Journal of Applied Spectroscopy, Vol. 72, No.

1, 2005

ANALYSIS OF HYDROGEN BONDS BY THE IR SPECTRA

OF THYMINE AND N1,N3-DEUTEROTHYMINE

G. N. Ten,a* T. G. Burova, a and V. I. Baranovb UDC 543.42+547.82

Calculations of the frequencies and absolute intensities of the IR bands of plane vibrations of thymine and
N1,N3-deuterothymine in various phase states have been carried out. It has been shown that in the polycrys-
talline state thymine forms hydrogen bonds C2=O8...HN1 and C2=O8...HN3, and in an aqueous solution the
intermolecular interaction is realized by means of the hydrogen bonds O8...HO and O...HN1.

Keywords: thymine, N1,N3-deuterothymine, IR spectrum, calculation, hydrogen bond.

Introduction. The vibrational spectra of thymine (T) have been the subject of a large number of experimental
and theoretical works. Earlier, the vibrational spectra of T were measured in the gas phase [1], in solutions [2], and
in the polycrystalline state [2–4], as well as by the matrix-isolation method [5–7]. At the same time, as the analysis
of the theoretical works has shown, the calculation of the normal vibrations performed with the use of various methods
(quantum-mechanical, semiempirical, and ab initio ones [2, 4, 7]) or on the basis of the valence-force approximation
[3] leads to a different assignment of the spectral lines, mainly in two frequency ranges: 1500–1700 and 1100–1300
cm−1 [2–4]. This is due to the fact that the spectra of condensed states of T, where hydrogen bonds are formed,
widely differ from the spectra of an isolated molecule, but in the calculations this fact was not taken into account to
the fullest extent: in the ab initio method, in assigning, a set of frequencies for polycrystalline T [2] was used, and
the calculation and analysis of the IR spectra on the basis of the valence-optical scheme were performed without using
the intensities, which, as is known, considerably decreases the reliability of the interpretation [3].
Earlier, to study the hydrogen bonds of the bases of nucleic acids, a method was proposed for modeling the
influence of hydrogen bonds on the IR spectra by changing the force constants in a molecular fragment adjoining the
region of H-bond formation (in particular, deformation angles of the RAH group) on passing from a monomer to an as-
sociate. Moreover, such an approach permits determining the possible structural-dynamic model of the molecule upon the
formation of a hydrogen bond. For example, the thus-obtained information on the changes in the parameters has shown
that in the polycrystalline state uracyl (U) forms hydrogen bonds of two types — involving N–H (C4=O10...HN1 and
C4=O10...HN3) and C–H (C2=O8...HC5) groups [8]. This method was later used in investigating the tautomeric forms
of purine, adenine, and cytosine in different phase states with the use of not only vibrational but also electronic-vibra-
tional spectra and demonstrated its efficiency [9, 10].
The aim of the present work is to analyze the influence of hydrogen bonds on the IR spectra of T and its
N1,N3-deutero analog (T-d2) by modeling the force and electrooptical parameters of the deformation vibrations and to
determine the structural-dynamic models of the molecules under consideration in various phase states.
Calculations of the Frequencies and Intensities of the IR Spectra of Thymine in Various Phase States.
The vibrations of T were calculated by the valence-optical method [11] — the most effective method for modeling the
IR spectra of complex molecules. Since T is a 5-methyl-substituted molecule of U, the fragmentary technique with the
use of the force and electrooptical parameters of U and ethane for isolated molecules was applied [8, 12]. For the
polycrystalline state and the aqueous solution of T, unlike the monomer, the changes in the force constants and elec-

*
To whom correspondence should be addressed.

a
N. G. Chernyshevskii Saratov State University, 155 Moskovskaya Str., Saratov, 410026, Russia; e-mail:
TenGN@info.sgu.ru; bV. I. Vernadsky Institute for Geochemistry and Analytical Chemistry, Moscow, Russia. Trans-
lated from Zhurnal Prikladnoi Spektroskopii, Vol. 72, No. 1, pp. 99–105, January–February, 2005. Original article sub-
mitted December 8, 2003.

104 0021-9037/05/7201-0104 ©2005 Springer Science+Business Media, Inc.

