Efficient and Substantial DNA Lesions From Near 0 ... - ACS Publications

Subscriber access provided by ISTANBUL TEKNIK UNIVERSITESI

Article

Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O-Hydrogenated Thymine Nucleotides: A DFT Study 4

Shoushan Wang, Changzhe Zhang, Peiwen Zhao, and Yuxiang Bu J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.5b06195 • Publication Date (Web): 06 Oct 2015 Downloaded from http://pubs.acs.org on October 15, 2015

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry B is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study Shoushan Wang, Changzhe Zhang, Peiwen Zhao, Yuxiang Bu1 School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China

ABSTRACT: Possible electron-induced ruptures of C3′-O3′, C5′-O5′, and N1-C1′ bonds in O4-hydrogenated

2′-deoxythymidine-3′-monophsphate

(3′-dT(O4H)MPH)

and

2′-deoxythymidine-5′-monophsphate (5′-dT(O4H)MPH) are investigated using density functional theory calculations and efficient pathways are proposed. structural relaxation in the thymine C6 site.

Electron attachment causes remarkable

A concerted process of intramolecular proton transfer

(IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3′-O3′ bond rupture is observed in [3′-dT(O4H)MPH]−.

A low activation barrier (9.32 kcal/mol) indicates that this pathway is the

most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3′-end thymine, which [3′-dT(O4H)MPH]−.

prevents the N1-C1′ bond cleavage in

However, essentially spontaneous N1-C1′ bond cleavage following similar

IPT is predicted in [5'-dT(O4H)MPH]−.

A moderate activation barrier (13.02 kcal/mol) for the

rate-controlling IPT step suggests that base release from the N1-C1′ cleavage arises readily at the 3′-end of a single strand DNA with the strand ended by a thymine. insignificant change in the IPT process.

The C5′-O5′ bond has only

Solvent effects are found to increase slightly the energy

requirements for either bond ruptures (11.23 kcal/mol (C3′-O3′) vs. 16.18 kcal/mol (N1-C1′) ), but not change their relative efficiencies.

Keywords: Low energy electron; O4-hydrogenated thymine nucleotide; intramolecular proton transfer; DNA damage and lesion; DFT calculation.

*

The corresponding author: Yuxiang Bu, e-mail: [email protected] 1

ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

INTRODUCTION The oxidizing OH˙ (H˙) radical addition and abstraction to various DNA components were once believed to be the primary pathways leading to DNA damage besides the minor pathway directly from the deposition of high-energy on DNA.1-3 However, low energy electrons (LEEs) with incident electron energies below 20 eV, which are the most abundant species among the secondary particles created along all the ionizing radiation tracks,4 were demonstrated to be able to trigger DNA singleand double-strand breaks (SSBs and DSBs) in dry conditions.5-7 Furthermore, DNA SSBs and DSBs induced by prehydrated electrons were observed directly in irradiated DNA aqueous solutions with the damage effectiveness per prehydrated electron nearly twice than that per OH•.8-9 Consequently, more efforts should be made on the interactions between LEEs and different building blocks of DNA for a better understanding of possible DNA damage mechanisms and further development of more efficient radiotherapy methods. Based on the functions of damage quantum-yield versus incident electron energy obtained from diverse DNA constituents,5-13 transient anionic resonances were considered to be responsible for the ejection of H˙ (or H¯) as well as DNA SSBs and DSBs via a mechanism of dissociative electron attachment.

Unfortunately, bond rupture processes are inevitably competitive with the

ultrafast electron autodetachment event occurring at a magnitude of 1014 s-1 in the transient anionic resonances.14 To circumvent this disadvantage, a viewpoint regarding the short-lived transient anionic resonances as doorways to electronically stable valence-bound anions was proposed.14 Moreover, the existence of electronically stable valence-bound anions of nucleobases has been confirmed experimentally15 and theoretically.16-18 The relative stability of bound anionic states ensures subsequent reaction processes proceeding without any competition with the ultrafast electron autodetachment event. Thymine derivatives have attracted more attention on DNA lesions induced by excess electron (EE) attachment due to the strongest electron affinity of thymine among the four DNA nucleobases.19-20 C3′-O3′, C5′-O5′, and N1-C1′ bond ruptures via a pathway of direct electron transfer from the initially localized base moiety to the σ* orbital of the bond being broken have been widely investigated.21-26 The estimated activation energies for the C3′-O3′ bond rupture are 7.06 kcal/mol in 3′-dTMPH− 23 and 6.04 kcal/mol in 3′,5′-dTDP−.26 In comparison, the activation energies for the C5′-O5′ bond rupture are estimated to be 9.8-13.84 kcal/mol in 5′-dTMPH− 22,24-25 and 13.39 kcal/mol 2


Page 2 of 23

Page 3 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


in 3′,5′-dTDP−.26 As for the cleavage of N1-C1′ bond, the calculated activation energies are 18.9 kcal/mol in dT−,21 22.8 kcal/mol in 5′-dTMPH−,25 and 19.19 kcal/mol in 3′,5′-dTDP−.26

Naturally,

the C3′-O3′ and C5′-O5′ bonds (especially the C3′-O3′ bond) were considered to be the most probable rupture sites resulting in substantial DNA SSBs with base release from the N1-C1′ bond cleavage being a minor damage source.

