry and Food Technology, Faculty of Engineering and Economics, Wrocław University of Economics,
118/120 Komandorska, Wrocław 53-345, Poland
b Faculty of Chemistry, University of Wrocław, 14 Joliot-Curie, Wrocław 50-383, Poland
c Institute of Low Temperature and Structure Research, Polish Academy of Sciences, 2 Okólna, Wrocław 50-422, Poland
g r a p h i c a l a b s t r a c t
h i g h l i g h t s
"
"
"
The crystal structures of 3- and
5-nitroderivatives of 2-amino-4-
methylpyridine were studied.
These structures exhibit layered
arrangement with a dimeric N–HꢀꢀꢀN
motif.
The IR and Raman wavenumbers
have been calculated from the
optimized geometry of monomers
and dimers.
"
X-ray, IR, Raman and DFT methods
confirm the existence of
intermolecular N–HꢀꢀꢀN bonds.
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 9 May 2012
Received in revised form 16 July 2012
Accepted 17 July 2012
Available online 8 August 2012
The crystal structures of 2-amino-4-methyl-3-nitropyridine (I), 2-amino-4-methyl-3,5-dinitropyridine
(II) and 2-amino-4-methyl-5-nitropyridine (III) have been determined. The compounds crystallize in
the monoclinic P21/n, triclinic P-1 and monoclinic C2/c space groups, respectively. These structures are
stabilized by a combination of N–HꢀꢀꢀN and N–HꢀꢀꢀO hydrogen bonds and exhibit layered arrangement
with a dimeric N–HꢀꢀꢀN motif in which the molecular units are related by inversion centre. The molecular
structures of the studied compounds have been determined using the DFT B3LYP/6-311G(2d,2p)
approach and compared to those derived from X-ray studies. The IR and Raman wavenumbers have been
calculated from the optimized geometry of monomers and dimers formed in the unit cell and compared
to the experimental values obtained from the spectra.
Keywords:
2-Amino-4-methyl-3-nitropyridine
2-Amino-4-methyl-3,5-dinitropyridine
2-Amino-4-methyl-5-nitropyridine
IR and Raman spectra
Ó 2012 Elsevier B.V. All rights reserved.
Crystal structures
Intra- and intermolecular hydrogen bonds
Introduction
interest of numerous studies [1–4]. The pyridine ring appears
in a large number of natural substances such as vitamin B5,
The pyridine derivatives are widely used in the syntheses
of various biologically active compounds and have attracted
vitamin B6, pyridoxal and pyridoxamine; and drugs such as
nifedipine, nichetamine, sulphapyridine. Some of pyridine
derivatives show antimicrobial, antifungal, antibacterial, pesti-
cidal, antiallergic, antihypertensive, antitumor or analgesic
properties [5–10].
On the other hand, substituted pyridine compounds such as 2-
aminopyridines [11–13] and their nitro derivatives are useful as
building blocks of nonlinear optical materials [14–18].
⇑
Corresponding author at: Department of Bioorganic Chemistry, Institute of
Chemistry and Food Technology, Faculty of Engineering and Economics, Wrocław
University of Economics, 118/120 Komandorska, Wrocław 536-345, Poland. Tel.:
+48 71 368 0301; fax: +48 71 368 0292.
E-mail addresses: isai@o2.pl, ibryndal@ue.wroc.pl (I. Bryndal).
1386-1425/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.saa.2012.07.121

I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
953
Scheme 1. The molecular formulas of I–III compounds.
The present work is a continuation of our systematic studies on
the 2-aminopyridine derivatives with different substituents at var-
ious ring positions [19–22]. The relationships between the struc-
ture of these compounds and their hybrid salts have also been
studied [23–26]. The knowledge of their crystal and molecular
structures and their relation to the vibrational characteristics can
be applied in the discussion of their biological activity and the role
of hydrogen bonds in it. Therefore we report the preparation meth-
ods, structures, spectroscopic properties and quantum chemical
calculations of 2-amino-4-methyl-3-nitropyridine (I), 2-amino-4-
methyl-3,5-dinitropyridine (II) and 2-amino-4-methyl-5-nitropyr-
idine (III) (Scheme 1).
The IR and Raman spectra of 2-amino-4-methyl-3-nitropyridine
(I) are reported in the Spectral Database for Organic Compounds
(SDBS), (SDBS No: 29780) [27]. These data have been compared
to the spectra of other derivatives studied in the present paper.
In the similar way, although the crystal structure of I has been
determined at ambient temperature by other authors [28] recently,
the complementary X-ray studies at low temperatures for I–III
derivatives are reported in this paper.
The residues were purified by crystallization from water to give
2-amino-4-methyl-3-nitropyridine, (Yield: (27% (10 g), m.p.
I
134(1) °C), 2-amino-4-methyl-3,5-dinitropyridine, II (Yield: 80%
(10.4 g), m.p. 197(1) °C) and 2-amino-4-methyl-5-nitropyridine,
III (Yield: 40% (15 g), m.p. 218(1) °C), respectively. Melting points
were determined using a Köfler apparatus. The chemical composi-
tion of the obtained compounds was checked using the Carlo Erba
Analyser, Model 1104.
X-ray data collection
Details of the data collections, analyses and refinements for the
studied compounds are given in Supplementary Table S1. X-ray
measurements of the I–III derivatives were performed at 120, 90
and 100 K, respectively, using graphite-monochromated CuK
a
(k = 1.5418 Å) for I and MoK (k = 0.71073 Å) radiation for II and
a
III, respectively. The instrument was equipped with Oxford Cryo-
systems low-temperature devices. Lattice parameters were deter-
mined from least-squares analysis, and reflection data were
integrated using the CrysAlis software [30]. For I, an empirical
absorption correction determined with the CrysAlis RED 1.171
was applied to the data using spherical harmonics, implemented
in SCALE3 ABSPACK scaling algorithm [30]. A correction for extinc-
tion was applied for crystal I. For II and III, no absorption correc-
tion was applied; only Lorentz and polarization effects were
taken into account.
