Nine Principles of Semantic Harmonization

Medical data is routinely collected, stored and recorded across different institutions and in a range of different formats. Semantic harmonization is the process of collating this data into a singular consistent logical view, with many approaches to harmonizing both possible and valid. The broad scope of possibilities for undertaking semantic harmonization do lead however to the development of bespoke and ad-hoc systems; this is particularly the case when it comes to cohort data, the format of which is often specific to a cohort's area of focus. Guided by work we have undertaken in developing the 'EMIF Knowledge Object Library', a semantic harmonization framework underpinning the collation of pan-European Alzheimer's cohort data, we have developed a set of nine generic guiding principles for developing semantic harmonization frameworks, the application of which will establish a solid base for constructing similar frameworks

Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials

A theoretical and experimental spectroscopy study on methanol and ethanol conversion over H-SAPO-34

The elucidation of the structure-activity relation of zeolites or zeotype materials remains very challenging. Recent advances in both theoretical and experimental techniques provide new opportunities to study these complex materials and any catalytic reaction occurring inside. In order to establish new active reaction routes, the knowledge of formed intermediates is crucial. The characterization of such intermediates can be done using a variety of spectroscopic techniques. In this contribution, methanol and ethanol conversion over H-SAPO-34 is investigated using IR and UV-VIS measurements. Calculated adsorption enthalpies of methanol and ethanol in a large SAPO 44T finite cluster show the stronger adsorption of the larger alcohol by 14 kJ mol-1. Dispersion contributions are found to be crucial. IR spectra are calculated for the clusters containing the adsorbed alcohols and matched with experimental data. In addition, the cluster is also loaded with singly methylated cationic hydrocarbons as these are representative reaction intermediates. A detailed normal mode analysis is performed, enabling to separate the framework-guest contributions. Based on the computed data in situ DRIFT experimental peaks could be assigned. Finally, contemporary DFT functionals such as CAM-B3LYP seem promising to compute gas phase UV-VIS spectra

Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development

Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g. obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Sheffler scheme for dispersion interactions.Comment: 61 pages, 12 figures, 2 table

Determination of the nature of the Cu coordination complexes formed in the presence of NO and NH3 within SSZ-13

Ammonia-selective catalytic reduction (NH3-SCR) using Cu zeolites is a well-established strategy for the abatement of NOx gases. Recent studies have demonstrated that Cu is particularly active when exchanged into the SSZ-13 zeolite, and its location in either the 6r or 8r renders it an excellent model system for fundamental studies. In this work, we examine the interaction of NH3-SCR relevant gases (NO and NH3) with the Cu2+ centers within the SSZ-13 structure, coupling powder diffraction (PD), X-ray absorption spectroscopy (XAFS), and density functional theory (DFT). This combined approach revealed that, upon calcination, cooling and gas exposure Cu ions tend to locate in the 8r window. After NO introduction, Cu-ions are seen to coordinate to two framework oxygens and one NO molecule, resulting in a bent Cu-nitrosyl complex with a Cu-N-O bond angle of similar to 150 degrees. Whilst Cu seems to be partially reduced/changed in coordination state, NO is partially oxidized. On exposure to NH3 while the PD data suggest the Cu2+ ion occupies a similar position, simulation and XAFS pointed toward the formation of a Jahn-Teller distorted hexaamine complex [Cu(NH3)(6)](2+) in the center of the cha cage. These results have important implications in terms of uptake and storage of these reactive gases and potentially for the mechanisms involved in the NH3-SCR process

Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals

Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often in experimental condensed-matter physics and materials engineering as data. These predictions are used to analyze recent measurements, or to plan future experiments. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such an ab initio prediction? Information and experience about this question is scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This leads to a practical protocol that allows any scientist - experimental or theoretical - to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Delta expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW with respect to WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains updated supplementary material