基于片段分子轨道的水合Cu(II)离子分子动力学(FMO-MD)模拟

IF 0.4 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
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":null,"pages":null},"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\":null,\"pages\":null},\"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}
引用次数: 4

摘要

采用基于片段分子轨道分子动力学(FMO-MD)的模拟方法,研究了由一个二价铜离子和64个水分子组成的液滴模型。在三体碎片校正(FMO3)下,在无限制Hartree-Fock (UHF)水平上评估总能量和力。在第一个水化壳中进行了两次MD运行:一次是六配位设置,另一次是五配位设置。两次运行均得到Cu-O径向分布函数的主峰位置为2.02 Å,与实验数据吻合较好。两种情况下的O-Cu-O角分布函数表现出不同的特征。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Chem-Bio Informatics Journal
Chem-Bio Informatics Journal BIOCHEMISTRY & MOLECULAR BIOLOGY-
CiteScore
0.60
自引率
0.00%
发文量
8
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信