Dipole-Bound Electron Attachment to Uracil−Water Complexes. Theoretical ab Initio Study

Abstract

Ab initio calculations performed in this work found positive electron affinities for all three possible doubly H-bonded complexes of the uracil molecule with a single water molecule. In all cases the excess electron is bound by the the dipole field of the complex. No conventional stable "valence" anionic states were found with the theoretical procedure used in this work (SCF + second-order perturbation theory corrections for the electron correlation effects). The attachment of the excess electron lowers the relative energy differences between the three complexes, making their coexistence more probable. Structural changes in the uracilwater complex upon attachment of an electron were also found. The anion's equilibrium geometry had noticeably shortened hydrogen-bond lengths and a shifted orientation of the water molecule with respect to the uracil molecule compared to the neutral system.

Ab Initio Molecular Dynamics Study of Uracil in Aqueous Solution

“…The latest studies consisted of ab initio geometry optimizations of small clusters composed of a nucleic acid base (uracil, thymine, cytosine, adenine, or guanine) surrounded by a few explicit water molecules. [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] Uracil, as the structurally most simple nucleic acid base, has received a great deal of attention. Recent examples are detailed geometry optimizations of uracil·n w H 2 O complexes.…”

“…Different theoretical levels of calculation (HF, MP2, and DFT) have been considered and their results compared. The uracil·H 2 O complex 21,22, [28][29][30]35,37,38 has been a major focus, in particular the determination of the hydrophilic sites that are energetically the most favorable for hydrogen bonding to the water molecule. Calculations involving several water molecules in a variety of arrangements 23, 31,35,37,38 have also been carried out in order to gain detailed insight into the structural patterns adopted by water molecules around uracil.…”

Electron Attachment to Hydrated Oligonucleotide Dimers: Guanylyl‐3′,5′‐Cytidine and Cytidylyl‐3′,5′‐Guanosine

“…[55] The DFT approach has also been applied to elucidate the electron-capturing abilities of the A:T pair and the mA:mT pair in their tautomeric forms by Radisic et al [34] The influence of water microsolvation on the electron attachment to nucleobases has also been investigated extensively at different levels of theory. [56][57][58][59][60][61][62][63][64][65][66][67][68][69] Recently, the electron affinities of the thymine-adenine base-pair stacking between different bases were studied by the "resolution of identity formulation of MP2" (RI-MP2) approach. [70] These investigations suggest that the pyrimidines in DNA fragments have a strong tendency to capture low-energy electrons and to form electronically stable radical anions.…”

Microsolvation Pattern of the Hydrated Radical Anion of Uracil: U-(H2O)n(n= 3−5)

“…Accordingly, this highly twisted base in U3-18a is expected to be less stable. 4 . Geometry optimization resulted in 13 stable conformers for the radical anion of tetrahydrated uracil complexes ( Figure 2).…”

“…Following the structures of the most stable conformers of U -(H 2 O) 3 and U -(H 2 O) 4 , the radical anions of pentahydrated uracil were constructed on the basis of the water clusters of triad, tetrad, and pentad patterns. Nine conformers were optimized as the local minima on the potential energy surface (Figure 3).…”