Valence- and Dipole-Bound Anions of the Thymine-Water Complex: Ab Initio Characterization of the Potential Energy Surfaces

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2916 J. Phys. Chem. A 2006, 110, Valence- and Dipole-Bound Anions of the Thymine-Water Complex: Ab Initio Characterization of the Potential Energy Surfaces Tomaso Frigato, Daniel Svozil,* and
2916 J. Phys. Chem. A 2006, 110, Valence- and Dipole-Bound Anions of the Thymine-Water Complex: Ab Initio Characterization of the Potential Energy Surfaces Tomaso Frigato, Daniel Svozil,* and Pavel Jungwirth Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, FlemingoVo nám. 2, , Prague 6, Czech Republic ReceiVed: July 25, 2005; In Final Form: NoVember 14, 2005 The potential energy surfaces of the neutral and anionic thymine-water complexes are investigated using high-level ab initio calculations. Both dipole-bound (DB) and valence-bound (VB) anionic forms are considered. Four minima and three first-order stationary points are located, and binding energies are computed. All minima, for both anions, are found to be vertically and adiabatically stable. The binding energies are much higher for valence-bound than for dipole-bound anions. Adiabatic electron affinities are in the mev range for VB anions and the 4-60 mev range for DB anions, and vertical detachment energies are in the mev and mev range for VB and DB anions, respectively. For cases where literature data are available, the computed values are in good agreement with previous experimental and theoretical studies. It is observed that electron attachment modifies the shape of the potential energy surfaces of the systems, especially for the valence-bound anions. Moreover, for both anions the size of the energy barrier between the two lowest energy minima is strongly reduced, rendering the coexistence of different structures more probable. 1. Introduction Electron trapping by nucleotide bases has a crucial importance in understanding the mechanism of DNA-base damage due to high energy radiation. Radical anions resulting from electron attachment to DNA and RNA bases may participate in a chain of chemical reactions that can lead to a permanent alteration of the original bases. Generally, two different types of anions can be produced by an excess electron attachment. 1 A conventional one, called a valence-bound (VB) anion, is obtained when the excess electron occupies a valence molecular orbital. VB anions are characterized by significant changes in geometry upon the capture of the electron. The second type, usually referred to as a dipole-bound (DB) anion, is found in polar molecules that exhibit a large dipole moment in their neutral form. The minimum value of the dipole moment needed to bind an electron was first estimated by Fermi and Teller in For molecular systems, this value depends on the molecular moment of inertia, 3 but as a rule of thumb the value 2.5 D is usually adopted. 4 In DB anions, the excess electron is loosely bound primarily because of the electrostatic charge-dipole interactions 5-7 and dispersion interactions 8-11 between the electron and the neutral molecule. The resulting anionic wave function is very diffuse, and only small geometrical relaxation occurs upon electron capture. Electron attachment to DNA bases has been studied extensively, both experimentally and theoretically (for a recent review, see ref 12). It is usually described in terms of properties such as adiabatic electron affinity (AEA), vertical electron affinity (VEA), and vertical detachment energy (VDE). Two main experimental techniques for the investigation of electronic properties of molecular anions are photoelectron spectroscopy (PES) and Rydberg electron-transfer spectroscopy Part of the special issue Jürgen Troe Festschrift. * Corresponding author. (RET). Recorded spectra of uracil (U) and thymine (T), obtained by PES 13 and RET experiments, 5 showed a typical feature of DB anions: a sharp, intense peak between 0 and 0.1 ev. This particular shape of the spectrum is a consequence of the fact that the attachment of an electron in a DB state does not perturb the geometry of the neutral precursor significantly. In a subsequent study, RET spectroscopy showed that it is possible to obtain a VB anion of isolated uracil by electron attachment to the Ar-U complex, followed by evaporation of argon. 14 The first theoretical calculations of electron attachment on isolated uracil 15 and thymine 16 were restricted to dipole-bound anions only. Later, a first positive estimate of AEA for the thymine VB anion was calculated. 17 Recently, we have reinvestigated both valence- and dipole-bound anions of thymine at a high level of theory. 18 This work supported the previous evidence for the simultaneous existence of both DB and VB adiabatically stable anions of isolated thymine, with the VB anion having a small adiabatic but a large vertical stability. The DB to VB orbital electron transfer has been studied by Sommerfeld, 19 who postulated the possibility, for isolated uracil, of a decay of the higher energy VB state via a vibrationally excited DB state. For systems where the VB anion is the most stable, like hydrated DNA bases, DB states may act as doorways to the formation of VB anions. 