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PAPER Faraday Discussions The effect of microhydration on ionization energies of thymine Kirill Khistyaev, a Ksenia B. Bravaya, a Eugene Kamarchik, ab Oleg Kostko, c Musahid Ahmed*

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PAPER Faraday Discussions The effect of microhydration on ionization energies of thymine Kirill Khistyaev, a Ksenia B. Bravaya, a Eugene Kamarchik, ab Oleg Kostko, c Musahid Ahmed* c and Anna I. Krylov* a Received 3rd November 2010, Accepted 26th January 2011 DOI: /c0fd00002g A combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron VUV radiation. The onsets of the PIE curves are , , , and ev for thymine, thymine mono-, di-, and trihydrates, respectively. The computed (EOM-IP-CCSD/cc-pVTZ) AIEs are 8.90, 8.51, 8.52, and 8.35 ev for thymine and the lowest isomers of thymine mono-, di-, and tri-hydrates. Due to large structural relaxation, the Franck Condon factors for the 0 ) 0 transitions are very small shifting the apparent PIE onsets to higher energies. Microsolvation strongly affects IEs of thymine the addition of each water molecule reduces the first vertical IE by ev. The adiabatic IE decreases even more (up to 0.4 ev). The magnitude of the effect varies for different ionized states and for different isomers. For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule. I. Introduction The ionization of nucleic acid bases (NABs) is involved in DNA radiation and photo-damage and may eventually lead to dangerous mutations with a risk for cancer and neurodegenerative diseases. Due to their relatively low ionization energies (IEs), individual nucleobases are the most likely components of DNA to be oxidized. Their IEs, however, are affected by coupling to DNA s sugar phosphate backbone, hydrogen-bonding and p-stacking between neighboring bases, as well as interactions with solvating water molecules and counter ions. Quantifying the exact nature of these effects has proven difficult, and even the values of IEs of solvated DNA are still controversial. For example, a recent computational study 1 that attempted to compute the IE of guanine in solvated DNA by a QM/MM approach reported a large increase (4 ev) of guanine s IE, contrary to the conclusions drawn from experimental studies. 2 As part of our effort to understand the role played by different interactions of NABs with the environment, 3 8 we recently characterized the effect of a Department of Chemistry, University of Southern California, Los Angeles, CA, , USA. b Department of Chemistry, C.L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia, 30322, USA c Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Electronic supplementary information (ESI) available. See DOI: /c0fd00002g This journal is ª The Royal Society of Chemistry 2011 Faraday Discuss., 2011, 150, hydrogen-bonding and p-stacking on the ionized states of the gas-phase dimers of AA, TT, AT, and CC in a combined experimental and theoretical study. 7,8 We found that stacking and hydrogen-bonding can reduce the IEs by ev via two distinct mechanisms: hole delocalization and electrostatic charge dipole interactions. We also analyzed ionization-induced structural changes in isolated nucleic acid bases 9 and in uracil dimers. 4,5 Consistent with delocalized character of the highest occupied molecular orbital (HOMO), structural changes involve several CC and CN bonds, the largest change being for the double CC bond. In bare NABs the relaxation energy is ev, whereas in the dimers the difference between adiabatic and vertical IEs is larger. To quantify the effect of structural relaxation on photoionization efficiency (PIE) curves, we computed Franck Condon factors (FCFs) for the lowest-energy tautomers of NABs. 9 In all cases, we observed that the 0 ) 0 transitions have non-negligible FCFs and that the onsets of the PIE curves indeed represent AIEs. Microsolvation has been found to decrease the IEs of nucleobases by about 0.1 ev per water molecule 6,10. The absolute values of IEs reported in VUV 6 and electron impact 10 studies are slightly different. An excellent agreement of the IE of isolated thymine determined from the PIE curve ( ev) 6 with the value derived from MATI spectra ( ev) 11 validates the accuracy of the synchrotron VUV measurements. 6 The computational studies 12,13 performed with B3LYP predicted similar magnitude shifts and pointed out substantial geometric relaxation in hydrated species leading to even larger changes in AIEs. These studies were motivated by differences between the results obtained by the two experimental approaches, i.e., using electron impact ionization and VUV photoionization. 