ORI GI NAL RESEARCH

Structural behavior of sugar radicals formed by proton transfer

reaction of deoxycytidine cation radical: detailed view from NBO
analysis
Marjan Jebeli Javan

Zahra Aliakbar Tehrani

Alireza Fattahi
Received: 25 June 2011 / Accepted: 27 December 2011 / Published online: 17 January 2012
Springer Science+Business Media, LLC 2012
Abstract The cation radicals of DNA constituents gen-
erated by the ionizing radiation initiate the alteration of the
bases, which is one main type of cytotoxic DNA lesions.
These cation radical spices are known for their role in
producing nucleic acid strand break, and it is important to
identify the cation radical formation at particular atomic
site in these molecules so that the major pathway for the
nucleic acid damage may be trapped. In the present study,
we explored theoretically energetic, structural, and elec-
tronic properties of the possible radicals formed via proton
atom abstraction at various sites of sugar part of deoxy-
cytidine cation radical by employing density functional
theory at B3LYP/6-311??G (d,p) level. The computation
revealed 0.022.6 kcal/mol energy disparity in these radi-
cals. Radical-centered carbon increases the extent of
bonding with its adjacent atoms. This tendency should be
important in predicting the reactivity of sugar-based radi-
cals. Based on DFT calculations, sugar radicals of deoxy-
cytidine have following stability order: raH1
0
[raH2
0
[
raH4
0
[raH3
0
[raH5
0
[raO5
0
H[raO3
0
H. Furthermore,
inuence of cation radical formation on acidities of mul-
tiple sites in deoxycytidine nucleosides was investigated.
For instance upon cation radical formation, DH
acidity
of
O3
0
H and O5
0
H sites of deoxycytidine varies from 348.6
and 351.5 to 228.8 and 227.5 kcal/mol, respectively.
Keywords Deoxycytidine Cation radical Hydrogen
atom abstraction Sugar puckering mode NBO analysis
Introduction
In biological system, ionizing radiation causes several
deleterious effects including reproductive cell death,
mutagenesis and transformation. These affects are mainly
dues to damages induced in cellular DNA, which is
believed to be the prime target for the action of ionizing
radiation [13]. Radiation damages in DNA and RNA
occurs by direct or indirect action of high-energy photons
or electrons on the nucleobase and, to a lesser extent,
carbohydrate residues [4]. In the direct mechanism, the
nucleobase is ionized by the radiation to form a cation
radical [4, 5].
Carbon-centered neutral sugar radicals in the DNA
deoxyribose backbone are known to lead to single strand-
ing breaks in DNA. These lesions are among the most
serious of DNA damages. Elucidation of the production
and nature of DNA sugar radicals is, therefore, critical to
understanding their damaging effects in DNA. The
deoxyribose radical formed by hydrogen atom loss at the
C1
0
position is known to result in an alkali-labile stranding
break, whereas the C3
0
, C4
0
, and C5
0
sugar radicals can lead
to frank strand breaks [68]. It was recently reported that
irradiation of DNA by a high-energy Argon ion-beam [9]
(high linear energy transfer, LET, radiation) produced a far
greater yield of sugar radicals than was found by c-irradi-
ation (a low LET radiation). Since these sugar radicals
were formed predominantly along the ion track, where
excitations and ionizations are in proximity, it was pro-
posed that excited-state cation radicals could be the pre-
cursors of the neutral sugar radicals [10, 11].
Shukla et al. [12] reported the formation of sugar radi-
cals on photoexcitation of guanine cation radical (G
?
) in
DNA. They proposed that excitation of guanine cation
radical results in delocalization of a signicant fraction of
M. Jebeli Javan Z. Aliakbar Tehrani A. Fattahi (&)
Department of Chemistry, Sharif University of Technology,
P.O. Box 11365-9516, Tehran, Iran
e-mail: fattahi@sharif.edu
1 3
Struct Chem (2012) 23:11851192
DOI 10.1007/s11224-011-9942-5
the spin and charge onto the sugar moiety to form a tran-
sient sugar cation radical that undergoes rapid deprotona-
tion resulting in a neutral sugar radical. This conversion
was found to be in high yields (50% in DNA and 80100%
in model systems) [9, 12, 13].
Several recent studies [1418] have validated the
mechanism of this reaction that visible photoexcitation of
G
?
(in dGuo) [13] and one-electron-oxidized adenine in
dAdo [14] in aqueous glassy systems lead to formation of
sugar radicals C5
0
and C3
0
as well as some C1
0
. Phosphate
groups at 3
0
or 5
0
were found to deactivate that site toward
sugar radical formation and as a consequence only C1
0
was
found in DNA, whereas C1
0
, C3
0
, and C5
0
were all found in
deoxyguanosine [9, 13]. Moreover, it was found that one-
electron oxidized adenine (A(H)

