Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249

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Spectrochimica Acta Part A: Molecular and

Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa

The temperature-dependent single-crystal Raman spectroscopy of a

model dipeptide: L-Alanyl-L-alanine
J.G. Silva a, L.M. Arruda a, G.S. Pinheiro a,b,⇑, C.L. Lima b, F.E.A. Melo a, A.P. Ayala a, J. Mendes Filho a,
P.T.C. Freire a
a
Departamento de Física, Universidade Federal do Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
b
Departamento de Física, Campus Ministro Petrônio Portella, Universidade Federal do Piauí, CEP 64049-550 Teresina, PI, Brazil

h i g h l i g h t s g r a p h i c a l a b s t r a c t

 Temperature dependent polarized

Raman spectra of the L-alanyl-L-
alanine.
 The crystal of L-alanyl-L-alanine
undergoes a structural phase
transition.
 The phase transition is observed
between 80 and 60 K.

a r t i c l e i n f o a b s t r a c t

Article history: A single-crystal of peptide L-alanyl-L-alanine (C6H12N2O3) was studied by Raman spectroscopy at low-
Received 16 December 2014 temperature, and a tentative assignment of the normal modes was given. Evidence of a second order
Received in revised form 4 April 2015 structural phase transition was found through Raman spectroscopy between the temperatures of 80 K
Accepted 7 April 2015
and 60 K. Group theory considerations suggest that the transition leads the sample from the tetragonal
Available online 11 April 2015
to a monoclinic structure. Additionally, our study suggests that the mechanism for the structural phase
transition is governed by the occupation of non-equivalent C1 local symmetry sites by the CH3 molecular
Keywords:
groups. Analysis based on group theory suggests L-alanyl-L-alanine presents C2 symmetry at low
Raman spectroscopy
Infrared spectroscopy
temperatures.
Peptide Ó 2015 Elsevier B.V. All rights reserved.
Phase transition

Introduction Additionally, they are important for being constituents of several

Peptides are important organic compounds not only because of
their ability to form proteins but because of the central role they
play in several biological and physiological processes in living
organisms [1]. Among the biological functions displayed by pep-
tides are their capabilities as neurotransmitters and hormones.
⇑ Corresponding author at: Departamento de Física, Universidade Federal do
Ceará, C.P. 6030, CEP 60455-760 Fortaleza, CE, Brazil. Tel.: +55 8533669906; fax:
+55 8533669450.
E-mail address: gardenia@fisica.ufc.br (G.S. Pinheiro).
protein chains and taking part in our biological metabolism. As a
consequence, peptides have received special attention from
researchers of the pharmacological area. Further uses as, for
instance, antibiotic and immunological agents are also active fields
of study for peptides [2].
As a consequence, the study of peptides has considerably grown
in importance in the last few decades. Although its origin is cred-
ited to Emil Fischer for his article on the synthesis of the dipeptide
glycylglycine in 1901 [3], the subject remained relatively dormant
for years due to difficulties the peptide synthesis presented. This
difficulty was solved gradually with increasingly efficient

http://dx.doi.org/10.1016/j.saa.2015.04.010
1386-1425/Ó 2015 Elsevier B.V. All rights reserved.
 J.G. Silva et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249 245

found in the literature, although some works performed at room

temperature were presented [15–18]. The understanding of vibra-
tional and structural properties of peptides is of relevance since
they have potential use in medicine. In this work, the vibrational
properties of Ala-Ala through Raman spectroscopy at low tempera-
tures are investigated, and an assignment of the vibrational modes
is provided. Careful analysis of the behavior of the vibrational
modes as a function of temperature is also furnished.

Fig. 1. Experimental and calculated powder X-ray diffractogram of L-alanyl-L- Experimental procedures
alanine crystal.