Experimental
Synthesis
The syntheses of several 2-aminonitropyridines were described
previously by Talik and Talik [29]. Their methods were applied in
the syntheses of I–III compounds using commercially available 2-
amino-4-methylpyridine (Fluka, >99%). These compounds were
obtained as follows: 25 g of appropriate 2-amino-4-methylpyri-
dine were dissolved in 125 cm3 of concentrated H2SO4 (Fluka,
96%). The reaction mixture was cooled under intensive stirring to
0 °C by adding ice mixed with NaCl. Subsequently, 37.5 cm3 of
HNO3 (Chempur, 65%, d = 1.4 g/cm3) were added in small portions
keeping the temperature below 10 °C. Then the mixture was stir-
red for 1.5 h with continuous cooling, and kept at ambient temper-
ature for 1 h. Next, the reaction mixture was heated in a water bath
for half an hour at 40 °C, 1 h in the temperature range 60–70 °C and
half an hour in a boiling water bath. Then, the whole reaction mix-
ture was cooled to ambient temperature, poured on ice and neu-
The structures were solved by direct methods using SHELXS-97
program [31] and refined on F2 by full-matrix least squares with
anisotropic thermal parameters for all non H-atoms using SHEL-
XL-97 [31]. The H atoms bound to C atoms were included in the
geometrically calculated positions, with the C–H distances of
0.95–0.98 Å, and refined using a riding model, with Uiso(H) =
1.2Ueq(Caryl) and Uiso(Hmethyl) = 1.5Ueq(C). The H atoms bounded
to N and O atoms were located from difference Fourier maps
and were freely refined with Uiso(H) = 1.2Ueq(N) and 1.5 Ueq(O),
respectively.
Full crystallographic details, including structures have been
deposited at the Cambridge Crystallographic Data Centre; CCDC
Reference Nos. 858904–858906. These data can be obtained free
of charge via <http://www.ccdc.cam.ac.uk/conts/retrieving.html>
(or from the Cambridge Crystallographic Data Centre, 12 Union
Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223 336033; e-mail:
deposit@ccdc.cam.uk).
tralized with ammonia to
a slightly alkaline pH. The solid
reaction product was filtered off under vacuum. Two nitro isomers
(3 and 5) were separated by steam distillation. More volatile 3- ni-
tro isomer (I) was distilled off and condensed as a pure compound
(obtained after drying 10 g), while residual 5-nitro isomer (III) was
filtered off and crystallized from water (with H2SO4 and active car-
bon added initially for dissolving the compound and removing
impurities). After neutralization, filtering off and drying, about
15 g of 5-nitro isomer (III) was obtained.
Spectroscopic measurements
IR spectra were recorded at room temperature in Nujol suspen-
sion in the 4000–50 cmꢁ1 range and potassium bromide pellet in
the 4000–400 cmꢁ1 range. The spectra were measured using a FTIR
The 2-amino-4-methyl-3,5-dinitropyridine (II) was obtained
from 2-amino-4-methyl-5-nitropyridine (III) by a similar proce-
dure (nitration and rearrangement to dinitropyridines).
Biorad 575C spectrometer with the resolution of 2.0 cmꢁ1
.
Raman spectra were measured in back scattering geometry in
the 4000–80 cmꢁ1 range using a FTRaman Bruker 110/S spectrom-

954
I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
eter. The resolution was 2.0 cmꢁ1. The YAG:Nd (excitation wave-
length 1064 nm) laser was used as an excitation source.
Quantum chemical calculations
The geometry optimisation of the molecular structures of the
studied compounds was performed for both the monomeric and
dimeric units with the use of Gaussian 03 programme package
[32]. All calculations were performed using density functional
three-parameters hybrid (B3LYP) methods [33–35] with the 6-
311G(d,p) [36,37] 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 computa-
tional level. The Potential Energy Distribution (PED) of the normal
modes among the respective internal coordinates has been calcu-
Fig. 2. The dimer of I formed by N–HꢀꢀꢀN hydrogen bonds. Dashed lines indicate
intra- and intermolecular hydrogen bonds (symmetry code as in Table 2).
lated for I–III using the BALGA [38] program. As the input data
the atomic coordinates from the X-ray studies were applied. The
dimers are built from two molecular units coupled via two hydro-
gen bonds between them. In this case the eight-atomic ring system
was formed (see Figs. 1 and 2).
The vector displacements of the atoms from their equilibrium
positions during the vibration and the graphical pictures of these
displacements were prepared using ANIMOL program that also
visualizes particular modes in animated way [39].
Linear correlation was used for scaling the theoretical wave-
numbers to compare them with the experimental values [40].
The mean square deviation between the experimental and calcu-
lated unscaled wavenumbers for I was 5.5 and 5.2 cmꢁ1, for II
was 6.01 and 5.7 cmꢁ1 and for III was 7.4 and 5.7 cmꢁ1, for the
IR and the Raman spectra, respectively. The scaling of the calcu-
lated waveꢁn1umbers improves this result to 2.0 cmꢁ1 for the IR
and 1.7 cm for the Raman spectra – for I, 2.8 cmꢁ1 for the IR
and 2.7 cmꢁ1 – for II, 4.4 cmꢁ1 for the IR and 3.3 cmꢁ1 – for III.
0.960, 0.957, 0.972 scaling factors were used for the 3600–
2900 cmꢁ1 range and 0.974, 0.979, 0.978 were used for the
1700–0 cmꢁ1 range of the monomers and the dimers of I–III,
respectively.
The theoretical Raman intensities were calculated using the
RAINT computer program [41] reported in [42].
Results and discussion
Structures description
The structure determinations of I–III revealed that the three
Fig. 1. The molecular structures of (a) I, (b) II and (c) III, with atom-numbering
schemes. Thermal ellipsoids are drawn at 50% probability level.
studied compounds crystallize in centrosymmetric space groups,

I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
955
ꢀ
P21/n, P1 and C2/c, respectively. Atom numbering schemes and
joined by C–HꢀꢀꢀO interactions involving one of the H atoms of
the methyl group as a donor and the nitro O atom as an acceptor,
forming a layer (Supplementary Fig. S1). Additionally, the appear-
molecular structures of the studied compounds are depicted in
Fig. 1(a)–(c). Selected geometric parameters are presented in Ta-
ble 1. The pyridine ring is slightly distorted from planarity; the
largest deviation (0.022(2) Å) from an aromatic ring plane occurs
for C3 atom. The amino N2 and methyl C7 atoms lie approximately
in the pyridine ring plane. The intramolecular N–HꢀꢀꢀO hydrogen
bond exists between the amino and nitro groups in I and II. Never-
theless, the nitro group is twisted with respect to the pyridine ring,
the dihedral angle between these planes is 16° in I, 40° and 26° in
II; probably as the result of the steric hindrance of the neighboring
nitro and methyl groups in the aromatic ring. For instance, the
twisting angle of the NO2 group is <10° in 2-amino-3-nitropyridine
compounds [13,14,43–46], and as large as 55° in 2-amino-4-
methyl-3-nitropyridininium trifluoroacetate [25]. The other geo-
metrical parameters for I–III may be regarded as normal and are
comparable with the values observed for 2-amino-3-nitropyridine
polymorphs [43,44] and also 2-amino-4-methyl-3-nitropyridine
[28].
