Molecular structures of thymidine isomers isolated in low-temperature inert matrices
The Fourier transform infrared spectra of 2`-deoxyribonucleoside — thymidine (dT) in low-temperature Ar matrices are obtained in the range 4000–1300 cm–¹. It is determined that anti-conformers of thymidine are dominant. The ribose rings of the main anti-conformers dT_a0, dT_a1 are in the C2`-endo co...
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irk-123456789-1289322018-01-15T03:03:43Z Molecular structures of thymidine isomers isolated in low-temperature inert matrices Ivanov, A.Yu. Krasnokutski, S.A. Sheina, G.G. Biological Systems at Low Temperatures The Fourier transform infrared spectra of 2`-deoxyribonucleoside — thymidine (dT) in low-temperature Ar matrices are obtained in the range 4000–1300 cm–¹. It is determined that anti-conformers of thymidine are dominant. The ribose rings of the main anti-conformers dT_a0, dT_a1 are in the C2`-endo conformation, but the ribose rings of minor anti-conformers dT_a2, dT_a3 have the C3`-endo conformation, stabilized by intramolecular hydrogen bonds O3`H…O5` and O5`H…O3`, respectively. The main syn-conformer dT_s2 is stabilized by the intramolecular hydrogen bond O5`H…O2 and has C2`-endo conformation of the ribose ring. 2003 Article Molecular structures of thymidine isomers isolated in low-temperature inert matrices / A.Yu. Ivanov, S.A. Krasnokutski, G.G. Sheina // Физика низких температур. — 2003. — Т. 29, № 9-10. — С. 1065-1070. — Бібліогр.: 24 назв. — англ. 0132-6414 PACS: 33.15.-e, 67.80.Cx http://dspace.nbuv.gov.ua/handle/123456789/128932 en Физика низких температур Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України |
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Biological Systems at Low Temperatures Biological Systems at Low Temperatures |
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Biological Systems at Low Temperatures Biological Systems at Low Temperatures Ivanov, A.Yu. Krasnokutski, S.A. Sheina, G.G. Molecular structures of thymidine isomers isolated in low-temperature inert matrices Физика низких температур |
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The Fourier transform infrared spectra of 2`-deoxyribonucleoside — thymidine (dT) in low-temperature Ar matrices are obtained in the range 4000–1300 cm–¹. It is determined that anti-conformers of thymidine are dominant. The ribose rings of the main anti-conformers dT_a0, dT_a1 are in the C2`-endo conformation, but the ribose rings of minor anti-conformers dT_a2, dT_a3 have the C3`-endo conformation, stabilized by intramolecular hydrogen bonds O3`H…O5` and O5`H…O3`, respectively. The main syn-conformer dT_s2 is stabilized by the intramolecular hydrogen bond O5`H…O2 and has C2`-endo conformation of the ribose ring. |
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Ivanov, A.Yu. Krasnokutski, S.A. Sheina, G.G. |
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Ivanov, A.Yu. Krasnokutski, S.A. Sheina, G.G. |
| author_sort |
Ivanov, A.Yu. |
| title |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices |
| title_short |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices |
| title_full |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices |
| title_fullStr |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices |
| title_full_unstemmed |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices |
| title_sort |
molecular structures of thymidine isomers isolated in low-temperature inert matrices |
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Фізико-технічний інститут низьких температур ім. Б.І. Вєркіна НАН України |
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2003 |
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Biological Systems at Low Temperatures |
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| citation_txt |
Molecular structures of thymidine isomers isolated in low-temperature inert matrices / A.Yu. Ivanov, S.A. Krasnokutski, G.G. Sheina // Физика низких температур. — 2003. — Т. 29, № 9-10. — С. 1065-1070. — Бібліогр.: 24 назв. — англ. |
