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

The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by hydrogen bonds. Such mechanism is sensitive to the structure of nucleotide hydrogen bonds, consequently only one nucleotide sort is captured by DNA-polimerase in each event.The algorithm of this multistep selection mechanism is also analysed...

The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling through the intermolecular potential barrier is essential. We argue that in this case the enzyme excitation and internal motion facilitate proton transfer between reactants by squeezing the potential barrier which otherwise is practically impen...

We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a X-ray cry...

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the ...

Quantum theory of hydrogen atoms distribution between two complementary nucleotide bases in DNA double helix at moment of replication has been proposed in this work. It bases on two mechanisms of proton tunneling: the Andreev-Meyerovich mechanism with spontaneous phonon radiation and the Kagan-Maximov (Flynn-Stoneham) mechanism at phonon scattering. According to the presented model, the probability of proton location in shallow potential well (point mutation form) is directly...

The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the network is confined or as water interacts with surfaces. These changes have been observed to be large on a chemical scale for water confined in carbon nanotubes and in the pores of xerogel, and may play a fundamental, and neglected, role in bi...

We analyze the influence of the charge and the degree of oxidation of the surface of graphene (Gr) on its interaction with cytosine and oligonucleotide r(C)10. This is a computational study involving DFT calculations and molecular dynamics simulations. It is shown that cytosine interacts stronger with graphene oxide (GO) than with Gr, while the energy of the interaction of cytosine with GO only weakly depends on the degree of the Gr oxidation. A correlation between the shifts...

We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotential...

Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important qua...

We report a benchmark theoretical investigation of both adiabatic and vertical electron affinities of five DNA and RNA nucleobases: adenine, guanine, cytosine, thymine and uracil using state-of-the-art equation of motion coupled cluster (EOMCC) method. We have calculated the vertical electron affinity values of first five electron attached states of the DNA and RNA nucleobases and only the first electron attached state is found to be energetically accessible in gas phase. An ...