arXiv subjects

Rocio Semino

Publications and source records attributed to Rocio Semino.

At least 19 recordsLinked to original sources

arXiv2026

Bottlenecks in Hamiltonian-Adaptive Resolution Simulation Method for Modeling Interfaces

The Hamiltonian-Adaptive Resolution Simulation (H-AdResS) method allows to combine atomistic and particle-based coarse-grained models in a single simulation box, which makes it very attractive to model systems containing interfaces or reactive regions surrounded by an interacting environment. In our previous work [arXiv:2604.21867], we implemented H-AdResS in LAMMPS 2023 and extended its use to interfaces, focusing on MOF/CO$_2$ interfaces as an example. We found that, despite its advantages, using this method properly for this kind of systems is not trivial. In this work, an in-depth analysis of the impact of the choice of thermostatting schemes and long-range electrostatics models is presented. Even though its Hamiltonian formulation enables performing H-AdResS simulations within constant temperatures ensembles, not every thermostat is appropriate. We demonstrate that Langevin thermostat is a reliable choice for this method, while Nos\'e-Hoover results in artifacts. In addition, we show that using short-range models such as the Damped Shifted Force method for electrostatics, a popular choice for H-AdResS simulations, can lead to non-physical results when modeling interfaces. The need of capping strategies to deal with discontinuities in forces and energies arising from abrupt changes in resolution is also discussed. Finally, the impossibility of changing the definition of the H-AdResS Hamiltonian to include a gradual interpolation of the bonded degrees of freedom is discussed. We hope that this contribution helps the reader to appropriately set up H-AdResS simulations and to assess if this method can be used to accurately model their system of interest.

cond-mat.mtrl-sci↗

arXiv2026

Partially reactive force field for the UiO-66 metal-organic framework

UiO-66 is the most widely studied metal-organic framework (MOF), on account of its structural tunability given by its capacity of sustaining high amounts of point defects in its structure. Its synthesis mechanism is largely unknown, with only a few works mostly focused on the formation of the Zr-oxide cluster. In this work, a partially reactive force field to model UiO-66, nb-UiO-FF, is introduced. This force field incorporates node--ligand reactivity via a Morse potential and the introduction of dummy atoms to reproduce the anisotropic charge distribution of the Zr atoms in the node. nb-UiO-FF reproduces structural features of both UiO-66 and its isoreticular analog UiO-67, mechanical properties and framework stability with or without defects, activated or filled with N,N-dimethylformamide or ethanol. The force field is further employed within a molecular dynamics scheme to study the early stages of solvothermal node--ligand binding. Transient structural motifs both thermodynamically and kinetically favored are identified. This force field enables studying the self-assembly of UiO-66, as well as the formation of its point defects.

cond-mat.mtrl-sci↗

arXiv2026

Machine Learning and Molecular Simulations Reveal Mechanisms of ZIFs Polymorph Selection

Zn(imidazolate)$_2$ metal-organic frameworks (MOFs) exhibit a remarkable degree of polymorphism. Because of their promising industrial applications, many research groups have investigated phase transitions, phase diagram and relative stability of these polymorphs. There is now wide consensus in the research community that these MOFs are solvothermally formed via non-classical nucleation mechanisms, in which pre-nucleation clusters are first formed, followed by an intermediate amorphous structure that subsequently reorganizes to yield the final crystalline MOF. However, no study up to date has uncovered which part of the synthesis process determines the final polymorph obtained. In this work, path collective variable metadynamics simulations performed with a partially reactive force field give insights into mechanistic and thermodynamic aspects of the self-assembly of these MOFs. Databases of transient and intermediate synthesis structures are built from the simulations. By developing and applying neural network classifiers over these databases, it is found that both pre-nucleation clusters and the amorphous intermediate structures are polymorph-dependent. These results suggest that polymorph selection happens as early as the pre-nucleation cluster stage.

cond-mat.mtrl-sci↗

arXiv2026

Extending Hamiltonian-Adaptive Resolution Simulation to Interfaces: An Updated LAMMPS Implementation and Application to Porous Solids

