A theoretical study using ab initio methods of tautomerism in cytosine in the gas phase and in water

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations. Two pathways were considered to explain the mechanism of this process, where the water molecule attacks the C–N bond to give an intermediate (an amino–hydroxy–oxo structure in the A-path, and a hydroxy–oxo in the B-path) as the determinant step of reaction. Stationary structures along both energy profiles were analyzed at molecular dynamics level, obtaining states with higher free energies than those from electronic calculations in the gas phase and in solution described as a continuous medium. From the results obtained, the more complex A-pathway, with five steps, was kinetically the most favorable (with an endergonic reaction energy of 7.41 kcal mol⁻¹, a high barrier of 67.53 kcal mol⁻¹, and a small velocity constant k₂ = 1.80 × 10⁻³⁷ s⁻¹), concluding that the uracil base can participate in a spontaneous genetic mutation since the uracil–ammonia complex has a long lifetime of 6.10 × 10²⁷ s. This process turns out exergonic and faster when carried out in gas phase simulation or electronic calculation with a continuous medium, due to the disappearance of explicit water molecules that can compete with the assistant molecule.

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell

A detailed quantum chemical investigation was undertaken to obtain the structure and energetics of cytosine hydrates Cyt·nH2O, with n = 1 to 7. The MP2(fc)/aug-cc-pVDZ level was used as the standard, with some DFT (B3LYP) and coupled cluster calculations, as well as calculations with the aug-cc-pVTZ basis set added for comparison. In a systematic search for microhydrated forms of cytosine, we have found that several structures have not yet been reported in the literature. The energies of different isomers, as well as binding energies are compared. When predicting the stability of a complex, we suggest using a scheme where the water molecules are extracted from a finite model of bulk water. Finally, based on energetic data, we suggest a rational definition of the first hydration shell; with this definition, it contains just six water molecules.

Infrared spectra of protonated uracil, thymine and cytosine

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.

Theoretical Studies on the Hydrolysis Mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) Formamide

Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

Elucidation of primary radiation damage in DNA through application of ab initio molecular orbital theory

This review summarizes the results of recent ab initio molecular orbital calculations performed on DNA constituents that attempt to further our understanding of the radiation-induced damage to DNA. The results reviewed include calculations performed on the four individual DNA bases, the base pairs in gas phase and modelled aqueous phase, the deoxyribose moiety, and a portion of the sugar-phosphate backbone. The emphasis is on the electron affinities and ionization potentials of the radical species calculated under various conditions (i.e. gas phase, aqueous phase, proton transfer, base stacking), as it has been shown that the initial ion radical distribution is largely a function of these two properties. Theoretical studies of the electronic excited states of the individual bases and radioprotection of the biomolecule by various thiol compounds are also reviewed. Finally, a summary is provided to allow for further elaboration of the current model for radiation damage to DNA and to show the present advantages and limitations of ab initio theory in the investigation of such processes.