Dana Nachtigallová

Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases

A comprehensive effort in photodynamical ab initio simulations of the ultrafast deactivation pathways for all five nucleobases adenine, guanine, cytosine, thymine, and uracil is reported. These simulations are based on a complete nonadiabatic surface-hopping approach using extended multiconfigurational wave functions. Even though all five nucleobases share the basic internal conversion mechanisms, the calculations show a distinct grouping into purine and pyrimidine bases as concerns the complexity of the photodynamics. The purine bases adenine and guanine represent the most simple photodeactivation mechanism with the dynamics leading along a diabatic ππ* path directly and without barrier to the conical intersection seam with the ground state. In the case of the pyrimidine bases, the dynamics starts off in much flatter regions of the ππ* energy surface due to coupling of several states. This fact prohibits a clear formation of a single reaction path. Thus, the photodynamics of the pyrimidine bases is much richer and includes also nπ* states with varying importance, depending on the actual nucleobase considered. Trapping in local minima may occur and, therefore, the deactivation time to the ground state is also much longer in these cases. Implications of these findings are discussed (i) for identifying structural possibilities where singlet/triplet transitions can occur because of sufficient retention time during the singlet dynamics and (ii) concerning the flexibility of finding other deactivation pathways in substituted pyrimidines serving as candidates for alternative nucleobases.

Coordination and siting of Cu+ ions in ZSM-5: A combined quantum mechanics/interatomic potential function study

Siting and coordination of Cu+ ions in zeolite ZSM-5 have been studied by a combined quantum mechanics/interatomic potential function technique. A new Cu(I)–O interaction potential has been parameterized based on abinitio data which is compatible with abinitio-parametrized shell model potentials for zeolites. Several different sites of Cu+ inside ZSM-5 have been found. The structure of the site and the coordination of the Cu+ ion depend on the T-site where the Si atom is replaced by an Al atom. If Al is at the edge of the main and sinusoidal channels the Cu+ ion prefers to occupy thc open space in the channel intersection and it is coordinated to two oxygen atoms of the AlO4 tetrahedron. The largest binding energy of Cu+ with ZSM-5 was found for Cu+ located inside a six-membered ring on the wall of the sinusoidal channel, where it can coordinate to three or four oxygen atoms of the zeolite framework. The Cu+ sites predicted are in accord with available experimental results.

Excited state dynamics of DNA bases

Biochemical reactions are subject to the particular environmental conditions of planet earth, including solar irradiation. How DNA responds to radiation is relevant to human health because radiation damage can affect genetic propagation and lead to cancer and is also important for our understanding of how life on earth developed. A reductionist approach to unravelling the detailed photochemistry seeks to establish intrinsic properties of individual DNA building blocks, followed by extrapolation to larger systems, to incorporate interactions between the building blocks and the role of the biomolecular environment. Advances in both experimental and computational techniques have lead to increasingly detailed insights in the excited state dynamics of DNA bases in isolation as well as the role of the solvent and intermolecular interactions. This review seeks to summarise current findings and understanding.

Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State†

Ab initio nonadiabatic dynamics simulations are reported for thymine with focus on the S(2) --> S(1) deactivation using the state-averaged CASSCF method. Supporting calculations have been performed on vertical excitations, S(1) and S(2) minima, and minima on the crossing seam using the MS-CASPT2, RI-CC2, MR-CIS, and MR-CISD methods. The photodynamical process starts with a fast (<100 fs) planar relaxation from the S(2) pipi* state into the pi(O)pi* minimum of the S(2) state. The calculations demonstrate that two pi-excited states (denoted pipi* and pi(O)pi*) are actually involved in this stage. The time in reaching the S(2)/S(1) intersections, through which thymine can deactivate to S(1), is delayed by both the change in character between the states as well as the flatness of the S(2) surface. This deactivation occurs in an average time of 2.6 ps at the lowest-energy region of the crossing seam. After that, thymine relaxes to the npi* minimum of the S(1) state, where it remains until the transfer to the ground state takes place. The present dynamics simulations show that not only the pi(O)pi* S(2) trapping but also the trapping in the npi* S(1) minimum contribute to the elongation of the excited-state lifetime of thymine.

Coordination of Cu+ and Cu2+ ions in ZSM-5 in the vicinity of two framework Al atoms

A combined quantum mechanics/interatomic potential function technique has been used to examine Cu+/Al− sites in the vicinity of H+Al− sites and Cu2+ in the vicinity of two framework Al atoms under dehydrated conditions. The symmetrical coordination of Cu2+ ions to four framework oxygen atoms is the most stable site and Cu2+ is hard to reduce at these sites. In agreement with EPR measurements a square-pyramidal coordination of Cu2+ at these sites is suggested. However, this symmetrical coordination is attained only for specific positions of the framework aluminium pair. Coordination changes upon reduction of divalent to monovalent copper ions and upon excitation of Cu+ ions in the first triplet excited state are also investigated. The coordination of the copper ions does not significantly change during reduction in the dehydrated state. Coordination changes of Cu+ upon excitation in the triplet state and calculated transition energies for Cu+/Al− sites in the vicinity of H+Al− sites are identical to those observed for isolated Cu+/Al− sites.

The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study

Electronic singlet excitations of stacked adenine–thymine (AT) and guanine–cytosine (GC) complexes have been investigated with respect to local excitation and charge‐transfer (CT) characters. Potential energy curves for rigid displacement of the nucleobases have been computed to establish the distance dependence of the CT states. The second‐order algebraic diagrammatic construction [ADC(2)] method served as reference approach for comparison to a selected set of density functionals used within the time‐dependent density functional theory (TD‐DFT). Particular attention was dedicated to the performance of the recently developed family of M06 functionals. The calculations for the stacked complexes show that at the ADC(2) level, the lowest CT state is S6 for the AT and as S4 for the GC pair. At the reference geometry, the actual charge transferred is found to be 0.73 e for AT. In case of GC, this amount is much smaller (0.17 e). With increasing separation of the two nucleobases, the CT state is strongly destabilized. The M06‐2X version provides a relatively good reproduction of the ADC(2) results. It avoids the serious overstabilization and overcrowding of the spectrum found with the B3LYP functional. On the other hand, M06‐HF destabilizes the CT state too strongly. TD‐DFT/M06‐2X calculations in solution (heptane, isoquinoline, and water) using the polarizable continuum model show a stabilization of the CT state and an increase in CT character with increasing polarity of the solvent.

The vibrational dynamics of carbon monoxide in a confined space—CO in zeolites

Based on theoretical calculations, and a survey of infrared spectra of CO adsorbed on different cation exchanged zeolites, a model is proposed to explain the influence of the zeolite framework on the vibrational behaviour of CO confined into small void spaces (zeolite channels and cavities). The concepts developed should help to understand a number of details relevant to both, precise interpretation of IR spectra and a better understanding of the vibrational dynamics of small molecules in a confined space.

Nonadiabatic dynamics of uracil: population split among different decay mechanisms.

Nonadiabatic dynamics simulations performed at the state-averaged CASSCF method are reported for uracil. Supporting calculations on stationary points and minima on the crossing seams have been performed at the MR-CISD and CASPT2 levels. The dominant mechanism is characterized by relaxation into the S(2) minimum of ππ* character followed by the relaxation to the S(1) minimum of nπ* character. This mechanism contributes to the slower relaxation with a decay constant larger than 1.5 ps, in good agreement with the long time constants experimentally observed. A minor fraction of trajectories decay to the ground state with a time constant of about 0.7 ps, which should be compared to the experimentally observed short constant. The major part of trajectories decaying with this time constant follows the ππ* channel and hops to the ground state via an ethylenic conical intersection. A contribution of the relaxation proceeding via a ring-opening conical intersection was also observed. The existence of these two latter channels together with a reduced long time constant is responsible for a significantly shorter lifetime of uracil compared to that of thymine.

The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study

Ab initio surface hopping dynamics calculations were performed for the biologically relevant tautomer of guanine in gas phase excited into the first ππ∗ state. The results show that the complete population of UV-excited molecules returns to the ground state following an exponential decay within ∼220 fs. This value is in good agreement with the experimentally obtained decay times of 148 and 360 fs. No fraction of the population remains trapped in the excited states. The internal conversion occurs in the ππ∗ state at two related types of conical intersections strongly puckered at the C2 atom. Only a small population of about 5% following an alternative pathway via a nπ∗ state was found in the dynamics.

Does Stacking Restrain the Photodynamics of Individual Nucleobases

Nonadiabatic photodynamical simulations of 4-aminopyrimidine (4-APy) used as a model for adenine were performed by embedding it between two stacking methyl-guanine (mGua) molecules to determine the effect of spatial restrictions on the ultrafast photodeactivation mechanism of this nucleobase. A hybrid multiconfigurational ab initio/molecular mechanical approach in combination with surface hopping was used. During the dynamics the formation of a significant fraction of intrastrand hydrogen bonding from 4-APy to mGua above and below is observed. These findings show that this type of hydrogen bond may play an important role for the photodynamics within one DNA strand and that it should be of interest even in irregular segments of double stranded nucleic acids structures. The relaxation mechanism of internal conversion to the ground state is dominated by ring puckering, and an overall elongation of the lifetime of the embedded system by approximately 20% as compared to the isolated 4-APy is computed.