Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil
Low-temperature matrix isolation Fourier-transform infrared spectroscopy and quantum-chemical calcula-tions with DFT/B3LYP and MP2 methods were used for investigation of isolated 5-bromouracil (BrU) mole-cules. Only one tautomeric form of BrU was dominated in the low-temperature Ne, Ar, and Kr matri...
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Ivanov, A.Yu. Rubin, Yu.V. Egupov, S.A. Belous, L.F. Karachevtsev, V.A. 2017-05-30T12:24:03Z 2017-05-30T12:24:03Z 2013 Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil / A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, V.A. Karachevtsev // Физика низких температур. — 2013. — Т. 39, № 6. — С. 704–711. — Бібліогр.: 43 назв. — англ. 0132-6414 PACS: 33.15.–e, 33.20.–t, 33.20.Ea, 82.30.Qt https://nasplib.isofts.kiev.ua/handle/123456789/118473 Low-temperature matrix isolation Fourier-transform infrared spectroscopy and quantum-chemical calcula-tions with DFT/B3LYP and MP2 methods were used for investigation of isolated 5-bromouracil (BrU) mole-cules. Only one tautomeric form of BrU was dominated in the low-temperature Ne, Ar, and Kr matrices. It was revealed that population of minor hydroxy-tautomers did not exceed 0.2%. Appearance of additional absorption bands in the region of stretching vibrations CO (about 1710 cm⁻¹) as well as of deformation ones (1297, 1093, 901 cm⁻¹) was explained by Fermi resonance. In Ne matrices the peak intensities of absorption bands assigned to the out-of-plane vibrations of the ring and exocyclic atoms were decreased sharply. For the first time, least square method with the using of polynomial was proposed for the corrective scaling of calculated frequencies of vibrations. It is shown that the correction of calculated frequencies with the polynomial of degree two permits to decrease the root-mean-square discrepancy between the calculated and experimental ones to 4–5 cm⁻¹ in the re-gion of 1500–500 cm⁻¹. The same polynomial may be applied for the correction of spectra of molecules with a similar structure. The present work was carried out due to the financial support (grant No. 0110U007895) of the National Acade-my of Sciences of Ukraine. The authors thank S.G. Stepa-nian for helpful discussions and R.I. Zubatyuk for his help in organization and carrying out of calculations. Quantum-chemical calculations were performed using computational cluster of B. Verkin Institute for Low Temperature Physics and Engineering of National Academy of Science of Ukraine and computational facilities of joint computational cluster of SSI “Institute for Single Crystals” and Institute for Scintillation Materials of National Academy of Science of Ukraine incorporated into Ukrainian National Grid. en Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України Физика низких температур Динамика кристаллической решетки Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil Article published earlier |
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Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil |
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Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil Ivanov, A.Yu. Rubin, Yu.V. Egupov, S.A. Belous, L.F. Karachevtsev, V.A. Динамика кристаллической решетки |
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Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil |
| title_full |
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil |
| title_fullStr |
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil |
| title_full_unstemmed |
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil |
| title_sort |
fermi resonance in ne, ar and kr-matrix infrared spectra of 5-bromouracil |
| author |
Ivanov, A.Yu. Rubin, Yu.V. Egupov, S.A. Belous, L.F. Karachevtsev, V.A. |
| author_facet |
Ivanov, A.Yu. Rubin, Yu.V. Egupov, S.A. Belous, L.F. Karachevtsev, V.A. |
| topic |
Динамика кристаллической решетки |
| topic_facet |
Динамика кристаллической решетки |
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2013 |
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English |
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Физика низких температур |
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Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України |
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Article |
| description |
Low-temperature matrix isolation Fourier-transform infrared spectroscopy and quantum-chemical calcula-tions with DFT/B3LYP and MP2 methods were used for investigation of isolated 5-bromouracil (BrU) mole-cules. Only one tautomeric form of BrU was dominated in the low-temperature Ne, Ar, and Kr matrices. It was revealed that population of minor hydroxy-tautomers did not exceed 0.2%. Appearance of additional absorption bands in the region of stretching vibrations CO (about 1710 cm⁻¹) as well as of deformation ones (1297, 1093, 901 cm⁻¹) was explained by Fermi resonance. In Ne matrices the peak intensities of absorption bands assigned to the out-of-plane vibrations of the ring and exocyclic atoms were decreased sharply. For the first time, least square method with the using of polynomial was proposed for the corrective scaling of calculated frequencies of vibrations. It is shown that the correction of calculated frequencies with the polynomial of degree two permits to decrease the root-mean-square discrepancy between the calculated and experimental ones to 4–5 cm⁻¹ in the re-gion of 1500–500 cm⁻¹. The same polynomial may be applied for the correction of spectra of molecules with a similar structure.
