A CASPT2 study of the excited states of adenine tautomers with silver ions

Nonconventional Hydrogen Bonds between Silver Anion and Nucleobases: Size-Selected Anion Photoelectron Spectroscopy and Density Functional Calculations

We conducted combined gas-phase anion photoelectron spectroscopy and density functional theory studies on nucleobase-silver complexes. The most probable structures of the nucleobase-Ag^- complexes were determined by comparing the theoretical calculations with the experimental measurements. The vertical detachment energies (VDEs) of uracil-Ag^-, thymine-Ag^-, cytosine-Ag^-, and guanine-Ag^- were estimated to be 2.18 ± 0.08, 2.11 ± 0.08, 2.04 ± 0.08, and 2.20 ± 0.08 eV, respectively, based on their photoelectron spectra. Adenine-Ag^- has two isomers coexisting in the experiment; the experimental VDEs of the two isomers are 2.18 and 2.53 eV, respectively. In the most probable isomers of nucleobases-Ag^-, uracil, thymine, and cytosine interact with Ag^- anion via N-H···Ag and C-H···Ag hydrogen bonds, while adenine and guanine interact with Ag^- anion through two N-H···Ag hydrogen bonds. The N-H···Ag hydrogen bonds can be characterized as medium or strong hydrogen bonds. It is found that binding sites of the Ag anion to the nucleobases are affected by the deprotonation energies and the steric effects of two adjacent X-H groups.

DFT study and topological analysis of the bonding in DNA Hoogsteen-type base pairs

The purpose of our work is to characterize and present a theoretical comparative study of a variety of compounds based on DNA base pairs linked with some transition metal ions in gas phase: C–M–G (Cytosine–metal–Guanine) where [Formula: see text](I), Zn(II), Cd(II) and A–M–T (Adenine–metal–Thyminate) where [Formula: see text](II), Ru(I), Ni(I), Y(II), Zn(I), Cd(I), Cu(II). Geometry optimization and frequency calculations were carried out at DFT/ZORA/BLYP-D/TZ2P level. M–N and M–O bonds were investigated with the quantum chemical topology (QCT): Quantum theory of atoms in molecules (QTAIM) and electron localization functions (ELF). The hydrogen bonds: N10–H[Formula: see text]O7 for A–M–T complexes and N7–H[Formula: see text]O10 for C–M–T ones were visualized and discussed, QTAIM and ELF prove the existence of O7–H[Formula: see text]N10 hydrogen bond for some A–M–T systems, since the bond critical point (BCP) of N7–H having [Formula: see text], so it has a covalent character confirming the existence of a tautomer process of these complexes. Bonding energy [Formula: see text], Pauli repulsion [Formula: see text], electrostatic [Formula: see text], and orbital [Formula: see text] interactions were represented and compared together. Hirschfeld’s charges showed the existence of charge transfer process in the bridge moieties. It seems that, in contrast to natural base pairs that are stabilized by hydrogen bonding, Hoogsteen-type base pairs are held together by coordinative bond with metal ions.

Cytidine-Ag+-purine base complexes as studied by electrospray ionization mass spectrometry

The complexes of cytidine (C) with Ag(+) and adenosine (A), guanosine (G), inosine (In) and caffeine (Caf) were studied by electrospray ionization mass spectrometry (ESI-MS). Both collision-induced dissociation (CID) "in- source" and CID MS/MS experiments were performed. The stability of [C + G + Ag](+) and [C + In + Ag](+) ions in the gas phase was found to be much higher than that of [C + A + Ag](+) and [C + Caf + Ag](+) ions. It is reasonable to conclude that guanosine and inosine form bidentate complex with silver cation, by N7 atom and O=C6 oxygen atom, whereas adenosine and caffeine form monodentate complexes, by N3 atom of adenine and N9 atom of caffeine.

On the Bonding of First-Row Transition Metal Cations to Guanine and Adenine Nucleobases

The binding of first-row transition metal monocations (Sc+-Cu+) to N7 of guanine and N7 or N3 of adenine nucleobases has been analyzed using the hybrid B3LYP density functional theory (DFT) method. The nature of the bonding is mainly electrostatic, the electronic ground state being mainly determined by metal-ligand repulsion. M+-guanine binding energies are 18-27 kcal/mol larger than those of M+-adenine, the difference decreasing along the row. Decomposition analysis shows that differences between guanine and adenine mainly arise from Pauli repulsion and the deformation terms, which are larger for adenine. Metal cation affinity values at this level of calculation are in very good agreement with experimental data obtained by Rodgers et al. (J. Am. Chem. Soc. 2002, 124, 2678) for adenine nucleobases.