• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

水溶液中磷酸离子振动光谱的第一性原理分子动力学研究。

Vibrational spectra of phosphate ions in aqueous solution probed by first-principles molecular dynamics.

机构信息

Institut für Physikalische Chemie, Universität Zürich.

出版信息

J Phys Chem A. 2012 Mar 15;116(10):2466-74. doi: 10.1021/jp211783z. Epub 2012 Mar 6.

DOI:10.1021/jp211783z
PMID:22352866
Abstract

We have carried out "first-principles" Born-Oppenheimer molecular dynamics (BOMD) simulations of the phosphate ions H₂PO₄⁻ and HPO₄²⁻ in liquid water and have calculated their IR spectra by Fourier transform techniques from the trajectories. IR bands were assigned by a so-called "generalized normal coordinate analysis". The effects of including Hartree-Fock (HF) exchange into the density functional theory (DFT) computation of forces were studied by comparing results obtained with the well-known BP, BLYP, and B3LYP functionals. The neglect of dispersion in the functionals was empirically corrected. The inclusion of HF exchange turned out to yield dramatically improved and, thus, quite accurate descriptions of the IR spectra observed for H₂PO₄⁻ and HPO₄²⁻ in aqueous solution. An analysis of earlier computational results (Klähn, M. et al. J. Phys. Chem. A 2004, 108, 6186-6194) on these vibrational spectra, which had been obtained in a hybrid setting combining a BP description of the respective phosphate with a simple molecular mechanics (MM) model of its aqueous environment, revealed three different sources of error, (i) the BP force field of the phosphates is much too soft and would have required a substantial scaling of frequencies, (ii) the oversimplified water force field entailed incorrect solvation structures and, thus, qualitatively wrong patterns of solvatochromic band shifts, and (iii) quantitative frequency computations additionally required the inclusion of HF exchange. Thus, the results of the B3LYP BOMD simulations do not only characterize physical properties like the IR spectra or the solvation structures of the phosphate systems but also provide clues for the future design of simplified but nevertheless reasonably accurate DFT/MM methods applicable to phosphates.

摘要

我们对磷酸离子 H₂PO₄⁻和 HPO₄²⁻在液态水中进行了“第一性原理”Born-Oppenheimer 分子动力学(BOMD)模拟,并通过轨迹的傅里叶变换技术计算了它们的红外光谱。通过所谓的“广义正则坐标分析”对红外带进行了分配。通过比较使用著名的 BP、BLYP 和 B3LYP 泛函获得的结果,研究了在密度泛函理论(DFT)计算力中包含 Hartree-Fock(HF)交换的影响。在泛函中忽略色散的影响通过经验进行了修正。结果表明,包含 HF 交换可以大大改进并因此相当准确地描述在水溶液中观察到的 H₂PO₄⁻和 HPO₄²⁻的红外光谱。对这些振动光谱的早期计算结果(Klähn,M. 等人。J. Phys. Chem. A 2004, 108, 6186-6194)的分析表明,在结合了分别对磷酸盐的 BP 描述和其水溶液的简单分子力学(MM)模型的混合设置中获得的这些计算结果存在三个不同的误差源,(i)磷酸盐的 BP 力场太软,需要对频率进行大量缩放,(ii)过于简化的水力场导致不正确的溶剂化结构,从而导致溶剂化带位移的定性错误模式,(iii)定量频率计算还需要包含 HF 交换。因此,B3LYP BOMD 模拟的结果不仅可以描述物理性质,如红外光谱或磷酸盐系统的溶剂化结构,还可以为未来设计简化但仍然相当准确的适用于磷酸盐的 DFT/MM 方法提供线索。

