David Quigley

Stable prenucleation mineral clusters are liquid-like ionic polymers

Calcium carbonate is an abundant substance that can be created in several mineral forms by the reaction of dissolved carbon dioxide in water with calcium ions. Through biomineralization, organisms can harness and control this process to form various functional materials that can act as anything from shells through to lenses. The early stages of calcium carbonate formation have recently attracted attention as stable prenucleation clusters have been observed, contrary to classical models. Here we show, using computer simulations combined with the analysis of experimental data, that these mineral clusters are made of an ionic polymer, composed of alternating calcium and carbonate ions, with a dynamic topology consisting of chains, branches and rings. The existence of a disordered, flexible and strongly hydrated precursor provides a basis for explaining the formation of other liquid-like amorphous states of calcium carbonate, in addition to the non-classical behaviour during growth of amorphous calcium carbonate.

Gas hydrate nucleation and cage formation at a water/methane interface

Nucleation of gas hydrates remains a poorly understood phenomenon, despite its importance as a critical step in understanding the performance and mode of action of low dosage hydrate inhibitors. We present here a detailed analysis of the structural and mechanistic processes by which gas hydrates nucleate in a molecular dynamics simulation of dissolved methane at a methane/water interface. It was found that hydrate initially nucleates into a phase consistent with none of the common bulk crystal structures, but containing structural units of all of them. The process of water cage formation has been found to correlate strongly with the collective arrangement of methane molecules.

Metadynamics simulations of ice nucleation and growth

The metadynamics method for accelerating rate events in molecular simulations is applied to the problem of ice freezing. We demonstrate homogeneous nucleation and growth of ice at 180 K in the isothermal-isobaric ensemble without the presence of external fields or surfaces. This result represents the first report of continuous and dynamic ice nucleation in a system of freely evolving density. Simulations are conducted using a variety of periodic simulation domains. In all cases the cubic polymorph ice I(c) is grown. The influence of boundary effects on estimates of the nucleation free energy barrier are discussed in relation to differences between this and earlier work.

Computational Techniques at the Organic−Inorganic Interface in Biomineralization

Just over ninety years ago, the first edition of D’Arcy Thompson’s book On Growth and Form appeared. Much of it is long out of date, but D’Arcy Thompson makes a point of fundamental importance in his discussion of the morphology of inorganic crystals in biological systems. He points out that the deposition of minerals in the living body, the complex shapes and symmetries often seen, cannot be explained by simple ideas of crystal packing. He speculates (and in 1919 it could be no more than speculation) on the importance of “directing forces”, using the analogy of ordering in liquid crystals discussed in the work of Lehman. In some cases, it was already clear that a pre-existing template controlled the growth of the inorganic material and D’Arcy Thompson shows how the complex forms of the silicate skeletons of sponges and radiolarians can be explained using simple models based on froths and bubbles that somehow constrain the growth of the inorganic material in their interstices. This presence of some controlling growth mechanism distinguishes two kinds of biomineralization process. Biologically induced mineralization occurs when minerals form as a byproduct of the activity of cells or their interaction with the surrounding environment. The morphologies and phases observed are usually similar to those seen in nonbiological systems. Biologically controlled mineralization is regulated by the organism, and the resulting structures have a physiological function (or sometimes functions). In this review, we are concerned only with the second case, biologically controlled mineralization. * Address for corresponding author: Department of Engineering Materials, Sir Robert Hadfield Building, University of Sheffield, Mappin St., Sheffield S1 3JD, U.K. Telephone: +44 114 222 5957. Fax: +44 114 222 5943. E-mail: j.harding@sheffield.ac.uk. Chem. Rev. 2008, 108, 4823–4854 4823

Free energy and structure of calcium carbonate nanoparticles during early stages of crystallization

We introduce a metadynamics based scheme for computing the free energy of nanoparticles as a function of their crystalline order. The method is applied to small nanoparticles of the biomineral calcium carbonate to determine the preferred structure during early stages of crystal growth. For particles 2 nm in diameter, we establish a large energetic preference for amorphous particle morphologies. Particles with partial crystalline order consistent with vaterite are also observed with substantially lower probability. The absence of the stable calcite phase and stability of the amorphous state support recent conjectures that calcite formation starts via the deposition of amorphous calcium carbonate.

