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

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

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

Abstract 5188: Lrig1, a cell surface negative regulator of ErbB1-4, marks both proliferative and quiescent intestinal stem cells and acts as a tumor suppressor

Abstract Whether proliferative and quiescent intestinal stem cells coexist in normal and cancerous tissue is controversial. Due to heightened transcript expression in the intestinal epithelial stem cell compartment, detection in quiescent hair follicle stem cells and frequent loss in breast cancer, we hypothesized that Leucine-rich repeats and immunoglobulin-like domain protein 1 (Lrig1) would mark a novel population of intestinal stem cells and may be important for intestinal homeostasis and in cancer. To study this, we generated Lrig1-CreERT2/+; R26R-LacZ mice to study the role of Lrig1. One day after Lrig1-CreERT2/+; R26R-LacZ mice received a single injection of tamoxifen, 1-2 cells were labeled in the progenitor zone. Three months after injection, 10% of colonic crypts were entirely labeled and 8% of crypts contained singly labeled, non-proliferative, Lgr5-negative cells at the crypt-base. In a regenerative response to gut injury, these singly labeled cells proliferated and gave rise to clusters of labeled daughter cells, demonstrating the ability of these quiescent stem cells to become activated. Loss of Lrig1 resulted in heightened expression of ErbB1-3 in the normal intestine, duodenal adenomas and carcinoma, supporting a functional role for Lrig1 in the maintenance of intestinal epithelial homeostasis and its ability to act as a tumor suppressor. In addition, driving stochastic loss of Apc in Lrig1-expressing cells results in multiple, large distal colonic tumors and less frequent, smaller intestinal tumors, which are common features of human familial polyposis. In summary, we show that Lrig1, a cell surface negative regulator of ErbB1-4, marks both proliferative and quiescent intestinal stem cells and acts as a tumor suppressor. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5188. doi:10.1158/1538-7445.AM2011-5188</jats:p

Water Adsorption in Flexible Gallium-Based MIL-53 Metal–Organic Framework

International audienc

The Pan-ErbB Negative Regulator Lrig1 Is an Intestinal Stem Cell Marker that Functions as a Tumor Suppressor

SummaryLineage mapping has identified both proliferative and quiescent intestinal stem cells, but the molecular circuitry controlling stem cell quiescence is incompletely understood. By lineage mapping, we show Lrig1, a pan-ErbB inhibitor, marks predominately noncycling, long-lived stem cells that are located at the crypt base and that, upon injury, proliferate and divide to replenish damaged crypts. Transcriptome profiling of Lrig1+ colonic stem cells differs markedly from the profiling of highly proliferative, Lgr5+ colonic stem cells; genes upregulated in the Lrig1+ population include those involved in cell cycle repression and response to oxidative damage. Loss of Apc in Lrig1+ cells leads to intestinal adenomas, and genetic ablation of Lrig1 results in heightened ErbB1-3 expression and duodenal adenomas. These results shed light on the relationship between proliferative and quiescent intestinal stem cells and support a model in which intestinal stem cell quiescence is maintained by calibrated ErbB signaling with loss of a negative regulator predisposing to neoplasia