However, this conclusion was suspected based on the experimental

observations from LEE-bombarded thin film oligonucleotides27-30 and the intrinsic deficiency of conventional DFT methods, the one-electron self-interaction error, which is apt to overstabilize the delocalized states.31

Extra charge distribution across several bonds from the initially localized

base moiety to the σ* orbital of C3′-O3′ or C5′-O5′ bond was, indeed, involved in the transition state of either bond rupture process.22-26 Most recently, a DFT benchmark study including the one-electron self-interaction correction31 reported comparable activation energies for the two phosphodiester bond ruptures (23.5 kcal/mol for the C3′-O3′ bond rupture and 24.4 kcal/mol for the C5′-O5′ bond rupture) to those for the N1-C1′ bond cleavage (the activation energies obtained previously were demonstrated to be reasonable) verifying formally the thin film experimental results. Nevertheless, it should be noted that the vertical detachment energy (VDE) of 5′-dTMPH− is unexpectedly smaller than the activation energy of the C5′-O5′ bond rupture estimated in the DFT benchmark study.31 The same situation also occurs for the N1-C1′ bond cleavage in 5′-dTMPH− 25 and 3′,5′-dTDP−.26 Thus, the possibility of the C5′-O5′ and N1-C1′ bond ruptures is considerably decreased due to the competitive electron detachment. Solvent effects were found to increase significantly the difficulty of the C3′-O3′, C5′-O5′, and N1-C1′ bond ruptures with the corresponding activation energies lying in the range 28.77-34.2 kcal/mol.26,31 Such high energy requirements for the C3′-O3′, C5′-O5′, and N1-C1′ bond ruptures both in the gas phase and aqueous solutions imply that DNA SSBs and base release via the above-mentioned pathways are essentially suppressed. In other words, alternative pathway or initial reactive species leading to efficient C3′-O3′, C5′-O5′, and N1-C1′ bond ruptures should be explored. Hydrogenated-thymine derivatives, produced from thymine derivatives via electron capture followed by protonation32-36 and direct H addition37 in irradiated aqueous solutions, LEE induced barrier-free PT with proton-donors,38-39 and being irradiated in solid states,40-45 were considered to be able to cause DNA damage.46-47 In C5-hydrogenated 3′-dTMP system, the possibility of the C3′-O3′ and N1-C1′ bond ruptures via a pathway of intramolecular H transfer from the C2′ site of 3



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 23

2′-deoxyribose to the C6 site followed by either bond cleavage was investigated.46 The calculated least energy requirements for C3′-O3′ and N1-C1′ bond ruptures were 23.9 and 29.1 kcal/mol, respectively. On the other hand, the activation energy for the same intramolecular H transfer in C5-hydrogenated 5′-dTMP system was estimated to be 29.1 kcal/mol.47 Such high energy requirements indicate that DNA damage resulting from C5-hydrogenated thymine derivatives via the above-mentioned pathways is essentially impossible, as pointed out by the same group in their another literature.48 In comparison, efficient N1-C1′ bond cleavage via a pathway of intramolecular PT from the C2′ site of 2′-deoxyribose to the C6 site followed by bond cleavage with the largest energy requirement smaller than 12.5 kcal/mol was predicted in anionic C5-hydrogenated 5′-dTMP,47 suggesting the important effect of further EE attachment. However, in contrast to the O4-hydrogenated species produced both in the solid phase and aqueous solutions, the C5-hydrogenated radicals are merely minor radiation products.32-36,38-44 Therefore, only little DNA damage comes from the decay of the C5-hydrogenated thymine derivatives.

On the contrary, the

consequence of EE attachment to the O4-hydrogenated thymine derivatives is, up to now, still unclear.

Recently, intramolecular PT from the C2′ site of 2′-deoxyribose to the C6 site

accompanied with C3′-O3′ bond rupture in [3′-dC(N3H)MPH]− anion14 and the same intramolecular PT process but followed by the N1-C1′ bond cleavage in [5′-dC(N3H)MPH]− anion48 were predicted. The activation energies for the rate-controlling intramolecular PT step are no more than 13.2 kcal/mol for both cases.

Based on the above results and the spin density distributions of the

O4-hydrogenated thymine derivatives,42-43,45 the decay of the O4-hydrogenated thymine nucleotides induced by EE attachment may cause efficient C3′-O3′ and N1-C1′ bond ruptures. Two model compounds, 3′-dT(O4H)MPH and 5′-dT(O4H)MPH (Scheme 1), are constructed in the present work to explore the possible bond rupture sites leading to DNA SSBs and base release induced by EE attachment.

Intramolecular PT from the C2′ site of 2′-deoxyribose to the C6 site

accompanied with the C3′-O3′ bond rupture is predicted in [3′-dT(O4H)MPH]− anion suggesting the efficient DNA SSBs at the non-3′-end T site of a single strand DNA.

As for the 3′-end thymine

residue of a single strand DNA, the results of [5′-dT(O4H)MPH]− anion predict efficient N1-C1′ bond cleavage via a pathway involving the same intramolecular PT process.

The least energy

requirement for either bond rupture is found to be increased slightly in the influence of solvent effects, but still moderate. 4


Page 5 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


COMPUTATIONAL DETAILS All geometry optimizations and energy calculations were carried out using Becke’s 3-parameter exchange functional (B3)49 combined with the correlation functional of Lee, Yang, and Parr (LYP).50 Double-ζ quality basis set augmented with polarization and diffuse functions (denoted as DZP++) was employed. The Huzinage-Dunning51-52 double-ζ basis set was augmented with one set of p-type polarization functions for each H atom and one set of d-type polarization functions for each C, N, O, and P atom (αp(H)=0.75, αd(C)=0.75, αd(N)=0.80, αd(O)=0.85, αd(P)=0.60). Even-tempered diffuse s function and s and p functions with the orbital exponents determined by the prescription of Lee and Schaefer53 were added to each H and heavy atom to complete the DZP++ basis set. The reliability of B3LYP/DZP++ level of theory has been verified in previous calculations.31,48,54 Frequency analyses were performed to assess the nature of stationary points on the potential energy surfaces. Natural population analysis (NPA) based on the natural bond orbital theory was used to calculate atomic charges.55 A proton was added to the phosphate group to mimic the function of a counterion such as Na+ or K+ existing in the vicinity of the phosphate group in the physiological conditions, as did in other similar computational studies.14,21-23,25-26,31,48,56 Polarizable continuum model (PCM) with ε=78.39 was employed to mimic the solvent environment. All results were calculated using the Gaussian 03 package.57

RESULTS AND DISCUSSION C3′-O3′ bond rupture in 3′-dT(O4H)MPH induced by EE attachment.

First, it is necessary

to study the properties of 3′-dT(O4H)MPH for a better understanding of subsequent EE attachment and bond rupture processes.

The unpaired electron occupies the highest occupied molecular

orbital (HOMO) with a π* orbital character localized primarily on the base moiety (Figure S1 in the Supporting Information (SI)).

The spin densities located at the C4, C5, and C6 atoms are 0.39,

-0.19, and 0.64, respectively (Figure S2 in the SI), which are in good agreement with the experimental estimations42-43 and theoretical calculations.45 As presented in Table 1, substantial electron affinity is predicted for 3′-dT(O4H)MPH.

The vertical electron affinity (VEA) is

estimated to be marginally negative (-0.09 eV), which is in between the values reported for 5



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

non-hydrogenated 3′-dTMPH (-0.15-0.26 eV).23,31

Page 6 of 23

However, it is significantly higher than those

for the C5-hydrogenated thymine derivatives (-1.6 ~ -1.7 eV).46

The adiabatic electron affinity

(AEA) is calculated to be 0.58 eV, slightly larger than those for 3′-dTMPH (0.44 ~ 0.58 eV).23,31 Thus, the ability of 3′-dT(O4H)MPH for binding an EE is ensured by these relatively higher VEA and AEA.

On the other hand, the VDE of the corresponding anion [3′-dT(O4H)MPH]− is

estimated to be 1.68 eV, 0.13 ~ 0.15 eV larger than those of [3′-dTMPH]− anion (1.53 ~ 1.56 eV).23,31 The considerable positive AEA and VDE indicate that the EE attached [3′-dT(O4H)MPH]− anion is electronically stable. The sizable energy difference between VEA and AEA of 3′-dT(O4H)MPH (0.62 eV) reflects a large amount of structural relaxation upon EE attachment.

The NPA charge distribution presented

in Table 2 shows that the extra negative charge is distributed mainly on the base moiety in [3′-dT(O4H)MPH]− anion.

A value of -0.89 on the base moiety relative to that in

3′-dT(O4H)MPH is estimated with nearly half extra charge (-0.43) located at the C6 atom. the spin density center, C6 atom, is also an extremely negative charge center.

Namely,

The enhanced

negative charge at the C6 atom alters the sum of the three angles ∠C5C6N1+∠C5C6H6+∠N1C6H6 from 359.5° in 3′-dT(O4H)MPH to 331.7° in the anion [3′-dT(O4H)MPH]−, indicating the transformation of C6 hybridization from sp2 to sp3 (Figure 1).

The pyramidalization structure

around the C6 site in the anion [3′-dT(O4H)MPH]− elongates the C6-C5 and C6-N1 bonds from 1.40 Å and 1.42 Å in 3′-dT(O4H)MPH to 1.48 Å and 1.48 Å with the other bond length changes insignificant (< 0.03 Å, Figure 1), respectively.

Notably, the large extra negative charge at the C6

atom in [3′-dT(O4H)MPH]− anion makes it a strong basic center for proton attacking.