|
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0132-6414 |
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https://nasplib.isofts.kiev.ua/handle/123456789/118473 |
| citation_txt |
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil / A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, V.A. Karachevtsev // Физика низких температур. — 2013. — Т. 39, № 6. — С. 704–711. — Бібліогр.: 43 назв. — англ. |
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2025-11-25T12:21:59Z |
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2025-11-25T12:21:59Z |
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| fulltext |
© A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, and V.A. Karachevtsev, 2013
Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6, pp. 704–711
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra
of 5-bromouracil
A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, and V.A. Karachevtsev
B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine
47 Lenin Ave., Kharkov 61103, Ukraine
E-mail: ivanov@ilt.kharkov.ua
Received December 21, 2012, revised February 13, 2013
Low-temperature matrix isolation Fourier-transform infrared spectroscopy and quantum-chemical calcula-
tions with DFT/B3LYP and MP2 methods were used for investigation of isolated 5-bromouracil (BrU) mole-
cules. Only one tautomeric form of BrU was dominated in the low-temperature Ne, Ar, and Kr matrices. It was
revealed that population of minor hydroxy-tautomers did not exceed 0.2%. Appearance of additional absorption
bands in the region of stretching vibrations CO (about 1710 cm
–1
) as well as of deformation ones (1297, 1093,
901 cm
–1
) was explained by Fermi resonance. In Ne matrices the peak intensities of absorption bands assigned to
the out-of-plane vibrations of the ring and exocyclic atoms were decreased sharply. For the first time, least
square method with the using of polynomial was proposed for the corrective scaling of calculated frequencies of
vibrations. It is shown that the correction of calculated frequencies with the polynomial of degree two permits to
decrease the root-mean-square discrepancy between the calculated and experimental ones to 4–5 cm
–1
in the re-
gion of 1500–500 cm
–1
. The same polynomial may be applied for the correction of spectra of molecules with a
similar structure.
PACS: 33.15.–e Properties of molecules;
33.20.–t Molecular spectra;
33.20.Ea Fourier transform spectra;
82.30.Qt Isomerization and rearrangement.
Keywords: FTIR spectroscopy, matrix isolation, DFT method, Fermi resonance.
1. Introduction
Modern science shows constant interest in studies of
biological molecules under conditions free of strong inter-
molecular interactions [1,2]. The low-temperature spectral
methods are the basis of this scientific direction [1–5].
Low-temperatures permit to freeze separate isomers of
biological molecules and their complexes in the inert sur-
rounding and to model biological processes in the space
[6]. Besides, absent of molecule rotation in the inert medi-
um permits essential improve of the resolution of vibra-
tional spectra. Owing to this, the low-temperature matrix
isolation infrared spectroscopy revealed self-descriptive-
ness technique during studies on tautomerism of deoxyri-
bonucleic acid (DNA) bases and of their biologically ac-
tive derivatives [7]. Such biologically active molecules as
halogen-substituted DNA bases and nucleosides have a vi-
tal part in the various biological processes [8]. For example,
5-haloderivatives of uracil are able to replace thymine in
DNA [8,9], have increased mutagenic activity [8,10] and
increase DNA sensitivity to ionizing radiation [11]. Some
works were devoted to studies of vibrational spectra of 5-bro-
mouracil (BrU ) molecules isolated in Ar matrices [12–14].
On the basis of these spectra, conclusions have been made
on BrU flat structure [12] and on Fermi resonance in the
region of CO stretching vibrations [13,14]. As well, the
conclusion on the predominance of the tautomeric structure
of BrU_0 was drawn (Fig. 1).
