Tag: DFT

Oct 29 2023

Materiomics Chronicles: week 6

After surviving week five, the sixth week of the academic year feels almost relaxing. However, all the effort is worth it, and I was happy to hear the students of our materiomics program at UHasselt appreciate the effort put into creating their classes, during an evaluation meeting.

The evolution of the Z position of a Be atom on Graphene. Periodic cell with 10 Angstrom vacuum along z direction. Z position is given in direct coordinates (0...1), with the graphene sheet positioned at z=0 (=1). The Be atom is van der Waals bonded, and moves through the vacuum to attach to the "bottom" side of the sheet, though originally positioned at the "top" side.

The evolution of the Z position of a Be atom on Graphene. Periodic cell with 10 Angstrom vacuum along z direction. Z position is given in direct coordinates (0…1), with the graphene sheet positioned at z=0 (=1). The Be atom is van der Waals bonded, and moves through the vacuum to attach to the “bottom” side of the sheet, though originally positioned at the “top” side.

Though the week was not as intense as the week before does not mean there were no classes at all. The second bachelor students in chemistry continued their studies of particles in simple potentials though the study of a particle in a square infinite potential well during the course introduction to quantum chemistry. During the course quantum and computational chemistry, the third bachelor chemistry, the He atom was now studied by means of the variational method, introducing the concepts of effective nuclear charge and shielding in a natural way.

While the bachelor students could take a backseat approach during the lectures (except for calculating some bbracket integrals), the master materiomics students had to do most of the heavy lifting during their classes. For the course on Density Functional Theory there was response lecture as well as a lab-session where they studied the dynamics of Be on and around graphene, while the first master students had their second presentation & discussion session on the computational aspects of the papers studied in the course Properties of functional materials.

At the end of this week, we added another 11h of live classes and ~2h of video lectures, putting our semester total at 85h of live lectures. Upwards and onward to week 7.

Permanent link to this article: https://dannyvanpoucke.be/materiomics-chronicles-week-6/

Oct 07 2023

Materiomics Chronicles: week 3

In week three of the academic year at the chemistry and materiomics programs of UHasselt, the students started to put their freshly gained new knowledge of weeks 1 and 2 into practice with a number of exercise classes.

For the second bachelor chemistry students, this meant performing their first calculations within the context of the course introduction to quantum chemistry. At this point this is still very mathematical (e.g., calculating commutators) and abstract (e.g., normalizing a wave function or calculating the probability of finding a particle, given a simple wave function), but this will change, and chemical/physical meaning will slowly be introduced into the mathematical formalism. For the third bachelor chemistry, the course quantum and computational chemistry continued with perturbation theory, and we started with the variational method as well. The latter was introduced through the example of the H atom, for which the exact variational ground state was recovered starting from a well chosen trial wave function.

Infinite polymethylene glycol (POM) chain.

Ball-and-stick representation of an infinite polymethylene glycol (POM) chain.

In the master materiomics, the first master course fundamentals of materials modelling, dove into the details underpinning DFT introducing concepts like pseudo-potentials, the frozen-core approximation, periodic boundary conditions etc. This knowledge was then put into practice during a second exercise session working on the supercomputer, as a last preparation for the practical lab exercise the following day. During this lab, the students used the supercomputer to calculate the Young modulus of two infinite linear polymers. An intense practical session which they all executed with great courage (remember 2 weeks ago they never heard of DFT, nor had they accessed a supercomputer). Their report for this practical will be part of their grade.

For the second master materiomics, the course focused on Density Functional Theory consisted of a discussion lecture, covering the topics the students studied during their self study assignments. In addition, I recorded two video lectures for the blended learning part of the course. For the course Machine learning and artificial intelligence in modern materials science self study topics were covered in such a discussion lecture as well. In addition, the QM9 data set was investigated during an exercise session, as preparation for further detailed study.

At the end of this week, we have added another 16h of live lectures and ~1h of video lectures, putting our semester total at 35h of live lectures. Upwards and onward to week 4.

Permanent link to this article: https://dannyvanpoucke.be/materiomics-chronicles-week-3/

Sep 30 2023

Materiomics Chronicles: week 2

After the more gentle introductions last week during the first lectures at UHasselt, this week we dove into the deep end.

