arXiv subjects

Michele Parrinello

Publications and source records attributed to Michele Parrinello.

At least 73 records · Page 4Linked to original sources

arXiv2019

Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

A widely spread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. Nucleation process, polymorph selection, and crystal habits depend crucially on this thermodynamic parameter. When performing simulations in the canonical ensemble as the crystalline phase is deposited the solution is depleted of solutes. This unavoidable modification of the thermodynamic conditions leads to significant artifact. Here we adopt the idea of the constant chemical potential molecular dynamics approach of Perego et al. [J. Chem. Phys. 2015, 142, 144113] to the study of nucleation. Our method allows determining the crystal nucleus size and nucleation rates at constant supersaturation. As an example we study the homogeneous nucleation of sodium chloride from its supersaturated aqueous solution.

cond-mat.soft↗

arXiv2019

Calculation of phase diagrams in the multithermal-multibaric ensemble

From the Ising model and the Lennard-Jones fluid, to water and the iron-carbon system, phase diagrams are an indispensable tool to understand phase equilibria. In spite of the effort of the simulation community the calculation of a large portion of a phase diagram using computer simulation is still today a significant challenge. Here we propose a method to calculate phase diagrams involving liquid and solid phases by the reversible transformation of the liquid and the solid. To this end we introduce an order parameter that breaks the rotational symmetry and we leverage our recently introduced method to sample the multithermal-multibaric ensemble. In this way in a single molecular dynamics simulation we are able to compute the liquid-solid coexistence line for entire regions of the temperature and pressure phase diagram. We apply our approach to the bcc-liquid phase diagram of sodium and the fcc-bcc-liquid phase diagram of aluminum.

cond-mat.stat-mech↗

arXiv2019

Kinetics of aqueous media reactions via ab initio enhanced molecular dynamics: the case of urea decomposition

Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants to the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.

physics.chem-ph↗

arXiv2019

Path Integral Molecular Dynamics for Bosons

Trapped Bosons exhibit fundamental physical phenomena and are potentially useful for quantum technologies. We present a method for simulating Bosons using path integral molecular dynamics. A main challenge for simulations is including all permutations due to exchange symmetry. We show that evaluation of the potential can be done recursively, avoiding explicit enumeration of permutations, and scales cubically with system size. The method is applied to Bosons in a 2D trap and agrees with essentially exact results. An analysis of the role of exchange with decreasing temperature is also presented.

cond-mat.quant-gas↗

arXiv2019

A local fingerprint for hydrophobicity and hydrophilicity: from methane to peptides

An important characteristic that determines the behavior of a solute in water is whether it is hydrophobic or hydrophilic. The traditional classification is based on chemical experience and heuristics. However, this does not reveal how the local environment modulates this important property. We present a local fingerprint for hydrophobicity and hydrophilicity inspired by the two body contribution to the entropy. This fingerprint is an inexpensive, quantitative and physically meaningful way of studying hydrophilicity and hydrophobicity that only requires as input the water-solute radial distribution functions. We apply our fingerprint to octanol, benzene and the 20 proteinogenic amino acids. Our measure of hydrophilicity is coherent with chemical experience and, moreover, it also shows how the character of an atom can change as its environment is changed. Lastly, we use the fingerprint as collective variable in a funnel metadynamics simulation of a host-guest system. The fingerprint serves as a desolvation collective variable that enhances transitions between the bound and unbound states.

physics.chem-ph↗

arXiv2019

Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics

Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics-based technique that addressed this issue and allows estimating affinities in the presence of multiple escape pathways. Our approach is shown on a Lysozyme T4 variant in complex with the benzene molecule. The calculated binding free energy is in agreement with experimental data. Remarkably, not only we were able to find all the previously identified ligand binding pathways, but also we uncovered 3 new ones. This results were obtained at a small computational cost, making this approach valuable for practical applications, such as screening of small compounds libraries.

physics.chem-ph↗

arXiv2019

Naphthalene crystal shape prediction from molecular dynamics simulations

We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys., 142, 2015, 144113]. To bring the crystal growth within the timescale of a molecular dynamics simulation we applied Well-Tempered Metadynamics with a spatially constrained collective variable, which focuses the sampling on the growing layer. We estimated that the resulting steady state crystal shape corresponds to a rhombic prism, which is in line with experiments. Further, we observed that at the investigated supersaturations, the $\{00\bar{1}\}$ face grows in a two step two dimensional nucleation mechanism while the considerably faster growing faces $\{1\bar{1}0\}$ and $\{20\bar{1}\}$ grow new layers with a one step two dimensional nucleation mechanism.

