Evidence of low temperature phase transition in 2,6-dimethylpyrazine - picric acid cocrystal by means of temperature dependent investigations: X-ray, DSC and IR

Article abstract of DOI:10.1016/j.molstruc.2020.129432

In the present paper the structural and dynamical properties of crystalline 2,6–dimethylpyrazine - picric acid cocrystal are described. The title cocrystal crystallizes in centrosymmetric monoclinic P2₁/c space group. The X-ray diffraction and

Full text of DOI:10.1016/j.molstruc.2020.129432

Journal Pre-proof
Evidence of low temperature phase transition in 2,6-dimethylpyrazine
- picric acid cocrystal by means of temperature dependent
investigations: X-ray, DSC and IR.
´
A. Pawlukojc Conceptualization;Methodology;Investigation;Writing–Oryginal Draft;Project administration ,
´
J. Hetmanczyk Investigation;Formal analysis;Writing–Review and Editing;Visualization ,
´
L. Hetmanczyk Investigation;Formal analysis;Writing–Review and Editing ,
J. Nowicka-Scheibe Concepualization;Resources ,
Jan K. Maurin Investigation;Formal analysis ,
W. Schilf Investigation;Formal analysis ,
´
D. Trzybinski Investigation;Formal analysis ,
K. Woz´niak Investigation;Formal analysis
PII:
S0022-2860(20)31747-6
DOI:
Reference:
https://doi.org/10.1016/j.molstruc.2020.129432
MOLSTR 129432
To appear in:
Journal of Molecular Structure
Received date:
Revised date:
Accepted date:
22 July 2020
7 October 2020
8 October 2020
´
Please cite this article as: A. Pawlukojc Conceptualization;Methodology;Investigation;Writing–Oryginal Draft;Project
´
J. Hetmanczyk Investigation;Formal analysis;Writing–Review and Editing;Visualization ,
´
L. Hetmanczyk Investigation;Formal analysis;Writing–Review and Editing , J. Nowicka-Scheibe Concepualization;R
Jan K. Maurin Investigation;Formal analysis , W. Schilf Investigation;Formal analysis ,
´
D. Trzybinski Investigation;Formal analysis , K. Woz´niak Investigation;Formal analysis , Evidence
of low temperature phase transition in 2,6-dimethylpyrazine - picric acid cocrystal by means of tem-
perature dependent investigations: X-ray, DSC and IR., Journal of Molecular Structure (2020), doi:
https://doi.org/10.1016/j.molstruc.2020.129432
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Highlights
 New 2,6-dimethylpyrazine - picric acid cocrystal was synthezed and investigated.
 DFT calculation for solids state model was performed.
 Low temperature phase transition was observed.
 Full vibrational analysis was performed.
 Activation energy for reorientation of C-CH3bending vibration was obtained.

Evidence of low temperature phase transition in 2,6-dimethylpyrazine - picric
acid cocrystal by means of temperature dependent investigations: X-ray, DSC
and IR.
A. Pawlukojća,b,1, J. Hetmańczyk c, Ł. Hetmańczyk c, J. Nowicka-Scheibe d, Jan K.
Maurine,f, W. Schilf g, D. Trzybiński h, K. Woźniaki
a Institute of Nuclear Chemistry and Technology, Dorodna 16 str., 03-195 Warsaw, Poland
b Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141-980 Dubna, Russia
c Faculty of Chemistry, Jagiellonian University, Ingardena 3 str., 30-060 Cracow, Poland
d West Pomeranian University of Technology, Szczecin, Faculty of Chemical Technology and Engineering,
Department of Organic and Physical Chemistry, Piastów Ave. 42, 71-065 Szczecin, Poland
e National Medicines Institute, Chełmska 30/34 str., 00-725 Warsaw, Poland
f National Centre for Nuclear Research, Sołtana 7 str., 05-400 Otwock, Poland
g Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44, 01-224 Warsaw, Poland
h Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101,
02-089 Warszawa, Poland
iFaculty of Chemistry, University of Warsaw, Pasteura 1 str., 02-093 Warsaw, Poland
1Corresponding author.
E-mail address:a.pawlukojc@ichtj.waw.pl (Andrzej Pawlukojć)

