Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832

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Spectrochimica Acta Part A:

Molecular and Biomolecular Spectroscopy
journal homepage: www.journals.elsevier.com/spectrochimica-acta-part-a-
molecular-and-biomolecular-spectroscopy

Computationally assisted vibrational spectroscopy of nucleic acid bases.

2. Thymine
Sergey A. Katsyuba *, Timur I. Burganov
Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia

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

• A cluster model of a solute surrounded

by 30 water molecules allows repro­
ducing experimental Raman spectra of
aqueous thymine.
• B3LYP-D3/def2-TZVP or B3LYP-D3/
aug-cc-pVDZ computations are suffi­
cient for the above purpose.
• The strong effect of water on vibrational
spectra of thymine is mainly a result of
hydrogen bonding with 6 nearest water
molecules.

A R T I C L E I N F O A B S T R A C T

Keywords: As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121–24128], Raman and infrared (IR) spectra of
Liquid aqueous thymine and its N-deuterated derivative, thymine-d2 have been computationally reproduced and
Clusters interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of
Explicit solvation
structure and IR spectra of liquids and solutions [J. Phys. Chem. B, 2020, 124, 6664–6670]. A cluster model of a
DFT
Hydrogen bonding
solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational fre­
Infrared and Raman spectra quencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ sim­
Deuteration ulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman
spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine,
caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water mol­
ecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules
that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be
ascribed to the joined action of solute–solvent and solvent–solvent interactions. Nevertheless, the moderate
number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, sug­
gests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced,
while the effect of bulk water is rather modest.

* Corresponding author.
E-mail address: skatsyuba@yahoo.com (S.A. Katsyuba).