| series |
Физика низких температур |
| work_keys_str_mv |
AT ivanovayu molecularstructuresofthymidineisomersisolatedinlowtemperatureinertmatrices AT krasnokutskisa molecularstructuresofthymidineisomersisolatedinlowtemperatureinertmatrices AT sheinagg molecularstructuresofthymidineisomersisolatedinlowtemperatureinertmatrices |
| first_indexed |
2025-07-09T10:15:16Z |
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Fizika Nizkikh Temperatur, 2003, v. 29, Nos. 9/10, p. 1065–1070
Molecular structures of thymidine isomers isolated in
low-temperature inert matrices
A.Yu. Ivanov1, S.A. Krasnokutski2, and G.G. Sheina1
1 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
2 Max-Planck-Institut für Strömungsforschung, Bunsenstraße 10, Göttingen 37073, Germany
The Fourier transform infrared spectra of 2’-deoxyribonucleoside — thymidine (dT) in
low-temperature Ar matrices are obtained in the range 4000–1300 ñm–1. It is determined that
anti-conformers of thymidine are dominant. The ribose rings of the main anti-conformers dT_a0,
dT_a1 are in the Ñ2’-endo conformation, but the ribose rings of minor anti-conformers dT_a2,
dT_a3 have the Ñ3’-endo conformation, stabilized by intramolecular hydrogen bonds O3’H…O5’
and O5’H…O3’, respectively. The main syn-conformer dT_s2 is stabilized by the intramolecular
hydrogen bond O5’H…O2 and has Ñ2’-endo conformation of the ribose ring.
PACS: 33.15.–e, 67.80.Cx
The structural components of DNA — nucleosides
and their derivatives — are important objects of inves-
tigation for the modern science of life [1–11]. The
main experimental methods of investigation of nucleo-
sides are NMR spectroscopy and crystallography [1].
But the results of investigations by these methods de-
pend strongly on the intermolecular interactions. For
example, only one form of several possible conformers
can be stabilized in crystals [1]. Owing to competing
interactions with the solvent, NMR spectroscopy gives
no way to obtain direct data about intramolecular hy-
drogen bonding [4,5]. These limitations are absent in
the method of matrix isolation, where molecular iso-
mers from the gas phase are trapped in low-tem-
perature inert matrices [12]. We previously used the
Fourier transform infrared (FTIR) matrix isolation
spectroscopy for the first time in the investigation of
pyrimidine nucleosides isolated in low-temperature in-
ert matrices [10,11]. The evaporation of uridine and
dT without thermodestruction was demonstrated, and
the intramolecular H-bond O5’H…O2 was detected
[10,11]. In the present research, FTIR spectra of dT
in Ar matrices were obtained by using an enhanced ex-
perimental setup. The new spectral data suggest the
existence of more types of isomers with intramolecular
H-bonds in the isolated pyrimidine nucleosides than
had been considered before [7–11].
Experimental and computational methods
The basic features of the FTIR spectrometer have
been described previously [11,13–15]. For this paper
the FTIR spectra of thymidine and the auxiliary sub-
stance 1-methyl-thymine were obtained in the ranges
4000–1300 cm–1 with a CaF2 beamsplitter at an
apodized resolution of 0.4 cm–1
. The matrix isolation
© A.Yu. Ivanov, S.A. Krasnokutski, and G.G. Sheina, 2003
1
2
3
4
5
6
7
He
8
Fig. 1. The general scheme of low-temperature setup
based on liquid He cryostat: rotating vacuum seal (1),
cryogenic block with cold mirrors and QCM (2), rotating
nitrogen shield (3), flange with indium seal (4), Knudsen
cell (5), electric heater of Knudsen cell (6), Ar flow
through Knudsen cell (7), outside Ar flow (8).
setup was based on a liquid helium cryostat with a ni-
trogen shield (Fig. 1). Two low-temperature differen-
tial quartz crystal microbalances (QCM) and two
metal mirrors were placed on the copper holder in the
vacuum chamber (Fig. 1) and had a working tempera-
ture in the range 5–40 K. The QCM was used for the
measurements of the absolute intensity of the molecu-
lar beams and the matrix-to-sample ratio (M/S) [13].
