8092
J. Phys. Chem. 1993,97, 8092-8097
Ab Initio Molecular Orbital Calculations on DNA Radical Ions. 3. Ionization Potentials and Ionization Sites in Components of the DNA Sugar Phosphate Backbone Anny-Odile Colson,t Brent Besler,* and Michael D. Sevilla'lf Department of Chemistry, Oakland University, Rochester, Michigan 48309, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202 Received: April 2, 1993
Ab initio molecular orbital calculations of various fragments of the DNA backbone have been performed to aid our understanding of charge localization and transfer following DNA irradiation. Koopmans ionization potentials of H3P04, H2P04- and several hydrated forms of the H2P04--Na+ complex were determined at the ROHF/3-21 G level. Counterion interaction and progressive hydration result in a substantial increase in the phosphate ionization potential, hence gradually disfavoring the phosphate group as a potential localization site for the hole. The binding energy of the waters of hydration progressively decreases as saturation is approached. In the triply hydrated system, the average water-sodium binding energy is 3 1.2 kcal/mol H2O while the average water-phosphate oxygen hydrogen bond energy is 9.4 kcal/mol H2O. The Koopmans ionization potential of 2'-deoxyribose was determined, leading to the following trend in IP: base < deoxyribose (D) < phosphate (P). Calculations performed on DP, DPD, and PDP reveal that the joining of D to D P results in a decrease in I P of D-P while joining of P to D-P raises its IP. Subsequent hydration of DP and DPD via a sodium counterion results in a slight decrease in Koopmans IP. Unpaired spin densities determined in D, DP, and DPD localize the hole at the sugar ring oxygen, while hole localization at the anionic phosphate oxygen is found in PDP. In deoxycytidine 3'-monophosphate, the spin is localized to the cytosine base ?r electron system. Koopmans ionization potentials determined for DP and PDP in Z-DNA are ca. 0.2 eV lower than their B-DNA analogues.
Introduction Studies of free radicals formed in irradiated DNA at low temperature have detected a number of DNA base radicals but have yet to find deoxyribose radicals. Indeed, even though over 50% of the DNA's mass is made up of the sugar-phosphate backbone and ionizing radiations are known to randomly ionize all available sites, the initial radicals thus far found by ESR spectroscopy are the radical anions and cations of the DNA bases.'-' On theother hand, low-temperaturestudiesof irradiated nucleotides and nucleosideshave revealed the existenceof a variety of sugar-centered radicals.*-14 Since damaged sugars are known to lead to strand breaks and subsequently cell death,l it is of importance to examine possible primary radicals formed in the sugar-phosphate backbone. Hydration of ionic groups on the polyanionic DNA sugar phosphate backbone and interaction of cations with the backbone electrostatic potential will both play an important role in any subsequent chemistryfollowing ionization of DNA. In this work, wecontinueour abinitiomolecularorbitalstudieson the properties of DNA ion radicals,15J6with calculations on the constituents of the polyanionic deoxyribose backbone of DNA. Our goals are to determine the most probable site of hole localization on the DNA backbone following exposure of the macromolecule to ionizing radiations and to elucidate the effects of hydration on the ionization potentials and unpaired electron distribution of several constituents of the DNA sugar phosphate backbone.
Method of Calculation The ab initio calculations presented in this work were performed at the ROHFf3-21G17 level utilizing Gaussian 901* and 9219 programs on Dec 5000/200, IBM RS 6000, and Cray-YMP computer systems. The spin-restricted open-shell HartreeFockZO method was applied throughout this study to avoid any substantial spin contamination previously observed with the use of unrestricted Oakland University. t Wayne State University.