physics.chem-ph↗

arXiv2019

Accurate quantum chemical free energies at affordable cost

Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new method that combining metadynamics and free energy perturbation allows calculating accurate quantum chemical free energies for chemical reactions. To prove the effectiveness of this new approach we study the S N 2 reaction of CH3F + Cl- -> CH3Cl + F- in vacuo and solvated by water. Comparisons are made with harmonic transition state theory to show how this method could provide accurate equilibrium and rate constants for complex systems.

physics.chem-ph↗

arXiv2019

Augmented Harmonic Linear Discriminant Analysis

Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation methods has been developed. A much-used class of methods relies on the use of collective variables. The efficiency of these methods relies critically on an educated guess of the collective variables. For this reason much effort has been devoted to the construction and improvement of collective variables. Among the many methods proposed, harmonic linear discriminant analysis has proven effective. This method builds the collective coordinates solely from the knowledge of the fluctuations in the different metastable state. In this Letter we propose to improve upon the harmonic linear discriminant analysis by adding to the construction of the collective coordinates an extra bit of information, namely that of the transition state ensemble. Configurations belonging to the transition state ensemble are harnessed by the use of the spring shooting transition path sampling algorithm. We show on a challenging example that these coordinates thus augmented not only perform better in the calculation of the static properties, but also accelerate considerably the calculation of reaction rates.

cond-mat.stat-mech↗

arXiv2019

Making the best of a bad situation: a multiscale approach to free energy calculation

Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently and reconstruct the free energy landscape. In methods like metadynamics, the quality of these collective variables plays a key role in convergence efficiency. Unfortunately in many systems of interest it is not possible to identify an optimal collective variable, and one must deal with the non-ideal situation of a system in which some slow modes are not accelerated. We propose a two-step approach in which, by taking into account the residual multiscale nature of the problem, one is able to significantly speed up convergence. To do so, we combine an exploratory metadynamics run with an optimization of the free energy difference between metastable states, based on the recently proposed variationally enhanced sampling method. This new method is well parallelizable and is especially suited for complex systems, because of its simplicity and clear underlying physical picture.

physics.comp-ph↗

arXiv2019

Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution

In the ongoing intense quest to increase the photoconversion efficiencies of lead halide perovskites, it has become evident that optimizing the morphology of the material is essential to achieve high peformance. Despite the fact that nucleation plays a key role in controlling the crystal morphology, very little is known about the nucleation and crystal growth processes. Here, we perform metadynamics simulations of nucleation of methylammonium lead triiodide (MAPI) in order to unravel the atomistic details of perovskite crystallization from a $γ$-butyrolactone solution. The metadynamics trajectories show that the nucleation process takes place in several stages. Initially, dense amorphous clusters mainly consisting of lead and iodide appear from the homogeneous solution. These clusters evolve into lead iodide (PbI$_{2}$) like structures. Subsequently, methylammonium (MA$^{+}$) ions diffuse into this PbI$_{2}$-like aggregates triggering the transformation into a perovskite crystal through a solid-solid transformation. Demonstrating the crucial role of the monovalent cations in crystallization, our simulations provide key insights into the evolution of the perovskite microstructure which is essential to make high-quality perovskite based solar cells and optoelectronics.

cond-mat.mtrl-sci↗

arXiv2019

Multithermal-multibaric molecular simulations from a variational principle

We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to construct a bias that leads to a uniform sampling in energy and volume. The intervals of temperature and pressure are taken as inputs and the relevant energy and volume regions are determined on the fly. In this way the method guarantees adequate statistics for the chosen TP region. We show that our multithermal-multibaric simulations can be used to calculate all static physical quantities for all temperatures and pressures in the targeted region of the TP plane. We illustrate our approach by studying the density anomaly of TIP4P/Ice water.

cond-mat.stat-mech↗

arXiv2019

The onset of dehydrogenation in solid Ammonia Borane, an ab-initio metadynamics study

