A close examination of the structure and dynamics of HC(NH2)2PbI3 by MD simulations and group theory.

The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal and fully anisotropic isobaric conditions. Two trajectories, one at 300 K and another at 450 K, were extended for over 50 ps in order to perform a detailed assessment of the rotational dynamics of organic cations. The characteristic rotations of the cation are analyzed by defining two rotation axes. It is found that the formamidinium molecules rotate preferentially around the direction parallel to the line connecting the two nitrogen atoms. The rotational dynamics shows some characteristics already observed in methylammonium lead iodide, like the heterogeneous dynamics at room temperature that disappears at 450 K. The orientational probability of the molecules is explored in terms of an expansion in cubic harmonics up to the 12th order. It reveals a strong directionality at room temperature that relaxes when increasing the temperature. These findings are further rationalized using Landau and group theories suggesting a mixed displacive/order-disorder structural instability at lower temperatures.

Molecular disorder and translation/rotation coupling in the plastic crystal phase of hybrid perovskites.

The complexity of hybrid organic perovskites calls for an innovative theoretical view that combines usually disconnected concepts in order to achieve a comprehensive picture: (i) the intended applications of this class of materials are currently in the realm of conventional semiconductors, which reveal the key desired properties for the design of efficient devices. (ii) The reorientational dynamics of the organic component resembles that observed in plastic crystals, therefore requiring a stochastic treatment that can be done in terms of pseudospins and rotator functions. (iii) The overall structural similarity with all inorganic perovskites suggests the use of the high temperature pseudo cubic phase as the reference platform on which further refinements can be built. In this paper we combine the existing knowledge on these three fields to define a general scenario based on which we can continue the quest towards a fundamental understanding of hybrid organic perovskites. With the introduction of group theory as the main tool to rationalize the different ideas and with the help of molecular dynamics simulations, several experimentally observed properties are naturally explained with possible suggestions for future work.

Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study.

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation.

Structure of supercooled water in clusters and bulk and its relation to the two-state picture of water: results from the TIP4P-ice model.

The structure of water clusters (H(2)O)(n) (n = 40-200) and bulk water were examined by molecular dynamics simulations using the TIP4P-ice water model. The analysis of the low-temperature structures in terms of the local structure index (LSI) showed a bimodal distribution. This finding supports the two-state picture derived from the analysis of the inherent dynamics of bulk SPC/E water. The water molecules at the outer interface of the coldest clusters are more structured than those in the inner core. The geometrical constraint of the interface forces the surface molecules to lose one neighbor and adopt a local angular distribution of hydrogen bonds resembling that found in the basal plane of ice Ih.

Brownian dynamics study of gel-forming colloidal particles.

Brownian dynamics simulations are used to study the formation process of colloidal gels and the effect of particle concentration on their rheological properties. To model the interaction between particles, we adopted an R-shifted 12-6 Lennard-Jones (LJ) potential, which allows independent control of the particle size and attractive range. For a short-ranged potential, the percolated network characteristic of a gel exhibited a viscoelastic behavior of weak gels. The storage modulus (G') increased with the particle concentration increase. Moreover, the dependency of storage modulus (G') on the particle concentration followed a power law function, which is commonly reported in the literature for experimental data. Simulating frequency sweep tests showed that the system behaved as a liquid-like or solid-like material, depending on the frequency applied. The crossover frequency, i.e., the frequency at which G' and G'' are equal, appears to shift slightly to lower values when the particle concentration increases, suggesting a more solid-like behavior for systems with higher particle concentration. During gelation, the storage modulus increases as a stretched exponential and reaches a constant value at long times.

On the uptake of ammonia by the water/vapor interface.

The passage of a single ammonia molecule from an infinitely dilute gas through the water/vapor interface is studied by constrained molecular dynamics simulations. The free energy of the system as a function of the distance between the ammonia and the interface has a minimum in the interfacial region. It is found that the preference of the ammonia for the interface is mainly due the disruption of the solvent structure caused by the ammonia in the bulk region, which results in an increase of the solvent internal energy.

Cluster structure and corralling effect driven by interaction mismatch in two dimensional mixtures.

The formation of clusters with crystal-like order in two dimensions is studied using Monte Carlo simulations. We find that the necessary conditions to induce the formation of clusters of one component is to add a second component that has a larger size and that has a long-range soft repulsive interaction with its own kind but not with the other one. The clusters of the small particles are found to be surrounded by a network of quasi-one-dimensional arrangements of the larger particles. The degree of order of the clusters is found to depend on the concentration of the larger particles. The findings explain recent experimental observations on lipid-poloxamer mixtures and they provide guidelines for how to form ordered clusters of nanoparticles in two dimensions.

Kinetic and thermodynamic control of protein adsorption.

Control of nonspecific protein adsorption is very important for the design of biocompatible and biomimetic materials as well as drug carriers. Grafted polymer layers can be used to prevent protein adsorption. We have studied the molecular factors that determine the equilibrium and kinetic control of protein adsorption by grafted polymer layers. We find that polymers that are not attracted to the surface are very effective for kinetic control but not very good for equilibrium reduction of protein adsorption. Polymers with attractions to the surface show exactly the opposite behavior. The implications for molecular design of biocompatible materials also are discussed in this paper.