Benchmarking Quantum Mechanical Methods for the Description of Charge-Transfer States in π-Stacked Nucleobases

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

We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.

Stimulated Resonance Raman and Excited-State Dynamics in an Excitonically Coupled Bodipy Dimer: A Test for TD-DFT and the Polarizable Continuum Model

Bodipy is one of the most versatile and studied functional dyes due to its myriad applications and tunable spectral properties. One of the strategies to adjust their properties is the formation of Bodipy dimers and oligomers whose properties differ significantly from the corresponding monomer. Recently, we have developed a novel strategy for synthesizing α,α-ethylene-bridged Bodipy dimers; however, their excited-state dynamics was heretofore unknown. This work presents the ultrafast excited-state dynamics of a novel α,α-ethylene-bridge Bodipy dimer and its monomeric parent. The dimer's steady-state absorption and fluorescence suggest a Coulombic interaction between the monomeric units' transition dipole moments (TDMs), forming what is often termed a "J-dimer". The excited-state properties of the dimer were studied using molecular excitonic theory and time-dependent density functional theory (TD-DFT). We chose the M06 exchange-correlation functional (XCF) based on its ability to reproduce the experimental oscillator strength and resonance Raman spectra. Ultrafast laser spectroscopy reveals symmetry-breaking charge separation (SB-CS) in the dimer in polar solvents and the subsequent population of the charge-separated ion-pair state. The charge separation rate falls into the normal regime, while the charge recombination is in the inverted regime. Conversely, in nonpolar solvents, the charge separation is thermodynamically not feasible. In contrast, the monomer's excited-state dynamics shows no dependence on the solvent polarity. Furthermore, we found no evidence of significant structural rearrangement upon photoexcitation, regardless of the deactivation pathway. After an extensive analysis of the electronic transitions, we concluded that the solvent fluctuations in the local environment around the dimer create an asymmetry that drives and stabilizes the charge separation. This work sheds light on the charge-transfer process in this new set of molecular systems and how excited-state dynamics can be modeled by combining the experiment and theory.

Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.

Target State Optimized Density Functional Theory for Electronic Excited and Diabatic States

A flexible self-consistent field method, called target state optimization (TSO), is presented for exploring electronic excited configurations and localized diabatic states. The key idea is to partition molecular orbitals into different subspaces according to the excitation or localization pattern for a target state. Because of the orbital-subspace constraint, orbitals belonging to different subspaces do not mix. Furthermore, the determinant wave function for such excited or diabatic configurations can be variationally optimized as a ground state procedure, unlike conventional ΔSCF methods, without the possibility of collapsing back to the ground state or other lower-energy configurations. The TSO method can be applied both in Hartree-Fock theory and in Kohn-Sham density functional theory (DFT). The density projection procedure and the working equations for implementing the TSO method are described along with several illustrative applications. For valence excited states of organic compounds, it was found that the computed excitation energies from TSO-DFT and time-dependent density functional theory (TD-DFT) are of similar quality with average errors of 0.5 and 0.4 eV, respectively. For core excitation, doubly excited states and charge-transfer states, the performance of TSO-DFT is clearly superior to that from conventional TD-DFT calculations. It is shown that variationally optimized charge-localized diabatic states can be defined using TSO-DFT in energy decomposition analysis to gain both qualitative and quantitative insights on intermolecular interactions. Alternatively, the variational diabatic states may be used in molecular dynamics simulation of charge transfer processes. The TSO method can also be used to define basis states in multistate density functional theory for excited states through nonorthogonal state interaction calculations. The software implementing TSO-DFT can be accessed from the authors.

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

In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K + $$ {}^{+} $$ cation in the calculation.

Flavin Charge Redistribution upon Optical Excitation Is Independent of Solvent Polarity

Flavin absorption spectra encode molecular details of the flavin's local environment through coupling of local electric fields with the chromophore's charge redistribution upon optical excitation. Translating experimentally measured field-tuned transition energies to local electric field magnitudes and directions across a wide range of field magnitudes requires that the charge redistribution be independent of the local field. We have measured the charge redistribution upon optical excitation of the derivatized flavin TPARF in the non-hydrogen-bonding, nonpolar solvent toluene, with and without a tridentate hydrogen-bonding ligand, DBAP, using electronic Stark spectroscopy. These measurements were interpreted using TD-DFT finite field and difference density calculations. In comparing our present results to previous Stark spectroscopic analyses of flavin in more polar solvents, we conclude that flavin charge redistribution upon optical excitation is independent of solvent polarity, indicating that dependence of flavin transition energies on local field magnitude is linear with local field magnitude.

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.

Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study

Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found to be important therapeutic targets and material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton-transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6-31++G**) and considered single layer of Gq [G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)] to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron-oxidized G4 and its various proton-transfer states: G^•+, G(N₁-H)^•, G(N₂-H')^•, G(N₂-H″)^•, G(N₁-H)^•-(H⁺O₆)G, and G(N₂-H)^•-(H⁺N₇)G. The present calculation predicts the formation of G(N₂-H)^•-(H⁺N₇)G, which is only ca. 0.8 kcal/mol higher in energy than the initially formed G^•+. The formation of G(N₂-H)^•-(H⁺N₇)G plays a key role in explaining the formation of 8-OG along with G(N₁-H)^• formation via tautomerization from G(N₂-H)^•, as proposed recently.

Spin-Orbit Natural Transition Orbitals and Spin-Forbidden Transitions

Natural transition orbitals (NTOs) are in widespread use for visualizing and analyzing electronic transitions. The present work introduces the analysis of formally spin-forbidden transitions with the help of complex-valued spin-orbit (SO) NTOs. The analysis specifically focuses on the components in such transitions that cause their intensity to be nonzero because of SO coupling. Transition properties such as transition dipole moments are partitioned into SO-NTO hole-particle pairs, such that contributions to the intensity from specific occupied and unoccupied orbitals are obtained. The method has been implemented within the restricted active space (RAS) self-consistent field wave function theory framework, with SO coupling treated by RAS state interaction. SO-NTOs have a broad range of potential applications, which is illustrated by the T₂-S₁ state mixing in pyrazine, spin-forbidden versus spin-allowed 4f-5d transitions in the Tb³⁺ ion, and the phosphorescence of tris(2-phenylpyridine) iridium [Ir(ppy)₃].

Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study

In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′^• > C1′^• > C5′^• > C3′^• > C2′^•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.