QM:QM partitioning for ONIOM non-adiabatic on-the-fly molecular dynamic simulations of the (6-4)-lesion containing dinucleotide T(6-4) C T.
ONIOM(QM:QM) partitioning for the NA-O-MD simulations.
Reactant (left) and product structure (right) of the (6-4)-lesion containing dinucleotide T(6-4) C T: the pyrimidinone core is treated on high level of theory (CAS(12/9)) and mechanically embedded in the complete dinucleotide. The latter one is treated on a lower level of theory (HF). As relevant coordinates in the ONIOM(QM:QM) NA-O-MD simulations the N3–C6 distance R, the hybridization angle at C4 (defined by the dihedral angle ϕ = ∢(N3, C4, C6′, C5) and indicated by the red tetrahedral), the out-of-plane motions of N3 (green plane), and C6 (blue plane, defined by the dihedral angles φ = ∢(C5, C2, C4, C3) and θ = ∢(C2, C5, N1, C6), respectively) emerged.
ONIOM non-adiabatic on-the-fly molecular dynamics of the (6-4)-lesion containing dinucleotide T(6-4) C T: the progression of the potential energy (in eV) is shown on top, a low-pass filter has been applied to separate the essential dynamics from the superimposed high-frequency C–H modes. Middle panel: time evolution of the re-hybridization coordinate at C4 (ϕ, red line), and the out-of-plane deformations of the pyrimidinone core (φ, green line and θ, blue line). Bottom panel: time evolution of the N3–C6 distance R.
ONIOM non-adiabatic on-the-fly molecular dynamics of the (6-4)-lesion containing dinucleotide T(6-4) C T started in the vicinity of the S 1/S 0 conical intersection. The top panel shows the evolution of the electronic states (S 0, red; S 1, green; S 2, blue). The populated electronic state is highlighted with cyan squares. Additionally the total energy E tot is depicted in light grey. Bottom panel: N3–C6 distance R.
Scheme summarizing the ONIOM NA-O-MD simulations on the (6-4)-lesion containing dinucleotide. Percentages refer to the consecutive branching events, which involve non-adiabatic transitions.
Decisive hybridization scheme leading to the photochemical Dewar-valence isomerization in (6-4)-lesion containing dinucleotides and photophysical deactivation in isolated 5M2P.
Vertical excitation energies (in eV) of 5M2P on sa5-CAS(12/9) and MS-PT2 level of theory. The excitation energies of T(6-4) C T are calculated on ONIOM(sa5-CAS(12/9):HF) and ONIOM(MS-PT2-CAS:HF) level of theory. Transition moments |⟨S i |μ x, y, z |S 0⟩|2 are given in debye, additionally the absolute energy of the electronic ground state S0 (HF optimized geometry) is presented (in hartree). Changes in the state order are indicated with (S i ).
Article metrics loading...
Full text loading...