For the students of the second bachelor chemistry  the course introduction to quantum chemistry dove into the postulates of quantum chemistry. They learned about the wave-function and operators, had their first contact with the mystics notation of quantum chemistry: the bra-ket notation. For the third bachelor chemistry, the course quantum and computational chemistry was centered around perturbation theory. In addition to the theory, we applied the method to the simple system of the infinite square potential.

The electron density in the primitive diamond unit cell.

In the master materiomics the course fundamentals of materials modeling was kicked into high gear, not only did the students learn the theory behind quantum mechanical modelling, they also had their fist experience on the supercomputers of the VSC. So in addition to the road from the standard Schrödinger equation to the Hohenberg-Kohn-Sham equations of DFT, they also traveled their first steps along the road from their somewhat familiar windows OS to the bash command-line environment of the HPC unix system.

Finally, as the course introduction into quantum chemistry is part of the preparatory program of the master materiomics, I started creating the narrated versions of those lectures as well (2h worth recording, corresponding to 4h of live lectures). As the available time is limited, we are going for single shot recordings which makes things exciting in that department as well.

At the end of this week, we have added another 7h of live lectures and 2h of video lectures, putting our semester total at 19h of lectures. Upwards and onward to week 3.

Permanent link to this article: https://dannyvanpoucke.be/materiomics-chronicles-week-2/

Jun 08 2023

Hydration sphere structure of architectural molecules: polyethylene glycol and polyoxymethylene oligomers

Authors: Ahmed M. Rozza, Danny E. P. Vanpoucke, Eva-Maria Krammer, Julie Bouckaert, Ralf Blossey, Marc F. Lensink, Mary Jo Ondrechen, Imre Bakó, Julianna Oláh, and Goedele Roos
Journal: Journal of Molecular Liquids 384, 122172 (2023)
doi: 10.1016/j.molliq.2023.122172
IF(2021): 6.633
export: bibtex
pdf: <JMolLiq>

 

Graphical Abstract: PEG or POM, similar in structure though very different in their solvation. Is this due to structure or charge(distribution)?

Abstract

Non-toxic, chemically inert, organic polymers as polyethylene glycol (PEG) and polyoxymethylene (POM) have versatile applications in basic research, industry and pharmacy. In this work, we aim to characterize the hydration structure of PEG and POM oligomers by exploring how the solute disturbs the water structure compared to the bulk solvent and how the solute chain interacts with the solvent. We explore the effect of (i) the C-C-O (PEG) versus CO (POM) constitution of the chain and (ii) chain length. To this end, MD simulations followed by clustering and topological analysis of the hydration network, as well as by quantum
mechanical calculations of atomic charges are used. We show that the hydration varies with chain conformation and length. The degree of folding of the chain impacts its degree of solvation, which is measurable by different parameters as for example the number of water molecules in the first solvation shell and the solvent accessible surface. Atomic charges calculated on the oligomers in gas phase are stable throughout conformation and chain length and seem not to determine solvation. Hydration however induces charge transfer from the solute molecule to the solvent, which depends on the degree of hydration.

 

Permanent link to this article: https://dannyvanpoucke.be/paper-roosg_peg-en/

Mar 10 2022

On the influence of water on THz vibrational spectral features of molecular crystals

Authors: Sergey Mitryukovskiy, Danny E. P. Vanpoucke, Yue Bai, Théo Hannotte, Mélanie Lavancier, Djamila Hourlier, Goedele Roos and Romain Peretti
Journal: Physical Chemistry Chemical Physics 24, 6107-6125 (2022)
doi: 10.1039/D1CP03261E
IF(2020): 3.676
export: bibtex
pdf: <PCCP>

 

Graphical Abstract: Comparison of the measured THz spectrum of 3 phases of Lactose-Monohydrate to the calculated spectra for several Lactose configurations with varying water content.

Abstract

The nanoscale structure of molecular assemblies plays a major role in many (µ)-biological mechanisms. Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from pharmaceuticals and agrochemicals, to nutraceuticals and cosmetics. The collective vibrations in such molecular crystals can be probed using terahertz spectroscopy, providing unique characteristic spectral fingerprints. However, the association of the spectral features to the crystal conformation, crystal phase and its environment is a difficult task. We present a combined computational-experimental study on the incorporation of water in lactose molecular crystals, and show how simulations can be used to associate spectral features in the THz region to crystal conformations and phases. Using periodic DFT simulations of lactose molecular crystals, the role of water in the observed lactose THz spectrum is clarified, presenting both direct and indirect contributions. A specific experimental setup is built to allow the controlled heating and corresponding dehydration of the sample, providing the monitoring of the crystal phase transformation dynamics. Besides the observation that lactose phases and phase transformation appear to be more complex than previously thought – including several crystal forms in a single phase and a non-negligible water content in the so-called anhydrous phase – we draw two main conclusions from this study. Firstly, THz modes are spread over more than one molecule and require periodic computation rather than a gas-phase one. Secondly, hydration water does not only play a perturbative role but also participates in the facilitation of the THz vibrations.

