Simulation of solid-state phase transition in<scp>dl</scp>-methionine

Ghasemlou, Saba; Ensing, Bernd; Cuppen, Herma M.

doi:10.1039/d3ce00227f

Cited by 2 publications

(9 citation statements)

References 72 publications

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“…Again in both studies, shifts are found to be cooperative, while the rotations in a defect-free crystal, as observed in our study, and the alteration of the hydrogen bonds in crystals with high defect density, observed in Shi’s study, both follow a nucleation-and-growth mechanism. In our previous study, we provided more experimental proof by reproducing the IR and Raman spectra of the stable states . Also, the energy barriers coming from Shi’s measurements and our calculations are also comparable as discussed above.…”

Section: Conclusion: What Is the Phase Transition Mechanism?supporting

confidence: 67%

“…We hence limit our study to the layer size dependence of the transition, and we do not include the dependence on the number of bilayers. A proof of concept on the adequacy of the employed cell size is that with a simulation cell containing 2 × 8 × 4, we could capture the critical cooperative segment and estimate the energy barrier as explained in our previous study . Our calculations returned a transition energy barrier of Eb /R = 1500 K per unit cell, which is almost twice the value obtained experimentally ( Eb /R = 44100 K) .…”

Section: Structure Of α and β-Dl-methionine And Collective Variablesmentioning

confidence: 51%

“…Table S1 summarizes the harmonic force constants for each CV and each system. The same fixed path-CV is used for all simulation box sizes and was converged for a system of 2 × 8 × 4 as described in ref ( 69 ). Each window starts with 100 ps of equilibration, while inner torsions and z (indicating the distance of the sampled configurations from the initial path) are restrained.…”

Section: Computational Setupmentioning

confidence: 99%

“…Previously we carried out a molecular dynamics study on dl -Met focusing on the phase transition in a defect-free crystal . We obtained energy landscapes, including free energy and potential energy contributions to the transition.…”

Section: Introductionmentioning

confidence: 99%

“…Previously we carried out a molecular dynamics study on dl -Met focusing on the phase transition in a defect-free crystal. 69 We obtained energy landscapes, including free energy and potential energy contributions to the transition. The free energy is suggestive of two distinct transition pathways; in one pathway, the transition initiates via shifts along the b axis followed by shifts along the c axis and conformational changes.…”

Section: Introductionmentioning

confidence: 99%

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Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations

Ghasemlou,

Cuppen

2024

ACS Omega

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The solid-state phase transition in DL-methionine has been extensively studied because of its atypical behavior. The transition occurs through changes in the molecular conformation and 3D packing of the molecules. Phase transitions in racemic aliphatic amino acid crystals are known to show different behaviors depending on whether conformational changes or packing changes are involved, where the former is thought to proceed through a nucleation-and-growth mechanism in a standard moleculeby-molecule picture, and the latter through a cooperative mechanism. The phase transition of DL-methionine resembles the thermodynamic, kinetic, and structural features of both categories: a conformational change and relative shifts between layers in two directions. The present paper presents molecular dynamics simulations of the phase transition to examine the underlying mechanism from two perspectives: (i) analysis of the scaling behavior of the free energy barriers involved in the phase transition and (ii) a structural inspection of the phase transition. Both methods can help to distinguish between a concerted phase change and a molecule-by-molecule or zip-like mechanism. The free energy predominantly scales with the system size, which suggests a cooperative mechanism. The structural changes draw, however, a slightly more complex picture. The conformational changes appear to occur in a molecule-by-molecule fashion, where the rotational movement is triggered by movement in the same layer. Conformational changes occur on a time scale nearly twice as long as the shifts between layers. Shifts in one direction appear to be less concerted than shifts in the perpendicular direction. We relate this to the edge-free energy involved in these shifts. We believe that the behavior observed in DL-methionine is likely applicable to phase transitions in other layered systems that interact through aliphatic chains as well.

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Section: Conclusion: What Is the Phase Transition Mechanism?supporting

confidence: 67%

Section: Structure Of α and β-Dl-methionine And Collective Variablesmentioning

confidence: 51%

Section: Computational Setupmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations

Ghasemlou,

Cuppen

2024

ACS Omega

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Identifying and controlling the order parameter for ultrafast photoinduced phase transitions in thermosalient materials

Ghasemlou,

Li,

Galimberti

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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The drastic shape deformation that accompanies the structural phase transition in thermosalient materials offers great potential for their applications as actuators and sensors. The microscopic origin of this fascinating effect has so far remained obscure, while for technological applications, it is important to learn how to drive transitions from one phase to another. Here, we present a combined computational and experimental study, in which we have successfully identified the order parameter for the thermosalient phase transition in the molecular crystal 2,7-di([1,1’-biphenyl]-4-yl)-fluorenone. Molecular dynamics simulations reveal that the transition barrier vanishes at the transition temperature. The simulations further show that two low-frequency vibrational–librational modes are directly related to the order parameter that describes this phase transition, which is supported by experimental Raman spectroscopy studies. By applying a computational THz pulse with the proper frequency and amplitude we predict that we can photoinduce this phase transition on a picosecond timescale.

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Simulation of solid-state phase transition indl-methionine

Abstract: Solid-to-solid polymorphic transitions are a common phenomenon in organic crystals. The different interactions that play a role in these transitions are however far from understood. In this computational study, we...

Cited by 2 publications

References 72 publications

Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations

Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations

Identifying and controlling the order parameter for ultrafast photoinduced phase transitions in thermosalient materials

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