Reply to ‘Comment on “Extending Hirshfeld-I to bulk and periodic materials” ‘

Authors: Danny E. P. Vanpoucke, Isabel Van Driessche, and Patrick Bultinck
Journal: J. Comput. Chem. 34(5), 422-427 (2013)
doi: 10.1002/jcc.23193
IF(2013): 3.601
export: bibtex
pdf: <J.Comput.Chem.> <arXiv>
Graphical Abstract: Hirshfeld-I atoms-in-molecules atoms in Ti doped CeO2. Graphical Abstract:The issues raised in the preceding comment are addressed. It is shown why Hirshfeld-I is, from a theoretical point of view, a good method for defining AIM and obtaining charges. Charges for a set of ionic systems are calculated using our presented method and shown to be chemically feasable. Comparison of pseudo-density to all-electron based results shows the pseudo-densities to be sufficient to obtain all-electron quality results. Timing results for systems containing hundreds of atoms.

Abstract

The issues raised in the comment by Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO3, and La2Ce2O7, using our previously presented method for calculating Hirshfeld-I charges in solids (Vanpoucke et al., J. Comput. Chem. doi: 10.1002/jcc.23088). It is shown that the use of pseudovalence charges is sufficient to retrieve the full all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over 200 atoms, underlining the relatively low cost for large systems. A number of theoretical issues are formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on “expectations” for atomic charges.

Extending Hirshfeld-I to bulk and periodic materials

Authors: Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche,
Journal: J. Comput. Chem. 34(5), 405-417 (2013)
doi: 10.1002/jcc.23088
IF(2013): 3.601
export: bibtex
pdf: <J.Comput.Chem.> <arXiv>
Graphical Abstract: Hirshfeld-I atoms-in-molecules carbon atoms in a graphene sheet. Graphical Abstract: The Hirshfeld-I method is extended to solids, allowing for the partitioning of a solid density into constituent atoms. The use of precalculated density grids makes the implementation code independent, and the use of pseudo-potential based electron density distributions is shown to give qualitatively the same results as all electron densities. Results for some simple solids/periodic systems like cerium oxide and graphene are presented.

Abstract

In this work, a method is described to extend the iterative Hirshfeld-I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudopotential-based electron density distributions, and it is shown that high-quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of grids containing (precalculated) electron densities makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems. The conceptual issue of obtaining reference densities for anions is discussed, and the delocalization problem for anionic reference densities originating from the use of a plane wave basis set is identified and handled.

New Functionalized Metal-Organic Frameworks MIL-47-X (X = -Cl, -Br, -CH3, -CF3, -OH, -OCH3): Synthesis, Characterization and CO2 Adsorption Properties

Authors: Shyam Biswas, Danny E. P. Vanpoucke, Toon Verstraelen, Matthias Vandichel, Sarah Couck, Karen Leus, Ying-Ya Liu, Michel Waroquier, Veronique Van Speybroeck, Joeri F. M. Denayer, and Pascal Van Der Voort
Journal: J. Phys. Chem. C 117(44), 22784-22796 (2013)
doi: 10.1021/jp406835n
IF(2013): 4.835
export: bibtex
pdf: <J.Phys.Chem.C>

Abstract

Six new functionalized vanadium hydroxo terephthalates [VIII(OH)(BDC-X)]·n(guests) (MIL-47(VIII)-X-AS) (BDC = 1,4-benzenedicarboxylate; X = −Cl, −Br, −CH3, −CF3, −OH, −OCH3; AS = as-synthesized) along with the parent MIL-47 were synthesized under rapid microwave-assisted hydrothermal conditions (170 °C, 30 min, 150 W). The unreacted H2BDC-X and/or occluded solvent molecules can be removed by thermal activation under vacuum, leading to the empty-pore forms of the title compounds (MIL-47(VIV)-X). Except pristine MIL-47 (+III oxidation state), the vanadium atoms in all the evacuated functionalized solids stayed in the +IV oxidation state. The phase purity of the compounds was ascertained by X-ray powder diffraction (XRPD), diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, Raman, thermogravimetric (TG), and elemental analysis. The structural similarity of the filled and empty-pore forms of the functionalized compounds with the respective forms of parent MIL-47 was verified by cell parameter determination from XRPD data. TGA and temperature-dependent XRPD (TDXRPD) experiments in an air atmosphere indicate high thermal stability in the 330–385 °C range. All the thermally activated compounds exhibit significant microporosity (SBET in the 305–897 m2 g–1 range), as verified by the N2 and CO2 sorption analysis. Among the six functionalized compounds, MIL-47(VIV)-OCH3 shows the highest CO2 uptake, demonstrating the determining role of functional groups on the CO2 sorption behavior. For this compound and pristine MIL-47(VIV), Widom particle insertion simulations were performed based on ab initio calculated crystal structures. The theoretical Henry coefficients show a good agreement with the experimental values, and calculated isosurfaces for the local excess chemical potential indicate the enhanced CO2 affinity is due to two effects: (i) the interaction between the methoxy group and CO2 and (ii) the collapse of the MIL-47(VIV)-OCH3 framework.