ance of aromatic
gested by the X-ray data.
p
–
p
stacking and short N–Oꢀꢀꢀ
p contact are sug-
In the crystal structure of II, the H22 atom of amino group is in-
volved in the intra- and intermolecular hydrogen bonds with three
O atoms of two nitro groups (Table 3). The N–HꢀꢀꢀO bonds between
the pyridine units form the ribbon as shown in Supplementary
Fig. S2. The packing of the whole crystal is stabilized by C–HꢀꢀꢀO
interactions and aromatic p–p stacking.
The crystal structure of III contains the dimers connected via N–
HꢀꢀꢀO hydrogen bonds involving one of the H atoms of amino group
as a donor and nitro O atoms as acceptors (Table 4). As a result of
such interactions the layered structure is characteristic for the
compound III (Supplementary Fig. S3).
Vibrational and DFT calculations
The main features of the crystal structures are the centrosym-
metric dimers formed by two identical N–HꢀꢀꢀN hydrogen bonds
(Tables 2–4) involving one H atom of NH2 group as a donor and
the pyridine N-atom as an acceptor. In such a way, the dimer
and two HBs form eight-membered ring denoted as R22(8) graph
set motif (Fig. 2, Table 2) [47]. Similar dimers appear in crystals
of 2-aminopyridine and its nitro derivatives [43,44,48].
In the crystal structure of I, another H atom of amino group is
engaged in the intramolecular interaction with the O1 atom of
the nitro group only (Table 2). In this compound the dimers are
The IR and Raman spectra of the studied compounds are com-
pared in Figs. 3 and 4. Experimental and calculated wavenumbers
of I–III compounds are collected in Table 5, in which the assign-
ment of the vibrational normal modes to the respective bands is
proposed.
The IR spectrum of I measured in the present study was com-
pared to the one that had been measured earlier and shown in
the Spectral Database for Organic Compounds (SDBS) [27]. Both
spectra of this compound are identical.
It should be noted that the majority of wavenumbers and PED
contributions calculated for the dimers and monomers are nearly
identical or very similar. They mainly differ by a few percent
admixture of other internal co-ordinates in the normal modes.
However, this does not influence the assignment of the normal
modes to the respective IR and Raman bands that are based on
the significant contribution of the definite internal co-ordinates.
Table 1
Selected geometric parameters (Å, °) in I–III.
I Exp.
Calc.
II Exp.
Calc.
III Exp.
Calc.
Distances
N1–C6
N1–C2
C2–N2
C2–C3
C3–C4
C3–N3
N3–O1
N3–O2
C4–C5
C4–C7
C5–C6
C5–N5
N5–O3
N5–O4
1.323(2)
1.357(2)
1.343(2)
1.432(2)
1.412(2)
1.448(2)
1.242(2)
1.226(2)
1.386(2)
1.508(2)
1.387(2)
–
1.322 1.3216(14) 1.316 1.3346(12) 1.324
1.355 1.3581(11) 1.357 1.3593(12) 1.353
1.336 1.3316(14) 1.332 1.3393(12) 1.344
1.437 1.4253(10) 1.431 1.4169(13) 1.413
1.390 1.3912(14) 1.404 1.3747(13) 1.379
Pyridine ring vibrations
The assignment of the pyridine ring vibrations for the studied
compounds is based on the comparative spectra of pyridine [49],
the results of DFT quantum chemical calculations reported by Ure-
na et al. [50], as well as a number of our works on the IR and Raman
spectra of several pyridine derivatives [16,19,22,23,51]. On that
basis the following description of the lines observed in the spectra
1.450 1.4549(11) 1.462
1.239 1.2287(12) 1.235
–
–
–
–
–
–
1.227 1.2266(9)
1.223
1.390 1.4024(11) 1.404 1.4212(12) 1.416
1.506 1.5042(11) 1.505 1.5057(13) 1.504
1.387 1.3901(11) 1.392 1.3921(13) 1.390
is proposed:
t(CH): 3207–3109; t(/): 1610–1521 and 1008–889;
t(/) + d(CH): 1280–1150; d(/): 1158–1103, 791–750 and 679–
–
–
–
1.4496(15) 1.462 1.4413(13) 1.454
529;
c(CH) +
c(/): 1013–951, 849–782, 770–720 and 505–454;
–
–
1.2294(9)
1.2316(9)
1.226 1.2325(11) 1.229
1.227 1.2377(11) 1.230
and
c
(/): 240–98 cmꢁ1. The detailed assignment of the observed
bands to the respective normal modes is given in Table 5.
Bond angles
C6–N1–C2
N2–C2–N1 114.5(2)
It should be noted that the breathing s(/) vibrations of the pyr-
t
118.5(2)
118.9 118.36(7)
115.5 115.77(8)
124.5 124.66(7)
120.1 119.56(7)
120.1 123.00(6)
120.2 119.27(7)
119.7 117.62(7)
122.0 123.72(7)
119.0 118.02(7)
118.9 118.22(7)
116.9 113.97(7)
125.3 122.59(7)
117.8 123.24(7)
118.8 116.97(8)
116.0 117.19(8)
124.3 120.98(8)
119.7 121.82(8)
121.9 121.69(8)
117.6
117.0
121.7
121.3
121.6
–
–
–
–
–
115.7
119.0
125.3
119.5
116.9
123.6
123.5
118.5
118.0
124.3
idine ring in the three studied compounds exhibit interesting con-
formity. These vibrations usually appear for benzene derivatives in
the range 1000–900 cmꢁ1 [52,53]. For pyridine derivatives they
usually appear in the range 900–750 cmꢁ1 depending on the num-
ber of substituents and their position at the heterocyclic ring [54].
