Shirin Faraji

Multistate vibronic interactions in difluorobenzene radical cations. II. Quantum dynamical simulations

The multistate vibronic dynamics in the X-D electronic states of all three difluorobenzene radical cations are investigated theoretically by an ab initio quantum dynamical approach. The vibronic coupling scheme and the ab initio values of the system parameters are adopted from Paper I [S. Faraji and H. Koppel, J. Chem. Phys. 129, 074310 (2008)]. Extensive calculations by wave-packet propagation have been performed with the aid of the multiconfiguration time-dependent Hartree method. Five coupled electronic potential energy surfaces and 10 (11 in the case of the orthoisomer) vibrational degrees of freedom have been included in these calculations. The nonadiabatic interactions lead to the restructuring of the photoelectron spectral envelopes. Ultrafast internal conversion processes within the electronic manifolds in question demonstrate the strength of the nonadiabatic coupling effects and complement the analogous findings for the electronic spectra. The internal conversion dynamics is characterized by a stepwise transfer of the electronic population to the lowest electronic state on a time scale of femtoseconds to picoseconds. A difference between the three isomers is found to be related to the weaker interaction between the sets of X-A and B-C-D states (with high-energy conical intersections) in the meta isomer, as compared to the other isomers. The implications of these findings for the qualitative understanding of the fluorescence dynamics of fluorinated benzene radical cations are discussed.

Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases

DNA photolyases are light-activated enzymes that repair DNA damage induced by ultraviolet (UV) radiation. UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photolesions. Photolyases selectively bind to DNA and initiate the splitting of mutagenic pyrimidine dimers via photoinduced electron transfer from a flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering its repair. This review discusses the consecutive steps of the repair process, from both experimental and theoretical points of view. It covers the following issues: the process of how photolyases accommodate the lesion into their binding pockets, excitation energy transfer between two involved catalytic cofactors, photoinduced electron transfer to the lesion, the splitting of the pyrimidine dimer radical anion, and the fate of the unstable radical species created after the splitting of the thymine dimer. In particular, mechanisms of the splitting and restoration of the original bases are described in detail, and the most probable repair pathways are outlined.

Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases.

Intermolecular coulombic decay (ICD) is an efficient mechanism of low-energy electron generation in condensed phases and is discussed as their potential source in living cells, tissues, and materials. The first example of ICD as an operating mechanism in real biological systems, that is, in the DNA repair enzymes photolyases, is presented. Photolyase function involves light-induced electron detachment from a reduced flavin adenine dinucleotide (FADH(-)), followed by its transfer to the DNA-lesion triggering repair of covalently bound nucleobase dimers. Modern quantum chemical methods are employed to demonstrate that the transferred electron is efficiently generated via a resonant ICD process between the antenna pigment and the FADH(-) cofactors.

Ab initio quantum dynamical study of the multi-state nonadiabatic photodissociation of pyrrole

There has been a substantial amount of theoretical investigations on the photodynamics of pyrrole, often relying on surface hopping techniques or, if fully quantal, confining the study to the lowest two or three singlet states. In this study we extend ab initio based quantum dynamical investigations to cover simultaneously the lowest five singlet states, two π-σ∗ and two π-π∗ excited states. The underlying potential energy surfaces are obtained from large-scale MRCI ab initio computations. These are used to extract linear and quadratic vibronic coupling constants employing the corresponding coupling models. For the N-H stretching mode Q(24) an anharmonic treatment is necessary and also adopted. The results reveal a sub-picosecond internal conversion from the S(4) (π-π∗) state, corresponding to the strongly dipole-allowed transition, to the S(1) and S(2) (π-σ∗) states and, hence, to the ground state of pyrrole. The significance of the various vibrational modes and coupling terms is assessed. Results are also presented for the dissociation probabilities on the three lowest electronic states.

A quantum chemical perspective on (6-4) photolesion repair by photolyases

(6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed.

On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein.