Owing to QCM, we have the capability of working
not only with an Ar flux passing through the Knudsen
cell but with an outside flux of cold Ar gas also
(Fig. 1).
All nucleosides are very thermally labile molecules,
and for their evaporation a special Knudsen cell with
reduced molecular beam losses was constructed. As is
shown in Fig. 2, the geometry of the Knudsen cell and
its disposition to low-temperature mirror are very im-
portant for effective operation. The data in Fig. 2
were obtained by the statistical Monte Carlo method,
which is very useful for the simulation of complicated
vacuum systems [16]. This evaporation cell is cha-
racterized by a working vapor pressure of around
10–5 Torr and Knudsen number of over 100. This evap-
oration cell is more effective by a factor of more than
500–1000 over one of the cells used in our previous ex-
periments with simple compounds [13–15]. In com-
parison with our previous work [11], for the present
experiments the distance L (Fig. 2) was decreased
from 4.5R to 2.5R. The typical intensities of molecu-
lar beams of thymidine were about 40–70 ng/(s·cm2)
at evaporation temperatures 410–430 K without any
thermodestruction. Thymidine (commercial substance
from Sigma) was used without additional purifica-
tion. The auxiliary substance 1-methyl-thymine was
synthesized at the Kharkov National University
(Kharkov, Ukraine). All substances were annealed to
remove impurities such as sorbed H2O, CO2, and N2 in
the initial phase of evaporation. The inert gas Ar was
more than 99.99% pure and deposited on the mirrors at
11 K. To improve the optical characteristics of the Ar
matrices, before the deposition of matrix samples a
thin layer of pure Ar was deposited on the mirrors over
a temperature range of 35–20 K [15]. The quan-
tum-chemical ab initio calculations of the relative en-
ergies and vibrational spectra of thymidine conformers
were performed by the program PC GAMESS version
6.0 [17] of the GAMESS (US) QC package [18].
Results and discussion
The peculiarities of vibrational spectra of dT con-
formers. As is evident from Fig. 3, in the region of the
stretching vibrations �(OÍ), �(NÍ), the frequency of
the �(N3H) stretching vibration of dT coincides well
with �(N3H) of 1-methyl-thymine. Because of this,
four absorption bands in this region (Fig. 3) can be-
long to two OH groups of 2’-deoxyribose — O3’H,
O5’H only (Fig. 3). The magnification of the number
of bands can be explained by intramolecular hydrogen
bonds in the conformational structures, which were
considered in this paper (Fig. 4). It is known that the
conformational-flexible ribose rings of nucleosides has
a puckered structure and C2’-endo, C3’-endo are the
1066 Fizika Nizkikh Temperatur, 2003, v. 29, Nos. 9/10
A.Yu. Ivanov, S.A. Krasnokutski, and G.G. Sheina
0 4 8
0
0.4
0.8
L(R)
I
H
2R
Nozzle
H = 2R
Fig. 2. The relationship of the efficiency of evaporation
cell (I) as function of the distances L between cell and
cold mirror. L is in units R, R is the radius of outlet noz-
zle of Knudsen cell.
3600 3500 3400
0,4
0,8
D
� , ñm–1
2
1
�O5'H
�O5'H
syn-conf.
�O3'H
�N3H
Fig. 3. The FTIR spectra of thymidine (1) and
1-methylthymine (2) isolated in Ar matrices (T = 12 K,
M/S = 700) in the O–H, N–H stretching region
(3690–3390 cm–1).
