Federico Giberti

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

Uncovering molecular details of urea crystal growth in the presence of additives

Controlling the shape of crystals is of great practical relevance in fields like pharmacology and fine chemistry. Here we examine the paradigmatic case of urea which is known to crystallize from water with a needle-like morphology. To prevent this undesired effect, inhibitors that selectively favor or discourage the growth of specific crystal faces can be used. In urea the most relevant faces are the {001} and the {110} which are known to grow fast and slow, respectively. The relevant growth speed difference between these two crystal faces is responsible for the needle-like structure of crystals grown in water solution. To prevent this effect, additives are used to slow down the growth of one face relative to another, thus controlling the shape of the crystal. We study the growth of fast {001} and slow {110} faces in water solution and the effect of shape controlling inhibitors like biuret. Extensive sampling through molecular dynamics simulations provides a microscopic picture of the growth mechanism and of the role of the additives. We find a continuous growth mechanism on the {001} face, while the slow growing {110} face evolves through a birth and spread process, in which the rate-determining step is the formation on the surface of a two-dimensional crystalline nucleus. On the {001} face, growth inhibitors like biuret compete with urea for the adsorption on surface lattice sites; on the {110} face instead additives cannot interact specifically with surface sites and play a marginal sterical hindrance of the crystal growth. The free energies of adsorption of additives and urea are evaluated with advanced simulation methods (well-tempered metadynamics) allowing a microscopic understanding of the selective effect of additives. Based on this case study, general principles for the understanding of the anisotropic growth of molecular crystals from solutions are laid out. Our work is a step toward a rational development of novel shape-affecting additives.

Fast Crystallization of the Phase Change Compound GeTe by Large-Scale Molecular Dynamics Simulations

Phase change materials are of great interest as active layers in rewritable optical disks and novel electronic nonvolatile memories. These applications rest on a fast and reversible transformation between the amorphous and crystalline phases upon heating, taking place on the nanosecond time scale. In this work, we investigate the microscopic origin of the fast crystallization process by means of large-scale molecular dynamics simulations of the phase change compound GeTe. To this end, we use an interatomic potential generated from a Neural Network fitting of a large database of ab initio energies. We demonstrate that in the temperature range of the programming protocols of the electronic memories (500-700 K), nucleation of the crystal in the supercooled liquid is not rate-limiting. In this temperature range, the growth of supercritical nuclei is very fast because of a large atomic mobility, which is, in turn, the consequence of the high fragility of the supercooled liquid and the associated breakdown of the Stokes-Einstein relation between viscosity and diffusivity.

Molecular-dynamics simulations of urea nucleation from aqueous solution

Significance Nucleation from solution is a ubiquitous process that plays important roles in physics, chemistry, engineering, and material science. Despite its importance, nucleation is far from being completely understood. In this work, we combine advanced molecular-dynamics simulation techniques and theory to provide a description of urea nucleation from aqueous solution. In particular, our analysis shows that a two-step nucleation mechanism is favorable and that two polymorphs are seen to compete in the early stages of the nucleation process. In our analysis, we have derived and validated a theoretical correction to finite-size effects to compute free-energy profiles in the limit of a macroscopic system at constant supersaturation. Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Metadynamics studies of crystal nucleation

Crystallization processes are characterized by activated events, thus the application of enhanced sampling techniques such as metadynamics in order to study phenomena occurring at the molecular scale through molecular modelling. This paper provides an introduction to metadynamics and an overview of its applications in the context of crystal nucleation.

The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water

In this work, we revisit the role of nuclear quantum effects on the structural and electronic properties of the excess proton in bulk liquid water using advanced molecular dynamics techniques. The hydronium ion is known to be a weak acceptor of a hydrogen bond which gives it some hydrophobic character. Quantum effects reduce the degree of this hydrophobicity which facilitates the fluctuations of the protons along the wires compared to the classical proton. Although the Eigen and Zundel species still appear to be dominant motifs, quantum fluctuations result in rather drastic events where both transient autoionization and delocalization over extended proton wires can simultaneously occur. These wild fluctuations also result in a significant change of the electronic properties of the system such as the broadening of the electronic density of states. An analysis of the Wannier functions indicate that quantum fluctuations of neat water molecules result in transient charging with subtle similarities and differences to that of the excess proton.

Transient Polymorphism in NaCl

We introduce a new collective variable (CV) that can be used to increase the frequency with which nucleation events are observed in biased atomistic simulations. This CV forces the ions to aggregate into clusters but does not force the ions to order themselves in a particular pattern. We perform metadynamics simulations using this CV in order to examine nucleation in a solution of sodium chloride and find that for small cluster sizes the usual bulk rocksalt structure is less stable than a structure that resembles wurtzite.

1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from metadynamics.

Recent experimental evidence has shown that the nucleation of 1,3,5-tris(4-bromophenyl)benzene (3BrY) follows a two-step mechanism. In this work, the formation of clusters of 3BrY from homogeneous water and methanol solutions is simulated using metadynamics. The local structure of 3BrY molecules in the clusters is then compared with the low-temperature crystal structure of 3BrY, as well as with an alternative 3BrY high-pressure crystal packing obtained through Parrinello-Rahaman molecular dynamics simulations. It is found that the interactions between the aromatic cores of 3BrY represent the main supramolecular motif observed in both the local structure of the prenucleation clusters and in the crystalline state. Within the clusters, these interactions lead to the presence of dimers and trimers locally arranged in crystal-like configurations.

Analyzing and Driving Cluster Formation in Atomistic Simulations

In this paper a set of computational tools for identifying the phases contained in a system composed of atoms or molecules is introduced. The method is rooted in graph theory and combines atom centered symmetry functions, adjacency matrices, and clustering algorithms to identify regions of space where the properties of the system constituents can be considered uniform. We show how this method can be used to define collective variables and how these collective variables can be used to enhance the sampling of nucleation events. We then show how this method can be used to analyze simulations of crystal nucleation and growth by using it to analyze simulations of the nucleation of the molecular crystal urea and simulations of nucleation in a semiconducting alloy. The semiconducting alloy example we discuss is particular challenging as multiple nucleation centers are formed. We show, however, that our algorithm is able to detect the grain boundaries in the resulting polycrystal.

Design of Heterogeneous Chalcogenide Nanostructures with Pressure-Tunable Gaps and without Electronic Trap States

Heterogeneous nanostructures, such as quantum dots (QDs) embedded in solid matrices or core-shell nanoparticles, are promising platforms for a wide variety of applications, including phosphors with increased quantum yield, photocatalysis, and solar energy conversion. However, characterizing and controlling their interfacial morphology and defects, which greatly influence their electronic properties, have proven difficult in numerous cases. Here we carried out atomistic calculations on chalcogenide nanostructured materials, i.e., PbSe QDs in CdSe matrices and CdSe embedded in PbSe, and we established how interfacial and core structures affect their electronic properties. In particular, we showed that defects present at interfaces of PbSe nanoparticles and CdSe matrices give rise to detrimental intragap states, degrading the performance of photovoltaic devices. Instead, the electronic gaps of the inverted system (CdSe dots in PbSe) are clean, indicating that this material has superior electronic properties for solar applications. In addition, our calculations predicted that the core structure of CdSe and in turn its band gap may be tuned by applying pressure to the PbSe matrix, providing a means to engineering the properties of new functional materials.