https://doi.org/10.1016/j.saa.2023.123832
Received 16 September 2023; Received in revised form 26 December 2023; Accepted 31 December 2023
Available online 4 January 2024
1386-1425/© 2024 Elsevier B.V. All rights reserved.
S.A. Katsyuba and T.I. Burganov
Fig. 1. B3LYP-D3/def2-TZVP optimized structure and atom numbering
of thymine.
1. Introduction
In a first paper of this series [1] we have reported our results on
computational modeling of vibrational infrared (IR) and Raman spectra
of a member of the family of nucleobases, cytosine, in aqueous solutions.
In this paper we present our results on DNA base thymine (Fig. 1), which
represents a methyl substituted derivative of the structurally simplest
nucleobase, i.e. uracil. The structures and properties of nucleobases are
dependent on their interaction with surrounding water,[2,3,4] which
also strongly affects their vibrational spectra. This makes the Raman and
IR spectra a valuable source of information on aqueous nucleobases and,
at the same time, extremely complicates the spectra interpretation. To
alleviate this task, input is required from quantum chemical calculations
at computational levels that match the experimental resolution and
accuracy. However, in all known computational studies of the vibra­
tional spectra of aqueous thymine, only frequencies [5] and IR in­
tensities[6] were analyzed, though Raman spectra are more suitable
probes of nucleobases in biologically relevant environment, since water
has broader windows of transparency in Raman spectra compared to IR
spectra.
The most probable reason for this situation is that the computation of
the intensities of vibrational bands is very problematic for the condensed
state. Implicit treatment of media effects, e.g. within the framework of
polarizable continuum models (PCM), usually fail with calculations of
intensities of the vibrational bands for the condensed phase.[7,8] Ab
initio molecular dynamics (AIMD) simulations of Raman spectra are
directly applicable to condensed phase systems, but the considerable
computational cost does not allow application of this protocol routinely.
Microsolvated solute structures embedded in a solvation continuum
were used for simulation of IR spectra of aqueous thymine, [6] but the
analogous simulation of the corresponding Raman spectra has not been
attempted.
Recently, we presented an efficient approach to an accurate, fully
quantum–mechanical (QM) modeling of IR spectra of condensed-phase
systems.[8] An automated cluster generation algorithm [9] was
applied to construct an ensemble of explicitly solvated molecular clus­
ters that were re-optimized at a reasonable but efficient level of Density
Functional Theory (DFT). The DFT simulated IR spectrum of the system
often matches the corresponding condensed-phase IR experiment even
better, than the theoretical spectrum of the isolated molecule compared
to the gas-phase IR spectrum. Application of the above protocol to mo­
lecular [10,11] and ionic [12] liquids, and various solutions of
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
structurally flexible compounds,[13] has demonstrated an accuracy of
such IR spectra simulations and efficiency of their use for interpretation
of the corresponding experimental spectra. Recently we estimated
within the framework of our cluster model a limited number of the
liquid-state Raman scattering cross sections, σ, of trans- and gauche-
conformers of 1,2-dichloroethane.[14] This molecule is not able to
pronounced hydrogen bonding (HB) with the solvent. In contrast, HB
effects are quite strong for aqueous nucleobases. Nevertheless, the
application of the same solvation model allowed us to quite satisfactorily
describe the influence of water on both IR, and Raman spectra of cyto­
sine.[1] We have shown that strong changes of frequencies and relative
intensities of Raman and IR bands of cytosine, caused by its hydration,
cannot be completely assigned to influence of HB with 7 or 8 closest
water molecules. They are rather ascribed to the joined effect of sol­
ute–solvent and solvent–solvent HB with participation of at least 30
water molecules separating cytosine from the bulk water. In other
words, we demonstrated that the vibrational modes and the derivatives
of the polarizability and dipole moment of a solute are mainly locally
influenced by its first hydration shell, while the effect of bulk water is
rather modest.
In the present study we intend to test the generality of the above
conclusions in another challenging case of vibrational spectra of
aqueous thymine. Thus, the purpose of our study is twofold: (i) to further
test our computational protocol of simulation of the IR and Raman
spectra of liquid-phase systems in general and, in particular, aqueous
solutions; (ii) obtain a better knowledge of the aqueous thymine struc­
ture and its HB pattern on the grounds of a complete QM-assisted
interpretation of the experimental vibrational spectra.
2. Computations
2.1. Clusters generation
Thymine and its N-deuterated species (thymine-d2) are investigated
in two types of environments: the gas phase, and in aqueous solutions
(H2O for thymine and D2O for thymine-d2). The liquid states are
approximated by a representative ensemble of molecular clusters. In
these clusters, solvation shells around the solute are formed by inter­
action with explicit solvent molecules. Clusters are generated by the
Quantum Cluster Growth (QCG) algorithm [9] with the use of the corre­
sponding QCG program,[15] which, in short, adds solvent molecules
around the solute at energetically favorable positions using an inter­
molecular force field docking algorithm (xTB-IFF).[16] The cluster
generation step is followed by MD simulations of 10 ps length with time
steps of 2 fs at 298 K with the use of the recently developed general force
field GFN-FF.[17] The equilibrated snapshots from the trajectory,
dumped in every 50 fs, are fully geometry optimized at the robust and
fast semi-empirical GFN2-xTB [18] level, forming an ensemble of low-
energy clusters. The cluster of lowest free energy (i.e., including ther­
mostatistical corrections) is used as starting point for the calculation of
IR and Raman spectra in solution. The thermostatistical contributions to
the free energy were obtained by single-point hessian calculations [19]
within the framework of the modified rigid-rotor-harmonic-oscillator
statistical treatment (ΔGmRRHO) [20,21] at the GFN2-xTB/ALPB [22]
level.
For a more accurate treatment of explicit solvent effects on the so­
lute, the GFN2-xTB generated clusters are re-optimized at higher DFT
level. This provides equilibrium geometries that are suitable for stan­
dard harmonic vibrational frequency calculations.
In previous studies [8,10–12] it has been suggested that vibrational
modes and dipole moment derivatives are mainly influenced by their
immediate local surroundings, which also holds for strongly hydrogen
bonded systems. Successful modeling [1] of Raman spectra of cytosine
and cytosine-d3 suggests that the same is true for derivatives of the
polarizability of a solute. The inclusion of the first solvation shell is
deemed to be sufficient to simulate solution phase vibrational spectra
S.A. Katsyuba and T.I. Burganov Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832

Fig. 2. Experimental IR spectra of aqueous solution of thymine [5] (top) and thymine isolated in Ar matrix [34] (bottom) in comparison with the spectrum (red)
computed with B3LYP-D3/aug-cc-pVDZ method for thymine cluster with 11 “heavy” water molecules (mH = mO = 400 aem, see subsection 2.2). In the domain
indicated by an asterisk, the peaks resulting from the subtraction of the water band are not reliable.

