Nucleation in the natural world often occurs in the presence of organic interfaces. In mineralized tissues, a range of macromolecular matrices are found in contact with inorganic phases and are believed to direct mineral formation. In geochemical settings, mineral surfaces, which are often covered with organic or biological films, surround the volume within which nucleation occurs. In the classical picture of nucleation, the presence of such interfaces is expected to have a profound effect on nucleation rates, simply because they can reduce the interfacial free energy, which controls the height of the thermodynamic barrier to nucleation of the solid phase. However, the recent discovery of a nearly monodisperse population of calcium carbonate clusters—so called pre-nucleation clusters—and the many observations of amorphous precursor phases have called into question the applicability of classical descriptions. Here we use in situ observations of nucleation on organothiol self-assembled monolayers (SAMs) to explore the energetics and pathways of calcite nucleation at organic interfaces. We find that carboxyl SAM-directed nucleation is described well in purely classical terms through a reduction in the thermodynamic barrier due to decreased interfacial free energy. Moreover, the differences in nucleation kinetics on odd and even chain-length carboxyl SAMs are attributable to relative differences in these energies. These differences arise from varying degrees of SAM order related to oxygen-oxygen interactions between SAM headgroups. In addition, amorphous particles formed prior to or during crystal nucleation do not grow and are not observed to act as precursors to the crystalline phase. Instead, calcite appears to nucleate independently. These results imply that the recently proposed model of calcite formation as a non-classical process, one which proceeds via aggregation of stable pre-nucleation clusters that form an amorphous precursor from which the crystalline phase emerges, is not applicable to template-directed nucleation on carboxyl SAMs and does not provide a universal description of calcite formation.

First-principles calculations and molecular-dynamics simulations are employed in this study to further our understanding of the crystal structure and orientational order of carbonate ions in vaterite, which is the least stable polymorph of calcium carbonate. The structural details of vaterite have been controversial but they are prerequisite for investigating and understanding the processes involving vaterite crystal nucleation, growth, and stabilization at a molecular level. The first-principles calculations, using density functional theory with the plane-wave pseudopotential method, are carried out to calculate relative thermodynamic stabilities of proposed structures. Molecular-dynamics simulations with classical empirical potentials, larger computational cells, and fully flexible models at different temperatures are performed to investigate the orientation and order-disorder of the carbonate ions. The results show that the previously accepted structure with disordered CO₃ ions, which are randomly distributed over three orientations parallel to the c axis, is only metastable. By applying a temperature annealing technique to the molecular dynamics simulations, a more stable structure with fully ordered carbonate ions is found that has a hexagonal superstructure. The space group of this newly derived vaterite structure is P6₅22 (no. 179) with Z = 18 and cell dimensions of √3 times in a, and 3 times in c of the previous suggested disordered structure. Comparison of experimental observations of X-ray diffraction patterns, enthalpies of transformation to calcite, and volume change by heat treatment with our theoretical calculations indicates that freshly made vaterite is often carbonate-disordered and metastable and can fully or partially transform to a carbonate-ordered structure by aging and heating.