Analyzing coordination preferences of Mg2+ complexes: insights from computational and database study

The phosphodiester dissociative hydrolysis of a DNA model promoted by metal dications

CONTEXT

Phosphodiester bonds, which form the backbone of DNA, are highly stable in the absence of catalysts. This stability is crucial for maintaining the integrity of genetic information. However, when exposed to catalytic agents, these bonds become susceptible to cleavage. In this study, we investigated the role of different metal dications (Ca2⁺, Mg2⁺, Zn2⁺, Mn2⁺, and Cu2⁺) in promoting the hydrolysis of phosphodiester bonds. A minimal DNA model was constructed using two pyrimidine nucleobases (cytosine and thymine), two deoxyribose units, one phosphate group, and one metallic dication coordinated by six water molecules. The results highlight that Cu2⁺ is the most efficient in lowering the energy barrier for bond cleavage, with an energy barrier of 183 kJ/mol, compared to higher barriers for metals like Zn2⁺ (202 kJ/mol), Mn2⁺ (202 kJ/mol), Mg2⁺ (210 kJ/mol), and Ca2⁺ (223 kJ/mol). Understanding the interaction between these metal ions and phosphodiester bonds offers insight into DNA stability and organic data storage systems.

METHODS

DFT calculations were employed using Gaussian 16 software, applying the B3LYP hybrid functional with def2-SVP basis sets and GD3BJ dispersion corrections. Full geometry optimizations were performed for the initial and transition states, followed by identifying energy barriers associated with phosphodiester bond cleavage. The optimization criteria included maximum force, root-mean-square force, displacement, and energy convergence thresholds.

Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion

An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc^+/2+–water bond as a noncovalent bond while Sc³⁺–OH₂, Sc²⁺–OH, and Sc⁺–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.

Assessing the Intrinsic Strengths of Ion–Solvent and Solvent–Solvent Interactions for Hydrated Mg2+ Clusters

Information resulting from a comprehensive investigation into the intrinsic strengths of hydrated divalent magnesium clusters is useful for elucidating the role of aqueous solvents on the Mg2+ ion, which can be related to those in bulk aqueous solution. However, the intrinsic Mg–O and intermolecular hydrogen bond interactions of hydrated magnesium ion clusters have yet to be quantitatively measured. In this work, we investigated a set of 17 hydrated divalent magnesium clusters by means of local vibrational mode force constants calculated at the ωB97X-D/6-311++G(d,p) level of theory, where the nature of the ion–solvent and solvent–solvent interactions were interpreted from topological electron density analysis and natural population analysis. We found the intrinsic strength of inner shell Mg–O interactions for [Mg(H2O)n]2+ (n = 1–6) clusters to relate to the electron density at the bond critical point in Mg–O bonds. From the application of a secondary hydration shell to [Mg(H2O)n]2+ (n = 5–6) clusters, stronger Mg–O interactions were observed to correspond to larger instances of charge transfer between the lp(O) orbitals of the inner hydration shell and the unfilled valence shell of Mg. As the charge transfer between water molecules of the first and second solvent shell increased, so did the strength of their intermolecular hydrogen bonds (HBs). Cumulative local vibrational mode force constants of explicitly solvated Mg2+, having an outer hydration shell, reveal a CN of 5, rather than a CN of 6, to yield slightly more stable configurations in some instances. However, the cumulative local mode stretching force constants of implicitly solvated Mg2+ show the six-coordinated cluster to be the most stable. These results show that such intrinsic bond strength measures for Mg–O and HBs offer an effective way for determining the coordination number of hydrated magnesium ion clusters.

QM/MM investigation of ATP hydrolysis in aqueous solution

Adenosine-5'-triphosphate (ATP) hydrolysis represents a most important reaction in biology. Despite extensive research efforts, the mechanism for ATP hydrolysis in aqueous solution still remains under debate. Previous theoretical studies often predefined reaction coordinates to characterize the mechanism for ATP hydrolysis in water with Mg(2+) by evaluating free energy profiles through these preassumed reaction paths. In the present work, a nudged elastic band method is applied to identify the minimum energy path calculated with a hybrid quantum mechanics and molecular mechanics approach. Along the reaction path, the free energy profile was obtained to have a single transition state and the activation energy of 32.5 kcal/mol. This transition state bears a four-centered structure that describes a concerted nature of the reaction. In the More-O'Ferrall-Jencks diagram, the results show that the reaction proceeds through a concerted path before the system reaches the transition state and along an associative path after the transition state. In addition, the calculated reaction free energy is -7.0 kcal/mol, in good agreement with experiment, capturing the exothermic feature of MgATP(2-) hydrolysis in aqueous solution, whereas the reaction was often shown to be endothermic in the previous theoretical studies. As Mg(2+) is required for ATP hydrolysis in cells, its role in the reaction is also elucidated.