{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Physics, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark",
    "Science Institute and Faculty of Physical Sciences",
    "University of Iceland",
    "Department of Chemistry, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark",
    "Department of Chemical and Pharmaceutical Sciences",
    "University of Trieste"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "A. O. Dohn"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "D. Llorena Prieto"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "E. Selenius"
    },
    {
      "affs": [
        0
      ],
      "name": "M. Haubro"
    },
    {
      "affs": [
        0
      ],
      "name": "K. Haldrup"
    },
    {
      "affs": [
        3
      ],
      "name": "K. B. Møller"
    },
    {
      "affs": [
        1,
        2,
        4,
        5
      ],
      "name": "G. Levi"
    },
    {
      "affs": [
        0
      ],
      "name": "M. M. Nielsen"
    },
    {
      "name": "Asmus Ougaard Dohn",
      "orcid": "0000-0002-5172-7168"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7e1j2fvw2f294.bib",
  "cited_by": 0,
  "doi": "10.26434/chemrxiv.15008382/v1",
  "fulltext_url": null,
  "id": "7e1j2fvw2f294",
  "issns": [],
  "landing_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008382/v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1606|Advanced Physical and Chemical Molecular Interactions"
    ]
  ],
  "openalex": "W7211871328",
  "pdf_url": "https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008382/v1",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-06",
  "publisher": "American Chemical Society (ACS)",
  "ris": "https://research.draconitic.com/paper/7e1j2fvw2f294.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:17Z",
      "native_id": "10.26434/chemrxiv.15008382",
      "source": "chemrxiv",
      "url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008382/v2"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1606|Advanced Physical and Chemical Molecular Interactions",
      "subfield": "physical"
    }
  ],
  "title": "Vicem: Automating Molecular Mechanics Modeling of Solvation Dynamics with Applications to Time-Resolved X-ray Scattering",
  "title_text": "Vicem: Automating Molecular Mechanics Modeling of Solvation Dynamics with Applications to Time-Resolved X-ray Scattering",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:19Z",
  "url": "https://research.draconitic.com/paper/7e1j2fvw2f294",
  "venue": "ChemRxiv",
  "versions": []
}