Electron Attachment to the DNA Bases Adenine and Guanine and Dehydrogenation of Their Anionic Derivatives: A Density Functional Study
Hujun Xie Zexing Cao*
Department of Chemistry, Xiamen University
Xiamen, P. R. China 361005
zxcao@xmu.edu.cn
Abstract
Density functional calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest-cost channel of hydrogen loss, and the N9-H bond scission has Gibbs free energies of dissociation ∆G° of 8.8 kcal mol-1 for the anionic adenine and 13.9 kcal mol-1 for the anionic guanine. The relatively high feasibility of low-energy electron-induced N9-H bond cleavage in the purine nucleobases arises from high electron affinities of their H-deleted counterparts. Unlike adenine, other N-H bond dissociations are competitive with the N9-H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9-H bond fragmentation.
Keywords: DNA bases; Electron attachment; Dehydrogenation; DFT calculations.
1 Introduction
The nucleic acid bases as basic constituents of biological species are very important in the process of DNA damage. Recent experiments show that low energy electrons (LEEs) can directly induce DNA strand breaks. Many experimental and theoretical studies have been performed to elucidate mechanisms of DNA cleavage [1-2].
Generally, the radiation damage of DNA does not arise from direct interaction of ionizing radiation with living cells. The initial high-energy radiation basically drives charge transfer and energy redistribution processes in the complex molecule and enhances radiation-induced chemical bond cleavage. The experimental study on electron attachment to uracil suggests that the hydrogen radical may be generated through the dissociative electron attachment (DEA) reaction [3]. This process represents an efficient way to decompose the bases by electrons at energies well below the ionization energy.
Experimental studies point out that the nonthermal secondary electrons at energies below 15 eV are a plentiful species produced in irradiated cells. The primary DNA damage induced by the free secondary
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electrons takes place through transient molecular resonances localized on the basic components of the DNA plasmid.
In the DEA reaction, the excess electrons generally occupy the lowest-energy empty π* molecular orbitals of the DNA bases and create transient anions [4]. Injection of the low-energy electrons not only causes DNA strand breaks, but also induces fragmentation of the DNA bases. The pyrimidine bases as representative components of biological species have been extensively studied [5-6], both experimentally and theoretically. The progress in fundamental aspects of multidisciplinary studies on low energy electron-induced damage in biomolecules has been reviewed .
Recent experimental observations show that the purine nucleobases adenine (A) and guanine (G) can be decomposed by very low energy electrons [7]. The decomposition of adenine produces three main fragments (A-H)−(134 amu), (A-HCN)−(108 amu) and CN−(26 amu), where the dehydrogenation processes represents about 95% of the total yield. On the contrary, more different anionic fragments are created in the fragmentation of guanine and the dehydrogenation channel stands for only about 5% of the total yield. A detailed understanding of such LEE-induced fragmentation features of the purines adenine and guanine requires further theoretical investigations.
The knowledge of the interaction between LEEs and individual components of DNA is quite useful in the molecular description of DNA damage and modification [8]. In the present work, extensive density functional calculations have been performed to unravel the dehydrogenation mechanisms in adenine and guanine by low energy electron impacts. The electron attachment to the purines adenine and guanine as well as energetics for different dehydrogenation channels has been explored theoretically.
2 Computational details
Full geometry optimizations of the purines and their derivatives have been carried out by the B3LYP method with 6-31+G(d,p) basis set. Vibrational frequency analyses have been employed to assess the nature of optimized structures. The energetics calculations by different functionals and basis sets have been performed for comparison. All calculations were performed using the Gaussian 98 program. Adiabatic electron affinities (AEA) were determined by the energy difference between the neutral and anionic species at their respective optimized geometries, i.e., AEA = Eneutral - Eanion. The zero-point energy (ZPE) correction has been considered in estimate of electron affinities.
The relative energy profiles along the C-H or N-H bond dissociation in the anionic purine bases of DNA have been investigated by potential energy surface (PES) scan. A series of constrained optimizations along the pathway of bond dissociation have been performed in the PES scan.
Natural population analyses (NPA) of the B3LYP/6-31+G(d,p) wavefunction were performed with the natural bond orbital (NBO) analysis of Reed and Weinhold.