main equilibrium conformations of the ribose ring in
solutions [1]. As is indicated in Fig. 4, the transition
C3’-endo � C2’-endo has no effect on the structure of
the H-bonds in the syn-conformers dT_s1, dT_s2
(Fig. 4). In the anti-conformers dT_a2, dT_a3 the
transition C2’-endo � C3’-endo leads to the formation
of the H-bonds O3’H…O5’, O5’H…O3’ (Fig. 4). The
choice of the structure dT_a1 with the orientation of
hydroxymethyl group gauche+ and torsion angle �
(< C3’–C4’–C5’O5’) = + 50o are close to the struc-
tures with hydrogen bonds C6H…O5’ in the anti-con-
formers of uridine and cytosine [7,8]. The structure
dT_a0 with the orientation of hydroxymethyl group
gauche— (< � � – 65o) and the lack of any classical lin-
ear H-bonds (Fig. 4) were considered also. The stabi-
lization of the position of the pyrimidine ring in the
dT_a0, dT_a2, dT_a3 conformation can be effected by
the electrostatic interaction between atoms: C6H ��
O4’ and C2O �� H1’. The orientation of the methyl
group with respect to the carbonyl group C2O are
close to the structure A from [19], where two hydro-
gen atoms positioned above and below N1–C2–O
plane (Fig. 4). All conformers from Fig. 4 may be con-
sidered as local minima, since they were stable at the
HF/3–21G(p), HF/6–31G(d,p), and MP2/6–31G(d,p)
levels of calculation and have no imaginary frequen-
cies in the calculated spectra.
The experimental and calculated spectra are com-
pared in the region of ��OÍ), ��NH), ��CH) (Ta-
ble 1). From this table we notice that the calculated
frequencies of the free O5’H, O3’H, and N3H groups
are in good agreement with the experimental frequen-
cies for all conformers. The band 3482 cm–1 (Fig. 3,
Table 1) can be assigned to the H-bonded vibration
O5’H…O2 in the syn-conformations. According to our
calculations, the vibration �(hb_O5’H) in conformer
dT_s2 has a frequency about 40 cm–1 lower than in the
dT_s1 conformer (Table 1). We can see in our experi-
mental spectra that the band at 3482 cm–1 does not
Molecular structures of thymidine isomers isolated in low-temperature inert matrices
Fizika Nizkikh Temperatur, 2003, v. 29, Nos. 9/10 1067
O
H
H
H
O
H
N
H
R
O4
N
H
O2
H
H
H
O
H
H
H
O
H
H
H
O
H
N
H
R O
N H
O
H
H
H
OH
HO
H H
H
O
H
N
H
R
O
N
H
O
H
H
H
O
H
O
H
H
H
O
H
N
H
R
ON
H
O
H
H
H
O
H
H
H
O
H H
H
O
H
N
H
R O
N H
OH
H
HO
H
O
H
H
H
O
H
N
H
R
O
N
H
O
H
H
HO
H
H
dT_a1
dT_s1
dT_a2
dT_s2
dT_a3
dT_a0
5' 1'
3'
4
3
2
1
6
5
Fig. 4. The conformational structures of thymidine
which are stable at the different level of calcu-
lation (HF/3–21G(p), HF/6–31G(d,p) and
MP2/6–31G(d,p)). Intramolecular H-bonds are repre-
sented with dashed lines. The symbol R – represents a
CH3 group.
Table 1
The parameters of experimental FTIR spectra in Ar matrices and calculated by the method 6–31G(d,p) spectral bands of
thymidine conformers in the 3700–3000 cm–1 region
Conformer
mode
Experiment dT_a0 dT_a1 dT_a2 dT_a3 dT_s1 dT_s2
�, ñm–1 I �, ñm–1 Ia �, ñm–1 Ia �, ñm–1 Ia �, ñm–1 Ia �, ñm–1 Ia �, ñm–1 I a
�O5’H 3665 3.1 3673 76 3367 72 3673 84
�O3’H 3641 1.8 3654 64 3659 54 3659 65 3681 76 3660 54
� hb_O3’H 3620* 0.8* 3638 107
� hb_O5’H 3597* 0.5* 3639 86
� hb_O5’H 3482 6.2 3626 161 3589 351
�N3H 3428 9.2 3439 106 3441 103 3438 106 3438 106 3435 103 3436 106
�C6H 3075 0.5 3059 4 3043 14 3071 7 3070 8 3022 6 3026 5
C o m m e n t: I — relative integral intensities. Ia — absolute integral intensities (km/mol). �hb_OH — bands of
groups involved in the intramolecular H-bonds. * — after deconvolution of the wide band 3598 cm–1 on the Gaussian
contours.
