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REVIEW 3 major objections 5 minor 42 references

Structural Stability of Sulfur Depleted MoS2

T0 review · 3 major / 5 minor · reviewed 2026-08-07 · deepseek-v4-flash

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Pith's one-line read After complete removal of its top sulfur layer, monolayer MoS2 remains stable because bottom sulfur atoms migrate through the molybdenum plane to the depleted side, forming a MoSx alloy.

desk verdict A real observation — S migration through the Mo plane after full top-layer removal — but the large-scale claims rest on an unidentified ReaxFF parameter set; fixable, but not reproducible as written. read the letter →

arxiv 2505.24644 v1 pith:JMJAFSSM submitted 2025-05-30 cond-mat.mtrl-sci cond-mat.mes-hall

Ygor M. Jaques , Cristiano F. Woellner , Lucas M. Sassi , Marcelo L. Pereira Jr , Luiz A. Ribeiro Jr , Pulickel M. Ajayan , Douglas S. Galvão This is my paper
classification cond-mat.mtrl-scicond-mat.mes-hall
keywords MoS2sulfurvacanciesmoleculardynamicsabinitiotransitionmetaldichalcogenidesstructuralstabilitydefectengineeringSxalloy
verification ladder T0 review T1 audit T2 compute T3 formal

The pith

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

The reading

The paper asks what happens to a monolayer of MoS2 when every sulfur atom on one side is removed. Using classical reactive molecular dynamics and ab initio molecular dynamics, it finds that the remaining sheet does not fall apart: bottom-layer sulfur atoms spontaneously cross the molybdenum layer within tens of picoseconds, partially refilling the empty top side and producing a MoSx alloy with line-like dislocation boundaries. The same migration occurs in large suspended sheets and on a MoS2 substrate once the depleted patch is larger than about 4 nm2; smaller defects locally contract and block migration. The result matters for controlled defect engineering because it predicts that deliberately desulfurized TMD monolayers can reorganize into alloys by internal sulfur transport, without foreign species.

What carries the argument

The central object is the fully top-sulfur-depleted monolayer, called MoS in the paper: a single molybdenum plane with only one sulfur plane remaining. The mechanism carrying the argument is sulfur trans-layer migration: in regions where top sulfur has been removed, Mo atoms pull closer together, shortening Mo-Mo distances and broadening the Mo-Mo coordination; sulfur atoms at those sites then move across to the empty top side and form boundary lines, until enough sulfur has crossed to stabilize the sheet. The evidence combines classical reactive molecular dynamics at 300 K with ab initio molecular dynamics on a small cell, and both methods show the same migration sequence: one sulfur atom moves first, followed by two others, after which the system reaches equilibrium.

What would settle it

A density-functional-theory calculation of the energy barrier for a single sulfur atom to hop through the molybdenum plane in a sulfur-depleted MoS2 monolayer would settle the mechanism: if the barrier is more than a few electronvolts, room-temperature migration within tens of picoseconds cannot occur, and the observed classical result would be a force-field artifact.

Watch

Extended reading notes

Core claim

The paper shows that a defect-engineered MoS2 monolayer with one complete sulfur layer removed, stoichiometrically 'MoS,' is structurally stable. In both classical reactive MD and ab initio MD, sulfur atoms from the remaining bottom layer start crossing through the Mo plane within a few picoseconds and continue until a partial restoration of the top layer is reached, creating a MoSx alloy with boundary lines of sulfur atoms rather than a uniform sheet. The migration is driven by structural stability: molybdenum atoms in sulfur-depleted regions contract toward each other, which opens pathways for sulfur to cross, and the system equilibrates with corrugation and shortened Mo-Mo distances. On a pristine MoS2 substrate, the repair only happens when the defect area is at least about 4 nm2; below that, local indentation prevents sulfur from moving. At elevated temperatures, molybdenum atoms from the depleted layer migrate onto the substrate and bond in AB or AA stacked islands, so heat transfers metal from the MoS layer to the support.

