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arxiv: 2605.19808 · v1 · pith:7Z3AK7FGnew · submitted 2026-05-19 · ❄️ cond-mat.mtrl-sci · physics.chem-ph

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

Akanksha Nawani (1) , Rocio Semino (1) ((1) Sorbonne Universit\'e , CNRS , Physicochimie des Electrolytes et Nanosyst\`emes Interfaciaux , PHENIX , Paris , France.) This is my paper

Pith reviewed 2026-05-20 04:16 UTC · model grok-4.3

classification ❄️ cond-mat.mtrl-sci physics.chem-ph
keywords UiO-66metal-organic frameworkforce fieldmolecular dynamicspoint defectsself-assemblynode-ligand bindingZr-based MOF
0
0 comments X

The pith

A new partially reactive force field models UiO-66 structure, stability, and early node-ligand assembly steps.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper introduces nb-UiO-FF, a classical force field for the UiO-66 metal-organic framework that adds partial reactivity between metal nodes and organic ligands. Reactivity is handled by a Morse potential for bond formation and breaking together with dummy atoms that reproduce the uneven charge distribution around zirconium. The model matches crystal structures and mechanical properties of both UiO-66 and the related UiO-67 framework, whether the material is empty, solvent-filled, or contains defects. Molecular dynamics simulations with the force field then follow the first stages of solvothermal binding and locate short-lived structural arrangements that are favored on both energy and time scales. The result supplies a practical tool for exploring how the framework grows and how its common point defects arise.

Core claim

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.

What carries the argument

The nb-UiO-FF force field, which adds a Morse potential to capture node-ligand reactivity and dummy atoms to represent the anisotropic charge distribution on zirconium atoms in the nodes.

If this is right

  • The force field supports molecular dynamics studies of UiO-66 self-assembly.
  • It identifies transient structural motifs that are both thermodynamically and kinetically favored during node-ligand binding.
  • The same parameters correctly describe the isoreticular UiO-67 framework.
  • Framework stability and mechanical properties remain accurate with or without defects and with different solvents.
  • The model can now be used to investigate point defect formation during synthesis.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • The same approach could be adapted to simulate synthesis of other zirconium MOFs that also form defects readily.
  • The favored motifs point to possible experimental levers, such as solvent choice, for controlling defect levels.
  • Longer simulations might show how these early arrangements grow into crystals or lead to disordered regions.
  • The force field offers a route to predict how synthesis conditions affect final porosity and stability without full quantum calculations.

Load-bearing premise

The Morse potential parameters and dummy-atom charges can be chosen such that the resulting classical model accurately captures the node-ligand reactivity and anisotropic Zr charge distribution across the range of conditions studied.

What would settle it

Molecular dynamics runs with nb-UiO-FF that produce transient structural motifs different from those observed in spectroscopy or ab initio calculations of early node-ligand binding would show the model does not correctly describe assembly.

Figures

Figures reproduced from arXiv: 2605.19808 by Akanksha Nawani (1), CNRS, France.), Paris, PHENIX, Physicochimie des Electrolytes et Nanosyst\`emes Interfaciaux, Rocio Semino (1) ((1) Sorbonne Universit\'e.

Figure 1
Figure 1. Figure 1: FIG. 1: Structural representation of UiO-66: (a) [PITH_FULL_IMAGE:figures/full_fig_p001_1.png] view at source ↗
Figure 3
Figure 3. Figure 3: FIG. 3: Parameter space exploration for the Morse [PITH_FULL_IMAGE:figures/full_fig_p003_3.png] view at source ↗
Figure 3
Figure 3. Figure 3: While certain parameter combinations yielded [PITH_FULL_IMAGE:figures/full_fig_p004_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: FIG. 4: RDFs for selected atomic pairs indicated in [PITH_FULL_IMAGE:figures/full_fig_p005_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: FIG. 5: Local coordination environment of the two [PITH_FULL_IMAGE:figures/full_fig_p006_5.png] view at source ↗
Figure 6
Figure 6. Figure 6: FIG. 6: 2 [PITH_FULL_IMAGE:figures/full_fig_p007_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: FIG. 7: Snapshots of UiO-66 self-assembly. Solvent was [PITH_FULL_IMAGE:figures/full_fig_p007_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: FIG. 8: Representative structural motifs observed [PITH_FULL_IMAGE:figures/full_fig_p008_8.png] view at source ↗
read the original abstract

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.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The manuscript introduces nb-UiO-FF, a partially reactive classical force field for UiO-66 that augments standard potentials with a Morse term for node-ligand reactivity and dummy atoms on Zr to capture anisotropic charge distribution. It reports that the model reproduces structural features of UiO-66 and the isoreticular UiO-67, mechanical properties, and framework stability both with and without defects and in the presence of DMF or ethanol. The force field is then used in molecular-dynamics simulations of solvothermal conditions to identify transient, thermodynamically and kinetically favored node-ligand binding motifs, with the broader goal of enabling studies of self-assembly and defect formation.

