S. Vandenbrande

Thermodynamic insight into stimuli-responsive behavior of soft porous crystals

L. Vanduyfhuys, S.M.J. Rogge, J. Wieme, S. Vandenbrande, G. Maurin, M. Waroquier, V. Van Speybroeck
Nature Communications
9, 1, 204
2018
A1

Abstract 

Knowledge of the thermodynamic potential in terms of the independent variables allows to characterize the macroscopic state of the system. However, in practice, it is difficult to access this potential experimentally due to irreversible transitions that occur between equilibrium states. A showcase example of sudden transitions between (meta)stable equilibrium states is observed for soft porous crystals possessing a network with long-range structural order, which can transform between various states upon external stimuli such as pressure, temperature and guest adsorption. Such phase transformations are typically characterized by large volume changes and may be followed experimentally by monitoring the volume change in terms of certain external triggers. Herein, we present a generalized thermodynamic approach to construct the underlying Helmholtz free energy as a function of the state variables that governs the observed behaviour based on microscopic simulations. This concept allows a unique identification of the conditions under which a material becomes flexible.

Open Access version available at UGent repository
Gold Open Access

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

C. Caratelli, J. Hajek, S.M.J. Rogge, S. Vandenbrande, E.J. Meijer, M. Waroquier, V. Van Speybroeck
ChemPhysChem
19 (4), 420-429
2018
A1

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

Methane Adsorption in Zr-Based MOFs: Comparison and Critical Evaluation of Force Fields

S. Vandenbrande, T. Verstraelen, J. J. Gutierrez-Sevillano, M. Waroquier, V. Van Speybroeck
Journal of Physical Chemistry C
121 (45), 25309-25322
2017
A1

Abstract 

The search for nanoporous materials that are highly performing for gas storage and separation is one of the contemporary challenges in material design. The computational tools to aid these experimental efforts are widely available and adsorption isotherms are routinely computed for huge sets of (hypothetical) frameworks. Clearly the computational results depend on the interactions between the adsorbed species and the adsorbent, which are commonly described using force fields. In this paper, an extensive comparison and in-depth investigation of several force fields from literature is reported for the case of methane adsorption in the Zr-based Metal-Organic Frameworks UiO-66, UiO-67, DUT-52, NU-1000 and MOF-808. Significant quantitative differences in the computed uptake are observed when comparing different force fields, but most qualitative features are common which suggests some predictive power of the simulations when it comes to these properties. More insight into to the host-guest interactions is obtained by benchmarking the force fields with an extensive number of ab initio computed single molecule interaction energies. This analysis at the molecular level reveals that especially ab initio derived force fields perform well in reproducing the ab initio interaction energies. Finally, the high sensitivity of uptake predictions on the underlying potential energy surface is explored.

Open Access version available at UGent repository
Gold Open Access

Alternating Copolymer of Double Four Ring Silicate and Dimethyl Silicone Monomer - PSS-1

S. Smet, S. Vandenbrande, P. Verlooy, S. Kerkhofs, E. Breynaert, C. Kirschhock, C. Martineau, F. Taulelle, V. Van Speybroeck, J.A. Martens
Chemistry - A European Journal
23 (47), 11286-11293
2017
A1

Abstract 

A new copolymer consisting of double four ring (D4R) silicate units linked by dimethylsilicone monomer referred to as polyoligosiloxysilicone number one (PSS-1) was synthesized. The D4R building unit is provided by hexamethyleneimine cyclosilicate hydrate crystals, which were dehydrated and reacted with dichlorodimethylsilane. The local structure of D4R silicate units and dimethyl silicone monomers was revealed by multidimensional solid-state NMR, FTIR and modeling. On average, D4R silicate units have 6.8 silicone linkages. Evidence for preferential unidirectional growth and chain ordering within the PSS-1 copolymer was provided by STEM and TEM. The structure of PSS-1 copolymer consists of twisted columns of D4R silicate units with or without cross-linking. Both models are consistent with the spectroscopic, microscopic and physical properties. PSS-1 chains are predicted to be mechanically strong compared to silicones such as PDMS, yet more flexible than rigid silica materials such as zeolites.

