PCCP PAPER. Electron interaction with a DNA duplex: dcpdc:dgpdg. Introduction. Jiande Gu,* a Jing Wang b and Jerzy Leszczynski* b

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1 PAPER Cite this: Phys. Chem. Chem. Phys., 2016, 18, Electron interaction with a DNA duplex: dcpdc:dgpdg Jiande Gu,* a Jing Wang b and Jerzy Leszczynski* b Received 29th February 2016, Accepted 14th April 2016 DOI: /c6cp01408a Electron attachment to double-stranded cytosine-rich DNA, dcpdc:dgpdg, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 ev. The excess electron may reside on the nucleobase at the 5 0 position (dc pdc:dgpdg) or at the 3 0 position (dcpdc :dgpdg). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dc 1H pdc:dg 2-H pdg and dcpdc 2H :dgpdg 1-H. These distonic radical anions are found to be approximately 1 to 4 kcal mol 1 more stable than the normal radical anions. Intra-strand cytosine p - p transition energies are below the electron detachment energy. Inter-strand p - p transitions of the excess electron from C to G are predicted to be less than 2.79 ev. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex. Introduction There are a number of possible mechanisms leading to DNA damage. Among them, electron attachment to DNA is considered to be one of the crucial factors that induce damages in DNA The study of such processes is important from both the basic viewpoint as well as due to possible environmental implications and medical applications. Understanding the process of electron attachment to DNA is also the key step to reveal the secrets of electron transfer through DNA. 15,16 It is well known that due to their relatively large electron affinity pyrimidine bases thymine (T) and cytosine (C) are the primary hosts for the excess electron during the process of electron attachment to DNA However, the electron capture ability of these pyrimidine bases is affected by their local environments. The experimental study by Ray et al. in 2005 revealed that that electron capture capability of pyrimidines in double-stranded DNA is less efficient than that in singlestranded CT-rich oligomers. Besides, the number of C bases in the strands seems to affect their electron capture ability. 25 Accordingly, a detailed description of the local structure at the a Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai , China. jiande@icnanotox.org b Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA. jerzy@icnanotox.org Electronic supplementary information (ESI) available. See DOI: /c6cp01408a electronic molecular orbital level for cytosine-rich fragments in both single-stranded and double-stranded DNA segments is essential for understanding and predicting the elementary mechanisms of electron attachment induced reactions in the cytosine-rich DNA oligomers. The last decade has been an eventful period for the electron attachment to the cytosine-centered DNA studies. Such investigations have been performed in a very systematic manner. The model systems adapted in these studies range from nucleobase, nucleoside, nucleotide monomers up to single-stranded nucleotide oligomers The studies of electrons interacting with the realistic models of DNA such as dinucleoside phosphate deoxycytidylyl-3 0,5 0 - deoxyguanosine (dcpdg), dinucleoside phosphate deoxyguanylyl- 3 0,5 0 -deoxycytidine (dgpdc), 23 and cytosine-centered trinucleoside phosphate (dgpdcpdg) 24 have been performed using reliable theoretical approaches. Recently, electron attachment to a cytosinerich DNA segment, dinucleoside phosphate deoxycytidylyl-3 0,5 0 - deoxycytidine (dcpdc), has been studied using the most appropriate (M06-2X) density functional method. 26 These studies suggest that the cytosine base is a substantial electron acceptor and the excess electron is distinctly localized in one of the cytosine bases in the electron attached DNA fragment. Electron attachment to DNA strongly affects the local structure of the base on which the electron is located, and also alters the corresponding base base stacking patterns. 23,24,26 Electron attachment to double-stranded cytosine-related DNA has been modeled using the G:C base-pair, the dg:dc This journal is the Owner Societies 2016 Phys. Chem. Chem. Phys., 2016, 18,

