Center for Molecular Modeling - D.E.P. Vanpoucke

First-principles study of antisite defect configurations in ZnGa2O4:Cr persistent phosphors

kurt — Wed, 27 Jan 2016 11:24:02 +0000

A. De Vos, K. Lejaeghere, D.E.P. Vanpoucke, J.J. Joos, P.F. Smet, K. Hemelsoet

Inorganic Chemistry

55 (5), 2402–2412

2016

Abstract

First-principles simulations on zinc gallate solid phosphors (ZGO) containing a chromium dopant and antisite defects rationalize the attractive interactions between the various elements. A large number of antisite pair configurations is investigated and compared with isolated antisite defects. Defect energies point out the stability of the antisite defects in ZGO. Local structural distortions are reported, and charge transfer mechanisms are analyzed based on theoretical density of states and Hirshfeld-I charges.

DOI

http://dx.doi.org/10.1021/acs.inorgchem.5b02805

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A Flexible Photoactive Titanium Metal-Organic Framework Based on a [Ti-3(IV)(mu(3)-O)(O)(2)(COO)(6)] Cluster

michel — Fri, 21 Aug 2015 19:59:38 +0000

B. Bueken, F. Vermoortele, D.E.P. Vanpoucke, H. Reinsch, C. Tsou, P. Valvekens, T. De Baerdemaeker, R. Ameloot, C. Kirschhock, V. Van Speybroeck, J. Mayer, D. De Vos

Angewandte Chemie int. Ed.

127, 14118 –14123

2015

Abstract

The synthesis of titanium-carboxylate metal-organic frameworks (MOFs) is hampered by the high reactivity of the commonly employed alkoxide precursors. Herein, we present an innovative approach to titanium-based MOFs by the use of titanocene dichloride to synthesize COK-69, the first breathing Ti MOF, which is built up from trans-1,4-cyclo-hexanedicarboxylate linkers and an unprecedented [Ti-3(IV)(mu(3)-O)(O)(2)(COO)(6)] cluster. The photoactive properties of COK-69 were investigated in depth by proton-coupled electron-transfer experiments, which revealed that up to one Ti-IV center per cluster can be photoreduced to Ti-III while preserving the structural integrity of the framework. The electronic structure of COK-69 was determined by molecular modeling, and a band gap of 3.77 eV was found.

DOI

http://dx.doi.org/10.1002/anie.201505512

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Bueken_et_al-2015-Angewandte_Chemie.pdf

Understanding Intrinsic Light Absorption Properties of UiO- 66 Frameworks: A Combined Theoretical and Experimental Study

kevin — Fri, 21 Aug 2015 15:49:51 +0000

K. Hendrickx, D.E.P. Vanpoucke, K. Leus, K. Lejaeghere, A. Van Yperen-De Deyne, V. Van Speybroeck, P. Van der Voort, K. Hemelsoet

Inorganic Chemistry

54, 22, 10701-10710

2015

Abstract

A combined theoretical and experimental study is performed in order to elucidate the effects of linker functional groups on the photoabsorption properties of UiO-66-type materials. This study, in which both mono- and di-functionalized linkers (with X= -OH, -NH2, -SH) are studied, aims to obtain a more complete picture on the choice of functionalization. Static Time-Dependent Density Functional Theory (TD-DFT) calculations combined with Molecular Dynamics simulations are performed on the linkers and compared to experimental UV/VIS spectra, in order to understand the electronic effects governing the absorption spectra. Di-substituted linkers show larger shifts compared to mono-substituted variants, making them promising candidates for further study as photocatalysts. Next, the interaction between the linker and the inorganic part of the framework is theoretically investigated using a cluster model. The proposed Ligand-to-Metal-Charge Transfer (LMCT) is theoretically observed and is influenced by the differences in functionalization. Finally, computed electronic properties of the periodic UiO-66 materials reveal that the band gap can be altered by linker functionalization and ranges from 4.0 down to 2.2 eV. Study of the periodic Density of States (DOS) allows to explain the band gap modulations of the framework in terms of a functionalization-induced band in the band gap of the original UiO-66 host.

DOI

http://dx.doi.org/10.1021/acs.inorgchem.5b01593

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Mechanical properties from periodic plane wave QM codes: the challenge of the flexible nanoporous MIL-47 (V) framework

michel — Wed, 15 Jul 2015 09:05:57 +0000

D.E.P. Vanpoucke, K. Lejaeghere, V. Van Speybroeck, M. Waroquier, A. Ghysels

Journal of Physical Chemistry C

119, 23752-23766

2015

Abstract

Modeling the flexibility of metal–organic frameworks (MOFs) requires the computation of mechanical properties from first principles, e.g., for screening of materials in a database, for gaining insight into structural transformations, and for force field development. However, this paper shows that computations with periodic density functional theory are challenged by the flexibility of these materials: guidelines from experience with standard solid-state calculations cannot be simply transferred to flexible porous frameworks. Our test case, the MIL-47(V) material, has a large-pore and a narrow-pore shape. The effect of Pulay stress (cf. Pulay forces) leads to drastic errors for a simple structure optimization of the flexible MIL-47(V) material. Pulay stress is an artificial stress that tends to lower the volume and is caused by the finite size of the plane wave basis set. We have investigated the importance of this Pulay stress, of symmetry breaking, and of k-point sampling on (a) the structure optimization and (b) mechanical properties such as elastic constants and bulk modulus, of both the large-pore and narrow-pore structure of MIL-47(V). We found that, in the structure optimization, Pulay effects should be avoided by using a fitting procedure, in which an equation of state E(V) (EOS) is fit to a series of energy versus volume points. Manual symmetry breaking could successfully lower the energy of MIL-47(V) by distorting the vanadium–oxide distances in the vanadyl chains and by rotating the benzene linkers. For the mechanical properties, the curvature of the EOS curve was compared with the Reuss bulk modulus, derived from the elastic tensor in the harmonic approximation. Errors induced by anharmonicity, the eggbox effect, and Pulay effects propagate into the Reuss modulus. The strong coupling of the unit cell axes when the unit cell deforms expresses itself in numerical instability of the Reuss modulus. For a flexible material, it is therefore advisible to resort to the EOS fit procedure.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1021/acs.jpcc.5b06809

