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J. Phys. Chem. B 2003, 107, 848-853
The Adenine-Thymine Base Pair Radical Anion: Adding an Electron Results in a Major Structural Change Nancy A. Richardson,† Steven S. Wesolowski,‡ and Henry F. Schaefer, III*,† Center for Computational Quantum Chemistry, UniVersity of Georgia, Athens, Georgia 30602-2525, and Department of Chemistry, Yale UniVersity, New HaVen, Connecticut 06520-8107 ReceiVed: September 20, 2002; In Final Form: NoVember 15, 2002
The adiabatic electron affinity (AEA) for the Watson-Crick adenine-thymine (AT) DNA base pair is predicted and contrasted to that of guanine-cytosine (GC) with a range of density functional methods with doubleand triple-ζ plus polarization plus diffuse (DZP++ and TZ2P++) basis sets. An estimate of the true AEA is provided using a bracketing method that has been calibrated against a comprehensive tabulation of experimental electron affinities [Rienstra-Kiracofe, J. C.; Tschumper, G. S.; Schaefer, H. F.; Nandi, S.; Ellison, G. B. Chem. ReV. 2002, 102, 10163]. Optimized structures for AT and the AT anion are compared to the neutral and anionic forms of the individual bases as well as Rich’s 1976 X-ray structure for the related sodium adenylyl-3′,5′-uridine hexahydrate, ApU‚6H2O. In contrast to the angular distortions (to nonplanarity) occurring in GC upon anion formation, the angular distortions for the AT anion are slight. However, in an analogous fashion to the GC anion, major changes in the AT anion hydrogen bond distances, from 0.27 to 0.32 Å, are predicted relative to neutral AT. Natural population analysis (NPA) charge distributions are also seen to shift. Those of the AT anion also indicate that the unpaired electron is localized on the pyrimidine (thymine). Density functional theory consistently predicts a substantial positiVe adiabatic electron affinity for the AT pair (e.g., TZ2P++/B3LYP: +0.31 eV). This contrasts to second-order perturbation theory (MP2) treatments which predict unbound base pair anions. Despite the greater AEA of isolated T relative to C (+0.15 vs -0.02 eV), the AEA of the AT pair is slightly smaller than that of GC (0.31 vs 0.48 eV). This difference is attributed to the weaker solvating capacity of A (A‚T-) relative to G (G‚C-). The pairing (dissociation to A + T-) energy of AT- is determined to be 14.8 kcal/mol. This value is slightly greater than previous estimates for neutral AT from theory (12.4 kcal/mol) and experiment (13.0 kcal/mol).
I. Introduction Interest in the electron affinities (EA) for fragments of DNA and RNA stems from both their significance in the anion formation that initiates events leading to radiation damage1-6 and their role in charge transfer along DNA which could be impaired by stable anion formation.7-15 One line of investigation has proceeded by considering the intrinsic effect of excess charge on the fundamental components of the nucleic acid and then analyzing changes that occur with additional elements of the system. Such theoretical work could complement current experimental efforts to study the DNA “π-way”.16 Early computational work by Colson, Besler, and Sevilla illustrated the qualitative effect of base pairing on proton-transfer energies, electron affinities, and ionization potentials.10 Subsequent work on nucleic acid bases and base pairs has emphasized the energetics and structure of the neutral molecules.17-19 However, steps toward understanding the effects of excess charge on DNA were made with determinations of the individual nucleic acid base (NAB) electron affinities. The individual NABs are experimentally observable in the gas phase.4,20-25 Theoretical EA determinations26-32 complemented the experimental work producing considerably varied results. The best estimates31 predict positive, covalently bound anions of uracil (U) and thymine (T) with EAs of about 0.19 and 0.16 eV, * Corresponding author. † University of Georgia. ‡ Yale University.