For the studied here compounds I–III the DFT calculations predict
the wavenumbers of these modes at 839, 814 and 813 cmꢁ1. The
respective Raman lines appear as medium strong bands at 866,
836 and 841 cmꢁ1, respectively. This sequence shows a good
agreement with the total dipole moments determined for the iso-
lated I–III molecules in DFT calculations. They are 1.3840, 0.5843
and 1.2519 D, respectively.
As far as vibrational dynamics of the studied compounds is con-
sidered, the problem of the breathing vibrations of the pyridine
ring in its derivatives can be also discussed taking into account
the shift of the gravity point of the pyridine ring in the derivative
according to its position in the unsubstituted pyridine. Supplemen-
N2–C2–C3
N1–C2–C3
C4–C3–C2
C4–C3–N3
C2–C3–N3
O2–N3–O1 121.2(2)
O1–N3–C3 119.0(2)
O2–N3–C3 119.8(2)
C3–C4–C5
C3–C4–C7
C5–C4–C7
C6–C5–C4
C6–C5–N5
C4–C5–N5
O3–N5–O4
O3–N5–C5
O4–N5–C5
N1–C6–C5
125.8(2)
119.7(2)
120.8(2)
119.9(2)
119.3(2)
119.7
118.4
123.4
118.2
118.3
–
–
–
–
–
116.4(2)
125.5(2)
118.1(2)
119.60(14) 119.7 121.28(7)
–
–
–
–
–
114.9 115.31(8)
122.7 118.79(8)
122.3 125.90(8)
120.6 120.31(8)
116.0 117.03(7)
123.5 122.65(8)
124.3 121.51(9)
118.5 119.16(8)
117.1 119.32(8)
124.0 123.88(8)
–
–
–
–
–
116.06(7)
122.59(7)
123.38(7)
118.83(7)
117.71(7)
124.8(2)
124.3 123.74(7)

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I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
Table 2
Geometrical parameters of hydrogen bonds and short interactions for I.
D–HꢀꢀꢀA
D–H
HꢀꢀꢀA
DꢀꢀꢀA
D–HꢀꢀꢀA
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Intermolecular
N2–H21ꢀꢀꢀN1a
C7–H73ꢀꢀꢀO1b
0.93(2)
0.98
1.02
1.09
2.09(2)
2.48
2.03
–
3.016(2)
3.457(2)
3.046
–
173(2)
174
177
–
Intramolecular
N2–H22ꢀꢀꢀO1
0.94(2)
1.00
1.98(2)
1.88
2.614(2)
2.615
124(2)
127
a
Symmetry codes: ꢁx + 1, ꢁy + 1, ꢁz + 2;
ꢁx + 1/2, yꢁ1/2, ꢁz + 1/2.
b
Table 3
Geometrical parameters of hydrogen bonds and short interactions for II.
D–HꢀꢀꢀA
D–H
HꢀꢀꢀA
DꢀꢀꢀA
D–HꢀꢀꢀA
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Intermolecular
N2–H21ꢀꢀꢀN1a
N2–H22ꢀꢀꢀ O3b
N2–H22ꢀꢀꢀ O4b
C6–H6ꢀꢀꢀO2c
0.88(2)
0.88(2)
0.88(2)
0.95
1.02
1.01
1.01
1.08
2.18(2)
2.49(2)
2.65(2)
2.51
2.03
–
–
3.057(2)
3.314(3)
3.082(2)
3.203(2)
3.045
176.9(10)
157.3(10)
111.9(9)
129.6
177.6
–
–
–
–
–
–
–
Intramolecular
N2–H22ꢀꢀꢀO1
C6–H6–O4
0.88(2)
0.95
0.98
1.01
1.08
1.08
1.08
2.09(2)
2.36
2.42
1.94
2.34
2.30
2.30
2.692(2)
2.687(2)
2.783(2)
2.799(2)
2.659
2.678
2.764
2.741
124.8(9)
99.6
101.0
102.6
125.6
96.2
103.4
101.9
C7–H71ꢀꢀꢀO3
C7–H72ꢀꢀꢀO2
0.98
2.42
a
b
c
Symmetry codes: ꢁx + 2, ꢁy + 1, ꢁz + 1;
x + 1, y + 1, z + 1;
x, y, zꢁ1.
Table 4
Geometrical parameters of hydrogen bonds and short interactions for III.
D–HꢀꢀꢀA
D–H
HꢀꢀꢀA
DꢀꢀꢀA
D–HꢀꢀꢀA
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Exp.
Calc.
Intermolecular
N2–H21ꢀꢀꢀN1a
N2–H22ꢀꢀꢀ O3b
N2–H22ꢀꢀꢀ O4b
0.96(2)
0.87(2)
0.87(2)
1.02
1.00
1.00
2.03(2)
2.52(2)
2.28(2)
1.99
–
–
2.993(2)
3.062(2)
3.140(2)
3.017
–
–
179.2(13)
121.6(12)
173.1(12)
179.8
–
–
Intramolecular
C6–H6ꢀꢀꢀO4
0.95
1.08
2.33
2.29
2.685(2)
2.665
101.1
97.8
a
Symmetry codes: ꢁx + 1, ꢁy + 1, ꢁz + 1;
x + 1/2, ꢁy + 3/2, zꢁ1/2.
b
tary Fig. S4 shows the position of these points in the analyzed mol-
ecules. The displacements of the gravity points are 0.9970, 0.8013
and 0.8392 Å for the compounds I–III, respectively. This sequence
gives the order I > III > II that agrees with the sequence of Raman
The asymmetric bending vibrations of the methyl groups should
appear between 1410 and 1550 cmꢁ1 [53,55]. This is true for the
compounds under study. das(CH3) vibration contributes to the
bands observed in the range 1473–1429 cmꢁ1 giving a 20–99%
contribution. The symmetric ds(CH3) vibrations also appear in a
typical range and are observed at 1436–1371 cmꢁ1 giving a 30–
99% contribution to the normal modes. The other bands involving
wavenumbers tI > tIII > t
II: 866 > 841 > 836 cmꢁ1 for the breathing
ring vibrations. It means, that the mass and place substitution sim-
ply influence the gravitation energy of this modes. In such a way,
the effect of the substituents’ mass and place of their substitution
on the gravity centre position can be analyzed.
the methyl groups are observed in the following regions:
q
s
(CH3):
(CH3):
1071–978,
c(/-CH3): 625–593, d(/-CH3): 407–395 and
221–202 cmꢁ1. The detailed assignment of the observed bands to
the respective normal modes is given in Table 5.