相似文献

1
Vibrational spectra of phosphate ions in aqueous solution probed by first-principles molecular dynamics.水溶液中磷酸离子振动光谱的第一性原理分子动力学研究。
J Phys Chem A. 2012 Mar 15;116(10):2466-74. doi: 10.1021/jp211783z. Epub 2012 Mar 6.
2
Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application.动力学模拟中原子涨落的振动光谱。I. 理论、局限性及一个示例应用。
J Chem Phys. 2004 Dec 22;121(24):12233-46. doi: 10.1063/1.1822914.
3
Density functional theory study on the structure and vibrational frequencies of glycylglycine.甘氨酰甘氨酸结构与振动频率的密度泛函理论研究
Spectrochim Acta A Mol Biomol Spectrosc. 2008 Jul;70(2):301-6. doi: 10.1016/j.saa.2007.08.009. Epub 2007 Aug 19.
4
Direct calculations of vibrational absorption and circular dichroism spectra of alanine dipeptide analog in water: quantum mechanical/molecular mechanical molecular dynamics simulations.水中丙氨酸二肽类似物振动吸收和圆二色光谱的直接计算:量子力学/分子力学分子动力学模拟
J Chem Phys. 2009 Oct 7;131(13):135102. doi: 10.1063/1.3243078.
5
Hydration of inorganic phosphates in crystal lattices and in aqueous solution. An experimental and theoretical study.晶格和水溶液中无机磷酸盐的水合作用。一项实验与理论研究。
Spectrochim Acta A Mol Biomol Spectrosc. 2007 Apr;66(4-5):1152-64. doi: 10.1016/j.saa.2006.05.029. Epub 2006 Jun 6.
6
IR spectra of flavins in solution: DFT/MM description of redox effects.溶液中黄素的红外光谱:氧化还原效应的 DFT/MM 描述。
J Phys Chem B. 2011 Mar 10;115(9):2117-23. doi: 10.1021/jp111334z. Epub 2011 Feb 10.
7
Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution.动力学模拟中原子涨落的振动光谱。II. 飞秒时间分辨率下溶剂诱导的频率涨落。
J Chem Phys. 2004 Dec 22;121(24):12247-58. doi: 10.1063/1.1822915.
8
A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.一种用于研究水中溶剂化酰胺基团分子动力学的可极化量子力学/分子力学方法。
J Chem Phys. 2016 Mar 21;144(11):114504. doi: 10.1063/1.4943972.
9
Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water.溶剂对螺旋肽红外光谱和振动圆二色光谱的影响:基于密度泛函理论的含显式水的静态光谱模拟
J Phys Chem B. 2005 Apr 28;109(16):8231-43. doi: 10.1021/jp0506078.
10
Ab initio HF and DFT simulations, FT-IR and FT-Raman vibrational analysis of alpha-chlorotoluene.从头算 HF 和 DFT 模拟,α-氯甲苯的 FT-IR 和 FT-Raman 振动分析。
Spectrochim Acta A Mol Biomol Spectrosc. 2010 Sep 15;77(1):150-9. doi: 10.1016/j.saa.2010.04.043. Epub 2010 May 6.

引用本文的文献

1
Characterizing biomolecular structure features through an innovative elliptical dichroism spectrometry for cancer detection.通过创新的椭圆偏振光谱法表征生物分子结构特征以用于癌症检测。
Heliyon. 2024 Sep 24;10(19):e38399. doi: 10.1016/j.heliyon.2024.e38399. eCollection 2024 Oct 15.
2
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy.利用实时红外光谱法原位监测植物乳杆菌生物膜的形成。
NPJ Biofilms Microbiomes. 2022 Nov 19;8(1):92. doi: 10.1038/s41522-022-00353-5.
3
Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.
采用QM/MM 混合计算方法对生物分子和溶剂化分子的非谐振动分析。
J Chem Theory Comput. 2019 Mar 12;15(3):1924-1938. doi: 10.1021/acs.jctc.8b01193. Epub 2019 Feb 21.
4
The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations.量子力学/分子力学模拟揭示镁在 GTP 水解中的几何和电荷作用。
Biophys J. 2012 Jul 18;103(2):293-302. doi: 10.1016/j.bpj.2012.06.015. Epub 2012 Jul 17.