A semiclassical dynamics simulation for a long-lived excimer state of π-stacked adenines

Aggregation of nucleobases and metabolites: Adenine-theobromine trimers

The selection of cytosine, guanine, thymine, and adenine as components of the information biopolymers was a complex process influenced by several factors. Among them, the intermolecular interactions may have played a determinant role. Thus, a deep understanding of the intermolecular interactions between nucleobases and other prebiotic molecules may help understand the first instants of chemical evolution. Following this hypothesis, we present here a combined spectroscopic and computational study of theobromine₂-adenine and thebromine-adenine₂ trimers. While adenine is a nucleobase, theobromine was probably part of the prebiotic chemistry. The trimers were formed in jets and probed by a combination of UV and IR spectroscopic techniques. The spectra were interpreted in light of the predictions obtained using density-functional methods. The results suggest the existence of a subtle balance between formation of hydrogen bonds and π-π interactions. Thus, while theobromine₂-adenine tends to form complex in stacked structures, theobromine-adenine₂ prefers formation of planar structures, maximizing the interaction by hydrogen bonds. The small energy difference between planar and stacked structures highlights the importance of accurately modeling the dispersion forces in the functionals to produce reliable predictions.

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.

Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides

A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.

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.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back

L_a and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.

Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations

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.

Thymine dimer splitting in the T<>T-G trinucleotide model system: a semiclassical dynamics and TD-DFT study

The mechanism leading to bond cleavage of a thymine-thymine cyclobutane dimer (T<>T) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5' and C6C6' bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale.

Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.

The effect of dimerization on the excited state behavior of methylated xanthine derivatives: a computational study

The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is investigated by means of the ADC(2), CASSCF, and CASPT2 methods. The results of the calculations of stationary points in the ground and excited states, minima on the S0/S1 crossing seams and the relaxation pathways are used to provide the interpretation of experimental observations of the monomer xanthine derivatives. The effect of dimerization on the excited state properties is studied for various relative orientations of the monomers in the dimer complexes in comparison with the relevant monomer species. A significant stabilization in the excited state minima of dimers is observed. These can act as trapping sites. Various types of conical intersections, with both localized and delocalized characters of wavefunctions, have been found, mainly energetically above the lowest bright excited state in the FC region. In addition, structures with the bonds formed between the two monomers were also found on the crossing seams. The possibility of ultrafast relaxation via these conical intersections is discussed.

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases

Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.

Detailed mechanism for photoinduced cytosine dimerization: a semiclassical dynamics simulation

Semiclassical dynamics simulation is used to study dimerization of two stacked cytosine molecules following excitation by ultrashort laser pulses (25 fs fwhm, Gaussian, 4.1 eV photon energy). The initial excited state was found to form an ultrashort exciton state, which eventually leads to the formation of an excimer state by charge transfer. When the interbase distance, defined as an average value of C(5)-C(5)' and C(6)-C(6)', becomes less than 3 Å, charge recombination occurs due to strong intermolecular interaction, eventually leading to an avoided crossing within 20-30 fs. Geometries at the avoided crossing, with average intermolecular distance of about 2.1 Å, are in accord with CASSCF/CASPT2 calculations. Results indicate that the C(2)-N(1)-C(6)-C(5) and C(2)'-N(1)'-C(6)'-C(5)' dihedral angles' bending vibrations play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to a nonadiabatic transition to the electronic ground state.