Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes.

Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.

Low-energy-barrier proton transfer induced by electron attachment to the guanine...cytosine base pair.

The photoelectron spectrum of the anion of the guanine...cytosine base pair (GC)(*-) is recorded for the first time. The observed variation in the spectral peak-height ratios with the source conditions suggests the presence of two or more anionic isomers. Two maxima of the broad bands in the photoelectron spectrum were measured at about 1.9 and about 2.6 eV. These values are very well reproduced by the vertical detachment energies of the B3LYP/6-31++G(d,p) calculated low-energy anionic structures, which are 1) the Watson-Crick base-pair anion with proton transferred from N1 of guanine to N3 of cytosine, 2) its analogue in which the proton is transferred from N9 of guanine to N7 of guanine, and 3) the global minimum geometry, which is formed from the latter anion by rotation of guanine about the axis approximately defined by C2 of guanine and C4 of cytosine. Furthermore, a minor difference in the stabilities of the two lowest energy anions explains the experimentally observed source (temperature) dependence of the PES spectrum. A rational procedure, based on the chemistry involved in the formation of anionic dimers, which enables the low-energy anions populated in the photoelectron spectrum to be identified is proposed. In contrast to the alternative combinatorial approach, which in the studied case would lead to carrying out quantum chemical calculations for 2000-2500 structures, the procedure described here reduces the computational problem to only 15 geometries.

Valence anions of 9-methylguanine-1-methylcytosine complexes. Computational and photoelectron spectroscopy studies.

The photoelectron spectrum for the radical anion of 9-methylguanine-1-methylcytosine, MGMC(-), was recorded for the first time. To interpret the experimental results, B3LYP/6-31++G(d,p) level computational studies were carried out for the neutral and anionic complexes of MGMC/MGMC(-) stabilized by three hydrogen bonds and comprising canonical or low-energy tautomeric forms of the methylated nucleobases. The visualization of singly occupied molecular orbitals for the MGMC(-) anions indicates that they are valence-bound species since the excess electron is localized on a pi* orbital of cytosine. All but one of the studied anionic complexes are adiabatically stable at the applied B3LYP level of theory. The intensity maximum of the broad band in the photoelectron spectrum was measured at 2.1 eV. This value is very well reproduced by the calculated vertical detachment energy of the calculated global minimum geometry of the MGMC(-) anion. This structure is the Watson-Crick base pair anion with proton transferred from the N1 atom of guanine to the N3 site of cytosine. The calculated adiabatic electron affinities span a range of 0.39-0.60 eV. The consequences of electron attachment to the AT or GC base pairs incorporated within DNA are briefly discussed in the context of DNA damage by low-energy electrons.

[Interactions of aluminofluoride complexes (ALFx) with high-energy compounds (ADP, ATP) as revealed by molecular modeling]. / Oddzialywanie kompleksów glinowo-fluorkowych (ALFXx) na zwiazki wysokoenergetyczne (ADP, ATP) oceniane przy zastosowaniu modelowania molekularnego.

INTRODUCTION: Aluminofluoride complexes (AlFx) are toxic substances at the cellular and subcellular level, apparently implicated in degeneration of the nervous system. The present study focused on direct interactions with A1Fx of two common adenine nucleotides: adenosine diphosphate and adenosine triphosphate, both of which play an important role in many biochemical processes. The aim was to search for interactions between ADP-AlIF and ATP-AlFx complexes depending on the environment of the reaction. MATERIAL AND METHODS: Modern HyperChem computer software was used allowing for the computation of heat of formation and bond energy. Results. The strongest bonds in vacuum were calculated for ADP-AIF4 ', ADP-AIF3 and ATP-AlF3. In water, the strongest bonds were found for ADP-AF3 and ATP-AlF3. Due to inhibition of metabolic processes, stable bonds between those molecules are less advantageous than labile ones. Nevertheless, strong bonds seem to be associated with reduced toxicity of AlFx complexes.