![]() ![]() ![]() Our study revealed that, although the N7 site of Guanine has a good protonation propensity, N7 protonated Guanine can not occur in the stable planar base pairs due to reasons explained by the protonation induced charge redistribution in Guanine. We have extensively studied the case of protonated base pairs involving N7 protonated purines. We have noticed that the stability and hence the occurrence frequency of protonated bases do not depend only on their protonation propensity but the protonation induced modifications of stabilizing factors, such as, hydrogen bonding and pi-stacking potentials play a role of greater importance. We have further tried to correlate the site specific protonation propensity data with the occurrence frequency of the protonated bases. It considers water molecule as proton donor. On the basis of the results obtained from advanced ab-initio quantum mechanical calculations, in this study, we therefore have proposed a physicochemically relevant method of studying the thermodynamics of the process of protonation in terms of estimation of site specific protonation propensities of RNA bases. For the sake of comparative analysis and completeness, in our study, we have considered deprotonation of RNA bases as well. ![]() Significance of local pKa values of different titrable sites of different RNA bases and influence of protonation on their stabilizing factors like noncovalent interactions, have not got much attention. Moreover, these studies mainly focus on describing the process of protonation as a function of the difference between pH of the local environment and average pKa of the nucleobase. We have observed that there is a lack of relevance with the physiological context in the methods adopted in most of those studies. Quite a few efforts has been made in recent years to understand the kinetics and thermodynamics of the process of protonation and stabilization of the protonated bases. It is therefore expected that, in order to compensate the cost of protonation, the protonation induced charge redistribution and geometric changes will help the protonated base to participate in different higher order interactions such as base pair, base triple, base stack, etc. But the process of protonation of nucleobases is energetically unfavourable in physiological pH. It has been shown that, apart from the normal and modified base and noncanonical base pairs involving them, protonated bases and protonated base pairs play an important role in shaping up the complex folded structure of the RNA molecule. With the discovery of regulatory roles of RNA molecules, several scientific efforts have been made to understand its structural diversity. Our results indicate that the BN and S doped DV-Gr defect sheet will be the considered as promising candidate materials in battery applications. The bonding between metal ions and doped graphene sheets have analyzed by using QTAIM and electron localization function. Moreover, the energy gap values are increased upon the adsorption of metal ions on BN, and S doped DV-Gr defect sheet. The energy gap opened in DV-Gr defect sheet upon BN codoping is found to be 0.42 eV and 0.51 eV for S doping. The interaction between different metal ions and the doped graphene sheet is illustrated by the negative region of ESP, and the more negative region is observed in DV-Gr defect sheet which implies the strength of the metal ion adsorption. It is found that the metal ions adsorption on BN and S doped DV-Gr defect sheet have higher adsorption energy. In this study, we show the role of defects and doping in enhancing the adsorption of alkali metal ions. ![]() Herein, we have investigated the effects of metal ions adsorption on Boron-Nitrogen (BN) codoped and Sulphur (S) doped pristine (Pr), and divacancy (DV) defected graphene (Gr) sheets using density functional theory calculation (DFT). Heteroatom doped carbon materials are one of the most prominent families of material that are used in various energy-related applications. ![]()
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