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浓度驱动过程的非平衡建模——恒化学势分子动力学模拟。

Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations.

机构信息

Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India.

Thomas Young Centre and Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom.

出版信息

Acc Chem Res. 2023 May 16;56(10):1156-1167. doi: 10.1021/acs.accounts.2c00811. Epub 2023 Apr 25.

DOI:10.1021/acs.accounts.2c00811
PMID:37120847
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10193523/
Abstract

ConspectusConcentration-driven processes in solution, i.e., phenomena that are sustained by persistent concentration gradients, such as crystallization and surface adsorption, are fundamental chemical processes. Understanding such phenomena is crucial for countless applications, from pharmaceuticals to biotechnology. Molecular dynamics (MD), both in- and out-of-equilibrium, plays an essential role in the current understanding of concentration-driven processes. Computational costs, however, impose drastic limitations on the accessible scale of simulated systems, hampering the effective study of such phenomena. In particular, due to these size limitations, closed system MD of concentration-driven processes is affected by solution depletion/enrichment that unavoidably impacts the dynamics of the chemical phenomena under study. As a notable example, in simulations of crystallization from solution, the transfer of monomers between the liquid and crystal phases results in a gradual depletion/enrichment of solution concentration, altering the driving force for phase transition. In contrast, this effect is negligible in experiments, given the macroscopic size of the solution volume. Because of these limitations, accurate MD characterization of concentration-driven phenomena has proven to be a long-standing simulation challenge. While disparate equilibrium and nonequilibrium simulation strategies have been proposed to address the study of such processes, the methodologies are in continuous development.In this context, a novel simulation technique named constant chemical potential molecular dynamics (CμMD) was recently proposed. CμMD employs properly designed, concentration-dependent external forces that regulate the flux of solute species between selected subregions of the simulation volume. This enables simulations of systems under a constant chemical drive in an efficient and straightforward way. The CμMD scheme was originally applied to the case of crystal growth from solution and then extended to the simulation of various physicochemical processes, resulting in new variants of the method. This Account illustrates the CμMD method and the key advances enabled by it in the framework of chemistry. We review results obtained in crystallization studies, where CμMD allows growth rate calculations and equilibrium shape predictions, and in adsorption studies, where adsorption thermodynamics on porous or solid surfaces was correctly characterized via CμMD. Furthermore, we will discuss the application of CμMD variants to simulate permeation through porous materials, solution separation, and nucleation upon fixed concentration gradients. While presenting the numerous applications of the method, we provide an original and comprehensive assessment of concentration-driven simulations using CμMD. To this end, we also shed light on the theoretical and technical foundations of CμMD, underlining the novelty and specificity of the method with respect to existing techniques while stressing its current limitations. Overall, the application of CμMD to a diverse range of fields provides new insight into many physicochemical processes, the study of which has been hitherto limited by finite-size effects. In this context, CμMD stands out as a general-purpose method that promises to be an invaluable simulation tool for studying molecular-scale concentration-driven phenomena.

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/baa7/10193523/4eeb5dbff14c/ar2c00811_0005.jpg
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摘要

概述

溶液中的浓度驱动过程,即由持续的浓度梯度维持的现象,如结晶和表面吸附,是基本的化学过程。理解这些现象对于从制药到生物技术的无数应用至关重要。分子动力学(MD),无论是在平衡态还是非平衡态,都在当前对浓度驱动过程的理解中发挥着重要作用。然而,计算成本对可模拟系统的规模施加了严格的限制,阻碍了对这些现象的有效研究。特别是,由于这些尺寸限制,对浓度驱动过程的封闭系统 MD 受到溶液耗尽/富集的影响,这不可避免地影响了所研究的化学现象的动力学。作为一个显著的例子,在溶液结晶的模拟中,单体在液相和晶相之间的转移导致溶液浓度的逐渐耗尽/富集,改变了相变的驱动力。相比之下,由于溶液体积的宏观尺寸,这种效应在实验中可以忽略不计。由于这些限制,对浓度驱动现象的准确 MD 特征描述已被证明是一个长期存在的模拟挑战。虽然已经提出了各种平衡和非平衡模拟策略来解决这些过程的研究,但这些方法仍在不断发展。

在这种情况下,最近提出了一种名为恒化学势分子动力学(CμMD)的新型模拟技术。CμMD 采用适当设计的、与浓度相关的外部力,调节溶质物种在模拟体积的选定子区域之间的通量。这使得可以以高效和直接的方式模拟在恒定化学驱动力下的系统。CμMD 方案最初应用于溶液中晶体生长的情况,然后扩展到各种物理化学过程的模拟,从而产生了该方法的新变体。本账户说明了 CμMD 方法及其在化学框架内实现的关键进展。我们回顾了在结晶研究中获得的结果,在这些研究中,CμMD 允许计算生长速率和平衡形状预测,以及在吸附研究中,通过 CμMD 正确地描述了多孔或固体表面上的吸附热力学。此外,我们将讨论 CμMD 变体在模拟多孔材料中的渗透、溶液分离和固定浓度梯度下的成核中的应用。在介绍该方法的众多应用的同时,我们对使用 CμMD 进行浓度驱动模拟进行了原创性和全面的评估。为此,我们还强调了 CμMD 的理论和技术基础,突出了该方法相对于现有技术的新颖性和特异性,同时强调了其当前的局限性。总的来说,CμMD 在各种领域的应用为许多物理化学过程提供了新的见解,这些过程的研究由于有限尺寸效应而受到限制。在这种情况下,CμMD 作为一种通用方法脱颖而出,有望成为研究分子尺度浓度驱动现象的宝贵模拟工具。

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