The H2a′

atom is the closest hydrogen atom in 2′-deoxyribose moiety to the C6 site with a distance being 2.82 Å.

Intramolecular PT from the C2′ site to the C6 site controls subsequent C3′-O3′ bond rupture

pathway.

The complete DNA SSBs starting from the neutral radical 3′-dT(O4H)MPH involving

EE attachment and intramolecular PT is depicted in Figure 1. The gas phase activation energy for the H2a′ proton transfer from the C2′ atom to the C6 site is estimated to be 9.32 kcal/mol (Table 3), which is comparable to the activation energy of the C3′-O3′ bond cleavage in the sugar-phosphate-sugar model (ca. 10 kcal/mol).58 In comparison, significantly high activation energies were predicted for the C3′-O3′ bond rupture in [3′-dTMPH]− anion (23.5 kcal/mol)31 and the C5-hydrogenated thymine derivatives (23.9-25.1 kcal/mol).46 In the transition 6


Page 7 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


state (TS) which is verified by having only one imaginary frequency -1224.2i cm-1, the transferred H2a′ proton is 1.34 Å away from the C2′ atom and 1.55 Å to the C6 atom (Figure 1). The HOMO of the TS state mainly consists of a mixture of the π* orbital of the base moiety, the π orbital around C1′, C2′ and C3′ atoms, and the σ* orbital of the C3′-O3′ bond (Figure 2a). Electron transfer induced by the intramolecular PT from the initially localized base moiety in the anion [3′-dT(O4H)MPH]− to the anti-bonding σ* orbital of the C3′-O3′ bond in the TS state (Figure S3 in the SI) destabilizes the C3′-O3′ bond making its bond length elongated from 1.48 Å to 1.60 Å. Meanwhile, electron transfer to the π orbital around C1′, C2′ and C3′ atoms makes the C2′-C3′ bond length shortened from 1.52 Å in [3′-dT(O4H)MPH]− anion to 1.46 Å in the TS state. In contrast, the N1-C1′ bond length stretches from 1.43 Å to 1.47 Å. (Figure 1).

The C3′-O3′ bond is already sufficiently elongated in the TS

state and the following C3′-O3′ bond rupture is a barrier-free, spontaneous process as confirmed by the intrinsic reaction coordinate (IRC) calculations. A similar situation was observed in the case of [3′-dC(N3H)MPH]− anion.14

The C3′-O3′ bond rupture product is a complex consisting of a

negatively charged phosphate group (with the NPA charge being -0.97, Table 2) and a neutral closed-shell O4-hydrogenated thymine derivative (Figure 1).

A representative C=C double bond

distance is observed for the C2′-C3′ bond (1.34 Å) in the neutral O4-hydrogenated species making the structure of 2′-deoxyribose moiety planar (Figure 1).

It should be noted that the N1-C1′ bond

length changes only slightly (in a rang 1.43-1.47 Å) along the C3′-O3′ bond rupture pathway.

The

relative stability of the N1-C1′ bond and the concerted C3′-O3′ bond rupture in the intramolecular PT process suggest the important effect of the phosphate group at the O3′ position on DNA SSBs.

The

importance of the O3′-phosphate group can be further verified by a higher energy requirement for the N1-C1′ bond cleavage in [5′-dT(O4H)MPH]− anion (see below).

The whole C3′-O3′ bond

rupture reaction is exothermal with the product 53.05 kcal/mol lower in energy than the anion [3′-dT(O4H)MPH]− (Table 3).

The lower activation energy and larger reaction energy release for

the C3′-O3′ bond rupture in the anion [3′-dT(O4H)MPH]− show that efficient and substantial DNA SSBs can occur at the non-3′-end T site of a single strand DNA through a pathway initiated from the O4-hydrogenated thymine nucleotides including EE attachment and intramolecular PT process. The gas phase potential energy surface along the C3′-O3′ bond rupture pathway is depicted in Figure 3a. The C3′-O3′ bond rupture process in aqueous phase 3′-dT(O4H)MPH induced by EE attachment 7



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

is very similar to that in the gas phase.

Page 8 of 23

Almost same spin density distribution in the aqueous phase

as that in the gas phase for 3′-dT(O4H)MPH is obtained (Figures S1-2 in the SI).

However,

significant increases of VEA, AEA, and VDE are predicted (Table 1) due to the enhanced stability of [3′-dT(O4H)MPH]− anion from the polarizable surroundings.

As in the gas-phase case, the

extra negative charge centered at the C6 atom results in considerable structural relaxation (Table 2 and Figure S4 in the SI).

The structural pyramidalization around the C6 site reflecting the

transformation of C6 hybridization from sp2 in 3′-dT(O4H)MPH to sp3 in [3′-dT(O4H)MPH]− anion is obvious.

In aqueous phase [3′-dT(O4H)MPH]− anion, the H2a′ proton transfer from the C2′ site

to the C6 site still controls subsequent C3′-O3′ bond rupture process.

