Electron-Impact Total Ionization Cross Sections of Molecular Ions.

The Binary-Encounter-Bethe (BEB) model for electron-impact total ionization cross sections of neutral molecules has been modified for molecular positive ions. The total ionization cross sections for [Formula: see text], [Formula: see text], CD(+), and CO(+) from the modified BEB formula are compared to available experimental data. The theory is in good agreement with experimental data on [Formula: see text], [Formula: see text], and CD(+), but the experimental data by Belic et al. on [Formula: see text], and CO(+) are lower than the theory. The large difference between the theory and experiment on CO(+) is a strong indication of the dominance of the dissociative ionization channel, CO(+)→C(+)+O(+), which was not included in the experiment.

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference.

The internal motions of the double-stranded DNA oligomer (dCdG)3 (dC, deoxycytidylate; dG, deoxyguanylate) in the B and Z forms have been calculated in the harmonic approximation. A complete vibrational analysis has been made, and the resulting normal mode frequencies have been used to evaluate the vibrational entropy of B and Z DNA. The greater flexibility of the B DNA hexamer leads to an entropic stabilization relative to the stiffer Z DNA hexamer of 22 calories per mole per kelvin at 300 K. The calculated value is of the same order as that (21 to 27 calories per mole per kelvin) obtained from nuclear magnetic resonance measurements on the methylated duplexes (m5dCdG)3 and (dCdGm5dCdGdCdG). This result demonstrates the importance of internal motions, which have been neglected in earlier studies of the transition from B to Z DNA, in the stability of different nucleic acid conformers.

Dynamics of DNA oligomers.

The techniques of molecular and harmonic dynamics are used to study the internal mobility of three double-stranded DNA hexamers. A 60 ps molecular dynamics simulation and a normal mode description of d(CpGpCpGpCpG)2 in the B conformation characterize the atomic fluctuations of this structure. A comparison between the two approaches validates the harmonic results at room temperature. Detailed examination of the normal modes indicates that only the low-frequency modes are needed to determine atomic fluctuations. A harmonic analysis is made of d(CpGpCpGpCpG)2 in the Z conformation and of d(TpApTpApTpA)2 in the B conformation using only the low-frequency modes. The atomic fluctuations of the three alternating pyrimidine-purine helices are compared and the dependence on conformation and sequence are discussed. The insights which theoretical calculations can provide for the interpretation of experimental results are explored.