2 Paper nucleoside-pair, 29 the phosphate deoxyguanyl-3 0,5 0 -deoxycytidine dimer [dgpdc] 2 31 and the cytosine-rich trinucleoside phosphate dimer dgpdgpdg:dcpdcpdc. 32 These studies reveal that electron attachment to the cytosine base in the double-stranded DNA tends to induce proton transfer from guanine to cytosine with excess electrons. Moreover, the base base stacking pattern seems to be interrupted, as a result of electron attachment. 31,32 Unfortunately, due to the limitations of the applied computational methodology (the B3LYP approach of density functional theory), in describing p p stacking, these studies are not able to provide detailed information related to the changes in the local base base stacking patterns. However, such information is necessary for understanding the mechanism of one electron migration from base to base through the DNA double-helix. In DNA oligomers, the excess electron may be located at different sites, forming various radical anions. 26,33 The studies of these local minimum structures of the radical anions could reveal the favored positions of an attached excess electron in DNA oligomers and reveal the local structural variations due to electron attachment. These data are imperative for understanding the details of electron migration along the DNA strands. As a primary step towards exploring the mechanism of electron capture and electron transfer mechanisms involving a cytosine-rich DNA double helix, here we report theoretical investigations of electron attachment to the cytosine-rich DNA double-strand segment dinucleoside phosphate deoxycytidylyl- 3 0,5 0 -deoxycytidine-dinucleoside phosphate deoxyguanylyl-3 0,5 0 - deoxyguanosine (dcpdc:dgpdg Fig. 1). This model represents the minimal meaningful unit of a cytosine-rich doublestranded DNA helix. Investigations of the different structures of the radical sites of this system provide information on how local structures are affected by excess electron migration from cytosine to cytosine, an important and basic step in electron transfer through DNA strands. Moreover, the information of electron excitations in these electron-localized radical anions revealed in the present study might eventually guide and lead to future experimental determination of the target systems. Theoretical methods Three basic issues should be considered when selecting a suitable approach in the quantum chemical study of electron interaction with DNA/RNA segments. The applied approach should be: (1) accurate in describing base base stacking, (2) reliable for predicting electron affinity of DNA/RNA bases, and (3) reasonable accurate in exploring the excitation of electrons. Recently developed Minnesota density functional M06-2X is the one of the methods that complies with the above criteria. Studies of the stacked bases have demonstrated that the geometrical parameters of the stacking patterns predicted using the M06-2X functional are very close to those predicted using the MP2 method (the differences in base base distances are less than 0.02 Å, and in base base angles less than 11). 37 The stacking energy differences between the M06-2X and MP2 methods are less than 1 kcal mol 1 (0.04 ev). 37 The electron affinities of the five PCCP Fig. 1 Two views of the optimized geometries of dcpdc:dgpdg in aqueous solution (PCM model). Here O 1 and O 2 are the geometric centers of atoms N3, N1, and C5 of dc 1 and of dc 2, and N1, N3, and C5 of dg 1 and of dg 2, respectively. v 1 and v 2 are the plane vectors defined by atoms N3, N1, and C5 of dc 1 and of dc 2, and N1, N3, and C5 of dg 1 and of dg 2, respectively. t 1 are the vectors of the bases pointing from O 1 to the atoms N4 of dc 1 and dg 1, respectively. t 2 are the vectors of the bases pointing from O 2 to the atoms N4 of dc 2 and dg 2, respectively. O 0 1 is the projection of O 1 on the base-plane of C 2 (or G 2 ). For base base stacking pattern parameters and inter-strand H-bonding parameters see Tables 1 and 2. Color conventions: grey: carbon; blue: nitrogen; red: oxygen; orange: phosphorous. nucleobases evaluated by the M06-2X approach are close to those predicted using the G4 method. 17 Specifically, the AEAs of cytosine predicted by the M06-2X/ G(d,p) approach is only 0.07 ev lower than G4 predictions. 17 Moreover, a recent benchmark exploration of the performance of time-dependent DFT (TDDFT) methods reveals that M06-2X is the best overall performing GH-mGGA functional among the 24 tested functionals. 38 In the present study the M06-2X functional and the valence double zeta basis set, augmented with d-type polarization functions as well as the diffuse functions for heavy elements and p-type polarization functions for H, namely 6-31+G(d,p), 39 were used in the calculations. Geometries of the nucleotide dimer dcpdc:dgpdg and the corresponding radical anions were optimized using the M06-2X/6-31+G(d,p) approach. The Barone Tomasi polarizable continuum model (PCM) 40 with the standard dielectric constant of water (e = 78.39) was used to simulate the solvated environment of an aqueous solution. The adiabatic electron affinity was computed as the difference between the absolute energies of the appropriate neutral and anion species at their respective optimized geometries, AEA = E neut E anion. The time-dependent density functional theory approach has become widely applied for studying electronic transitions because of its remarkably low computational cost and high reliability as compared to other Phys. Chem. Chem. Phys., 2016, 18, This journal is the Owner Societies 2016

