Paolo Raiteri

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes.

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.

Water Is the Key to Nonclassical Nucleation of Amorphous Calcium Carbonate

Calcium carbonate is a ubiquitous mineral that represents one of the most significant biominerals, a major contributor to carbon sequestration through geological deposits, and a technological hindrance as a result of scale formation. Amorphous calcium carbonate is intimately involved in the nucleation and growth of this material, yet much remains undiscovered regarding the atomic detail. Through dynamical simulation we demonstrate that nucleation of amorphous calcium carbonate follows a nonclassical pathway. This arises from the addition of ion pairs to clusters exhibiting a consistently exothermic free energy that persists with increasing particle size. Furthermore, the disruption of the surrounding water of solvation by the atomically rough surface reduces the barrier to growth to the order of ambient thermal energy, thereby allowing the amorphous phase to grow faster than crystalline polymorphs. Amorphous calcium carbonate nanoparticles are also found to exploit size-dependent water content to render itself more stable than the favored bulk phase, calcite, below a critical diameter of close to 4 nm.

Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions

Making Crystals The initial transition from a disordered solution to the formation of nuclei that grow into crystals continues to be a puzzle. Recent experiments suggested the formation of stable ordered clusters that appear prior to the formation of the first nuclei. Wallace et al. (p. 885; see the Perspective by Myerson and Trout) used molecular dynamics to look at the potential structure and dynamics of these clusters and lattice gas simulations to explore the population dynamics of the cluster populations prior to nucleation. A liquid-liquid phase separation process was observed whereby one phase becomes more concentrated in ions and becomes the precursor for nuclei to form. The preordering seen during calcium carbonate crystallization may be due to a liquid-liquid separation process. [Also see Perspective by Myerson and Trout] Recent experimental observations of the onset of calcium carbonate (CaCO3) mineralization suggest the emergence of a population of clusters that are stable rather than unstable as predicted by classical nucleation theory. This study uses molecular dynamics simulations to probe the structure, dynamics, and energetics of hydrated CaCO3 clusters and lattice gas simulations to explore the behavior of cluster populations before nucleation. Our results predict formation of a dense liquid phase through liquid-liquid separation within the concentration range in which clusters are observed. Coalescence and solidification of nanoscale droplets results in formation of a solid phase, the structure of which is consistent with amorphous CaCO3. The presence of a liquid-liquid binodal enables a diverse set of experimental observations to be reconciled within the context of established phase-separation mechanisms.

Anisotropy of Earth's D'' layer and stacking faults in the MgSiO3 post-perovskite phase.

The post-perovskite phase of (Mg,Fe)SiO3 is believed to be the main mineral phase of the Earths lowermost mantle (the D″ layer). Its properties explain numerous geophysical observations associated with this layer—for example, the D″ discontinuity, its topography and seismic anisotropy within the layer. Here we use a novel simulation technique, first-principles metadynamics, to identify a family of low-energy polytypic stacking-fault structures intermediate between the perovskite and post-perovskite phases. Metadynamics trajectories identify plane sliding involving the formation of stacking faults as the most favourable pathway for the phase transition, and as a likely mechanism for plastic deformation of perovskite and post-perovskite. In particular, the predicted slip planes are {010} for perovskite (consistent with experiment) and {110} for post-perovskite (in contrast to the previously expected {010} slip planes). Dominant slip planes define the lattice preferred orientation and elastic anisotropy of the texture. The {110} slip planes in post-perovskite require a much smaller degree of lattice preferred orientation to explain geophysical observations of shear-wave anisotropy in the D″ layer.

Dehydroxylation of kaolinite to metakaolin—a molecular dynamics study

The thermally induced transformation of kaolinite to metakaolin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal of structural water through dehydroxylation produces a distortion or buckling effect in the 1 : 1 Al–Si layers, which is due to the migration of the aluminium into vacant sites provided by the inter-layer spacing. The structural change is characterized by a loss of crystallinity and a concomitant change in aluminium coordination from octahedral to tetrahedral, with this study confirming the presence of 5-fold aluminium within the metakaolin structure. The degree and probability of Al migration are proportional to the amount of local disorder within the structure, which is governed by the degree of local hydroxyl group loss. This results in the formation of aluminium clusters within the layers. This study proposes that instead of a uniform structure, metakaolin exhibits regions of differing aluminium concentrations, which can have major effects in the reaction chemistry at those sites.

Simulation of structural phase transitions by metadynamics

Abstract We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illus trated on various kinds of crystals and the advantages with respect to previous schemes are emphasized. The relevance of the new method for the problem of crystal structure prediction is also discussed.

Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories

Mineral growth and dissolution are often treated as occurring via a single reversible process that governs the rate of reaction. We show that multiple distinct intermediate states can occur during both growth and dissolution. Specifically, we used metadynamics, a method for efficiently exploring the free-energy landscape of a system, coupled to umbrella sampling and reactive flux calculations to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped barite (BaSO(4)) surface. The activation energies calculated for the rate-limiting reactions, which are different for attachment and detachment, precisely match those measured experimentally during both growth and dissolution. These results can potentially explain anomalous non-steady-state mineral reaction rates observed experimentally and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.

The thermal stability of lattice-energy minima of 5-fluorouracil: Metadynamics as an aid to polymorph prediction

This paper reports a novel methodology for the free-energy minimization of crystal structures exhibiting strong, anisotropic interactions due to hydrogen bonding. The geometry of the thermally expanded cell was calculated by exploiting the dependence of the free-energy derivatives with respect to cell lengths and angles on the average pressure tensor computed in short molecular dynamics simulations. All dynamic simulations were performed with an elaborate anisotropic potential based on a distributed multipole analysis of the isolated molecule charge density. Changes in structure were monitored via simulated X-ray diffraction patterns. The methodology was used to minimize the free energy at ambient conditions of a set of experimental and hypothetical 5-fluorouracil crystal structures, generated in a search for lattice-energy minima with the same model potential. Our results demonstrate that the majority ( approximately 75%) of lattice-energy minima are thermally stable at ambient conditions, and hence, the free-energy (like the lattice-energy) surface is complex and highly undulating. Metadynamics trajectories (Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562) started from the free-energy minima only produced transitions that preserved the hydrogen-bonding motif, and thus, further developments are needed for this method to efficiently explore such free-energy surfaces. The existence of so many free-energy minima, with large barriers for the alteration of the hydrogen-bonding motif, is consistent with the range of motifs observed in crystal structures of 5-fluorouracil and other 5-substituted uracils.

A new structural model for disorder in vaterite from first-principles calculations

Both of the previously proposed Pbnm and P6522 ordered structures for vaterite are found to be unstable transition states using first-principles methods. Five stable structures are located, the lowest energy one being of P3221 symmetry. Since interconversion between these structures requires only thermal energy, this provides an additional source of disorder within the vaterite structure.