Abstract
In the present paper the structural and dynamical properties of crystalline 2,6–
dimethylpyrazine - picric acid cocrystal are described. The title cocrystal crystallizes in
centrosymmetric monoclinic P21/c space group. The X-ray diffraction and NMR spectroscopy
show the presence of protonated form of 2,6-dimethypyrazine and deprotonated form of picric
acid molecules. The Hirshfeld surface analysis for determine of intermolecular contacts was
performed. Low temperature phase transition was observed and described by temperature
dependent investigations: X-ray diffraction, different scanning calorimetry (DSC) and IR
spectroscopy. The vibrational properties of cocrystal were investigated by use of IR and Raman
spectroscopies, as well as density functional theory (DFT) with periodic boundary conditions.
Activation energy for reorientational motion of CH3 group was determined from the band shape
analysis of C–CH3 bending vibration.
Keywords: 2,6-dimethylpyrazine-picric acid cocrystal; X-ray diffraction; Raman spectroscopy;
temperature dependent IR spectroscopy, DFT calculation; phase transition.

1.Introduction
In this report a synthesis and investigation of 2,6-dimethylpyrazine with picric acid
cocrystal was presented. Picric acid forms crystalline picrate through ionic, hydrogen bonding
and π-π interactions, favors the formation of the salts with various organic bases. In recent years
the studies on growth and nonlinear optical properties cocrystals of picric acid with amino acids
[1-9] were presented. They were investigated by structural, spectroscopic, thermal, optical and
theoretical calculation methods. All of them show SHG (second harmonic generation) effect
more than for KDP (potassium dideuterium phosphate) crystal. Picrate salts crystallize with other
organic bases in the non-centrosymmetric space groups and show nonlinear optical properties
(second harmonic generation, third harmonic generation) also [10-14]. In these crystals picric
acid appears in the form of anion and forms intermolecular hydrogen bonds type of O-H···O or
N-H···O with cation molecules. Another class of the picric acid cocrystals is centrosymmetric
crystals characterized by intermolecular hydrogen bonds and weak stacking interaction
between symmetry related picric benzene ring and aromatic ring of charge donors [15-21]. The
distance of  interaction is observed in the range of 3.4Å - 3.9Å. The picric acid as well as
2,6-dimethylpyrazine are interesting compounds for materials engineering [22-26]. Their
organometallic complexes show luminescence, fluorescence and magnetic properties. As all
pyrazine methyl derivatives, 2,6-dimethylpyrazine is interesting molecule for investigation of
methyl group’s dynamics [27, 28] performed by IR, Raman, inelastic neutron scattering and
theoretical DFT methods.
The main goal of this work is determination and description of structural and dynamical
properties as well as low temperature phase transition of 2,6-dimethylpyrazine - picric acid
cocrystal. Crystallography studies by X-ray diffraction at several temperatures, DSC and infrared
temperature dependent spectroscopy were performed. Additionally, NMR spectroscopies in solid
states, CDCl3 and acetone solution, Raman spectroscopy as well as DFT calculation with
periodic boundary conditions for an experimental data analysis were used.
2.Experimental
2.1. Sample preparation
Picric acid (moistened with water) and 2,6-dimethylpyrazine were purchased from
Sigma-Aldrich Chemical Companies and were used without further purification. Methanol,
chloroform and ethyl alcohol of HPLC grade were also from Aldrich. Two mmol of 2,6-
dimethylpyrazine (20 ml) were added to 20 ml of methanol solutions containing picric acid (2
mmol) and mixture was stirred at 40°C temperature for 1 h. The resulting solution was allowed