The complete DNA SSBs

occurred in aqueous solutions initiated from 3′-dT(O4H)MPH involving EE attachment and intramolecular PT process is depicted in Figure S4 in the SI.

In the influence of solvent effects,

the energy requirement for the rate-controlling intramolecular PT step is increased to be 11.23 kcal/mol, 1.91 kcal/mol larger than that in the gas phase (Table 3). In comparison, the least energy requirements for the aqueous phase C3′-O3′ bond rupture are estimated to be 30.1 kcal/mol in [3′-dTMPH]− anion31 and 24.2-25.3 kcal/mol in the C5-hydrogenated thymine derivatives.46

The

HOMO of the TS state in the aqueous phase is also a mixed orbital consisting of nearly the same components as those in the gas phase (Figure S5a in the SI). Electron transfer from the initially localized base moiety in [3′-dT(O4H)MPH]− anion to the anti-bonding σ* orbital of the C3′-O3′ bond and the π orbital around C1′, C2′ and C3′ atoms in the TS state (Figure S6 in the SI) makes bond length changes similar to those in the gas phase. The already stretched C3′-O3′ bond (1.56 Å) in the transition state implies that the following C3′-O3′ bond rupture is also a spontaneous process, as confirmed by the IRC calculations.

Solvent effects further decrease the total reaction energy of the

C3′-O3′ bond rupture to be -58.04 kcal/mol (Table 3).

The moderate activation energy and large

reaction energy release indicate that EE attached O4-hydrogenated thymine nucleotides rather than the C5-hydrogenated radicals and canonical anionic thymine derivatives are the most probable species in aqueous solutions leading to efficient and substantial DNA SSBs at the non-3′-end T site of a single strand DNA via a pathway involving intramolecular PT process. The aqueous phase potential energy surface along the C3′-O3′ bond rupture pathway is depicted in Figure S7a in the SI. N1-C1′ bond cleavage in 5′-dT(O4H)MPH induced by EE attachment. 8


The results obtained

Page 9 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


from 3′-dT(O4H)MPH demonstrate that the inclusion of 2′-deoxyribose and O3'-phosphate group has negligible effects on the spin density distribution localized primarily on the base moiety.

Thus,

nearly the same spin density distribution as that in 3′-dT(O4H)MPH could be expected in the radical 5′-dT(O4H)MPH. The HOMO of the gaseous 5′-dT(O4H)MPH confirms the above expectation with spin densities located at the C4, C5, and C6 atoms being 0.41, -0.20, and 0.65, respectively (Figures S8-9 in the SI).

Compared to the case of 3′-dT(O4H)MPH, relatively weak

electron affinity is estimated in 5′-dT(O4H)MPH (Table 1).

The VEA is calculated to be -0.37 eV,

which is smaller than those VEAs of non-hydrogenated 5′-dTMPH (-0.28 ~ 0.28 eV)22,25,31 In contrast, the AEA is estimated to be positive (0.40 eV), which is larger than those AEAs of 5′-dTMPH (0.17 ~ 0.40 eV)22,25,31 and the C5-hydrogenated thymine derivatives (-1.37 ~ -1.46 eV).47

The VDE of the corresponding anion [5′-dT(O4H)MPH]− is predicted to be slightly lower

(1.40 eV, Table 1) than that of [3′-dT(O4H)MPH]− anion, but much higher than those VDEs of [5′-dTMPH]− anion (0.58 ~ 0.99 eV).22,25,31 The substantial positive AEA and VDE ensure the formation of electronically stable [5′-dT(O4H)MPH]− anion.

It should be noted that the higher

VEA, AEA and VDE in 3′-dT(O4H)MPH compared to those in 5′-dT(O4H)MPH are partly due to the existence of intramolecular hydrogen-bond between the O5′-H proton and the extra negative charge localized on the base moiety in [3′-dT(O4H)MPH]− anion.22,31 Therefore, not only 3′-dT(O4H)MPH but also 5′-dT(O4H)MPH has sufficient electron affinity to form respective corresponding anion that has considerable electronic stability for subsequent C3′-O3′ or N1-C1′ bond rupture. Nearly same spin density distributions between 3′-dT(O4H)MPH and 5′-dT(O4H)MPH imply an analogous NPA charge distribution in [5′-dT(O4H)MPH]− anion to that in [3′-dT(O4H)MPH]− anion (Table 4).

The extra negative charge distributed on the base moiety is -0.88 with nearly half

(-0.39) located at the C6 atom.

As a result, a very similar structural alteration around the C6 site to

that in [3′-dT(O4H)MPH]− anion occurs in [5′-dT(O4H)MPH]− anion.

The C6 hybridization is

also forced to be transformed from sp2 in 5′-dT(O4H)MPH to sp3 in [5′-dT(O4H)MPH]− anion with the sum of the three angles ∠C5C6N1+∠C5C6H6+∠N1C6H6 being changed from 359.9° to 336.6° (Figure 4).