Langevin Dynamics in Constant Pressure Extended Systems

The advantages of performing Langevin dynamics in extended systems are discussed. A simple Langevin dynamics scheme for producing the canonical ensemble is reviewed, and is then extended to the Hoover ensemble. We show that the resulting equations of motion generate the isobaric-isothermal ensemble. The Parrinello-Rahman ensemble is then discussed and we show that despite the presence of intrinsic probability gradients in this system, a Langevin dynamics approach samples the extended phase space in the correct fashion. The implementation of these methods in the ab initio plane wave density functional theory code CASTEP [M. D. Segall, P. L. D. Lindan, M. J. Probert, C. J. Pickard, P. J. Hasnip, S. J. Clarke, and M. C. Payne, J. Phys.: Condens. Matter 14, 2717 (2003)] is demonstrated.

Metadynamics simulations of calcite crystallization on self-assembled monolayers

We show that recent developments in the application of metadynamics methods to direct simulations of crystallization make it possible to predict the orientation of crystals grown on self-assembled monolayers. In contrast to previous studies, the method allows for dynamic treatment of the organic component and the inclusion of explicit surface water without the need for computationally intensive interfacial energy calculations or prior knowledge of the interfacial structure. The method is applied to calcite crystallization on carboxylate terminated alkanethiols arrayed on Au (111). We demonstrate that a dynamic treatment of the monolayer is sufficient to reproduce the experimental results without the need to impose epitaxial constraints on the system. We also observe an odd-even effect in the variation of selectivity with organic chain length, reproducing experimentally observed orientations in both cases. Analysis of the ordering process in our simulations suggests a cycle of mutual control in which both the organic and mineral components induce complementary local order across the interface, leading to the formation of a critical crystalline region. The influence of pH, together with some factors that might affect the range of applicability of our method, is discussed.

Sampling the structure of calcium carbonate nanoparticles with metadynamics

Metadynamics is employed to sample the configurations available to calcium carbonate nanoparticles in water, and to map an approximate free energy as a function of crystalline order. These data are used to investigate the validity of bulk and ideal surface energies in predicting structure at the nanoscale. Results indicate that such predictions can determine the structure and morphology of particles as small as 3-4 nm in diameter. Comparisons are made to earlier results on 2 nm particles under constant volume conditions which support nanoconfinement as a mechanism for enhancing the stability of amorphous calcium carbonate. Our results indicate that crystalline calcitelike structure is thermodynamically preferred for nanoparticles as small as 2 nm in the absence of nanoconfinement.

A metadynamics based approach to sampling crystallisation events

We discuss the practicalities of applying the metadynamics method to sampling crystallisation events in molecular systems. Suitable choices for collective coordinates are presented along with criteria for their parameterisation. Issues arising from finite-size effects are discussed with particular reference to the generation of multiple clusters when biasing global order parameters. We also consider the applicability of two methods for enhancing the accuracy of the reconstructed free-energy landscape. The discussion is illustrated with example data from freezing in the Lennard-Jones and ice–water systems.

Protein binding on stepped calcite surfaces : simulations of ovocleidin-17 on calcite {31.16} and {31.8}

Simulations using classical molecular dynamics are reported on the binding of the protein Ovocleidin-17 to calcite stepped surfaces. vicinal surfaces ({31.8} and {31.16}) are used to obtain acute and obtuse steps. The simulations demonstrate that binding is greater at the obtuse step. A range of analytical methods is used to show the importance of surface and local water structure for protein binding. We discuss the general features of molecular binding in the light of these results. Our analysis shows that it is unlikely that Ovocleidin-17 is important in controlling crystal morphology; its main role is likely to be in controlling calcite nucleation.