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

We show that the origin of electronic transitions of molecular many-body systems can be revealed by a quantified natural transition orbitals (QNTO) analysis and the electronic excitations of the total system can be mapped onto a standard orbitals set of a reference system. We further illustrate QNTO on molecular systems by studying the origin of electronic transitions of DNA moiety, thymine and thymidine. This QNTO analysis also allows us to assess the performance of various ...

This Chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full quantum dynamics to various flavours of semiclassical or ab initio molecular dynamics, each with its advantages and its limitations. As this contribution shows, the most common approach employed up-to-date to learn about the deactivation of nucl...

We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the base pairs because they account for site specificity of the binding. We adopt the Morse potential with coupling terms to construct the Hamiltonian. This model gives rise to a breather excitation, corresponding to the DNA bubble formation, wh...

In this study, structural stability, electronic, optical and vibrational properties of DNA nucleobase adsorbed Graphene Quantum Dot (GQD) has been investigated using density functional theory. Based on state-of-art electronic structure calculations, we predict order of GQD sensitivity for DNA nucleobase as Thymine > Cytosine > Guanine > Adenine. An interaction of GQD with DNA nucleobase leads to modulation in electronic energy gap. Our calculated UV/vis and IR vibrational spe...

Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced electronic overlaps or from small activation energies. In particular, we examine A- vs B-DNA, the ribbon-like structures proposed to arise from molecular stretching, the potential role of counterions in hole doping the DNA orbitals, the possibility ...

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here we employ first-principles real-time time-dependent density functional theory simulation, using a m...

We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding biomolecule, structure-dynamics-function can be reformatted as structure-stability-function. It should be specially noted that such an approach highly simplifies end widens the time interval of investigation of dynamic characteristics of macr...

On the basis of first-principles GW calculations, we study the quasiparticle properties of the guanine, adenine, cytosine, thymine, and uracil DNA and RNA nucleobases. Beyond standard G0W0 calculations, starting from Kohn-Sham eigenstates obtained with (semi)local functionals, a simple self-consistency on the eigenvalues allows to obtain vertical ionization energies and electron affinities within an average 0.11 eV and 0.18 eV error respectively as compared to state-of-the-ar...

Protons in the gap between base pairs of the double helix store the code of life by breaking the chiral symmetry that swaps the sense strand with its complementary partner. When these hydrogen bonds break during replication and transcription, pairs of protons switch sides restoring chiral symmetry and destroying genetic information. Using time-independent second-order perturbation theory, we show that the observed rate of such spontaneous mutations follows in the sudden appro...

Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the breathing of DNA, are generally localized and, microscopically, are due to the breaking of the hydrogen bonds linking the base pairs (\emph{bps}). I apply imaginary time path integral techniques to a mesoscopic Hamiltonian which accounts for ...