0022-3654/93/2097-8092$04.00/0
determinants.21 Spin densities were calculated using Mulliken population analysis.2' Figure 1 presents the structures of various DNA components and fragments examined in this study. With the exception of as, these structures were fully optimized (bon,d distancesand angles), and their geometries are reported in the supplementarymaterial. As part of this work, we report KoopmansZ2ionizationpotentials of several structures. These values are simply the energy of the HOMO in the optimized neutral systems. In the present study, we have chosen to limit our calculations totheROHF/3-21Glevelsincein previous works15J6weobserved that results obtainedat this level compared well with experimental values of ionization potentials. For example, Koopmans ionization potentials for the DNA bases at the 3-21G level show only an average 0.15-eV deviation from experimental values whereas at the 6-31G*//3-21G level the deviation is 0.24 eV.15
Results and Discussion 1. Ionization Potential of the Phosphate Group and Effects of Hydration. We first focus our interest on calculating the ionization potential of the smallest building block of the DNA backbone, the phosphategroup. H3P04 and its corresponding anion H2P04were fully geometry optimized at the ROHF/3-21G level. Their respective Koopmans ionization potentials are 12.10 and 5.23 eV. The latter value agrees well with that of Yu et al. and Tasaki et al.23,24This result indicates that, once the energy necessary for abstracting a proton has been provided to H3P04, ionization of H2PO4- will easily occur. More importantly, H2PO4- is the anionic form of the phosphate group encountered in the DNA backbone; it is therefore relevant to compare its Koopmans ionization potential to that of the four DNA bases calculated in our previous study.15 Surprisingly, the ionization potential of H2P04- is much lower than that of any DNA base, guanine having the lowest Koopmans IP of 8.04 eV at the ROHFf3-21G 1 e ~ e l . l ~ Consequently, this result seemingly points to a very facile ionization of the DNA backbone phosphate as opposed to the regular DNA bases. However, for this comparison to be relevant 0 1993 American Chemical Society
MO Calculations on DNA Radical Ions - a1
a I
I
HO-P=O
I
I
RO-P=O
I OR
as
I
OR
4
4 -
Na'(HzOh
-
Na'(Hz0)3
0
I
Na*(HzO)r
0
I
HO-P=O
RO-P=O
I
I
OR
Na'
I
RO-P=O
I OR
RO-P=O
Q
-0
0
OR
-0
The Journal of Physical Chemistry, Vol. 97, No. 30, 1993 8093
OR
OH
OH
I
OH
I
R,O-P=O
OH
I
OH
I
HO-P=O
e d Hz@
l
f
P
"D' o
I I 0
R1O-P=O
0
0
HO-P=O
HO-P=O
I I
OH
I I
6H
6H
Figure 1. ROHF/3-21G geometry optimized structures treated in this work. Structures a through a4 were fully optimized, but convergence criteria were not met for as (see text). Dihedral angles in b through f were kept fmed in the appropriate DNA configuration.
in a biological context, effects of the environment must also be accounted f0r.2~Thus, we introduce a counterion in the H2PO4system. Sodium was chosen to play this role, since it is the most readily available cation in the vicinity of the DNA molecule. The sodium ion was placed halfway in between the two anionic oxygens bonded to the phosphorus, all four atoms being coplanar. The starting Na-P distance was set at 2.3 A. Upon geometry optimization,the sodium atom simply pulled away from the system to an optimized distance from the phosphorus of 2.69 A, but no preferred interaction with either anionic oxygen was observed (Figure 2A). The introduction of a counterion in the system significantlyaffected the Koopmans ionizationpotential. Indeed, a 5.5-eV increase in IP resulted from the presence of sodium, with a calculated Koopmans value for the sodium-phosphate complex of 10.73 eV. DNA studies widely agree on the importance of the solvation layer on stabilizing base stacking and the DNA double helix itself.2"' For this reason, we proceeded to hydrate the sodium phosphate system in a stepwise manner up to four waters per sodium ion (Figure 2C,B,D). Although interactions in hydrated sodium phosphate systems have been investigated,BJ8J9no details of gradual hydration effects on the ionization potentials of such complexes has been reported. Other studies have shown that the free phosphate oxygen atoms have a higher affinity for water molecules than the esterified 03' and 0 5 ' phosphate oxygen atoms.3s33 For this reason, hydration of the anionic oxygens is considered in this study. In a first step, two waters were allowed to interact with the system. They were initially placed symmetrically with respect to a plane formed by Na, P, and the two anionic phosphate oxygens, their oxygen atom interacting with the sodium ion, and each of their proton hydrogen-bonding to the phosphate oxygens. During the course of optimization, both waters significantly rearranged so both hydrogen bonded only to