3 sophisticated quantum chemical methods for the valenceexcited states In the performed test calculations the TDDFT approach was used with the M06-2X functional. We predicted a value of 254 nm for the first electronic transition in the neutral dcpdc:dgpdg duplex in the PCM modeled polarizable surroundings. This is about 3 nm less than the experimental peak value of 257 nm for the same complex in aqueous solutions (see In the present study, the TDDFT approach (M06-2X functional) was employed to calculate the electronic transition energies of the electron attached species. The number of excited states included in the TDDFT calculations amounts to 40. The symmetric properties (s, p, lone pair, or Rydberg state) of the excited states were examined by the corresponding orbitals. The GAUSSIAN 09 system of DFT programs 44 was used for all computations. Results and discussion A. Neutral dcpdc:dgpdg Theinitialstructureoftheneutral dcpdc:dgpdg was constructed based on our previous studies of the B-form of a single-stranded DNA dimer dcpdc by pairing dgpdg through the Watson Crick type G:C H-bonding pair. Geometric optimizations without constrains of this initial structure were performed both in aqueous solutions (modeled by the PCM) and in the gas phase. The optimized geometry of dcpdc:dgpdg in the neutral form in aqueous solution is depicted in Fig. 1 and the base base stacking pattern parameters are reported in Table 1, along with those in the gas phase. Of course, this structure is only one of the possible local minima on the potential energy surface. However, it represents a DNA helical unit in the B-form, which is of biological importance. In the presence of a polarized medium, in neutral dcpdc: dgpdg, the base-center of dc 1 (O 1, defined as the geometric center of N3, N1, and C5 of dc 1 ) is located Å away from the base-plane of dc 2 (C 2 : defined by N3, N1, and C5 of dc 2 ). The larger distance (4.106 Å) between the base-centers, R(O 1,O 2 ), indicates that the bases slide considerably away along the base-planes (R(O 2,O 0 1 ) amounts to Å for the projected base base center distance). Cytosine base planes are found to be located noticeably away from parallel configuration. The angle between the base-plane vectors (f(v 1, v 2 ), v 1 and v 2, defined by N3, N1, and C5 of dc 1 and that of dc 2, respectively) is calculated to be In dcpdc:dgpdg the base-center of dg 1 (O 1, defined as the geometric center of N1, N3, and C5 of dg 1 ) is Å away from the base-plane of dg 2 (G 2 : defined by N1, N3, and C5 of dg 2 ). The distance of Å between the base-centers, R(O 1,O 2 ), indicates that the bases slide away along the base-planes R(O 2, O 0 1 ) by Å. However, guanine base planes are not far away from parallel configuration; the stacked guanine bases tilt by 2.31 in dcpdc:dgpdg. The twist between the stacked bases (f(t 1, t 2 ), see Table 1) is computed to be for dcpdc and for dgpdg. These parameters are close to the typical values observed in B-DNA. 27,33,45 Table 1 Geometric parameters of the base base stacking pattern of the optimized structures of the neutral and the anionic dcpdc:dgpdg. Distances in (Å) and angles in (1). Plain: in PCM modeled aqueous solutions; italic: in gas-phase Species R(O 1,O 2 ) a R(O 1,B 2 ) b R(O 2,O 1 0 ) c f(v 1, v 2 ) d f(t 1, t 2 ) e dcpdc:dgpdg C strand G strand dc pdc:dgpdg C strand G strand dcpdc :dgpdg C strand G strand Paper a R(O 1,O 2 ): distance between the base-centers O 1 and O 2, see Fig. 1. b R(O 1,B 2 ): distance between the base-center and the base-plane of the stacked base. c R(O 2,O 1 0 ): distance between the base-center O 2 and the projected base-center O 1 (projected on the base-plane of B 2 ), defined as (R(O 1,O 2 ) 2 R(O 1,B 2 ) 2 ) 1/2. d f(v 1, v 2 ): angle between the base-plane vectors. e f(t 1, t 2 ): angle between the base-direction vectors lying on the base-plane. H-bond lengths in this helix unit are computed to span from Å to Å. H-bonding in the dc 1 :dg 2 pair is slightly weaker than that in dc 2 :dg 1, as suggested by the somewhat longer H-bond distances in the dc 1 :dg 2 pair (Table 2). The propeller twist, depictured by the angle between the H-bonded C and G base-plane vectors, is evaluated to be for the dc 1 :dg 2 pair and for the dc 2 :dg 1 pair. Due to their different local environments the base rotation in pdc 2 seems to be less constrained than in dc 1 p. A relatively large propeller twist in the dc 2 :dg 1 pair compliments stronger H-bonding interactions. Interestingly, cytosine cytosine stacking is perturbed by the presence of H-bonding in the double stranded dcpdc:dgpdg, as compared to the cytosine-rich DNA single strand segment dcpdc. In dcpdc the base base slide is shorter (2.279 Å vs Å) and the base base tilt is smaller (8.61 vs ). 