Spectroscopic identification of 2,4-pyrimidinedithiol; an experimental matrix isolation and ab initio Hartree-Fock and density functional theory study

Article abstract of DOI:10.1016/S1386-1425(97)00278-3

2,4-Pyrimidinedithiol (the dithiol form of 2,4-dithiouracil) was generated by UV (λ > 335 nm) irradiation of the dithione form of 2,4-dithiouracil isolated in low-temperature argon or nitrogen matrices. The IR and UV spectra of the photoproduct are reported. The dithiol form of 2,4-dithiouracil was identified by comparison of the experimental spectrum with the spectrum theoretically predicted for this form at the HF/6-31 (d,p) and DFT(B-3LYP)/6-31 (d,p) levels. This comparison resulted also in assignment of the bands observed in the IR spectrum of 2,4-pyrimidinedithiol to the theoretically predicted normal modes.

Full text of DOI:10.1016/S1386-1425(97)00278-3

Spectrochimica Acta Part A 54 (1998) 685–693
Spectroscopic identification of 2,4-pyrimidinedithiol; an
experimental matrix isolation and ab initio Hartree–Fock and
density functional theory study
a
a,
b
c
Leszek Lapinski , Maciej J. Nowak *, Robert Kołos , J o´ zef S. Kwiatkowski ,
d
Jerzy Leszczy n´ ski
a
Institute of Physics, Polish Academy of Sciences, A1. Lotnikow 32/46, 02-668 Warsaw, Poland
Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44, 01-224 Warsaw, Poland
Institute of Physics, N. Copernicus Uni6ersity, Grudziadzka 5, 87-100 Toru n´ , Poland
Department of Chemistry, Jackson State Uni6ersity, 1400 Lynch Street, Jackson Mississippi 39217, USA
b
c
d
Received 28 October 1997; received in revised form 28 October 1997; accepted 18 November 1997
Abstract
,4-Pyrimidinedithiol (the dithiol form of 2,4-dithiouracil) was generated by UV (u\335 nm) irradiation of the
2
dithione form of 2,4-dithiouracil isolated in low-temperature argon or nitrogen matrices. The IR and UV spectra of
the photoproduct are reported. The dithiol form of 2,4-dithiouracil was identified by comparison of the experimental
spectrum with the spectrum theoretically predicted for this form at the HF/6-31 (d,p) and DFT(B-3LYP)/6-31 (d,p)
levels. This comparison resulted also in assignment of the bands observed in the IR spectrum of 2,4-pyrimidinedithiol
to the theoretically predicted normal modes. © 1998 Elsevier Science B.V. All rights reserved.
Keywords: 2,4-Dihiouracil; 2,4-Pyrimidinedithiol; Photochemistry; Proton transfer; Matrix isolation; Infrared spectra;
UV spectra; Ab initio; Density functional theory
1
. Introduction
the gas phase tautomeric equilibria are frozen
during deposition of the matrix, this technique
has proven to be very useful for the studies of
tautomerism of the nucleic acid bases [1–5].
Along with the ‘normal’ forms of cytosine and
guanine, the ‘rare’ tautomers of these compounds
were found in rare gas low-temperature matrices
[2,3,5,6]. Adenine, uracil and thymine were ob-
served in matrices exclusively in their ‘normal’
tautomeric forms [1,7,8]. An inert, low-tempera-
ture environment can also stabilize the ‘rare’ tau-
The chemical and physical properties of nucleic
acid bases and their derivatives are of continuous
interest. Among numerous experimental methods
the matrix-isolation offers the possibility of inves-
tigation of the bases in conditions in which the
intermolecular interactions are minimized. Since
*
Corresponding author. Tel.: +4822 843 70001; fax:
+
4822 843 0922; e-mail: mjnow@ifpan.edu.pl
1
386-1425/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved.
PII S1386-1425(97)00278-3

6
86
L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
tomeric forms produced photochemically in the
matrix. A UV induced proton transfer from the
nitrogen atom in the heterocyclic ring to the
exocyclic oxygen, changing the oxo form into the
hydroxy tautomer, was discovered in this labora-
tory for 4(3H)-pyrimidinone isolated in low-tem-
perature inert gas matrices [9]. Next, similar
photoreactions were found for matrix-isolated
mal dithione form in a reaction presented in
Scheme 1. This is the first example of a photoin-
duced double proton transfer of the type quoted
above.
The nucleic acid bases with a sulfur atom in-
stead of oxygen in uracil have been a subject of
considerable interest since they were detected in
natural tRNAs [18]. Thiouracil’s derivatives at-
tract attention not only because of their unclear
role in nucleic acid structures but also because of
exhibited pharmacological activities. For example
a series of 1-amino-5-substituted 4-thio or 2,4-
dithio uracil analogues were assayed for anti-
conflict and anestethic activity in rats or mice [19].
2,4-Dithiouracil was found to be a melanoma-
seeking agent owing to its specific incorporation
in nascent melanin [20].
The UV absorption spectra of 2,4-dithiouracil
in water solutions and IR spectra of the com-
pound in DMSO solutions were reported by
Psoda and Shugar [21]. Ultraviolet absorption,
circular dichroism and magnetic circular dichro-
ism spectra of 2,4-dithiouracil in aqueous and
acetonitrile solutions were measured by Igarashi-
Yamamoto et al. [22]. The UV absorption and
phosphorescence spectra of this compound in
EPA glass were collected by Pownall et al. [23].
Phosphorescence and ODMR spectra of 2,4-
dithiouracil were reported by Taherian and Maki
2(1H)-pyridinone [10], 3(2H)-pyridazinone [11]
and cytosine [2]. Similar photoreactions were
subsequently observed for a number of thione
compounds: 2(1H)-pyridinethione [12], 3(2H)-
pyridazinethione [13], 4(3H)-pyrimidinethione [13]
and 2(1H)-quinolinethione [14]. The phototau-
tomeric reactions, listed above, are entirely differ-
ent from those known as ESIPT (excited state
intramolecular proton transfer) processes [15,16].
ESIPT always occurs in systems having proton
donor and acceptor linked by hydrogen bond.
Proton transfer undergoes from excited singlet
state which is placed higher in energy scale than
the respective excited singlet state of the product
(
tautomer). The obtained form (tautomer) is not
stable in the ground state and a back proton
transfer ends ESIPT process. None of this fea-
tures concerns oxo“hydroxy or thione“thiol
phototautomeric reactions mentioned in Refs.
[
2,9–14]. ln these cases no intramolecular hydro-
gen bonds are present. The possibility of existence
of intermolecular hydrogen bonds is excluded
since the phototautomeric reactions were ob-
served only for monomeric, isolated in low-tem-
perature matrices, molecules. The mechanism of
proton transfer is different than that in the case of
ESIPT because the energy of the first excited
singlet state of produced tautomer is higher than
the energy of the first excited singlet state of the
substrate. In low-temperature matrices the pro-
duced enol (or thiol) tautomers are stable and
were detected in their ground states.
[24]. Vibrational spectra of 2,4-dithiouracil in wa-
ter neutral solutions were studied by means of
resonance Raman spectroscopy by Ghomi et al.
[25].
The IR spectra of 2,4-dithiouracil isolated in
low-temperature matrices were previously re-
Up to now the ‘rare’ hydroxy forms of uracil
(
or thymine) and the corresponding ‘rare’ hy-
droxy-thiol forms of thiouracils have never been
obtained by thermal (in the vapour state) or pho-
tochemical population method. The dithiol form
of 2 4-dithiouracil is the first case for which the
‘
rare’ uracil tautomer of them was formed [17].
This tautomeric form was obtained from the nor-
Scheme 1.