The related C6-C5 and C6-N1 bonds are elongated separately from 1.40 Å and 1.42 Å in

5′-dT(O4H)MPH to 1.47 Å and 1.48 Å in [5′-dT(O4H)MPH]− anion with the other bonds in the base moiety only slightly changed.

In the anion [5′-dT(O4H)MPH]−, the H2a′ atom is also the 9



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 23

closest hydrogen atom in 2′-deoxyribose moiety to the negative charge center C6 with a distance being 2.50 Å.

However, it is now the N1-C1′ bond cleavage through a pathway involving the same

intramolecular PT from the C2′ site to the C6 site dominates subsequent reaction process due to the absence of O3′-phosphate group in [5′-dT(O4H)MPH]− anion.

The complete N1-C1′ bond cleavage

pathway initiated from the neutral radical 5′-dT(O4H)MPH including EE attachment and intramolecular PT is depicted in Figure 4. The gas phase activation energy for the H2a′ proton transfer from the C2′ site to the C6 site is estimated to be 13.02 kcal/mol (Table 3), which is larger than those corresponding to the same PT process

occurred

in

[3′-dT(O4H)MPH]−

anion

(9.32

C5-hydrogenated thymine derivatives (5.8 ~ 12.5 kcal/mol).47

kcal/mol)

and

the

EE-attached

In this transition state (denoted as

TS1, verified by having only one imaginary frequency -1362.7i cm-1), the transferred H2a′ proton is 1.41 Å away from the C2′ atom and 1.44 Å to the C6 atom.

The HOMO of the TS1 state mainly

consists of a mixture of the π* orbital of the base moiety and the π orbital of the C1′-C2′ bond (Figure 2b). Electron transfer from the initially localized base moiety in the anion [5′-dT(O4H)MPH]− to the π orbital of the C1′-C2′ bond in the TS1 state (Figure S10 in the SI) shrinks the C1′-C2′ bond length from 1.54 Å to 1.51 Å. In the meanwhile, the N1-C1′ bond length is elongated from 1.43 Å to 1.48 Å with the other bonds keeping nearly unaltered (Figure 4).

The proton transferred intermediate

[5′-dT(O4H,C6H)MPH]− is 3.88 kcal/mol lower in energy than [5′-dT(O4H)MPH]− anion indicating that the intramolecular PT process is thermodynamically favorable (Table 3).

In the

intermediate [5′-dT(O4H,C6H)MPH]−, the extra negative charge is distributed mainly on the 2′-deoxyribose moiety (-0.85) based on the NPA charge distribution analysis (Table 4).

The

HOMO is now mixed mainly by the σ* orbital of the N1-C1′ bond and the p-type orbital of C2′ atom (Figure 2c). Electron transfer to the anti-bonding σ* orbital of the N1-C1′ bond (Figure S10 in the SI) elongates significantly the N1-glycosidic bond from 1.43 Å in [5′-dT(O4H)MPH]− anion to 1.52 Å in [5′-dT(O4H,C6H)MPH]− anion. The C1′-C2′ bond length continuously shrinks from 1.51 Å at the TS1 state to 1.49 Å in the intermediate [5′-dT(O4H,C6H)MPH]−.

However, it is predicted that the

alteration of the C5′-O5′ bond length is negligible (ca. 0.01 Å) in the intramolecular PT process (Figure 4).

Therefore, the sufficiently long N1-C1′ bond length and the nearly unchanged C5′-O5′

bond collectively suggest that the next reaction step is the cleavage of the N1-C1′ bond. The gas phase activation energy for the N1-glycosidic bond cleavage is estimated to be only 10


Page 11 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


2.21 kcal/mol (Table 3), which can be readily surmounted by the reaction energy released in the previous PT process (3.88 kcal/mol).

In this transition state (TS2, verified by having only one

imaginary frequency -234.4i cm-1), the N1-C1′ bond distance is extended to be 1.80 Å.

The C1′-C2′

bond continuously shrinks from 1.49 Å in the intermediate [5′-dT(O4H,C6H)MPH]− to 1.43 Å in the TS2 state having a tendency of forming C1′=C2′ double bond (Figure 4).

The N1-glycosidic

bond cleavage product is a complex consisting of a negatively charged closed-shell base analog (with the total NPA charge being -0.95) and a neutral closed-shell abasic nucleotide (Figure 4, Table 4).

A representative C1′=C2′ double bond (1.35 Å) causing the structure of 2′-deoxyribose moiety

planar is observed in the abasic nucleotide.

The reaction energy concerning the N1-C1′ bond

cleavage is 15.46 kcal/mol exothermal. The released total reaction energy from [5′-dT(O4H)MPH]− anion is 19.34 kcal/mol, indicating that the base release in 5′-dT(O4H)MPH induced by EE attachment is also thermodynamically favorable (Table 3).

Note that the C5′-O5′ bond length

changes only slightly (in a rang of 1.44~1.46 Å) along the N1-glycosidic bond cleavage pathway suggesting its relative stability in [5′-dT(O4H)MPH]− anion (Figure 4).

The gas phase potential

energy surface along the N1-C1′ bond cleavage pathway is depicted in Figure 3b.

Notably, the

activation energy for the rate-controlling intramolecular PT step is lower than those (18.9 ~ 26.6 kcal/mol) for the direct N1-C1′ bond cleavage in canonical anionic thymine derivatives.21,25-26,31 Although the energy requirements for the N1-glycosidic bond cleavage in EE-attached C5-hydrogenated thymine derivatives are even lower,47 these C5-hydrogenated species are only minor radiation products as mentioned above.41-43 Accordingly, the O4-hydrogenated thymine nucleotides are the most probable species leading to efficient and substantial base release at the 3′-end of a single strand DNA with the strand ended by a thymine residue induced by EE attachment through a pathway involving intramolecular PT process. The changes induced by solvent effects on the spin density distribution of 5′-dT(O4H)MPH and the NPA charge distribution along the whole N1-C1′ bond cleavage process are insignificant (Table 4 and Figures S8-9 in the SI).

Nevertheless, significant increases of VEA, AEA, and VDE

are predicted due to the enhanced stability of [5′-dT(O4H)MPH]− anion from the polarizable surroundings (Table 1).

In the aqueous phase, EE attachment also causes considerable structural

relaxation including the transformation of C6 hybridization from sp2 in 5′-dT(O4H)MPH to sp3 in [5′-dT(O4H)MPH]− anion (Figure S11 in the SI).

The augmented negative charge at the C6 atom

11



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

makes it a strong basic center for proton attacking.

Page 12 of 23

The aqueous phase activation energy for the

intramolecular PT from the C2′ site to the C6 site is estimated to be 16.18 kcal/mol, 3.16 kcal/mol larger than that in the gas phase (Table 3).

In the TS1 state, a mixed HOMO consisting of nearly

the same components as those in the gas phase is observed (Figure S5b in the SI).

Electron

transfer from the initially localized base moiety in the anion [5′-dT(O4H)MPH]− to the π orbital of the C1′-C2′ bond in the TS1 state makes bond length changes analogous to those in the gas phase (Figure S12 in the SI).

The proton transferred intermediate [5′-dT(O4H,C6H)MPH]− is 4.36

kcal/mol lower in energy than the anion [5′-dT(O4H)MPH]− (Table 3).

In the aqueous phase

intermediate [5′-dT(O4H,C6H)MPH]−, electron transfer to the anti-bonding σ* orbital of the N1-C1′ bond and the p-type orbital of C2′ atom makes relevant bond length changes analogous to those occurred in the gas-phase (Figures S5c and S11 in the SI).

The N1-C1′ bond in the intermediate

[5′-dT(O4H,C6H)MPH]− is readily stretched to be 1.83 Å in the TS2 state with the activation energy being only 4.99 kcal/mol, which is nearly surmounted by the reaction energy released in the last intramolecular PT process (Table 3). Closed-shell negatively charged base analog and neutral abasic nucleotide as N1-glycosidic bond cleavage products are predicted with the total reaction energy 22.32 kcal/mol exothermal (Tables 3-4, Figure S11 in the SI).

The aqueous phase potential

energy surface along the N1-C1′ bond cleavage pathway is depicted in Figure S7b in the SI. Notably, the activation energy for the rate-controlling intramolecular PT step is comparable to those (11.3 ~ 14.7 kcal/mol) occurred in the EE-attached C5-hydrogenated thymine derivatives.47

In

comparison, higher activation energies (17.5 ~ 28.8 kcal/mol) for the direct N1-C1′ bond cleavage in canonical anionic thymine derivatives are required.25-26,31 Consequently, the O4-hydrogenated thymine nucleotides are also the most probable species in aqueous solutions leading to efficient and substantial base release at the 3′-end of a single strand DNA with the strand ended by a thymine residue induced by EE attachment through a pathway involving intramolecular PT process.

CONCLUSIONS In the present work, DNA SSBs and base release induced by EE attachment to the O4-hydrogenated thymine nucleotides (3′-dT(O4H)MPH and 5′-dT(O4H)MPH) are investigated using the B3LYP/DZP++ level of theory.

Substantial electron attachment and detachment energies 12


Page 13 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


ensure the formation of the corresponding anions having sufficient electronic stability for subsequent C3′-O3′ and N1-C1′ bond ruptures. The attached EE is distributed mainly on the base moiety with the C6 atom being the extremely negative charge center.

Considerable structural

relaxation after EE attachment including the transformation of C6 hybridization from sp2 to sp3 is observed.

The enhanced negative charge located at the C6 atom makes it a strong basic center for

proton attacking.

Intramolecular PT from the C2′ site of 2′-deoxyribose moiety to the C6 site

controls reaction pathways. In [3′-dT(O4H)MPH]− anion, the intramolecular PT process is accompanied by the C3′-O3′ bond rupture.

The low activation energy (9.32 kcal/mol) for this

concerted process indicates that this pathway is, to date, the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3′-end T site.