with similar accuracy as for individual molecules in vacuum. To find out
whether this applies to aqueous thymine, the cluster size was increased
from 4 to 39 solvent molecules. The number of solvating molecules in
each cluster and Cartesian coordinates of all generated clusters can be
found in ESI.
2.2. Vibrational spectra computation
All DFT calculations were carried out using the Turbomole-7.5.1
program package.[23] Both isolated molecules and the solute–solvent
clusters used in the computation of vibrational spectra were optimized
with two DFT methods: hybrid DFT functional B3LYP-D3 – one of the
best performing DFT methods for the calculation of vibrational fre­
quencies, Raman activities and IR intensities of organic molecules;
[7,24,25] and less computationally demanding GGA functional PBE-D3
[26] successfully used for simulation of Raman spectra of various solu­
tions of 1,2-dichloroethane [14] and IR spectra of aqueous cytosine. [1]
The D3 London dispersion correction in the Becke-Johnson sampling
scheme (indicated by “-D3” appended to the functional name) [27,28]
was used in all cases. B3LYP-D3 and PBE-D3 methods were combined
with double-zeta basis set aug-cc-pVDZ [29] recommended for the
computation of Raman spectra,[30] and triple-zeta basis set def2-TZVP,
[31,32,33] providing good quality of vibrational spectra simulations for
various liquid-state systems.[1,11,14].
For the explicit treatment of solvent effects on the structure and
vibrational spectra of solvated molecules, the generated clusters were re-
optimized at DFT level and harmonic vibrational frequencies and IR and
Raman intensities were calculated for the lowest-energy cluster. Initially
[8] we calculated the IR spectrum of any system, modeled within the
framework of our cluster approach, as a thermodynamic average of the
individual spectra computed for each complete cluster at the DFT level.
Nevertheless, further studies [1,10–14] have shown that the difference
between the spectrum of the lowest-energy cluster and that averaged
from all clusters in the final ensemble is negligible, and hence the

3
S.A. Katsyuba and T.I. Burganov Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832

Fig. 3. Experimental IR spectra of solution of thymine-d2[5] in D2O (top) and thymine-d2 isolated in Ar matrix [35] (bottom) in comparison with the spectrum (red)
computed with B3LYP-D3/aug-cc-pVDZ method for thymine-d2 cluster with 11 “heavy” water molecules (mD = mO = 400 aem, see subsection 2.2). In the domain
indicated by an asterisk, the peaks resulting from the subtraction of the water band are not reliable.

averaging was avoided to minimize computational expenses. The same
turned out to be true for the present case, which is clearly seen in Fig. S1,
where the spectra simulated for the lowest-energy and the second lowest
energy clusters are compared. For comparison with the experiment the
computed frequencies and relative intensities were plotted with a Lor­
entzian broadening (fwhm = 10 cm− 1). To facilitate comparison of the
simulated spectra with the corresponding experimental spectra obtained
after subtraction of the spectrum of water,[5] we separated the spectra
of the solute molecule from the spectra of the surrounding water mol­
ecules. To achieve such separation, the atomic masses of all species in
the cluster, except for the solute, were increased to 400 amu, and thus
their spectra were shifted to the low-frequency region. This strategy only
marginally affects the possible coupling between the vibrational modes
of solvent and solute molecules, and hence insignificantly changes
relative intensities of the solute vibrational bands.[1,8].
3. Results and discussion
3.1. IR and Raman spectra of isolated thymine and thymine-d2
IR spectra of isolated thymine (Fig. S2, ESI) and thymine-d2 (Fig. S3,
ESI) simulated with the use of B3LYP-D3/def2-TZVP, PBE-D3/aug-cc-
pVDZ and B3LYP-D3/aug-cc-pVDZ methods practically coincide with
each other and with experimental IR spectra of thymine [34] and
thymine-d2[35] monomers isolated in Ar matrix. The best agreement
between experimental and computed frequencies of the strongest bands
in the spectral region 600–1800 cm− 1 was achieved after global scaling
of the B3LYP-D3/def2-TZVP theoretical frequencies by 0.981 for
thymine and thymine-d2. The scaling factor of 0.985 was used for
B3LYP-D3/aug-cc-pVDZ computations. Moderate deviations of the fre­
quencies computed with the use of B3LYP-D3 method from their
experimental counterparts do not exceed analogous deviations of the
experimental frequencies of gaseous thymine [36,37] from the fre­
quencies measured for thymine in Ar matrix.[34] Slightly worse
agreement with the experiment for thymine-d2 was provided by PBE-
D3/aug-cc-pVDZ simulations (Fig. S3), in which case the scaling factor
of 1.027 was used.
Similarly to the case of IR spectra simulations, Raman spectra of
isolated thymine (Fig. S4, ESI) simulated with the use of PBE-D3/aug-cc-
pVDZ and B3LYP-D3/aug-cc-pVDZ methods practically coincide with
each other and match experimental Raman spectrum of thymine
monomers isolated in Ar matrix [34] quite well. In contrast, B3LYP-D3/
def2-TZVP calculations (Fig. S4) predict wrong relative intensities for
two strongest bands in the spectral region of 1600–1800 cm− 1, which