to stand at room temperature. The formed complex was isolated, filtered off and washed with
minimum amounts of chloroform to obtain the pure product and dried under vacuum over
anhydrous CaCl2. Cocrystal in a molar ratio 1:1 was synthesized and needle yellow crystals were
obtained.
2.2. X-Ray diffraction
Good quality single crystal of investigated system was selected for the X-ray diffraction
experiments at T = 100, 120, 140, 160, 200, 250 and 295 K. Diffraction data were collected on
the Agilent Technologies SuperNova Dual Source diffractometer with CuKα radiation (λ =
1.54184 Å) using CrysAlis RED software [29]. The multi-scan empirical absorption correction
using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm, was applied
[29]. The structural determination procedure was carried out using the SHELX package [30].
The structures were solved with direct methods and then successive least-square refinement was
carried out based on the full-matrix least-squares method on F2 using the SHELXL program
[30]. The H-atoms linked to the N-atom in all cases were located on Fourier difference maps and
refined as riding on heavy atoms with Uiso(H) = 1.2Ueq(N). Other H-atoms were positioned
geometrically, with C–H equal to 0.93 and 0.96 Å for the aromatic and methyl H-atoms,
respectively, and constrained to ride on their parent atoms with Uiso(H) = xUeq(C), where x = 1.2
for the aromatic and 1.5 for the methyl-H-atoms.
2.3. NMR spectroscopy
The solid state CPMAS spectra were run on a Bruker Avance 500 MHz spectrometer
using 4 mm CPMAS Bruker probehead. The typical spectral condition for natural abundance
nitrogen CPMAS NMR spectra were: spectral width 28 kHz, acquisition time 40ms, spin rate 6-
12 kHz, contact time for spin-lock 5ms, relaxation delay 10 to 120 s depending on relaxation
condition for particular sample, estimated from carbon measurement. The typical experimental
condition for carbon CPMAS were: spectral width 31 kHz, acquisition time 20 ms, contact time
2 ms, spin rate 12 kHz. For differentiation of protonated and quaternary carbon atoms, the short
contact time spectra with contact time 40s were done. In SCT (semi constant time) experiments
only protonated carbon signals are displayed. Originally, the solid-state spectra were referenced
to the solid glycine sample and then the obtained chemical shifts of appropriate signals were
recalculated to TMS (tetramethylsilane) scale for carbon, and nitromethane for nitrogen
measurements, respectively.
All solution state NMR experiments were performed on Varian-Agilent 600 MHz
VNMRS instrument using 5 mm inverse probehead equipped with Z-gradient coil. The nitrogen
chemical shifts were obtained from 2D GHMBC experiments. For data acquisition and spectra
processing standard Varian-Agilent software was used. The proton and carbon spectra were

referenced with respect to internal TMS as a standard. For nitrogen-15 external nitromethane
was applied as a standard.
2.4. Differential scanning calorimetry (DSC)
DSC measurement below room temperature was performed using a Mettler-Toledo 822e
calorimeter. The sample weighing 6.40 mg was placed in standard alumina 40 µl crucibles
(closed by compression) and heated at a rate of 10 K min−1 under a dry N2 atmosphere at a
constant flow (50 ml min−1). The DSC measurements were made both during heating and
cooling of the sample. Transition temperatures were taken as the onset temperature (Tonset).
2.5. Raman spectroscopy
The Raman spectrum was recorded on the Horiba LabRam HR Evolution Raman
microscope with 633 nm HeNe laser (17mW power) as an excitation source. The resolution was
set up to 2 cm-1. An Olympus microscope objective lens SLWD with a focus x50 and a
numerical aperture of NA = 0.35 were used to focus the laser beam on the sample surface. The
spectrum was obtained using 20 scans (50-4000 cm-1 wavenumber) with an acquisition time of
72 s of each.
2.6. Infrared spectroscopy
Fourier transforms far and middle infrared (FT-FIR, FT-MIR) absorption measurements
were performed using a Bruker Vertex 70v vacuum Fourier Transform spectrometer. The
transmission spectra were collected with a resolution of 2 cm-1 and with 32 scans per each
spectrum for FIR and MIR, respectively. The FT-FIR spectra (600-50 cm-1 wavenumber range)
were collected for sample suspended in Apiezon N grease and placed on polyethylene (PE) disc.
The FT-MIR spectra were collected for sample suspended in Nujol between KBr pellets. The
Nujol and Apiezon additionally preserve the sample from decomposition and the influence of
atmospheric conditions. Temperature measurements were carried out using Advanced Research
System cryostat DE-202A and water-cooled helium compressor ARS-2HW working in a closed
cycle manner. The sample was loaded at room temperature and measurements were performed
on cooling down to ca. 9 K. The desired temperature was measured with accuracy of ±0.1 K and
stabilized for ca. 3 minutes before the measurements were taken. The LakeShore 331S
temperature controller equipped with silicon diode sensor was used to control the temperature.
The cooling rate between desired temperatures was ca. 3 Kmin-1. The PE and KRS5 windows
were used in a cryostat in the case of FT-FIR and FT-MIR measurements, respectively.
2.7. Quantum chemical calculations
The total energy optimization and the frequency calculations were performed using the
density functional theory (DFT) [31,32] as implemented in the CASTEP [33] program. The unit
cell parameters were held constant, only atomic coordinates were optimized using the BFGS