Load-bearing premise

The main result assumes the classical molybdenum-sulfur interaction model used for the large simulations correctly describes sulfur atoms moving through the molybdenum layer, and the paper does not identify which parameter set produced that model, with the ab initio check limited to a tiny cell for a few picoseconds.

Editorial extensions

If this is right

  • A fully top-layer-sulfur-depleted MoS2 monolayer remains intact over nanosecond timescales, with sulfur redistribution rather than structural collapse.
  • The equilibrated sheet is a MoSx alloy with local composition variations and line-dislocation boundaries, not a uniform MoS stoichiometry.
  • On a MoS2 substrate, sulfur migration is suppressed for defect areas below about 4 nm2 but proceeds for larger patches, giving a size threshold for controlled repair.
  • At elevated temperatures, molybdenum atoms from the depleted layer detach and adsorb onto the substrate in AB or AA stacked islands, so heating degrades the MoS layer by metal transfer.
  • In constant-pressure simulations, the MoS monolayer contracts in-plane and develops pronounced corrugation, indicating that compaction is part of the stabilization response.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

  • The paper leaves implicit that the same self-repair mechanism could be used to pattern MoSx regions laterally by varying the size of the desulfurized patch, without needing a second chalcogen source.
  • The ~4 nm2 threshold is a testable prediction: damage spots below this size should heal by local contraction, while larger spots should show sulfur crossover between layers.
  • If the migration is real, high-temperature operation of defective MoS2 devices could slowly transfer molybdenum and sulfur between adjacent layers or substrates, changing stacking order and local electronic properties over time.
  • A direct computational check is to repeat the 300 K classical simulation with a different published Mo-S interaction model to see whether the sulfur-crossing mechanism is parameterization-independent.
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Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, and a circularity audit.

Referee Report

3 major / 5 minor

Summary. The paper uses classical ReaxFF MD and AIMD to study monolayer MoS2 with one complete sulfur layer removed. The authors report that S atoms from the remaining layer spontaneously migrate through the Mo plane within about 10 ps, producing line-like S dislocations and a locally mixed MoSx structure; they further report that this behavior persists in systems up to 100 nm, that supported monolayers show migration only above a defect area of roughly 4 nm2, and that at 600-1000 K Mo atoms from the depleted layer adsorb onto a pristine MoS2 substrate in AB/AA stacking regions. The central claim is that the S-depleted monolayer is dynamically stable and reorganizes via S migration rather than remaining a static MoS sheet.

Significance. If the central claim is correct, the work provides a concrete atomic mechanism for the response of MoS2 to severe chalcogen depletion, with implications for defect engineering and Janus/alloy synthesis. The paper has real strengths: it combines two independent simulation methods, shows the same S-migration event in a small 3x3 cell in both ReaxFF and AIMD, extends the classical simulations to large (10 nm and 100 nm) systems, includes a substrate geometry with variable defect size, and supplies MD videos in the Supporting Information. The simulations do not fit any parameter to the target result, so circularity is not a concern. However, the large-scale and stability conclusions rest on an unidentified ReaxFF parameter set and on very short single trajectories, so the significance is conditional on those points being fixed.

