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An introduction to classical molecular dynamics simulation for experimental scattering users.

ABSTRACT: Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a 'black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.

SUBMITTER: McCluskey AR

PROVIDER: S-EPMC6557182 | biostudies-other | 2019 Jun

REPOSITORIES: biostudies-other

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An introduction to classical molecular dynamics simulation for experimental scattering users.

McCluskey Andrew R AR Grant James J Symington Adam R AR Snow Tim T Doutch James J Morgan Benjamin J BJ Parker Stephen C SC Edler Karen J KJ

Journal of applied crystallography 20190507 Pt 3

Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a 'black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamic ...[more]

PMID: 31236095

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Project description:Zeolite ZSM-5 is a key catalyst in commercially relevant processes including the widely studied methanol to hydrocarbon reaction, and molecular diffusion in zeolite pores is known to be a crucial factor in controlling catalytic reactions. Here, we present critical analyses of recent quasi-elastic neutron scattering (QENS) data and complementary molecular dynamics (MD) simulations. The QENS experiments show that the nature of methanol diffusion dynamics in ZSM-5 pores is dependent both on the Si/Al ratio (11, 25, 36, 40 and 140), which determines the Brønsted acid site density of the zeolite, and that the nature of the type of motion observed may vary qualitatively over a relatively small temperature range. At 373 K, on increasing the ratio from 11 to 140, the observed mobile methanol fraction increases and the nature of methanol dynamics changes from rotational (in ZSM-5 with Si/Al of 11) to translational diffusion. The latter is either confined localized diffusion within a pore in zeolites with ratios up to 40 or non-localized, longer-range diffusion in zeolite samples with the ratio of 140. The complementary MD simulations conducted over long time scales (1 ns), which are longer than those measured in the present study by QENS (≈1-440 ps), at 373 K predict the occurrence of long-range translational diffusion of methanol in ZSM-5, independent of the Si/Al ratios (15, 47, 95, 191 and siliceous MFI). The rate of diffusion increases slightly by increasing the ratio from 15 to 95 and thereafter does not depend on zeolite composition. Discrepancies in the observed mobile methanol fraction between the MD simulations (100% methanol mobility in ZSM-5 pores across all Si/Al ratios) and QENS experiments (for example, ≈80% immobile methanol in ZSM-5 with Si/Al of 11) are attributed to the differences in time resolutions of the techniques. This perspective provides comprehensive information on the effect of acid site density on methanol dynamics in ZSM-5 pores and highlights the complementarity of QENS and MD, and their advantages and limitations. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

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An introduction to classical molecular dynamics simulation for experimental scattering users.

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An introduction to classical molecular dynamics simulation for experimental scattering users.

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