Structures and Energetics of the Deprotonated Adenine−Uracil Base Pair, Including Proton-Transferred Systems

Intramolecular vibrational energy redistribution in nucleobases: Excitation of NH stretching vibrations in adenine–uracil + H2O

Redistribution of vibrational energy in the adenine–uracil base pair is studied when the base pair undergoes an intermolecular interaction with an overtone-bending vibration excited H2O(2[Formula: see text]bend) molecule. Energy transfer is calculated using the structural information obtained from density functional theory in the solution of the equations of motion. Intermolecular vibrational energy transfer (VET) from H2O(2[Formula: see text]bend) to the uracil–NH stretching mode is efficient and rapidly followed by intramolecular vibrational energy redistribution (IVR) resulting from coupling between vibrational modes. An important pathway is IVR carrying energy to the NH-stretching mode of the adenine moiety in a subpicosecond scale, the energy build-up being sigmoidal, when H2O interacts with the uracil–NH bond. The majority of intermolecular hydrogen bonds between the base pair and H2O are weakened but unbroken during the ultrafast energy redistribution period. Lifetimes of intermolecular HB are on the order of 0.5 ps. The efficiency of IVR in the base pair is due to near-resonance between coupled CC and CN vibrations. The resonance also exists between the frequencies of H2O bend and NH stretch, thus facilitating VET. When H2O interacts with the NH bond at the adenine end of the base pair, energy flow in the reverse direction to the uracil–NH stretch is negligible, the unidirectionality discussed in terms of the effects of uracil CH stretches. The energy distributed in the CH bonds is found to be significant. The IVR process is found to be nearly temperature independent between 200 and 400 K.

Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine

Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N₄₄₄₄]⁺) or tetrabutylphosphonium ([P₄₄₄₄]⁺) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N₄₄₄₄][Ad]·2H₂O, and thymine, [P₄₄₄₄][Thy]·2H₂O, as well as the double salt cocrystal, [P₄₄₄₄]₂[Ad][Thy]·3H₂O·2HThy. The cocrystal includes the anionic [Ad^-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.

Energy decomposition analysis based on broken symmetry unrestricted density functional theory

In this paper, the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme is extended to molecular interactions in open shell singlet states, which is a challenge for many popular EDA methods due to the multireference character. Based on broken symmetry (BS) unrestricted density functional theory with a spin projection approximation, the extension scheme, named GKS-EDA(BS) in this paper, divides the total interaction energy into electrostatic, exchange-repulsion, polarization, correlation, and dispersion terms. Test examples include the pancake bond in the phenalenyl dimer, the ligand interactions in the Fe(ii)-porphyrin complexes, and the radical interactions in dehydrogenated guanine-cytosine base pairs and show that GKS-EDA(BS) is a practical EDA tool for open shell singlet systems.

Elementary lesions in DNA subunits: electron, hydrogen atom, proton, and hydride transfers

When DNA is damaged by ionizing radiation, the genes in a cell may acquire mutations or the cell could die. The smallest known DNA-damaging unit is an electron, often low-energy secondary electrons. Additional electrons and transfers involving hydrogen atoms, protons, and hydride anions can damage DNA subunits, including individual nucleobases and nucleoside pairs. Researchers would like to better understand the molecular mechanisms involved in DNA damage from ionizing radiation. In this Account, we highlight our theoretical investigations of the molecular mechanisms of DNA damage using quantum mechanical models. Our investigations use robust theoretical methods with computations conducted in the gas phase and with solution models. We calculate adiabatic electron affinities (AEAs), which describe the energetics of electronic attachment to closed-shell DNA subunits, for the free bases, nucleosides, nucleotides, base pairs, and single and double DNA strand units. Electron affinities for free nucleobases yield the order uracil > thymine > cytosine > guanine > adenine and the same order for the DNA nucleosides, mononucleotides, and nucleoside 3',5'-diphosphates. AEA values increase steadily with the size and complexity of the system because of greater hydration, glycosylation, nucleotide formation, and base pairing. We predict and experimental results partially confirm that most of the more complex and hydrated species are observable as radical anions. Our modeling studies indicate that depyrimidination reactions of radical anion nucleosides release cytosine more often than thymine. Recent experimental results support those findings. Our theoretical studies of DNA base-pair radical anions predict increases in electron affinity accompanying H bonding and solvation. Electron addition facilitates some proton transfers in these pairs, which results in strongly perturbed pairing configurations. Of all nucleobase moieties within the more complex radical anion systems, thymine is best able to retain a negative charge. Charge and spin are well-separated in some of these systems. Radical species derived via hydrogen abstraction from DNA subunits yield large AEA values because they form closed-shell anions. Our studies predict single-strand breaks following H abstraction from nucleotides. Some H-abstraction processes in the DNA base pairs lead to severe distortions in pairing configuration based on our calculations. This body of systematic theoretical studies provides realistic descriptions of some events that lead to elementary DNA lesions, while providing rationalizations for many observed phenomena. Such approaches can lead to the design of new experiments, which would contribute to our understanding of the chemical physics of nucleic acids.