The 0.5THz finger-print mode of alpha-Lactose Monohydrate.

The 0.5 THz finger-print mode of alpha-lactose monohydrate.

Permanent link to this article: https://dannyvanpoucke.be/paper-lactosethz_romain-en/

Jan 23 2020

Investigation of structural, electronic and magnetic properties of breathing metal–organic framework MIL-47(Mn): a first principles approach

Authors: Mohammadreza Hosseini, Danny E. P. Vanpoucke, Paolo Giannozzi, Masoud Berahman  and Nasser Hadipour
Journal: RSC Adv. 10, 4786-4794 (2020)
doi: 10.1039/C9RA09196C
IF(2019): 3.119
export: bibtex
pdf: <RSC Adv.> (Open Access)

 

Graphical abstract: MIL-47(Mn) paper
Graphical Abstract: The breathing MIL-47(Mn) Metal-Organic Framework. Upon breathing, the electronic structure of this MOF undergoes a transition from an anti-ferromagnetic semiconductor, to a ferromagnetic semi-metal.

Abstract

The structural, electronic and magnetic properties of the MIL-47(Mn) metal–organic framework are investigated using first principles calculations. We find that the large-pore structure is the ground state of this material. We show that upon transition from the large-pore to the narrow-pore structure, the magnetic ground-state configuration changes from antiferromagnetic to ferromagnetic, consistent with the computed values of the intra-chain coupling constant. Furthermore, the antiferromagnetic and ferromagnetic configuration phases have intrinsically different electronic behavior: the former is semiconducting, the latter is a metal or half-metal. The change of electronic properties during breathing posits MIL-47(Mn) as a good candidate for sensing and other applications. Our calculated electronic band structure for MIL-47(Mn) presents a combination of flat dispersionless and strongly dispersive regions in the valence and conduction bands, indicative of quasi-1D electronic behavior. The spin coupling constants are obtained by mapping the total energies onto a spin Hamiltonian. The inter-chain coupling is found to be at least one order of magnitude smaller than the intra-chain coupling for both large and narrow pores. Interestingly, the intra-chain coupling changes sign and becomes five times stronger going from the large pore to the narrow pore structure. As such MIL-47(Mn) could provide unique opportunities for tunable low-dimensional magnetism in transition metal oxide systems.

Permanent link to this article: https://dannyvanpoucke.be/paper_mil47mn_moh-en/

Sep 05 2019

Book Chapter on Zeolites: Now Open Access

  • Filed under blog

  • September 5, 2019

Zeolites and Metal-Organic Frameworks

Zeolites and Metal-Organic Frameworks

Some good new news: The book on zeolites and porous frameworks for which I wrote a chapter on modeling with Bartlomiej Szyja has become open access and can be found here.

Permanent link to this article: https://dannyvanpoucke.be/book-chapter-on-zeolites-now-open-access/

Sep 23 2017

A combined experimental and theoretical investigation of the Al-Melamine reactive milling system: a mechanistic study towards AlN-based ceramics

Authors: Seyyed Amin Rounaghi, Danny E.P. Vanpoucke, Hossein Eshghi, Sergio Scudino, Elaheh Esmaeili, Steffen Oswald and Jürgen Eckert
Journal: J. Alloys Compd. 729, 240-248 (2017)
doi: 10.1016/j.jallcom.2017.09.168
IF(2017): 3.779
export: bibtex
pdf: <J.Alloys Compd.>

 

Graphical Abstract: Evolution of the end products as function of Al and N content during ball-milling synthesis of AlN.
Graphical Abstract: Evolution of the end products as function of Al and N content during ball-milling synthesis of AlN.