Many natural phenomena involve processes that happen simultaneously at different characteristic length- and timescales. Typically, the region where the process of interest happens is affected by fluctuations in its surroundings. Modeling these systems requires an effective combination of simulation resolutions. The Hamiltonian-Adaptive Resolution Simulation (H-AdResS) method allows to model dual-resolution systems in length- and time-scales compatible with molecular diffusion, by combining atomistic and particle-based coarse graining models in the same simulation box. In this work, a new implementation of H-AdResS is provided in LAMMPS 2023. New features extend the usage to more diverse interaction potentials and simplify the preparation of input files via dedicated lammps input commands, while keeping the efficiency gain of the basis method. The implementation is benchmarked by reproducing water properties from a reference atomistic simulation. Importantly, the new implementation includes changes in compensation routines allowing to simulate systems with fluctuating density. As an example, the method in its new implementation is applied to modeling a porous metal-organic framework and its gas adsorption structure and transport properties. We demonstrate that structural and dynamic properties in the atomistic region of the dual-resolution scheme are unaffected and remain those of the fully atomistic system, while increasing simulation efficiency. This paves the way for using H-AdResS to simulate complex interfaces across applications in energy storage, electrocatalysis, and membrane technologies.

cond-mat.mtrl-sci↗

arXiv2026

Systematic Study of Machine Learning Classification Algorithms of Zeolitic Imidazolate Framework Polymorphs

Zeolitic Imidazolate Frameworks (ZIFs) are a family of metal--organic frameworks that feature metal centers tetrahedrally linked to imidazole-based ligands and adopt zeolite-like topologies. ZIFs formed by Zinc cations and imidazolate linkers exhibit a remarkable degree of polymorphism, which can be modulated by varying synthesis parameters or thermodynamic conditions (i.e., temperature and pressure). Computer simulations provide a unique way of studying these materials and their phase transitions from the microscopic standpoint, revealing their underlying molecular mechanisms. However, studying these mechanisms requires to be able to classify the phase of each molecular entity in an agnostic and automatic fashion, which is particularly challenging when the two phases involved are structurally very similar. In this work, we systematically study neural network classifiers to classify ZIF phases on-the-fly during molecular dynamics simulations. We test a variety of input features, differing both in the dimensionality and nature of the descriptors and in the kind of force field used for building the training/testing database. We reveal that even with low-dimensional descriptors the classification is highly accurate, while the use of high-dimensional descriptors leads to an even better performance. Training the classifier with configurations coming from different force fields we can remove force field bias and enhance the classifier performance and general applicability. Finally, we apply our classifiers to reveal mechanistic details of the ZIF-4-cp $\xrightarrow{}$ ZIF-4-cp-II phase transition.

cond-mat.mtrl-sci↗

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

Computer Simulation of the Growth of a Metal-Organic Framework Proto-crystal at Constant Chemical Potential

Designing metal-organic frameworks (MOFs) synthesis protocols is currently largely driven by trial-and-error, since we lack fundamental understanding of the molecular level mechanisms that underlie their self-assembly processes. Previous works have studied the nucleation of MOFs, but their growth has never been studied by means of computer simulations, which provide molecular level detail. In this work, we combine constant chemical potential simulations with a particle insertion method to model the growth of the ZIF-8 MOF at varying synthesis temperatures and concentrations of the reactants. Non-classical growth mechanisms triggered by oligomer attachments were detected, with a higher predominance in the most concentrated setups. The newly formed layers preserve the pore-like density profile of the seed crystal but contain defective sites characterized by the presence of 3, 5 and 7 membered rings, typical of amorphous phases. Compared to the amorphous intermediate species obtained at the nucleation part of the self-assembly process previously investigated in our group [Chem. Mater., doi: 10.1021/acs.chemmater.5c02028, 2025], larger-sized rings are more common in the grown layer. Moreover, these are favored by increasing reactant concentration and temperature, as is the degree of deviation with respect to the original crystal structure. We computed growth rates for the steady-state regime, and the non-linear tendency with respect to concentration leads us to hypothesize that in these conditions the growth is controlled by the adsorption rather than by the diffusion processes.

cond-mat.mtrl-sci↗

arXiv2025

Intermolecular Interactions between Polyethylene, Water, and Potential Antistatic and Slip Additives: a Molecular Dynamics Study