Single-crystal samples of Ala-Ala (C6H12N2O3) were grown by

temporary protections for the amino group. After the synthesis of
an active hormone, the octapeptide oxytocin, by du Vigneaud
et al. in 1954 [4], the variety of synthesized natural occurring pep-
tides and analogs grew along with the demand for them and the
study of their properties. The study of peptides is varied in scope
and methods [5–9]. Vibrational spectroscopy has become an
important tool for the investigation of protein and peptide science
and as such, several studies on vibrational properties of peptides
have been conducted [10–14].
L-Alanyl-L-alanine (Ala-Ala) is one of the simplest peptides but
any study of its vibrational properties at low temperatures are
the vapor-diffusion technique at controlled temperature (278 K).
The crystals obtained were thin platelets shape and colorless. The
crystal structure of the samples obtained was confirmed through
an X-ray powder diffraction experiment using a D8 Advance
(Bruker) diffractometer using Cu Ka radiation operating at 40 kV,
40 mA. The Raman spectra of Ala-Ala were obtained using a
T64000 Jobin Yvon spectrometer equipped with a liquid N2-cooled
charged coupled device detection system and a 514.5 nm argon ion
laser. The slit of the spectrometer allowed a resolution of 2 cm1. In
order to obtain low temperatures, the sample was placed in a
helium flux cryostat (model DE202S, from Air Products and
Chemicals), and the temperature was monitored in the interval

Fig. 2. (a) Molecular structure of Ala-Ala; (b) unit cell of Ala-Ala crystal.

(a) (b)

Fig. 3. Raman spectra of Ala-Ala crystal in the 50–600 cm1 spectral region for several temperatures for the (a) ðx  yÞðz; zÞðx  yÞ and (b) ðx  yÞðx þ y; zÞðx  yÞ scattering
geometries.
246 J.G. Silva et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249

20–300 K by a digital temperature controller unit having a stability Table 1

of 0.1 K. Vibrational wavenumbers (cm1) and tentative assignment for the Ala-Ala from
spectra recorded at room temperature.

Scattering geometry Assignment

Results and discussion
ðx  yÞðz; zÞðx  yÞ ðx  yÞðx þ y; zÞðx  yÞ
(cm1) (cm1)
Ala-Ala crystallizes in the tetragonal structure belonging to the
I4 (C54) space group [19]. The lattice parameters are a = b = 17.985 Å – 78 Lattice mode
92 92 Lattice mode
and c = 5.154 Å, and contains eight formulas per unit cell. Fig. 1 – 97 Lattice mode
shows the Ala-Ala X-ray diffraction pattern obtained at room tem- 114 112 Lattice mode
perature, refined by Rietveld method with R-factors Rwp = 10.3% 154 s(CO2 )
and S = 1.2 for the goodness of fit. The data obtained is good agree- 243 241 s(CH3)
262 260 s(CH3)
ment with the pattern previously published [19]. The molecular
304 304 d(esq.)
structure and a view of the unit cell are shown in 319 317 d(esq.)
Fig. 2(a) and (b). The structures were visualized by VESTA [20]. 339 338 d(esq.)
The molecular packaging of Ala-Ala is formed by eight hydrogen 376 376 d(esq.)
bonds between the nitrogen of one molecule with carboxylate oxy- 391 392 d(esq.)
402 402 d(esq.)
gens from four different molecules. Factor group analysis shows 468 469 s(NH+3)
that the 273 optical modes predicted decompose into the irre- 553 555 r(CO 2)
ducible representations as C = 68A + 69B + 68E. All representations 651 650 d(CO 2)

are Raman active and the A and E representations are also infrared 679 680 do.p.(CONH)
731 729 do.p.(CONH)
active.
802 800 x(CO2 )
The axes of the crystal were defined according to the following 852 851 r(CH3) + m(C–CH3)
convention: the z-axis was that perpendicular to the plane of the 887 886 m(C–CH3) + m(C–
platelet, the y-axis was defined as the axis coincident with the NH+3)
longest dimension of the crystal and the x-axis was defined per- 912 912 m(C–CO) + m(C–CO2 )
955 956 x(NH+3)
pendicular to the y- and z-axes. The Raman spectra were taken 1008 1009 x(NH+3)
for two scattering geometries: ðx  yÞðz; zÞðx  yÞ and 1049 1048 m(C–CH3) + d(CH3)
ðx  yÞðx þ y; zÞðx  yÞ, which provide data on the modes with A 1097 1097 x(CH3)
1118 1119 m(CN)
and E symmetries, respectively. In this work, the usual Porto’s 1153 1151 r(NH+3)
notation [21] was used for describing the scattering geometries. 1260 1261 d(CH)
Because of the platelet form of the crystals obtained, the z(xy)z 1284 1283 d(CH)
geometry was not available, and the phonons of the B irreducible 1320 1320 d(CH) + d(NH)
1338 1338 ds(CH3)
representation are not presented in this work.
1369 1369 ds(CH3)
Fig. 3 shows the Raman spectra of Ala-Ala for several tempera- 1405 1405 ms(CO2 )
tures in the spectral range 50–600 cm1, for (a) the 1451 1451 da(CH3)
ðx  yÞðz; zÞðx  yÞ and (b) the ðx  yÞðx þ y; zÞðx  yÞ scattering 1551 1551 d(NH) + m(CN)
1602 1603 ma(CO2 )
geometries. All the spectra presented in this work were taken in 1627 1627 da(NH+3)
the cooling cycle. This region is characterized by the external 1681 1681 m(C@O)
modes of the crystal and by internal modes of low-energy. These 2887 2884 m(CH)
bands provide important insights about the structural stability of 2904 2904 ms(CH3)
the material [22–24]. The band at 153 cm1 is associated with 2935 2933 ms(CH3)
2974 2975 ma(CH3)
the torsion of CO 
2 unit, s(CO2 ), and the band at 242 cm
1
is 2989 ma(CH3)
assigned as the torsion of CH3, s(CH3). A band of great importance 3012 3013 ms(NH+3)
due to its relationship with the hydrogen bond is torsion of NH+3, 3015 ms(NH+3)
s(NH+3), which is observed at 473 cm1 in the Raman spectrum. 3216 3216 ma(NH+3)
Table 1 presents the tentative assignment of the bands observed
in the Raman spectra of Ala-Ala at room temperature for the two
scattering geometries. Additionally, it is worth to note that bands associated with CH3
Under cooling, the Raman spectra in Fig. 3 show great changes group change as a consequence of the phase transition. In fact, an
in both scattering geometries between 60 and 80 K. An increase in inelastic scattering study performed on L-alanine showed an anom-
the number of the modes in the region 50–200 cm1 is observed aly of the mean-square displacement of the scattering nuclei
indicating a change of symmetry of the crystal. Furthermore, in between 160 and 220 K. Such an anomaly was interpreted as a
the region 200–600 cm1, the splitting of bands associated with phase transition (or a structural rearrangement) probably related
both the torsion of CH3 group, s(CH3), at 242 and 262 cm1 to thermally activated reorientation of NH3 and CH3 groups [25].
(marked by asterisks), and the deformation of the skeletal struc- In other words, while the CH3 group in L-alanine can be responsible
ture of Ala-Ala, d(skel.), at 401 cm1 (marked by square) are also for a structural rearrangement at low temperatures, it also seems
observed. It is interesting to remember that a similar phenomenon to play some roles in Ala-Ala. This point will be discussed below.
was already observed in the L-valine crystal at low temperatures; Another relevant point related to spectra in Fig. 3 concerns the
the appearance of modes in the low-wavenumber region was band associated with rocking of CO 
2 unit, r(CO2 ), observed at
associated with a phase transition undergone by the crystal 555 cm1 at room temperature. Such a band in both scattering
between 100 and 120 K [23]. Such a phase transition observed in geometries studied in the present work can be fitted by one peak
Ala-Ala can have an explanation similar to those presented for at high temperatures while at low temperatures two peaks are
other amino acid crystals. The contraction of the unit cell due to needed to fit it. This can be understood as a lower order for CO 2
cooling changes the intermolecular bonds of the crystal leading groups at low temperatures.
to modification of the crystal symmetry [23,24].
 J.G. Silva et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249 247

(a) (b)

Fig. 4. Raman spectra of Ala-Ala crystal in the 600–1200 cm1 spectral region for several temperatures for the (a) ðx  yÞðz; zÞðx  yÞ and (b) ðx  yÞðx þ y; zÞðx  yÞ scattering
geometries.

(a) (b)

Fig. 5. Raman spectra of Ala-Ala crystal in the 1200–1800 cm1 spectral region for several temperatures for the (a) ðx  yÞðz; zÞðx  yÞ and (b) ðx  yÞðx þ y; zÞðx  yÞ scattering
geometries.