) in deoxynucleosides
and deoxynucleotides also is readily converted by visible
light to sugar radicals in almost complete conversion to
sugar radicals, predominantly C5
0
radical with a small
contribution of C3
0
radical with the C5
0
radical being the
most abundant [9].
Furthermore, numerous investigations have revealed
that the cation radical formed by electron loss from DNA
migrate a long distance through the DNA duplex by a
hopping mechanism [1924]. Intrabase-pair proton transfer
processes have been proposed to slow or stop by excess
electron transfer through the helix and thereby act as a
crucial restriction on such spin and charge transfer [19, 25
28]. Such proton transferred processes will strongly depend
on the pK
a
of the nucleobase ion-radical involved. The pK
a
values of cation radicals were found to be invariably lower
than those of parent compounds. For example, the pK
a
of
guanine (N1H) is reported as 9.6, whereas the corre-
sponding pK
a
of the guanine cation radical (G
?
) in H
2
O at
ambient temperature is about 3.9 [25, 29].
Moreover, the gas phase represents a suitable reference
medium in which the reaction energetic can be established
without solvent effects and other interferences. There have
been recent reports on ionmolecule reactions of gas-phase
nucleobase cation radicals with several neutral counterparts
and neutral nucleobases with gas-phase cation radicals that
showed electron and proton transfer as well as radical
addition reactions. Since mass spectrometry technique is a
powerful experimental method for determination of ther-
mochemical values for ions and neutral compounds,
examinations of the intrinsic (solvent-free) reactivity of
cation radical species using this technique are valuable
[3033].
In this paper
1
we examine the chemistry nature of the
deoxycytidine (dC) cation radicals as the basic components
of DNA by using quantum chemical calculations. Scheme 1
displays the atom numbering and chemical structure of
neutral deoxycytidine. Structure, geometry (including
puckering and conformation changes of furanose ring) and
electronic properties of deoxycytidine cation radicals were
investigated employing B3LYP exchangecorrelation
functional with 6-311??G (d,p) orbital basis sets. Because
of the cationic and radical nature of deoxycytidine cation
radical, its ionmolecule reactions may involve electron,
proton, hydride, hydrogen atom, or larger radical transfer.
Consequently, we explored energetic and structural proper-
ties of the possible carbon-centered radicals formed via
proton transfer at various sites of sugar part of deoxycytidine
cation radical. Furthermore, the inuence of cation radical
formation on the acidities of multiple sites in deoxycytidine
nucleoside was examined.
Theoretical method
Initial searches of minima on the potential energy surface
for deoxycytidine cation radicals and radicals resulting
from proton transfer reaction at the relative energy range of
10 kcal/mol were carried out using the MMFF force eld
with the Spartan software [34]. The most stable conformers
were optimized by DFT method using the Beckes [35, 36]
hybrid functional (B3LYP) and the 6-311??G (d,p) basis
set. Spin-unrestricted calculations (UB3LYP) were used
for open-shell systems. Harmonic frequency analysis
characterized the optimized structures as local minima (all
frequencies are real) or rst order saddle points (one
imaginary frequency). Vibration frequencies were used to
correct all calculations to 298.15 k.
To analyze the distribution of the unpaired electron,
molecular orbitals, spin density, and atomic charges, the nat-
ural bond orbital (NBO) were determined using 6-311??G
(d,p) orbital basis set. In this context, a study of hyperconju-
gative interactions has been completed. Hyperconjugation
Deoxycytidine
Scheme 1 Schematic diagram showing atom numbering scheme of
deoxycytidine nucleoside. The letters a and b are used to distinguish
between hydrogens linked to the same atom
1
Presented in the proceeding of the spring 2010 meeting of the ACS
division of Carbohydrate Chemistry.
1186 Struct Chem (2012) 23:11851192
1 3
may be given as a stabilizing affect that arises froman overlap
between the BD
*
orbital and the half-lled P orbital of the
radical center. The NBO analysis reveals hyperconjugation
interaction. This non-covalent bondingantibonding interac-
tion can be quantitatively described in terms of the NBO
approach which is expressed by using the second-order per-
turbation interaction energy (E
(2)
) [3741]. This energy rep-
resents the estimate of the off-diagonal NBO Fock matrix
elements. It could be deducted from the second-order pertur-
bation approach [41]:
E
2
DE
ij
q
i
Fi; j
2
e
j
e
i
;
where q
i
is the donor orbital occupancy, e
i
; e
j
are diagonal
elements (orbital energies) and F(i, j) is the off-diagonal
NBO Fock matrix element.
Results and discussion
Geometrical aspects of deoxycytidine cation radical
The molecular geometry of deoxycytidine can be discussed
in terms of the following structural units: (1) cytosine
ring (2) furanose ring conformation or pseudorotation angle
(P angle) which represents, the puckering amplitude of
pseudorotation of the sugar ring. The furanose ring puck-
ering can be described using the terms endo and exo which
refer to the displacement of an atom above or below the
mean plane of the ring. (endo: on the same side as C5
0
atom, exo: on the opposite side). The following equation
calculated this value: (when m
2
is negative one should add
180 to the calculated value of P) [42, 43].
tanP
m
4
m
1
m
3
m
0

