Formation of spiroiminodihydantoin due to the reaction between 8-oxoguanine and carbonate radical anion: A quantum computational study

Initial decomposition pathways of 1,1-diamino-2,2-dinitroethylene (α-FOX-7) in the condensed phase

The initial decomposition pathways of α-FOX-7 in the condensed phase (crystal) were investigated via density functional theory. Calculations were carried out using three FOX-7 systems with increasing complexity from 1-layer (sheet) via 2-layer (surface) to 3-layer (bulk). The encapsulated environment of the central α-FOX-7 molecule, where decomposition takes place, is reconstructed by neighbouring molecules following a crystal structure. A minimal number of neighbouring molecules that have an impact on the energetics of decomposition are identified among all surrounding molecules. The results show that the presence of intermolecular hydrogen bonds due to the encapsulated environment in the condensed phase decreases the sensitivity of α-FOX-7, i.e. it increases the barrier of decomposition, but it does not alter the initial decomposition pathways of the reaction compared to the gas phase. Moreover, increasing the complexity of the system from a single gas phase molecule via sheet and surface to bulk increases the decomposition barriers. The calculations reveal a remarkable agreement with experimental data [A. M. Turner, Y. Luo, J. H. Marks, R. Sun, J. T. Lechner, T. M. Klapötke and R. I. Kaiser, Exploring the Photochemistry of Solid 1, 1-Diamino-2, 2-Dinitroethylene (FOX-7) Spanning Simple Bon Ruptures, Nitro-to-Nitrite Isomerization, and Nonadiabatic Dynamics, J. Phys. Chem. A, 2022, 126, 29, 4747-4761] and suggest that the initial decomposition of α-FOX-7 likely takes place at the surface of the crystal.

An Exploration of the Transformation of the 8-Oxo-7,8-Dihydroguanine Radical Cation to Protonated 2-Amino-5-Hydroxy-7,9-Dihydropurine-6,8-Dione in a Base Pair

A theoretical investigation was performed to disclose the transformation mechanism of 8-oxo-7,8-dihydroguanine radical cation (8-oxoG⋅⁺ ) to protonated 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-8-oxoG) in base pair. The energy profiles for three possible pathways of the events were mapped. It is shown that direct loss of H7 from base paired 8-oxoG⋅⁺ is the only energetically favorable pathway to generate neutral radical, 8-oxoG(-H7)⋅. Further oxidation of 8-oxoG(-H7)⋅ : C to 8-oxoG(-H7)⁺  : C is exothermic. However, the 8-oxoG(-H7)⁺  : C deprotonation from all possible active sites is infeasible, indicating the inaccessible second proton loss and the lack of essential intermediate 2-amino-7,9-dihydropurine-6,8-dione (8-oxoG^OX ). This makes 8-oxoG(-H7)⁺ act as the precursor of hydration leading to the generation of protonated 5-HO-8-oxoG by stepwise fashion in base pair, which would initiate the step down guanidinohydantoin (Gh) pathway. These results clearly specify the structure-dependent transformation for 8-oxoG⋅⁺ and verify the emergence of protonated 5-HO-8-oxoG in base pair.

Computational Study of the pH-Dependent Competition between Carbonate and Thymine Addition to the Guanine Radical

When oligonucleotides are oxidized by carbonate radical, thymine and carbonate can add to guanine radical, yielding either a guanine-thymine cross-link product (G∧T) or 8-oxo-7,8-dehydroguanine (8oxoG) and its further oxidation products such as spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). The ratio of thymine addition to carbonate addition depends strongly on the pH. Details of the mechanism have been explored by density functional calculations using the ωB97XD/6-31+G(d,p) level of theory with the SMD implicit solvation method, augmented with a few explicit waters. Free energies of intermediates and transition states in aqueous solution have been calculated along the pathways for addition of thymine, CO₃^2-/HCO₃^- and carbonate radical to guanine radical. The pH dependence was examined by using appropriate explicit proton donors/acceptors as computational models for buffers at pH 2.5, 7, and 10. Deprotonation of thymine is required for nucleophilic addition at C8 of guanine radical, and thus is favored at higher pH. The barrier for carbonate radical addition is lower than for bicarbonate or carbonate dianion addition; however, for low concentrations of carbonate radical, the reaction may proceed by addition of bicarbonate/carbonate dianion to guanine radical. Thymine and bicarbonate/carbonate dianion addition are followed by oxidation by O₂, loss of a proton from C8 and decarboxylation of the carbonate adduct. At pH 2.5, guanine radical cation can be formed by oxidization with sulfate radical. Water addition to guanine radical cation is the preferred path for forming 8oxoG at pH 2.5.

The R- and S-diastereoisomeric effects on the guanidinohydantoin-induced mutations in DNA

Although, Gh (Gh1 or Gh2) in DNA would induce mainly G to C mutations, other mutations cannot be ignored.