L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
687
ported [26–28]. From the analysis of those spectra
it was clear that the compound adopts exclusively
the dithione form while isolated in low-tempera-
ture matrices.
Relative energies of different 2,4-dithiouracil
tautomers were theoretically predicted by
Leszczy n´ ski and Lammertsma at the MP2/6-
31G*//3-21G(*) level with inclusion of zero-point
energy corrections [29]. The dithione tautomer
was found to be the most stable structure and the
difference with the dithiol tautomer was predicted
−
1
to be as high as 28 kJ mol
.
Scheme 2. Atom numbering for: 2,4-pyrimidinedithiol.
density functional theory with the Becke’s three-
parameter exchange functional and gradient-cor-
rected functional of Lee, Yang and Parr
2
. Experimental section
The 2,4-dithiouracil used in this study was
(
DFT(B3-LYP)) [31]. In the calculations a split-
kindly made available to us by Professor D.
Shugar (Warsaw). The compound was heated in a
microoven placed in the vacuum chamber of the
cryostat. The vapors of 2,4-dithiouracil were de-
posited, together with large excess of argon, on a
CsI (or sapphire for UV spectroscopy) window
cooled to 10 K. The matrix gases argon and
nitrogen of the spectral purity were supplied by
Linde AG, and Technische Gase (Berlin, Ger-
many), respectively. The infrared spectra were
recorded with a Perkin-Elmer 580B grating spec-
trometer or with FTIR spectrometer Nicolet 170
SX. Integral intensities of the IR absorption
bands were measured by numerical integration.
UV absorption spectra were taken using a 480
mm focal length monochromator (Digikroem
valence basis set augmented by a set of six d
functions on heavy atoms and three p functions
on hydrogens (the 6-31G(d,p) basis set) was used
[30]. The HF and DFT(B3-LYP) approaches were
used to predict the harmonic vibrational
wavenumbers and absolute intensities at the cor-
responding optimized geometries of the molecule.
All quantum-mechanical calculations were per-
formed using the GAUSSIAN 92/DFT program
[32]. Note that the DFT-optimization was carried
out with the options Opt=Tight and Int=Fine-
Grid, and the vibrational calculations were done
with the option Int=FineGrid.
The predicted vibrational wavenumbers were
scaled down by a single factor of 0.98 or 0.9 in the
case of DFT(B3-LYP) or HF calculations, respec-
tively (to correct for systematic shortcomings of
the quantum-mechanical methodology, mainly to
correct for anharmonicity). The theoretically cal-
culated force constant matrices in Cartesian coor-
dinates were transformed to molecular internal
coordinates in order to enable standard potential
energy distribution (PED) analysis [33] of the
normal modes. The internal coordinate set used in
the PED calculation is the same as that used in
Ref. [25], except for the coordinates associated
with the SH group (the SH stretching (wSH),
in-plane bending (iSH) and out-of-plane tor-
sional (~SH) modes). These coordinates were
defined in a standard way, the same as that
480), deuterium lamp and Philips XP2020 photo-
multiplier. The signal was registered in the single
photon counting mode.
Matrices were irradiated with the light from the
high pressure mercury lamp HBO 200 fitted with
a water filter and a cut-off filter (WG 335) trans-
mitting the light with u\335 nm. The time of
irradiation was 1 h.
3. Computational details
The geometry of planar dithiol form of 2,4-
dithiouracil (Scheme 2) was optimized at the ab
initio Hartree–Fock (HF) [30] level and using the

6
88
L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
Table 1
Experimental wavenumbers ( w˜ ), integral intensities (I) and theoretically calculated wavenumbers, absolute intensities (Ath) and
potential energy distribution (PED) of the absorption bands of 2,4-pyrimidinedithiol
Experimental
Ar matrix
Calculated
Calculated
N2 matrix
DFT/6-31G(d,p)
HF/6-31G(d,p)
−
1
w˜ cm−1 I rel.
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ cm
I rel
3
3
163
112
1
20
w C5H (97)
w C6H (97)
3061
3023
2
23
w C5H (95)
w C6H (95)
Â
Ã
2
2
2
617
614
610
Ã
Ì
Ã
2615Â
Á2657
Í
0.4
0.1
w S8H (100)
w S10H (100)
2632
2631
0.4
0.8
w S8H (100)
w S10H (100)
1
5
Ì
24
2
2
603
599
2602Å
Ä2647
Ã
Å
1
1
627
586
10
3
1628
1599
14
3
1
1
1
1
557
554
545
542
416
1556
1543
444
1574
1551
337
w C5C6 (33),
i C6H (17),
w C6N1 (15),
w N3C4 (13),
w C2N3 (10)
1600
1577
454
w C5C6 (30),
w C6N1 (15),
i C6H (15),
w C2N3 (14),
w CN3C4 (13)
1
1
1
530
526
521
57
1529
1524
69
168
132
w C4C5 (34),
w N1C2 (16),
w C6N1 (12),
w C5H (10)
268
w C4C5 (27),
w N1C2 (24),
w N3C4 (13),
w C6N1 (12)
1
450
4
1448
6
1
1
1
1
421
417
413
399
1423
1415
164
146
1422
i C6H (29),
i C5H (26),
w N3C4 (23),
w N1C2 (15)
1438
1354
130
276
i C5H (31),
i C6H (23),
w N3C4 (20),
w N1C2 (12)
1
335
202
6
1335
1271
202
7
1347
1239
197
30
w C2N3 (42),
i C6H (20),
i R1 (13)
w C2N3 (41),
i C6H (21),
w C6N1 (11)
1
265
260
w N1C2 (32),
1
w N3C4 (24),
w C6N1 (13)
1
230
78
i C6H (23),
i R1 (22),
w N1C2 (21),
w C2S (13)
1
1
224
222
1233
1224
99
112
1220
103
w C6N1 (20),
i R1 (19),
1
216
i C6H (18),
w C2N3 (13),
w C2S (11)
1
176
48
w C4C5 (18),
i R1 (16),
w C4S (14),
w C5C6 (13),
w N3C4 (12),
i C6H (11)

L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
689
Table 1 (Continued)
Experimental
Ar matrix
Calculated
Calculated
N2 matrix
DFT/6-31G(d,p)
HF/6-31G(d,p)
−
1
w˜ cm−1 I rel.
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ cm
I rel
"
1
1
1
185
181
177
1187
1185
1180
24
38
73
1173
1103
57
w C4C5 (23),
i R1 (20),
w C4S (14),
w C5C6 (12)
1
116
076
3
w C6N1 (33),
i C5H (26),
w N3C4 (18)
1
101
3
1101
3
5
i C5H (48),
w C5C6 (25),
w C6N1 (10)
1
26
w C5C6 (38),
i C5H (17),
w C4C5 (11)
9
77
75
0.1
k C6H (93),
k C5H (20)
1017
982
0.1
k C6H (95),
k C5H (17)
9
0.4
i R1 (43),
3
i R1 (42),
w N1C2 (12),
w C2N3 (11),
w N3C4 (11),
w C6N1 (10)
w C6N1 (12),
w C2N3 (12),
w N1C2 (10)
9
61
3
9
8
14
94
1
i S8H (59),
i S10H (26)
931
3
i S8H (75)
9
9
8
12
00
71
4
5
6
909
886
3
5
21
i S10H (62),
i S8H (29)
912
826
25
27
i S10H (78),
i S8H (10)
Á 813
17
81
k C5H (87),
k C6H (13)
k C5H (89),
k C6H (11)
Ã
Í
Ã
8
8
8
24
15
06
826
817
809
104
78
Ä 810
i R2 (23),
i R3 (20),
w C2S (19),
w C4S (19)
814
60
i R2 (21),
w C2S (20),
i R3 (20),
w C4S (19)
7
6
71
89
4
772
689
3
771
683
7
~ R1 (82),
k C2S (19)
787
679
19
19
~ R1 (78),
k C2S (21)
22
22
20
i R3 (44),
i R2 (24),
w C4C5 (10),
w C4S (10)
i R3 (43),
i R2 (24),
w C4C5 (11),
w C4S (10)
606
0.7
k C4S (45),
k C2S (37),
616
1
k C4S (44),
k C2S (35),
~ R2 (17)
~
R2 (16)

6
90
L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
Table 1 (Continued)
Experimental
Ar matrix
Calculated
Calculated
N2 matrix
DFT/6-31G(d,p)
HF/6-31G(d,p)
−
1
w˜ cm−1 I rel.
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ † cm−1 Ath km mol−1 PED (%)
w˜ cm
I rel
434
1
w C2S (42),
i R2 (26),
i R3 (18)
434
1
w C2S (41),
i R2 (27),
i R3 (18)
429
0.6
~ R3 (62),
k C2S (14),
436
2
~ R3 (63),
k C2S (12),
~ R2 (12),
~
R2 (11)
~
R1 (10)
4
02
0.1
6
w C4S (41),
k C2S (17),
i R2 (16)
402
0.5
7
w C4S (39),
w C2S (17),
i R2 (16)
3
47
14
6
346
6
343
i C2S (45),
i C4S (44)
343
305
i C2S (45),
i C4S (43)
3
17
13
~ S8H (94)
20
~ S8H (99)
Á
3
13
Í
Ä294
36
1
~ S10H (94)
258
182
37
1
~ S10H (99)
1
84
i C2S (44),
i C4S (44)
i C4S (45),
i C2S (43)
1
65
0.2
~ R3 (38),
k C4S (34),
170
164
0.3
~ R2 (40),
~ R3 (31),
k C4S (27)
~
R1 (15),
k C2S (12)
1
55
2
~ R2 (79),
k C2S (18)
2
~ R2 (38),
k C2S (33),
~
R1 (13)
a
Theoretical positions of absorption bands were scaled: for DFT calculations by a factor 0.98 and for HF by 0.9. PED’s lower than
0% are not included.
1
Abbreviations: I, internal absorbances of IR bands normalized in such a way that the observed intensity sum of all assigned bands
th
is equal to the calculated (at the DFT(B3-LYP)/6-31G(d,p) level) intensity sum of the corresponding bands. A , calculated
intensities; rel, relative; w, stretching; i, bending in-plane; ~, wagging; k, bending out-of-plane.
applied in Refs. [12,14]. The contributions to the
PED values of less than 10% (Table 1) are not
included.
The spectra resulting after 1 h of UV (u\335
nm) irradiation of the matrix are shown in Fig.
1B. The remarkable feature of the spectra of the
photoproduct is the absence of any absorptions in
the high frequency region, in which for the spectra
of the dithione form the bands due to NH stretch-
ing vibrations were present. At 2610 and 2603
4. Results and discussion
−
1
cm
(Fig. 1B and 2) a weak absorption band,
The survey IR spectra of 2,4-dithiouracil iso-
split into several components, due to SH stretch-
ing vibrations was observed in the spectrum col-
lected after UV irradiation of the matrix. In this
spectral region no bands due to other vibrations
lated in the Ar matrix are presented in Fig. 1A.
These spectra are identical with those previously
reported [26].