Methyl group vibrations
Three fundamental t(CH3) bands corresponding to one symmet-
ric and two asymmetric vibrations are usually observed in the
Nitro-group vibrations
The nitro group bonded to the pyridine ring (C/–NO2) gives rise
to the eight vibrational normal modes. They are described as
range between 2950 and 2990 cmꢁ1 [53,55]. Our DFT calculations
locate these modes at the following bands:
(97–100% contribution) and
s(CH3) 2836–2828 cmꢁ1 (100% con-
tribution). They agree well with the experimental values found at
3107–2979 cmꢁ1 for as(CH3) and 2992–2932 cmꢁ1 for
s(CH3).
tas(CH3) 2921–2884
t
stretching
plane vibrations: bending d(NO2), rocking
NO2) and out-of-plane wagging (NO2), twisting
sional (/-NO2). Observed main IR and (RS) modes of the C/–
NO2 group have been identified and assigned to the following IR
t
as(NO2),
t
s(NO2) and
t
(C–NO2) vibrations and five in-
(NO2), bending d(/-
(NO2) and tor-
x
t
t
q
s
The other weak bands in this range arise from a Fermi resonance
with the bending vibrations of these groups.
c

I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
957
Fig. 3. Experimental and calculated IR spectra of I–III in the range 3700–50 cmꢁ1
.
Fig. 4. Experimental and calculated Raman spectra of I–III in the range 3600–80 cmꢁ1
.
peaks for I–III, respectively:
1441; 1429; 1452 and the second range 1314; 1323; 1291;
d(NO2) 866 (866), 835 (836); 841 (841), (NO2) 786 (791); 785
t
as(NO2) 1559; 1556; 1543;
t
s(NO2)
t
as(NO2): 1596 (1597),
ts(NO2): 1348 (1348) and d(NO2): 894
(894) cmꢁ1
.
x
Presented here results differ from the data reported earlier for
2-amino-5-nitropyridine [56], for which other assignment of bands
(782); 765 (764) cmꢁ1. The respective theoretical wavenumbers
of these vibrations calculated for the dimeric model are expected
in the ranges 1613–1428, 1311–1215, 870–840, 778–704, 626–
426, 400–365, 328–232 and 278–67 cmꢁ1. These modes involve
the most significant PED contributions of the C–NO2 and NO2 coor-
dinates into the normal modes. Some different modes also contain
lower contribution of these atomic displacements and respective
internal coordinates. This situation appears for the modes observed
in the range 680–650, 635–600 and 480–460 cmꢁ1 (Table 5). The
significant shifts to the higher wavenumbers are observed for
the compound II for which the following vibrations are observed:
were proposed: tas(NO2): 1493 (1499), t .
s(NO2): 1285 (1274) cmꢁ1
It probably follows from the differences of their crystallographic
structures and other programs used in the DFT calculations.
Hydrogen bonds and short contacts vibrations
The series of the materials studied here creates a unique possi-
bility to compare the structures and vibrational properties of the
compounds with different substitution place of nitro groups. From
the X-ray studies it follows that the position of this chromophore
influences both the unit cell structure, space arrangement of the

Table 5
Experimental and calculated wavenumbers (cmꢁ1) and assignments of I–III compounds.
I
II
III
Calc*
IR spectra
RS spectra
–
Calc*
IR spectra
3426 m
RS spectra
3426 vw
Calc*
IR spectra
3407 m
RS spectra
3406 vw
Assignment
1
2
–
3
4
5
6
–
–
7
8
9
10
11
12
13
14
–
3371
3370
–
3112
3085
2963
2963
–
3479 sh
3458 m
3388 sh
3264 m
3208 sh
3118 m
1
2
–
3
4
5
6
–
–
–
3354
3354
–
3099
3074
2945
2945
–
1
2
–
3
4
5
6
–
–
7
8
9
10
11
12
13
14
–
3418
3418
–
3055
3021
2964
2964
–
m
NH2 + mN–HꢀꢀꢀN/
–
3392 sh
3292 w
3235 sh
3162 m
–
3322 w
3274 vw
–
–
m
m
N–HꢀꢀꢀN/
N–HꢀꢀꢀN/
3257 vw
3286 vw
3109 vw
3157 vw
3207 sh
–
m
CH
3068 vw
–
3031 vw
3064 w
3048 sh
–
–
–
–
–
–
–
3166 sh
–
3120 m
–
–
Combination
Combination
–
–
–
–
2908
2908
2891
2891
2885
2885
2828
2828
–
2940
2940
2891
2891
2884
2884
2828
2828
–
3112 vw
m
CH
2996 vw
2981 vw
3005 w
2979 w
7
8
9
10
11
12
–
2921
2921
2892
2892
2836
2836
–
3099 sh
3045 sh
3099 vw
3014 vw
2992 vw
3107 sh
3065 sh
2984 sh
2973 m
2945 sh
3065 w
2991 vw
m
asCH3
2932 vw
–
2937 m
–
2992 vw
–
2945 w
–
2936 w
–
m
sCH3
2878 w
2865 sh
2844 w
2719 vw
2669 vw
1668 sh
1654 m
1608 m
1601 sh
1579 sh
1543m
1528 vw
1504 sh
1493 vw
–
Combination
–
–
–
15
16
17
18
–
–
–
–
–
–
–
–
–
–
13
14
15
16
–
–
–
–
–
–
–
–
–
–
–
–
15
16
17
18
–
–
–
–
–
–
Combination
Combination
Combination
d/-NH2HB
2736 vw
–
1618 vs
1594
1591
1561
1550
1620 sh
1612 vw
1590 w
1613
1611
1576
1567
1633 s
1630 w
1639
1630
1568