However, in spite of the predominance BrU_0 tauto-
mer, the number of absorption bands in the experimental
vibrational spectra of BrU exceeds noticeably theoretically
possible 3N-6 fundamental vibrations. Also, quantitative
data on BrU tautomeric equilibrium and on low-intensity
spectral bands in the deformation range of 1500–500 cm
–1
were absent. Meanwhile, analysis of the uracil spectra reveals
Fermi resonance in this spectral region (1550–500 cm
–1
)
too [15]. Besides, spectra of BrU were obtained only for
Ar matrices, and this is able to complicate their analysis
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil
Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6 705
owing to the matrix effect on the vibrational spectrum. The
matrix induces frequency shifts of spectral bands. As a
result, the multiplex structure of contour of absorption
band may occur. The appearance of multiplexes is often
associated with stable conformations of the matrix sites
[16,17] as well with the interaction with the matrix through
libration of the impurity molecules [18]. It is evident that
the more lattice parameters of inert matrices will differ the
more noticeable differences in spectra of molecules isolat-
ed in matrices will be. Therefore, in our work, the vibra-
tional spectra of isolated BrU molecules were obtained not
only in the matrices with relatively close lattice parameters
(Ar, Kr) but in Ne matrices also. To calculate vibrational
spectra by the DFT/B3LYP method, in addition to correla-
tion consistent basis sets, 6–311++G(df, pd) one was used,
revealed the best results in some works [19,20]. For the first
time, to scale the calculated frequencies, we employed the
least square method with the corrective multiplier as the
polynomial. On the basis of the vibrational spectrum of iso-
lated molecules, the proposed scheme of investigation in-
terprets structure of isolated BrU molecules more reliably.
2. Experimental and computer modeling methods
Main details of the low-temperature experiment were
presented in works [21–24]. In the present investigation
Fourier-transform infrared (FTIR) spectra were measured
in the range of 3800–500 cm
–1
, with apodized resolution
being 0.25 cm
–1
. Matrix deposition onto cryogenic mirrors
was controlled with the low-temperature quartz crystal
microbalance (QCM) [25]. The molecular flow intensity
and the concentration of impurity molecules were meas-
ured by QCM (the matrix-to-sample ratio = M/S). The in-
tensity of the molecular flow of commercial BrU samples
(Sigma) was about (50–60)·10
–9
g/(s·cm
2
) at evaporation
temperatures 440–460 K. In this temperature range thermal
destruction of BrU molecules was not observed. The purity
of inert gases (Ne, Ar, and Kr) exceeds 99.99%. The tem-
peratures of cryogenic mirrors were 5 K for Ne matrices
and 12 K for Ar and Kr matrices.
Quantum-chemical calculations were performed with
Gaussian 09 [26] and Firefly QC (version 7.1.G) [27] pro-
gram packages. Firefly QC package is partially used
the GAMESS (US) program code [28]. Structures of the
BrU were optimized at the density functional theory
DFT/B3LYP [29] and Möller–Plesset perturbation theory
(MP2) level of theory. As well, CCSD(T) and complete
basis set (CBS) methods [30] and correlation consistent
basis sets aug-cc-pVDZ, aug-cc-pVTZ [31] were used.
DFT/B3LYP method with basis sets aug-cc-pVDZ and
aug-cc-VTZ and 6–311++G(df,pd) was applied to calcu-
late vibrational spectra.
Standard capabilities of Firefly program were used for
the estimation of Gibbs free energies (∆G) of BrU tauto-
mers. At analysis of spectra the representing normal modes
through internal coordinates by INTC program were used
[32,33]. Calculated spectra were synthesized by SYNSPEC
program [34] for the visual comparison of experiment and
calculations.
3. Results and discussion
3.1. Scaling of DFT/B3LYP frequencies with the least
square method
A frequently used density functional theory (DFT)
method of calculation was applied to assign the absorp-
tion bands of the experimental vibrational spectra. In
comparison with MP2 method, DFT one not only reduces
the computation time but partly compensates the manifes-
tation of the anharmonicity of real vibrations [35]. Actu-
ally for comparison with the experiment, multiplication
of calculated frequencies by the corrective multiplier λ
(the “scaling factor”) is necessary. Besides, as indicated
above, additional frequency shifts are caused by the ma-
trix. It is known that, in comparison with the gas phase,
for frequencies higher than 1000 cm
–1
matrix shifts as a
rule are negative and can be positive for frequencies low-
er than 1000 cm
–1
[16]. In our experiments the shifts fre-
quency of the spectral bands of BrU isolated in Ar and Kr
matrices with regard to the spectrum in Ne matrix were
determined (Fig. 2). For the stretching vibrations in the
region 3500–1600 cm
–1
these shifts are negative and de-
pend monotonically on the frequency (Fig. 2). In the de-
formation region of 1500–500 cm
–1
the shifts may be
different signs and may depend on frequency no monoto-
nous (Fig. 2).
