FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices
The Fourier transform infrared spectra in the range 4000–200 cm⁻¹ of pyrimidine nucleoside 2'-deoxyuridine (dU) have been obtained in the low temperature inert Kr matrices. For the first time, instead of a usual flat mirror, a low temperature one-coordinate retroreflector was used as the matr...
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Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України
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| Цитувати: | FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices / A.Yu. Ivanov, V.A. Karachevtsev // Физика низких температур. — 2007. — Т. 33, № 6-7. — С. 772-777. — Бібліогр.: 34 назв. — англ. |
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Ivanov, A.Yu. Karachevtsev, V.A. 2017-06-16T07:59:22Z 2017-06-16T07:59:22Z 2007 FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices / A.Yu. Ivanov, V.A. Karachevtsev // Физика низких температур. — 2007. — Т. 33, № 6-7. — С. 772-777. — Бібліогр.: 34 назв. — англ. 0132-6414 PACS: 33.15.–e; 67.80.Cx https://nasplib.isofts.kiev.ua/handle/123456789/121790 The Fourier transform infrared spectra in the range 4000–200 cm⁻¹ of pyrimidine nucleoside 2'-deoxyuridine (dU) have been obtained in the low temperature inert Kr matrices. For the first time, instead of a usual flat mirror, a low temperature one-coordinate retroreflector was used as the matrix substrate. Owing to this, the matrix setup is insensitive to dip angle vibrations of the cryostat and is favourable to work with thinner matrix layers. Of two syn-conformers with dU_s1 and dU_s2 (stabilized by the intramolecular hydrogen bond O5'H…O2), only dT_s2 conformer with C2'-endo structure of the ribose ring was uniquely quenched. The height of the interconversion barrier of the minor syn-conformer dU_s1 was estimated to be below 0.7 kcal/mole. It was shown that the energy relaxation of impurities in Kr is slower than in Ar matrices. This investigation was supported by the National Academy of Sciences of Ukraine. en Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України Физика низких температур Classical Cryocrystals FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices Article published earlier |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices Ivanov, A.Yu. Karachevtsev, V.A. Classical Cryocrystals |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices |
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FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices |
| title_sort |
ftir spectra and conformations of 2`-deoxyuridine in kr matrices |
| author |
Ivanov, A.Yu. Karachevtsev, V.A. |
| author_facet |
Ivanov, A.Yu. Karachevtsev, V.A. |
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Classical Cryocrystals |
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Classical Cryocrystals |
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2007 |
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English |
| container_title |
Физика низких температур |
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Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України |
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Article |
| description |
The Fourier transform infrared spectra in the range 4000–200 cm⁻¹ of pyrimidine nucleoside 2'-deoxyuridine
(dU) have been obtained in the low temperature inert Kr matrices. For the first time, instead of a
usual flat mirror, a low temperature one-coordinate retroreflector was used as the matrix substrate. Owing to
this, the matrix setup is insensitive to dip angle vibrations of the cryostat and is favourable to work with thinner
matrix layers. Of two syn-conformers with dU_s1 and dU_s2 (stabilized by the intramolecular hydrogen
bond O5'H…O2), only dT_s2 conformer with C2'-endo structure of the ribose ring was uniquely quenched.
The height of the interconversion barrier of the minor syn-conformer dU_s1 was estimated to be below 0.7
kcal/mole. It was shown that the energy relaxation of impurities in Kr is slower than in Ar matrices.
