ORIGINAL RESEARCH

Structural behavior of sugar radicals formed by proton transferreaction of deoxycytidine cation radical: detailed view from NBOanalysis

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 0.0–22.6 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: raH10[ raH20[raH40[ raH30[ raH50[ raO50H [ raO30H. Furthermore,

influence of cation radical formation on acidities of mul-

tiple sites in deoxycytidine nucleosides was investigated.

For instance upon cation radical formation, DHacidity of

O30H and O50H 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 [1–3]. 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

C10 position is known to result in an alkali-labile stranding

break, whereas the C30, C40, and C50 sugar radicals can lead

to frank strand breaks [6–8]. 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 significant 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

123

Struct Chem (2012) 23:1185–1192

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 80–100%

in model systems) [9, 12, 13].

Several recent studies [14–18] 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 C50 and C30 as well as some C10. Phosphate

groups at 30 or 50 were found to deactivate that site toward

sugar radical formation and as a consequence only C10 was

found in DNA, whereas C10, C30, and C50 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 C50 radical with a small

contribution of C30 radical with the C50 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 [19–24]. 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 pKa of the nucleobase ion-radical involved. The pKa

values of cation radicals were found to be invariably lower

than those of parent compounds. For example, the pKa of

guanine (N1–H) is reported as 9.6, whereas the corre-

sponding pKa of the guanine cation radical (G•?) in H2O 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 ion–molecule 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

[30–33].

In this paper1 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 exchange–correlation

functional with 6-311??G (d,p) orbital basis sets. Because

of the cationic and radical nature of deoxycytidine cation

radical, its ion–molecule 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 influence 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 field

with the Spartan software [34]. The most stable conformers

were optimized by DFT method using the Becke’s [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 first 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 hydrogen’s 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) 23:1185–1192

123

may be given as a stabilizing affect that arises from an overlap

between the BD* orbital and the half-filled P orbital of the

radical center. The NBO analysis reveals hyperconjugation

interaction. This non-covalent bonding–antibonding 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)) [37–41]. 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]:

Eð2Þ ¼ DEij � qiFði; jÞ2

ej � ei;

where qi is the donor orbital occupancy, ei; ej 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 C50

atom, exo: on the opposite side). The following equation

calculated this value: (when m2 is negative one should add

180� to the calculated value of P) [42, 43].

tanðPÞ ¼ ðm4 þ m1Þ � ðm3 þ m0Þ2m2ðsin 36ð Þ þ sin 72ð ÞÞ

where mi is dihedral angles i.e., m0 = C40–O40–C10–C20,m1 = O40–C10–C20–C30, m2 = C10–C20–C30–C40, m3 = C20–C30–C40–O40, and m4 = O30–C40–O40–C10. (3) The glyco-

sidic bond connecting these units. The glycosyl torsion angle

v is defined as v = O40–C10–N1–C2 in pyrimidine nucleo-

sides and as v = O40–C10–N9–C4 in purine nucleosides,

allowing the orientation of the base with respect to the sugar

to be determined. (4) Rotation around the C40–C50 bond

leads to three possible conformers: ‘‘gauche-trans’’ (gt),

‘‘trans-gauche’’ (tg), and ‘‘gauche–gauche’’ (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 first 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 C20-endo/syn

which consists of two (1.834 A) O2…HO50 and

O40…HO50 (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 O2…HO50

group [44–51]. 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 O2…HO50 hydrogen bond in neutral

deoxycytidine molecule.

The adiabatic ionization energy (AIE or IEa) 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 simplification, the following

notations are adopted in this article to better clarifying

geometries and energetic aspects of radicals: The carbon

and oxygen centers (i.e., C10–H, C20–H, C30–H, C40–H,

C50–H, O30–H and O50–H) chosen for generating radical on

H

OHH

H

C3 O

H

HHO

H

C3 O

OH

HH

H

C3 O

gt tg gg

Scheme 2 Definition of three possible rotamers about C40–C50 bond

Struct Chem (2012) 23:1185–1192 1187

123

deoxycytidine cation radical are simplified as raH10,raH20, raH30, raH40, raH50, raO30H, and raO50H,

respectively. For example, raH10 and raO20H radicals

show that proton abstraction occurred through C10 and O20

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 raH10 from Fig. 2 is the most stable ribose radicals of

deoxycytidine from an energetic point of view. This radical

is stabilized by C = O…O20H hydrogen bond which sig-

nificantly 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 (raH10) and structure raH40 is only

about 1.9 kcal/mol. Geometry optimization of raH40, leads

to the formation of O30H…O50 hydrogen bond with the

length 2.206 A. On DFT calculation, raH40 is followed by

raH30, raH50, and raH20 radicals. They are located at 4.8,

6.9, and 11.5 kcal/mol above raH10, respectively. It is

worth to mention that the C40 sugar radical (i.e., raH40) 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-filled P orbital of the radical center

and the r* orbital of sugar or nucleoabse parts in radicals

can take place. For raH10 radical center of deoxycytidine

stabilizing interactions are as follow: n (1)C10 ? r* C20–H20

(4.3 kcal/mol), n (1)C10 ? r* C30–O30 (5.1 kcal/mol), and n

(1)C10 ? r* N1–C2 (6.0 kcal/mol). The most important

hyperconjugation interaction that stabilizes raH40 radical,

which corresponds with removal of the hydrogen atom at

the C40 position of sugar part of deoxycytidine, are n

C40 ? r* C20–C30 (2.3 kcal/mol), n C40 ? r* C30–C40

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) 23:1185–1192

123

(19.2 kcal/mol), and n C30 ? r* C30–O30 (3.2 kcal/mol). In

radical raH30, which corresponds with removal of the

hydrogen atom at the C30 position of sugar part of deox-

ycytidine, the important interactions between ‘‘half filled’’