For scaling of calculated frequencies the constant value
of λ is usually used, fitted for one or two frequencies of the
Fig. 1. Molecular structure and atom numbering of the main BrU
tautomers.
A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, and V.A. Karachevtsev
706 Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6
spectral range. To optimize λ in the whole range, it was
proposed to use the least square method [36] in which the
minimum of error function S is the optimum criterion [37]:
2
min
N
i i
i
S , (1)
where ωi is the experimental frequency, νi is the calculated
frequency.
Minimum of the expression (1) is found from condition
∂S/∂λ = 0:
2
N N
i i i
i i
. (2)
It is seen from the representation of frequency shifts
(Fig. 2) that correction by the constant λ is satisfactory
only in the narrow frequency range. Frequency scaling for
the deformation range must be performed with the nonmo-
notonous function. Therefore, the computer program was
elaborated for the correction of frequencies with the poly-
nomial of degree M: X0+X1f…+Xmf
M
. Then, the error
function S may be presented as
2
0
min
N M
k
i k i i
i k
S X f . (3)
From conditions of minimum of the expression (3) the sys-
tem of linear equations is obtained:
0... 0
2 ( ) 0
N M
jk
i k i i ii
j M i k
S
X f f
X
. (4)
Gaussian method [38] was used for the numerical solu-
tion of the system of linear algebraic equations (Eq. (4)).
Next, the computer program determined the mean deviation
( )/m i N , maximum deviation max max | |i m
and root-mean-square deviation 2 1/2[( ( – ) )/ ]rms i m N
of the corrected raw of calculated frequencies from the
experimental ones of the vibrational spectrum.
The vibrational spectra for the dominating structure of
BrU were calculated by DFT/B3LYP method. Statistical
results of the frequency correction with the fixed multiplier
as well as with polynomials of degree one and two in the
range of 1550–500 cm
–1
are presented in Table 1. It fol-
lows from these results that linear regression (M = 1) is
practically no better than scaling with the fixed λ (M = 0).
However, regression with the polynomial of degree two
which is a nonmonotonous function profits markedly for
the all parameters (Table 1). Relative to the linear regres-
sion, advantage of nonmonotonous one for aug-cc-pVTZ
basis is higher than that for aug-cc-pVDZ basis. However,
both the correlation bases rank below to 6–311++G(df,pd)
not only in the nonmonotonous regression but in the least
values of ∆max, δrms and K (Table 1). This verified the
conclusion of the previous works on efficiency of the
DFT/B3LYP/6–311++G(df,pd) method for calculations of
vibrational spectra [19,20]. Besides, 6–311++G(df,pd)
basis requires smaller computational cost than aug-cc-
pVTZ one. The tapping of the more time consuming the
DFT/B3LYP/aug-cc-pVTZ/anharmonic method only af-
fects the results of the frequency correction (Table 1). The
best approximation of calculation to experiment is obtained
for BrU in Ne matrices. The values ∆max and δrms for Ar
and Kr matrices coincide practically (Table 1). In spite of
the nonmonotonous frequency shift of spectral bands in Ar
and Kr matrices (Fig. 2), the increasing of δrms does not
exceed 20% in comparison with Ne matrix (Table 1).
To check polynomials obtained for BrU on other mole-
cules, the spectral data for glycine [39] and uracil [21]
were used. Linear regression demonstrates close results for
both molecules (Table 1). The polynomial of degree two
increases sharply value of ∆max and δrms for glycine. How-
ever, for uracil, magnitudes of the values of ∆max and δrms
decrease (Table 1). Evidently, the increase of the polyno-
mial degree restricts the range of its use by molecules of
the similar structure.
The scaling of calculated spectra allows us to perform
the reliable assignment of the absorption bands in FTIR
spectra. The absorption bands of the stretching and bend-
ing vibrations of the ring and exocyclic groups are ar-
ranged in the range of 1500–1000 cm
–1
. A comparison of
the calculated and experimental spectrum in this region
shows a good agreement of the frequencies of spectral
bands (Fig. 3). Only two weak absorption bands at 1297
and 1093 cm
–1
require the further discussion. In the range
of 1000–500 cm
–1
half of absorption bands belong out-of-
plane bending vibrations of the ring and exocyclic groups.