|
| issn |
0132-6414 |
| url |
https://nasplib.isofts.kiev.ua/handle/123456789/121790 |
| citation_txt |
FTIR spectra and conformations of 2`-deoxyuridine in Kr matrices / A.Yu. Ivanov, V.A. Karachevtsev // Физика низких температур. — 2007. — Т. 33, № 6-7. — С. 772-777. — Бібліогр.: 34 назв. — англ. |
| work_keys_str_mv |
AT ivanovayu ftirspectraandconformationsof2deoxyuridineinkrmatrices AT karachevtsevva ftirspectraandconformationsof2deoxyuridineinkrmatrices |
| first_indexed |
2025-11-27T04:21:43Z |
| last_indexed |
2025-11-27T04:21:43Z |
| _version_ |
1850799690498441216 |
| fulltext |
Fizika Nizkikh Temperatur, 2007, v. 33, Nos. 6/7, p. 772–777
FTIR spectra and conformations of 2�-deoxyuridine
in Kr matrices
A.Yu. Ivanov 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 November 20, 2006
The Fourier transform infrared spectra in the range 4000–200 ñì
–1
of pyrimidine nucleoside 2�-deo-
xyuridine (dU) have been obtained in the low temperature inert Kr matrices. For the first time, instead of a
usual flat mirror, a low temperature one-coordinate retroreflector was used as the matrix substrate. Owing to
this, the matrix setup is insensitive to dip angle vibrations of the cryostat and is favourable to work with thin-
ner matrix layers. Of two syn-conformers with dU_s1 and dU_s2 (stabilized by the intramolecular hydrogen
bond O5�H…O2), only dT_s2 conformer with Ñ2�-endo structure of the ribose ring was uniquely quenched.
The height of the interconversion barrier of the minor syn-conformer dU_s1 was estimated to be below 0.7
kcal/mole. It was shown that the energy relaxation of impurities in Kr is slower than in Ar matrices.
PACS: 33.15.–e Properties of molecules;
67.80.Cx Structure, lattice dynamics, and sound propagation.
Keywords: Fourier transform infrared spectra, matrix isolation, low temperature retroreflector, nucleoside.
Introduction
The structure and stability of molecular fragments of
biomolecules in the gas phase, which are of great interest
for understanding life on the molecular level, are inves-
tigated by different modern experimental methods [1], in-
cluding such methods as He nanodroplets isolation
(HENDI) [2,3], cavity ring-down spectroscopy (CRDS)
[4,5], and conventional Fourier transform infrared
(FTIR) spectroscopy. In spite of distinctions between
these methods, cooling of preliminary evaporated mole-
cules is common to these methods. Owing to fast cooling,
the molecular structures may be fixed in the isolated state
at low temperatures, but interconversion processes are
observed between low barrier conformers [6,7]. Previ-
ously we used FTIR spectroscopy in inert matrices to in-
vestigate conformers of pyrimidine nucleosides [8–10]:
2`-deoxyuridine [9] and thymidine [10]. Three confor-
mers with anti-orientation of the pyrimidine ring were
found in Ar and Ne matrices [9,10], but among the two
possible syn-conformations with intramolecular hydro-
gen bond O5�H…O2 (Fig. 1), only dU_s2 with C2�-endo
conformation of 2�-deoxyribose ring were found in inert
matrices. The transitions between C2�-endo and C3�-endo
conformations of the sugar ring were subject of numerous
© A.Yu. Ivanov and V.A. Karachevtsev, 2007
O
C
N
O
O
O
O
CC
C
C
C
C
C
C 2 4
O
O
O
O
O
C
C
C
C
C
C C
C
C
N
N
a
1
3
b
N
Fig. 1. The molecular structure and atom numbering of syn-con-
formations 2�-deoxyuridine: dU_s2 conformer with C2�-endo
conformation of 2�-deoxyribose (a); dU_s1 conformer with
C3�-endo conformation of 2�-deoxyribose (b). Intramolecular
H-bonds O5�H—O2 are represented with dashed lines.
calculations and experiments [11–14]. The first calcula-
tion [11] was made by the method of molecular mechanics
and the height of the barrier �E
�
between C2�-endo and
C3�-endo conformations of 2�-deoxyribose was estimated
to be 0.6 kcal/mole. In more recent molecular mechanics
calculations with a stochastic difference equation algo-
rithm [12], the value �E
�
= 2 kcal/mole was obtained. Ab
initio calculations at the MP2/6-31G* level gave �E
#
4 kcal/mole [13]. NMR studies of purine nucleosides in
solutions showed this barrier to be 4.7 kcal/mole [14]. For
this work we performed ab initio calculations at DFT and
MP2 levels with correlated consistent basis sets as well as
experiments in Kr matrices, using a more advanced expe-
rimental method.