Additives are essential to enhance or modify the properties of plastics for target applications. However, finding appropriate additives may be challenging, since we lack knowledge on their interactions with plastics and moisture, and the interplay between them. In this work, we study stearoyl diethanolamine as well as two amphiphilic molecules as potential new additives for their antistatic or slip properties in polyethylene by means of atomistic molecular dynamics simulations. We reveal that additive/water interactions and relative solubility are strongly determined by their relative ratio. The polyethylene model thin film adopts a crystalline core and an amorphous-like surface, with polymer chain terminations predominantly located at the surface of the slab. Water forms a layer on top of the polymer surface or droplets when its concentration is lowered, but it never enters the polymer matrix. All additives interact with water mainly by their polar heads, with water acting as a hydrogen bond acceptor or donor depending on the additive. The additives studied exhibit remarkably different structures when they are mixed with the polymer: two of them enter the polymer matrix to various degrees, either by intercalating their chains with the polyethylene ones or by forming micellar-like structures, while the third one stays at the surface. When water is incorporated into the system, the structure of some of the additive/polyethylene systems changes. The magnitude and nature of these changes depend on the relative concentrations of all species and on the nature of the additive. We propose that one of our two modeled molecules could have promising properties as a slip agent, as its behavior in the PE matrix resembles that of the industrial slip agent erucamide.

physics.chem-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↗

arXiv2025

Unveiling ZIF-8 nucleation mechanisms through molecular simulation: role of temperature, solvent and reactant concentration

Synthesizing new metal-organic frameworks (MOFs) is a challenging task, as the size, morphology, polymorph and type and number of defects present on the synthesis product may depend on many variables, including temperature, solvent, concentration and nature of reactants, among others. A deeper understanding on how synthesis conditions determine the obtained material is crucial to optimize the use of resources when synthesizing new MOFs. In this contribution, we study the impact of changing concentration, solvent and temperature on the molecular level mechanisms of the solvothermal nucleation process of ZIF-8 relying on molecular dynamics simulations using a force field that incorporates metal-ligand reactivity. We find that the nucleation is faster when the synthesis is performed in dimethylsulfoxide than when it is performed in methanol, in alignment with experimental observations. In the early steps of the nucleation process, we observe the formation of linear oligomers containing metal ions and ligands, which start forming cycles later on. All simulations lead to the formation of a final state that is highly-connected and partially amorphous, which could be correlated to an intermediate species observed in direct experiments. The mechanism of formation of this phase mainly consists of the merging of smaller nuclei. Even though increasing temperature and the reactants concentration lead to a similar nucleation speedup, there are differences in ring populations and lifetimes within the highly-connected amorphous intermediate phases that are formed in each case. Finally, important differences in the free energy of Zn-2-methylimidazolate versus Zn-imidazolate subsequent binding events are revealed and discussed.

physics.chem-ph↗

arXiv2024

Thermodynamic Insights into the Self-assembly of Zeolitic Imidazolate Frameworks from Computer Simulations

New metal-organic frameworks (MOFs) are periodically synthesized all over the world due to the wide range of societally and environmentally relevant applications they possess. However, the mechanisms and thermodynamics associated to MOF self-assembly are poorly understood because of the difficulties in studying such a multi-scale process with molecular-level resolution. In this work, we performed well-tempered metadynamics simulations of the early nucleation and late growth steps of the self-assembly of ZIF-4 using a reactive force field. We found that the formation of building blocks is a complex, multi-step process that involves changes in the coordination of the metal ion. Saturating the ligand coordination of a metal ion is more energetically favorable during growth than during early nucleation. The addition of a fourth ligand is less exergonic than it is for the first three and the associated free energy is highly dependent on the local environment of the undercoordinated metal ion. The stability of this bond depends on the strength of the solvent--metal ion interaction. Incorporating a ligand to a ZIF-1 crystal is less favorable compared to the more stable ZIF-4 polymorph. Milder differences were found when comparing the growth of (100), (010) and (001) ZIF-4 surfaces.

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↗

arXiv2024

Phase Diagram of ZIF-4 Computed via Well-tempered Metadynamics

Well-tempered metadynamics simulations are employed to explore the phase diagram of ZIF-4, a porous crystalline metal-organic framework of industrial relevance. Despite the vast amount of experimental efforts, the phase diagram that includes ZIF-4 and its related polymorphs has not yet been fully determined. For example, the crystalline phase called ZIF-4-cp is not experimentally observed when high pressure ramps are applied. Our simulations shed light into the phase diagram topology and allow us to further look into the collective degrees of freedom that drive the phase transitions in the T=150-450 K and P=0-200 MPa region. The porous ZIF-4 phase transforms into ZIF-4-cp through pore closure, while the latter has a phase transition at higher pressures regimes to ZIF-4-cp-II, a transformation which involves subtle changes in swing dihedral angles.