(donor) Lewis type NBOs and ‘‘empty’’ (acceptor) non-

Lewis NBOs are nC30 ? r* C20-C30, n C30 ? r*C20–H20, and

nC30 ? r* C30-O30 with charge-transfer energy values of 9.7,

3.5, and 19.1 kcal/mol, respectively.

The two least stable radical species raO50H and raO20Hare 15.9 and 22.6 kcal/mol higher in energy than raC10H.

To examine the lifetime of raO50H and raO30H 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 O30H = 3.0 eV and radical O50H = 2.9 eV.

On NBO analysis the most important delocalization inter-

actions of raO30H radical are n O30 ? r* C20–C30 (2.6 kcal/

mol) and n O30 ? r* C30–C40 (6.4 kcal/mol) while in

raO20H radical delocalization interactions are n O50 ?r* C40–C50 (5.2 kcal/mol) and n O30 ? r* C50–H50 (4.2 kcal/mol).

As seen in Fig. 2, the raH20, raH30, raH50, and raO50Hradicals of deoxycytidine molecule are qualitatively similar

in their structures. These structures obviously differ in

sugar puckering modes and rotamers around C40–C50 bond

(see Table 1 for more details). For example raH20, raH50

radicals have ‘‘gauche-trans’’ (gt) conformation around

C40–C50 bond whereas, raH30 and raO50H radicals have

‘‘gauche- gauche’’ (gg) and ‘‘trans-gauche’’ (tg) arrange-

ment about C40–C50 bond, respectively. In the optimized

structures of raH40 and raO50H radicals of deoxycytidine

O50H…O30 and O50H…O30 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 C40–C50 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-

ified 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 flexible

segments of deoxycytidine. The values of bond lengths and

angles within the furanose ring strongly depend on the ring

conformation.

The values of the C–C 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 bpositions. This tendency might be important in predicting

the reactivity of the sugar based radicals. In addition, the

values of the C–C 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 significantly 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 raH10 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 vvalues 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 C30

atom (i.e., raH10, raH40 radicals), and two possible con-

formations of the furanose ring with endo orientation of the

C30 atom (i.e., raH30 and raH50 radicals). The raH20 rad-

ical of deoxycytidine has O40-endo conformation whereas

raO30H and raO50H radicals have C40-exo and C20-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 C40–C50

bond

Conformation

raH10 -815.5291936 0.0 (0.0) 7.2 gg syn/C30-exo

raH20 -815.5093698 11.5 (6.3) 7.6 gt anti/O40-endo

raH30 -815.5211156 4.8 (2.3) 4.4 gg anti/C30-endo

raH40 -815.3028884 1.9 (0.8) 8.1 tg anti/C30-exo

raH50 -815.5176049 6.9 (4.2) 5.6 gt anti/C30-endo

raO30H -815.4916404 22.6 (11.6) 5.9 tg anti/C40-exo

raO50H -815.5022536 15.5 (10.5) 6.0 tg anti/C20-endo

Struct Chem (2012) 23:1185–1192 1189

123

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

C20, C30, and O50 atoms of deoxyribose sugar part.

Even more direct evidence for the distribution of the sin-

gle radical comes from molecular 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 SOMO of 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 raH30, raH40, and raH50 radicals the SOMO well located

at deoxyribose sugar part (typical r radical) while in raH10

and raH20 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 (DHacidity) 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 Mg2?, Ca2?, Zn2? (as Lewis acids) in

organic and biological medium originates in the formation

of a donor–acceptor 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 pKa 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 pKa of cation radicals

invariably were found to be lower than its parent compound.

For example, the pKa of guanine (N1–H) is reported as 9.6,

while the corresponding pKa of the guanine cation radical

(G•?) in H2O 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:

DH298 ¼ DE298 þ D PVð Þ ¼ DE298 þ DngRT

DH298 ¼ EðA�Þ298 � EðHþÞ298 � E HA�þð Þ298þ 5=2ð ÞRT

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) 23:1185–1192

123

where E298 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 N4Ha is the most

favored deprotonation site with the gas-phase acidity of

345.5 kcal mol-1, followed by O30 and O05 protons. It is

worth nothing that removal of Ha and Hb 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

O03H is the most favored deprotonation site with a

DHacidity of 227.0 kcal mol-1 and the N4Ha is the least

acidic site with a DHacidity 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, DHacidity of H2SO4

(known as a super acid in the gas phase) is 299.0 kcal/

mol [57]; however, the acidities of all O–H and N–H

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: raH10[ raH20[ raH40[raH30[ raH50[ raO50H [ raO30H. 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 raH30, raH40, and raH50 radicals are

well located at deoxyribose sugar part (typical rradical) while in raH10 and raH20 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 raH10 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.

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