26 Notably, solvent effects have only minor influence on the stacking patterns of the neutral dcpdc:dgpdg complex (see Table 1). The twist angle of guanine guanine stacking is about 21 larger in the gas phase than that in aqueous solutions. However, solvent effects are significant for the H-bonding pattern between the strands. In the gas phase the H-bond distances between O2 of C and H(N2) of G (h1) are about 0.06 to 0.09 Å longer than those in the PCM level model (1.923 Å vs Å for dc 1 :dg 2 ; Å vs Å for dc 2 :dg 1 ). Meanwhile, the gas phase H-bond distances between H(N4) of C and O4 of G (h3) are about 0.10 to 0.15 Å shorter than those revealed by the PCM approach (1.790 Å vs Å for dc 1 :dg 2 ; Å vs Å for dc 2 :dg 1 ). However, no significant variations are observed in the comparison of the H-bond This journal is the Owner Societies 2016 Phys. Chem. Chem. Phys., 2016, 18,

4 Paper PCCP Table 2 Geometric parameters of the inter-strand H-bonding patterns of the optimized structures of the neutral and the anionic dcpdc:dgpdg. Distances in (Å) and angles in (1). Plain: in PCM modeled aqueous solutions; italic: in gas-phase Species h1 a h2 b h3 c f(v 1, v 2 ) d dcpdc:dgpdg dc 1 :dg dc 2 :dg dc pdc:dgpdg dc 1 :dg dc 2 :dg dcpdc :dgpdg dc 1 :dg dc 2 :dg Fig. 2 The optimized structure of dc pdc:dgpdg and the corresponding SOMO in aqueous solution. For geometric parameters see Tables 1 and 2. For color conventions see Fig. 1. a h 1 : H-bond distance between O2 of C and H(N2) of G, see Fig. 1. b h 2 : H-bond distance between N3 of C and H(N1) of G, see Fig. 1. c h 3 : H-bond distance between H(N4) of C and O6 of G, see Fig. 1. d f(v 1, v 2 ): angle between the H-bonded C and G base-plane vectors. distance between N3 of C and H(N3) of G (h2) in the gas phase and in aqueous solutions. Solvent effects seem to weaken the H-bonding between the strands. This is further confirmed by the analysis of the H-bonding energy of the dcpdc:dgpdg complex. Based on the optimized dimer and monomers, the binding energy of the neutral duplex is computed to be kcal mol 1 (2.43 ev) in the gas phase while it is kcal mol 1 (1.40 ev) in aqueous solutions. Overall, the influences of the solvent effects on the structural characteristics are limited. Considering that large molecular complexes such as dcpdc:dgpdg are difficult to be prepared in the gas-phase experiments, solvated dcpdc:dgpdg complexes are more realistic models representing DNA related experiments. Therefore, unless addressed, the following discussion will be based on the results derived from the studies in aqueous solutions modeled by the PCM approach. B. Cytosine-centered radical anions of dcpdc:dgpdg The excess electron in the radical anions of the duplex unit is found to reside on the nucleobase of either dc 1 (dc pdc: dgpdg, Fig. 2) or dc 2 (dcpdc :dgpdg, Fig. 3). The optimized geometry of dc pdc:dgpdg demonstrates that due to electron attachment the structure of the cytosine in dc 1 (C 1 ) is significantly different from that in the neutral species. The elongated bond lengths for C2QO2 (1.26 Å vs Å), N3 C4 (1.38 Å vs Å), C4 N4 (1.39 Å vs Å), and C5 C6 (1.40 Å vs Å) are determined in the C 1 cytosine of dc pdc:dgpdg. Meanwhile, the geometric parameters of nucleobase C 2 are literally the same as those in the neutral form. The geometric feature of dc pdc strongly indicates that the nucleobase C 1 is the principal host of the unpaired electron. The Natural Population Analysis (NPA) reveals that over 0.84 negative charge resides on the C 1 moiety in Fig. 3 The optimized structure of dcpdc :dgpdg and the corresponding SOMO in aqueous solution. For geometric parameters see Tables 1 and 2. For color conventions see Fig. 1. dc pdc:dgpdg (see Table 3). Meanwhile, 0.06 extra negative charge is on the ribose connecting the C 1, and 0.06 extra negative charge is on the G 2 group (H-bonding to the C 1 )in dc pdc:dgpdg. Molecular orbital analysis reveals that the excess electron occupies the first p anti-bonding orbital of C 1, as illustrated by the singly-occupied molecular orbital (SOMO) in Fig. 2. Analogously, the geometric feature and the SOMO of dcpdc :dgpdg (see ESI and Fig. 3) suggest that the excess electron is trapped mainly on the C 2 moiety. The corresponding NPA charge analysis indicates that the C 2 fragment attracts about 0.85 negative charge (Table 3) in the radical anion dcpdc :dgpdg. The C 2 H-bonded base, G 1, hosts about 0.05 extra negative charge in this radical anion. C. Base base stacking pattern Electron attachment to the bases of the cytidine oligomer induces alterations in the base-stacking pattern in dcpdc: dgpdg. While the stacked guanine bases remain parallel to each other, the cytosine base planes are located significantly away from parallel configuration. The base-planes tilt by in dcpdc :dgpdg and by in dc pdc:dgpdg. The large value of the cytosine cytosine tilt angle in dc pdc:dgpdg results from the existence of a center of the negative charge of C 1 that attracts the positively charged H to C5 and N4 of C 2, Phys. Chem. Chem. Phys., 2016, 18, This journal is the Owner Societies 2016

