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Phonon density of states of silica (SiO2) nanopore via molecular dynamics simulations

Pablo Galaviz, Dehong Yu, Nicolas de Souza, Sho Kimura, Yoshitomo Kojima, Seiji Mori, Akira Yamaguchi

TL;DR

The paper addresses the vibrational density of states (VDOS) of SiO2 nanopores and how force field choice, crustal structure, and surface-adsorbed water reshape the vibrational spectra. It combines classical molecular dynamics with three force fields (VFF1990, ReaxFF2023, PoreMS) and benchmarks against density functional theory (DFT) and inelastic neutron scattering (INS), including comparisons for nanopore and bulk silica. Key findings show that ReaxFF2023 and PoreMS reproduce amorphous SiO2 PDOS well, that the dry nanopore VDOS is largely harmonic between 100 and 300 K, and that adding surface water introduces a dominant mode near $60\mathrm{meV}$ with strong temperature- and loading-dependent spectral changes and diffusion. The work provides a practical reference framework for simulating silica nanopores and guiding interpretation of VDOS measurements from neutron or X-ray scattering, with public data and scripts to extend to similar nanomaterials.

Abstract

This study presents a comprehensive computational investigation of the vibration density of states (VDOS) of a silica nanopore, systematically evaluating a range of force fields against inelastic neutron scattering results. We analyze the influence of temperature, crustal structure, and surface-adsorbed water molecules on the nanopore's structural and dynamic properties. We performed classical molecular dynamics simulations of nanopore and bulk silica, and used density functional theory (DFT) calculations for bulk silica for comparison. The resulting VDOS shows relatively good agreement with DFT and experimental data. The temperature has a relatively low effect on the dry nanopore. The inclusion of H2O molecules significantly affects the VDOS. The low-energy modes are dominated by H2O VDOS and increase with loading. This work is an essential step towards characterizing silica nanopores via molecular dynamics and provides a valuable reference for experimental comparison with X-ray and neutron scattering VDOS results.

Phonon density of states of silica (SiO2) nanopore via molecular dynamics simulations

TL;DR

The paper addresses the vibrational density of states (VDOS) of SiO2 nanopores and how force field choice, crustal structure, and surface-adsorbed water reshape the vibrational spectra. It combines classical molecular dynamics with three force fields (VFF1990, ReaxFF2023, PoreMS) and benchmarks against density functional theory (DFT) and inelastic neutron scattering (INS), including comparisons for nanopore and bulk silica. Key findings show that ReaxFF2023 and PoreMS reproduce amorphous SiO2 PDOS well, that the dry nanopore VDOS is largely harmonic between 100 and 300 K, and that adding surface water introduces a dominant mode near with strong temperature- and loading-dependent spectral changes and diffusion. The work provides a practical reference framework for simulating silica nanopores and guiding interpretation of VDOS measurements from neutron or X-ray scattering, with public data and scripts to extend to similar nanomaterials.

Abstract

This study presents a comprehensive computational investigation of the vibration density of states (VDOS) of a silica nanopore, systematically evaluating a range of force fields against inelastic neutron scattering results. We analyze the influence of temperature, crustal structure, and surface-adsorbed water molecules on the nanopore's structural and dynamic properties. We performed classical molecular dynamics simulations of nanopore and bulk silica, and used density functional theory (DFT) calculations for bulk silica for comparison. The resulting VDOS shows relatively good agreement with DFT and experimental data. The temperature has a relatively low effect on the dry nanopore. The inclusion of H2O molecules significantly affects the VDOS. The low-energy modes are dominated by H2O VDOS and increase with loading. This work is an essential step towards characterizing silica nanopores via molecular dynamics and provides a valuable reference for experimental comparison with X-ray and neutron scattering VDOS results.

Paper Structure

This paper contains 17 sections, 12 equations, 15 figures, 3 tables.

Table of Contents

  1. Introduction
  2. Notation and abbreviations
  3. Methods
  4. Force fields
  5. Analysis
  6. Surface vibrations
  7. Density functional theory calculation
  8. Results
  9. Force field dependency
  10. Temperature dependency
  11. Nanopore vs bulk comparison
  12. H2O loading dependency
  13. H2O monolayer analysis
  14. Conclusions
  15. Acknowledgment
  16. ...and 2 more sections

Figures (15)

  • Figure 1: Anneling procedure. Each stage shows the thermodynamical thermostat employed
  • Figure 2: Quick simulation protocol.
  • Figure 3: Phonon density of states for $\alpha$-quartz comparison using three force fields and DFT calculations. Panels (a)-(b) show the comparison between VFF1990 and the DFT calculations for Incoherent and Coherent scattering, respectively. Panels (c)-(d), and (e)-(f) shows the corresponding result for ReaxFF2023 and PoreMS force fields, respectively.
  • Figure 4: Neutron scattering function for $\alpha$-quartz and amorphous SiO2 comparison using three force fields and INS results. Panels (a)-(b) show the comparison between the INS experiment and the calculated VFF1990 for $\alpha$-quartz and amorphous SiO2, respectively. Panels (c)-(d), and (e)-(f) shows the corresponding result for ReaxFF2023 and PoreMS force fields, respectively.
  • Figure 5: VDOS temperature dependency for $\alpha$-quartz and amorphous SiO2. Panels (a)-(b) show the VDOS temperature dependency using VFF1990 for $\alpha$-quartz and amorphous SiO2, respectively. Panels (c)-(d), and (e)-(f) show the corresponding result for ReaxFF2023 and PoreMS force fields, respectively. In each panel, the temperature is indicated by the line style.
  • ...and 10 more figures