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We studied water confined in naphthalene diimide (NDI)-based molecular crystals via classical molecular dynamics simulations. We examined NDIs functionalized with either hydrophilic linear triethylene glycol side chains (NDI-TEG) or hydrophobic n-hexyl chains (NDI-C6), increasing the hydration (i.e., amount of water molecules within each crystal) up to a 1:3 NDI:water molar ratio. Static and dynamical properties of confined water are compared to those of room-temperature and supercooled (200\u00a0K) bulk water, which serve as references for liquid and glassy states, respectively. The impact of confinement is analyzed through structural order parameters, time-dependent correlation functions, and hydrogen-bond (HB) analyses. At low hydration (\u22481:1 NDI:water), confined water assumes a structural order that is far from the tetrahedral one, showing different spatial organizations when inserted within hydrophilic NDI-TEG or hydrophobic NDI-C6 crystals. By increasing the hydration level (\u22481:3 NDI:water), the structure of confined water clusters shifts toward a more bulk-like (liquid) arrangement, while the chemical nature of the NDI side chains plays a marginal role. Notably, fast (sub-ps) and slow (hundreds of ns) water dynamics are not much influenced by the hydrophilicity\/hydrophobicity of the side chains but rather by confinement effects. The analysis of the HB network autocorrelation functions highlights how finite-size effects and restricted connectivity are the main factors controlling HB dynamics. Our study paves the way toward an atomistic understanding of both structural and dynamical functions of water confined in molecular crystals, opening new paths for the rationalization of transport phenomena in the emerging class of organic mixed ionic-electronic conductors.<\/jats:p>","DOI":"10.1063\/5.0318997","type":"journal-article","created":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T11:38:21Z","timestamp":1778585901000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Structure and dynamics of confined water in naphthalene-diimide based molecular crystals"],"prefix":"10.1063","volume":"164","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-0135-0135","authenticated-orcid":false,"given":"Filippo Tommaso","family":"Garattoni","sequence":"first","affiliation":[{"name":"Department of Chemistry \u201cGiacomo Ciamician,\u201d University of Bologna 1 , via Piero Gobetti 85, 40129 Bologna,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9133-939X","authenticated-orcid":false,"given":"Marco","family":"Severi","sequence":"additional","affiliation":[{"name":"Department of Chemistry \u201cGiacomo Ciamician,\u201d University of Bologna 1 , via Piero Gobetti 85, 40129 Bologna,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Amante","sequence":"additional","affiliation":[{"name":"Institute for Chemical-Physical Processes, National Research Council of Italy 2 , viale Ferdinando Stagno d\u2019Alcontres 37, 98158 Messina,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8591-1203","authenticated-orcid":false,"given":"Christian B.","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Queen Mary University of London 3 , Mile End Road, London E1 4NS,","place":["United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1895-2950","authenticated-orcid":false,"given":"Giuseppe","family":"Cassone","sequence":"additional","affiliation":[{"name":"Institute for Chemical-Physical Processes, National Research Council of Italy 2 , viale Ferdinando Stagno d\u2019Alcontres 37, 98158 Messina,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8515-4214","authenticated-orcid":false,"given":"Daniele","family":"Fazzi","sequence":"additional","affiliation":[{"name":"Department of Chemistry \u201cGiacomo Ciamician,\u201d University of Bologna 1 , via Piero Gobetti 85, 40129 Bologna,","place":["Italy"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"317","published-online":{"date-parts":[[2026,5,12]]},"reference":[{"issue":"11","key":"2026051207381566400_c1","doi-asserted-by":"publisher","first-page":"110401","DOI":"10.1063\/5.0292407","article-title":"Advances in unveiling water\u2019s molecular mysteries","volume":"163","year":"2025","journal-title":"J.\u00a0Chem. 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