QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester A_N + D_N Associative Mechanism with an O2′ H Internal Proton Transfer

The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2′ oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3′–O2′ cyclic phosphate and a O5′ hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2′ migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) A_N + D_N mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10¹¹ difference in rate strongly supporting the less accepted triester mechanism

Ion Association in AlCl₃ Aqueous Solutions from Constrained First-Principles Molecular Dynamics

The Car–Parrinello-based molecular dynamics (CPMD) method was used to investigate the ion-pairing behavior between Cl^– and Al³⁺ ions in an aqueous AlCl₃ solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, with the internuclear separation (<i>r</i>_Al–Cl) between the Al³⁺ ion and one of the Cl^– ions held constant. The calculated potential of mean force (PMF) of the Al³⁺–Cl^– ion pair shows a global minimum at <i>r</i>_Al–Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent-separated ion pairs (SSIPs) are identified at <i>r</i>_Al–Cl = 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration-shell intervals of the Al³⁺ cation, suggesting that the Cl^– ion is inclined to reside in regions with low concentrations of water molecules, that is, between the first and second hydration shells of Al³⁺ and between the second shell and the bulk. A detailed analysis of the solvent structure around the Al³⁺ and Cl^– ions as a function of <i>r</i>_Al–Cl is presented. The results are compared to structural data from X-ray measurements and unconstrained CPMD simulations of single Al³⁺ and Cl^– ions and AlCl₃ solutions. The dipole moments of the water molecules in the first and second hydration shells of Al³⁺ and in the bulk region and those of Cl^– ions were calculated as a function of <i>r</i>_Al–Cl. Major changes in the electronic structure of the system were found to result from the removal of Cl^– from the first hydration shell of the Al³⁺ cation. Finally, two unconstrained CPMD simulations of aqueous AlCl₃ solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes were observed in these systems, confirming their stability

Near-Quantitative Agreement of Model-Free DFT-MD Predictions with XAFS Observations of the Hydration Structure of Highly Charged Transition-Metal Ions

First-principles dynamics simulations (DFT, PBE96, and PBE0) and electron scattering calculations (FEFF9) provide near-quantitative agreement with new and existing XAFS measurements for a series of transition-metal ions interacting with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This analysis does not require either the development of empirical interparticle interaction potentials or structural models of hydration. However, it provides consistent parameter-free analysis and improved agreement with the higher-<i>R</i> scattering region (first- and second-shell structure, symmetry, dynamic disorder, and multiple scattering) for this comprehensive series of ions. DFT+GGA MD methods provide a high level of agreement. However, improvements are observed when exact exchange is included. Higher accuracy in the pseudopotential description of the atomic potential, including core polarization and reducing core radii, was necessary for very detailed agreement. The first-principles nature of this approach supports its application to more complex systems