The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Non-Covalent Interactions

S. Vandenbrande, M. Waroquier, V. Van Speybroeck, T. Verstraelen
Journal of Chemical Theory and Computation (JCTC)
13 (1), 161–179
2017
A1

Abstract 

We propose a methodology to derive pairwise-additive noncovalent force fields from monomer electron densities without any empirical input. Energy expressions are based on the symmetry-adapted perturbation theory (SAPT) decomposition of interaction energies. This ensures a physically motivated force field featuring an electrostatic, exchange repulsion, dispersion, and induction contribution, which contains two types of parameters. First, each contribution depends on several fixed atomic parameters, resulting from a partitioning of the monomer electron density. Second, each of the last three contributions (exchange-repulsion, dispersion, and induction) contains exactly one linear fitting parameter. These three so-called interaction parameters in the model are initially estimated separately using SAPT reference calculations for the S66x8 database of noncovalent dimers. In a second step, the three interaction parameters are further refined simultaneously to reproduce CCSD(T)/CBS interaction energies for the same database. The limited number of parameters that are fitted to dimer interaction energies (only three) avoids ill-conditioned fits that plague conventional parameter optimizations. For the exchange repulsion and dispersion component, good results are obtained for all dimers in the S66x8 database using one single value for the associated interaction parameters. The values of those parameters can be considered universal and can also be used for dimers not present in the original database used for fitting. For the induction component such an approach is only viable for the dispersion dominated dimers in the S66x8 database. For other dimers (such as hydrogen-bonded complexes), we show that our methodology remains applicable. However, the interaction parameter needs to be determined on a case-specific basis. As an external validation:, the force field predicts interaction energies in good agreement with CCSD(T)/CBS values for dispersion dominated dimers extracted from an HIV-II protease crystal structure with a bound ligand (indinavir). Furthermore, experimental second virial coefficients of small alkanes and alkenes are well reproduced.

Open Access version available at UGent repository
Green Open Access

Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion

S.M.J. Rogge, J. Wieme, L. Vanduyfhuys, S. Vandenbrande, G. Maurin, T. Verstraelen, M. Waroquier, V. Van Speybroeck
Chemistry of Materials
28 (16), 5721-5732
2016
A1

Abstract 

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal–organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials.

This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
http://pubs.acs.org/doi/abs/10.1021/acs.chemmater.6b01956

Open Access version available at UGent repository
Gold Open Access

Minimal Basis Iterative Stockholder: Atoms-in-Molecules for Force-Field Development

T. Verstraelen, S. Vandenbrande, F. Heidar-Zadeh, L. Vanduyfhuys, V. Van Speybroeck, M. Waroquier, P.W. Ayers
Journal of Chemical Theory and Computation (JCTC)
12(8), 3894-3912
2016
A1

Abstract 

Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g. obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Sheffler scheme for dispersion interactions.

QuickFF: A program for a quick and easy derivation of force fields for Metal-Organic Frameworks from ab initio input

L. Vanduyfhuys, S. Vandenbrande, T. Verstraelen, R. Schmid, M. Waroquier, V. Van Speybroeck
Journal of Computational Chemistry
36, 13, 1015–1027
2015
A1

Abstract 

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort.

Open Access version available at UGent repository

Direct Computation of Parameters for Accurate Polarizable Force Fields

T. Verstraelen, S. Vandenbrande, P.W. Ayers
Journal of Chemical Physics
141, 194144
2014
A1

Abstract 

We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham DFT, approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.

QuickFF: toward a generally applicable methodology to quickly derive accurate force fields for Metal-Organic Frameworks from ab initio input

L. Vanduyfhuys, S. Vandenbrande, T. Verstraelen, R. Schmid, M. Waroquier, V. Van Speybroeck
Journal of Computational Chemistry
2015
A1
Published while none of the authors were employed at the CMM

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