Theoretical studies of the base pair fidelity of selenium-modified DNA

Heavy Chalcogen Properties of Sulfur and Selenium Enhance Nucleic Acid-Based Therapeutics

The Group 16 elements of the periodic table have a characteristic valence shell configuration instrumental to their chemical properties and reactivities. The electrostatic potentials of these so-called chalcogens have been exploited in the design of materials that require the efficient passage of electrons including supermagnets, photocatalytic dyes, and solar panels. Likewise, the incorporation of the heavy chalcogen selenium into organic frameworks has been shown to increase the reactivities of double bonds and heterocyclic rings, while its interactions with aromatic side chains in the hydrophobic core of proteins via selenomethionine impart a stabilizing effect. Typically present in the active site, the hypervalence of selenocysteine enables it to further stabilize the folded protein and mediate electron transfer. Selenium's native occurrence in bacterial tRNA maintains base pair fidelity, most notably during oxidative stress, through its electronic and steric effects. Such native modifications at the positions 2 and 5 of uridine render these sites relevant in the design of RNA-based therapeutics. Innocuous selenium substitution for oxygen in the former and the standard methods of selenium-derivatized oligonucleotide synthesis and detection have led to the establishment of a novel class of therapeutics. In this review, we summarize some progress in this area.

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water

Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S₂ state that converts internally to the dark S₁ state, from which the population is transferred to the triplet T₂ state via intersystem crossing and finally to the lowest T₁ state. This S₂ → S₁ → T₂ → T₁ deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T₁ lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T₁/S₀ crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ₁ = 131 fs and τ₂ = 191 fs) that are in excellent agreement with the experimentally reported value (τ_exp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.

Mechanistic photophysics and photochemistry of unnatural bases and sunscreen molecules: insights from electronic structure calculations

Photophysics and photochemistry are basic subjects in the study of light-matter interactions and are ubiquitous in diverse fields such as biology, energy, materials, and environment. A full understanding of mechanistic photophysics and photochemistry underpins many recent advances and applications. This contribution first provides a short discussion on the theoretical calculation methods we have used in relevant studies, then we introduce our latest progress on the mechanistic photophysics and photochemistry of two classes of molecular systems, namely unnatural bases and sunscreens. For unnatural bases, we disclose the intrinsic driving forces for the ultrafast population to reactive triplet states, impacts of the position and degree of chalcogen substitutions, and the effects of complex environments. For sunscreen molecules, we reveal the photoprotection mechanisms that dissipate excess photon energy to the surroundings by ultrafast internal conversion to the ground state. Finally, relevant theoretical challenges and outlooks are discussed.

Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations

Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.

Excited-State Properties and Relaxation Pathways of Selenium-Substituted Guanine Nucleobase in Aqueous Solution and DNA Duplex

The excited-state properties and relaxation mechanisms after light irradiation of 6-selenoguanine (6SeG) in water and in DNA have been investigated using a quantum mechanics/molecular mechanics (QM/MM) approach with the multistate complete active space second-order perturbation theory (MS-CASPT2) method. In both environments, the S₁ ¹(n_Seπ₅^*) and S₂ ¹(π_Seπ₅^*) states are predicted to be the spectroscopically dark and bright states, respectively. Two triplet states, T₁ ³(π_Seπ₅^*) and T₂ ³(n_Seπ₅^*), are found energetically below the S₂ state. Extending the QM region to include the 6SeG-Cyt base pair slightly stabilizes the S₂ state and destabilizes the S₁, due to hydrogen-bonding interactions, but it does not affect the order of the states. The optimized minima, conical intersections, and singlet-triplet crossings are very similar in water and in DNA, so that the same general mechanism is found. Additionally, for each excited state geometry optimization in DNA, three kind of structures ("up", "down", and "central") are optimized which differ from each other by the orientation of the C═Se group with respect to the surrounding guanine and thymine nucleobases. After irradiation to the S₂ state, 6SeG evolves to the S₂ minimum, near to a S₂/S₁ conical intersection that allows for internal conversion to the S₁ state. Linear interpolation in internal coordinates indicate that the "central" orientation is less favorable since extra energy is needed to surmount the high barrier in order to reach the S₂/S₁ conical intersection. From the S₁ state, 6SeG can further decay to the T₁ ³(π_Seπ₅^*) state via intersystem crossing, where it will be trapped due to the existence of a sizable energy barrier between the T₁ minimum and the T₁/S₀ crossing point. Although this general S₂ → T₁ mechanism takes place in both media, the presence of DNA induces a steeper S₂ potential energy surface, that it is expected to accelerate the S₂ → S₁ internal conversion.

Selenium substitution effects on excited-state properties and photophysics of uracil: a MS-CASPT2 study

The photophysics of selenium-substituted nucleobases has attracted recent experimental attention because they could serve as potential photosensitizers in photodynamic therapy. Herein, we present a comprehensive MS-CASPT2 study on the spectroscopic and excited-state properties, and photophysics of 2-selenouracil (2SeU), 4-selenouracil (4SeU), and 2,4-selenouracil (24SeU). Relevant minima, conical intersections, crossing points, and excited-state relaxation paths in the lowest five electronic states (i.e., S₀, S₁, S₂, T₂, and T₁) are explored. On the basis of these results, their photophysical mechanisms are proposed. Upon photoirradiation to the bright S₂ state, 2SeU quickly relaxes to its S₂ minimum and then moves in an essentially barrierless way to a nearby S₂/S₁ conical intersection near which the S₁ state is populated. Next, the S₁ system arrives at an S₁/T₂/T₁ intersection where a large S₁/T₁ spin-orbit coupling of 430.8 cm^-1 makes the T₁ state populated. In this state, a barrier of 6.8 kcal mol^-1 will trap 2SeU for a while. In parallel, for 4SeU or 24SeU, the system first relaxes to the S₂ minimum and then overcomes a small barrier to approach an S₂/S₁ conical intersection. Once hopping to the S₁ state, there exists an extended region with very close S₁, T₂, and T₁ energies. Similarly, a large S₁/T₁ spin-orbit coupling of 426.8 cm^-1 drives the S₁→ T₁ intersystem crossing process thereby making the T₁ state populated. Similarly, an energy barrier heavily suppresses electronic transition to the S₀ state. The present work manifests that different selenium substitutions on uracil can lead to a certain extent of different vertical and adiabatic excitation energies, excited-state properties, and relaxation pathways. These insights could help understand the photophysics of selenium-substituted nucleobases.

Structural insights of non-canonical U*U pair and Hoogsteen interaction probed with Se atom

Unlike DNA, in addition to the 2′-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine (^SeU) phosphoramidite and Se-nucleobase-modified RNAs (^SeU-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4^…H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.