关于Ca2+在Ab Initio分子动力学解决方案中的局部结构平衡
Hugo Moison1, Julie Aufort1,2, Magali Benoit3
1GET, OMP, Université Paul Sabatier, 14, avenue Édouard Belin, 31400 Toulouse, France.
The journal of physical chemistry. B
|March 25, 2024
概括
稳定的同位素分析对气候,健康和农业至关重要. 这项研究使用了ab initio分子动力学来模拟水中的离子协调,发现温度显著影响结果,并突出了以前的模拟问题.
科学领域:
- 计算化学的计算化学
- 物理化学 物理化学
- 生物地质化学生物地质化学
背景情况:
- 稳定的 (Ca) 同位素比例对于包括气候重建,骨癌诊断和农业营养管理在内的应用至关重要.
- 在水中Ca2+的协调对于其分化特性至关重要,但仍有争议.
- 对Ca2+水合的准确建模对于解释各种科学学科的同位素数据至关重要.
研究的目的:
- 使用ab initio分子动力学模拟来建模水中的Ca2+协调.
- 研究不同交换相关函数和温度对Ca2+协调的影响.
- 评估模拟结果的趋同性和可靠性,特别是关于水分子交换的模拟结果.
主要方法:
- 采用了ab initio分子动力学模拟,以在水溶液中的Ca2+模型.
- 测试了各种交换和相关函数,选择了BLYP与Grimme-D2校正,因为其在重现水性质方面的准确性.
- 系统地研究温度效应 (300600 K),并实施方法以确保模拟趋同,包括马尔科夫链分析.
主要成果:
- 功能性选择显著影响计算的平均Ca2+协调.
- 在较低温度 (300400 K) 的模拟显示了潜在的平衡问题,限制了趋同和可靠性.
- 估计的Ca2+协调值在300K的6.2到高温 (450600K) 的6.7-6.8之间.
结论:
- 具有Grimme-D2校正的BLYP函数提供了水中的Ca2+的可靠模型.
- 温度显著影响Ca2+协调,而模拟交换不足可能导致错误的结论.
- 结果强调需要在同位素研究中仔细验证模拟参数,特别是温度和平衡.
相关概念视频
Feedback Regulation of Calcium Concentration
3.4K
Calcium is an essential signaling molecule required for various cellular functions. Calcium pumps and ion channels on cell and organellar membranes, such as those on the endoplasmic reticulum (ER), regulate calcium concentrations inside the cell. They remain closed, keeping the cytosolic calcium levels low at a resting state.
Various transmembrane receptors, such as G protein-coupled receptors (GPCRs), elicit a response to extracellular signals by increasing cytosolic calcium. Activated GPCRs...
Various transmembrane receptors, such as G protein-coupled receptors (GPCRs), elicit a response to extracellular signals by increasing cytosolic calcium. Activated GPCRs...
3.4K
Complexation Equilibria: Overview
672
Complexation reactions take place when dative or coordinate covalent bonds form between metal ions and ligands. The compounds formed in these reactions are called coordination compounds. The number of bonds formed between the metal ion and the ligands is called its coordination number. Generally, most metal ions in an aqueous solution are solvated by water molecules and thus exist as aqua complexes.
The equilibrium constant of the complexation reaction is represented as the formation constant...
The equilibrium constant of the complexation reaction is represented as the formation constant...
672
Chemical Equilibria: Systematic Approach to Equilibrium Calculations
689
Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
The first step is to identify all the chemical reactions involved, The...
The first step is to identify all the chemical reactions involved, The...
689
Calmodulin-dependent Signaling
5.1K
Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
5.1K


