Tag: Metal-Organic Frameworks

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.

Book Chapter on Zeolites: Now Open Access

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.

Book chapter: Computational Chemistry Experiment Possibilities

Authors: Bartłomiej M. Szyja and Danny Vanpoucke
Book: Zeolites and Metal-Organic Frameworks, (2018)
Chapter Ch 9, p 235-264
Title Computational Chemistry Experiment Possibilities
ISBN: 978-94-629-8556-8
export: bibtex
pdf: <Amsterdam University Press>
<Open Access>

 

Zeolites and Metal-Organic Frameworks (the hard-copy)

Abstract

Thanks to a rapid increase in the computational power of modern CPUs, computational methods have become a standard tool for the investigation of physico-chemical phenomena in many areas of chemistry and technology. The area of porous frameworks, such as zeolites, metal-organic frameworks (MOFs) and covalent-organic frameworks (COFs), is not different. Computer simulations make it possible, not only to verify the results of the experiments, but even to predict previously inexistent materials that will present the desired experimental properties. Furthermore, computational research of materials provides the tools necessary to obtain fundamental insight into details that are often not accessible to physical experiments.

The methodology used in these simulations is quite specific because of the special character of the materials themselves. However, within the field of porous frameworks, density functional theory (DFT) and force fields (FF)
are the main actors. These methods form the basis of most computational studies, since they allow the evaluation of the potential energy surface (PES) of the system.

Related:

Newsflash: here

Newsflash: Book-chapter on MOFs and Zeolites en route to bookstores near you.

It is almost a year ago that I wrote a book-chapter, together with Bartek Szyja, on MOFs and Zeolites. Coming March 2018, the book will be available through University press. It is interesting to note that in a 13 chapter book, ours was the only chapter dealing with the computational study and simulation of these materials…so there is a lot more that can be done by those who are interested and have the patience to perform these delicate and often difficult but extremely rewarding studies. From my time as a MOF researcher I have learned two important things:

  1. Any kind of interesting/extreme/silly physics you can imagine will be present in some MOFs. In this regard, the current state of the MOF/COF field is still in its infancy as most experimental work focuses on  simple applications such as catalysis and gas storage, for which other materials may be better suited. These porous materials may be theoretically interesting for direct industrial application, but the synthesis cost generally will be a bottleneck. Instead, looking toward the fundamental physics applications: Low dimensional magnetism, low dimensional conduction, spin-filters, multiferroics, electron-phonon interactions, interactions between spin and mechanical properties,…. MOFs are a true playground for the theoretician.
  2. MOFs are very hard to simulate correctly, so be wary of all (published) results that come computationally cheap and easy. Although the unit-cell of any MOF is huge, with regard to standard solid state materials, the electron interactions are also quite long range, so the first Brillouin zone needs very accurate sampling (something often neglected). Also spin-configurations can have a huge influence, especially in systems with a rather flat potential energy surface.

In the book-chapter, we discuss some basic techniques used in the computational study of MOFs, COFs, and Zeolites, which will be of interest to researchers starting in the field. We discuss molecular dynamics and Monte Carlo, as well as Density Functional Theory and all its benefits and limitations.

Open Access version of the book.

Bachelor Projects Completed: 2 new computational materials scientists initialised

The black arts of computational materials science.

Black arts of computational materials science.

Just over half a year ago, I mentioned that I presented two computational materials science related projects for the third bachelor physics students at the UHasselt. Both projects ended up being chosen by a bachelor student, so I had the pleasure of guiding two eager young minds in their first steps into the world of computational materials science. They worked very hard, cursed their machine or code (as any good computational scientist should do once in a while, just to make sure that he/she is still at the forefront of science) and survived. They actually did quite a bit more than “just surviving”, they grew as scientists and they grew in self-confidence…given time I believe they may even thrive within this field of research.

