Electron ionization of the nucleobases adenine and hypoxanthine near the threshold: a combined experimental and theoretical study.

Electron ionization of the DNA nucleobase, adenine, and the tRNA nucleobase, hypoxanthine, was investigated near the threshold region (∼5-20 eV) using a high-resolution hemispherical electron monochromator and a quadrupole mass spectrometer. Ion efficiency curves of the threshold regions and the corresponding appearance energies (AEs) are presented for the parent cations and the five most abundant fragment cations of each molecule. The experimental ionization energies (IEs) of adenine and hypoxanthine were determined to be 8.70 ± 0.3 eV and 8.88 ± 0.5 eV, respectively. Quantum chemical calculations (B3LYP/6-311+G(2d,p)) yielded a vertical IE of 8.08 eV and an adiabatic IE of 8.07 eV for adenine and a vertical IE of 8.51 eV and an adiabatic IE of 8.36 eV for hypoxanthine, and the lowest energy optimized structures of the fragment cations and their respective neutral species were calculated. The enthalpies of the possible reactions from the adenine and hypoxanthine cations were also obtained computationally, which assisted in determining the most likely electron ionization pathways leading to the major fragment cations. Our results suggest that the imidazole ring is more stable than the pyrimidine ring in several of the fragmentation reactions from both adenine and hypoxanthine. This electron ionization study contributes to the understanding of the biological effects of electrons on nucleobases and to the database of the electronic properties of biomolecules, which is necessary for modeling the damage of DNA in living cells that is induced by ionizing radiation.

Factors Contributing to the Accuracy of Harmonic Force Field Calculations for Water.

An analysis of the major factors affecting the accuracy of harmonic force field computations of water is presented. By systematically varying the level of approximation in the basis set, treatment of electron correlation, core electron correlation, and relativistic correction, the underlying sources of error in the computation of harmonic vibrational frequencies for water were quantified. The convergence error due to wavefunction description with a cc-pVQZ basis set in the absence of electron correlation was 1.6 cm(-1), as determined from extending the Hartree-Fock computations to larger basis sets. The convergence error due to neglecting higher-order electronic correlation terms than are included at the CCSD(T) level using the cc-pVTZ basis set was estimated to be 4.7 cm(-1), as determined from frequency calculations up to CCSDTQ for water and literature results up to CCSDTQP for diatomic molecules. The convergence error due to omitting higher-order diffuse functions than included in aug-cc-pVQZ was found to be 3.7 cm(-1), as determined by adding more diffuse functions in larger basis sets. The error associated with neglecting core electron correlation effects (i.e., "freezing" core electrons) was 5.0 cm(-1) and with neglecting relativistic effects was 2.2 cm(-1). Due to a cancellation among these various sources of error, the harmonic frequencies for H2O computed using the CCSD(T)/aug-cc-pVQZ model chemistry were on average within 2 cm(-1) of experimentally inferred vibrational frequencies.

Molecular recognition of trigonal oxyanions using a ditopic salt receptor: evidence for anisotropic shielding surface around nitrate anion.

A ditopic, macrobicyclic receptor with adjacent anion and cation binding sites is able to extract a range of monovalent salts into chloroform solution. The structures of the receptor complexed with KAcO, LiNO(3), NaNO(3), KNO(3), and NaNO(2) are characterized in solution by NMR spectroscopy and in the solid state by X-ray crystallography. The sodium and potassium salts are bound to the receptor as contact ion-pairs, with the metal cation located in the receptor's crown ether ring and the trigonal oxyanion hydrogen bonded to the receptor NH residues. The solid-state structure of the LiNO(3) complex has a bridging water molecule between the cation and anion. In all solid-state structures, the trigonal oxyanion is not located symmetrically inside the receptor cavity. It appears that anion orientation is controlled by a complex interplay of steric factors, coordination bonding to the metal cation, and hydrogen bonding with the receptor NH residues. An important feature with this latter effect is the fact that hydrogen bonds directed toward the oxygen lone pairs on a trigonal oxyanion are stronger than hydrogen bonds to the pi-electrons. In solution, the (1)H NMR spectra of the nitrate and nitrite salt complexes are noteworthy because several receptor signals, including the NH protons, undergo unusual upfield movements in chemical shift upon complexation. This is a reflection of the diamagnetic anisotropy of these trigonal oxyanions. The magnetic shielding surface for the NO(3)(-) anion is calculated using density functional theory and shown to have a shielding region directly above the central nitrogen.