Center for Molecular Modeling - S. Caroes

The Importance of Cell Shape Sampling To Accurately Predict Flexibility in Metal-Organic Frameworks

michel — Sat, 11 Nov 2017 15:06:22 +0000

S.M.J. Rogge, S. Caroes, R. Demuynck, M. Waroquier, V. Van Speybroeck, A. Ghysels

Journal of Chemical Theory and Computation

14 (3), 1186-1197

2018

Abstract

In this work, the influence of cell shape sampling on the predicted stability of the different metastable phases in flexible metal–organic frameworks at finite temperatures is investigated. The influence on the free energy by neglecting cell shape sampling is quantified for the prototypical MIL-53(Al) and the topical DUT-49(Cu). This goal is achieved by constructing free energy profiles in ensembles either in which the phase space associated with the cell shape is sampled explicitly or in which the cell shape is kept fixed. When neglecting cell shape sampling, thermodynamic integration of the hydrostatic pressure yields unreliable free energy profiles that depend on the choice of the fixed cell shape. In this work, we extend the thermodynamic integration procedure via the introduction of a generalized pressure, derived from the Lagrangian strain tensor and the second Piola–Kirchhoff tensor. Using this generalized procedure, the dependence on the unit cell shape can be eliminated, and the inaccuracy in free energy stemming from the lack of cell shape sampling can be uniquely quantified. Finally, it is shown that the inaccuracy in free energy when fixing the cell shape at room temperature stems mainly from entropic contributions for both MIL-53(Al) and DUT-49(Cu).

DOI

http://dx.doi.org/10.1021/acs.jctc.7b01134

Private attachment

main.pdf

Starters grant

wim — Wed, 29 Mar 2017 08:25:37 +0000

Project promotor

A. Ghysels

Financierende instantie

BOF

Project data

01/09/2016 to 31/10/2020

Bedrag

€73 000,00

Project titel

BOF/STA/030

Personeel

S. Caroes

Project ref.

BOF A.Ghysels BOFSTA2016001601

The importance of unit cell fluctuations for free energy profiles of flexible crystals

senne — Wed, 22 Mar 2017 14:46:32 +0000

S. Caroes, S.M.J. Rogge, R. Demuynck, L. Vanduyfhuys, V. Van Speybroeck, A. Ghysels

ISBN/ISSN:

Poster

Conference / event / venue

MolSim 2017

Amsterdam The Netherlands

Monday, 9 January, 2017 to Friday, 20 January, 2017

Abstract (private)

Poster_SenneCaroes_Final.pdf

Model reduction by coarse-graining the diffusion propagator in complex media

wim — Wed, 08 Mar 2017 13:49:40 +0000

Understanding the Activity of Spinorphin Derivatives with Markov State Models

wim — Wed, 08 Mar 2017 10:44:11 +0000

Where classical meets quantum: developing diagnostic tools for mass transport simulations at the atomic scale

wim — Mon, 07 Mar 2016 14:51:52 +0000

Modeling oxygen diffusion through biological lipid membranes using inverse Monte Carlo

wim — Mon, 07 Mar 2016 13:20:24 +0000

Model reduction by coarse-graining the diffusion propagator in complex media

wim — Mon, 07 Mar 2016 13:15:20 +0000

Senne Caroes

wim — Mon, 31 Aug 2015 08:36:15 +0000

Explicit sampling of the unit cell shape for a more accurate estimation of the free energy profile for flexible crystals

wim — Mon, 31 Aug 2015 07:08:20 +0000

S. Caroes

Master of Science in Physics and Astronomy

2016

Supervisors

Prof. Dr. ir. A. Ghysels, Prof. Dr. ir. Veronique Van Speybroeck

Attachment (private)

scriptie(1).pdf