2m
2
sin 36 sin 72
where m
i
is dihedral angles i.e., m
0
= C4
0
O4
0
C1
0
C2
0
,
m
1
= O4
0
C1
0
C2
0
C3
0
, m
2
= C1
0
C2
0
C3
0
C4
0
, m
3
= C2
0

C3
0
C4
0
O4
0
, and m
4
= O3
0
C4
0
O4
0
C1
0
. (3) The glyco-
sidic bond connecting these units. The glycosyl torsion angle
v is dened as v = O4
0
C1
0
N1C2 in pyrimidine nucleo-
sides and as v = O4
0
C1
0
N9C4 in purine nucleosides,
allowing the orientation of the base with respect to the sugar
to be determined. (4) Rotation around the C4
0
C5
0
bond
leads to three possible conformers: gauche-trans (gt),
trans-gauche (tg), and gauchegauche (gg) (Scheme 2)
concerning the intramolecular hydrogen bonds involving
hydroxyl groups. Their orientations depend on the endo or
exo character of the ribose part and on the nature of the
possible interaction of hydroxyl group with the cytosine
heterocycle.
The rst step was to identify the minima on the con-
formational potential energy surface for deoxycytidine and
its ionized form starting form several low-lying confor-
mations. The optimized structures of neutral deoxycyti-
dine, its cation radical form obtained at B3LYP/6-311??G
(d,p) level of theory are sketched in Fig. 1, which high-
lights the most interesting structural features. The lowest
energy conformer in neutral deoxycytidine is C2
0
-endo/syn
which consists of two (1.834 A

) O2HO5
0
and
O4
0
HO5
0
(2.782 A

) intramolecular hydrogen bonds. The

syn orientation of the base unit with respect to the sugar
unit is strongly stabilized by formation of the intramolec-
ular hydrogen bond with participation of the O2HO5
0
group [4451]. As seen in Fig. 1, the obvious geometrical
variations during cation radical formation involve struc-
tural features in hydrogen bonding. In fact cytosine base
unit should turn around the glycosyl linkage to make for-
mation of cation radical and consequently cleavage of
intramolecular O2HO5
0
hydrogen bond in neutral
deoxycytidine molecule.
The adiabatic ionization energy (AIE or IE
a
) was pre-
dicted as the difference between the total energy of the
appropriate neutral and cation radical at their respective
optimized geometries (i.e., AIE = E
cation radical
- E
neutral
).
The B3LYP/6-311??G (d,p) adiabatic ionization energy of
the deoxycytidine (8.3 eV) exhibits substantial decrease as
compared to the cytosine nucleobase 8.6 eV [52]. The
decrease of the AIP from cytosine nucleobase to deoxycyt-
idine nucleoside amounts to 0.3 eV, demonstrating the
addition of deoxyribose to cytosine nucleobase decreases the
ionization potential. The relatively high ionization energy of
neutral deoxycytidine (8.3 eV) makes the cation radical a
reactive species for charge-transfer ionization of neutral
molecules as well as cytosine nucleobase.
Abstraction of proton at various sites of deoxycytidine
cation radical leads to neutral radicals which may capture
electrons, forming closed shell anions. To differentiate the
reactivity of radicals formed at deoxycytidine cation radi-
cal, a number of atomic sites are arbitrarily chosen for
generating radicals. Two types of free radicals may be
found by hydrogen abstraction: carbon centered and oxy-
gen centered radicals. For simplication, the following
notations are adopted in this article to better clarifying
geometries and energetic aspects of radicals: The carbon
and oxygen centers (i.e., C1
0
H, C2
0
H, C3
0
H, C4
0
H,
C5
0
H, O3
0
H and O5
0
H) chosen for generating radical on
H
OH H
H
C
3
O
H
H HO
H
C
3
O
OH
H H
H
C
3
O
gt tg gg
Scheme 2 Denition of three possible rotamers about C4
0
C5
0
bond
Struct Chem (2012) 23:11851192 1187
1 3
deoxycytidine cation radical are simplied as raH1
0
,
raH2
0
, raH3
0
, raH4
0
, raH5
0
, raO3
0
H, and raO5
0
H,
respectively. For example, raH1
0
and raO2
0
H radicals
show that proton abstraction occurred through C1
0
and O2
0
atoms of deoxycytidine cation radical, respectively.
Stability and energetic aspects of deoxycytidine sugar
radicals
The optimized structures of the most stable conformers of
various radicals of deoxycytidine are depicted in Fig. 2
which highlights the most interesting structural features.
For an easier characterization of stability of radicals and
comparison geometrical changes after radical formation,
absolute energies (E in a.u), relative energies (DE in kcal/
mol), dipole moments (l in Debye), and relevant optimized
parameters for radicals of deoxycytidine were calculated at
B3LYP/6-311??G (d,p) level of theory which are shown
in Table 1. Bulk solvation effects were included in the
series of single-point energy calculations on the optimized
structures obtained from gas phase, through the integral
equation formalism of the polarized model (IEF-PCM)
[53]. The dielectric constant e = 78.4 was employed to
model aqueous solution. The aqueous solvation effects on
the stability order of these radicals are given in parentheses
as shown in Table 1. Results of calculation performed at
solution phase revealed that the stability order of deoxy-
cytidine radicals is the same in comparison with that in gas
phase. However, the energy gap and relative stability pre-
dicted by these methods are different.
As shown in Table 1, energies of deoxycytidine sugar
radicals are spread over a range of 23 kcal/mol. One gen-
eral trend is that radicals produced on the carbon center are
more stable than those produced on oxygen center. Struc-
ture raH1
0
from Fig. 2 is the most stable ribose radicals of
deoxycytidine from an energetic point of view. This radical
is stabilized by C = OO2
0
H hydrogen bond which sig-
nicantly weakened during radical formation as compared
with free deoxycytidine (for comparison see Figs. 1, 2).
As demonstrated by DE values reported in Table 1, for
deoxycytidine sugar radicals the energetic gap among the
most stable conformer (raH1
0
) and structure raH4
0
is only
about 1.9 kcal/mol. Geometry optimization of raH4
0
, leads
to the formation of O3
0
HO5
0
hydrogen bond with the
length 2.206 A