5 Paper Table 3 Natural population analysis of charge distributions of dcpdc:dgpdg and the corresponding radical anions (in a.u.) a Species C 1 C 2 s 1 s 2 p G 1 G 2 S 1 S 2 P dcpdc:dgpdg dc pdc:dgpdg D dcpdc :dgpdg D a C 1 and C 2 are the nucleobases of dc 1 and dc 2,s 1 and s 2 are the corresponding sugar moieties, and p is the phosphate group of the dcpdc strand. G 1 and G 2 are the nucleobases of dg 1 and dg 2,S 1 and S 2 are the corresponding sugar moieties, and P is the phosphate group of the dcpdc strand. D is the difference between anion and neutral species. causing the rotation of the base C 2 around the glycosidic bond. It is important to note that, although there is no intra-strand H-bonding type interaction between the successive cytosine bases in dcpdc :dgpdg, the base-planes still tilt by a large angle (19.21). This implies that an excess electron is not a beneficial addition to the stability of the stacked bases. This conclusion is consistent with the results of the previous studies of the cytosine-rich oligomer (dcpdc), guanine-rich oligomers (dgpdg and dgpdcpdg), and the GC oligomers. 24,26,33 It is important to note that the base base stacking pattern of the dgpdg strand in the radical anions of dcpdc:dgpdg is not affected by the excess electron which resides on cytosine. Therefore, electron attachment to cytosine sites in DNA double strands seems to cause stacking pattern disturbances only within the strand. D. Inter-strand H-bonding pattern The values of calculated geometrical parameters indicate that electron attachment to the cytosine in the double stranded oligomer alter the inter-strand H-bonding pattern. The H-bonds h1 and h2 of dc :dg are reduced to 1.77 Å and 1.78 Å in dc pdc:dgpdg, and to 1.78 Å and 1.78 Å in dcpdc :dgpdg, respectively. The corresponding bond lengths in the neutral dcpdc:dgpdg range from 1.84 Å to 1.89 Å. On the other hand, the H-bond h3 of dc :dg increases to 2.13 Å in dc pdc:dgpdg, and to 1.90 Å in dcpdc :dgpdg, respectively. The corresponding bond lengths in the neutral dcpdc:dgpdg are 1.94 Å and 1.84 Å, respectively. Similar variations have also been reported in the previous studies of G:C and dg:dc pairs Slight elongations of h1, h2, and h3 bonds are observed for the neutral base-pairs (dc 2 :dg 1 of dc pdc:dgpdg and dc 1 :dg 2 of dcpdc:dgpdg ), in the radical anions of the helix segment. The excess negative charge on cytosine is found to increase the propeller deformation of dc 1 :dg 2 by ca. 101 in both dc pdc:dgpdg and dcpdc: dgpdg. Nevertheless, the propeller angle of dc 2 :dg 1 is less affected by the extra negative charge accumulation on cytosine. Compared to the base base stacking pattern, the area of influence of electron attachment to the cytosine sites on the H-bonding pattern is more diffused. It may affect the adjacent base-pairs through H-bonding interactions. E. Inter-strand proton transfer Electron attachment to the cytosine in the double stranded oligomer increases the negative charge distributions on the excess electron hosts. Consequently, these accumulated negative charges improve the proton accepting ability of the cytosine bases. In the radical anions of dcpdc:dgpdg the proton linked to N3 of G has been found to have a tendency to shift to N3 of the cytosine that possesses the excess electron, forming the charge-radical separated radical anions dc 1H pdc:dg 2-H pdg in dc pdc:dgpdg (Fig. 4), and dcpdc 2H :dgpdg 1-H in dcpdc :dgpdg (Fig. 5). The natural population analysis confirms that due to proton transfer over 0.84 negative charge resides on the G 2-H moiety in dc 1H pdc:dg 2-H pdg (see Table 4), and the corresponding SOMO in Fig. 4 indicates that the radical remains on the C 1H moiety. Analogously, over 0.84 negative charge is determined on the G 1-H moiety by the NPA study and Fig. 4 The optimized structure of dc 1H pdc:dg 2-H pdg and the corresponding SOMO in aqueous solution. For geometric parameters see Tables 5 and 6. For color conventions see Fig. 1. Fig. 5 The optimized structure of dcpdc 2H :dgpdg 1-H and the corresponding SOMO in aqueous solution. For geometric parameters see Tables 5 and 6. For color conventions see Fig. 1. This journal is the Owner Societies 2016 Phys. Chem. Chem. Phys., 2016, 18,

