Ionization energy, nucleotides

Murray JS, Peralta-Inga Z, Politzer P, Ekanayake K, LeBreton P (2001) Computational characterization of nucleotide bases Molecular surfaceelectrostatic potentials and local ionization energies, and local polarization energies, Int. J. Quantum Chem. 83 245-254... 

Keywords electron propagator quasiparticle approximations renormalized approximations quasiparticle virtual orbitals C60 fullerene ionization energies correlation states nucleotide electron detachment energies... 

Much of the biochemistry and biophysics of DNA relies on the electron donating properties of nucleotides, which, in the simplest sense, are reflected in ionization energies. For example, electron donation, as reflected in the susceptibility of nucleotides to electrophilic attack, plays a ubiquitous role in mechanisms of chemical mutagenesis and carcinogenesis (1,2). Similarly, nucleotide ionization is an initiating step associated with radiation induced DNA strand scission (3-6). Nucleotide electron donation and ionization is also central to mechanisms responsible for electron transport in oligonucleotides (7). 

Starting from the comparative study of the ionization constants of uracil itself as well as of its several methylated or ethylated derivatives (representing models of tautomeric forms), it may be seen (Table XVII) that uracil and uridine exist in aqueous solution in the diketo form 32. The pX values are not known for the model tautomers 27, 29, and 30, but these forms have been ruled out on the basis of UV studies. Recently the ionization constants of uracil, thymine, their derivatives and nucleotides were determined over the range 10-50°, and thermodynamic enthalpy, entropy, and free energy changes for protonation and depro-tonation of these compounds have been evaluated.93-95,332... 

The effect of solvation on the IPs of nucleotides has been investigated by Le-Breton and coworkers using a combination of photoelectron spectroscopy and computational methods. They conclude that the first and second ionization potentials of the nucleotides deoxycytidine 5 -phosphate (CMP) and deoxythymidine 5 -phosphate (TMP) arise from ionization of the negatively charged phosphate group and nucleobase, respectively, both in the gas phase and in solution. The difference in the calculated first and second ionization potentials is smaller for the hydrated versus gas phase nucleosides as a consequence of the larger solvation energy for the zwit-terion formed upon ionization of the nucleobase versus the neutral radical formed upon ionization of the phosphate. The calculated adiabatic ionization potentials for the hydrated nucleobases CMP and TMP are 5.8 and 6.0 eV, respectively, considerably lower than the gas phase nucleobase ionization potentials (Table 1). 

There is currently much interest in field desorption (FD) which describes the process of field ionization from the adsorbed state with desorption as an ion. Field desorption takes place at lower temperatures than are normally required for evaporation of a molecule and since there is also only a low energy transfer in the ionization process itself, molecular ions of high intensity are formed. A number of underivatised polar compounds of low volatility have been investigated without thermal decomposition these include nucleosides and nucleotides [132], pesticides [133] and glycosides [134]. The method has also been extended by combining pyrolysis with FD to distinguish the five bases and some of the nucleotide fragments of deoxyribonucleic acid [135]. 

FAB is a method of relatively soft ionization that has been applied to many volatile and thermally labile, biologically important compovmds over a large mass range. Although FAB-MS provides information on the molecular mass of cyclic nucleotides, it does not allow detailed structural identification. For instance, isomers often provide similar spectra. For example, the FAB mass spectra of the two isomers 3, 5 - and 2, 3 -cyclic adenosine monophosphate are practically identical. The employment of CID of ions results in mass-analyzed kinetic energy spectra (MIKES), which provide the means of differentiating these cyclic nucleotide isomers. 

The potential of laser microprobe mass spectrometry (LMMS) has been investigated for structural characterization of nucleosides and nucleotides. This technique is based on the measurement of ions formed promptly by direct desorption and ionization (DI) of solid microscopic samples. The DI process is very fast for nucleosides, which makes it possible to apply a relatively high laser energy to the sample. In the case of nucleosides, LMMS gives... 

Results from self-consistent field (SCF) molecular orbital calculations, in combination with gas-phase photoelectron data and results from post-SCF calculations have provided a basis for descriptions of the valence electronic structure of gas-phase nucleotides and of nucleotides in water-counterion clusters. These descriptions contain values for 11 to 14 of the lowest energy ionization events in the DNA nucleotides 5 -dGMP , 5 -dAMP, 5 -dCMP and 5 -dTMP . When used with an evaluation of the difference between the Gibbs free energies of hydration for the initial and final states associated with ionization, this approach also describes the influence of hydration on the energetic ordering of ionization events in nucleotides. 

The Influence of Aqueous Bulk Solvation on Nucleotide Gibbs Free Energies of Ionization... 

In the gas-phase, the lowest energy ionization event in all four of the DNA nucleotides is associated with removal of an electron from phosphate. This is consistent with the observation that the phosphate group is more negatively charged than the sugar or base groups. 

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