The discovery of effective hydrogen storage materials is fundamental for the progress of a clean energy economy. Ammonia borane ($\mathrm{H_3BNH_3}$) has attracted great interest as a promising candidate but the reaction path that leads from its solid phase to hydrogen release is not yet fully understood. To address the need for insights in the atomistic details of such a complex solid state process, in this work we use \textit{ab-initio} molecular dynamics and metadynamics to study the early stages of AB dehydrogenation. We show that the formation of ammonia diborane ($\mathrm{H_3NBH_2(}$$μ$$\mathrm{-H)BH_3}$) leads to the release of $\mathrm{NH_4^+}$, which in turn triggers an autocatalytic $\mathrm{H_2}$ production cycle. Our calculations provide a model for how complex solid state reactions can be theoretically investigated and rely upon the presence of multiple ammonia borane molecules, as substantiated by standard quantum-mechanical simulations on a cluster.

physics.chem-ph↗

arXiv2019

Homogeneous nucleation of ice

Ice nucleation is a process of great relevance in physics, chemistry, technology and environmental sciences, much theoretical and experimental efforts have been devoted to its understanding, but still it remains a topic of intense research. We shed light on this phenomenon by performing atomistic based simulations. Using metadynamics and a carefully designed set of collective variables, reversible transitions between water and ice are able to be simulated. We find that water freezes into a stacking disordered structure with the all-atom TIP4P/Ice model, and the features of the critical nucleus of nucleation at the microscopic level are revealed. Our results are in agreement with recent experimental and other theoretical works and confirm that nucleation is preceded by a large increase in tetrahedrally coordinated water molecules.

cond-mat.soft↗

arXiv2019

A microscopic description of acid-base equilibrium

Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the molecular behaviour. Atomistic simulations could complement experiments and shed precious light on microscopic mechanisms. The large free energy barriers connected to proton dissociation however make the use of enhanced sampling methods mandatory. Here we perform an ab initio molecular dynamics (MD) simulation and enhance sampling with the help of methadynamics. This has been made possible by the introduction of novel descriptors or collective variables (CVs) that are based on a conceptually new outlook on acid-base equilibria. We test successfully our approach on three different aqueous solutions of acetic acid, ammonia, and bicarbonate. These are representative of acid, basic, and amphoteric behaviour.

physics.chem-ph↗

arXiv2019

Silicon liquid structure and crystal nucleation from ab-initio deep Metadynamics

Studying the crystallization process of silicon is a challenging task since empirical potentials are not able to reproduce well the properties of both semiconducting solid and metallic liquid. On the other hand, nucleation is a rare event that occurs in much longer timescales than those achievable by ab-initio molecular dynamics. To address this problem, we train a deep neural network potential based on a set of data generated by Metadynamics simulations using a classical potential. We show how this is an effective way to collect all the relevant data for the process of interest. In order to drive efficiently the crystallization process, we introduce a new collective variable based on the Debye structure factor. We are able to encode the long-range order information in a local variable which is better suited to describe the nucleation dynamics. The reference energies are then calculated using the SCAN exchange-correlation functional, which is able to get a better description of the bonding complexity of the Si phase diagram. Finally, we recover the free energy surface with a DFT accuracy, and we compute the thermodynamics properties near the melting point, obtaining a good agreement with experimental data. In addition, we study the early stages of the crystallization process, unveiling features of the nucleation mechanism.

physics.comp-ph↗

arXiv2018

Enhanced sampling of transition states

The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods are able to obtain sufficient sampling in order to draw the free energy, the transition states are often sparsely sampled. We propose an approach based on the Variationally Enhanced Sampling Method to enhance sampling in the transition region. To this effect, we introduce a dynamic target distribution which uses the derivative of the instantaneous free energy surface to locate the transition regions on the fly and modulate the probability of sampling different regions. Finally, we exemplify the effectiveness of this approach in enriching the number of configurations in the transition state region in the cases of a chemical reaction and of a nucleation process.

physics.chem-ph↗

arXiv2018

Combining Metadynamics and Integrated Tempering Sampling

The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In metadynamics the fluctuations of a carefully chosen collective variable are amplified, while in integrated tempering sampling the system is pushed to visit an approximately uniform interval of energies and allows exploring a range of temperatures in a single run. We describe our ap-proach and apply it to the two prototypical systems a SN2 chemical reaction and to the freezing of silica. The combination of metadynamics and integrated tempering sampling leads to a powerful method. In par-ticular in the case of silica we have measured more than one order of magnitude acceleration.

physics.chem-ph↗