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用密度泛函理论分子动力学研究催化异质界面的动力学:常用恒温器导致的异常温度分布

Addressing Dynamics at Catalytic Heterogeneous Interfaces with DFT-MD: Anomalous Temperature Distributions from Commonly Used Thermostats.

作者信息

Korpelin Ville, Kiljunen Toni, Melander Marko M, Caro Miguel A, Kristoffersen Henrik H, Mammen Nisha, Apaja Vesa, Honkala Karoliina

机构信息

Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YN), FI-40014 Jyväskylä, Finland.

Department of Electrical Engineering and Automation, Aalto University, FIN-02150 Espoo, Finland.

出版信息

J Phys Chem Lett. 2022 Mar 24;13(11):2644-2652. doi: 10.1021/acs.jpclett.2c00230. Epub 2022 Mar 17.

DOI:10.1021/acs.jpclett.2c00230
PMID:35297635
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8959310/
Abstract

Density functional theory-based molecular dynamics (DFT-MD) has been widely used for studying the chemistry of heterogeneous interfacial systems under operational conditions. We report frequently overlooked errors in thermostated or constant-temperature DFT-MD simulations applied to study (electro)catalytic chemistry. Our results demonstrate that commonly used thermostats such as Nosé-Hoover, Berendsen, and simple velocity-rescaling methods fail to provide a reliable temperature description for systems considered. Instead, nonconstant temperatures and large temperature gradients within the different parts of the system are observed. The errors are not a "feature" of any particular code but are present in several molecular dynamics implementations. This uneven temperature distribution, due to inadequate thermostatting, is well-known in the classical MD community, where it is ascribed to the failure in kinetic energy equipartition among different degrees of freedom in heterogeneous systems (Harvey . 1998, 726-740) and termed the flying ice cube effect. We provide tantamount evidence that interfacial systems are susceptible to substantial flying ice cube effects and demonstrate that the traditional Nosé-Hoover and Berendsen thermostats should be applied with care when simulating, for example, catalytic properties or structures of solvated interfaces and supported clusters. We conclude that the flying ice cube effect in these systems can be conveniently avoided using Langevin dynamics.

摘要

基于密度泛函理论的分子动力学(DFT-MD)已被广泛用于研究实际操作条件下多相界面体系的化学性质。我们报告了在用于研究(电)催化化学的恒温或等温DFT-MD模拟中经常被忽视的错误。我们的结果表明,常用的热浴方法,如诺西-胡佛(Nosé-Hoover)、贝伦德森(Berendsen)和简单的速度重标方法,无法为所考虑的体系提供可靠的温度描述。相反,会观察到体系不同部分存在非恒定温度和较大的温度梯度。这些错误并非任何特定代码的“特性”,而是在多个分子动力学实现中都存在。由于热浴不足导致的这种不均匀温度分布在经典分子动力学领域是众所周知的,在该领域中,它被归因于多相体系中不同自由度之间动能均分的失败(哈维,1998年,726 - 740页),并被称为“飞冰块效应”。我们提供了同等的证据表明界面体系容易受到显著的飞冰块效应影响,并证明在模拟例如溶剂化界面和负载簇的催化性质或结构时,应谨慎使用传统的诺西-胡佛和贝伦德森热浴。我们得出结论,使用朗之万动力学可以方便地避免这些体系中的飞冰块效应。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/684fec97adcd/jz2c00230_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/1cd71ce18dc5/jz2c00230_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/9205dbcece90/jz2c00230_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/e6edcac3e460/jz2c00230_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/684fec97adcd/jz2c00230_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/1cd71ce18dc5/jz2c00230_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/9205dbcece90/jz2c00230_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/e6edcac3e460/jz2c00230_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b703/8959310/684fec97adcd/jz2c00230_0004.jpg

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