 Fig. 1. Numbering of atoms (a) and natural vibration coordinates (b) of
thymine.

trooptical parameters of the molecule upon the superposition on it of additional, namely, hydrogen bonds were taken
into account.
As the calculation shows, in joining fragments for making the frequencies and intensities of the IR spectra of
an isolated T molecular consistent with the data of the experiment performed by the matrix-isolation method [5, 7]
(Table 1), it is necessary to increase by ,15% the force constants of the C4C5, C5C6 (K4, K5) bonds and the defor-
mation angles C4C5C11, C6C5C11 (K24, K25), as well as change the electrooptical parameters ∂µi ⁄ ∂qj for the C4C5 and
C5C6 bonds compared to the analogous parameters of U [8]. This is due to the addition of the methyl group CH3. The
numbering of atoms and natural coordinates of T is given in Fig. 1. The inverse vibration problems for the polycrys-
talline state and the solution were not solved, since the use of quantitative estimates of changes in the force and elec-
trooptical parameters obtained previously for U in considering the influence of the hydrogen bond on the IR spectrum
[8] gives a good reproduction of the values of frequencies and intensities of the IR spectra of T and T-d2 of the con-
densed states (Tables 2 and 3). Table 4 gives only those force constants and electrooptical parameters of T for various
phase states whose values differ from the values of the analogous parameters of U [8].
For an isolated molecule of T, the experimental and calculated values of the absolute intensities of vibrations
ν6 and ν7 agree only qualitatively (Table 1), since in the 1600–1800-cm−1 range Fermi resonance takes place [5], and
its influence on the redistribution of the absorption-band intensities was ignored in our calculation. Moreover, as for
U, for T there is a strong interaction of vibrations of C=O carbonyl bonds and a C=C double bond [12, 13]. There-
fore, the intensity of vibration ν8, whose mode is determined by the stretching vibrations Q(C4O10) and Q(C5C6) and
their interaction, depends on both the experimental conditions and the force field used. Indeed, the intensity of the ab-
sorption band interpreted in the experiment in [8] as vibration ν8 doubles in the N2-matrix as compared to Ar and has
a value comparable to the data of [7] and correlating with the results of our calculation (Table 1).
−1 −1
Three vibrations in the 300–1600-cm range for T (1472, 1405, and 1183 cm ) [7] and U (1473, 1401, and
−1
1186 cm [8]) are characteristics: they retain their frequency value, have a high intensity, and their mode is deter-
mined by the deformation vibrations of the N1H and N3H bonds.
In general, the interpretation of the IR spectrum for an isolated molecule of T coincides with the assignment
made by other authors [5–7], which gives reason to carry out an adequate assignment of the absorption bands [5] of
an isolated molecule of T-d2. Deuteration causes a shift of the deformation vibrations of the N1D and N3D bonds into
the 800–1200-cm−1 range with a simultaneous decrease in the intensities of the corresponding absorption bands com-
pared to T. This is due to the increase in the contribution to their modes of the stretching vibrations of the pyrimidine
ring and the deformation vibrations of the CH3 methyl group. Deuteration leads to a small shift into the low-frequency
region of the absorption bands determined by the deformation vibrations of the C6H bond (1653, 1494, 1414, 1365,
−1 −1
1193 cm for T and 1639, 1488, 1390, 1327, 1174 cm for T-d2) because of their mixing with the deformation vi-
brations of the N1D and N3D bonds. Moreover, while for T in the IR spectrum characteristic deformation vibrations
of the CH3 methyl group (1466, 1336, 991 cm−1) are observed; for T-d2 the calculation shows their splitting and mix-
−1
ing with the stretching and deformation vibrations of the pyrimidine ring (1488, 1463, 1343, 1327, 1026, 935 cm ).
−1
As for U-d2, in the IR spectrum of the isolated molecule of T-d2 in the 300–1500-cm range three high-intensity vi-
brations (1461, 1393, 1314 cm−1 for U-d2 and 1488, 1463, 1327 cm−1 for T-d2) are observed, but unlike T and U,
they are not frequency-characteristic and their mode is determined by the changes in different functional groups.

105