Fig. 2. Frequency shifts (Δi, см
–1
) of absorption bands of the
experimental BrU spectra in Kr (1) and Ar (2) matrices in relation
to Ne matrix. The dotted lines between Δi are drawn for clear
illustration.
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil
Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6 707
Here comparison demonstrates a good agreement between
the calculated and experimental bands too, except the weak
band at 901 cm
–1
(Fig. 4).
3.2. Occupation of BrU tautomers in the low-temperature
matrices
The calculations show that the hydroxy tautomers have
considerably greater energy than the major diketoform.
Varying methods of calculation and basis sets does not
lead to the significant changes (< 2 kJ/mol) of relative en-
ergies (Table 2). Also, consideration of Gibbs free energy
does not change the relative stability of the BrU tautomers.
Based on these data, using the standard formula, we can
calculate the population of tautomer j at temperature T [40]:
0
exp ( ( ) / )
( ) 100%
exp ( ( ) / )
j
j n
i
i
G T RT
O T
G T RT
. (5)
The temperature plots of population minor of the BrU
tautomers were obtained by using Eq. (5). According to
these plots the population of the BrU_1–BrU_2 tautomers
Table 1. Statistical parameters of discrepancies between experimental frequencies of BrU in Ne, Ar, Kr matrices and frequencies
calculated by DFT/B3LYP method with different basis sets and polynomial corrections
Basis sets
Degree
of polynomial
m , cm
–1
rms , cm
–1
max , cm
–1
K
Ne Ar Kr Ne Ar Kr Ne Ar Kr Ar
aug–cc–pVDZ M = 1 –0.3 –0.3 –0.3 11.2 11.6 11.4 25.8 24.8 24.5 9
aug–cc–pVDZ M = 2 0.1 0.2 0.1 9.6 9.6 9.4 22.8 21.3 21.3 7
aug–cc–pVTZ M = 0 –0.7 0.3 –0.6 7.6 8.4 8.3 14.9 13.8 13.5 8
aug–cc–pVTZ M = 1 –0.3 –0.3 –0.3 7.6 8.3 8.3 13.8 12.8 12.9 8
aug–cc–pVTZ M = 2 0.1 0.1 0.1 5.6 6.1 6.1 11.2 13.0 13.7 6
aug–cc–pVTZ
a
M = 1 –0.5 –0.6 –0.6 10.5 11.2 11.2 21.4 22.2 21.9 10
aug–cc–pVTZ
a
M = 2 0.0 0.0 0.0 7.2 8.0 8.0 13.5 16.1 16.9 8
6–311++G(df,pd) M = 0 0.3 –0.6 0.4 7.1 8.1 8.2 12.3 17.8 19.0 10
6–311++G(df,pd) M = 1 –0.4 –0.4 –0.4 6.7 7.8 7.8 10.7 16.8 18.0 9
6–311++G(df,pd) M = 2 0.0 0.0 0.0 4.3
d
5.1 5.2 9.9 12.0 12.8 4
aug–cc–pVDZ
b
M = 1 –1 8.2 17.3
aug–cc–pVDZ
b
M = 2 –1.4 12.0 25.4
aug–cc–pVDZ
c
M = 1 –1.4 10.4 23.2
aug–cc–pVDZ
c
M = 2 –0.7 8.7 21.0
Notes :
a
anharmonic calculation;
b
correction of glycine frequencies [39] by BrU polynomial for Ar matrices;
c
correction of uracil
frequencies [21] by BrU polynomial for Ar matrices;
d
for Ne matrices the polynomial may be presented as 0.9267 + ν(1.38·10
–4
) –
– ν
2
(6.86·10
–8
); K is the number of bands with discrepancy greater than 6 cm
–1
.
Fig. 3. Vibrational spectra in the region of stretching vibrations of py-
rimidine ring and BrU deformation vibrations (1500–1000 cm
–1
):
Ar matrix (Т = 11 K, M/S = 800:1) (1); calculation by
DFT/B3LYP/ 6–311++G(df,pd) method with frequency correc-
tion of the polynomial of degree two (2). FR is combination
bands enhanced by Fermi resonance.
Fig. 4. Vibrational spectra in the BrU deformation region (1000–
500 cm
–1
): Ar matrix (Т = 11 K, M/S = 800:1) (1); calculation by
DFT/B3LYP/ 6–311++G(df,pd) method with frequency correc-
tion of the polynomial of degree two (2). FR is combination
bands enhanced by Fermi resonance.