Probability of inconsistencies in theory revision,
A multi-agent model for updating logically interconnected beliefs under bounded confidence

Authors: Sylvia Wenmackers, Danny E. P. Vanpoucke, and Igor Douven
Journal: Eur. Phys. J. B 85, 44 (2012)
doi: 10.1140/epjb/e2011-20617-8
IF(2012): 1.282
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pdf: <Eur.Phys.J.B>

Abstract

We present a model for studying communities of epistemically interacting agents who update their belief states by averaging (in a specified way) the belief states of other agents in the community. The agents in our model have a rich belief state, involving multiple independent issues which are interrelated in such a way that they form a theory of the world. Our main goal is to calculate the probability for an agent to end up in an inconsistent belief state due to updating (in the given way). To that end, an analytical expression is given and evaluated numerically, both exactly and using statistical sampling. It is shown that, under the assumptions of our model, an agent always has a probability of less than 2% of ending up in an inconsistent belief state. Moreover, this probability can be made arbitrarily small by increasing the number of independent issues the agents have to judge or by increasing the group size. A real-world situation to which this model applies is a group of experts participating in a Delphi-study.

Tuning of CeO2 buffer layers for coated superconductors through doping

Authors: Danny E. P. Vanpoucke, Stefaan Cottenier, Veronique Van Speybroeck, Patrick Bultinck, and Isabel Van Driessche,
Journal: Appl. Surf. Sci. 260, 32-35 (2012)
doi: 10.1016/j.apsusc.2012.01.032
IF(2012): 2.112
export: bibtex
pdf: <Appl.Surf.Sci.> <arXiv>

Abstract

The appearance of microcracks in cerium oxide (CeO2) buffer layers, as used in buffer layer architectures for coated superconductors, indicates the presence of stress between this buffer layer and the substrate. This stress can originate from the differences in thermal expansion or differences in lattice parameters between the CeO2 buffer layer and the substrate. In this article, we study, by means of ab initio density functional theory calculations, the influence of group IV doping elements on the lattice parameter and bulk modulus of CeO2. Vegard’s law behavior is found for the lattice parameter in systems without oxygen vacancies, and the Shannon crystal radii for the doping elements are retrieved from the lattice expansions. We show that the lattice parameter of the doped CeO2 can be matched to that of the La2Zr2O7 coated NiW substrate substrate for dopant concentrations of about 5%, and that bulk modulus matching is either not possible or would require extreme doping concentrations.

Models and simulations in material science: two cases without error bars

Authors: Sylvia Wenmackers and Danny E. P. Vanpoucke
Journal: Statistica Neerlandica 66, 339-355 (2012)
doi: 10.1111/j.1467-9574.2011.00519.x
IF(2012): 0.585
export: bibtex
pdf: <Stat.Neer.> <arXiv>

Abstract

We discuss two research projects in material science in which the results cannot be stated with an estimation of the error: a spectroscopic ellipsometry study aimed at determining the orientation of DNA molecules on diamond and a scanning tunneling microscopy study of platinum-induced nanowires on germanium. To investigate the reliability of the results, we apply ideas from the philosophy of models in science. Even if the studies had reported an error value, the trustworthiness of the result would not depend on that value alone.

Aqueous CSD approach for the growth of novel, lattice-tuned LaxCe1- xOδ epitaxial layers

Authors: Vyshnavi Narayanan, Petra Lommens, Klaartje De Buysser, Danny E.P. Vanpoucke, Ruben Huehne, Leopoldo Molina, Gustaaf Van Tendeloo , Pascal Van Der Voort, Isabel Van Driessche
Journal: J. Mater. Chem. 22, 8476-8483 (2012)
doi: 10.1039/C2JM15752G
IF(2012): 6.101
export: bibtex
pdf: <J.Mater.Chem.>