Experimental and computational methods
Most of the important features of our matrix isolation
setup have been described elsewhere [9,10,15,16]. Nu-
cleosides are very thermally labile molecules and for their
evaporation a special evaporation system with a short dis-
tance to the low temperature mirror and with reduced mo-
lecular beam losses was used [8–10] (Fig. 2). Further-
more, FTIR matrix isolation spectroscopy of nonplanar
conformational-flexible molecules (like sugar, nucleo-
sides, nucleotides…) encounters some additional prob-
lems. Such molecules have relatively broad spectral
bands in FTIR spectra (5–10 cm
–1
in comparison with
0.3–1 cm
–1
in the spectra of nucleic acid bases, which
have flat pyrimidine rings [15]) and the sensitivity of
spectral experiments is lower. Consequently, thick matrix
samples (thicker than 0.1–0.5 mm) must be prepared
to improve sensitivity, jet thick matrices have poorer opti-
cal quality (especially in the short-wave region above
2000 cm
–1
) and a tendency to mechanical collapse. For
one, it is so for large guest molecules like 4-pen-
thyl-4�cyanobiphenyl [17].
Previously, in order to improve the optical characteris-
tics of Ar matrices, prior to matrix samples preparation,
we deposed a thin layer of pure Ar on the cold mirrors
over the temperature range of 35–20 K [16]. As the next
step, in this investigation we, for the first time, used a
retroreflector (functioning as an Amichi prism, Fig. 2).
Owing to the additional reflection, the retroreflector per-
mits work with thinner layers than those with a flat mirror.
Unfortunately, the evaporation cell in this design has an
expanding beam and a strong dependence of the molecu-
lar beam density on the distance between the cell and
cryomirror (Fig. 2). Because of this design, the advantage
in absorption band intensities was not realized. The
unique peculiarity of the retroreflector is in that the tilt
has no influence on the parallelism of the incoming and
outcoming beams [18]. Therefore, the matrix setup with
retroreflector is insensitive to the tilt . However, if there is
a need to work at grazing angle there is a possibility to ad-
just the retroreflector so that work at grazing angles be-
comes feasible. It is well known that reflection at grazing
angles [19] is necessary for efficient spectroscopy of thin
films, for example, in surface enhanced infrared absorp-
tion (SEIRA) spectroscopy. With retroreflector, work at
grazing angles can be peformed without an additional op-
tical window in the vacuum chamber and without align-
ment of the additional spectrometer optics.
In this work, FTIR spectra of pyrimidine nucleoside
2�-deoxyuridine (dU) were obtained in low temperature
inert Kr matrices in the range 4000–200 cm
–1
. The low
temperature differential quartz crystal microbalance
(QCM) was used to measure absolute intensities of mo-
lecular beams and matrix-to-sample ratio (M/S) [15]. The
M/S ratio was about 600:1 for all experiments in Kr matri-
ces. Owing to QCM, we were able to work not only with
Ar flux passing through the Knudsen cell but with extra
flux of cold Ar gas also. The Kr gas was 99.99% pure, Kr
matrices were deposited at the temperatures of the mir-
rors: namely, 9 K for the flat mirror, and 6 K for the
retroreflector.
