Abstract
Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26–27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine–cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal·mol−1, vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal·mol−1 lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H···O2 distance dramatically reduced from 1.88 to 1.58 Å, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a “reverse wobble” incorporating two N-H···N hydrogen bonds. Three different types of relaxation energies (4.3–54 kcal·mol−1) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.
Keywords: electron affinities, nucleic acid bases, radiation damage, strand breaks
Lesions in DNA caused by both high- and low-energy electrons are thought to result in cancer cell formation. Consequently, the mechanisms of primary and secondary damage to purine–pyrimidine base pairs have been under intense investigation in recent years (1–15). Radical and anion formation in DNA are thought to be steps in pathways arising from radiation damage, which can lead to mutations (15). This mutation can happen in several different ways, including direct radiation damage, secondary ballistic electron damage, or chemical damage by oxidative species (15). Additionally, electronic properties of DNA have been under scrutiny with the hopes of using DNA strands in molecular electronic devices (16–18).
Illenberger and coworkers (3, 4) have noted, based on electron/nucleobase collision experiments, that dehydrogenation of bases is the predominant dissociative channel for DNA. High-energy photons, for example in the form of UV radiation from the sun, release electrons, which, in turn, may induce alterations such as single- and double-strand breaks in DNA or deletions of entire segments of the strand (19). This process can occur through a number of pathways, one of which is dissociative electron attachment (DEA), whereby electrons formed as secondary products of radiation bind to nucleobases and cause bonds to break.
Abdoul-Carime et al. (3) have shown that DEA yields bases that are dehydrogenated predominantly at nitrogen sites. Furthermore, their work notes that the N–H bond that is cleaved in the isolated base pairs is at the same site as the glycosidic N–C bond between the base pair and the sugar phosphate backbone in the double-helical form of DNA and that the N–C bond should be even more easily cleaved.
The works of Sanche (20) and of Folkard et al. (21) have shown that indirect damage to DNA can be caused in a number of ways, including oxidative damage through hydrogen peroxide, hydroxyl radicals, and hydrated electrons produced from ionization of water molecules surrounding DNA in vivo. Of these, low-energy electrons with energies <20 eV (1 eV = 1.602 × 10−19 J) have been shown to be the most abundant secondary species (22). It has recently been demonstrated that even very low energy electrons (0–5 eV) can induce strand breaks in DNA (2, 5, 20, 23, 24).
Prior theoretical research has explored the structures and energetics of both the closed shell (14, 25, 26), H-abstracted (1), and deprotonated (8) A-T and guanine–cytosine (G-C) base pairs, as well as the closed shell (13, 27) and H-abstracted (7, 11–13) individual bases. Bera and Schaefer (1) investigated the structures and energetics of the open shell H-abstracted G-C radicals. Richardson et al. (14, 25) predicted the adiabatic electron affinities (AEAs) of the G-C and A-T base pairs to be 0.60 and 0.36 eV, respectively, by using density functional theory with a double-ζ plus polarization and diffuse functions basis set (DZP++). Kumar et al. (8) have reported structures, dissociation energies, and electron affinities (EAs) of three different base pairs by using a self-consistent-charge density functional tight binding method, yielding EAs ranging from 0.42 to 1.57 eV.
Luo et al. (12) found the AEA of guanine with a hydrogen abstracted from the N9 site to be the highest, at 2.99 eV. Luo et al. (11) found similar results for cytosine, with a hydrogen removed from the N1 site yielding the highest AEA of 2.98 eV. In this work, we employ the same reliable methods to compute AEAs for radicals of the G-C base pair obtained by H-abstraction.
Understanding the energetics and structural changes involved in possible reaction pathways will further elucidate the underlying cause and mechanism of DNA strand breaking. The possibility of using DNA as a molecular wire in microscale electronic devices is also a topic of current interest (16, 17). Although we are growing accustomed to ever-shrinking electronic devices, there exist size restrictions below which currently used materials fail to function effectively. Mindful of this present limitation, many researchers are looking for different materials with desirable properties in the microscale to nanoscale size range. Knowledge of the electronic characteristics of DNA and its components can be useful in tailoring its charge transport properties (16, 28).
Results and Discussion
Fig. 1 illustrates the International Union of Pure and Applied Chemistry (IUPAC) atom-numbering scheme used. The formalism used to denote the individual H-abstracted radicals is as follows: the hydrogen is removed from G-C at the site mentioned in parentheses, from the base preceding the parentheses. For example, the H-abstracted radical G(N9)·-C is generated by homolytic cleavage of the N9–H bond of guanine.
Fig. 1.
The standard IUPAC G-C base pair numbering scheme.
As an indication of the effect of anion formation on the overall base pair geometry, two dihedral angles were considered: the G(C6-C2)-C(C2-C4) angle and the G(C6-N1)-C(N3-C4) angle. Because the G-C base pair is planar in neutral DNA, a significant change in the dihedral angle on anion formation could lead to formation of a strand break or lesion in DNA.
The stabilizing effects of an added electron on the G-C radicals are noted as we consider the energetic and geometric changes manifest in the closed-shell deprotonated G-C anions. The closed-shell anions were generated by homolytic bond cleavage to dehydrogenate the G-C base pair with subsequent anion formation by addition of a single electron. Geometric parameters, relative energies with respect to the lowest-energy anion of the series, and relaxation energies are given in Tables 1–5. AEAs, dissociation energies, and gas-phase acidities (GPAs) of the anions are reported in Table 6. EAs are predicted for all of the base pair radicals to be much greater than that for G-C itself.
Table 1.
Total energies, relative energies, vertical detachment energies, and relaxation energies ER1 of the deprotonated G-C base pair structures
| H-abstracted radical | Deprotonated G-C energy at its optimized geometry, hartree | Vertical detachment energy, eV | Relative energy, kcal·mol−1 | Deprotonated G-C energy at the optimized neutral closed shell G-C geometry, hartree | Relaxation energy ER1, kcal·mol−1 |
|---|---|---|---|---|---|
| G-C(N1)· | −937.17994 | 3.79 | 0.0 | −937.16381 | 10.1 |
| G(N2a)·-C | −937.16156 | 3.57 | 11.5 | −937.10980 | 32.5 |
| G(N9)·-C | −937.16123 | 3.15 | 11.7 | −937.14584 | 9.7 |
| G-C(N4b)· | −937.16028 | 3.74 | 12.3 | −937.13869 | 13.6 |
| G(N1)·-C | −937.15951 | 3.47 | 12.8 | −937.12402 | 22.3 |
| G-C(N4a)· | −937.14825 | 3.77 | 19.9 | −937.12152 | 16.8 |
| G(N2b)·-C | −937.13695 | 2.70 | 27.0 | −937.11372 | 14.6 |
| G-C(C6)· | −937.13639 | 3.53 | 27.3 | −937.12291 | 8.5 |
| G-C(C5)· | −937.12248 | 3.23 | 36.1 | −937.10938 | 8.2 |
| G(C8)·-C | −937.09627 | 2.53 | 52.5 | −937.08267 | 8.5 |
Table 2.
A second set of relaxation energies ER2 and vertical EA for the deprotonated G-C base pair structures
| H-abstracted radical | Deprotonated G-C energy at optimized neutral radical geometry, hartree | Vertical EA, eV | Relaxation energy ER2, kcal·mol−1 |
|---|---|---|---|
| G-C(N1)· | −937.173 10 | 3.47 | 4.3 |
| G(N2a)·-C | −937.128 10 | 2.34 | 21.0 |
| G(N9)·-C | −937.143 75 | 2.10 | 11.0 |
| G-C(N4b)· | −937.144 17 | 3.10 | 10.1 |
| G(N1)·-C | −937.145 64 | 2.65 | 8.7 |
| G-C(N4a)· | −937.141 24 | 3.45 | 4.4 |
| G(N2b)·-C | −937.126 85 | 2.11 | 6.3 |
| G-C(C6)· | −937.111 94 | 2.24 | 15.3 |
| G-C(C5)· | −937.101 94 | 2.12 | 12.9 |
| G(C8)·-C | −937.077 01 | 1.41 | 12.1 |
Table 3.
A third set of relaxation energies ER3 for the deprotonated G-C base pair structures
| H-abstracted radical | Deprotonated G-C energy at optimized G-C radical anion geometry, hartree | Relaxation energy ER3, kcal·mol−1 |
|---|---|---|
| G-C(N1)· | −937.154 92 | 15.7 |
| G(N2a)·-C | −937.076 69 | 53.3 |
| G(N9)·-C | −937.111 48 | 31.2 |
| G-C(N4b)· | −937.123 93 | 22.8 |
| G(N1)·-C | −937.095 98 | 39.9 |
| G-C(N4a)· | −937.110 66 | 23.6 |
| G(N2b)·-C | −937.077 36 | 37.4 |
| G-C(C6)· | −937.128 27 | 5.1 |
| G-C(C5)· | −937.100 79 | 13.6 |
| G(C8)·-C | −937.048 16 | 30.2 |
Table 4.
