Yuji. Kato, T. Fujiwara, Y. Komeiji, T. Nakano, H. Mori, Yoshio Okiyama, Y. Mochizuki
{"title":"基于片段分子轨道的水合Cu(II)离子分子动力学(FMO-MD)模拟","authors":"Yuji. Kato, T. Fujiwara, Y. Komeiji, T. Nakano, H. Mori, Yoshio Okiyama, Y. Mochizuki","doi":"10.1273/CBIJ.14.1","DOIUrl":null,"url":null,"abstract":"A simulation protocol based on fragment molecular orbital−based molecular dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water molecules. The total energy and forces were evaluated at the unrestricted Hartree-Fock (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the experimental data. The O-Cu-O angular distribution function showed different characteristics between the two cases.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"2021 1","pages":"1-13"},"PeriodicalIF":0.4000,"publicationDate":"2014-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"4","resultStr":"{\"title\":\"Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion\",\"authors\":\"Yuji. Kato, T. Fujiwara, Y. Komeiji, T. Nakano, H. Mori, Yoshio Okiyama, Y. Mochizuki\",\"doi\":\"10.1273/CBIJ.14.1\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"A simulation protocol based on fragment molecular orbital−based molecular dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water molecules. The total energy and forces were evaluated at the unrestricted Hartree-Fock (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the experimental data. The O-Cu-O angular distribution function showed different characteristics between the two cases.\",\"PeriodicalId\":40659,\"journal\":{\"name\":\"Chem-Bio Informatics Journal\",\"volume\":\"2021 1\",\"pages\":\"1-13\"},\"PeriodicalIF\":0.4000,\"publicationDate\":\"2014-07-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"4\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Chem-Bio Informatics Journal\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1273/CBIJ.14.1\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chem-Bio Informatics Journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1273/CBIJ.14.1","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion
A simulation protocol based on fragment molecular orbital−based molecular dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water molecules. The total energy and forces were evaluated at the unrestricted Hartree-Fock (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the experimental data. The O-Cu-O angular distribution function showed different characteristics between the two cases.