Experimental data were compared with ab initio calcu-
lations, which were performed by PC GAMESS version
7.0 [20] of GAMESS program [21]. Large part of calcula-
tions were performed on a dual AMD Athlon-MP worksta-
tion run in SMP mode. The stability of 2�-deoxyuridine
conformers (Fig. 1) were estimated with correlated consis-
tent basis cc-pvdz basis sets [22,23] within DFT/cc-pvdz
and MP2/cc-pvdz. The DFT/cc-pvdz method was used for
to calculate vibrational spectra and estimate the free Gibbs
FTIR spectra and conformations of 2�-deoxyuridine in Kr matrices
Fizika Nizkikh Temperatur, 2007, v. 33, Nos. 6/7 773
2R
L= 1.6R
L= 3R
Flat
cryomirror
Retroreflector
Nozzle
90
O
0 2 4
L(R)
I
Nitrogen
shield
0
0.4
0.8
I,
ar
b
.
u
n
it
s
Fig. 2. The evaporation scheme with flat cryomirror and
cryoretroreflector with the relationship of the intensity of mo-
lecular beam (I) as function of the distances L between the cell
and cold substrate. L is in the unit of radius (R) of the outlet
nozzle of cell. This scheme reflects actual distances of cryo-
substrates L(R) from the nozzle of evaporation cell.
energy G (harmonic oscillator-rigid rotor approximation)
by using the standard capabilities of the PC-GAMESS.
Results and discussion
For conformations of nucleosides, the region of stret-
ching (�) vibrations �OH, �NH (3600–3400 cm
–1
) is the
most informative. As can be seen in Fig. 3, spectra of dU
in Kr matrices are quite similar to those in Ar matrices [9],
while all bands in Kr have low frequency shifts. The
shape of the spectral lines of H-bonded �O5�H of dU_s2
conformer in Ar and Kr matrices does not differ signifi-
cantly (Fig. 3). However, spectra in Kr matrix on the flat
mirror at 9 K contain a new weak band at 3514 cm
–1
(Fig. 3, curve 2). The intensity of this band increased
(Fig. 4) after a long infrared irradiation by the globar of
the Fourier spectrometer in the range 400–4500 cm
–1
(as
determined by selective properties of KBr beamsplitter).
It is significant that this IR-induced effect was not ob-
served for dU conformers in Ar and Ne matrices [9].
IR-induced interconversions in the low temperature ma-
trices are known for many compounds [24,25]. Similar
to these data, the spectral changes can be explained
by IR-induced conformational transition from dU_s2 to
dU_s1 conformer with C3 �-endo conformation of
2�-deoxyribose. According to DFT/cc-pvdz calculations
of the vibrational spectra (Table 1) the 3514 cm
–1
band
may be assigned to H-bonded �O5�H of dU_s1 conformer
(Fig. 1) as well.
Table 1. The frequencies and intensities of experimental spectral
bands in the FTIR spectra of 2�-deoxyuridine in Kr matrices and
calculated ones (DFT/cc-pvdz) for dU_s1 and dU_s2 conformers
Conformer
mode
Experiment dU_s1* dU_s1 dU_s2* dU_s2
�� ñì
–1
I �� ñì
–1
I
a �� ñì
–1
I
a
�O5�H 3654 1.5
�O3�H 3633 1 3644 36 3633 25
� hb_O3�H
� hb_O5�H
3580
3615
0.5
3514 0.2
� hb_O5� 3480 1.6 3528 317 3482 507
�N3H 3422 2.5 3443 68 3444 72
Comment: I — relative integral intensities; I
a
— absolute integral intensities
[km/mol]; �hb_OH — bands of groups involved in the intramolecular
H-bonds. * — Scaling factor for calculated frequencies = 0.962.
But furthermore, it was found that the intensity of this
band is not well reproducable. As shown in Fig. 3, the
3514 cm
–1
band in Kr on the retroreflector at 6 K (Fig. 3,
curve 3) is practically absent. It was so in some experi-
ments with a flat mirror as well. To explain this discrep-
ancy, we focused our attention on the spectral behavior of
a water impurity. The weak donor band of a water dimer at
3568.7 cm
–1
[26] is present in the dU spectra in Kr matri-
ces (Fig. 3,4). Under IR-irradiation this band increased in
intensity together with the 3514 cm
–1
band (Fig. 4). In ad-
ditional, according to Engdall and Nelander [26], the wa-
ter trimer band is also at 3514.2 cm
–1
. As a rule, a small
774 Fizika Nizkikh Temperatur, 2007, v. 33, Nos. 6/7
A.Yu. Ivanov and V.A. Karachevtsev
3600 3500 3400
0
0.2
0.4
0.6
3514 cm
–1
3
2
1
D
�, cm
–1
�O5'H
�O5'H
syn-conf
�O3'H
�N3H
Fig. 3. The comparison of FTIR spectra of 2�-deoxyuridine in:
Ar matrix at flat mirror (T = 5 K, M/S = 700) (1), Kr matrices
at flat mirror (T = 9 K, M/S = 600) (2), Kr matrices at
retroreflector (T = 6 K, M/S = 600) (3) in the O–H, N–H
stretching region (3690–3390 cm
–1
).