On

the other hand, essentially spontaneous (activation energy requirement can be overcome by the reaction energy released in the last reaction step) N1-glycosidic bond cleavage following the intramolecular PT process is predicted in [5′-dT(O4H)MPH]− anion.

The moderate activation

energy (13.02 kcal/mol) for the rate-controlling intramolecular PT step suggests that base release from the N1-C1′ bond cleavage arises readily at the 3′-end of a single strand DNA with the strand ended by a thymine residue.

Solvent effects are found to increase slightly the least energy

requirements for both bond ruptures (11.23 kcal/mol for the C3′-O3′ bond rupture vs. 16.18 kcal/mol for the N1-C1′ bond cleavage), but do not change the high efficiency feature of either bond rupture. In a word, both in the gas phase and aqueous solutions, O4-hydrogenated thymine nucleotides rather than C5-hydrogenated radicals and canonical anionic thymine derivatives are the most probable species leading to efficient and substantial DNA lesions in a single strand DNA via a pathway including EE attachment and intramolecular PT process.

13



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 14 of 23

ASSOCIATED CONTENT (S) Supporting Information The calculated structures, molecular orbitals, and spin density distributions of relevant molecules including initial reactants, transition state and products in the gas phase and aqueous phase.

This

material is available free of charge via the Internet at htpp://pubs.acs.org.

AUTHOR INFORMATION Corresponding Author *E-mail: [email protected]. Notes The authors declare no competing financial interest.

ACKNOWLEDGMENTS This work was supported by NSFC (21373123, 20633060, and 20973101), NSF (ZR2013BM027) of Shandong Province. A part of the calculations were carried out at National Supercomputer Center in Jinan, Shanghai Supercomputer Center, and High-Performance Supercomputer Center at SDU-Chem.

REFERENCES (1) Steenken, S. Purine Bases, Nucleosides, and Nucleotides: Aqueous Solution Redox Chemistry and Transformation Reactions of Their Radical Cations and e− and OH Adducts. Chem. Rev. 1989, 89, 503-520. (2) Ito, T.; Baker, S. C.; Stickley, C. D.; Peak, J. G.; Peak, M. J. Dependence of the Yield of Strand Breaks Induced by γ-Rays in DNA on the Physical Conditions of Exposure: Water Content and Temperature. Int. J. Radiat. Biol. 1993, 63, 289-296. (3) Burrows, C. J.; Muller, J. G. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem. Rev. 1998, 98, 1109-1152. (4) ICRU Report Vol. 31, International Commission on Radiation Units and Measurements, 14


Page 15 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Washington, DC (1979). (5) Boudaı̈ ffa, B.; Cloutier, P.; Hunting, D.; Huels, M. A.; Sanche, L. Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20 eV) Electrons. Science 2000, 287, 1658-1660. (6) Pan, X.; Cloutier, P.; Hunting, D.; Sanche, L. Dissociative Electron Attachment to DNA. Phys. Rev. Lett. 2003, 90, 208102. (7) Martin, F.; Burrow, P. D.; Cai, Z.; Cloutier, P.; Hunting, D.; Sanche, L. DNA Strand Breaks Induced by 0-4 eV Electrons: The Role of Shape Resonances. Phys. Rev. Lett. 2004, 93, 068101. (8) Wang, C.-R.; Nguyen, J.; Lu, Q.-B. Bond Breaks of Nucleotides by Dissociative Electron Transfer of Nonequilibrium Prehydrated Electrons: A New Molecular Mechanism for Reductive DNA Damage. J. Am. Chem. Soc. 2009, 131, 11320-11322. (9) Nguyen, J.; Ma, Y.; Luo, T.; Bristow, R. G.; Jaffray, D. A.; Lu, Q.-B. Direct Observation of Ultrafast-Electron-Transfer Reactions Unravels High Effectiveness of Reductive DNA Damage. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 11778-11783. (10) Abdoul-Carime, H.; Gohlke, S.; Illenberger, E. Site-Specific Dissociation of DNA Bases by Slow Electrons at Early Stages of Irradiation. Phys. Rev. Lett. 2004, 92, 168103. (11) Ptasińska, S.; Denifl, S.; Grill, V.; Märk, T. D.; Illenberger, E.; Scheier, P. Bond- and Site-Selective Loss of H− from Pyrimidine Bases. Phys. Rev. Lett. 2005, 95, 093201. (12) Ptasińska, S.; Denifl, S.; Grill, V.; Märk, T. D.; Scheier, P.; Gohlke, S.; Huels, M. A.; Illenberger, E. Bond-Selective H− Ion Abstraction from Thymine. Angew. Chem. Int. Ed. 2005, 44, 1647-1650. (13) Ptasinska, S.; Denifl, S.; Scheier, P.; Illenberger, E.; Märk, T. D. Bond- and Site-Selective Loss of H Atoms from Nucleobases by Very-Low-Energy Electrons (

Efficient and Substantial DNA Lesions From Near 0 ... - ACS Publications

Recommend Documents