. On DFT calculation, raH4

0
is followed by
raH3
0
, raH5
0
, and raH2
0
radicals. They are located at 4.8,
6.9, and 11.5 kcal/mol above raH1
0
, respectively. It is
worth to mention that the C4
0
sugar radical (i.e., raH4
0
) is
probably one of the most important DNA damaged radicals
due to its central role in the fabrication of detrimental
strand break.
The NBO analysis reveals that hyperconjugation inter-
action between the half-lled P orbital of the radical center
and the r* orbital of sugar or nucleoabse parts in radicals
can take place. For raH1
0
radical center of deoxycytidine
stabilizing interactions are as follow: n
(1)C1
0 ? r*
C2
0
H2
0
(4.3 kcal/mol), n
(1)C1
0 ? r*
C3
0
O3
0 (5.1 kcal/mol), and n
(1)C1
0 ? r*
N1C2
(6.0 kcal/mol). The most important
hyperconjugation interaction that stabilizes raH4
0
radical,
which corresponds with removal of the hydrogen atom at
the C4
0
position of sugar part of deoxycytidine, are n
C4
0 ? r*
C2
0
C3
0 (2.3 kcal/mol), n
C4
0 ? r*
C3
0
C4
0
Fig. 1 Optimized geometries at B3LYP/6-311??G(d,p) level of
theory for neutral and cation radical forms of deoxycytidine
raH1' raH2'
raH3' raH4'
raH5' raO3'H
raO5'H
Fig. 2 The optimized structures of the most stable conformers of
sugar radicals resulted from proton transfer reaction of deoxycytidine
cation radical calculated at B3LYP/6-311??G (d,p). Bond lengths
are in angstrom
1188 Struct Chem (2012) 23:11851192
1 3
(19.2 kcal/mol), and n
C3
0 ? r*
C3
0
O3
0 (3.2 kcal/mol). In
radical raH3
0
, which corresponds with removal of the
hydrogen atom at the C3
0
position of sugar part of deox-
ycytidine, the important interactions between half lled
(donor) Lewis type NBOs and empty (acceptor) non-
Lewis NBOs are n
C3
0 ? r*
C2
0
-C3
0 , n
C3
0 ? r*
C2
0
H2
0 , and
n
C3
0 ? r*
C3
0
-O3
0 with charge-transfer energy values of 9.7,
3.5, and 19.1 kcal/mol, respectively.
The two least stable radical species raO5
0
H and raO2
0
H
are 15.9 and 22.6 kcal/mol higher in energy than raC1
0
H.
To examine the lifetime of raO5
0
H and raO3
0
H radicals,
the AEA of these radicals have been evaluated at B3LYP/
6-311??G (d,p) level of theory. These values were found
to be: radical O3
0
H = 3.0 eV and radical O5
0
H = 2.9 eV.
On NBO analysis the most important delocalization inter-
actions of raO3
0
H radical are n
O3
0 ? r*
C2
0
C3
0 (2.6 kcal/
mol) and n
O3
0 ? r*
C3
0
C4
0 (6.4 kcal/mol) while in
raO2
0
H radical delocalization interactions are n
O5
0 ?
r*
C4
0
C5
0 (5.2 kcal/mol) andn
O3
0 ? r*
C5
0
H5
0 (4.2 kcal/mol).
As seen in Fig. 2, the raH2
0
, raH3
0
, raH5
0
, and raO5
0
H
radicals of deoxycytidine molecule are qualitatively similar
in their structures. These structures obviously differ in
sugar puckering modes and rotamers around C4
0
C5
0
bond
(see Table 1 for more details). For example raH2
0
, raH5
0
radicals have gauche-trans (gt) conformation around
C4
0
C5
0
bond whereas, raH3
0
and raO5
0
H radicals have
gauche- gauche (gg) and trans-gauche (tg) arrange-
ment about C4
0
C5
0
bond, respectively. In the optimized
structures of raH4
0
and raO5
0
H radicals of deoxycytidine
O5
0
HO3
0
and O5
0
HO3
0
intramolecular hydrogen
bonds with bond lengths of 2.206 and 2.260 A