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Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction

michel — Wed, 15 Jul 2015 08:58:36 +0000

T. Bogaerts, L. Vanduyfhuys, D.E.P. Vanpoucke, J. Wieme, M. Waroquier, P. Van der Voort, V. Van Speybroeck

CrystEngComm

17, 8612–8622

2015

Abstract

The structural characterization of complex crystalline materials such as metal organic frameworks can prove a very difficult challenge both for experimentalists as for theoreticians. From theory, the flat potential energy surface of these highly flexible structures often leads to different geometries that are energetically very close to each other. In this work a distinction between various computationally determined structures is made by comparing experimental and theoretically derived X-ray diffractograms which are produced from the materials geometry. The presented approach allows to choose the most appropriate geometry of a MIL-47(V) MOF and even distinguish between different electronic configurations that induce small structural changes. Moreover the techniques presented here are used to verify the applicability of a newly developed force field for this material. The discussed methodology is of significant importance for modelling studies where accurate geometries are crucial, such as mechanical properties and adsorption of guest molecules.

DOI

http://dx.doi.org/10.1039/C5CE01388G

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Comment on 'Europium doping induced symmetry deviation and its impact on the second harmonic generation of doped ZnO nanowires'

danny — Thu, 28 May 2015 09:02:12 +0000

D.E.P. Vanpoucke

Nanotechnology

Vol 25, Issue 45, article number 458001

2014

Abstract

In Dhara et al 2014 Nanotechnology 25 225202, the authors reported on the synthesis of Eu-doped ZnO nanowires (NWs) and investigated the influence of Eu doping on the second harmonic generation (SHG). Maximum SHG was found to correlate strongly with the structural deformation attributed to Eu3+ doping. In this comment, we show the deformation of interest is due to the presence of Eu2+ dopants, based on both the experimental data presented by Dhara et al and ab-initio density functional theory calculations.

DOI

http://dx.doi.org/10.1088/0957-4484/25/45/458001

On the convergence of atomic charges with the size of the enzymatic environment

wim — Wed, 11 Feb 2015 13:08:42 +0000

D.E.P. Vanpoucke, J. Olah, F. De Proft, V. Van Speybroeck, G. Roos

Journal of Chemical Information and Modeling (JCIM)

Volume 55 Issue 3 page 564–571

2015

Abstract

Atomic charges are a key concept to give more insight into the electronic structure and chemical reactivity. The Hirshfeld-I partitioning scheme applied to the model protein human 2-cysteine peroxiredoxin thioredoxin peroxidase B is used to investigate how large a protein fragment needs to be in order to achieve convergence of the atomic charge of both, neutral and negatively charged residues. Convergence in atomic charges is rapidly reached for neutral residues, but not for negatively charged ones. This study pinpoints difficulties on the road towards accurate modeling of negatively charged residues of large biomolecular systems in a multiscale approach.

DOI

http://dx.doi.org/10.1021/ci5006417

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Aliovalent doping of CeO2: DFT study of oxidation state and vacancy effects

danny — Thu, 03 Jul 2014 14:02:03 +0000

D.E.P. Vanpoucke, P. Bultinck, S. Cottenier, V. Van Speybroeck, I. Van Driessche

Journal of Materials Chemistry A

2 (3), 13723-13737

2014

Abstract

The modification of CeO₂ properties by means of aliovalent doping is investigated within the ab initio density functional theory framework. Lattice parameters, dopant atomic radii, bulk moduli and thermal expansion coefficients of fluorite type Ce_1-xM_xO_2-y (with M = Mg, V, Co, Cu, Zn, Nb, Ba, La, Sm, Gd, Yb, and Bi) are presented for 0.00 < x < 0.25. The relative stability of the doped systems is discussed, and the influence of oxygen vacancies is investigated. It is shown that oxygen vacancies tend to increase the lattice parameter, and strongly decrease the bulk modulus. Defect formation energies are correlated with calculated crystal radii and covalent radii of the dopants, and are shown to present no simple trend. The previously observed inverse relationship between the thermal expansion coefficient and the bulk modulus in group IV doped CeO2 [J. Am. Ceram. Soc., 2014, 97(1), 258] is shown to persist independent of the inclusion of charge compensating vacancies.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1039/c4ta02449d

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Rationality: A Social-Epistemology Perspective

danny — Thu, 03 Jul 2014 13:24:29 +0000

S. Wenmackers, D.E.P. Vanpoucke, I. Douven

Frontiers in Psychology

Volume 5, Article 581

2014

Published while none of the authors were employed at the CMM

DOI

http://dx.doi.org/10.3389/fpsyg.2014.00581

Quasi-1D physics in Metal-Organic Frameworks: MIL-47(V) from first principles

kurt — Thu, 03 Jul 2014 06:53:14 +0000

D.E.P. Vanpoucke, J. Jaeken, S. De Baerdemacker, K. Lejaeghere, V. Van Speybroeck

Beilstein Journal of Nanotechnology

5, 1738–1748

2014

Abstract

The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å³. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO₆ chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.3762/bjnano.5.184

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