Far-red fluorescent proteins (FPs) enable deep-tissue in vivo imaging. Combining FPs with large and small Stokes shifts enables single-excitation/dual-emission multicolor applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the origin of an extended Stokes shift (0.2 eV) observed in mPlum, one of the most far-red-shifted FPs. We demonstrated that the red shift of emission is largely due to the excited-state relaxation of the chromophore itself. Rigid protein environment suppresses the relaxation; however, if the hydrogen-bond network around the chromophore is sufficiently flexible, it can rearrange upon electronic excitation, allowing the chromophore to relax. The reorganization of the hydrogen-bond network is driven by changes in bonding and charge distributions of the chromophore in the excited state. The ILE65 and GLU16 residues play the most important role. The MD simulations reveal two ground-state populations with the direct (Chro-ILE65···GLU16) and water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond patterns. In the excited state, both populations relax to a single emitting state with the water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond pattern, which provides a better match for the excited-state charge distribution (the acylimines oxygen has a larger negative charge in S1 than in S0). The extended Stokes shift arises due to the conversion of the direct hydrogen-bond pattern to the water-mediated one accompanied by large structural relaxation of the electronically excited chromophore. This conclusion is supported by calculations for the GLU16LEU mutant, which has only one hydrogen-bond pattern. Consequently, no interconversion is possible, and the computed Stokes shift is small, in agreement with the experiment. Our theoretical findings provide support to a recent study of the Stokes shifts in mPlum and its mutants.

Multistate vibronic interactions in difluorobenzene radical cations. I. Electronic structure calculations

The multimode multistate vibronic interactions between the five lowest electronic states of all three isomers of the difluorobenzene radical cation are investigated theoretically, based on ab initio electronic structure data, and employing a well-established vibronic coupling model. The approach rests on the linear vibronic coupling scheme, augmented by quadratic coupling terms for the totally symmetric modes. The underlying ionization potentials and coupling constants are obtained from ab initio coupled-cluster calculations. Low-energy conical intersections and strong vibronic couplings are found to prevail within the sets of X-A and B-C-D cationic states, while the interactions between these two sets of states are found to be weaker and depend on the isomer. The inclusion of the aforementioned quadratic couplings is found to be essential to correctly reproduce the lowest-energy conical intersections between the two different sets of electronic states. Differences between the three isomers regarding these quantities are pointed out. The results will be used as basis for multidimensional wave-packet dynamical simulations for these coupled potential energy surfaces to be presented in the following paper (Paper II).

Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory

Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6‐4 photoproducts. (6‐4) Photolyases are light‐activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6‐4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH−) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron‐induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.

Multi-Mode Jahn–Teller and Pseudo-Jahn–Teller Effects in Benzenoid Cations

The multi-state multi-mode vibronic interactions in the benzene radical cation and some of its fluorinated derivatives are surveyed from a theoretical point of view.While the parent system is a prototypical example for the multi-mode dynamical Jahn–Teller effect, partial fluorination leads to a reduction of symmetry and a ‘disappearance’ of the Jahn–Teller effect. Nevertheless, strong vibronic interactions prevail also there and lead to marked effects in the spectral intensity distributions and to an ultrafast electronic population dynamics. These phenomena have been analyzed theoretically in our group by means of a well-established vibronic coupling scheme, combined with an ab initio quantum dynamical approach (namely, ab initio coupled cluster calculations for the underlying potential energy surfaces and coupling constants, and the so-called MCTDH wavepacket propagation technique for the nuclear motion). The results are presented and discussed, putting emphasis on their dependence on the respective system, especially the degree of fluorination. They shed new light on the substitutional effects on vibronic interactions and demonstrate the degree of sophistication that can be achieved nowadays in their theoretical treatment.

Emission turn-on and solubility turn-off in conjugated polymers: one- and two-photon-induced removal of fluorescence-quenching solubilizing groups.

The synthesis of highly efficient two-photon uncaging groups and their potential use in functional conjugated polymers for post-polymerization modification are reported. Careful structural design of the employed nitrophenethyl caging groups allows to efficiently induce bond scission by a two-photon process through a combination of exceptionally high two-photon absorption cross-sections and high reaction quantum yields. Furthermore, π-conjugated polyfluorenes are functionalized with these photocleavable side groups and it is possible to alter their emission properties and solubility behavior by simple light irradiation. Cleavage of side groups leads to a turn-on of the fluorescence while solubility of the π-conjugated materials is drastically reduced.