are formed
involving hydroxyl groups of sugar part of deoxycytidine.
The tg orientation about C4
0
C5
0
bond allows stabilization
interaction in these radicals.
Geometrical changes on these radicals are different for
each fragment (i.e., the rings of cytosine and sugar unit). In
the former, variations occur on bond distances, whereas in
the latter the endocyclic torsion angles are the main mod-
ied parameters. The results of calculations revealed that
the cytosine ring to be in a planar shape and it has been
demonstrated to undergo less deformation or conformation
change when compared to furanose ring and other exible
segments of deoxycytidine. The values of bond lengths and
angles within the furanose ring strongly depend on the ring
conformation.
The values of the CC bond lengths are not equal within
the furanose ring of radical and neutral molecules. At least
one general trend may be seen from geometries of the
deoxycytidine radicals: while the radical-centered atom
increases the bond orders with its adjacent atoms, it usually
weakens the chemical bonds between the atoms on a and b
positions. This tendency might be important in predicting
the reactivity of the sugar based radicals. In addition, the
values of the CC bond lengths in sugar part of deoxy-
cytidine depend on the conformation of the sugar unit. The
results of DFT calculations have shown that the deoxy-
cytidine sugar conformation is changed signicantly during
radical formation (see Table 1 for more details). It should
be emphasized that these conformers of sugar unit have
rarely been observed in standard pyrimidine nucleosides.
Furthermore, on the DFT calculations, for deoxycytidine
radicals, in all cases (except raH1
0
radical which has syn
orientation about glycosyl bond) the v angles which char-
acterize the orientation of the base with respect to the sugar
unit remains anti conformation, since the corresponding v
values vary within the -165.4 B v B -170.0 range.
Moreover, the pseudorotation angle (P) is varied within a
large range of values which cover two possible confor-
mations of the furanose ring with exo orientation of the C3
0
atom (i.e., raH1
0
, raH4
0
radicals), and two possible con-
formations of the furanose ring with endo orientation of the
C3
0
atom (i.e., raH3
0
and raH5
0
radicals). The raH2
0
rad-
ical of deoxycytidine has O4
0
-endo conformation whereas
raO3
0
H and raO5
0
H radicals have C4
0
-exo and C2
0
-endo
conformations for their sugar part.
Molecular orbital and charge distributions
Delocalization of positive charge seems to further stabi-
lizing the cation radical. The result of calculation revealed
that the single positive charge on deoxycytidine cation
radical is redistributed between the cytosine nucleobase and
Table 1 B3LYP/6-311??G
(d,p) absolute energies (E in
a.u), relative energies (DE in
kcal/mol), dipole moments
(l in Debye), and relevant
geometrical parameters for
various sugar radicals of
deoxycytidine
Relative energy values using
IEF-PCM are given in
parenthesis
System E DE l C4
0
C5
0
bond
Conformation
raH1
0
-815.5291936 0.0 (0.0) 7.2 gg syn/C3
0
-exo
raH2
0
-815.5093698 11.5 (6.3) 7.6 gt anti/O4
0
-endo
raH3
0
-815.5211156 4.8 (2.3) 4.4 gg anti/C3
0
-endo
raH4
0
-815.3028884 1.9 (0.8) 8.1 tg anti/C3
0
-exo
raH5
0
-815.5176049 6.9 (4.2) 5.6 gt anti/C3
0
-endo
raO3
0
H -815.4916404 22.6 (11.6) 5.9 tg anti/C4
0
-exo
raO5
0
H -815.5022536 15.5 (10.5) 6.0 tg anti/C2
0
-endo
Struct Chem (2012) 23:11851192 1189