One week ago, they presented their results in a final presentation for their classmates and supervisors. The self-confidence of Giel, and the clarity of his story was impressive. Giel has a knack for storytelling in (a true Pan Narrans as Terry Pratchett would praise him). His report included an introduction to various topics of solid state physics and computational materials science in which you never notice how complicated the topic actually is. He just takes you along for the ride, and the story unfolds in a very natural fashion. This shows how well he understands what he is writing about.

This, in no way means his project was simple or easy. Quite soon, at the start of his project Giel actually ran into a previously unknown VASP bug. He had to play with spin-configurations of defects and of course bumped into a hand full of rookie mistakes which he only made once *thumbs-up*. (I could have warned him for them, but I believe people learn more if they bump their heads themselves. This project provided the perfect opportunity to do so in a safe environment. 😎 )  His end report was impressive and his results on the Ge-defect in diamond are of very good quality.

The second project was brought to a successful completion by Asja. This very eager student actually had to learn how to program in fortran before he could even start. He had to implement code to calculate partial phonon densities with the existing HIVE code. Along the way he also discovered some minor bugs (Thank you very much 🙂  ) and crashed into a rather unexpected hard one near the end of the project. For some time, things looked very bleak indeed: the partial density of equivalent atoms was different, and the sum of all partial densities did not sum to the total density. As a result there grew some doubts if it would be possible to even fulfill the goal of the project. Luckily, Asja never gave up and stayed positive, and after half a day of debugging on my part the culprit was found (in my part of the code as well). Fixing this he quickly started torturing his own laptop calculating partial phonon densities of state for Metal-organic frameworks and later-on also the Ge-defect in diamond, with data provided by Giel. Also these results are very promising and will require some further digging, but they will definitely be very interesting.

For me, it has been an interesting experience, and I count myself lucky with these two brave and very committed students. I wish them all the best of luck for the future, and maybe we meet again.

VSC-user day 2017: The Poster Edition

Last Friday, the HPC infrastructure in Flanders got celebrated by the VSC user day. Being one of the Tier-1 supercomputer users at UHasselt, I was asked if I could present a poster at the meeting, showcasing the things I do here. Although I was very interested in this event, educational obligations (the presentations of the bachelor projects, on which I will post later) prevented me from attending the meeting.

As means of a compromise, I created a poster for the meeting which Geert Jan Bex, our local VSC/HPC support team, would be so nice to put up at the event. The poster session was preceded by a set of 1-minute presentations of the posters, for which a slide had to be made. As I could not be physically present, I provided the organizers a slide which contained a short description that could be used as the 1-minute presentation. Unfortunately, things got a little mixed up, as Geert Jan accidentally printed this slide as the poster (which gave rise to some difficulties in the printing process 🙄 ). So for those who might have had an interest in the actual poster, let me put it up here:

This poster presents my work on linker functionalisation of the MIL-47, which got recently published in the Journal of physical chemistry C, and the diamond work on the C-vacancy, which is currently submitted. Clicking on the poster above will provide you the full size image. The 1-minute slide presentation, which erroneously got printed as poster:

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.

VASP tutor: Structure optimization through Equation-of-State fitting

Materials properties, such as the electronic structure, depend on the atomic structure of a material. For this reason it is important to optimize the atomic structure of the material you are investigating. Generally you want your system to be in the global ground state, which, for some systems, can be very hard to find. This can be due to large barriers between different conformers, making it easy to get stuck in a local minimum. However, a very shallow energy surface will be problematic as well, since optimization algorithms can get stuck wandering these plains forever, hopping between different local minima (Metal-Organic Frameworks (MOFs) and other porous materials like Covalent-Organic Frameworks and Zeolites are nice examples).