Dihedral angles of the deprotonated G-C base pair structures
| Deprotonated G-C structure | G(C6-C2)-C(C2-C4) dihedral, ° | G(C6-N1)-C(N3-C4) dihedral, ° |
|---|---|---|
| G-C(N1)− | 8.0 (0.0) | 5.3 (0.0) |
| G(N2a)−-C | 0.1 (30.6) | 0.0 (39.4) |
| G(N9)−-C | 6.7 (0.0) | 10.9 (0.0) |
| G-C(N4b)− | 0.0 (0.2) | 0.0 (0.3) |
| G(N1)−-C | 7.2 (0.0) | 16.0 (0.0) |
| G-C(N4a)− | 45.3 (31.7) | 32.2 (15.9) |
| G(N2b)−-C | 0.0 (0.0) | 0.0 (0.0) |
| G-C(C6)− | 6.2 (0.1) | 4.3 (0.2) |
| G-C(C5)− | 0.0 (0.0) | 0.0 (0.1) |
| G(C8)−-C | 5.8 (0.0) | 9.4 (0.0) |
Angles for the neutral radicals are given in parentheses.
Table 5.
H-bond distances of the deprotonated G-C structures
| H-abstracted anion | G(O6)··· C(H4a), Å | C(N3)··· G(H1), Å | C(O2)··· G(H2a), Å |
|---|---|---|---|
| G-C neutral | 1.724 | 1.886 | 1.884 |
| G-C(N1)− | 1.905 (1.730) | 1.803 (1.839) | 1.576 (1.811) |
| G(N2a)−-C | – (1.819) | – (1.932) | – (–) |
| G(N9)−-C | 1.525 (1.790) | 1.978 (1.854) | 2.219 (1.616) |
| G-C(N4b)− | 2.255 (1.878) | 1.902 (1.944) | 1.647 (1.920) |
| G(N1)−-C | – (–) | – (–) | – (–) |
| G-C(N4a)− | – (–) | 1.846 (1.909) | 1.792 (1.751) |
| G(N2b)−-C | 1.528 (1.777) | 1.956 (1.916) | 2.152 (2.035) |
| G-C(C6)− | 1.919 (1.714) | 1.801 (1.901) | 1.653 (1.917) |
| G-C(C5)− | 1.935 (1.717) | 1.817 (1.909) | 1.646 (1.885) |
| G(C8)−-C | 1.528 (1.733) | 1.956 (1.881) | 2.152 (1.871) |
H-bond lengths for neutral radicals are given in parentheses. A dash (–) indicates that the H-bond has been removed upon radical or anion formation.
Table 6.
AEAs of the G-C base pair H-abstracted radicals, deprotonated G-C dissociation energies (De) to the respective base plus deprotonated base, and GPAs (G-C → anion + H+) for the G-C base pair
| H-abstracted G-C radical | Optimized neutral radical energy, hartree | AEA, eV | De of corresponding anion, kcal·mol−1 | GPA, eV |
|---|---|---|---|---|
| G-C(N1)· | −937.04565 | 3.65 | 41.6 | 14.66 |
| G(N2a)·-C | −937.04205 | 3.25 | 22.8 | 15.16 |
| G(N9)·-C | −937.06641 | 2.58 | 23.7 | 15.17 |
| G-C(N4b)· | −937.03039 | 3.53 | 32.4 | 15.20 |
| G(N1)·-C | −937.04565 | 3.03 | 22.1 | 15.22 |
| G-C(N4a)· | −937.01447 | 3.64 | 30.8 | 15.52 |
| G(N2b)·-C | −937.04933 | 2.38 | 12.8 | 15.83 |
| G-C(C6)· | −937.02946 | 2.91 | 37.1 | 15.85 |
| G-C(C5)· | −937.02386 | 2.68 | 36.9 | 16.22 |
| G(C8)·-C | −937.02521 | 1.93 | 23.7 | 16.94 |
Energies and Geometries.