4
S.A. Katsyuba and T.I. Burganov
Fig. 4. Experimental Raman spectra of aqueous solution of thymine[5] (top) and thymine isolated in Ar matrix[34] (bottom) and the corresponding simulated
spectrum (red) of thymine cluster with 30 “heavy” water molecules (mH = mO = 400 aem, see subsection 2.2) calculated with B3LYP-D3/def2-TZVP method.
suggests that the choice of basis set is more critical for simulation of
Raman spectra of isolated thymine than the choice of DFT functional.
3.2. IR and Raman spectra of aqueous thymine and thymine-d2
In the cluster simulations of the spectra of aqueous thymine and
thymine-d2, the scaling factors optimized in the course of modeling of
the spectra of isolated thymine species (vide supra) were used without
any changes. Variation of the number of water molecules (n) in cluster
models of solvated thymine produces rather essential changes in the
computed spectra for n = 4, 5 and 6, while the effect of further increase
of n is comparatively moderate (Figs. S5 – S7, ESI). It should be noted
that in all previous applications of our cluster approach,[1,8,10–14] the
number of explicit solvent molecules was steadily increased until the
solute surface was completely covered by the solvent, and this stage was
regarded as the formation of the first solvation shell. In the case of
thymine, its molecule remains only partially covered by water molecules
even in clusters with n = 39: namely, the hydrophobic methyl group of
thymine is not completely shielded from the outside space. Similarly, in
the AIMD simulation [3] of aqueous thymine, the methyl group of the
solute did not form active short contacts with the solvent, despite the
inclusion of 54 water molecules in the model.
In such a situation, we prefer not to define the first hydration shell of
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
thymine, but simply choose the clusters, allowing to obtain spectra best
matching their experimental counterparts. In the case of IR spectra, the
best simulation quality was obtained for clusters containing 11 water
molecules (Figs. 2 and 3). Since a correct comparison with experiment is
hampered by the unreliable subtraction of the strong water bands in the
experimental IR spectra,[5] we can only state that the simulations
reasonably well reproduce the differences in the positions of the stron­
gest experimental IR bands in the spectra of isolated [34,35] and
aqueous [5] thymine.
As water is quite transparent solvent for Raman spectroscopy, and
the experimental Raman spectra of aqueous thymine [5] show many
more peaks than the IR spectra, it was essential to test our cluster
approach on the Raman spectra simulations. The simulated Raman
spectra demonstrated rather moderate dependence on the choice of
basis set, DFT functional, and the size of the cluster for n > 5 (Figs. S6 -
S13, ESI). Nevertheless, similarly to simulation of Raman vibrational
characteristics of aqueous cytosine and cytosine-d3,[1] the best
computed spectra of aqueous thymine and thymine-d2 were obtained
with the use of B3LYP-D3 functional for clusters containing 30 water
molecules (Figs. 4 and 5). In contrast to the case of isolated thymine, the
spectra of the above clusters computed with the use of B3LYP-D3/def2-
TZVP or B3LYP-D3/aug-cc-pVDZ levels of theory were practically equal
in quality. PBE-D3 simulations produced spectra of slightly worse, but
S.A. Katsyuba and T.I. Burganov
Fig. 5. Experimental Raman spectrum (black) of solution of thymine-d2[5] in D2O and the corresponding simulated spectrum (red) of thymine-d2 cluster with 30
“heavy” water molecules (mD = mO = 400 aem, see subsection 2.2) calculated with B3LYP-D3/def2-TZVP method.
still acceptable quality (Figs. S12, S13, ESI).
Thus, the technical outcome of our study is that successful simulation
of Raman spectra of aqueous thymine is possible with the use of B3LYP-
D3 or PBE-D3 levels of DFT in combination with def2-TZVP or aug-cc-
pVDZ basis sets, if 30 water molecules are explicitly modeled,
although even the inclusion of only 6 water molecules in the hydration
shell of the solute allows to obtain spectra of acceptable quality (Figs. S6,
S7, ESI).
Simultaneous good match of experimental liquid-state frequencies
and Raman intensities with the corresponding parameters computed
with the use of our protocol for both thymine in H2O and thymine-d2 in
D2O, strongly suggests good quality of the calculated force constants
and, hence, of the normal modes of aqueous thymine and deuterated
thymine. Figs. 6 and 7 show the pictures of the harmonic normal modes
corresponding to the strongest Raman bands of hydrated thymine and
thymine-d2, respectively, computed for clusters including 11 water
molecules using the B3LYP-D3/aug-cc-pVDZ method.
3.3. The structure of thymine and its hydration shell in aqueous solution
Good match of the simulated and experimental spectra suggests a
close structural correspondence of the hydration shell of the actual
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
aqueous solution of thymine and model clusters thymine:11H2O (shown
in Figs. 6 and 7) or thymine:30H2O. Part of the latter cluster is shown in
Fig. 8 (A), where all water molecules, except those participating in im­
mediate HB with thymine, are omitted for clarity. Fig. 8 (B) also dem­
onstrates the thymine:6H2O structure, representing the minimal-size
cluster allowing to simulate the spectra of aqueous thymine with
reasonable accuracy (Figs. S6 and S7).
The following feature is common for all three structures: each of the
N–H groups of thymine is H-bonded to only one water molecule. This is
fully consistent with the data obtained by AIMD computations, where
aqueous thymine was modeled using periodic boundary conditions for
cubic box containing one thymine molecule and 54 water molecules.
[3,4] As shown in Figs. 6, 7 and 8 (B), C = O groups of thymine form
from one to two H-bonds with water in small clusters comprising 11 and
6 water molecules, respectively. The same result was obtained by Dan­
ilov et al.[38] for the B3LYP/6–31 + G(d) optimized cluster thymi­
ne:11H2O. According to AIMD data,[3,4] an average number of H-bonds
per carbonyl group is about 2, although for certain period of time oxygen
atom of carbonyl group forms three H-bonds in 3D arrangement, similar
to one shown in Fig. 8 (A). This latter fragment comprises 8 water
molecules H-bonded to thymine. A coordination number of thymine in
bulk water environment, averaged along AIMD trajectory,[3,4] amounts
S.A. Katsyuba and T.I. Burganov
Fig. 6. The harmonic normal modes corresponding to the strongest Raman bands shown in Fig. 4 and assigned to in-plane vibrations of aqueous thymine. Hydrogen
bonds are shown with dotted lines.
to 6.42 water molecules. This probably explains why the spectra simu­
lated for clusters, comprising less than 6 water molecules, strongly
deviate from their experimental counterparts (vide supra), whilst simu­
lations for clusters with n ≥ 6 reasonably well match experimental
spectra of aqueous thymine and thymine-d2.
Interaction with surrounding water molecules changes the structure
of thymine itself compared to isolated thymine: e.g., the C = O bonds
lengthen, while C-N bonds shorten (see Table S1, ESI, for details). It
should be noted that changes of bond lengths of thymine upon hydration
presented in Table S1 for cluster thymine:6H2O are closer to the changes
reported for the AIMD [3,4] results, than the corresponding changes
calculated for cluster thymine:30H2O. This suggests that the structural
changes of aqueous thymine relative to the isolated molecule are caused
mainly by a small number (n ≈ 6) of water molecules immediately H-
bonded to thymine. At the same time, the quality of simulated spectra
improves if n is increased to 30. Thus, the Raman spectra of the solute
represent a more sensitive probe of the hydration shell than the structure
of the solute.
4. Conclusions
In this work, the explicit modeling has been used to evaluate the
structure of aqueous thymine, and vibrational frequencies and relative
IR and Raman intensities of bands in its spectra. Difficulties with the
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
subtraction of the water IR bands in the experimental spectra of aqueous
solutions [5] does not allow reliable assessment of quality of our liquid-
state IR spectra simulations, but to reproduce the Raman spectra of
aqueous thymine and thymine-d2 it was sufficient to take into account a
limited number of explicit water molecules. Namely, even inclusion of 6
water molecules in the model hydration shell of thymine allows to
reproduce experimental Raman spectra for this strongly H-bonded spe­
cies fairly well. Further improvement of the simulated spectra of
aqueous thymine, and especially thymine-d2, was achieved for clusters
including 30 molecules of water. Successful computations of not only
the positions of the experimental Raman bands, but also their relative