VASP, as well as other ab initio software, provides multiple settings and possibilities to perform structure optimization. Let’s give a small overview, which I also present in my general VASP introductory tutorial, in order of increasing workload on the user:

  1. Experimental Structure: This the most lazy option, as it entails just taking an experimentally obtained structure and not optimizing it at all. This should be avoided unless you have a very specific reason why you want to use specifically this geometry. (In this regard, Force-Field optimized structures fall into the same category.)
  2. Simple VASP Optimization: You can let VASP do the heavy lifting. There are several parameters which help with this task.
    1. IBRION = 1 (RMM-DIIS, good close to a minimum), 2 (conjugate gradient, safe for difficult problems, should always work), 3 (damped molecular dynamics, useful if you start from a bad initial guess) The IBRION tag determines how ions are moved during relaxation.
    2. ISIF = 2 (Ions only, fixed shape and volume), 4 (Ions and cell shape, fixed volume), 3 (ions, shape and volume relaxed) The ISIF tag determines how the stress tensor is calculated, and which degrees of freedom can change during a relaxation.
    3. ENCUT = max(ENMAX)x1.3  To reduce Pulay stresses, it is advised to increase the basis set to 1.3x the default value, which is the largest ENMAX value for the atoms used in your system.
  1. Volume Scan (Quick and dirty): For many systems, especially simple systems, the internal coordinates of the ions are often well represented in available structure files. The main parameter which needs optimization is the lattice parameter. This is also often the main change if different functional are used. In a quick and dirty volume scan, one performs a set of static calculations, only the volume of the cell is changed. The shape of the cell and the internal atom coordinates are kept fixed. Fitting a polynomial to the resulting Energy-Volume data can then be used to obtain the optimum volume. This option is mainly useful as an initial guess and should either be followed by option 2, or improved to option 4.
  2. Equation of state fitting to fixed volume optimized structures: This approach is the most accurate (and expensive) method. Because you make use of fixed volume optimizations (ISIF = 4), the errors due to Pulay stresses are removed. They are still present for each separate fixed volume calculation, but the equation of state fit will average out the basis-set incompleteness, as long as you take a large enough volume range: 5-10%. Note that the 5-10% volume range is generally true for small systems. In case of porous materials, like MOFs, ±4% can cover a large volume range of over 100 Å3. Below you can see a pseudo-code algorithm for this setup. Note that the relaxation part is split up in several consecutive relaxations. This is done to further reduce basis-set incompleteness errors. Although the cell volume does not change, the shape does, and the original sphere of G-vectors is transformed into an ellipse. At each restart this is corrected to again give a sphere of G-vectors. For many systems the effect may be very small, but this is not always the case, and it can be recognized as jumps in the energy going from one relaxation calculation to the next. The convergence is set the usual way for a relaxation in VASP (EDIFF and EDIFFG parameters) and a threshold in the number of ionic steps should be set as well (5-10 for normal systems is reasonable, while for porous/flexible materials you may prefer a higher value). There exist several possible equations-of-state which can be used for the fit of the E(V) data. The EOSfit option of HIVE-4 implements 3:
    1. Birch-Murnaghan third order isothermal equation of state
    2. Murnaghan equation of state
    3. Rose-Vinet equation of state (very well suited for (flexible) MOFs)

    Using the obtained equilibrium volume a final round of fixed volume relaxations should be done to get the fully optimized structure.

For (set of Volumes: equilibrium volume ±5%){
	Step 1          : Fixed Volume relaxation
	(IBRION = 2, ISIF=4, ENCUT = 1.3x ENMAX, LCHARG=.TRUE., NSW=100)
	Step 2→n-1: Second and following fixed Volume relaxation (until a threshold is crossed and the structure is relaxed in fewer than N ionic steps) (IBRION = 2, ISIF=4, ENCUT = 1.3x ENMAX, ICHARG=1, LCHARG=.TRUE., NSW=100) 
	Step n : Static calculation (IBRION = -1, no ISIF parameter, ICHARG=1, ENCUT = 1.3x ENMAX, ICHARG=1, LCHARG=.TRUE., NSW=0) 
} 
Fit Volume-Energy to Equation of State.
Fixed volume relaxation at equilibrium volume. (With continuations if too many ionic steps are required.) 
Static calculation at equilibrium volume
EOS-fitting Diamond and Graphite

Top-left: Volume scan of Diamond. Top-right: comparison of volume scan and equation of state fitting to fixed volume optimizations, showing the role of van der Waals interactions. Bottom: Inter-layer binding in graphite for different functionals.