1 3
deoxyribose sugar part (total positive charge increases by
0.36 and 0.64 on cytosine moiety and sugar part, respec-
tively). The location of the positive charge on sugar part is
expected to decrease the negative charge density near atoms
C2
0
, C3
0
, and O5
0
atoms of deoxyribose sugar part.
Even more direct evidence for the distribution of the sin-
gle radical comes frommolecular orbital analysis of the singly
occupied molecular orbital (SOMO). Plots of the singly
occupied molecular orbital of deoxycytidine cation radicals
and carbon-centered radicals generated during proton
abstraction of cation radical are shown in Figs. 3 and 4. The
most striking feature of the SOMOof deoxycytidine revealed
that the single electron density is well-located on the deoxy-
ribose part (see Fig. 3).
Comparison of the SOMO plots for carbon-centered
radicals of deoxycytidine illustrates three kinds of delocal-
ization methods for stabilization of radicals: (1) delocaliza-
tion of unpaired electron on the cytosine nucleobase moiety
via the p conjugation features (2) on the sugar part of
deoxycytidine molecule via typical r radical features (3)
combinations of p conjugation and typical r radical features
are due to delocalization of unpaired electron to both cyto-
sine moiety and sugar part. For instance, as shown in Fig. 4,
in raH3
0
, raH4
0
, and raH5
0
radicals the SOMO well located
at deoxyribose sugar part (typical r radical) while in raH1
0
and raH2
0
radicals unpaired electron is located in both the
cytosine moiety and sugar part of deoxycytidne through both
p conjugation and typical r radical features. Furthermore, as
seen in Fig. 4, the SOMO of these radicals differ from the
SOMO of their parent cation radical. The results of calcu-
lation revealed that the SOMO of deoxycytidine cation
radical is well located at deoxyribose sugar part whereas of
the SOMO of radicals of deoxycytidine cation radical are
mainly located at the cytosine nucleobase part.
Effect of cation radical formation on acidity
enhancement of deoxycytidine
The various parameters are affected by the gas-phase
acidities (DH
acidity
) of organic and bioorganic molecules
such as metal cationization, hydrogen bonding, cation
radical formation and so on. For example catalytic activity
of metal ions such as Mg
2?
, Ca
2?
, Zn
2?
(as Lewis acids) in
organic and biological medium originates in the formation
of a donoracceptor complex between the cation and the
reactant, which must act as a Lewis base [54, 55]. Fur-
thermore, we have recently demonstrated that multiple
hydrogen bonds can enhance the acidity of organic mole-
cules [56]. Computations, gas-phase acidity measurements,
and pK
a
determinations in DMSO on a series of polyols
show that multiple hydrogen bond to a single charged
center lead to greatly enhanced acidities and consequently
produced the new class of Bronsted acids was proposed.
Moreover, as mentioned in introduction section, results of
previous studies demonstrated that the pK
a
of cation radicals
invariably were found to be lower than its parent compound.
For example, the pK
a
of guanine (N1H) is reported as 9.6,
while the corresponding pK
a
of the guanine cation radical
(G
?
) in H
2
O at ambient temperature is ca. 3.9 [25, 29].
Consequently, we decided to explore how acidity of deox-
ycytidine cation radical changes during deprotonation. For
proton transfer reaction of deoxycytidine cation radical the
HA
?
? H
?
1 A