6 Paper PCCP Table 4 Natural population analysis of charge distributions of dc 1H pdc:dg 2-H pdg and dcpdc 2H :dgpdg 1-H (in a.u.) a Species C 1 C 2 s 1 s 2 p G 1 G 2 S 1 S 2 P dc 1H pdc:dg 2-H pdg D dcpdc 2H :dgpdg 1-H D a C 1 is protonated (C 1H ) and G 2 is deprotonated (G 2-H )indc 1H pdc:dg 2-H pdg and C 2 is protonated (C 2H ) and G 1 is deprotonated (G 1-H )in dcpdc 2H :dgpdg 1-H. D is the difference between anion and neutral species. See Table 3. the radical is found on the C 1H moiety by molecular orbital analysis in dc 1H pdc:dg 2-H pdg (see Table 4 and Fig. 5). Inter-strand proton transfer modifies the inter-strand H-bonding pattern (Table 5). The length of H-bonds h1 of dc 1 :dg 2 (1.77 Å) increases to 1.92 Å in dc 1H :dg 2-H. Contrarily, the length of h3 of dc 1 :dg 2 (2.13 Å) reduces to 1.95 Å in dc 1H :dg 2-H. Similar changes are also observed in dc 2 :dg 1 and dc 2H : dg 1-H (see Table 5). It is crucial that the inter-strand proton transfer does not cause large disturbances in the base base stacking patterns of the radical anions of dcpdc:dgpdg (see Table 6). The changes in base base separations are within 0.05 Å and those in base base tilt angles are limited to 21. Using various models previous studies suggest that the proton transfer in the G:C radical anions tends to result in the formation of an anion-radical-center separated stable distonic radical anion C H :G -H In the present study, the total energy of the distonic radical anion dc 1H pdc:dg 2-H pdg is about 0.95 kcal mol 1 (0.04 ev) below dc pdc:dgpdg, and that of dcpdc 2H :dgpdg 1-H is 3.58 kcal mol 1 (0.16 ev) below dcpdc :dgpdg, in aqueous solutions. However, the stability preference of the distonic radical anion is not revealed for dcpc:dgpdg radical anions in the gas phase. The total energy of dc 1H pdc:dg 2-H pdg is about 2.01 kcal mol 1 (0.08 ev) above dc pdc:dgpdg, and that of dcpdc 2H :dgpdg 1-H is literally the same as dcpdc :dgpdg in the gas phase study. Similar results have also been observed for the sandwiched dg:dc pair in the study of (dg:dc) This phenomenon Table 5 Geometric parameters of the inter-strand H-bonding patterns of the optimized structures of the distonic radical anions dc 1H pdc: dg 2-H pdg and dcpdc 2H :dgpdg 1-H. Distances in (Å) and angles in (1). Plain: in PCM modeled aqueous solutions; italic: in gas-phase Species h1 a h2 b h3 c f(v 1, v 2 ) d dc 1H pdc:dg 2-H pdg dc 1H :dg 2-H dc 2 :dg dcpdc 2H :dgpdg 1-H dc 1 :dg dc 2H :dg 1-H a h 1 : H-bond distance between O2 of C and H(N2) of G, see Fig. 1. b h 2 : H-bond distance between N3 of C and H(N1) of G in neutral dc:dg and H(N3)ofCandN1ofGinprotontransferreddC H :dg -H,seeFig.1and3. c h 3 : H-bond distance between H(N4) of C and O6 of G, see Fig. 1. d f(v 1, v 2 ): angle between the H-bonded C and G base-plane vectors. Table 6 Geometric parameters of the base base stacking pattern of the optimized structures of the distonic radical anions dc 1H pdc:dg 2-H pdg and dcpdc 2H :dgpdg 1-H. Distances in (Å) and angles in (1). Plain: in PCM modeled aqueous solutions; italic: in gas-phase Species R(O 1,O 2 ) a R(O 1,B 2 ) b R(O 2,O 1 0 ) c f(v 1, v 2 ) d f(t 1, t 2 ) e dc 1H pdc:dg 2-H pdg C strand G strand dcpdc 2H :dgpdg 1-H C strand G strand a R(O 1,O 2 ): distance between the base-centers O 1 and O 2, see Fig. 1. b R(O 1,B 2 ): distance between the base-center and the base-plane of the stacked base. c R(O 2,O 1 0 ): distance between the base-center O 2 and the projected base-center O 1 (projected on the base-plane of B 2 ), defined as (R(O 1,O 2 ) 2 R(O 1,B 2 ) 2 ) 1/2. d f(v 1, v 2 ): angle between the base-plane vectors. e f(t 1, t 2 ): angle between the base-direction vectors lying on the base-plane. suggests the strong environment dependence of the interstrand proton transfer. F. Electron affinities The predicted stability (from an energetic point of view) of the radical anions follows the order: dc pdc:dgpdg 4 dcpdc : dgpdg (Table 7). The AEA is predicted to be 2.23 ev for the formation of dc pdc:dgpdg and 2.13 ev for the formation of the dcpdc :dgpdg anion. The AEA of dc pdc:dgpdg amounts to approximately 0.25 ev more than the value of the corresponding single strand anions dc pdc (1.98 ev without zero-point energy correction 33 ). Parallel to dc pdc:dgpdg, the value of AEA of dcpdc :dgpdg is 0.24 ev larger than that of dcpdc (1.89 ev without zero-point energy correction 33 ). Thus, the pairing between dcpdg and dgpdg increases the electron capture ability of dcpdc by 0.24 to 0.25 ev in aqueous solutions. It should be noted that in aqueous solutions the AEA of the cytosine nucleobase is very close to that of the cytosine:- guanine base pair (1.89 ev vs ev). Therefore, the electron capture ability enhancement in the radical anions of dcpdc: dgpdg should not be attributed to the H-bonding between the base-pairs, rather, it reflects the collective effects of the pairing between the nucleotide oligomers. The AEA of dcpdc :dgpdg is about 0.1 ev smaller than that for dc pdc:dgpdg. Since the cytosine bases in dcpdc Phys. Chem. Chem. Phys., 2016, 18, This journal is the Owner Societies 2016

