Suppr超能文献

多尺度反应分子动力学。

Multiscale reactive molecular dynamics.

机构信息

Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, USA.

出版信息

J Chem Phys. 2012 Dec 14;137(22):22A525. doi: 10.1063/1.4743958.

Abstract

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

摘要

许多对化学、材料科学和生物学很重要的过程,如果不考虑电子和核级别的动力学及其与系统较慢、协作运动的耦合,就无法描述。这些固有的多尺度问题需要计算效率高且准确的方法来收敛统计性质。本文提出了一种方法,该方法使用来自凝聚相从头算模拟的直接数据来开发反应性分子动力学模型,而不需要预定义的经验函数。相反,反应性模型中使用的相互作用表示为通过使用线性最小二乘算法进行优化的插值函数的线性组合。这里概述的过程的一个显著优点是能够最小化需要非线性优化的参数数量。该方法可一般应用于多尺度问题,并通过直接基于凝聚相从头算分子动力学模拟为水合过剩质子和氢氧根离子生成反应性模型来证明。由此产生的模型忠实地再现了从头算模拟中的水-离子结构特性和扩散常数。此外,质子转移的自由能曲线也被再现,质子转移对两个离子在水中的结构扩散很敏感。这些模型与从头算模拟的高度一致性将允许以比当前从头算模拟方法高几个数量级的计算效率对凝聚相系统中的一般化学反应进行精确建模,从而有效地对系统较慢、大规模运动的耦合进行统计抽样。

相似文献

1
Multiscale reactive molecular dynamics.多尺度反应分子动力学。
J Chem Phys. 2012 Dec 14;137(22):22A525. doi: 10.1063/1.4743958.
5
On the recombination of hydronium and hydroxide ions in water.在水合氢离子和氢氧根离子的重组。
Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20410-5. doi: 10.1073/pnas.1112486108. Epub 2011 Dec 5.
6
The curious case of the hydrated proton.水合质子的奇案。
Acc Chem Res. 2012 Jan 17;45(1):101-9. doi: 10.1021/ar200140h. Epub 2011 Aug 22.

引用本文的文献

1
Classical Models of Hydroxide for Proton Hopping Simulations.用于质子跳跃模拟的氢氧化物经典模型。
J Phys Chem B. 2024 Dec 12;128(49):12161-12170. doi: 10.1021/acs.jpcb.4c05499. Epub 2024 Dec 3.
2
Activation of the Influenza B M2 Proton Channel (BM2).乙型流感病毒 M2 质子通道(BM2)的激活。
Biochemistry. 2024 Nov 19;63(22):3011-3019. doi: 10.1021/acs.biochem.4c00607. Epub 2024 Nov 3.
4
Activation of the influenza B M2 proton channel (BM2).乙型流感病毒M2质子通道(BM2)的激活
bioRxiv. 2024 Jul 26:2024.07.26.605324. doi: 10.1101/2024.07.26.605324.

本文引用的文献

5
On Ion and Molecular Polarization of Halides in Water.论卤化物在水中的离子与分子极化
J Chem Theory Comput. 2009 Jun 9;5(6):1449-53. doi: 10.1021/ct900096n.
8
The curious case of the hydrated proton.水合质子的奇案。
Acc Chem Res. 2012 Jan 17;45(1):101-9. doi: 10.1021/ar200140h. Epub 2011 Aug 22.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验