process was used, where HA

1
and A

represents deoxycytidine cation radical and its oxygen cen-

tered radicals, the enthalpy changes can be calculated as:
DH
298
DE
298
D PV DE
298
Dn
g
RT
DH
298
EA

298
EH

298
E HA

298
5=2 RT
Neutral Deoxycytidine Deoxycytidine Cation
Radical
Fig. 3 Plots of the HOMO of neutral deoxycytidine and SOMOs of
deoxycytidine cation radical
raH2' raH1'
raH4' raH3'
raH5'
Fig. 4 Plots of the singly occupied molecular orbitals (SOMOs) for
carbon-centered radicals of deprotonateed deoxycytidine
1190 Struct Chem (2012) 23:11851192
1 3
where E
298
represents the calculated energy including
thermal vibrational corrections of HA
?
and A

. The (5/2)
RT term includes the translation energy of the proton and
the D (PV) term. It is worth to mention that gas-phase
acidities vary over a wide range, for instance, from 420.0
to 350.0 kcal/mol for hydrocarbons and from 340.0 to
309.0 kcal/mol for carboxylic acids.
The gas-phase acidities for various deprotonation sites
of neutral and cation radical forms of deoxycytidine are
summarized in Table 2. The predicted acidity for neutral
form of deoxycytidine shows that the N4H
a
is the most
favored deprotonation site with the gas-phase acidity of
345.5 kcal mol
-1
, followed by O3
0
and O
0
5 protons. It is
worth nothing that removal of H
a
and H
b
from N4 in
deoxycytidine was converged to the same structure during
the geometry optimization. The predicted acidity values
for cation radical form of deoxycytidine show that the
O
0
3H is the most favored deprotonation site with a
DH
acidity
of 227.0 kcal mol
-1
and the N4H
a
is the least
acidic site with a DH
acidity
of 228.8 kcal mol
-1
. Thus, the
acidity values of these weak polar protons may be
enhanced on the average by more than 120 kcal/mol (i.e.,
it becomes less endothermic) upon cation radical forma-
tion. Furthermore, it is worth mentioning that upon cation
radical formation, the gas-phase acidity strength of OH
and NH groups of deoxycytidine molecule drastically
increases to the extent that it converts the weak acids of
interest to a super acid. For instance, DH
acidity
of H
2
SO
4
(known as a super acid in the gas phase) is 299.0 kcal/
mol [57]; however, the acidities of all OH and NH
groups examined herein are considerably enhanced
when deoxycytidine was ionized and converted to cation
radical.
Conclusions
In this study, we explored theoretically structure and
electronic properties of deoxycytidine cation radical as
well as structure, relative stability, puckering of furanose
ring of its possible radicals formed via proton abstraction at
various sites of sugar part by employing density functional
theory (B3LYP) with the 6-31??G(d,p) basis set. It is
worth to mention that this body of systematic theoretical
studies provides realistic description of some events that
leads to elementary DNA lesions, while providing ratio-
nalizations for many observed phenomena. The results of
calculations in this study can be outlined as follows:
1. Radical-centered radicals generated during proton
atom abstraction of deoxycytidine cation radical have
following stability order: raH1
0
[raH2
0
[raH4
0
[
raH3
0
[raH5
0
[raO5
0
H[raO3
0
H. Furthermore,
results of calculation performed in solution phase
(through the integral equation formalism of the
polarized model or IEF-PCM) revealed that the
stability order of deoxycytidine radicals is the same
in comparison with that in gas phase.
2. SOMO orbitals of raH3
0
, raH4
0
, and raH5
0
radicals are
well located at deoxyribose sugar part (typical r
radical) while in raH1
0
and raH2
0
radicals unpaired
electron is located in both the cytosine moiety and
sugar part of deoxycytidne through both p conjugation
and typical r radical features.
3. All radicals generated during proton abstraction of
deoxycytidine cation radical have anti orientation
about glycosyl bond (except raH1
0
radical which has
syn orientation about glycosyl bond).
4. It is worth mentioning that upon cation radical
formation, the gas-phase acidity strength of OH and
NH groups of deoxycytidine molecule drastically
increases to the extent that it converts the weak acids
of interest to a super acid.
Acknowledgment Support from Sharif University of Technology is
gratefully acknowledged.
References
1. Von Sonntag C (2006) Free-radical-induced DNA damage and its
repair. Springer, Berlin
2. Yan M, Becker D, Summereld S, Renke P, Sevilla MD (1992)
J Phys Chem 96:1983
3. Little JB (2000) Carcinogenesis 21:397
4. Von Sonntag C (1991) In: Glass WA, Varma MN (eds) Physical
and chemical mechanism in molecular radiation biology. Plenum
Press, New York, p 287
Table 2 B3LYP/6-311??G
(d,p) gas-phase acidities
(DH
acidity
in kcal/mol), relevant
geometrical parameters, and