Abstract

Lanthanum–cerium oxide (LCO) films were deposited on Ni-5%W substrates by chemical solution deposition (CSD) from water-based precursors. LCO films containing different ratios of lanthanum and cerium ions (from CeO2 to La2Ce2O7) were prepared. The composition of the layers was optimized towards the formation of LCO buffer layers, lattice-matched with the superconducting YBa2Cu3Oy layer, useful for the development of coated conductors. Single, crack-free LCO layers with a thickness of up to 140 nm could be obtained in a single deposition step. The crystallinity and microstructure of these lattice-matched LCO layers were studied by X-ray diffraction techniques, RHEED and SEM. We find that only layers with thickness below 100 nm show a crystalline top surface although both thick and thin layers show good biaxial texture in XRD. On the most promising layers, AFM and (S)TEM were performed to further evaluate their morphology. The overall surface roughness varies between 3.9 and 7.5 nm, while the layers appear much more dense than the frequently used La2Zr2O7 (LZO) systems, showing much smaller nanovoids (1–2 nm) than the latter system. Their effective buffer layer action was studied using XPS. The thin LCO layers supported the growth of superconducting YBCO deposited using PLD methods.

Investigation of tunable buffer layers for coated superconductors:
from solid state physics to quantum chemistry

Authors: Danny E.P. Vanpoucke
Ph.D. Thesis at Ghent University, Belgium
date: October 5th, 2012
Promoters Prof. Dr. Isabel Van Driessche and Prof. Dr. Patrick Bultinck
#pages 218
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pdf: <PhD.Thesis>
research page with more information

Abstract

High temperature ceramic superconductors can be grown in layered structures on metallic wires to provide the mechanical flexibility required for industrial applications. To prevent the metal atoms of diffusing into the superconductor—destroying its superconductivity—buffer layers are grown between the metal substrate and the superconductor. Recently, cerium oxide has been used as such a buffer layer. However, the layer thickness of these buffer layers is limited by the formation of cracks during deposition. This behaviour has been linked to internal stress due to lattice mismatch and different thermal expansion coefficients of the substrate and the buffer layer. A simple way to reduce these mismatches is through metal doping.

In this work, we study the influence of dopants on the properties of cerium oxide through the use of ab initio calculations. Trends in the stability, lattice parameter, bulk modulus and thermal expansion coefficient of cerium oxide doped with different dopants are investigated. In addition, the influence of charge compensating oxygen vacancies is studied, and their role in the stability of heavily La-doped cerium oxide (La2Ce2O7) is presented. The use of dopants with different valences also leads to a modification of the charge distribution around the dopant sites. A way to have a more quantitative estimate of the charge transfer induced by dopants is via the introduction of the chemical concept of ‘atoms in a molecule’ into solids. This can be considered a first step in the direction of answering the experimental question: What is the charge of a given atom in a certain compound? In this work we present an implementation of this Hirshfeld method for solids, and calculate the atomic charges in doped cerium oxides.

Front cover of the PhD thesis.

Density functional theory study of La2Ce2O7: disordered fluorite vs pyrochlore structure

Authors: Danny E. P. Vanpoucke, Patrick Bultinck, Stefaan Cottenier, Veronique Van Speybroeck and Isabel Van Driessche,
Journal: Phys. Rev. B 84, 054110 (2011)
doi: 10.1103/PhysRevB.84.054110
IF(2011): 3.691
export: bibtex
pdf: <Phys.Rev.B.> <arXiv>

Abstract

The crystal structure of lanthanum cerium oxide (La2Ce2O7) is investigated using ab initio density functional theory calculations. The relative stability of fluorite- and pyrochlore-like structures is studied through comparison of their formation energies. These formation energies show the pyrochlore structure to be favored over the fluorite structure, apparently contradicting the conclusions based on experimental neutron and x-ray diffraction (XRD).
By calculating and comparing XRD spectra for a set of differently ordered and random structures, we show that the pyrochlore structure is consistent with diffraction experiments. For these reasons, we suggest the pyrochlore structure as the ground-state crystal structure for La2Ce2O7.

Pt Nanowires on Ge(001): Sheep in Wolf’s Clothing?

Authors: Danny E. P. Vanpoucke
Journal: Belgian Physical Society Magazine 3, 11-16 (2011)
(Featured Article for the BΦ)
pdf: <local>

Abstract

The deposition of small amounts of platinum on a germanium (001) surface gives rise to the formation of monatomic nanowires. These nanowires are defect–and kink-free and their length is only limited by the underlying terrace, to which they are uniquely connected. Using ab initio calculations and simulated scanning tunneling microscopy (STM) images we model these nanowires, and show them to consist of germanium atoms, in contrast to earlier proposed models.