one anionic oxygen. On the other hand, the sodium ion which was equidistant from both anionicoxygensin the starting geometry favored interaction with the "nonhydrated" oxygen. The optimized geometry is shown in Figure 2B. These first two waters of hydration were responsible for a 0.46-eV increase in the Koopmans ionization potential of the complex. The combined effect of both water molecules and Na+ resulted in a total increase in the ionization potential of H2P04- of 5.96 eV. Tasaki et al.24 determined this overall effect to be responsible for an 8.25-eV increasein the ionization potential of H2P04-, but the optimization of the structure29 used for this calculation did not allow for free rearrangement of the water molecules around the sodium ion. We further hydrated the system by allowing an additional water molecule to interact with the sodium counterion and the unhydrated phosphate anionic oxygen. This resulted in one doubly and one singly hydrated phosphate oxygen. Although hydration patterns of the phosphate group are experimentally difficult to identify due to the thermal vibration of the later group?' it is not unusual to observe one of the anionic phosphate oxygens being more heavily hydrated than the other in DNA.30Jlb-3'36 The optimized configurationof the three water oxygens and the sodium counterion shown in Figure 2C closely resembled that of a trigonal planar structure. The additional water which contributed to pull the counterion further away from the phosphorus atom also increased the Koopmans ionization potential of the hydrated sodium phosphate group by 0.25 eV. The energeticsof this system will be discussed later. We further hydrated the model by incorporating a fourth water molecule. In this case, only interaction between the counterion and the water oxygen was possible since the water hydrogens pointed away from the system as shown in Figure 2D. No full optimization of the complex was possible due to a flat multidimensional potential surface caused by the rotation of the fourth water around its C2 axis. The calculation predicts a slight decrease in Koopmans ionization potential to a final value of 11.30 eV. This result is not surprising since the fourth water molecule acts solely as an electron donor. Dimethylation of the phosphate complexes (Figure l a through la,) resulted in a slight lowering of the Koopmans ionization potentials by an average of 0.3 eV (Figure 3), the anionic system undergoing little change. These results are in reasonable agreement with the vertical I P Sof various substituted phosphate groups obtained from photoelectron spectra.37 These results summarized in Figure 3 suggest that, in a biologically relevant environment, the phosphate group is not likely to be a stable localizationsite for the "hole" (radical cation). This provides a theoretical explanationfor the lack of experimental evidence for phosphate-centered radical cations in DNA. Comparison to previously calculated Koopmans ionization potentials of the DNA bases'5J6 shows guanine to remain the preferred center for hole localization in irradiated DNA. ( a ) Gas-Phase Hydration Energies of NaH2P0,. Successive hydration energies of the sodium phosphate complex are summarized in Table I. The average binding energy of each water molecule is 33 kcal/mol. However, this energy gradually decreases as subsequent waters are added to the hydrated system. Indeed, the first two waters are each bound by 35.4 kcal/mol, while the third water's binding energy is 31.1 kcal/mol. The fourth water which exclusively interacts with the counterion, involves only 19.7 kcal/mol in binding to the complex. ( b ) Energetics of the Triply Hydrated Sodium Phosphate Complex. Table I1 presents the energies of interaction between several subsystems of the N a H ~ P 0 4 ( H 2 0 complex. )~ In the gas phase, ca. 6.8 eV account for the electrostatic interaction between the counterion and the phosphate group in the isolated system, but the waters of hydration slightly pull the Na+ away from the phosphate and hence weaken this interaction to 6.15 eV. Prasad et al. calculated a binding energy of 6.73 eV29 in the nonhydrated system, while Pullman et al. observed a weaker interaction2*due
Colson et al.
8094 The Journal of Physical Chemistry, Vol. 97,No. 30, 1993
A
B
Fi-2. ROHF/3-2lGgeometryoptimizedconfigurationsofthesodiumphosphatecomplexes in nonhydratedand hydratedstates. No fulloptimization of Na(Hz0)4HzP04 was achieved (see text). l4
1
TABLE Ik Calculated Interaction Energies within NaHdWAH~O) - -. - ,"(eVP . I
N & ~ ~ oNaH2P04 ~
....................
Ndi2P04
11.65
...........
Na(CH3)2P04 10.53
41
(H2O)Z 11.19
...........
(H20)3
NaH2P04 (H20)4 11.30
1 1 . 4 4.....................
Na(2$2p04 10.93
Na(CH3)2P04 (HzOb 11.21
5.23
Figure 3. Calculated ROHF/3-2 1G Koopmans ionization potentials of phosphoricacid, phosphate anion, sodium phosphate complex, and their dimethylanalogsin unhydratedand hydrated optimizedgeometries(ev).
