arXiv subjects

Cecilia M. S. Alvares

Publications and source records attributed to Cecilia M. S. Alvares.

6 recordsLinked to original sources

arXiv2026

Reactive Coarse Grained Force Field for Metal-Organic Frameworks applied to Modeling ZIF-8 Self-Assembly

Decoding the self-assembly mechanism of metal-organic frameworks is a crucial step in reducing trial-and-error tests in their synthesis protocols. Atomistic simulations have proven essential in revealing molecular-level features of MOF nucleation, but they still exhibit limitations in the simulation setups due to size constraints (inability of reaching realistic concentrations or exploring non-stoichiometric metal:ligand ratios). In this contribution, we develop a methodology to derive reactive coarse grained force fields based on multiscale coarse graining methods. We apply our novel methodology to the case of the archetypal zeolitic-imidazolate framework ZIF-8. Our coarse grained force field, which we call nb-CG-ZIF-FF, does not contain any explicit connectivity information, but learns the tetrahedral Zn-connectivity from many body correlations within an atomistic benchmark. nb-CG-ZIF-FF quantitatively reproduces the features of bulk, crystalline ZIF-8 as well as the structural evolution of pre-nucleation species in terms of Zn n-fold coordination populations from the atomistic benchmark. While the range of rings that are formed along the synthesis process are well captured by nb-CG-ZIF-FF, the model cannot exactly reproduce ring populations. Our reactive CG force field fitting approach can be applied to any MOF, opening new research avenues in modeling MOF formation, decomposition, defect dynamics and phase transition processes.

cond-mat.mtrl-sci↗

arXiv2025

A Set of Tutorials for the LAMMPS Simulation Package

The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While molecular simulations thus become accessible to a larger audience, the `black box' nature of such software packages and wide array of options and features can make it challenging to use them correctly, particularly for beginners in the topic of MD simulations. LAMMPS is one such versatile molecular simulation code, designed for modeling particle-based systems across a broad range of materials science and computational chemistry applications, including atomistic, coarse-grained, mesoscale, grid-free continuum, and discrete element models. LAMMPS is capable of efficiently running simulations of varying sizes from small desktop computers to large-scale supercomputing environments. Its flexibility and extensibility make it ideal for complex and extensive simulations of atomic and molecular systems, and beyond. This article introduces a suite of tutorials designed to make learning LAMMPS more accessible to new users. The first four tutorials cover the basics of running molecular simulations in LAMMPS with systems of varying complexities. The second four tutorials address more advanced molecular simulation techniques, specifically the use of a reactive force field, grand canonical Monte Carlo, enhanced sampling, and the REACTER protocol. In addition, we introduce LAMMPS-GUI, an enhanced cross-platform graphical text editor specifically designed for use with LAMMPS and able to run LAMMPS directly on the edited input. LAMMPS-GUI is used as the primary tool in the tutorials to edit inputs, run LAMMPS, extract data, and visualize the simulated systems.

physics.comp-ph↗

arXiv2025

MARTINI-based force fields for predicting gas separation performances of MOF/polymer composites

MOF/polymer composites have been widely investigated in the past decade for gas separation applications. However, the impact of MOF nanoparticle morphology and size in gas separation have not yet been systematically studied by computer simulation techniques. In this work, coarse grained simulations are deployed to study gas adsorption in ZIF-8/PVDF at the nanoparticle level. Nanoparticles of different morphologies and sizes are explored, and adsorption of CO2, N2 and CH4 is investigated throughout the extension of the bulk and surface of the nanoparticle as well as of the polymer phase. Results reproduce the expected preference for CO2 over the other two gasses. Nanoparticles of smaller sizes provide better separation performance at ambient conditions, while rhombic dodecahedron nanoparticles perform better than cubic ones. This work presents a perspective on the merits and limitations of modelling gas adsorption in MOF/polymer composites at the nanoparticle level via particle-based coarse graining approaches, and provides a methodological set-up which can be integrated into high-throughput schemes, bringing us closer to reaching time- and length scales that can be directly compared with experimental data.