3 Results and discussion
Optimized structures of the purines adenine and guanine are displayed in Figure 1. The charge populations of their neutral and anionic forms are presented in Figure 2. Predicted potential energy profiles along different dehydrogenation pathways are depicted in Figures 3-6. The fragments from hydrogen loss are labeled according to the site of dissociative hydrogen atom in the parent anions. For example, (N9-H) and (N10-H11) denote fragments to lose the hydrogen atom at the N9 site and N10 site.Structures and Stabilities of Bimetallic Species 3.1 Natural Population Analysis
Figure 2 shows the charge distribution of the neutral and anionic forms of adenine and guanine determined by Weinhold′s natural population analysis. As Figure 2 shows, the excess charges are distributed over all the anionic adenine, while for the anion of guanine, the excess charges are mainly
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http://www.paper.edu.cn found around NH2 and NH sites in the six-membered ring of guanine. Such distinct charge distributions indicate that both purine anions have different electronic structures. Neutral1.007Anion1.016H111.386N71.3611.31281.3665Neutral1.221N101.354Anion1.2301.438H1.3821.4111.423N71.3871.01461.0816N11.02251.3091.346N11.1021.3721.3441.347H81.3101.3781.33724H111.01021.3861.027N1.384N910N31.3761.010N31.313H1.0871.0111.0881.0121.326H121.0191.360 HH121.0081.015OH1.0821.0871.38141.434N91.0091.008Hadenine guanine Figure 1: The structures of the purine DNA bases Neutral0.444Anion0.407H-0.487-0.011-0.580N0.001H0.3940.439N-0.837-0.9050.4200.294N-0.5660.2400.1270.227H0.190-0.5540.2370.192-0.593N-0.646H0.198-0.063H0.1740.039Neutral-0.600OAnion-0.321-0.4400.649-0.232-0.0560.301N-0.0420.6200.0890.4480.172H-0.384N-0.661H0.101H0.1700.4420.425 adenine guanine 0.3500.349N-0.531H0.459-0.6180.4220.2360.103-0.589N-0.3360.342N0.135N-0.869-0.577-0.6950.456H0.200-0.298 Figure 2: Charge populations in the neutral and anionic purine bases by NPA 3.2 Stabilities of H-deleted Radicals and Anions The relative energies of optimized neutral and anionic fragments formed by stripping one H atom from the purine DNA bases are shown in Table I. The ZPE corrections are included in estimate of relative energies. In adenine and guanine, the hydrogen abstraction and electron attachment to its fragment may generate five neutral radicals and anions, respectively. Predicted relative energies in Table I indicate that the H-deleted species of adenine at the N9 position has relatively high stability, which is a sugar-binding site in the adenine moiety. In contrast to adenine, guanine exhibits different features in elimination of one hydrogen atom. The N10 site for neutral species and the N9 site for anion are relatively more accessible for H abstraction. As Table I displays, for the anionic species, there are larger energy differences with respect to the neutral radicals, suggesting that the electron attachment to adenine has a significant effect on the dehydrogenation activity. On the contrary, the relative energies for both neutral and anionic H-deleted forms of guanine are comparable except for the H abstraction at C8. The stabilities of anionic adenine and its fragments 3http://www.paper.edu.cn
have been investigated in previous studies [9]. Experimental and computational studies point out that the radicals generated by hydrogen abstraction at nitrogen centers are more stable than those at carbon centers [10].
Table 1: Relative energies (RE in kcal mol-1) of the H-deleted neutral and anionic radicals from adenine and guanine
H site AdenineN10-H11N10-H12
RE
neutral anion
N9 0.0 0.0
2.9 18.4 4.1 18.9
C2 10.1 62.5 C8 17.2 36.9 GuanineN10-H11N10-H12
N9 2.2 0.0
0.0 1.4 4.9 6.8
N1 4.0 2.2 C8 27.1 41.9
3.3 Electron Affinities and Energetics
The adiabatic electron affinities for the dehydrogenated radicals of the purine are the dominating factor in the N-H or C-H bond selective scission induced by LEEs. Tables II and III list the adiabatic electron affinities (AEA) of these radicals determined by different DFT calculations. Previous investigations have shown that these approaches can predict reasonable adiabatic electron affinities. And the present results agree with other theoretical calculations quite well. As Tables II and III show, the H-deleted fragment (N9-H) for both adenine and guanine has the highest electron affinities among all radicals considered here. Such high electron affinities may facilitate hydrogen atom loss induced by LEEs. Note that the AEA of radicals from hydrogen elimination at different sites of guanine is less changed, whereas for adenine the AEA of radical from H loss at the N9 site is remarkable higher than other fragments. This suggests that the dehydrogenation process at the N9 site of anionic adenine is quite facile. Such substantial differences of AEA among H-abstracted species of adenine and guanine anions may be responsible for their distinct fragmentation properties.
To have more accurate description of the dehydrogenating feature of adenine and guanine, we calculated the relative energies and thermodynamic values for different bond scission channels to lose one hydrogen atom. Selected DFT results are collected in Tables IV and V. All calculations conclude that the N9-H bond dissociation is the lowest-cost process for both purine DNA bases. As Tables IV and V show, the hydrogen loss at the N9, N1 and N10-H11 sites of guanine is mutually competitive, while the hydrogen elimination at the N9 site of adenine anion is a dominant fragmentation process. In particular, at the B3LYP/6-311++G(d,p) level, the N9-H bond dissociation has Gibbs free energies of reaction ∆G° of 8.8 kcal mol-1 for adenine anion and 13.9 kcal mol-1 for guanine anion, respectively. Table 2: Predicted adiabatic electron affinities (in eV) of H-deleted radicals of adenine a
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Method(C2-H)(C8-H)2.362.372.262.422.28(N9-H)3.223.253.013.243.23(N10-H11) (N10-H12) 2.552.592.432.652.542.57 2.61 2.46 2.68 2.57 B3LYP/6-31+G(d,p) 0.95B3LYP/6-311++G(d,p) 0.94BLYP/6-31+G(d,p) 0.91BP86/6-31+G(d,p) 1.04B3PW91/6-31+G(d,p) 0.82a
The ZPV correction included.
Table3: Predicted adiabatic electron affinities (in eV) of H-deleted radicalsof guanine a
Method (C8-H) (N1-H) (N9-H) (N10-H11)(N10-H12) B3LYP/6-31+G(d,p) B3LYP/6-311++G(d,p) BLYP/6-31+G(d,p) BP86/6-31+G(d,p) B3PW91/6-31+G(d,p)
a
2.20 2.20 2.12 2.27 2.10
2.92 2.94 2.71 2.92 2.91
2.93 2.97 2.76 2.98 2.93
2.75 2.79 2.68 2.79 2.74
2.77 2.80 2.59 2.80 2.77
The ZPV correction included.
Table4: Selected energetics and thermodynamic values (kcal mol-1) for different dehydrogenation channels of adenine anion: A− → (A−H)− + H
B3LYP/6-31+G(d,p)
H site ∆H° ∆G° H site ∆H° ∆G° H site ∆H° ∆G°
C2 C8N913.114.07.3N9N10-H11 31.532.425.5N10-H11 N10-H12 32.1 33.0 26.0 N10-H12 ∆E 75.6 50.0
76.9 51.169.5 44.0C2 C8B3LYP/6-311++G(d,p)
∆E 77.2 51.5 14.9 33.0 33.5
78.8 52.9 16.1 34.3 34.8 70.8 45.3 8.8 N926.7 27.2 BLYP/6-31+G(d,p)
C2 C8N10-H11 N10-H12 ∆E 74.8 50.3 14.2 31.1 31.7
76.1 51.3 15.1 32.1 32.7 68.6 44.3 8.4 25.1 25.7 5
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Table5: Selected energetics and thermodynamic values (kcal mol-1) for different dehydrogenation channels of guanine anion: G− → (G−H)− + H
B3LYP/6-31+G(d,p)
H site ∆H° ∆G° H site ∆H° ∆G° H site ∆H° ∆G° C8
N1
N914.315.68.1N921.4 13.9 N9
N10-H1115.717.09.5N10-H1122.815.2N10-H11
N10-H12 21.1 22.4 14.8 N10-H12 26.7 28.0 20.3 N10-H12
∆E 56.1 13.8
57.6 14.949.8 8.6C8 63.3 55.4 C8
N123.6 16.0 N1
B3LYP/6-311++G(d,p)
∆E 61.8 22.2 20.1 21.5
BLYP/6-31+G(d,p)
∆E 56.1 18.4 15.8 17.1 21.9
57.6 19.7 17.0 18.3 23.2 49.7
12.2
9.6
10.8
15.6
3.4 Potential Energy Surfaces
The low energy electron attachment to the purine bases can form transient anions, along with excitation
of related vibrational modes, which may cause the fission of specific bond in anion. The bond dissociation can be described by the potential energy surface (PES) along the dissociation path. Figures 3-6 display the PES profiles along selected N-H and C-H dissociations in adenine and guanine anions. As Figure 3 shows, the barrier of the N9-H bond dissociation in adenine and guanine anions is about 18.1 and 20.2 kcal mol-1, respectively. As the N9-H bond length increases, the PES rises sharply at first and then reaches its maximum at about 1.45 Å for the adenine anion or at about 1.50 Å for the guanine anion. Followed by a region of plateau minimum (∼2.10 Å for adenine and ∼2.05 Å for guanine), the PES becomes relatively flat. The stretch of N9-H bond to the plateau minimum is endothermic by 15.5 kcal mol-1 for the adenine anion and 18.1 kcal mol-1 for the guanine anion at the B3LYP/6-31+G(d,p) level. All DFT calculations here predict quite similar PES profiles.