7 Paper Table 7 (italic) Theoretical predictions for the AEAs (in ev) of cytidine oligomers dcpdc:dgpdg and dcpdc in aqueous solutions (plain) and in the gas phase Process AEA VEA a VDE b dcpdc:dgpdg - dc pdc:dgpdg 2.23 (0.89) 1.56 (0.21) 2.85 (1.81) dcpdc:dgpdg - dcpdc :dgpdg 2.13 (0.56) 2.64 (1.43) dcpdc:dgpdg - dc 1H pdc:dg 2-H pdg 2.27 (0.80) 3.39 (2.42) dcpdc:dgpdg - dcpdc 2H :dgpdg 1-H 2.88 (0.57) 3.26 (2.11) dcpdc - dc pdc 1.98 c 1.32 c 2.59 c dcpdc - dcpdc 1.89 c 2.40 c a VEA = E(neutral) E(anion); the energies are evaluated using the optimized neutral structures. b VDE = E(neutral) E(anion); the energies are evaluated using the optimized anion structures. c Ref. 26. are more efficiently stacked than those in dc pdc this 0.1 ev difference might be attributed to the stacking interaction between the bases that usually reduces the electron affinity of cytosine in DNA. This reducing effect of electron capture ability due to stacking interactions can also be seen in the single strands of DNA. 26 The dgpdc stacked oligomers possess smaller AEA values ( ev), 14,17 as compared to the data revealed in the present study of dcpdc:dgpdg. This is consistent with the experimental observations that the number of C bases affects the electron capture ability of the single strand of DNA in a monolayer. 25 The vertical attachment energy (VEA) and the corresponding electron state of dcpdc:dgpdg have been studied to understand the very first step of electron attachment. The VEA value is calculated to be 1.56 ev in the PCM level modeled aqueous solutions. The molecular orbital analysis demonstrates that the excess electron is captured by the coupled p anti-bonding orbitals of the stacked cytosine bases in the nascent stage of electron attachment (Fig. 6). Subsequent geometric distortions and de-coupling of the molecular orbitals of cytosine bases lead to the more stable one-base-centered radical anions. This scenario is consistent with the previous suggestion that the excess electron tends to disrupt the stacking pattern. A similar phenomenon is seen in the dcpdc single strand study. 26 Basepairing between dcpdc and dgpdg does not encourage the excess electron to be accumulated between the stacked cytosine bases. A previous study concludes that the AEA for the formation of the phosphate-centered radical anion in DNA is between 1.20 ev and 1.60 ev. 17,33 The formation of phosphate-centered radical anions in general results in large structural distortions in the phosphate group. The excess electron trapped in the coupled p anti-bonding orbitals of the cytosine moieties at the Fig. 6 The SOMO of the dcpdc:dgpg with an electron vertically attached (radical anion with the stable structure of the neutral dcpdc:dgpdg) in aqueous solutions. first stage of attachment excludes its redistribution to the far side phosphate groups. In this case, electron attachment to the phosphate group of dcpdc:dgpdg is less viable. The cytosine-centered radical anions of dcpdc:dgpdg are electronically stable. The vertical electron detachment energy (VDE) is predicted to be 2.85 ev for dc pdc:dgpdg and 2.64 ev for dcpdc :dgpdg, respectively. In this case, interstrand proton transfer is viable because the corresponding energy barriers have been estimated to be less than 4 kcal mol 1 (0.17 ev) in aqueous solutions. 28,29,32 The inter-strand proton transferred radical anions are even more stable. The VDE of dc 1H pdc:dg 2-H pdgis3.39evandthatofdcpdc 2H :dgpdg 1-H is 3.26 ev in aqueous solutions. Detachment of the excess electron from the radical anions is difficult due to thermal motions. As expected, the electron accepting ability of dcpdc:dgpdg is smaller in the gas phase than in aqueous solutions. The AEA of the formation of dc pdc:dgpdg is 0.89 ev and that of dcpdc :dgpdg amounts to 0.56 ev. The electron affinity of this complex has a strong site preference. This site preference is partly related to the position of the phosphate group in the nucleotides, as can be seen from the studies of electron attachment to 3 0 -dcmp (AEA = 0.44 ev) and 5 0 -dcmp (AEA = 0.34 ev) in the gas phase Significant VDEs of the radical anions of dcpdc:dgpdg (ranging from 1.43 to 2.42 ev) suggest that such processes as electron migration through bases are feasible in the gas phase. G. Electronic spectra The neutral dcpdc:dgpdg duplex is colorless. TDDFT calculations predict that its excitation energy of the first electronic transition is 4.9 ev (254 nm, about 3 nm less than the experimental peak value of 257 nm) in aqueous solutions. The corresponding radical anions of dcpdc:dgpdg are expected to have much lower excitation states due to the excess electron that locates on the p* anti-bonding orbital of cytosine bases. Since the VDE of dc pdc:dgpdg is 2.85 ev and that of dcpdc :dgpdg is 2.64 ev, only the first five observable transitions will be presented and discussed below (Table 8). The computed electronic transition energies of dc pdc:dgpdg and dcpdc :dgpdg are lowforthefirstexcitation:1.70ev(727nm)fordc pdc:dgpdg, and1.47ev(843nm)fordcpdc :dgpdg, respectively. Molecular orbital analysis indicates that this first excitation corresponds to the p - p transition of the unpaired electron between the nucleobase C 1 and C 2 in the radical anions of dcpdc:dgpdg. This journal is the Owner Societies 2016 Phys. Chem. Chem. Phys., 2016, 18,