minimizer installed within CASTEP [34]. The results were obtained for the crystalline state
within the generalized gradient approximation (GGA) at PBE (Perdew–Burke–Ernzerhof
correlation) functional [35]. An essentially semiempirical dispersion correction introduced by
Tkatchenko and Scheffler (TS) [36] was used to include the van der Waals interactions in the
molecular crystal. Calculations were performed using on the fly generated norm-conserving
pseudopotentials as implemented in CASTEP. The density functional perturbation theory
(DFPT) [37] was used to calculate the vibrational properties at Gamma point. The plane-wave
cut-off energy was 1012 eV. Brillouin zone sampling of electronic states was performed on a
1×3×1 Monkhorst-Pack grid where k-point grip was kept to maintain a spacing of ca. 0.07 Å-1.
The convergence threshold for self-consistent iterations was set at 5×10-10 eV/atom. The
optimization parameters were set as follows: total energy convergence tolerance: 5×10-7
eV/atom, maximum force tolerance: 0.01 eV/Å, and maximum displacement tolerance: 5×10-4 Å
[38]. The IR and Raman spectra were generated from the CASTEP frequency calculation results.
As initial data for calculated properties the crystal structure determined at 100 K was applied.
3. Results and discussion
3.1. X-ray diffraction studies
Crystal data, data collection and structure refinements details for cocrystal of 2,6-
dimethylpyrazine with picric acid for different temperatures are collected in Table 1. The
crystals structures have been deposited at the Cambridge Crystallographic Data Centre
(deposition numbers CCDC 1968087, 1968088, 1968089, 1968090, 1968091, 1968092 and
1968382).
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).
The cocrystal of 2,6-dimethylpyrazine – picric acid in the temperature 295 K crystallizes
in monoclinic P21/c space group with a=15.3303(5)Å, b=5.70917(19)Å, c=16.8234(6)Å,
=101.2704(7)° and Z=4. The asymmetric part of the unit cell contains one 2,6-
dimethylpyrazinium(+) cation and one picrate(-) anion as shown in Fig 1. The arrangement of
the molecules in the unit cell is depicted in Fig 2. The bond lengths, bond and torsion angles for
cocrystal observed in the room temperature and calculated for PBE + vdW level are presented in
Table 2. In the 2,6-dimethylpyrazine – picric acid cocrystal the pyrazine N4 atom forms
bifurcated hydrogen bonds, N5-H5A···O1 and N5-H5A···O7, with the picrate anion. The
corresponding distances are equal to 2.628Å and 2.925 Å (see Table 3). The nitro group in
position 1, being in the vicinity of the acidic oxygen acid, is twisting by ca. 47° around C-N
bond, while nitro groups in positions 2 and 3 are twisting by 0.45° and 4.63° respectively (see
Table 2). In the crystalline lattice ions form a columnar packing along c-axis with the motif

