Supporting Information for A Multiscale Simulation Workflow for Molecular Solvated Systems in ChemShell: Application to Orthosilicic Acid Condensation

Simulation data accompanying the article: You Lu, Chin Yong, Xu Zhang, Thomas W. Keal, Alexey A. Sokol, and C. Richard A. Catlow, "A Multiscale Simulation Workflow for Molecular Solvated Systems in ChemShell: Application to Orthosilicic Acid Condensation," Journal of Chemical Theory and Computation (2026). DOI: [article DOI to be added on publication]. The work models the first condensation (Si–O–Si bond formation) of orthosilicic acid, Si(OH)₄, in an acidic water–methanol solution (pH < 1, 333.15 K). Solution models were built and equilibrated by classical molecular dynamics with DL_FIELD and DL_POLY, and a non-periodic QM/MM cluster was cut from the equilibrated snapshot. The reactive free energy surface was sampled by well-tempered, multiple-walker metadynamics (20 walkers) at the GFN2-xTB/OpenMM QM/MM level, driven through PLUMED within ChemShell. The two biased collective variables are the O–Si attack distance d(O1898, Si2112) and the coordination number n of the electrophilic silicon Si2112. This deposit holds the structural models, the metadynamics output, and the collective-variable time series needed to reproduce and reanalyze the reported results: md_snapshot.xyz — PBC-wrapped classical MD snapshot used as the starting configuration (20,205 atoms). shell_model.xyz and shell_model_optimized.xyz — the 8,026-atom QM/MM cluster before and after QM/MM optimization. qm_region_optimized.xyz — the optimized 119-atom QM region (B3LYP-D3/6-31+G**). animation_walker00–walker19_qm.xyz — QM-region trajectories for the 20 metadynamics walkers (2,001 frames each, 119 atoms, 100 fs stride). HILLS — accumulated Gaussian hills from the 20-walker run (8,000 entries; Bohr, Ha). COLVAR_walker00–walker19 — collective-variable time series per walker (d, n, n₂–n₅; 200,001 entries each; Bohr). fes_d1.dat — one-dimensional free energy projection along d from PLUMED sum_hills (Å, kcal/mol). plumed_metadynamics.dat — the ChemShell-generated PLUMED input for the metadynamics production run. Cartesian coordinates in the XYZ files are in Angstroms, and atom labels follow the shell model's 0-based sequential numbering. In the raw PLUMED files the column headers d1 and c1–c5 correspond to d and n, n₂–n₅, respectively. Please cite the article above when using these data.