Motion of the hydrogen bond proton in cytosine and the transition between its normal and imino states

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base...

We propose a model for the photo-deactivation mechanism for DNA based upon accurate quantum chemical and molecular dynamical evaluations of model Watson/Crick nucleoside pairs and stacked pairs. Our results corroborate recent ultrafast experimental studies on DNA oligonucleotides and suggest that following photo-excitation to a local $\pi-\pi^*$ state, the excitation is rapidly delocalized over several (3-4) bases on an ultrafast time-scale. However, this delocalized state is...

Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of protonation on the electronic properties of the DNA basepairs to probe for possible molecular electronics applications. We find that, under mild acidic pH conditions, the A:T basepair shows excellent rectification behaviour which is, however, ab...

Ab initio molecular dynamics including non-adiabatic and spin-orbit couplings on equal footing is used to unravel the deactivation of cytosine after UV light absorption. Intersystem crossing (ISC) is found to compete directly with internal conversion in tens of femtoseconds, thus making cytosine the organic compound with the fastest triplet population calculated so far. It is found that close degeneracy between singlet and triplet states can more than compensate for very smal...

The conformational and vibrational properties of 6-azaCytidine (6-azaC) and Cytidine (Cyt) have been studied in gas phase and aqueous environment. The two most stable conformers of each molecule have been identified and investigated in more details. The stability order of the two most stable conformers of both molecules is changing going from gas phase to solution. The first solvation shell of both molecules has been studied using QM/MM-MD (Quantum Mechanics/Molecular Mechani...

We have analyzed the low-energy electron attachment to wobble base pairs using the equation motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electro...

Work on the chemical evolution of pre-biotic molecules remains incomplete since the major obstacle is the lack of adequate knowledge of rate coefficients of various reactions which take place in interstellar conditions. In this work, we study the possibility of forming three pyrimidine bases, namely, cytosine, uracil and thymine in interstellar regions. Our study reveals that the synthesis of uracil from cytosine and water is quite impossible under interstellar circumstances....

In a recent article, Zikic {\it et al.} [Phys. Rev. E {\bf 74}, 011919 (2006)] present first-principles calculations of the DNA nucleotides electrical conductance. They report qualitative and quantitative differences with previous work, in particular with that of Zwolak and Di Ventra [Nano Lett. {\bf 5}, 421 (2005)] and Lagerqvist {\it et al.} [Nano Lett. {\bf 6}, 779 (2006)]. In this comment we address the alleged discrepancies and show that Zikic {\it et al.} have seriously...

We report on our study of the electronic properties of guanine traps in the DNA surrounded by adenines. We have shown that for a typical range of DNA parameters, formation of the bound state of two holes at the same guanine trap is possible for the GGG and GGGG traps if the hole-hole interaction is weak, which can be achieved for the DNA in solutions. The origin of the two-hole bound state is the competition between the Coulomb repulsion and the phonon mediated attraction bet...

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenin...