Adélia J. A. Aquino

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.

The nonadiabatic deactivation paths of pyrrole

Multireference configuration interaction (MRCI) calculations have been performed for pyrrole with the aim of providing an explanation for the experimentally observed photochemical deactivation processes. Potential energy curves and minima on the crossing seam were determined using the analytic MRCI gradient and nonadiabatic coupling features of the COLUMBUS program system. A new deactivation mechanism based on an out-of-plane ring deformation is presented. This mechanism directly couples the charge transfer 1pipi* and ground states. It may be responsible for more than 50% of the observed photofragments of pipi*-excited pyrrole. The ring deformation mechanism should act complementary to the previously proposed NH-stretching mechanism, thus offering a more complete interpretation of the pyrrole photodynamics.

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.

Electronically excited states and photodynamics: a continuing challenge

The purpose of this contribution is the description of the progress in theoretical investigations on electronically excited states in connection with photodynamical simulations made within the last years and to provide an outlook on the scope of future applications and challenges. An overview over excited-state phenomenology is given and the applicability of different computational methods is discussed. Both electronic structure- and dynamics methods are considered. The examples presented comprise the explanation of the photostability of individual DNA nucleobases, the photodynamics of DNA including excitonic and charge-transfer processes, the primary processes of vision and the broad field of photovoltaics, photodevices, and molecular machines.

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.

UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions

A detailed investigation of the excited states accessed by UV absorption in alternating DNA duplexes was performed by means of an extensive sampling of intra- and intermolecular degrees of freedom. The excited states were computed using the algebraic diagrammatic construction method to second-order (ADC(2)). A realistic DNA environment was included through an electrostatic embedding QM/MM coupling scheme. The results indicate that (i) most excited states are delocalized over at most two bases, (ii) charge transfer states are located at higher energies than the bright states in the Franck-Condon region, but (iii) coupling between locally excited and charge transfer states may provide a route to dynamical charge separation, and (iv) spectral broadening is mainly caused by intramolecular vibrations.

Electronically excited states in poly(p-phenylenevinylene): vertical excitations and torsional potentials from high-level ab initio calculations.

Ab initio second-order algebraic diagrammatic construction (ADC(2)) calculations using the resolution of the identity (RI) method have been performed on poly-(p-phenylenevinylene) (PPV) oligomers with chain lengths up to eight phenyl rings. Vertical excitation energies for the four lowest π–π* excitations and geometry relaxation effects for the lowest excited state (S1) are reported. Extrapolation to infinite chain length shows good agreement with analogous data derived from experiment. Analysis of the bond length alternation (BLA) based on the optimized S1 geometry provides conclusive evidence for the localization of the defect in the center of the oligomer chain. Torsional potentials have been computed for the four excited states investigated and the transition densities divided into fragment contributions have been used to identify excitonic interactions. The present investigation provides benchmark results, which can be used (i) as reference for lower level methods and (ii) give the possibility to parametrize an effective Frenkel exciton Hamiltonian for quantum dynamical simulations of ultrafast exciton transfer dynamics in PPV type systems.

Ab initio modeling of excitonic and charge-transfer states in organic semiconductors: the PTB1/PCBM low band gap system.

A detailed quantum chemical simulation of the excitonic and charge-transfer (CT) states of a bulk heterojunction model containing poly(thieno[3,4-b]thiophene benzodithiophene) (PTB1)/[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) is reported. The largest molecular model contains two stacked PTB1 trimer chains interacting with C60 positioned on top of and lateral to the (PTB1)3 stack. The calculations were performed using the algebraic diagrammatic construction method to second order (ADC(2)). One main result of the calculations is that the CT states are located below the bright inter-chain excitonic state, directly accessible via internal conversion processes. The other important aspects of the calculations are the formation of discrete bands of CT states originating from the lateral C60s and the importance of inter-chain charge delocalization for the stability of the CT states. A simple model for the charge separation step is also given, revealing the energetic feasibility of the overall photovoltaic process.

A Zwitterionic Carbanion Frustrated by Boranes – Dihydrogen Cleavage with Weak Lewis Acids via an “Inverse” Frustrated Lewis Pair Approach

The synthesis, structural characterization, and acid-base chemistry of [C(SiMe2OCH2CH2OMe)3]Na (2), a sterically encumbered zwitterionic organosodium compound, is reported. 2 is a strong Brønsted base that forms frustrated Lewis pairs (FLPs) with a number of boron-containing Lewis acids ranging from weakly Lewis acidic aryl and alkyl boranes to various alkyl borates. These intermolecular FLPs readily cleave H2, which confirms that even poor Lewis acids can engage in FLP-mediated H2 cleavage provided that the present bulky base is of sufficiently high Brønsted basicity.