Interaction of cations with 2′-deoxythymidine nucleoside and analysis of the nature and strength of cation bonds

Dual-Metal Electrolytes for Hybrid-Ion Batteries: Synergism or Antagonism?

The construction of hybrid metal-ion batteries faces a plethora of challenges. A critical one is to unveil the solvation/desolvation processes at the molecular level in electrolytes that ensure efficient transfer of several types of charge carriers. This study reports first results on simulations of mixed-ion electrolytes. All combinations of homo- and hetero-binuclear complexes of Li⁺ , Na⁺ and Mg²⁺ , solvated with varying number of ethylene carbonate (EC) molecules are modeled in non-polar and polar environment by means of first principles calculations and compared to the mononuclear analogues in terms of stability, spatial organization, charge distribution and solvation/desolvation behavior. The used PF₆ ^- counterion is shown to have minor impact on the geometry of the complexes. The desolvation energy penalty of binuclear complexes can be lowered by the fluoride ions, emerging upon the PF₆ ^- decay. These model investigations could be extended to rationalize the solvation structure and ionic mobility in dual-ion electrolytes.

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results.

Electronic Structure Insights into the Solvation of Magnesium Ions with Cyclic and Acyclic Carbonates

A computational framework to rank the solvation behavior of Mg(2+) in carbonates by using molecular dynamics simulations and density functional theory is reported. Based on the binding energies and enthalpies of solvation calculated at the M06-2X/6-311++G(d,p) level of theory and the free energies of solvation from ABF-MD simulations, we find that ethylene carbonate (EC) and the ethylene carbonate:propylene carbonate (EC:PC) binary mixture are the best carbonate solvents for interacting with Mg(2+) . Natural bond orbital and quantum theory of atoms in molecules analyses support the thermochemistry calculations with the highest values of charge transfer, perturbative stabilization energies, electron densities, and Wiberg bond indices being observed in the Mg(2+) (EC) and Mg(2+) (EC:PC) complexes. The plots of the noncovalent interactions indicate that those responsible for the formation of Mg(2+) carbonate complexes are strong-to-weak attractive interactions, depending on the regions that are interacting. Finally, density of state calculations indicate that the interactions between Mg(2+) and the carbonate solvents affects the HOMO and LUMO states of all carbonate solvents and moves them to more negative energy values.

Glycosidic bond cleavage in deoxynucleotides: effects of solvent and the DNA phosphate backbone in the computational model

Density functional theory (B3LYP) was employed to examine the hydrolysis of the canonical 2'-deoxynucleotides in varied environments (gas phase or water) using different computational models for the sugar residue (methyl or phosphate group at C5') and nucleophile (water activated through full or partial proton abstraction). Regardless of the degree of nucleophile activation, our results show that key geometrical parameters along the reaction pathway are notably altered upon direct inclusion of solvent effects in the optimization routine, which leads to significant changes in the reaction energetics and better agreement with experiment. Therefore, despite the wide use of gas-phase calculations in the literature, small model computational work, as well as large-scale enzyme models, that strive to understand nucleotide deglycosylation must adequately describe the environment. Alternatively, although inclusion of the phosphate group at C5' also affects the geometries of important stationary points, the effects cancel to yield unchanged deglycosylation barriers, and therefore smaller computational models can be used to estimate the energy associated with nucleotide deglycosylation, with the 5' phosphate group included if full (geometric) details of the reaction are desired. Hydrogen-bonding interactions with the nucleobase can significantly reduce the barrier to deglycosylation, which supports suggestions that discrete hydrogen-bonding interactions with active-site amino acid residues can play a significant role in enzyme-catalyzed nucleobase excision. Taken together with previous studies, the present work provides vital clues about the components that must be included in future studies of the deglycosylation of isolated noncanonical nucleotides, as well as the corresponding enzyme-catalyzed reactions.