Determining the Complete Stability of Calcite Kink Sites: Real vs Ideal

Abstract

Kink sites play a pivotal role in the growth and dissolution of materials at the solid−liquid interface. Despite this, little is known about the thermodynamic stability of such sites. Calcium carbonate, in the form of calcite, is one of the most abundant biominerals and a natural means of carbon sequestration in the environment. Here, we present a complete determination of the standard free energies for all 16 individual kink sites for the significant case of the calcite (101̅ 4)−water interface using both alchemical-and pathway-based simulation techniques. The results reveal the importance of distinguishing between real and ideal ionbinding free energies at surfaces, especially for calcite−water, where the interfacial potential can alter values by more than 100 kJ/mol per site. Individual kink site stabilities are found to show variations in excess of 60 kJ/mol, which can help explain the observed differences in growth rates between the two distinct steps of calcite.

High-Throughput Computational Screening of Solid-Binding Peptides

“…In addition to high sensitivity and being robust to a range of binding affinity and reasonable polypeptide lengths, an essential characteristic of a screening tool is efficiency. Enhanced sampling provides excellent accuracy and can be used on various systems as long as the method is carefully selected. , However, a new calculation needs to be performed for even the slightest change (cf. Car9 and K8AK11A), and each calculation is rather expensive and time-consuming.…”

New Insights into Calcite Dissolution Mechanisms under Water, Proton, or Carbonic Acid-Dominated Conditions

“…A number of atomic level simulations including molecular dynamics (MD) and density functional theory (DFT) calculations have been performed to unravel the mechanisms of calcite dissolution and precipitation, along with their corresponding kinetics. − These efforts include investigation of the structure of water molecules on the calcite surface, in conjunction with X-ray reflectivity (XR) and surface X-ray diffraction (SXRD). ,− Building on this foundational work, several H 2 O-promoted dissolution models have been proposed based on experimental evidence and MD or DFT calculations, as well as surface complexation models (SCM). Shiraki et al proposed, based on AFM results, that dissociative adsorption of water followed by nucleophilic attack by water breaks the bond between Ca and O of carbonate, which leads to a detachment of a hydrated [HCO 3 ·Ca] + ion pair .…”

Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling

“…The CVs represent the progress of the reaction in a low-dimensional space. The problem of slow solvent dynamics is usually addressed by including the solvent coordination numbers of relevant solutes as CVs. − However, the cost of this approach means that it can only be applied to accelerate the solvent exchange of one or two solute atoms. Moreover, since the dynamics of coordination numbers are not strictly Markovian, this approach could produce dubious free energies, especially when applied to solutes with large coordination numbers and complex solvation shells.…”