6,10 A number of tautomers were calculated to interpret the early electron impact results, while attempts were made to fit the appearance energy measurements to various vertical and adiabatic values. In other nucleobases, microhydration leads to similar effects, 6 although the magnitude of the IE drop varies. For example, the changes in AIE in adenine water clusters 6,14 are smaller than those for thymine. The effect of microsolvation on electronically excited states and photoinduced dynamics in nuclear bases and other model chromophores has been investigated theoretically and experimentally In addition to perturbations to the electronic spectrum and differential stabilization of excited states, microsolvation can open up new relaxation channels including, among others, hydrogen/proton and electron transfer, charge-transfer-to-solvent states, and zwitter-ion formation. The theoretical treatment of ionized species is challenging owing to their openshell character and electronic near-degeneracies. 23,24 Wave-function approaches using doublet references often suffer from spin-contamination and symmetrybreaking, which result in hole over-localization. 23 DFT methods are affected by self-interaction error leading to charge over-delocalization. Owing to these defects, computational studies often observe artifacts of electronic structure methodology rather than real physical properties of these systems. We employ the EOM-IP method that is free from the above problems and is the method of choice for these systems. EOM-IP describes open-shell target states as ionized states derived from well behaved closed-shell neutral reference wave functions (see Section II.A). We also use DFT with a range-separated functional (ub97x-d) that greatly reduces self-interaction errors. 25,26 The appearance energies of microhydrated thymine ions [T(H 2 O) n, n ¼ 1 3)] have been reported previously by our group. 6 In the present work we have performed the measurements with a broader energy range and report improved error bars. Furthermore, derivation of the PIE curves as reported by us for NABs and their dimers, allows for qualitative interpretation of the VIEs for thymine and hydrated thymine as a maxima at the obtained curves. In the earlier experimental work, 6 the beam contained mixed adenine thymine and water clusters, and in the new experiments reported here thymine alone was microhydrated with water. 314 Faraday Discuss., 2011, 150, This journal is ª The Royal Society of Chemistry 2011 Previous experimental and theoretical studies on the microhydration of thymine do not provide a detailed physical picture of the ionization processes. Hence, the focus of this work is on quantifying the effect of microsolvation on IEs and on understanding its origin. We consider several isomers of the microhydrates shown in Fig. 1 (all structures correspond to the lowest-energy tautomer of thymine). In order to unambiguously compare with the experimental measurements, we also perform modeling of the FCFs for the lowest electronic state of the cations. Accurate FCF calculations for hydrogen-bonded systems of such complexity are rare and provide important benchmarks as well as insight into the spectroscopy of biologically relevant species. II. Experimental and computational techniques A. Electronic structure calculations Open-shell doublet wave functions can be formally derived from a closed-shell systems by addition or subtraction of an electron. As such, they can be described accurately and efficiently by the ionization potential (IP) and electron affinity (EA) variants of equation-of-motion coupled-cluster (EOM-CC) methods EOM-IP, which relies on the N-electron closed-shell reference, is free from the symmetry breaking and spin-contamination problems that are ubiquitous in openshell calculations, and is capable of describing charge localization patterns in ionized clusters. 4,7,23,31 EOM-IP simultaneously includes dynamical and non-dynamical correlation, describes multiple electronic states in one calculation, and treats states with different number of electrons on the same footing. Using the EOM-CC family of methods, electronically excited, ionized, or attached states of the thymine-water clusters can be computed starting from the same closed-shell CCSD (coupled-cluster with singles and doubles) reference wave function of the neutral. 24,32 The target open-shell wave functions are generated by a Koopmans-like excitation operator R acting on the reference CC wave function: J EOM IP (N 1) ¼ ^Re ^T F 0 (N) (1) where F 0 (N) is the reference determinant of the N -electron neutral system, T is the coupled-cluster excitation operator including single and double substitutions, and R Fig. 1 Structures and binding energies (D e, kcal mol 1 ) of the considered thymine water monohydrates, dihydrates and trihydrates, CCSD/cc-pVTZ at RI-MP2/cc-pVTZ geometry. This journal is ª The Royal Society of Chemistry 2011 Faraday Discuss., 2011, 150, consists of 1h and 2h1p (1-hole and 2-hole-1-particle) operators generating (N 1)- electron determinants from the N-electron reference. Amplitudes T are found by solving CCSD equations for the ground-state wave function of the neutral, while amplitudes R are obtained by subsequent diagonalization of the similarity transformed Hamiltonian, H ¼ e T He T. EOM-IP-CCSD yields accurate energy splittings and smooth potential energy surfaces along charge transfer coordinates. 23 This method has been successfully applied to describe electronic structure of ionized benzene dimers, 31,33 water clusters and dimers of nucleobases. 3 5,7,8 Typical errors in excitation energies associated with single excitation processes for EOM-CC with single and double substitutions are in the ev range. 37,38 However, energy differences between different ionized states are described much better (errors below 0.05 ev). 23 In our recent joint experimental and theoretical study of the four gas-phase nucleobases, the errors in computed adiabatic IEs relative to the experimental values were found to be below 0.1 ev. 9 We also employed DFT with the long-range and dispersion-corrected ub97x-d functional 26 (for geometry optimization and frequency calculations). Long-range Hartree Fock exchange included in ub97x-d mitigates the effect of self-interaction error yielding accurate structures and frequencies. 7,9 There are several tautomers of thymine; however, the energy gap between the canonical form and the next most stable tautomer is more than 10 kcal mol 1 (ref. 39) in the gas phase. Since we used thermal vaporization to generate thymine in the gas phase, there is not enough energy to populate higher-lying tautomers. Thus, the canonical form should be predominantly present in a molecular beam. We considered the three most stable monohydrated thymine isomers (T1-T3, see Fig. 1) and the two thymine-(h 2 O) 2 structures (T11, T12) obtained by Hobza et al. using the molecular dynamics/quenching technique. 39 The fourth most stable monohydrate structure (T4) shown in Fig. 1 is 4.4 kcal mol 1 higher in energy than the most stable T1. Therefore we excluded T4 from further consideration. Thymine trihydrate structures (T111 and T112) were obtained by addition of a water molecule to dihydrate structures. All ground-state geometries were optimized using the RI- MP2/cc-pVTZ 40,41 and ub97x-d/cc-pvtz methods, which yielded similar results. For example, the differences in all bond lengths for the thymine molecule in T1 is less than 0.01 A; the hydrogen bond between the N H group of thymine and the oxygen of water is A shorter and the hydrogen bond between C¼O of thymine and the hydrogen of water is A shorter for RI-MP2 (1.871 and A, respectively) than for ub97x-d (1.899 and A, respectively). Fig. 2 and 3 show the RI-MP2 ground states geometries. The respective Cartesian coordinates as well as ub97x-d structures are given in the ESI. The equilibrium structures of the cations were computed with ub97x-d/cc-pvtz (see Fig. 4 and 5). This functional, when used with the G(3df,3pd) basis set, was shown to describe geometries and binding energies of the weakly bound complexes with mean absolute errors of A and 0.22 kcal mol 1, respectively. 26 For the ionized thymine monohydrates, this functional (with the cc-pvtz basis) yields structures that are similar to those obtained with EOM-IP-CCSD/6-311+G (d,p), 42 i.e., the mean absolute errors are 0.01 A for the thymine moiety and 0.11 A for thymine water hydrogen bond. All IEs were calculated using EOM-IP-CCSD/cc-pVTZ at the equilibrium geometries described above. The cc-pvtz basis set provides a good balance between accuracy and computational efficiency. The first IE of thymine computed using EOM-IP-CCSD with the extended cc-pvtz basis [augmented by diffuse s and p functions from G(d,p) as was done in ref. 43] is 9.20 ev, which is 0.07 ev higher than the cc-pvtz value. Zero point energy (ZPE) correction lowers AIEs of thymine and thymine monohydrates (T1 and T2) by 0.08 ev. Thus, due to error cancellation, non ZPE-corrected AIEs computed with cc-pvtz are very close to the ZPE-corrected AIEs obtained with the extended cc-pvtz basis set. 316 Faraday Discuss., 2011, 150, This journal is ª The Royal Society of Chemistry 2011 Fig. 2 Equilibrium structures of thymine and three thymine monohydrates optimized by RI- MP2/cc-pVTZ. Bond lengths and changes in bond lengths due to interactions with water are shown (in A). The charge distribution analysis were performed using Natural Bond Orbital Package (NBO v.5.0). 44 All calculations were conducted using the Q-CHEM electronic structure package. 45 Molecular structures, frequencies, and relevant total energies are given in the ESI. B. Calculation of the Franck Condon factors and PIE curves Unambiguous comparison with the experimental PIE curves requires calculation of FCFs. While in molecular systems (i.e., ionized NABs), FCFs can be reliably computed using the double-harmonic approximation with Duschinsky rotations, 46 as was done in ref. 9, the calculations in clusters are more challenging due to large structural relaxation of soft (and anharmonic) inter-fragment degrees of freedom. To correctly describe these effects, we combine double-harmonic treatment of the thymine moiety and water with a one-dimensional quantum treatment of the inter-fragment coordinate assuming that the water thymine and intramolecular thymine vibrations are uncoupled and that the respective FCFs are multiplicative. Using the ezspectrum program, 47 we first compute FCFs for the thymine moiety using double-harmonic approximation with Duschinsky rotations 46 at the C s geometry using normal modes and frequencies for the non-planar structures with one hydrogen of water out of the plane. The water molecule itself was excluded from this calculation and only the geometry of the thymine moiety (from the monohydrate) was used. Duschinsky rotations are important because the normal-mode overlap matrix for the neutral and the ionized states is significantly non-diagonal. In these calculations, we used harmonic frequencies and structures computed by ub97x-d/cc-pvtz for both the neutral and the 1st ionized states of the monohydrates. The effect of water-thymine degrees of freedom on FCFs is described by a onedimensional model, which takes into account anharmonicity and large structural This journal is ª The Royal Society of Chemistry 2011 Faraday Discuss., 2011, 150, Fig. 3 Equilibrium structures of thymine dihydrate and trihydrate optimized by RI-MP2/ccpVTZ. Bond lengths and changes in bond lengths due to microhydration are shown (in A). Fig. 4 Equilibrium structures of ionized thymine and thymine monohydrates optimized by ub97x-d/cc-pvtz. Bond lengths and changes in bond lengths due to ionization are shown (in A). relaxation. This treatment is similar to the intrinsic reaction coordinate connecting the initial and final state. Water thymine motion is defined by three coordinates: r, the distance between the water oxygen and the nearest hydrogen in thymine; q, the angle formed by the NH bond in thymine and the oxygen in water; and 4, the rotation of the water center-of-mass relative to the axis defined by r (Fig. 6). In the neutral thymine monohydrate (T1), these coordinates obtain the values r ¼ A, q ¼ 36.7, 318 Faraday Discuss., 2011, 150, This journal is ª The Royal Society of Chemistry 2011 Fig. 5 Equilibrium structures of ionized thymine and thymine di- and trihydrates optimized by ub97x-d/cc-pvtz. Bond lengths and changes in bond lengths due to ionization are shown (in A). and 4 ¼ 40.6, while in the cation they equal r ¼ A, q ¼ 1.6, and 4 ¼ 2.2. Along the simplest path, each coordinate is described by a linear equation connecting the values in the neutral and in the cation. This path is used to evaluate two potential surfaces, V(r), one with the thymine held at its equilibrium neutral geometry and Fig. 6 Coordinates describing relative water thymine motion. This journal is ª The Royal Society of Chemistry 2011 Faraday Discuss., 2011, 150, the second with thymine held at its equilibrium cation geometry. The effective onedimensional Hamiltonian describing this motion is: bh ¼ 1 v 2mr vr 1 v 2 2m vr 1 v 2 2 2mr 2 vq 1 v 2 2 2I vf þ V b ðrþ; (2) 2 where m is the mass of water and I is the moment of inertia of water rotating in the plane of the molecule. This equation was then solved to obtain vibrational eigenstates for the water motion on the neutral and cation surfaces which, in turn, were used to compute FCFs. Within the approximation that the vibrational mode corresponding to the water motion is decoupled from the vibrational modes of the thymine, the energy associated with the water-water vibrational transitions is additive to the thymine-only spectra and the FCFs are multiplicative. Each peak appearing in the spectrum associated with the thymine moiety thus has the spectrum for the water fragment superimposed on top of it. This leads to both qualitative and quantitative changes in the theoretical spectrum, since the peaks with the largest FCFs in the water vibrational motion are the 1 ) 0 and 2 ) 0 peaks. C. Experimental details The experiments were performed on a molecular beam apparatus coupled to a 3 meter VUV monochromator on the Chemical Dynamics Beamline at the Advanced Light Source (ALS). The thermal vaporization source has been described recently in a publication detailing the microsolvation of DNA bases. 6 The nozzle consisted of a cm diameter disk (1 mm thick) with a 100 mm diameter center hole welded on to one end of a closed stainless steel tube of cm OD and cm long. This front end of the stainless steel tube contained thymine and could be heated to between 298 and 700 K with a cartridge heater mounted in an aluminum heating block. The temperature of the tube was monitored with a thermocouple to the heating block. To produce the water complexes, Ar carrier gas at 58.7 kpa was passed over a water reservoir held at room temperature and directed into the stainless steel nozzle. The temperature utilized for generating thymine vapor was 503 K. Shown in Fig. 7 is a representative mass spectrum of

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