Significance. A transferable, reactive force field for UiO-66 would be a useful addition to the MOF modeling toolkit, particularly for exploring synthesis pathways and defect chemistry that are difficult to access with static DFT or non-reactive potentials. The combination of a Morse interaction with dummy-atom charges is a pragmatic way to introduce limited reactivity without moving to reactive bond-order potentials. If the parameterization proves robust outside the fitting set, the work could support falsifiable predictions about motif populations during early-stage assembly.

major comments (2)
  1. [Abstract / Parameterization] Abstract and parameter-fitting section: no quantitative validation metrics (RMSD for lattice parameters, percentage errors on bulk moduli, or defect formation energies) or error bars are supplied, nor is the target data set used to determine the Morse well depth, range, and dummy-atom charges described. Without these, it is impossible to judge whether the reported reproduction of structures, mechanics, and stability is within acceptable tolerances or merely qualitative.
  2. [MD Simulations of Node-Ligand Binding] MD results on transient motifs: the central claim that certain binding motifs are both thermodynamically and kinetically favored rests on the transferability of the fitted Morse parameters and dummy charges to non-equilibrium node-ligand approach trajectories. No independent test (e.g., comparison of approach energies or barriers to ab initio metadynamics or to a separate DFT data set) is reported, leaving open the possibility that the observed motif ranking is an artifact of the fitting procedure.
minor comments (2)
  1. [Methods] Notation for the dummy-atom charges and positions should be defined explicitly in a table or equation rather than only in the text.
  2. [Results] Figure captions for the motif snapshots should state the simulation temperature, solvent model, and time window over which the motif is observed.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive review and for recognizing the potential utility of a partially reactive force field for studying UiO-66 assembly and defects. We address each major comment below and have revised the manuscript accordingly where the points identify clear gaps in presentation or validation.

read point-by-point responses

  1. Referee: [Abstract / Parameterization] Abstract and parameter-fitting section: no quantitative validation metrics (RMSD for lattice parameters, percentage errors on bulk moduli, or defect formation energies) or error bars are supplied, nor is the target data set used to determine the Morse well depth, range, and dummy-atom charges described. Without these, it is impossible to judge whether the reported reproduction of structures, mechanics, and stability is within acceptable tolerances or merely qualitative.

    Authors: We agree that explicit quantitative metrics and a clear description of the fitting data are necessary for rigorous assessment. In the revised manuscript we have added a dedicated parameterization subsection that specifies the DFT-derived target data set (optimized node-ligand geometries, interaction energies, and partial charges) used to determine the Morse parameters and dummy-atom charges. We have also inserted a validation table reporting RMSD values for lattice parameters of UiO-66 and UiO-67, percentage deviations in bulk moduli and defect formation energies relative to reference DFT and experimental data, and standard deviations from replicate simulations. revision: yes

  2. Referee: [MD Simulations of Node-Ligand Binding] MD results on transient motifs: the central claim that certain binding motifs are both thermodynamically and kinetically favored rests on the transferability of the fitted Morse parameters and dummy charges to non-equilibrium node-ligand approach trajectories. No independent test (e.g., comparison of approach energies or barriers to ab initio metadynamics or to a separate DFT data set) is reported, leaving open the possibility that the observed motif ranking is an artifact of the fitting procedure.

    Authors: We acknowledge the referee’s concern about transferability to non-equilibrium trajectories. The force field was fitted exclusively to equilibrium structures and energies; its use in solvothermal MD therefore relies on the assumption that the Morse term remains physically reasonable during approach. While a full ab initio metadynamics benchmark was outside the scope of the present study, we have added to the revised manuscript (i) a limitations paragraph discussing this assumption and (ii) a supplementary comparison of binding energies extracted from selected MD snapshots against single-point DFT calculations on the same geometries. These additions provide partial independent support for the motif ranking while making the transferability caveat explicit. revision: partial

Circularity Check

0 steps flagged

No circularity: standard force-field parameterization with independent validation targets

full rationale

The paper introduces nb-UiO-FF by adding a Morse term for node-ligand reactivity and dummy atoms for Zr anisotropy, then reports that the resulting model reproduces equilibrium structures, moduli, defect stability, and solvent-filled behavior for UiO-66/67 while also generating new MD observations of transient binding motifs. No equation or claim in the abstract or described workflow equates a reported prediction to a fitted input by construction, nor does any load-bearing step rest on a self-citation chain that itself assumes the target result. The derivation therefore remains self-contained: parameters are chosen to match selected reference data, and the subsequent structural, mechanical, and dynamical results are presented as applications rather than tautological restatements of those choices.

Axiom & Free-Parameter Ledger

2 free parameters · 1 axioms · 1 invented entities

The central claim depends on conventional classical force-field assumptions plus newly introduced parameters for reactivity and charge anisotropy that are not independently derived from first principles.

free parameters (2)
  • Morse potential parameters for node-ligand interaction
    Used to model partial reactivity; values are chosen to reproduce binding behavior.
  • Dummy atom charges and positions on Zr
    Introduced to capture anisotropic charge distribution; parameters fitted or assigned to match target properties.
axioms (1)
  • domain assumption Standard classical force-field terms (harmonic bonds, angles, Lennard-Jones non-bonded interactions) remain valid for all interactions not involving the added Morse term.
    The paper augments rather than replaces the underlying force-field framework.
invented entities (1)
  • Dummy atoms attached to Zr nodes no independent evidence
    purpose: To reproduce the anisotropic charge distribution of the zirconium atoms.
    New modeling device added to the force field; no independent experimental signature provided in the abstract.

pith-pipeline@v0.9.0 · 5777 in / 1411 out tokens · 45638 ms · 2026-05-20T04:16:00.376625+00:00 · methodology

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Reference graph

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