have a high-frequency shoulder in Ar matrices (Fig. 3)
and the occupancy of conformer dT_s1 can be ne-
glected. The calculated frequencies and intensities of
the characteristic bands of the conformers dT_a2 and
dT_a3 are in close agreement (Table 1). This result is
supported by the experiment in Ar matrices, where we
can see only the one wide band 3598 cm–1 with a
high-frequency shoulder (Fig. 3). Contrary to the cal-
culated parameters of �C6H (Table 1), only one band
of �C6H vibration was detected in the experimental
spectrum (Fig. 5). The influence of the intramolecular
hydrogen bonds C6H…O5’ in conformer dT_a1 on the
�C6H parameters was not detected experimentally, as
the free C6H group in 1-methyl-thymine has Fermi
resonance splitting in the spectra (Fig. 5). Conse-
quently, it may be considered that the anti-conformers
dT_a0 and dT_a1 are practically indistinguishable in
the investigated region.
The populations of dT conformers in the low-tem-
perature matrices. It is known that the conformers’
occupancies in matrices may differ widely from those
in the gas phase. The effect of interconversion is ob-
served at low barriers between conformational isomers
[12]. We tested the interconversion by using the an-
nealing of matrix samples. The annealing of matrix
samples at 30 K has no influence on the
conformational equilibrium. It follows that the barrier
heights of dT conformers > 2.5–3 kcal/mole and their
conformational equilibrium in the gas phase at the
evaporation temperature must be close to equilibrium
in Ar matrices at 12 K. For comparison with the real
experimental data the relative free Gibbs energy �G
was estimated by the standard method [20]:
� � � � �G T E ZPE CdT T S TAB
T
( ) ( )�
�
0
.
The relative electronic energy �E was estimated at
the MP2/6–31G(d,p) level of ab initio calculation,
and the relative zero-point vibrational energy �ZPE
and temperature-dependent contributions of rotation
and vibration were estimated at the HF/6–31G(d,p)
level for temperatures of 298 and 420 K (Table 2).
The association of �G and the experimental spec-
tral data can be expressed by the standard equation:
�G T RT K RT /AB AB A B( ) ln ln ( )�
�
� � ,
where KA,B is the equilibrium constant of conformers
A, B, and �A, �B are the populations of these confor-
mers.
To define the equilibrium constants by using the
experimental spectra it is necessary to know the molar
extinction coefficients of the characteristic spectral
bands or their ratios. The ratios of molar extinction
coefficients of characteristic bands may be determined
through the redistribution of the intensities of the
characteristic bands under the influence of changing
evaporation temperature or through the UV irradia-
tion of matrix samples. If the corresponding experi-
ments are difficult, the ab initio calculations of the in-
tensities of the characteristic spectral bands may be
used. Ab initio calculations usually overestimate the
absolute infrared intensity of vibrational bands
[21,22], but the ratio of the experimental and calcu-
lated intensities I coincides much better. The equilib-
rium constant of isomers a and b has been presented as
[23,24]:
K
I
I
I
I
AB
a
a
b
b
�
�
�
�
�
�
�
�
�
�
�
�
�
�
�
(exp)
( )
( )
(exp)calc
calc �
�
�
� . (1)
Unlike some studies [23,24], we have used Eq. (1)
with the intensities of the ��OH), ��NH), and ��CH)
stretching vibrations only. With our data the best
agreement between the calculated and experimental
results is observed for the ratio of the intensities of
stretching vibrations. For determination of KAB dif-
ferent combinations of the experimental and calcu-
lated intensities from Table 1 were used. As discussed
above, the anti-conformers in the pairs: dT_a0 and
dT_a1, dT_a2 and dT_a3 are practically indistin-
guishable in the matrix spectra. Therefore, for the
sake of simplicity, the conformer dT_a0 was ignored.
