Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations

Abstract

In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

“…Properties of Franck-Condon excited states of NAs have been a subject of extensive quantum mechanical (QM) studies with the use of ab initio methods and timedependent density functional theory (TD DFT) [11][12][13][14][15][16][17][18][19][20] . NA stacked dimers, as a main model system in the high level ab initio calculations of vertical transitions, exhibit no markedly red-shifted transitions compared to monomer absorption, apart from a small ~ 0.1 eV exciton splitting in homodimers 11-13 , resulting in a weak wavelength tail 11 relative to the monomer's spectrum.…”

“…The experimental results also show that nearest base-base interactions can indeed satisfactory describe absorption 21 and circular dichroism spectra 22 . It has also been shown that only delocalized excitonic ππ* states contribute to the low-energy part of the absorption spectra, while charge-transfer (CT) transitions appear to be blue-shifted relative to absorption maximum 11,12,[15][16][17][18] . Meantime, a significant deviation of the fluorescence excitation spectra of some dinucleotides and oligonucleotides from their absorption spectra in the 290-310 nm region 21,23,24 , a long-wavelength tail in DNA absorption spectra 25,26 suggested possible electronic transitions in that spectral range.…”

“…All the theoretical studies however dealt with classical A or B stacking geometries 11-13 , artificial 14,15 , optimized or molecular dynamics (MD) sampled geometries [15][16][17][18][19][20] with inter-base distances close to canonical stacking forms. As an exception, it is worth noticing ref.…”

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations

“…well above the L a and L b bands (Fig. 2) 32 . They are found to mix with the energetically close lying bright B a and B b bands borrowing partially their oscillator strength.…”

“…Although this mechanism is not supported by QM/MM computations 31,32,58 , other groups have considered the possibility to populate low lying CT states directly in the FC region 8,64 . In this regard we would like to draw attention to a recent paper by Rohlfing and co-workers which argues that aqueous solvation may lower CT states by more than 1 eV based on many-body Green's function computations 64 .…”