John H. Harding

Growth of ZnO thin films: Experiment and theory

Many recent studies of ZnO thin film growth have highlighted a propensity for forming c-axis aligned material, with the crystal morphology dominated by the polar {0001} surface. This is illustrated here for ZnO thin films grown by pulsed laser deposition methods, and put to advantage by using such films as templates for aligned growth of ZnO nanorods. Complementary to such experiments, we report results of periodic ab initio density functional theory calculations on thin films of ZnO which terminate with the (0001), (000), (100) and (110) surfaces. Thin (<18 layer) films which terminate with the polar (0001) and (000) surfaces are found to be higher in energy than corresponding films in which these polar surfaces flatten out forming a new ‘graphitic’-like structure in which the Zn and O atoms are coplanar and the dipole is removed. For thinner (<10 layer) slab sizes this coplanar surface is found to be lower in energy than the non-polar (100) and (110) surfaces also. The transition between the lowest energy geometries as the ZnO film thickness increases is investigated, and possible consequences for the growth mechanism discussed.

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 Much of it is long out of date, but D’Arcy Thompson makes a point of fundamental importance in his discussion of the morphology of inorganic crystals in biological systems.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

A new potential model for barium titanate and its implications for rare-earth doping

We present a new set of interatomic potentials for modelling the BaTiO3 perovskite system. The potential model is fitted using multiple parameters to a range of experimental and ab initio data including the cohesive energy and lattice parameters of BaTiO3, BaO and rutile TiO2. This procedure provides internal consistency to the potential model for studying the energetics of the defect chemistry of BaTiO3. This is tested by examining rare-earth cation doping in BaTiO3 and considering all five possible compensation schemes. Our simulations are in agreement with experiment and predict small rare-earth cations to dope exclusively on the Ti site; medium sized rare-earth cations to dope on both the Ti and Ba sites and large rare-earth cation doping exclusively on the Ba-site. For Ba-site substitution the simulations predict electron compensation to be energetically unfavourable compared to the formation of Ti vacancies.

Tuning hardness in calcite by incorporation of amino acids

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

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.

The challenge of biominerals to simulations

Biomaterials are hierarchical systems whose structure and properties represent a major challenge to simulation. We briefly discuss the remarkable experimental data now available both on the structure, formation and properties of biominerals. In the light of this we discuss current attempts to simulate biomaterials at atomic and meso length scales and timescales and the range of physical effects that are important in producing biomaterials. We emphasise the importance of obtaining robust forcefields for these systems and the sensitivity of simulations to the forcefields used. We conclude by suggesting future directions for the field and remaining problems to be solved.

Effects of cationic substitution on structural defects in layered cathode materials LiNiO2

The electrochemical properties of layered rock salt cathode materials are strongly influenced by defects. The three most common defects in LiNiO2-based compounds, namely extra Ni, Li–Ni anti-site and oxygen vacancy defects have been investigated. The calculated defect formation energies are very low in LiNiO2, consistent with the difficulty in synthesizing stoichiometric defect-free LiNiO2. A systematic study is conducted to examine the effect of Co, Mn and Al substitution on defect formation. It is shown that the presence of Ni2+ in the Li layer can be rationalized using ideas of superexchange interactions. In addition, a correlation between oxygen vacancy formation energy and oxygen charge is noted. This explains the better thermal stability obtained by early transition metal or Al substitutions.

Protein sequences bound to mineral surfaces persist into deep time

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI: http://dx.doi.org/10.7554/eLife.17092.001

Simulations of calcite crystallization on self-assembled monolayers.

This paper presents simulations of calcium carbonate ordering in contact with self-assembled monolayers. The calculations use potential-based molecular dynamics to model the crystallization of calcium carbonate to calcite expressing both the (00.1) and (01.2) surfaces. The effect of monolayer properties: ionization; epitaxial matching; charge density; and headgroup orientation on the crystallization process are examined in detail. The results demonstrate that highly charged surfaces are vital to stimulate ordering and crystallization. Template directed crystallization requires charge epitaxy between both the crystal surface and the monolayer. The orientation of the headgroup appears to make no contribution to the selection of the crystal surface.