L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
691
Fig. 1. The infrared spectra of 2,4-dithiouracil isolated in Ar matrix; (A) before irradiation, (B) after UV (u\335 nm) irradiation
of the matrix.
are expected, and that is why the assignment of
the observed spectral feature to wSH vibrations
seems reliable. The other vibrations of SH groups
give rise to the bands of even lower intensity. The
bands due to torsional vibration of SH groups
The UV absorption spectra of 2,4-dithiouracil
isolated in Ar matrix are shown in Fig. 4. These
spectra are quite similar to those of the compound
in the EPA glass [23], water solution [21,22,25]
and to the spectra of 2,4-dithiouracil in the gas
phase [37]. The maximum of the strong band due
to the yy* transition is placed at 276 nm. At
longer wavelengths a weaker band is observed in
which the vibrational structure may be seen. The
−
1
expected near 300 cm
could only be traced in
an Ar matrix. For other thiol heterocyclic com-
pounds the usually weak ~SH bands were ob-
served only in very few cases [12–14,34–36]. Also
in thiol compounds the bands due to SH bending
in plane vibration are very weak and were rarely
detected in IR matrix spectra [12–14,34–36].
Comparison of the experimental spectrum of
the photoproduct with the spectrum theoretically
predicted (at the DFT(B-3LYP)/6-31G(d,p) and
HF/6-31G(d,p) levels) for the 2,4-pyrim-
idinedithiol structure is shown in Figs. 2 and 3. A
good overall agreement between these spectra is
clearly seen. The most intense bands in the exper-
imental spectrum (1530, 1413, 1335, 1222, 1177
−
1
and 815 cm ) have their well predicted counter-
parts in the spectra theoretically calculated at
both DFT and HF levels. The lack of any high or
medium intensity bands in the ranges 1100–800
−
1
−1
cm
and 600–300 cm
is a further similarity
between experimental and theoretical spectra.
The frequencies and intensities of the bands
observed in the experimental spectrum of the pho-
toproduct are collected in Table 1 together with
those of the IR bands theoretically predicted for
the 2,4-pyrimidinedithiol structure. The proposed
assignment is also shown in this table.
Fig. 2. The 2700–2550 cm−1 region (where the bands due to
wSH vibration are expected) of the infrared spectrum of 2,4-
pyrimidinedithiol: (A) isolated in N matrix; (B) isolated in Ar
2
matrix; (C) isolated in Ar matrix (high resolution FTIR mea-
surement); (D) the bands due to wSH vibrations theoretically
calculated at the DFT(B3-LYP)/6-31G(d,p) level; (E) calcu-
lated at the HF/6-31G(d,p) level.

6
92
L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
ably. In comparison with the initial spectrum the
bands in the spectrum recorded after UV irradia-
tion are observed (Fig. 4) at shorter wavelengths
(
227, 287 and 299 nm for the two maxima and a
long wavelength end, respectively). The studies
38] of the UV spectra of thio-derivatives of
[
pyridine and pyrimidine in the gas phase indicate
that the long wavelength (ꢀ350 nm) band is
characteristic for the thione tautomer, while no
absorptions are present at these wavelengths in
the spectra of the thiol tautomer. Hence, the effect
observed in the present work is in agreement with
what one can expect assuming a dithione“dithiol
photoreaction.
5
. Conclusion
Fig. 3. (A) The infrared spectrum of 2,4-pyrimidinedithiol
isolated in N2 matrix; (B) isolated in Ar matrix; (C) IR
spectrum of 2,4-pyrimidinedithiol theoretically calculated at
the DFT(B3-LYP)/6-31G(d,p) level; (D) calculated at the HF/
The following reasons allow for a conclusion
that the photoproduct of the UV irradiation of
,4-dithiouracil is dithiol form of the
compound:
2
a
6
-31G(d,p) level.
“
appearance of the bands due to SH stretching
in the spectrum after irradiation;
the overall agreement between the observed IR
spectrum of the photoproduct and the theoreti-
cal predictions;
long wavelength end of this band is at 379 nm.
After UV irradiation of the matrix, with the light
“
(
u\335 nm) from the high pressure mercury
lamp, the UV absorption spectra change consider-
“
“
similar thione“thiol photoreactions were pre-
viously observed though for single proton
transfer only;
the UV spectra of the photoproduct are in
agreement with the spectra of other thiol hete-
rocyclic compounds.
Acknowledgements
This study has been supported at Warsaw by
the European Union grant No. CIPA-CT 93-
0
108; at Torun by the internal grant of the Insti-
tute of Physics, and at Jackson by the NIH grant
cS06-GM08047 and by the contract (DAAL 03-
8
9-0038) between the Army Research Office and
the University of Minnesota for the Army High
Performance Computing Research Center under
the auspices of the Department of the Army
Research Laboratory cooperative agreement num-
Fig. 4. The UV absorption spectra of 2,4-dithiouracil isolated
in Ar matrix; (A) before irradiation, (B) after UV (u\335 nm)
irradiation of the matrix, (C) expanded fragment of the spec-
trum before irradiation recorded using Xe lamp as a light
source.
ber
DAAH04-95-2-0003/contract
number

L. Lapinski et al. / Spectrochimica Acta Part A 54 (1998) 685–693
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