Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.     

Quantitative detection of singlet O2 by cavity-enhanced absorption

A method for the practical determination of the absolute concentration of single (a1delta(g)) oxygen is discussed. The method is based on sensitive off-axis integrated-cavity-output spectroscopy (ICOS). Off-axis ICOS allows narrowband, continuous-wave lasers to be used in conjunction with optical cavities to record sensitive absorption measurements. The details of the method as well as spectroscopic data confirming the first observation of the (1, 0) band of the b1sigma(g)(+) - a1delta(g) Noxon system are presented. The absolute transition probabilities for the b1sigma(g)(+) - a1delta(g) Noxon system, which are not known precisely from experiments, are determined by quantum chemistry theory.     

Interpreting ultrafast molecular fragmentation dynamics with ab initio electronic structure calculations

High-level ab initio electronic structure calculations are used to interpret the fragmentation dynamics of CHBr(2)COCF(3), following excitation with an intense ultrafast laser pulse. The potential energy surfaces of the ground and excited cationic states along the dissociative C-CF(3) bond have been calculated using multireference second order perturbation theory methods. The calculations confirm the existence of a charge transfer resonance during the evolution of a dissociative wave packet on the ground state potential energy surface of the molecular cation and yield a detailed picture of the dissociation dynamics observed in earlier work. Comparisons of the ionic spectrum for two similar molecules support a general picture in which molecules are influenced by dynamic resonances in the cation during dissociation.     

6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase

Cyclobutylpyrimidine dimers (CPDs) are formed between adjacent pyrimidines in DNA when it absorbs ultraviolet light. CPDs can be directly repaired by DNA photolyase (PL) in the presence of visible light. How PL recognizes and binds its substrate is still not well understood. Fluorescent nucleic acid base analogues are powerful probes of DNA structure. We have used the fluorescent adenine analogue 6MAP, a pteridone, to probe the local double helical structure of the CPD substrate when bound by photolyase. Duplex melting temperatures were obtained by both UV-vis absorption and fluorescence spectroscopies to ascertain the effect of the probe and the CPD on DNA stability. Steady-state fluorescence measurements of 6MAP-containing single-stranded and doubled-stranded oligos with and without protein show that the local region around the CPD is significantly disrupted. 6MAP shows a different quenching pattern compared to 2-aminopurine, another important adenine analogue, although both probes show that the structure of the complementary strand opposing the 5'-side of the CPD lesion is more destacked than that opposing the 3'-side in substrate/protein complexes. We also show that 6MAP/CPD duplexes are substrates for PL. Vertical excitation energies and transition dipole moment directions for 6MAP were calculated using time-dependent density functional theory. Using these results, the F?rster resonance energy transfer efficiency between the individual adenine analogues and the oxidized flavin cofactor was calculated to account for the observed intensity pattern. These calculations suggest that energy transfer is highly efficient for the 6MAP probe and less so for the 2Ap probe. However, no experimental evidence for this process was observed in the steady-state emission spectra.     

On the accessibility to conical intersections in purines: hypoxanthine and its singly protonated and deprotonated forms

The dynamics following electronic excitation of hypoxanthine and its nucleoside inosine were studied by femtosecond fluorescence up-conversion. Our objective was to explore variants of the purinic DNA bases in order to determine the molecular parameters that increase or reduce the accessibility to ground state conical intersections. From experiments in water and methanol solution we conclude that both dominant neutral tautomers of hypoxanthine exhibit ultrashort excited state lifetimes (τ < 0.2 ps), which are significantly shorter than in the related nucleobase guanine. This points to a more accessible conical intersection for the fluorescent state upon removal of the amino group, present in guanine but absent in hypoxanthine. The excited state dynamics of singly protonated hypoxanthine were also studied, showing biexponential decays with a 1.1 ps component (5%) besides a sub-0.2 ps ultrafast component. On the other hand, the S(1) lifetimes of the singly deprotonated forms of hypoxanthine and inosine show drastic differences, where the latter remains ultrafast but the singly deprotonated hypoxanthine shows a much longer lifetime of 19 ps. This significant variation is related to the different deprotonation sites in hypoxanthine versus inosine, which gives rise to significantly different resonance structures. In our study we also include multireference perturbation theory (MRMP2) excited state calculations in order to determine the nature of the initial electronic excitation in our experiments and clarify the ordering of the states in the singlet manifold at the ground state geometry. In addition, we performed multireference configuration interaction calculations (MR-CIS) that identify the presence of low-lying conical intersections for both prominent neutral tautomers of hypoxanthine. In both cases, the surface crossings occur at geometries reached by out of plane opposite motions of C2 and N3. The study of this simpler purine gives several insights into how small structural modifications, including amino substitution and protonation site and state, determine the accessibility to conical intersections in this kind of heterocycles.     

Nuclear dynamics for a three-state Jahn-Teller model system

We report wavepacket dynamics on a model system with a three-state conical intersection. Quantum wavepacket dynamics using the multiconfigurational time-dependent Hartree method have been carried out for the T ? (e + t(2)) Jahn-Teller problem, using a Jahn-Teller vibronic model Hamiltonian. The effects of the magnitude of the coupling parameters and of the initial position of the wavepacket on the dynamics around the three-state conical intersection have been considered. It was found that the effect of the coupling strength is not dramatic for the population transfer in most cases, but the details of the dynamics and the involvement of the different modes are affected by it.     

Three-state conical intersections in nucleic acid bases

The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S(0), S(1), and S(2) states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S(2) and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S(1), S(2), and S(3) states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.     

Beyond two-state conical intersections. Three-state conical intersections in low symmetry molecules: the allyl radical

Using multireference configuration interaction expansions comprised of over 7 million configuration state functions, three-state conical intersections are reported for the closely spaced, spectroscopically observed (tilde)B(2A1), (tilde)C(2B1), and (tilde)D(2B2) states (in C(2v) symmetry) of the allyl radical. These conical intersections of states which were previously assigned as the 3,4,5(2)A states and are here reassigned as the 4,5,6(2)A states, are expected to be accessible using optical probes. This conclusion is obtained from the structure of the minimum energy point on the 4,5,6(2)A three-state conical intersection seam which is similar to the equilibrium structure of the ground (tilde)X(2A2) state and only 1.1 eV above the (tilde)D(2B2) state at its equilibrium geometry. The seam of three-state degeneracies joins two two-state seams of conical intersection, the 4,5(2)A and 5,6(2)A conical intersection seams. The energy of the minimum energy point on the 4,5(2)A two-state seam is only 0.15 eV above that of the (tilde)D(2B2) state at its equilibrium structure. Three-state intersections are also reported for the 3,4,5(2)A states.     

Excited electronic states of the cyclic isomers of O2 and SO2

The low-lying electronic states of O3 and SO2 in their bent and cyclic isomers up to about 10 eV are calculated using the multireference configuration interaction (MRCI) method with a standard Gaussian correlation consistent polarized triple-zeta (cc-pVTZ) basis set. The vertical excitation energies, electron configurations, and oscillator strengths of these states are reported. The molecular orbital structures and excited states of the cyclic isomers are discussed in relation to the bent ones. Coherent anti-Stokes Raman spectroscopy (CARS) schemes for detecting the synthesis of the cyclic isomers are suggested.