major comments (3)
  1. [Computational Details, ReaxFF paragraph] The classical MD results, including the large 10 nm and 100 nm NVT/NPT runs, the defect-area threshold of about 4 nm2, and the 2 ns elevated-temperature runs, are all produced with ReaxFF, but the Mo-S parameter set is not identified. Reference 39 is Chenoweth et al., a ReaxFF parameterization for hydrocarbon oxidation, not for MoS2, and no parameter file is given in the paper or the Supplementary Material. Because the migration barrier for an S atom to cross the Mo plane is the key physical quantity for the main claim, the reader cannot check whether the force field describes that barrier correctly. This is a reproducibility gap that blocks verification of the abstract's strongest statement; the authors should supply the actual parameter file and cite the correct ReaxFF parametrization for Mo/S, or rerun the central simulations with a published MoS2 ReaxFF set and compare.
  2. [Results, second paragraph and Figure 2] The claim that 'consistently, for both methodologies, a single S atom moves first, followed by two others' appears to be based on one classical trajectory and one AIMD trajectory. No replicate runs with different initial velocities, no ensemble averages, and no quantitative order parameter are reported. Given that the migration event occurs on a roughly 10 ps timescale, the sequence of single versus multiple S hops could easily be thermal noise; the paper should report at least several independent trajectories and show that the migration sequence and the final distribution of S atoms on L1 are reproducible.
  3. [Results, NVT/NPT equilibration and Figures 1-3] The 'remarkable stability' of suspended MoS is supported only by about 100 ps of equilibration, and by 20 ps for the 100 nm video, while the observed migration events occur within about 10 ps. A 100 ps trajectory is too short to establish kinetic or thermodynamic stability, and the AIMD validation covers only a 3x3 cell for a few picoseconds. The paper should provide longer trajectories for at least the representative system sizes and report the time evolution of a stability measure, such as the number of S atoms on the depleted side or the potential energy, to demonstrate a plateau rather than a transient.
minor comments (5)
  1. [Computational Details, AIMD paragraph] The AIMD simulations do not state the temperature, the thermostat, the total simulation time, or the number of MD steps; the caption of Figure 2 only says 'a few picoseconds.' These details are needed to judge the cross-method comparison.
  2. [Results, substrate simulations and Figure 4] The defect-area threshold of approximately 4 nm2 is derived from a single simulation at 1 nm2 compared with a single simulation at 4 nm2; at minimum one intermediate size and repeated runs would make the threshold statement quantitative.
  3. [Results, NPT ensemble paragraph] It is not stated whether the classical NPT simulations used semi-isotropic or fully anisotropic pressure coupling, nor how the z-dimension, which must contain a free surface, is treated; this matters for the reported structural contraction and corrugation heights.
  4. [Introduction and Results, line dislocation terminology] The term 'line dislocations' is used loosely for the one-dimensional arrays of S atoms that migrate through the Mo layer; these are not crystallographic dislocations in the usual sense, so a more neutral term such as 'S-rich line defects' or 'domain boundaries' would be clearer.
  5. [Figure 5] The y-axis label of Figure 5(a) is described only as 'number of Mo atoms from MoS added to the MoS2 layer'; the axis unit/range and the exact simulation time points should be printed on the figure or given in the caption.

Circularity Check

0 steps flagged · score 0.0 of 10

No significant circularity: the S-migration and stability claims are direct simulation observations, not outputs forced by fitted parameters or self-citation.

full rationale

The paper's central claims are direct observations of molecular dynamics trajectories, namely sulfur migration through the Mo plane, the line-dislocation morphology, the substrate-size threshold near 4 nm2, and high-temperature Mo adsorption onto the underlying MoS2. No parameter in the reported simulations is fitted to the target outcome, and no 'prediction' is algebraically or statistically forced by construction. The authors did not define MoS stability in terms of the simulation output beyond reporting the observed structural evolution, and no load-bearing argument relies on a self-citation chain. The ReaxFF citation issue (Ref. 39 describes a hydrocarbon force field rather than a Mo/S parameterization) is a reproducibility and transferability concern, not a circularity concern, because the force field is an external model input whose accuracy is not established by the paper's own derivation. The AIMD cross-check independently supports the small-cell migration behavior. Accordingly, no circular step is identified and the score is 0.

Assumptions & free parameters 2 free parameters · 5 assumptions · 0 invented entities

The central claim rests on simulation methodology rather than on fitted target quantities. The key unvalidated step is the transferability of the ReaxFF force field to a heavily S-depleted MoS2 structure, plus the assumption that very short trajectories establish stability. No new physical entities are introduced, and no parameters are fit to the target observation.

