Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material

Ergebnisse atomistischer Modellierung von Geomaterialien

The present thesis deals with two aspects which are related to the present Earth's chemical and thermal heterogeneity: trace element partitioning and the lattice thermal conductivity of the lower mantle. We use atomistic computer simulations, first, to elucidate the microscopic mechanisms governing the incorporation of trace elements into silicate melts and their partitioning behavior in the presence of silicate melts. Second, the atomistic modeling approach is employed to obtain the lattice thermal conductivity of lower- mantle minerals at high pressures and temperatures. In chapter 1, the structure of aluminosilicate melts and glasses with 76 mol% SiO2 and varying amounts of Y and La is studied by means of ab-initio and classical molecular dynamics (MD) simulations as well as x-ray and neutron diffraction experiments. The following structural trends are found: the average coordination numbers of Y and La decrease with increasing REE content, and so does the average coordination number of Al. Furthermore, the distribution of Al coordination numbers is shifted to lower values in La-bearing melts, as compared to Y-bearing melts. These trends are rationalized in terms of cation field strengths. The ab-initio MD simulations also show that the Al avoidance rule is not valid for the studied REE-bearing aluminosilicate melts. Chapter 2 is devoted to the incorporation of Y as a trace element into calcium aluminosilicate melts. The aim is to understand how the melt composition, in particular the Ca content and the degree of melt polymerization, influences the partitioning behavior of Y between minerals and melts or between different melts. The local environment of Y in different melts is studied by means of classical MD and EXAFS spectroscopy. Using thermodynamic integration, we determine the equilibrium constant for an exchange reaction of Y and Al between two different melts. The results are consistent with experimental data and provide an atomic-scale explanation of the observed partitioning trends. Chapter 3 deals with the thermal conductivity of the Earth's lower mantle. We determine the lattice thermal conductivities of iron-free lower-mantle phases by means of classical equilibrium MD simulations, in conjunction with the Green-Kubo approach, over a wide pressure and temperature range. The conductivities of the individual phases are then parameterized as a function of density and temperature, and the thermal conductivity of the lower-mantle aggregate is calculated along a model geotherm. Assuming that the presence of iron impurities in the minerals reduce their thermal conductivity by 50%, as suggested by experimental results, we obtain the lattice thermal conductivity of an iron-bearing lower-mantle aggregate, down to the core-mantle boundary, where it reaches 8 W/(mK). The lattice contribution to the global heat flux across the core-mantle boundary is estimated to be 11 terawatts.Die vorliegende Arbeit behandelt zwei Aspekte der chemischen und thermischen Heterogenität der gegenwärtigen Erde: die Verteilung von Spurenelementen und die thermische Leitfähigkeit des unteren Mantels. Wir verwenden atomistische Computersimulationen, um erstens die mikroskopischen Mechanismen aufzuklären, die den Einbau von Spurenelementen in Silikatschmelzen und ihr Verteilungsverhalten in Gegenwart von Silikatschmelzen steuern. Zum zweiten benutzen wir die Methode der atomistischen Modellierung, um den Gitterbeitrag zur Wärmeleitfähigkeit von Mineralen des unteren Mantels bei hohen Drücken und Temperaturen zu erhalten. In Kapitel 1 untersuchen wir die Struktur von Aluminosilikat-Schmelzen und -Gläsern mit 76 mol% SiO2 und unterschiedlichem Y- und La-Gehalt mit Hilfe sowohl von Ab-initio- und klassischer Molekulardynamik (MD) als auch von Röntgen- und Neutronenbeugung. Folgende Trends werden beobachtet: Die durchschnittlichen Koordinationszahlen von Y und La nehmen mit zunehmendem REE-Gehalt ab, ebenso die durchschnittliche Koordinationszahl von Al. Außerdem ist die Verteilung der Al- Koordinationszahlen in den La-haltigen Schmelzen im Vergleich zu den Y-haltigen Schmelzen zu kleineren Werten verschoben. Diese Trends werden anhand der Feldstärken der beteiligten Kationen erklärt. Die Ab-initio- Simulationen zeigen außerdem, dass die Al-Vermeidungsregel in den hier untersuchten REE-haltigen Aluminosilikatschmelzen verletzt ist. Kapitel 2 widmet sich dem Einbau von Y als Spurenelement in Calcium- Aluminosilikatschmelzen. Ziel ist es zu verstehen, wie die Schmelzzusammensetzung, insbesondere der Ca-Gehalt und die Polymerisierung der Schmelze, das Verteilungsverhalten von Y zwischen Mineralen und Schmelzen oder zwischen verschiedenen Schmelzen beeinflusst. Die lokale Umgebung von Y in verschiedenen Schmelzen wird mit Hilfe klassischer MD und EXAFS-Spektroskopie untersucht. Die Technik der thermodynamischen Integration erlaubt es, die Gleichgewichtskonstante einer Austauschreaktion von Y und Al zwischen zwei unterschiedlichen Silikatschmelzen zu bestimmen. Die Ergebnisse stehen im Einklang mit experimentellen Daten und liefern eine Erklärung der beoachteten Verteilungstendenzen durch Prozesse auf atomarer Ebene. Kapitel 3 behandelt die Wärmeleitfähigkeit des unteren Erdmantels. Wir bestimmen den Gitterbeitrag zur Wärmeleitfähigkeit der eisenfreien Phasen des unteren Mantles mittels klassischer Gleichgewichts-MD und der Green-Kubo-Methode in einem weiten Druck- und Temperaturbereich. Die Leitfähigkeiten der einzelnen Phasen werden dann als Funktion der Dichte und der Temperatur parametrisiert, und die Leitfähigkeit des Mantelaggregats wird entlang einer Modellgeotherme berechnet. Unter der Annahme, dass der Eisengehalt der Minerale ihre Wärmeleitfähigkeit um 50% reduziert, wie es experimentelle Ergebnisse nahelegen, erhalten wir den Gitterbeitrag zur Wärmeleitfähigkeit eines eisenhaltigen Aggregats mit der mineralogischen Zusammensetzung des unteren Mantels bis hinunter zur Kern-Mantel-Grenze, wo er 8 W/(mK) beträgt. Wir schätzen den Gitterbeitrag zum globalen Wärmefluss durch die Kern-Mantel- Grenze auf 11 Terawatt

Trace element partitioning between silicate melts - A molecular dynamics approach

Knowledge of trace element partition coefficients is crucial for our understanding of global element cycles. While a great number of experimental studies on mineral-melt partitioning have been performed in the past, the influence of melt structure on partitioning has mostly been considered empirically. This is mainly due to the lack of reliable structure models for typical melts at the relevant pressure and temperature conditions. Molecular dynamics simulations on the other hand may open a new window into this problem as they provide a unique approach to both structural and thermodynamic properties of minerals and melts. In this contribution, we employ first-principles and classical molecular dynamics simulations to (1) explore further a new approach to predict trace element partitioning between several silicate melts and (2) simultaneously investigate the structural controls of the observed partitioning. Specifically, we use a thermodynamic integration scheme to investigate the partitioning behavior of various trace elements (Y, La, As) in a granitic and gabbroic as well as two Ti-bearing melts and compare our data to experimental findings. Our results indicate that, similar to the lattice strain model, partitioning in melts as well seems to depend on an ideal coordination environment for each trace element and on how well this environment can be accommodated in a specific melt. (C) 2017 Elsevier Ltd. All rights reserved

Investigation of structure and dynamics of the hydrated metal–organic framework MIL-53(Cr) using first-principles molecular dynamics

International audienceThe hydration behavior of metal–organic frameworks (MOFs) is of interest both from a practical and from a fundamental point of view: it is linked, on the one hand, to the hydrothermal stability (or instability) of the nanoporous material, which might limit its use in technological applications. On the other hand, it sheds light on the behavior of water in a strongly confined environment. Here, we use first-principles molecular dynamics (MD) to investigate two hydrated phases of the flexible MOF MIL-53(Cr), which adopts a narrow- or a large-pore form, depending on the water loading. Structure and dynamics of the two phases are thoroughly analyzed and compared, with a focus on the hydroxyl group of MIL-53(Cr) and the water molecules in the nanopores. Furthermore, the behavior of the confined water is compared to that of bulk water. Whereas in the narrow-pore form, water is adsorbed at specific crystalline sites, it shows a more disordered, bulk-like structure in the large-pore form. However, reorientation dynamics of water molecules in the latter is considerably slowed down with respect to bulk water, which highlights the confinement effect of the nanoporous framework

Molecular dynamics simulations of Y in silicate melts and implications for trace element partitioning

Element partitioning depends strongly on composition and structure of the involved phases. In this study, we use molecular dynamics simulations to investigate the local environment of Y as an exemplary trace element in four silicate melts with different compositions and thus varying degrees of polymerization. Based on these structural results, we propose a mechanism which explains the observed partitioning trends of Y and other rare-earth elements between crystals and melts or between two melts. With our computational approach, we found a systematic correlation between melt composition and Y coordination as well as Y―O bond lengths, a result which was corroborated by EXAFS spectroscopy on glasses with the same compositions as the simulated melts. Our simulations revealed, moreover, the affinity of Y for network modifiers as second-nearest neighbors (Ca in this study) and the tendency to avoid network formers (Si and Al). This is consistent with the observation that Y (and other rare-earth elements) in general prefer depolymerized to polymerized melts in partitioning experiments (see, e.g., Schmidt et al. (2006)). Furthermore, we used the method of thermodynamic integration to calculate the Gibbs free energy which governs Y partitioning between two exemplary melts. These more quantitative results, too, are in line with the observed partitioning trend

Hydrothermal Breakdown of Flexible Metal–Organic Frameworks: A Study by First-Principles Molecular Dynamics

Flexible metal–organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53­(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability

The structure of Y- and La-bearing aluminosilicate glasses and melts: A combined molecular dynamics and diffraction study

To understand the behavior of rare earth elements (REE) in magmatic systems it is important to characterize in a systematic way their incorporation into silicate melts and glasses. Here, we study the structural environment of the REE Y and La in four aluminosilicate glasses and melts with varying REE content, using a combined simulation and diffraction approach. Glasses are investigated by X-ray and neutron diffraction as well as classical molecular dynamics simulations using two different polarizable ion potentials. Structure models of the corresponding melts are derived from classical and first-principles molecular dynamics simulations. We discuss the effect of temperature on coordination numbers and rationalize the structural changes in response to variations in melt/glass composition in terms of cation field strengths. We find robust evidence that REE and Al coordination numbers decrease with increasing REE content in the investigated melts and glasses. Comparing the two classical potentials, one of them is able to reproduce features of the experimental structure factors with a mixture of corner- and edge-sharing Al-O/REE-O polyhedra, whereas the other potential predicts corner-sharing Al-O/REE-O polyhedra only. (C) 2016 Elsevier B.V. All rights reserved