intensities for both thymine and N-deuterated aqueous species, means
that we were able to correctly model not only the potential energy
surface, but also the derivatives of the polarizability of these systems.
This is in parallel with the outcome of our very recent studies of aqueous
cytosine, [1] and suggests that the vibrational modes and derivatives of
the polarizability of a solute are mainly locally influenced by its im­
mediate environment, while the effect of bulk water is rather modest.
The same was shown earlier for the dipole moment derivatives of
various solutes in a broad set of solvents.[8,10–14] This knowledge not
only improves our understanding of solute–solvent interactions, but also
allows minimization of the computational costs of QM simulations of the
liquid-state vibrational spectra. The successful use for this purpose of
moderate-size basis sets def2-TZVP and aug-cc-pVDZ, both for thymine
S.A. Katsyuba and T.I. Burganov
Fig. 7. The harmonic normal modes corresponding to the strongest Raman bands shown in Fig. 5 and assigned to in-plane vibrations of aqueous thymine-d2.
Hydrogen bonds are shown with dotted lines.
and cytosine, gives hope for affordable cluster computations of
condensed-state Raman spectra of other systems, in particular, aqueous
nucleobases.
Good quality of the Raman spectroscopic characteristics of the hy­
drated thymine, represented within the framework of our approach by
clusters thymine:nH2O with n ≥ 6, especially with n = 30, suggests a
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
close structural correspondence of both the solute and its hydration shell
of the actual aqueous solution of thymine and our model clusters. The
geometry of the central part of these clusters, “thymine + water mole­
cules directly H-bonded to thymine”, practically coincides with
dynamically averaged structure of larger model of aqueous thymine
revealed during the course of AIMD simulations. [3,4] The good
S.A. Katsyuba and T.I. Burganov
Fig. 8. B3LYP/def2-TZVP optimized clusters thymine:30H2O (A) and thymine:6H2O (B); only water molecules forming H-bonds with thymine are shown in (A). H-
bonds are shown with dotted lines.
agreement between the spectroscopic fingerprint of the model structure
and the real liquid-state vibrational spectra can be considered as proof of
the correctness of the structural outcomes of both approaches. The same
good agreement between our cluster and AIMD models, demonstrated
earlier for aqueous cytosine, [1] suggests that our comparatively simple
approach [9] is able to capture the main structural, spectroscopic and
HB features of aqueous nucleobases. Its application to studies of other
representatives of these species is planned for the near future.
CRediT authorship contribution statement
Sergey A. Katsyuba: Conceptualization, Data curation, Formal
analysis, Funding acquisition, Investigation, Methodology, Project
administration, Resources, Supervision, Validation, Writing – review &
editing, Writing – original draft. Timur I. Burganov: Data curation,
Investigation, Visualization, Writing – original draft.
Declaration of competing interest
The authors declare the following financial interests/personal re­
lationships which may be considered as potential competing interests:
Sergey Katsyuba reports financial support was provided by Russian
Science Foundation. Sergey Katsyuba reports a relationship with Russ­
sian Science Foundation that includes: funding grants. If there are other
authors, they declare that they have no known competing financial in­
terests or personal relationships that could have appeared to influence
the work reported in this paper.
Data availability
No data was used for the research described in the article.
Acknowledgement
The financial support of this study by the Russian Science Foundation
(grant 22-23-00970) is gratefully acknowledged. Special thanks are due
to Dr. S. Scpicher for his valuable advice.
9
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 309 (2024) 123832
Appendix A. Supplementary data
Cartesian coordinates of various quantum chemically optimized
clusters explicitly modeling hydrated thymine, the IR and Raman
spectra of various clusters simulated with various DFT functionals and
basis sets are given. This material is available free of charge via the
Internet. Supplementary data to this article can be found online at htt
ps://doi.org/10.1016/j.saa.2023.123832.
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