respectively. The cytosine (C) anion is also predicted to be covalent but slightly unbound with an EA of -0.02 eV. Guanine (G) and adenine (A) were found to have EAs of 0.07 and -0.17 eV, respectively, with some debate as to whether these were dipole or covalently bound anions. In covalent anions the additional electron fills the LUMO in a conventional way, whereas in dipole bound anions, the electron is held in a diffuse orbital not influencing structure.33 Li, Cai, and Sevilla have reported that the purine anions exhibit a mixed covalent-dipole character when large, diffuse basis sets are employed.34 Therefore, until these sytems are treated using methods that account for this mixture, the covalent (negative) electron affinities of the purines are perhaps best estimated using small basis sets that constrain the electron density on the molecular framework. In analyzing the isolated NABs, these experiments indicated that excess negative charge in DNA would be found on the pyrimidines and that significant geometrical distortion of the anion would occur to accommodate the negative charge. Further progress in studying excess charge in DNA extends to the determination of the electron affinity of the WatsonCrick base pairs. Experimental observations for some of the gas-phase base pairs was accomplished35 and an identification of vibrational frequencies for one pair, GC, was recently reported in Nature;36 however, experimental EAs were not determined. Theoretical attempts to determine the EA of GC37-40 ranged from quite negative to slightly positive. Similarly, the EA of AT has been variously estimated from -1.05 eV to -0.4 eV at several levels of theory.37,41 The MP2 work may have been
10.1021/jp022111l CCC: $25.00 © 2003 American Chemical Society Published on Web 12/28/2002
Adenine-Thymine Base Pair Radical Anion
Figure 1. Atomic numbering scheme for the AT base pair.
hinderd by problems associated with spin contamination for the anions.30,42 The controversy of the EA for GC was addressed by our well-tested DFT bracketing technique43 that showed GC to form a covalently bound anion with an adiabatic EA of about 0.5 eV.44 This might be surprising since both G and C have EAs close to zero. The combination of molecules results in a complex with different properties than either individually. The explanation of the appreciable EA of GC lies in an examination of the microsolvation data. Since microsolvation had been shown to affect electron affinities of the individual bases U, T, and C,24 a reason for the stability of the GC anion seems to be that the presence of another hydrogen-bonded molecule affects the electron affinity of cytosine in the guaninecytosine (GC) base pair. The influence of G increased the EA of C by an amount equivalent to about two water molecules. In contrast to the GC pair where both bases have electron affinities close to zero, the adenine-thymine (AT) base pair is composed of a base with a significantly negative predicted EA, A ) -0.17 eV, and of a base with a relatively positive EA, T ) 0.16 eV. Extension of the bracketing technique to the AT pair should provide a reliable estimate of the adiabatic EA as well as insight into reasons for the preferred location of excess charge. In this study we again use our systematic procedure to predict the adiabatic electron affinity of AT, whose structure is shown in Figure 1. We also explore the consequences of negative charge in terms of structural fluctuations, energetic changes, harmonic vibrational frequencies variations, and natural population analysis (NPA) charge differences. We contrast AT to the previously studied GC. II. Theoretical Methods In accord with our previous work31,43,44 employing a DFT bracketing technique, five generalized gradient approximation (GGA) exchange-correlation density functionals were used to optimize geometries, determine absolute energies, and generate natural charges for the hydrogen-bonded Watson-Crick base pair adenine-thymine (AT). These functionals are denoted B3LYP, B3P86, BHLYP, BLYP, and BP86 and are combinations of one of Becke’s exchange functionals: the 3-parameter HF/DFT hybrid exchange functional (B3),45 a modified halfand-half HF/DFT hybrid method (BH)46 as implemented in GAUSSIAN 94, or the pure DFT exchange functional (B)47 with the dynamical correlation functional of Lee, Yang, and Parr (LYP)48 or that of Perdew (P86).49,50 The GAUSSIAN 94 system of DFT programs51 was used for all results. In general, BHLYP underestimates AEAs, while B3P86 always overestimates AEAs. The hybrid functionals that incorporate exact exchange are susceptible to spin contamination; therefore the use of all five functionals gives some assurance that the weakness of one functional has not produced spurious data and led to erroneous conclusions. Two basis sets were used. Geometry optimizations and harmonic vibrational frequency analyses were carried out with double-ζ quality basis sets with polarization and diffuse functions (denoted DZP++). The DZP++ basis sets were
J. Phys. Chem. B, Vol. 107, No. 3, 2003 849 constructed by augmenting the Huzinaga-Dunning52,53 set of contracted double-ζ Gaussian functions with one set of p-type polarization functions for each H atom and one set of five d-type polarization functions for each C, N, and O atom (Rp(H) ) 0.75, Rd(C) ) 0.75, Rd(N) ) 0.80, Rd(O) ) 0.85). To complete the DZP++ basis, one even tempered s diffuse function was added to each H atom while sets of even tempered s and p diffuse functions were centered on each heavy atom. The even tempered orbital exponents were determined according to the prescription of Lee and Schaefer:54
Rdiffuse )
(
)
1 R1 R2 + R 2 R2 R3 1
(1)
where R1, R2, and R3 are the three smallest Gaussian orbital exponents of the s- or p-type primitive functions for a given atom (R1 < R2 < R3). The final DZP++ set contains six functions per H atom (5s1p/3s1p) and nineteen functions per C, N, or O atom (10s6p1d/5s3p1d), yielding a total of 428 contracted functions for the AT pair. This basis has the tactical advantage that it has previously been used in comprehensive calibrative studies43 of a wide range of electron affinities. In addition, single-point energies at the DZP++ optimized geometries were computed using a triple-ζ plus double polarization plus diffuse quality basis set (TZ2P++). This basis was formed from the Huzinaga-Dunning52,53 sp sets augmented with two sets of polarization functions (two sets of five d-type functions on C, N, and O, and two sets of p functions on H). The exponents for the polarization functions are Rp(H) ) 1.50, 0.375, Rd(C) ) 1.50, 0.375, Rd(N) ) 1.60, 0.40, and Rd(O) ) 1.70, 0.425. Even tempered diffuse s- and p-type functions were added in a fashion analogous to the DZP++ set. The final TZ2P++ set contains 10 functions per H atom (6s2p/4s2p) and 28 functions per C, N, or O atom (11s7p2d/6s4p2d), yielding a total of 642 contracted functions for the AT pair. Both the neutral and anion stationary points were optimized via analytic gradients until the residual RMS gradient was less than 10-4 hartree/bohr. Numerical integration was performed using the GAUSSIAN 9451 default grid consisting of 75 radial shells with 302 angular points per shell. Each valence 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 ) Eneut - Eanion
(2)
All molecular orbital plots were constructed with the TZ2P++ basis using the MOLDEN software package55 and utilized the appropriate B3LYP/DZP++ optimized structures. Natural Population Atomic (NPA) charges were determined at the B3LYP/DZP++ level using the Natural Bond Order (NBO) analysis of Reed and Weinhold.56-59 III. Results A. Geometry. In considering the effects of excess charge, analysis of geometric changes provides insight into its molecular accommodation. Our previous work44 showed reasonable accuracy for DFT bond lengths in NABs and NAB pairs. Complete B3LYP/DZP++ geometry optimizations of neutral and anionic AT bond lengths are shown in Figure 2. Only infinitesimal variations occur in the purine while differences in the pyrimidine bond lengths are more significant. These changes provide some assurance that the AT anion is covalently rather than valence bound; the excess electron density significantly perturbs the
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Richardson et al.
Figure 4. Selected bond lengths of the adenine-thymine anion base pair with five DFT functionals using the DZP++ basis set. (Comparison is made to the related experimental distances61 which contain two inequivalent A-U pairs as determined by crystallography for the structure shown in Figure 1.) Figure 2. B3LYP/DZP++ optimized bond lengths of the neutral and anion AT pairs. Distances are reported in angstroms.
TABLE 1: Harmonic Vibrational Frequencies (in cm-1) Corresponding to the Six “New” Vibrational Modes Introduced upon AT and AT- Pairinga BHLYP/DZP++ BLYP/DZP++ B3LYP/DZP++ BP86/DZP++ B3P86/DZP++
ω1
ω2
ω3
ω4
ω6
ω7
27, 23 24,29, 23 29, 18 29, 22
37, 33 40,37, 33 37, 37 38, 34
58, 43 78,60, 43 64, 48 63, 48
77, 64 94,79, 53 79, 50 80, 70
107, 96 130,107, 95 113, 99 114, 98
121, 112 133,118, 110 114, 106 118, 111
38 38
68 67
82 83
114 115
122 119
BP86/6-311Gb (AT) 27 B3PW(91)/6-311Gb (AT) 27
Figure 3. Significant (>0.010 Å) changes in AT base pair bond lengths (anion - neutral). Differences are reported in angstroms.
molecular framework and occupancies. Figure 3 illustrates significant (>0.010 Å) bond length changes that occur between the neutral and anionic AT pair. Some changes occur in the thymine ring with a 0.060 Å lengthening of the C5-C6 bond and a slightly smaller lengthening of the C6-N1 bond. Such changes are also observable upon formation of excited electronic states in which electrons are promoted into the C5-C6 obitals of T.60 Other significant changes occur for the covalent heavyatom-to-hydrogen distances as well as for the atoms adjacent to those atoms participating in hydrogen bonds. The greatest changes, however, occur in the actual hydrogen bond lengths. Figure 4 shows the neutral and anionic bond lengths for the heavy atom distances and for the hydrogen-bonded heavy-atomto-hydrogen distances for the five DFT functionals and for the closest experimental work available, the sodium adenylyl-3′,5′uridine hexahydrate (ApU) X-ray structure.61 This work and the sodium guanylyl-3′,5′-cytidine nonahydrate (GpC) crystal62 have previously served as the primary comparisons for theoretical studies of bases and base pairs.17,18,40,63-65 (Uracil differs from thymine only in the absence of the methyl group attached to C5.) The changes in hydrogen-bonded distances could be taken as evidence for increasing charge density on T: distance between the T O4 and the A H6 decreases while the A N1 and T H3 distance increases, indicating a weaking of this bond. The
a Entries given as pairs correspond to the neutral and anion GC values, respectively. A thorough description of these vibrational modes is provided in ref 66. b Ref 66.
O4 has become more negative, thus shortening the distance to the H6. Since the charge transfer in the oxygen hydrogen bond is more significant than that in the nitrogen-hydrogen bond, overall stabilization is achieved. Do such charge shifts impact the angles in AT? Consideration of the angular changes provides another and more curious perspective. In the individual NABs, ring distortion (to nonplanarity) occurs for both the A and T molecules. However, in the AT anion, almost no ring distortion occurs. (Detailed comparisons are available as Supporting Information.) This is in contrast to the GC anion in which C is significantly distorted. The accommodation of excess charge apparently occurs in such a fashion as not to perturb the ring angles, at least in the DFT model. Such lack of distortion might suggest that excess charge on AT would cause less disruption of DNA than excess charge on GC, where the angles are perturbed significantly. B. Vibrational Frequencies and Pairing Energetics. Changes relative to neutral AT also occur in the harmonic vibrational frequencies and the pairing energy. Table 1 shows the AT and AT- harmonic vibrational frequencies of modes related to the interaction of A and T/T- for the five DFT functionals, plus a comparison with previous work. No experimental determinations of vibrational frequencies are available for AT. The differences between the neutral molecule and the anion for these “new modes” are small with the greatest decrease (about 15 cm-1)
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J. Phys. Chem. B, Vol. 107, No. 3, 2003 851
TABLE 2: Pairing Energies (in kcal/mol) for the Neutral and Anionic A, T, ATa AT f A+T
AT- f A + T-
AT- f A + e- + T
BHLYP/DZP++ BLYP/DZP++b B3LYP/DZP++ BP86/DZP++ B3P86/DZP++
-12.7 (-14.1) - (-13.1) -12.5 (-13.8) -13.3 (-14.3) -13.9 (-15.1)
-15.7 (-16.6) - (-13.5) -16.1 (-16.7) -20.4 (-20.4) -18.0 (-18.3)
-15.8 (-13.6) - (-19.0) -20.7 (-18.2) -26.7 (-23.7) -34.3 (-31.6)
TZ2P++/B3LYP HF/6-31G(d)c MP2/6-31G*d Expt.e
-10.6 (-11.9) -10.03 -12.4 -13.0
-14.3 (-14.8) -8.79
-17.8 (-15.3)
a Nonzero-point vibrationally corrected pairing energies are given in parentheses. b Zero-point correction is not available for the BLYP. c Ref 37. d Ref 70. e From field-ionization mass spectroscopy, ref 68.
occurring for the out-of-plane torsion of the AT molecule. As noted in our previous work,44 the inclusion of diffuse functions reduces the magnitude of the vibrational frequencies compared to those determined with the 6-311G basis set.66 However, our theoretical harmonic vibrational frequencies here will likely exceed those determined by experiment since these low energy modes are expected to be very anharmonic.67 In contrast to the vibrational frequencies, experimental results for pairing energies have been reported. Pairing energetics of AT (along with a number of other base pairs) were originally estimated by Yanson, Teplitsky, and Sukhodub using fieldionization mass spectroscopy68 to be about 13.0 kcal/mol. Table 2 provides the pairing energies of AT and AT- for all five functionals as well as comparison with the previous MP2/631G* results of Sˇ poner, Leszczynski, and Hobza who found the neutral AT dissociation energy to be 12.4 kcal/mol. BSSE corrections are not considered in our work, but are generally less for DFT than MP2.17 Agreement of the DFT values with
TABLE 3: Zero-Point Vibrationally Corrected Adiabatic Electron Affinities (in eV) for Isolated A, T, and the AT Base Pair Using the DZP++ Basis Seta Ab BHLYP BLYP B3LYP BP86 B3P86 B3LYP/TZ2P++ UMP2/6-31++G**(6d)c
T
AT
-0.65(-0.66)