Abstract

A versatile ball milling process was employed for the synthesis of hexagonal aluminum nitride (h-AlN) through the reaction of metallic aluminum with melamine. A combined experimental and theoretical study was carried out to evaluate the synthesized products. Milling intermediates and products were fully characterized via various techniques including XRD, FTIR, XPS, Raman and TEM. Moreover, a Boltzmann distribution model was proposed to investigate the effect of milling energy and reactant ratios on the thermodynamic stability and the proportion of different milling products. According to the results, the reaction mechanism and milling products were significantly influenced by the reactant ratio. The optimized condition for AlN synthesis was found to be at Al/M molar ratio of 6, where the final products were consisted of nanostructured AlN with average crystallite size of 11 nm and non-crystalline heterogeneous carbon.

Permanent link to this article: https://dannyvanpoucke.be/paperdoped-nitrides-iii-en/

Apr 28 2017

Mechanochemical synthesis of nanostructured metal nitrides, carbonitrides and carbon nitride: A combined theoretical and experimental study

Authors: Seyyed Amin Rounaghi, Danny E.P. Vanpoucke, Hossein Eshghi, Sergio Scudino, Elaheh Esmaeili, Steffen Oswald and Jürgen Eckert
Journal: Phys. Chem. Chem. Phys. 19, 12414-12424 (2017)
doi: 10.1039/C7CP00998D
IF(2017): 3.906
export: bibtex
pdf: <Phys.Chem.Chem.Phys.>

Abstract

Nowadays, the development of highly efficient routes for the low cost synthesis of nitrides is greatly growing. Mechanochemical synthesis is one of those promising techniques which is conventionally employed for the synthesis of nitrides by long term milling of metallic elements under pressurized N2 or NH3 atmosphere (A. Calka and J. I. Nikolov, Nanostruct. Mater., 1995, 6, 409-412). In the present study, we describe a versatile, room-temperature and low cost mechanochemical process for the synthesis of nanostructured metal nitrides (MNs), carbonitrides (MCNs) and carbon nitride (CNx). Based on this technique, melamine as a solid nitrogen-containing organic compound (SNCOC) is ball milled with four different metal powders (Al, Ti, Cr and V) to produce nanostructured AlN, TiCxN1-x, CrCxN1-x, and VCxN1-x (x~0.05). Both theoretical and experimental techniques are implemented to determine the reaction intermediates, products, by-products and finally, the mechanism underling this synthetic route. According to the results, melamine is polymerized in the presence of metallic elements at intermediate stages of the milling process, leading to the formation of a carbon nitride network. The CNx phase subsequently reacts with the metallic precursors to form MN, MCN or even MCN-CNx nano-composites depending on the defect formation energy and thermodynamic stability of the corresponding metal nitride, carbide and C/N co-doped structures.

Permanent link to this article: https://dannyvanpoucke.be/doped-nitrides-ii-en/

Mar 30 2017

Linker Functionalization in MIL-47(V)-R Metal–Organic Frameworks: Understanding the Electronic Structure

Authors: Danny E. P. Vanpoucke
Journal: J. Phys. Chem. C 121(14), 8014-8022 (2017)
doi: 10.1021/acs.jpcc.7b01491
IF(2017): 4.484
export: bibtex
pdf: <J.Phys.Chem.C>
Graphical Abstract: Evolution of the electronic band structure of MIL-47(V) upon OH-functionalization of the BDC linker.
Graphical Abstract: Evolution of the electronic band structure of MIL-47(V) upon OH-functionalization of the BDC linker. The π-orbital of the BDC linker splits upon functionalisation, and the split-off π-band moves up into the band gap, effectively reducing the latter.

Abstract

Metal–organic frameworks (MOFs) have gained much interest due to their intrinsic tunable nature. In this work, we study how linker functionalization modifies the electronic structure of the host MOF, more specifically, the MIL-47(V)-R (R = −F, −Cl, −Br, −OH, −CH3, −CF3, and −OCH3). It is shown that the presence of a functional group leads to a splitting of the π orbital on the linker. Moreover, the upward shift of the split-off π-band correlates well with the electron-withdrawing/donating nature of the functional groups. For halide functional groups the presence of lone-pair back-donation is corroborated by calculated Hirshfeld-I charges. In the case of the ferromagnetic configuration of the host MIL-47(V+IV) material a half-metal to insulator transition is noted for the −Br, −OCH3, and −OH functional groups, while for the antiferromagnetic configuration only the hydroxy group results in an effective reduction of the band gap.

Permanent link to this article: https://dannyvanpoucke.be/mof-mil47-linkerfunct-en/