···ADADAD···, where A - denote picric acid anion and D - 2,6-dimethylpyrazine cation. 2,6-
dimethylpyrazine and picric acid ions forms charge transfer (CT) complex with distance between
center of rings 3.849 Å and angle between ring planes 1.1°. The angle between pair of CT
complexes is equal to 66.11°. The temperature dependence of unit cell parameters as well as
volume of unit cell and hydrogen bond length (N5-H5A···O1) during heating cycle are presented
in Fig.3. It can be seen that the nonlinear temperature dependence for a, b, c and parameter of
unit cell can suggest the existence of phase transition at about 160 K. The temperature
dependence of hydrogen bond N5-H5A···O1 length show the same behavior.
3.2. Hirshfeld surface analysis
Fig.4 shows Hirshfeld surface generated with the aim of CrystalExplorer program [39]
for crystal packing determined at 295 K. Hirshfeld surface is an excellent tool and provides
valuable information on molecular interactions presented in the studied system. A
crystallographic data file (CIF) is needed in order to calculate this surface. Many properties can
be mapped on such surface. Similar analyses were performed for many molecular systems, for
example see Ref [40] where reader can find additional explanations. The hydrogen interactions
in Fig. 4 were marked as green dashed lines. The so called dnorm parameter, which gives
information about intermolecular contacts between atoms, was mapped on the surfaces. For the
contacts closer than the sum of van der Waals radii of atoms the red spot appears on surface.
These regions correspond to hydrogen bonds. Surface colored in blue means no close contact
between atoms enclosed by the surface and outside atoms occur. This additionally proofs the
assumption made earlier that picric acid and 2,6-dimethylpyrazine molecules do not interact
strongly in the discussed cocrystal besides of the hydrogen bonds. Very similar results were
obtained for di and de parameters mapped onto surface. Parameter di denotes distance from the
surface to the nearest atom inside the surface whereas de is the distance from the surface to the
nearest external atom. In the Figure 5 fingerprints plots (de versus di) for investigated cocrystal
are shown. Namely, Fig 5a displays all the intercontact presented in the discussed system. Fig 5
b-d depicts the most important interactions found in the studied cocrystal. Only contributions
higher than 10% were shown in this figure. The main contribution to the fingerprint gives the O-
H interactions (43.1%, Fig. 5b). Two characteristic sharp spikes are clearly visible. The H-H, C-
O and N-O interactions contribute to the fingerprint in the following amounts: 20.8%, 10.2% and
5.3%, respectively. It is worth noting that H-H interactions occupy the second position among
the highest contribution. The contribution of the remaining intermolecular contacts was found to
be less than 5% of the total surface (C-C 2.3%, C-H 4.8%, C-N 4.8%, H-N 3.1%, N-N 1%, O-O
4.7%). It can be concluded that hydrogen bonds are the most important interaction found in the
26DMP-PA cocrystal. The π-π interactions are rather small.

3.3. NMR spectroscopy
The structure of 2,6-dimethylpyrazine - picric acid cocrystal was investigated in CDCl3
solution, acetone solution and the solid state. The results of this study are collected in Table 4.
Due to intermolecular interaction with chloroform some signals for cocrystal were severe
broadened or missed, therefore the measurements were repeated in acetone solution. The signal
assignments for aromatic carbon atoms were done on the base of signal intensity comparing
(intensity of protonated carbon atoms are few times more intensive than those of quaternary
atoms). For picric acid anion the C1, C2, C3 and C4 atoms signals were distinguished by
13
intensity as well. In CPMAS C spectra the protonated and quaternary carbon atoms signals
were assigned using SCT experiments, where only protonated carbon signals are present. The
chemical shift observed on the C1 carbon atom in picric acid, at the CPMAS investigation, is
about 161 ppm, while for solutions is 154 ppm. On the other hand, the chemical shift on N5
shows -160.4 ppm in the CPMAS, it is lower than for solutions. Those both effects, upfield on
carbon and downfield on nitrogen signals, indicate that some proton transfer from picric acid to
pyrazine nitrogen sites can take place [41]. Since this process does not change symmetry of the
compounds it should be considered as fast on NMR time scale dynamic exchange of protons. In
investigated cocrystal this effect is different on both nonequivalent nitrogen atoms, which means
that position N5 (stronger upfield effect detected) is preferred in protonation reaction.
3.4. DSC investigation
The phase situation for the 2,6–dimethylopyrazine - picric acid cocrystal was probed using
differential scanning calorimetry (DSC) method in the temperature range 120–295 K.
Investigations were performed on heating and cooling of sample. Fig.6 shows the temperature
dependencies of the heat flow obtained on heating (pink curve) and on cooling (blue curve) of
the titled compound. The heating/cooling rate for the sample was 10 K min−1. One distinct
h
Tc
anomaly on each of these two DSC curves was registered at:
= 163.5 K (onset on heating)
and c = 153.1 K (onset on cooling). Thus, the title compound has two solid phases. The thermal
Tc
hysteresis of the phase transition temperature Tc equal to ca. 10.4 K and the heat flow anomaly
sharpness suggest that the detected phase transition is a first-order one. The relatively high
entropy change (S = 3.95 J·mol-1·K-1) connected with observed phase transition indicates high
degree of dynamical disorder of high temperature phase.
3.5. Vibrational spectral studies
The investigated 2,6-dimethylopyrazine - picric acid cocrystal contains 140 atoms in a
crystallographic unit cell. It’s implying that 420 normal modes are expected where 372 of them
described normal vibration modes, 45 described translation and rotation modes and 3 are non-
active acoustic modes. Due to selection rules in the C2h crystallographic symmetry group the