1562
1660 vw
1589 m
1596 m
1597 m
1610 w
m
/ +
/ +
m
asNO2I,II
19
20
21
22
–
1519
1519
1498
1490
–
1559 m
1513 s
–
1559 m
1507 w
–
17
18
19
20
21
22
23
24
25
26
27
28
29
30
1534
1534
1517
1514
1485
1484
1446
1442
1433
1432
1412
1411
1381
1381
1556 m
1536 m
1552 w
1523 m
1499 w
1473 sh
1462 sh
1435 vw
1413 vw
19
20
21
22
–
1501
1498
1463
1457
–
1538 w
1521 vw
1499 m
1496 sh
–
m
m
m
masNO2II,III + dCHI
asNO2I,II
asNO2II
+ m/ + dCH
1512 m
1505 sh
1480 w
+
m
/
23
24
25
26
27
28
29
30
1435
1428
1415
1414
1411
1411
1398
1396
1473 vw
1456 sh
1441 m
1459 sh
1445 w
23
24
25
26
27
28
29
30
1456
1450
1431
1430
1417
1417
1395
1389
1475 sh
1470 sh
1452 m
1480 sh
1478 vw
1458 vw
1426 vw
dasCH3I
dasCH3
dasCH3
+
m
/-NH2
+ masNO2III
HB
1459 vw
1429 w
1414 w
+
m
sNO2I
1424 sh
1420 sh
1436 w
1431 sh
1426 sh
1406 sh
1372 w
dsCH3
+
m
/ + dNH2HB
31
32
33
34
35
36
1356
1356
1319
1319
1284
1284
1371 w
1350 w
1383 m
1346 w
1312 vs
31
32
33
34
35
36
37
38
–
1360
1360
1326
1325
1311
1311
1295
1294
–
1375 w
1351 m
1384 vw
–
31
32
33
34
35
36
1370
1370
1300
1297
1286
1285
1372 vw
1352 sh
dsCH3
dCH +
1341 sh
m/ + dNH2HB
1314 m
1302 sh
1348 m
1323 vs
1311 sh
1291 sh
–
1348 m
1323 vs
1293 sh
1332 m
1291 s
1335 m
1292 vs
m
sNO2 + m/
37
38
39
40
1235
1233
1217
1215
1267 m
1267 s
–
37
38
39
40
1255
1253
1244
1241
1274 vs
1266 sh
1237 sh
1273 s
m
m
/ + dCH +
/ + sNO2
msNO2I
1239 s
1196 sh
1234 vs
1195 sh
39
40
1246
1244
1280 sh
1278 w
m

41
42
43
44
–
1121
1119
1081
1079
–
1150 w
1153 w
41
42
43
44
45
46
–
1203
1202
1112
1111
1084
1078
–
1236 w
1132 vw
1109 w
–
1233 m
41
42
43
44
45
46
–
1152
1151
1081
1080
1061
1056
–
1188 w
1189 m
m
/ + dCH
d/ + /-NO2
NH2HBII,III
d/ + CH3
CH3
1120 w
1100 sh
–
1121 w
1103 sh
–
1139 w
1118 vw
1093 vw
1083 vw
–
1156 sh
1136 w
1109 m
1092 sh
–
1158 vw
m
+
qNH2HB,I + m(/-NH2)HB
1110 m
1084 sh
–
q
+
m
/
45
46
47
48
49
50
53
54
1042
1041
1010
1010
993
991
947
947
1068 w
1061 m
q
1044 w
1009 w
997 sh
1031 w
1027 sh
47
48
49
50
53
54
1016
1014
1010
1010
950
1042 vw
1030 vw
1041 w
1026 sh
47
48
49
50
51
52
1027
1026
998
998
956
1071 w
1045 sh
1029 vw
1041 vw
1031vw
q
+ m/
982 vw
981 vw
954 w
951 w
1013 vw
998 sh
974 sh
–
1013 m
975 vw
c
CH + c/
949
956
51
52
–
950
949
–
977 vw
–
978 vw
–
51
52
–
983
980
–
1002 vw
–
1008 w
–
–
–
–
m
m
/ + qCH3
53
54
–
922
921
–
955 m
889 sh
–
952 m
–
/
–
–
–
–
55
56
57
58
–
870
870
814
814
–
894 w
835 m
–
895 w
836 w
–
dNO2
dNO2 + d/
55
56
57
58
59
60
61
62
63
64
65
–
839
838
784
783
771
771
768
767
751
717
711
–
866 m
821 w
786 m
866 w
819 vw
791 m
57
58
55
56
–
813
813
840
840
–
849 sh
841 m
841 m
c
c
CH +
/ +
c/
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
778
778
764
763
755
751
743
710
704
697
664
661
626
617
588
587
785 w
779 w
782 m
–
–
–
x
NO2
/ -CH3 + dNO2I,II
NO2
62
63
61
59
60
64
65
66
67
68
–
743
742
749
763
760
725
709
693
636
628
–
750 vw
d/ + m
756 w
721 w
–
756 w
741 vw
754 w
765 w
770 w
764 m
s
x
h
+
x
HB
731 vw
NO2
+
m
/
+ sh
I,III HB
–
–
–
–
–
–
721 vw
–
735 vw
x
x
sh
NO2
NO2
+
+
c
c
/ + cCHIII
/
–
–
720 w
681 sh
652 w
66
67
68
–
699
596
590
–
707 sh
667 w
610 vw
–
710 w
679 w
668 vw
638 w
–
HB
606 m
–
679 w
645 vw
d/ + dNO2 + breathing hHB
NO2 + d/-NH2HB
/-CH3
630 w
599 w
–
–
–
q
69
70
579
578
593 vw
593 vw
601 vw
–
69
70
587
587
625 sh
613 w
600 w
583 m
568 sh
532 m
c
+ c/
71
72
73
74
75
76
77
78
–
556
550
522
522
501
488
466
462
–
570 vw
544 m
526 m
478 w
–
567 vw
544 m
532 sh
481 w
–
–
–
–
71
72
73
74
–
568
567
520
516
–
588 w
529 w
–
q
NO2 + d/-NH2HB + d/
/ -CH3
75
76
77
78
79
80
81
82
83
84
–
548
548
520
511
484
479
463
462
418
411
–
559 w
566 sh
536 sh
561 w
–
d/ +
NH2HB
m
–
x
+
c
(N–HꢀꢀꢀN/)
502 w
467 w
428 w
–
505 vw
465 w
423 vw
–
75
76
77
78
–
458
454
438
426
–
454 sh
448 m
–
452 vw
440 vw
–
c
/ +
c/-CH3 (N–
+ c
HꢀꢀꢀN/) + NO2II
q
+ xNH2HBI,II
q
NO2 + d/ -NH2HB
–
–
–
–
d/ -NH2HB + qNO2
79
80
–
411
408
–
419 w
–
415 m
–
79
80
81
82
83
378
377
356
352
328
379 vw
369 vw
336 vw
376 w
–
x
NH2HB + c/
HB
–
–
–
–
d/ + m/ -NO2
81
382
396 sh
395 w
85
400
404 vw
407 w
336 vw
d/ -CH3 + d/ + m/ -NO2I
(continued on next page)

Table 5 (continued)
I
II
III
Calc*
IR spectra
RS spectra
Calc*
IR spectra
361 vw
RS spectra
362 vw
Calc*
IR spectra
RS spectra
Assignment
82
83
84
85
86
381
356
353
293
292
86
87
88
89
90
91
92
93
94
95
399
369
365
328
327
311
305
265
262
232
84
–
326
–
356 vw
294 w
365 w
294 w
–
–
–
–
d/ + m/ -NO2 + d/ -CH3I
