Benchmark Studies on the Building Blocks of DNA. 3. Watson–Crick and Stacked Base Pairs

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.

Excited state properties of an A-D-A non-fullerene electron acceptor: a LC-TD-DFTB study

Understanding charge transfer processes is essential to estimate the performance of organic photovoltaic technologies. Although experimental production is on the rise, predictability strongly relies on theoretical modeling, which is limited to the size of semiconductors. As a computationally favorable approach, we benchmarked the long-range corrected (LC) time-dependent (TD) formulation of the semi-empirical density functional-based tight-binding method (DFTB) for three polycyclic aromatic hydrocarbons (PAHs) and studied the DTP-IC-4Ph molecule, a PAH-based non-fullerene electron acceptor (NFA) with an A-D-A backbone structure. After a thorough investigation into the long-range parameter (ω) tuning for naphthalene, anthracene and pyrene, the excitation energies, oscillator strengths and Natural Transition Orbitals (NTOs) were compared with the standard ωB97X-D/6-31G(d,p) level of theory and the ADC2/6-31G(d,p) multiconfigurational method. We estimated mobility-related properties of the NFA and considered 1000 thermally accessible configurations to qualitatively reproduce the experimental absorption profile and investigate the energetic disorder. Finally, we conducted a fragment-based analysis using the one-electron transition density matrix (1TDM) to determine the character of the excited states and investigate the effect of side chains on exciton formation. Our results are sensitive to the level of theory and highly dependent on the long-range parameter but suggest that the presence of alkyl chains promotes a higher average charge delocalization and allows for additional hopping mechanisms, favoring the charge transfer dynamics.

Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair

We introduce a method (FrD-LVC) based on a fragment diabatization (FrD) for the parametrization of a linear vibronic coupling (LVC) model suitable for studying the photophysics of multichromophore systems. In combination with effective quantum dynamics (QD) propagations with multilayer multiconfigurational time-dependent Hartree (ML-MCTDH), the FrD-LVC approach gives access to the study of the competition between intrachromophore decays, like those at conical intersections, and interchromophore processes, like exciton localization/delocalization and the involvement of charge-transfer (CT) states. We used FrD-LVC parametrized with time-dependent density functional theory (TD-DFT) calculations, adopting either CAM-B3LYP or ωB97X-D functionals, to study the ultrafast photoexcited QD of a guanine-cytosine (GC) hydrogen-bonded pair, within a Watson-Crick arrangement, considering up to 12 coupled diabatic electronic states and the effect of all of the 99 vibrational coordinates. The bright excited states localized on C and, especially, on G are predicted to be strongly coupled to the G → C CT state, which is efficiently and quickly populated after an excitation to any of the four lowest energy bright local excited states. Our QD simulations show that more than 80% of the excited population on G and ∼50% of that on C decay to this CT state in less than 50 fs. We investigate the role of vibronic effects in the population of the CT state and show that it depends mainly on its large reorganization energy so that it can occur even when it is significantly less stable than the bright states in the Franck-Condon region. At the same time, we document that the formation of the GC pair almost suppresses the involvement of dark nπ* excited states in the photoactivated dynamics.

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

Assessment of local coupled cluster methods for excited states of BODIPY/Aza-BODIPY families

It was previously reported that Laplace transformed local CC2 (LCC2*) provided the best agreement (MAE = 0.145 eV) when comparing vertical excitation energies to experimental λ_max for a benchmark set of 17 BODIPY/Aza-BODIPY molecules. However, these energies did not agree with values obtained from canonical CC2. Here we report LCC2* computations of vertical excitation energies on the same benchmark set of molecules using a newly implemented treatment of the ground state. Comparison with resolution-of-identity approximate coupled cluster to second-order (RI-CC2) results demonstrate that the new LCC2* results agree quantitatively. Furthermore, these values can easily be corrected empirically to also provide excellent agreement with the experiment. We show that the local algebraic diagrammatic construction to second-order (LADC(2)) method exhibits the same differences between implementations as seen for LCC2. The source of the difference is traced to an improved treatment of the ground state in the local methods, which decreases agreement with the experiment (as attributed to a fortuitous cancellation of errors) but significantly improves agreement with RI-CC2. While the absolute vertical excitation energies now show larger deviations, there remains a strong linear correlation between the LCC2* results and the experiment. For the 17 BODIPY/Aza-BODIPY molecules vertical excitation energies are determined using DLPNO-STEOM-CCSD and shown to have excellent agreement with experimental λ_max (MAE = 0.145 eV), which is the best of all the single-reference methods. The vertical excitation energies are determined using LCC2*, empirically corrected LCC2*, and RI-CC2 for a series of eight large BODIPYs and Aza-BODIPYs.