3550 3500 3450
0.1
H O dimer
2
D
� O5'H
syn-conf
3514 cm
–1
�, cm
–1
Fig. 4. The influence of globar irradiation on the water bands
in Kr matrices with 2�-deoxyuridine (T = 9 K, M/S = 600.) The
temporal interval — 30 min.
amount of H2O molecules can be trapped in the matrix at
a quickened performance of experiment. Nevertheless,
water dimers in Ar matrices (and especially trimers) did
not practically form and did not interfere with experiment
(Fig. 5). For a more sophisticated solution of this problem,
as before [9], we used UV irradiation to shift the
conformational equilibrium of dU. The UV-induced
interconversion and some decomposition were previously
observed for dU samples in Ar matrices [9]. In comparison
with that work, a pronounced UV decomposition of dU in
Kr matrices was obvious (Fig. 6). Unlike experiments in
Ar matrices [9], the UV decomposition in Kr was accom-
panied by an increase of the intensities of the 3568 cm
–1
and 3514 cm
–1
spectral bands (Fig. 6) and of the water
monomer bands in the region 3800–3650 cm
–1
(not dis-
played). It should be also noted that, owing to thinner matri-
ces the efficiency of UV irradiation of the matrix samples on
retroreflector was somewhat higher than on flat mirror.
These results correlate with the known data for the ef-
ficiency of photoprocesses in different matrix media. As a
rule, the quantum yield of photoisomerization decreases
in the sequence Xe, Kr, Ar, N2 [24,25]. Previously, we ob-
served a drop in the efficiency of the UV-induced inter-
conversion of glycine conformers in Kr, Ar, Ne [9]. These
results may be in part explained by the influence of the
size of the matrix cage, since the heavier gases with a
larger cage interact weaker with impurity molecules [25].
Hence, the stronger UV decomposition of dU in Kr, as
compared to Ar, and the formation of water dimers might
be caused by slower energy relaxation from impurity to
the matrix. However, the results of Fig. 4 cannot be ex-
plained by the cage effect. As can be seen in Fig. 4, despite
more stronger interaction between the Kr atom and the
water molecule, water dimers and trimers formed more ef-
fectively on the surface of Kr matrices than Ar ones. This
process is not practically affected by cage dimentios. Ob-
viously, water impurities have longer relaxation times
and longer diffusion paths on the Kr surface than with Ar.
It is interesting to note in this connection the result of
Reva et al. [27] who demonstrated depletion of the
low-barrier (�0.7 kcal/mole) cyanoacetic acid gauche
conformers in the sequence of matrices Xe, Kr, Ar. It can
be therefore inferred that relaxation on the surface of ma-
trices plays an important role in depopulation of the
low-barrier conformers.
To understand the above problems qualitatively, sim-
plified transition kinetics between dU_s1 and dU_s2 con-
formers of dU was considered. The energy relaxation
profile along the dihedral angle C1�C2�C3�C4� (or �3, ac-
cording to [11]) is shown in Fig. 7. It was assumed that the
transition takes place in the framework of syn-conforma-
tion, without breaking H-bond O5�H–O2. The position of
the pyrimidine ring is important since the C2O group may
influence the position of O4� in the ribose ring and, hence,
the barrier height. Therefore, our results (Fig. 7) are no-
ticeably distinct from calculations by Foloppe and
MacKerell [12] for model compounds of 2�-deoxyribose.