338 vw
328 sh
292 sh
337 w
303 vw
–
–
d/ -NO2
–
–
–
–
274 sh
274 w
–
–
–
–
–
–
d/ -NO2
+ c/ -NH2HB
87
88
–
245
245
–
–
264 w
–
240 w
–
–
c
c
c
/-NO2
/-CH3
/-NO2
+
c
/ -CH3
+ c/
–
–
–
–
–
–
85
86
87
88
89
90
91
92
–
282
281
278
277
254
251
200
199
–
280 vw
287 vw
–
–
–
–
–
–
–
–
–
–
–
–
–
–
+ c
/ -CH3
–
–
–
–
–
–
–
261 vw
d/-NO2
/ + /-CH3
d/-NO2
–
–
96
225
226 sh
–
207 vw
219 vw
c
c
–
–
97
98
99
100
101
102
103
104
206
203
197
197
109
108
97
–
216 vw
–
–
–
–
89
90
91
92
93
237
236
196
192
88
–
257 sh
221 w
141 m
202 w
–
–
–
–
–
s
s
c
CH3
NO2
–
–
142 sh
126 sh
–
–
+ c/
I
132 vw
133 sh
–
94
95
–
108
102
–
130 vw
–
132 sh
121 m
/-NO2
+
c
/ +
c
/-NH2II,IIIHB
92
–
94
95
96
–
86
85
74
–
d/
+
qNH2
+
c
/-NO2I
HB
HB
120 vw
–
110 m
–
105
107
78
63
–
–
114 m
98 sh
93
96
97
–
99
98
–
114
80
78
–
58
62
–
–
–
m
c
NHꢀꢀꢀN HB + d/HB
/-NO2
99 m
–
–
97
–
–
–
55
–
–
–
–
–
–
–
106
108
–
109
110
111
112
67
56
–
52
52
48
31
–
–
–
c
/-NO2
+
x
NH2HB
NHꢀꢀꢀNHB
Waving / HB
NO2
81 sh
81 w
69 vw
68 w
d/HB + m
91 m
–
s
100
98
99
101
102
39
45
41
16
11
88 vw
68 sh
82 m
–
101
100
53
56
Waving /HB
Wagging /, / + sNO2
+
s
NO2
–
–
–
–
–
–
113
114
17
7
–
–
–
–
102
–
28
–
–
–
–
–
Flapping /, /
Twisting /, /
In-plane vibrations:
m
, stretching; d, bending;
q
, rocking. Out-of-plane vibrations:
c, torsional; x, wagging; s, twisting. /, pyridine ring; h, eight-membered ring.
*
Scaling factor: fsc = 0.963 (3600–2500 cmꢁ1), fsc = 0.978 (2499–0 cmꢁ1) for I–III compounds.

I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
961
molecules in it, as well as the configuration and strength of the
hydrogen bonds inside the unit cell. The studied compounds differ
in the number and type of HBs appearing in their structure. The
pyridine units of the compound I are joined via two types of HBs
in which two hydrogen atoms of NH2 group are involved: intermo-
lecular NHꢀꢀꢀN/ (/ = pyridine ring, N/ - pyridine nitrogen) and
intramolecular N–HꢀꢀꢀON (ON – oxygen atom of the nitro group),
see Supplementary Fig. S5. The compound III contains two HBs
of the same type but both have inter-molecular nature joining
two adjacent pyridine units. Finally, according to the X-ray data
three types of HBs exist in III: two inter-molecular of the N–HꢀꢀꢀN/
and N–HꢀꢀꢀO0N types and the third of the N–HꢀꢀꢀO0N0 type. The com-
mon feature of all these structures is the eight membered system
built from two N2–H22ꢀꢀꢀN1 hydrogen bonds that join two pyridine
rings. This system strongly affects the structure and vibrational
properties of the studied compounds. Such a ring contains weak
bonds. It seems problematic to handle it as a relatively indepen-
dent part (the whole unit) of an atomic system, like e.g., the ben-
zene ring. Of course, it may be possible to define likely internal
coordinates of the eight-atomic ring but this is not well estab-
lished. The hydrogen bonds cannot compete with the covalent
bonds. Parts of this ring belong to better-organized atomic sys-
tems, i.e., to molecules. The experimental and calculated geometri-
cal parameters of all appearing HBs are collected in Tables 2–4. The
X-ray data indicate that the length of the N–HꢀꢀꢀN/ HB is 3.016(2) Å
for I, 3.057(2) Å for II and 2.993(2) Å for III. On the other hand, the
respective IR bands are observed at the wavenumbers 3458 and
3264 cmꢁ1 for I, 3426 and 3292 cmꢁ1 for II and 3407 and
3322 cmꢁ1 for III. It is clearly seen that good correlation exists be-
tween the X-ray parameters and the vibrational data. It means that
other approach should be applied in the assignment of IR bands in
which the eight-membered h ring formed from the eight atoms
sequence fits well to the wavenumbers for the IR bands observed
in the range 3460 – 3200 cmꢁ1. The bands at 3458, 3426,
3407 cmꢁ1 exhibit low-frequency shift, whereas the sequence
3264, 3292, 3322 cmꢁ1 shows high-frequency shift, respectively
for the compounds I–III. It means that the splitting between
respective bands
Dt
equals to 194, 134 and 85 cmꢁ1. Such an
excellent fitting between the spectroscopic and X-ray data proves
that two HBs appeared in the h ring could not be considered sepa-
rately in the discussion of the vibrational spectra. The agreement
between the structural (N/(i)ꢀꢀꢀN/(ii) distance) and spectroscopic
(doublet of bands in the range 3460–3200 cmꢁ1) results could be
obtained when the bridge h ring is discussed as a whole unit.
