T. Verstraelen

Charting the Complete Thermodynamic Landscape of Gas Adsorption for a Responsive Metal-Organic Framework

R. Goeminne, S. Krause, S. Kaskel, T. Verstraelen, J.D. Evans
JACS (Journal of the American Chemical Society)
143, 11, 4143–4147
2021
A1

Abstract 

New nanoporous materials have the ability to revolutionize adsorption and separation processes. In particular, materials with adaptive cavities have high selectivity and may display previously undiscovered phenomena, such as negative gas adsorption (NGA), in which gas is released from the framework upon an increase in pressure. Although the thermodynamic driving force behind this and many other counterintuitive adsorption phenomena have been thoroughly investigated in recent years, several experimental observations remain difficult to explain. This necessitates a comprehensive analysis of gas adsorption akin to the conformational free energy landscapes used to understand the function of proteins. We have constructed the complete thermodynamic landscape of methane adsorption on DUT-49. Traversing this complex landscape reproduces the experimentally observed structural transitions, temperature dependence, and the hysteresis between adsorption and desorption. The complete thermodynamic description presented here provides unparalleled insight into adsorption and provides a framework to understand other adsorbents that challenge our preconceptions.

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files

T. Verstraelen, W. Adams, L. Pujal, A. Tehrani, B. D. Kelly, L. Macaya, F. Meng, M. Richer, R. Hernández-Esparza, X. D. Yang, M. Chan, T. D. Kim, M. Cools-Ceuppens, V. Chuiko, E. Vohringer-Martinez, P.W. Ayers, F. Heidar-Zadeh
Journal of Computational Chemistry
45, 6, 458--464
2021
A1

Abstract 

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

Cation−π Interactions Accelerate the Living Cationic Ring-Opening Polymerization of Unsaturated 2-Alkyl-2-oxazolines

E. Van den Broeck, B. Verbraeken, K. Dedecker, P. Cnudde, L. Vanduyfhuys, T. Verstraelen, K. Van Hecke, V. V. Jerca, S. Catak, R. Hoogenboom, V. Van Speybroeck
Macromolecules
53, 10, 3832-3846
2020
A1

Abstract 

Cation–dipole interactions were previously shown to have a rate-enhancing effect on the cationic ring-opening polymerization (CROP) of 2-oxazolines bearing a side-chain ester functionality. In line with this, a similar rate enhancement—via intermolecular cation−π interactions—was anticipated to occur when π-bonds are introduced into the 2-oxazoline side-chains. Moreover, the incorporation of π-bonds allows for facile postfunctionalization of the resulting poly(2-oxazoline)s with double and triple bonds in the side-chains via various click reactions. Herein, a combined molecular modeling and experimental approach was used to study the CROP reaction rates of 2-oxazolines with side-chains having varying degrees of unsaturation and side-chain length. The presence of cation−π interactions and the influence of the degree of unsaturation were initially confirmed by means of regular molecular dynamics simulations on pentameric systems. Furthermore, a combination of enhanced molecular dynamics simulations, static calculations, and a thorough analysis of the noncovalent interactions was performed to unravel to what extent cation−π interactions alter the reaction kinetics. Additionally, the observed trends were confirmed also in the presence of acetonitrile as solvent, in which experimentally the polymerization is performed. Most intriguingly, we found only a limited effect on the intrinsic reaction kinetics of the CROP and a preorganization effect in the reactive complex region. The latter effect was established by the unsaturated side-chains and the cationic center through a complex interplay between cation−π, π–π, π–induced dipole, and cation–dipole interactions. These findings led us to propose a two-step mechanism comprised of an equilibration step and a CROP reaction step. The influence of the degree of unsaturation, through a preorganization effect, on the equilibration step was determined with the following trend for the polymerization rates: n-ButylOx < ButenOx < ButynOx ≥ PentynOx. The trend was experimentally confirmed by determining the polymerization rate constants.

Open Access version available at UGent repository
Gold Open Access

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

G. Shchygol, A. Yakovlev, T. Trnka, A.C.T. van Duin, T. Verstraelen
Journal of Chemical Theory and Computation
15, 12, 6799-6812
2019
A1

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

Modeling Gas Adsorption in Flexible Metal–Organic Frameworks via Hybrid Monte Carlo / Molecular Dynamics Schemes

S.M.J. Rogge, R. Goeminne, R. Demuynck, J.J. Gutiérrez-Sevillano, S. Vandenbrande, L. Vanduyfhuys, M. Waroquier, T. Verstraelen, V. Van Speybroeck
Advanced Theory and Simulations
2 (4), 1800177
2019
A1