8 Paper Table 8 The predicted transition energies (DE) and the oscillator strengths (f) of the first five transitions of the radical anions of dcpdc:dgpdg a PCCP dc pdc:dgpdg dcpdc :dgpdg dc 1H pdc:dg 2-H pdg dcpdc 2H :dgpdg 1-H State DE (ev) f DE (ev) f DE (ev) f DE (ev) f S (726) (843) (615) (575) (727) (801) S (584) (601) (537) (525) (584) (612) S (513) (552) (448) (435) (554) (577) S (445) (484) (398) (382) S (443) (383) (371) a Numbers in parentheses are in nm. Bold is for radical anions of single stranded dcpdc (ref. 26) for comparison. Fig. 7 The predicted absorption spectra of dc pdc:dgpdg and dcpdc :dgpdg. Therefore, this excitation can be viewed as the electron migration along DNA. For comparison, C 1H and C 2 p - p transition energies are 2.02 ev (615 nm) and 2.16 ev (575 nm) for the corresponding inter-strand proton transferred radical anions. Also other p - p transitions of the excess electron are predicted from C to G, with the excitation energy of 2.79 ev or 445 nm (the fourth excitation) in dc pdc:dgpdg, and with 2.56 ev or 484 nm in dcpdc :dgpdg. The analogous transition is also calculated for dc 1H pdc:dg 2-H pdg (3.12 ev or 398 nm) and dcpdc 2H :dgpdg 1-H (3.25 ev or 382 nm). The simulated visible absorption spectra of the radical anions of dcpdc:dgpdg (ranging from 500 nm to 700 nm) are depicted in Fig. 7. Thus, the cytosine-rich radical anions of the duplexes are expected to exhibit a unique color in aqueous solutions. Conclusions Electron attachment to double-stranded cytosine-rich DNA has been studied computationally, employing density functional theory with the M06-2X functional. Electron distribution patterns for the radical anions of dcpdc:dgpdg have been explored both in the gas phase and in aqueous solution. In aqueous solutions a significant value (2.2 ev) of electron affinity for the formation of the cytosinecentered radical anion in DNA is revealed. Without the influence of the polarizable medium the corresponding AEA values range from 0.56 to 0.89 ev. Solvent effects are vital for the stabilization of the radical anions. The excess electron may reside on the nucleobase at the 5 0 position (dc pdc:dgpdg) or at the 3 0 position (dcpdc :dgpdg). Inter-strand proton transfer between the radical anion centered cytosine and the paired guanine results in formation of the radical anion center separated complexes dc 1H pdc:dg 2-H pdg and dcpdc 2H :dgpdg 1-H. In aqueous solutions these distonic radical anions are found to be about 1 to 4 kcal mol 1 (0.04 to 0.17 ev) more stable than the normal radical anions of dcpdc:dgpdg. The base base stacking pattern of the dgpdg strand is not affected by the excess electron that resides on cytosine. Electron attachment to cytosine sites in DNA double strands causes stacking pattern disturbances only within the affected strand. However, the influence of electron attachment to cytosine sites on the H-bonding pattern is more diffused. The excess negative charges on cytosine increases the propeller distortion of dc 1 :dg 2 by ca. 101 in both dc pdc:dgpdg and dcpdc :dgpdg. Nevertheless, the propeller angle of dc 2 :dg 1 is less affected by the extra negative charge accumulation on cytosine. This information is vital for understanding and exploring the cytosine cytosine electron migration mechanism. Energies of electron p - p transition from intra-strand cytosine to its neighboring cytosine (1.47 ev to 2.16 ev) are below the electron detachment energy. Inter-strand proton transfer from dg to dc is therefore unlikely to block the electron transfer through DNA at the cytosine sites. Other p - p transitions of the excess electron from C to G with the excitation energy of 2.56 ev to 2.79 ev are predicted, suggesting that electron transfer might also occur through the inter-strand base base jumping mode. Detection of the existence of the base-centered radical anion is crucial for experimental studies of DNA. An analysis of absorption visible spectra reveals the absorption bands ranging Phys. Chem. Chem. Phys., 2016, 18, This journal is the Owner Societies 2016

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