cond-mat.mtrl-sci↗

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

Microscopic Mechanism of the Thermal Amorphization of ZIF-4 and Melting of ZIF-zni Revealed via Molecular Dynamics and Machine Learning Techniques

We investigate the microscopic mechanism of the thermally induced ambient pressure ordered-disordered phase transitions of two zeolitic imidazolate frameworks of formula Zn(C$_3$H$_3$N$_2$)$_2$: a porous (ZIF-4) and a dense, non-porous (ZIF-zni) polymorph via a combination of data science and computer simulation approaches. Molecular dynamics simulations are carried out at the atomistic level through the nb-ZIF-FF force field that incorporates ligand-metal reactivity and relies on dummy atoms to reproduce the correct tetrahedral topology around Zn$^{2+}$ centres. The force field is capable of reproducing the structure of ZIF-4, ZIF-zni and the amorphous (ZIF$\_$a) and liquid (ZIF$\_$liq) phases that respectively result when these crystalline materials are heated. Symmetry functions computed over a database of structures of the four phases, are used as inputs to train a neural network that predicts the probabilities of belonging to each of the four phases at the local Zn$^{2+}$ level with 90$\%$ accuracy. We apply this methodology to follow the time-evolution of the amorphization of ZIF-4 and the melting of ZIF-zni along a series of molecular dynamics trajectories. We first computed the transition temperature and determined associated thermodynamic state functions. Subsequently, we studied the mechanisms. Both processes consist of two steps: (i) for ZIF-4, a low-density amorphous phase is first formed, followed by the final ZIF$\_$a phase while (ii) for ZIF-zni, a ZIF$\_$a-like phase precedes the formation of the liquid phase. These processes involve connectivity changes in the first neighbour ligands around the central Zn$^{2+}$ cations. We find that the amorphization of ZIF-4 is a non-isotropic processes and we trace back the origins of this anisotropic behaviour to density and lability of coordination bonds.

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↗

arXiv2022

Computer Simulation of the Early Stages of Self-Assembly and Thermal Decomposition of ZIF-8

We employ all-atom well-tempered metadynamics simulations to study the mechanistic details of both the early stages of nucleation and crystal decomposition for the benchmark metal-organic framework ZIF-8. To do so, we developed and validated a force field that reliably models the modes of coordination bonds via a Morse potential functional form and employs cationic and anionic dummy atoms to capture coordination symmetry. We also explored a set of physically relevant collective variables and carefully selected an appropriate subset for our problem at hand. After a rapid increase of the Zn-N connectivity, we observe the evaporation of small clusters in favor of a few large clusters, that lead to the formation of an amorphous highly-connected aggregate. Zn(MIm)42- and Zn(MIm)3- complexes are observed, with lifetimes in the order of a few picoseconds, while larger structures, such as 4-, 5- and 6-membered rings, have substantially longer lifetimes of a few nanoseconds. The free ligands act as ``templating agents'' for the formation of the sodalite cages. ZIF-8 crystal decomposition results in the formation of a vitreous phase. Our findings contribute to a fundamental understanding of MOF's synthesis that paves the way to controlling synthesis products. Furthermore, our developed force field and methodology can be applied to model solution processes that require coordination bond reactivity for other ZIFs besides ZIF-8.

physics.chem-ph↗

arXiv2021

Ranking the Synthesizability of Hypothetical Zeolites with the Sorting Hat

Zeolites are nanoporous alumino-silicate frameworks widely used as catalysts and adsorbents. Even though millions of distinct siliceous networks can be generated by computer-aided searches, no new hypothetical framework has yet been synthesized. The needle-in-a-haystack problem of finding promising candidates among large databases of predicted structures has intrigued materials scientists for decades; most work to date on the zeolite problem has been limited to intuitive structural descriptors. Here, we tackle this problem through a rigorous data science scheme-the "zeolite sorting hat"-that exploits interatomic correlations to produce a 95% real versus theoretical zeolites classification accuracy. The hypothetical frameworks that are grouped together with known zeolites are promising candidates for synthesis, that can be further ranked by estimating their thermodynamic stability. A critical analysis of the classifier reveals the decisive structural features. Further partitioning into compositional classes provides guidance in the design of synthetic strategies.

cond-mat.mtrl-sci↗