Abstract 

Herein, a hybrid Monte Carlo (MC)/molecular dynamics (MD) simulation protocol that properly accounts for the extraordinary structural flexibility of metal–organic frameworks (MOFs) is developed and validated. This is vital to accurately predict gas adsorption isotherms and guest‐induced flexibility of these materials. First, the performance of three recent models to predict adsorption isotherms and flexibility in MOFs is critically investigated. While these methods succeed in providing qualitative insight in the gas adsorption process in MOFs, their accuracy remains limited as the intrinsic flexibility of these materials is very hard to account for. To overcome this challenge, a hybrid MC/MD simulation protocol that is specifically designed to handle the flexibility of the adsorbent, including the shape flexibility, is introduced, thereby unifying the strengths of the previous models. It is demonstrated that the application of this new protocol to the adsorption of neon, argon, xenon, methane, and carbon dioxide in MIL‐53(Al), a prototypical flexible MOF, substantially decreases the inaccuracy of the obtained adsorption isotherms and predicted guest‐induced flexibility. As a result, this method is ideally suited to rationalize the adsorption performance of flexible nanoporous materials at the molecular level, paving the way for the conscious design of MOFs as industrial adsorbents.

Gold Open Access

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

M. Riquelme, A. Lara, D.L. Mobley, T. Verstraelen, A.R. Matamala, E. Vohringer-Martinez
Journal of Chemical Information and Modeling (JCIM)
58 (9), 1779-1797
2018
A1

Abstract 

Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, non polarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol(-1) for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.

Multiscale partial charge estimation on graphene for neutral, doped and charged flakes

A. Maslechko, T. Verstraelen, T.S. van Erp, E. Riccardi
Physical Chemistry Chemical Physics (PCCP)
20 (31) 20678-20687
2018
A1

Abstract 

The minimal-basis iterative stockholder (MBIS) and restrained electrostatic potential (RESP) methods were applied to examine the effects of edges and of nitrogen and boron dopants on the atomic partial charges of neutral and charged graphene flakes. The results provided the parameters to fit a second-order atom-condensed Kohn-Sham DFT model (ACKS2), accurately determining the partial charges, the dipole and local electric fields in large graphene flakes with negligible cost. Our approach can lead to improvements of graphene force fields in charged conditions and guide the design of media for catalytic applications.

Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes

F. Heidar-Zadeh, P.W. Ayers, T. Verstraelen, I. Vinogradov, E. Vohringer-Martinez, P. Bultinck
Journal of Physical Chemistry A
112 (17) 4219-4245
2018
A1

Abstract 

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way, that clarifies the enormous freedom one has within the information-theoretic ansatz.

Ab initio evaluation of Henry coefficients using importance sampling

S. Vandenbrande, M. Waroquier, V. Van Speybroeck, T. Verstraelen
Journal of Chemical Theory and Computation
14 (12), 6359–6369
2018
A1

Abstract 

We present a new algorithm that allows for an efficient evaluation of the Henry coefficient of a guest molecule inside a porous material, which permits to use ab initio energy calculations. The Widom insertion method, which is currently used to compute these Henry coefficients, typically requires millions of energy evaluations. Our new methodology reduces this number by more than 1 order of magnitude, enabling the use of an ab initio potential energy surface. The methodology we propose is reminiscent of the well-known importance sampling technique which is frequently used in Monte Carlo integrations. First, a conventional Widom insertion simulation is performed using a force field. In the second step, the Widom results are used to select a limited number of configurations and only for these configurations the ab initio evaluation of the energy is required. Finally, by appropriately reweighting the latter energies, an accurate estimation of the ab initio Henry coefficient is possible at a moderate computational cost. We apply our methodology to the adsorption of CO2 in Mg-MOF-74, a prototypical case where interactions of a polar guest molecule with unsaturated metal sites dominate the adsorption mechanism. In this case generic force fields such as UFF or Dreiding are inappropriate and the use of ab initio methods is indispensable. In a second case study, we compute Henry coefficients of methane in UiO-66 using different levels of theory. We pay particular attention to the influence of the dispersion corrections and the role of many-body effects. For the final example, we qualitatively investigate adsorption features for a series of functionalized UiO-66 frameworks. Overall the cases we present show that accurate computations of Henry coefficients is extremely challenging, as different levels of theory provide strongly varying results. At the same time ab initio calculations have added value compared to force fields, as they provide a physically more sound description of the adsorption mechanism and in some cases clearly improve correspondence with experiment.

Open Access version available at UGent repository
Gold Open Access

Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of Metal Organic Frameworks

L. Vanduyfhuys, S. Vandenbrande, J. Wieme, M. Waroquier, T. Verstraelen, V. Van Speybroeck
Journal of Computational Chemistry
39 (16), p. 999-1011
2018
A1

Abstract 

QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal-organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparant workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster-based models. This is essential for an accurate description of MOFs with one dimensional metal-oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL-53(Al), MOF-5, CAU-13 and NOTT-300. As expected, periodic input data is proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL-53(Al). Bulk moduli and thermal expansion coefficients of MOF-5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU-13 and NOTT-300, the transition pressure is accurately
predicted provided cross terms are taken into account.

Open Access version available at UGent repository
Gold Open Access

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