According to the relative electronic energy
calculations, the syn-conformer dT_s2 with the
1068 Fizika Nizkikh Temperatur, 2003, v. 29, Nos. 9/10
A.Yu. Ivanov, S.A. Krasnokutski, and G.G. Sheina
3120 3080 3040
0
0.04
D
� , ñm–1
2
1
� C H6
Fig. 5. The FTIR spectra of thymidine (1) and
1-methylthymine (2) isolated in Ar matrices (T = 12 K,
M/S = 700) in the C5–H, C6–H stretching region
(3140–3040 cm–1).
intramolecular hydrogen bond O5’H…O2 and confor-
mation of the sugar ring — C2’-endo has the minimal
energy among all conformers at all levels of optimiza-
tion (Table 2). The data in Table 2 demonstrate dis-
agreement between the experimental and calculated
occupancies of the dT_a1 and dT_s2 conformers, but
the experimental and calculated data coincide well for
the minor anti-conformers dT_a2 and dT_a3 (Ta-
ble 2). The influence of the vibrational-rotational con-
tribution to the free energy reduces the difference of
conformers’ energies significantly, and this is espe-
cially noticeable with increasing evaporation tempera-
ture (Table 2). Because of this, conformers dT_s2 may
have an essential effect on biological processes at the
relatively low physiological temperatures.
Conclusions
It was shown that FTIR matrix isolation spectros-
copy is a helpful method for the investigation of the
molecular structure of nucleoside conformational iso-
mers. It was established that at evaporation tempera-
tures of up to 430 K thymidine may be evaporated for
an appreciable length of time and trapped in inert ma-
trices without any thermodestruction. Anti-conform-
ers of thymidine are dominant in the isolated state.
The main anti-conformer dT_a1, has the Ñ2’-endo con-
formation of the ribose ring. The minor anti-conform-
ers dT_a2, dT_a3 have the Ñ3’-endo conformation of
the ribose ring, stabilized by intramolecular hydrogen
bonds O3’H…O5’ and O5’H…O3’ respectively.
The intramolecular hydrogen bonds O3’H…O5’, and
O5’H…O3’ may be regarded as an indicator of the
transition Ñ2’-endo � Ñ3’-endo between conforma-
tions of ribose ring in the anti-conformers of
thymidine. The thymidine dT_s2 syn-conformer is sta-
bilized by the intramolecular hydrogen bond
O5’H…O2 and the dominant conformation of ribose
ring is Ñ2’-endo.
Acknowledgement
This investigation was supported by the
Ukrainian Academy of Sciences and in part by
the INTAS-International Association under grant
No. INTAS 00–00911.
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Fizika Nizkikh Temperatur, 2003, v. 29, Nos. 9/10 1069
Table 2
Calculated and experimental relative energies (kcal/mole) of the thymidine conformers in the isolated state
Conformer
method
dT_a0 dT_a1 dT_a2 dT_a3 dT_s1 dT_s2
HF/3–21G(p) 5.4 2.4 2.6 4.6 3.3 0
(–865.3452)*
HF/6–31G(d,p) 2.9 1.6 1.8 3.4 1.5 0
(–870.1091)*
MP2/6–31G(d,p) 5.7 3.0 3.8 4.9 2.6 0
(–872.6776)*
�G (298 K)**
MP2/6–31G(d,p)
3.3 1.8 2.1 3.4 1.6 0
�G (420 K)**
MP2/6–31G(d,p)
2.4 1.4 1.6 2.9 1.2 0
�G (420 K)
Experiment
— 0 1.8 2.2 — 1.1
* — absolute energies in a.u. are indicate in brackets. ** — vibrational-rotational contribution was estimated at
HF/6–31G(d,p) level.
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