The Raman spectra of Ala-Ala crystal in both ðx  yÞðz; zÞðx  yÞ as additional evidences that Ala-Ala crystal undergoes a phase
and ðx  yÞðx þ y; zÞðx  yÞ scattering geometries for several tem- transition at T < 80 K.
peratures in the 600–1200 cm1 spectral region is shown in Fig. 5 shows the Raman spectra of Ala-Ala crystal in the spectral
Fig. 4. In this region, one expects to observe vibrations associated range 1200–1800 cm1 for several temperatures for two scattering
with bending of CO + geometries. In this spectral region, one expects to observe the
2 unit, deformation of CONH, wagging of NH3
and CO + bands associated with bending vibrations of NH, CH, CH3 and
2 and rocking of NH3 and CH3 groups, among others
[26,27]. In this figure, modifications in the Raman spectrum similar NH+3 units, as well as stretching vibrations of CO2 and C@O units

to those noted in the previous spectral region are observed. As
temperature decrease, one observes between 60 and 80 K the fol-
lowing phenomena: (i) the splitting of the band at 682 cm1
(marked by an arrow) which is associated with the out-of-plane
deformation of CONH, do.p.(CONH); (ii) the splitting of the band
marked by a star and associated with wagging vibration of CH3,
x(CH3), located at 1096 cm1 at room temperature. It is worth also
to mention the splitting of a band localized at 1050 cm1, which
was tentatively associated with stretching of C–CH3 and bending of
CH3, m(C–CH3) + d(CH3). In fact, between 300 and 100 K on cooling,
the band shows a symmetric profile, but below 80 K it appears
with an asymmetric shape; in the spectrum recorded at 11 K, the
band splits into two peaks. These set of modifications can be seen
[23,28]. Bands at 1261 and 1283 cm1 are assigned as the deforma-
tion of CH, d(CH). The symmetric deformations of CH3 group,
ds(CH3), are located at 1338 and 1369 cm1, while the anti-sym-
metric deformation of the same unit, da(CH3), is observed at
1451 cm1. The intense band observed at 1681 cm1 is associated
with stretching of C@O, m(C@O), in accordance with several other
studies on amino acid crystals [17,29,30]. From the analysis of tem-
perature evolution of the bands in Fig. 5, it is also possible to
observe the appearance of a band at 1301 cm1. The new band
strongly supports the hypothesis of the occurrence of a phase tran-
sition undergone by Ala-Ala crystal. The clarity of the changes is in
contrast with the behavior of the Raman spectra of other amino
acid crystals in the same spectral region where the observed
248 J.G. Silva et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249
(a)
Fig. 6. Raman spectra of Ala-Ala crystal in the 2700–3300 cm1 spectral region for several temperatures for the (a) ðx  yÞðz; zÞðx  yÞ and (b) ðx  yÞðx þ y; zÞðx  yÞ scattering
geometries.
modifications are subtle: for example, although L-histidine pre-
sents a conformational phase transition at low temperatures, their
Raman spectra between 1200 and 1800 cm1 do not show appear-
ance of any new band nor splitting of peaks [28].
Fig. 6 presents the Raman spectra of Ala-Ala in the spectral
region 2700–3300 cm1 for several temperatures for two scatter-
ing geometries. In this spectral region, it is possible to observe
bands associated with stretching of CH, CH3 and NH+3 units (see
the tentative assignment in Table 1) [17,26,27]. The changes in
the Raman spectra upon variation of the temperature are not
impressive. It is important to remember that, in general, great
modifications in this spectral region could be associated with con-
formational changes of the molecules in the unit cell of the crystal
[31,32]. In the case of the Ala-Ala crystal, only changes of intensi-
ties of the bands are observed. Such behavior is similar to that veri-
fied for DL-alanine crystal where only small change of intensities
are observed at low temperatures [27]. However, differently from
Ala-Ala crystal, in DL-alanine the modifications presented by the
material is associated with slight changes of the CO 2 group ori-
entation, not to a solid-solid phase transition.
According to the group theory analysis, at room temperature,
one expects to observe in the Raman spectrum 69 normal modes
on each of the ðx  yÞðz; zÞðx  yÞ and ðx  yÞðx þ y; zÞðx  yÞ scatter-
ing geometries. Such a number is in agreement with the number of
modes observed at room temperature and listed in Table 1.
However, below 80 K, the number of modes observed in the
Raman spectrum of Ala-Ala is increased. In the spectrum recorded
at 20 K, one can clearly observe several new bands (at 132, 170,
176, 186, 195, 209, 216 and 222 cm1) in the lattice modes region.
The total number of modes at low temperatures is not compatible
with the C4 tetragonal structure. One possible way to explain the
increase in the number of normal modes is supposing the occur-
rence of a phase transition from the tetragonal structure to a struc-
