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The molecular structures of 40-mer poly(N-isopropylacrylamide) (PNIPAM) chains in solutions were obtained using molecular dynamics simulations. The 5-mer PNIPAM chains with terminated H atoms, including the second coordination shells of the solvent methanol and water molecules, were extracted from the 40-mer PNIPAM chains in solutions. The O K-edge inner-shell spectra of the 5-mer PNIPAM chains were obtained by averaging the inner-shell spectra of 9700 extracted polymer structures. This calculation method can be used to precisely evaluate the energy shifts of the C=O \u03c0* peaks of PNIPAM caused by the structural changes of the polymer chains, the substitutions of the hydrogen bonds of the C=O groups in PNIPAM from methanol to water molecules, and the increase in the coordination numbers of solvent molecules with the C=O groups, which were observed in the O K-edge XAS experiments.<\/jats:p>","DOI":"10.1063\/5.0245456","type":"journal-article","created":{"date-parts":[[2025,2,3]],"date-time":"2025-02-03T11:34:11Z","timestamp":1738582451000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Oxygen K-edge inner-shell calculations of polymers in solutions realized by the extraction of local structures from molecular dynamics simulations"],"prefix":"10.1063","volume":"162","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6249-6553","authenticated-orcid":false,"given":"Masanari","family":"Nagasaka","sequence":"first","affiliation":[{"name":"Institute for Molecular Science 1 , Myodaiji, Okazaki 444-8585,","place":["Japan"]},{"name":"Graduate Institute for Advanced Studies, SOKENDAI 2 , Myodaiji, Okazaki 444-8585,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2197-3883","authenticated-orcid":false,"given":"Yifeng","family":"Yao","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Zhejiang University 3 , Hangzhou 310028,","place":["People\u2019s Republic of China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8947-9980","authenticated-orcid":false,"given":"Kenji","family":"Mochizuki","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Zhejiang University 3 , Hangzhou 310028,","place":["People\u2019s Republic of China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"317","published-online":{"date-parts":[[2025,2,3]]},"reference":[{"key":"2025020311340966200_c1","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1146\/annurev.physchem.58.032806.104614","article-title":"Protein-folding dynamics: Overview of molecular simulation techniques","volume":"58","year":"2007","journal-title":"Annu. 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