UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.

The photophysics of roseoflavin in three different environments is investigated by using ab initio and quantum mechanics/molecular mechanics methods. Intramolecular charge transfer is shown to be responsible for the quenching of the fluorescence in the gas phase, and in the water environment. However, for the roseoflavin incorporated into the blue light using flavin (BLUF) protein environment (substituting the native flavin) no such deactivation is found. The conical intersection between the locally excited state of the chromophore and the charge transfer state involving the tyrosine residue, which in the native BLUF domain is responsible for initiating the photocycle, is missing for the roseoflavin substituted protein. This explains the experimental observations of the lack of any photocycle, and the loss of the biological function of the BLUF photoreceptor reported earlier.

Charge transfer in DNA cannot be understood without addressing the complex conformational flexibility, which occurs on a wide range of timescales. In order to reduce this complexity four dinucleotide models 1X consisting of benzophenone linked by a phosphodiester to one of the natural nucleosides X = A, G, T, C were studied in water and methanol. The theoretical work focuses on the dynamics and electronic structure of 1G. Predominant conformations in the two solvents were obtained by molecular dynamics simulations. 1G in MeOH adopts mainly an open geometry with a distance of 12-16 Å between the two aromatic parts. In H 2 O the two parts of 1G form primarily a stacked conformation yielding a distance of 5-6 Å. The low-lying excited states were investigated by electronic structure theory in a QM/MM environment for representative snapshots of the trajectories. Photo-induced intramolecular charge transfer in the S 1 state occurs exclusively in the stacked conformation. Ultrafast transient absorption spectroscopy with 1X reveals fast charge transfer from S 1 in both solvents with varying yields. Significant charge transfer from the T 1 state is only found for the nucleobases with the lowest oxidation potential: in H 2 O, charge transfer occurs with 3.2 Â 10 9 s À1 for 1A and 6.0 Â 10 9 s À1 for 1G. The reorganization energy remains nearly unchanged going from MeOH to the more polar H 2 O. The electronic coupling is rather low even for the stacked conformation with H AB = 3 meV and explains the moderate charge transfer rates. The solvent controls the conformational distribution and therefore gates the charge transfer due to differences in distance and stacking.

We present a density functional theory (B3LYP) study of the isomerization of 4-hydroxybenzylidene-1,2-dimethyl-imidazolinone (HOBDI), which is to mimic the green fluorescent protein (GFP) chromophore, in the ground state promoted by a nucleophile. Four solvents with different polarity, water, DMSO, methanol, and benzene, have been used to characterize the nucleophile assisted mechanism. The former three solvents have been used as nucleophile to participate in the reaction, while in benzene, we use n-propylamine as the nucleophile. When water, methanol and n-propylamine are used as nucleophile, the isomerization is characterized as a three-step process and the addition of the nucleophile is the rate-determining step. A proton transfer from the nucleophile to the oxygen of imidazolinone (O(1)) is observed during the addition step, which stabilizes the negative charge on O(1) due to the reduction of the C(1)[double bond, length as m-dash]C(2) double bond. The energy barrier to the reaction increases in the order of CH(3)OH

Abstract-The Radial Point Interpolation Time-Domain (RPITD) method is a flavor of meshless domain discretization methods applicable to computational electromagnetics. Meshless methods do not require an explicit mesh topology, but rather rely on a representation of a physical model as a node distribution. This is firstly advantageous for modeling of conformal boundaries and multi-scale geometries. But as the most attractive feature, the node arrangements can be adapted on-the-fly. The RPITD method is based on interpolation of the field distribution using radial and monomial basis functions. This paper introduces a technique to model arbitrarily shaped dielectric interfaces in the framework of meshless methods. Using the proposed technique, errors associated to the interpolation of non-smooth fields at material interfaces are reduced, as demonstrated for 2D-TE modes. This allows for accurate modeling of interfaces with dielectric contrast. Unlike previous publications which modify the basis functions at interfaces, a physically motivated correction term is introduced here. Errors in the vicinity of material interfaces decrease significantly and simulation accuracy is generally improved.

Abstract The theoretical treatment of molecules in electronically excited states is much more complicated than in the ground state (GS) and remains a challenge. In contrast to the GS, electronically excited states can hardly be treated by a single determinant or configuration state function, not even near equilibrium geometry. This calls for multireference methods, or, alternatively, for time-dependent response methods, such as time-dependent density functional theory, or time-dependent coupled cluster response theory. In this contribution, we provide an overview on the latter techniques and illustrate on several examples how these methods can be used to theoretically investigate photoreactions.

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