TABLE I: Gas-Phase Hydration Energies of NaHzP04 (kcal/mol) increAE av mental NaHzPOd#+2Hz0 NaHzP04(Hz0)zb -70.8 -35.4 -35.4 NaHzPO4#+ 3H20 N ~ H ~ P O ~ ( H Z-101.9 O ) ~ ~ -34.0 -31.1 NaHzPOP + 4H20 NaH2P04(H20)4d -121.6 -30.4 -19.7 0 Figure 2A. Figure 2B. Figure 2C. Figure 2D.
--
to the association of the counterion with only one of the anionic phosphate oxygens. The hydration energy of Na+ calculated in thegeometry of the hydrated sodium phosphate complex without the presence of the ph,w6hate anion amounts to 3.87 eV (29.7 kcal/mol HzO) whik the hydration energy of H2PO4-determined under similar conditions and omitting the interaction with the counterion amounts to 1.03 eV (7.9 kcal/mol H2O). The average hydrogen bond strength from water to phosphate oxygen is 7.9 kcal/mol. We find the Na+...OHZ bonds are strengthened only slightly to 3 1.2 kcal/mol H2O (5%) as the phosphate group enters the system, while each PO-HOH hydrogen bond energy increases by 1.5 kcal/mol (19%) upon Na+ introduction. It is interesting to note that the hydration energy for Na+ is 106 kcal/moP while
--- -
AE
AEb
(gas phase) (solution) Na+ + H2PO4- NaHzPO4 -6.83 -0.65 Na+ + H2P04- NaHzP04' -6.15 -0.39 + 3H20 &PO4-(H20)3' -1 -03 Na+ + 3H20 Na+(HzO)f -3.87 Na+(H20)sc+ H2PO4- NaHzPO4(Hz0)3 -7.38 a Products and reactants fully optimized at the 3-21G level except when indicatedotherwise. Hydration of reactants and productsmodeled by the Born charge term added to the Onsager reaction field model. Single-point calculations performed in the appropriate portion of the 3-21G optimized geometry of NaH2POd(H20)3. the first four hydration waters in our calculation contribute ca. 109 kcal/mol. Full solvation effects (e = 78) on the interaction energies between Na+ and HzPO4- (reactions 1 and 2 in Table 11) were accounted for by using the Born39 charge term added to the Onsager reaction field modelsm This self-consistent reaction field (SCRF) technique required prior computation of a suitable solute radius which was obtained in a gas-phase molecular volume c a l c ~ l a t i o nSolvation .~~ of the ions results in a nearly equal energy to the ion pair interaction so that only 0.39 eV remains for the net energy of stabilization of NaHzPO4. 2. 2'-DeoxyriborJe. The neutral and cation radical 2'deoxyribose structures (Figure lb) were geometry optimized a t the ROHF/3-21G level. The starting geometries were obtained from the optimized structure of 2'-deoxyribose 5'-phosphate described in the next section. All dihedral angles were kept fixed during the course of optimization in the C2t-endo puckering conformation. The optimized bond distances of the neutral sugar were all within 0.03 Aof well-refined C2-endocrystal structures4' with the sole exception of the C1'44'distance which was slightly longer than the experimentally observed one in nucleosides41( 1.48 vs 1.42 A). All optimized angles lay within 5 O of those reported by Saenger.41 The Koopmans ionization potential resulting from the optimization of the neutral system was found to be 10.96 eV. This result lies between the ionization potentials of NaHzP04
MO Calculations on DNA Radical Ions
The Journal of Physical Chemistry, Vol. 97, No. 30, 1993 8095
OH
I
OH
R1O-P=O
I b
OH
cAo
12
P-D-P
H2t-l
11
h
% v
6
I
I
OH
OH
HO-P=O
1
b
a
1
I OH t
OH
I
OH
HO-P
I
HzQ‘
I P
R10 -P
1
I
I
7 ‘
=0
Figure 5. Calculated ROHF/3-21 G Koopmans ionization potentials of the regular DNA bases15 and various fragments of the DNA backbone. Single-point calculations were performed on the hydrated systems.
TABLE III: DNA Backbone Torsion Angles (in degrees) torsion anglesu
0
I HO-P=O
I
OH
OH
e
d
a
B Y
6
I
€
R ~ H, = N~(H~o)~(
Figure 4. Hole localization sites obtained from ROHF calculations.The unpaired spin density localized exclusivelyon the oxygen atom p orbitals in structures a, b, d, e. In structure c, the spin delocalized over the cytosine ring.
and NaH2P04(H20), (Figure 3). Hence, it appears that waters of hydration will play a decisive role in determining the preferred site of hole localization between the phosphate and the sugar group. Electron spin densities were calculated to determine the preferred site of hole localization within the deoxyribose cation radical. In both semiempirical UHF calculations at the INDO level and ROHF calculationsat the 3-21G level, the spin density localized on the p orbitals of 04’ (Figure 4a) (99.8 and 95.3%, respectively). Such a pattern of hole localization has previously been observed in cyclicether radical cations where the ring oxygen is found to be the site of the unpaired electron The localizationon 04’ was accompanied by a C4’44‘ bond stretching of ca. 0.1 A (1.45 (3-21G optimized neutral geometry) to 1.56 A (3-21G optimized cation radical geometry) and a C1’-04’ bond stretching from 1.48 A (3-2 1G optimized neutral geometry) to 1.56 A (3-21G optimized cation radical geometry). As shown in Figure 5, any one of the four DNA bases are preferred sites for hole localization (guanine being favored) over the deoxyribose group. Kwiatkowskiet al.43presented the energiesof the occupied molecular orbitals of gauche-trans 3‘-endo ribose and gauchegauche 3’-endo ribose from which Koopmans IPcan be calculated. The resulting IP’s were 12.26 and 13.41 eV, respectively. If correction to the discrepancies observed between the absolute values of the calculated and measured potentials of adenine43 (1.9 eV) can be applied to the ionization potentials of the sugar group, the resulting corrected IP’s become in good agreement with our values. Others24 have used tetrahydrofuran to model the deoxyribosegroup and calculated ionization potentials which are in reasonable agreement with our values. 3. Phosphorylated Deoxyribose and Deoxycytidine 3’-Monophosphate. 2’-Deoxyribose 5’-phosphate was geometry optimized at the ROHF/3-21G level (Figure IC) in order to gain insight into the site of hole localization in the cation radical system. Starting bond distances and bond angles for the neutral structure
l
B-DNA this work
Drew-Dickersonb
-58.8 177.0 51.0 129.0 175.5 -93.4
-63 171 54 123 191 -108
-
rangesC -41 -68.6 136 213 36 61.8 122-139 155 227 -91 - 4 5 7
+
Z-DNA this work 92.7 -167.0 156.7 93.0 -178.3 55.5
Defined in ref 41, p 17. Average torsion angles from the DrewDickerson d ~ d e c a m e r . ~ ~Ranges . ~ ’ of torsion anglesreported for B-DNA structures models.47~48*50~53
were obtained from X-ray crystallography data.44 The torsion angles utilized in this structure and the fragments subsequently studied in this work were obtained from the B-DNA structure included in the molecular modeling package Alchemy III.45 Several measurements of torsion angles along the backbone were averaged, rejecting any inconsistent value. Although some variations in conformation arise depending on the B-DNA sequencestudied, the dihedralangles utilized in our model compare well with experimentally and theoretically determined v a l ~ e s ~ ~ 5 3 as shown in Table 111. Throughout this study, optimizations were performed on bond distances and angles, while the backbone torsion angles were kept fixed at values presented in Table 111. Also, the sugar moiety remained in a Czt-endo puckering conformationin all B-DNA structures. The calculatedKoopmans ionization potential obtained from the geometry optimization of the neutral 2’-deoxyribose 5’-phosphate fragment was 11.32 eV, ca. 0.4 eV higher than that of the deoxyribose group. Geometry optimization of the cation radical gave rise to bond distortions similar to those observed in the optimization of the sugar cation radical. Indeed, the C1’-04’ and C4’-04’ bonds of the deoxyribose ring lengthened to 1.56 upon optimizationas compared to 1.45 and 1.48 A in the optimized neutral molecule. As previously observed in the deoxyribose radical cation, 04’ of the sugar ring accounted for ca. 95% of the spin which localized in the p orbitals at the ROHF/3-21G level (Figure 4b). To gain further information on possible charge delocalization between the base and the sugar group in nucleosides, we performed a single-point calculation (no parameter optimization) on the deoxycytidine 3’-monophosphate cation radical. Cytosine was chosen not only for its small size as compared to the other DNA bases but also because of its relatively high ionization potentiaP which should promote spin delocalizationinto the sugar phosphate backbone. The 3’dCMP structure (Figure Id) was obtained by binding the ROHF/3-2 1G geometry optimized neutral cytosine15 to a neutral phosphorylated sugar group, using a N 1-C l’distance
8096
The Journal of Physical Chemistry, Vol. 97, No. 30, 1993
TABLE IV: Koopmans 3-216 Ionization Potentials of Various B- and Z-DNA Backbone Fragments (eV) B-DNA Z-DNA 10.96 D 11.32 11.10 DP DP-Na(H20)p 11.13 11.44 11.18 PDP 11.20 DPD 10.83 DPD-Na(H20)p Single-point calculations. of 1.5 A which is an average glycosyl bond length for pyrimidine bases.55 The base-sugar torsion angle x4I was chosen to be -1 19.0°. This value is an average of the glycosyl torsion angles between various cytosine residues and Czl-endo sugar groups in a B-DNA dodecamer determined by Dickerson and Drew.sl The resulting spin localized entirely on cytosine (99.6%)54(Figure 4c). The deoxyribose phosphate backbone only slightly affects the Koopmans IP of cytosine since the calculated Koopmans IP of the nucleotide (8.92 eV) is only 0.08 eV lower than that found for the individual cytosine a t the same basis set. This clearly shows how critical the DNA base is in determining the lowest energy site of ionization. 4. 2’-Deoxyribose5’,3’-Biphosphate and Bis(2’-deaxyribose) 3’,5’-Monophospbate, Two fragments of the DNA backbone comprising different proportions of the phosphate and 2’deoxyribose groups were investigated in this study to determine the favored site of hole localization following irradiation (Figure 1e,f). For more convenience, the 2’-deoxyribose 5’,3’-biphosphate fragment will be referred to as PDP and the bis(2’-deoxyribose) 3’,5’-monophosphate fragment as DPD. The initial bond distances and angles of PDP were obtained from X-ray crystallography data@while those of DPD arose from the optimized structure of the neutral 2’-deoxyribose 5'-phosphate described above. Torsion angles utilized are presented in Table 111. Protonation of the phosphate groups in PDP and DPD was implemented to achieve neutrality. We performed ROHF/3-21 G geometry optimization of the neutral and cation radical fragments, allowing bond distances and angles to vary, while keeping the torsion angles fixed to respect the B-DNA conformation of the systems. The Koopmans ionization potentials obtained are presented in Table IV. As expected, the values of 11.44 and 11.20 eV for PDP and DPD, respectively, clearly show little dependence of the ionization potentials on the backbone sequence. Surprisingly, the preferred site of hole localization depends on the backbone composition (Figure 4d, e). Indeed, ROHF/3-21G electron spin densities calculated for each cation radical structure show the preferred site of hole localization to be the anionic oxygen of the 5’-phosphate group in PDP (ca. 97%), while the ring oxygen of the deoxyribose group located at the 3’ end of the strand in DPD is the site of highest unpaired electron density (ca. 95%). In both cases, the spin distributes among the px, py, and pz orbitals. The spin localization is accompanied by important bond variations in the cation radical systems. Indeed, although bond angles of the PDP cation radical compare well with those of the neutral PDP, a 0.1 5-A stretching of the P-O(anionic) bond in the 5’-phosphate group occurs upon ionization of the system. Similarly, ionization of the DPD fragment results in a ca. 0.10-A stretch of the C4’04’ and C1’44’ bonds of the sugar ring which contains the unpaired spin as found for DP. These calculations show subtle differences in relative ionization based on DNA backbone sequence, DPD being more easily ionized than PDP (Figure 5 ) . A likely reaction of the phosphate radical (Figure 4d) is hydrogen abstraction from the deoxyribose group of the DNA molecule by the phosphate oxygen radical site. From the lengthening of the C1’-04’ bond upon cation formation we suggest a likely reaction of the ring oxygen radicals (Figure 4a,b,e) may be a rupture of a C-0 bond in the sugar ring. Formation
Colson et al. of these ribose radicals will likely lead to DNA single strand breaks. 1~ 5 6 Hydration effects on hole localization in the phosphorylated sugar and DPD were investigated. Hydration of 2’-deoxyribose 5’-phosphate was achieved by piecing together a deoxyribose group from the optimized DPD neutral backbone and the ROHF/32 1Goptimized neutral geometry of the triply hydrated phosphate sodium complex obtained in the present study. We performed single-pint calculations on the neutral and cation radical forms of this complex. The calculated Koopmans ionization potential obtained was slightly lower than that of the nonhydrated complex as shown in Table IV and Figure 5. N o delocalization of the hole resulted from hydration, 04’ carrying over 92% of the electron spin density (Figure 4b). The neutral DPD system was hydrated in a similar fashion, using the optimized geometry of the triply hydrated sodium phosphate complex. The Koopmans ionization potential resulting from a single-point calculation performed on the neutral system (10.83 eV) is lower than that of theunhydrated optimized neutral structure (1 1.20 eV). In the hydrated DPD backbone the hole localizes on one deoxyribose ring (located at the 3’ end) with 04’ of this ring accounting for over 92% of the spin (Figure 4e). Hydration effects on the Koopmans ionization potentials of DP and DPD follow the trend previously observed between H3PO, and NaHzPO,(H20)3 systems, the latter system undergoing a 0.66-eV decrease in Koopmans IP (Figure 3). In a study of charge transfer in nucleic acids, Clementi et al. have calculated the first ionization potentials of NH2-DPDbase.57 The low Koopmans IP’s obtained in this study$’ (ranging from 4.5 1 to 4.87 eV dependingon the nature of the base attached to the backbone fragment) are likely due to the anionic state of the phosphate group. 5. Z-DNA. Full ROHF/3-21G geometry optimization of the phosphorylated deoxyribose and PDP structures (Figure lc,e) was reiterated with the dihedral angles fixed a t values obtained froin a Z-DNA dodecamer58 and presented in Table 111. These values led to a C3’-endo puckering conformation of the sugar moiety. The Koopmans ionization potentials presented in Table IV did not vary significantly as a result of B-to-Z conformation transition, although a slight decrease of ca. 0.2 eV was observed in both cases. Moreover, the unpaired electron largely localized on the anionic oxygen of the phosphate group in PDP at the ROHF/3-21G level (97%) (Figure 4d),while 04’ remained the favored site of spin localization (94%) in the phosphorylated sugar complex (Figure 4b). Hence, although B-to-Z transition results in significant changes of conformation, no shift in site of hole localization ensues.
Conclusion In this work, ionization potentials and hole localization of various components of the DNA molecule and their hydration complexes have been investigated using ab initio molecular orbital calculations. In Figure 5, we present a summaryof theKoopmans ionization potentials of various DNA components investigated here and in our previous ~ t u d i e s . * ~Results J ~ obtained during the course of this study lead to the following tentative conclusions. 1. The trend in Koopmans ionization potential among the DNA building blocks can be summarized as base < deoxyribose C phosphate. It clearly appears from this trend that the four natural DNA bases will be more easily ionized than any other components of the DNA molecule. Ionization potentials determined in 5’-dGMP by LeBreton et al. and Yu et al.59,23follow a similar trend, although the ionization potentials of guanine and the sugar group within the complex are lower than the values found in this work and other studies of the individual components. 15,24,43,60-62 2. Thejoining of a deoxyribose to a phosphorylated deoxyribose complex in a superstructure lowers the IP by 0.12 eV, whereas
MO Calculations on DNA Radical Ions the joining of a phosphate group raises the IP of the system by 0.12 eV. The increase of IP upon phosphate addition to the phosphorylated sugar is also observed in Z-DNA but to a lesser extent. The B-to-Z-DNA transition is responsible for a slight decrease (ca. 0.2 eV) in ionization potential of the complexes considered in this study. 3. The ring oxygen of the deoxyribose group is predicted to be the favored site of unpaired electron spin localizationin all the DNA base free cation radical systems we have investigatedwith the exception of the diphosphorylated sugar in which the hole will more likely localize on the anionic oxygen of the phosphate group. However, the investigation of electron spin densities (calculated using the Mulliken population analysisz1 at the ROHF/3-21G level) in a nucleotide reveals a delocalization of the spin only over the DNA base ring. Ionization of the DNA double helix will therefore likely result in a transitory hole localization on 04’ of the deoxyribose ring or on a nonbonded phosphate oxygen. At low temperature, rapid transfer of the hole to the DNA base is expected to be competitive with any chemical rearrangement of the deoxyribose phosphate cation, which likely explains the lack of observation of sugar radicals in the low-temperatureESR experiments. At higher temperatures, sufficient activation energy may be available for rearrangements which could then become competitive with hole transfer to the base.
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