Characterising the geometric diversity of functional groups in chemical databases

Summary We have developed a program, HookSpace, which provides a simplistic approach to assessing the diversity of molecular databases. The spatial relationship between pairs of intramolecular functional groups can be analysed in a variety of ways to provide both qualitative and quantitative measures of diversity. Results are described and contrasted for two commercially available databases and a combinatorial library of benzodiazepam derivatives. HookSpace highlights the main differences in molecular content of these data sets.     

Molecular beam surface ionization detection: II. Field reversal and surface ionization study of Na on Re with adsorbed oxygen

The desorption and surface ionization of Na on a polycrystalline Re surface with various amounts of adsorbed oxygen have been studied by field reversal, surface ionization and thermoelectronic emission methods. In this work the unique properties of the field reversal method are taken advantage of, i.e. that both neutral and ionic desorption rate constants can be determined simultaneously. Absolute ionization coefficients have been measured by field reversal and have been compared with values found by the “oxygen coverage” method and by static surface ionization. The application to beam flux density determinations is discussed. The simultaneous variation of the neutral and ionic desorption rate constants during oxygen adsorption and the temperature dependence of them have been studied. The Re surface in 2 × 10^?8 Torr of oxygen and at 1300–1500 K is shown to be very stable and to behave differently than in studies at higher temperatures. The very rapid change in both desorption rate constants at an effective work function Φ^e = 5.35 V is here correlated with the results of LEED experiments (Gorodetskii and Knysh) and is proposed to indicate a change from a stable Re oxide surface at low Φ^e (and oxygen coverage) to a different surface structure at higher Φ^e. Desorption energies have been determined at various values of Φ^e. The neutral desorption energy at low oxygen pressure is 2.70 ± 0.06 eV, which agress well with earlier, here corrected modulated beam results. The energy (Schottky) cycle for surface ionization is shown to be closed at low Φ^e, which has been difficult to show with other methods in any other case.     

The role of nucleobase carboradical and carbanion on DNA lesions: a theoretical study

DNA base release induced by H and OH radical addition to thymine and their corresponding electron adducts is studied at the DFT B3LYP/6-31+G(d,p) level in gas phase and in solution. H atom transfer after radical formation from C2' on the sugar to the C6 site on the base is shown to be prohibited for the radical species. Their corresponding electron adducts, albeit minor events in cellular systems, show excellent capabilities to proton transfer from C2' on the sugar to the C6 site on the base. The barriers for subsequent N-glycosidic bond dissociation range from 0.1 to 1.6 kcal mol(-1) at the B3LYP level and around 5 kcal mol(-1) using the BB1K functional, implying that these reactions can serve as a source to abasic sites. Analysis of bond dissociation energies show that all the reactions are exothermic, which is consistent with the changes in N-glycosidic bond lengths during the proton-transfer reactions. Bulk solvation plays a reverse influence on proton transfer and the bond rupture reactions. Molecular orbitals, NPA charges, and electron affinities are calculated to shed further light on the properties leading up to the intramolecular reactions.