physics.chem-ph↗

arXiv2024

Coarse grained modeling of a metal-organic framework/polymer composite and its gas adsorption at the nanoparticle level

Simulations have acted as a cornerstone to understand MOF/polymer interface structure, however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/Force Matching (FM) force field was developed and successfully implemented to model the ZIF-8/PVDF composite at a coarse grained resolution. Inter-phase interactions were modeled using FM potentials, which strive to reasonably reproduce the forces from an atomistic benchmark model, while intraphase interactions are modeled using the general-purpose MARTINI potentials. Systems made of a ZIF-8 nanoparticle embedded into a PVDF matrix were considered to evaluate the effect of nanoparticle size and morphology in the polymer structure and in the CO2 adsorption. Results show that simulations at the nanoparticle level are crucial for depicting the polymer penetration. Notably, the smallest nanoparticle exhibited the least extent of polymer penetration, while the cubic nanoparticle exhibited the highest amount. Polymer conformation and local density values change similarly in all ZIF-8/PVDF systems depending on whether the polymer lies inside or outside of the nanoparticle domain. All composite models present more significant CO2 adsorption in the nanoparticle domain than in the PVDF phase, in agreement with experiments. More remarkably, the small rhombic dodecahedron ZIF-8/PVDF system presents a larger equilibrium amount of gas adsorbed at ambient condition compared to the other two systems, in alignment with the observed polymer penetration trend. On the other hand, the amount of CO2 adsorbed at equilibrium is lower for the rhombic dodecahedron morphology than for the cubic one, contrary to the intuitive expectation founded in the polymer penetration trend. This result could be a reflection of a difference in the number of surface adsorption sites.

physics.chem-ph↗

arXiv2023

Force Matching and Iterative Boltzmann Inversion Coarse Grained Force Fields for ZIF-8

Despite the intense activity at the electronic and atomistic resolutions, coarse grained (CG) modeling of MOFs remains largely unexplored. One of the main reasons for this is the lack of adequate CG force fields. In this work, we present Iterative Boltzmann Inversion (IBI) and Force Matching (FM) force fields for modeling ZIF-8 in three different coarse grained resolutions. Their ability of reproducing structure, elastic tensor and thermal expansion is evaluated and compared with that of MARTINI force-fields considered in previous work.[C. M. S. Alvares et al, J. Chem. Phys., 158, 194107 (2023).] Moreover, MARTINI and FM are evaluated in their ability of depicting the swing effect, a subtle phase transition ZIF-8 undergoes when loaded with guest molecules. Overall, we found that all our force fields reproduce structure reasonably well. Elastic constants and volume expansion results are analyzed and the technical and conceptual challenges in reproducing them are explained. Force matching exhibits promising results for capturing the swing effect. This is the first time these CG methods, widely applied in polymer and biomolecules communities, are deployed to model porous solids. We highlight the challenges of fitting CG force fields for these materials. This work opens the door to a whole new line of developments in the field of modeling MOFs and other porous crystalline solids.

cond-mat.mtrl-sci↗

arXiv2023

Coarse Grained modeling of Zeolitic Imidazolate Framework-8 using MARTINI Force Fields

In this contribution, the well-known MARTINI particle-based coarse graining approach is tested for its ability to model the ZIF-8 metal-organic framework. Its capability to describe structure, lattice parameters, thermal expansion, elastic constants and guest-induced swing effect is evaluated. We find that MARTINI force fields successfully capture the structural properties of the MOF for different degrees of coarsening. Lattice parameter at ambient conditions is overall well reproduced, with MARTINI 2.0 models however having the tendency to slightly overestimate it. The trend of having higher values of C11 elastic constants than C12 is well reproduced by all models, although no particular model excelled in accurately reproducing all elastic constants simultaneously. Amongst the possibilities tested, the choice of bead flavors within a particular MARTINI version appears to have a less critical impact in the simulated properties. None of the CG models investigated were able capture the swing effect within the scope of MD simulations. A perspective on the importance of having a proper LJ parametrization for modeling guest-MOF and MOF-MOF interactions is highlighted. We hope that this work will act as a springboard to the use of MARTINI models within the MOF simulations community.

physics.chem-ph↗