In our calculations the barrier height of transition dU_s1
and dU_s2 is about 0.7 kcal/mole at DFT level and 1.3
kcal/mole at MP2 level (Fig. 7).
FTIR spectra and conformations of 2�-deoxyuridine in Kr matrices
Fizika Nizkikh Temperatur, 2007, v. 33, Nos. 6/7 775
3700 3600 3500
0
0.2
0.4
3
2
1
monomer
D
�O5'H
�O5'H
syn-conf
�O3'H
�N3H
H O
dimer
2
�, cm
–1
H O
2
Fig. 5. The manifestation of water impurity bands in the differ-
ent matrices: Ar matrix with 1-methyluracil (T = 11 K) (1), Ar
matrix with 2�-deoxyuridine (T = 11 K) (2), Kr matrices at flat
mirror (T = 9 K) (3).
3600 3500 3400
0
0.06
0.12
0.18
3
2
1
D
�O5'H �O5'H
syn-conf�O3'H
�N3H
3514 cm
–1
�, cm
–1
(H O)
2 2
Fig. 6. Effect of UV irradiation on the FTIR of spectrum of
2�-deoxyuridine isolated in Kr matrix (T = 6 K, M/S = 600) in
the O–H, N–H stretching region (3690–3390 cm
–1
): spectrum
before UV irradiation (1); spectrum after UV irradiation (2);
difference spectrum after UV irradiation (t = 20 min) (3).
According to the conventional transition state theory
(TST), the classical rate constants KTST can be estimated
from the Eyring equation [28]:
K
k T
h
TST
B G /RT� �e � #
,
(1)
where �G
#
is the free energy of the barrier, h and kB are
the Planck and Boltzmann constants.
Similarly as was done by Jensen and Gordon for
glycine [28], the Wigner correction for quantum tunnel-
ing effects is:
K K
h
k T
RT
G
TST
w
TST
B
�
�
��
�
��
�
�
�
�
�
�
�
�
�
�
�
�
1
1
24
1
2
�
� #
, (2)
where the imaginary frequency at the saddle point is de-
noted by �. Assuming that only one-way transitions oc-
cur, the number of molecules dN which passed through
the barrier during dt is:
dN K NdtTST
w� � (3)
Integration of Eq. (3) with the initial number of molecules
N0 leads to:
N t N
K t
TST
w
( ) �
�
0e . (4)
The time of transition of one-half of molecules T1/2 from
one conformer to another has the form
T
K K
/
TST
w
TST
w1 2
2 0 693
� �
ln .
. (5)
Obviously, depopulation of the low-barrier conformer
(or, in other words, «conformational cooling» [6,27]) will
occur if the energy relaxation time is close to T1/2. The re-
sults of calculations using Eqs. (1)–(5) for different tem-
peratures and barriers heights are summarized in Table 2.
One can see that, by extrapolations the reported experi-
mental data [7,27], the conformers with barriers of about
0.7 kcal/mole can be easily conserved in the isolated state
at 6 K. But it is possible only if the energy relaxation is
very fast, otherwise, the population of conformers will
change.
Table 2. The time (s) of T1/2 of transition of one-half number of
molecules from the one conformer to another calculated by
Eqs. (1)–(5) (the reverse transition was ignored)
Barrier,
kcal/mole
The time (s) of T1/2 of transition for different temperature (K)
430 K 300 K 200 K 12 K 6 K
0.3 1.1�10
–13
1.9�10
–13
3.7�10
–13
1.2�10
–6
9.0
0.7 1.7�10
–13
3.5�10
–13
10
–12
9.9 2.5�10
13
1.3 3.4�10
–13
10
–12
4.6�10
–12
8�10
11
>2.5�10
13
2.0 8�10
–13
3�10
–12
2.5�10
–11
>8�10
11
>2.5�10
13
3.0 2.6�10
–12
1.7�10
–11
3�10
–10
>8�10
11
>2.5�10
13
Among the above-mentioned methods (HENDI,
CRDS, and matrix isolation), the process of cooling is the
longest in CRDS, which used seeded molecular beams,
since gas-dynamic cooling occurs due to numerous colli-
sions in the supersonic part of nozzle [29]. The super-
sonic cooling typically quenches the population of con-
formers if the barrier exceeds 1 kcal/mole [30]. In
addition, the carrier gas and the backing pressure influ-
ence this process. As was shown by Ruoff et al. [30], the
«conformational cooling» increase in the sequence He,
Ar, Kr, Xe. From the gas-dynamic investigations [31] it is
known that the energy thermal accommodation coeffi-
cient decreases in the reverse sequence of these atoms.
Because of this, a small coefficient of accommodation is
to be compensated by higher frequency of collisions.
The faster energy relaxation and, consequently, the
effecient «conformational quenching» may result in a di-
rect contact of impurity molecules with superfluid helium
nanodroplets in HENDI [32] or with the surface of low
temperature matrices. As noted by Poliakoff and Turner
[33], the energy relaxation rate is subject to variations di-
rectly as frequencies of the phonon spectrum. The fre-
quencies of the phonon spectrum increase in the sequence
of matrices — Xe, Kr, Ar [34]. It is interesting that the
phonon spectrum of solid Ne is between those of Kr and
Ar (Fig. 20.8 in [34]). These facts interpret in general the
above-discussed data for photoisomerization of dU con-
formers and behavior of water impurity. At the same time,
despite a relatively high barrier (Fig. 7), no reliable evi-
dence of dU_s1 «conformational quenching» in Ar or Kr
matrices was found. It may be due to two different factors.
Firstly, the actual barrier height may be significantly
lower than calculated (Fig. 7). Secondly, the cooling rate
776 Fizika Nizkikh Temperatur, 2007, v. 33, Nos. 6/7
A.Yu. Ivanov and V.A. Karachevtsev
– 50 – 40– 30 – 20 –10 0 10 20 30 40
– 0.5
0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
dU_s1
dU_s2
2.1
kcal/mole
0.7
kcal/mole
1.3
kcal/mole
E
,
k
ca
l/
m
o
le
Fig. 7. The energy relaxation profile between dU_s2 and dU_s1
conformers along dihedral angle C1�C2�C3�C4� calculated by
the methods DFT/cc-pvdz (circles) and MP2/cc-pvdz (squares).
of endocyclic torsion vibrations of dU_s1 may be rela-
tively slow resulting in «conformational cooling». Using
molecular matrices is likely to remove the first factor. As
discussed by Poliakoff and Turner [33], these matrices
can support additional channels of energy relaxation of
impurities via vibrations of host molecules.
Conclusions
The conformational equilibrium of dU conformers with
intramolecular hydrogen bonds in Kr matrices at 6–9 K is
close to the observed equilibrium in Ne and Ar matrices at
5–30 K [9]. Basically, it may be thought that comparison
with the gas phase is true also, with one exception for
dU_s1 conformer with C3�-endo conformation of the ribose
ring. The 3514 cm
–1
band was assigned to the water trimer,
but its overlap with H-bonded �O5�H of dU_s1 conformer is
not completely excluded. For a reliable «conformational
quenching» of dU_s1, use the H2 or N2 molecular matrices
at lower temperatures (< 4 K) might be helpful.
It has been shown that a retroreflector enables work
with thin Ar matrices, correlation with the evaporation
system of thermally labile biomolecules, and improves
the optical stability of the cryogenic matrix isolation
setup. It is important that the retroreflector simplifies
measurements at grazing angles and consequently
enables investigations of very thin matrices. Use of the
retroreflector scheme for surface enhanced infrared ab-
sorption (SEIRA) spectroscopy at low temperatures is
promising for further investigation.
This investigation was supported by the National
Academy of Sciences of Ukraine.
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