Center for Molecular Modeling - DEFNET (641887) H20ITN2015000201

ReaxFF Parameter Optimization with Monte-Carlo and Evolutionary Algorithms: Guidelines and Insights

toon — Thu, 28 Nov 2019 11:31:09 +0000

G. Shchygol, A. Yakovlev, T. Trnka, A.C.T. van Duin, T. Verstraelen

Journal of Chemical Theory and Computation

15, 12, 6799-6812

2019

Abstract

ReaxFF is a computationally efficient force field to simulate complex reactive dynamics in extended molecular models with diverse chemistries, if reliable force-field parameters are available for the chemistry of interest. If not, they must be optimized by minimizing the error ReaxFF makes on a relevant training set. Because this optimization is far from trivial, many methods, in particular, genetic algorithms (GAs), have been developed to search for the global optimum in parameter space. Recently, two alternative parameter calibration techniques were proposed, that is, Monte-Carlo force field optimizer (MCFF) and covariance matrix adaptation evolutionary strategy (CMA-ES). In this work, CMA-ES, MCFF, and a GA method (OGOLEM) are systematically compared using three training sets from the literature. By repeating optimizations with different random seeds and initial parameter guesses, it is shown that a single optimization run with any of these methods should not be trusted blindly: nonreproducible, poor or premature convergence is a common deficiency. GA shows the smallest risk of getting trapped into a local minimum, whereas CMA-ES is capable of reaching the lowest errors for two-third of the cases, although not systematically. For each method, we provide reasonable default settings, and our analysis offers useful guidelines for their usage in future work. An important side effect impairing parameter optimization is numerical noise. A detailed analysis reveals that it can be reduced, for example, by using exclusively unambiguous geometry optimization in the training set. Even without this noise, many distinct near-optimal parameter vectors can be found, which opens new avenues for improving the training set and detecting overfitting artifacts.

DOI

10.1021/acs.jctc.9b00769

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

CMM's publication on the nature of active sites of UiO-66 in the catalysis of Fischer esterification was ranked second most downloaded in Journal of Catalysis

chiara — Mon, 20 Nov 2017 09:31:10 +0000

CMM's publication entitled "Nature of active sites and beneficial influence of water in the catalysis of Fischer esterification" by Chiara Caratelli, Julianna Hajek, Francisco G. Cirujano, Michel Waroquier, Francesc X. Llabres i Xamena and Veronique Van Speybroeck was the second most downloaded article of the last 90 days in Journal of Catalysis.

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

Highlighted Chemical Society Reviews contribution showcases the potential of metal-organic and covalent organic frameworks as single-site heterogeneous catalysts

wim — Tue, 18 Apr 2017 08:05:00 +0000

While metal-organic and covalent organic frameworks are still in their infancy compared to zeolites, their versatility and nearly unlimited tunability endow these materials with an enormous potential as heterogeneous catalysts. In a recent review, to be published in Chemical Society Reviews, we highlight how recent advances, both in synthetic conditions as well as in modelling and characterization tools, contribute to unprecedented insight in heterogeneous catalysis and may be a game changer in catalyst design for a number of processes currently dominated by homogeneous catalysts. This review, which is part of a Chemical Society Reviews special issue on MOFs and is featured on the front cover, was coordinated by prof. Jorge Gascon from TU Delft and prof. Veronique Van Speybroeck from the Center for Molecular Modeling, in collaboration with the experimental groups of Francesc X. Llabrés i Xamena, Enrique V. Ramos-Fernandez, and Marco Daturi. This review forms a milestone within the ERC DYNPOR grant and DEFNET programme, which focus on the investigation of complex chemical transformations in nanoporous materials.

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

Missing linkers: an alternative pathway to UiO-66 electronic structure engineering

kurt — Sun, 05 Feb 2017 10:38:54 +0000

A. De Vos, K. Hendrickx, P. Van der Voort, V. Van Speybroeck, K. Lejaeghere

Chemistry of Materials

29 (7), 3006–3019

2017

Abstract

UiO-66 is a promising metal-organic framework for photocatalytic applications. However, the ligand-to-metal charge transfer of an excited electron is inefficient in the pristine material. Herein we assess the influence of missing linker defects on the electronic structure of UiO-66 and discuss their ability to improve ligand-to-metal charge transfer. Using a new defect classification system, which is transparent and easily extendable, we identify the most promising photocatalysts by considering both relative stability and electronic structure. We find the properties of UiO-66 defect structures largely to depend on the coordination of the constituent nodes, and the nodes with the strongest local distortions to alter the electronic structure most. Defects hence provide an alternative pathway to tune UiO-66 for photocatalytic purposes, besides linker modification and node metal substitution. In addition, the decomposition of MOF properties into node- and linker-based behavior is more generally valid, so we propose orthogonal electronic structure tuning as a paradigm in MOF electronic structure engineering.

Open Access version available at UGent repository

Gold Open Access

DOI

http://dx.doi.org/10.1021/acs.chemmater.6b05444

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acs%2Echemmater%2E6b05444(1).pdf

Metal-organic and covalent organic frameworks as single-site catalysts

sven — Fri, 13 Jan 2017 12:53:35 +0000

S.M.J. Rogge, A. Bavykina, J. Hajek, H. Garcia, A.I. Olivos-Suarez, A. Sepúlveda-Escribano, A. Vimont, G. Clet, P. Bazin, F. Kapteijn, M. Daturi, E.V. Ramos-Fernandez, F.X. Llabres i Xamena, V. Van Speybroeck, J. Gascon

Chemical Society Reviews

46 (11), 3134-3184

2017

Abstract

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions.

Open Access version available at UGent repository

Gold Open Access

DOI

http://dx.doi.org/10.1039/C7CS00033B

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Rogge_MOF_2017.pdf