Absolute and relative energies of all of the anions are presented in Table 1. Analogous to the results of Bera and Schaefer (1) for the neutral radicals, the lowest-energy deprotonated G-C species (shown in Fig. 2) is G-C(N1)−, in which a proton has been abstracted from a sugar-binding site on the cytosine moiety. These findings are consistent with experiments showing that the nitrogen sites are more likely to hold the excess charge (3). In all structures in which the proton removed was not involved in one of the three H-bonds, the H-bonds lengthen if the hydrogen-donating base is the site of dehydrogenation, whereas the other H-bond(s) shorten. It is interesting to note that there does not appear to be any energetic trend in the proton being removed from the guanine rather than the cytosine moiety. The relative ordering, extent of relaxation, and resultant geometric changes for each can be rationalized as follows: The lowest-energy anion was found to be G-C(N1)−; shown in Fig. 2, this anion is resonance-stabilized by the carbonyl group on one side and C
C double bond on the other side. This conclusion is supported by the fact that, when compared with the geometries of both neutral G-C (Fig. 3) and the G-C(N1) radical (1), both of the N–C bonds adjacent to N1 have shortened significantly. The corresponding hydrogen-abstracted neutral radical is the fourth-most energetically favorable radical. The rather large change in relative stability between the radical and the anion should be reflected in the EA of the neutral radical, which we discuss in the next section. Despite being the lowest-energy H-abstracted anion, this structure deviates from planarity, with the two dihedral angles (defined above) predicted to be 8.0° and 5.3°. This deprotonated base pair also has the highest dissociation energy, 41.6 kcal·mol−1.
Fig. 2.
G-C(N1)− optimized anion. All bond lengths are given in Å.
Fig. 3.
The (closed-shell neutral) G-C base pair optimized geometry. All bond lengths are given in Å.
Possibly the most dramatic change in geometry due to anion formation is for the second-lowest-energy structure, G(N2a)−-C, shown in Fig. 4. This structure lies ≈11.5 kcal·mol−1 higher in energy than G-C(N1)−. One of the three hydrogens involved in G-C H-bonding is removed (from the N2 site on guanine) leaving two H-bonds in the optimized radical. Anion formation causes the next nearest H-bond to break, and the two structures rotate away from each other and form a new, second H-bond. The length of the remaining original H-bond is 1.761 Å. Although the corresponding dehydrogenated neutral radical structure displayed significant dihedral angles, 30.6° and 39.4°, on anion formation the structure returns to planarity.
Fig. 4.
G(N2a)-C− optimized anion. All bond lengths are given in Å.
The N9 position on guanine is used for the base-sugar-binding site in the Watson-Crick structure. The anion generated at this position, G(N9)−-C, is shown in Fig. 5. This structure is ≈11.7 kcal·mol−1 higher in energy than the most stable structure and only 0.2 kcal·mol−1 above the second-lowest structure. Again, the H-bonds adjacent to the site of dehydrogenation shorten considerably.
Fig. 5.
G(N9)-C− optimized anion. All bond lengths are given in Å.
As shown in Fig. 6, removal of a hydrogen from the N4 site on cytosine results in the next-lowest-energy structure. The other hydrogen on N4 is involved in H-bonding in the G-C base pair, and the distance between the hydrogen and the O6 position on guanine lengthens by ≈0.4 Å upon anion formation. The other two H-bonds both decrease in length.
Fig. 6.
G-C(N4b)− optimized anion. All bond lengths are given in Å.
The fifth-lowest-energy structure is G(N1)−-C, shown in Fig. 7. This structure involves removal of the middle of the three hydrogens involved in H-bonding. Significant structural changes occur: the base pairs “slide” relative to each other in the plane (forming a “reverse wobble” structure) in such a way that they can still form two H-bonds and avoid the repulsion of the two nitrogen lone pairs. The two resulting H-bonds in this deprotonated structure are of N−···H-N and N-H···N character. This result may be surprising because neutral N–H···N H-bonds are considered to be weaker than neutral O–H···O H-bonds. The two dihedral angles between the bases are 7° and 16°.
Fig. 7.
G(N1)-C− optimized anion. All bond lengths are given in Å.
The next-highest-energy structure (shown in Fig. 8) is almost 20 kcal·mol−1 above the lowest-energy anion. Like the fourth-lowest structure, it involves removal of a hydrogen from the N4 site on cytosine. However, this structure exhibits the largest deviation from planarity upon anion formation, with the two dihedral angles predicted to be 45° and 32°, respectively. The four remaining anions are >25 kcal·mol−1 above the lowest-energy anion and display relatively little dihedral distortion.