Figures 4 and 5 present the PES profiles for different bond dissociations in adenine and guanine anions. Apparently, the N9-H bond scission is much favored energetically in the dehydrogenation of adenine anion. For guanine, the N9-H bond cleavage and other several N-H dissociations are mutually competitive energetically. Predicted Gibbs free energies in Tables IV and V show that the dehydrogenation from the N9-H bond in both purine bases is the lowest-cost channel thermodynamically.
To evaluate the effect of ring substituent on dehydrogenation, substitution of F as well as OCH3 for H at C8 has been considered. As Figure 6 displays, the substitution of F for H in the adenine anion will increase the barrier by ∼4 kcal mol-1 for the N9-H bond dissociation, while substitution of OCH3 for H may lower the barrier by ∼4 kcal mol-1. However, the substitution of OCH3 for H in guanine almost does not change energetics of the N9-H bond dissociation. Such different effects of substituted groups can be ascribed into their distinct push-electron and pull-electron properties and interactions with
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http://www.paper.edu.cn purine. These results show that the LEE-induced fragmentation of the DNA bases may be modified by replacement of the group in the ring. 454035302545 B3LYP/6-31+G(d,p) B3LYP/gen:aug-cc-pvdz for N9 & H,others 6-31+G(d,p) BLYP/6-31+G(d,p) B3PW91/6-31+G(d,p)Relative Energy (kcal mol)Relative Energy (kcal mol) B3LYP/6-31+G(d,p) B3LYP/gen:aug-cc-pvdz for N9 & H,others 6-31+G(d,p) B3PW91/6-31+G(d,p) BLYP/6-31+G(d,p)4035302520151050-1 -1201510501.01.52.02.53.01.01.52.02.53.0N9-H distance (Angstrom) aN9-H distance (Angstrom) b Figure3: The PES profiles along the N9-H bond dissociation for the adenine (a) and guanine (b) anions by different DFT calculations
8070Relative Energy(kcal mol)60504030201001.0 C2-H C8-H N9-H N10-H11 N10-H12-11.52.02.53.0Bond distance (Angstrom)Figure4: Potential energy surface profiles along the N-H and C-H bond dissociations in the anionic adenine by B3LYP/6-31+G(d) 60Relative Energy (kcal mol)50 C8-H N1-H N9-H N10-H11 N10-H12-14030201001.01.52.02.53.0Bond distance (Angstrom)7 http://www.paper.edu.cn
Figure5: Potential energy surface profiles along the N-H and C-H bond dissociations in the anionic guanine by B3LYP/6-31+G(d) 4035 4035Relative Energy (kcal mol)Relative Energy(kcal mol)-1-13025203025201510501.01.52.02.53.0 1510500.81.01.21.41.61.82.02.22.42.62.83.0 C8-H C8-F C8-OCH3C8-H C8-F C8-OCH3N9-H Bond distance (Angstrom)aN9-H Bond distance (Angstrom) bFigure6: Comparison of the PES profiles for the N9-H bond dissociation of the adenine (a) and guanine (b) anions with different substituents at the C8 site
3.5 Electronic Structure
On the basis of electronic structure analysis, we noticed that the electronic configuration of the DNA base could change during the bond dissociation. Relevant molecular orbitals at representative N9-H separations in adenine and guanine anions are depicted in Figure 7. As Figure 7 displays, at the equilibrium geometry (RN9-H=1.01 Å) of the adenine anion, the excess electron enters into a low-energy π* orbital, and thus the adenine anion can be characterized as a π* state. Previous SCF calculations coupled with MP2 energy corrections indicate that adenine tautomers accommodate an excess electron through dipole moment interactions [11]. At the plateau minimum (2.10 Å), the electronic configuration has the character of σ* state. Therefore, the electronic structure transition should take place as the N9-H bond stretches. In the H-deleted species, the excess electron is coupled with one unpaired electron at N9 to form a σ lone pair. Such change of electronic structure in the bond cleavage has been investigated in previous studies.