A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, and V.A. Karachevtsev
708 Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6
should not exceed 0.02% in the temperature range of this
work (440–460 K) (Fig. 5). The data of calculation are in a
good agreement with experiment. The search of character-
istic absorption bands was performed in the range of CO
stretching vibrations, which are the most intense vibrations
of the BrU tautomers. Comparison of experimental and
calculated data demonstrates absence of characteristic
bands of CO vibrations for the BrU_1 and BrU_2 tauto-
mers (accuracy of estimation at 0.2% population).
Тable 2. Full (E, a.u) and relative energies (E, G, kJ/mol)
of main BrU tautomers calculated by the different ab initio me-
thods
T
au
to
m
er
M
et
h
o
d
E
,
M
P
2
/a
u
g
-c
c-
p
V
T
Z
E
,
M
P
2
/C
B
S
E
,
C
C
S
D
(T
)/
M
P
2
/a
u
g
-c
c-
p
V
D
Z
G
(
4
6
0
K
)*
,
k
J/
m
o
l
BrU_0
(E, –2986.2276)
0
(E, –2986.5215)
0
(E, –2985.8023 )
0
0
BrU_1 36.2 35.5 35.4 35.6
BrU_2 36.7 35.0 37.9 37.3
BrU_3 47.5 46.8 47.2 46.9
Notes : *averaging of E over the first three columns of table
was used at calculations of G.
3.3. Fermi resonance in the νСО range and the range
of deformation vibrations
The overwhelming dominance of the BrU_0 tautomer
over other tautomer structures permits to suggest that addi-
tional spectral bands, not assigned to calculated ones, have
a resonance nature. Splitting of bands due to Fermi reso-
nance can be observed in the vibrational spectra of the pyri-
midine bases in the low-temperature matrices [19,21,41,42].
By analogy with these studies, the BrU_0 absorption bands
about 1710 см
–1
(Figs. 6(а), (с)) may belong to combina-
tion bands enhanced by Fermi resonance. For the rigorous
proof of this fact, it is necessary to consider as intensities
of vibrations involved in the Fermi resonance are changed.
Under resonance, redistribution of intensities of the fun-
damental If and combination Ic vibrations is taking place
[43]:
0 0/ ( ) / ( )c fI I , (6)
where 0 is the initial difference of frequencies between
the fundamental and combination vibration, and is the
total splitting of bands. Since = res + 0, Eq. (6) can be
transformed to
res res 0/ / ( 2 )c fI I , (7)
where res is the resonance splitting of bands.
It follows from Eq. (7) that ratio of intensities can be
changed if you change the 0, for example, using matrix
shifts of vibration frequencies. It depends on the nature of
interacting vibrations. Fundamental and combination vi-
brations that have the same properties of symmetry are
involved in Fermi resonance [43]. For example, the νCO
fundamental vibrations and combination vibrations formed
by stretching and flat deformation vibrations of pyrimidine
Fig. 5. Temperature evaporation dependent of the population of
minor BrU tautomers.
Fig. 6. Vibrational spectra in the νCO stretching region of BrU:
(a) Ar matrix (Т = 11 K, M/S = 800:1); vertical dotted line in-
dicate the possible combination bands; (b) calculation by
DFT/B3LYP/ 6–311++G(df,pd) method for BrU_0 (1); BrU_1
(2), and BrU_3 (3); (c) Kr matrix (Т = 11 K, M/S = 800:1) (1);
Ne matrix (Т = 5 K, M/S = 700:1) (2).
Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil
Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6 709
ring or side groups. The Fig. 2 presents that frequency of
νCO increases in Ne matrix in comparison with Ar or Kr
matrices. In comparison with the νCO, the absolute value
of frequency shifts of the deformation vibrations is less and
can have a different sign. Consequently, if the initial fre-
quency of combination vibration in Ar matrix is less than
frequency of fundamental vibration νCO, then under going
to Ne matrix the 0 value may increases. Then, according
to Eq. (7), the intensity of the combination band should de-
crease. It is precisely these changes in the intensity of the
absorption bands about 1710 см
–1
were observed in the BrU
experimental spectra BrU (Fig. 6, Table 3). Integral inten-
sities of combination bands in Ar and Kr matrices are the
same, but they sharply decrease in the Ne matrix (Table 3).
