New model for aspartic acid species in aqueous calcium carbonate growth environments: challenges and perspectives.

The lack of experimental data on the dynamics of aspartic acid species in water for its range of protonation states and the details of their atomic-level interaction with aqueous calcium carbonate species is a driver for accurate force field development. A classical model that is consistent with the few pieces of experimental data available and with first principles calculations has been developed. The complex dynamics of the aspartate anions relevant to biomineralization and calcium carbonate crystal growth has been explored in water, providing a quantitative description of solvation structure and free energies, including conformational free energy profiles and pairing free energies. The model has been used to probe the structure and dynamics of aqueous calcium aspartate homo- and hetero-chiral clusters, confirming their unlikelihood due to weak and water-mediated interactions. This supports the hypothesis that the formation of such clusters, observed while growing vaterite in the presence of acidic chiral amino acids, is favoured by the presence of the crystal surface.

Simulating the binding of key organic functional groups to aqueous calcium carbonate species.

The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.

Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture.

Since Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid L-Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when D-Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality amplification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.

Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.

A general method for parametrizing atomic interaction functions is presented. The method is based on an analysis of surfaces corresponding to the difference between calculated and target data as a function of alternative combinations of parameters (parameter space mapping). The consideration of surfaces in parameter space as opposed to local values or gradients leads to a better understanding of the relationships between the parameters being optimized and a given set of target data. This in turn enables for a range of target data from multiple molecules to be combined in a robust manner and for the optimal region of parameter space to be trivially identified. The effectiveness of the approach is illustrated by using the method to refine the chlorine 6-12 Lennard-Jones parameters against experimental solvation free enthalpies in water and hexane as well as the density and heat of vaporization of the liquid at atmospheric pressure for a set of 10 aromatic-chloro compounds simultaneously. Single-step perturbation is used to efficiently calculate solvation free enthalpies for a wide range of parameter combinations. The capacity of this approach to parametrize accurate and transferrable force fields is discussed.

Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.

To test and validate the Automated force field Topology Builder and Repository (ATB; http://compbio.biosci.uq.edu.au/atb/ ) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies.