An In-Situ Neutron Diffraction and DFT Study of Hydrogen Adsorption in a Sodalite-Type Metal-Organic Framework, Cu-BTTri

Herein we present a detailed study of the hydrogen adsorption properties of Cu‐BTTri, a robust crystalline metal–organic framework containing open metal‐coordination sites. Diffraction techniques, carried out on the activated framework, reveal a structure that is different from what was previously reported. Further, combining standard hydrogen adsorption measurements with in‐situ neutron diffraction techniques provides molecular level insight into the hydrogen adsorption process. The diffraction experiments unveil the location of four D2 adsorption sites in Cu‐BTTri and shed light on the structural features that promote hydrogen adsorption in this material. Density functional theory (DFT), used to predict the location and strength of binding sites, corroborate the experimental findings. By decomposing binding energies in different sites in various energetic contributions, we show that van der Waals interactions play a crucial role, suggesting a possible route to enhancing the binding energy around open metal coordination sites.

Understanding How Ligand Functionalization Influences CO2 and N-2 Adsorption in a Sodalite Metal-Organic Framework

Mehrdad Asgari, Michele Ceriotti, Ilia Kochetygov, Wendy Lee Queen, Pascal Alexander Schouwink, Rocio Semino Barbaresi, Olga Trukhina

In this work, a detailed study is conducted to understand how ligand substitution influences the CO, and N-2 adsorption properties of two highly crystalline sodalite metal-organic frameworks (MOFs) known as Cu-BTT (BTT-3 = 1,3,5-benzenetristetrazolate) and Cu-BTTri (BTTri(-3) = 1,3,5-benzenetristriazolate). The enthalpy of adsorption and observed adsorption capacities at a given pressure are significantly lower for Cu-BTTri compared to its tetrazole counterpart, Cu-BTT. In situ X-ray and neutron diffraction, which allow visualization of the CO2 and N-2 binding sites on the internal surface of Cu-BTTri, provide insights into understanding the subtle differences. As expected, slightly elongated distances between the open Cu2+ sites and surface-bound CO, in Cu-BTTri can be explained by the fact that the triazolate ligand is a better electron donor than the tetrazolate. The more pronounced Jahn-Teller effect in Cu-BTTri leads to weaker guest binding. The results of the aforementioned structural analysis were complemented by the prediction of the binding energies at each CO2 and N-2 adsorption site by density functional theory calculations. In addition, variable temperature in situ diffraction measurements shed light on the fine structural changes of the framework and CO2 occupancies at different adsorption sites as a function of temperature. Finally, simulated breakthrough curves obtained for both sodalite MOFs demonstrate the materials' potential performance in dry postcombustion CO2 capture. The simulation, which considers both framework uptake capacity and selectivity, predicts better separation performance for Cu-BTT. The information obtained in this work highlights how ligand substitution can influence adsorption properties and hence provides further insights into the material optimization for important separations.

AMER CHEMICAL SOC2020

Characterization of metal organic frameworks of interest for gas adsorption/separation applications

Mehrdad Asgari

Metal-Organic Frameworks (MOFs) are a class of porous materials that are applicable in many energy and environmentally relevant areas, due to their unique features including unprecedented internal surface areas and easy chemical tunability. Gas separation and storage are among the most important applications for which MOFs have been extensively studied. Considering the large number of potential MOFs that can be accessed, through a combination of numerous metal clusters and organic linkers, determining the relationship between their structural features (such as pore size and shape and chemical functionalities) and corresponding gas adsorption properties is of utmost importance. In this regard, in-situ characterization, especially diffraction, can be advantageous. MOFs can offer high crystallinity, and so their structure can readily be characterized via diffraction. In addition, due to the presence of metal ions, and predefined molecular building blocks, which exhibit multiple chemical moieties, the potential energy surface for a guest molecule within a MOF cavity possesses multiple minima that correspond to well-defined adsorption sites with varying binding energies. This makes diffraction the most direct way to probe static site-specific binding properties. Given this, the focus of this work is on understanding the structure-derived function of MOFs of interest in gas separation/storage applications. To do this, standard adsorption experiments are coupled with in-situ diffraction techniques. The latter is able to reveal the location and orientation of adsorbed guest species inside the framework, provide insights into the framework response to varying pressure, temperature, and atmosphere, and allow one to determine the relative differences in binding energy between neighboring adsorption sites. The aforementioned information can then be used to rationalize the relationship between different physiochemical features of a given framework and their performance in an adsorption process. In addition to establishing structure-property relations for the usage of MOFs, the obtained experimental results are used to corroborate those calculated by DFT methods, providing a stress test for computational methods aimed at predicting the structures and properties of hypothetical MOFs. The first chapter of this thesis, the introduction, offers a brief review of different characterization methods for studying gas adsorption/separation applications in MOFs. Although the focus of this chapter is on carbon dioxide capture as the application, these characterization methods are also used to study other adsorption processes. The next three chapters, chapters 2-4, present several prominent MOF families that are of interest in hydrogen storage and carbon dioxide capture applications. These case studies demonstrate how using in-situ diffraction techniques coupled with adsorption measurements and DFT calculations can be used to gain molecular level insight into how small molecules bind inside the selected MOF structures. Further, these structure-property correlation studies are able to help unveil how altering MOF building blocks, such as metals and ligands, gives rise to enhanced or diminished adsorption properties. The last chapter, chapter 5, is a study of the response of an activated MOF to varying temperature; in this chapter various structural motions, which are responsible for a large negative thermal expansion (NTE), are elucidated.

EPFL2020

In silico DNA-binding and rational design of ruthenium-arene anticancer drugs

Christian Gossens

Organometallic ruthenium(II)-arene (RA) antitumour compounds of the general type [Ru(II)(η6-arene)(X)2(pta)], RA-pta, and [Ru(II)(η6-arene)X(en)], RA-en, (X=leaving group; pta=1,3,5-triaza-7-phosphaadamantane, en=ethylenediamine) have been investigated computationally. The main focus has been i.e. the hydrolysis properties, ligand exchange reactions, binding to DNA and the analysis of the resulting structural perturbations. The goal of this thesis was to elucidate key steps in the reactivity of the above drugs that are not readily accessible by experimental techniques. The methodologies employed cover tailor made force fields in classical molecular dynamics (MD), density functional theory (DFT) MD simulations in implicit and explicit solvent as well as combined classical/quantum (QM/MM) MD simulations. For RA-pta compounds, binding energies between the metal centres and the surrounding ligands were calculated. The calculated energies rationalize the experimentally observed tendencies for arene loss, and show that the pta ligands are relatively strongly bound. Exchange of metal centre, methylation or protonation of the pta-ligand, or change of the arene result in significant differences in the metal-arene binding energies while leaving the metalphosphine bond strength essentially unchanged. Significantly lower binding energies and reduced hapticity are predicted for the exchange of arene by nucleobases. The latter show higher binding energies for nitrogen π-bonding than for p-bonding. No influence on the ruthenium-arene interaction was observed for RA-pta complexes bearing arenes with functionalized side chains. A combined DFT/continuum electrostatics approach has been used to estimate the protonation states and absolute pKa values of a series of RA-pta compounds and their hydrolysis products. Our results suggest that the selective in vivo activity towards cancer cells and the observed pH dependent DNA damage is due to a pH dependent activation/deactivation mechanism. In the context of rational drug design, it is hypothesised that analogues with fluorinated arene rings should result in improved selectivity towards hypoxic cancer cells. For RA-en complexes, we rationalized the chemoselectivity towards guanine. The calculated DFT binding energies for the three investigated nucleobases (G, A, C) decreases in the order G(N7) >> C(O2) ∼ C(N3) > A(N7) > G(O6) > OH2. The G(N7) complex is the most stable product due to a C6=O-HNen hydrogen bond while the corresponding C6-NH2-HNen interaction in adenine is repulsive. A study of the reaction of [(η6-benzene)Ru(en)(OH2)]2+ (1) towards the nucleobases G, A and C reveals a strong preference for a formation of an H-bonded cis vs. trans reactant adduct. Only guanine can form a thermally stable trans reactant adduct. The potential reaction sites of adenine and cytosine might loose their nucleophilicity by protonation while simultaneously the aqua leaving group of 1 is converted into an unreactive hydroxo ligand. For the reaction of 1 with guanine three different reaction pathways were identified, however, a "direct trans" reaction pathway is probably the most biologically relevant. Using classical and QM/MM MD we showed that both investigated ruthenium compounds, RA-pta and RA-en, can bind to the major groove of duplex DNA and are stable in this position. The DNA is highly flexible, adapts very fast and widens the major groove to accommodate the ruthenium complex. The local and global structural changes of the DNA (e.g. bending towards the major groove) observed for the RA-pta series are similar to those reported for cisplatin. A severe perturbation of the Watson-Crick base pairing adjacent to the binding site of RA-en was observed that can be linked to recent experimental results. Finally, a tailor made force field for RA-en was derived from our QM/MM trajectories using a force matching approach.

EPFL2007