Table 3. Frequencies and intensities of absorption bands
measured in the νCO stretching region in Ne, Ar and Kr matrices
Vibration
Ar matrix Kr matrix Ne matrix
ν
a
, см
–1 I
b ν, см
–1
I
b
ν, см
–1
I
b
νC2O 1763.4 1 1760.1 1 1774.1 1
νC4O 1729.5 0.4 1725.7 0.4 1735.3 0.49
Combination
band
1711.4 0.28 1708.7 0.29 1707.9 0.12
Notes :
a
Frequency of the most intensive band in multiplet
(Fig. 6(a), 6(c));
b
integral intensity is normalized to νC2O in-
tensity.
This is strong evidence that absorption bands about
1710 cm
–1
are among the combination vibrations. These
vibrations may be formed by the normal mode Q11
(Fig. 3), Q14, Q16, and Q23 (Fig. 4). Hitherto, to study the
Fermi resonance of νCO vibrations for uracil [21] and
isocytosine [20] we used the same method of matrix shits.
The weak bands 1297, 1093 cm
–1
(Fig. 3) and 901 cm
–1
(Fig. 4) may also be assigned to the Fermi resonance-
enhanced combination bands. Previously, Fermi resonance
has been demonstrated in this area for uracil [19] and
isocytosine [20].
Besides absorption bands, which do not correspond to the
calculated spectra we can see close satellites of fundamental
vibrations in the experimental spectra (Figs. 3, 4, 6, 7). The
interaction with the matrix through librations of the impu-
rity molecule may be a probable hypothesis of complex
structure of multiplets. It was shown previously, that due to
librations one of bending vibrations of methane molecules
in Xe matrix undergoes a dramatic broadening of absorp-
tion band with a corresponding decreasing of peak intensi-
ty. As well, a decreasing of peak intensities of some bands
in the deformation region was found in the FTIR spectra
of BrU in Ne matrices. The most characteristic changes are
related to the out-of-plane bending vibrations of NH groups
(Fig. 7). The band of N3H group bending vibration not
only dramatically reduces the peak intensity in the Ne ma-
trix, but is shifted to lower frequencies region (Fig. 7(а)).
The band of bending vibration of N1H group almost disap-
pears from the spectrum in Ne matrix, and as well, its fre-
quency is also reduced. Reduction of peak intensity in Ne
matrix was observed for all out-of plane vibrations of BrU.
4. Conclusions
It was established that only one tautomeric form of 5-bro-
mouracil dominated in the low-temperature matrices, as
the population of the minor tautomers does not exceed
0.2%.
The least squares method was used for the scaling of cal-
culated frequencies by using polynomial. It is shown that the
use of the polynomial to adjust the frequency obtained by
the DFT/B3LYP method reduces the mean square discrep-
ancy between theory and experiment to 4–5 см
–1
. The
common polynomial may be used to scale frequencies of
vibrations of molecules with similar structure. The use of
the 6–311++G(df,pd) basis set and Ar matricrs may be an
optimal choice for the investigations of vibrational spectra
of biological molecules.
Owing to Fermi resonance in the BrU spectra, some ad-
ditional absorption bands appear in the νCO stretching
vibrations region (~ 1710 см
–1
), and region of bending
vibrations (1297, 1093, 901 см
–1
). It was found that in the
Fig. 7. The variation frequency and intensity of BrU deformation
vibration of NH groups in the Ar (1), Kr (2) and Ne (3) matrices:
(a) out-of-plane vibration of N3H; (b) out-of-plane vibration of
N1H.
A.Yu. Ivanov, Yu.V. Rubin, S.A. Egupov, L.F. Belous, and V.A. Karachevtsev
710 Low Temperature Physics/Fizika Nizkikh Temperatur, 2013, v. 39, No. 6
Ne matrix, the peak intensities of the absorption bands of
out-of-plane bending vibrations of the ring and exocyclic
atoms of BrU decreases sharply.
Acknowledgment
The present work was carried out due to the financial
support (grant No. 0110U007895) of the National Acade-
my of Sciences of Ukraine. The authors thank S.G. Stepa-
nian for helpful discussions and R.I. Zubatyuk for his help
in organization and carrying out of calculations. Quantum-
chemical calculations were performed using computational
cluster of B. Verkin Institute for Low Temperature Physics
and Engineering of National Academy of Science of
Ukraine and computational facilities of joint computational
cluster of SSI “Institute for Single Crystals” and Institute
for Scintillation Materials of National Academy of Science
of Ukraine incorporated into Ukrainian National Grid.
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