Table 6 presents the wavenumbers of other normal modes that
in our opinion should be assigned to the vibrations of this intermo-
lecular interaction.
The stretching vibration of the HꢀꢀꢀN/ HB bonds, i.e., the
t
(HꢀꢀꢀN/) mode, according to the results of the quantum chemical
calculations should be observed in the range 114–74 cmꢁ1 (see Ta-
ble 5). These values are in good agreement with the wavenumbers
of IR bands observed in the range 200–68 cmꢁ1. The shapes of
these broad contours are typical for those observed for other HB
systems [57–61].
Apart from the bands in the region above 3200 cmꢁ1, the se-
quence of IR bands at 3118, 3162 and 3120 cmꢁ1 is observed,
respectively. They are broad and multi-componential what proba-
bly arises from the participation of a few vibrations corresponding
to different HBs appearing in the structure of the studied com-
pounds. X-ray studies suggest the existence of the interactions be-
tween the CH3 and NO2 groups (intermolecular) as well as NH2 and
NO2 groups (intramolecular) for the compound I. For the derivative
II short contacts appear for the intermolecular interactions NH2-
ꢀꢀꢀNO2 (3.082(2), 3.314(3) Å) and CHꢀꢀꢀNO2 (3.203(2) Å) as well as
intramolecular interactions NH2ꢀꢀꢀNO2 (2.692(2) Å), CHꢀꢀꢀNO2
(2.687(2) Å) and CH3ꢀꢀꢀNO2 (2.783(2), 2.799(2) Å). Finally, in the
compound III the short intermolecular contacts NH2ꢀꢀꢀNO2
(3.062(2), 3.140(2) Å) and intramolecular CHꢀꢀꢀNO2 (2.685(2) Å)
are proposed (see Tables 2–4). These interactions seem to be weak-
er than those realized in the eight-membered bridge. Therefore the
wavenumbers of respective bands should be red shifted. These
interactions are probably reflected in the broad contour at about
3100 cmꢁ1. This problem should be answered when the IR and Ra-
man spectra recorded at low temperature will be completed.
N2–H22ꢀꢀꢀN1–C2–N2–H22ꢀꢀꢀN1–C2 should be considered as
whole unit. 18 normal modes characterize the vibrations of such
system. Among them there are nine stretching modes: two (N–
HꢀꢀꢀN/), two (C–N), two (/) describing the vibration of the C@N
bonds of the pyridine ring, two (h) breathing
(HꢀꢀꢀN/) and one
mode of the whole ring. Nine bending modes can be characterized
as two in-plane d(NHꢀꢀꢀN/), two out-of-plane (NHꢀꢀꢀN/) and five
torsions of the whole HB bridge ring (h). Because this ring has pla-
a
t
t
t
t
t
c
s
nar arrangement, the Ci symmetry can be adopted in the descrip-
tion of its vibrational normal modes described by the 9Ag + 9Au
representation, where Ag modes are Raman active and Au modes
are IR active. Basing on the above consideration Table 6 lists the
wavenumbers and their assignment to respective vibrations of
the eight-membered h ring. These data should be related to the
structure of the ring for which the N/(i)ꢀꢀꢀN/(ii) distance is the most
characteristic parameter. It is the closest distance between the
adjacent pyridine rings. From the X-ray studies it follows that
these distances are 3.609(3) Å for the compound I, 3.662(3) Å for
the compound II and 3.765(3) Å for the compound III. This
Conclusions
(1) X-ray, IR and Raman studies as well as quantum chemical
calculations performed for the studied compounds confirm
the existence of intermolecular N–HꢀꢀꢀN hydrogen bonds in
structures in which the NH2 groups and pyridine nitrogen
atoms are engaged. As a result, dimeric arrangement from
adjacent pyridine units is formed consisting of eight-mem-
bered ring as a bridge system. The vibrations of this system
are responsible for
a characteristic sequence of bands
Table 6
observed in the defined ranges of the IR spectrum.
(2) X-ray studies suggest the existence of the interactions
between the CH3 and NO2 groups (intermolecular) as well
as NH2 and NO2 groups (intramolecular) for the studied
compounds. These interactions seem to be weaker than
those realized in the eight membered bridge and therefore
the broad contour at about 3100 cmꢁ1 probably corresponds
to the vibrations of these HBs.
(3) The quantum chemical calculations predict well the forma-
tion of the eight-membered bridge system built from hydro-
gen bonds but also exhibit good agreement between the
theoretical and experimental wavenumbers of their normal
IR experimental wavenumbers [cmꢁ1] assigned to the vibrations of eight-membered
ring built from to HBs.
I
II
III
m
m
q
(N–HꢀꢀꢀN/)
(NHꢀꢀꢀN)
3458, 3264
120, –
3426, 3292
–, 81
3407, 3322
–, 69
(NH2)HB
+
1120, 1100
1109, –
1109, 1092
m(/-NH2)HB
m(/)
1473, 1456
667
1480, 1414
679
1475, 1431
652
Breathing hHB
d(N–HꢀꢀꢀN/)
–, 1618
526, 478
1633, –
536, 502
1668, 1654
454, 379
c
s
(N–HꢀꢀꢀN/)
(h)HB
756, –, 721, 707, – 756, 741, –, 710, – 770, 765, –, 681

962
I. Bryndal et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 96 (2012) 952–962
of Advanced Industrial Science and Technology (AIST), Japan (SDBS No:
modes. It should be pointed out that the quantum chemical
29780).
calculations refer to the molecules and their dimers in vac-
uum. However, the X-ray results refer to molecules in chem-
ical environment. Therefore these results have to differ
theoretically since the states of the molecules are different.
Besides, the quantum chemical methods are approxima-
tions; they yield only approximate results. The scaling tries
to equalize these deviations.
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Acknowledgement
This work was financially supported by Ministry of Science and
Higher Education (Grant No. PBZ/MEiN/01/2006/21).
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.saa.2012.07.121.
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