free parameters (2)
  • ReaxFF Mo/S parameter set = not disclosed (ref 39 is hydrocarbon ReaxFF)
    All classical MD results depend on it; the paper does not identify the parameter file or the MoS2 ReaxFF development reference.
  • Substrate restraint force constant = 10 kcal/mol along z
    Applied to bottom S atoms of the pristine MoS2 layer to mimic a substrate; chosen by hand, not derived from a substrate model.
assumptions (5)
  • domain assumption PBE/GGA with PAW accurately captures Mo-S bonding and migration barriers.
    Used in all AIMD; no benchmark against experiments or higher-level theory. Invoked in Computational Details.
  • domain assumption ReaxFF potential is transferable to heavily S-depleted MoS2 despite being parameterized on other chemistries.
    Classical MD is the main tool; no validation of the force field against AIMD for these configurations is shown. Invoked in Computational Details and Results.
  • domain assumption 100 ps classical and few ps AIMD trajectories are long enough to conclude structural stability.
    Conclusions call the system stable; no free-energy barriers, elastic constants, or long-time extrapolation are provided. Invoked in Results and Conclusions.
  • domain assumption Supercell periodicity (3x3 and ~10 nm cells) does not control the migration mechanism.
    Line dislocations and migration may depend on cell size; only two sizes are checked. Invoked in Results.
  • ad hoc to paper The pristine MoS2 layer with restrained bottom S atoms faithfully represents a substrate.
    A force constant is applied in the bilayer setup, but real substrates have different interactions. Invoked in Computational Details.

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Cite this review

Pith. "Pith review of Structural Stability of Sulfur Depleted MoS2." pith.science (2026). https://pith.science/paper/JMJAFSSM

@misc{pith2026250524644,
  author       = {Pith},
  title        = {Pith review of: Structural Stability of Sulfur Depleted MoS2},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/JMJAFSSM}},
  note         = {Machine review of arXiv:2505.24644}
}
read the original abstract

Transition metal dichalcogenides (TMDs), particularly monolayer MoS2, have received increased attention in materials science and have been exploited in diverse applications from photonics to catalysis. Defects in TMDs play a crucial role in modulating their properties, and understanding defect-induced dynamics is of great importance. This study investigates the dynamics of sulfur depletion in defective monolayer MoS2, which yields stable MoS monolayers. Various defect sizes, temperature regimes, and substrate effects were investigated. Through comprehensive classical molecular (ReaxFF) molecular dynamics (MD) and ab initio MD (AIMD) simulations, we elucidate the dynamics of sulfur vacancy formation in MoS2 lattices. After removing all sulfur atoms from the top layer, several sulfur atoms from the bottom layer spontaneously migrate to the top layer as a response to increase structural stability, thus creating a MoSx alloy. These findings deepen our understanding of defect dynamics in TMDs, offering valuable insights into the controlled engineering of their properties for nanotechnology applications.

Figures

Figures reproduced from arXiv: 2505.24644 by the authors.

Figure 1
Figure 1. (a) A schematic representation of a MoS2 monolayer with one of its sulfur layers (L1) removed, leading to the formation of a MOS structure containing only one Mo layer (L2) and one S layer (L3). (b) Top and (c) side views of equilibrated MoS configuration after 100 ps of classical MD in the NVT ensemble. (d) Detailed view of two regions within the MoS structure, illustrating areas where the initial MoS configuration… view at source ↗
Figure 2
Figure 2. Dynamics of a 3 × 3 supercell of MoS for classical and ab initio MD simulations. Both systems reached equilibrium within a few picoseconds, during which sulfur (S) atoms transverse through the Mo layer. 5 [PITH_FULL_IMAGE:figures/full_fig_p005_2.png] view at source ↗
Figure 3
Figure 3. (a) Equilibrated MoS configuration after 100 ps of classical MD in the NPT [PITH_FULL_IMAGE:figures/full_fig_p006_3.png] view at source ↗
Figures from the paper (2 more)
Figure 4
Figure 4. Figure 4: Equilibrated configurations after NPT runs for systems with varying defect sizes, [PITH_FULL_IMAGE:figures/full_fig_p008_4.png]
Figure 5
Figure 5. Figure 5: (a) The number of Mo atoms from MoS added to the MoS [PITH_FULL_IMAGE:figures/full_fig_p009_5.png]

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Pith tools

Reviewed August 7, 2026 · model on record in the stance chip above.