Tag: Materials Science

Helium flash: the beginning of a new chapter.

During the past two and a half years, part of being a delocalized physicist has meant for me that I had to work at one end of the country while my girlfriend and son lived at the other. Today this situation drastically changed, as I moved with my FWO-postdoctoral project from my alma mater to the University of Hasselt, where I started in the Wide Band Gap Materials group of Prof. Ken Haenen.

My delocalization will now take the form of Metal-Organic Frameworks on the one side and Diamond based materials on the other. As the sole computational solid state physicist in an otherwise entirely experimental group (and even institute) I seem to have returned to a well known configuration (At Ghent university I was initially the house-theoretician of the SCRiPTS group). Also the idea of performing calculations on diamond brings back memories, since this allotrope of carbon lives two levels above the germanium on which Pt nanowires grow. All-in-all I look forward to an exciting time. But first things first: getting my HPC credentials and data safely transported from the one end of the country to the other.

First-Principles Study of Antisite Defect Configurations in ZnGa2O4:Cr Persistent Phosphors

Authors: Arthur De Vos, Kurt Lejaeghere, Danny E. P. Vanpoucke, Jonas J. Joos, Philippe F. Smet, and Karen Hemelsoet
Journal: Inorg. Chem. 55(5), 2402-2412 (2016)
doi: 10.1021/acs.inorgchem.5b02805
IF(2016): 4.857
export: bibtex
pdf: <Inorg.Chem>
Graphical Abstract: (left) Ball-and-stick model of zinc gallate (right) density of states of Cr doped zinc gallate.
Graphical Abstract: First-principles simulations on zinc gallate solid phosphors (ZGO) containing a chromium dopant and antisite defects (left) 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 (right) and Hirshfeld-I charges.

Abstract

Zinc gallate doped with chromium is a recently developed near-infrared emitting persistent phosphor, which is now extensively studied for in vivo bioimaging and security applications. The precise mechanism of this persistent luminescence relies on defects, in particular, on antisite defects and antisite pairs. A theoretical model combining the solid host, the dopant, and/or antisite defects is constructed to elucidate the mutual interactions in these complex materials. Energies of formation as well as dopant, and defect energies are calculated through density-functional theory simulations of large periodic supercells. The calculations support the chromium substitution on the slightly distorted octahedrally coordinated gallium site, and additional energy levels are introduced in the band gap of the host. Antisite pairs are found to be energetically favored over isolated antisites due to significant charge compensation as shown by calculated Hirshfeld-I charges. Significant structural distortions are found around all antisite defects. The local Cr surrounding is mainly distorted due to a ZnGa antisite. The stability analysis reveals that the distance between both antisites dominates the overall stability picture of the material containing the Cr dopant and an antisite pair. The findings are further rationalized using calculated densities of states and Hirshfeld-I charges.

Virtual Winterschool 2016: Computational Solid State Physics & Chemistry

In just an hour, I’ll be presenting my talk at the virtual winterschool 2016. In an attempt to tempt fate as much as possible I will try to give/run real-time examples on our HPC in Gent, however at this moment no nodes are available yet to do so. Let’s keep our fingers crossed and see if it all works out.

Abstract

Modern materials research has evolved to the point where it is now common practice to manipulate materials at nanometer scale or even at the atomic scale (e.g. Intel’s skylake architecture with 14nm features, atomic layer deposition and surface structure manipulations with an STM-tip). At these scales, quantum mechanical effects become ever more relevant, making their prediction important for the field of materials science.

In this session, we will discuss how advanced quantum mechanical calculations can be performed for solids and indicate some differences with standard quantum chemical approaches. We will touch upon the relevant concepts for performing such calculations (plane-wave basis-sets, pseudo-potentials, periodic boundary conditions,…) and show how the basic calculations are performed with the VASP-code. You will familiarize yourself with the required input files and we will discuss several of the most important output-files and the data they contain.

At the end of this session you should be able to set up a single-point calculation, a structure optimization, a density of states and band structure calculation.

