{
  "abstract": "The absorption spectrum of aqueous indole contains contributions from the two lowest-lying excited states, La and lower-energy Lb. The corresponding fluorescence spectrum exhibits a large Stokes shift attributed to solvent-induced inversion of the excited-state ordering followed by emission from the La state. However, modeling excited-state relaxation mechanisms in aqueous indole is challenging because the two excited states are strongly coupled in a condensed-phase environment. Here we employ the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA) to simulate the finite-temperature quantum dynamics of molecular systems with two vibrationally-coupled electronic excited states. We consider indole, 2-cyanoindole (2CNI), and L-tryptophan (Trp) to examine effects of substitution on the optical properties of indole. In all three chromophores, ultrafast population transfer occurs from the brighter La state to the darker Lb state. In indole and Trp, the La state has pronounced charge-transfer character and is stabilized by the polar solvent, leading to its repopulation during solvent relaxation and predominantly La emission. In 2CNI, the reduced charge-transfer character of La weakens its solvent stabilization, suppressing population transfer back to La and resulting in Lb emission. T-TEDOPA reproduces the experimentally supported excited-state relaxation mechanisms and emissive state assignments. The moderate underestimation of the Stokes shifts for systems with strong solute-solvent interactions, such as indole and Trp, is attributed to limitations of the electronic-structure method and the QM/MM solvent treatment. These results further establish T-TEDOPA as a robust framework for simulating photophysical properties in complex condensed-phase systems.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry",
    "Oregon State University",
    "Department of Physics"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Dayana Bashirova"
    },
    {
      "affs": [
        2,
        1
      ],
      "name": "Evan Lambertson"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Bianca Dawson"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Tim J. Zuehlsdorff"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/4b5sypq8a3f5r.bib",
  "cited_by": 0,
  "doi": "10.26434/chemrxiv.15008292/v1",
  "fulltext_url": null,
  "id": "4b5sypq8a3f5r",
  "issns": [],
  "landing_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008292/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|Photochemistry and Electron Transfer Studies"
    ]
  ],
  "openalex": "W7208772458",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-04",
  "publisher": "American Chemical Society (ACS)",
  "ris": "https://research.draconitic.com/paper/4b5sypq8a3f5r.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:17Z",
      "native_id": "10.26434/chemrxiv.15008292",
      "source": "chemrxiv",
      "url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008292/v1"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1606|Photochemistry and Electron Transfer Studies",
      "subfield": "physical"
    }
  ],
  "title": "Computational Elucidation of System-Dependent Excited-State Relaxation Mechanisms and Stokes Shifts in Indole-Based Chromophores",
  "title_text": "Computational Elucidation of System-Dependent Excited-State Relaxation Mechanisms and Stokes Shifts in Indole-Based Chromophores",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:17Z",
  "url": "https://research.draconitic.com/paper/4b5sypq8a3f5r",
  "venue": "ChemRxiv",
  "versions": []
}