Transferable force field for metal-organic frameworks from first-principles: BTW-FF

We present an ab-initio derived force field to describe the structural and mechanical properties of metal-organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted

Transferable force field for metal-organic frameworks from first-principles:BTW-FF

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted

Defect chemistry of Ti and Fe impurities and aggregates in Al2O3

We report a theoretical evaluation of the properties of iron and titanium impurities in sapphire (corundum structured α-Al2O3). Calculations using analytical force fields have been performed on the defect structure with the metals present in isolated, co-doped and tri-cluster configurations. Crystal field parameters have been calculated with good agreement to available experimental data. When titanium and iron are present in neighbouring face and edge-sharing orientations, the overlap of the d-orbitals facilitates an intervalence charge transfer (FeIII/TiIII → FeII/TiIV) with an associated optical excitation energy of 1.85 eV and 1.76 eV in the respective configurations. Electronic structure calculations based on density functional theory confirm that FeIII/TiIII is the ground-state configuration for the nearest-neighbour pairs, in contrast to the often considered FeII/TiIV pair. Homonuclear intervalence charge transfer energies between both FeIII/FeII and TiIV/TiIII species have also been calculated, with the energy lying in the infra-red region. Investigation of multiple tri-clusters of iron and titanium identified one stable configuration, TiIII–(TiIV/FeII), with the energy of electron transfer remaining unchanged

Free energy of ligand removal in the metal-organic framework UiO-66

We report an investigation of the "missing-linker phenomenon" in the Zr-based metal organic framework UiO-66 using atomistic force field and quantum chemical methods. For a vacant benzene dicarboxylate ligand, the lowest energy charge-capping mechanism involves acetic acid or Cl-/H2O. The calculated defect free energy of formation is remarkably low, consistent with the high defect concentrations reported experimentally. A dynamic structural instability is identified for certain higher defect concentrations. In addition to the changes in material properties upon defect formation, we assess the formation of molecular aggregates, which provide an additional driving force for ligand loss. These results are expected to be of relevance to a wide range of metal-organic frameworks

Compositional control of pore geometry in multivariate metal-organic frameworks: an experimental and computational study

A new approach is reported for tailoring the pore geometry in five series of multivariate metal-organic frameworks (MOFs) based on the structure [Zn-2(bdc)(2)(dabco)] (bdc = 1,4-benzenedicarboxylate, dabco = 1,8-diazabicyclooctane), DMOF-1. A doping procedure has been adopted to form series of MOFs containing varying linker ratios. The series under investigation are [Zn-2(bdc)(2-x)(bdc-Br)(x)(dabco)]center dot nDMF 1 (bdc-Br = 2-bromo-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-I)(x)(dabco)]center dot nDMF 2 (bdc-I = 2-iodo-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-NO2)(x)(dabco)]center dot nDMF 3 (bdc-NO2 = 2-nitro-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-NH2)(x)(dabco)]center dot nDMF 4 (bdc-NH2 = 2-amino-1,4-benzenedicarboxylate) and [Zn-2(bdc-Br)(2-x)(bdc-I)(x)(dabco)] nDMF 5. Series 1-3 demonstrate a functionality-dependent pore geometry transition from the square, open pores of DMOF-1 to rhomboidal, narrow pores with increasing proportion of the 2-substituted bdc linker, with the rhomboidal-pore MOFs also showing a temperature-dependent phase change. In contrast, all members of series 4 and 5 have uniform pore geometries. In series 4 this is a square pore topology, whilst series 5 exhibits the rhomboidal pore form. Computational analyses reveal that the pore size and shape in systems 1 and 2 is altered through non-covalent interactions between the organic linkers within the framework, and that this can be controlled by the ligand functionality and ratio. This approach affords the potential to tailor pore geometry and shape within MOFs through judicious choice of ligand ratios

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

Integrated genomic characterization of oesophageal carcinoma

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies