Mario Barbatti

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.

Nonadiabatic dynamics with trajectory surface hopping method

The trajectory surface hopping (TSH) method is a general methodology for dynamics propagation of nonadiabatic systems. It is based on the hypothesis that the time evolution of a wave packet through a potential‐energy branching region can be approximated by an ensemble of independent semiclassical trajectories stochastically distributed among the branched surfaces. As it was proposed about 40 years ago, the TSH methodology has become one of the main tools for nonadiabatic dynamics propagation in molecular physics and chemistry. One reason for this success lies on its intuitive conceptual background allied to its high computational efficiency when compared to full quantum mechanical propagation. In this work, the TSH method is reviewed and applications from different fields are surveyed.

Nonadiabatic Deactivation of 9H-Adenine: A Comprehensive Picture Based on Mixed Quantum−Classical Dynamics

Mixed quantum-classical dynamics simulations at the multireference configuration interaction (MR-CIS) level were performed for 9 H-adenine in order to understand its ultrafast nonradiative decay process. Dynamics simulations were also performed for the model system 6-aminopyrimidine. MR-CIS and complete active space perturbation theory (CASPT2) have been employed to characterize a large variety of qualitatively different conical intersections, the branches of the crossing seam connecting them, and the reaction paths from the Franck-Condon region for 9 H-adenine. The results show a two-step process consisting of ultrashort deactivation from S 3 to S 1 and a longer exponential decay step corresponding to the conversion from S 1 to S 0.

Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adenine

In spite of the importance of nonadiabatic dynamics simulations for the understanding of ultrafast photo-induced phenomena, simulations based on different methodologies have often led to contradictory results. In this work, we proceed through a comprehensive investigation of on-the-fly surface-hopping simulations of 9H-adenine in the gas phase using different electronic structure theories (ab initio, semi-empirical, and density functional methods). Simulations that employ ab initio and semi-empirical multireference configuration interaction methods predict the experimentally observed ultrafast deactivation of 9H-adenine with similar time scales, however, through different internal conversion channels. Simulations based on time-dependent density functional theory with six different hybrid and range-corrected functionals fail to predict the ultrafast deactivation. The origin of these differences is analyzed by systematic calculations of the relevant reaction pathways, which show that these discrepancies can always be traced back to topographical features of the underlying potential energy surfaces.

Photochemistry of ethylene: A multireference configuration interaction investigation of the excited-state energy surfaces

Multireference configuration interaction with singles and doubles (MR-CISD) calculations have been performed for the optimization of conical intersections and stationary points on the ethylene excited-state energy surfaces using recently developed methods for the computation of analytic gradients and nonadiabatic coupling terms. Basis set dependence and the effect of various choices of reference spaces for the MR-CISD calculations have been investigated. The crossing seam between the S0 and S1 states has been explored in detail. This seam connects all conical intersections presently known for ethylene. Major emphasis has been laid on the hydrogen-migration path. Starting in the V state of twisted-orthogonal ethylene, a barrierless path to ethylidene was found. The feasibility of ethylidene formation will be important for the explanation of the relative yield of cis and trans H2 elimination.

Newton-X: a surface-hopping program for nonadiabatic molecular dynamics

The Newton‐X program is a general‐purpose program package for excited‐state molecular dynamics, including nonadiabatic methods. Its modular design allows Newton‐X to be easily linked to any quantum‐chemistry package that can provide excited‐state energy gradients. At the current version, Newton‐X can perform nonadiabatic dynamics using Columbus, Turbomole, Gaussian, and Gamess program packages with multireference configuration interaction, multiconfigurational self‐consistent field, time‐dependent density functional theory, and other methods. Nonadiabatic dynamics simulations with a hybrid combination of methods, such as Quantum‐Mechanics/Molecular‐Mechanics, are also possible. Moreover, Newton‐X can be used for the simulation of absorption and emission spectra. The code is distributed free of charge for noncommercial and nonprofit uses at www.newtonx.org. WIREs Comput Mol Sci 2014, 4:26–33. doi: 10.1002/wcms.1158

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.

Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study

Surface hopping dynamics methods using the coupled cluster to approximated second order (CC2), the algebraic diagrammatic construction scheme to second order (ADC(2)), and the time-dependent density functional theory (TDDFT) were developed and implemented into the program system Newton-X. These procedures are especially well-suited to simulate nonadiabatic processes involving various excited states of the same multiplicity and the dynamics in the first excited state toward an energetic minimum or up to the region where a crossing with the ground state is found. 9H-adenine in the gas phase was selected as the test case. The results showed that dynamics with ADC(2) is very stable, whereas CC2 dynamics fails within 100 fs, because of numerical instabilities present in the case of quasi-degenerate excited states. ADC(2) dynamics correctly predicts the ultrafast character of the deactivation process. It predicts that C2-puckered conical intersections should be the preferential pathway for internal conversion for low-energy excitation. C6-puckered conical intersection also contributes appreciably to internal conversion, becoming as important as C2-puckered for high-energy excitations. In any case, H-elimination plays only a minor role. TDDFT based on a long-range corrected functional fails to predict the ultrafast deactivation. In the comparison with several other methods previously used for dynamics simulations of adenine, ADC(2) has the best performance, providing the most consistent results so far.

Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran

A formal derivation of the nuclear-ensemble method for absorption and emission spectrum simulations is presented. It includes discussions of the main approximations employed in the method and derivations of new features aiming at further developments. Additionally, a method for spectrum decomposition is proposed and implemented. The method is designed to provide absolute contributions of different classes of states (localized, diffuse, charge-transfer, delocalized) to each spectral band. The methods for spectrum simulation and decomposition are applied to the investigation of UV absorption of benzene, furan, and 2-phenylfuran, and of fluorescence of 2-phenylfuran.

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.