Electronic couplings for photo-induced processes from subsystem time-dependent density-functional theory: The role of the diabatization

Subsystem time-dependent density-functional theory (sTDDFT) making use of approximate non-additive kinetic energy (NAKE) functionals is known to be capable of describing excitation energy transfer processes in a variety of applications. Here, we show that sTDDFT, especially when combined with projection-based embedding (PbE), can be employed for the entire range of photo-induced electronic couplings essential for modeling photophysical properties of complex chemical and biological systems and therefore represents a complete toolbox for this class of problems. This means that it is capable of capturing the interaction/coupling associated with local- and charge-transfer (CT) excitons. However, this requires the choice of a reasonable diabatic basis. We therefore propose different diabatization strategies of the virtual orbital space in PbE-sTDDFT and show how CT excitations can be included in sTDDFT using NAKE functionals via a phenomenological approach. Finally, these electronic couplings are compared to couplings from a multistate fragment excitation difference (FED)-fragment charge difference (FCD) diabatization procedure. We show that both procedures, multistate FED-FCD and sTDDFT (with the right diabatization procedure chosen), lead to an overall good agreement for the electronic couplings, despite differences in their general diabatization strategy. We conclude that the entire range of photo-induced electronic couplings can be obtained using sTDDFT (with the right diabatization procedure chosen) in a black-box manner.

Excited States of One-Electron Oxidized Guanine-Cytosine Base Pair Radicals: A Time Dependent Density Functional Theory Study

One-electron oxidized guanine (G^•+) in DNA generates several short-lived intermediate radicals via proton transfer reactions resulting in the formation of neutral guanine radicals. The identification of these radicals in DNA is of fundamental interest to understand the early stages of DNA damage. Herein, we used time-dependent density functional theory (TD-ωB97XD-PCM/6-31G(3df,p)) to calculate the vertical excitation energies of one-electron oxidized G and G-cytosine (C) base pair in various protonation states: G^•+, G(N1-H)^•, and G(N2-H)^•, as well as G^•+-C, G(N1-H)^•-(H⁺)C, G(N1-H)^•-(N4-H⁺)C), G(N1-H)^•-C, and G(N2-H)^•-C in aqueous phase. The calculated UV-vis spectra of these radicals are in good agreement with the experiment for the G radical species when the calculated values are red-shifted by 40-70 nm. The present calculations show that the lowest energy transitions of proton transfer species (G(N1-H)^•-(H⁺)C, G(N1-H)^•-(N4-H⁺)C, and G(N1-H)^•-C) are substantially red-shifted in comparison to the spectrum of G^•+-C. The calculated spectrum of G(N2-H)^•-C shows intense absorption (high oscillator strength), which matches the strong absorption in the experimental spectra of G(N2-H)^• at 600 nm. The present calculations predict the lowest charge transfer transition of C → G^•+ is π → π* in nature and lies in the UV region (3.4-4.3 eV) with small oscillator strength.

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.

Photophysical deactivation pathways in adenine oligonucleotides

In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

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

DNA building blocks consisting of up to four nucleobases are investigated using the EOM-CCSD and CC2-LR methods in two B-DNA-like arrangements of a poly-adenine:poly-thymine (poly-A:poly-T) system. Excitation energies and oscillator strengths are presented and the characteristics of the excited states are discussed. Excited states of single-stranded poly-A systems are highly delocalized, especially the spectroscopically bright states, where delocalization over up to four fragments can be observed. In the case of poly-T systems, the states are somewhat less delocalized, extending to maximally about three fragments. A single A:T Watson-Crick pair has highly localized states, while delocalization over base pairs can be observed for some excited states of the (A)2:(T)2 system, but intrastrand delocalization is more pronounced in this case, as well. As for the characteristics of the simulated UV absorption spectra, a significant decrease of intensity can be observed in the case of single strands with increasing chain length; this is due to the stacking interactions and is in accordance with previous results. On the other hand, the breaking of H-bonds between the two strands does not alter the spectral intensity considerably, it only causes a redshift of the absorption band, thus it is unable to explain the experimentally observed DNA hyperchromism on its own, and stacking interactions need to be considered for the description of this effect as well.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

The nonadditivity of stacking interactions in adenine–thymine and guanine–cytosine stacked structures: Study by MP2 and SCS-MP2 calculations

The nonadditivity of stacking interactions in stacked structures of adenine–thymine and guanine–cytosine base pairs is investigated by MP2 and SCS-MP2 calculations with 6-311++G** and aug-cc-pvdz basis sets. The calculation results indicate that the intermolecular distances in the multi-stacked structures do not become shorter obviously as the stacked structure added. The middle stacking interaction energies in the multi-stacked structures also become weaker than that of dimer structures. It is found that the total stacking interaction energies of the trimer and tetramer stacked structures do not increase proportionally. Based on the results, we suggest that there is negative cooperativity of the stacking interactions in the adenine–thymine and guanine–cytosine stacked structures.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Photochemistry of methyl hypobromite (CH3OBr): excited states and photoabsorption spectrum

From photoabsorption to photodissociation, from MRCI to TDDFT; a comprehensive benchmark on the photochemistry of methyl hypobromite (CH₃OBr) is provided.

Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory

It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.