number of modes equals to vib = 105Ag + 104Au + 105Bg + 103Bu, where modes with
symmetry Ag and Au are active only in IR while Bu and Bg modes are active only in Raman
spectra for k = 0. Details are described in Table 5.
IR spectra collected at 9.8K and 290K, Raman spectrum at 290K as well as IR and
Raman spectra calculated in periodic boundary conditions in far infra-red region are presented in
Fig. 7. These same spectra in the energy range 3600-600 cm-1 are show on Fig. 8. Observed IR
and Raman frequencies as well as calculated one and their tentative assignments are listed in
Table 6. The assignment was done based on available literature data [28, 42-44] and
visualization of particular modes in Jmol software [45]. For the high wavenumbers internal
vibrations of both constituting building blocks i.e. picric acid (PA-) anion and 2,6-
dimethylpyrazine (26DMP+) cation can be treated independently, so the total spectrum can be
obtained as a sum coming from particular molecular parts. For far infrared region the vibrations
origin from PA- and 26DMP+ are mixed. In the 3300 – 3000 cm-1 range C-H stretching vibration
from aromatic hydrogen are visible. The calculated IR spectrum describes well this region. In the
Raman experimental spectrum only one low intensity peak is presented at 2934 cm-1 (CH3 str.
sym. 26DMP+). This peak is visible at 2978 cm-1 in the calculated spectrum. In the IR spectra
hydrogen bonds vibrations, overlapping with continuous absorption and Fermi resonance, are
represented by the very broad maximum between 1700 and 2700 cm-1. Peaks at 2199, 2173,
1989 and 1961 cm-1 at 9.8K in IR spectra are connected to overtone (2 x CH bend.) and summation
(CH bend.+ CH wagg.) vibrations modes while at 290 K these peaks are observed at 2170 and 1972
cm-1 respectively. In the Raman spectrum there is no visible bands in this region (see Fig. 8). In
the calculated IR spectrum one can observe sharp very intensive peak at about 2800 cm-1 which
is connected with N-H stretching vibration. In the theoretical RS spectrum band of low intensity
is observed (not visible in the experimental data). The ring stretching, CH3 bending, CH3 rocking
of 2,6-dimethylpyrazine cation as well as C=O stretching, ring stretching, NO2 stretching, C-N
stretching of picric acid anion modes are observed in the wavenumber range 1700–850 cm−1 in
the IR and Raman spectra. In this range there is a good agreement between experimental and
predicted IR and Raman spectra. The N-H bend. (26DMP+) and N-H wagg. (26DMP+) modes are
observed at 1113 cm-1 and 869 cm-1 in the room temperature respectively. In the far infrared
region C-CH3 bending and wagging modes, CH3 torsion modes as well as ring deformation and
ring torsion modes for 2,6-dimethylpyrazine cation are observed. In this same region for the
picric acid anion the NO2 bending, rocking, wagging and torsion modes and C-NO2 bending and
wagging modes as well as ring deformation and ring torsion modes are observed. The region 600
– 200 cm-1 (both IR and Raman) is very well reproduced by computations. Below 200 cm-1 the