On the contrary, the guanine anion displays dipole-bound character as Figure 7 shows. The excess electron in guanine is around NH2, but it is off the molecular framework. Therefore, the guanine anion can be viewed as dipole bound species. As a consequence, the excess electron in guanine exerts little influence on guanine, and unlike adenine the dehydrogenation activity of guanine is less affected by LEE. In recent computational studies, valence and dipole-bound anions of guanine tautomers have been examined, and a valence anionic π* state was predicted to be vertically bound for the canonical tautomer. Such electronic stability arises from bucking of the ring skeleton and rotation of the NH2 group out of the ring plane.
The PES profiles of pure π* and σ* states in the adenine anion have been investigated to understand the electronic structural feature in dehydrogenation. As Figure 8 shows, the curves of both π* and σ* states lie above the neutral energy curve in the region of N9-H bond length less than 1.35 Å, where the π* anion state is metastable. As the N9-H bond stretches, the σ* energy curve descends and the π* energy curve rises, and the σ*-π* state crossing occurs at about 1.22 Å, giving rise to a barrier for the N9-H bond cleavage. For comparison, such energy curves have been calculated using the so-called stabilization method at the self-consistent field level using the 6-31+G(d,p) basis set. The results
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obtained from stabilization extrapolations indicate that the anion energy curves are similar to those depicted in Figure 8 and the σ* state intersects the neutral energy curve at about 1.43 Å. The notable difference is that the σ* energy curve from the stabilization method has larger descent curvature than that in Figure 8.
π* state (1.01 Å ) in adenine σ* state (2.10 Å) in adenine dipole bound state (1.01 Å ) in guanineFigure7: Singly occupied molecular orbitals of the adenine and guanine anions
140120Relative Energy (kcal mol)-1 neutral adenine a mixed σ*-π* state anion a pure σ* state anion a pure π* state anion1008060402000.81.01.21.41.61.82.02.22.4N9-H distance (Angstrom) Figure8: Potential energy surface profiles of neutral, π* and σ* states anion in the adenine along the N9-H bond dissociation by B3LYP/6-31+G(d,p), a pure σ* and π* state derived from the TD-DFT method
4 Concluding Remarks
The electron attachment to the purine DNA bases adenine and guanine has been investigated by the DFT approach. Possible N-H and C-H bond dissociations in both purine anions have been studied theoretically. The lowest-cost bond scission channel is the dehydrogenation process from the N9-H bond in adenine and guanine anions. Predicted thermodynamic values point out that certain bond scissions in the guanine anion are mutually competitive unlike the adenine anion. The N9-H bond cleavage has Gibbs free energies of dissociation ∆G° of 8.8 kcal mol-1 for the anionic adenine and 13.9 kcal mol-1 for the anionic guanine, respectively. In comparison with neutral purines, the N9-H bond fragmentation in their anions is much favored energetically. Such feasibility of the bond scission in the purine anions arises from the relatively high electron affinities of the H-deleted fragments.
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For the adenine anion, as the N9-H bond stretches, the electron configuration may change, giving rise to the σ* SOMO localized at N9 site, and the σ* energy curve intersects the neutral energy curve at about 1.35 Å. While the guanine anion has a character of dipole-bound state, and its fragmentation is not sensitive to the low energy electron attachment. The present results support the experimental finding that adenine and guanine exhibit different features in decomposition induced by the very low energy electrons. Furthermore, the ring substituent in the purine DNA bases has a notable effect on their bond dissociations.
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