Characterization of the excited states of DNA building blocks: a coupled cluster computational study

Theoretical insight into photodeactivation mechanisms of adenine-uracil and adenine-thymine nucleobase pairs

In this work, several plausible intra- and intermolecular photoinduced processes of the Watson-Crick base pairs of adenine with uracil (A-U) or thymine (A-T) according to the results of spin component scaling variant of algebraic diagrammatic construction up to the second order [SCS-ADC(2)] calculations are discussed. Although widely explored, these systems lack complete characterization of possible intramolecular relaxation channels perturbed by intermolecular interactions. In particular, we address the still open debate on photodeactivation via purine-ring puckering at the C2 or C6-atom position of adenine. We also show that the presence of low-lying, long-lived 1nπ* states can be a significant factor in hindering relaxation via an electron-driven proton transfer process, as the population of these states can lead to an efficient intersystem crossing to a triplet manifold, the estimated rate of which is 1.6 × 1010 s-1 which exceeds the corresponding internal conversion to the ground state by an order of magnitude. Additionally, the SCS variant of the ADC(2) method is shown to provide a more balanced description of valence and charge-transfer excited states.

Ab initio investigation of excited state charge transfer pathways in differently capped bithiophene cages

The electronic excitations of conformationally constrained bithiophene cage systems as previously investigated by Lewis et al. (J. Am. Chem. Soc. 143, 18548 (2021)) are revisited, employing the correlated ab initio Scaled Opposite-Spin Algebraic Diagrammatic Construction Second Order electronic structure method. Quantitative descriptors are determined to assess the extent of charge transfer between the bithiophene moieties and the capping domains, represented by either phenyl or triazine groups. The investigation substantiates intrinsic differences in the photophysical behavior of these two structural variants and reveals the presence of lower-energy excited states characterized by noteworthy charge transfer contributions in the triazine cage system. The manifestation of this charge transfer character is discernible even at the Franck-Condon geometry, persisting throughout the relaxation of the excited state. By examining isolated monomer building blocks, we confirm the existence of analogous charge transfer contributions in their excitations. Employing this methodological approach facilitates the prospective identification of potential wall/cap chromophore pairs, wherein charge transfer pathways can be accessed within the energetically favorable regime.

Benchmarking Aspects of Ab Initio Fragment Models for Accurate Excimer Potential Energy Surfaces

While Coupled-Cluster methods have been proven to provide an accurate description of excited electronic states, the scaling of the computational costs with the system size limits the degree for which these methods can be applied. In this work different aspects of fragment-based approaches are studied on noncovalently bound molecular complexes with interacting chromophores of the fragments, such as π-stacked nucleobases. The interaction of the fragments is considered at two distinct steps. First, the states localized on the fragments are described in the presence of the other fragment(s); for this we test two approaches. One method is founded on QM/MM principles, only including the electrostatic interaction between the fragments in the electronic structure calculation with Pauli repulsion and dispersion effects added separately. The other model, a Projection-based Embedding (PbE) using the Huzinaga equation, includes both electrostatic and Pauli repulsion and only needs to be augmented by dispersion interactions. In both schemes the extended Effective Fragment Potential (EFP2) method of Gordon et al. was found to provide an adequate correction for the missing terms. In the second step, the interaction of the localized chromophores is modeled for a proper description of the excitonic coupling. Here the inclusion of purely electrostatic contributions appears to be sufficient: it is found that the Coulomb part of the coupling provides accurate splitting of the energies of interacting chromophores that are separated by more than 4 Å.

The Ultrafast Quantum Dynamics of Photoexcited Adenine-Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model

In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine-thymine (AT) in a Watson-Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Dependent Density Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization scheme (FrD) we have developed to define diabatic states on the basis of individual chromophores in a multichromophoric system. Wavepacket propagations were run with the multilayer extension of the Multiconfiguration Time-Dependent Hartree method. We considered excitations to the three lowest bright states, a ππ* state of thymine and two ππ* states (La and Lb) of adenine, and we found that on the 100 fs time scale the main decay pathways involve intramonomer population transfers toward nπ* states of the same nucleobase. In AT this transfer is less effective than in the isolated nucleobases, because hydrogen bonding destabilizes the nπ* states. The population transfer to the A → T charge transfer state is negligible, making the ultrafast (femtosecond) decay through the proton coupled electron transfer mechanism unlikely, in line with experimental results in apolar solvents. The excitation energy transfer is also very small. We carefully compare the predictions of LVC Hamiltonians obtained with different sets of diabatic states, defined so to match either local states of the two separated monomers or the base pair adiabatic states in the Franck-Condon region. To that end we also extend the flexibility of the FrD-LVC approach, introducing a new strategy to define fragments diabatic states that account for the effect of the rest of the multichromohoric system through a Molecular Mechanics potential.

Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis

The characterization of the electronically excited states of DNA strands populated upon solar UV light absorption is essential to unveil light-induced DNA damage and repair processes. We report a comprehensive analysis of the electronic properties of the UV spectrum of single-stranded polyadenine based on theoretical calculations that include excitations over eight nucleobases of the DNA strand and environmental effects by a multiscale quantum mechanics/molecular mechanics scheme, conformational sampling by molecular dynamics, and a meaningful interpretation of the electronic structure by quantitative wavefunction analysis. We show that electronic excitations are extended mainly over two nucleobases with additional important contributions of monomer-like excitations and excitons delocalized over three monomers. Half of the spectral intensity derives from locally excited and Frenkel exciton states, while states with partial charge-transfer character account for the other half and pure charge-transfer states represent only a minor contribution. The hypochromism observed when going from the isolated monomer to the strand occurs independently from delocalization and charge transfer and is instead explained by long-range environmental perturbations of the monomer states.

Solvent effects on the excited state characteristics of adenine–thymine base pairs

A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.

Challenges in Simulating Light-Induced Processes in DNA

In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.