ture with lower symmetry. In particular, a monoclinic C2 symmetry
is compatible with the number of normal modes observed in the
Raman spectrum of Ala-Ala at low temperatures. Supposing a
C4 ? C2 phase transition it is expected that the number of modes
in the monoclinic phase be twice the number of modes in the
tetragonal phase. When the group theory analysis for Ala-Ala is
performed using the factor group C2, one obtains that the 276
degrees of freedom are now distributed as C = 138A + 138B.
For the monocrystalline sample, it was possible to identify
about 93 distinct modes (45 modes with A symmetry and 48
(b)
modes with E symmetry) in the spectrum of a polarized experi-
ment. It is seen that the increasing of the number of observed
modes is completely explained by group theory if we suppose
the new symmetry C2 for the Ala-Ala at low temperatures.
It is interesting to note that the changes were observed in
almost all ranges of the Raman spectrum. By the analysis of
Table 1, one sees that many of the important variations found in
the spectra are related to the CH3 groups. In the presented work,
it is suggested that the phase transition mechanism for this peptide
crystal is the occupation of non-equivalents sites by the CH3
groups located in the center of the unit cell and those located near
the borders, as seen in Fig. 2(b).
At this point, it is worth to compare the phase transition under-
gone by Ala-Ala with the behavior of some simple amino acid crys-
tals. For example, studies on the L-alanine crystal under low
temperature do not present strong evidence that the material
undergoes phase transition, although the splitting of infrared
active bands at those conditions suggests that in the crystalline
material there is a disorder due to protons occupying different
positions in the hydrogen bonds formed by NH+3 group [33]. It is
also interesting to remember that anomalies at low temperature
were interpreted as opposite competing interactions from crystal
packing forces and charge-phonon coupling like a Jahn–Teller
effect [34]. The most important aspect is that although L-alanine
exhibits some anomalies at low temperatures we can ascribe the
orthorhombic room-temperature phase of L-alanine is stable down
to 10 K. Similarly, when a-glycine is investigated under the scru-
tiny of Raman spectroscopy, no evidence of phase transition is
observed under low-temperature conditions, although an increase
in the interlayer hydrogen bond length is verified through the
analysis of the N–H stretching vibration [35]. Another example of
an amino acid crystal where it is observed a stable structure at
low temperature is DL-serine. On the other hand, when L-serine
was investigated by Raman spectroscopy, it was verified that the
crystal undergoes a dynamic transition at 140 K [36]. This transi-
tion was interpreted as the orientation of the side chain–CH2OH
fragments of the zwitterion with respect to the skeletal C–C bonds;
as a result positional disorder of the O–H  O intermolecular
hydrogen bond was observed [36].
On the other hand, a Raman spectroscopic study showed that
the amino acid L-valine seems to undergo a phase transition at
100 K, as indicated by the disappearance of a lattice mode for
low temperatures [23]. This glance at the stability of some simple
 J.G. Silva et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 148 (2015) 244–249
amino acids at low temperatures highlights our result that in the
simple dipeptide Ala-Ala, an instability is verified. Our Raman
spectroscopic study indicates that the Ala-Ala crystal undergoes a
continuous second order phase transition, going presumably from
the tetragonal C4 structure to a monoclinic C2 structure. In such a
phase transition one would expect the correlations (i) 69A + 69B
from the C4 factor group to 138A in the C2 factor group and (ii)
69E from C4 symmetry to 138B in the C2 symmetry. Obviously, this
is not definitive, future studies are needed to elucidate this issue
conclusively.
Conclusions
In this work, the vibrational behavior of crystalline samples of L-
alanyl-L-alanine was investigated as a function of temperature
through Raman spectroscopy. A table with the tentative assign-
ments for the Raman normal modes of vibration observed in the
spectra for two different scattering geometries is presented. It
was found that the sample remains stable down to a temperature
of about 80 K, when it begins to undergo a slow second order phase
transition from the tetragonal structure with factor group C4 to
presumably a monoclinic structure with factor group C2. It is sug-
gested that the governing mechanism of this transition is the
occupation of non-equivalent sites by the CH3 groups present in
the Ala-Ala molecule.
Acknowledgments
The authors would like to thank FUNCAP and CNPq Brazilian
agencies for the financial support.
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