{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T03:01:26Z","timestamp":1791342086365,"version":"4.3.1"},"reference-count":86,"publisher":"AIP Publishing","issue":"15","funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0022884"],"award-info":[{"award-number":["DE-SC0022884"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006377","name":"Purdue University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006377","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,4,21]]},"abstract":"<jats:p>Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter\u2019s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna\u2013Matthews\u2013Olson protein, and ring deformation in photosystems I and II.<\/jats:p>","DOI":"10.1063\/5.0198443","type":"journal-article","created":{"date-parts":[[2024,4,19]],"date-time":"2024-04-19T09:55:17Z","timestamp":1713520517000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":5,"title":["PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations"],"prefix":"10.1063","volume":"160","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4688-4721","authenticated-orcid":false,"given":"S.","family":"Ahad","sequence":"first","affiliation":[{"name":"Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-6550-900X","authenticated-orcid":false,"given":"C.","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7390-3652","authenticated-orcid":false,"given":"M.","family":"Reppert","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2024,4,19]]},"reference":[{"key":"2024041909550951700_c1","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1039\/c1fd00078k","article-title":"Design principles of photosynthetic light-harvesting","volume":"155","year":"2012","journal-title":"Faraday Discuss."},{"key":"2024041909550951700_c2","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/nature22012","article-title":"Quantum design of photosynthesis for bio-inspired solar-energy conversion","volume":"543","year":"2017","journal-title":"Nature"},{"key":"2024041909550951700_c3","doi-asserted-by":"publisher","first-page":"35","DOI":"10.4137\/aci.s32151","article-title":"On the conflicting estimations of pigment site energies in photosynthetic complexes: A case study of the CP47 complex","volume":"11","year":"2016","journal-title":"Anal. 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