Fig. 8.
G-C(N4a)− optimized anion. All bond lengths are given in Å.
Relaxation Energies.
Three distinct relaxation energies (ER1, ER2, and ER3) have been computed (shown in Tables 1–3) corresponding to different potential pathways from G-C to the deprotonated anions: relaxation energy ER1 corresponds to the energy lowering after deprotonation of neutral G-C; ER2 is the energy released through relaxation after electron attachment to hydrogen abstracted G-C; and ER3 gives the relaxation energy after hydrogen atom abstraction from the G-C radical anion.
Remarkably, the nonconventional structure G(N2a)·-C exhibits the largest relaxation energies of the 10 structures considered, presumably due to the stability afforded by the confounding C–H···N H-bond. Given the extensive rearrangement that occurs upon electron attachment in this structure, the magnitude of the relaxation energies is not too surprising. The relaxation energies for the global minimum anion structure, G-C(N1)−, are more modest: ER1 = 10.1 kcal·mol−1, ER2 = 4.3 kcal·mol−1, and ER3 = 15.7 kcal·mol−1, corresponding to the relatively minor changes in geometry after anion formation for this species. Overall, the size of the predicted relaxation energies for all structures considered is an indication of the magnitude of the driving force behind the observed geometrical relaxations upon anion formation.
EAs and GPA.
The theoretical AEAs of the H-abstracted G-C radicals range from 1.93 to 3.65 eV and are listed in Table 6. The three radicals having the highest EAs (3.65, 3.64, and 3.53 eV) all result from H-abstraction from a nitrogen site on cytosine. The general trend shows that the EAs of the radicals generated on the nitrogen sites are higher than those generated on carbon centers, a finding readily attributed to the greater electronegativity of nitrogen. All of the radicals display significantly larger AEAs than the closed-shell G-C base pair.
The radical with the highest AEA, 3.65 eV at the B3LYP/DZP++ level, results from the removal of hydrogen from the N1 site on cytosine [G-C(N1)·]. The N1 of cytosine in double-stranded DNA would be linked to the sugar–phosphate backbone. The corresponding anion is the lowest energy of the 10 studied here. That the radical with the lowest AEA results from H-abstraction from cytosine is not surprising, because cytosine has been shown to have a higher AEA than guanine and to function as something of a sink for negative charge (29, 30).
The G-C(N4a)· radical has the second-highest AEA (3.64 eV). Electron addition to the radical results in the sixth-lowest-energy anion of the 10 considered, suggesting that the large AEA arises (Fig. 8) primarily through destabilization of the radical rather than through stabilization of the anion. With an AEA of 3.53 eV, the radical G-C(N4b)· comes in a close third. Like the structure previously discussed, the hydrogen was also lost from the N4 site on cytosine. The next-two-highest-predicted EAs are 3.25 and 3.03 eV, exhibited by the G(N2a)·-C and G(N1)·-C radicals, respectively. The extra electron in both the anions is resonance delocalized by the C2N3 double bond.
These EAs are in very good agreement with the results obtained for the single bases by Abdoul-Carime et al. in their 2004 study (3), in which EAs of the N-dehydrogenated radicals were predicted to be between 3.5 and 4.0 eV. The present work further supports the DEA mechanism for the generation of the proton-abstracted base pair anions as proposed by Abdoul-Carime et al. (3). The moderate EAs of the G-C base pair (25) make the electron capture successful. The large energy lowering of the anions and subsequently high EAs of the base pair attests to the plausibility of the DEA process.
GPAs also have been computed and are shown in Table 6. They range from 14.66 to 16.94 eV and are very similar to GPAs predicted for isolated adenine (7). However, we do not find any correlation between relative acidity and deprotonation site (e.g., carbon vs. nitrogen).
Dissociation Energies.
The predicted dissociation energies of the deprotonated G-C structures are given in Table 6. The first seven anions in Table 6 are more difficult (higher dissociation energies) to dissociate into their component base and deprotonated base. The neutral radicals corresponding to these deprotonated structures have the highest EAs, reported in Table 6. It is interesting that, despite losing one H-bond, the dissociation energy of the G-C(N4a)− anion (30 kcal·mol−1) is greater than the dissociation energy of the neutral G-C (27.2 kcal·mol−1) (25, 31).