Some examples

Let us start with a simple and well behaved system: Diamond. This material has a very simple internal structure. As a result, the internal coordinates should not be expected to change with reasonable volume variations. As such, a simple volume scan (option 3), will allow for a good estimate of the equilibrium volume. The obtained bulk modulus is off by about 2% which is very good.

Switching to graphite, makes things a lot more interesting. A simple volume scan gives an equilibrium volume which is a serious overestimation of the experimental volume (which is about 35 Å3), mainly due to the overestimation of the c-axis. The bulk modulus is calculated to be 233 GPa a factor 7 too large. Allowing the structure to relax at fixed volume changes the picture dramatically. The bulk modulus drops by 2 orders of magnitude (now it is about 24x too small) and the equilibrium volume becomes even larger. We are facing a serious problem for this system. The origin lies in the van der Waals interactions. These weak forces are not included in standard DFT, as a result, the distance between the graphene sheets in graphite is gravely overestimated. Luckily several schemes exist to include these van der Waals forces, the Grimme D3 corrections are one of them. Including these the correct behavior of graphite can be predicted using an equation of state fit to fixed volume optimizations.(Note that the energy curve was shifted upward to make the data-point at 41 Å3 coincide with that of the other calculations.) In this case the equilibrium volume is correctly estimated to be about 35 Å3 and the bulk modulus is 28.9 GPa, a mere 15% off from the experimental one, which is near perfect compared to the standard DFT values we had before.

In case of graphite, the simple volume scan approach can also be used for something else. As this approach is well suited to check the behaviour of 1 single internal parameter, we use it to investigate the inter-layer interaction. Keeping the a and b lattice vectors fixed, the c-lattice vector is scanned. Interestingly the LDA functional, which is known to overbind, finds the experimental lattice spacing, while both PBE and HSE06 overestimate it significantly. Introducing D3 corrections for these functionals fixes the problem, and give a stronger binding than LDA.

EOS-fitting for MIL53-MOFs

Comparison of a volume scan and an EOS-fit to fixed volume optimizations for a Metal-Organic Framework with MIL53/47 topology.

We just saw that for simple systems, the simple volume scan can already be too simple. For more complex systems like MOFs, similar problems can be seen. The simple volume scan, as for graphite gives a too sharp potential (with a very large bulk modulus). In addition, internal reordering of the atoms gives rise to very large changes in the energy, and the equilibrium volume can move quite a lot. It even depends on the spin-configuration.

In conclusion: the safest way to get a good equilibrium volume is unfortunately also the most expensive way. By means of an equation of state fit to a set of fixed volume structure optimizations the ground state (experimental) equilibrium volume can be found. As a bonus, the bulk modulus is obtained as well.

Colloquium on Porous Frameworks: Day 2

Program Porous Frameworks ColloquiumOn Monday, we had the second day of our colloquium on Porous Frameworks, containing no less than 4 full sessions, covering all types of frameworks. We started the day with the invited presentation of Prof. Dirk De Vos of the KU Leuven, who discussed the breathing behavior in Zr and Ti containing MOFs, including the work on the COK-69 in which I was involved myself. In the MOFs presented, the breathing behavior was shown to originate from the folding of the linkers, in contrast to breathing due to the hinging motion of the chains in MIL-47/53 MOFs.

After the transition metals, things were stepped up even further by Dr. Stefania Tanase who talked about the use of lanthanide ions in MOFs. These lanthanides give rise to coordinated water molecules which appear to be crucial to their luminescence. Prof. Donglin Jiang, of JAIST in Japan, changed the subject to the realm of COFs, consisting of 2D porous sheets which, through Van Der Waals interactions form 3D structures (similar to graphite). The tunability of these materials would make them well suited for photoconductors and photoenergy conversion (i.e. solar cells).