predicted bands are slightly shifted toward higher wavenumber range relative to experimental
spectra.
3.6. Temperature-dependent IR spectroscopy
Figures 9 and 10a show the selected IR spectra of the 2,6–dimethylopyrazine-picric acid
cocrystal, within the wavenumber range 1700–850 cm−1 and 2250–1900 cm−1respectively,
registered during the cooling of the sample from 290K to 9.8K. In the middle infrared spectra,
some evident changes can be noticed. The narrowing of the peaks and the appearing of some
new bands can be observed. The narrowing of bands with lowering of temperature indicates
slowing of their fast reorientational motions. Fig. 10b presents contour plot of bands connected
to overtone (2 x CH bend.) and summation (CH bend. + CH wagg.) vibrations modes. In the vicinity of
phase transition the changes of intensity as well as splitting of broad bands into two components
are visible. Moreover, the maxima of emerging doublets in particular peaks are moving away
from each other. Fig. 11 presents the temperature dependence of the bands position in a 1680–
840 cm-1 region. As can be seen in Figs. 9 and 11, some bands (at 1635 cm-1, 1464 cm-1, 1113
cm-1 and 869 cm-1) start to split in the spectra at temperature close to Tc = 153.1 K. The band at
1635 cm-1 is assigned to C=O stretching mode of picric acid anion. During cooling a new band
emerges and two well distinguishable bands are observed at 1639 and 1632 cm-1 in the lowest
temperature. The band at 1464 cm-1 which relates to stretching asymmetric N-O mode of picric
acid anion, splits into two components. Interesting features can be noticed for hydrogen bond at
1113 cm-1 (N-H in-plane deformation) and at 869 cm-1 (N-H out-of-plane deformation) for
26DMP+ cation. For both bands a splitting in the vicinity of phase transition is visible. This may
mean that the dynamics of hydrogen bonds is changing in the phase transition. The and shape
analysis contain information concerning molecular reorientational motions of molecules in
condensed phases, when the reorientational correlation time τR is of an order 10-13 - 10-11
seconds. For this, the analysis of FWHM which is based on the formula used for the damping
associated with the order-disorder transition [46, 47] was performed. The reorientational
correlation time c is the mean time between instantaneous jumps from one potential well to the
other, and it is defined by the following formula:
Ea
c = ·exp(
),
(1)
RT
where:  is the relaxation time at an infinite temperature T, Ea is the potential barrier height for
reorienting group, R = NA·kB = 8.314472 JK-1mol-1 is the gas constant, and NA and kB are
2
Avogadro’s and Boltzmann’s constants, respectively. When 2·R >> 1, where  = 2πν and ν is
the frequency of a particular phonon mode, the temperature dependence of the FWHM of the
infrared bands connected with this mode is determined by following expression [46-48]:

Ea
FWHM(T) = (a + bT) + c·exp(-
),
(2)
RT
where: a, b, c and Ea are fitting parameters. Here the Ea is activation energy of the reorientation
process. The linear part of equation (2) is associated with the vibrational relaxation and the
exponential term is associated with rotational relaxation and corresponds to the thermal
reorientational motions of a diffusion nature.
In the studied system two groups belonging to different molecules, namely the methyl
CH3 from 2,6-dimethylpyrazine and nitro NO2 from picric acid may potentially reorientate.
However, the rotation of NO2 is less probable. These groups take part in the formation of
hydrogen bonds network and are rather immobilized due to this effect. On the other hand, CH3
groups are not engaged in the formation of such bonds and moreover there is no steric effect.
The rotation of methyl groups is not strongly hindered and affected by the environmental effects
such as close contact. This is the reason why the rotation of methyl group is much more probable
and can be responsible for the narrowing of particular bands.
Analysis of the temperature dependency of the full-width-at-half-maximum (FWHM)
was carried out for the band at 294 cm-1 associated with C–CH3 bending mode. In order to
perform analysis of FWHM a few conditions must be fulfilled. Firstly, the analyzed peak should
be well isolated from others (energy separated). Secondly, it should be connected with only one
mode. In other words, it should describe only one process i.e. motion of particular group whereas
the remaining atoms should not be involved (engaged) in this vibration. The third condition
states that intensity of analyzed peak should not be very small; it means that investigated
transition should be connected with noticeable change of dipole moment. Figure 12 presents the
temperature dependence of the FWHM of the analyzed infrared band at 294 cm-1. The shape of
the analyzed peak was approximated by a Lorentz function. It can be seen that during the cooling
of the sample from the room temperature, FWHM of this band decreases exponentially down to
the temperature 150 K. Below Tc the changes of FWHM are small and it can be said that this
temperature dependency reaches plateau. This indicates that below ~150 K, reorientational
motion of the C-CH3 groups is slowed down. The fitting Eq. (2) to FWHM vs. T dependence
was done to all experimental points in the temperature range 290–9.8 K. The fitted parameters
are listed in Table 7. The mean value of activation energy Ea(I/II) obtained from the analysis of
this band is equal to 5.2 kJmol‒1. The obtained Ea is characteristic for methyl groups which
exhibit tunneling behavior. It is interesting to notice that very similar value (Ea~3.5 kJmol-1) was
obtained for 2,6-dimethylpyrazine (DMP) and chloranilic acid (CLA) complex [27] from the
analysis of neutron scattering data. FT-IR analysis for the 2,6–dimethylopyrazine-picric acid