Additional Files/Info

Computational Materials Science: Where Theory Meets Experiments

Authors: Danny E. P. Vanpoucke,
Journal: Developments in Strategic Ceramic Materials:
Ceramic Engineering and Science Proceedings 36(8), 323-334 (2016)
(ICACC 2015 conference proceeding)
Editors: Waltraud M. Kriven, Jingyang Wang, Dongming Zhu,Thomas Fischer, Soshu Kirihara
ISBN: 978-1-119-21173-0
webpage: Wiley-VCH
export: bibtex
pdf: <preprint> 

Abstract

In contemporary materials research, we are able to create and manipulate materials at ever smaller scales: the growth of wires with nanoscale dimensions and the deposition of layers with a thickness of only a few atoms are just two examples that have become common practice. At this small scale, quantum mechanical effects become important, and this is where computational materials research comes into play. Using clever approximations, it is possible to simulate systems with a scale relevant for experiments. The resulting theoretical models provide fundamental insights in the underlying physics and chemistry, essential for advancing modern materials research. As a result, the use of computational experiments is rapidly becoming an important tool in materials research both for predictive modeling of new materials and for gaining fundamental insights in the behavior of existing materials. Computer and lab experiments have complementary limitations and strengths; only by combining them can the deepest fundamental secrets of a material be revealed.

In this paper, we discuss the application of computational materials science for nanowires on semiconductor surfaces, ceramic materials and flexible metal-organic frameworks, and how direct comparison can advance insight in the structure and properties of these materials.

Doping of CeO2 as a Tunable Buffer Layer for Coated Superconductors: A DFT Study of Mechanical and Electronic Properties

Authors: Danny E. P. Vanpoucke,
Journal: Developments in Strategic Ceramic Materials:
Ceramic Engineering and Science Proceedings 36(8), 169-177 (2016)
(ICACC 2015 conference proceeding)
Editors: Waltraud M. Kriven, Jingyang Wang, Dongming Zhu,Thomas Fischer, Soshu Kirihara
ISBN: 978-1-119-21173-0
webpage: Wiley-VCH
export: bibtex
pdf: <preprint> 

Abstract

In layered ceramic superconductor architectures, CeO2 buffer layers are known to form micro cracks during the fabrication process. To prevent this crack formation, doping of the CeO2 layer has been suggested. In this theoretical study, the influence of dopants (both tetravalent and aliovalent) on the mechanical and structural properties of CeO2 is investigated by means of density functional theory. Group IVa and IVb dopants show clearly distinct stability, with the former favouring interface and surface doping, while the latter favour uniform bulk doping. This behaviour is linked to the dopant electronic structure. The presence of charge compensating vacancies is shown to complicate the mechanical and structural picture for aliovalent dopants. We find that the vacancies often counteract the dopant modifications of the host material. In contrast, all dopants show an inverse relation between the bulk modulus and thermal expansion coefficient, independent of their valency and the presence of oxygen vacancies. Based on the study of these idealized systems, new dopants are suggested for applications.

A Flexible Photoactive Titanium Metal-Organic Framework Based on a [TiIV33-O)(O)2(COO)6] Cluster

Authors: Bart Bueken, Frederik Vermoortele, Danny E. P. Vanpoucke, Helge Reinsch, Chih-Chin Tsou, Pieterjan Valvekens, Trees De Baerdemaeker, Rob Ameloot, Christine E. A. Kirschhock, Veronique Van Speybroeck, James M. Mayer and Dirk De Vos
Journal: Angew. Chem. Int. Ed. 54(47), 13912-13917 (2015)
doi: 10.1002/anie.201505512
IF(2015): 11.705
export: bibtex
pdf: <Angew.Chem.Int.Ed.> 

Abstract

The synthesis of titanium-carboxylate metal-organic frameworks (MOFs) is hampered by the high reactivity of the commonly employed alkoxide precursors. Here, we present an innovative approach to Ti-based MOFs using titanocene dichloride to synthesize COK-69, the first breathing Ti-MOF built up of trans-1,4- cyclohexanedicarboxylate linkers and an unprecedented [TiIV33-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 TiIV per cluster can be photoreduced to TiIII, while preserving the structural integrity of the framework. From molecular modeling, the electronic structure of COK-69 was determined and a band gap of 3.77 eV was found.

Cover Image of Crystal Engineering Communications: Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction

Authors: Thomas Bogaerts, Louis Vanduyfhuys, Danny E.P. Vanpoucke, Jelle Wieme, Michel Waroquier, Pascal Van Der Voort, and Veronique Van Speybroeck,
Journal: CrystEngComm. 17(45), 8565 (2015)
doi: 10.1039/C5CE90198G
IF(2015): 3.849
export: bibtex
pdf: <CrystEngComm>

Abstract

The cover image depicts an X-ray beam hitting a sample of MIL-47(V) Metal-Organic Framework (reddish powder), resulting in an X-ray diffraction pattern. This leads to the atomic structure on the left, Where the spin-densities are indicated for the anti-ferromagnetic ground state.  (The related paper can be found here.)


Cover of CrystEngComm: Volume 17, Issue 45, dec. 7, 2015

Understanding intrinsic light absorption properties of UiO-66 frameworks: A combined theoretical and experimental study

Authors: Kevin Hendrickx, Danny E.P. Vanpoucke, Karen Leus, Kurt Lejaeghere,
Andy Van Yperen-De Deyne, Veronique Van Speybroeck, Pascal Van Der
Voort, and Karen Hemelsoet
Journal: Inorg. Chem. 54(22), 10701-10710 (2015)
doi: 10.1021/acs.inorgchem.5b01593
IF(2015): 4.820
export: bibtex
pdf:  <Inorg.Chem.>

Abstract

Linker-functionalization of UiO-66 modifies the optical band gap and thus the color of the MOF.

Linker-functionalization of UiO-66 modifies the optical band gap and thus the color of the MOF.

A combined theoretical and experimental study is performed in order to elucidate the eff ects 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 eff ects 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.

Mechanical Properties from Periodic PlaneWave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework

Authors: Danny E. P. Vanpoucke, Kurt Lejaeghere, Veronique Van Speybroeck, Michel Waroquier, and An
Ghysels
Journal: J. Phys. Chem. C 119(41), 23752-23766 (2015)
doi: 10.1021/acs.jpcc.5b06809
IF(2015): 4.509
export: bibtex
pdf: <J.Phys.Chem.C> 
Graphical Abstract: Pulay stresses complicate the structure optimization of the breathing MIL-47(V) Metal-Organic Framework.
Graphical Abstract: Pulay stresses complicate the structure optimization of the breathing MIL-47(V) Metal-Organic Framework.

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.

Experimental truths

In statistics there exist a well known aphorism:

All models are wrong but some are useful.

— George Edward Pelham Box, 1919-2013

 

"George E. P. Box" by DavidMCEddy

“George E. P. Box” by DavidMCEddy

From the point of view of the definition of the word “model” this is true in an absolute sense, since a model implicitly means approximations are made, and as such discrepancies with “the real system” exist. As a result, this real system is considered as the only “not wrong” description of itself. In the exact sciences, the real system is often nature. This may lead some scientists to believe that experimental results, and by extension conclusions based on them, are true by default. When confronted with theoretical results in disagreement with experimental conclusions, the quick response entails a failure of the theoretical model used since it is not real nature that was worked with, but only a model.

Quite often this is true, and leads to the formulation of new and better models of reality: This allowed, for example, Newton’s laws of motion to evolve to special relativity and further to general relativity. However, equally often (in materials science at least) something else may be going on: The scientist may have forgotten that the experimentalist is also using a model to create his/her experimental results. Broadly speaking, experimental results can be categorized as either being direct or indirect results. Direct results are what you could call “WYSIWYG”-results. What you measure is the quantity you are interested in: e.g. contact angles of liquids by measuring the angle between a drop of the liquid and the substrate surface, the scanning tunneling and atomic force microscopy pictures of a surface,… Indirect results on the other hand, require some post-processing of a direct result to obtain the quantity of interest. This post-processing step includes the use of a model which links the direct result to the property of interest. e.g. The atomic structure of a material. Here the direct result would be the measured X-ray diffraction (XRD) spectrum, while the model and its assumptions are nowadays neatly hidden in well-performing software. This software will try to fit known crystal models to obtain lattice parameters and atomic positions for the XRD spectrum provided. This means however that the obtained result is the best fit that can be obtained, which is not necessarily the actual atomic structure.

Graphical Abstract for paper: Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction.

Graphical Abstract for paper: Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction.

Another important aspect to remember in regard to experimental results is the fact that different samples are truly different systems. For example, a material grown as a single crystal or synthesized as a powder may give subtly different XRD-spectra. In a recent paper with Thomas Bogaerts, we investigated how well different models for the MIL-47(V) Metal Organic Framework (MOF) fitted to experimental XRD spectra of this material. We found that depending on which experimental spectrum (single crystal or powder XRD) we fitted to, a different model was preferred, showing nature to have multiple truths for the same system. The structural difference between these models is minute, since the models entail different spin configurations on the same topology. However, the effort required for the more extended fitting procedure performed by Thomas is well worth it, since it provided a new (indirect) method for determining the spin-configuration in these rather complex structure, giving access to slightly less-wrong models for the future.