dipole moments (l in Debye) at
298 K for various deprotonation
sites of neutral and cation
radical forms of deoxycytidine
System Deprotonation site E DH
acidity
l Conformation
dC N4H
a
-816.176380 345.5 10.50 syn/C2
0
-endo
O3
0
H -815.613854 348.6 12.34 anti/C3
0
-endo
O5
0
H -815.608898 351.5 2.68 anti/C3
0
-exo
dC cation radical N4H
a
-815.5005309 228.8 3.97 anti/C1
0
-exo
O3
0
H -815.5036466 227.0 6.07 anti/C4
0
-exo
O5
0
H -815.5022536 227.5 6.03 anti/C3
0
-exo
Struct Chem (2012) 23:11851192 1191
1 3
5. Steenken S (1989) Chem Rev 89:503
6. Pogozelski WK, Tullius TD (1998) Chem Rev 98:1089
7. Tronche C, Goodman BK, Greenberg MM (1998) Chem Biol
5:263
8. Von Sonntag C (1987) The chemical basis of radiation biology.
Taylor and Francis, London
9. Adhikary A, Collins S, Koppen J, Becker D, Sevilla MD (2006)
Nucleic Acid Res 34:1501
10. Becker D, Bryant-Friedrich A, Trzasko C, Sevilla MD (2003)
Radiat Res 160:174
11. Becker D, Razskazovskii Y, Callaghan MU, Sevilla MD (1996)
Radiat Res 146:361
12. Shukla LI, Pazdro R, Huang J, De Vreugd C, Becker D, Sevilla
MD (2004) Radiat Res 161:582
13. Adhikary A, Malkhasian AYS, Collins S, Koppen J, Becker D,
Sevilla MD (2005) Nucleic Acids Res 33:5553
14. Adhikary A, Kumar A, Sevilla MD (2006) Radiat Res 165:479
15. Kumar A, Sevilla MD (2006) J Phys Chem B 110:24181
16. Adhikary A, Collins S, Khanduri D, Sevilla MD (2007) J Phys
Chem B 111:74157421
17. Becker D, Adhikary A, Sevilla MD (2007) In: Rao BSM, Wishart
J (eds) Recent trends in radiation chemistry. World Scientic
Publishing Co, Singapore
18. Kumar A, Sevilla MD (2007) In: Shukla MK, Leszczynski J (eds)
Radiation induced molecular phenomena in nucleic acid: a
comprehensive theoretical and experimental analysis. Springer,
Berlin
19. Henderson PT, Jones D, Hampikian G, Kan Y, Schuster GB
(1999) Proc Natl Acad Sci USA 96:8353
20. ONeill MA, Barton JK (2004) J Am Chem Soc 126:11471
21. Lewis FD, Letinger RL, Wasielewski MR (2001) Acc Chem Res
34:159
22. Giese B, Amaudrut J, Kohler AK, Spomann M, Wessely S (2001)
Nature 412:318
23. Sharovich V, Cadet J, Gasparutto D, Dourandin A, Huang W,
Geacintov NE (2001) J Phys Chem B 105:586
24. Takada T, Kawai K, Fujitsuka M, Majima T (2004) Proc Natl
Acad Sci USA 101:14002
25. Steenken S (1992) Free Radical Res Commun 16:349
26. Steenken S (1997) Biol Chem 378:1293
27. Colson A, Besler B, Close DM, Sevilla MD (1992) J Phys Chem
96:661
28. Bertran J, Oliva A, Rodriguez-Santiago L, Sodupe M (1998)
J Am Chem Soc 120:8159
29. Nelson WH, Sagstuen E, Hole EO, Close DM (1998) Radiat Res
149:75
30. Hwang CT, Stumpf CL, Yu YQ, Kenttamaa HI (1999) Int J Mass
Spectrom 183:253
31. Liu J, Crawford K, Petzold CJ, Kenttamaa HI (2001) Proceedings
of the 49th ASMS conference on mass spectrometry and allied
topics, Chicago 2001. American society for mass spectrometry:
Santa Fe, New Mexico, Presentation No. ThPB 038
32. Harrison AG (1997) Mass Spectrom Rev 16:201
33. Lias SG (1988) Ionization energy evaluation, NIST standard
reference database number 69. In: Mallard WG, Linstrom PJ
(eds) National Institute of Standards and Technology, Gathers-
burg MD, 20899 (http://webbook.nist.gov)
34. Spartan 06V102. Wavefunction, Inc.: Irvine, CA
35. Becke AD (1993) J Chem Phys 98:5648
36. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785
37. Reed AE, Weinhold F (1985) J Chem Phys 83:1736
38. Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys
83:735
39. Reed AE, Weinhold F (1983) J Chem Phys 78:4066
40. Foster JP, Weinhold F (1980) J Am Chem Soc 102:7211
41. Chocholousova J, Vladimir Spirko V, Hobza P (2004) Phys Chem
Chem Phys 6:37
42. Altona C, Sundaralingam M (1972) J Am Chem Soc 94:8205
43. Saenger W (1984) Principles of nucleic acid structure. Springer,
New York
44. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J
(2000) J Mol Struct (Theochem) 526:329
45. Knowles D, Foloppe N, Matassova BN, Murchie A (2002) Curr
Opin Pharmacol 2:501
46. Brameld KA, Goddard WA (1999) J Am Chem Soc 121:985
47. Hernandez B, Elass A, Navarro R, Vergoten G, Hernanz A (1998)
J Phys Chem B 102:4233
48. Grana AM, Rios MA (1995) J Mol Struct (Theochem) 334:37
49. Hocquet A (2001) Phys Chem Chem Phys 3:3192
50. Louit G, Hocquet A, Ghomi M (2002) Phys Chem Chem Phys
4:3843
51. Zhang C, Xue Y (2007) J Mol Struct (Theochem) 802:35
52. Dougherty RC (1968) J Am Chem Soc 90:5780
53. Tomasi J, Persico M (1994) Chem Rev 94:2027
54. Pena DA, Uphade BS, Reddy EP, Smirniotis PG (2004) J Phys
Chem B 108:9927
55. Kennedy JW, Hall DG (2002) J Am Chem Soc 124:11586
56. Tian Zh, Fattahi A, Lis L, Kass SR (2009) J Am Chem Soc
131:16984
57. Wang XB, Nicholas JB, Wang LS (2000) J Phys Chem A
104:504
1192 Struct Chem (2012) 23:11851192
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