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

Effect of A-DNA and B-DNA Conformation on the Interplay between Local Excitations and Charge-Transfer States in the Ultrafast Decay of Guanine-Cytosine Stacked Dimers: A Quantum Dynamical Investigation

We here simulate in the gas phase the population dynamics of guanine/cytosine (GC) and cytosine/guanine (CG) stacked dimers in B-DNA and A-DNA arrangement, following excitation in the lowest-energy band, and considering the four lowest-energy ππ* bright excited states, the three lowest-energy nπ* states, and the G → C charge-transfer (CT) state. We resort to a generalized Linear Vibronic Coupling (LVC) model parametrized with time-dependent density functional theory (TD-DFT) computations, exploiting a fragment-based diabatization and we run nonadiabatic quantum dynamical simulations with the multilayer version of the Multiconfigurational Time-Dependent Hartree (ML-MCTDH) approach. G → C CT results in a major decay process for GC in B-DNA but less in A-DNA arrangement, where also the population transfer to the lowest-energy excited state localized on C is an important intermonomer process. In CG arrangements, mostly intramonomeric decays take place. We simulate the dynamics of several other GC structures whose arrangement is intermediate between B-DNA and A-DNA, obtaining further insights on the effect that the sequence and, especially, the stacking geometry have on the population transfer to the G → C CT.

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.

Mind the GAP: quantifying the breakdown of the linear vibronic coupling Hamiltonian

Excited state dynamics play a critical role across a broad range of scientific fields. Importantly, the highly non-equilibrium nature of the states generated by photoexcitation means that excited state simulations should usually include an accurate description of the coupled electronic-nuclear motion, which often requires solving the time-dependent Schrödinger equation (TDSE). One of the biggest challenges for these simulations is the requirement to calculate the PES over which the nuclei evolve. An effective approach for addressing this challenge is to use the approximate linear vibronic coupling (LVC) Hamiltonian, which enables a model potential to be parameterised using relatively few quantum chemistry calculations. However, this approach is only valid provided there are no large amplitude motions in the excited state dynamics. In this paper we introduce and deploy a metric, the global anharmonicity parameter (GAP), which can be used to assess the accuracy of an LVC potential. Following its derivation, we illustrate its utility by applying it to three molecules exhibiting different rigidity in their excited states.

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

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.

Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform

We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population.

Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies

ConspectusThe interaction between light and multichromophoric assemblies (MCAs) is the primary event of many fundamental processes, from photosynthesis to organic photovoltaics, and it triggers dynamical processes that share remarkable similarities at the molecular scale: light absorption, energy and charge transfer, internal conversions, emission, and so on. Those events often involve many chromophores and different excited electronic states that are coupled on an ultrafast time scale. This Account aims to discuss some of the chemical physical effects ruling these processes, a fundamental step toward their control, based on our experience on nucleic acids.In the last 15 years, we have, indeed, studied the photophysics and photochemistry of DNA and its components. By combining different quantum mechanical methods, we investigated the molecular processes responsible for the damage of the genetic code or, on the contrary, those preventing it by dissipating the excess energy deposited in the system by UV absorption. Independently of its fundamental biological role, DNA, with its fluctuating closely stacked bases stabilized by weak nonbonding interactions, can be considered a prototypical MCA. Therefore, it allows one to tackle within a single system many of the conceptual and methodological challenges involved in the study of photoinduced processes in MCA.In this Account, by using the outcome of our studies on oligonucleotides as a guideline, we thus highlight the most critical modellistic issues to be faced when studying, either experimentally or computationally, the interaction between UV light and DNA and, at the same time, bring out their general relevance for the study of MCAs.We first discuss the rich photoactivated dynamics of nucleobases (the chromophores), highlighting the main effects modulating the interplay between their excited states and how the latter can affect the photoactivated dynamics of the polynucleotides, either providing effective monomer-like nonradiative decay routes or triggering reactive processes (e.g., triplet generation).We then tackle the reaction paths involving multiple bases, showing that in the DNA duplex the most important ones involve two stacked bases, forming a neutral excimer or a charge transfer (CT) state, which exhibit different spectral signatures and photochemical reactivity. In particular, we analyze the factors affecting the dynamic equilibrium between the excimer and CT, such as the fluctuations of the backbone or the rearrangement of the solvent.Next, we highlight the importance of the effects not directly connected to the chromophores, such as the flexibility of the backbone or the solvent effect. The former, affecting the stacking geometry of the bases, can determine the preference between different deactivation paths. The latter is particularly influential for CT states, making very important an accurate treatment of dynamical solvation effects, involving both the solvent bulk and specific solute-solvent interactions.In the last section, we describe the main methodological challenges related to the study of polynucleotide excited states and stress the benefits derived by the integration of complementary approaches, both computational and experimental. Only exploiting different point of views, in our opinion, it is possible to shed light on the complex phenomena triggered by light absorption in DNA, as in every MCA.