Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study

Abstract

Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC) 5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50−100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

“…On the other hand, the largest source of error is the adopted computational approach (e.g., density functional, basis set). The overestimation of the transition energies is a systematic feature of M052X, 29 and a similar blue shift is found also for cytosine 30,51 . In fact, we correctly reproduce the solvent shift associated with N3 protonation.…”

“…The overestimation of the transition energies is a systematic feature of M052X, 29 and a similar blue shift is found also for cytosine. 30,51 In fact, we correctly reproduce the solvent shift associated with N3 protonation.…”

Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization

“…Moreover, when coupled with Molecular Dynamics (MD) simulations, FrDEx has provided useful information on the effect that the loops and thermal fluctuations of the structure have on the ECD spectral signal 27 . Very recently, we have also profitably used FrDEx to compute the ECD spectra of a GC B‐DNA duplex 28 . These promising results have however been obtained only on two particular systems, a sample too small to fully assess the performances of FrDEx in simulating the electronic spectra of GQs and test its limitations.…”

“…27 Very recently, we have also profitably used FrDEx to compute the ECD spectra of a GC B-DNA duplex. 28 These promising results have however been obtained only on two particular systems, a sample too small to fully assess the performances of FrDEx in simulating the electronic spectra of GQs and test its limitations.…”

Ag+-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes

“…Each stick transitions broadened with a Gaussian with HWHM of 0.2 eV. Ref [ 34 ] is cited in Supplementary Materials.…”