Center for Molecular Modeling - C. Caratelli

Elucidation of the pre-nucleation phase directing metal-organic framework formation

leen — Tue, 07 Dec 2021 08:43:52 +0000

M. Filez, C. Caratelli, M. Rivera-Torrente, F. Muniz-Miranda, M. Hoek, M. Altelaar, A.J.R. Heck, V. Van Speybroeck, B.M. Weckhuysen

Cell Reports Physical Science

2, 12, 100680

2021

Abstract

Metal-organic framework (MOF) crystallization is governed by molecular assembly processes in the pre-nucleation stage. Yet, unravelling these pre-nucleation pathways and rationalizing their impact on crystal formation poses a great challenge since probing molecular-scale assemblies and macroscopic particles simultaneously is very complex. Herein, we present a multimodal, integrated approach to monitor MOF nucleation across multiple length scales by combining in situ optical spectroscopy, mass spectrometry, and molecular simulations. This approach allows tracing initial metal-organic complexes in solution and their assembly into oligomeric nuclei and simultaneously probing particle formation. During Co-ZIF-67 nucleation, a metal-organic pool forms with a variety of complexes caused by ligand exchange and symmetry reduction reactions. We discriminate complexes capable of initiating nucleation from growth species required for oligomerization into frameworks. Co4-nuclei are observed, which grow into particles following autocatalytic kinetics. The geometric and compositional variability of metal-organic pool species clarifies long-debated amorphous zeolitic imidazolate framework (ZIF)-particle nucleation and non-classic pathways of MOF crystallization.

DOI

dx.doi.org/10.1016/j.xcrp.2021.100680

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FilezetalCellReportsPhysicalScience2021.pdf

FengetalMatter2021.pdf

Dynamic interplay between defective UiO-66 and protic solvents in activated processes

chiara — Fri, 23 Aug 2019 13:17:09 +0000

C. Caratelli, J. Hajek, E.J. Meijer, M. Waroquier, V. Van Speybroeck

Chemistry - A European Journal

25 (67), 15315-15325

2019

Abstract

UiO‐66, composed by Zr‐oxide inorganic bricks [Zr6(μ3‐O)4(μ3‐OH)4] and organic terephthalate linkers, is one of the most studied metal–organic frameworks (MOFs) due to its exceptional thermal, chemical, and mechanical stability. Thanks to its high connectivity, the material can withstand structural deformations during activation processes such as linker exchange, dehydration, and defect formation. These processes do alter the zirconium coordination number in a dynamic way, creating open metal sites for catalysis and thus are able to tune the catalytic properties. In this work, it is shown, by means of first‐principle molecular‐dynamics simulations at operating conditions, how protic solvents may facilitate such changes in the metal coordination. Solvent can induce structural rearrangements in the material that can lead to undercoordinated but also overcoordinated metal sites. This is demonstrated by simulating activation processes along well‐chosen collective variables. Such enhanced MD simulations are able to track the intrinsic dynamics of the framework at realistic conditions.

DOI

http://dx.doi.org/10.1002/chem.201903178

Active Role of Methanol in Post-Synthetic Linker Exchange in the Metal-Organic Framework UiO-66

wim — Wed, 14 Nov 2018 08:06:51 +0000

J. Marreiros, C. Caratelli, J. Hajek, A. Krajnc, G. Fleury, B. Bueken, D. De Vos, G. Mali, M. Roeffaers, V. Van Speybroeck, R. Ameloot

Chemistry of Materials

31 (4), 1359-1369

2019

Abstract

UiO-66 is known as one of the most robust metal-organic framework materials. Nevertheless, UiO-66 has also been shown to undergo post-synthetic exchange of structural linkers with surprising ease in some sol-vents. To date the exchange mechanism has not yet been fully elucidated. Here, we show how time-resolved monitoring grants insight into the selected case of exchanging 2-aminoterephthalic acid into UiO-66 in methanol. Analysis of both the solid and liquid phase, complemented by computational insights, revealed the active role of methanol in the creation and stabilization of metastable states in which dangling linkers are similar to monocarboxylate defects that can be introduced during UiO-66 synthesis, such dangling link-ers undergo fast exchange. The presence of missing linker or missing cluster defects at the start of the ex-change process was shown to have no considerable impact on the equilibrium composition. After the ex-change process, the incoming 2-aminoterephthalate and remaining terephthalate linkers were distributed homogeneously in the framework for the typical small crystal size of UiO-66 (≈500nm).

Open Access version available at UGent repository

Green Open Access

DOI

http://dx.doi.org/10.1021/acs.chemmater.8b04734

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acs.chemmater.8b04734.pdf

On the intrinsic dynamic nature of the rigid UiO-66 metal-organic framework

chiara — Wed, 06 Dec 2017 09:54:36 +0000

J. Hajek, C. Caratelli, R. Demuynck, K. De Wispelaere, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck

Chemical Science

9 (10), 2723-2732

2018

Abstract

UiO-66 is a showcase example of an extremely stable metal–organic framework, which maintains its structural integrity during activation processes such as linker exchange and dehydration. The framework can even accommodate a substantial number of defects without compromising its stability. These observations point to an intrinsic dynamic flexibility of the framework, related to changes in the coordination number of the zirconium atoms. Herein we follow the dynamics of the framework in situ, by means of enhanced sampling molecular dynamics simulations such as umbrella sampling, during an activation process, where the coordination number of the bridging hydroxyl groups capped in the inorganic Zr6(μ3-O)4(μ3-OH)4 brick is reduced from three to one. Such a reduction in the coordination number occurs during the dehydration process and in other processes where defects are formed. We observe a remarkable fast response of the system upon structural changes of the hydroxyl group. Internal deformation modes are detected, which point to linker decoordination and recoordination. Detached linkers may be stabilized by hydrogen bonds with hydroxyl groups of the inorganic brick, which gives evidence for an intrinsic dynamic acidity even in the absence of protic guest molecules. Our observations yield a major step forward in the understanding on the molecular level of activation processes realized experimentally but that is hard to track on a purely experimental basis.

Open Access version available at UGent repository

Green Open Access

DOI

http://dx.doi.org/10.1039/C7SC04947A

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c7sc04947a.pdf

Insights on the Realgar Crystal Under Pressure from XP-PCM and Periodic Model Calculations

chiara — Fri, 10 Nov 2017 15:38:36 +0000

C. Caratelli, R. Cammi, R. Chelli, M. Pagliai, G. Cardini, V. Schettino

Journal of Physical Chemistry A

121 (46), pp 8825–8834

2017

Published while none of the authors were employed at the CMM

DOI

DOI:10.1021/acs.jpca.7b08868

Insights on the Realgar Crystal Under Pressure from XP-PCM and Periodic Model Calculations

chiara — Thu, 02 Nov 2017 12:16:32 +0000

C. Caratelli, R. Cammi, R. Chelli, M. Pagliai, G. Cardini, V. Schettino

Journal of Physical Chemistry A

2017

Published while none of the authors were employed at the CMM

Abstract

The spectroscopic properties of As₄S₄ with pressure have been computed by the quantum mechanical XP-PCM method and by density functional theory periodic calculations. The comparison has allowed the interpretation of the available experimental data. By comparison of the two methods and with experiments, we show that the XP-PCM method is able to reproduce the same behaviour of the periodic calculations with much lower computational cost allowing to be adopted as a first choice computational tool or a qualitative interpretation of molecular crystals properties under pressure.

DOI

10.1021/acs.jpca.7b08868

Influence of a confined methanol solvent on the reactivity of active sites in UiO-66

chiara — Thu, 12 Oct 2017 13:59:10 +0000

C. Caratelli, J. Hajek, S.M.J. Rogge, S. Vandenbrande, E.J. Meijer, M. Waroquier, V. Van Speybroeck

ChemPhysChem

19 (4), 420-429

2018

Abstract

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this contribution, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites.

Open Access version available at UGent repository

Gold Open Access

DOI

http://dx.doi.org/10.1002/cphc.201701109

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Caratelli_et_al-2018-ChemPhysChem.pdf

Nature of active sites on UiO-66 and beneficial influence of water in the catalysis of Fischer esterification

michel — Mon, 13 Feb 2017 14:07:11 +0000

C. Caratelli, J. Hajek, F. G. Cirujano, M. Waroquier, F. X. Llabres i Xamena, V. Van Speybroeck

Journal of Catalysis

352, 401-414

2017

Abstract

Zirconium terephthalate UiO-66 type metal organic frameworks (MOFs) are known to be highly active, stable and reusable catalysts for the esterification of carboxylic acids with alcohols. Moreover, when defects are present in the structure of these MOFs, coordinatively unsaturated Zr ions with Lewis acid properties are created, which increase the catalytic activity of the resulting defective solids. In the present work, molecular modeling techniques combined with new experimental data on various defective hydrated and dehydrated materials allow to unravel the nature and role of defective active sites in the Fischer esterification and the role of coordinated water molecules to provide additional Brønsted sites. Periodic models of UiO-66 and UiO-66-NH2 catalysts have been used to unravel the reaction mechanism on hydrated and dehydrated materials. Various adsorption modes of water and methanol are investigated. The proposed mechanisms are in line with experimental observations that amino groups yield a reduction in the reaction barriers, although they have a passive role in modulating the electronic structure of the material. Water has a beneficial role on the reaction cycle by providing extra Brønsted sites and by providing stabilization for various intermediates through hydrogen bonds.

Open Access version available at UGent repository

Gold Open Access

DOI

http://dx.doi.org/10.1016/j.jcat.2017.06.014

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1-s2.0-S002195171730221X-main-1.pdf

MOFSIM2019

sven — Mon, 17 May 2021 10:11:33 +0000

Ghent, Belgium

Wednesday, 10 April, 2019 to Friday, 12 April, 2019

Participant(s)

V. Van Speybroeck, L. Vanduyfhuys, C. Caratelli, J. Cerutti Torres, R. Goeminne, J. Hajek, A. De Vos, K. Lejaeghere, S. Borgmans, K. Dedecker, J. De Vos, A.E.J. Hoffman, A. Lamaire, J. Wieme, M. Cools-Ceuppens, S.M.J. Rogge

Project ref.

ERC DYNPOR H20ERC2015000301

Towards a Molecular Level Understanding of Active Sites for Catalysis and the Interactions with Solvents in Zirconium Based Metal-Organic Frameworks at Operating Conditions

samuel — Tue, 26 Nov 2019 10:45:43 +0000

C. Caratelli

Wed, 02/10/2019

Het Pand, Onderbergen, Ghent

https://biblio.ugent.be/publication/8642697

Supervisors

Prof. Dr. ir. Veronique Van Speybroeck

Attachment (private)

Caratelli_compressed.pdf