cocrystal, suggests that the rapid C-CH3 group reorientation is slowing down below 150 K
(correlation time τ> 10-12 s).

4. Conclusion
The new molecular cocrystal 2,6–dimethylopyrazine - picric acid crystallizes in P21/c
space group with Z=4, a=15.3303(5)Å, b=5.70917(19)Å, c=16.8234(6)Å and =101.2704(7)°.
From NMR and X-ray investigations it was found that 2,6–dimethylopyrazine exists in the cation
form and picric acid exists in anion form. They are bonded to each other by hydrogen bonds N-
H+···O- with the length 2.628Å and 2.925Å. Hirshfeld surface analysis shows that intermolecular
contacts are performed mainly by hydrogen bonds (43.1% contribution). On the base of
temperature dependent measurements (DSC, X-ray and IR) low temperature phase transition at
153.1K on cooling and at 163.5K on heating was observed. The temperature dependent overtone
(2 x CH bend.), summation (CH bend. + CH wagg.), C=O str., NO2 str., N-H bend. and N-H wagg. vibrational
modes were observed. IR, Raman and DFT calculation for periodic boundary condition were
used for determination of cocrystal dynamic structure. The normal modes were described and
analyzed as a function of temperature. Activation energy for C-CH3 group bending reorientation
was obtained to be equal 5.2 ± 0.5kJmol-1.

5. Acknowledgements
The infrared absorption (FT-FIR and FT-MIR) researches were carried out with the
equipment purchased thanks to the financial support of the European Regional Development
Fund in the framework of the Polish Innovation Economy Operational Program (contract no.
POIG.02.01.00-12-023/08).

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Figure captions
Fig.1. The molecular structure and the atom numbering scheme in the 2,6–dimethylopyrazine-
picric acid cocrystal.

Fig.2. The packing of 2,6–dimethylopyrazine-picric acid cocrystal in the crystalline lattice.

Fig.3. Temperature dependence for a, b, c and parameters of unit cell, volume of unit cell and
N5-H5A···O1hydrogen bond length for 2,6–dimethylopyrazine-picric acid cocrystal.

Fig.4. Hirshfeld surfaces analysis for 2,6-dimethylpyrazine-picric acid cocrystal. Parameters
mapped onto the surface, a) dnorm b) di and c) de.
Fig.5. Fingerprint generated for 2,6-dimethylpyrazine-picric acid cocrystal with relative
percentage contributions of particular intermolecular contacts to Hirshfeld surface area: a) all
interactions (100%), b) O-H (43.1%), c) H-H (20.8%) d) C-O (10.2%).

Fig.6. DSC curves for 2,6–dimethylopyrazine-picric acid cocrystal.

Fig.7. Comparison of Raman, IR and calculated IR spectra in the far infra-red region for 2,6–

dimethylopyrazine-picric acid cocrystal.