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Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field.

ABSTRACT: In this study, we develop a reactive force field (ReaxFF) for a Si/O/H/F system to perform etching simulations of SiO₂ with an HF etchant. Quantum mechanical (QM) training sets from density functional theory calculations, which contain structures of reactant/product and energies with bond dissociation, valence angle distortions, and reactions between SiO₂ clusters and SiO₂ slab with HF gases, are used to optimize the ReaxFF parameters. Structures and energies calculated using the ReaxFF match well with the QM training sets. Using the optimized ReaxFF, we conduct molecular dynamics simulations of the etching process of SiO₂ substrates with active HF molecules. The etching yield and number of reaction products with different incident energies of the HF etchant are investigated. These simulations show that the developed ReaxFF offers insights into the atomistic surface reaction of the SiO₂ etching process.

SUBMITTER: Kim DH

PROVIDER: S-EPMC8223409 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field.

Kim Dong Hyun DH Kwak Seung Jae SJ Jeong Jae Hun JH Yoo Suyoung S Nam Sang Ki SK Kim YongJoo Y Lee Won Bo WB

ACS omega 20210608 24

In this study, we develop a reactive force field (ReaxFF) for a Si/O/H/F system to perform etching simulations of SiO2 with an HF etchant. Quantum mechanical (QM) training sets from density functional theory calculations, which contain structures of reactant/product and energies with bond dissociation, valence angle distortions, and reactions between SiO2 clusters and SiO2 slab with HF gases, are used to optimize the ReaxFF parameters. Structures and energies cal ...[more]

PMID: 34179646

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Project description:BACKGROUND:After the discovery of membrane-reversible electroporation decades ago, the procedure has been used extensively in biology, biotechnology and medicine. The research on the basic mechanism has increasingly attracted attention. Although most research has focused on models that consider all atomic and molecular interactions and much atomic-level information can be obtained, the huge computational demand limits the models to simulations of only a few nanometers on the spatial scale and a few nanoseconds on the time scale. In order to more comprehensively study the reversible electroporation mechanism of phospholipid membrane on the nanoscale and at longer time intervals of up to 100 ns, we developed a dipalmitoylphosphatidylcholine (DPPC) phospholipid membrane model with the coarse-grained Martini force field. The model was tested by separately examining the morphology of the phospholipid membrane, the hydrophilic channel size, the distribution of the voltage potential on both sides of the membrane, and the movement of water molecules and ions during electroporation. RESULTS:The results showed that the process went through several stages: (1) the formation of the pore with defects originating on the surface. (2) The maintenance of the pore. The defects expanded to large pores and the size remains unchanged for several nanoseconds. (3) Pore healing stage due to self-assembly. Phospholipid membrane shrunk and the pore size decreased until completely closed. The pores were not circular in cross-section for most of the time and the potential difference across the membrane decreased dramatically after the pores formed, with almost no restoration of membrane integrity even when the pores started to close. CONCLUSIONS:The mechanism of the reversible electroporation process on the nanoscale level, including defects, expansion, stability, and pore closing stages on a longer time scale of up to 100 ns was demonstrated more comprehensively with the coarse-grained Martini force field, which took both the necessary molecular information and the calculation efficiency into account.

Project description:The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.

Dataset Information

Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field.

Publications

Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field.

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