The very low dissociation energies of some of the anions generated indicate that DEA could greatly alter structural and energetic characteristics of the base pairs and consequently of the DNA strand. Even very-low-energy secondary electrons (0–3 eV) would be able to split the base pairing.
Conclusions
In view of the complexity of biological systems, it is highly desirable (although difficult) to be able to discern the main chemical and physical events that are responsible for damage to genetic material. This complexity is enhanced because of exposure of the systems under study to UV or x-ray radiation or to an electron beam, because such conditions can cause many chemical changes, including cleavage of bonds and production of radicals and free electrons. Low-energy free electrons also can be produced by various other mechanisms in chemical and biochemical systems, and, therefore, a study of effects of their attachment to molecules poses an interesting problem. Formation of radicals, anions, or cations of the bases can induce strong effects on the structure of DNA, and the elucidation and exploration of these myriad effects represent an important avenue of research.
The B3LYP density functional with the DZP++ basis set has been used to study the EAs and geometrical perturbations of the 10 H-abstracted neutral doublet G-C base pair radicals upon electron attachment. The energetically most favored of these anions is created by removing a proton from the N1 site on cytosine. This result is concordant with previous experimental work showing dehydrogenation of the nucleic acid bases to be most likely to occur at nitrogen sites that are also the sites of the glycosidic bond in DNA (3). The EAs of the various H-deleted radicals ranged from 1.93 to 3.65 eV. DEA could cause significant damage to DNA, with torsional angles indicative of deviation from planarity between guanine and cytosine ranging from <1° up to ≈45°. Changes in H-bond distances by as much as 0.5 Å also occur. These significant geometrical perturbations indicate that H-abstraction by means of irradiative damage to DNA at G-C base pair sites, possibly caused by high- or low-energy electrons, could have major detrimental effects on the overall DNA structure. This effect in turn may result in mutagenesis in living cells by alteration or termination of a DNA sequence upon an attempt to replicate. The large AEAs also suggest that radical creation could potentially alter the function of microscale electronic devices made by using DNA.
Methods
Geometry optimizations and absolute energy analyses were performed by using the q-chem 2.1 suite of programs (32). A fine grid was used for geometry optimizations, consisting of 75 radial shells and 590 angular points. Becke’s three-parameter hybrid density functional (B3) (33), was used with the correlation functional of Lee, Yang, and Parr (LYP) (34). All computations used the DZP++ basis set, which contains 6 basis functions per H atom and 19 functions per C, N, or O atom, constructed by augmenting the double-ζ Huzinaga–Dunning (35–37) set of contracted Gaussian functions with one set of d-type polarization functions and even-tempered diffuse functions for each C, N, and O, and one set of p-type polarization functions as well as one even-tempered s diffuse function for each H (38). Molecular structure figures were generated by using a code written by S.E.W. (39).
The physical properties of special interest in this study rely on energetic differences as described by the following.
AEA of Dehydrogenated G-C.
AEA = E(optimized neutral radical) − E(optimized deprotonated G-C).
Vertical Detachment Energy (VDE) of Deprotonated G-C.
VDE = E(neutral radical at optimized deprotonated G-C geometry) − E(optimized deprotonated G-C).
Vertical EA (VEA) of Dehydrogenated G-C.
VEA = E(optimized neutral radical) − E(deprotonated G-C at optimized neutral radical geometry).
Anion Relaxation Energies (ER).
ER1 = E(deprotonated G-C at optimized G-C geometry) − E(optimized deprotonated G-C); ER2 = E(deprotonated G-C at optimized neutral radical geometry) − E(optimized deprotonated G-C); ER3 = E(deprotonated G-C at optimized G-C radical anion geometry) − E(optimized deprotonated G-C).
Dissociation Energy (De) of Deprotonated G-C.
De = E[(G-H+)− − C] − E[(G-H+)−] − E(C) and De = E[G − (C-H+)−] − E(G) − E[(C-H+)−].
GPA of G-C.
GPA = E(optimized G-C) − E(optimized deprotonated G-C).
Acknowledgments
This work was supported by National Science Foundation Grant CHE 0451445.
Abbreviations
- EA
electron affinity
- AEA
adiabatic EA
- DEA
dissociative electron attachment
- GPA
gas-phase acidity
- G-C
guanine–cytosine.
Footnotes
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
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