19 Hydration of nucleic acid bases is of fundamental importance because biological processes take place in an aqueous environment. A consistent number of studies have focused on the microhydration of uracil, which is the structurally simplest base. Neutral complexes composed of up to seven water molecules have been studied by ab initio and DFT methods Recently, a system consisting of uracil and 49 H 2 O molecules has been investigated using ab initio molecular dynamics simulations, 32 raising interesting questions about the role of finite temperature and system size on DNA bases hydration. Thy /jp054090b CCC: $ American Chemical Society Published on Web 12/22/2005 Anions of the Thymine-Water Complex J. Phys. Chem. A, Vol. 110, No. 9, mine-water complexes were considered as well in some of the aforementioned works. 21,23 Regarding the composite effects of hydration and electron attachment, it was shown experimentally by Bowen et al., 33 that the addition of a single water molecule strongly stabilizes the valence-bound anion of uracil. Very similar results were obtained for microhydrated thymine: 34 the onset of the PES spectrum for a singly hydrated thymine, corresponding to the AEA value, was found around 0.3 ev, while the maximum (VDE) was located around 0.9 ev. The first theoretical calculations by Adamowicz et al. 35 failed to reproduce the stabilization effect of hydration on the valencebound anion of uracil. Three structures, corresponding to three energy minima of the complex, were considered, and calculations converged to adiabatically and vertically stable DB anions in all configurations. The reason VB anions were not found is probably due to the fact that geometry optimizations were performed only at the HF level of theory. The addition of two water molecules allowed one to converge the calculations to a VB anion U-(H 2 O) 3 -, the energy of which approached the energy of the neutral system, 36 although a still slightly negative value of the AEA was computed. This result is in disagreement with experimental findings. 34 Ortiz et al. 37 performed calculations of the uracil-water complex at the / G** level of theory. Four minimal structures of the complex (plus three isomeric forms) were considered. Only valence-bound anions were obtained, and three out of the four minima were found to be adiabatically stable. Although these results are in better agreement with experiments than previous calculations, the authors anticipated that larger basis sets and more complete correlation methods are likely to produce larger VDEs and AEAs. 37 VDEs of the same four U-H 2 O complexes were computed by Gutowski et al. 38 The authors found that the level of theory used, B3LYP/6-31++G**(5d), overestimates the VDE of bare uracil by approximatively 200 mev and, therefore, they assumed that the same error may affect the results obtained for the hydrated uracil. An interesting anionic form of the U-H 2 O complex was discovered by Adamowicz et al., 39 who found a structure (called AISE, anion with internally suspended electron) with the electron positioned between uracil and water; this structure has a high VDE but a quite large negative AEA and, therefore, can only exist as a metastable state that will interconvert to either a stable valence form of anion or that will lead to electron detachment. To the best of our knowledge, only minimum energy configurations were considered so far in theoretical calculations of anionic hydrated uracil (or thymine); first-order transition states were characterized for the uracil-water complex, 20 but only in its neutral form. The energy barriers were found to be too high for thermal transitions between adjacent minima at room temperature. In the present contribution, the methodology applied to isolated thymine previously 18 is used to investigate electronic affinities of the thymine-water complex. Combining the two studies, we present an accurate investigation of the influence on thymine of electron attachment, microhydration by a single water molecule, and microhydration and electron attachment at one time. Four minima and three transition-state structures are considered, and for all geometries both DB and VB anions are found. Moreover, energies of transition states of the neutral and anionic forms are determined to elucidate the role of electron Figure 1. Chemical formula and atom numbering of thymine. Atoms of water are indicated in text as O w and H w. In nucleoside, the sugar is bonded to the N1 atom. Adenine is bonded to H-N3 and OdC4. Minor and a major groove edges are indicated. Positions of water in our system are denoted with A, B, C, and D. attachment on the shape of the potential energy surface of the thymine-water complex. 2. Methods Figure 1 shows the structure and atom numbering of the thymine molecule; atoms of water are denoted in the text as O w and H w. First, four minimum energy structures, obtained exploring the potential energy surface of the neutral thyminewater complex by a molecular dynamics/quenching technique, were taken from a previous study of Hobza et al. 23 Structures were then reoptimized at level with the 6-31G* basis set, and vibrational frequencies were computed at the same level to ensure the minimum character of the stationary points. Three transition-state (TS) structures connecting pairs of minima were optimized at the same level of theory. Intrinsic reaction path (IRC) calculations 40 were performed to compute a minimum energy path passing through the seven (four minima and three TS) stationary points. Different levels of theory (in particular basis sets) were used to study VB and DB anions of the thymine-water complex. In both cases, the frozen core approximation was used for correlated calculations, and VEA, AEA, and VDE were obtained from the supermolecular approach using the following relationships (T-H VEA ) E 2 O) (T-H (T-H2 O) - E 2 O) (T-H2 O)- where the subscript indicates whether the energy has been computed for the neutral or anionic complex, and the superscript defines at what geometry the energy is evaluated. This also implies that the calculations of stationary points of the neutral complex were refined at the higher level of theory used for the anions, specified in the following subsections. (1) (T-H AEA ) E 2 O) (T-H (T-H2 O) - E 2 O) - (T-H2 (2) O)- (T-H VDE ) E 2 O) - (T-H (T-H2 O) - E 2 O) - (T-H2 (3) O)- 2918 J. Phys. Chem. A, Vol. 110, No. 9, 2006 Frigato et al. Resolution of the identity (RI-) optimizations were carried out with the computer code Turbomole All of the remaining calculations were performed using Gaussian Dipole-Bound Anions. To describe dipole-bound electrons properly, standard basis sets (in our case 6-31+G* and aug-cc-pvdz 43 ) have to be augmented with an additional set composed of very diffuse functions. The nonspherical character of the excess electron necessitates the inclusion of higher angular momentum functions. It has been shown previously 44 that the inclusion of S and P functions already accounts for more than 90% of the binding energy at the level of theory. Therefore, only S and P additional diffuse sets were added. Within relatively broad margins, the exact position of the diffuse sets has little influence on the results. 15,16,18,45 Because the orbital occupied by a DB electron is centered outside the molecule toward the positive end of its dipole moment, it is common practice to place them there. In our calculations, the additional diffuse functions were placed on the atom closest to the positive end of the dipole moment of the neutral complex. The additional S and P diffuse functions have exponents R i )R 1 q i-1, i ) 1...n. 45 Three parameters have to be determined: the lowest exponent, R 1, the progression parameter, q, and the length of the sequence (i.e., the number of additional S and P sets), n. To obtain these parameters, we followed the procedure developed by Gutowski et al. 45 The value of the highest exponent should be smaller than the exponent of the most diffuse function in the standard basis set by at least a factor of 2. In the present work, its value was obtained simply by halving the value of the smallest exponent appearing in the standard basis set. The value of the progression parameter depends on the value of the dipole moment of the neutral molecule. 45 For molecules with dipole moments in the D range, q adopts values between 3.0 and ,45 To increase the numerical stability and the efficiency of our calculations, 18 we utilized a value of q ) 5.0. To determine the length of sequence n, SCF orbitals of the neutral complex were computed with the diffuse set present, and n was increased until the molecular orbital coefficients of the most diffuse sets were not dominant, that is, the extra diffuse basis set became saturated. 45 Because electron correlation effects change the properties of DB anions significantly, 8,11,45 and because the computation of electronic affinities requires the use of size-extensive methods, geometry optimizations were performed at the /aug-ccpvdzx level (X indicates the additional diffuse basis set). Assuming that the difference between CCSD(T) and energies exhibits only a small basis set dependency, 46,47 CCSD- (T) energies can be approximated as CCSD(T) E aug-cc-pvdzx ) CCSD(T) where E 6-31+G*X E aug-cc-pvdzx and E 6-31+G*X CCSD(T) + (E 6-31+G*X are computed at /aug-ccpvdzx geometries. Because no substantial spin contamination was observed in any calculations of DB anions, unrestricted CCSD(T) and methods were used. To improve convergency, the HF/aug-ccpVDZX orbitals of the neutral complex were used as a starting orbital guess. Because of the negligible geometry difference between DB and neutral complexes, we assumed that zero point energy (ZPE) corrections are the same for DB and neutral complexes (as a check, we found that in the structure denoted below as D, ZPEs of neutral and anionic thymine-water complexes differ by less than 2 mev) Valence-Bound Anions. Because of the relatively high computational demands of calculations with the employed basis sets, the approximate resolution of the identity (RI- ) method 48,49 was used for geometry optimizations. In the RI- approximation, two-electron four-center integrals are replaced by linear combinations of two-electron three-center integrals, which are easier to compute, via the introduction of an auxiliary fitting basis set, and a lower number of integrals needs to be computed and stored This allows a speedup of RI- calculations compared with standard that depends on the details of the calculations but reaches 1 order of magnitude easily. 48,50,51 Regarding the accuracy, it has been shown on several systems that, with an accurate choice of the auxiliary fitting basis set, energies and structures computed with and RI- methods do not show significant differences. 48,51,52 In particular, interaction energies of selected H-bonded and stacked DNA base pairs, computed with and RI- methods, are almost identical, 50 and we showed in a previous contribution that the AEA of the VB thymine anion differs only marginally ( 1 mev) when computed with and RI- methods. 18 A procedure similar to that adopted in our previous study of isolated thymine 18 was applied to the geometry optimization of VB anions. Geometries of the neutral complex were used as starting structures and were first optimized at the RI-/6-31G* level. Subsequent optimizations were performed at the RI-/aug-cc-pVTZ level. The preliminary optimizations with the 6-31G* basis set converged to complexes characterized by a nonplanar ring, and the following optimizations at RI-/ aug-cc-pvtz converged to the correct VB structures. In this way, we avoided artifacts of direct optimizations at the RI-/ aug-cc-pvtz level, that tend to converge to higher energies, corresponding to hybrid dipole-bound-valence-bound structures. 18 In the case of TS calculations, a proper choice of starting guess structures proved to be particularly important. Thymine atomic coordinates were taken from the RI-/aug-cc-pVTZ optimized geometry of one of the two minima connected directly to the transition structure. The water molecule was initially placed in the same relative position to the thymine molecule as in the neutral TS structure (optimized at the same level of theory). Compatibly with minima calculations, final optimizations were performed at the RI-/aug-cc-pVTZ level. Complete basis set (CBS) energies were estimated using the extrapolation scheme developed by Helgaker et al. 53,54 utilizing Dunning s augmented correlation consistent basis sets of double- and triple-ζ quality: 43 - E 6-31+G*X ) (4) E HF HF ) E aug-cc-pvdz + E ) E aug-cc-pvdz HF (E aug-cc-pvtz + (E aug-cc-pvtz HF - E aug-cc-pvdz )/ (5) - E aug-cc-pvdz )/ (6) Because of the presence of a nonnegligible spin contamination ( Ŝ ), single point energy calculations were performed for optimized structures with the spin-projected method (P) with the aug-cc-pvdz and aug-cc-pvtz basis sets. 18 Because no substantial spin contamination was observed at the CCSD(T) level, unrestricted CCSD(T) was used in our calcula- Anions of the Thymine-Water Complex J. Phys. Chem. A, Vol. 110, No. 9, Figure 2. Relative energies and optimized geometries of stationary points of the neutral complex. TABLE 1: Relative Energies, Expressed in kcal/mol, of Neutral Complexes Computed at Different Levels of Theory + E a CC complex 6-31G* aug-cc-pvdz aug-cc-pvtz CBS CBS CBS+ZPE A B C D T T T a CCSD(T) E CC ) E 6-31+G* - E 6-31+G* tions. As explained above, CCSD(T) energies were extrapolated as follows: E CCSD(T) ) E + (E CCSD(T) 6-31+G* - E 6-31+G* ) (7) Finally, because of the significant differences between neutral and VB optimized geometries, ZPE corrections, calculated at the RI-/aug-cc-pVDZ level without the inclusion of any scaling factor, were added to computed energies. We notice at this point that, for both VB anions and neutral complexes, the ZPE values of the TS structures were computed without including the contribution of the single imaginary frequency. 3. Results and Discussion Neutral Complex. Figure 2 shows the minima and transitionstate structures for the neutral complex, optimized at the RI- /aug-cc-pvtz level. All structures are characterized by a planar thymine ring. In structures B-D, the water molecule interacts with thymine via O w H w O and NH O w hydrogen bonds. The water hydrogen and oxygen atoms involved in the H bond are coplanar with the thymine molecule, whereas the second H atom is pointing out of the plane. Because of the presence of the methyl group, structure A is somewhat different because the water is positioned outside of the thymine plane, and one of the two H bonds is substituted by two weak CH O w interactions. Regarding transition-state geometries, it can be noticed that one hydrogen bond is always broken. In structures T1 and T3, the water molecule lies outside the thymine plane and is bound through a CO H w
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