With Prof. Rochus Schmid of the University of Bochum we delved into the nitty-gritty details of developing Force-Fields for MOFs. He noted that such force-fields can provide good first approximations for structure determination of new MOFs, and if structure related terms are missing in the force-field these will pop up as missing phonon-frequencies.

Prof. Monique Van der Veen showed us how non-polar guest molecules can make a MOF polar, while Agnes Szecsenyi bravely tackled the activity in Iron based MIL-53 MOFs from the DFT point of view. The row of 3 TU Delft contributions was closed by the invited presentation of Prof. Jorge Gascon who provided an overview of the work in his group and discussed how the active sites in MOFs can be improved through cooperative effects.

Prof. Jaroslaw Handzlik provided the last invited contribution, with a comparative theoretical study of Cr-adsorption on various silicate based materials (from amorphous silicate to zeolites). The final session was then closed by the presentations of Dr. Katrine Svane (Bath University) who discussed the effect of defects in UiO-66 MOFs in further detail and Marcus Rose presenting his findings on hyper-crosslinked Polymers, a type of COFs with an amorphous structure and a wide distribution in different pore sizes.

This brought us to a happy end of a successful colloquium, which was celebrated with a drink in the city center of Groningen. Tuesday we traveled back home, such that Wednesday Sylvia could start at the third part of the conference-holiday roller coaster by leaving for Saltzburg.

Colloquium on Porous Frameworks: Day 1

Program Porous Frameworks ColloquiumToday the CMD26 conference started in Groningen, and with its kick-off also our own 2-day colloquium on porous frameworks (aka MOFs, COFs and Zeolites) was launched. During the two sessions of the day, the focus mainly went out to the Zeolites, with Prof. Emiel Hensen of the Technical university of Eindhoven introducing us to the subject and discussing how new zeolites could be designed in a more rational way. He showed us how the template used during synthesis plays a crucial role in the final growth and structure. Dr. Nakato explained how alkali-metal nanoclusters can undergo insulator to metal transitions when incorporated in zeolites (it is due to the competition between electron-electron repulsion and electron-phonon coupling), while Dr. De Wijs informed us on how Al T-sites need to be ordered and assigned in zeolites to allow for the prediction of NMR parameters.

After the coffee break Dr. Palcic, from the Rudjer Boskovic Institute in Croatia, taught us about the role of heteroatoms in zeolites. She told us that even though more than 2 million theoretical structures exist, only 231 have officially been recognized as having been synthesized, so there is a lot more work to be done. She also showed that to get stable zeolites with pores larger than 7-8 Angstrom one needs to have 3 and 4-membered rings in the structure, since these lead to more rigid configurations. Unfortunately these rings are themselves less stable, and need to be stabilized by different atoms at the T-sites.

Dr. Vandichel, still blushing from his tight traveling scheme, changed the subject from zeolites to MOFs, in providing new understanding in the role of defects in MOFs on their catalytic performance. Dr. Liu changed the subject even further with the introduction of COFs and showing us how Hydrogen atoms migrate through these materials. Using the wisdom of Bruce Lee :

You must be shapeless, formless, like water. When you pour water in a cup, it becomes the cup. When you pour water in a bottle, it becomes the bottle. When you pour water in a teapot, it becomes the teapot.

he clarified how water behaves inside these porous materials. Our first colloquium day was closed by Ir. Rohling, who took us back to the zeolite scene (although he was comparing the zeolites to enzymes). He discussed how reactivity in zeolites can be tweaked by the confinement of the reacting agents, and how this can be used for molecule identification. More importantly he showed how multiple active site collaborate, making chemical reactions much easier than one would expect from single active site models.

After all was said and done, it was time to relax a little during the conference welcome reception. And now time to prepare for tomorrow, day 2 of our colloquium on porous frameworks.