利用 mW 模型进行 MD 模拟,研究封闭对超亲水孔隙中水特性的影响。

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-09-24 DOI:10.1007/s00894-024-06145-2
Vikas Kumar Sinha, Chandan Kumar Das
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引用次数: 0

摘要

背景:我们利用单原子水(mW)模型,探讨了强亲水约束对水的各种特性的影响,如密度、焓、势能、径向分布函数、熵、比热容、结构动力学和转变温度(凝固和熔化温度)。研究发现,水的特性取决于封闭性和壁-流体表面的相互作用。在过渡温度附近观察到密度、焓、势能和熵的滞后环,而滞后环的大小随封闭性和表面相互作用而变化。在孔径较小(H ≤ 20)的情况下,固相的密度比液相的密度高,这是与散装水系统相比非常规的行为,原因是封闭表面具有明显的亲水性。与散装水相比,封闭系统中的比热容表现出更大的振荡,这是由于在相等的温度区间内焓差不均匀造成的。在加热和淬火过程中的相变过程中,比热容会发生突变。在固相中,封闭对熵有显著影响,但在液相中,其影响可以忽略不计。同样,在孔径较小(H 25 Å)的熔化温度中也观察到更多的振荡行为。在淬火过程中,面内取向参数和四面体有序参数的突然跳变表明形成了有序相,特别是金刚石晶体结构。不同晶体结构(立方金刚石、六方金刚石和二维六方)的百分比随约束尺寸和壁流体相互作用强度而变化:在 100-350 K 的温度范围内,使用 LAMMPS 对不同纳米级禁锢分离尺寸(从 8.5 Å 到 70 Å)的 mW 水模型进行冷却和加热模拟。使用模拟实验获得的 RDF 数据计算每个温度点的熵,熵的增减幅度为 2.5 K。
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Effect of confinement on water properties in super-hydrophilic pores using MD simulations with the mW model

Context

We explore the influence of strongly hydrophilic confinement on various properties of water, such as density, enthalpy, potential energy, radial distribution function, entropy, specific heat capacity, structural dynamics, and transition temperatures (freezing and melting temperatures), using monatomic water (mW) model. The properties of water are found to be dependent on confinement and the wall-fluid surface interaction. Hysteresis loops are observed for density, enthalpy, potential energy, and entropy around the transition temperatures, while the size of hysteresis loops varies with confinement and surface interaction. In smaller pore sizes (H ≤ 20), the solid phase displays a higher density compared to the liquid phase, which is unconventional behavior compared to bulk water systems due to the pronounced hydrophilic properties of the confinement surface. Specific heat capacity exhibits more oscillations in the confined system compared to bulk water, stemming from uneven enthalpy differences across equal temperature intervals. During phase transformation in both heating and quenching processes, there is an abrupt change observed in specific heat capacity. Confinement exerts a notable impact on entropy in the solid phase, but its influence is negligible in the liquid phase. At lower pore sizes (H < 25 Å), there is more fluctuation in freezing temperature for all wall-fluid interactions, which diminishes beyond pore sizes of H > 25 Å. Similarly, more oscillatory behavior is observed in melting temperatures at lower pore sizes (H < 40 Å), which diminishes at higher pore sizes (H > 40 Å). During the quenching process, a sudden jump in the in-plane orientational and tetrahedral order parameters indicates the formation of an ordered phase, specifically a diamond crystalline structure. The percentages of different crystalline structures (cubic diamond, hexagonal diamond, and 2D hexagonal) vary with both the confinement size and the wall-fluid interaction strength.

Methods

Cooling and heating simulations are conducted with the mW water model using LAMMPS for different nanoscale confinement separation sizes ranging from 8.5 to 70 Å within the temperature range of 100–350 K. The water is modeled using two-body and three-body interaction potential (Stillinger–Weber potential) and the confinement is introduced using LJ 9–3 water-wall interaction potential. Entropy is calculated using RDF data obtained from the simulation experiments for each temperature point with increments or decrements of 2.5 K. The transition temperatures are estimated using the specific heat capacity analysis.

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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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