Vicem: Automating Molecular Mechanics Modeling of Solvation Dynamics with Applications to Time-Resolved X-ray Scattering
6 affiliations
- 1Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
- 2Science Institute and Faculty of Physical Sciences
- 3University of Iceland
- 4Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
- 5Department of Chemical and Pharmaceutical Sciences
- 6University of Trieste
Abstract
Time-resolved X-ray solution scattering (trXSS) probes molecular-scale structural dynamics in solution, but its interpretation requires efficient computational methodologies and models for assessing how changes in solute structure and charge distribution affect the surrounding solvent shell and the resulting scattering signal. We present VICEM, an OpenMM/ASE-based software suite for constructing solvated molecular models, running molecular dynamics simulations, inspecting and analyzing the resulting trajectories, while exposing solute geometry, partial charges, Lennard–Jones parameters, and bonded terms as editable variables for model refinement. VICEM includes an approximate restrained-solute model designed for rapid solvent-shell sampling around prescribed solute geometries, together with utilities for correcting the potential energy along selected intramolecular coordinates. We benchmark the restrained model against established force fields for 244 systems comprising neutral organic molecules, charged organic solutes, and transition-metal complexes. Across 5018 solute-water radial distribution functions, the effect of restraining the solute structure on the solvent shell is generally comparable to differences between established flexible force fields, and diagnostic cases are scrutinized to identify when reference geometry, nonbonded assignment, or suppressed solute flexibility controls the solvent response. For a prototypical iron complex, VICEM is used to scan candidate geometries and quantify the effect of the structure on solvent-shell radial distribution functions and the corresponding scattering signal, showing how VICEM can be used to tune molecular models for structural refinement. VICEM is therefore shown to provide a platform for reproducible solvent-shell modeling and targeted force-field refinement with particular focus on trXSS analysis.
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BibTeX
@misc{dohn2026vicem,
title = {{Vicem: Automating Molecular Mechanics Modeling of Solvation Dynamics with Applications to Time-Resolved X-ray Scattering}},
author = {A. O. Dohn and D. Llorena Prieto and E. Selenius and M. Haubro and K. Haldrup and K. B. Møller and G. Levi and M. M. Nielsen and Asmus Ougaard Dohn},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15008382/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008382/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Vicem: Automating Molecular Mechanics Modeling of Solvation Dynamics with Applications to Time-Resolved X-ray Scattering
AU - A. O. Dohn
AU - D. Llorena Prieto
AU - E. Selenius
AU - M. Haubro
AU - K. Haldrup
AU - K. B. Møller
AU - G. Levi
AU - M. M. Nielsen
AU - Asmus Ougaard Dohn
PY - 2026
DA - 2026/09/06
PB - ChemRxiv
DO - 10.26434/chemrxiv.15008382/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008382/v1
AB - Time-resolved X-ray solution scattering (trXSS) probes molecular-scale structural dynamics in solution, but its interpretation requires efficient computational methodologies and models for assessing how changes in solute structure and charge distribution affect the surrounding solvent shell and the resulting scattering signal. We present VICEM, an OpenMM/ASE-based software suite for constructing solvated molecular models, running molecular dynamics simulations, inspecting and analyzing the resulting trajectories, while exposing solute geometry, partial charges, Lennard–Jones parameters, and bonded terms as editable variables for model refinement. VICEM includes an approximate restrained-solute model designed for rapid solvent-shell sampling around prescribed solute geometries, together with utilities for correcting the potential energy along selected intramolecular coordinates. We benchmark the restrained model against established force fields for 244 systems comprising neutral organic molecules, charged organic solutes, and transition-metal complexes. Across 5018 solute-water radial distribution functions, the effect of restraining the solute structure on the solvent shell is generally comparable to differences between established flexible force fields, and diagnostic cases are scrutinized to identify when reference geometry, nonbonded assignment, or suppressed solute flexibility controls the solvent response. For a prototypical iron complex, VICEM is used to scan candidate geometries and quantify the effect of the structure on solvent-shell radial distribution functions and the corresponding scattering signal, showing how VICEM can be used to tune molecular models for structural refinement. VICEM is therefore shown to provide a platform for reproducible solvent-shell modeling and targeted force-field refinement with particular focus on trXSS analysis.
ER -